def CGM1_UpperLimb(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\full-PiG\\"
staticFilename = "PN01NORMSTAT.c3d"
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model=cgm.CGM1()
model.configure(bodyPart=enums.BodyPart.UpperLimb)
markerDiameter=14
mp={
'LeftShoulderOffset' : 50,
'LeftElbowWidth' : 91,
'LeftWristWidth' : 56 ,
'LeftHandThickness' : 28 ,
'RightShoulderOffset' : 45,
'RightElbowWidth' : 90,
'RightWristWidth' : 55 ,
'RightHandThickness' : 30 }
model.addAnthropoInputParameters(mp)
# -----------CGM STATIC CALIBRATION--------------------
scp=modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp,acqStatic,model,headFlat= True).compute()
csp = modelFilters.ModelCoordinateSystemProcedure(model)
# --- motion ----
gaitFilename="PN01NORMSS01.c3d"
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
modMotion=modelFilters.ModelMotionFilter(scp,acqGait,model,enums.motionMethod.Determinist)
modMotion.compute()
csdf = modelFilters.CoordinateSystemDisplayFilter(csp,model,acqGait)
csdf.setStatic(False)
csdf.display()
# thorax
R_thorax= model.getSegment("Thorax").anatomicalFrame.motion[10].getRotation()
R_thorax_vicon = getViconRmatrix(10, acqGait, "TRXO", "TRXA", "TRXL", "XZY")
np.testing.assert_almost_equal( R_thorax,
R_thorax_vicon, decimal =3)
# head
R_head= model.getSegment("Head").anatomicalFrame.motion[10].getRotation()
R_head_vicon = getViconRmatrix(10, acqGait, "HEDO", "HEDA", "HEDL", "XZY")
np.testing.assert_almost_equal( R_head,
R_head_vicon, decimal =2)
def calibrate(DATA_PATH, calibrateFilenameLabelled, translators, required_mp,
optional_mp, leftFlatFoot, rightFlatFoot, headFlat,
markerDiameter, pointSuffix, **kwargs):
"""
Calibration of the CGM1.1
:param DATA_PATH [str]: path to your data
:param calibrateFilenameLabelled [str]: c3d file
:param translators [dict]: translators to apply
:param required_mp [dict]: required anthropometric data
:param optional_mp [dict]: optional anthropometric data (ex: LThighOffset,...)
:param leftFlatFoot [bool]: enable of the flat foot option for the left foot
:param rightFlatFoot [bool]: enable of the flat foot option for the right foot
:param headFlat [bool]: enable of the head flat option
:param markerDiameter [double]: marker diameter (mm)
:param pointSuffix [str]: suffix to add to model outputs
"""
# --------------------------ACQUISITION ------------------------------------
# --- btk acquisition ----
if "forceBtkAcq" in kwargs.keys():
acqStatic = kwargs["forceBtkAcq"]
else:
acqStatic = btkTools.smartReader(
(DATA_PATH + calibrateFilenameLabelled))
btkTools.checkMultipleSubject(acqStatic)
if btkTools.isPointExist(acqStatic, "SACR"):
translators["LPSI"] = "SACR"
translators["RPSI"] = "SACR"
logging.info("[pyCGM2] Sacrum marker detected")
acqStatic = btkTools.applyTranslators(acqStatic, translators)
# ---detectedCalibrationMethods----
dcm = cgm.CGM.detectCalibrationMethods(acqStatic)
# ---definition---
model = cgm.CGM1()
model.setVersion("CGM1.1")
model.configure(acq=acqStatic, detectedCalibrationMethods=dcm)
model.addAnthropoInputParameters(required_mp, optional=optional_mp)
# --store calibration parameters--
model.setStaticFilename(calibrateFilenameLabelled)
model.setCalibrationProperty("leftFlatFoot", leftFlatFoot)
model.setCalibrationProperty("rightFlatFoot", rightFlatFoot)
model.setCalibrationProperty("headFlat", headFlat)
model.setCalibrationProperty("markerDiameter", markerDiameter)
# --------------------------STATIC CALBRATION--------------------------
scp = modelFilters.StaticCalibrationProcedure(
model) # load calibration procedure
# ---initial calibration filter----
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=leftFlatFoot,
rightFlatFoot=rightFlatFoot,
headFlat=headFlat,
markerDiameter=markerDiameter,
).compute()
# ---- Decorators -----
decorators.applyBasicDecorators(dcm, model, acqStatic, optional_mp,
markerDiameter)
# ----Final Calibration filter if model previously decorated -----
if model.decoratedModel:
# initial static filter
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=leftFlatFoot,
rightFlatFoot=rightFlatFoot,
headFlat=headFlat,
markerDiameter=markerDiameter).compute()
# ----------------------CGM MODELLING----------------------------------
# ----motion filter----
# notice : viconCGM1compatible option duplicate error on Construction of the foot coordinate system
modMotion = modelFilters.ModelMotionFilter(scp,
acqStatic,
model,
enums.motionMethod.Determinist,
markerDiameter=markerDiameter)
modMotion.compute()
if "displayCoordinateSystem" in kwargs.keys(
) and kwargs["displayCoordinateSystem"]:
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csdf = modelFilters.CoordinateSystemDisplayFilter(
