def noIK_6dof(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM2\\cgm2.4\\fullBody\\"
staticFilename = "PN01OP01S01STAT.c3d"
gaitFilename = "PN01OP01S01STAT.c3d"
markerDiameter = 14
mp = {
'Bodymass': 83.0,
'LeftLegLength': 874.0,
'RightLegLength': 876.0,
'LeftKneeWidth': 106.0,
'RightKneeWidth': 103.0,
'LeftAnkleWidth': 74.0,
'RightAnkleWidth': 72.0,
'LeftSoleDelta': 0,
'RightSoleDelta': 0,
}
# --- Calibration ---
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
translators = files.getTranslators(MAIN_PATH, "CGM2_4.translators")
acqStatic = btkTools.applyTranslators(acqStatic, translators)
model = cgm2.CGM2_4()
model.configure()
model.addAnthropoInputParameters(mp)
# ---- Calibration ----
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute()
print "----"
print model.getSegment("Left Shank").getReferential(
"TF").relativeMatrixAnatomic
print "----"
# # cgm decorator
modelDecorator.HipJointCenterDecorator(model).hara()
modelDecorator.KneeCalibrationDecorator(model).midCondyles(
acqStatic, markerDiameter=markerDiameter, side="both")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic, markerDiameter=markerDiameter, side="both")
#
# # final
modelFilters.ModelCalibrationFilter(
scp, acqStatic, model, markerDiameter=markerDiameter).compute()
# ------ Fitting -------
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
acqGait = btkTools.applyTranslators(acqGait, translators)
# Motion FILTER
modMotion = modelFilters.ModelMotionFilter(
scp, acqGait, model, enums.motionMethod.Sodervisk)
modMotion.compute()
btkTools.smartWriter(acqGait, "cgm24_noIK6dof_staticMotion.c3d")
def cgm24(cls):
"""
"""
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "operations\\markerDecomposition\\CGM24decomposeTracking\\"
#
staticFilename = "PN01OP01S01STAT.c3d"
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model=cgm2.CGM2_4LowerLimbs()
model.setVersion("CGM2.4e")
model.configure()
markerDiameter=14
mp={
'Bodymass' : 83.0,
'LeftLegLength' : 874.0,
'RightLegLength' : 876.0 ,
'LeftKneeWidth' : 106.0,
'RightKneeWidth' : 103.0,
'LeftAnkleWidth' : 74.0,
'RightAnkleWidth' : 72.0,
'LeftSoleDelta' : 0,
'RightSoleDelta' : 0,
}
model.addAnthropoInputParameters(mp)
# CALIBRATION
scp=modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp,acqStatic,model,
leftFlatFoot = 1, rightFlatFoot = 1,
markerDiameter=markerDiameter,
).compute()
modelDecorator.KneeCalibrationDecorator(model).midCondyles(acqStatic, markerDiameter=markerDiameter, side="left")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, markerDiameter=markerDiameter, side="left")
modelDecorator.KneeCalibrationDecorator(model).midCondyles(acqStatic, markerDiameter=markerDiameter, side="right")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, markerDiameter=markerDiameter, side="right")
modelDecorator.HipJointCenterDecorator(model).hara(side = "Both")
scp=modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp,acqStatic,model,
leftFlatFoot = 1, rightFlatFoot = 1,
markerDiameter=markerDiameter,
).compute()
# --- Test 1 Motion Axe X -------
gaitFilename="PN01OP01S01SS01.c3d"
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
modMotion=modelFilters.ModelMotionFilter(scp,acqGait,model,pyCGM2Enums.motionMethod.Sodervisk )
modMotion.compute()
mtf = modelFilters.TrackingMarkerDecompositionFilter(model,acqGait)
mtf.decompose()
btkTools.smartWriter(acqGait, "cgm24-decompose.c3d")
def basicCGM1_manualOffset_thighRotationOFF_shankRotationON_tibialTorsionON(cls):
"""
CGM1 manual offset behaviour :
=> - Manual Thigh Rotation must modify ShankRotation.
- If zero TibialTorsion inputs -> flag RightTibialTorsion must be off and TibialTorsion keep zero value
"""
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\basic-manualOffsets-thiOFF_shaON_torsionON\\"
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={
'InterAsisDistance' : 0,
'LeftAsisTrocanterDistance' : 0,
'LeftThighRotation' : 0,
'LeftShankRotation' : -10,
'LeftTibialTorsion' : -30,
'RightAsisTrocanterDistance' : 0,
'RightThighRotation' : 0,
'RightShankRotation' : -10,
'RightTibialTorsion' : -30
}
model.addAnthropoInputParameters(mp,optional=optional_mp)
# -----------CGM STATIC CALIBRATION--------------------
scp=modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp,acqStatic,model).compute()
# decorators
modelDecorator.Cgm1ManualOffsets(model).compute(acqStatic,"left",model.mp["LeftThighRotation"],markerDiameter,model.mp["LeftTibialTorsion"],model.mp["LeftShankRotation"])
modelDecorator.Cgm1ManualOffsets(model).compute(acqStatic,"right",model.mp["RightThighRotation"],markerDiameter,model.mp["RightTibialTorsion"],model.mp["RightShankRotation"])
# finql calibration
modelFilters.ModelCalibrationFilter(scp,acqStatic,model ).compute()
# TESTS
np.testing.assert_equal(model.m_useRightTibialTorsion,True )
np.testing.assert_equal(model.m_useLeftTibialTorsion,True )
np.testing.assert_almost_equal(model.mp_computed["LeftShankRotationOffset"] ,0, decimal = 3)
np.testing.assert_almost_equal(model.mp_computed["RightShankRotationOffset"] ,0, decimal = 3)
def noIK_6dof_Garches(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "Datasets Tests\\didier\\08_02_18_Vincent Pere\\"
staticFilename = "08_02_18_Vincent_Pere_Statique_000_MOKKA.c3d"
gaitFilename = "08_02_18_Vincent_Pere_Statique_000_MOKKA.c3d"
markerDiameter = 14
mp = {
'Bodymass': 70.0,
'LeftLegLength': 890.0,
'RightLegLength': 890.0,
'LeftKneeWidth': 150.0,
'RightKneeWidth': 150.0,
'LeftAnkleWidth': 88.0,
'RightAnkleWidth': 99.0,
'LeftSoleDelta': 0,
'RightSoleDelta': 0,
}
# --- Calibration ---
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model = cgm2.CGM2_4()
model.configure()
model.addAnthropoInputParameters(mp)
# ---- Calibration ----
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute()
print "----"
print model.getSegment("Left Shank").getReferential(
"TF").relativeMatrixAnatomic
print "----"
# # cgm decorator
modelDecorator.HipJointCenterDecorator(model).hara()
modelDecorator.KneeCalibrationDecorator(model).midCondyles(
acqStatic, markerDiameter=markerDiameter, side="both")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic, markerDiameter=markerDiameter, side="both")
#
# # final
modelFilters.ModelCalibrationFilter(
scp, acqStatic, model, markerDiameter=markerDiameter).compute()
# ------ Fitting -------
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
# Motion FILTER
modMotion = modelFilters.ModelMotionFilter(
scp, acqGait, model, enums.motionMethod.Sodervisk)
