def main():
NEXUS = ViconNexus.ViconNexus()
NEXUS_PYTHON_CONNECTED = NEXUS.Client.IsConnected()
if NEXUS_PYTHON_CONNECTED: # run Operation
DATA_PATH, filenameLabelledNoExt = NEXUS.GetTrialName()
logging.info("data Path: " + DATA_PATH)
logging.info("file: " + filenameLabelledNoExt)
subject = NEXUS.GetSubjectNames()[0]
logging.info("Gap filling for subject %s" % (subject))
# btkAcq builder
nacf = nexusFilters.NexusConstructAcquisitionFilter(
DATA_PATH, filenameLabelledNoExt, subject)
acq = nacf.build()
#acq = btkTools.smartReader(str(DATA_PATH+filenameLabelledNoExt+".c3d"))
gfp = gapFilling.LowDimensionalKalmanFilterProcedure()
gff = gapFilling.GapFillingFilter(gfp, acq)
gff.fill()
filledAcq = gff.getFilledAcq()
filledMarkers = gff.getFilledMarkers()
for marker in filledMarkers:
nexusTools.setTrajectoryFromAcq(NEXUS, subject, marker, filledAcq)
else:
raise Exception("NO Nexus connection. Turn on Nexus")
def main():
parser = argparse.ArgumentParser(description='')
parser.add_argument('--markers', nargs='+')
parser.add_argument('--noCorrection',
action='store_true',
help='disable correction')
args = parser.parse_args()
NEXUS = ViconNexus.ViconNexus()
NEXUS_PYTHON_CONNECTED = NEXUS.Client.IsConnected()
if NEXUS_PYTHON_CONNECTED: # run Operation
DATA_PATH, filename = NEXUS.GetTrialName()
LOGGER.logger.info(" Path: " + DATA_PATH)
LOGGER.logger.info(" file: " + filename)
# --------------------------SUBJECT ------------------------------------
subjects = NEXUS.GetSubjectNames()
subject = nexusTools.getActiveSubject(
NEXUS) #checkActivatedSubject(NEXUS,subjects)
Parameters = NEXUS.GetSubjectParamNames(subject)
# --------------------------PULL ------------------------------------
nacf = nexusFilters.NexusConstructAcquisitionFilter(
DATA_PATH, filename, subject)
acq = nacf.build()
# --------------------------process ------------------------------------
# Work with BTK Here
markers = args.markers
# markers = cgm.CGM1.LOWERLIMB_TRACKING_MARKERS
madp = AnomalyDetectionProcedure.MarkerAnomalyDetectionRollingProcedure(
markers, plot=False, window=5, threshold=3)
adf = AnomalyFilter.AnomalyDetectionFilter(acq, filename, madp)
anomaly = adf.run()
if not args.noCorrection:
macp = AnomalyCorrectionProcedure.MarkerAnomalyCorrectionProcedure(
markers, anomaly["Output"], plot=False, distance_threshold=20)
acf = AnomalyFilter.AnomalyCorrectionFilter(acq, filename, macp)
acqo = acf.run()
# --------------------------PUSH ------------------------------------
for marker in markers:
nexusTools.setTrajectoryFromAcq(NEXUS, subject, marker, acqo)
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"