def test_sample0(self):
DATA_PATH = MAIN_PATH = pyCGM2.TEST_DATA_PATH + "GaitModels\CGM1\\fullBody-native-noOptions\\"
staticFilename = "static.c3d"
acqStatic = btkTools.smartReader(DATA_PATH + staticFilename)
markerDiameter = 14
leftFlatFoot = False
rightFlatFoot = False
headStraight = False
pointSuffix = "test"
vskFile = vskTools.getVskFiles(DATA_PATH)
vsk = vskTools.Vsk(DATA_PATH + "New Subject.vsk")
required_mp, optional_mp = vskTools.getFromVskSubjectMp(vsk,
resetFlag=True)
# calibration according CGM1
model, finalAcqStatic = cgm1.calibrate(DATA_PATH,
staticFilename,
None,
required_mp,
optional_mp,
leftFlatFoot,
rightFlatFoot,
headStraight,
markerDiameter,
pointSuffix,
displayCoordinateSystem=True)
# no fitting operation, only checking of forceplateAssembly
gaitFilename = "gait1.c3d"
acqGait = btkTools.smartReader(DATA_PATH + gaitFilename)
mfpa = None
mappedForcePlate = forceplates.matchingFootSideOnForceplate(acqGait,
mfpa=mfpa)
forceplates.addForcePlateGeneralEvents(acqGait, mappedForcePlate)
logging.warning("Manual Force plate assignment : %s" %
mappedForcePlate)
# assembly foot and force plate
modelFilters.ForcePlateAssemblyFilter(
model,
acqGait,
mappedForcePlate,
leftSegmentLabel="Left Foot",
rightSegmentLabel="Right Foot").compute(
pointLabelSuffix=pointSuffix)
testingUtils.plotComparisonOfPoint(acqGait, "RGroundReactionForce",
"test")
testingUtils.plotComparisonOfPoint(acqGait, "RGroundReactionMoment",
"test")
def test_FullBody_noOptions(self):
DATA_PATH = MAIN_PATH = pyCGM2.TEST_DATA_PATH + "LowLevel\\uncropped data\\cgm1\\"
staticFilename = "static.c3d"
DATA_PATH_OUT = pyCGM2.TEST_DATA_PATH_OUT+"LowLevel\\uncropped data\\cgm1\\"
files.createDir(DATA_PATH_OUT)
markerDiameter=14
leftFlatFoot = True
rightFlatFoot = True
headStraight = True
pointSuffix = ""
vskFile = vskTools.getVskFiles(DATA_PATH)
vsk = vskTools.Vsk(DATA_PATH + "New Subject.vsk")
required_mp,optional_mp = vskTools.getFromVskSubjectMp(vsk, resetFlag=True)
model,finalAcqStatic = cgm1.calibrate(DATA_PATH,
staticFilename,
None,
required_mp,
optional_mp,
leftFlatFoot,
rightFlatFoot,
headStraight,
markerDiameter,
pointSuffix,
displayCoordinateSystem=True)
# btkTools.smartWriter(finalAcqStatic, str( staticFilename[:-4]+"-pyCGM2modelled.c3d"))
# logging.info("Static Calibration -----> Done")
gaitFilename="gait1.c3d"
acqGait0 = btkTools.smartReader(DATA_PATH + gaitFilename)
trackingMarkers = model.getTrackingMarkers(acqGait0)
validFrames,vff,vlf = btkTools.findValidFrames(acqGait0,trackingMarkers)
mfpa = None
reconstructFilenameLabelled = gaitFilename
acqGait = cgm1.fitting(model,DATA_PATH, reconstructFilenameLabelled,
None,
markerDiameter,
pointSuffix,
mfpa,
enums.MomentProjection.Proximal,
displayCoordinateSystem=True)
btkTools.smartWriter(acqGait, DATA_PATH_OUT+"//gait1-processed.c3d")
def test_CGM1_FullBody_noOptions_uncorrectUpperLimbMarker(self):
DATA_PATH = pyCGM2.TEST_DATA_PATH + "Scenarii\different static and dynamic marker set\CGM1-fullBody\\"
staticFilename = "static.c3d"
acqStatic = btkTools.smartReader(DATA_PATH + staticFilename)
markerDiameter = 14
leftFlatFoot = False
rightFlatFoot = False
headStraight = False
pointSuffix = "test"
vskFile = vskTools.getVskFiles(DATA_PATH)
vsk = vskTools.Vsk(DATA_PATH + "New Subject.vsk")
required_mp, optional_mp = vskTools.getFromVskSubjectMp(vsk,
resetFlag=True)
model, finalAcqStatic, error = cgm1.calibrate(
DATA_PATH,
staticFilename,
None,
required_mp,
optional_mp,
leftFlatFoot,
rightFlatFoot,
headStraight,
markerDiameter,
pointSuffix,
displayCoordinateSystem=True)
# btkTools.smartWriter(finalAcqStatic, str( staticFilename[:-4]+"-pyCGM2modelled.c3d"))
LOGGER.logger.info("Static Calibration -----> Done")
# case 1 - one marker on the upper limb misses
gaitFilename = "gait1_noRFIN.c3d"
mfpa = None
reconstructFilenameLabelled = gaitFilename
acqGait, error = cgm1.fitting(model,
DATA_PATH,
reconstructFilenameLabelled,
None,
markerDiameter,
pointSuffix,
mfpa,
enums.MomentProjection.Proximal,
displayCoordinateSystem=True)
assert model.m_bodypart == enums.BodyPart.FullBody
def test_CGM1_FullBody_noOptions_noFP(self):
DATA_PATH = pyCGM2.TEST_DATA_PATH + "GaitModels\CGM1\\fullBody-native-noOptions - noFP\\"
staticFilename = "static.c3d"
acqStatic = btkTools.smartReader(DATA_PATH + staticFilename)
markerDiameter=14
leftFlatFoot = False
rightFlatFoot = False
headStraight = False
pointSuffix = "test"
vskFile = vskTools.getVskFiles(DATA_PATH)
vsk = vskTools.Vsk(DATA_PATH + "New Subject.vsk")
required_mp,optional_mp = vskTools.getFromVskSubjectMp(vsk, resetFlag=True)
model,finalAcqStatic = cgm1.calibrate(DATA_PATH,
staticFilename,
None,
required_mp,
optional_mp,
leftFlatFoot,
rightFlatFoot,
headStraight,
markerDiameter,
pointSuffix,
displayCoordinateSystem=True)
# btkTools.smartWriter(finalAcqStatic, str( staticFilename[:-4]+"-pyCGM2modelled.c3d"))
# logging.info("Static Calibration -----> Done")
gaitFilename="gait1.c3d"
mfpa = None
reconstructFilenameLabelled = gaitFilename
acqGait = cgm1.fitting(model,DATA_PATH, reconstructFilenameLabelled,
None,
markerDiameter,
pointSuffix,
mfpa,
enums.MomentProjection.Proximal,
displayCoordinateSystem=True)
btkTools.smartWriter(acqGait, "gait1-pyCGM2modelled.c3d")
def main(sessionFilename,
createPDFReport=True,
checkEventsInMokka=True,
anomalyException=False):
detectAnomaly = False
LOGGER.set_file_handler("pyCGM2-QTM-Workflow.log")
LOGGER.logger.info("------------QTM - pyCGM2 Workflow---------------")
sessionXML = files.readXml(os.getcwd() + "\\", sessionFilename)
sessionDate = files.getFileCreationDate(os.getcwd() + "\\" +
sessionFilename)
#---------------------------------------------------------------------------
#management of the Processed foldercd
DATA_PATH = os.getcwd() + "\\" + "processed\\"
files.createDir(DATA_PATH)
staticMeasurement = qtmTools.findStatic(sessionXML)
calibrateFilenameLabelled = qtmTools.getFilename(staticMeasurement)
if not os.path.isfile(DATA_PATH + calibrateFilenameLabelled):
shutil.copyfile(os.getcwd() + "\\" + calibrateFilenameLabelled,
DATA_PATH + calibrateFilenameLabelled)
LOGGER.logger.info(
"qualisys exported c3d file [%s] copied to processed folder" %
(calibrateFilenameLabelled))
if qtmTools.findKneeCalibration(
sessionXML, "Left") is not None or qtmTools.findKneeCalibration(
sessionXML, "Right") is not None:
LOGGER.logger.info(
" the %s not accept functional knee calibration !!" % (MODEL))
dynamicMeasurements = qtmTools.findDynamic(sessionXML)
for dynamicMeasurement in dynamicMeasurements:
reconstructFilenameLabelled = qtmTools.getFilename(dynamicMeasurement)
# marker
order_marker = int(
float(dynamicMeasurement.Marker_lowpass_filter_order.text))
fc_marker = float(
dynamicMeasurement.Marker_lowpass_filter_frequency.text)
if not os.path.isfile(DATA_PATH + reconstructFilenameLabelled):
shutil.copyfile(os.getcwd() + "\\" + reconstructFilenameLabelled,
DATA_PATH + reconstructFilenameLabelled)
LOGGER.logger.info(
"qualisys exported c3d file [%s] copied to processed folder" %
(reconstructFilenameLabelled))
acq = btkTools.smartReader(
str(DATA_PATH + reconstructFilenameLabelled))
acq, zeniState = eventDetector.zeni(
acq,
fc_lowPass_marker=fc_marker,
order_lowPass_marker=order_marker)
if zeniState:
btkTools.smartWriter(
acq, str(DATA_PATH + reconstructFilenameLabelled))
if checkEventsInMokka:
cmd = "Mokka.exe \"%s\"" % (
str(DATA_PATH + reconstructFilenameLabelled))
os.system(cmd)