modMotion.compute()
btkTools.smartWriter(acqGait,
"cgm24_noIK6dof_staticMotion_Garches.c3d")
def calibration_GarchesFlatFoot(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "Datasets Tests\\didier\\08_02_18_Vincent Pere\\"
staticFilename = "08_02_18_Vincent_Pere_Statique_000_MOKKA.c3d"
markerDiameter = 14
mp = {
'Bodymass': 70.0,
'LeftLegLength': 890.0,
'RightLegLength': 890.0,
'LeftKneeWidth': 150.0,
'RightKneeWidth': 150.0,
'LeftAnkleWidth': 88.0,
'RightAnkleWidth': 99.0,
'LeftSoleDelta': 0,
'RightSoleDelta': 0,
"LeftToeOffset": 0,
"RightToeOffset": 0,
}
# --- Calibration ---
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model = cgm2.CGM2_4()
model.configure()
model.addAnthropoInputParameters(mp)
# ---- Calibration ----
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute()
# cgm decorator
modelDecorator.HipJointCenterDecorator(model).hara()
modelDecorator.KneeCalibrationDecorator(model).midCondyles(
acqStatic, markerDiameter=markerDiameter, side="both")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic, markerDiameter=markerDiameter, side="both")
# final
modelFilters.ModelCalibrationFilter(scp,
acqStatic,
model,
markerDiameter=markerDiameter,
leftFlatFoot=True,
rightFlatFoot=True).compute()
# display CS
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csf = modelFilters.CoordinateSystemDisplayFilter(csp, model, acqStatic)
csf.setStatic(True)
csf.display()
btkTools.smartWriter(acqStatic, "cgm2.4_GarchesFlatFoot.c3d")
def customLocalPosition(cls):
"""
GOAL : compare Joint centres and foot Offset
"""
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM2\\cgm2.1\\native\\"
staticFilename = "static.c3d"
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model=cgm2.CGM2_1LowerLimbs()
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--------------------
# initial
scp=modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp,acqStatic,model).compute()
pos0_L = model.getSegment("Pelvis").getReferential("TF").static.getNode_byLabel("LHJC").getLocal()
pos0_R = model.getSegment("Pelvis").getReferential("TF").static.getNode_byLabel("RHJC").getLocal()
# cgm decorator
modelDecorator.HipJointCenterDecorator(model).custom(position_Left = np.array([1,2,3]),
position_Right = np.array([1,2,3]), methodDesc = "us") # add node to pelvis
# final
modelFilters.ModelCalibrationFilter(scp,acqStatic,model).compute()
pos_L = model.getSegment("Pelvis").getReferential("TF").static.getNode_byLabel("LHJC").getLocal()
pos_R = model.getSegment("Pelvis").getReferential("TF").static.getNode_byLabel("RHJC").getLocal()
# ---- tests ----
np.testing.assert_equal(model.getSegment("Pelvis").getReferential("TF").static.getNode_byLabel("LHJC").getDescription() ,"us")
np.testing.assert_equal(model.getSegment("Left Thigh").getReferential("TF").static.getNode_byLabel("LHJC").getDescription() ,"us")
np.testing.assert_equal(model.getSegment("Pelvis").getReferential("TF").static.getNode_byLabel("RHJC").getDescription() ,"us")
np.testing.assert_equal(model.getSegment("Right Thigh").getReferential("TF").static.getNode_byLabel("RHJC").getDescription() ,"us")
np.testing.assert_equal(np.all(pos_L == pos0_L) == False, True)
np.testing.assert_equal(np.all(pos_R == pos0_R) ==False, True)
def calibration_FlatFoot(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM2\\cgm2.4\\medial\\"
staticFilename = "static.c3d"
markerDiameter = 14
mp = {
'Bodymass': 69.0,
'LeftLegLength': 930.0,
'RightLegLength': 930.0,
'LeftKneeWidth': 94.0,
'RightKneeWidth': 64.0,
'LeftAnkleWidth': 67.0,
'RightAnkleWidth': 62.0,
'LeftSoleDelta': 0,
'RightSoleDelta': 0,
"LeftToeOffset": 0,
"RightToeOffset": 0,
}
# --- Calibration ---
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model = cgm2.CGM2_4()
model.configure()
model.addAnthropoInputParameters(mp)
# ---- Calibration ----
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute()
# cgm decorator
modelDecorator.HipJointCenterDecorator(model).hara()
modelDecorator.KneeCalibrationDecorator(model).midCondyles(
acqStatic, markerDiameter=markerDiameter, side="both")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic, markerDiameter=markerDiameter, side="both")
# final
modelFilters.ModelCalibrationFilter(scp,
acqStatic,
model,
markerDiameter=markerDiameter,
leftFlatFoot=True,
rightFlatFoot=True).compute()
# display CS
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csf = modelFilters.CoordinateSystemDisplayFilter(csp, model, acqStatic)
csf.setStatic(True)
csf.display()
btkTools.smartWriter(acqStatic, "cgm2.4_FlatFoot.c3d")
def 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 advancedCGM11_KneeMedKad(cls):
"""
"""
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\CGM1.1\medial\\"
staticFilename = "static-all.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 = {
'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.KneeCalibrationDecorator(model).midCondyles_KAD(
acqStatic)
#modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, side="both")
modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute()
btkTools.smartWriter(acqStatic, "advancedCGM11_KneeMedKad.c3d")
def basicCGM1_manualTibialTorsion(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\basic-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,
}
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,
viconCGM1compatible=True).compute()
# TESTS ------------------------------------------------
# offset testing
offsetTesting(acqStatic,model,display = True, unitTesting=True)
# nodes
# 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.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 basicCGM1_manualTibialTorsion(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\KAD-basic\\"
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()
#TESTS
np.testing.assert_equal(model.m_useRightTibialTorsion,True )
np.testing.assert_equal(model.m_useLeftTibialTorsion,True )
# np.testing.assert_almost_equal(model.mp["InterAsisDistance"],model.mp_computed["InterAsisDistance"] , decimal = 3)
# np.testing.assert_almost_equal(model.mp["LeftAsisTrocanterDistance"],model.mp_computed["LeftAsisTrocanterDistance"] , decimal = 3)
# np.testing.assert_almost_equal(model.mp["LeftThighRotation"],-1.0*model.mp_computed["LeftThighRotationOffset"] , decimal = 3)
# np.testing.assert_almost_equal(model.mp["LeftShankRotation"],-1.0*model.mp_computed["LeftShankRotationOffset"] , decimal = 3)
np.testing.assert_almost_equal(model.mp["LeftTibialTorsion"],-1.0*model.mp_computed["LeftTibialTorsionOffset"] , decimal = 3)
