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 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 applyHJCDecorators(model,method):
if method["Left"] == "Hara":
logging.info("[pyCGM2] Left HJC : Hara")
modelDecorator.HipJointCenterDecorator(model).hara(side = "left")
elif len(method["Left"]) == 3:
logging.info("[pyCGM2] Left HJC : Custom")
logging.warning(method["Left"])
modelDecorator.HipJointCenterDecorator(model).custom(position_Left = np.array(method["Left"]), methodDesc = "custom",side="left")
if method["Right"] == "Hara":
logging.info("[pyCGM2] Right HJC : Hara")
modelDecorator.HipJointCenterDecorator(model).hara(side = "right")
elif len(method["Right"]) == 3:
logging.info("[pyCGM2] Right HJC : Custom")
logging.warning(method["Right"])
modelDecorator.HipJointCenterDecorator(model).custom(position_Right = np.array(method["Right"]), methodDesc = "custom",side="right")
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_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 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 applyHJCDecorators(model, method):
if model.getBodyPart() != enums.BodyPart.UpperLimb:
if method["Left"] == "Hara":
LOGGER.logger.info("[pyCGM2] Left HJC : Hara")
modelDecorator.HipJointCenterDecorator(model).hara(side="left")
elif len(method["Left"]) == 3:
LOGGER.logger.info("[pyCGM2] Left HJC : Custom")
LOGGER.logger.debug(method["Left"])
modelDecorator.HipJointCenterDecorator(model).custom(
position_Left=np.array(method["Left"]),
methodDesc="custom",
side="left")
if method["Right"] == "Hara":
LOGGER.logger.info("[pyCGM2] Right HJC : Hara")
modelDecorator.HipJointCenterDecorator(model).hara(side="right")
elif len(method["Right"]) == 3:
LOGGER.logger.info("[pyCGM2] Right HJC : Custom")
LOGGER.logger.debug(method["Right"])
modelDecorator.HipJointCenterDecorator(model).custom(
position_Right=np.array(method["Right"]),
methodDesc="custom",
side="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_4LowerLimbs()
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",
cgm1Behaviour=True)
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, pyCGM2Enums.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, pyCGM2Enums.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,
RotateLeftThighFlag=True,
RotateRightThighFlag=True).compute()
# save static c3d with update KJC
btkTools.smartWriter(acqStatic, "Static-SARA.c3d")
# ------ Fitting -------
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
# Motion FILTER
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", "RASI", "RPSI", "LPSI"])
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqGait,
segmentLabels=["Left HindFoot", "Right HindFoot", "Pelvis"],
angleLabels=["LFootProgress", "RFootProgress", "Pelvis"],
eulerSequences=["TOR", "TOR", "ROT"],
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix="cgm1_6dof")
# ------- OPENSIM IK --------------------------------------
# --- osim builder ---
cgmCalibrationprocedure = opensimFilters.CgmOpensimCalibrationProcedures(
model)
markersetFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_4\\cgm2_4-markerset.xml"
osimfile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\osim\\lowerLimb_ballsJoints.osim"
oscf = opensimFilters.opensimCalibrationFilter(
osimfile, model, cgmCalibrationprocedure)
oscf.addMarkerSet(markersetFile)
scalingOsim = oscf.build(exportOsim=False)
# --- fitting ---
#procedure
cgmFittingProcedure = opensimFilters.CgmOpensimFittingProcedure(model)
iksetupFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_4\\cgm2_4-ikSetUp_template.xml"
osrf = opensimFilters.opensimFittingFilter(iksetupFile, scalingOsim,
cgmFittingProcedure,
MAIN_PATH)
acqIK = osrf.run(acqGait,
str(MAIN_PATH + gaitFilename),
exportSetUp=False)
# -------- NEW MOTION FILTER ON IK MARKERS ------------------
modMotion_ik = modelFilters.ModelMotionFilter(
scp,
acqIK,
model,
pyCGM2Enums.motionMethod.Sodervisk,
useForMotionTest=True)
modMotion_ik.compute()
finalJcs = modelFilters.ModelJCSFilter(model, acqIK)
finalJcs.setFilterBool(False)
