def sortedEvents(acq):
evs = acq.GetEvents()
contextLst = [] # recuperation de tous les contextes
for it in btk.Iterate(evs):
if it.GetContext() not in contextLst:
contextLst.append(it.GetContext())
valueFrame = [] # recuperation de toutes les frames SANS doublons
for it in btk.Iterate(evs):
if it.GetFrame() not in valueFrame:
valueFrame.append(it.GetFrame())
valueFrame.sort() # trie
events = []
for frame in valueFrame:
for it in btk.Iterate(evs):
if it.GetFrame() == frame:
events.append(it)
newEvents = btk.btkEventCollection()
for ev in events:
newEvents.InsertItem(ev)
acq.ClearEvents()
acq.SetEvents(newEvents)
def sortedEvents(acq):
evs = acq.GetEvents()
contextLst=[] # recuperation de tous les contextes
for it in btk.Iterate(evs):
if it.GetContext() not in contextLst:
contextLst.append(it.GetContext())
valueFrame=[] # recuperation de toutes les frames SANS doublons
for it in btk.Iterate(evs):
if it.GetFrame() not in valueFrame:
valueFrame.append(it.GetFrame())
valueFrame.sort() # trie
events =[]
for frame in valueFrame:
for it in btk.Iterate(evs):
if it.GetFrame()==frame:
events.append(it)
#
# import ipdb; ipdb.set_trace()
# events =[]
# for contextLst_it in contextLst:
# for frameSort in valueFrame:
# for it in btk.Iterate(evs):
# if it.GetFrame()==frameSort and it.GetContext()==contextLst_it:
# events.append(it)
return events
def applyTranslators(acq, translators):
"""
Rename marker from translators
:Parameters:
- `acq` (btkAcquisition) - a btk acquisition instance
- `translators` (dict) - translators
"""
acqClone = btk.btkAcquisition.Clone(acq)
if translators is not None:
modifiedMarkerList = list()
# gather all labels
for it in translators.items():
wantedLabel,initialLabel = it[0],it[1]
if wantedLabel != initialLabel and initialLabel !="None":
modifiedMarkerList.append(it[0])
modifiedMarkerList.append(it[1])
# Remove Modified Markers from Clone
for point in btk.Iterate(acq.GetPoints()):
if point.GetType() == btk.btkPoint.Marker:
label = point.GetLabel()
if label in modifiedMarkerList:
acqClone.RemovePoint(utils.str(label))
logging.debug("point (%s) remove in the clone acq " %((label)))
# Add Modify markers to clone
for it in translators.items():
wantedLabel,initialLabel = it[0],it[1]
if initialLabel !="None":
if isPointExist(acq,wantedLabel):
smartAppendPoint(acqClone,(wantedLabel+"_origin"),acq.GetPoint(utils.str(wantedLabel)).GetValues(),PointType=btk.btkPoint.Marker) # modified marker
logging.warning("wantedLabel (%s)_origin created" %((wantedLabel)))
if isPointExist(acq,initialLabel):
if initialLabel in translators.keys():
if translators[initialLabel] == "None":
logging.warning("Initial point (%s)and (%s) point to similar values" %((initialLabel), (wantedLabel)))
smartAppendPoint(acqClone,(wantedLabel),acq.GetPoint(utils.str(initialLabel)).GetValues(),PointType=btk.btkPoint.Marker)
smartAppendPoint(acqClone,(initialLabel),acq.GetPoint(utils.str(initialLabel)).GetValues(),PointType=btk.btkPoint.Marker) # keep initial marker
elif translators[initialLabel] == wantedLabel:
logging.warning("Initial point (%s) swaped with (%s)" %((initialLabel), (wantedLabel)))
initialValue = acq.GetPoint(utils.str(initialLabel)).GetValues()
wantedlValue = acq.GetPoint(utils.str(wantedLabel)).GetValues()
smartAppendPoint(acqClone,(wantedLabel),initialValue,PointType=btk.btkPoint.Marker)
smartAppendPoint(acqClone,("TMP"),wantedlValue,PointType=btk.btkPoint.Marker)
