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 folder
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_1-pyCGM2.settings"):
settings = files.openFile(pyCGM2.PYCGM2_APPDATA_PATH,
"CGM1_1-pyCGM2.settings")
else:
settings = files.openFile(pyCGM2.PYCGM2_SETTINGS_FOLDER,
"CGM1_1-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_1.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_1.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
elif momentProjection_text == "JCS":
momentProjection = enums.MomentProjection.JCS
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_1.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 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_1.translators"):
translators = files.openFile(DATA_PATH,"CGM1_1.translators")
else:
translators = None
# --- Manager ----
manager = ModelManager.CGM1_1ConfigManager(userSettings,localInternalSettings=internalSettings,localTranslators=translators)
manager.contruct()
finalSettings = manager.getFinalSettings()
files.prettyDictPrint(finalSettings)
logging.info("=============Calibration=============")
model,finalAcqStatic = cgm1_1.calibrate(DATA_PATH,
manager.staticTrial,
manager.translators,
manager.requiredMp,
manager.optionalMp,
manager.leftFlatFoot,
manager.rightFlatFoot,
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_1.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("CGM1.1 [%s].completeSettings" % i):
i += 1
filename = "CGM1.1 [" + str(i)+"].completeSettings"
files.saveJson(DATA_PATH, filename, finalSettings)
logging.info("---->complete settings (%s) exported" %(filename))
raw_input("Press return to exit..")
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_1-pyCGM2.settings"):
settings = files.openFile(pyCGM2.PYCGM2_APPDATA_PATH,
"CGM1_1-pyCGM2.settings")
else:
settings = files.openFile(pyCGM2.PYCGM2_SETTINGS_FOLDER,
"CGM1_1-pyCGM2.settings")
# --------------------------CONFIG ------------------------------------
argsManager = CgmArgsManager.argsManager_cgm(settings, args)
markerDiameter = argsManager.getMarkerDiameter()
pointSuffix = argsManager.getPointSuffix("cgm1_1")
momentProjection = argsManager.getMomentProjection()
DATA_PATH, reconstructFilenameLabelledNoExt = NEXUS.GetTrialName()
reconstructFilenameLabelled = reconstructFilenameLabelledNoExt + ".c3d"
logging.info("data Path: " + DATA_PATH)
logging.info("calibration file: " + reconstructFilenameLabelled)
# --------------------------SUBJECT ------------------------------------
# Notice : Work with ONE subject by session
subjects = NEXUS.GetSubjectNames()
subject = nexusTools.checkActivatedSubject(NEXUS, subjects)
logging.info("Subject name : " + subject)
# --------------------pyCGM2 MODEL ------------------------------
model = files.loadModel(DATA_PATH, subject)
# --------------------------CHECKING -----------------------------------
# check model is the CGM1
logging.info("loaded model : %s" % (model.version))
if model.version != "CGM1.1":
raise Exception(
"%s-pyCGM2.model file was not calibrated from the CGM1.1 calibration pipeline"
% model.version)
# --------------------------SESSION INFOS ------------------------------------
# translators management
translators = files.getTranslators(DATA_PATH, "CGM1_1.translators")
if not translators: translators = settings["Translators"]
# btkAcq builder
nacf = nexusFilters.NexusConstructAcquisitionFilter(
DATA_PATH, reconstructFilenameLabelledNoExt, subject)
acq = nacf.build()
#force plate assignement from Nexus
mfpa = nexusTools.getForcePlateAssignment(NEXUS)
# --------------------------MODELLING PROCESSING -----------------------
acqGait = cgm1_1.fitting(model,
DATA_PATH,
reconstructFilenameLabelled,
translators,
markerDiameter,
pointSuffix,
mfpa,
momentProjection,
forceBtkAcq=acq)
# ----------------------SAVE-------------------------------------------
# Todo: pyCGM2 model : cpickle doesn t work. Incompatibility with Swig. ( see about BTK wrench)
# ----------------------DISPLAY ON VICON-------------------------------
nexusFilters.NexusModelFilter(NEXUS, model, acqGait, subject,
pointSuffix).run()
nexusTools.createGeneralEvents(NEXUS, subject, acqGait,
["Left-FP", "Right-FP"])
# ========END of the nexus OPERATION if run from Nexus =========
else:
raise Exception("NO Nexus connection. Turn on Nexus")
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_1.translators"):
translators = files.openFile(DATA_PATH, "CGM1_1.translators")
else:
translators = None
# --- Manager ----
manager = ModelManager.CGM1_1ConfigManager(
userSettings,
localInternalSettings=internalSettings,
localTranslators=translators)
manager.contruct()
finalSettings = manager.getFinalSettings()
# files.prettyDictPrint(finalSettings)
# logging.info("=============Calibration=============")
model, finalAcqStatic = cgm1_1.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]) +
'.C3D') #+"-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_1.fitting(model,
DATA_PATH,
reconstructFilenameLabelled,
manager.translators,
manager.markerDiameter,
manager.pointSuffix,
mfpa,
manager.momentProjection,
displayCoordinateSystem=True)
btkTools.smartWriter(
acqGait,
str(DATA_PATH + reconstructFilenameLabelled[:-4]) +
'.C3D') #+"-pyCGM2modelled.c3d"
def main():