# --------------------------GLOBAL SETTINGS ------------------------------------
# global setting ( in user/AppData)
if os.path.isfile(pyCGM2.PYCGM2_APPDATA_PATH + "CGM1-pyCGM2.settings"):
settings = files.openFile(pyCGM2.PYCGM2_APPDATA_PATH,
"CGM1-pyCGM2.settings")
else:
settings = files.openFile(pyCGM2.PYCGM2_SETTINGS_FOLDER,
"CGM1-pyCGM2.settings")
# --------------------------MP ------------------------------------
required_mp, optional_mp = qtmTools.SubjectMp(sessionXML)
# translators management
translators = files.getTranslators(os.getcwd() + "\\", "CGM1.translators")
if not translators: translators = settings["Translators"]
# --------------------------MODEL CALIBRATION -----------------------
LOGGER.logger.info(
"--------------------------MODEL CALIBRATION -----------------------")
staticMeasurement = qtmTools.findStatic(sessionXML)
calibrateFilenameLabelled = qtmTools.getFilename(staticMeasurement)
LOGGER.logger.info("----- CALIBRATION- static file [%s]--" %
(calibrateFilenameLabelled))
leftFlatFoot = utils.toBool(
sessionXML.Left_foot_normalised_to_static_trial.text)
rightFlatFoot = utils.toBool(
sessionXML.Right_foot_normalised_to_static_trial.text)
headFlat = utils.toBool(sessionXML.Head_normalised_to_static_trial.text)
markerDiameter = float(sessionXML.Marker_diameter.text) * 1000.0
pointSuffix = None
acqStatic = btkTools.smartReader(DATA_PATH + calibrateFilenameLabelled)
# Calibration operation
# --------------------
model, acqStatic, detectAnomaly = cgm1.calibrate(
DATA_PATH,
calibrateFilenameLabelled,
translators,
required_mp,
optional_mp,
leftFlatFoot,
rightFlatFoot,
headFlat,
markerDiameter,
pointSuffix,
anomalyException=anomalyException)
LOGGER.logger.info("----- CALIBRATION- static file [%s]-----> DONE" %
(calibrateFilenameLabelled))
# --------------------------MODEL FITTING ----------------------------------
LOGGER.logger.info(
"--------------------------MODEL FITTING ----------------------------------"
)
dynamicMeasurements = qtmTools.findDynamic(sessionXML)
modelledC3ds = list()
for dynamicMeasurement in dynamicMeasurements:
reconstructFilenameLabelled = qtmTools.getFilename(dynamicMeasurement)
LOGGER.logger.info("----Processing of [%s]-----" %
(reconstructFilenameLabelled))
mfpa = qtmTools.getForcePlateAssigment(dynamicMeasurement)
momentProjection_text = sessionXML.Moment_Projection.text
if momentProjection_text == "Default":
momentProjection_text = settings["Fitting"]["Moment Projection"]
if momentProjection_text == "Distal":
momentProjection = enums.MomentProjection.Distal
elif momentProjection_text == "Proximal":
momentProjection = enums.MomentProjection.Proximal
elif momentProjection_text == "Global":
momentProjection = enums.MomentProjection.Global
acq = btkTools.smartReader(DATA_PATH + reconstructFilenameLabelled)
# filtering
# -----------------------
# marker
order_marker = int(
float(dynamicMeasurement.Marker_lowpass_filter_order.text))
fc_marker = float(
dynamicMeasurement.Marker_lowpass_filter_frequency.text)
# force plate
order_fp = int(
float(dynamicMeasurement.Forceplate_lowpass_filter_order.text))
fc_fp = float(
dynamicMeasurement.Forceplate_lowpass_filter_frequency.text)
if dynamicMeasurement.First_frame_to_process.text != "":
vff = int(dynamicMeasurement.First_frame_to_process.text)
else:
vff = None
if dynamicMeasurement.Last_frame_to_process.text != "":
vlf = int(dynamicMeasurement.Last_frame_to_process.text)
else:
vlf = None
# fitting operation
# -----------------------
acqGait, detectAnomaly = cgm1.fitting(
model,
DATA_PATH,
reconstructFilenameLabelled,
translators,
markerDiameter,
pointSuffix,
mfpa,
momentProjection,
fc_lowPass_marker=fc_marker,
order_lowPass_marker=order_marker,
fc_lowPass_forcePlate=fc_fp,
order_lowPass_forcePlate=order_fp,
anomalyException=anomalyException,
frameInit=vff,
frameEnd=vlf)
outFilename = reconstructFilenameLabelled
btkTools.smartWriter(acqGait, str(DATA_PATH + outFilename))
modelledC3ds.append(outFilename)
LOGGER.logger.info("----Processing of [%s]-----> DONE" %
(reconstructFilenameLabelled))
# --------------------------GAIT PROCESSING -----------------------
LOGGER.logger.info(
"---------------------GAIT PROCESSING -----------------------")
if createPDFReport:
nds = normativeDatasets.NormativeData("Schwartz2008", "Free")
types = qtmTools.detectMeasurementType(sessionXML)
for type in types:
modelledTrials = list()
for dynamicMeasurement in dynamicMeasurements:
if qtmTools.isType(dynamicMeasurement, type):
filename = qtmTools.getFilename(dynamicMeasurement)
# event checking
# -----------------------
acq = btkTools.smartReader(DATA_PATH + filename)
geap = AnomalyDetectionProcedure.GaitEventAnomalyProcedure(
)
adf = AnomalyFilter.AnomalyDetectionFilter(
acq, filename, geap)
anomaly_events = adf.run()
if anomaly_events["ErrorState"]:
detectAnomaly = True
LOGGER.logger.warning(
"file [%s] not used for generating the gait report. bad gait event detected"
% (filename))
else:
modelledTrials.append(filename)
try:
report.pdfGaitReport(DATA_PATH,
model,
modelledTrials,
nds,
pointSuffix,
title=type)
LOGGER.logger.error("Generation of Gait report complete")
except:
LOGGER.logger.error("Generation of Gait report failed")
LOGGER.logger.info(
"-------------------------------------------------------")
if detectAnomaly:
LOGGER.logger.error(
"Anomalies has been detected - Find Error messages, then check warning message in the log file"
)
else:
LOGGER.logger.info("workflow return with no detected anomalies")
def main(sessionFilename, createPDFReport=True):
logging.info("------------------------------------------------")
logging.info("------------QTM - pyCGM2 Workflow---------------")
logging.info("------------------------------------------------")
sessionXML = files.readXml(os.getcwd() + "\\", sessionFilename)
sessionDate = files.getFileCreationDate(os.getcwd() + "\\" +
sessionFilename)
#---------------------------------------------------------------------------
#management of the Processed foldercd
DATA_PATH = os.getcwd() + "\\" + "processed\\"
files.createDir(DATA_PATH)
staticMeasurement = qtmTools.findStatic(sessionXML)
calibrateFilenameLabelled = qtmTools.getFilename(staticMeasurement)
if not os.path.isfile(DATA_PATH + calibrateFilenameLabelled):
shutil.copyfile(os.getcwd() + "\\" + calibrateFilenameLabelled,
DATA_PATH + calibrateFilenameLabelled)
logging.info(
"qualisys exported c3d file [%s] copied to processed folder" %
(calibrateFilenameLabelled))
dynamicMeasurements = qtmTools.findDynamic(sessionXML)
for dynamicMeasurement in dynamicMeasurements:
reconstructFilenameLabelled = qtmTools.getFilename(dynamicMeasurement)
if not os.path.isfile(DATA_PATH + reconstructFilenameLabelled):
shutil.copyfile(os.getcwd() + "\\" + reconstructFilenameLabelled,
DATA_PATH + reconstructFilenameLabelled)
logging.info(
"qualisys exported c3d file [%s] copied to processed folder" %
(reconstructFilenameLabelled))
acq = btkTools.smartReader(
str(DATA_PATH + reconstructFilenameLabelled))
acq, zeniState = eventDetector.zeni(acq)
if zeniState:
btkTools.smartWriter(
acq, str(DATA_PATH + reconstructFilenameLabelled))
cmd = "Mokka.exe \"%s\"" % (str(DATA_PATH +
reconstructFilenameLabelled))
os.system(cmd)
# --------------------------GLOBAL SETTINGS ------------------------------------
# global setting ( in user/AppData)
if os.path.isfile(pyCGM2.PYCGM2_APPDATA_PATH + "CGM1-pyCGM2.settings"):
settings = files.openFile(pyCGM2.PYCGM2_APPDATA_PATH,
"CGM1-pyCGM2.settings")
else:
settings = files.openFile(pyCGM2.PYCGM2_SETTINGS_FOLDER,
