def optionalMp(self):
if self._vsk is None:
return self._userSettings["MP"]["Optional"]
else:
required_mp,optional_mp = vskTools.getFromVskSubjectMp(self._vsk, resetFlag=True)
self._userSettings["MP"]["Optional"].update(optional_mp)
return optional_mp
def test_CGM24_FullBody_noOptions_uncorrectLowerLimbMarker(self):
DATA_PATH = pyCGM2.TEST_DATA_PATH + "Scenarii\\different static and dynamic marker set\\CGM24-fullBody\\"
staticFilename = "static.c3d"
acqStatic = btkTools.smartReader(DATA_PATH + staticFilename)
markerDiameter=14
leftFlatFoot = False
rightFlatFoot = False
headStraight = False
pointSuffix = "test"
vskFile = vskTools.getVskFiles(DATA_PATH)
vsk = vskTools.Vsk(DATA_PATH + "PN07.vsk")
required_mp,optional_mp = vskTools.getFromVskSubjectMp(vsk, resetFlag=True)
settings = files.openFile(pyCGM2.PYCGM2_SETTINGS_FOLDER,"CGM2_4-pyCGM2.settings")
hjcMethod = settings["Calibration"]["HJC"]
translators = files.getTranslators(DATA_PATH,"CGM2_4.translators")
# if not translators: translators = settings["Translators"]
model,finalAcqStatic = cgm2_4.calibrate(DATA_PATH,
staticFilename,
translators,
settings,
required_mp,
optional_mp,
False,
leftFlatFoot,
rightFlatFoot,
headStraight,
markerDiameter,
hjcMethod,
pointSuffix,
displayCoordinateSystem=True)
# btkTools.smartWriter(finalAcqStatic, str( staticFilename[:-4]+"-pyCGM2modelled.c3d"))
logging.info("Static Calibration -----> Done")
gaitFilename="gait1_noLASI.c3d"
mfpa = None
reconstructFilenameLabelled = gaitFilename
acqGait = cgm2_4.fitting(model,DATA_PATH, reconstructFilenameLabelled,
translators,
settings,
False,
markerDiameter,
pointSuffix,
mfpa,
enums.MomentProjection.Proximal,
displayCoordinateSystem=True)
assert model.m_bodypart == enums.BodyPart.UpperLimb
def test_sample0(self):
DATA_PATH = MAIN_PATH = pyCGM2.TEST_DATA_PATH + "GaitModels\CGM1\\fullBody-native-noOptions\\"
staticFilename = "static.c3d"
acqStatic = btkTools.smartReader(DATA_PATH + staticFilename)
markerDiameter = 14
leftFlatFoot = False
rightFlatFoot = False
headStraight = False
pointSuffix = "test"
vskFile = vskTools.getVskFiles(DATA_PATH)
vsk = vskTools.Vsk(DATA_PATH + "New Subject.vsk")
required_mp, optional_mp = vskTools.getFromVskSubjectMp(vsk,
resetFlag=True)
# calibration according CGM1
model, finalAcqStatic = cgm1.calibrate(DATA_PATH,
staticFilename,
None,
required_mp,
optional_mp,
leftFlatFoot,
rightFlatFoot,
headStraight,
markerDiameter,
pointSuffix,
displayCoordinateSystem=True)
# no fitting operation, only checking of forceplateAssembly
gaitFilename = "gait1.c3d"
acqGait = btkTools.smartReader(DATA_PATH + gaitFilename)
mfpa = None
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)
testingUtils.plotComparisonOfPoint(acqGait, "RGroundReactionForce",
"test")
testingUtils.plotComparisonOfPoint(acqGait, "RGroundReactionMoment",
"test")
def test_FullBody_noOptions(self):
DATA_PATH = MAIN_PATH = pyCGM2.TEST_DATA_PATH + "LowLevel\\uncropped data\\cgm1\\"
staticFilename = "static.c3d"
DATA_PATH_OUT = pyCGM2.TEST_DATA_PATH_OUT+"LowLevel\\uncropped data\\cgm1\\"
files.createDir(DATA_PATH_OUT)
markerDiameter=14
leftFlatFoot = True
rightFlatFoot = True
headStraight = True
pointSuffix = ""
vskFile = vskTools.getVskFiles(DATA_PATH)
vsk = vskTools.Vsk(DATA_PATH + "New Subject.vsk")
required_mp,optional_mp = vskTools.getFromVskSubjectMp(vsk, resetFlag=True)
model,finalAcqStatic = cgm1.calibrate(DATA_PATH,
staticFilename,
None,
required_mp,
optional_mp,
leftFlatFoot,
rightFlatFoot,
headStraight,
markerDiameter,
pointSuffix,
displayCoordinateSystem=True)
# btkTools.smartWriter(finalAcqStatic, str( staticFilename[:-4]+"-pyCGM2modelled.c3d"))
# logging.info("Static Calibration -----> Done")
gaitFilename="gait1.c3d"
acqGait0 = btkTools.smartReader(DATA_PATH + gaitFilename)
trackingMarkers = model.getTrackingMarkers(acqGait0)
