def applyDecorators_CGM1(smc, model,acqStatic,optional_mp,markerDiameter):
# native but thighRotation altered in mp
if smc["left"] == enums.CgmStaticMarkerConfig.Native and optional_mp["LeftThighRotation"] !=0:
logging.warning("CASE FOUND ===> Left Side = NATIVE CGM1 + manual Thigh ")
modelDecorator.Cgm1ManualOffsets(model).compute(acqStatic,"left",optional_mp["LeftThighRotation"],
markerDiameter, optional_mp["LeftTibialTorsion"], optional_mp["LeftShankRotation"])
if smc["right"] == enums.CgmStaticMarkerConfig.Native and optional_mp["RightThighRotation"] !=0:
logging.warning("CASE FOUND ===> Right Side = NATIVE CGM1 + manual Thigh ")
modelDecorator.Cgm1ManualOffsets(model).compute(acqStatic,"right",optional_mp["RightThighRotation"],
markerDiameter,optional_mp["RightTibialTorsion"],optional_mp["RightShankRotation"])
# KAD
if smc["left"] == enums.CgmStaticMarkerConfig.KAD:
logging.warning("CASE FOUND ===> Left Side = KAD")
modelDecorator.Kad(model,acqStatic).compute(markerDiameter=markerDiameter, side="left")
if smc["right"] == enums.CgmStaticMarkerConfig.KAD:
logging.warning("CASE FOUND ===> Right Side = KAD")
modelDecorator.Kad(model,acqStatic).compute(markerDiameter=markerDiameter, side="right")
# KADmed
if smc["left"] == enums.CgmStaticMarkerConfig.KADmed:
logging.warning("CASE FOUND ===> Left Side = KAD+med")
modelDecorator.Kad(model,acqStatic).compute(markerDiameter=markerDiameter, side="left")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, markerDiameter=markerDiameter, side="left")
if smc["right"] == enums.CgmStaticMarkerConfig.KADmed:
logging.warning("CASE FOUND ===> Right Side = KAD+med")
modelDecorator.Kad(model,acqStatic).compute(markerDiameter=markerDiameter, side="right")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, markerDiameter=markerDiameter, side="right")
def applyBasicDecorators(dcm, model,acqStatic,optional_mp,markerDiameter,cgm1only=False):
# native but thighRotation altered in mp
if dcm["Left Knee"] == enums.JointCalibrationMethod.Basic and dcm["Left Ankle"] == enums.JointCalibrationMethod.Basic and optional_mp["LeftThighRotation"] !=0:
logging.warning("CASE FOUND ===> Left Side = NATIVE CGM1 + manual Thigh ")
modelDecorator.Cgm1ManualOffsets(model).compute(acqStatic,"left",optional_mp["LeftThighRotation"],
markerDiameter, optional_mp["LeftTibialTorsion"], optional_mp["LeftShankRotation"])
if dcm["Right Knee"] == enums.JointCalibrationMethod.Basic and dcm["Right Ankle"] == enums.JointCalibrationMethod.Basic and optional_mp["RightThighRotation"] !=0:
logging.warning("CASE FOUND ===> Right Side = NATIVE CGM1 + manual Thigh ")
modelDecorator.Cgm1ManualOffsets(model).compute(acqStatic,"right",optional_mp["RightThighRotation"],
markerDiameter,optional_mp["RightTibialTorsion"],optional_mp["RightShankRotation"])
# KAD - and Kadmed
if dcm["Left Knee"] == enums.JointCalibrationMethod.KAD:
logging.warning("CASE FOUND ===> Left Side = KAD")
modelDecorator.Kad(model,acqStatic).compute(markerDiameter=markerDiameter, side="left")
if dcm["Left Ankle"] == enums.JointCalibrationMethod.Medial:
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, markerDiameter=markerDiameter, side="left")
if dcm["Right Knee"] == enums.JointCalibrationMethod.KAD:
logging.warning("CASE FOUND ===> Right Side = KAD")
modelDecorator.Kad(model,acqStatic).compute(markerDiameter=markerDiameter, side="right")
if dcm["Right Ankle"] == enums.JointCalibrationMethod.Medial:
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, markerDiameter=markerDiameter, side="right")
if not cgm1only:
#Kad-like (KneeMed)
if dcm["Left Knee"] == enums.JointCalibrationMethod.Medial and dcm["Left Ankle"] == enums.JointCalibrationMethod.Basic:
modelDecorator.KneeCalibrationDecorator(model).midCondyles_KAD(acqStatic, markerDiameter=markerDiameter, side="left")
if dcm["Right Knee"] == enums.JointCalibrationMethod.Medial and dcm["Right Ankle"] == enums.JointCalibrationMethod.Basic:
modelDecorator.KneeCalibrationDecorator(model).midCondyles_KAD(acqStatic, markerDiameter=markerDiameter, side="right")