"CGM1-pyCGM2.settings")
# --------------------------MP ------------------------------------
required_mp, optional_mp = qtmTools.SubjectMp(sessionXML)
# --Check MP
inspectprocedure = inspectProcedures.AnthropometricDataQualityProcedure(
required_mp)
inspector = inspectFilters.QualityFilter(inspectprocedure)
inspector.run()
# translators management
translators = files.getTranslators(os.getcwd() + "\\", "CGM1.translators")
if not translators: translators = settings["Translators"]
# --------------------------MODEL CALIBRATION -----------------------
logging.info(
"--------------------------MODEL CALIBRATION -----------------------")
staticMeasurement = qtmTools.findStatic(sessionXML)
calibrateFilenameLabelled = qtmTools.getFilename(staticMeasurement)
logging.info("----- CALIBRATION- static file [%s]--" %
(calibrateFilenameLabelled))
leftFlatFoot = utils.toBool(
sessionXML.Left_foot_normalised_to_static_trial.text)
rightFlatFoot = utils.toBool(
sessionXML.Right_foot_normalised_to_static_trial.text)
headFlat = utils.toBool(sessionXML.Head_normalised_to_static_trial.text)
markerDiameter = float(sessionXML.Marker_diameter.text) * 1000.0
pointSuffix = None
# Calibration checking
# --------------------
acqStatic = btkTools.smartReader(DATA_PATH + calibrateFilenameLabelled)
for key in MARKERSETS.keys():
logging.info("[pyCGM2] Checking of the %s" % (key))
# presence
ip_presence = inspectProcedures.MarkerPresenceQualityProcedure(
acqStatic, markers=MARKERSETS[key])
inspector = inspectFilters.QualityFilter(ip_presence)
inspector.run()
if ip_presence.markersIn != []:
ip_gap = inspectProcedures.GapQualityProcedure(
acqStatic, markers=ip_presence.markersIn)
inspector = inspectFilters.QualityFilter(ip_gap)
inspector.run()
ip_swap = inspectProcedures.SwappingMarkerQualityProcedure(
acqStatic, markers=ip_presence.markersIn)
inspector = inspectFilters.QualityFilter(ip_swap)
inspector.run()
ip_pos = inspectProcedures.MarkerPositionQualityProcedure(
acqStatic, markers=ip_presence.markersIn)
inspector = inspectFilters.QualityFilter(ip_pos)
# Calibration operation
# --------------------
logging.info("[pyCGM2] --- calibration operation ---")
model, acqStatic = cgm1.calibrate(DATA_PATH, calibrateFilenameLabelled,
translators, required_mp, optional_mp,
leftFlatFoot, rightFlatFoot, headFlat,
markerDiameter, pointSuffix)
logging.info("----- CALIBRATION- static file [%s]-----> DONE" %
(calibrateFilenameLabelled))
# --------------------------MODEL FITTING ----------------------------------
logging.info(
"--------------------------MODEL FITTING ----------------------------------"
)
dynamicMeasurements = qtmTools.findDynamic(sessionXML)
modelledC3ds = list()
eventInspectorStates = list()
for dynamicMeasurement in dynamicMeasurements:
reconstructFilenameLabelled = qtmTools.getFilename(dynamicMeasurement)
logging.info("----Processing of [%s]-----" %
(reconstructFilenameLabelled))
mfpa = qtmTools.getForcePlateAssigment(dynamicMeasurement)
momentProjection_text = sessionXML.Moment_Projection.text
if momentProjection_text == "Default":
momentProjection_text = settings["Fitting"]["Moment Projection"]
if momentProjection_text == "Distal":
momentProjection = enums.MomentProjection.Distal
elif momentProjection_text == "Proximal":
momentProjection = enums.MomentProjection.Proximal
elif momentProjection_text == "Global":
momentProjection = enums.MomentProjection.Global
acq = btkTools.smartReader(DATA_PATH + reconstructFilenameLabelled)
# Fitting checking
# --------------------
for key in MARKERSETS.keys():
if key != "Calibration markers":
logging.info("[pyCGM2] Checking of the %s" % (key))
# presence
ip_presence = inspectProcedures.MarkerPresenceQualityProcedure(
acq, markers=MARKERSETS[key])
inspector = inspectFilters.QualityFilter(ip_presence)
inspector.run()
if ip_presence.markersIn != []:
ip_gap = inspectProcedures.GapQualityProcedure(
acq, markers=ip_presence.markersIn)
inspector = inspectFilters.QualityFilter(ip_gap)
inspector.run()
ip_swap = inspectProcedures.SwappingMarkerQualityProcedure(
acq, markers=ip_presence.markersIn)
inspector = inspectFilters.QualityFilter(ip_swap)
inspector.run()
ip_pos = inspectProcedures.MarkerPositionQualityProcedure(
acq, markers=ip_presence.markersIn)
inspector = inspectFilters.QualityFilter(ip_pos)
# filtering
# -----------------------
# marker
order_marker = int(
float(dynamicMeasurement.Marker_lowpass_filter_order.text))
fc_marker = float(
dynamicMeasurement.Marker_lowpass_filter_frequency.text)
# force plate
order_fp = int(
float(dynamicMeasurement.Forceplate_lowpass_filter_order.text))
fc_fp = float(
dynamicMeasurement.Forceplate_lowpass_filter_frequency.text)
# event checking
# -----------------------
inspectprocedureEvents = inspectProcedures.GaitEventQualityProcedure(
acq)
inspector = inspectFilters.QualityFilter(inspectprocedureEvents)
inspector.run
eventInspectorStates.append(inspectprocedureEvents.state)
# fitting operation
# -----------------------
logging.info("[pyCGM2] --- Fitting operation ---")
acqGait = cgm1.fitting(model,
DATA_PATH,
reconstructFilenameLabelled,
translators,
markerDiameter,
pointSuffix,
mfpa,
momentProjection,
fc_lowPass_marker=fc_marker,
order_lowPass_marker=order_marker,
fc_lowPass_forcePlate=fc_fp,
order_lowPass_forcePlate=order_fp)
outFilename = reconstructFilenameLabelled
btkTools.smartWriter(acqGait, str(DATA_PATH + outFilename))
modelledC3ds.append(outFilename)
logging.info("----Processing of [%s]-----> DONE" %
(reconstructFilenameLabelled))
# --------------------------GAIT PROCESSING -----------------------
if not all(eventInspectorStates):
raise Exception(
"[pyCGM2] Impossible to run Gait processing. Badly gait event detection. check the log file"
)
logging.info(
"---------------------GAIT PROCESSING -----------------------")
if createPDFReport:
nds = normativeDatasets.Schwartz2008("Free")
types = qtmTools.detectMeasurementType(sessionXML)
for type in types:
modelledTrials = list()
for dynamicMeasurement in dynamicMeasurements:
if qtmTools.isType(dynamicMeasurement, type):
filename = qtmTools.getFilename(dynamicMeasurement)
modelledTrials.append(filename)
report.pdfGaitReport(DATA_PATH,
model,
modelledTrials,
nds,
pointSuffix,
title=type)
logging.info("----- Gait Processing -----> DONE")
def test_FullBody_noOptions_global(self):
DATA_PATH = MAIN_PATH = pyCGM2.TEST_DATA_PATH + "GaitModels\\CGM1\\LowerLimb-medMed_Yprogression\\"
staticFilename = "static.c3d"
acqStatic = btkTools.smartReader(DATA_PATH + staticFilename)
markerDiameter = 14
leftFlatFoot = False
rightFlatFoot = False
headStraight = False
pointSuffix = "test"
vskFile = vskTools.getVskFiles(DATA_PATH)
vsk = vskTools.Vsk(DATA_PATH + "Subject.vsk")
required_mp, optional_mp = vskTools.getFromVskSubjectMp(vsk,
resetFlag=True)
model, finalAcqStatic = cgm1.calibrate(DATA_PATH,
staticFilename,
None,
required_mp,
optional_mp,
leftFlatFoot,
rightFlatFoot,
headStraight,
markerDiameter,
pointSuffix,
displayCoordinateSystem=True)
# btkTools.smartWriter(finalAcqStatic, str( staticFilename[:-4]+"-pyCGM2modelled.c3d"))
# logging.info("Static Calibration -----> Done")
gaitFilename = "gait1.Global.c3d"
mfpa = "RLX"
reconstructFilenameLabelled = gaitFilename
acqGait = cgm1.fitting(model,
DATA_PATH,
reconstructFilenameLabelled,
None,
markerDiameter,
pointSuffix,
mfpa,
enums.MomentProjection.Global,
displayCoordinateSystem=True)
testingUtils.plotComparison_ForcePanel(acqGait, None, "test", "Left")
