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 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 CGM1_UpperLimb(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\full-PiG\\"
staticFilename = "PN01NORMSTAT.c3d"
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model=cgm.CGM1()
model.configure(bodyPart=enums.BodyPart.UpperLimb)
markerDiameter=14
mp={
'LeftShoulderOffset' : 50,
'LeftElbowWidth' : 91,
'LeftWristWidth' : 56 ,
'LeftHandThickness' : 28 ,
'RightShoulderOffset' : 45,
'RightElbowWidth' : 90,
'RightWristWidth' : 55 ,
'RightHandThickness' : 30 }
model.addAnthropoInputParameters(mp)
# -----------CGM STATIC CALIBRATION--------------------
scp=modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp,acqStatic,model,headFlat= True).compute()
csp = modelFilters.ModelCoordinateSystemProcedure(model)
# --- motion ----
gaitFilename="PN01NORMSS01.c3d"
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
modMotion=modelFilters.ModelMotionFilter(scp,acqGait,model,enums.motionMethod.Determinist)
modMotion.compute()
csdf = modelFilters.CoordinateSystemDisplayFilter(csp,model,acqGait)
csdf.setStatic(False)
csdf.display()
# thorax
R_thorax= model.getSegment("Thorax").anatomicalFrame.motion[10].getRotation()
R_thorax_vicon = getViconRmatrix(10, acqGait, "TRXO", "TRXA", "TRXL", "XZY")
np.testing.assert_almost_equal( R_thorax,
R_thorax_vicon, decimal =3)
# head
R_head= model.getSegment("Head").anatomicalFrame.motion[10].getRotation()
R_head_vicon = getViconRmatrix(10, acqGait, "HEDO", "HEDA", "HEDL", "XZY")
np.testing.assert_almost_equal( R_head,
R_head_vicon, decimal =2)
def CGM1_upperLimb(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\full-PiG\\"
staticFilename = "PN01NORMSTAT.c3d"
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model = cgm.CGM1()
model.configure(bodyPart=enums.BodyPart.UpperLimb)
markerDiameter = 14
mp = {
'LeftShoulderOffset': 50,
'LeftElbowWidth': 91,
'LeftWristWidth': 56,
'LeftHandThickness': 28,
'RightShoulderOffset': 45,
'RightElbowWidth': 90,
'RightWristWidth': 55,
'RightHandThickness': 30
}
model.addAnthropoInputParameters(mp)
# -----------CGM STATIC CALIBRATION--------------------
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp,
acqStatic,
model,
headHorizontal=False).compute()
# --- motion ----
gaitFilename = "PN01NORMSS01.c3d"
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
modMotion = modelFilters.ModelMotionFilter(
scp, acqGait, model, enums.motionMethod.Determinist)
modMotion.compute()
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csdf = modelFilters.CoordinateSystemDisplayFilter(csp, model, acqGait)
csdf.setStatic(False)
csdf.display()
modelFilters.ModelJCSFilter(model, acqGait).compute(
description="vectoriel", pointLabelSuffix="cgm1_6dof")
#plot("LNeckAngles",acqGait,"cgm1_6dof")
np.testing.assert_almost_equal(
acqGait.GetPoint("LShoulderAngles").GetValues(),
acqGait.GetPoint("LShoulderAngles_cgm1_6dof").GetValues(),
decimal=3)
np.testing.assert_almost_equal(
acqGait.GetPoint("RShoulderAngles").GetValues(),
acqGait.GetPoint("RShoulderAngles_cgm1_6dof").GetValues(),
decimal=3)
np.testing.assert_almost_equal(
acqGait.GetPoint("RElbowAngles").GetValues(),
acqGait.GetPoint("RElbowAngles_cgm1_6dof").GetValues(),
decimal=3)
np.testing.assert_almost_equal(
acqGait.GetPoint("LElbowAngles").GetValues(),
acqGait.GetPoint("LElbowAngles_cgm1_6dof").GetValues(),
decimal=3)
np.testing.assert_almost_equal(
acqGait.GetPoint("RWristAngles").GetValues(),
acqGait.GetPoint("RWristAngles_cgm1_6dof").GetValues(),
decimal=3) # fail on transverse
np.testing.assert_almost_equal(
acqGait.GetPoint("LWristAngles").GetValues(),
acqGait.GetPoint("LWristAngles_cgm1_6dof").GetValues(),
decimal=3) # fail on transverse
np.testing.assert_almost_equal(
acqGait.GetPoint("RNeckAngles").GetValues(),
acqGait.GetPoint("RNeckAngles_cgm1_6dof").GetValues(),
decimal=1) # fail on coronal
np.testing.assert_almost_equal(
acqGait.GetPoint("LNeckAngles").GetValues(),
acqGait.GetPoint("LNeckAngles_cgm1_6dof").GetValues(),
decimal=1) # fail on coronal
btkTools.smartWriter(acqGait, "upperLimb_angle.c3d")
def CGM1_fullbody_static(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\full-PiG\\"
staticFilename = "PN01NORMSTAT.c3d"
# CALIBRATION ###############################
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
markerDiameter = 14
# Lower Limb
mp = {
'Bodymass': 83,
'LeftLegLength': 874,
'RightLegLength': 876.0,
'LeftKneeWidth': 106.0,
'RightKneeWidth': 103.0,
'LeftAnkleWidth': 74.0,
'RightAnkleWidth': 72.0,
'LeftSoleDelta': 0,
'RightSoleDelta': 0,
'LeftShoulderOffset': 50,
'LeftElbowWidth': 91,
'LeftWristWidth': 56,
'LeftHandThickness': 28,
'RightShoulderOffset': 45,
'RightElbowWidth': 90,
'RightWristWidth': 55,
'RightHandThickness': 30
}
model = cgm.CGM1()
model.configure(bodyPart=enums.BodyPart.FullBody)
model.addAnthropoInputParameters(mp)
scp = modelFilters.StaticCalibrationProcedure(
model) # load calibration procedure
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=True,
rightFlatFoot=True,
markerDiameter=14,
viconCGM1compatible=True).compute()
# MOTION ###############################
gaitFilename = "PN01NORMSTAT.c3d"
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
modMotion = modelFilters.ModelMotionFilter(
scp,
acqGait,
model,
enums.motionMethod.Determinist,
markerDiameter=14,
viconCGM1compatible=False)
modMotion.compute()
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csdf = modelFilters.CoordinateSystemDisplayFilter(csp, model,
acqGait).display()
modelFilters.ModelJCSFilter(model, acqGait).compute(
description="vectoriel", pointLabelSuffix="cgm1_6dof")
plot("RSpineAngles", acqGait, "cgm1_6dof")
plot("LSpineAngles", acqGait, "cgm1_6dof")
np.testing.assert_almost_equal(
acqGait.GetPoint("RSpineAngles").GetValues(),
acqGait.GetPoint("RSpineAngles_cgm1_6dof").GetValues(),
decimal=2)
np.testing.assert_almost_equal(
acqGait.GetPoint("LSpineAngles").GetValues(),
acqGait.GetPoint("LSpineAngles_cgm1_6dof").GetValues(),
decimal=2)
btkTools.smartWriter(acqGait, "fullbody.c3d")
def KadMed_TrueEquinus_leftSkinMarkers(cls):
DATA_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\kad-med-TrueEquinus-leftSkinMarkers\\"
staticFilename = "static.c3d"
markerDiameter=14
required_mp={
'Bodymass' : 36.9,
'LeftLegLength' : 665.0,
'RightLegLength' : 655.0 ,
'LeftKneeWidth' : 102.7,
'RightKneeWidth' : 100.2,
'LeftAnkleWidth' : 64.5,
'RightAnkleWidth' : 63.0,
'LeftSoleDelta' : 0,
'RightSoleDelta' : 0,
}
optional_mp={
'InterAsisDistance' : 0,
'LeftAsisTrocanterDistance' : 0,
'LeftThighRotation' : 0,
'LeftShankRotation' : 0 ,
'LeftTibialTorsion' : 0,
'RightAsisTrocanterDistance' : 0,
'RightThighRotation' : 0,
'RightShankRotation' : 0,
'RightTibialTorsion' : 0
}
settings = files.openJson(pyCGM2.PYCGM2_APPDATA_PATH,"CGM1_1-pyCGM2.settings")
translators = settings["Translators"]
pointSuffix = "cgm1_6dof"
model,acqStatic = cgm1.calibrate(DATA_PATH,staticFilename,translators,
required_mp,optional_mp,
False,False,markerDiameter,
pointSuffix)
mcsp = modelFilters.ModelCoordinateSystemProcedure(model)
mcsf = modelFilters.CoordinateSystemDisplayFilter(mcsp,model,acqStatic)
mcsf.setStatic(False)
mcsf.display()
btkTools.smartWriter(acqStatic,"CGM1-KadMed-TrueEquinus-leftSkin-static.c3d")
#motion
gaitFilename="gait trial 01.c3d"
mfpa = None
momentProjection=enums.MomentProjection.Distal
acqGait = cgm1.fitting(model,DATA_PATH, gaitFilename,
translators,
markerDiameter,
pointSuffix,
mfpa,
momentProjection)
mcsp = modelFilters.ModelCoordinateSystemProcedure(model)
mcsf = modelFilters.CoordinateSystemDisplayFilter(mcsp,model,acqGait)
mcsf.setStatic(False)
mcsf.display()
#mcsp = modelFilters.ModelCoordinateSystemProcedure(model)
#modelFilters.CoordinateSystemDisplayFilter(mcsp,model,acqGait).display()
btkTools.smartWriter(acqGait, "CGM1-KadMed-TrueEquinus-leftSkin-gait.c3d")
# testings
offsetTesting(acqStatic,model,display = True, unitTesting=True)
testJointCentres(acqGait)
testRelativesAngles(acqGait,pointSuffix)
def CGM1_fullbody(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\Full PIG - StephenL5_C7\\"
staticFilename = "PN01NORMSTAT.c3d"
# CALIBRATION ###############################
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
markerDiameter = 14
# Lower Limb
mp = {
'Bodymass': 83,
'LeftLegLength': 874,
'RightLegLength': 876.0,
'LeftKneeWidth': 106.0,
'RightKneeWidth': 103.0,
'LeftAnkleWidth': 74.0,
'RightAnkleWidth': 72.0,
'LeftSoleDelta': 0,
'RightSoleDelta': 0,
'LeftShoulderOffset': 50,
'LeftElbowWidth': 91,
'LeftWristWidth': 56,
'LeftHandThickness': 28,
'RightShoulderOffset': 45,
'RightElbowWidth': 90,
'RightWristWidth': 55,
'RightHandThickness': 30