csp, model, acqStatic)
csdf.setStatic(False)
csdf.display()
if "noKinematicsCalculation" in kwargs.keys(
) and kwargs["noKinematicsCalculation"]:
logging.warning(
"[pyCGM2] No Kinematic calculation done for the static file")
return model, acqStatic
else:
#---- Joint kinematics----
# relative angles
modelFilters.ModelJCSFilter(model, acqStatic).compute(
description="vectoriel", pointLabelSuffix=pointSuffix)
# detection of traveling axis + absolute angle
if model.m_bodypart != enums.BodyPart.UpperLimb:
pfp = progressionFrame.PelvisProgressionFrameProcedure()
else:
pfp = progressionFrame.ThoraxProgressionFrameProcedure()
pff = progressionFrame.ProgressionFrameFilter(acqStatic, pfp)
pff.compute()
globalFrame = pff.outputs["globalFrame"]
forwardProgression = pff.outputs["forwardProgression"]
if model.m_bodypart != enums.BodyPart.UpperLimb:
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqStatic,
segmentLabels=["Left Foot", "Right Foot", "Pelvis"],
angleLabels=["LFootProgress", "RFootProgress", "Pelvis"],
eulerSequences=["TOR", "TOR", "ROT"],
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix=pointSuffix)
if model.m_bodypart == enums.BodyPart.LowerLimbTrunk:
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqStatic,
segmentLabels=["Thorax"],
angleLabels=["Thorax"],
eulerSequences=["YXZ"],
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix=pointSuffix)
if model.m_bodypart == enums.BodyPart.UpperLimb or model.m_bodypart == enums.BodyPart.FullBody:
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqStatic,
segmentLabels=["Thorax", "Head"],
angleLabels=["Thorax", "Head"],
eulerSequences=["YXZ", "TOR"],
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix=pointSuffix)
# BSP model
bspModel = bodySegmentParameters.Bsp(model)
bspModel.compute()
if model.m_bodypart == enums.BodyPart.FullBody:
modelFilters.CentreOfMassFilter(
model, acqStatic).compute(pointLabelSuffix=pointSuffix)
return model, acqStatic
def CGM1_fullbody_static(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\full-PiG\\"
staticFilename = "PN01NORMSTAT.c3d"
# CALIBRATION ###############################
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
markerDiameter = 14
# Lower Limb
mp = {
'Bodymass': 83,
'LeftLegLength': 874,
'RightLegLength': 876.0,
'LeftKneeWidth': 106.0,
'RightKneeWidth': 103.0,
'LeftAnkleWidth': 74.0,
'RightAnkleWidth': 72.0,
'LeftSoleDelta': 0,
'RightSoleDelta': 0,
'LeftShoulderOffset': 50,
'LeftElbowWidth': 91,
'LeftWristWidth': 56,
'LeftHandThickness': 28,
'RightShoulderOffset': 45,
'RightElbowWidth': 90,
'RightWristWidth': 55,
'RightHandThickness': 30
}
model = cgm.CGM1()
model.configure(bodyPart=enums.BodyPart.FullBody)
model.addAnthropoInputParameters(mp)
scp = modelFilters.StaticCalibrationProcedure(
model) # load calibration procedure
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=True,
rightFlatFoot=True,
markerDiameter=14,
viconCGM1compatible=True).compute()
# MOTION ###############################
gaitFilename = "PN01NORMSTAT.c3d"
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
modMotion = modelFilters.ModelMotionFilter(
scp,
acqGait,
model,
enums.motionMethod.Determinist,
markerDiameter=14,
viconCGM1compatible=False)
modMotion.compute()
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csdf = modelFilters.CoordinateSystemDisplayFilter(csp, model,
acqGait).display()
modelFilters.ModelJCSFilter(model, acqGait).compute(
description="vectoriel", pointLabelSuffix="cgm1_6dof")
plot("RSpineAngles", acqGait, "cgm1_6dof")
plot("LSpineAngles", acqGait, "cgm1_6dof")
np.testing.assert_almost_equal(
acqGait.GetPoint("RSpineAngles").GetValues(),
acqGait.GetPoint("RSpineAngles_cgm1_6dof").GetValues(),
decimal=2)
np.testing.assert_almost_equal(
acqGait.GetPoint("LSpineAngles").GetValues(),
acqGait.GetPoint("LSpineAngles_cgm1_6dof").GetValues(),
decimal=2)
btkTools.smartWriter(acqGait, "fullbody.c3d")
def CGM1_upperLimb(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\full-PiG\\"
staticFilename = "PN01NORMSTAT.c3d"
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model = cgm.CGM1()
model.configure(bodyPart=enums.BodyPart.UpperLimb)
markerDiameter = 14
mp = {
'LeftShoulderOffset': 50,
'LeftElbowWidth': 91,
'LeftWristWidth': 56,
'LeftHandThickness': 28,
'RightShoulderOffset': 45,
'RightElbowWidth': 90,
'RightWristWidth': 55,
'RightHandThickness': 30
}
model.addAnthropoInputParameters(mp)
# -----------CGM STATIC CALIBRATION--------------------
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp,
acqStatic,
model,
headHorizontal=False).compute()
# --- motion ----
gaitFilename = "PN01NORMSS01.c3d"
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