acqClone.GetPoint(utils.str("TMP")).SetLabel(initialLabel)
acqClone.RemovePoint(utils.str(wantedLabel+"_origin"))
acqClone.RemovePoint(utils.str(initialLabel+"_origin"))
else:
logging.warning("Initial point (%s) renamed (%s) added into the c3d" %((initialLabel), (wantedLabel)))
smartAppendPoint(acqClone,(wantedLabel),acq.GetPoint(utils.str(initialLabel)).GetValues(),PointType=btk.btkPoint.Marker)
smartAppendPoint(acqClone,(initialLabel),acq.GetPoint(utils.str(initialLabel)).GetValues(),PointType=btk.btkPoint.Marker)
else:
logging.warning("initialLabel (%s) doesn t exist " %((initialLabel)))
#raise Exception ("your translators are badly configured")
return acqClone
def createEvents(NEXUS,subject,acq,labels):
freq = acq.GetPointFrequency()
events= acq.GetEvents()
for ev in btk.Iterate(events):
if ev.GetLabel() in labels:
NEXUS.CreateAnEvent( subject, ev.GetContext(), ev.GetLabel(), int(ev.GetTime()*freq), 0.0 )
def changeSubjectName(btkAcq,subjectName):
# change subject name in the metadata
md = btkAcq.GetMetaData()
if "SUBJECTS" in _getSectionFromMd(md):
subjectMd = btkAcq.GetMetaData().FindChild(utils.str("SUBJECTS")).value()
if "NAMES" in _getSectionFromMd(subjectMd):
subjectMd.FindChild(utils.str("NAMES")).value().GetInfo().SetValue(0,utils.str(subjectName))
if "USES_PREFIXES" not in _getSectionFromMd(subjectMd):
btk.btkMetaDataCreateChild(subjectMd, utils.str("USES_PREFIXES"), 0)
if "ANALYSIS" in _getSectionFromMd(md):
analysisMd = btkAcq.GetMetaData().FindChild(utils.str("ANALYSIS")).value()
if "SUBJECTS" in _getSectionFromMd(analysisMd):
anaSubMdi = analysisMd.FindChild(utils.str("SUBJECTS")).value().GetInfo()
for i in range(0,anaSubMdi.GetDimension(1) ):
anaSubMdi.SetValue(i,utils.str(subjectName))
events = btkAcq.GetEvents()
for ev in btk.Iterate(events):
ev.SetSubject(utils.str(subjectName))
# Do not work
# eventMd = btkAcq.GetMetaData().FindChild("EVENT").value()
# eventMdi = eventMd.FindChild("SUBJECTS").value().GetInfo()
# for i in range(0,eventMdi.GetDimension(1) ):
# eventMdi.SetValue(i,"TEST")
return btkAcq
def run(self):
fa = self.m_acq.GetAnalogFrequency()
for analog in btk.Iterate(self.m_acq.GetAnalogs()):
for label in self.m_labels:
if analog.GetLabel() == label:
values = analog.GetValues()
# stop 50hz
value50 = signal_processing.remove50hz(values, fa)
# high pass and compensation with mean
hpLower = self.m_hpf_low
hpUpper = self.m_hpf_up
valuesHp = signal_processing.highPass(
value50, hpLower, hpUpper, fa)
btkTools.smartAppendAnalog(self.m_acq,
label + "_HPF",
valuesHp,
desc="high Pass filter")
# rectification
btkTools.smartAppendAnalog(self.m_acq,
label + "_Rectify",
np.abs(valuesHp),
desc="rectify")
def isKineticFlag(acq):
"""
Flag up if correct kinetics available
:Parameters:
- `trial` (openma.trial) - an openma trial instance
:Return:
- `` (bool) - flag if kinetic available
- `kineticEvent_times` (lst) - time of maximal Normal reaction Forces for both context
- `kineticEvent_times_left` (lst) - time of maximal Normal reaction Forces for the Left context
- `kineticEvent_times_right` (lst) - time of maximal Normal reaction Forces for the Right context
"""
kineticEvent_frames = []
kineticEvent_frames_left = []
kineticEvent_frames_right = []
events = acq.GetEvents()
for ev in btk.Iterate(events):
if ev.GetContext() == "General":
if ev.GetLabel() in ["Left-FP", "Right-FP"]:
kineticEvent_frames.append(ev.GetFrame())
if ev.GetLabel() in ["Left-FP"]:
kineticEvent_frames_left.append(ev.GetFrame())
if ev.GetLabel() in ["Right-FP"]:
kineticEvent_frames_right.append(ev.GetFrame())
if kineticEvent_frames == []:
return False, 0, 0, 0
else:
return True, kineticEvent_frames, kineticEvent_frames_left, kineticEvent_frames_right
def markerFiltering(btkAcq, order=2, fc=6):
"""
Low-pass filtering of all points in an acquisition
:Parameters:
- `btkAcq` (btkAcquisition) - btk acquisition instance
- `fc` (double) - cut-off frequency
- `order` (double) - order of the low-pass filter
"""
fp = btkAcq.GetPointFrequency()
bPoint, aPoint = signal.butter(order, fc / (fp * 0.5), btype='lowpass')
for pointIt in btk.Iterate(btkAcq.GetPoints()):
if pointIt.GetType() == btk.btkPoint.Marker:
x = signal.filtfilt(bPoint,
aPoint,
pointIt.GetValues()[:, 0],
axis=0)
y = signal.filtfilt(bPoint,
aPoint,
pointIt.GetValues()[:, 1],
axis=0)
z = signal.filtfilt(bPoint,
aPoint,
pointIt.GetValues()[:, 2],
axis=0)
pointIt.SetValues(np.array([x, y, z]).transpose())
def isPointExist(acq, label, ignorePhantom=True):
"""
Check if a point label exists inside an acquisition
:Parameters:
- `acq` (btkAcquisition) - a btk acquisition inctance
- `label` (str) - point label
"""
try:
acq.GetPoint(label)
except RuntimeError:
return False
else:
frameNumber = acq.GetPointFrameNumber()
for it in btk.Iterate(acq.GetPoints()):
if it.GetLabel() == label:
LOGGER.logger.debug("[pyCGM2] marker (%s) is a phantom " %
label)
values = it.GetValues()
residuals = it.GetResiduals()
if not ignorePhantom:
if all(residuals == -1):
return False
else:
return True
else:
return True
def GetMarkerNames(acq):
"""
"""
markerNames=[]
for it in btk.Iterate(acq.GetPoints()):
if it.GetType() == btk.btkPoint.Marker and it.GetLabel()[0] !="*":
markerNames.append(it.GetLabel())
return markerNames
def createGeneralEvents(NEXUS, subject, acq, labels):
freq = acq.GetPointFrequency()
events = acq.GetEvents()
for ev in btk.Iterate(events):
if ev.GetLabel() in labels:
#print ev.GetTime()*freq
NEXUS.CreateAnEvent(str(subject), "General", str(ev.GetLabel()),
int(ev.GetTime() * freq), 0.0)
def smartGetEvents(acq, label, context):
evs = acq.GetEvents()
out = list()
for it in btk.Iterate(evs):
if it.GetContext() == context and it.GetLabel() == label:
out.append(it.GetFrame())
return out
def globalTransformationLabToOsim(acq, R_LAB_OSIM):
points = acq.GetPoints()
for it in btk.Iterate(points):
if it.GetType() == btk.btkPoint.Marker:
values = np.zeros(it.GetValues().shape)
for i in range(0, it.GetValues().shape[0]):
values[i, :] = np.dot(R_LAB_OSIM, it.GetValues()[i, :])
it.SetValues(values)
def applyValidFramesOnOutput(acq,validFrames):
validFrames = np.asarray(validFrames)
for it in btk.Iterate(acq.GetPoints()):
if it.GetType() in [btk.btkPoint.Angle, btk.btkPoint.Force, btk.btkPoint.Moment,btk.btkPoint.Power]:
values = it.GetValues()
for i in range(0,3):
values[:,i] = values[:,i] * validFrames
it.SetValues(values)
def clearEvents(acq,labels):
events= acq.GetEvents()
newEvents=btk.btkEventCollection()
for ev in btk.Iterate(events):
if ev.GetLabel() not in labels:
newEvents.InsertItem(ev)
acq.ClearEvents()
acq.SetEvents(newEvents)
def applyTranslators(acq, translators,keepInitial=False):
"""
Rename marker from translators
:Parameters:
- `acq` (btkAcquisition) - a btk acquisition instance
- `translators` (dict) - translators
- `keepInitial` (bool) - flag for avoiding to remove initial markers
example of translators :
"Translators" : {