}
model = cgm.CGM1()
model.configure(bodyPart=enums.BodyPart.FullBody)
model.addAnthropoInputParameters(mp)
scp = modelFilters.StaticCalibrationProcedure(
model) # load calibration procedure
csp = modelFilters.ModelCoordinateSystemProcedure(model)
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=False,
rightFlatFoot=False,
markerDiameter=14,
viconCGM1compatible=True,
).compute()
#headHorizontal=True
# --- motion ----
gaitFilename = "PN01NORMSS01_stephen.c3d"
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
modMotion = modelFilters.ModelMotionFilter(
scp, acqGait, model, enums.motionMethod.Determinist)
modMotion.compute()
csdf = modelFilters.CoordinateSystemDisplayFilter(csp, model, acqGait)
csdf.setStatic(False)
csdf.display()
# TESTING
# thorax
R_thorax = model.getSegment(
"Thorax").anatomicalFrame.motion[10].getRotation()
R_thorax_vicon = getViconRmatrix(10, acqGait, "TRXO", "TRXA", "TRXL",
"XZY")
np.testing.assert_almost_equal(R_thorax, R_thorax_vicon, decimal=3)
# head
R_head = model.getSegment(
"Head").anatomicalFrame.motion[10].getRotation()
R_head_vicon = getViconRmatrix(10, acqGait, "HEDO", "HEDA", "HEDL",
"XZY")
np.testing.assert_almost_equal(R_head, R_head_vicon, decimal=2)
btkTools.smartWriter(acqStatic, "FullBody_motion_CGM1_fullbody.c3d")
def calibrate(DATA_PATH,calibrateFilenameLabelled,translators,weights,
required_mp,optional_mp,
ik_flag,leftFlatFoot,rightFlatFoot,headFlat,
markerDiameter,hjcMethod,
pointSuffix,**kwargs):
"""
Calibration of the CGM2.3
: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
"""
# --------------------------STATIC FILE WITH TRANSLATORS --------------------------------------
if "Fitting" in weights.keys():
weights = weights["Fitting"]["Weight"]
# --- btk acquisition ----
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"
logging.info("[pyCGM2] Sacrum marker detected")
acqStatic = btkTools.applyTranslators(acqStatic,translators)
# ---check marker set used----
dcm = cgm.CGM.detectCalibrationMethods(acqStatic)
# --------------------------MODEL--------------------------------------
# ---definition---
model=cgm2.CGM2_3()
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 "noKinematicsCalculation" in kwargs.keys() and kwargs["noKinematicsCalculation"]:
logging.warning("[pyCGM2] No Kinematic calculation done for the static file")
return model, acqStatic
else:
if model.getBodyPart() == enums.BodyPart.UpperLimb:
ik_flag = False
logging.warning("[pyCGM2] Fitting only applied for the upper limb")
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_3\\cgm2_3-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_3\\cgm2_3-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"])
osrf = opensimFilters.opensimFittingFilter(iksetupFile,
scalingOsim,
cgmFittingProcedure,
(DATA_PATH) )
acqStaticIK = osrf.run(acqStatic,(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:
pfp = progressionFrame.PelvisProgressionFrameProcedure()
else:
pfp = progressionFrame.ThoraxProgressionFrameProcedure()
pff = progressionFrame.ProgressionFrameFilter(finalAcqStatic,pfp)
pff.compute()
globalFrame = pff.outputs["globalFrame"]
forwardProgression = pff.outputs["forwardProgression"]
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 fitting(model, DATA_PATH, reconstructFilenameLabelled, translators,
markerDiameter, pointSuffix, mfpa, momentProjection, **kwargs):
"""
Fitting of the CGM1.1
:param model [str]: pyCGM2 model previously calibrated
:param DATA_PATH [str]: path to your data
:param reconstructFilenameLabelled [string list]: c3d files
:param translators [dict]: translators to apply
:param mfpa [str]: manual force plate assignement
:param markerDiameter [double]: marker diameter (mm)
:param pointSuffix [str]: suffix to add to model outputs
:param momentProjection [str]: Coordinate system in which joint moment is expressed
"""
# --------------------------ACQUISITION ------------------------------------
# --- btk acquisition ----
if "forceBtkAcq" in kwargs.keys():
acqGait = kwargs["forceBtkAcq"]
else:
acqGait = btkTools.smartReader(
(DATA_PATH + reconstructFilenameLabelled))
btkTools.checkMultipleSubject(acqGait)
if btkTools.isPointExist(acqGait, "SACR"):
translators["LPSI"] = "SACR"
translators["RPSI"] = "SACR"
logging.info("[pyCGM2] Sacrum marker detected")
acqGait = btkTools.applyTranslators(acqGait, translators)
trackingMarkers = model.getTrackingMarkers(acqGait)
validFrames, vff, vlf = btkTools.findValidFrames(acqGait, trackingMarkers)
# filtering
# -----------------------
if "fc_lowPass_marker" in kwargs.keys(
) and kwargs["fc_lowPass_marker"] != 0:
fc = kwargs["fc_lowPass_marker"]
order = 4
if "order_lowPass_marker" in kwargs.keys():
order = kwargs["order_lowPass_marker"]
signal_processing.markerFiltering(acqGait,
trackingMarkers,
order=order,
fc=fc)
if "fc_lowPass_forcePlate" in kwargs.keys(
) and kwargs["fc_lowPass_forcePlate"] != 0:
fc = kwargs["fc_lowPass_forcePlate"]
order = 4
if "order_lowPass_forcePlate" in kwargs.keys():
order = kwargs["order_lowPass_forcePlate"]
signal_processing.forcePlateFiltering(acqGait, order=order, fc=fc)
scp = modelFilters.StaticCalibrationProcedure(model) # procedure
# ---Motion filter----
modMotion = modelFilters.ModelMotionFilter(scp,
acqGait,
model,
enums.motionMethod.Determinist,
markerDiameter=markerDiameter)
modMotion.compute()
if "displayCoordinateSystem" in kwargs.keys(
) and kwargs["displayCoordinateSystem"]:
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csdf = modelFilters.CoordinateSystemDisplayFilter(csp, model, acqGait)
csdf.setStatic(False)
csdf.display()
if "NaimKneeCorrection" in kwargs.keys() and kwargs["NaimKneeCorrection"]:
# Apply Naim 2019 method
if type(kwargs["NaimKneeCorrection"]) is float:
nmacp = modelFilters.Naim2019ThighMisaligmentCorrectionProcedure(
model, "Both", threshold=(kwargs["NaimKneeCorrection"]))
else:
nmacp = modelFilters.Naim2019ThighMisaligmentCorrectionProcedure(
model, "Both")
mmcf = modelFilters.ModelMotionCorrectionFilter(nmacp)
mmcf.correct()
# btkTools.smartAppendPoint(acqGait,"LNaim",mmcf.m_procedure.m_virtual["Left"])
# btkTools.smartAppendPoint(acqGait,"RNaim",mmcf.m_procedure.m_virtual["Right"])
#---- Joint kinematics----
# relative angles
modelFilters.ModelJCSFilter(model,
acqGait).compute(description="vectoriel",
pointLabelSuffix=pointSuffix)
# detection of traveling axis + absolute angle
if model.m_bodypart != enums.BodyPart.UpperLimb:
pfp = progressionFrame.PelvisProgressionFrameProcedure()
else:
pfp = progressionFrame.ThoraxProgressionFrameProcedure()
pff = progressionFrame.ProgressionFrameFilter(acqGait, pfp)
pff.compute()
globalFrame = pff.outputs["globalFrame"]
forwardProgression = pff.outputs["forwardProgression"]
if model.m_bodypart != enums.BodyPart.UpperLimb:
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqGait,
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,
acqGait,
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,
acqGait,
segmentLabels=["Thorax", "Head"],
angleLabels=["Thorax", "Head"],
eulerSequences=["YXZ", "TOR"],
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix=pointSuffix)
#---- Body segment parameters----
bspModel = bodySegmentParameters.Bsp(model)
bspModel.compute()
if model.m_bodypart == enums.BodyPart.FullBody:
modelFilters.CentreOfMassFilter(
model, acqGait).compute(pointLabelSuffix=pointSuffix)
# Inverse dynamics
if btkTools.checkForcePlateExist(acqGait):
if model.m_bodypart != enums.BodyPart.UpperLimb:
# --- force plate handling----
# find foot in contact
mappedForcePlate = forceplates.matchingFootSideOnForceplate(
acqGait, mfpa=mfpa)
forceplates.addForcePlateGeneralEvents(acqGait, mappedForcePlate)
logging.warning("Manual Force plate assignment : %s" %
mappedForcePlate)
# assembly foot and force plate
modelFilters.ForcePlateAssemblyFilter(
model,
acqGait,
mappedForcePlate,
leftSegmentLabel="Left Foot",
rightSegmentLabel="Right Foot").compute(
pointLabelSuffix=pointSuffix)
#---- Joint kinetics----
idp = modelFilters.CGMLowerlimbInverseDynamicProcedure()
modelFilters.InverseDynamicFilter(
model,
acqGait,
procedure=idp,
projection=momentProjection,
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix=pointSuffix)
#---- Joint energetics----
modelFilters.JointPowerFilter(
model, acqGait).compute(pointLabelSuffix=pointSuffix)
#---- zero unvalid frames ---
btkTools.applyValidFramesOnOutput(acqGait, validFrames)
return acqGait
def fitting(model, DATA_PATH, reconstructFilenameLabelled, translators,
weights, ik_flag, markerDiameter, pointSuffix, mfpa,
momentProjection, **kwargs):
"""
Fitting of the CGM2.5
:param model [str]: pyCGM2 model previously calibrated
:param DATA_PATH [str]: path to your data
