def fitting(model,DATA_PATH, reconstructFilenameLabelled,
translators,weights,
ik_flag,markerDiameter,
pointSuffix,
mfpa,
momentProjection,**kwargs):
"""
Fitting of the CGM2.3
:param model [str]: pyCGM2 model previously calibrated
:param DATA_PATH [str]: path to your data
:param reconstructFilenameLabelled [string list]: c3d files
:param translators [dict]: translators to apply
:param ik_flag [bool]: enable the inverse kinematic solver
:param mfpa [str]: manual force plate assignement
:param markerDiameter [double]: marker diameter (mm)
:param pointSuffix [str]: suffix to add to model outputs
:param momentProjection [str]: Coordinate system in which joint moment is expressed
"""
if "Fitting" in weights.keys():
weights = weights["Fitting"]["Weight"]
# --------------------------ACQ WITH TRANSLATORS --------------------------------------
# --- btk acquisition ----
if "forceBtkAcq" in kwargs.keys():
acqGait = kwargs["forceBtkAcq"]
else:
acqGait = btkTools.smartReader((DATA_PATH + reconstructFilenameLabelled))
btkTools.checkMultipleSubject(acqGait)
if btkTools.isPointExist(acqGait,"SACR"):
translators["LPSI"] = "SACR"
translators["RPSI"] = "SACR"
logging.info("[pyCGM2] Sacrum marker detected")
acqGait = btkTools.applyTranslators(acqGait,translators)
trackingMarkers = model.getTrackingMarkers(acqGait)
validFrames,vff,vlf = btkTools.findValidFrames(acqGait,trackingMarkers)
# filtering
# -----------------------
if "fc_lowPass_marker" in kwargs.keys() and kwargs["fc_lowPass_marker"]!=0 :
fc = kwargs["fc_lowPass_marker"]
order = 4
if "order_lowPass_marker" in kwargs.keys():
order = kwargs["order_lowPass_marker"]
signal_processing.markerFiltering(acqGait,trackingMarkers,order=order, fc =fc)
if "fc_lowPass_forcePlate" in kwargs.keys() and kwargs["fc_lowPass_forcePlate"]!=0 :
fc = kwargs["fc_lowPass_forcePlate"]
order = 4
if "order_lowPass_forcePlate" in kwargs.keys():
order = kwargs["order_lowPass_forcePlate"]
signal_processing.forcePlateFiltering(acqGait,order=order, fc =fc)
# --- initial motion Filter ---
scp=modelFilters.StaticCalibrationProcedure(model)
# section to remove : - copy motion of ProximalShank from Shank with Sodervisk
modMotion=modelFilters.ModelMotionFilter(scp,acqGait,model,enums.motionMethod.Sodervisk)
modMotion.compute()
# /section to remove
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 tl 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) )
logging.info("-------INVERSE KINEMATICS IN PROGRESS----------")
acqIK = osrf.run(acqGait,(DATA_PATH + reconstructFilenameLabelled ))
logging.info("-------INVERSE KINEMATICS DONE-----------------")
# eventual gait acquisition to consider for joint kinematics
finalAcqGait = acqIK if ik_flag else acqGait
# --- final pyCGM2 model motion Filter ---
# use fitted markers
modMotionFitted=modelFilters.ModelMotionFilter(scp,finalAcqGait,model,enums.motionMethod.Sodervisk ,
markerDiameter=markerDiameter)
modMotionFitted.compute()
if "displayCoordinateSystem" in kwargs.keys() and kwargs["displayCoordinateSystem"]:
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csdf = modelFilters.CoordinateSystemDisplayFilter(csp,model,finalAcqGait)
csdf.setStatic(False)
csdf.display()
#---- Joint kinematics----
# relative angles
modelFilters.ModelJCSFilter(model,finalAcqGait).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(finalAcqGait,pfp)
pff.compute()
globalFrame = pff.outputs["globalFrame"]
forwardProgression = pff.outputs["forwardProgression"]
if model.m_bodypart != enums.BodyPart.UpperLimb:
modelFilters.ModelAbsoluteAnglesFilter(model,finalAcqGait,
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,finalAcqGait,
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,finalAcqGait,
segmentLabels=["Thorax","Head"],