validFrames,vff,vlf = btkTools.findValidFrames(acqGait0,trackingMarkers)
mfpa = None
reconstructFilenameLabelled = gaitFilename
acqGait = cgm1.fitting(model,DATA_PATH, reconstructFilenameLabelled,
None,
markerDiameter,
pointSuffix,
mfpa,
enums.MomentProjection.Proximal,
displayCoordinateSystem=True)
btkTools.smartWriter(acqGait, DATA_PATH_OUT+"//gait1-processed.c3d")
def test_CGM1_FullBody_noOptions_uncorrectUpperLimbMarker(self):
DATA_PATH = pyCGM2.TEST_DATA_PATH + "Scenarii\different static and dynamic marker set\CGM1-fullBody\\"
staticFilename = "static.c3d"
acqStatic = btkTools.smartReader(DATA_PATH + staticFilename)
markerDiameter = 14
leftFlatFoot = False
rightFlatFoot = False
headStraight = False
pointSuffix = "test"
vskFile = vskTools.getVskFiles(DATA_PATH)
vsk = vskTools.Vsk(DATA_PATH + "New Subject.vsk")
required_mp, optional_mp = vskTools.getFromVskSubjectMp(vsk,
resetFlag=True)
model, finalAcqStatic, error = cgm1.calibrate(
DATA_PATH,
staticFilename,
None,
required_mp,
optional_mp,
leftFlatFoot,
rightFlatFoot,
headStraight,
markerDiameter,
pointSuffix,
displayCoordinateSystem=True)
# btkTools.smartWriter(finalAcqStatic, str( staticFilename[:-4]+"-pyCGM2modelled.c3d"))
LOGGER.logger.info("Static Calibration -----> Done")
# case 1 - one marker on the upper limb misses
gaitFilename = "gait1_noRFIN.c3d"
mfpa = None
reconstructFilenameLabelled = gaitFilename
acqGait, error = cgm1.fitting(model,
DATA_PATH,
reconstructFilenameLabelled,
None,
markerDiameter,
pointSuffix,
mfpa,
enums.MomentProjection.Proximal,
displayCoordinateSystem=True)
assert model.m_bodypart == enums.BodyPart.FullBody
def test_CGM1_FullBody_noOptions_noFP(self):
DATA_PATH = pyCGM2.TEST_DATA_PATH + "GaitModels\CGM1\\fullBody-native-noOptions - noFP\\"
staticFilename = "static.c3d"
acqStatic = btkTools.smartReader(DATA_PATH + staticFilename)
markerDiameter=14
leftFlatFoot = False
rightFlatFoot = False
headStraight = False
pointSuffix = "test"
vskFile = vskTools.getVskFiles(DATA_PATH)
vsk = vskTools.Vsk(DATA_PATH + "New Subject.vsk")
required_mp,optional_mp = vskTools.getFromVskSubjectMp(vsk, resetFlag=True)
model,finalAcqStatic = cgm1.calibrate(DATA_PATH,
staticFilename,
None,
required_mp,
optional_mp,
leftFlatFoot,
rightFlatFoot,
headStraight,
markerDiameter,
pointSuffix,
displayCoordinateSystem=True)
# btkTools.smartWriter(finalAcqStatic, str( staticFilename[:-4]+"-pyCGM2modelled.c3d"))
# logging.info("Static Calibration -----> Done")
gaitFilename="gait1.c3d"
mfpa = None
reconstructFilenameLabelled = gaitFilename
acqGait = cgm1.fitting(model,DATA_PATH, reconstructFilenameLabelled,
None,
markerDiameter,
pointSuffix,
mfpa,
enums.MomentProjection.Proximal,
displayCoordinateSystem=True)
btkTools.smartWriter(acqGait, "gait1-pyCGM2modelled.c3d")
calibrateFilenameLabelled = args.trial
logging.info( "data Path: "+ DATA_PATH )
logging.info( "calibration file: "+ calibrateFilenameLabelled)
# --------------------------SUBJECT ------------------------------------
# translators management
translators = files.getTranslators(DATA_PATH,"CGM1.translators")
if not translators: translators = settings["Translators"]
# --------------------------SUBJECT ------------------------------------
if os.path.isfile(DATA_PATH+subject+".vsk"):
logging.info("vsk file found")
vsk = vskTools.Vsk(str(DATA_PATH + subject+".vsk"))
required_mp,optional_mp = vskTools.getFromVskSubjectMp(vsk, resetFlag=args.resetMP)
mpInfo,mpFilename = files.getJsonFileContent(DATA_PATH,"mp.pyCGM2",subject)
else:
logging.info("no vsk found")
mpInfo,mpFilename = files.getJsonFileContent(DATA_PATH,"mp.pyCGM2",subject)
required_mp,optional_mp = files.getMp(mpInfo, resetFlag=args.resetMP)
#---------------------------------------------------------------------------