:param reconstructFilenameLabelled [string list]: c3d files
:param translators [dict]: translators to apply
:param ik_flag [bool]: enable the inverse kinematic solver
:param mfpa [str]: manual force plate assignement
:param markerDiameter [double]: marker diameter (mm)
:param pointSuffix [str]: suffix to add to model outputs
:param momentProjection [str]: Coordinate system in which joint moment is expressed
"""
detectAnomaly = False
if "anomalyException" in kwargs.keys():
anomalyException = kwargs["anomalyException"]
else:
anomalyException = False
if "forceFoot6DoF" in kwargs.keys() and kwargs["forceFoot6DoF"]:
forceFoot6DoF_flag = True
else:
forceFoot6DoF_flag = False
if "Fitting" in weights.keys():
weights = weights["Fitting"]["Weight"]
# --- btk acquisition ----
if "forceBtkAcq" in kwargs.keys():
acqGait = kwargs["forceBtkAcq"]
else:
acqGait = btkTools.smartReader(
(DATA_PATH + reconstructFilenameLabelled))
btkTools.checkMultipleSubject(acqGait)
if btkTools.isPointExist(acqGait, "SACR"):
translators["LPSI"] = "SACR"
translators["RPSI"] = "SACR"
LOGGER.logger.info("[pyCGM2] Sacrum marker detected")
acqGait = btkTools.applyTranslators(acqGait, translators)
trackingMarkers = cgm2.CGM2_5.LOWERLIMB_TRACKING_MARKERS + cgm2.CGM2_5.THORAX_TRACKING_MARKERS + cgm2.CGM2_5.UPPERLIMB_TRACKING_MARKERS
actual_trackingMarkers, phatoms_trackingMarkers = btkTools.createPhantoms(
acqGait, trackingMarkers)
vff, vlf = btkTools.getFrameBoundaries(acqGait, actual_trackingMarkers)
if "frameInit" in kwargs.keys() and kwargs["frameInit"] is not None:
vff = kwargs["frameInit"]
LOGGER.logger.info("[pyCGM2] first frame forced to frame [%s]" %
(vff))
if "frameEnd" in kwargs.keys() and kwargs["frameEnd"] is not None:
vlf = kwargs["frameEnd"]
LOGGER.logger.info("[pyCGM2] end frame forced to frame [%s]" % (vlf))
flag = btkTools.getValidFrames(acqGait,
actual_trackingMarkers,
frameBounds=[vff, vlf])
LOGGER.logger.info("[pyCGM2] Computation from frame [%s] to frame [%s]" %
(vff, vlf))
# --------------------ANOMALY------------------------------
for marker in actual_trackingMarkers:
if marker not in model.getStaticTrackingMarkers():
LOGGER.logger.warning(
"[pyCGM2-Anomaly] marker [%s] - not used during static calibration - wrong kinematic for the segment attached to this marker. "
% (marker))
# --marker presence
markersets = [
cgm2.CGM2_5.LOWERLIMB_TRACKING_MARKERS,
cgm2.CGM2_5.THORAX_TRACKING_MARKERS,
cgm2.CGM2_5.UPPERLIMB_TRACKING_MARKERS
]
for markerset in markersets:
ipdp = InspectorProcedure.MarkerPresenceDetectionProcedure(markerset)
idf = InspectorFilter.InspectorFilter(acqGait,
reconstructFilenameLabelled,
ipdp)
inspector = idf.run()
# --marker outliers
if inspector["In"] != []:
madp = AnomalyDetectionProcedure.MarkerAnomalyDetectionRollingProcedure(
inspector["In"], plot=False, window=5, threshold=3)
adf = AnomalyFilter.AnomalyDetectionFilter(
acqGait,
reconstructFilenameLabelled,
madp,
frameRange=[vff, vlf])
anomaly = adf.run()
anomalyIndexes = anomaly["Output"]
if anomaly["ErrorState"]: detectAnomaly = True
if btkTools.checkForcePlateExist(acqGait):
afpp = AnomalyDetectionProcedure.ForcePlateAnomalyProcedure()
adf = AnomalyFilter.AnomalyDetectionFilter(acqGait,
reconstructFilenameLabelled,
afpp,
frameRange=[vff, vlf])
anomaly = adf.run()
if anomaly["ErrorState"]: detectAnomaly = True
if detectAnomaly and anomalyException:
raise Exception(
"Anomalies has been detected - Check Warning message of the log file"
)
# --------------------MODELLING------------------------------
# filtering
# -----------------------
if "fc_lowPass_marker" in kwargs.keys(
) and kwargs["fc_lowPass_marker"] != 0:
fc = kwargs["fc_lowPass_marker"]
order = 4
if "order_lowPass_marker" in kwargs.keys():
order = kwargs["order_lowPass_marker"]
signal_processing.markerFiltering(acqGait,
trackingMarkers,
order=order,
fc=fc)
if "fc_lowPass_forcePlate" in kwargs.keys(
) and kwargs["fc_lowPass_forcePlate"] != 0:
fc = kwargs["fc_lowPass_forcePlate"]
order = 4
if "order_lowPass_forcePlate" in kwargs.keys():
order = kwargs["order_lowPass_forcePlate"]
signal_processing.forcePlateFiltering(acqGait, order=order, fc=fc)
# --- initial motion Filter ---
scp = modelFilters.StaticCalibrationProcedure(model)
modMotion = modelFilters.ModelMotionFilter(scp, acqGait, model,
enums.motionMethod.Sodervisk)
modMotion.compute()
progressionFlag = False
if btkTools.isPointExist(acqGait, 'LHEE',
ignorePhantom=False) or btkTools.isPointExist(
acqGait, 'RHEE', ignorePhantom=False):
pfp = progressionFrame.PointProgressionFrameProcedure(marker="LHEE") \
if btkTools.isPointExist(acqGait, 'LHEE',ignorePhantom=False) \
else progressionFrame.PointProgressionFrameProcedure(marker="RHEE")
pff = progressionFrame.ProgressionFrameFilter(acqGait, pfp)
pff.compute()
progressionAxis = pff.outputs["progressionAxis"]
globalFrame = pff.outputs["globalFrame"]
forwardProgression = pff.outputs["forwardProgression"]
progressionFlag = True
elif btkTools.isPointsExist(acqGait, ['LASI', 'RASI', 'RPSI', 'LPSI'],
ignorePhantom=False) and not progressionFlag:
LOGGER.logger.info(
"[pyCGM2] - progression axis detected from Pelvic markers ")
pfp = progressionFrame.PelvisProgressionFrameProcedure()
pff = progressionFrame.ProgressionFrameFilter(acqGait, pfp)
pff.compute()
globalFrame = pff.outputs["globalFrame"]
forwardProgression = pff.outputs["forwardProgression"]
progressionFlag = True
elif btkTools.isPointsExist(acqGait, ['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(acqGait, 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 "
)
for target in weights.keys():
if target not in actual_trackingMarkers or target not in model.getStaticIkTargets(
):
weights[target] = 0
LOGGER.logger.warning(
"[pyCGM2] - the IK targeted marker [%s] is not labelled in the acquisition [%s]"
% (target, reconstructFilenameLabelled))
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 tl 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, acqGait)
osrf.setTimeRange(acqGait, beginFrame=vff, lastFrame=vlf)
if "ikAccuracy" in kwargs.keys():
osrf.setAccuracy(kwargs["ikAccuracy"])
LOGGER.logger.info("-------INVERSE KINEMATICS IN PROGRESS----------")
try:
acqIK = osrf.run(DATA_PATH + reconstructFilenameLabelled,
progressionAxis=progressionAxis,
forwardProgression=forwardProgression)
LOGGER.logger.info("[pyCGM2] - IK solver complete")
except:
LOGGER.logger.error("[pyCGM2] - IK solver fails")
acqIK = acqGait
detectAnomaly = True
LOGGER.logger.info(
"---------------------------------------------------")
# eventual gait acquisition to consider for joint kinematics
finalAcqGait = acqIK if ik_flag else acqGait
if "displayCoordinateSystem" in kwargs.keys(
) and kwargs["displayCoordinateSystem"]:
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csdf = modelFilters.CoordinateSystemDisplayFilter(
csp, model, finalAcqGait)
csdf.setStatic(False)
csdf.display()
# --- final pyCGM2 model motion Filter ---
# use fitted markers
modMotionFitted = modelFilters.ModelMotionFilter(
scp,
finalAcqGait,
model,
enums.motionMethod.Sodervisk,
markerDiameter=markerDiameter,
forceFoot6DoF=forceFoot6DoF_flag)
modMotionFitted.compute()
#---- Joint kinematics----
# relative angles
modelFilters.ModelJCSFilter(model, finalAcqGait).compute(
description="vectoriel", pointLabelSuffix=pointSuffix)
modelFilters.ModelAbsoluteAnglesFilter(
model,
finalAcqGait,
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)
#---- Body segment parameters----
bspModel = bodySegmentParameters.Bsp(model)
bspModel.compute()
modelFilters.CentreOfMassFilter(
model, finalAcqGait).compute(pointLabelSuffix=pointSuffix)
# Inverse dynamics
if btkTools.checkForcePlateExist(acqGait):
# --- force plate handling----
# find foot in contact
mappedForcePlate = forceplates.matchingFootSideOnForceplate(
finalAcqGait, mfpa=mfpa)
forceplates.addForcePlateGeneralEvents(finalAcqGait, mappedForcePlate)
LOGGER.logger.warning("Manual Force plate assignment : %s" %
mappedForcePlate)
# assembly foot and force plate
modelFilters.ForcePlateAssemblyFilter(
model,
finalAcqGait,
mappedForcePlate,
leftSegmentLabel="Left Foot",
rightSegmentLabel="Right Foot").compute(
pointLabelSuffix=pointSuffix)
#---- Joint kinetics----
idp = modelFilters.CGMLowerlimbInverseDynamicProcedure()
modelFilters.InverseDynamicFilter(
model,
finalAcqGait,
procedure=idp,
projection=momentProjection,
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix=pointSuffix)
#---- Joint energetics----
modelFilters.JointPowerFilter(
model, finalAcqGait).compute(pointLabelSuffix=pointSuffix)
#---- zero unvalid frames ---
btkTools.cleanAcq(finalAcqGait)
btkTools.applyOnValidFrames(finalAcqGait, flag)
if detectAnomaly and not anomalyException:
LOGGER.logger.error(