angleLabels=["Thorax", "Head"],
eulerSequences=["YXZ","TOR"],
globalFrameOrientation = globalFrame,
forwardProgression = forwardProgression).compute(pointLabelSuffix=pointSuffix)
#---- Body segment parameters----
bspModel = bodySegmentParameters.Bsp(model)
bspModel.compute()
if model.m_bodypart == enums.BodyPart.FullBody:
modelFilters.CentreOfMassFilter(model,finalAcqGait).compute(pointLabelSuffix=pointSuffix)
# Inverse dynamics
if btkTools.checkForcePlateExist(acqGait):
if model.m_bodypart != enums.BodyPart.UpperLimb:
# --- force plate handling----
# find foot in contact
mappedForcePlate = forceplates.matchingFootSideOnForceplate(finalAcqGait,mfpa=mfpa)
forceplates.addForcePlateGeneralEvents(finalAcqGait,mappedForcePlate)
logging.warning("Manual Force plate assignment : %s" %mappedForcePlate)
# assembly foot and force plate
modelFilters.ForcePlateAssemblyFilter(model,finalAcqGait,mappedForcePlate,
leftSegmentLabel="Left Foot",
rightSegmentLabel="Right Foot").compute(pointLabelSuffix=pointSuffix)
#---- Joint kinetics----
idp = modelFilters.CGMLowerlimbInverseDynamicProcedure()
modelFilters.InverseDynamicFilter(model,
finalAcqGait,
procedure = idp,
projection = momentProjection,
globalFrameOrientation = globalFrame,
forwardProgression = forwardProgression
).compute(pointLabelSuffix=pointSuffix)
#---- Joint energetics----
modelFilters.JointPowerFilter(model,finalAcqGait).compute(pointLabelSuffix=pointSuffix)
#---- zero unvalid frames ---
btkTools.applyValidFramesOnOutput(finalAcqGait,validFrames)
return finalAcqGait
def fitting(model, DATA_PATH, reconstructFilenameLabelled, translators,
markerDiameter, pointSuffix, mfpa, momentProjection, **kwargs):
"""
Fitting of the CGM1.1
:param model [str]: pyCGM2 model previously calibrated
:param DATA_PATH [str]: path to your data
:param reconstructFilenameLabelled [string list]: c3d files
:param translators [dict]: translators to apply
:param mfpa [str]: manual force plate assignement
:param markerDiameter [double]: marker diameter (mm)
:param pointSuffix [str]: suffix to add to model outputs
:param momentProjection [str]: Coordinate system in which joint moment is expressed
"""
# --------------------------ACQUISITION ------------------------------------
# --- btk acquisition ----
if "forceBtkAcq" in kwargs.keys():
acqGait = kwargs["forceBtkAcq"]
else:
acqGait = btkTools.smartReader(
(DATA_PATH + reconstructFilenameLabelled))
btkTools.checkMultipleSubject(acqGait)
if btkTools.isPointExist(acqGait, "SACR"):
translators["LPSI"] = "SACR"
translators["RPSI"] = "SACR"
logging.info("[pyCGM2] Sacrum marker detected")
acqGait = btkTools.applyTranslators(acqGait, translators)
trackingMarkers = model.getTrackingMarkers(acqGait)
validFrames, vff, vlf = btkTools.findValidFrames(acqGait, trackingMarkers)
# filtering
# -----------------------
if "fc_lowPass_marker" in kwargs.keys(
) and kwargs["fc_lowPass_marker"] != 0:
fc = kwargs["fc_lowPass_marker"]
order = 4
if "order_lowPass_marker" in kwargs.keys():
order = kwargs["order_lowPass_marker"]
signal_processing.markerFiltering(acqGait,
trackingMarkers,
order=order,
fc=fc)
if "fc_lowPass_forcePlate" in kwargs.keys(
) and kwargs["fc_lowPass_forcePlate"] != 0:
fc = kwargs["fc_lowPass_forcePlate"]
order = 4
if "order_lowPass_forcePlate" in kwargs.keys():
order = kwargs["order_lowPass_forcePlate"]
signal_processing.forcePlateFiltering(acqGait, order=order, fc=fc)
scp = modelFilters.StaticCalibrationProcedure(model) # procedure
# ---Motion filter----
modMotion = modelFilters.ModelMotionFilter(scp,
acqGait,
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, acqGait)
csdf.setStatic(False)
csdf.display()
if "NaimKneeCorrection" in kwargs.keys() and kwargs["NaimKneeCorrection"]:
# Apply Naim 2019 method
if type(kwargs["NaimKneeCorrection"]) is float:
nmacp = modelFilters.Naim2019ThighMisaligmentCorrectionProcedure(
model, "Both", threshold=(kwargs["NaimKneeCorrection"]))
else:
nmacp = modelFilters.Naim2019ThighMisaligmentCorrectionProcedure(
model, "Both")
mmcf = modelFilters.ModelMotionCorrectionFilter(nmacp)
mmcf.correct()
# btkTools.smartAppendPoint(acqGait,"LNaim",mmcf.m_procedure.m_virtual["Left"])
# btkTools.smartAppendPoint(acqGait,"RNaim",mmcf.m_procedure.m_virtual["Right"])
#---- Joint kinematics----
# relative angles
modelFilters.ModelJCSFilter(model,
acqGait).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(acqGait, pfp)
pff.compute()
globalFrame = pff.outputs["globalFrame"]
forwardProgression = pff.outputs["forwardProgression"]
if model.m_bodypart != enums.BodyPart.UpperLimb:
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqGait,
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,
acqGait,
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,
acqGait,
segmentLabels=["Thorax", "Head"],
angleLabels=["Thorax", "Head"],
eulerSequences=["YXZ", "TOR"],
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix=pointSuffix)
#---- Body segment parameters----
bspModel = bodySegmentParameters.Bsp(model)
bspModel.compute()
if model.m_bodypart == enums.BodyPart.FullBody:
modelFilters.CentreOfMassFilter(
model, acqGait).compute(pointLabelSuffix=pointSuffix)
# Inverse dynamics
if btkTools.checkForcePlateExist(acqGait):
if model.m_bodypart != enums.BodyPart.UpperLimb:
# --- force plate handling----
# find foot in contact
mappedForcePlate = forceplates.matchingFootSideOnForceplate(
acqGait, mfpa=mfpa)
forceplates.addForcePlateGeneralEvents(acqGait, mappedForcePlate)
logging.warning("Manual Force plate assignment : %s" %
mappedForcePlate)
# assembly foot and force plate
modelFilters.ForcePlateAssemblyFilter(
model,
acqGait,
mappedForcePlate,
leftSegmentLabel="Left Foot",
rightSegmentLabel="Right Foot").compute(
pointLabelSuffix=pointSuffix)
#---- Joint kinetics----
idp = modelFilters.CGMLowerlimbInverseDynamicProcedure()
modelFilters.InverseDynamicFilter(
model,
acqGait,
procedure=idp,
projection=momentProjection,
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix=pointSuffix)
#---- Joint energetics----
modelFilters.JointPowerFilter(
model, acqGait).compute(pointLabelSuffix=pointSuffix)
#---- zero unvalid frames ---
btkTools.applyValidFramesOnOutput(acqGait, validFrames)
return acqGait
def fitting(model,DATA_PATH, reconstructFilenameLabelled,
translators,settings,
ik_flag,markerDiameter,
pointSuffix,
mfpa,
momentProjection):
# --- btk acquisition ----
acqGait = btkTools.smartReader(str(DATA_PATH + reconstructFilenameLabelled))
btkTools.checkMultipleSubject(acqGait)
acqGait = btkTools.applyTranslators(acqGait,translators)
validFrames,vff,vlf = btkTools.findValidFrames(acqGait,cgm2.CGM2_4LowerLimbs.TRACKING_MARKERS)
# --- initial motion Filter ---
scp=modelFilters.StaticCalibrationProcedure(model)
modMotion=modelFilters.ModelMotionFilter(scp,acqGait,model,enums.motionMethod.Sodervisk)
modMotion.compute()
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_4\\cgm2_4-markerset.xml" # markerset
cgmCalibrationprocedure = opensimFilters.CgmOpensimCalibrationProcedures(model) # procedure
oscf = opensimFilters.opensimCalibrationFilter(osimfile,
model,
cgmCalibrationprocedure,
str(DATA_PATH))
oscf.addMarkerSet(markersetFile)
scalingOsim = oscf.build()
# --- opensim Fitting Filter ---
iksetupFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm2_4\\cgm2_4-ikSetUp_template.xml" # ik tl file
cgmFittingProcedure = opensimFilters.CgmOpensimFittingProcedure(model) # procedure
cgmFittingProcedure.updateMarkerWeight("LASI",settings["Fitting"]["Weight"]["LASI"])