#knee and ankle Med
if dcm["Left Knee"] == enums.JointCalibrationMethod.Medial and dcm["Left Ankle"] == enums.JointCalibrationMethod.Medial:
modelDecorator.KneeCalibrationDecorator(model).midCondyles(acqStatic, markerDiameter=markerDiameter, side="left")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, markerDiameter=markerDiameter, side="left")
if dcm["Right Knee"] == enums.JointCalibrationMethod.Medial and dcm["Right Ankle"] == enums.JointCalibrationMethod.Medial:
modelDecorator.KneeCalibrationDecorator(model).midCondyles(acqStatic, markerDiameter=markerDiameter, side="right")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, markerDiameter=markerDiameter, side="right")
def advancedCGM11_KneeMedKad_TrueEquinus(cls):
"""
"""
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\kad-med-TrueEquinus\\"
staticFilename = "static.c3d"
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model = cgm.CGM1
model.configure()
markerDiameter = 14
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
}
model.addAnthropoInputParameters(mp, optional=optional_mp)
# -----------CGM STATIC CALIBRATION--------------------
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute()
# cgm decorator
modelDecorator.Kad(model, acqStatic).compute()
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic, side="both")
modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute()
btkTools.smartWriter(acqStatic, "Kad-med-TrueEquinus.c3d")
def advancedCGM1_kadMed_manualTibialTorsion(cls):
"""
- constraints on both tibial Torsion But application of a KAD-med calibration
=> tibial Torsion has to be udpated
"""
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\KAD-Med\\"
staticFilename = "MRI-US-01, 2008-08-08, 3DGA 02.c3d"
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model=cgm.CGM1LowerLimbs()
model.configure()
markerDiameter=14
mp={
'Bodymass' : 71.0,
'LeftLegLength' : 860.0,
'RightLegLength' : 865.0 ,
'LeftKneeWidth' : 102.0,
'RightKneeWidth' : 103.4,
'LeftAnkleWidth' : 75.3,
'RightAnkleWidth' : 72.9,
'LeftSoleDelta' : 0,
'RightSoleDelta' : 0,
}
optional_mp={
'InterAsisDistance' : 0,
'LeftAsisTrocanterDistance' : 0,
'LeftThighRotation' : 0,
'LeftShankRotation' : 0 ,
'LeftTibialTorsion' : -10,
'RightAsisTrocanterDistance' : 0,
'RightThighRotation' : 0,
'RightShankRotation' : 0,
'RightTibialTorsion' : 15
}
model.addAnthropoInputParameters(mp,optional=optional_mp)
# -----------CGM STATIC CALIBRATION--------------------
scp=modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp,acqStatic,model).compute()
# cgm decorator
modelDecorator.Kad(model,acqStatic).compute()
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, side="both")
modelFilters.ModelCalibrationFilter(scp,acqStatic,model).compute()
np.testing.assert_equal(model.m_useRightTibialTorsion,True )
np.testing.assert_equal(model.m_useLeftTibialTorsion,True )
np.testing.assert_equal(model.mp["LeftTibialTorsion"],0 ) # cancel by the decorator
np.testing.assert_equal(model.mp["RightTibialTorsion"],0)
ltt_vicon = np.rad2deg(acqStatic.GetMetaData().FindChild("PROCESSING").value().FindChild("LTibialTorsion").value().GetInfo().ToDouble()[0])
rtt_vicon =np.rad2deg(acqStatic.GetMetaData().FindChild("PROCESSING").value().FindChild("RTibialTorsion").value().GetInfo().ToDouble()[0])
np.testing.assert_almost_equal(-1.0*model.mp_computed["LeftTibialTorsionOffset"],ltt_vicon, decimal = 3)
np.testing.assert_almost_equal(model.mp_computed["RightTibialTorsionOffset"],rtt_vicon, decimal = 3)
def kadMedCGM1_proximal(cls, plotFlag=False):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\PIG advanced\\KAD-tibialTorsion\\"
staticFilename = "MRI-US-01, 2008-08-08, 3DGA 02.c3d"
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model = cgm.CGM1
model.configure()
markerDiameter = 14
mp = {
'Bodymass': 71.0,
'LeftLegLength': 860.0,
'RightLegLength': 865.0,
'LeftKneeWidth': 102.0,
'RightKneeWidth': 103.4,
'LeftAnkleWidth': 75.3,
'RightAnkleWidth': 72.9,
'LeftSoleDelta': 0,
'RightSoleDelta': 0,
}