"Anomalies has been detected - Check Warning messages of the log file"
)
return finalAcqGait, detectAnomaly
def calibrate(DATA_PATH, calibrateFilenameLabelled, translators, weights,
required_mp, optional_mp, ik_flag, leftFlatFoot, rightFlatFoot,
headFlat, markerDiameter, hjcMethod, pointSuffix, **kwargs):
"""
Calibration of the CGM2.5
: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
if "Fitting" in weights.keys():
weights = weights["Fitting"]["Weight"]
# ---btk acquisition---
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_5.LOWERLIMB_TRACKING_MARKERS + cgm2.CGM2_5.THORAX_TRACKING_MARKERS + cgm2.CGM2_5.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_5.LOWERLIMB_TRACKING_MARKERS,
cgm2.CGM2_5.THORAX_TRACKING_MARKERS,
cgm2.CGM2_5.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_5()
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)
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)
# BSP model
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
def fitting(model, DATA_PATH, reconstructFilenameLabelled, translators,
settings, markerDiameter, pointSuffix, mfpa, momentProjection,
**kwargs):
"""
Fitting of the CGM2.2
:param model [str]: pyCGM2 model previously calibrated
:param DATA_PATH [str]: path to your data
:param reconstructFilenameLabelled [string list]: c3d files
:param translators [dict]: translators to apply
:param mfpa [str]: manual force plate assignement
:param markerDiameter [double]: marker diameter (mm)
:param pointSuffix [str]: suffix to add to model outputs
:param momentProjection [str]: Coordinate system in which joint moment is expressed
"""
# --------------------------ACQUISITION ------------------------------------
# --- btk acquisition ----
if "forceBtkAcq" in kwargs.keys():
acqGait = kwargs["forceBtkAcq"]
else:
acqGait = btkTools.smartReader(
str(DATA_PATH + reconstructFilenameLabelled))
btkTools.checkMultipleSubject(acqGait)
acqGait = btkTools.applyTranslators(acqGait, translators)
trackingMarkers = model.getTrackingMarkers()
validFrames, vff, vlf = btkTools.findValidFrames(acqGait, trackingMarkers)
# --- initial motion Filter ---
scp = modelFilters.StaticCalibrationProcedure(model)
modMotion = modelFilters.ModelMotionFilter(scp, acqGait, model,
enums.motionMethod.Determinist)
modMotion.compute()
# ---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\\cgm1\\cgm1-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\\cgm1\\cgm1-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"])
osrf = opensimFilters.opensimFittingFilter(iksetupFile, scalingOsim,
cgmFittingProcedure,
str(DATA_PATH))
logging.info("-------INVERSE KINEMATICS IN PROGRESS----------")
acqIK = osrf.run(acqGait, str(DATA_PATH + reconstructFilenameLabelled))
logging.info("-------INVERSE KINEMATICS DONE-----------------")
# --- final pyCGM2 model motion Filter ---
# use fitted markers
modMotionFitted = modelFilters.ModelMotionFilter(
scp,
acqIK,
model,
enums.motionMethod.Determinist,
markerDiameter=markerDiameter)
modMotionFitted.compute()
if "displayCoordinateSystem" in kwargs.keys(
) and kwargs["displayCoordinateSystem"]:
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csdf = modelFilters.CoordinateSystemDisplayFilter(csp, model, acqIK)
csdf.setStatic(False)
csdf.display()
#---- Joint kinematics----
# relative angles
modelFilters.ModelJCSFilter(model,
acqIK).compute(description="vectoriel",
pointLabelSuffix=pointSuffix)
# detection of traveling axis + absolute angle
if model.m_bodypart != enums.BodyPart.UpperLimb:
longitudinalAxis, forwardProgression, globalFrame = btkTools.findProgressionAxisFromPelvicMarkers(
acqIK, ["LASI", "LPSI", "RASI", "RPSI"])
else:
longitudinalAxis, forwardProgression, globalFrame = btkTools.findProgressionAxisFromLongAxis(
acqIK, "C7", "CLAV")
if model.m_bodypart != enums.BodyPart.UpperLimb:
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqIK,
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,
acqIK,
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,
acqIK,
segmentLabels=["Thorax", "Head"],
angleLabels=["Thorax", "Head"],
eulerSequences=["YXZ", "TOR"],
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix=pointSuffix)
#---- Body segment parameters----
bspModel = bodySegmentParameters.Bsp(model)
bspModel.compute()
if model.m_bodypart == enums.BodyPart.FullBody:
modelFilters.CentreOfMassFilter(
model, acqIK).compute(pointLabelSuffix=pointSuffix)
# Inverse dynamics
if model.m_bodypart != enums.BodyPart.UpperLimb:
# --- force plate handling----
# find foot in contact
mappedForcePlate = forceplates.matchingFootSideOnForceplate(acqIK,
mfpa=mfpa)
forceplates.addForcePlateGeneralEvents(acqIK, mappedForcePlate)
logging.warning("Manual Force plate assignment : %s" %
mappedForcePlate)
# assembly foot and force plate
modelFilters.ForcePlateAssemblyFilter(
model,
acqIK,
mappedForcePlate,
leftSegmentLabel="Left Foot",
rightSegmentLabel="Right Foot").compute()
#---- Joint kinetics----
idp = modelFilters.CGMLowerlimbInverseDynamicProcedure()
modelFilters.InverseDynamicFilter(
model,
acqIK,
procedure=idp,
projection=momentProjection,
).compute(pointLabelSuffix=pointSuffix)
#---- Joint energetics----
modelFilters.JointPowerFilter(
model, acqIK).compute(pointLabelSuffix=pointSuffix)
#---- zero unvalid frames ---
btkTools.applyValidFramesOnOutput(acqIK, validFrames)
return acqIK
def CGM1_fullbody_onStatic(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\Full PIG - StephenL5_C7\\"
staticFilename = "PN01NORMSTAT.c3d"
# CALIBRATION ###############################
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
markerDiameter = 14
# Lower Limb
mp = {
'Bodymass': 83,
'LeftLegLength': 874,
'RightLegLength': 876.0,
'LeftKneeWidth': 106.0,
'RightKneeWidth': 103.0,
'LeftAnkleWidth': 74.0,
'RightAnkleWidth': 72.0,
'LeftSoleDelta': 0,
'RightSoleDelta': 0,
'LeftShoulderOffset': 50,
'LeftElbowWidth': 91,
'LeftWristWidth': 56,
'LeftHandThickness': 28,
'RightShoulderOffset': 45,
'RightElbowWidth': 90,
'RightWristWidth': 55,
'RightHandThickness': 30
}
model = cgm.CGM1()
model.configure(bodyPart=enums.BodyPart.FullBody)
model.addAnthropoInputParameters(mp)
scp = modelFilters.StaticCalibrationProcedure(
model) # load calibration procedure
csp = modelFilters.ModelCoordinateSystemProcedure(model)
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=False,
rightFlatFoot=False,
markerDiameter=14,
viconCGM1compatible=True,
).compute()
#headHorizontal=True
# --- motion ----
gaitFilename = "PN01NORMSTAT_stephen.c3d"
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
modMotion = modelFilters.ModelMotionFilter(
scp, acqGait, model, enums.motionMethod.Determinist)
modMotion.compute()
csdf = modelFilters.CoordinateSystemDisplayFilter(csp, model, acqGait)
csdf.setStatic(False)
csdf.display()
# angles
modelFilters.ModelJCSFilter(model, acqGait).compute(
description="vectoriel", pointLabelSuffix="cgm1_6dof")
longitudinalAxis, forwardProgression, globalFrame = btkTools.findProgressionAxisFromLongAxis(
acqGait, "C7", "CLAV")
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqGait,
segmentLabels=["Thorax"],
angleLabels=[
"Thorax",
],
eulerSequences=["YXZ"],
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix="cgm1_6dof")
# testing
np.testing.assert_equal(longitudinalAxis, "X")
np.testing.assert_equal(forwardProgression, True)
np.testing.assert_equal(globalFrame, "XYZ")
# BSP model
bspModel = bodySegmentParameters.Bsp(model)
bspModel.compute()
btkTools.smartAppendPoint(
acqGait, "pelvisCOM_py",
model.getSegment("Pelvis").getComTrajectory())
btkTools.smartAppendPoint(acqGait, "headCOM_py",
model.getSegment("Head").getComTrajectory())
btkTools.smartAppendPoint(
acqGait, "ThoraxCOM_py",
model.getSegment("Thorax").getComTrajectory())
btkTools.smartAppendPoint(
acqGait, "LhumCOM_py",
model.getSegment("Left UpperArm").getComTrajectory())
btkTools.smartAppendPoint(
acqGait, "LforeCom_py",
model.getSegment("Left ForeArm").getComTrajectory())
btkTools.smartAppendPoint(
acqGait, "LhandCom_py",
model.getSegment("Left Hand").getComTrajectory())
btkTools.smartAppendPoint(
acqGait, "RhumCOM_py",
model.getSegment("Right UpperArm").getComTrajectory())
btkTools.smartAppendPoint(
acqGait, "RforeCom_py",
model.getSegment("Right ForeArm").getComTrajectory())
btkTools.smartAppendPoint(
acqGait, "RhandCom_py",
model.getSegment("Right Hand").getComTrajectory())
modelFilters.CentreOfMassFilter(
model, acqGait).compute(pointLabelSuffix="py2")
TL5_pelvis = model.getSegment(
"Pelvis").anatomicalFrame.getNodeTrajectory("TL5")
TL5_thorax = model.getSegment(
"Thorax").anatomicalFrame.getNodeTrajectory("TL5")
C7o_thorax = model.getSegment(
"Thorax").anatomicalFrame.getNodeTrajectory("C7o")