modMotion = modelFilters.ModelMotionFilter(
scp, acqGait, model, enums.motionMethod.Determinist)
modMotion.compute()
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csdf = modelFilters.CoordinateSystemDisplayFilter(csp, model, acqGait)
csdf.setStatic(False)
csdf.display()
modelFilters.ModelJCSFilter(model, acqGait).compute(
description="vectoriel", pointLabelSuffix="cgm1_6dof")
#plot("LNeckAngles",acqGait,"cgm1_6dof")
np.testing.assert_almost_equal(
acqGait.GetPoint("LShoulderAngles").GetValues(),
acqGait.GetPoint("LShoulderAngles_cgm1_6dof").GetValues(),
decimal=3)
np.testing.assert_almost_equal(
acqGait.GetPoint("RShoulderAngles").GetValues(),
acqGait.GetPoint("RShoulderAngles_cgm1_6dof").GetValues(),
decimal=3)
np.testing.assert_almost_equal(
acqGait.GetPoint("RElbowAngles").GetValues(),
acqGait.GetPoint("RElbowAngles_cgm1_6dof").GetValues(),
decimal=3)
np.testing.assert_almost_equal(
acqGait.GetPoint("LElbowAngles").GetValues(),
acqGait.GetPoint("LElbowAngles_cgm1_6dof").GetValues(),
decimal=3)
np.testing.assert_almost_equal(
acqGait.GetPoint("RWristAngles").GetValues(),
acqGait.GetPoint("RWristAngles_cgm1_6dof").GetValues(),
decimal=3) # fail on transverse
np.testing.assert_almost_equal(
acqGait.GetPoint("LWristAngles").GetValues(),
acqGait.GetPoint("LWristAngles_cgm1_6dof").GetValues(),
decimal=3) # fail on transverse
np.testing.assert_almost_equal(
acqGait.GetPoint("RNeckAngles").GetValues(),
acqGait.GetPoint("RNeckAngles_cgm1_6dof").GetValues(),
decimal=1) # fail on coronal
np.testing.assert_almost_equal(
acqGait.GetPoint("LNeckAngles").GetValues(),
acqGait.GetPoint("LNeckAngles_cgm1_6dof").GetValues(),
decimal=1) # fail on coronal
btkTools.smartWriter(acqGait, "upperLimb_angle.c3d")
def calibrate(DATA_PATH, calibrateFilenameLabelled, translators, required_mp,
optional_mp, leftFlatFoot, rightFlatFoot, headFlat,
markerDiameter, pointSuffix, **kwargs):
"""
Calibration of the CGM1
:param DATA_PATH [str]: path to your data
:param calibrateFilenameLabelled [str]: c3d file
:param translators [dict]: translators to apply
:param required_mp [dict]: required anthropometric data
:param optional_mp [dict]: optional anthropometric data (ex: LThighOffset,...)
:param leftFlatFoot [bool]: enable of the flat foot option for the left foot
:param rightFlatFoot [bool]: enable of the flat foot option for the right foot
:param headFlat [bool]: enable of the head flat option
:param markerDiameter [double]: marker diameter (mm)
:param pointSuffix [str]: suffix to add to model outputs
"""
# --------------------------ACQUISITION ------------------------------------
if "forceBtkAcq" in kwargs.keys():
acqStatic = kwargs["forceBtkAcq"]
else:
# ---btk acquisition---
acqStatic = btkTools.smartReader(
str(DATA_PATH + calibrateFilenameLabelled))
btkTools.checkMultipleSubject(acqStatic)
acqStatic = btkTools.applyTranslators(acqStatic, translators)
# ---check marker set used----
dcm = cgm.CGM.detectCalibrationMethods(acqStatic)
# ---definition---
model = cgm.CGM1()
model.configure(acq=acqStatic, detectedCalibrationMethods=dcm)
model.addAnthropoInputParameters(required_mp, optional=optional_mp)
# --store calibration parameters--
model.setStaticFilename(calibrateFilenameLabelled)
model.setCalibrationProperty("leftFlatFoot", leftFlatFoot)
model.setCalibrationProperty("rightFlatFoot", rightFlatFoot)
model.setCalibrationProperty("headFlat", headFlat)
model.setCalibrationProperty("markerDiameter", markerDiameter)
# --------------------------STATIC CALBRATION--------------------------
scp = modelFilters.StaticCalibrationProcedure(
model) # load calibration procedure
# ---initial calibration filter----
modelFilters.ModelCalibrationFilter(scp,
acqStatic,
model,
leftFlatFoot=leftFlatFoot,
rightFlatFoot=rightFlatFoot,
markerDiameter=markerDiameter,
headFlat=headFlat,
viconCGM1compatible=True).compute()
# ---- Decorators -----
decorators.applyBasicDecorators(dcm,
model,
acqStatic,
optional_mp,
markerDiameter,
cgm1only=True)
pigStaticMarkers = cgm.CGM.get_markerLabelForPiGStatic(dcm)
# ----Final Calibration filter if model previously decorated -----
if model.decoratedModel:
# initial static filter
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=leftFlatFoot,
rightFlatFoot=rightFlatFoot,
headFlat=headFlat,
markerDiameter=markerDiameter,
viconCGM1compatible=True).compute()
# ----------------------CGM MODELLING----------------------------------
# ----motion filter----
# notice : viconCGM1compatible option duplicate error on Construction of the foot coordinate system
modMotion = modelFilters.ModelMotionFilter(
scp,
acqStatic,
model,
enums.motionMethod.Determinist,
markerDiameter=markerDiameter,
viconCGM1compatible=False,
pigStatic=True,