# --------------------------MODELLING PROCESSING ---------------------------
model,acqStatic = cgm1.calibrate(DATA_PATH,calibrateFilenameLabelled,translators,required_mp,optional_mp,
leftFlatFoot,rightFlatFoot,markerDiameter,
pointSuffix)
#---------------------------------------------------------------------------
#---------------------------------------------------------------------------
def test_FullBody_noOptions_global(self):
DATA_PATH = MAIN_PATH = pyCGM2.TEST_DATA_PATH + "GaitModels\\CGM1\\LowerLimb-medMed_Yprogression\\"
staticFilename = "static.c3d"
acqStatic = btkTools.smartReader(DATA_PATH + staticFilename)
markerDiameter = 14
leftFlatFoot = False
rightFlatFoot = False
headStraight = False
pointSuffix = "test"
vskFile = vskTools.getVskFiles(DATA_PATH)
vsk = vskTools.Vsk(DATA_PATH + "Subject.vsk")
required_mp, optional_mp = vskTools.getFromVskSubjectMp(vsk,
resetFlag=True)
model, finalAcqStatic = cgm1.calibrate(DATA_PATH,
staticFilename,
None,
required_mp,
optional_mp,
leftFlatFoot,
rightFlatFoot,
headStraight,
markerDiameter,
pointSuffix,
displayCoordinateSystem=True)
# btkTools.smartWriter(finalAcqStatic, str( staticFilename[:-4]+"-pyCGM2modelled.c3d"))
# logging.info("Static Calibration -----> Done")
gaitFilename = "gait1.Global.c3d"
mfpa = "RLX"
reconstructFilenameLabelled = gaitFilename
acqGait = cgm1.fitting(model,
DATA_PATH,
reconstructFilenameLabelled,
None,
markerDiameter,
pointSuffix,
mfpa,
enums.MomentProjection.Global,
displayCoordinateSystem=True)
testingUtils.plotComparison_ForcePanel(acqGait, None, "test", "Left")
testingUtils.plotComparison_ForcePanel(acqGait, None, "test", "Right")
gaitFilename = "gait2.Global.c3d"
mfpa = "XLR"
reconstructFilenameLabelled = gaitFilename
acqGait = cgm1.fitting(model,
DATA_PATH,
reconstructFilenameLabelled,
None,
markerDiameter,
pointSuffix,
mfpa,
enums.MomentProjection.Global,
displayCoordinateSystem=True)
testingUtils.plotComparison_ForcePanel(acqGait, None, "test", "Left")
testingUtils.plotComparison_ForcePanel(acqGait, None, "test", "Right")
def test_issue_signAbdAddOffset(self):
DATA_PATH = pyCGM2.TEST_DATA_PATH + "Issues\\StephenM\\signedAbdAdd-KadMed\\"
staticFilename = "Static.c3d"
acqStatic = btkTools.smartReader(str(DATA_PATH + staticFilename))
markerDiameter = 14
leftFlatFoot = True
rightFlatFoot = True
headStraight = True
pointSuffix = "test"
vskFile = vskTools.getVskFiles(DATA_PATH)
vsk = vskTools.Vsk(DATA_PATH + "Nick.vsk")
required_mp, optional_mp = vskTools.getFromVskSubjectMp(vsk,
resetFlag=True)
# required_mp={
# 'Bodymass' : 65.0,
# 'LeftLegLength' : 800.0,
# 'RightLegLength' : 800.0 ,
# 'LeftKneeWidth' : 120.0,
# 'RightKneeWidth' : 120.0,
# 'LeftAnkleWidth' : 100.0,
# 'RightAnkleWidth' : 100.0,
# 'LeftSoleDelta' : 0,
# 'RightSoleDelta' : 0,
# 'LeftShoulderOffset' : 40,
# 'LeftElbowWidth' : 74,
# 'LeftWristWidth' : 55 ,
# 'LeftHandThickness' : 34 ,
# 'RightShoulderOffset' : 40,
# 'RightElbowWidth' : 74,
# 'RightWristWidth' : 55 ,
# 'RightHandThickness' : 34}
#
# optional_mp={
# 'InterAsisDistance' : 0,#0,
# 'LeftAsisTrocanterDistance' : 0,#0,
# 'LeftTibialTorsion' : 0,#0,
# 'LeftThighRotation' : 0,#0,
# 'LeftShankRotation' : 0,#0,ipdb
# 'RightAsisTrocanterDistance' : 0,#0,
# 'RightTibialTorsion' : 0,#0,
# 'RightThighRotation' : 0,#0,
# 'RightShankRotation' : 0}
model, finalAcqStatic = cgm1.calibrate(DATA_PATH,
staticFilename,
None,
required_mp,
optional_mp,
leftFlatFoot,
rightFlatFoot,
headStraight,
markerDiameter,
pointSuffix,
displayCoordinateSystem=True)
testingUtils.test_offset(
model.mp_computed["LeftThighRotationOffset"],
acqStatic,
"LThighRotation",
decimal=1) # not enought accurate but unsignificant
testingUtils.test_offset(model.mp_computed["RightThighRotationOffset"],
acqStatic,
"RThighRotation",
decimal=1)
testingUtils.test_offset(model.mp_computed["LeftShankRotationOffset"],
acqStatic,
"LShankRotation",
decimal=1)