cgmFittingProcedure.updateMarkerWeight("RASI",settings["Fitting"]["Weight"]["RASI"])
cgmFittingProcedure.updateMarkerWeight("LPSI",settings["Fitting"]["Weight"]["LPSI"])
cgmFittingProcedure.updateMarkerWeight("RPSI",settings["Fitting"]["Weight"]["RPSI"])
cgmFittingProcedure.updateMarkerWeight("RTHI",settings["Fitting"]["Weight"]["RTHI"])
cgmFittingProcedure.updateMarkerWeight("RKNE",settings["Fitting"]["Weight"]["RKNE"])
cgmFittingProcedure.updateMarkerWeight("RTIB",settings["Fitting"]["Weight"]["RTIB"])
cgmFittingProcedure.updateMarkerWeight("RANK",settings["Fitting"]["Weight"]["RANK"])
cgmFittingProcedure.updateMarkerWeight("RHEE",settings["Fitting"]["Weight"]["RHEE"])
cgmFittingProcedure.updateMarkerWeight("RTOE",settings["Fitting"]["Weight"]["RTOE"])
cgmFittingProcedure.updateMarkerWeight("LTHI",settings["Fitting"]["Weight"]["LTHI"])
cgmFittingProcedure.updateMarkerWeight("LKNE",settings["Fitting"]["Weight"]["LKNE"])
cgmFittingProcedure.updateMarkerWeight("LTIB",settings["Fitting"]["Weight"]["LTIB"])
cgmFittingProcedure.updateMarkerWeight("LANK",settings["Fitting"]["Weight"]["LANK"])
cgmFittingProcedure.updateMarkerWeight("LHEE",settings["Fitting"]["Weight"]["LHEE"])
cgmFittingProcedure.updateMarkerWeight("LTOE",settings["Fitting"]["Weight"]["LTOE"])
cgmFittingProcedure.updateMarkerWeight("LTHAP",settings["Fitting"]["Weight"]["LTHAP"])
cgmFittingProcedure.updateMarkerWeight("LTHAD",settings["Fitting"]["Weight"]["LTHAD"])
cgmFittingProcedure.updateMarkerWeight("LTIAP",settings["Fitting"]["Weight"]["LTIAP"])
cgmFittingProcedure.updateMarkerWeight("LTIAD",settings["Fitting"]["Weight"]["LTIAD"])
cgmFittingProcedure.updateMarkerWeight("RTHAP",settings["Fitting"]["Weight"]["RTHAP"])
cgmFittingProcedure.updateMarkerWeight("RTHAD",settings["Fitting"]["Weight"]["RTHAD"])
cgmFittingProcedure.updateMarkerWeight("RTIAP",settings["Fitting"]["Weight"]["RTIAP"])
cgmFittingProcedure.updateMarkerWeight("RTIAD",settings["Fitting"]["Weight"]["RTIAD"])
cgmFittingProcedure.updateMarkerWeight("LSMH",settings["Fitting"]["Weight"]["LSMH"])
cgmFittingProcedure.updateMarkerWeight("LFMH",settings["Fitting"]["Weight"]["LFMH"])
cgmFittingProcedure.updateMarkerWeight("LVMH",settings["Fitting"]["Weight"]["LVMH"])
cgmFittingProcedure.updateMarkerWeight("RSMH",settings["Fitting"]["Weight"]["RSMH"])
cgmFittingProcedure.updateMarkerWeight("RFMH",settings["Fitting"]["Weight"]["RFMH"])
cgmFittingProcedure.updateMarkerWeight("RVMH",settings["Fitting"]["Weight"]["RVMH"])
# cgmFittingProcedure.updateMarkerWeight("LTHL",settings["Fitting"]["Weight"]["LTHL"])
# cgmFittingProcedure.updateMarkerWeight("LTHLD",settings["Fitting"]["Weight"]["LTHLD"])
# cgmFittingProcedure.updateMarkerWeight("LPAT",settings["Fitting"]["Weight"]["LPAT"])
# cgmFittingProcedure.updateMarkerWeight("LTIBL",settings["Fitting"]["Weight"]["LTIBL"])
# cgmFittingProcedure.updateMarkerWeight("RTHL",settings["Fitting"]["Weight"]["RTHL"])
# cgmFittingProcedure.updateMarkerWeight("RTHLD",settings["Fitting"]["Weight"]["RTHLD"])
# cgmFittingProcedure.updateMarkerWeight("RPAT",settings["Fitting"]["Weight"]["RPAT"])
# cgmFittingProcedure.updateMarkerWeight("RTIBL",settings["Fitting"]["Weight"]["RTIBL"])
osrf = opensimFilters.opensimFittingFilter(iksetupFile,
scalingOsim,
cgmFittingProcedure,
str(DATA_PATH) )
logging.info("-------INVERSE KINEMATICS IN PROGRESS----------")
acqIK = osrf.run(acqGait,str(DATA_PATH + reconstructFilenameLabelled ))
logging.info("-------INVERSE KINEMATICS DONE-----------------")
# eventual gait acquisition to consider for joint kinematics
finalAcqGait = acqIK if ik_flag else acqGait
# --- final pyCGM2 model motion Filter ---
# use fitted markers
modMotionFitted=modelFilters.ModelMotionFilter(scp,finalAcqGait,model,enums.motionMethod.Sodervisk ,
