def test_functions(self):
filename = pyCGM2.TEST_DATA_PATH + "LowLevel\\IO\\Hånnibøl_c3d\\gait1.c3d"
acq = btkTools.smartReader(filename, translators=None)
btkTools.GetMarkerNames(acq)
btkTools.findNearestMarker(acq, 0, "LASI")
btkTools.GetAnalogNames(acq)
btkTools.isGap(acq, "LASI")
btkTools.findMarkerGap(acq)
btkTools.isPointExist(acq, "LASI")
btkTools.isPointsExist(acq, ["LASI", "RASI"])
btkTools.clearPoints(acq, ["LASI", "RASI"])
btkTools.checkFirstAndLastFrame(acq, "LASI")
btkTools.isGap_inAcq(acq, ["LASI", "RASI"])
btkTools.findValidFrames(acq, ["LASI", "RASI"])
btkTools.checkMultipleSubject(acq)
btkTools.checkMarkers(acq, ["LASI", "RASI"])
btkTools.clearEvents(acq, ["Foot Strike"])
btkTools.modifyEventSubject(acq, "Hän")
btkTools.modifySubject(acq, "Han")
btkTools.getVisibleMarkersAtFrame(acq, ["LASI", "RASI"], 0)
btkTools.isAnalogExist(acq, "emg-Hän")
btkTools.createZeros(acq, ["LASI", "RASI"])
btkTools.constructEmptyMarker(acq, "zéros", desc="Hän")
btkTools.getStartEndEvents(acq, "Left")
btkTools.changeSubjectName(acq, "Hän")
btkTools.smartGetMetadata(acq, "SUBJECTS", "USED")
btkTools.smartSetMetadata(acq, "SUBJECTS", "USED", 0, "Hän")
def fill(self, acq):
logging.info("----LowDimensionalKalmanFilter gap filling----")
btkmarkersLoaded = btkTools.GetMarkerNames(acq)
ff = acq.GetFirstFrame()
lf = acq.GetLastFrame()
pfn = acq.GetPointFrameNumber()
btkmarkers = []
for ml in btkmarkersLoaded:
if btkTools.isPointExist(acq, ml):
btkmarkers.append(ml)
# --------
logging.debug("Populating data matrix")
rawDatabtk = np.zeros((pfn, len(btkmarkers) * 3))
for i in range(0, len(btkmarkers)):
values = acq.GetPoint(btkmarkers[i]).GetValues()
residualValues = acq.GetPoint(btkmarkers[i]).GetResiduals()
rawDatabtk[:, 3 * i - 3] = values[:, 0]
rawDatabtk[:, 3 * i - 2] = values[:, 1]
rawDatabtk[:, 3 * i - 1] = values[:, 2]
E = residualValues[:, 0]
rawDatabtk[np.asarray(E) == -1, 3 * i - 3] = np.nan
rawDatabtk[np.asarray(E) == -1, 3 * i - 2] = np.nan
rawDatabtk[np.asarray(E) == -1, 3 * i - 1] = np.nan
Y2 = self._smooth(rawDatabtk, tol=1e-2, sigR=1e-3, keepOriginal=True)
logging.debug("writing trajectories")
# Create new smoothed trjectories
filledMarkers = list()
for i in range(0, len(btkmarkers)):
targetMarker = btkmarkers[i]
if btkTools.isGap(acq, targetMarker):
logging.info("marker (%s) --> filled" % (targetMarker))
filledMarkers.append(targetMarker)
val_final = np.zeros((pfn, 3))
val_final[:, 0] = Y2[:, 3 * i - 3]
val_final[:, 1] = Y2[:, 3 * i - 2]
val_final[:, 2] = Y2[:, 3 * i - 1]
btkTools.smartAppendPoint(acq, targetMarker, val_final)
logging.info(
"----LowDimensionalKalmanFilter gap filling [complete]----")
return acq, filledMarkers
def nexus_x2d(cls):
NEXUS = ViconNexus.ViconNexus()
NEXUS_PYTHON_CONNECTED = NEXUS.Client.IsConnected()
DATA_PATH = "C:\\Users\\HLS501\\Documents\\VICON DATA\\pyCGM2-Data\\operations\\gapFilling\\gaitWithGaps_withX2d\\"
filenameNoExt = "gait_GAP"
NEXUS.OpenTrial(str(DATA_PATH + filenameNoExt), 30)
acq_filled = btkTools.smartReader(
str(DATA_PATH + "gait_GAP.-moGap.c3d"))
subject = NEXUS.GetSubjectNames()[0]
print "Gap filling for subject ", subject
markersLoaded = NEXUS.GetMarkerNames(
subject) # nexus2.7 return all makers, even calibration only
frames = NEXUS.GetFrameCount()
markers = []