testingUtils.test_offset(model.mp_computed["RightShankRotationOffset"],
acqStatic,
"RShankRotation",
decimal=1)
testingUtils.test_offset(model.mp_computed["LeftTibialTorsionOffset"],
acqStatic,
"LTibialTorsion",
decimal=1)
testingUtils.test_offset(model.mp_computed["RightTibialTorsionOffset"],
acqStatic,
"RTibialTorsion",
decimal=1)
testingUtils.test_offset(model.mp_computed["LeftAnkleAbAddOffset"],
acqStatic,
"LAnkleAbAdd",
decimal=1)
testingUtils.test_offset(model.mp_computed["RightAnkleAbAddOffset"],
acqStatic,
"RAnkleAbAdd",
decimal=1)
testingUtils.test_offset(
model.mp_computed["LeftStaticPlantFlexOffset"],
acqStatic,
"LStaticPlantFlex",
decimal=1)
testingUtils.test_offset(
model.mp_computed["RightStaticPlantFlexOffset"],
acqStatic,
"RStaticPlantFlex",
decimal=1)
testingUtils.test_offset(model.mp_computed["LeftStaticRotOffset"],
acqStatic,
"LStaticRotOff",
decimal=1)
testingUtils.test_offset(model.mp_computed["RightStaticRotOffset"],
acqStatic,
"RStaticRotOff",
decimal=1)
def test_issue_jointForce_CGM24(self):
"""
synopsis : inverted sign of the x-component of the joint force with CGM1.1 to CGM2.4
"""
DATA_PATH = MAIN_PATH = pyCGM2.TEST_DATA_PATH + "Issues\\StephenM\\sign_jointForce_CGM24\\"
staticFilename = "FullBody CGM2 data Cal 01.c3d"
acqStatic = btkTools.smartReader(DATA_PATH + staticFilename)
markerDiameter = 14
leftFlatFoot = False
rightFlatFoot = False
headStraight = False
pointSuffix = "test"
vskFile = vskTools.getVskFiles(DATA_PATH)
vsk = vskTools.Vsk(DATA_PATH + "Nick.vsk")
required_mp, optional_mp = vskTools.getFromVskSubjectMp(vsk,
resetFlag=True)
settings = files.openFile(pyCGM2.PYCGM2_APPDATA_PATH,
"CGM2_4-pyCGM2.settings")
model, finalAcqStatic = cgm2_4.calibrate(DATA_PATH,
staticFilename,
None,
settings,
required_mp,
optional_mp,
True,
leftFlatFoot,
rightFlatFoot,
headStraight,
markerDiameter, {
"Left": "Hara",
"Right": "Hara"
},
pointSuffix,
displayCoordinateSystem=True)
# btkTools.smartWriter(finalAcqStatic, str( staticFilename[:-4]+"-pyCGM2modelled.c3d"))
# logging.info("Static Calibration -----> Done")
gaitFilename = "Capture 02.Distal.c3d"
mfpa = "R"
reconstructFilenameLabelled = gaitFilename
acqGait = cgm2_4.fitting(model,
DATA_PATH,
reconstructFilenameLabelled,
None,
settings,
True,
markerDiameter,
pointSuffix,
mfpa,
enums.MomentProjection.Distal,
displayCoordinateSystem=True)
testingUtils.plotComparisonOfPoint(acqGait,
"RAnkleForce",
"test",
title="RAnkleForce PiG - CGM24")
testingUtils.plotComparisonOfPoint(acqGait,
"RKneeForce",
"test",
title="RKneeForce PiG - CGM24")
testingUtils.plotComparisonOfPoint(acqGait,
"RHipForce",
"test",
title="RHipForce PiG - CGM24")
def test_FullBody_noOptions(self):
DATA_PATH = pyCGM2.TEST_DATA_PATH + "GaitModels\CGM1\\fullBody-native-Options\\"
staticFilename = "static.c3d"
acqStatic = btkTools.smartReader(DATA_PATH + staticFilename)
markerDiameter=14
leftFlatFoot = True
rightFlatFoot = True
headStraight = True
pointSuffix = "test"
vskFile = vskTools.getVskFiles(DATA_PATH)
vsk = vskTools.Vsk(DATA_PATH + "New Subject.vsk")
required_mp,optional_mp = vskTools.getFromVskSubjectMp(vsk, resetFlag=True)
model,finalAcqStatic,error = cgm1.calibrate(DATA_PATH,
staticFilename,
None,
required_mp,
optional_mp,
leftFlatFoot,
rightFlatFoot,
headStraight,
markerDiameter,
pointSuffix,
displayCoordinateSystem=True)
testingUtils.test_offset(model.mp_computed["LeftThighRotationOffset"],acqStatic,"LThighRotation", decimal=3)
testingUtils.test_offset(model.mp_computed["RightThighRotationOffset"],acqStatic,"RThighRotation", decimal=3)
testingUtils.test_offset(model.mp_computed["LeftShankRotationOffset"],acqStatic,"LShankRotation", decimal=3)
testingUtils.test_offset(model.mp_computed["RightShankRotationOffset"],acqStatic,"RShankRotation", decimal=3)
testingUtils.test_offset(model.mp_computed["LeftTibialTorsionOffset"],acqStatic,"LTibialTorsion", decimal=3)
