def applyDecorators_CGM1(smc, model,acqStatic,optional_mp,markerDiameter):
# native but thighRotation altered in mp
if smc["left"] == enums.CgmStaticMarkerConfig.Native and optional_mp["LeftThighRotation"] !=0:
logging.warning("CASE FOUND ===> Left Side = NATIVE CGM1 + manual Thigh ")
modelDecorator.Cgm1ManualOffsets(model).compute(acqStatic,"left",optional_mp["LeftThighRotation"],
markerDiameter, optional_mp["LeftTibialTorsion"], optional_mp["LeftShankRotation"])
if smc["right"] == enums.CgmStaticMarkerConfig.Native and optional_mp["RightThighRotation"] !=0:
logging.warning("CASE FOUND ===> Right Side = NATIVE CGM1 + manual Thigh ")
modelDecorator.Cgm1ManualOffsets(model).compute(acqStatic,"right",optional_mp["RightThighRotation"],
markerDiameter,optional_mp["RightTibialTorsion"],optional_mp["RightShankRotation"])
# KAD
if smc["left"] == enums.CgmStaticMarkerConfig.KAD:
logging.warning("CASE FOUND ===> Left Side = KAD")
modelDecorator.Kad(model,acqStatic).compute(markerDiameter=markerDiameter, side="left")
if smc["right"] == enums.CgmStaticMarkerConfig.KAD:
logging.warning("CASE FOUND ===> Right Side = KAD")
modelDecorator.Kad(model,acqStatic).compute(markerDiameter=markerDiameter, side="right")
# KADmed
if smc["left"] == enums.CgmStaticMarkerConfig.KADmed:
logging.warning("CASE FOUND ===> Left Side = KAD+med")
modelDecorator.Kad(model,acqStatic).compute(markerDiameter=markerDiameter, side="left")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, markerDiameter=markerDiameter, side="left")
if smc["right"] == enums.CgmStaticMarkerConfig.KADmed:
logging.warning("CASE FOUND ===> Right Side = KAD+med")
modelDecorator.Kad(model,acqStatic).compute(markerDiameter=markerDiameter, side="right")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, markerDiameter=markerDiameter, side="right")
def 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 applyBasicDecorators(dcm, model,acqStatic,optional_mp,markerDiameter,cgm1only=False):
# native but thighRotation altered in mp
if dcm["Left Knee"] == enums.JointCalibrationMethod.Basic and dcm["Left Ankle"] == enums.JointCalibrationMethod.Basic and optional_mp["LeftThighRotation"] !=0:
logging.warning("CASE FOUND ===> Left Side = NATIVE CGM1 + manual Thigh ")
modelDecorator.Cgm1ManualOffsets(model).compute(acqStatic,"left",optional_mp["LeftThighRotation"],
markerDiameter, optional_mp["LeftTibialTorsion"], optional_mp["LeftShankRotation"])
if dcm["Right Knee"] == enums.JointCalibrationMethod.Basic and dcm["Right Ankle"] == enums.JointCalibrationMethod.Basic and optional_mp["RightThighRotation"] !=0:
logging.warning("CASE FOUND ===> Right Side = NATIVE CGM1 + manual Thigh ")
modelDecorator.Cgm1ManualOffsets(model).compute(acqStatic,"right",optional_mp["RightThighRotation"],
markerDiameter,optional_mp["RightTibialTorsion"],optional_mp["RightShankRotation"])
# KAD - and Kadmed
if dcm["Left Knee"] == enums.JointCalibrationMethod.KAD:
logging.warning("CASE FOUND ===> Left Side = KAD")
modelDecorator.Kad(model,acqStatic).compute(markerDiameter=markerDiameter, side="left")
if dcm["Left Ankle"] == enums.JointCalibrationMethod.Medial:
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, markerDiameter=markerDiameter, side="left")
if dcm["Right Knee"] == enums.JointCalibrationMethod.KAD:
logging.warning("CASE FOUND ===> Right Side = KAD")
modelDecorator.Kad(model,acqStatic).compute(markerDiameter=markerDiameter, side="right")
if dcm["Right Ankle"] == enums.JointCalibrationMethod.Medial:
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, markerDiameter=markerDiameter, side="right")
if not cgm1only:
#Kad-like (KneeMed)
if dcm["Left Knee"] == enums.JointCalibrationMethod.Medial and dcm["Left Ankle"] == enums.JointCalibrationMethod.Basic:
modelDecorator.KneeCalibrationDecorator(model).midCondyles_KAD(acqStatic, markerDiameter=markerDiameter, side="left")
if dcm["Right Knee"] == enums.JointCalibrationMethod.Medial and dcm["Right Ankle"] == enums.JointCalibrationMethod.Basic:
modelDecorator.KneeCalibrationDecorator(model).midCondyles_KAD(acqStatic, markerDiameter=markerDiameter, side="right")
#knee and ankle Med
if dcm["Left Knee"] == enums.JointCalibrationMethod.Medial and dcm["Left Ankle"] == enums.JointCalibrationMethod.Medial:
modelDecorator.KneeCalibrationDecorator(model).midCondyles(acqStatic, markerDiameter=markerDiameter, side="left")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, markerDiameter=markerDiameter, side="left")
if dcm["Right Knee"] == enums.JointCalibrationMethod.Medial and dcm["Right Ankle"] == enums.JointCalibrationMethod.Medial:
modelDecorator.KneeCalibrationDecorator(model).midCondyles(acqStatic, markerDiameter=markerDiameter, side="right")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(acqStatic, markerDiameter=markerDiameter, side="right")
def 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_manualTibialTorsion_withDecorator(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={
'InterAsisDistance' : 0,
'LeftAsisTrocanterDistance' : 0,
'LeftThighRotation' : 0,
'LeftShankRotation' : 0,
'LeftTibialTorsion' : -30.0,
'RightAsisTrocanterDistance' : 0,
'RightThighRotation' : 0,
'RightShankRotation' : 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()
# 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"])
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 applyBasicDecorators(dcm,
model,
acqStatic,
optional_mp,
markerDiameter,
cgm1only=False):
if model.getBodyPart() != enums.BodyPart.UpperLimb:
# native but thighRotation altered in mp
if dcm["Left Knee"] == enums.JointCalibrationMethod.Basic and dcm[
"Left Ankle"] == enums.JointCalibrationMethod.Basic and optional_mp[
"LeftThighRotation"] != 0:
LOGGER.logger.debug(
"CASE FOUND ===> Left Side = NATIVE CGM1 + manual Thigh ")
modelDecorator.Cgm1ManualOffsets(model).compute(
acqStatic, "left", optional_mp["LeftThighRotation"],
markerDiameter, optional_mp["LeftTibialTorsion"],
optional_mp["LeftShankRotation"])
if dcm["Right Knee"] == enums.JointCalibrationMethod.Basic and dcm[
"Right Ankle"] == enums.JointCalibrationMethod.Basic and optional_mp[
"RightThighRotation"] != 0:
LOGGER.logger.debug(
"CASE FOUND ===> Right Side = NATIVE CGM1 + manual Thigh ")
modelDecorator.Cgm1ManualOffsets(model).compute(
acqStatic, "right", optional_mp["RightThighRotation"],
markerDiameter, optional_mp["RightTibialTorsion"],
optional_mp["RightShankRotation"])
# KAD - and Kadmed
if dcm["Left Knee"] == enums.JointCalibrationMethod.KAD:
LOGGER.logger.debug("CASE FOUND ===> Left Side = Knee-KAD")
modelDecorator.Kad(model, acqStatic).compute(
markerDiameter=markerDiameter, side="left")
if dcm["Left Ankle"] == enums.JointCalibrationMethod.Medial:
LOGGER.logger.debug("CASE FOUND ===> Left Side = Ankle-Med")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic, markerDiameter=markerDiameter, side="left")
if dcm["Right Knee"] == enums.JointCalibrationMethod.KAD:
LOGGER.logger.debug("CASE FOUND ===> Right Side = Knee-KAD")
modelDecorator.Kad(model, acqStatic).compute(
markerDiameter=markerDiameter, side="right")
if dcm["Right Ankle"] == enums.JointCalibrationMethod.Medial:
LOGGER.logger.debug("CASE FOUND ===> Right Side = Ankle-Med")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic, markerDiameter=markerDiameter, side="right")
if not cgm1only:
if model.getBodyPart() != enums.BodyPart.UpperLimb:
#Kad-like (KneeMed)
if dcm["Left Knee"] == enums.JointCalibrationMethod.Medial and dcm[
"Left Ankle"] == enums.JointCalibrationMethod.Basic:
modelDecorator.KneeCalibrationDecorator(model).midCondyles_KAD(
acqStatic, markerDiameter=markerDiameter, side="left")
if dcm["Right Knee"] == enums.JointCalibrationMethod.Medial and dcm[
"Right Ankle"] == enums.JointCalibrationMethod.Basic:
modelDecorator.KneeCalibrationDecorator(model).midCondyles_KAD(
acqStatic, markerDiameter=markerDiameter, side="right")
#knee and ankle Med
if dcm["Left Knee"] == enums.JointCalibrationMethod.Medial and dcm[
"Left Ankle"] == enums.JointCalibrationMethod.Medial:
LOGGER.logger.info(
"[pyCGM2] Left Knee : Medial - Left Ankle : Medial")
modelDecorator.KneeCalibrationDecorator(model).midCondyles(
acqStatic, markerDiameter=markerDiameter, side="left")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic, markerDiameter=markerDiameter, side="left")
if dcm["Right Knee"] == enums.JointCalibrationMethod.Medial and dcm[
"Right Ankle"] == enums.JointCalibrationMethod.Medial:
LOGGER.logger.info(
"[pyCGM2] Right Knee : Medial - Right Ankle : Medial")
modelDecorator.KneeCalibrationDecorator(model).midCondyles(
acqStatic, markerDiameter=markerDiameter, side="right")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic, markerDiameter=markerDiameter, side="right")