testingUtils.plotComparison_ForcePanel(acqGait, None, "test", "Right")
gaitFilename = "gait2.Global.c3d"
mfpa = "XLR"
reconstructFilenameLabelled = gaitFilename
acqGait = cgm1.fitting(model,
DATA_PATH,
reconstructFilenameLabelled,
None,
markerDiameter,
pointSuffix,
mfpa,
enums.MomentProjection.Global,
displayCoordinateSystem=True)
testingUtils.plotComparison_ForcePanel(acqGait, None, "test", "Left")
testingUtils.plotComparison_ForcePanel(acqGait, None, "test", "Right")
def test_issue_signAbdAddOffset(self):
DATA_PATH = pyCGM2.TEST_DATA_PATH + "Issues\\StephenM\\signedAbdAdd-KadMed\\"
staticFilename = "Static.c3d"
acqStatic = btkTools.smartReader(str(DATA_PATH + staticFilename))
markerDiameter = 14
leftFlatFoot = True
rightFlatFoot = True
headStraight = True
pointSuffix = "test"
vskFile = vskTools.getVskFiles(DATA_PATH)
vsk = vskTools.Vsk(DATA_PATH + "Nick.vsk")
required_mp, optional_mp = vskTools.getFromVskSubjectMp(vsk,
resetFlag=True)
# required_mp={
# 'Bodymass' : 65.0,
# 'LeftLegLength' : 800.0,
# 'RightLegLength' : 800.0 ,
# 'LeftKneeWidth' : 120.0,
# 'RightKneeWidth' : 120.0,
# 'LeftAnkleWidth' : 100.0,
# 'RightAnkleWidth' : 100.0,
# 'LeftSoleDelta' : 0,
# 'RightSoleDelta' : 0,
# 'LeftShoulderOffset' : 40,
# 'LeftElbowWidth' : 74,
# 'LeftWristWidth' : 55 ,
# 'LeftHandThickness' : 34 ,
# 'RightShoulderOffset' : 40,
# 'RightElbowWidth' : 74,
# 'RightWristWidth' : 55 ,
# 'RightHandThickness' : 34}
#
# optional_mp={
# 'InterAsisDistance' : 0,#0,
# 'LeftAsisTrocanterDistance' : 0,#0,
# 'LeftTibialTorsion' : 0,#0,
# 'LeftThighRotation' : 0,#0,
# 'LeftShankRotation' : 0,#0,ipdb
# 'RightAsisTrocanterDistance' : 0,#0,
# 'RightTibialTorsion' : 0,#0,
# 'RightThighRotation' : 0,#0,
# 'RightShankRotation' : 0}
model, finalAcqStatic = cgm1.calibrate(DATA_PATH,
staticFilename,
None,
required_mp,
optional_mp,
leftFlatFoot,
rightFlatFoot,
headStraight,
markerDiameter,
pointSuffix,
displayCoordinateSystem=True)
testingUtils.test_offset(
model.mp_computed["LeftThighRotationOffset"],
acqStatic,
"LThighRotation",
decimal=1) # not enought accurate but unsignificant
testingUtils.test_offset(model.mp_computed["RightThighRotationOffset"],
acqStatic,
"RThighRotation",
decimal=1)
testingUtils.test_offset(model.mp_computed["LeftShankRotationOffset"],
acqStatic,
"LShankRotation",
decimal=1)
testingUtils.test_offset(model.mp_computed["RightShankRotationOffset"],
acqStatic,
"RShankRotation",
decimal=1)
testingUtils.test_offset(model.mp_computed["LeftTibialTorsionOffset"],
acqStatic,
"LTibialTorsion",
decimal=1)
testingUtils.test_offset(model.mp_computed["RightTibialTorsionOffset"],
acqStatic,
"RTibialTorsion",
decimal=1)
testingUtils.test_offset(model.mp_computed["LeftAnkleAbAddOffset"],
acqStatic,
"LAnkleAbAdd",
decimal=1)
testingUtils.test_offset(model.mp_computed["RightAnkleAbAddOffset"],
acqStatic,
"RAnkleAbAdd",
decimal=1)
testingUtils.test_offset(
model.mp_computed["LeftStaticPlantFlexOffset"],
acqStatic,
"LStaticPlantFlex",
decimal=1)
testingUtils.test_offset(
model.mp_computed["RightStaticPlantFlexOffset"],
acqStatic,
"RStaticPlantFlex",
decimal=1)
testingUtils.test_offset(model.mp_computed["LeftStaticRotOffset"],
acqStatic,
"LStaticRotOff",
decimal=1)
testingUtils.test_offset(model.mp_computed["RightStaticRotOffset"],
acqStatic,
"RStaticRotOff",
decimal=1)
def test_Kad_noOptions(self):
DATA_PATH = pyCGM2.TEST_DATA_PATH + "GaitModels\CGM1\\kad-noOptions\\"
staticFilename = "static.c3d"
acqStatic = btkTools.smartReader(DATA_PATH + staticFilename)
markerDiameter=14
leftFlatFoot = False
rightFlatFoot = False
headStraight = False
pointSuffix = "test"
# vskFile = vskTools.getVskFiles(DATA_PATH)
# vsk = vskTools.Vsk(str(DATA_PATH + "PIG-KAD.vsk"))
# required_mp,optional_mp = vskTools.getFromVskSubjectMp(vsk, resetFlag=True)
required_mp={
'Bodymass' : 71.0,
'LeftLegLength' : 860.0,
'RightLegLength' : 865.0 ,
'LeftKneeWidth' : 102.0,
'RightKneeWidth' : 103.4,
'LeftAnkleWidth' : 75.3,
'RightAnkleWidth' : 72.9,
'LeftSoleDelta' : 0,
'RightSoleDelta' : 0,
'LeftShoulderOffset' : 40,
'LeftElbowWidth' : 74,
'LeftWristWidth' : 55 ,
'LeftHandThickness' : 34 ,
'RightShoulderOffset' : 40,
'RightElbowWidth' : 74,
'RightWristWidth' : 55 ,
'RightHandThickness' : 34}
optional_mp={
'InterAsisDistance' : 0,#0,
'LeftAsisTrocanterDistance' : 0,#0,
'LeftTibialTorsion' : 0,#0,
'LeftThighRotation' : 0,#0,
'LeftShankRotation' : 0,#0,
'RightAsisTrocanterDistance' : 0,#0,
'RightTibialTorsion' : 0,#0,
'RightThighRotation' : 0,#0,
'RightShankRotation' : 0}
model,finalAcqStatic,error = cgm1.calibrate(DATA_PATH,
staticFilename,
None,
required_mp,
optional_mp,
leftFlatFoot,
rightFlatFoot,
headStraight,
markerDiameter,
pointSuffix,
displayCoordinateSystem=True)
testingUtils.test_offset(model.mp_computed["LeftThighRotationOffset"],acqStatic,"LThighRotation", decimal=3)
testingUtils.test_offset(model.mp_computed["RightThighRotationOffset"],acqStatic,"RThighRotation", decimal=3)
testingUtils.test_offset(model.mp_computed["LeftShankRotationOffset"],acqStatic,"LShankRotation", decimal=3)
testingUtils.test_offset(model.mp_computed["RightShankRotationOffset"],acqStatic,"RShankRotation", decimal=3)
testingUtils.test_offset(model.mp_computed["LeftTibialTorsionOffset"],acqStatic,"LTibialTorsion", decimal=3)
testingUtils.test_offset(model.mp_computed["RightTibialTorsionOffset"],acqStatic,"RTibialTorsion", decimal=3)
testingUtils.test_offset(model.mp_computed["LeftAnkleAbAddOffset"],acqStatic,"LAnkleAbAdd", decimal=3)
testingUtils.test_offset(model.mp_computed["RightAnkleAbAddOffset"],acqStatic,"RAnkleAbAdd", decimal=3)
testingUtils.test_offset(model.mp_computed["LeftStaticPlantFlexOffset"],acqStatic,"LStaticPlantFlex", decimal=3)
testingUtils.test_offset(model.mp_computed["RightStaticPlantFlexOffset"],acqStatic,"RStaticPlantFlex", decimal=3)
testingUtils.test_offset(model.mp_computed["LeftStaticRotOffset"],acqStatic,"LStaticRotOff", decimal=3)
testingUtils.test_offset(model.mp_computed["RightStaticRotOffset"],acqStatic,"RStaticRotOff", decimal=3)
np.testing.assert_equal(model.getSegment("Left Thigh").getReferential("TF").static.getNode_byLabel("LHJC").m_desc ,"Davis")
np.testing.assert_equal(model.getSegment("Right Thigh").getReferential("TF").static.getNode_byLabel("RHJC").m_desc ,"Davis")
np.testing.assert_equal(model.getSegment("Left Thigh").getReferential("TF").static.getNode_byLabel("LKJC").m_desc ,"KAD")
np.testing.assert_equal(model.getSegment("Right Thigh").getReferential("TF").static.getNode_byLabel("RKJC").m_desc ,"KAD")
np.testing.assert_equal(model.getSegment("Left Shank").getReferential("TF").static.getNode_byLabel("LKJC").m_desc ,"KAD")
np.testing.assert_equal(model.getSegment("Right Shank").getReferential("TF").static.getNode_byLabel("RKJC").m_desc ,"KAD")
np.testing.assert_equal(model.getSegment("Left Shank").getReferential("TF").static.getNode_byLabel("LAJC").m_desc ,"KAD")
np.testing.assert_equal(model.getSegment("Right Shank").getReferential("TF").static.getNode_byLabel("RAJC").m_desc ,"KAD")
np.testing.assert_equal(model.getSegment("Left Foot").getReferential("TF").static.getNode_byLabel("LAJC").m_desc ,"KAD")
np.testing.assert_equal(model.getSegment("Right Foot").getReferential("TF").static.getNode_byLabel("RAJC").m_desc ,"KAD")
# btkTools.smartWriter(finalAcqStatic, str( staticFilename[:-4]+"-pyCGM2modelled.c3d"))
# LOGGER.logger.info("Static Calibration -----> Done")
gaitFilename="gait1.c3d"
mfpa = None
reconstructFilenameLabelled = gaitFilename
