def calculateRawEMG(self):
origEMGNames = list()
emgData = {}
noSignals = 0
for filename in self.fileNames:
acq = qtools.fileOpen(filename)
noSignals = acq.GetAnalogNumber()
for number in range(
noSignals): # it is assumed same signals are in all trials
signal = acq.GetAnalog(number)
signalLabel = signal.GetLabel()
if "Moment" not in signalLabel and "Force" not in signalLabel:
origEMGNames.append(signal.GetLabel())
for origSigName, ourSigName in signalMapping.emgNameMap.iteritems():
if origSigName in origEMGNames and ourSigName is not "":
emgData[ourSigName] = {}
for filename in self.fileNames:
acq = qtools.fileOpen(filename)
measurementName = path.basename(filename)
measurementName = measurementName.replace('.c3d', '')
signal = acq.GetAnalog(origSigName)
values = np.array(signal.GetValues()[:, 0])
emgData[ourSigName][measurementName] = {}
emgData[ourSigName][measurementName] = values
return emgData
def getForceData(self, acq, frame, noFrames):
pfe = btk.btkForcePlatformsExtractor()
grwf = btk.btkGroundReactionWrenchFilter()
pfe.SetInput(acq)
pfc = pfe.GetOutput()
grwf.SetInput(pfc)
grwc = grwf.GetOutput()
grwc.Update()
for filename in self.fileNames:
forceData = []
acq = qtools.fileOpen(filename)
for forceNumber in range(grwc.GetItemNumber()):
forceData.append({
"id": forceNumber + 1,
"forceCount": 1,
"forcenumber": 2951,
"data": {
"force":
list(
self.resampleForceData(grwc, forceNumber, 0,
noFrames)[frame, :]),
"moment":
list(
self.resampleForceData(grwc, forceNumber, 1,
noFrames)[frame, :]),
"position":
list(
self.resampleForceData(grwc, forceNumber, 2,
noFrames)[frame, :])
}
})
return forceData
def getValidC3dList(self, basenameOnly):
measurementNames = []
fileNames = []
# check that pluginGait model calculations exist
# check that events exist
for filename in self.c3dFileList:
origLabelNames = []
acq = qtools.fileOpen(filename)
noMarkers = range(acq.GetPointNumber())
measurementName = path.basename(filename)
measurementName = measurementName.replace('.c3d', '')
for number in noMarkers: # it is assumed that same signals are in all trials
marker = acq.GetPoint(number)
origLabelNames.append(marker.GetLabel())
if "LAnkleAngles" in origLabelNames and acq.GetEventNumber() > 0:
measurementNames.append(measurementName)
fileNames.append(filename)
if basenameOnly == True:
out = measurementNames
else:
out = fileNames
return out
def getMetaValue(self, measurementName, groupLabelName, scalarName):
acq = qtools.fileOpen(self.workingDirectory + measurementName + ".c3d")
md = acq.GetMetaData()
fieldFormat = md.FindChild(groupLabelName).value().FindChild(
scalarName).value().GetInfo().GetFormatAsString()
scalarValue = list()
if fieldFormat == "Char":
sValue = md.FindChild(groupLabelName).value().FindChild(
scalarName).value().GetInfo().ToString()
sValue = list(sValue)
scalarValue = [i.rstrip() for i in sValue]
else:
scalarValue = md.FindChild(groupLabelName).value().FindChild(
scalarName).value().GetInfo().ToDouble()
return scalarValue
def getSegAngles(self):
for filename in self.fileNames:
measurementName = os.path.basename(filename)
measurementName = measurementName.replace('.c3d', '')
if '1' in measurementName: #temporaty
acq = qtools.fileOpen(filename)
noFrames = acq.GetLastFrame() - acq.GetFirstFrame()
sig = {}
for sigName in self.segmentRotList:
if qtools.isPointExist(acq, sigName + 'O'):
sig[sigName] = np.array([0, 0, 0])
for frame in range(noFrames):
sig[sigName] = np.vstack(
(sig[sigName],
self.combineCardanSeqPerFrame(
acq, sigName.split(), frame)))
return sig
def calculateEvents(self, forceThreshold):
