def main():
qtm_folder = os.getcwd()
sessionXML = files.readXml(qtm_folder + "\\", "session.xml")
# --------------------------MP ------------------------------------
required_mp, _ = qtmTools.SubjectMp(sessionXML)
# --------------------------Check MP ----------------------------------
logging.info("--MP Checking--")
inspectprocedure1 = inspectProcedures.AnthropometricDataQualityProcedure(
required_mp)
inspector = inspectFilters.QualityFilter(inspectprocedure1)
inspector.run()
# --------------------------FILES -----------------------
staticMeasurement = utils.find_static(sessionXML)
staticFilename = qtmTools.getFilename(staticMeasurement)
dynamicFilenames = []
dynamicMeasurements = qtmTools.findDynamic(sessionXML)
for dynamicMeasurement in dynamicMeasurements:
reconstructFilenameLabelled = qtmTools.getFilename(dynamicMeasurement)
dynamicFilenames.append(reconstructFilenameLabelled)
# --------------------------CHECKING -----------------------
# static is only in qtm folder and does not get processed
runAllQualityProcedures(qtm_folder, [staticFilename])
runAllQualityProcedures(os.path.join(qtm_folder, "processed"),
dynamicFilenames)
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 = utils.find_static(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 + "CGM2_2-pyCGM2.settings"):
settings = files.openFile(pyCGM2.PYCGM2_APPDATA_PATH,
"CGM2_2-pyCGM2.settings")
else:
settings = files.openFile(pyCGM2.PYCGM2_SETTINGS_FOLDER,
"CGM2_2-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() + "\\",
"CGM2_2.translators")
if not translators:
translators = settings["Translators"]
# ikweight
ikWeight = files.getIKweightSet(DATA_PATH, "CGM2_2.ikw")
if not ikWeight:
ikWeight = settings["Fitting"]["Weight"]
# --------------------------MODEL CALIBRATION -----------------------
logging.info(
"--------------------------MODEL CALIBRATION -----------------------")
staticMeasurement = utils.find_static(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
hjcMethod = settings["Calibration"]["HJC"]
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 = cgm2_2.calibrate(DATA_PATH, calibrateFilenameLabelled,
translators, settings, required_mp,
optional_mp, False, leftFlatFoot,
rightFlatFoot, headFlat,
markerDiameter, hjcMethod, 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 = cgm2_2.fitting(model, DATA_PATH, reconstructFilenameLabelled,
translators, settings, 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 -----------------------")
return model
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():
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 + "CGM2_2-pyCGM2.settings"):
settings = files.openFile(pyCGM2.PYCGM2_APPDATA_PATH,
"CGM2_2-pyCGM2.settings")
else:
settings = files.openFile(pyCGM2.PYCGM2_SETTINGS_FOLDER,
"CGM2_2-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() + "\\",
"CGM2_2.translators")
if not translators: translators = settings["Translators"]
# ikweight
ikWeight = files.getIKweightSet(DATA_PATH, "CGM2_2.ikw")
if not ikWeight: ikWeight = settings["Fitting"]["Weight"]
# --------------------------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
hjcMethod = settings["Calibration"]["HJC"]
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 = cgm2_2.calibrate(DATA_PATH, calibrateFilenameLabelled,
translators, settings, required_mp,
optional_mp, False, leftFlatFoot,
rightFlatFoot, headFlat,
markerDiameter, hjcMethod, 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 = cgm2_2.fitting(model, DATA_PATH, reconstructFilenameLabelled,
translators, settings, 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 test(cls):
DATA_PATH ="C:\\Users\\HLS501\\Documents\\VICON DATA\\pyCGM2-Data\\operations\\inspection\\sample0\\"
filename = "static.c3d"
logging.info("TEST")
mp={
'Bodymass' : 70.0,
'LeftLegLength' : 900.0,
'RightLegLength' : 900.0 ,
'LeftKneeWidth' : 100.0,
'RightKneeWidth' : 100.0,
'LeftAnkleWidth' : 70.0,
'RightAnkleWidth' : 70.0,
'LeftSoleDelta' : 0,
'RightSoleDelta' : 0,
'LeftShoulderOffset' : 0,
'LeftElbowWidth' : 0,
'LeftWristWidth' : 0 ,
'LeftHandThickness' : 0 ,
'RightShoulderOffset' : 0,
'RightElbowWidth' : 0,
'RightWristWidth' : 0 ,
'RightHandThickness' : 0}
inspectprocedure1 = inspectProcedures.AnthropometricDataQualityProcedure(mp)
inspector = inspectFilters.QualityFilter(inspectprocedure1)
inspector.run()
acq = btkTools.smartReader(DATA_PATH+"gait_gap.c3d")
inspectprocedure1 = inspectProcedures.GapQualityProcedure(acq)
inspector = inspectFilters.QualityFilter(inspectprocedure1)
inspector.run()
acq = btkTools.smartReader(DATA_PATH+"gait_swapped.c3d")
inspectprocedure2 = inspectProcedures.SwappingMarkerQualityProcedure(acq)
inspector = inspectFilters.QualityFilter(inspectprocedure2)
inspector.run()
# acq = btkTools.smartReader(DATA_PATH+"gait_noEvents.c3d")
# inspectprocedure2 = inspectProcedures.GaitEventQualityProcedure(acq)
# inspector = inspectFilters.QualityFilter(inspectprocedure2)
# inspector.run()
acq = btkTools.smartReader(DATA_PATH+"gait_wrongEvent.c3d")
inspectprocedure2 = inspectProcedures.GaitEventQualityProcedure(acq)
inspector = inspectFilters.QualityFilter(inspectprocedure2)
inspector.run()
acq = btkTools.smartReader(DATA_PATH+"gait_PelvisSwapped.c3d")
inspectprocedure2 = inspectProcedures.MarkerQualityProcedure(acq)
inspector = inspectFilters.QualityFilter(inspectprocedure2)
inspector.run()