model.addAnthropoInputParameters(mp)
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute()
# cgm decorator
modelDecorator.Kad(model, acqStatic).compute()
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic, side="both")
modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute()
# ------ Test 1 Motion Axe X -------
gaitFilename = "MRI-US-01, 2008-08-08, 3DGA 14.Proximal.c3d"
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
# Motion FILTER
# optimisation segmentaire et calibration fonctionnel
modMotion = modelFilters.ModelMotionFilter(
scp,
acqGait,
model,
pyCGM2Enums.motionMethod.Determinist,
viconCGM1compatible=False)
modMotion.compute()
# Joint kinematics
modelFilters.ModelJCSFilter(model, acqGait).compute(
description="vectoriel", pointLabelSuffix="cgm1_6dof")
# BSP model
bspModel = bodySegmentParameters.Bsp(model)
bspModel.compute()
# force plate -- construction du wrench attribue au pied
forceplates.appendForcePlateCornerAsMarker(acqGait)
mappedForcePlate = forceplates.matchingFootSideOnForceplate(acqGait)
modelFilters.ForcePlateAssemblyFilter(
model,
acqGait,
"RL",
leftSegmentLabel="Left Foot",
rightSegmentLabel="Right Foot").compute()
idp = modelFilters.CGMLowerlimbInverseDynamicProcedure()
modelFilters.InverseDynamicFilter(
model,
acqGait,
procedure=idp,
projection=pyCGM2Enums.MomentProjection.Proximal,
viconCGM1compatible=True).compute(pointLabelSuffix="cgm1_6dof")
modelFilters.JointPowerFilter(
model, acqGait).compute(pointLabelSuffix="cgm1_6dof")
# writer
btkTools.smartWriter(acqGait, "testInvDyn_kadMed.c3d")
if plotFlag:
plotMoment(acqGait, "LAnkleMoment", "LAnkleMoment_cgm1_6dof",
"kadMedCGM1_proximal-LAnkleMoment")
plotMoment(acqGait, "RAnkleMoment", "RAnkleMoment_cgm1_6dof",
"kadMedCGM1_proximal-RAnkleMoment")
plt.show()
def advancedCGM1_kad_manualTibialTorsion(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\KAD-manualTibialTorsion\\"
staticFilename = "MRI-US-01, 2008-08-08, 3DGA 02.c3d"
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model=cgm.CGM1
model.configure()
markerDiameter=14
mp={
'Bodymass' : 71.0,
'LeftLegLength' : 860.0,
'RightLegLength' : 865.0 ,
'LeftKneeWidth' : 102.0,
'RightKneeWidth' : 103.4,
'LeftAnkleWidth' : 75.3,
'RightAnkleWidth' : 72.9,
'LeftSoleDelta' : 0,
'RightSoleDelta' : 0,
}
optional_mp={
'LeftTibialTorsion' : -30.0,
'RightTibialTorsion' : -30.0
}
model.addAnthropoInputParameters(mp,optional=optional_mp)
# -----------CGM STATIC CALIBRATION--------------------
scp=modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp,acqStatic,model).compute()
# cgm decorator
modelDecorator.Kad(model,acqStatic).compute()
modelFilters.ModelCalibrationFilter(scp,acqStatic,model,
viconCGM1compatible=True).compute()
# TESTS ------------------------------------------------
# offset testing
offsetTesting(acqStatic,model,display =True, unitTesting=True)
# node description
np.testing.assert_equal(model.getSegment("Left Thigh").getReferential("TF").static.getNode_byLabel("LKJC").m_desc ,"KAD")
np.testing.assert_equal(model.getSegment("Right Thigh").getReferential("TF").static.getNode_byLabel("RKJC").m_desc ,"KAD")
np.testing.assert_equal(model.getSegment("Left Shank").getReferential("TF").static.getNode_byLabel("LKJC").m_desc ,"KAD")
np.testing.assert_equal(model.getSegment("Right Shank").getReferential("TF").static.getNode_byLabel("RKJC").m_desc ,"KAD")
np.testing.assert_equal(model.getSegment("Left Shank").getReferential("TF").static.getNode_byLabel("LAJC").m_desc ,"KAD-manualTT")
np.testing.assert_equal(model.getSegment("Right Shank").getReferential("TF").static.getNode_byLabel("RAJC").m_desc ,"KAD-manualTT")
np.testing.assert_equal(model.getSegment("Left Foot").getReferential("TF").static.getNode_byLabel("LAJC").m_desc ,"KAD-manualTT")
np.testing.assert_equal(model.getSegment("Right Foot").getReferential("TF").static.getNode_byLabel("RAJC").m_desc ,"KAD-manualTT")
np.testing.assert_equal(model.m_useRightTibialTorsion,True )
np.testing.assert_equal(model.m_useLeftTibialTorsion,True )