parser = argparse.ArgumentParser(description='CGM1.1 Fitting')
parser.add_argument(
'--proj',
type=str,
help='Moment Projection. Choice : Distal, Proximal, Global')
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('-ae',
'--anomalyException',
action='store_true',
help='stop if anomaly detected ')
parser.add_argument('-fi',
'--frameInit',
type=int,
help='first frame to process')
parser.add_argument('-fe',
'--frameEnd',
type=int,
help='last frame to process')
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_1-pyCGM2.settings"):
settings = files.openFile(pyCGM2.PYCGM2_APPDATA_PATH,
"CGM1_1-pyCGM2.settings")
else:
settings = files.openFile(pyCGM2.PYCGM2_SETTINGS_FOLDER,
"CGM1_1-pyCGM2.settings")
# --------------------------CONFIG ------------------------------------
argsManager = CgmArgsManager.argsManager_cgm(settings, args)
markerDiameter = argsManager.getMarkerDiameter()
pointSuffix = argsManager.getPointSuffix("cgm1_1")
momentProjection = argsManager.getMomentProjection()
DATA_PATH, reconstructFilenameLabelledNoExt = NEXUS.GetTrialName()
reconstructFilenameLabelled = reconstructFilenameLabelledNoExt + ".c3d"
LOGGER.logger.info("data Path: " + DATA_PATH)
LOGGER.set_file_handler(DATA_PATH + "pyCGM2-Fitting.log")
LOGGER.logger.info("calibration file: " + reconstructFilenameLabelled)
# --------------------------SUBJECT ------------------------------------
# Notice : Work with ONE subject by session
subjects = NEXUS.GetSubjectNames()
subject = nexusTools.getActiveSubject(NEXUS)
LOGGER.logger.info("Subject name : " + subject)
# --------------------pyCGM2 MODEL ------------------------------
model = files.loadModel(DATA_PATH, subject)
# -------------------------- MP ------------------------------------
# allow alteration of thigh offset
model.mp_computed[
"LeftThighRotationOffset"] = NEXUS.GetSubjectParamDetails(
subject, "LeftThighRotation")[0]
model.mp_computed[
"RightThighRotationOffset"] = NEXUS.GetSubjectParamDetails(
subject, "RightThighRotation")[0]
# --------------------------CHECKING -----------------------------------
# check model is the CGM1
LOGGER.logger.info("loaded model : %s" % (model.version))
if model.version != "CGM1.1":
raise Exception(
"%s-pyCGM2.model file was not calibrated from the CGM1.1 calibration pipeline"
% model.version)
# --------------------------SESSION INFOS ------------------------------------
# translators management
translators = files.getTranslators(DATA_PATH, "CGM1_1.translators")
if not translators: translators = settings["Translators"]
# btkAcq builder
nacf = nexusFilters.NexusConstructAcquisitionFilter(
DATA_PATH, reconstructFilenameLabelledNoExt, subject)
acq = nacf.build()
#force plate assignement from Nexus
mfpa = nexusTools.getForcePlateAssignment(NEXUS)
# --------------------------MODELLING PROCESSING -----------------------
acqGait, detectAnomaly = cgm1_1.fitting(
model,
DATA_PATH,
reconstructFilenameLabelled,
translators,
markerDiameter,
pointSuffix,
mfpa,
momentProjection,
forceBtkAcq=acq,
anomalyException=args.anomalyException,
frameInit=args.frameInit,
frameEnd=args.frameEnd)
# ----------------------SAVE-------------------------------------------
# Todo: pyCGM2 model : cpickle doesn t work. Incompatibility with Swig. ( see about BTK wrench)
# ----------------------DISPLAY ON VICON-------------------------------
nexusFilters.NexusModelFilter(NEXUS, model, acqGait, subject,
pointSuffix).run()
nexusTools.createGeneralEvents(NEXUS, subject, acqGait,
["Left-FP", "Right-FP"])
# ========END of the nexus OPERATION if run from Nexus =========
else:
raise Exception("NO Nexus connection. Turn on Nexus")
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 folder
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_1-pyCGM2.settings"):
settings = files.openFile(pyCGM2.PYCGM2_APPDATA_PATH,
"CGM1_1-pyCGM2.settings")
else:
settings = files.openFile(pyCGM2.PYCGM2_SETTINGS_FOLDER,
"CGM1_1-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_1.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_1.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
elif momentProjection_text == "JCS":
momentProjection = enums.MomentProjection.JCS
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_1.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(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 folder
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_1-pyCGM2.settings"):
settings = files.openFile(pyCGM2.PYCGM2_APPDATA_PATH,
"CGM1_1-pyCGM2.settings")
else:
settings = files.openFile(pyCGM2.PYCGM2_SETTINGS_FOLDER,
"CGM1_1-pyCGM2.settings")
# --------------------------MP ------------------------------------
required_mp, optional_mp = qtmTools.SubjectMp(sessionXML)
# translators management
translators = files.getTranslators(os.getcwd() + "\\",
"CGM1_1.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_1.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()
eventInspectorStates = 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
elif momentProjection_text == "JCS":
momentProjection = enums.MomentProjection.JCS
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_1.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))
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")