C7_thorax = model.getSegment(
"Thorax").anatomicalFrame.getNodeTrajectory("C7")
C7_head = model.getSegment("Head").anatomicalFrame.getNodeTrajectory(
"C7")
btkTools.smartAppendPoint(acqGait, "TL5_pelvis", TL5_pelvis, desc="")
btkTools.smartAppendPoint(acqGait, "TL5_thorax", TL5_thorax, desc="")
btkTools.smartAppendPoint(acqGait, "C7o_thorax", C7o_thorax, desc="")
btkTools.smartAppendPoint(acqGait, "C7_thorax", C7_thorax, desc="")
btkTools.smartAppendPoint(acqGait, "C7_head", C7_thorax, desc="")
btkTools.smartWriter(acqGait,
"FullBody_COM_CGM1_fullbody_onStatic.c3d")
def CGM1_fullbody(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\Full PIG - StephenL5_C7\\"
staticFilename = "PN01NORMSTAT.c3d"
# CALIBRATION ###############################
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
markerDiameter = 14
# Lower Limb
mp = {
'Bodymass': 83,
'LeftLegLength': 874,
'RightLegLength': 876.0,
'LeftKneeWidth': 106.0,
'RightKneeWidth': 103.0,
'LeftAnkleWidth': 74.0,
'RightAnkleWidth': 72.0,
'LeftSoleDelta': 0,
'RightSoleDelta': 0,
'LeftShoulderOffset': 50,
'LeftElbowWidth': 91,
'LeftWristWidth': 56,
'LeftHandThickness': 28,
'RightShoulderOffset': 45,
'RightElbowWidth': 90,
'RightWristWidth': 55,
'RightHandThickness': 30
}
model = cgm.CGM1()
model.configure(bodyPart=enums.BodyPart.FullBody)
model.addAnthropoInputParameters(mp)
scp = modelFilters.StaticCalibrationProcedure(
model) # load calibration procedure
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=False,
rightFlatFoot=False,
markerDiameter=14,
viconCGM1compatible=True,
).compute()
#headHorizontal=True
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csdf = modelFilters.CoordinateSystemDisplayFilter(
csp, model, acqStatic)
csdf.setStatic(True)
csdf.display()
# joint centres
np.testing.assert_almost_equal(
acqStatic.GetPoint("TRXO").GetValues().mean(axis=0),
acqStatic.GetPoint("OT").GetValues().mean(axis=0),
decimal=3)
np.testing.assert_almost_equal(
acqStatic.GetPoint("LCLO").GetValues().mean(axis=0),
acqStatic.GetPoint("LSJC").GetValues().mean(axis=0),
decimal=3)
np.testing.assert_almost_equal(
acqStatic.GetPoint("LHUO").GetValues().mean(axis=0),
acqStatic.GetPoint("LEJC").GetValues().mean(axis=0),
decimal=3)
np.testing.assert_almost_equal(
acqStatic.GetPoint("LCLO").GetValues().mean(axis=0),
acqStatic.GetPoint("LSJC").GetValues().mean(axis=0),
decimal=3)
np.testing.assert_almost_equal(
acqStatic.GetPoint("RCLO").GetValues().mean(axis=0),
acqStatic.GetPoint("RSJC").GetValues().mean(axis=0),
decimal=3)
np.testing.assert_almost_equal(
acqStatic.GetPoint("RHUO").GetValues().mean(axis=0),
acqStatic.GetPoint("REJC").GetValues().mean(axis=0),
decimal=3)
np.testing.assert_almost_equal(
acqStatic.GetPoint("RCLO").GetValues().mean(axis=0),
acqStatic.GetPoint("RSJC").GetValues().mean(axis=0),
decimal=3)
btkTools.smartWriter(acqStatic, "FullBody_Static_CGM1_fullbody.c3d")
def CGM1_fullbody(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\Full PIG - StephenL5_C7\\"
staticFilename = "PN01NORMSTAT.c3d"
# CALIBRATION ###############################
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
markerDiameter = 14
# Lower Limb
mp = {
'Bodymass': 83,
'LeftLegLength': 874,
'RightLegLength': 876.0,
'LeftKneeWidth': 106.0,
'RightKneeWidth': 103.0,
'LeftAnkleWidth': 74.0,
'RightAnkleWidth': 72.0,
'LeftSoleDelta': 0,
'RightSoleDelta': 0,
'LeftShoulderOffset': 50,
'LeftElbowWidth': 91,
'LeftWristWidth': 56,
'LeftHandThickness': 28,
'RightShoulderOffset': 45,
'RightElbowWidth': 90,
'RightWristWidth': 55,
'RightHandThickness': 30
}
model = cgm.CGM1()
model.configure(bodyPart=enums.BodyPart.FullBody)
model.addAnthropoInputParameters(mp)
scp = modelFilters.StaticCalibrationProcedure(
model) # load calibration procedure
csp = modelFilters.ModelCoordinateSystemProcedure(model)
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=False,
rightFlatFoot=False,
markerDiameter=14,
viconCGM1compatible=True,
).compute()
#headHorizontal=True
# --- motion ----
gaitFilename = "PN01NORMSS01_stephen.c3d"
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
modMotion = modelFilters.ModelMotionFilter(
scp, acqGait, model, enums.motionMethod.Determinist)
modMotion.compute()
csdf = modelFilters.CoordinateSystemDisplayFilter(csp, model, acqGait)
csdf.setStatic(False)
csdf.display()
# angles
modelFilters.ModelJCSFilter(model, acqGait).compute(
description="vectoriel", pointLabelSuffix="cgm1_6dof")
longitudinalAxis, forwardProgression, globalFrame = btkTools.findProgressionAxisFromLongAxis(
acqGait, "C7", "CLAV")
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqGait,
segmentLabels=["Thorax"],
angleLabels=[
"Thorax",
],
eulerSequences=["YXZ"],
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix="cgm1_6dof")
# testing
np.testing.assert_equal(longitudinalAxis, "X")
np.testing.assert_equal(forwardProgression, False)
np.testing.assert_equal(globalFrame, "XYZ")
#plot("LNeckAngles",acqGait,"cgm1_6dof")
# relative angles
np.testing.assert_almost_equal(
acqGait.GetPoint("RSpineAngles").GetValues(),
acqGait.GetPoint("RSpineAngles_cgm1_6dof").GetValues(),
decimal=2)
np.testing.assert_almost_equal(
acqGait.GetPoint("LSpineAngles").GetValues(),
acqGait.GetPoint("LSpineAngles_cgm1_6dof").GetValues(),
decimal=2)
np.testing.assert_almost_equal(
acqGait.GetPoint("LShoulderAngles").GetValues(),
acqGait.GetPoint("LShoulderAngles_cgm1_6dof").GetValues(),
decimal=3)
np.testing.assert_almost_equal(
acqGait.GetPoint("RShoulderAngles").GetValues(),
acqGait.GetPoint("RShoulderAngles_cgm1_6dof").GetValues(),
decimal=3)
np.testing.assert_almost_equal(
acqGait.GetPoint("RElbowAngles").GetValues(),
acqGait.GetPoint("RElbowAngles_cgm1_6dof").GetValues(),
decimal=3)
np.testing.assert_almost_equal(
acqGait.GetPoint("LElbowAngles").GetValues(),
acqGait.GetPoint("LElbowAngles_cgm1_6dof").GetValues(),
decimal=3)
# np.testing.assert_almost_equal( acqGait.GetPoint("RWristAngles").GetValues(),
# acqGait.GetPoint("RWristAngles_cgm1_6dof").GetValues(), decimal =3) # fail on transverse
# np.testing.assert_almost_equal( acqGait.GetPoint("LWristAngles").GetValues(),
# acqGait.GetPoint("LWristAngles_cgm1_6dof").GetValues(), decimal =3)# fail on transverse
#
# np.testing.assert_almost_equal( acqGait.GetPoint("RNeckAngles").GetValues(),
# acqGait.GetPoint("RNeckAngles_cgm1_6dof").GetValues(), decimal =1) # fail on coronal
# np.testing.assert_almost_equal( acqGait.GetPoint("LNeckAngles").GetValues(),
# acqGait.GetPoint("LNeckAngles_cgm1_6dof").GetValues(), decimal =1) # fail on coronal
# absolute angles
np.testing.assert_almost_equal(
acqGait.GetPoint("LThoraxAngles").GetValues(),
acqGait.GetPoint("LThoraxAngles_cgm1_6dof").GetValues(),
decimal=3)
np.testing.assert_almost_equal(
acqGait.GetPoint("RThoraxAngles").GetValues(),
acqGait.GetPoint("RThoraxAngles_cgm1_6dof").GetValues(),
decimal=3)
btkTools.smartWriter(acqStatic, "FullBody_Angles_CGM1_fullbody.c3d")
def calibrate(DATA_PATH,calibrateFilenameLabelled,translators,
required_mp,optional_mp,
leftFlatFoot,rightFlatFoot,headFlat,
markerDiameter,hjcMethod,
pointSuffix,**kwargs):
"""
Calibration of the CGM2.1
: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 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
# --------------------------ACQUISITION ------------------------------------
# ---btk acquisition---
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 = cgm.CGM1.LOWERLIMB_TRACKING_MARKERS + cgm.CGM1.THORAX_TRACKING_MARKERS+ cgm.CGM1.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 = [cgm.CGM1.LOWERLIMB_TRACKING_MARKERS, cgm.CGM1.THORAX_TRACKING_MARKERS, cgm.CGM1.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)
# ---definition---
model=cgm2.CGM2_1()
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,
markerDiameter=markerDiameter,
headFlat= headFlat,
).compute()
modMotion=modelFilters.ModelMotionFilter(scp,acqStatic,model,enums.motionMethod.Determinist,
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 ")
if "displayCoordinateSystem" in kwargs.keys() and kwargs["displayCoordinateSystem"]:
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csdf = modelFilters.CoordinateSystemDisplayFilter(csp,model,acqStatic)
csdf.setStatic(False)
csdf.display()
# ----------------------CGM MODELLING----------------------------------
# ----motion filter----
# notice : viconCGM1compatible option duplicate error on Construction of the foot coordinate system
if "noKinematicsCalculation" in kwargs.keys() and kwargs["noKinematicsCalculation"]:
LOGGER.logger.warning("[pyCGM2] No Kinematic calculation done for the static file")
return model, acqStatic
else:
#---- Joint kinematics----