markerDiameter=markerDiameter)
modMotionFitted.compute()
#---- Joint kinematics----
# relative angles
modelFilters.ModelJCSFilter(model,finalAcqGait).compute(description="vectoriel", pointLabelSuffix=pointSuffix)
# detection of traveling axis
longitudinalAxis,forwardProgression,globalFrame = btkTools.findProgressionAxisFromPelvicMarkers(finalAcqGait,["LASI","LPSI","RASI","RPSI"])
# absolute angles
modelFilters.ModelAbsoluteAnglesFilter(model,finalAcqGait,
segmentLabels=["Left Foot","Right Foot","Pelvis"],
angleLabels=["LFootProgress", "RFootProgress","Pelvis"],
eulerSequences=["TOR","TOR", "ROT"],
globalFrameOrientation = globalFrame,
forwardProgression = forwardProgression).compute(pointLabelSuffix=pointSuffix)
#---- Body segment parameters----
bspModel = bodySegmentParameters.Bsp(model)
bspModel.compute()
# --- force plate handling----
# find foot in contact
mappedForcePlate = forceplates.matchingFootSideOnForceplate(finalAcqGait)
forceplates.addForcePlateGeneralEvents(finalAcqGait,mappedForcePlate)
logging.info("Force plate assignment : %s" %mappedForcePlate)
if mfpa is not None:
if len(mfpa) != len(mappedForcePlate):
raise Exception("[pyCGM2] manual force plate assignment badly sets. Wrong force plate number. %s force plate require" %(str(len(mappedForcePlate))))
else:
mappedForcePlate = mfpa
forceplates.addForcePlateGeneralEvents(finalAcqGait,mappedForcePlate)
logging.warning("Manual Force plate assignment : %s" %mappedForcePlate)
# assembly foot and force plate
modelFilters.ForcePlateAssemblyFilter(model,finalAcqGait,mappedForcePlate,
leftSegmentLabel="Left Foot",
rightSegmentLabel="Right Foot").compute()
#---- Joint kinetics----
idp = modelFilters.CGMLowerlimbInverseDynamicProcedure()
modelFilters.InverseDynamicFilter(model,
finalAcqGait,
procedure = idp,
projection = momentProjection
).compute(pointLabelSuffix=pointSuffix)
#---- Joint energetics----
modelFilters.JointPowerFilter(model,finalAcqGait).compute(pointLabelSuffix=pointSuffix)
#---- zero unvalid frames ---
btkTools.applyValidFramesOnOutput(finalAcqGait,validFrames)
return finalAcqGait
def fitting(model, DATA_PATH, reconstructFilenameLabelled, translators,
markerDiameter, pointSuffix, mfpa, momentProjection):
# --------------------------ACQUISITION ------------------------------------
# --- btk acquisition ----
acqGait = btkTools.smartReader(str(DATA_PATH +
reconstructFilenameLabelled))
btkTools.checkMultipleSubject(acqGait)
acqGait = btkTools.applyTranslators(acqGait, translators)
validFrames, vff, vlf = btkTools.findValidFrames(
acqGait, cgm.CGM1LowerLimbs.TRACKING_MARKERS)
scp = modelFilters.StaticCalibrationProcedure(model)
# ---Motion filter----
modMotion = modelFilters.ModelMotionFilter(scp,
acqGait,
model,
enums.motionMethod.Determinist,
markerDiameter=markerDiameter)
modMotion.compute()
#---- Joint kinematics----
# relative angles
modelFilters.ModelJCSFilter(model,
acqGait).compute(description="vectoriel",
pointLabelSuffix=pointSuffix)
# detection of traveling axis
longitudinalAxis, forwardProgression, globalFrame = btkTools.findProgressionAxisFromPelvicMarkers(
acqGait, ["LASI", "LPSI", "RASI", "RPSI"])
# absolute angles
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqGait,
segmentLabels=["Left Foot", "Right Foot", "Pelvis"],
angleLabels=["LFootProgress", "RFootProgress", "Pelvis"],
eulerSequences=["TOR", "TOR", "ROT"],
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix=pointSuffix)
#---- Body segment parameters----
bspModel = bodySegmentParameters.Bsp(model)
bspModel.compute()
# --- force plate handling----
# find foot in contact
mappedForcePlate = forceplates.matchingFootSideOnForceplate(acqGait)
forceplates.addForcePlateGeneralEvents(acqGait, mappedForcePlate)