useLeftKJCmarker=pigStaticMarkers[0],
useLeftAJCmarker=pigStaticMarkers[1],
useRightKJCmarker=pigStaticMarkers[2],
useRightAJCmarker=pigStaticMarkers[3])
modMotion.compute()
if "displayCoordinateSystem" in kwargs.keys(
) and kwargs["displayCoordinateSystem"]:
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csdf = modelFilters.CoordinateSystemDisplayFilter(
csp, model, acqStatic)
csdf.setStatic(False)
csdf.display()
#---- Joint kinematics----
# relative angles
modelFilters.ModelJCSFilter(model, acqStatic).compute(
description="vectoriel", pointLabelSuffix=pointSuffix)
# detection of traveling axis + absolute angle
if model.m_bodypart != enums.BodyPart.UpperLimb:
longitudinalAxis, forwardProgression, globalFrame = btkTools.findProgressionAxisFromPelvicMarkers(
acqStatic, ["LASI", "LPSI", "RASI", "RPSI"])
else:
longitudinalAxis, forwardProgression, globalFrame = btkTools.findProgressionAxisFromLongAxis(
acqStatic, "C7", "CLAV")
if model.m_bodypart != enums.BodyPart.UpperLimb:
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqStatic,
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,
acqStatic,
segmentLabels=["Thorax"],
angleLabels=["Thorax"],
eulerSequences=["YXZ"],
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix=pointSuffix)
if model.m_bodypart == enums.BodyPart.UpperLimb or model.m_bodypart == enums.BodyPart.FullBody:
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqStatic,
segmentLabels=["Thorax", "Head"],
angleLabels=["Thorax", "Head"],
eulerSequences=["YXZ", "TOR"],
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix=pointSuffix)
# BSP model
bspModel = bodySegmentParameters.Bsp(model)
bspModel.compute()
if model.m_bodypart == enums.BodyPart.FullBody:
modelFilters.CentreOfMassFilter(
model, acqStatic).compute(pointLabelSuffix=pointSuffix)
return model, acqStatic
def CGM1_upperLimb_absoluteAngles_static(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\full-PiG\\"
staticFilename = "PN01NORMSTAT.c3d"
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
model = cgm.CGM1()
model.configure(bodyPart=enums.BodyPart.UpperLimb)
markerDiameter = 14
mp = {
'LeftShoulderOffset': 50,
'LeftElbowWidth': 91,
'LeftWristWidth': 56,
'LeftHandThickness': 28,
'RightShoulderOffset': 45,
'RightElbowWidth': 90,
'RightWristWidth': 55,
'RightHandThickness': 30
}
model.addAnthropoInputParameters(mp)
# -----------CGM STATIC CALIBRATION--------------------
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(scp,
acqStatic,
model,
headHorizontal=False).compute()
# --- motion ----
gaitFilename = "PN01NORMSTAT.c3d"
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
modMotion = modelFilters.ModelMotionFilter(
scp, acqGait, model, enums.motionMethod.Determinist)
modMotion.compute()
longitudinalAxis, forwardProgression, globalFrame = btkTools.findProgressionAxisFromLongAxis(
acqGait, "C7", "CLAV")
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqGait,
segmentLabels=["Thorax"],
angleLabels=[
"Thorax",
],
eulerSequences=["YXZ"],
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix="cgm1_6dof")
np.testing.assert_equal(longitudinalAxis, "X")
np.testing.assert_equal(forwardProgression, True)
np.testing.assert_equal(globalFrame, "XYZ")
# plot("LHeadAngles",acqGait,"cgm1_6dof")
# plot("RHeadAngles",acqGait,"cgm1_6dof")
plot("RThoraxAngles", acqGait, "cgm1_6dof")
plot("LThoraxAngles", acqGait, "cgm1_6dof")
def calibrate(DATA_PATH, calibrateFilenameLabelled, translators, required_mp,
optional_mp, leftFlatFoot, rightFlatFoot, headFlat,
markerDiameter, pointSuffix, **kwargs):
"""
Calibration of the CGM1.1
:param DATA_PATH [str]: path to your data
:param calibrateFilenameLabelled [str]: c3d file
:param translators [dict]: translators to apply
:param required_mp [dict]: required anthropometric data
:param optional_mp [dict]: optional anthropometric data (ex: LThighOffset,...)
:param leftFlatFoot [bool]: enable of the flat foot option for the left foot
:param rightFlatFoot [bool]: enable of the flat foot option for the right foot
:param headFlat [bool]: enable of the head flat option
:param markerDiameter [double]: marker diameter (mm)
:param pointSuffix [str]: suffix to add to model outputs
"""
detectAnomaly = False
if "anomalyException" in kwargs.keys():
anomalyException = kwargs["anomalyException"]
else:
anomalyException = False
# --------------------------ACQUISITION ------------------------------------
# ---btk acquisition---
if "forceBtkAcq" in kwargs.keys():
acqStatic = kwargs["forceBtkAcq"]
else:
acqStatic = btkTools.smartReader(
(DATA_PATH + calibrateFilenameLabelled))
btkTools.checkMultipleSubject(acqStatic)
if btkTools.isPointExist(acqStatic, "SACR"):
translators["LPSI"] = "SACR"
