def CGM23(cls):
TRACKING_MARKERS = ["LASI", "RASI","RPSI", "LPSI",
"LTHI","LKNE","LTHAP","LTHAD",
"LTIB","LANK","LTIAP","LTIAD",
"LHEE","LTOE",
"RTHI","RKNE","RTHAP","RTHAD",
"RTIB","RANK","RTIAP","RTIAD",
"RHEE","RTOE"]
model=cgm2.CGM2_3LowerLimbs()
model.configure()
trackingMarkers = model.getTrackingMarkers()
np.testing.assert_equal(trackingMarkers,
TRACKING_MARKERS)
def noIK_6dof(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()
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()
#import ipdb; ipdb.set_trace()
# ------ 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()
csp = modelFilters.ModelCoordinateSystemProcedure(model)
modelFilters.CoordinateSystemDisplayFilter(csp, model,
acqGait).display()
btkTools.smartWriter(acqGait, "cgm23_noIK6dof_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_3_SARA_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_3LowerLimbs()
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 -------
acqLeftKnee = btkTools.smartReader(str(MAIN_PATH + leftKneeFilename))
# Motion of only left
modMotionLeftKnee=modelFilters.ModelMotionFilter(scp,acqLeftKnee,model,pyCGM2Enums.motionMethod.Sodervisk)
modMotionLeftKnee.segmentalCompute(["Left Thigh","Left Shank"])
# decorator
modelDecorator.KneeCalibrationDecorator(model).sara("Left",indexFirstFrame = 489, indexLastFrame = 1451 )
# ----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(acqLeftKnee,"Left" +"_KneeFlexionOri",Or_inThigh)
btkTools.smartAppendPoint(acqLeftKnee,"Left" +"_KneeFlexionAxis",axis_inThigh)
btkTools.smartWriter(acqLeftKnee, "Left Knee-Sara.c3d")
# ------ RIGHT KNEE CALIBRATION -------
acqRightKnee = btkTools.smartReader(str(MAIN_PATH + rightKneeFilename))
# Motion of only left
modMotionRightKnee=modelFilters.ModelMotionFilter(scp,acqRightKnee,model,pyCGM2Enums.motionMethod.Sodervisk)
modMotionRightKnee.segmentalCompute(["Right Thigh","Right Shank"])
# decorator
modelDecorator.KneeCalibrationDecorator(model).sara("Right",indexFirstFrame = 25, indexLastFrame = 1060 )
# ----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(acqRightKnee,"Right" +"_KneeFlexionOri",Or_inThigh)
btkTools.smartAppendPoint(acqRightKnee,"Right" +"_KneeFlexionAxis",axis_inThigh)
btkTools.smartWriter(acqRightKnee, "Right Knee-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 Foot","Right Foot","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_3\\cgm2_3-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_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,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")