"LASI":"L_ASIS",
"RASI":"",
}
2nd line means RASI is with the acq
"""
acqClone = btk.btkAcquisition.Clone(acq)
modifiedMarkerList = list()
# gather all labels
for it in translators.items():
wantedLabel,initialLabel = it[0],it[1]
if wantedLabel != initialLabel and initialLabel !="":
modifiedMarkerList.append(it[0])
modifiedMarkerList.append(it[1])
# Remove Modified Markers from Clone
for point in btk.Iterate(acq.GetPoints()):
if point.GetType() == btk.btkPoint.Marker:
label = point.GetLabel()
if label in modifiedMarkerList:
acqClone.RemovePoint(label)
# Add Modify markers to clone
for it in translators.items():
wantedLabel,initialLabel = it[0],it[1]
logging.debug("wantedLabel (%s) initialLabel (%s) " %(str(wantedLabel), str(initialLabel)))
if wantedLabel != initialLabel and initialLabel !="":
if isPointExist(acq,initialLabel):
logging.debug("Initial point (%s) renamed (%s) added into the c3d" %(str(initialLabel), str(wantedLabel)))
smartAppendPoint(acqClone,str(wantedLabel),acq.GetPoint(str(initialLabel)).GetValues(),PointType=btk.btkPoint.Marker) # modified marker
if keepInitial:
smartAppendPoint(acqClone,str(initialLabel),acq.GetPoint(str(initialLabel)).GetValues(),PointType=btk.btkPoint.Marker) # keep initial marker
else :
logging.debug("initialLabel (%s) doesn t exist " %(str(initialLabel)))
return acqClone
def applyOnValidFrames(acq, validFrames):
frameNumber = acq.GetPointFrameNumber()
for it in btk.Iterate(acq.GetPoints()):
if it.GetType() in [
btk.btkPoint.Angle, btk.btkPoint.Force, btk.btkPoint.Moment,
btk.btkPoint.Power
]:
for i in range(0, frameNumber):
if not validFrames[i]:
it.SetResidual(i, -1)
it.SetValue(i, 0, 0)
it.SetValue(i, 1, 0)
it.SetValue(i, 2, 0)
def run(self):
fa = self.m_acq.GetAnalogFrequency()
for analog in btk.Iterate(self.m_acq.GetAnalogs()):
for label in self.m_labels:
if analog.GetLabel() == label:
values = analog.GetValues()
valuesFilt = signal_processing.enveloppe(
values, self.m_fc, fa)
btkTools.smartAppendAnalog(self.m_acq,
label + "_Env",
valuesFilt,
desc="fc(" + str(self.m_fc) +
")")
def cleanAcq(acq):
nframes = acq.GetPointFrameNumber()
for it in btk.Iterate(acq.GetPoints()):
if it.GetType() in [
btk.btkPoint.Marker, btk.btkPoint.Scalar, btk.btkPoint.Angle,
btk.btkPoint.Force, btk.btkPoint.Moment, btk.btkPoint.Power
]:
values = it.GetValues()
if np.all(values == np.zeros(3)) or np.all(
values == np.array([180, 0, 180])):
LOGGER.logger.debug("point %s remove from acquisition" %
(it.GetLabel()))
acq.RemovePoint(it.GetLabel())
def getStartEndEvents(btkAcq,context,startLabel="Start", endLabel="End"):
events= btkAcq.GetEvents()
start=[]
end=[]
for ev in btk.Iterate(events):
if ev.GetContext()== utils.str(context) and ev.GetLabel()==utils.str(startLabel) :
start.append(ev.GetFrame())
if ev.GetContext()==utils.str(context) and ev.GetLabel()==utils.str(endLabel) :
end.append(ev.GetFrame())
if start==[] or end==[]:
return None,None
if len(start)>1 or len(end)>1:
raise("[pyCGM2]: You can t have multiple Start and End events" )
elif end<start:
raise("[pyCGM2]: wrong order ( start<end)" )
else:
return start[0],end[0]
def hasChild(md,mdLabel):
"""
Check if a label is within metadata
.. note::
btk has a HasChildren method. HasChild doesn t exist, you have to use MetadataIterator to loop metadata
:Parameters:
- `md` (btkMetadata) - a btk metadata instance
- `mdLabel` (str) - label of the metadata you want to check
"""
outMd = None