translators["RPSI"] = "SACR"
LOGGER.logger.info("[pyCGM2] Sacrum marker detected")
acqStatic = btkTools.applyTranslators(acqStatic, translators)
trackingMarkers = cgm.CGM1.LOWERLIMB_TRACKING_MARKERS + cgm.CGM1.THORAX_TRACKING_MARKERS + cgm.CGM1.UPPERLIMB_TRACKING_MARKERS
actual_trackingMarkers, phatoms_trackingMarkers = btkTools.createPhantoms(
acqStatic, trackingMarkers)
vff = acqStatic.GetFirstFrame()
vlf = acqStatic.GetLastFrame()
# vff,vlf = btkTools.getFrameBoundaries(acqStatic,actual_trackingMarkers)
flag = btkTools.getValidFrames(acqStatic,
actual_trackingMarkers,
frameBounds=[vff, vlf])
gapFlag = btkTools.checkGap(acqStatic,
actual_trackingMarkers,
frameBounds=[vff, vlf])
if gapFlag:
raise Exception(
"[pyCGM2] Calibration aborted. Gap find during interval [%i-%i]. Crop your c3d "
% (vff, vlf))
# --------------------ANOMALY------------------------------
# --Check MP
adap = AnomalyDetectionProcedure.AnthropoDataAnomalyProcedure(required_mp)
adf = AnomalyFilter.AnomalyDetectionFilter(None, None, adap)
mp_anomaly = adf.run()
if mp_anomaly["ErrorState"]: detectAnomaly = True
# --marker presence
markersets = [
cgm.CGM1.LOWERLIMB_TRACKING_MARKERS, cgm.CGM1.THORAX_TRACKING_MARKERS,
cgm.CGM1.UPPERLIMB_TRACKING_MARKERS
]
for markerset in markersets:
ipdp = InspectorProcedure.MarkerPresenceDetectionProcedure(markerset)
idf = InspectorFilter.InspectorFilter(acqStatic,
calibrateFilenameLabelled, ipdp)
inspector = idf.run()
# # --marker outliers
if inspector["In"] != []:
madp = AnomalyDetectionProcedure.MarkerAnomalyDetectionRollingProcedure(
inspector["In"], plot=False, window=4, threshold=3)
adf = AnomalyFilter.AnomalyDetectionFilter(
acqStatic, calibrateFilenameLabelled, madp)
anomaly = adf.run()
anomalyIndexes = anomaly["Output"]
if anomaly["ErrorState"]: detectAnomaly = True
if detectAnomaly and anomalyException:
raise Exception(
"Anomalies has been detected - Check Warning message of the log file"
)
# --------------------MODELLING------------------------------
# ---detectedCalibrationMethods----
dcm = cgm.CGM.detectCalibrationMethods(acqStatic)
# ---definition---
model = cgm.CGM1()
model.setVersion("CGM1.1")
model.configure(detectedCalibrationMethods=dcm)
model.addAnthropoInputParameters(required_mp, optional=optional_mp)
if dcm["Left Knee"] == enums.JointCalibrationMethod.KAD:
actual_trackingMarkers.append("LKNE")
if dcm["Right Knee"] == enums.JointCalibrationMethod.KAD:
actual_trackingMarkers.append("RKNE")
model.setStaticTrackingMarkers(actual_trackingMarkers)
# --store calibration parameters--
model.setStaticFilename(calibrateFilenameLabelled)
model.setCalibrationProperty("leftFlatFoot", leftFlatFoot)
model.setCalibrationProperty("rightFlatFoot", rightFlatFoot)
model.setCalibrationProperty("headFlat", headFlat)
model.setCalibrationProperty("markerDiameter", markerDiameter)
# --------------------------STATIC CALBRATION--------------------------
scp = modelFilters.StaticCalibrationProcedure(
model) # load calibration procedure
# ---initial calibration filter----
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=leftFlatFoot,
rightFlatFoot=rightFlatFoot,
headFlat=headFlat,
markerDiameter=markerDiameter,
).compute()
# ---- Decorators -----
decorators.applyBasicDecorators(dcm, model, acqStatic, optional_mp,
markerDiameter)
# ----Final Calibration filter if model previously decorated -----
if model.decoratedModel:
# initial static filter
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=leftFlatFoot,
rightFlatFoot=rightFlatFoot,
headFlat=headFlat,
markerDiameter=markerDiameter).compute()
# ----------------------CGM MODELLING----------------------------------
# ----motion filter----
# notice : viconCGM1compatible option duplicate error on Construction of the foot coordinate system
modMotion = modelFilters.ModelMotionFilter(scp,
acqStatic,
model,
enums.motionMethod.Determinist,
markerDiameter=markerDiameter)
modMotion.compute()
# ----progression Frame----
progressionFlag = False
if btkTools.isPointsExist(acqStatic, ['LASI', 'RASI', 'RPSI', 'LPSI'],
ignorePhantom=False):
LOGGER.logger.info(
"[pyCGM2] - progression axis detected from Pelvic markers ")
pfp = progressionFrame.PelvisProgressionFrameProcedure()
pff = progressionFrame.ProgressionFrameFilter(acqStatic, pfp)
pff.compute()
progressionAxis = pff.outputs["progressionAxis"]
globalFrame = pff.outputs["globalFrame"]
forwardProgression = pff.outputs["forwardProgression"]
progressionFlag = True
elif btkTools.isPointsExist(acqStatic, ['C7', 'T10', 'CLAV', 'STRN'],
ignorePhantom=False) and not progressionFlag:
LOGGER.logger.info(
"[pyCGM2] - progression axis detected from Thoracic markers ")
pfp = progressionFrame.ThoraxProgressionFrameProcedure()