# relative angles
modelFilters.ModelJCSFilter(model,acqStatic).compute(description="vectoriel", pointLabelSuffix=pointSuffix)
modelFilters.ModelAbsoluteAnglesFilter(model,acqStatic,
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)
# BSP model
bspModel = bodySegmentParameters.Bsp(model)
bspModel.compute()
modelFilters.CentreOfMassFilter(model,acqStatic).compute(pointLabelSuffix=pointSuffix)
btkTools.cleanAcq(acqStatic)
if detectAnomaly and not anomalyException:
LOGGER.logger.error("Anomalies has been detected - Check Warning messages of the log file")
return model, acqStatic,detectAnomaly
def fitting(model,DATA_PATH, reconstructFilenameLabelled,
translators,
markerDiameter,
pointSuffix,
mfpa,
momentProjection,**kwargs):
"""
Fitting of the CGM2.1
:param model [str]: pyCGM2 model previously calibrated
:param DATA_PATH [str]: path to your data
:param reconstructFilenameLabelled [string list]: c3d files
:param translators [dict]: translators to apply
:param mfpa [str]: manual force plate assignement
:param markerDiameter [double]: marker diameter (mm)
:param pointSuffix [str]: suffix to add to model outputs
:param momentProjection [str]: Coordinate system in which joint moment is expressed
"""
detectAnomaly = False
if "anomalyException" in kwargs.keys():
anomalyException = kwargs["anomalyException"]
else:
anomalyException=False
# --------------------------ACQUISITION ------------------------------------
# --- btk acquisition ----
if "forceBtkAcq" in kwargs.keys():
acqGait = kwargs["forceBtkAcq"]
else:
acqGait = btkTools.smartReader((DATA_PATH + reconstructFilenameLabelled))
btkTools.checkMultipleSubject(acqGait)
if btkTools.isPointExist(acqGait,"SACR"):
translators["LPSI"] = "SACR"
translators["RPSI"] = "SACR"
LOGGER.logger.info("[pyCGM2] Sacrum marker detected")
acqGait = btkTools.applyTranslators(acqGait,translators)
trackingMarkers = cgm.CGM1.LOWERLIMB_TRACKING_MARKERS + cgm.CGM1.THORAX_TRACKING_MARKERS+ cgm.CGM1.UPPERLIMB_TRACKING_MARKERS
actual_trackingMarkers,phatoms_trackingMarkers = btkTools.createPhantoms(acqGait, trackingMarkers)
vff,vlf = btkTools.getFrameBoundaries(acqGait,actual_trackingMarkers)
if "frameInit" in kwargs.keys() and kwargs["frameInit"] is not None:
vff = kwargs["frameInit"]
LOGGER.logger.info("[pyCGM2] first frame forced to frame [%s]"%(vff))
if "frameEnd" in kwargs.keys() and kwargs["frameEnd"] is not None:
vlf = kwargs["frameEnd"]
LOGGER.logger.info("[pyCGM2] end frame forced to frame [%s]"%(vlf))
flag = btkTools.getValidFrames(acqGait,actual_trackingMarkers,frameBounds=[vff,vlf])
LOGGER.logger.info("[pyCGM2] Computation from frame [%s] to frame [%s]"%(vff,vlf))
# --------------------ANOMALY------------------------------
for marker in actual_trackingMarkers:
if marker not in model.getStaticTrackingMarkers():
LOGGER.logger.warning("[pyCGM2-Anomaly] marker [%s] - not used during static calibration - wrong kinematic for the segment attached to this marker. "%(marker))
# --marker presence
markersets = [cgm.CGM1.LOWERLIMB_TRACKING_MARKERS, cgm.CGM1.THORAX_TRACKING_MARKERS, cgm.CGM1.UPPERLIMB_TRACKING_MARKERS]
for markerset in markersets:
ipdp = InspectorProcedure.MarkerPresenceDetectionProcedure( markerset)
idf = InspectorFilter.InspectorFilter(acqGait,reconstructFilenameLabelled,ipdp)
inspector = idf.run()
# --marker outliers
if inspector["In"] !=[]:
madp = AnomalyDetectionProcedure.MarkerAnomalyDetectionRollingProcedure( inspector["In"], plot=False, window=5,threshold = 3)
adf = AnomalyFilter.AnomalyDetectionFilter(acqGait,reconstructFilenameLabelled,madp, frameRange=[vff,vlf])
anomaly = adf.run()
anomalyIndexes = anomaly["Output"]
if anomaly["ErrorState"]: detectAnomaly = True
if btkTools.checkForcePlateExist(acqGait):
afpp = AnomalyDetectionProcedure.ForcePlateAnomalyProcedure()
adf = AnomalyFilter.AnomalyDetectionFilter(acqGait,reconstructFilenameLabelled,afpp, frameRange=[vff,vlf])
anomaly = adf.run()
if anomaly["ErrorState"]: detectAnomaly = True
if detectAnomaly and anomalyException:
raise Exception ("Anomalies has been detected - Check Warning message of the log file")
# --------------------MODELLING------------------------------
# filtering
# -----------------------
if "fc_lowPass_marker" in kwargs.keys() and kwargs["fc_lowPass_marker"]!=0 :
fc = kwargs["fc_lowPass_marker"]
order = 4
if "order_lowPass_marker" in kwargs.keys():
order = kwargs["order_lowPass_marker"]
signal_processing.markerFiltering(acqGait,trackingMarkers,order=order, fc =fc)
if "fc_lowPass_forcePlate" in kwargs.keys() and kwargs["fc_lowPass_forcePlate"]!=0 :
fc = kwargs["fc_lowPass_forcePlate"]
order = 4
if "order_lowPass_forcePlate" in kwargs.keys():
order = kwargs["order_lowPass_forcePlate"]
signal_processing.forcePlateFiltering(acqGait,order=order, fc =fc)
scp=modelFilters.StaticCalibrationProcedure(model)
# ---Motion filter----
modMotion=modelFilters.ModelMotionFilter(scp,acqGait,model,enums.motionMethod.Determinist,
markerDiameter=markerDiameter)
modMotion.compute()
progressionFlag = False
if btkTools.isPointExist(acqGait, 'LHEE',ignorePhantom=False) or btkTools.isPointExist(acqGait, 'RHEE',ignorePhantom=False):
pfp = progressionFrame.PointProgressionFrameProcedure(marker="LHEE") \
if btkTools.isPointExist(acqGait, 'LHEE',ignorePhantom=False) \
else progressionFrame.PointProgressionFrameProcedure(marker="RHEE")
pff = progressionFrame.ProgressionFrameFilter(acqGait,pfp)
pff.compute()
progressionAxis = pff.outputs["progressionAxis"]
globalFrame = pff.outputs["globalFrame"]
forwardProgression = pff.outputs["forwardProgression"]
progressionFlag = True
elif btkTools.isPointsExist(acqGait, ['LASI', 'RASI', 'RPSI', 'LPSI'],ignorePhantom=False) and not progressionFlag:
LOGGER.logger.info("[pyCGM2] - progression axis detected from Pelvic markers ")
pfp = progressionFrame.PelvisProgressionFrameProcedure()
pff = progressionFrame.ProgressionFrameFilter(acqGait,pfp)
pff.compute()
globalFrame = pff.outputs["globalFrame"]
forwardProgression = pff.outputs["forwardProgression"]
progressionFlag = True
elif btkTools.isPointsExist(acqGait, ['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(acqGait,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 ")
if "displayCoordinateSystem" in kwargs.keys() and kwargs["displayCoordinateSystem"]:
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csdf = modelFilters.CoordinateSystemDisplayFilter(csp,model,acqGait)
csdf.setStatic(False)
csdf.display()
#---- Joint kinematics----
# relative angles
modelFilters.ModelJCSFilter(model,acqGait).compute(description="vectoriel", pointLabelSuffix=pointSuffix)
modelFilters.ModelAbsoluteAnglesFilter(model,acqGait,
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)
#---- Body segment parameters----
bspModel = bodySegmentParameters.Bsp(model)
bspModel.compute()
modelFilters.CentreOfMassFilter(model,acqGait).compute(pointLabelSuffix=pointSuffix)
# Inverse dynamics
if btkTools.checkForcePlateExist(acqGait):
if model.m_bodypart != enums.BodyPart.UpperLimb:
# --- force plate handling----
# find foot in contact
mappedForcePlate = forceplates.matchingFootSideOnForceplate(acqGait,mfpa=mfpa)
forceplates.addForcePlateGeneralEvents(acqGait,mappedForcePlate)
LOGGER.logger.info("Manual Force plate assignment : %s" %mappedForcePlate)
# assembly foot and force plate
modelFilters.ForcePlateAssemblyFilter(model,acqGait,mappedForcePlate,
leftSegmentLabel="Left Foot",
rightSegmentLabel="Right Foot").compute(pointLabelSuffix=pointSuffix)
#---- Joint kinetics----
idp = modelFilters.CGMLowerlimbInverseDynamicProcedure()
modelFilters.InverseDynamicFilter(model,
acqGait,
procedure = idp,
projection = momentProjection,
globalFrameOrientation = globalFrame,
forwardProgression = forwardProgression
).compute(pointLabelSuffix=pointSuffix)
#---- Joint energetics----
modelFilters.JointPowerFilter(model,acqGait).compute(pointLabelSuffix=pointSuffix)
btkTools.cleanAcq(acqGait)
btkTools.applyOnValidFrames(acqGait,flag)
if detectAnomaly and not anomalyException:
LOGGER.logger.error("Anomalies has been detected - Check Warning messages of the log file")
return acqGait,detectAnomaly
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")
def fitting(model, DATA_PATH, reconstructFilenameLabelled, translators,
markerDiameter, pointSuffix, mfpa, momentProjection, **kwargs):
"""
Fitting of the CGM1
:param model [str]: pyCGM2 model previously calibrated
:param DATA_PATH [str]: path to your data
:param reconstructFilenameLabelled [string list]: c3d files
:param translators [dict]: translators to apply
:param mfpa [str]: manual force plate assignement
:param markerDiameter [double]: marker diameter (mm)
:param pointSuffix [str]: suffix to add to model outputs
:param momentProjection [str]: Coordinate system in which joint moment is expressed