# np.testing.assert_almost_equal(model.mp["RightAsisTrocanterDistance"],model.mp_computed["RightAsisTrocanterDistance"] , decimal = 3)
# np.testing.assert_almost_equal(model.mp["RightThighRotation"],model.mp_computed["RightThighRotationOffset"] , decimal = 3)
# np.testing.assert_almost_equal(model.mp["RightShankRotation"],model.mp_computed["RightShankRotationOffset"] , decimal = 3)
np.testing.assert_almost_equal(model.mp["RightTibialTorsion"],model.mp_computed["RightTibialTorsionOffset"] , decimal = 3)
def basicCGM1_bodyBuilderFoot(cls):
"""
goal : know effet on Foot kinematics of a foot referential built according ta sequence metionned in some bodybuilder code:
LFoot = [LTOE,LAJC-LTOE,LAJC-LKJC,zyx]
"""
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\basic\\"
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,
useBodyBuilderFoot=True).compute()
# ------ 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, "testuseBodyBuilderFoot.c3d")
def CGM1_UpperLimb(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\full-PiG\\"
staticFilename = "PN01NORMSTAT.c3d"
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model=cgm.CGM1()
model.configure(bodyPart=enums.BodyPart.UpperLimb)
markerDiameter=14
mp={
'LeftShoulderOffset' : 50,
'LeftElbowWidth' : 91,
'LeftWristWidth' : 56 ,
'LeftHandThickness' : 28 ,
'RightShoulderOffset' : 45,
'RightElbowWidth' : 90,
'RightWristWidth' : 55 ,
'RightHandThickness' : 30 }
model.addAnthropoInputParameters(mp)
# -----------CGM STATIC CALIBRATION--------------------
scp=modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp,acqStatic,model,headFlat= True).compute()
csp = modelFilters.ModelCoordinateSystemProcedure(model)
# --- motion ----
gaitFilename="PN01NORMSS01.c3d"
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
modMotion=modelFilters.ModelMotionFilter(scp,acqGait,model,enums.motionMethod.Determinist)
modMotion.compute()
csdf = modelFilters.CoordinateSystemDisplayFilter(csp,model,acqGait)
csdf.setStatic(False)
csdf.display()
# thorax
R_thorax= model.getSegment("Thorax").anatomicalFrame.motion[10].getRotation()
R_thorax_vicon = getViconRmatrix(10, acqGait, "TRXO", "TRXA", "TRXL", "XZY")
np.testing.assert_almost_equal( R_thorax,
R_thorax_vicon, decimal =3)
# head
R_head= model.getSegment("Head").anatomicalFrame.motion[10].getRotation()
R_head_vicon = getViconRmatrix(10, acqGait, "HEDO", "HEDA", "HEDL", "XZY")
np.testing.assert_almost_equal( R_head,
R_head_vicon, decimal =2)
def cgm1(cls):
"""
GOAL : compare Joint centres and foot Offset
"""
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "operations\\markerDecomposition\\CGM1decomposeTracking\\"
#
staticFilename = "static.c3d"
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model = cgm.CGM1LowerLimbs()
model.configure()
markerDiameter = 14
mp = {
'Bodymass': 36.9,
'LeftLegLength': 665,
'RightLegLength': 655.0,
'LeftKneeWidth': 102.7,
'RightKneeWidth': 100.2,
'LeftAnkleWidth': 64.5,
'RightAnkleWidth': 63.4,
'LeftSoleDelta': 0,
'RightSoleDelta': 0,
}
model.addAnthropoInputParameters(mp)
# CALIBRATION
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute()
print model.m_useRightTibialTorsion
# --- Test 1 Motion Axe X -------
gaitFilename = "gait trial 01.c3d"
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
modMotion = modelFilters.ModelMotionFilter(
scp,
acqGait,
model,
pyCGM2Enums.motionMethod.Determinist,
useForMotionTest=True)
modMotion.compute()
mtf = modelFilters.TrackingMarkerDecompositionFilter(model, acqGait)
mtf.decompose()
btkTools.smartWriter(acqGait, "cgm1-decompose.c3d")
def basicCGM1(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\basic\\"
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)
# -----------CGM STATIC CALIBRATION--------------------
scp=modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp,acqStatic,model).compute()
#btkTools.smartWriter(acqStatic, "CGM1_calibrationTest-basicCGM1.c3d")
# TESTS ------------------------------------------------
# offset testing
offsetTesting(acqStatic,model,display = True, unitTesting=True)
np.testing.assert_equal(model.m_useRightTibialTorsion,False )
np.testing.assert_equal(model.m_useLeftTibialTorsion,False )
# 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)
def GeneralScoreTest(cls):
"""
GOAL : compare Joint centres and foot Offset
"""
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\basic\\"
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)
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute()
# ------ 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, enums.motionMethod.Determinist)
modMotion.compute()
# score
msrp = modelQualityFilter.GeneralScoreResidualProcedure(model)
msrp.setDefinition("LHJC", "Pelvis", "Left Thigh")
srf = modelQualityFilter.ScoreResidualFilter(acqGait, msrp)
srf.compute()
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 basicCGM1_global(cls, plotFlag=False):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\basic-filtered\\"
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,
}
model.addAnthropoInputParameters(mp)
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute()
# ------ Test 1 Motion Axe X -------
gaitFilename = "MRI-US-01, 2008-08-08, 3DGA 14.global.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()
# 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.Global).compute(
pointLabelSuffix="cgm1_6dof")
modelFilters.JointPowerFilter(
model, acqGait).compute(pointLabelSuffix="cgm1_6dof")
#btkTools.smartWriter(acqGait,"testInvDyn.c3d")
if plotFlag:
plotMoment(acqGait, "LHipMoment", "LHipMoment_cgm1_6dof")
plotMoment(acqGait, "LKneeMoment", "LKneeMoment_cgm1_6dof")
plotMoment(acqGait, "LAnkleMoment", "LAnkleMoment_cgm1_6dof")
plotMoment(acqGait, "RHipMoment", "RHipMoment_cgm1_6dof")
plotMoment(acqGait, "RKneeMoment", "RKneeMoment_cgm1_6dof")
plotMoment(acqGait, "RAnkleMoment", "RAnkleMoment_cgm1_6dof")
plt.show()
# TEST ------
compareKinetics(acqGait, 5, -5, 0.2, 40.0, 0.1)
def calibrate(DATA_PATH,calibrateFilenameLabelled,translators,weights,
required_mp,optional_mp,
ik_flag,leftFlatFoot,rightFlatFoot,headFlat,
markerDiameter,hjcMethod,
pointSuffix,**kwargs):
"""
Calibration of the CGM2.3
:param DATA_PATH [str]: path to your data
:param calibrateFilenameLabelled [str]: c3d file
:param translators [dict]: translators to apply
:param required_mp [dict]: required anthropometric data
:param optional_mp [dict]: optional anthropometric data (ex: LThighOffset,...)