pff = progressionFrame.ProgressionFrameFilter(acqStatic, pfp)
pff.compute()
progressionAxis = pff.outputs["progressionAxis"]
globalFrame = pff.outputs["globalFrame"]
forwardProgression = pff.outputs["forwardProgression"]
else:
globalFrame = "XYZ"
progressionAxis = "X"
forwardProgression = True
LOGGER.logger.error(
"[pyCGM2] - impossible to detect progression axis - neither pelvic nor thoracic markers are present. Progression set to +X by default "
)
if "displayCoordinateSystem" in kwargs.keys(
) and kwargs["displayCoordinateSystem"]:
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csdf = modelFilters.CoordinateSystemDisplayFilter(
csp, model, acqStatic)
csdf.setStatic(False)
csdf.display()
if "noKinematicsCalculation" in kwargs.keys(
) and kwargs["noKinematicsCalculation"]:
LOGGER.logger.warning(
"[pyCGM2] No Kinematic calculation done for the static file")
return model, acqStatic
else:
#---- Joint kinematics----
# relative angles
modelFilters.ModelJCSFilter(model, acqStatic).compute(
description="vectoriel", pointLabelSuffix=pointSuffix)
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqStatic,
segmentLabels=[
"Left Foot", "Right Foot", "Pelvis", "Thorax", "Head"
],
angleLabels=[
"LFootProgress", "RFootProgress", "Pelvis", "Thorax", "Head"
],
eulerSequences=["TOR", "TOR", "ROT", "YXZ", "TOR"],
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix=pointSuffix)
# BSP model
bspModel = bodySegmentParameters.Bsp(model)
bspModel.compute()
modelFilters.CentreOfMassFilter(
model, acqStatic).compute(pointLabelSuffix=pointSuffix)
btkTools.cleanAcq(acqStatic)
if detectAnomaly and not anomalyException:
LOGGER.logger.error(
"Anomalies has been detected - Check Warning messages of the log file"
)
return model, acqStatic, detectAnomaly
def CGM1_fullbody_onStatic(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\Full PIG - StephenL5_C7\\"
staticFilename = "PN01NORMSTAT.c3d"
# CALIBRATION ###############################
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
markerDiameter = 14
# Lower Limb
mp = {
'Bodymass': 83,
'LeftLegLength': 874,
'RightLegLength': 876.0,
'LeftKneeWidth': 106.0,
'RightKneeWidth': 103.0,
'LeftAnkleWidth': 74.0,
'RightAnkleWidth': 72.0,
'LeftSoleDelta': 0,
'RightSoleDelta': 0,
'LeftShoulderOffset': 50,
'LeftElbowWidth': 91,
'LeftWristWidth': 56,
'LeftHandThickness': 28,
'RightShoulderOffset': 45,
'RightElbowWidth': 90,
'RightWristWidth': 55,
'RightHandThickness': 30
}
model = cgm.CGM1()
model.configure(bodyPart=enums.BodyPart.FullBody)
model.addAnthropoInputParameters(mp)
scp = modelFilters.StaticCalibrationProcedure(
model) # load calibration procedure
csp = modelFilters.ModelCoordinateSystemProcedure(model)
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=False,
rightFlatFoot=False,
markerDiameter=14,
viconCGM1compatible=True,
).compute()
#headHorizontal=True
# --- motion ----
gaitFilename = "PN01NORMSTAT_stephen.c3d"
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
modMotion = modelFilters.ModelMotionFilter(
scp, acqGait, model, enums.motionMethod.Determinist)
modMotion.compute()
csdf = modelFilters.CoordinateSystemDisplayFilter(csp, model, acqGait)
csdf.setStatic(False)
csdf.display()
# angles
modelFilters.ModelJCSFilter(model, acqGait).compute(
description="vectoriel", pointLabelSuffix="cgm1_6dof")
longitudinalAxis, forwardProgression, globalFrame = btkTools.findProgressionAxisFromLongAxis(
acqGait, "C7", "CLAV")
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqGait,
segmentLabels=["Thorax"],
angleLabels=[
"Thorax",
],
eulerSequences=["YXZ"],
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix="cgm1_6dof")
# testing
np.testing.assert_equal(longitudinalAxis, "X")
np.testing.assert_equal(forwardProgression, True)
np.testing.assert_equal(globalFrame, "XYZ")
# BSP model
bspModel = bodySegmentParameters.Bsp(model)
bspModel.compute()
btkTools.smartAppendPoint(
acqGait, "pelvisCOM_py",
model.getSegment("Pelvis").getComTrajectory())
btkTools.smartAppendPoint(acqGait, "headCOM_py",
model.getSegment("Head").getComTrajectory())
btkTools.smartAppendPoint(
acqGait, "ThoraxCOM_py",
model.getSegment("Thorax").getComTrajectory())
btkTools.smartAppendPoint(
acqGait, "LhumCOM_py",
model.getSegment("Left UpperArm").getComTrajectory())
btkTools.smartAppendPoint(
acqGait, "LforeCom_py",
model.getSegment("Left ForeArm").getComTrajectory())
btkTools.smartAppendPoint(
acqGait, "LhandCom_py",
model.getSegment("Left Hand").getComTrajectory())
btkTools.smartAppendPoint(
acqGait, "RhumCOM_py",
model.getSegment("Right UpperArm").getComTrajectory())
btkTools.smartAppendPoint(
acqGait, "RforeCom_py",
model.getSegment("Right ForeArm").getComTrajectory())