testingUtils.test_offset(model.mp_computed["RightTibialTorsionOffset"],acqStatic,"RTibialTorsion", decimal=3)
testingUtils.test_offset(model.mp_computed["LeftAnkleAbAddOffset"],acqStatic,"LAnkleAbAdd", decimal=3)
testingUtils.test_offset(model.mp_computed["RightAnkleAbAddOffset"],acqStatic,"RAnkleAbAdd", decimal=3)
testingUtils.test_offset(model.mp_computed["LeftStaticPlantFlexOffset"],acqStatic,"LStaticPlantFlex", decimal=3)
testingUtils.test_offset(model.mp_computed["RightStaticPlantFlexOffset"],acqStatic,"RStaticPlantFlex", decimal=3)
testingUtils.test_offset(model.mp_computed["LeftStaticRotOffset"],acqStatic,"LStaticRotOff", decimal=3)
testingUtils.test_offset(model.mp_computed["RightStaticRotOffset"],acqStatic,"RStaticRotOff", decimal=3)
np.testing.assert_equal(model.getSegment("Left Thigh").getReferential("TF").static.getNode_byLabel("LHJC").m_desc ,"Davis")
np.testing.assert_equal(model.getSegment("Right Thigh").getReferential("TF").static.getNode_byLabel("RHJC").m_desc ,"Davis")
np.testing.assert_equal(model.getSegment("Left Thigh").getReferential("TF").static.getNode_byLabel("LKJC").m_desc ,"Chord")
np.testing.assert_equal(model.getSegment("Right Thigh").getReferential("TF").static.getNode_byLabel("RKJC").m_desc ,"Chord")
np.testing.assert_equal(model.getSegment("Left Shank").getReferential("TF").static.getNode_byLabel("LKJC").m_desc ,"Chord")
np.testing.assert_equal(model.getSegment("Right Shank").getReferential("TF").static.getNode_byLabel("RKJC").m_desc ,"Chord")
np.testing.assert_equal(model.getSegment("Left Shank").getReferential("TF").static.getNode_byLabel("LAJC").m_desc ,"Chord")
np.testing.assert_equal(model.getSegment("Right Shank").getReferential("TF").static.getNode_byLabel("RAJC").m_desc ,"Chord")
np.testing.assert_equal(model.getSegment("Left Foot").getReferential("TF").static.getNode_byLabel("LAJC").m_desc ,"Chord")
np.testing.assert_equal(model.getSegment("Right Foot").getReferential("TF").static.getNode_byLabel("RAJC").m_desc ,"Chord")
testingUtils.test_point(finalAcqStatic,"LPelvisAngles","LPelvisAngles_test",decimal = 3)
testingUtils.test_point(finalAcqStatic,"RPelvisAngles","RPelvisAngles_test",decimal = 3)
testingUtils.test_point(finalAcqStatic,"LHipAngles","LHipAngles_test",decimal = 3)
testingUtils.test_point(finalAcqStatic,"LKneeAngles","LKneeAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"LAnkleAngles","LAnkleAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"RHipAngles","RHipAngles_test",decimal = 3)
testingUtils.test_point(finalAcqStatic,"RKneeAngles","RKneeAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"RAnkleAngles","RAnkleAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"LFootProgressAngles","LFootProgressAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"RFootProgressAngles","RFootProgressAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"LThoraxAngles","LThoraxAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"RThoraxAngles","RThoraxAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"LSpineAngles","LSpineAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"RSpineAngles","RSpineAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"LShoulderAngles","LShoulderAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"RShoulderAngles","RShoulderAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"LElbowAngles","LElbowAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"RElbowAngles","RElbowAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"LHeadAngles","LHeadAngles_test",decimal = 3)
testingUtils.test_point(finalAcqStatic,"RHeadAngles","RHeadAngles_test",decimal = 3)
# btkTools.smartWriter(finalAcqStatic, str( staticFilename[:-4]+"-pyCGM2modelled.c3d"))
# LOGGER.logger.info("Static Calibration -----> Done")
gaitFilename="gait1.c3d"