logging.info("Automatic Force plate assignment : %s" % mappedForcePlate)
if mfpa is not None:
if len(mfpa) != len(mappedForcePlate):
raise Exception(
"[pyCGM2] manual force plate assignment badly sets. Wrong force plate number. %s force plate require"
% (str(len(mappedForcePlate))))
else:
mappedForcePlate = mfpa
forceplates.addForcePlateGeneralEvents(acqGait, mappedForcePlate)
logging.warning("Manual Force plate assignment : %s" %
mappedForcePlate)
# assembly foot and force plate
modelFilters.ForcePlateAssemblyFilter(
model,
acqGait,
mappedForcePlate,
leftSegmentLabel="Left Foot",
rightSegmentLabel="Right Foot").compute()
#---- Joint kinetics----
idp = modelFilters.CGMLowerlimbInverseDynamicProcedure()
modelFilters.InverseDynamicFilter(
model, acqGait, procedure=idp,
projection=momentProjection).compute(pointLabelSuffix=pointSuffix)
#---- Joint energetics----
modelFilters.JointPowerFilter(
model, acqGait).compute(pointLabelSuffix=pointSuffix)
#---- zero unvalid frames ---
btkTools.applyValidFramesOnOutput(acqGait, validFrames)
return acqGait
def fitting(model, DATA_PATH, reconstructFilenameLabelled, translators,
markerDiameter, pointSuffix, mfpa, momentProjection, **kwargs):
"""
Fitting of the CGM1
:param model [str]: pyCGM2 model previously calibrated
:param DATA_PATH [str]: path to your data
:param reconstructFilenameLabelled [string list]: c3d files
:param translators [dict]: translators to apply
:param mfpa [str]: manual force plate assignement
:param markerDiameter [double]: marker diameter (mm)
:param pointSuffix [str]: suffix to add to model outputs
:param momentProjection [str]: Coordinate system in which joint moment is expressed
"""
# --------------------------ACQUISITION ------------------------------------
if "forceBtkAcq" in kwargs.keys():
acqGait = kwargs["forceBtkAcq"]
else:
# --- btk acquisition ----
acqGait = btkTools.smartReader(
str(DATA_PATH + reconstructFilenameLabelled))
btkTools.checkMultipleSubject(acqGait)
acqGait = btkTools.applyTranslators(acqGait, translators)
trackingMarkers = model.getTrackingMarkers()
validFrames, vff, vlf = btkTools.findValidFrames(acqGait, trackingMarkers)
scp = modelFilters.StaticCalibrationProcedure(model) # procedure
# ---Motion filter----
modMotion = modelFilters.ModelMotionFilter(scp,
acqGait,
model,
enums.motionMethod.Determinist,
markerDiameter=markerDiameter,
viconCGM1compatible=True)
modMotion.compute()
if "displayCoordinateSystem" in kwargs.keys(
) and kwargs["displayCoordinateSystem"]:
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csdf = modelFilters.CoordinateSystemDisplayFilter(csp, model, acqGait)
csdf.setStatic(False)
csdf.display()
#---- Joint kinematics----
# relative angles
modelFilters.ModelJCSFilter(model,
acqGait).compute(description="vectoriel",
pointLabelSuffix=pointSuffix)
# detection of traveling axis + absolute angle
if model.m_bodypart != enums.BodyPart.UpperLimb:
longitudinalAxis, forwardProgression, globalFrame = btkTools.findProgressionAxisFromPelvicMarkers(
acqGait, ["LASI", "LPSI", "RASI", "RPSI"])
else:
longitudinalAxis, forwardProgression, globalFrame = btkTools.findProgressionAxisFromLongAxis(
acqGait, "C7", "CLAV")
if model.m_bodypart != enums.BodyPart.UpperLimb:
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqGait,
segmentLabels=["Left Foot", "Right Foot", "Pelvis"],
angleLabels=["LFootProgress", "RFootProgress", "Pelvis"],
eulerSequences=["TOR", "TOR", "TOR"],
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix=pointSuffix)
if model.m_bodypart == enums.BodyPart.LowerLimbTrunk:
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqGait,
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,
acqGait,
segmentLabels=["Thorax", "Head"],
angleLabels=["Thorax", "Head"],