btkTools.smartAppendPoint(
acqGait, "RhandCom_py",
model.getSegment("Right Hand").getComTrajectory())
modelFilters.CentreOfMassFilter(
model, acqGait).compute(pointLabelSuffix="py2")
TL5_pelvis = model.getSegment(
"Pelvis").anatomicalFrame.getNodeTrajectory("TL5")
TL5_thorax = model.getSegment(
"Thorax").anatomicalFrame.getNodeTrajectory("TL5")
C7o_thorax = model.getSegment(
"Thorax").anatomicalFrame.getNodeTrajectory("C7o")
C7_thorax = model.getSegment(
"Thorax").anatomicalFrame.getNodeTrajectory("C7")
C7_head = model.getSegment("Head").anatomicalFrame.getNodeTrajectory(
"C7")
btkTools.smartAppendPoint(acqGait, "TL5_pelvis", TL5_pelvis, desc="")
btkTools.smartAppendPoint(acqGait, "TL5_thorax", TL5_thorax, desc="")
btkTools.smartAppendPoint(acqGait, "C7o_thorax", C7o_thorax, desc="")
btkTools.smartAppendPoint(acqGait, "C7_thorax", C7_thorax, desc="")
btkTools.smartAppendPoint(acqGait, "C7_head", C7_thorax, desc="")
btkTools.smartWriter(acqGait,
"FullBody_COM_CGM1_fullbody_onStatic.c3d")
def CGM1_fullbody(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\Full PIG - StephenL5_C7\\"
staticFilename = "PN01NORMSTAT.c3d"
# CALIBRATION ###############################
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
markerDiameter = 14
# Lower Limb
mp = {
'Bodymass': 83,
'LeftLegLength': 874,
'RightLegLength': 876.0,
'LeftKneeWidth': 106.0,
'RightKneeWidth': 103.0,
'LeftAnkleWidth': 74.0,
'RightAnkleWidth': 72.0,
'LeftSoleDelta': 0,
'RightSoleDelta': 0,
'LeftShoulderOffset': 50,
'LeftElbowWidth': 91,
'LeftWristWidth': 56,
'LeftHandThickness': 28,
'RightShoulderOffset': 45,
'RightElbowWidth': 90,
'RightWristWidth': 55,
'RightHandThickness': 30
}
model = cgm.CGM1()
model.configure(bodyPart=enums.BodyPart.FullBody)
model.addAnthropoInputParameters(mp)
scp = modelFilters.StaticCalibrationProcedure(
model) # load calibration procedure
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=False,
rightFlatFoot=False,
markerDiameter=14,
viconCGM1compatible=True,
).compute()
#headHorizontal=True
csp = modelFilters.ModelCoordinateSystemProcedure(model)
csdf = modelFilters.CoordinateSystemDisplayFilter(
csp, model, acqStatic)
csdf.setStatic(True)
csdf.display()
# joint centres
np.testing.assert_almost_equal(
acqStatic.GetPoint("TRXO").GetValues().mean(axis=0),
acqStatic.GetPoint("OT").GetValues().mean(axis=0),
decimal=3)
np.testing.assert_almost_equal(
acqStatic.GetPoint("LCLO").GetValues().mean(axis=0),
acqStatic.GetPoint("LSJC").GetValues().mean(axis=0),
decimal=3)
np.testing.assert_almost_equal(
acqStatic.GetPoint("LHUO").GetValues().mean(axis=0),
acqStatic.GetPoint("LEJC").GetValues().mean(axis=0),
decimal=3)
np.testing.assert_almost_equal(
acqStatic.GetPoint("LCLO").GetValues().mean(axis=0),
acqStatic.GetPoint("LSJC").GetValues().mean(axis=0),
decimal=3)
np.testing.assert_almost_equal(
acqStatic.GetPoint("RCLO").GetValues().mean(axis=0),
acqStatic.GetPoint("RSJC").GetValues().mean(axis=0),
decimal=3)
np.testing.assert_almost_equal(
acqStatic.GetPoint("RHUO").GetValues().mean(axis=0),
acqStatic.GetPoint("REJC").GetValues().mean(axis=0),
decimal=3)
np.testing.assert_almost_equal(
acqStatic.GetPoint("RCLO").GetValues().mean(axis=0),
acqStatic.GetPoint("RSJC").GetValues().mean(axis=0),
decimal=3)
btkTools.smartWriter(acqStatic, "FullBody_Static_CGM1_fullbody.c3d")
def CGM1_fullbody(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\Full PIG - StephenL5_C7\\"
staticFilename = "PN01NORMSTAT.c3d"
# CALIBRATION ###############################
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
markerDiameter = 14
# Lower Limb
mp = {
'Bodymass': 83,
'LeftLegLength': 874,
'RightLegLength': 876.0,
'LeftKneeWidth': 106.0,
'RightKneeWidth': 103.0,
'LeftAnkleWidth': 74.0,
'RightAnkleWidth': 72.0,
'LeftSoleDelta': 0,
'RightSoleDelta': 0,
'LeftShoulderOffset': 50,
'LeftElbowWidth': 91,
'LeftWristWidth': 56,
'LeftHandThickness': 28,
'RightShoulderOffset': 45,
'RightElbowWidth': 90,
'RightWristWidth': 55,
'RightHandThickness': 30
}
model = cgm.CGM1()
model.configure(bodyPart=enums.BodyPart.FullBody)
model.addAnthropoInputParameters(mp)
scp = modelFilters.StaticCalibrationProcedure(
model) # load calibration procedure
csp = modelFilters.ModelCoordinateSystemProcedure(model)
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=False,
rightFlatFoot=False,
markerDiameter=14,
viconCGM1compatible=True,
).compute()
#headHorizontal=True
# --- motion ----
gaitFilename = "PN01NORMSS01_stephen.c3d"
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
modMotion = modelFilters.ModelMotionFilter(
scp, acqGait, model, enums.motionMethod.Determinist)
modMotion.compute()
csdf = modelFilters.CoordinateSystemDisplayFilter(csp, model, acqGait)