for itMd in btk.Iterate(md):
if itMd.GetLabel() == utils.str(mdLabel):
outMd = itMd
break
return outMd
def run(self, acq, filename, options):
ff = acq.GetFirstFrame()
lf = acq.GetLastFrame()
if "frameRange" in options.keys():
frameInit = options["frameRange"][0] - ff
frameEnd = options["frameRange"][1] - ff + 1
else:
frameInit = ff - ff
frameEnd = lf - ff + 1
errorState = False
indexes = []
# --- ground reaction force wrench ---
pfe = btk.btkForcePlatformsExtractor()
grwf = btk.btkGroundReactionWrenchFilter()
pfe.SetInput(acq)
pfc = pfe.GetOutput()
grwf.SetInput(pfc)
grwc = grwf.GetOutput()
grwc.Update()
fp_counter = 1
for fpIt in btk.Iterate(grwc):
force_Z = fpIt.GetForce().GetValues()[frameInit:frameEnd, 2]
max = np.max(force_Z)
if max != 0:
indexes = np.where(force_Z == max)
if indexes[0].shape[0] > 1:
LOGGER.logger.warning(
"[pyCGM2-Anomaly] - check Force plate (%s) of file [%s] - signal Fz seems saturated"
% (str(fp_counter), filename))
errorState = True
fp_counter += 1
self.anomaly["Output"] = indexes
self.anomaly["ErrorState"] = errorState
def getNumberOfModelOutputs(acq):
n_angles = 0
n_forces = 0
n_moments = 0
n_powers = 0
for it in btk.Iterate(acq.GetPoints()):
if it.GetType() == btk.btkPoint.Angle:
n_angles += 1
if it.GetType() == btk.btkPoint.Force:
n_forces += 1
if it.GetType() == btk.btkPoint.Moment:
n_moments += 1
if it.GetType() == btk.btkPoint.Power:
n_powers += 1
return n_angles, n_forces, n_moments, n_powers
def findNearestMarker(acq,i,marker,markerNames=None):
values = acq.GetPoint(utils.str(marker)).GetValues()[i,:]
if markerNames is None:
markerNames=[]
for it in btk.Iterate(acq.GetPoints()):
if it.GetType() == btk.btkPoint.Marker and it.GetLabel()[0] !="*" and it.GetLabel() != utils.str(marker):
markerNames.append(it.GetLabel())
j=0
out = np.zeros((len(markerNames),3))
for name in markerNames :
out[j,:] = acq.GetPoint(name).GetValues()[i,:]
j+=1
tree = spatial.KDTree(out)
dist,index = tree.query(values)
return markerNames[index],dist
def temporalPlot(figAxis,
acq,
pointLabel,
axis,
pointLabelSuffix=None,
color=None,
title=None,
xlabel=None,
ylabel=None,
ylim=None,
legendLabel=None,
customLimits=None):
'''
**Description :** plot descriptive statistical (average and sd corridor) gait traces from a pyCGM2.Processing.analysis.Analysis instance
:Parameters:
- `figAxis` (matplotlib::Axis )
- `acq` (ma.Trial) - a Structure item of an Analysis instance built from AnalysisFilter
:Return:
- matplotlib figure
**Usage**
.. code:: python
'''
pointLabel = pointLabel + "_" + pointLabelSuffix if pointLabelSuffix is not None else pointLabel
flag = btkTools.isPointExist(acq, pointLabel)
if flag:
point = acq.GetPoint(pointLabel)
lines = figAxis.plot(point.GetValues()[:, axis], '-', color=color)
appf = 1
else:
flag = btkTools.isAnalogExist(acq, pointLabel)
if flag:
analog = acq.GetAnalog(pointLabel)
lines = figAxis.plot(analog.GetValues()[:, axis], '-', color=color)
appf = acq.GetNumberAnalogSamplePerFrame()
if legendLabel is not None and flag: lines[0].set_label(legendLabel)
if title is not None: figAxis.set_title(title, size=8)
figAxis.tick_params(axis='x', which='major', labelsize=6)
figAxis.tick_params(axis='y', which='major', labelsize=6)
if xlabel is not None: figAxis.set_xlabel(xlabel, size=8)
if ylabel is not None: figAxis.set_ylabel(ylabel, size=8)
if ylim is not None: figAxis.set_ylim(ylim)
if flag:
for ev in btk.Iterate(acq.GetEvents()):