:param ik_flag [bool]: enable the inverse kinematic solver
:param leftFlatFoot [bool]: enable of the flat foot option for the left foot
:param rightFlatFoot [bool]: enable of the flat foot option for the right foot
:param headFlat [bool]: enable of the head flat option
:param markerDiameter [double]: marker diameter (mm)
:param hjcMethod [str or list of 3 float]: method for locating the hip joint centre
:param pointSuffix [str]: suffix to add to model outputs
"""
# --------------------------STATIC FILE WITH TRANSLATORS --------------------------------------
if "Fitting" in weights.keys():
weights = weights["Fitting"]["Weight"]
# --- btk acquisition ----
if "forceBtkAcq" in kwargs.keys():
acqStatic = kwargs["forceBtkAcq"]
else:
acqStatic = btkTools.smartReader((DATA_PATH+calibrateFilenameLabelled))
btkTools.checkMultipleSubject(acqStatic)
if btkTools.isPointExist(acqStatic,"SACR"):
translators["LPSI"] = "SACR"
translators["RPSI"] = "SACR"
logging.info("[pyCGM2] Sacrum marker detected")
acqStatic = btkTools.applyTranslators(acqStatic,translators)
# ---check marker set used----
dcm = cgm.CGM.detectCalibrationMethods(acqStatic)
# --------------------------MODEL--------------------------------------
# ---definition---
model=cgm2.CGM2_3()
model.configure(acq=acqStatic,detectedCalibrationMethods=dcm)
model.addAnthropoInputParameters(required_mp,optional=optional_mp)
# --store calibration parameters--
model.setStaticFilename(calibrateFilenameLabelled)
model.setCalibrationProperty("leftFlatFoot",leftFlatFoot)
model.setCalibrationProperty("rightFlatFoot",rightFlatFoot)
model.setCalibrationProperty("headFlat",headFlat)
model.setCalibrationProperty("markerDiameter",markerDiameter)
# --------------------------STATIC CALBRATION--------------------------
scp=modelFilters.StaticCalibrationProcedure(model) # load calibration procedure
# ---initial calibration filter----
# use if all optional mp are zero
modelFilters.ModelCalibrationFilter(scp,acqStatic,model,
leftFlatFoot = leftFlatFoot, rightFlatFoot = rightFlatFoot,
headFlat= headFlat,
markerDiameter=markerDiameter,
).compute()
# ---- Decorators -----
decorators.applyBasicDecorators(dcm, model,acqStatic,optional_mp,markerDiameter)
decorators.applyHJCDecorators(model,hjcMethod)
# ----Final Calibration filter if model previously decorated -----
if model.decoratedModel:
# initial static filter
modelFilters.ModelCalibrationFilter(scp,acqStatic,model,
leftFlatFoot = leftFlatFoot, rightFlatFoot = rightFlatFoot,
headFlat= headFlat,
markerDiameter=markerDiameter).compute()
# ----------------------CGM MODELLING----------------------------------
# ----motion filter----
modMotion=modelFilters.ModelMotionFilter(scp,acqStatic,model,enums.motionMethod.Sodervisk,
markerDiameter=markerDiameter)
modMotion.compute()
if "noKinematicsCalculation" in kwargs.keys() and kwargs["noKinematicsCalculation"]:
logging.warning("[pyCGM2] No Kinematic calculation done for the static file")
return model, acqStatic
else:
if model.getBodyPart() == enums.BodyPart.UpperLimb:
ik_flag = False
logging.warning("[pyCGM2] Fitting only applied for the upper limb")
if ik_flag:
# ---OPENSIM IK---
# --- opensim calibration Filter ---
osimfile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\osim\\lowerLimb_ballsJoints.osim" # osimfile
markersetFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_3\\cgm2_3-markerset.xml" # markerset
cgmCalibrationprocedure = opensimFilters.CgmOpensimCalibrationProcedures(model) # procedure
oscf = opensimFilters.opensimCalibrationFilter(osimfile,
model,
cgmCalibrationprocedure,
(DATA_PATH))
oscf.addMarkerSet(markersetFile)
scalingOsim = oscf.build()
# --- opensim Fitting Filter ---
iksetupFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_3\\cgm2_3-ikSetUp_template.xml" # ik tool file
cgmFittingProcedure = opensimFilters.CgmOpensimFittingProcedure(model) # procedure
cgmFittingProcedure.updateMarkerWeight("LASI",weights["LASI"])
cgmFittingProcedure.updateMarkerWeight("RASI",weights["RASI"])
cgmFittingProcedure.updateMarkerWeight("LPSI",weights["LPSI"])
cgmFittingProcedure.updateMarkerWeight("RPSI",weights["RPSI"])
cgmFittingProcedure.updateMarkerWeight("RTHI",weights["RTHI"])
cgmFittingProcedure.updateMarkerWeight("RKNE",weights["RKNE"])
cgmFittingProcedure.updateMarkerWeight("RTIB",weights["RTIB"])
cgmFittingProcedure.updateMarkerWeight("RANK",weights["RANK"])
cgmFittingProcedure.updateMarkerWeight("RHEE",weights["RHEE"])
cgmFittingProcedure.updateMarkerWeight("RTOE",weights["RTOE"])
cgmFittingProcedure.updateMarkerWeight("LTHI",weights["LTHI"])
cgmFittingProcedure.updateMarkerWeight("LKNE",weights["LKNE"])
cgmFittingProcedure.updateMarkerWeight("LTIB",weights["LTIB"])
cgmFittingProcedure.updateMarkerWeight("LANK",weights["LANK"])
cgmFittingProcedure.updateMarkerWeight("LHEE",weights["LHEE"])
cgmFittingProcedure.updateMarkerWeight("LTOE",weights["LTOE"])
cgmFittingProcedure.updateMarkerWeight("LTHAP",weights["LTHAP"])
cgmFittingProcedure.updateMarkerWeight("LTHAD",weights["LTHAD"])
cgmFittingProcedure.updateMarkerWeight("LTIAP",weights["LTIAP"])
cgmFittingProcedure.updateMarkerWeight("LTIAD",weights["LTIAD"])
cgmFittingProcedure.updateMarkerWeight("RTHAP",weights["RTHAP"])
cgmFittingProcedure.updateMarkerWeight("RTHAD",weights["RTHAD"])
cgmFittingProcedure.updateMarkerWeight("RTIAP",weights["RTIAP"])
cgmFittingProcedure.updateMarkerWeight("RTIAD",weights["RTIAD"])
osrf = opensimFilters.opensimFittingFilter(iksetupFile,
scalingOsim,
cgmFittingProcedure,
(DATA_PATH) )
acqStaticIK = osrf.run(acqStatic,(DATA_PATH + calibrateFilenameLabelled ))
# eventual static acquisition to consider for joint kinematics
finalAcqStatic = acqStaticIK if ik_flag else acqStatic
# --- final pyCGM2 model motion Filter ---
# use fitted markers
modMotionFitted=modelFilters.ModelMotionFilter(scp,finalAcqStatic,model,enums.motionMethod.Sodervisk)
modMotionFitted.compute()
if "displayCoordinateSystem" in kwargs.keys() and kwargs["displayCoordinateSystem"]:
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csdf = modelFilters.CoordinateSystemDisplayFilter(csp,model,finalAcqStatic)
csdf.setStatic(False)
csdf.display()
#---- Joint kinematics----