self.forceThreshold = forceThreshold
eventLabels = dict()
eventsGroupped = dict()
eventData = dict()
null = None
for filename in self.fileNames:
acq = qtools.fileOpen(filename)
measurementName = path.basename(filename)
measurementName = measurementName.replace('.c3d', '')
eventLabels[measurementName] = []
frameRate = acq.GetPointFrequency()
noEvents = range(acq.GetEventNumber())
eventTimesLHS = list()
eventTimesRHS = list()
eventTimesLTO = list()
eventTimesRTO = list()
for number in noEvents:
firstFrame = acq.GetFirstFrame()
lastFrame = acq.GetLastFrame()
# extract the event of the aquisition
event = acq.GetEvent(number)
eventFrame = event.GetFrame() - firstFrame
eventTime = eventFrame / frameRate
eventName = event.GetLabel()
eventSide = event.GetContext(
) # return a string representing the Context
eventLabelOrig = eventSide + " " + eventName
eventLabel = qtools.renameSignal(signalMapping.eventNameMap,
eventLabelOrig)
if eventLabel not in eventLabels[
measurementName] and eventLabel != 'None':
eventLabels[measurementName].append(eventLabel)
if eventLabel == "LHS":
eventTimesLHS.append(eventTime)
eventsGroupped[measurementName + "_" +
eventLabel] = eventTimesLHS
if self.checkSignalExists(acq, measurementName,
'LGroundReactionForce'):
eventTimeLON = self.getOnOffEvent(
acq, measurementName, 'LGroundReactionForce',
frameRate, firstFrame, lastFrame, eventFrame,
eventTime, 'on')
if eventTimeLON:
eventsGroupped[measurementName +
"_LON"] = eventTimeLON
eventLabels[measurementName].append('LON')
elif eventLabel == "RHS":
eventTimesRHS.append(eventTime)
eventsGroupped[measurementName + "_" +
eventLabel] = eventTimesRHS
if self.checkSignalExists(acq, measurementName,
'RGroundReactionForce'):
eventTimeRON = self.getOnOffEvent(
acq, measurementName, 'RGroundReactionForce',
frameRate, firstFrame, lastFrame, eventFrame,
eventTime, 'on')
if eventTimeRON:
eventsGroupped[measurementName +
"_RON"] = eventTimeRON
eventLabels[measurementName].append('RON')
elif eventLabel == "LTO":
eventTimesLTO.append(eventTime)
eventsGroupped[measurementName + "_" +
eventLabel] = eventTimesLTO
if self.checkSignalExists(acq, measurementName,
'LGroundReactionForce'):
eventTimeLOFF = self.getOnOffEvent(
acq, measurementName, 'LGroundReactionForce',
frameRate, firstFrame, lastFrame, eventFrame,
eventTime, 'off')
if eventTimeLOFF:
eventsGroupped[measurementName +
"_LOFF"] = eventTimeLOFF
eventLabels[measurementName].append('LOFF')
elif eventLabel == "RTO":
eventTimesRTO.append(eventTime)
eventsGroupped[measurementName + "_" +
eventLabel] = eventTimesRTO
if self.checkSignalExists(acq, measurementName,
'RGroundReactionForce'):
eventTimeROFF = self.getOnOffEvent(
acq, measurementName, 'RGroundReactionForce',
frameRate, firstFrame, lastFrame, eventFrame,
eventTime, 'off')
if eventTimeROFF:
eventsGroupped[measurementName +
"_ROFF"] = eventTimeROFF
eventLabels[measurementName].append('ROFF')
for eventLabel in eventLabels[measurementName]:
eventData[measurementName + "_" + eventLabel] = {
"measurement": measurementName,
"values":
eventsGroupped[measurementName + "_" + eventLabel],
"rate": null
}
return (eventData, eventLabels)
def getFrameAndAnalogRateFromC3D(filePath):
acq = qtools.fileOpen(filePath)
frameRate = acq.GetPointFrequency()
analogRate = acq.GetAnalogFrequency()
return frameRate, analogRate
def createJson(self):
sig = {}
for filename in self.fileNames:
measurementName = os.path.basename(filename)
measurementName = measurementName.replace('.c3d', '')
if '1' in measurementName: #temporaty
acq = qtools.fileOpen(filename)