# joint centres
np.testing.assert_almost_equal(acqStatic.GetPoint("LFEP").GetValues().mean(axis=0),acqStatic.GetPoint("LHJC").GetValues().mean(axis=0),decimal = 3)
np.testing.assert_almost_equal(acqStatic.GetPoint("RFEP").GetValues().mean(axis=0),acqStatic.GetPoint("RHJC").GetValues().mean(axis=0),decimal = 3)
np.testing.assert_almost_equal(acqStatic.GetPoint("LFEO").GetValues().mean(axis=0),acqStatic.GetPoint("LKJC").GetValues().mean(axis=0),decimal = 3)
np.testing.assert_almost_equal(acqStatic.GetPoint("RFEO").GetValues().mean(axis=0),acqStatic.GetPoint("RKJC").GetValues().mean(axis=0),decimal = 3)
np.testing.assert_almost_equal(acqStatic.GetPoint("LTIO").GetValues().mean(axis=0),acqStatic.GetPoint("LAJC").GetValues().mean(axis=0),decimal = 3)
np.testing.assert_almost_equal(acqStatic.GetPoint("RTIO").GetValues().mean(axis=0),acqStatic.GetPoint("RAJC").GetValues().mean(axis=0),decimal = 3)
btkTools.smartWriter(acqStatic, "outStatic_advancedCGM1_kad_manualTibial.c3d")
def advancedCGM11_KadMed_TrueEquinus(cls):
"""
"""
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\kad-med-TrueEquinus\\"
staticFilename = "static.c3d"
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model=cgm.CGM1LowerLimbs()
model.configure()
markerDiameter=14
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
}
model.addAnthropoInputParameters(mp,optional=optional_mp)
# -----------CGM STATIC CALIBRATION--------------------
scp=modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp,acqStatic,model).compute()
# cgm decorator
modelDecorator.Kad(model,acqStatic).compute()
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, side="both")
modelFilters.ModelCalibrationFilter(scp,acqStatic,model).compute()
# tibial torsion
ltt_vicon = np.rad2deg(acqStatic.GetMetaData().FindChild("PROCESSING").value().FindChild("LTibialTorsion").value().GetInfo().ToDouble()[0])
rtt_vicon =np.rad2deg(acqStatic.GetMetaData().FindChild("PROCESSING").value().FindChild("RTibialTorsion").value().GetInfo().ToDouble()[0])
logging.info(" LTibialTorsion : Vicon (%.6f) Vs pyCGM2 (%.6f)" %(ltt_vicon,model.mp_computed["LeftTibialTorsionOffset"]))
logging.info(" RTibialTorsion : Vicon (%.6f) Vs pyCGM2 (%.6f)" %(rtt_vicon,model.mp_computed["RightTibialTorsionOffset"]))
# thigh and shank Offsets
lto = model.getViconThighOffset("Left")
lso = model.getViconShankOffset("Left")
rto = model.getViconThighOffset("Right")
rso = model.getViconShankOffset("Right")
lto_vicon = np.rad2deg(acqStatic.GetMetaData().FindChild("PROCESSING").value().FindChild("LThighRotation").value().GetInfo().ToDouble()[0])
lso_vicon = np.rad2deg(acqStatic.GetMetaData().FindChild("PROCESSING").value().FindChild("LShankRotation").value().GetInfo().ToDouble()[0])
rto_vicon = np.rad2deg(acqStatic.GetMetaData().FindChild("PROCESSING").value().FindChild("RThighRotation").value().GetInfo().ToDouble()[0])
rso_vicon = np.rad2deg(acqStatic.GetMetaData().FindChild("PROCESSING").value().FindChild("RShankRotation").value().GetInfo().ToDouble()[0])
logging.info(" LThighRotation : Vicon (%.6f) Vs pyCGM2 (%.6f)" %(lto_vicon,lto))
logging.info(" LShankRotation : Vicon (%.6f) Vs pyCGM2 (%.6f)" %(lso_vicon,lso))
logging.info(" RThighRotation : Vicon (%.6f) Vs pyCGM2 (%.6f)" %(rto_vicon,rto))
logging.info(" RShankRotation : Vicon (%.6f) Vs pyCGM2 (%.6f)" %(rso_vicon,rso))
btkTools.smartWriter(acqStatic,"Kad-med-TrueEquinus.c3d")
gaitFilename="gait trial 01.c3d"
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
# Motion FILTER
# optimisation segmentaire et calibration fonctionnel
modMotion=modelFilters.ModelMotionFilter(scp,acqGait,model,pyCGM2Enums.motionMethod.Determinist)
modMotion.compute()
# relative angles
modelFilters.ModelJCSFilter(model,acqGait).compute(description="vectoriel", pointLabelSuffix="cgm1_6dof")
# absolute angles
longitudinalAxis,forwardProgression,globalFrame = btkTools.findProgressionAxisFromPelvicMarkers(acqGait,["LASI","LPSI","RASI","RPSI"])
modelFilters.ModelAbsoluteAnglesFilter(model,acqGait,
segmentLabels=["Left Foot","Right Foot","Pelvis"],