eulerSequences=["YXZ", "TOR"],
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix=pointSuffix)
#---- Body segment parameters----
bspModel = bodySegmentParameters.Bsp(model)
bspModel.compute()
#---- CentreOfMass----
if model.m_bodypart == enums.BodyPart.FullBody:
modelFilters.CentreOfMassFilter(
model, acqGait).compute(pointLabelSuffix=pointSuffix)
# Inverse dynamics
if model.m_bodypart != enums.BodyPart.UpperLimb:
# --- force plate handling----
# find foot in contact
mappedForcePlate = forceplates.matchingFootSideOnForceplate(acqGait,
mfpa=mfpa)
forceplates.addForcePlateGeneralEvents(acqGait, mappedForcePlate)
logging.warning("Manual Force plate assignment : %s" %
mappedForcePlate)
# assembly foot and force plate
modelFilters.ForcePlateAssemblyFilter(
model,
acqGait,
mappedForcePlate,
leftSegmentLabel="Left Foot",
rightSegmentLabel="Right Foot").compute()
#---- Joint kinetics----
idp = modelFilters.CGMLowerlimbInverseDynamicProcedure()
modelFilters.InverseDynamicFilter(
model,
acqGait,
procedure=idp,
projection=momentProjection,
viconCGM1compatible=True).compute(pointLabelSuffix=pointSuffix)
#---- Joint energetics----
modelFilters.JointPowerFilter(
model, acqGait).compute(pointLabelSuffix=pointSuffix)
#---- zero unvalid frames ---
btkTools.applyValidFramesOnOutput(acqGait, validFrames)
return acqGait
def fitting(model, DATA_PATH, reconstructFilenameLabelled, translators,
settings, markerDiameter, pointSuffix, mfpa, momentProjection,
**kwargs):
"""
Fitting of the CGM2.2
:param model [str]: pyCGM2 model previously calibrated
:param DATA_PATH [str]: path to your data
:param reconstructFilenameLabelled [string list]: c3d files
:param translators [dict]: translators to apply
:param mfpa [str]: manual force plate assignement
:param markerDiameter [double]: marker diameter (mm)
:param pointSuffix [str]: suffix to add to model outputs
:param momentProjection [str]: Coordinate system in which joint moment is expressed
"""
# --------------------------ACQUISITION ------------------------------------
# --- btk acquisition ----
if "forceBtkAcq" in kwargs.keys():
acqGait = kwargs["forceBtkAcq"]
else:
acqGait = btkTools.smartReader(
str(DATA_PATH + reconstructFilenameLabelled))
btkTools.checkMultipleSubject(acqGait)
acqGait = btkTools.applyTranslators(acqGait, translators)
trackingMarkers = model.getTrackingMarkers()
validFrames, vff, vlf = btkTools.findValidFrames(acqGait, trackingMarkers)
# --- initial motion Filter ---
scp = modelFilters.StaticCalibrationProcedure(model)
modMotion = modelFilters.ModelMotionFilter(scp, acqGait, model,
enums.motionMethod.Determinist)
modMotion.compute()
# ---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\\cgm1\\cgm1-markerset.xml" # markerset
cgmCalibrationprocedure = opensimFilters.CgmOpensimCalibrationProcedures(
model) # procedure
oscf = opensimFilters.opensimCalibrationFilter(osimfile, model,
cgmCalibrationprocedure,
str(DATA_PATH))
oscf.addMarkerSet(markersetFile)
scalingOsim = oscf.build()
# --- opensim Fitting Filter ---
iksetupFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\settings\\cgm1\\cgm1-ikSetUp_template.xml" # ik tool file
cgmFittingProcedure = opensimFilters.CgmOpensimFittingProcedure(
model) # procedure
cgmFittingProcedure.updateMarkerWeight(
"LASI", settings["Fitting"]["Weight"]["LASI"])
cgmFittingProcedure.updateMarkerWeight(
"RASI", settings["Fitting"]["Weight"]["RASI"])
cgmFittingProcedure.updateMarkerWeight(
"LPSI", settings["Fitting"]["Weight"]["LPSI"])
cgmFittingProcedure.updateMarkerWeight(
"RPSI", settings["Fitting"]["Weight"]["RPSI"])
cgmFittingProcedure.updateMarkerWeight(
"RTHI", settings["Fitting"]["Weight"]["RTHI"])
cgmFittingProcedure.updateMarkerWeight(
"RKNE", settings["Fitting"]["Weight"]["RKNE"])