mfpa = None
reconstructFilenameLabelled = gaitFilename
acqGait,error = cgm1.fitting(model,DATA_PATH, reconstructFilenameLabelled,
None,
markerDiameter,
pointSuffix,
mfpa,
enums.MomentProjection.Proximal,
displayCoordinateSystem=True)
testingUtils.test_point(acqGait,"LPelvisAngles","LPelvisAngles_test",decimal = 3)
testingUtils.test_point(acqGait,"RPelvisAngles","RPelvisAngles_test",decimal = 3)
testingUtils.test_point(acqGait,"LHipAngles","LHipAngles_test",decimal = 3)
testingUtils.test_point(acqGait,"LKneeAngles","LKneeAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"LAnkleAngles","LAnkleAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"RHipAngles","RHipAngles_test",decimal = 3)
testingUtils.test_point(acqGait,"RKneeAngles","RKneeAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"RAnkleAngles","RAnkleAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"LFootProgressAngles","LFootProgressAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"RFootProgressAngles","RFootProgressAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"LThoraxAngles","LThoraxAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"RThoraxAngles","RThoraxAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"LSpineAngles","LSpineAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"RSpineAngles","RSpineAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"LShoulderAngles","LShoulderAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"RShoulderAngles","RShoulderAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"LElbowAngles","LElbowAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"RElbowAngles","RElbowAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"LHeadAngles","LHeadAngles_test",decimal = 3)
testingUtils.test_point(acqGait,"RHeadAngles","RHeadAngles_test",decimal = 3)
# testingUtils.test_point(acqGait,"LWristAngles","LWristAngles_test",decimal = 3) fail on z!
# testingUtils.test_point(acqGait,"RWristAngles","RWristAngles_test",decimal = 3) fail on Z!
# testingUtils.test_point(acqGait,"CentreOfMass","CentreOfMass_test",decimal = 3)
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())
def modelling(manager,DATA_PATH,DATA_PATH_OUT,vskFile=None):
modelVersion = manager.getModelVersion()
logging.info("model version : %s" %(modelVersion))
# --------------------------MODELLING ------------------------------------
# manage global settings and translators
if modelVersion == "CGM1.0":
translatorFiles= "CGM1.translators"
globalPyCGM2settingFile = "CGM1-pyCGM2.settings"
elif modelVersion == "CGM1.1":
translatorFiles= "CGM1_1.translators"
globalPyCGM2settingFile = "CGM1_1-pyCGM2.settings"
elif modelVersion == "CGM2.1":
translatorFiles= "CGM2_1.translators"
globalPyCGM2settingFile = "CGM2_1-pyCGM2.settings"
elif modelVersion == "CGM2.2":
translatorFiles= "CGM2_2.translators"
globalPyCGM2settingFile = "CGM2_2-pyCGM2.settings"
elif modelVersion == "CGM2.2e":
translatorFiles= "CGM2_2.translators"
globalPyCGM2settingFile = "CGM2_2-Expert-pyCGM2.settings"
elif modelVersion == "CGM2.3":
translatorFiles= "CGM2_3.translators"
globalPyCGM2settingFile = "CGM2_3-pyCGM2.settings"
elif modelVersion == "CGM2.3e":
translatorFiles= "CGM2_3.translators"
globalPyCGM2settingFile = "CGM2_3-Expert-pyCGM2.settings"
elif modelVersion == "CGM2.4":
translatorFiles= "CGM2_4.translators"
globalPyCGM2settingFile = "CGM2_4-pyCGM2.settings"
elif modelVersion == "CGM2.4e":
translatorFiles= "CGM2_4.translators"
globalPyCGM2settingFile = "CGM2_4-Expert-pyCGM2.settings"
else:
raise Exception( "model version not known")
settings = files.openJson(pyCGM2.PYCGM2_APPDATA_PATH,globalPyCGM2settingFile)
translators = files.getTranslators(DATA_PATH,translatorFiles)
if not translators: translators = settings["Translators"]
# mp file
if vskFile is None:
logging.info("mp from pipeline file")