angleLabels=["LFootProgress", "RFootProgress","Pelvis"],
eulerSequences=["TOR","TOR", "TOR"],
globalFrameOrientation = globalFrame,
forwardProgression = forwardProgression).compute(pointLabelSuffix="cgm1_6dof")
btkTools.smartWriter(acqGait, "Kad-med-TrueEquinus-angles.c3d")
def kad_midMaleolus(cls):
"""
"""
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\KAD-Med\\"
staticFilename = "MRI-US-01, 2008-08-08, 3DGA 02.c3d"
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model=cgm.CGM1LowerLimbs()
model.configure()
mp={
'Bodymass' : 71.0,
'LeftLegLength' : 860.0,
'RightLegLength' : 865.0 ,
'LeftKneeWidth' : 102.0,
'RightKneeWidth' : 103.4,
'LeftAnkleWidth' : 75.3,
'RightAnkleWidth' : 72.9,
'LeftSoleDelta' : 0,
'RightSoleDelta' : 0,
}
model.addAnthropoInputParameters(mp)
scp=modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp,acqStatic,model).compute()
# cgm decorator
modelDecorator.Kad(model,acqStatic).compute()
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, side="both")
modelFilters.ModelCalibrationFilter(scp,acqStatic,model).compute()
# tibial torsion
ltt_vicon = np.rad2deg(acqStatic.GetMetaData().FindChild("PROCESSING").value().FindChild("LTibialTorsion").value().GetInfo().ToDouble()[0])
rtt_vicon =np.rad2deg(acqStatic.GetMetaData().FindChild("PROCESSING").value().FindChild("RTibialTorsion").value().GetInfo().ToDouble()[0])
logging.info(" LTibialTorsion : Vicon (%.6f) Vs pyCGM2 (%.6f)" %(ltt_vicon,model.mp_computed["LeftTibialTorsionOffset"]))
logging.info(" RTibialTorsion : Vicon (%.6f) Vs pyCGM2 (%.6f)" %(rtt_vicon,model.mp_computed["RightTibialTorsionOffset"]))
# foot offsets
spf_l,sro_l = model.getViconFootOffset("Left")
spf_r,sro_r = model.getViconFootOffset("Right")
vicon_spf_l = np.rad2deg(acqStatic.GetMetaData().FindChild("PROCESSING").value().FindChild("LStaticPlantFlex").value().GetInfo().ToDouble()[0])
vicon_spf_r = np.rad2deg(acqStatic.GetMetaData().FindChild("PROCESSING").value().FindChild("RStaticPlantFlex").value().GetInfo().ToDouble()[0])
vicon_sro_l = np.rad2deg(acqStatic.GetMetaData().FindChild("PROCESSING").value().FindChild("LStaticRotOff").value().GetInfo().ToDouble()[0])
vicon_sro_r = np.rad2deg(acqStatic.GetMetaData().FindChild("PROCESSING").value().FindChild("RStaticRotOff").value().GetInfo().ToDouble()[0])
logging.info(" LStaticPlantFlex : Vicon (%.6f) Vs bodyBuilderFoot (%.6f)" %(spf_l,vicon_spf_l))
logging.info(" RStaticPlantFlex : Vicon (%.6f) Vs bodyBuilderFoot (%.6f)" %(spf_r,vicon_spf_r))
logging.info(" LStaticRotOff : Vicon (%.6f) Vs bodyBuilderFoot (%.6f)" %(sro_l,vicon_sro_l))
logging.info(" RStaticRotOff : Vicon (%.6f) Vs bodyBuilderFoot (%.6f)" %(sro_r,vicon_sro_r))
# thigh and shank Offsets
lto = model.getViconThighOffset("Left")
lso = model.getViconShankOffset("Left")
rto = model.getViconThighOffset("Right")
rso = model.getViconShankOffset("Right")
lto_vicon = np.rad2deg(acqStatic.GetMetaData().FindChild("PROCESSING").value().FindChild("LThighRotation").value().GetInfo().ToDouble()[0])
lso_vicon = np.rad2deg(acqStatic.GetMetaData().FindChild("PROCESSING").value().FindChild("LShankRotation").value().GetInfo().ToDouble()[0])
rto_vicon = np.rad2deg(acqStatic.GetMetaData().FindChild("PROCESSING").value().FindChild("RThighRotation").value().GetInfo().ToDouble()[0])
rso_vicon = np.rad2deg(acqStatic.GetMetaData().FindChild("PROCESSING").value().FindChild("RShankRotation").value().GetInfo().ToDouble()[0])
logging.info(" LThighRotation : Vicon (%.6f) Vs pyCGM2 (%.6f)" %(lto_vicon,lto))
logging.info(" LShankRotation : Vicon (%.6f) Vs pyCGM2 (%.6f)" %(lso_vicon,lso))
logging.info(" RThighRotation : Vicon (%.6f) Vs pyCGM2 (%.6f)" %(rto_vicon,rto))
logging.info(" RShankRotation : Vicon (%.6f) Vs pyCGM2 (%.6f)" %(rso_vicon,rso))
# ------ Test 1 Motion Axe X -------
gaitFilename="MRI-US-01, 2008-08-08, 3DGA 14.c3d"
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
# Motion FILTER
# optimisation segmentaire et calibration fonctionnel
modMotion=modelFilters.ModelMotionFilter(scp,acqGait,model,pyCGM2Enums.motionMethod.Determinist)
