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")