for i in range(0, len(markersLoaded)):
data = NEXUS.GetTrajectory(subject, markersLoaded[i])
if data != ([], [], [], []):
markers.append(markersLoaded[i])
#---------
acq = btkTools.smartReader(str(DATA_PATH + filenameNoExt + ".c3d"))
btkmarkersLoaded = btkTools.GetMarkerNames(acq)
ff = acq.GetFirstFrame()
lf = acq.GetLastFrame()
pfn = acq.GetPointFrameNumber()
btkmarkers = []
for ml in btkmarkersLoaded:
if btkTools.isPointExist(acq, ml):
btkmarkers.append(ml)
#---------
print "Populating data matrix"
rawData = np.zeros((frames, len(markers) * 3))
for i in range(0, len(markers)):
print i
rawData[:, 3 * i -
3], rawData[:, 3 * i -
2], rawData[:, 3 * i -
1], E = NEXUS.GetTrajectory(
subject, markers[i])
rawData[np.asarray(E) == 0, 3 * i - 3] = np.nan
rawData[np.asarray(E) == 0, 3 * i - 2] = np.nan
rawData[np.asarray(E) == 0, 3 * i - 1] = np.nan
Y = smooth(rawData, tol=1e-2, sigR=1e-3, keepOriginal=True)
print "Writing new trajectories"
# Create new smoothed trjectories
for i in range(0, len(markers)):
if markers[i] == "LTHAD":
E = np.ones((len(E), 1)).tolist()
val0 = Y[:, 3 * i - 3].tolist()
val1 = Y[:, 3 * i - 2].tolist()
val2 = Y[:, 3 * i - 1].tolist()
#NEXUS.SetTrajectory(subject,markers[i],Y[:,3*i-3].tolist(),Y[:,3*i-2].tolist(),Y[:,3*i-1].tolist(),E)
print "Done"
# --------
print "Populating data matrix"
rawDatabtk = np.zeros((pfn, len(btkmarkers) * 3))
for i in range(0, len(btkmarkers)):
values = acq.GetPoint(btkmarkers[i]).GetValues()
residualValues = acq.GetPoint(btkmarkers[i]).GetResiduals()
rawDatabtk[:, 3 * i - 3] = values[:, 0]
rawDatabtk[:, 3 * i - 2] = values[:, 1]
rawDatabtk[:, 3 * i - 1] = values[:, 2]
E = residualValues[:, 0]
rawDatabtk[np.asarray(E) == -1, 3 * i - 3] = np.nan
rawDatabtk[np.asarray(E) == -1, 3 * i - 2] = np.nan
rawDatabtk[np.asarray(E) == -1, 3 * i - 1] = np.nan
Y2 = smooth(rawDatabtk, tol=1e-2, sigR=1e-3, keepOriginal=True)
print "Writing new trajectories"
# Create new smoothed trjectories
for i in range(0, len(btkmarkers)):
targetMarker = btkmarkers[i]
if btkTools.isGap(acq, targetMarker):
val_final = np.zeros((pfn, 3))
val_final[:, 0] = Y2[:, 3 * i - 3]
val_final[:, 1] = Y2[:, 3 * i - 2]
val_final[:, 2] = Y2[:, 3 * i - 1]
btkTools.smartAppendPoint(acq, targetMarker, val_final)
nexusTools.setTrajectoryFromAcq(NEXUS, subject, targetMarker,
acq)
print "Done"
def kinematicFitting_oneFile_cgmProcedure(cls):
DATA_PATH = pyCGM2.TEST_DATA_PATH + "CGM2\\LowerLimb\\subject10_S1A1_julieDataSet_noModelOutputs\\"
config = dict()
config["static"] = "StaticR010S1A1.c3d"
config["dynamicTrial"] = [
"R010S1A1Gait001.c3d", "R010S1A1Gait003.c3d",
"R010S1A1Gait004.c3d", "R010S1A1Gait005.c3d",
"R010S1A1Gait007.c3d", "R010S1A1Gait010.c3d"
]
configMP = {
"Bodymass": 64.0,
"LeftLegLength": 865.0,
"RightLegLength": 855.0,
"LeftKneeWidth": 100.0,
"RightKneeWidth": 101.0,
"LeftAnkleWidth": 69.0,
"RightAnkleWidth": 69.0
}
requiredMarkers = [
"LASI", "RASI", "LPSI", "RPSI", "RTHIAP", "RTHIAD", "RTHI", "RKNE",
"RSHN", "RTIAP", "RTIB", "RANK", "RHEE", "RTOE", "RCUN", "RD1M",
"RD5M"
]
acqStatic = btkTools.smartReader(DATA_PATH + config["static"])
# model
model = cgm2Julie.CGM2ModelInf()
model.configure()
markerDiameter = 14
mp = {
'Bodymass': configMP["Bodymass"],
'LeftLegLength': configMP["LeftLegLength"],