required_mp,optional_mp = manager.getMP()
else:
logging.warning("mp from vsk file")
vsk = vskTools.Vsk(str(DATA_PATH + vskFile))
required_mp,optional_mp = vskTools.getFromVskSubjectMp(vsk, resetFlag=True)
fileSuffix = manager.getFileSuffix()
pointSuffix = manager.getPointSuffix()
ik_flag = manager.isIkFitting()
#------calibration--------
leftFlatFoot = manager.getLeftFlatFoot()
rightFlatFoot = manager.getRightFlatFoot()
markerDiameter = manager.getMarkerDiameter()
calibrateFilenameLabelled = manager.getStaticTial()
if modelVersion == "CGM1.0":
model,finalAcqStatic = cgm1.calibrate(DATA_PATH,calibrateFilenameLabelled,translators,required_mp,optional_mp,
leftFlatFoot,rightFlatFoot,markerDiameter,
pointSuffix)
elif modelVersion == "CGM1.1":
model,finalAcqStatic = cgm1_1.calibrate(DATA_PATH,calibrateFilenameLabelled,translators,required_mp,optional_mp,
leftFlatFoot,rightFlatFoot,markerDiameter,
pointSuffix)
elif modelVersion == "CGM2.1":
hjcMethods = manager.getHJC()
hjcMethods["Left"] = "Hara" if hjcMethods["Left"] == [] else hjcMethods["Left"]
hjcMethods["Right"] = "Hara" if hjcMethods["Right"] == [] else hjcMethods["Right"]
model,finalAcqStatic = cgm2_1.calibrate(DATA_PATH,calibrateFilenameLabelled,translators,required_mp,optional_mp,
leftFlatFoot,rightFlatFoot,markerDiameter,hjcMethods,
pointSuffix)
elif modelVersion == "CGM2.2":
hjcMethods = manager.getHJC()
hjcMethods["Left"] = "Hara" if hjcMethods["Left"] == [] else hjcMethods["Left"]
hjcMethods["Right"] = "Hara" if hjcMethods["Right"] == [] else hjcMethods["Right"]
model,finalAcqStatic = cgm2_2.calibrate(DATA_PATH,calibrateFilenameLabelled,translators,settings,
required_mp,optional_mp,
True,leftFlatFoot,rightFlatFoot,markerDiameter,hjcMethods,
pointSuffix)
elif modelVersion == "CGM2.2e":
hjcMethods = manager.getHJC()
hjcMethods["Left"] = "Hara" if hjcMethods["Left"] == [] else hjcMethods["Left"]
hjcMethods["Right"] = "Hara" if hjcMethods["Right"] == [] else hjcMethods["Right"]
model,finalAcqStatic = cgm2_2e.calibrate(DATA_PATH,calibrateFilenameLabelled,translators,settings,
required_mp,optional_mp,
True,leftFlatFoot,rightFlatFoot,markerDiameter,hjcMethods,
pointSuffix)
elif modelVersion == "CGM2.3":
hjcMethods = manager.getHJC()
hjcMethods["Left"] = "Hara" if hjcMethods["Left"] == [] else hjcMethods["Left"]
hjcMethods["Right"] = "Hara" if hjcMethods["Right"] == [] else hjcMethods["Right"]
model,finalAcqStatic = cgm2_3.calibrate(DATA_PATH,calibrateFilenameLabelled,translators,settings,
required_mp,optional_mp,
ik_flag,leftFlatFoot,rightFlatFoot,markerDiameter,hjcMethods,
pointSuffix)
elif modelVersion == "CGM2.3e":
hjcMethods = manager.getHJC()
hjcMethods["Left"] = "Hara" if hjcMethods["Left"] == [] else hjcMethods["Left"]
hjcMethods["Right"] = "Hara" if hjcMethods["Right"] == [] else hjcMethods["Right"]
model,finalAcqStatic = cgm2_3e.calibrate(DATA_PATH,calibrateFilenameLabelled,translators,settings,
required_mp,optional_mp,
ik_flag,leftFlatFoot,rightFlatFoot,markerDiameter,hjcMethods,
pointSuffix)
elif modelVersion == "CGM2.4":
hjcMethods = manager.getHJC()
hjcMethods["Left"] = "Hara" if hjcMethods["Left"] == [] else hjcMethods["Left"]
hjcMethods["Right"] = "Hara" if hjcMethods["Right"] == [] else hjcMethods["Right"]
model,finalAcqStatic = cgm2_4.calibrate(DATA_PATH,calibrateFilenameLabelled,translators,settings,
required_mp,optional_mp,
ik_flag,leftFlatFoot,rightFlatFoot,markerDiameter,hjcMethods,
pointSuffix)
elif modelVersion == "CGM2.4e":
hjcMethods = manager.getHJC()
hjcMethods["Left"] = "Hara" if hjcMethods["Left"] == [] else hjcMethods["Left"]
hjcMethods["Right"] = "Hara" if hjcMethods["Right"] == [] else hjcMethods["Right"]
model,finalAcqStatic = cgm2_4e.calibrate(DATA_PATH,calibrateFilenameLabelled,translators,settings,
required_mp,optional_mp,