finalJcs.compute(description="ik", pointLabelSuffix="2_ik") #
btkTools.smartWriter(acqIK, "gait trial 01 - Fitting.c3d")
def calibrate(self, aquiStatic, dictRef, dictAnatomic, options=None):
# add markers
valSACR = (aquiStatic.GetPoint("LPSI").GetValues() +
aquiStatic.GetPoint("RPSI").GetValues()) / 2.0
btkTools.smartAppendPoint(aquiStatic, "SACR", valSACR, desc="")
valMidAsis = (aquiStatic.GetPoint("LASI").GetValues() +
aquiStatic.GetPoint("RASI").GetValues()) / 2.0
btkTools.smartAppendPoint(aquiStatic, "midASIS", valMidAsis, desc="")
valLMET = (aquiStatic.GetPoint("LFMH").GetValues() +
aquiStatic.GetPoint("LVMH").GetValues()) / 2.0
btkTools.smartAppendPoint(aquiStatic, "LMET", valLMET, desc="")
valRMET = (aquiStatic.GetPoint("RFMH").GetValues() +
aquiStatic.GetPoint("RVMH").GetValues()) / 2.0
btkTools.smartAppendPoint(aquiStatic, "RMET", valRMET, desc="")
ff = aquiStatic.GetFirstFrame()
lf = aquiStatic.GetLastFrame()
frameInit = ff - ff
frameEnd = lf - ff + 1
# calibrate technical
self._calibrateTechnicalSegment(aquiStatic,
"Pelvis",
dictRef,
frameInit,
frameEnd,
options=options)
self._calibrateTechnicalSegment(aquiStatic,
"Left Thigh",
dictRef,
frameInit,
frameEnd,
options=options)
self._calibrateTechnicalSegment(aquiStatic,
"Right Thigh",
dictRef,
frameInit,
frameEnd,
options=options)
self._calibrateTechnicalSegment(aquiStatic,
"Left Shank",
dictRef,
frameInit,
frameEnd,
options=options)
self._calibrateTechnicalSegment(aquiStatic,
"Right Shank",
dictRef,
frameInit,
frameEnd,
options=options)
self._calibrateTechnicalSegment(aquiStatic,
"Left Foot",
dictRef,
frameInit,
frameEnd,
options=options)
self._calibrateTechnicalSegment(aquiStatic,
"Right Foot",
dictRef,
frameInit,
frameEnd,
options=options)
# # ---- decorator ----
modelDecorator.HipJointCenterDecorator(self).greatTrochanterOffset(
aquiStatic)
modelDecorator.KneeCalibrationDecorator(self).midCondyles(aquiStatic)
modelDecorator.AnkleCalibrationDecorator(self).midMaleolus(aquiStatic)
# calibrate anatomic
self._calibrateAnatomicalSegment(aquiStatic,
"Pelvis",
dictAnatomic,
frameInit,
frameEnd,
options=options)
self._calibrateAnatomicalSegment(aquiStatic,
"Left Thigh",
dictAnatomic,
frameInit,
frameEnd,
options=options)
self._calibrateAnatomicalSegment(aquiStatic,
"Right Thigh",
dictAnatomic,
frameInit,
frameEnd,
options=options)
self._calibrateAnatomicalSegment(aquiStatic,
"Left Shank",
dictAnatomic,
frameInit,
frameEnd,
options=options)
self._calibrateAnatomicalSegment(aquiStatic,
"Right Shank",
dictAnatomic,
frameInit,
frameEnd,
options=options)
self._calibrateAnatomicalSegment(aquiStatic,
"Left Foot",
dictAnatomic,
frameInit,
frameEnd,
options=options)
self._calibrateAnatomicalSegment(aquiStatic,
"Right Foot",
dictAnatomic,
frameInit,
frameEnd,
options=options)
def full_IK(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM2\\cgm2.4\\medial\\"
staticFilename = "static.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,
}
# --- Calibration ---
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model = cgm2.CGM2_4LowerLimbs()
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).compute()
# ------ Fitting -------
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
# Motion FILTER
modMotion = modelFilters.ModelMotionFilter(
scp, acqGait, model, pyCGM2Enums.motionMethod.Sodervisk)
modMotion.compute()
# relative angles
modelFilters.ModelJCSFilter(model, acqGait).compute(
description="vectoriel", pointLabelSuffix="cgm1_6dof")
# absolute angles
longitudinalAxis, forwardProgression, globalFrame = btkTools.findProgressionAxisFromPelvicMarkers(
acqGait, ["LASI", "RASI", "RPSI", "LPSI"])
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")
# ---Marker decomp filter----
mtf = modelFilters.TrackingMarkerDecompositionFilter(model, acqGait)
mtf.decompose()
# ------- OPENSIM IK --------------------------------------
# --- osim builder ---
cgmCalibrationprocedure = opensimFilters.CgmOpensimCalibrationProcedures(
model)
markersetFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_4\\cgm2_4-markerset - expert.xml"