modMotion.compute()
# relative angles
modelFilters.ModelJCSFilter(model,acqGait).compute(description="vectoriel", pointLabelSuffix="cgm1_6dof")
# absolute angles
longitudinalAxis,forwardProgression,globalFrame = btkTools.findProgressionAxisFromPelvicMarkers(acqGait,["LASI","LPSI","RASI","RPSI"])
modelFilters.ModelAbsoluteAnglesFilter(model,acqGait,
segmentLabels=["Left Foot","Right Foot","Pelvis"],
angleLabels=["LFootProgress", "RFootProgress","Pelvis"],
eulerSequences=["TOR","TOR", "TOR"],
globalFrameOrientation = globalFrame,
forwardProgression = forwardProgression).compute(pointLabelSuffix="cgm1_6dof")
btkTools.smartWriter(acqGait, "advancedCGM1_kad_midMaleolus-14.c3d")
# tests on joint angles
np.testing.assert_almost_equal( acqGait.GetPoint("RHipAngles").GetValues(),
acqGait.GetPoint("RHipAngles_cgm1_6dof").GetValues(), decimal =3)
np.testing.assert_almost_equal( acqGait.GetPoint("LHipAngles").GetValues(),
acqGait.GetPoint("LHipAngles_cgm1_6dof").GetValues(), decimal =3)
np.testing.assert_almost_equal( acqGait.GetPoint("RKneeAngles").GetValues(),
acqGait.GetPoint("RKneeAngles_cgm1_6dof").GetValues(), decimal =2)
np.testing.assert_almost_equal( acqGait.GetPoint("LKneeAngles").GetValues(),
acqGait.GetPoint("LKneeAngles_cgm1_6dof").GetValues(), decimal =2)
np.testing.assert_almost_equal( acqGait.GetPoint("RPelvisAngles").GetValues(),
acqGait.GetPoint("RPelvisAngles_cgm1_6dof").GetValues(), decimal =3)
np.testing.assert_almost_equal( acqGait.GetPoint("LPelvisAngles").GetValues(),
acqGait.GetPoint("LPelvisAngles_cgm1_6dof").GetValues(), decimal =3)
# # tests on angles influence by Vicon error
# np.testing.assert_almost_equal( acqGait.GetPoint("RAnkleAngles").GetValues(),
# acqGait.GetPoint("RAnkleAngles_cgm1_6dof").GetValues(), decimal =3)
# np.testing.assert_almost_equal( acqGait.GetPoint("LAnkleAngles").GetValues(),
# acqGait.GetPoint("LAnkleAngles_cgm1_6dof").GetValues(), decimal =3)
#
# np.testing.assert_almost_equal( acqGait.GetPoint("LFootProgressAngles").GetValues(),
# acqGait.GetPoint("LFootProgressAngles_cgm1_6dof").GetValues(), decimal =3)
# np.testing.assert_almost_equal( acqGait.GetPoint("RFootProgressAngles").GetValues(),
# acqGait.GetPoint("RFootProgressAngles_cgm1_6dof").GetValues(), decimal =3)
# ------ Test 2 Motion Axe -X -------
gaitFilename="MRI-US-01, 2008-08-08, 3DGA 12.c3d"
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
# Motion FILTER
# optimisation segmentaire et calibration fonctionnel
modMotion=modelFilters.ModelMotionFilter(scp,acqGait,model,pyCGM2Enums.motionMethod.Determinist)
modMotion.compute()
# relative angles
modelFilters.ModelJCSFilter(model,acqGait).compute(description="vectoriel", pointLabelSuffix="cgm1_6dof")
# absolute angles
longitudinalAxis,forwardProgression,globalFrame = btkTools.findProgressionAxisFromPelvicMarkers(acqGait,["LASI","LPSI","RASI","RPSI"])
modelFilters.ModelAbsoluteAnglesFilter(model,acqGait,
segmentLabels=["Left Foot","Right Foot","Pelvis"],
angleLabels=["LFootProgress", "RFootProgress","Pelvis"],
globalFrameOrientation = globalFrame,
eulerSequences=["TOR","TOR", "TOR"],
forwardProgression = forwardProgression).compute(pointLabelSuffix="cgm1_6dof")
#btkTools.smartWriter(acqGait, "test.c3d")
# tests on joint angles
np.testing.assert_almost_equal( acqGait.GetPoint("RHipAngles").GetValues(),
acqGait.GetPoint("RHipAngles_cgm1_6dof").GetValues(), decimal =3)
np.testing.assert_almost_equal( acqGait.GetPoint("LHipAngles").GetValues(),
acqGait.GetPoint("LHipAngles_cgm1_6dof").GetValues(), decimal =3)
np.testing.assert_almost_equal( acqGait.GetPoint("RKneeAngles").GetValues(),
acqGait.GetPoint("RKneeAngles_cgm1_6dof").GetValues(), decimal =2)
np.testing.assert_almost_equal( acqGait.GetPoint("LKneeAngles").GetValues(),
acqGait.GetPoint("LKneeAngles_cgm1_6dof").GetValues(), decimal =2)
np.testing.assert_almost_equal( acqGait.GetPoint("RPelvisAngles").GetValues(),
acqGait.GetPoint("RPelvisAngles_cgm1_6dof").GetValues(), decimal =3)
np.testing.assert_almost_equal( acqGait.GetPoint("LPelvisAngles").GetValues(),