cgmFittingProcedure.updateMarkerWeight(
"RTIB", settings["Fitting"]["Weight"]["RTIB"])
cgmFittingProcedure.updateMarkerWeight(
"RANK", settings["Fitting"]["Weight"]["RANK"])
cgmFittingProcedure.updateMarkerWeight(
"RHEE", settings["Fitting"]["Weight"]["RHEE"])
cgmFittingProcedure.updateMarkerWeight(
"RTOE", settings["Fitting"]["Weight"]["RTOE"])
cgmFittingProcedure.updateMarkerWeight(
"LTHI", settings["Fitting"]["Weight"]["LTHI"])
cgmFittingProcedure.updateMarkerWeight(
"LKNE", settings["Fitting"]["Weight"]["LKNE"])
cgmFittingProcedure.updateMarkerWeight(
"LTIB", settings["Fitting"]["Weight"]["LTIB"])
cgmFittingProcedure.updateMarkerWeight(
"LANK", settings["Fitting"]["Weight"]["LANK"])
cgmFittingProcedure.updateMarkerWeight(
"LHEE", settings["Fitting"]["Weight"]["LHEE"])
cgmFittingProcedure.updateMarkerWeight(
"LTOE", settings["Fitting"]["Weight"]["LTOE"])
osrf = opensimFilters.opensimFittingFilter(iksetupFile, scalingOsim,
cgmFittingProcedure,
str(DATA_PATH))
logging.info("-------INVERSE KINEMATICS IN PROGRESS----------")
acqIK = osrf.run(acqGait, str(DATA_PATH + reconstructFilenameLabelled))
logging.info("-------INVERSE KINEMATICS DONE-----------------")
# --- final pyCGM2 model motion Filter ---
# use fitted markers
modMotionFitted = modelFilters.ModelMotionFilter(
scp,
acqIK,
model,
enums.motionMethod.Determinist,
markerDiameter=markerDiameter)
modMotionFitted.compute()
if "displayCoordinateSystem" in kwargs.keys(
) and kwargs["displayCoordinateSystem"]:
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csdf = modelFilters.CoordinateSystemDisplayFilter(csp, model, acqIK)
csdf.setStatic(False)
csdf.display()
#---- Joint kinematics----
# relative angles
modelFilters.ModelJCSFilter(model,
acqIK).compute(description="vectoriel",
pointLabelSuffix=pointSuffix)
# detection of traveling axis + absolute angle
if model.m_bodypart != enums.BodyPart.UpperLimb:
longitudinalAxis, forwardProgression, globalFrame = btkTools.findProgressionAxisFromPelvicMarkers(
acqIK, ["LASI", "LPSI", "RASI", "RPSI"])
else:
longitudinalAxis, forwardProgression, globalFrame = btkTools.findProgressionAxisFromLongAxis(
acqIK, "C7", "CLAV")
if model.m_bodypart != enums.BodyPart.UpperLimb:
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqIK,
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,
acqIK,
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,
acqIK,
segmentLabels=["Thorax", "Head"],
angleLabels=["Thorax", "Head"],
eulerSequences=["YXZ", "TOR"],
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix=pointSuffix)
#---- Body segment parameters----
bspModel = bodySegmentParameters.Bsp(model)
bspModel.compute()
if model.m_bodypart == enums.BodyPart.FullBody:
modelFilters.CentreOfMassFilter(
model, acqIK).compute(pointLabelSuffix=pointSuffix)
# Inverse dynamics
if model.m_bodypart != enums.BodyPart.UpperLimb:
# --- force plate handling----
# find foot in contact
mappedForcePlate = forceplates.matchingFootSideOnForceplate(acqIK,
mfpa=mfpa)
forceplates.addForcePlateGeneralEvents(acqIK, mappedForcePlate)
logging.warning("Manual Force plate assignment : %s" %
mappedForcePlate)
# assembly foot and force plate
modelFilters.ForcePlateAssemblyFilter(
model,
acqIK,
mappedForcePlate,
leftSegmentLabel="Left Foot",
rightSegmentLabel="Right Foot").compute()
#---- Joint kinetics----
idp = modelFilters.CGMLowerlimbInverseDynamicProcedure()
modelFilters.InverseDynamicFilter(
model,
acqIK,
procedure=idp,
projection=momentProjection,
).compute(pointLabelSuffix=pointSuffix)
#---- Joint energetics----
modelFilters.JointPowerFilter(
model, acqIK).compute(pointLabelSuffix=pointSuffix)
#---- zero unvalid frames ---
btkTools.applyValidFramesOnOutput(acqIK, validFrames)
return acqIK