csdf.setStatic(False)
csdf.display()
# angles
modelFilters.ModelJCSFilter(model, acqGait).compute(
description="vectoriel", pointLabelSuffix="cgm1_6dof")
longitudinalAxis, forwardProgression, globalFrame = btkTools.findProgressionAxisFromLongAxis(
acqGait, "C7", "CLAV")
modelFilters.ModelAbsoluteAnglesFilter(
model,
acqGait,
segmentLabels=["Thorax"],
angleLabels=[
"Thorax",
],
eulerSequences=["YXZ"],
globalFrameOrientation=globalFrame,
forwardProgression=forwardProgression).compute(
pointLabelSuffix="cgm1_6dof")
# testing
np.testing.assert_equal(longitudinalAxis, "X")
np.testing.assert_equal(forwardProgression, False)
np.testing.assert_equal(globalFrame, "XYZ")
#plot("LNeckAngles",acqGait,"cgm1_6dof")
# relative angles
np.testing.assert_almost_equal(
acqGait.GetPoint("RSpineAngles").GetValues(),
acqGait.GetPoint("RSpineAngles_cgm1_6dof").GetValues(),
decimal=2)
np.testing.assert_almost_equal(
acqGait.GetPoint("LSpineAngles").GetValues(),
acqGait.GetPoint("LSpineAngles_cgm1_6dof").GetValues(),
decimal=2)
np.testing.assert_almost_equal(
acqGait.GetPoint("LShoulderAngles").GetValues(),
acqGait.GetPoint("LShoulderAngles_cgm1_6dof").GetValues(),
decimal=3)
np.testing.assert_almost_equal(
acqGait.GetPoint("RShoulderAngles").GetValues(),
acqGait.GetPoint("RShoulderAngles_cgm1_6dof").GetValues(),
decimal=3)
np.testing.assert_almost_equal(
acqGait.GetPoint("RElbowAngles").GetValues(),
acqGait.GetPoint("RElbowAngles_cgm1_6dof").GetValues(),
decimal=3)
np.testing.assert_almost_equal(
acqGait.GetPoint("LElbowAngles").GetValues(),
acqGait.GetPoint("LElbowAngles_cgm1_6dof").GetValues(),
decimal=3)
# np.testing.assert_almost_equal( acqGait.GetPoint("RWristAngles").GetValues(),
# acqGait.GetPoint("RWristAngles_cgm1_6dof").GetValues(), decimal =3) # fail on transverse
# np.testing.assert_almost_equal( acqGait.GetPoint("LWristAngles").GetValues(),
# acqGait.GetPoint("LWristAngles_cgm1_6dof").GetValues(), decimal =3)# fail on transverse
#
# np.testing.assert_almost_equal( acqGait.GetPoint("RNeckAngles").GetValues(),
# acqGait.GetPoint("RNeckAngles_cgm1_6dof").GetValues(), decimal =1) # fail on coronal
# np.testing.assert_almost_equal( acqGait.GetPoint("LNeckAngles").GetValues(),
# acqGait.GetPoint("LNeckAngles_cgm1_6dof").GetValues(), decimal =1) # fail on coronal
# absolute angles
np.testing.assert_almost_equal(
acqGait.GetPoint("LThoraxAngles").GetValues(),
acqGait.GetPoint("LThoraxAngles_cgm1_6dof").GetValues(),
decimal=3)
np.testing.assert_almost_equal(
acqGait.GetPoint("RThoraxAngles").GetValues(),
acqGait.GetPoint("RThoraxAngles_cgm1_6dof").GetValues(),
decimal=3)
btkTools.smartWriter(acqStatic, "FullBody_Angles_CGM1_fullbody.c3d")
def CGM1_fullbody(cls):
MAIN_PATH = pyCGM2.TEST_DATA_PATH + "CGM1\\CGM1-TESTS\\Full PIG - StephenL5_C7\\"
staticFilename = "PN01NORMSTAT.c3d"
# CALIBRATION ###############################
acqStatic = btkTools.smartReader(str(MAIN_PATH + staticFilename))
markerDiameter = 14
# Lower Limb
mp = {
'Bodymass': 83,
'LeftLegLength': 874,
'RightLegLength': 876.0,
'LeftKneeWidth': 106.0,
'RightKneeWidth': 103.0,
'LeftAnkleWidth': 74.0,
'RightAnkleWidth': 72.0,
'LeftSoleDelta': 0,
'RightSoleDelta': 0,
'LeftShoulderOffset': 50,
'LeftElbowWidth': 91,
'LeftWristWidth': 56,
'LeftHandThickness': 28,
'RightShoulderOffset': 45,
'RightElbowWidth': 90,
'RightWristWidth': 55,
'RightHandThickness': 30
}
model = cgm.CGM1()
model.configure(bodyPart=enums.BodyPart.FullBody)
model.addAnthropoInputParameters(mp)
scp = modelFilters.StaticCalibrationProcedure(
model) # load calibration procedure
csp = modelFilters.ModelCoordinateSystemProcedure(model)
modelFilters.ModelCalibrationFilter(
scp,
acqStatic,
model,
leftFlatFoot=False,
rightFlatFoot=False,
markerDiameter=14,
viconCGM1compatible=True,
).compute()
#headHorizontal=True
# --- motion ----
gaitFilename = "PN01NORMSS01_stephen.c3d"
acqGait = btkTools.smartReader(str(MAIN_PATH + gaitFilename))
modMotion = modelFilters.ModelMotionFilter(
scp, acqGait, model, enums.motionMethod.Determinist)
modMotion.compute()
csdf = modelFilters.CoordinateSystemDisplayFilter(csp, model, acqGait)
csdf.setStatic(False)
csdf.display()
# TESTING
# thorax
R_thorax = model.getSegment(
"Thorax").anatomicalFrame.motion[10].getRotation()
R_thorax_vicon = getViconRmatrix(10, acqGait, "TRXO", "TRXA", "TRXL",
"XZY")
np.testing.assert_almost_equal(R_thorax, R_thorax_vicon, decimal=3)
# head
R_head = model.getSegment(
"Head").anatomicalFrame.motion[10].getRotation()
R_head_vicon = getViconRmatrix(10, acqGait, "HEDO", "HEDA", "HEDL",
"XZY")
np.testing.assert_almost_equal(R_head, R_head_vicon, decimal=2)
btkTools.smartWriter(acqStatic, "FullBody_motion_CGM1_fullbody.c3d")