noFrames = acq.GetLastFrame() - acq.GetFirstFrame()
frames = []
sig[measurementName] = {}
for frame in range(noFrames):
fr = frame + 1
frames.append({
"frame":
fr,
"markers":
self.getMarkersPerFrame(acq, self.markerList, frame),
"segmentPos":
self.getMarkersPerFrame(acq, self.segmentList, frame),
"segmentRot":
self.combineCardanSeqPerFrame(acq, self.segmentRotList,
frame),
"force":
self.getForceData(acq, frame, noFrames)
})
sig[measurementName] = self.combineCardanSeqPerFrame(
acq, self.segmentRotList, frame)
root = {
"startTime":
acq.GetFirstFrame() / acq.GetPointFrequency(),
"endTime": (acq.GetLastFrame() - acq.GetFirstFrame()) /
acq.GetPointFrequency(),
"frameRate":
acq.GetPointFrequency(),
"uncroppedLength":
acq.GetLastFrame() / acq.GetPointFrequency(),
"labels": [self.labels(acq, self.markerList)],
"bones":
self.bones(acq),
"segments":
self.segments(acq),
"frames":
frames,
"force": {
"lengthUnit": "mm",
"forceUnit": "F",
"plates": self.calculateForcePlateInfo(acq)
}
}
# with open(self.workingDirectory + measurementName + '-3d-data.json', 'w') as f:
# json.dump(root, f, indent=4,sort_keys=True)
with open(
'E:\\Qualisys_repository\\q3dv\\examples\\data\\plugingait.js',
'w') as f: #temporaty
f.write('var plugingait = ') #temporaty
with open(
'E:\\Qualisys_repository\\q3dv\\examples\\data\\plugingait.js',
'a') as f: #temporaty
json.dump(root, f, indent=4, sort_keys=True) #temporaty
return root
def getAllGVS(self):
mapSignalNames = [
"Left Pelvic Angles", "Left Hip Angles", "Left Knee Angles",
"Left Ankle Angles", "Left Foot Progression",
"Right Pelvic Angles", "Right Hip Angles", "Right Knee Angles",
"Right Ankle Angles", "Right Foot Progression"
]
components = {'X', 'Y', 'Z'}
measuredValuesNormalized = {}
gvs = {}
gvsLn = {}
tree = ET.parse(
path.join(qtmWebGaitReport.GAIT_WEB_REPORT_PATH,
"qtmWebGaitReport", "Normatives", "normatives.xml"))
xmlRoot = tree.getroot()
for sigName in mapSignalNames:
measuredValuesNormalized[sigName] = {}
for component in components:
gvs[sigName + "_" + component + "_gvs"] = {}
gvsLn[sigName + "_" + component + "_gvs_ln_mean"] = {}
normValues = self.getNormValuesFromV3DXml(
xmlRoot, sigName + "_" + component)
if normValues is not "":
if component == "X":
i = 0
elif component == "Y":
i = 1
elif component == "Z":
i = 2
for filename in self.fileNames:
acq = qtools.fileOpen(filename)
measurementName = path.basename(filename)
measurementName = measurementName.replace('.c3d', '')
measuredValuesNormalized[sigName][measurementName] = {}
gvs[sigName + "_" + component +
"_gvs"][measurementName] = {}
gvsLn[sigName + "_" + component +
"_gvs_ln_mean"][measurementName] = {}
for origSigName, ourSigName in signalMapping.sigNameMap.iteritems(
):
if ourSigName == sigName:
pigSigName = origSigName
signal = acq.GetPoint(pigSigName)
measuredValues = scipy.signal.resample(
signal.GetValues(), 101) # normalize to 101 points
measuredValuesNormalized[sigName][
measurementName] = measuredValues
sub = measuredValuesNormalized[sigName][
measurementName][:, i] - normValues
gvs[sigName + "_" + component +
"_gvs"][measurementName] = qtools.rootMeanSquared(
sub)
gvsLn[sigName + "_" + component +
"_gvs_ln_mean"][measurementName] = np.log(
gvs[sigName + "_" + component +
"_gvs"][measurementName])
return (gvs, gvsLn)
def measurementInfo(self, extra_settings={}):
info = []
for filename in self.fileNames:
acq = qtools.fileOpen(filename)
measurementName = path.basename(filename)
measurementName = measurementName.replace('.c3d', '')
val = acq.GetDuration()
startOffset = acq.GetFirstFrame() / acq.GetPointFrequency()