# relative angles
modelFilters.ModelJCSFilter(model,finalAcqStatic).compute(description="vectoriel", pointLabelSuffix=pointSuffix)
# detection of traveling axis + absolute angle
if model.m_bodypart != enums.BodyPart.UpperLimb:
pfp = progressionFrame.PelvisProgressionFrameProcedure()
else:
pfp = progressionFrame.ThoraxProgressionFrameProcedure()
pff = progressionFrame.ProgressionFrameFilter(finalAcqStatic,pfp)
pff.compute()
globalFrame = pff.outputs["globalFrame"]
forwardProgression = pff.outputs["forwardProgression"]
if model.m_bodypart != enums.BodyPart.UpperLimb:
modelFilters.ModelAbsoluteAnglesFilter(model,finalAcqStatic,
segmentLabels=["Left Foot","Right Foot","Pelvis"],
angleLabels=["LFootProgress", "RFootProgress","Pelvis"],
eulerSequences=["TOR","TOR", "ROT"],
globalFrameOrientation = globalFrame,
forwardProgression = forwardProgression).compute(pointLabelSuffix=pointSuffix)
if model.m_bodypart == enums.BodyPart.LowerLimbTrunk:
modelFilters.ModelAbsoluteAnglesFilter(model,finalAcqStatic,
segmentLabels=["Thorax"],
angleLabels=["Thorax"],
eulerSequences=["YXZ"],
globalFrameOrientation = globalFrame,
forwardProgression = forwardProgression).compute(pointLabelSuffix=pointSuffix)
if model.m_bodypart == enums.BodyPart.UpperLimb or model.m_bodypart == enums.BodyPart.FullBody:
modelFilters.ModelAbsoluteAnglesFilter(model,finalAcqStatic,
segmentLabels=["Thorax","Head"],
angleLabels=["Thorax", "Head"],
eulerSequences=["YXZ","TOR"],
globalFrameOrientation = globalFrame,
forwardProgression = forwardProgression).compute(pointLabelSuffix=pointSuffix)
# BSP model
bspModel = bodySegmentParameters.Bsp(model)
bspModel.compute()
if model.m_bodypart == enums.BodyPart.FullBody:
modelFilters.CentreOfMassFilter(model,finalAcqStatic).compute(pointLabelSuffix=pointSuffix)
return model, finalAcqStatic
def calibration2Dof(model, DATA_PATH, reconstructFilenameLabelled, translators,
side, beginFrame, endFrame, jointRange, **kwargs):
# --- btk acquisition ----
if "forceBtkAcq" in kwargs.keys():
acqFunc = kwargs["forceBtkAcq"]
else:
acqFunc = btkTools.smartReader(
(DATA_PATH + reconstructFilenameLabelled))
btkTools.checkMultipleSubject(acqFunc)
acqFunc = btkTools.applyTranslators(acqFunc, translators)
# filtering
# -----------------------
if "fc_lowPass_marker" in kwargs.keys(
) and kwargs["fc_lowPass_marker"] != 0:
trackingMarkers = model.getTrackingMarkers(acqFunc)
fc = kwargs["fc_lowPass_marker"]
order = 4
if "order_lowPass_marker" in kwargs.keys():
order = kwargs["order_lowPass_marker"]
signal_processing.markerFiltering(acqFunc,
trackingMarkers,
order=order,
fc=fc)
#---get frame range of interest---
ff = acqFunc.GetFirstFrame()
lf = acqFunc.GetLastFrame()
# motion
if side is None:
side = detectSide(acqFunc, "LANK", "RANK")
LOGGER.logger.info("Detected motion side : %s" % (side))
start, end = btkTools.getStartEndEvents(acqFunc, side)
if start is not None:
LOGGER.logger.info("Start event detected")
initFrame = start
else:
initFrame = beginFrame if beginFrame is not None else ff
if end is not None:
LOGGER.logger.info("End event detected")
endFrame = end
else:
endFrame = endFrame if endFrame is not None else lf
iff = initFrame - ff
ilf = endFrame - ff
if model.version in ["CGM1.0", "CGM1.1", "CGM2.1", "CGM2.2"]:
validFrames, vff, vlf = btkTools.findValidFrames(
acqFunc, cgm.CGM1.LOWERLIMB_TRACKING_MARKERS)
# --------------------------RESET OF THE STATIC File---------
# load btkAcq from static file
staticFilename = model.m_staticFilename
acqStatic = btkTools.smartReader((DATA_PATH + staticFilename))
btkTools.checkMultipleSubject(acqStatic)
acqStatic = btkTools.applyTranslators(acqStatic, translators)
# initial calibration ( i.e calibration from Calibration operation)
leftFlatFoot = model.m_properties["CalibrationParameters"]["leftFlatFoot"]
rightFlatFoot = model.m_properties["CalibrationParameters"][
"rightFlatFoot"]
headFlat = model.m_properties["CalibrationParameters"]["headFlat"]
markerDiameter = model.m_properties["CalibrationParameters"][
"markerDiameter"]
if side == "Left":
# remove other functional calibration
model.mp_computed["LeftKneeFuncCalibrationOffset"] = 0
if side == "Right":
# remove other functional calibration
model.mp_computed["RightKneeFuncCalibrationOffset"] = 0
# no rotation on both thigh - re init anatonical frame
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=leftFlatFoot,
rightFlatFoot=rightFlatFoot,
headFlat=headFlat,
markerDiameter=markerDiameter).compute()
if model.version in ["CGM1.0", "CGM1.1", "CGM2.1", "CGM2.2"]:
modMotion = modelFilters.ModelMotionFilter(
scp, acqFunc, model, enums.motionMethod.Determinist)
modMotion.compute()
elif model.version in ["CGM2.3", "CGM2.4", "CGM2.5"]:
if side == "Left":
thigh_markers = model.getSegment("Left Thigh").m_tracking_markers
shank_markers = model.getSegment("Left Shank").m_tracking_markers
elif side == "Right":
thigh_markers = model.getSegment("Right Thigh").m_tracking_markers
shank_markers = model.getSegment("Right Shank").m_tracking_markers
validFrames, vff, vlf = btkTools.findValidFrames(
acqFunc, thigh_markers + shank_markers)
proximalSegmentLabel = (side + " Thigh")
distalSegmentLabel = (side + " Shank")
# Motion
modMotion = modelFilters.ModelMotionFilter(
scp, acqFunc, model, enums.motionMethod.Sodervisk)
modMotion.segmentalCompute([proximalSegmentLabel, distalSegmentLabel])
# calibration decorators
modelDecorator.KneeCalibrationDecorator(model).calibrate2dof(
side, indexFirstFrame=iff, indexLastFrame=ilf, jointRange=jointRange)
# --------------------------FINAL CALIBRATION OF THE STATIC File---------
# ---- Calibration
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=leftFlatFoot,
rightFlatFoot=rightFlatFoot,
headFlat=headFlat,
markerDiameter=markerDiameter).compute()
return model, acqFunc, side
def calibrate(DATA_PATH, calibrateFilenameLabelled, translators, required_mp,
optional_mp, leftFlatFoot, rightFlatFoot, headFlat,
markerDiameter, pointSuffix, **kwargs):
"""
Calibration of the CGM1.1
:param DATA_PATH [str]: path to your data
:param calibrateFilenameLabelled [str]: c3d file
:param translators [dict]: translators to apply
:param required_mp [dict]: required anthropometric data
:param optional_mp [dict]: optional anthropometric data (ex: LThighOffset,...)