colorContext = plotUtils.colorContext(ev.GetContext())
if ev.GetLabel() == "Foot Strike":
figAxis.axvline(x=(ev.GetFrame() - acq.GetFirstFrame()) * appf,
color=colorContext,
linestyle="-")
if ev.GetLabel() == "Foot Off":
figAxis.axvline(x=(ev.GetFrame() - acq.GetFirstFrame()) * appf,
color=colorContext,
linestyle="--")
def markerFiltering(btkAcq, markers, order=2, fc=6, zerosFiltering=True):
"""
Low-pass filtering of all points in an acquisition
:Parameters:
- `btkAcq` (btkAcquisition) - btk acquisition instance
- `fc` (double) - cut-off frequency
- `order` (double) - order of the low-pass filter
"""
def filterZeros(array, b, a):
N = len(array)
indexes = list(range(0, N))
for i in range(0, N):
if array[i] == 0:
indexes[i] = -1
splitdata = [
x[x != 0] for x in np.split(array,
np.where(array == 0)[0])
if len(x[x != 0])
]
splitIndexes = [
x[x != -1] for x in np.split(indexes,
np.where(indexes == -1)[0])
if len(x[x != -1])
]
filtValues_section = list()
for data in splitdata:
padlen = 3 * max(
len(a), len(b)
) # default as defined in https://docs.scipy.org/doc/scipy/reference/generated/scipy.signal.filtfilt.html
if len(data) <= padlen:
padlen = len(data) - 1
filtValues_section.append(
signal.filtfilt(b, a, data, padlen=padlen, axis=0))
indexes = np.concatenate(splitIndexes) if splitIndexes != [] else []
values = np.concatenate(
filtValues_section) if filtValues_section != [] else []
out = np.zeros((N))
j = 0
for i in indexes:
out[i] = values[j]
j += 1
return out
fp = btkAcq.GetPointFrequency()
bPoint, aPoint = signal.butter(order, fc / (fp * 0.5), btype='lowpass')
for pointIt in btk.Iterate(btkAcq.GetPoints()):
if pointIt.GetType() == btk.btkPoint.Marker and pointIt.GetLabel(
) in markers:
label = pointIt.GetLabel()
if zerosFiltering:
x = filterZeros(pointIt.GetValues()[:, 0], bPoint, aPoint)
y = filterZeros(pointIt.GetValues()[:, 1], bPoint, aPoint)
z = filterZeros(pointIt.GetValues()[:, 2], bPoint, aPoint)
else:
x = signal.filtfilt(bPoint,
aPoint,
pointIt.GetValues()[:, 0],
axis=0)
y = signal.filtfilt(bPoint,
aPoint,
pointIt.GetValues()[:, 1],
axis=0)
z = signal.filtfilt(bPoint,
aPoint,
pointIt.GetValues()[:, 2],
axis=0)
btkAcq.GetPoint(label).SetValues(np.array([x, y, z]).transpose())
def GetAnalogNames(acq):
analogNames=[]
for it in btk.Iterate(acq.GetAnalogs()):
analogNames.append(it.GetLabel())
return analogNames
def check(self):
events = self.acq.GetEvents()
if events != []:
events_L = list()
events_R = list()
for ev in btk.Iterate(events):
if ev.GetContext() == "Left":
events_L.append(ev)
if ev.GetContext() == "Right":
events_R.append(ev)
if events_L != [] and events_R != []:
labels = [
it.GetLabel() for it in btk.Iterate(events)
if it.GetLabel() in ["Foot Strike", "Foot Off"]
]
frames = [
it.GetFrame() for it in btk.Iterate(events)
if it.GetLabel() in ["Foot Strike", "Foot Off"]
]
init = labels[0]
for i in range(1, len(labels)):
label = labels[i]
frame = frames[i]
if label == init:
LOGGER.logger.error(
"[pyCGM2-Checking] two consecutive (%s) detected at frame (%i)"
% ((label), frame))
if self.exceptionMode:
raise Exception(
"[pyCGM2-Checking] two consecutive (%s) detected at frame (%i)"
% ((label), frame))
self.state = False
init = label
if events_L != []:
init = events_L[0].GetLabel()
if len(events_L) > 1:
for i in range(1, len(events_L)):
label = events_L[i].GetLabel()
if label == init:
LOGGER.logger.error(
"[pyCGM2-Checking] Wrong Left Event - two consecutive (%s) detected at frane (%i)"