'RightLegLength': configMP["RightLegLength"],
'LeftKneeWidth': configMP["LeftKneeWidth"],
'RightKneeWidth': configMP["RightKneeWidth"],
'LeftAnkleWidth': configMP["LeftAnkleWidth"],
'RightAnkleWidth': configMP["RightAnkleWidth"],
}
#offset 2ndToe Joint
toe = acqStatic.GetPoint("RTOE").GetValues()[:, :].mean(axis=0)
mp["rightToeOffset"] = (toe[2] - markerDiameter / 2.0) / 2.0
model.addAnthropoInputParameters(mp)
# -----------CGM STATIC CALIBRATION--------------------
# --- Initial calibration
scp = modelFilters.StaticCalibrationProcedure(model)
modelFilters.ModelCalibrationFilter(
scp, acqStatic, model,
rightFlatHindFoot=True).compute() # Initial calibration
# --- decorator
modelDecorator.KneeCalibrationDecorator(model).midCondyles(
acqStatic, leftMedialKneeLabel="LKNM", rightMedialKneeLabel="RKNM")
modelDecorator.AnkleCalibrationDecorator(model).midMaleolus(
acqStatic,
leftMedialAnkleLabel="LMMA",
rightMedialAnkleLabel="RMMA")
# --- Updated calibration
modelFilters.ModelCalibrationFilter(scp,
acqStatic,
model,
useLeftKJCnode="LKJC_mid",
useRightKJCnode="RKJC_mid",
useLeftAJCnode="LAJC_mid",
useRightAJCnode="RAJC_mid",
rightFlatHindFoot=True).compute()
# ---- optional -update static c3d
#btkTools.smartWriter(acqStatic, "StaticCalibrated.c3d")
# -----------CGM MOTION 6dof--------------------
# --- reader and checking
acqGait = btkTools.smartReader(DATA_PATH + config["dynamicTrial"][0])
btkTools.checkMarkers(acqGait, requiredMarkers)
btkTools.isGap(acqGait, requiredMarkers)
btkTools.checkFirstAndLastFrame(acqGait, "LASI")
logging.info("dyn Acquisition ---> OK ")
# --- filters
modMotion = modelFilters.ModelMotionFilter(
scp, acqGait, model, pyCGM2Enums.motionMethod.Determinist)
modMotion.compute()
modelFilters.ModelJCSFilter(model,
acqGait).compute(description="vectoriel",
pointLabelSuffix="2_6dof")
# --- writer
#btkTools.smartWriter(acqGait, "motionCalibrated.c3d")
# ------- OPENSIM IK --------------------------------------
cgmprocedure = opensimFilters.CgmOpensimCalibrationProcedures(model)
markersetFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\draft-opensimPreProcessing\\cgm2-markerset.xml"
osimfile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\draft-opensimPreProcessing\\cgm2-model.osim"
oscf = opensimFilters.opensimCalibrationFilter(osimfile, model,
cgmprocedure)
oscf.addMarkerSet(markersetFile)
fittingOsim = oscf.build()
filename = config["dynamicTrial"][0]
cgmFittingProcedure = opensimFilters.CgmOpensimFittingProcedure(model)
cgmFittingProcedure.updateMarkerWeight("LASI", 100)
iksetupFile = pyCGM2.OPENSIM_PREBUILD_MODEL_PATH + "models\\draft-opensimPreProcessing\\ikSetUp_template.xml"
osrf = opensimFilters.opensimFittingFilter(iksetupFile, fittingOsim,
cgmFittingProcedure,
DATA_PATH)
acqIK = osrf.run(acqGait, str(DATA_PATH + filename))
# -------- NEW MOTION FILTER ON IK MARKERS ------------------
modMotion_ik = modelFilters.ModelMotionFilter(
scp, acqIK, model, pyCGM2Enums.motionMethod.Sodervisk)
modMotion_ik.compute()
finalJcs = modelFilters.ModelJCSFilter(model, acqIK)
finalJcs.setFilterBool(False)
finalJcs.compute(description="ik", pointLabelSuffix="2_ik") #
# recup du mot file
motFilename = str(DATA_PATH + config["dynamicTrial"][0][:-4] + ".mot")
comparisonOpensimVsCGM(motFilename, acqIK, "2_ik")