:param leftFlatFoot [bool]: enable of the flat foot option for the left foot
:param rightFlatFoot [bool]: enable of the flat foot option for the right foot
:param headFlat [bool]: enable of the head flat option
:param markerDiameter [double]: marker diameter (mm)
:param pointSuffix [str]: suffix to add to model outputs
"""
# --------------------------ACQUISITION ------------------------------------
# --- btk acquisition ----
if "forceBtkAcq" in kwargs.keys():
acqStatic = kwargs["forceBtkAcq"]
else:
acqStatic = btkTools.smartReader(
(DATA_PATH + calibrateFilenameLabelled))
btkTools.checkMultipleSubject(acqStatic)
if btkTools.isPointExist(acqStatic, "SACR"):
translators["LPSI"] = "SACR"
translators["RPSI"] = "SACR"
logging.info("[pyCGM2] Sacrum marker detected")
acqStatic = btkTools.applyTranslators(acqStatic, translators)
# ---detectedCalibrationMethods----
dcm = cgm.CGM.detectCalibrationMethods(acqStatic)
# ---definition---
model = cgm.CGM1()
model.setVersion("CGM1.1")
model.configure(acq=acqStatic, detectedCalibrationMethods=dcm)
model.addAnthropoInputParameters(required_mp, optional=optional_mp)
# --store calibration parameters--
model.setStaticFilename(calibrateFilenameLabelled)
model.setCalibrationProperty("leftFlatFoot", leftFlatFoot)
model.setCalibrationProperty("rightFlatFoot", rightFlatFoot)
model.setCalibrationProperty("headFlat", headFlat)
model.setCalibrationProperty("markerDiameter", markerDiameter)
# --------------------------STATIC CALBRATION--------------------------
scp = modelFilters.StaticCalibrationProcedure(
model) # load calibration procedure
# ---initial calibration filter----
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=leftFlatFoot,
rightFlatFoot=rightFlatFoot,
headFlat=headFlat,
markerDiameter=markerDiameter,
).compute()
# ---- Decorators -----
decorators.applyBasicDecorators(dcm, model, acqStatic, optional_mp,
markerDiameter)
# ----Final Calibration filter if model previously decorated -----
if model.decoratedModel:
# initial static filter
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=leftFlatFoot,
rightFlatFoot=rightFlatFoot,
headFlat=headFlat,
markerDiameter=markerDiameter).compute()
# ----------------------CGM MODELLING----------------------------------
# ----motion filter----
# notice : viconCGM1compatible option duplicate error on Construction of the foot coordinate system
modMotion = modelFilters.ModelMotionFilter(scp,
acqStatic,
model,
enums.motionMethod.Determinist,
markerDiameter=markerDiameter)
modMotion.compute()
if "displayCoordinateSystem" in kwargs.keys(
) and kwargs["displayCoordinateSystem"]:
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csdf = modelFilters.CoordinateSystemDisplayFilter(
csp, model, acqStatic)
csdf.setStatic(False)
csdf.display()
if "noKinematicsCalculation" in kwargs.keys(
) and kwargs["noKinematicsCalculation"]:
logging.warning(
"[pyCGM2] No Kinematic calculation done for the static file")
return model, acqStatic
else:
#---- Joint kinematics----
# relative angles
modelFilters.ModelJCSFilter(model, acqStatic).compute(
description="vectoriel", pointLabelSuffix=pointSuffix)
# detection of traveling axis + absolute angle
if model.m_bodypart != enums.BodyPart.UpperLimb:
pfp = progressionFrame.PelvisProgressionFrameProcedure()
else:
pfp = progressionFrame.ThoraxProgressionFrameProcedure()
pff = progressionFrame.ProgressionFrameFilter(acqStatic, pfp)
pff.compute()
globalFrame = pff.outputs["globalFrame"]
forwardProgression = pff.outputs["forwardProgression"]
if model.m_bodypart != enums.BodyPart.UpperLimb:
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqStatic,
segmentLabels=["Left Foot", "Right Foot", "Pelvis"],
angleLabels=["LFootProgress", "RFootProgress", "Pelvis"],
eulerSequences=["TOR", "TOR", "ROT"],
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix=pointSuffix)
if model.m_bodypart == enums.BodyPart.LowerLimbTrunk:
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqStatic,
segmentLabels=["Thorax"],
angleLabels=["Thorax"],
eulerSequences=["YXZ"],
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix=pointSuffix)
if model.m_bodypart == enums.BodyPart.UpperLimb or model.m_bodypart == enums.BodyPart.FullBody:
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqStatic,
segmentLabels=["Thorax", "Head"],
angleLabels=["Thorax", "Head"],
eulerSequences=["YXZ", "TOR"],
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix=pointSuffix)
# BSP model
bspModel = bodySegmentParameters.Bsp(model)
bspModel.compute()
if model.m_bodypart == enums.BodyPart.FullBody:
modelFilters.CentreOfMassFilter(
model, acqStatic).compute(pointLabelSuffix=pointSuffix)
return model, acqStatic
def advancedCGM1_kad_midMaleolus_markerDiameter(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\KAD-Med-markerDiameter\\"
staticFilename = "MRI-US-01, 2008-08-08, 3DGA 02.c3d"
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model=cgm.CGM1
model.configure()
markerDiameter=25.0
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,markerDiameter=markerDiameter,
leftFlatFoot = False, rightFlatFoot = False).compute()
# cgm decorator
modelDecorator.Kad(model,acqStatic).compute(markerDiameter=markerDiameter, side="both")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic,markerDiameter=markerDiameter, side="both")
modelFilters.ModelCalibrationFilter(scp,acqStatic,model,
markerDiameter=markerDiameter).compute()
# TESTS ------------------------------------------------
offsetTesting(acqStatic,model,display = True, unitTesting=True)
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 ,"mid")
np.testing.assert_equal(model.getSegment("Right Shank").getReferential("TF").static.getNode_byLabel("RAJC").m_desc ,"mid")
np.testing.assert_equal(model.getSegment("Left Foot").getReferential("TF").static.getNode_byLabel("LAJC").m_desc ,"mid")
np.testing.assert_equal(model.getSegment("Right Foot").getReferential("TF").static.getNode_byLabel("RAJC").m_desc ,"mid")
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_midMaleolus_markerDiameter.c3d")
def basicCGM1_manualOffset_thighRotationON_shankRotationOFF_tibialTorsionON(cls):
"""
CGM1 manual offset behaviour :
=> - Manual Thigh Rotation must modify ShankRotation.