acqGait,error = cgm1.fitting(model,DATA_PATH, reconstructFilenameLabelled,
None,
markerDiameter,
pointSuffix,
mfpa,
enums.MomentProjection.Proximal,
displayCoordinateSystem=True)
testingUtils.test_point(acqGait,"LHipAngles","LHipAngles_test",decimal = 3)
testingUtils.test_point(acqGait,"LKneeAngles","LKneeAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"LAnkleAngles","LAnkleAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"RHipAngles","RHipAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"RKneeAngles","RKneeAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"RAnkleAngles","RAnkleAngles_test",decimal = 2)
def test_FullBody_noOptions(self):
DATA_PATH = pyCGM2.TEST_DATA_PATH + "GaitModels\CGM1\\fullBody-native-Options\\"
staticFilename = "static.c3d"
acqStatic = btkTools.smartReader(DATA_PATH + staticFilename)
markerDiameter=14
leftFlatFoot = True
rightFlatFoot = True
headStraight = True
pointSuffix = "test"
vskFile = vskTools.getVskFiles(DATA_PATH)
vsk = vskTools.Vsk(DATA_PATH + "New Subject.vsk")
required_mp,optional_mp = vskTools.getFromVskSubjectMp(vsk, resetFlag=True)
model,finalAcqStatic,error = cgm1.calibrate(DATA_PATH,
staticFilename,
None,
required_mp,
optional_mp,
leftFlatFoot,
rightFlatFoot,
headStraight,
markerDiameter,
pointSuffix,
displayCoordinateSystem=True)
testingUtils.test_offset(model.mp_computed["LeftThighRotationOffset"],acqStatic,"LThighRotation", decimal=3)
testingUtils.test_offset(model.mp_computed["RightThighRotationOffset"],acqStatic,"RThighRotation", decimal=3)
testingUtils.test_offset(model.mp_computed["LeftShankRotationOffset"],acqStatic,"LShankRotation", decimal=3)
testingUtils.test_offset(model.mp_computed["RightShankRotationOffset"],acqStatic,"RShankRotation", decimal=3)
testingUtils.test_offset(model.mp_computed["LeftTibialTorsionOffset"],acqStatic,"LTibialTorsion", decimal=3)
testingUtils.test_offset(model.mp_computed["RightTibialTorsionOffset"],acqStatic,"RTibialTorsion", decimal=3)
testingUtils.test_offset(model.mp_computed["LeftAnkleAbAddOffset"],acqStatic,"LAnkleAbAdd", decimal=3)
testingUtils.test_offset(model.mp_computed["RightAnkleAbAddOffset"],acqStatic,"RAnkleAbAdd", decimal=3)
testingUtils.test_offset(model.mp_computed["LeftStaticPlantFlexOffset"],acqStatic,"LStaticPlantFlex", decimal=3)
testingUtils.test_offset(model.mp_computed["RightStaticPlantFlexOffset"],acqStatic,"RStaticPlantFlex", decimal=3)
testingUtils.test_offset(model.mp_computed["LeftStaticRotOffset"],acqStatic,"LStaticRotOff", decimal=3)
testingUtils.test_offset(model.mp_computed["RightStaticRotOffset"],acqStatic,"RStaticRotOff", decimal=3)
np.testing.assert_equal(model.getSegment("Left Thigh").getReferential("TF").static.getNode_byLabel("LHJC").m_desc ,"Davis")
np.testing.assert_equal(model.getSegment("Right Thigh").getReferential("TF").static.getNode_byLabel("RHJC").m_desc ,"Davis")
np.testing.assert_equal(model.getSegment("Left Thigh").getReferential("TF").static.getNode_byLabel("LKJC").m_desc ,"Chord")
np.testing.assert_equal(model.getSegment("Right Thigh").getReferential("TF").static.getNode_byLabel("RKJC").m_desc ,"Chord")
np.testing.assert_equal(model.getSegment("Left Shank").getReferential("TF").static.getNode_byLabel("LKJC").m_desc ,"Chord")
np.testing.assert_equal(model.getSegment("Right Shank").getReferential("TF").static.getNode_byLabel("RKJC").m_desc ,"Chord")
np.testing.assert_equal(model.getSegment("Left Shank").getReferential("TF").static.getNode_byLabel("LAJC").m_desc ,"Chord")
np.testing.assert_equal(model.getSegment("Right Shank").getReferential("TF").static.getNode_byLabel("RAJC").m_desc ,"Chord")
np.testing.assert_equal(model.getSegment("Left Foot").getReferential("TF").static.getNode_byLabel("LAJC").m_desc ,"Chord")
np.testing.assert_equal(model.getSegment("Right Foot").getReferential("TF").static.getNode_byLabel("RAJC").m_desc ,"Chord")
testingUtils.test_point(finalAcqStatic,"LPelvisAngles","LPelvisAngles_test",decimal = 3)
testingUtils.test_point(finalAcqStatic,"RPelvisAngles","RPelvisAngles_test",decimal = 3)
testingUtils.test_point(finalAcqStatic,"LHipAngles","LHipAngles_test",decimal = 3)
testingUtils.test_point(finalAcqStatic,"LKneeAngles","LKneeAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"LAnkleAngles","LAnkleAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"RHipAngles","RHipAngles_test",decimal = 3)
testingUtils.test_point(finalAcqStatic,"RKneeAngles","RKneeAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"RAnkleAngles","RAnkleAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"LFootProgressAngles","LFootProgressAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"RFootProgressAngles","RFootProgressAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"LThoraxAngles","LThoraxAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"RThoraxAngles","RThoraxAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"LSpineAngles","LSpineAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"RSpineAngles","RSpineAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"LShoulderAngles","LShoulderAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"RShoulderAngles","RShoulderAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"LElbowAngles","LElbowAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"RElbowAngles","RElbowAngles_test",decimal = 2)
testingUtils.test_point(finalAcqStatic,"LHeadAngles","LHeadAngles_test",decimal = 3)
testingUtils.test_point(finalAcqStatic,"RHeadAngles","RHeadAngles_test",decimal = 3)
# btkTools.smartWriter(finalAcqStatic, str( staticFilename[:-4]+"-pyCGM2modelled.c3d"))
# LOGGER.logger.info("Static Calibration -----> Done")
gaitFilename="gait1.c3d"
mfpa = None
reconstructFilenameLabelled = gaitFilename
acqGait,error = cgm1.fitting(model,DATA_PATH, reconstructFilenameLabelled,
None,
markerDiameter,
pointSuffix,
mfpa,
enums.MomentProjection.Proximal,
displayCoordinateSystem=True)
testingUtils.test_point(acqGait,"LPelvisAngles","LPelvisAngles_test",decimal = 3)
testingUtils.test_point(acqGait,"RPelvisAngles","RPelvisAngles_test",decimal = 3)
testingUtils.test_point(acqGait,"LHipAngles","LHipAngles_test",decimal = 3)
testingUtils.test_point(acqGait,"LKneeAngles","LKneeAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"LAnkleAngles","LAnkleAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"RHipAngles","RHipAngles_test",decimal = 3)
testingUtils.test_point(acqGait,"RKneeAngles","RKneeAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"RAnkleAngles","RAnkleAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"LFootProgressAngles","LFootProgressAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"RFootProgressAngles","RFootProgressAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"LThoraxAngles","LThoraxAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"RThoraxAngles","RThoraxAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"LSpineAngles","LSpineAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"RSpineAngles","RSpineAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"LShoulderAngles","LShoulderAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"RShoulderAngles","RShoulderAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"LElbowAngles","LElbowAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"RElbowAngles","RElbowAngles_test",decimal = 2)
testingUtils.test_point(acqGait,"LHeadAngles","LHeadAngles_test",decimal = 3)
testingUtils.test_point(acqGait,"RHeadAngles","RHeadAngles_test",decimal = 3)
