def __init__(self, acq, markers=None):
self.acq = acq
self.markers = markers if markers is not None else btkTools.GetMarkerNames(
acq)
self.state = True
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 __init__(self, acq, markers=None, title=None):
self.acq = acq
self.markers = markers if markers is not None else btkTools.GetMarkerNames(
acq)
self.exceptionMode = False
self.state = True
self.title = "Marker position" if title is None else title
def __init__(self, acq, markers=None, title=None, plot=False):
self.acq = acq
self.markers = markers if markers is not None else btkTools.GetMarkerNames(
acq)
self.exceptionMode = False
self.title = "Swapping marker" if title is None else title
self.state = True
self.plot = plot
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"