- If zero TibialTorsion inputs -> flag RightTibialTorsion must be off and TibialTorsion keep zero value
"""
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\basic-manualOffsets-thiON_shaOFF_torsionON\\"
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={
'InterAsisDistance' : 0,
'LeftAsisTrocanterDistance' : 0,
'LeftThighRotation' : 10,
'LeftShankRotation' : 0,
'LeftTibialTorsion' : -30.0,
'RightAsisTrocanterDistance' : 0,
'RightThighRotation' : 10,
'RightShankRotation' : 0,
'RightTibialTorsion' : -30.0
}
model.addAnthropoInputParameters(mp,optional=optional_mp)
# -----------CGM STATIC CALIBRATION--------------------
scp=modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp,acqStatic,model).compute()
# decorators
modelDecorator.Cgm1ManualOffsets(model).compute(acqStatic,"left",model.mp["LeftThighRotation"],markerDiameter,model.mp["LeftTibialTorsion"],model.mp["LeftShankRotation"])
modelDecorator.Cgm1ManualOffsets(model).compute(acqStatic,"right",model.mp["RightThighRotation"],markerDiameter,model.mp["RightTibialTorsion"],model.mp["RightShankRotation"])
# finql calibration
modelFilters.ModelCalibrationFilter(scp,acqStatic,model,viconCGM1compatible=True ).compute()
# TESTS
# offset testing
offsetTesting(acqStatic,model,display = True, unitTesting=True)
np.testing.assert_equal(model.getSegment("Left Thigh").getReferential("TF").static.getNode_byLabel("LKJC").m_desc ,"manual ThighOffset")
np.testing.assert_equal(model.getSegment("Right Thigh").getReferential("TF").static.getNode_byLabel("RKJC").m_desc ,"manual ThighOffset")
np.testing.assert_equal(model.getSegment("Left Shank").getReferential("TF").static.getNode_byLabel("LKJC").m_desc ,"manual ThighOffset")
np.testing.assert_equal(model.getSegment("Right Shank").getReferential("TF").static.getNode_byLabel("RKJC").m_desc ,"manual ThighOffset")
np.testing.assert_equal(model.getSegment("Left Shank").getReferential("TF").static.getNode_byLabel("LAJC").m_desc ,"manualTHIoffset-manualTT")
np.testing.assert_equal(model.getSegment("Right Shank").getReferential("TF").static.getNode_byLabel("RAJC").m_desc ,"manualTHIoffset-manualTT")
np.testing.assert_equal(model.getSegment("Left Foot").getReferential("TF").static.getNode_byLabel("LAJC").m_desc ,"manualTHIoffset-manualTT")
np.testing.assert_equal(model.getSegment("Right Foot").getReferential("TF").static.getNode_byLabel("RAJC").m_desc ,"manualTHIoffset-manualTT")
np.testing.assert_equal(model.m_useRightTibialTorsion,True )
np.testing.assert_equal(model.m_useLeftTibialTorsion,True )
def basicCGM1_absoluteAngles_pelikin(cls):
"""
"""
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\Pelikin\\"
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)
scp=modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp,acqStatic,model).compute()
# ------ 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()
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", "ROT"],
globalFrameOrientation = globalFrame,
forwardProgression = forwardProgression).compute(pointLabelSuffix="cgm1_6dof")
#btkTools.smartWriter(acqGait, "verifX.c3d")
# --- tests on angles
np.testing.assert_almost_equal( acqGait.GetPoint("RNewPelAngles").GetValues(),
acqGait.GetPoint("RPelvisAngles_cgm1_6dof").GetValues(), decimal =3)
np.testing.assert_almost_equal( acqGait.GetPoint("LNewPelAngles").GetValues(),
acqGait.GetPoint("LPelvisAngles_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()
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", "ROT"],
globalFrameOrientation = globalFrame,
forwardProgression = forwardProgression).compute(pointLabelSuffix="cgm1_6dof")
# --- tests on angles
np.testing.assert_almost_equal( acqGait.GetPoint("RNewPelAngles").GetValues(),
acqGait.GetPoint("RPelvisAngles_cgm1_6dof").GetValues(), decimal =3)
np.testing.assert_almost_equal( acqGait.GetPoint("LNewPelAngles").GetValues(),
acqGait.GetPoint("LPelvisAngles_cgm1_6dof").GetValues(), decimal =3)
def basicCGM1_global(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\basic_pathologicalSubject\\"
staticFilename = "BOVE Vincent Cal 01.c3d"
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model = cgm.CGM1
model.configure()
markerDiameter = 14
mp = {
'Bodymass': 72.0,
'LeftLegLength': 840.0,
'RightLegLength': 850.0,
'LeftKneeWidth': 105.0,
'RightKneeWidth': 110.4,
'LeftAnkleWidth': 74.0,
'RightAnkleWidth': 74.0,
}
model.addAnthropoInputParameters(mp)
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute()
# ------ Travelling Axis Y -------
gaitFilename = "20120213_BV-PRE-S-NNNN-I-dyn 04.global2.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()
# 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,
mappedForcePlate,
leftSegmentLabel="Left Foot",
rightSegmentLabel="Right Foot").compute()
idp = modelFilters.CGMLowerlimbInverseDynamicProcedure()
modelFilters.InverseDynamicFilter(
model,
acqGait,
procedure=idp,
projection=pyCGM2Enums.MomentProjection.Global).compute(
pointLabelSuffix="cgm1_6dof")
modelFilters.JointPowerFilter(
model, acqGait).compute(pointLabelSuffix="cgm1_6dof")
btkTools.smartWriter(acqGait, "testInvDynPatho.c3d")
# TEST ------
compareKinetics(acqGait, 5, -5, 0.2, 40.0, 0.1)
'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)
#----CALIBRATION----
# initial calibration
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute()
# motion
gaitFilename = "MRI-US-01, 2008-08-08, 3DGA 14.c3d"
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
modMotion = modelFilters.ModelMotionFilter(scp,
acqGait,
model,
enums.motionMethod.Determinist,
usePyCGM2_coordinateSystem=True)
modMotion.compute()
# calibration decorators
modelDecorator.KneeCalibrationDecorator(model).calibrate2dof("Left")
modelDecorator.KneeCalibrationDecorator(model).calibrate2dof("Right")
def CGM2_4_SARA_test(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM2\\cgm2.4\\Knee Calibration\\"
staticFilename = "static.c3d"
funcFilename = "functional.c3d"
gaitFilename = "gait trial 01.c3d"
markerDiameter = 14
mp = {
'Bodymass': 69.0,
'LeftLegLength': 930.0,
'RightLegLength': 930.0,
'LeftKneeWidth': 94.0,
'RightKneeWidth': 64.0,
'LeftAnkleWidth': 67.0,
'RightAnkleWidth': 62.0,
'LeftSoleDelta': 0,
'RightSoleDelta': 0,
"LeftToeOffset": 0,