# testingUtils.test_point(acqGait,"LWristAngles","LWristAngles_test",decimal = 3) fail on z!
# testingUtils.test_point(acqGait,"RWristAngles","RWristAngles_test",decimal = 3) fail on Z!
# testingUtils.test_point(acqGait,"CentreOfMass","CentreOfMass_test",decimal = 3)
btkTools.smartAppendPoint(acqGait,"headCOM_py",model.getSegment("Head").getComTrajectory())
btkTools.smartAppendPoint(acqGait,"ThoraxCOM_py",model.getSegment("Thorax").getComTrajectory())
btkTools.smartAppendPoint(acqGait,"LhumCOM_py",model.getSegment("Left UpperArm").getComTrajectory())
btkTools.smartAppendPoint(acqGait,"LforeCom_py",model.getSegment("Left ForeArm").getComTrajectory())
btkTools.smartAppendPoint(acqGait,"LhandCom_py",model.getSegment("Left Hand").getComTrajectory())
btkTools.smartAppendPoint(acqGait,"RhumCOM_py",model.getSegment("Right UpperArm").getComTrajectory())
btkTools.smartAppendPoint(acqGait,"RforeCom_py",model.getSegment("Right ForeArm").getComTrajectory())
btkTools.smartAppendPoint(acqGait,"RhandCom_py",model.getSegment("Right Hand").getComTrajectory())
def main(args):
DATA_PATH = os.getcwd() + "\\"
# User Settings
if os.path.isfile(DATA_PATH + args.userFile):
userSettings = files.openFile(DATA_PATH, args.userFile)
else:
raise Exception("user setting file not found")
# internal (expert) Settings
if args.expertFile:
if os.path.isfile(DATA_PATH + args.expertFile):
internalSettings = files.openFile(DATA_PATH, args.expertFile)
else:
raise Exception("expert setting file not found")
else:
internalSettings = None
# translators
if os.path.isfile(DATA_PATH + "CGM1.translators"):
translators = files.openFile(DATA_PATH, "CGM1.translators")
else:
translators = None
if args.vskFile:
vsk = vskTools.Vsk(str(DATA_PATH + args.vskFile))
else:
vsk = None
# --- Manager ----
manager = ModelManager.CGM1ConfigManager(
userSettings,
localInternalSettings=internalSettings,
localTranslators=translators,
vsk=vsk)
manager.contruct()
finalSettings = manager.getFinalSettings()
files.prettyDictPrint(finalSettings)
logging.info("=============Calibration=============")
model, finalAcqStatic = cgm1.calibrate(DATA_PATH,
manager.staticTrial,
manager.translators,
manager.requiredMp,
manager.optionalMp,
manager.leftFlatFoot,
manager.rightFlatFoot,
manager.headFlat,
manager.markerDiameter,
manager.pointSuffix,
displayCoordinateSystem=True)
btkTools.smartWriter(
finalAcqStatic,
str(DATA_PATH + finalSettings["Calibration"]["StaticTrial"][:-4] +
"-pyCGM2modelled.c3d"))
logging.info("Static Calibration -----> Done")
manager.updateMp(model)
#files.prettyDictPrint(manager.finalSettings)
logging.info("=============Fitting=============")
for trial in manager.dynamicTrials:
mfpa = None if trial["Mfpa"] == "Auto" else trial["Mfpa"]
reconstructFilenameLabelled = trial["File"]
acqGait = cgm1.fitting(model,
DATA_PATH,
reconstructFilenameLabelled,
manager.translators,
manager.markerDiameter,
manager.pointSuffix,
mfpa,
manager.momentProjection,
displayCoordinateSystem=True)
btkTools.smartWriter(
acqGait,
str(DATA_PATH + reconstructFilenameLabelled[:-4] +
"-pyCGM2modelled.c3d"))
logging.info("---->dynamic trial (%s) processed" %
(reconstructFilenameLabelled))
logging.info("=============Writing of final Settings=============")
i = 0
while os.path.exists("CGM1 [%s].completeSettings" % i):
i += 1
filename = "CGM1 [" + str(i) + "].completeSettings"
files.saveJson(DATA_PATH, filename, finalSettings)
logging.info("---->complete settings (%s) exported" % (filename))
def main():
logging.info("------------------------------------------------")
logging.info("------------QTM - pyCGM2 Workflow---------------")
logging.info("------------------------------------------------")
file = "session.xml"
sessionXML = files.readXml(os.getcwd() + "\\", file)
sessionDate = files.getFileCreationDate(os.getcwd() + "\\" + file)
#---------------------------------------------------------------------------
#management of the Processed foldercd
DATA_PATH = os.getcwd() + "\\" + "processed\\"
files.createDir(DATA_PATH)
staticMeasurement = qtmTools.findStatic(sessionXML)
calibrateFilenameLabelled = qtmTools.getFilename(staticMeasurement)
if not os.path.isfile(DATA_PATH + calibrateFilenameLabelled):
shutil.copyfile(os.getcwd() + "\\" + calibrateFilenameLabelled,
DATA_PATH + calibrateFilenameLabelled)
logging.info(
"qualisys exported c3d file [%s] copied to processed folder" %
(calibrateFilenameLabelled))
dynamicMeasurements = qtmTools.findDynamic(sessionXML)
for dynamicMeasurement in dynamicMeasurements:
reconstructFilenameLabelled = qtmTools.getFilename(dynamicMeasurement)
if not os.path.isfile(DATA_PATH + reconstructFilenameLabelled):
shutil.copyfile(os.getcwd() + "\\" + reconstructFilenameLabelled,
DATA_PATH + reconstructFilenameLabelled)
logging.info(
"qualisys exported c3d file [%s] copied to processed folder" %
(reconstructFilenameLabelled))
acq = btkTools.smartReader(
str(DATA_PATH + reconstructFilenameLabelled))
if btkTools.checkForcePlateExist(acq):
if "5" in btkTools.smartGetMetadata(acq, "FORCE_PLATFORM",
"TYPE"):
forceplates.correctForcePlateType5(acq)
acq, zeniState = eventDetector.zeni(acq)
if zeniState:
btkTools.smartWriter(
acq, str(DATA_PATH + reconstructFilenameLabelled))
cmd = "Mokka.exe \"%s\"" % (str(DATA_PATH +
reconstructFilenameLabelled))
os.system(cmd)
# --------------------------GLOBAL SETTINGS ------------------------------------
# global setting ( in user/AppData)
if os.path.isfile(pyCGM2.PYCGM2_APPDATA_PATH + "CGM1-pyCGM2.settings"):
settings = files.openFile(pyCGM2.PYCGM2_APPDATA_PATH,
"CGM1-pyCGM2.settings")
else:
settings = files.openFile(pyCGM2.PYCGM2_SETTINGS_FOLDER,
"CGM1-pyCGM2.settings")
# --------------------------MP ------------------------------------
required_mp, optional_mp = qtmTools.SubjectMp(sessionXML)
# --Check MP
inspectprocedure = inspectProcedures.AnthropometricDataQualityProcedure(
required_mp)
inspector = inspectFilters.QualityFilter(inspectprocedure)
inspector.run()
# translators management
translators = files.getTranslators(os.getcwd() + "\\", "CGM1.translators")
if not translators: translators = settings["Translators"]
# --------------------------MODEL CALIBRATION -----------------------
logging.info(
"--------------------------MODEL CALIBRATION -----------------------")
staticMeasurement = qtmTools.findStatic(sessionXML)
calibrateFilenameLabelled = qtmTools.getFilename(staticMeasurement)
logging.info("----- CALIBRATION- static file [%s]--" %
(calibrateFilenameLabelled))
leftFlatFoot = toBool(
staticMeasurement.Left_foot_normalised_to_static_trial.text)
rightFlatFoot = toBool(
staticMeasurement.Right_foot_normalised_to_static_trial.text)
headFlat = toBool(staticMeasurement.Head_normalised_to_static_trial.text)
markerDiameter = float(staticMeasurement.Marker_diameter.text) * 1000.0
pointSuffix = None