osimfile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\osim\\lowerLimb_ballsJoints.osim"
oscf = opensimFilters.opensimCalibrationFilter(
osimfile, model, cgmCalibrationprocedure, MAIN_PATH)
oscf.addMarkerSet(markersetFile)
scalingOsim = oscf.build(exportOsim=False)
# --- fitting ---
#procedure
cgmFittingProcedure = opensimFilters.CgmOpensimFittingProcedure(
model, expertMode=True)
iksetupFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_4\\cgm2_4-expert-ikSetUp_template.xml"
osrf = opensimFilters.opensimFittingFilter(iksetupFile, scalingOsim,
cgmFittingProcedure,
MAIN_PATH)
acqIK = osrf.run(acqGait,
str(MAIN_PATH + gaitFilename),
exportSetUp=False)
# -------- NEW MOTION FILTER ON IK MARKERS ------------------
modMotion_ik = modelFilters.ModelMotionFilter(
scp,
acqIK,
model,
pyCGM2Enums.motionMethod.Sodervisk,
useForMotionTest=True)
modMotion_ik.compute()
finalJcs = modelFilters.ModelJCSFilter(model, acqIK)
finalJcs.setFilterBool(False)
finalJcs.compute(description="ik", pointLabelSuffix="2_ik") #
btkTools.smartWriter(acqIK, "cgm24e_fullIK.c3d")
pointLabelOrigin="LHEE")
gcp.setDefinition("Right Foot",
"TF",
sequence="ZXY",
pointLabel1="RSMH",
pointLabel2="RHEE",
pointLabel3="RVMH",
pointLabelOrigin="RHEE")
#---Initial Calibration Filter---
smf0 = modelFilters.ModelCalibrationFilter(gcp, acqStatic, bioMechModel)
smf0.setBoolOption("technicalReferentialOnly")
smf0.compute()
# ---- decorator ----
modelDecorator.HipJointCenterDecorator(bioMechModel).greatTrochanterOffset(
acqStatic)
modelDecorator.KneeCalibrationDecorator(bioMechModel).midCondyles(
acqStatic)
modelDecorator.AnkleCalibrationDecorator(bioMechModel).midMaleolus(
acqStatic)
gcp.setAnatomicalDefinition("Pelvis",
sequence="YZX",
nodeLabel1="RASI",
nodeLabel2="LASI",
nodeLabel3="SACR",
nodeLabelOrigin="midASIS")
gcp.setAnatomicalDefinition("Left Thigh",
sequence="ZXiY",
nodeLabel1="LKJC_mid",
nodeLabel2="LHJC_gt",
}
# --- Calibration ---
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model = cgm2.CGM2_2LowerLimbs()
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).compute()
# ------ Fitting -------
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
# Motion FILTER
modMotion = modelFilters.ModelMotionFilter(
scp, acqGait, model, pyCGM2Enums.motionMethod.Determinist)
def test_lowLevel(self):
DATA_PATH = pyCGM2.TEST_DATA_PATH + "GaitModels\CGM2.3\\Hannibal-medial\\"
staticFilename = "static.c3d"
gaitFilename= "gait1.c3d"
markerDiameter=14
required_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,
'LeftShoulderOffset' : 0,
'RightShoulderOffset' : 0,
'LeftElbowWidth' : 0,
'LeftWristWidth' : 0,
'LeftHandThickness' : 0,
'RightElbowWidth' : 0,
'RightWristWidth' : 0,
'RightHandThickness' : 0
}
optional_mp = {
'LeftTibialTorsion' : 0,
'LeftThighRotation' : 0,
'LeftShankRotation' : 0,
'RightTibialTorsion' : 0,
'RightThighRotation' : 0,
'RightShankRotation' : 0
}
# --- Calibration ---
# ---check marker set used----
acqStatic = btkTools.smartReader(DATA_PATH + staticFilename)
dcm = cgm.CGM.detectCalibrationMethods(acqStatic)
model=cgm2.CGM2_3()
model.configure(detectedCalibrationMethods=dcm)
model.addAnthropoInputParameters(required_mp,optional=optional_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).compute()
# ------ Fitting -------
acqGait = btkTools.smartReader(DATA_PATH + gaitFilename)
# Motion FILTER
modMotion=modelFilters.ModelMotionFilter(scp,acqGait,model,enums.motionMethod.Sodervisk)
modMotion.compute()
# ------- OPENSIM IK --------------------------------------
# --- osim builder ---
cgmCalibrationprocedure = opensimFilters.CgmOpensimCalibrationProcedures(model)
markersetFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_3\\cgm2_3-markerset.xml"
osimfile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\osim\\lowerLimb_ballsJoints.osim"
oscf = opensimFilters.opensimCalibrationFilter(osimfile,
model,
cgmCalibrationprocedure,
DATA_PATH)
oscf.addMarkerSet(markersetFile)
scalingOsim = oscf.build(exportOsim=False)