ik_flag,leftFlatFoot,rightFlatFoot,markerDiameter,hjcMethods,
pointSuffix)
btkTools.smartWriter(finalAcqStatic, str(DATA_PATH_OUT+"calibrated.c3d"))
logging.info("Static Calibration -----> Done")
# knee calibration
leftEnable = manager.isKneeCalibrationEnable("Left")
rightEnable = manager.isKneeCalibrationEnable("Right")
if leftEnable:
method, trial,begin,end,jointRange = manager.getKneeCalibration("Left")
if method == "Calibration2Dof":
model,acqFunc,side = kneeCalibration.calibration2Dof(model,
DATA_PATH,trial,translators,
"Left",begin,end,jointRange)
logging.info("Left knee Calibration (Calibration2Dof) -----> Done")
elif method == "SARA":
model,acqFunc,side = kneeCalibration.sara(model,
DATA_PATH,trial,translators,
"Left",begin,end)
logging.info("Left knee Calibration (SARA) -----> Done")
if rightEnable:
method, trial,begin,end,jointRange = manager.getKneeCalibration("Right")
if method == "Calibration2Dof":
model,acqFunc,side = kneeCalibration.calibration2Dof(model,
DATA_PATH,trial,translators,
"Right",begin,end,jointRange)
logging.info("Right knee Calibration (Calibration2Dof) -----> Done")
elif method == "SARA":
model,acqFunc,side = kneeCalibration.sara(model,
DATA_PATH,trial,translators,
"Right",begin,end)
logging.info("Right knee Calibration (SARA) -----> Done")
# update mp
manager.updateMp(model)
# save settings
if manager.m_pipelineFile is not None:
manager.save(DATA_PATH,str( manager.m_pipelineFile+"-saved"))
logging.info("pipeline file -----> Save")
# Fitting
trials = manager.getFittingTrials()
momentProjection = manager.getMomentProjection()
if modelVersion not in ["CGM1.0", "CGM1.1", "CGM2.1"]:
ikwf = manager.getIkWeightFile()
if ikwf is not None:
ikWeight = files.openJson(DATA_PATH,ikwf)
settings["Fitting"]["Weight"]=ikWeight["Weight"]
for trial in trials:
mfpa = None if trial["Mfpa"] == "Auto" else trial["Mfpa"]
reconstructFilenameLabelled = trial["File"]
if modelVersion == "CGM1.0":
acqGait = cgm1.fitting(model,DATA_PATH, reconstructFilenameLabelled,
translators,
markerDiameter,
pointSuffix,
mfpa,momentProjection)
elif modelVersion == "CGM1.1":
acqGait = cgm1_1.fitting(model,DATA_PATH, reconstructFilenameLabelled,
translators,
markerDiameter,
pointSuffix,
mfpa,momentProjection)
elif modelVersion == "CGM2.1":
acqGait = cgm2_1.fitting(model,DATA_PATH, reconstructFilenameLabelled,
translators,
markerDiameter,
pointSuffix,
mfpa,momentProjection)
elif modelVersion == "CGM2.2":
acqGait = cgm2_2.fitting(model,DATA_PATH, reconstructFilenameLabelled,
translators,settings,
markerDiameter,
pointSuffix,
mfpa,
momentProjection)
elif modelVersion == "CGM2.2e":
acqGait = cgm2_2e.fitting(model,DATA_PATH, reconstructFilenameLabelled,
translators,settings,
markerDiameter,
pointSuffix,
mfpa,
momentProjection)
elif modelVersion == "CGM2.3":
acqGait = cgm2_3.fitting(model,DATA_PATH, reconstructFilenameLabelled,
translators,settings,
ik_flag,markerDiameter,
pointSuffix,
mfpa,
momentProjection)
elif modelVersion == "CGM2.3e":
acqGait = cgm2_3e.fitting(model,DATA_PATH, reconstructFilenameLabelled,
translators,settings,
ik_flag,markerDiameter,
pointSuffix,
mfpa,
momentProjection)
elif modelVersion == "CGM2.4":
acqGait = cgm2_4.fitting(model,DATA_PATH, reconstructFilenameLabelled,
translators,settings,
ik_flag,markerDiameter,
pointSuffix,
mfpa,
momentProjection)
elif modelVersion == "CGM2.4e":
acqGait = cgm2_4e.fitting(model,DATA_PATH, reconstructFilenameLabelled,
translators,settings,
ik_flag,markerDiameter,
pointSuffix,
mfpa,
momentProjection)
logging.info("Fitting -----> Done")
if fileSuffix is not None:
c3dFilename = str(reconstructFilenameLabelled[:-4]+"-modelled-"+fileSuffix+".c3d")
else:
c3dFilename = str(reconstructFilenameLabelled[:-4]+"-modelled.c3d")
btkTools.smartWriter(acqGait, str(DATA_PATH_OUT+c3dFilename))
logging.info("c3d file (%s) generated" %(c3dFilename) )