frameRate = acq.GetPointFrequency()
originalDuration = acq.GetDuration()
creation_date = datetime.fromtimestamp(get_creation_date(filename))
creationDate = str(creation_date.date())
creationTime = str(creation_date.time())
diagnosis = ""
patientName = "UNSPECIFIED"
bodyHeight = 0
bodyWeight = 0
video_filenames = get_mp4_filenames(
get_parent_folder_absolute_path(self.workingDirectory))
resources = create_resources(video_filenames, extra_settings)
fields = [
{
"id": "Creation date",
"value": creationDate,
"type": "text"
},
{
"id": "Creation time",
"value": creationTime,
"type": "text"
},
{
"id": "Diagnosis",
"value": diagnosis,
"type": "text"
},
{
"id": "Last name",
"value": patientName,
"type": "text"
},
{
"id": "Height",
"value": bodyHeight,
"type": "text"
},
{
"id": "Weight",
"value": bodyWeight,
"type": "text"
},
]
info.append({
"duration": val,
"startOffset": startOffset,
"originalDuration": originalDuration,
"rate": frameRate,
"id": measurementName,
"fields": fields,
"resources": resources
})
return info
def calculateTimeseries(self):
#metaObj = metadata.Metadata(self.workingDirectory)
timeseries = dict()
components = {'X', 'Y', 'Z'}
origLabelNames = list()
origLabels = {}
for filename in self.fileNames: # create list of signals. Make sure that missing signal in one of trial will not break it
measurementName = path.basename(filename)
measurementName = measurementName.replace('.c3d', '')
origLabels[measurementName] = {}
origLabelNamesSelected = list()
acq = qtools.fileOpen(filename)
md = acq.GetMetaData()
if "PROCESSING" in _getSectionFromMd(md):
processingMd = acq.GetMetaData().FindChild(
"PROCESSING").value()
if "Weight" in _getSectionFromMd(processingMd):
mass = processingMd.FindChild(
"Weight").value().GetInfo().ToString()
elif "Bodymass" in _getSectionFromMd(processingMd):
mass = processingMd.FindChild(
"Bodymass").value().GetInfo().ToString()
noMarkers = range(acq.GetPointNumber())
for number in noMarkers:
marker = acq.GetPoint(number)
origLabelNames.append(marker.GetLabel())
for origLabelName in origLabelNames:
if origLabelName in signalMapping.sigNameMap and signalMapping.sigNameMap.get(
origLabelName) is not "":
origLabelNamesSelected.append(origLabelName)
origLabels[measurementName] = origLabelNamesSelected
for origLabelNameSelected in origLabelNamesSelected:
if signalMapping.sigNameMap.get(origLabelNameSelected) is not "":
ourSigName = signalMapping.sigNameMap.get(
origLabelNameSelected)
for component in components:
timeseries[ourSigName + "_" + component] = {}
for filename in self.fileNames:
acq = qtools.fileOpen(filename)
measurementName = path.basename(filename)
measurementName = measurementName.replace('.c3d', '')
if component == "X":
i = 0
elif component == "Y":
i = 1
elif component == "Z":
i = 2
bodyMass = float(mass[0])
constant2 = 0
if "Moment" in ourSigName:
constant1 = 1000 # converts from mm to m
elif "GRF" in ourSigName:
if component == "X":
i = 1
constant1 = bodyMass * 9.81 * -1
elif component == "Y":
i = 0
constant1 = bodyMass * 9.81 * -1
else:
constant1 = bodyMass * 9.81
elif "Ankle Angles" in ourSigName and component == "Y":
constant1 = -1
elif "Prog" in ourSigName and component == "X":
constant1 = -1
constant2 = -90
else:
constant1 = 1
if "Power" in ourSigName:
i = 2
if origLabelNameSelected in origLabels[
measurementName]:
marker = acq.GetPoint(origLabelNameSelected)
values = (np.array(marker.GetValues()[:, i]) /
constant1) + constant2
timeseries[ourSigName + "_" +
component][measurementName] = {}
timeseries[ourSigName + "_" +
component][measurementName] = values
return timeseries