acqGait.GetPoint("LPelvisAngles_cgm1_6dof").GetValues(), decimal =3)
def applyBasicDecorators(dcm,
model,
acqStatic,
optional_mp,
markerDiameter,
cgm1only=False):
if model.getBodyPart() != enums.BodyPart.UpperLimb:
# native but thighRotation altered in mp
if dcm["Left Knee"] == enums.JointCalibrationMethod.Basic and dcm[
"Left Ankle"] == enums.JointCalibrationMethod.Basic and optional_mp[
"LeftThighRotation"] != 0:
LOGGER.logger.debug(
"CASE FOUND ===> Left Side = NATIVE CGM1 + manual Thigh ")
modelDecorator.Cgm1ManualOffsets(model).compute(
acqStatic, "left", optional_mp["LeftThighRotation"],
markerDiameter, optional_mp["LeftTibialTorsion"],
optional_mp["LeftShankRotation"])
if dcm["Right Knee"] == enums.JointCalibrationMethod.Basic and dcm[
"Right Ankle"] == enums.JointCalibrationMethod.Basic and optional_mp[
"RightThighRotation"] != 0:
LOGGER.logger.debug(
"CASE FOUND ===> Right Side = NATIVE CGM1 + manual Thigh ")
modelDecorator.Cgm1ManualOffsets(model).compute(
acqStatic, "right", optional_mp["RightThighRotation"],
markerDiameter, optional_mp["RightTibialTorsion"],
optional_mp["RightShankRotation"])
# KAD - and Kadmed
if dcm["Left Knee"] == enums.JointCalibrationMethod.KAD:
LOGGER.logger.debug("CASE FOUND ===> Left Side = Knee-KAD")
modelDecorator.Kad(model, acqStatic).compute(
markerDiameter=markerDiameter, side="left")
if dcm["Left Ankle"] == enums.JointCalibrationMethod.Medial:
LOGGER.logger.debug("CASE FOUND ===> Left Side = Ankle-Med")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic, markerDiameter=markerDiameter, side="left")
if dcm["Right Knee"] == enums.JointCalibrationMethod.KAD:
LOGGER.logger.debug("CASE FOUND ===> Right Side = Knee-KAD")
modelDecorator.Kad(model, acqStatic).compute(
markerDiameter=markerDiameter, side="right")
if dcm["Right Ankle"] == enums.JointCalibrationMethod.Medial:
LOGGER.logger.debug("CASE FOUND ===> Right Side = Ankle-Med")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic, markerDiameter=markerDiameter, side="right")
if not cgm1only:
if model.getBodyPart() != enums.BodyPart.UpperLimb:
#Kad-like (KneeMed)
if dcm["Left Knee"] == enums.JointCalibrationMethod.Medial and dcm[
"Left Ankle"] == enums.JointCalibrationMethod.Basic:
modelDecorator.KneeCalibrationDecorator(model).midCondyles_KAD(
acqStatic, markerDiameter=markerDiameter, side="left")
if dcm["Right Knee"] == enums.JointCalibrationMethod.Medial and dcm[
"Right Ankle"] == enums.JointCalibrationMethod.Basic:
modelDecorator.KneeCalibrationDecorator(model).midCondyles_KAD(
acqStatic, markerDiameter=markerDiameter, side="right")
#knee and ankle Med
if dcm["Left Knee"] == enums.JointCalibrationMethod.Medial and dcm[
"Left Ankle"] == enums.JointCalibrationMethod.Medial:
LOGGER.logger.info(
"[pyCGM2] Left Knee : Medial - Left Ankle : Medial")
modelDecorator.KneeCalibrationDecorator(model).midCondyles(
acqStatic, markerDiameter=markerDiameter, side="left")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic, markerDiameter=markerDiameter, side="left")
if dcm["Right Knee"] == enums.JointCalibrationMethod.Medial and dcm[
"Right Ankle"] == enums.JointCalibrationMethod.Medial:
LOGGER.logger.info(
"[pyCGM2] Right Knee : Medial - Right Ankle : Medial")
modelDecorator.KneeCalibrationDecorator(model).midCondyles(
acqStatic, markerDiameter=markerDiameter, side="right")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic, markerDiameter=markerDiameter, side="right")
def basicCGM1_KAD_tibialTorsion(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\KAD-tibialTorsion-static_StaticVsDynamicAngles\\"
staticFilename = "MRI-US-01, 2008-08-08, 3DGA 02.c3d"
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model = cgm.CGM1LowerLimbs()
model.configure()
markerDiameter = 14
mp = {
'Bodymass': 71.0,
'LeftLegLength': 860.0,
'RightLegLength': 865.0,
'LeftKneeWidth': 102.0,
'RightKneeWidth': 103.4,
'LeftAnkleWidth': 75.3,
'RightAnkleWidth': 72.9,
'LeftSoleDelta': 0,
'RightSoleDelta': 0,
}
model.addAnthropoInputParameters(mp)