"RightToeOffset": 0,
}
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model = cgm2.CGM2_4()
model.configure()
model.addAnthropoInputParameters(mp)
# --- INITIAL CALIBRATION ---
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp, acqStatic, model).compute()
# cgm decorator
modelDecorator.HipJointCenterDecorator(model).hara()
modelDecorator.KneeCalibrationDecorator(model).midCondyles(
acqStatic, markerDiameter=markerDiameter, side="both")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic, markerDiameter=markerDiameter, side="both")
# final
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
seLeftHJCnode="LHJC_Hara",
useRightHJCnode="RHJC_Hara",
useLeftKJCnode="LKJC_mid",
useLeftAJCnode="LAJC_mid",
useRightKJCnode="RKJC_mid",
useRightAJCnode="RAJC_mid",
markerDiameter=markerDiameter).compute()
# ------ LEFT KNEE CALIBRATION -------
acqFunc = btkTools.smartReader(str(MAIN_PATH + funcFilename))
# Motion of only left
modMotionLeftKnee = modelFilters.ModelMotionFilter(
scp, acqFunc, model, enums.motionMethod.Sodervisk)
modMotionLeftKnee.segmentalCompute(["Left Thigh", "Left Shank"])
# decorator
modelDecorator.KneeCalibrationDecorator(model).sara(
"Left", indexFirstFrame=831, indexLastFrame=1280)
# ----add Point into the c3d----
Or_inThigh = model.getSegment("Left Thigh").getReferential(
"TF").getNodeTrajectory("KneeFlexionOri")
axis_inThigh = model.getSegment("Left Thigh").getReferential(
"TF").getNodeTrajectory("KneeFlexionAxis")
btkTools.smartAppendPoint(acqFunc, "Left" + "_KneeFlexionOri",
Or_inThigh)
btkTools.smartAppendPoint(acqFunc, "Left" + "_KneeFlexionAxis",
axis_inThigh)
# ------ RIGHT KNEE CALIBRATION -------
# Motion of only left
modMotionRightKnee = modelFilters.ModelMotionFilter(
scp, acqFunc, model, enums.motionMethod.Sodervisk)
modMotionRightKnee.segmentalCompute(["Right Thigh", "Right Shank"])
# decorator
modelDecorator.KneeCalibrationDecorator(model).sara("Right",
indexFirstFrame=61,
indexLastFrame=551)
# ----add Point into the c3d----
Or_inThigh = model.getSegment("Right Thigh").getReferential(
"TF").getNodeTrajectory("KneeFlexionOri")
axis_inThigh = model.getSegment("Right Thigh").getReferential(
"TF").getNodeTrajectory("KneeFlexionAxis")
btkTools.smartAppendPoint(acqFunc, "Right" + "_KneeFlexionOri",
Or_inThigh)
btkTools.smartAppendPoint(acqFunc, "Right" + "_KneeFlexionAxis",
axis_inThigh)
btkTools.smartWriter(acqFunc, "acqFunc-Sara.c3d")
#--- FINAL CALIBRATION ---
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
useLeftHJCnode="LHJC_Hara",
useRightHJCnode="RHJC_Hara",
useLeftKJCnode="KJC_Sara",
useLeftAJCnode="LAJC_mid",
useRightKJCnode="KJC_Sara",
useRightAJCnode="RAJC_mid",
markerDiameter=markerDiameter).compute()
# save static c3d with update KJC
btkTools.smartWriter(acqStatic, "Static-SARA.c3d")
# print functional Offsets
print model.mp_computed["LeftKneeFuncCalibrationOffset"]
print model.mp_computed["RightKneeFuncCalibrationOffset"]
def sara(model, DATA_PATH, reconstructFilenameLabelled, translators, side,
beginFrame, endFrame, **kwargs):
# --- btk acquisition ----
if "forceBtkAcq" in kwargs.keys():
acqFunc = kwargs["forceBtkAcq"]
else:
acqFunc = btkTools.smartReader(
str(DATA_PATH + reconstructFilenameLabelled))
btkTools.checkMultipleSubject(acqFunc)
acqFunc = btkTools.applyTranslators(acqFunc, translators)
#---get frame range of interest---
ff = acqFunc.GetFirstFrame()
lf = acqFunc.GetLastFrame()
start, end = btkTools.getStartEndEvents(acqFunc, side)
if start is not None:
logging.info("Start event detected")
initFrame = start
else:
initFrame = beginFrame if beginFrame is not None else ff
if end is not None:
logging.info("End event detected")
endFrame = end
else:
endFrame = endFrame if endFrame is not None else lf
iff = initFrame - ff
ilf = endFrame - ff
#---motion side of the lower limb---
if side is None:
side = detectSide(acqFunc, "LANK", "RANK")
logging.info("Detected motion side : %s" % (side))
# --------------------------RESET OF THE STATIC File---------
# load btkAcq from static file
staticFilename = model.m_staticFilename
acqStatic = btkTools.smartReader(str(DATA_PATH + staticFilename))
btkTools.checkMultipleSubject(acqStatic)
acqStatic = btkTools.applyTranslators(acqStatic, translators)
# initial calibration ( i.e calibration from Calibration operation)
leftFlatFoot = model.m_properties["CalibrationParameters"]["leftFlatFoot"]
rightFlatFoot = model.m_properties["CalibrationParameters"][
"rightFlatFoot"]
markerDiameter = model.m_properties["CalibrationParameters"][
"markerDiameter"]
headFlat = model.m_properties["CalibrationParameters"]["headFlat"]
if side == "Left":
model.mp_computed["LeftKneeFuncCalibrationOffset"] = 0
if side == "Right":
model.mp_computed["RightKneeFuncCalibrationOffset"] = 0
# initial calibration ( zero previous KneeFunc offset on considered side )
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=leftFlatFoot,
rightFlatFoot=rightFlatFoot,
headFlat=headFlat,
markerDiameter=markerDiameter).compute()
if model.version in ["CGM2.3", "CGM2.4", "CGM2.5"]:
if side == "Left":
thigh_markers = model.getSegment("Left Thigh").m_tracking_markers
shank_markers = model.getSegment("Left Shank").m_tracking_markers
elif side == "Right":
thigh_markers = model.getSegment("Right Thigh").m_tracking_markers
shank_markers = model.getSegment("Right Shank").m_tracking_markers
validFrames, vff, vlf = btkTools.findValidFrames(
acqFunc, thigh_markers + shank_markers)
proximalSegmentLabel = str(side + " Thigh")
distalSegmentLabel = str(side + " Shank")
# segment Motion
modMotion = modelFilters.ModelMotionFilter(
scp, acqFunc, model, enums.motionMethod.Sodervisk)
modMotion.segmentalCompute([proximalSegmentLabel, distalSegmentLabel])
# decorator
modelDecorator.KneeCalibrationDecorator(model).sara(
side, indexFirstFrame=iff, indexLastFrame=ilf)
# --------------------------FINAL CALIBRATION OF THE STATIC File---------
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=leftFlatFoot,
rightFlatFoot=rightFlatFoot,
headFlat=headFlat,
markerDiameter=markerDiameter).compute()
return model, acqFunc, side
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 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")