"""
# --------------------------ACQUISITION ------------------------------------
if "forceBtkAcq" in kwargs.keys():
acqGait = kwargs["forceBtkAcq"]
else:
# --- btk acquisition ----
acqGait = btkTools.smartReader(
str(DATA_PATH + reconstructFilenameLabelled))
btkTools.checkMultipleSubject(acqGait)
acqGait = btkTools.applyTranslators(acqGait, translators)
trackingMarkers = model.getTrackingMarkers()
validFrames, vff, vlf = btkTools.findValidFrames(acqGait, trackingMarkers)
scp = modelFilters.StaticCalibrationProcedure(model) # procedure
# ---Motion filter----
modMotion = modelFilters.ModelMotionFilter(scp,
acqGait,
model,
enums.motionMethod.Determinist,
markerDiameter=markerDiameter,
viconCGM1compatible=True)
modMotion.compute()
if "displayCoordinateSystem" in kwargs.keys(
) and kwargs["displayCoordinateSystem"]:
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csdf = modelFilters.CoordinateSystemDisplayFilter(csp, model, acqGait)
csdf.setStatic(False)
csdf.display()
#---- Joint kinematics----
# relative angles
modelFilters.ModelJCSFilter(model,
acqGait).compute(description="vectoriel",
pointLabelSuffix=pointSuffix)
# detection of traveling axis + absolute angle
if model.m_bodypart != enums.BodyPart.UpperLimb:
longitudinalAxis, forwardProgression, globalFrame = btkTools.findProgressionAxisFromPelvicMarkers(
acqGait, ["LASI", "LPSI", "RASI", "RPSI"])
else:
longitudinalAxis, forwardProgression, globalFrame = btkTools.findProgressionAxisFromLongAxis(
acqGait, "C7", "CLAV")
if model.m_bodypart != enums.BodyPart.UpperLimb:
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqGait,
segmentLabels=["Left Foot", "Right Foot", "Pelvis"],
angleLabels=["LFootProgress", "RFootProgress", "Pelvis"],
eulerSequences=["TOR", "TOR", "TOR"],
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix=pointSuffix)
if model.m_bodypart == enums.BodyPart.LowerLimbTrunk:
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqGait,
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,
acqGait,
segmentLabels=["Thorax", "Head"],
angleLabels=["Thorax", "Head"],
eulerSequences=["YXZ", "TOR"],
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix=pointSuffix)
#---- Body segment parameters----
bspModel = bodySegmentParameters.Bsp(model)
bspModel.compute()
#---- CentreOfMass----
if model.m_bodypart == enums.BodyPart.FullBody:
modelFilters.CentreOfMassFilter(
model, acqGait).compute(pointLabelSuffix=pointSuffix)
# Inverse dynamics
if model.m_bodypart != enums.BodyPart.UpperLimb:
# --- force plate handling----
# find foot in contact
mappedForcePlate = forceplates.matchingFootSideOnForceplate(acqGait,
mfpa=mfpa)
forceplates.addForcePlateGeneralEvents(acqGait, mappedForcePlate)
logging.warning("Manual Force plate assignment : %s" %
mappedForcePlate)
# assembly foot and force plate
modelFilters.ForcePlateAssemblyFilter(
model,
acqGait,
mappedForcePlate,
leftSegmentLabel="Left Foot",
rightSegmentLabel="Right Foot").compute()
#---- Joint kinetics----
idp = modelFilters.CGMLowerlimbInverseDynamicProcedure()
modelFilters.InverseDynamicFilter(
model,
acqGait,
procedure=idp,
projection=momentProjection,
viconCGM1compatible=True).compute(pointLabelSuffix=pointSuffix)
#---- Joint energetics----
modelFilters.JointPowerFilter(
model, acqGait).compute(pointLabelSuffix=pointSuffix)
#---- zero unvalid frames ---
btkTools.applyValidFramesOnOutput(acqGait, validFrames)
return acqGait
def calibrate(DATA_PATH, calibrateFilenameLabelled, translators, required_mp,
optional_mp, leftFlatFoot, rightFlatFoot, headFlat,
markerDiameter, pointSuffix, **kwargs):
"""
Calibration of the CGM1.1
: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 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 pointSuffix [str]: suffix to add to model outputs
"""
# --------------------------ACQUISITION ------------------------------------
# --- btk acquisition ----
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"
logging.info("[pyCGM2] Sacrum marker detected")
acqStatic = btkTools.applyTranslators(acqStatic, translators)
# ---detectedCalibrationMethods----
dcm = cgm.CGM.detectCalibrationMethods(acqStatic)
# ---definition---
model = cgm.CGM1()
model.setVersion("CGM1.1")
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----
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=leftFlatFoot,
rightFlatFoot=rightFlatFoot,
headFlat=headFlat,
markerDiameter=markerDiameter,
).compute()
# ---- Decorators -----
decorators.applyBasicDecorators(dcm, model, acqStatic, optional_mp,
markerDiameter)
# ----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----
# notice : viconCGM1compatible option duplicate error on Construction of the foot coordinate system
modMotion = modelFilters.ModelMotionFilter(scp,
acqStatic,
model,
enums.motionMethod.Determinist,
markerDiameter=markerDiameter)
modMotion.compute()
if "displayCoordinateSystem" in kwargs.keys(
) and kwargs["displayCoordinateSystem"]:
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csdf = modelFilters.CoordinateSystemDisplayFilter(
csp, model, acqStatic)
csdf.setStatic(False)
csdf.display()
if "noKinematicsCalculation" in kwargs.keys(
) and kwargs["noKinematicsCalculation"]:
logging.warning(
"[pyCGM2] No Kinematic calculation done for the static file")
return model, acqStatic
else:
#---- Joint kinematics----
# relative angles
modelFilters.ModelJCSFilter(model, acqStatic).compute(
description="vectoriel", pointLabelSuffix=pointSuffix)
# detection of traveling axis + absolute angle
if model.m_bodypart != enums.BodyPart.UpperLimb:
pfp = progressionFrame.PelvisProgressionFrameProcedure()
else:
pfp = progressionFrame.ThoraxProgressionFrameProcedure()
pff = progressionFrame.ProgressionFrameFilter(acqStatic, pfp)
pff.compute()
globalFrame = pff.outputs["globalFrame"]
forwardProgression = pff.outputs["forwardProgression"]
if model.m_bodypart != enums.BodyPart.UpperLimb:
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqStatic,
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,
acqStatic,
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,
acqStatic,
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, acqStatic).compute(pointLabelSuffix=pointSuffix)
return model, acqStatic
def calibrate(DATA_PATH, calibrateFilenameLabelled, translators, required_mp,
optional_mp, leftFlatFoot, rightFlatFoot, headFlat,
markerDiameter, pointSuffix, **kwargs):
"""
Calibration of the CGM1
: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 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 pointSuffix [str]: suffix to add to model outputs
"""
# --------------------------ACQUISITION ------------------------------------
if "forceBtkAcq" in kwargs.keys():
acqStatic = kwargs["forceBtkAcq"]
else:
# ---btk acquisition---
acqStatic = btkTools.smartReader(
str(DATA_PATH + calibrateFilenameLabelled))
btkTools.checkMultipleSubject(acqStatic)
acqStatic = btkTools.applyTranslators(acqStatic, translators)
# ---check marker set used----
dcm = cgm.CGM.detectCalibrationMethods(acqStatic)
# ---definition---
model = cgm.CGM1()
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----
modelFilters.ModelCalibrationFilter(scp,
acqStatic,
model,
leftFlatFoot=leftFlatFoot,
rightFlatFoot=rightFlatFoot,
markerDiameter=markerDiameter,
headFlat=headFlat,
viconCGM1compatible=True).compute()
# ---- Decorators -----
decorators.applyBasicDecorators(dcm,
model,
acqStatic,
optional_mp,
markerDiameter,
cgm1only=True)
pigStaticMarkers = cgm.CGM.get_markerLabelForPiGStatic(dcm)
# ----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,
viconCGM1compatible=True).compute()
# ----------------------CGM MODELLING----------------------------------
# ----motion filter----
# notice : viconCGM1compatible option duplicate error on Construction of the foot coordinate system
modMotion = modelFilters.ModelMotionFilter(
scp,
acqStatic,
model,
enums.motionMethod.Determinist,
markerDiameter=markerDiameter,
viconCGM1compatible=False,
pigStatic=True,
useLeftKJCmarker=pigStaticMarkers[0],
useLeftAJCmarker=pigStaticMarkers[1],
useRightKJCmarker=pigStaticMarkers[2],
useRightAJCmarker=pigStaticMarkers[3])
modMotion.compute()
if "displayCoordinateSystem" in kwargs.keys(
) and kwargs["displayCoordinateSystem"]:
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csdf = modelFilters.CoordinateSystemDisplayFilter(
csp, model, acqStatic)
csdf.setStatic(False)
csdf.display()
#---- Joint kinematics----
# relative angles
modelFilters.ModelJCSFilter(model, acqStatic).compute(
description="vectoriel", pointLabelSuffix=pointSuffix)
# detection of traveling axis + absolute angle
if model.m_bodypart != enums.BodyPart.UpperLimb:
longitudinalAxis, forwardProgression, globalFrame = btkTools.findProgressionAxisFromPelvicMarkers(
acqStatic, ["LASI", "LPSI", "RASI", "RPSI"])
else:
longitudinalAxis, forwardProgression, globalFrame = btkTools.findProgressionAxisFromLongAxis(
acqStatic, "C7", "CLAV")
if model.m_bodypart != enums.BodyPart.UpperLimb:
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqStatic,
segmentLabels=["Left Foot", "Right Foot", "Pelvis"],
angleLabels=["LFootProgress", "RFootProgress", "Pelvis"],
eulerSequences=["TOR", "TOR", "TOR"],
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix=pointSuffix)
if model.m_bodypart == enums.BodyPart.LowerLimbTrunk:
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqStatic,
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,
acqStatic,
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, acqStatic).compute(pointLabelSuffix=pointSuffix)
return model, acqStatic
def fitting(model,DATA_PATH, reconstructFilenameLabelled,
translators,weights,
ik_flag,markerDiameter,
pointSuffix,
mfpa,
momentProjection,**kwargs):
"""
Fitting of the CGM2.3
:param model [str]: pyCGM2 model previously calibrated
:param DATA_PATH [str]: path to your data
:param reconstructFilenameLabelled [string list]: c3d files
:param translators [dict]: translators to apply
:param ik_flag [bool]: enable the inverse kinematic solver
:param mfpa [str]: manual force plate assignement
:param markerDiameter [double]: marker diameter (mm)
:param pointSuffix [str]: suffix to add to model outputs
:param momentProjection [str]: Coordinate system in which joint moment is expressed
"""
if "Fitting" in weights.keys():
weights = weights["Fitting"]["Weight"]
# --------------------------ACQ WITH TRANSLATORS --------------------------------------
# --- btk acquisition ----
if "forceBtkAcq" in kwargs.keys():
acqGait = kwargs["forceBtkAcq"]
else:
acqGait = btkTools.smartReader((DATA_PATH + reconstructFilenameLabelled))
btkTools.checkMultipleSubject(acqGait)
if btkTools.isPointExist(acqGait,"SACR"):
translators["LPSI"] = "SACR"
translators["RPSI"] = "SACR"
logging.info("[pyCGM2] Sacrum marker detected")
acqGait = btkTools.applyTranslators(acqGait,translators)
trackingMarkers = model.getTrackingMarkers(acqGait)
validFrames,vff,vlf = btkTools.findValidFrames(acqGait,trackingMarkers)
# filtering
# -----------------------
if "fc_lowPass_marker" in kwargs.keys() and kwargs["fc_lowPass_marker"]!=0 :
fc = kwargs["fc_lowPass_marker"]
order = 4
if "order_lowPass_marker" in kwargs.keys():
order = kwargs["order_lowPass_marker"]
signal_processing.markerFiltering(acqGait,trackingMarkers,order=order, fc =fc)
if "fc_lowPass_forcePlate" in kwargs.keys() and kwargs["fc_lowPass_forcePlate"]!=0 :
fc = kwargs["fc_lowPass_forcePlate"]
order = 4
if "order_lowPass_forcePlate" in kwargs.keys():
order = kwargs["order_lowPass_forcePlate"]
signal_processing.forcePlateFiltering(acqGait,order=order, fc =fc)
# --- initial motion Filter ---
scp=modelFilters.StaticCalibrationProcedure(model)
# section to remove : - copy motion of ProximalShank from Shank with Sodervisk
modMotion=modelFilters.ModelMotionFilter(scp,acqGait,model,enums.motionMethod.Sodervisk)
modMotion.compute()
# /section to remove
if model.getBodyPart() == enums.BodyPart.UpperLimb:
ik_flag = False
logging.warning("[pyCGM2] Fitting only applied for the upper limb")
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_3\\cgm2_3-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_3\\cgm2_3-ikSetUp_template.xml" # ik tl 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"])
osrf = opensimFilters.opensimFittingFilter(iksetupFile,
scalingOsim,
cgmFittingProcedure,
(DATA_PATH) )
logging.info("-------INVERSE KINEMATICS IN PROGRESS----------")
acqIK = osrf.run(acqGait,(DATA_PATH + reconstructFilenameLabelled ))
logging.info("-------INVERSE KINEMATICS DONE-----------------")
# eventual gait acquisition to consider for joint kinematics
finalAcqGait = acqIK if ik_flag else acqGait
# --- final pyCGM2 model motion Filter ---
# use fitted markers
modMotionFitted=modelFilters.ModelMotionFilter(scp,finalAcqGait,model,enums.motionMethod.Sodervisk ,
markerDiameter=markerDiameter)
modMotionFitted.compute()
if "displayCoordinateSystem" in kwargs.keys() and kwargs["displayCoordinateSystem"]:
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csdf = modelFilters.CoordinateSystemDisplayFilter(csp,model,finalAcqGait)
csdf.setStatic(False)
csdf.display()
#---- Joint kinematics----
# relative angles
modelFilters.ModelJCSFilter(model,finalAcqGait).compute(description="vectoriel", pointLabelSuffix=pointSuffix)
# detection of traveling axis + absolute angle
if model.m_bodypart != enums.BodyPart.UpperLimb:
pfp = progressionFrame.PelvisProgressionFrameProcedure()
else:
pfp = progressionFrame.ThoraxProgressionFrameProcedure()
pff = progressionFrame.ProgressionFrameFilter(finalAcqGait,pfp)
pff.compute()
globalFrame = pff.outputs["globalFrame"]
forwardProgression = pff.outputs["forwardProgression"]
if model.m_bodypart != enums.BodyPart.UpperLimb:
modelFilters.ModelAbsoluteAnglesFilter(model,finalAcqGait,
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,finalAcqGait,
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,finalAcqGait,
segmentLabels=["Thorax","Head"],
angleLabels=["Thorax", "Head"],
eulerSequences=["YXZ","TOR"],
globalFrameOrientation = globalFrame,
forwardProgression = forwardProgression).compute(pointLabelSuffix=pointSuffix)
#---- Body segment parameters----
bspModel = bodySegmentParameters.Bsp(model)
bspModel.compute()
if model.m_bodypart == enums.BodyPart.FullBody:
modelFilters.CentreOfMassFilter(model,finalAcqGait).compute(pointLabelSuffix=pointSuffix)
# Inverse dynamics
if btkTools.checkForcePlateExist(acqGait):
if model.m_bodypart != enums.BodyPart.UpperLimb:
# --- force plate handling----
# find foot in contact
mappedForcePlate = forceplates.matchingFootSideOnForceplate(finalAcqGait,mfpa=mfpa)
forceplates.addForcePlateGeneralEvents(finalAcqGait,mappedForcePlate)
logging.warning("Manual Force plate assignment : %s" %mappedForcePlate)
# assembly foot and force plate
modelFilters.ForcePlateAssemblyFilter(model,finalAcqGait,mappedForcePlate,
leftSegmentLabel="Left Foot",
rightSegmentLabel="Right Foot").compute(pointLabelSuffix=pointSuffix)
#---- Joint kinetics----
idp = modelFilters.CGMLowerlimbInverseDynamicProcedure()
modelFilters.InverseDynamicFilter(model,
finalAcqGait,
procedure = idp,
projection = momentProjection,
globalFrameOrientation = globalFrame,
forwardProgression = forwardProgression
).compute(pointLabelSuffix=pointSuffix)
#---- Joint energetics----
modelFilters.JointPowerFilter(model,finalAcqGait).compute(pointLabelSuffix=pointSuffix)
#---- zero unvalid frames ---
btkTools.applyValidFramesOnOutput(finalAcqGait,validFrames)
return finalAcqGait
def CGM1_UpperLimb(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\full-PiG\\"
staticFilename = "PN01NORMSTAT.c3d"
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model = cgm.CGM1
model.configure(bodyPart=enums.BodyPart.UpperLimb)
markerDiameter = 14
mp = {
'LeftShoulderOffset': 50,
'LeftElbowWidth': 91,
'LeftWristWidth': 56,
'LeftHandThickness': 28,
'RightShoulderOffset': 45,
'RightElbowWidth': 90,
'RightWristWidth': 55,
'RightHandThickness': 30
}
model.addAnthropoInputParameters(mp)
# -----------CGM STATIC CALIBRATION--------------------
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute()
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csdf = modelFilters.CoordinateSystemDisplayFilter(
csp, model, acqStatic)
csdf.setStatic(True)
csdf.display()
btkTools.smartWriter(acqStatic, "upperLimb_calib.c3d")
# joint centres
np.testing.assert_almost_equal(
acqStatic.GetPoint("TRXO").GetValues().mean(axis=0),
acqStatic.GetPoint("OT").GetValues().mean(axis=0),
decimal=3)
np.testing.assert_almost_equal(
acqStatic.GetPoint("LCLO").GetValues().mean(axis=0),
acqStatic.GetPoint("LSJC").GetValues().mean(axis=0),
decimal=3)
np.testing.assert_almost_equal(
acqStatic.GetPoint("LHUO").GetValues().mean(axis=0),
acqStatic.GetPoint("LEJC").GetValues().mean(axis=0),
decimal=3)
np.testing.assert_almost_equal(
acqStatic.GetPoint("LCLO").GetValues().mean(axis=0),
acqStatic.GetPoint("LSJC").GetValues().mean(axis=0),
decimal=3)
np.testing.assert_almost_equal(
acqStatic.GetPoint("RCLO").GetValues().mean(axis=0),
acqStatic.GetPoint("RSJC").GetValues().mean(axis=0),
decimal=3)
np.testing.assert_almost_equal(
acqStatic.GetPoint("RHUO").GetValues().mean(axis=0),
acqStatic.GetPoint("REJC").GetValues().mean(axis=0),
decimal=3)
np.testing.assert_almost_equal(
acqStatic.GetPoint("RCLO").GetValues().mean(axis=0),
acqStatic.GetPoint("RSJC").GetValues().mean(axis=0),
decimal=3)