# Calibration checking
# --------------------
acqStatic = btkTools.smartReader(DATA_PATH + calibrateFilenameLabelled)
for key in MARKERSETS.keys():
logging.info("[pyCGM2] Checking of the %s" % (key))
# presence
ip_presence = inspectProcedures.MarkerPresenceQualityProcedure(
acqStatic, markers=MARKERSETS[key])
inspector = inspectFilters.QualityFilter(ip_presence)
inspector.run()
if ip_presence.markersIn != []:
ip_gap = inspectProcedures.GapQualityProcedure(
acqStatic, markers=ip_presence.markersIn)
inspector = inspectFilters.QualityFilter(ip_gap)
inspector.run()
ip_swap = inspectProcedures.SwappingMarkerQualityProcedure(
acqStatic, markers=ip_presence.markersIn)
inspector = inspectFilters.QualityFilter(ip_swap)
inspector.run()
ip_pos = inspectProcedures.MarkerPositionQualityProcedure(
acqStatic, markers=ip_presence.markersIn)
inspector = inspectFilters.QualityFilter(ip_pos)
# Calibration operation
# --------------------
logging.info("[pyCGM2] --- calibration operation ---")
model, acqStatic = cgm1.calibrate(DATA_PATH, calibrateFilenameLabelled,
translators, required_mp, optional_mp,
leftFlatFoot, rightFlatFoot, headFlat,
markerDiameter, pointSuffix)
logging.info("----- CALIBRATION- static file [%s]-----> DONE" %
(calibrateFilenameLabelled))
# --------------------------MODEL FITTING ----------------------------------
logging.info(
"--------------------------MODEL FITTING ----------------------------------"
)
dynamicMeasurements = qtmTools.findDynamic(sessionXML)
modelledC3ds = list()
eventInspectorStates = list()
for dynamicMeasurement in dynamicMeasurements:
reconstructFilenameLabelled = qtmTools.getFilename(dynamicMeasurement)
logging.info("----Processing of [%s]-----" %
(reconstructFilenameLabelled))
mfpa = qtmTools.getForcePlateAssigment(dynamicMeasurement)
momentProjection_text = dynamicMeasurement.Moment_Projection.text
if momentProjection_text == "Default":
momentProjection_text = settings["Fitting"]["Moment Projection"]
if momentProjection_text == "Distal":
momentProjection = enums.MomentProjection.Distal
elif momentProjection_text == "Proximal":
momentProjection = enums.MomentProjection.Proximal
elif momentProjection_text == "Global":
momentProjection = enums.MomentProjection.Global
acq = btkTools.smartReader(DATA_PATH + reconstructFilenameLabelled)
# Fitting checking
# --------------------
for key in MARKERSETS.keys():
if key != "Calibration markers":
logging.info("[pyCGM2] Checking of the %s" % (key))
# presence
ip_presence = inspectProcedures.MarkerPresenceQualityProcedure(
acq, markers=MARKERSETS[key])
inspector = inspectFilters.QualityFilter(ip_presence)
inspector.run()
if ip_presence.markersIn != []:
ip_gap = inspectProcedures.GapQualityProcedure(
acq, markers=ip_presence.markersIn)
inspector = inspectFilters.QualityFilter(ip_gap)
inspector.run()
ip_swap = inspectProcedures.SwappingMarkerQualityProcedure(
acq, markers=ip_presence.markersIn)
inspector = inspectFilters.QualityFilter(ip_swap)
inspector.run()
ip_pos = inspectProcedures.MarkerPositionQualityProcedure(
acq, markers=ip_presence.markersIn)
inspector = inspectFilters.QualityFilter(ip_pos)
# filtering
# -----------------------
# marker
order = int(float(dynamicMeasurement.Marker_lowpass_filter_order.text))
fc = float(dynamicMeasurement.Marker_lowpass_filter_frequency.text)
signal_processing.markerFiltering(acq, order=order, fc=fc)
# management of force plate type 5 and force plate filtering
order = int(
float(dynamicMeasurement.Forceplate_lowpass_filter_order.text))
fc = float(dynamicMeasurement.Forceplate_lowpass_filter_frequency.text)
if order != 0 and fc != 0:
acq = btkTools.smartReader(DATA_PATH + reconstructFilenameLabelled)
if btkTools.checkForcePlateExist(acq):
if "5" in btkTools.smartGetMetadata(acq, "FORCE_PLATFORM",
"TYPE"):
forceplates.correctForcePlateType5(acq)
signal_processing.markerFiltering(acq, order=order, fc=fc)
else:
if btkTools.checkForcePlateExist(acq):
if "5" in btkTools.smartGetMetadata(acq, "FORCE_PLATFORM",
"TYPE"):
forceplates.correctForcePlateType5(acq)
btkTools.smartWriter(acq, DATA_PATH + reconstructFilenameLabelled)
# event checking
# -----------------------
inspectprocedureEvents = inspectProcedures.GaitEventQualityProcedure(
acq)
inspector = inspectFilters.QualityFilter(inspectprocedureEvents)
inspector.run
eventInspectorStates.append(inspectprocedureEvents.state)
# fitting operation
# -----------------------
logging.info("[pyCGM2] --- Fitting operation ---")
acqGait = cgm1.fitting(model, DATA_PATH, reconstructFilenameLabelled,
translators, markerDiameter, pointSuffix, mfpa,
momentProjection)
outFilename = reconstructFilenameLabelled #[:-4] + "_CGM1.c3d"
btkTools.smartWriter(acqGait, str(DATA_PATH + outFilename))
modelledC3ds.append(outFilename)
logging.info("----Processing of [%s]-----> DONE" %
(reconstructFilenameLabelled))
# --------------------------GAIT PROCESSING -----------------------
if not all(eventInspectorStates):
raise Exception(
"[pyCGM2] Impossible to run Gait processing. Badly gait event detection. check the log file"
)
logging.info(
"---------------------GAIT PROCESSING -----------------------")
nds = normativeDatasets.Schwartz2008("Free")
types = qtmTools.detectMeasurementType(sessionXML)
for type in types:
modelledTrials = list()
for dynamicMeasurement in dynamicMeasurements:
if qtmTools.isType(dynamicMeasurement, type):
filename = qtmTools.getFilename(dynamicMeasurement)
modelledTrials.append(filename) #.replace(".c3d","_CGM1.c3d"))
subjectMd = {
"patientName":
sessionXML.find("Last_name").text + " " +
sessionXML.find("First_name").text,
"bodyHeight":
sessionXML.find("Height").text,
"bodyWeight":
sessionXML.find("Weight").text,
"diagnosis":
sessionXML.find("Diagnosis").text,
"dob":
sessionXML.find("Date_of_birth").text,
"sex":
sessionXML.find("Sex").text,
"test condition":
type,
"gmfcs":
sessionXML.find("Gross_Motor_Function_Classification").text,
"fms":
sessionXML.find("Functional_Mobility_Scale").text
}
analysisInstance = analysis.makeAnalysis(DATA_PATH,
modelledTrials,
subjectInfo=None,
experimentalInfo=None,
modelInfo=None,
pointLabelSuffix=None)
title = type
# spatiotemporal
plot.plot_spatioTemporal(DATA_PATH,
analysisInstance,
exportPdf=True,
outputName=title,
show=None,
title=title)
#Kinematics
if model.m_bodypart in [
enums.BodyPart.LowerLimb, enums.BodyPart.LowerLimbTrunk,
enums.BodyPart.FullBody
]:
plot.plot_DescriptiveKinematic(DATA_PATH,
analysisInstance,
"LowerLimb",
nds,
exportPdf=True,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
plot.plot_ConsistencyKinematic(DATA_PATH,
analysisInstance,
"LowerLimb",
nds,
exportPdf=True,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
if model.m_bodypart in [
enums.BodyPart.LowerLimbTrunk, enums.BodyPart.FullBody
]:
plot.plot_DescriptiveKinematic(DATA_PATH,
analysisInstance,
"Trunk",
nds,
exportPdf=True,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