# --- fitting ---
#procedure
cgmFittingProcedure = opensimFilters.CgmOpensimFittingProcedure(model)
iksetupFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_3\\cgm2_3-ikSetUp_template.xml"
osrf = opensimFilters.opensimFittingFilter(iksetupFile,
scalingOsim,
cgmFittingProcedure,
DATA_PATH,
acqGait )
acqIK = osrf.run(str(DATA_PATH + gaitFilename ),exportSetUp=False)
# -------- NEW MOTION FILTER ON IK MARKERS ------------------
modMotion_ik=modelFilters.ModelMotionFilter(scp,acqIK,model,enums.motionMethod.Sodervisk,
useForMotionTest=True)
modMotion_ik.compute()
finalJcs =modelFilters.ModelJCSFilter(model,acqIK)
finalJcs.compute(description="ik", pointLabelSuffix = "2_ik")#
btkTools.smartWriter(acqIK,"cgm23_fullIK_Motion.c3d")
def full_IK(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM2\\cgm2.3\\fullBody\\"
staticFilename = "PN01OP01S01STAT.c3d"
gaitFilename = "PN01OP01S01SS01.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_3.translators")
acqStatic = btkTools.applyTranslators(acqStatic, translators)
model = cgm2.CGM2_3LowerLimbs()
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).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()
# ------- OPENSIM IK --------------------------------------
# --- osim builder ---
cgmCalibrationprocedure = opensimFilters.CgmOpensimCalibrationProcedures(
model)
markersetFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_3\\cgm2_3-markerset.xml"
osimfile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\osim\\lowerLimb_ballsJoints.osim"
oscf = opensimFilters.opensimCalibrationFilter(
osimfile, model, cgmCalibrationprocedure, MAIN_PATH)
oscf.addMarkerSet(markersetFile)
scalingOsim = oscf.build(exportOsim=False)
# --- fitting ---
#procedure
cgmFittingProcedure = opensimFilters.CgmOpensimFittingProcedure(model)
iksetupFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_3\\cgm2_3-ikSetUp_template.xml"
osrf = opensimFilters.opensimFittingFilter(iksetupFile, scalingOsim,
cgmFittingProcedure,
MAIN_PATH)
acqIK = osrf.run(acqGait,
str(MAIN_PATH + gaitFilename),
exportSetUp=False)
# -------- NEW MOTION FILTER ON IK MARKERS ------------------
modMotion_ik = modelFilters.ModelMotionFilter(
scp,
acqIK,
model,
enums.motionMethod.Sodervisk,
useForMotionTest=True)
modMotion_ik.compute()
finalJcs = modelFilters.ModelJCSFilter(model, acqIK)
finalJcs.setFilterBool(False)
finalJcs.compute(description="ik", pointLabelSuffix="2_ik") #
btkTools.smartWriter(acqIK, "cgm23_fullIK_Motion.c3d")
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 CGM23_2DOF_test(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM2\\cgm2.3\\Knee Calibration\\"
staticFilename = "Static.c3d"
leftKneeFilename = "Left Knee.c3d"
rightKneeFilename = "Right Knee.c3d"
gaitFilename = "gait trial 01.c3d"
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,
}
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model = cgm2.CGM2_3()
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 -------
acqLeftKnee = btkTools.smartReader(str(MAIN_PATH + leftKneeFilename))
# Motion of only left
modMotionLeftKnee = modelFilters.ModelMotionFilter(
scp, acqLeftKnee, model, enums.motionMethod.Sodervisk)
modMotionLeftKnee.segmentalCompute(["Left Thigh", "Left Shank"])
# decorator
modelDecorator.KneeCalibrationDecorator(model).calibrate2dof(
"Left", indexFirstFrame=489, indexLastFrame=1451)
# ----add Point into the c3d----
btkTools.smartWriter(acqLeftKnee, "Left Knee-2dof.c3d")
# ------ RIGHT KNEE CALIBRATION -------
acqRightKnee = btkTools.smartReader(str(MAIN_PATH + rightKneeFilename))
# Motion of only left
modMotionRightKnee = modelFilters.ModelMotionFilter(
scp, acqRightKnee, model, enums.motionMethod.Sodervisk)
modMotionRightKnee.segmentalCompute(["Right Thigh", "Right Shank"])
# decorator
modelDecorator.KneeCalibrationDecorator(model).calibrate2dof(
"Right", indexFirstFrame=25, indexLastFrame=1060)
# ----add Point into the c3d----
btkTools.smartWriter(acqRightKnee, "Right Knee-2dof.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-2DOF.c3d")