% ((label), events_L[i].GetFrame()))
if self.exceptionMode:
raise Exception(
"[pyCGM2-Checking] Wrong Left Event - two consecutive (%s) detected at frane (%i)"
% ((label), events_L[i].GetFrame()))
self.state = False
init = label
else:
LOGGER.logger.warning("Only one left events")
self.state = False
if events_R != []:
init = events_R[0].GetLabel()
if len(events_R) > 1:
for i in range(1, len(events_R)):
label = events_R[i].GetLabel()
if label == init:
LOGGER.logger.error(
"[pyCGM2-Checking] Wrong Right Event - two consecutive (%s) detected at frane (%i)"
% ((label), events_R[i].GetFrame()))
if self.exceptionMode:
raise Exception(
"[pyCGM2-Checking] Wrong Right Event - two consecutive (%s) detected at frane (%i)"
% ((label), events_R[i].GetFrame()))
self.state = False
init = label
else:
LOGGER.logger.warning("Only one right events ")
self.state = False
else:
LOGGER.logger.error("[pyCGM2-Checking] No events are in trial")
if self.exceptionMode:
raise Exception(
"[pyCGM2-Checking] No events are in the trials")
self.state = False
def markerUnitConverter(acq,unitOffset):
for it in btk.Iterate(acq.GetPoints()):
if it.GetType() == btk.btkPoint.Marker:
values = it.GetValues()
it.SetValues(values*unitOffset)
def convertBtkAcquisition(acq, returnType="Trial"):
root = ma.Node('root')
trial = ma.Trial("Trial", root)
framerate = acq.GetPointFrequency()
firstFrame = acq.GetFirstFrame()
numberAnalogSamplePerFrame = acq.GetNumberAnalogSamplePerFrame()
analogFramerate = acq.GetAnalogFrequency()
if firstFrame == 1:
time_init = 0.0
else:
time_init = firstFrame / framerate
for it in btk.Iterate(acq.GetPoints()):
label = it.GetLabel()
values = it.GetValues()
residuals = it.GetResiduals()
desc = it.GetDescription()
data = np.zeros((values.shape[0], 4))
data[:, 0:3] = values
data[:, 3] = residuals[:, 0]
if it.GetType() == btk.btkPoint.Marker:
ts = ma.TimeSequence(str(label), 4, data.shape[0], framerate,
time_init, ma.TimeSequence.Type_Marker, "mm",
trial.timeSequences())
elif it.GetType() == btk.btkPoint.Angle:
ts = ma.TimeSequence(str(label), 4, data.shape[0], framerate,
time_init, ma.TimeSequence.Type_Angle, "Deg",
trial.timeSequences())
elif it.GetType() == btk.btkPoint.Force:
ts = ma.TimeSequence(str(label), 4, data.shape[0], framerate,
time_init, ma.TimeSequence.Type_Force,
"N.Kg-1", trial.timeSequences())
elif it.GetType() == btk.btkPoint.Moment:
ts = ma.TimeSequence(str(label), 4, data.shape[0], framerate,
time_init, ma.TimeSequence.Type_Moment,
"Nmm.Kg-1", trial.timeSequences())
elif it.GetType() == btk.btkPoint.Power:
ts = ma.TimeSequence(str(label), 4, data.shape[0], framerate,
time_init, ma.TimeSequence.Type_Power,
"Watt.Kg-1", trial.timeSequences())
else:
logging.warning(
"[pyCGM2] point [%s] not copied into openma trial" % (label))
ts.setData(data)
ts.setDescription(desc)
for it in btk.Iterate(acq.GetAnalogs()):
label = it.GetLabel()
values = it.GetValues()
desc = it.GetDescription()
data = values
ts = ma.TimeSequence(str(label), 1, data.shape[0], analogFramerate,
time_init, ma.TimeSequence.Type_Analog, "V", 1.0,
0.0, [-10.0, 10.0], trial.timeSequences())
ts.setData(data)
ts.setDescription(desc)
for it in btk.Iterate(acq.GetEvents()):
label = it.GetLabel()
time = it.GetTime()
context = it.GetContext()
subject = it.GetSubject()
ev = ma.Event(label, time, context, str(subject), trial.events())
sortedEvents(trial)
if returnType == "Trial":
return trial
else:
return root