plot.plot_ConsistencyKinematic(DATA_PATH,
analysisInstance,
"Trunk",
nds,
exportPdf=True,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
if model.m_bodypart in [
enums.BodyPart.UpperLimb, enums.BodyPart.FullBody
]:
pass # TODO plot upperlimb panel
#Kinetics
if model.m_bodypart in [
enums.BodyPart.LowerLimb, enums.BodyPart.LowerLimbTrunk,
enums.BodyPart.FullBody
]:
plot.plot_DescriptiveKinetic(DATA_PATH,
analysisInstance,
"LowerLimb",
nds,
exportPdf=True,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
plot.plot_ConsistencyKinetic(DATA_PATH,
analysisInstance,
"LowerLimb",
nds,
exportPdf=True,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
#MAP
plot.plot_MAP(DATA_PATH,
analysisInstance,
nds,
exportPdf=True,
outputName=title,
pointLabelSuffix=pointSuffix,
show=False,
title=title)
plt.show(False)
logging.info("----- Gait Processing -----> DONE")
def main():
parser = argparse.ArgumentParser(description='CGM1 Calibration')
parser.add_argument('-l',
'--leftFlatFoot',
type=int,
help='left flat foot option')
parser.add_argument('-r',
'--rightFlatFoot',
type=int,
help='right flat foot option')
parser.add_argument('-hf', '--headFlat', type=int, help='head flat option')
parser.add_argument('-md',
'--markerDiameter',
type=float,
help='marker diameter')
parser.add_argument('-ps',
'--pointSuffix',
type=str,
help='suffix of model outputs')
parser.add_argument('--check',
action='store_true',
help='force model output suffix')
parser.add_argument('--resetMP',
action='store_true',
help='reset optional mass parameters')
parser.add_argument('-ae',
'--anomalyException',
action='store_true',
help='stop if anomaly detected ')
args = parser.parse_args()
NEXUS = ViconNexus.ViconNexus()
NEXUS_PYTHON_CONNECTED = NEXUS.Client.IsConnected()
if NEXUS_PYTHON_CONNECTED: # run Operation
# --------------------------GLOBAL SETTINGS ------------------------------------
# global setting ( in user/AppData)
if os.path.isfile(pyCGM2.PYCGM2_APPDATA_PATH + "CGM1-pyCGM2.settings"):
settings = files.openFile(pyCGM2.PYCGM2_APPDATA_PATH,
"CGM1-pyCGM2.settings")
else:
settings = files.openFile(pyCGM2.PYCGM2_SETTINGS_FOLDER,
"CGM1-pyCGM2.settings")
# --------------------------CONFIG ------------------------------------
argsManager = CgmArgsManager.argsManager_cgm1(settings, args)
leftFlatFoot = argsManager.getLeftFlatFoot()
rightFlatFoot = argsManager.getRightFlatFoot()
headFlat = argsManager.getHeadFlat()
markerDiameter = argsManager.getMarkerDiameter()
pointSuffix = argsManager.getPointSuffix("cgm1")
DATA_PATH, calibrateFilenameLabelledNoExt = NEXUS.GetTrialName()
calibrateFilenameLabelled = calibrateFilenameLabelledNoExt + ".c3d"
LOGGER.logger.info("data Path: " + DATA_PATH)
LOGGER.set_file_handler(DATA_PATH + "pyCGM2-Calibration.log")
LOGGER.logger.info("calibration file: " + calibrateFilenameLabelled)
# --------------------------SUBJECT ------------------------------------
subjects = NEXUS.GetSubjectNames()
subject = nexusTools.getActiveSubject(
NEXUS) #checkActivatedSubject(NEXUS,subjects)
Parameters = NEXUS.GetSubjectParamNames(subject)
required_mp, optional_mp = nexusUtils.getNexusSubjectMp(
NEXUS, subject, resetFlag=args.resetMP)
# -------------------------- INFOS ------------------------------------
mpInfo, mpFilename = files.getMpFileContent(DATA_PATH, "mp.pyCGM2",
subject)
# translators management
translators = files.getTranslators(DATA_PATH, "CGM1.translators")
if not translators: translators = settings["Translators"]
# btkAcq builder
nacf = nexusFilters.NexusConstructAcquisitionFilter(
DATA_PATH, calibrateFilenameLabelledNoExt, subject)
acq = nacf.build()
# --------------------------MODELLING PROCESSING -----------------------
model, acqStatic, detectAnomaly = cgm1.calibrate(
DATA_PATH,
calibrateFilenameLabelled,
translators,
required_mp,
optional_mp,
leftFlatFoot,
rightFlatFoot,
headFlat,
markerDiameter,
pointSuffix,
forceBtkAcq=acq,
anomalyException=args.anomalyException)
# ----------------------SAVE-------------------------------------------
#pyCGM2.model
files.saveModel(model, DATA_PATH, subject)
# save mp
files.saveMp(mpInfo, model, DATA_PATH, mpFilename)
# ----------------------DISPLAY ON VICON-------------------------------
nexusUtils.updateNexusSubjectMp(NEXUS, model, subject)
nexusFilters.NexusModelFilter(NEXUS,
model,
acqStatic,
subject,
pointSuffix,
staticProcessing=True).run()
def main(args):
NEXUS = ViconNexus.ViconNexus()
NEXUS_PYTHON_CONNECTED = NEXUS.Client.IsConnected()
if NEXUS_PYTHON_CONNECTED: # run Operation
# --------------------------GLOBAL SETTINGS ------------------------------------
# global setting ( in user/AppData)
if os.path.isfile(pyCGM2.PYCGM2_APPDATA_PATH + "CGM1-pyCGM2.settings"):
settings = files.openFile(pyCGM2.PYCGM2_APPDATA_PATH,"CGM1-pyCGM2.settings")
else:
settings = files.openFile(pyCGM2.PYCGM2_SETTINGS_FOLDER,"CGM1-pyCGM2.settings")
# --------------------------CONFIG ------------------------------------
argsManager = CgmArgsManager.argsManager_cgm1(settings,args)
leftFlatFoot = argsManager.getLeftFlatFoot()
rightFlatFoot = argsManager.getRightFlatFoot()
headFlat = argsManager.getHeadFlat()
markerDiameter = argsManager.getMarkerDiameter()
pointSuffix = argsManager.getPointSuffix("cgm1")
DATA_PATH, calibrateFilenameLabelledNoExt = NEXUS.GetTrialName()
calibrateFilenameLabelled = calibrateFilenameLabelledNoExt+".c3d"
logging.info( "data Path: "+ DATA_PATH )
logging.info( "calibration file: "+ calibrateFilenameLabelled)
# --------------------------SUBJECT ------------------------------------
subjects = NEXUS.GetSubjectNames()
subject = nexusTools.checkActivatedSubject(NEXUS,subjects)
Parameters = NEXUS.GetSubjectParamNames(subject)
required_mp,optional_mp = nexusUtils.getNexusSubjectMp(NEXUS,subject,resetFlag=args.resetMP)
# -------------------------- INFOS ------------------------------------
mpInfo,mpFilename = files.getMpFileContent(DATA_PATH,"mp.pyCGM2",subject)
# translators management
translators = files.getTranslators(DATA_PATH,"CGM1.translators")
if not translators: translators = settings["Translators"]
# btkAcq builder
nacf = nexusFilters.NexusConstructAcquisitionFilter(DATA_PATH,calibrateFilenameLabelledNoExt,subject)
acq = nacf.build()
# --------------------------MODELLING PROCESSING -----------------------
model,acqStatic = cgm1.calibrate(DATA_PATH,calibrateFilenameLabelled,translators,
required_mp,optional_mp,
leftFlatFoot,rightFlatFoot,headFlat,markerDiameter,
pointSuffix,forceBtkAcq=acq)
# ----------------------SAVE-------------------------------------------
#pyCGM2.model
files.saveModel(model,DATA_PATH,subject)
# save mp
files.saveMp(mpInfo,model,DATA_PATH,mpFilename)
# ----------------------DISPLAY ON VICON-------------------------------
nexusUtils.updateNexusSubjectMp(NEXUS,model,subject)
nexusFilters.NexusModelFilter(NEXUS,
model,acqStatic,subject,
pointSuffix,
staticProcessing=True).run()