# -----------CGM STATIC CALIBRATION--------------------
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp,
acqStatic,
model,
leftFlatFoot=False,
rightFlatFoot=False).compute()
# cgm decorator
modelDecorator.Kad(model, acqStatic).compute()
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic, side="both")
# final calibration
modelFilters.ModelCalibrationFilter(scp,
acqStatic,
model,
leftFlatFoot=False,
rightFlatFoot=False).compute()
spf_l, sro_l = model.getViconFootOffset("Left")
spf_r, sro_r = model.getViconFootOffset("Right")
# TESTS ------------------------------------------------
np.testing.assert_equal(model.m_useRightTibialTorsion, True)
np.testing.assert_equal(model.m_useLeftTibialTorsion, True)
# joint centres
np.testing.assert_almost_equal(
acqStatic.GetPoint("LFEP").GetValues().mean(axis=0),
acqStatic.GetPoint("LHJC").GetValues().mean(axis=0),
decimal=3)
np.testing.assert_almost_equal(
acqStatic.GetPoint("RFEP").GetValues().mean(axis=0),
acqStatic.GetPoint("RHJC").GetValues().mean(axis=0),
decimal=3)
np.testing.assert_almost_equal(
acqStatic.GetPoint("LFEO").GetValues().mean(axis=0),
acqStatic.GetPoint("LKJC").GetValues().mean(axis=0),
decimal=3)
np.testing.assert_almost_equal(
acqStatic.GetPoint("RFEO").GetValues().mean(axis=0),
acqStatic.GetPoint("RKJC").GetValues().mean(axis=0),
decimal=3)
np.testing.assert_almost_equal(
acqStatic.GetPoint("LTIO").GetValues().mean(axis=0),
acqStatic.GetPoint("LAJC").GetValues().mean(axis=0),
decimal=3)
np.testing.assert_almost_equal(
acqStatic.GetPoint("RTIO").GetValues().mean(axis=0),
acqStatic.GetPoint("RAJC").GetValues().mean(axis=0),
decimal=3)
# foot offsets
vicon_spf_l = np.rad2deg(
acqStatic.GetMetaData().FindChild("PROCESSING").value().FindChild(
"LStaticPlantFlex").value().GetInfo().ToDouble()[0])
vicon_spf_r = np.rad2deg(
acqStatic.GetMetaData().FindChild("PROCESSING").value().FindChild(
"RStaticPlantFlex").value().GetInfo().ToDouble()[0])
vicon_sro_l = np.rad2deg(
acqStatic.GetMetaData().FindChild("PROCESSING").value().FindChild(
"LStaticRotOff").value().GetInfo().ToDouble()[0])
vicon_sro_r = np.rad2deg(
acqStatic.GetMetaData().FindChild("PROCESSING").value().FindChild(
"RStaticRotOff").value().GetInfo().ToDouble()[0])
logging.info(" LStaticPlantFlex : Vicon (%.6f) Vs pyCGM2 (%.6f)" %
(spf_l, vicon_spf_l))
logging.info(" RStaticPlantFlex : Vicon (%.6f) Vs pyCGM2 (%.6f)" %
(spf_r, vicon_spf_r))
logging.info(" LStaticRotOff : Vicon (%.6f) Vs pyCGM2 (%.6f)" %
(sro_l, vicon_sro_l))
logging.info(" RStaticRotOff : Vicon (%.6f) Vs pyCGM2 (%.6f)" %
(sro_r, vicon_sro_r))
np.testing.assert_almost_equal(spf_l, vicon_spf_l, decimal=3)
np.testing.assert_almost_equal(spf_r, vicon_spf_r, decimal=3)
np.testing.assert_almost_equal(sro_l, vicon_sro_l, decimal=3)
np.testing.assert_almost_equal(sro_r, vicon_sro_r, decimal=3)
# -------- CGM FITTING -------------------------------------------------
# ---- on c3d processed vicon static-pig operation
# Motion FILTER
# optimisation segmentaire et calibration fonctionnel
modMotion = modelFilters.ModelMotionFilter(
scp,
acqStatic,
model,
pyCGM2Enums.motionMethod.Determinist,
markerDiameter=markerDiameter,
pigStatic=True,
useRightKJCmarker="RKJC_KAD",
useRightAJCmarker="RAJC_KAD",
useLeftKJCmarker="LKJC_KAD",
useLeftAJCmarker="LAJC_MID",
viconCGM1compatible=False)
modMotion.compute()
# relative angles
modelFilters.ModelJCSFilter(model, acqStatic).compute(
description="vectoriel", pointLabelSuffix="cgm1_6dof")
btkTools.smartWriter(acqStatic,
"test_basicCGM1_KADmed-staticAngles.c3d")
# ---- on c3d processed vicon dynamic-pig operation
gaitFilename = "MRI-US-01, 2008-08-08, 3DGA 02 -dynamic.c3d" #"staticComparisonPipelines.c3d"
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
# Motion FILTER
# optimisation segmentaire et calibration fonctionnel
# output and plot
#btkTools.smartWriter(acqGait, "test_basicCGM1_KADmed-staticAngles.c3d")
plotComparison(acqGait, acqStatic, "LHipAngles")
plotComparison(acqGait, acqStatic, "LKneeAngles")
plotComparison(acqGait, acqStatic, "LAnkleAngles")