def main():
parser = argparse.ArgumentParser(description='CGM2.4 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('--noIk', action='store_true', help='cancel inverse kinematic')
parser.add_argument('--resetMP', action='store_true', help='reset optional mass parameters')
parser.add_argument('--forceLHJC', nargs='+')
parser.add_argument('--forceRHJC', nargs='+')
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 ------------------------------
# ( in user/AppData)
if os.path.isfile(pyCGM2.PYCGM2_APPDATA_PATH + "CGM2_4-pyCGM2.settings"):
settings = files.openFile(pyCGM2.PYCGM2_APPDATA_PATH,"CGM2_4-pyCGM2.settings")
else:
settings = files.openFile(pyCGM2.PYCGM2_SETTINGS_FOLDER,"CGM2_4-pyCGM2.settings")
argsManager = CgmArgsManager.argsManager_cgm(settings,args)
leftFlatFoot = argsManager.getLeftFlatFoot()
rightFlatFoot = argsManager.getRightFlatFoot()
headFlat = argsManager.getHeadFlat()
markerDiameter = argsManager.getMarkerDiameter()
pointSuffix = argsManager.getPointSuffix("cgm2.4")
ik_flag = argsManager.enableIKflag()
hjcMethod = settings["Calibration"]["HJC"]
lhjc = argsManager.forceHjc("left")
rhjc = argsManager.forceHjc("right")
if lhjc is not None:
hjcMethod["Left"] = lhjc
if rhjc is not None:
hjcMethod["Right"] = rhjc
# --------------------------LOADING------------------------------
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 -----------------------------------
# Notice : Work with ONE subject by session
subjects = NEXUS.GetSubjectNames()
subject = nexusTools.getActiveSubject(NEXUS)
Parameters = NEXUS.GetSubjectParamNames(subject)
required_mp,optional_mp = nexusUtils.getNexusSubjectMp(NEXUS,subject,resetFlag=args.resetMP)
# --------------------------SESSION INFOS -----------------------------
# --------------------------SESSIONS INFOS -----------------------------------
mpInfo,mpFilename = files.getMpFileContent(DATA_PATH,"mp.pyCGM2",subject)
# translators management
translators = files.getTranslators(DATA_PATH,"CGM2_4.translators")
if not translators: translators = settings["Translators"]
# btkAcq builder
nacf = nexusFilters.NexusConstructAcquisitionFilter(DATA_PATH,calibrateFilenameLabelledNoExt,subject)
acq = nacf.build()
# --------------------------CONFIG ------------------------------------
model,finalAcqStatic,detectAnomaly = cgm2_4.calibrate(DATA_PATH,calibrateFilenameLabelled,translators,settings,
required_mp,optional_mp,
ik_flag,leftFlatFoot,rightFlatFoot,headFlat,
markerDiameter,
hjcMethod,
pointSuffix,forceBtkAcq=acq, anomalyException=args.anomalyException)
# ----------------------SAVE-------------------------------------------
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,finalAcqStatic,subject,
pointSuffix,
staticProcessing=True).run()
# ========END of the nexus OPERATION if run from Nexus =========
else:
raise Exception("NO Nexus connection. Turn on Nexus")
else:
DATA_PATH, calibrateFilenameLabelledNoExt = NEXUS.GetTrialName()
calibrateFilenameLabelled = calibrateFilenameLabelledNoExt + ".c3d"
logging.info("data Path: " + DATA_PATH)
logging.info("calibration file: " + calibrateFilenameLabelled)
# --------------------------SUBJECT ------------------------------------
# Notice : Work with ONE subject by session
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.getJsonFileContent(DATA_PATH, "mp.pyCGM2",
subject)
# translators management
translators = files.getTranslators(DATA_PATH, "CGM2_1.translators")
if not translators: translators = settings["Translators"]
# --------------------------MODELLING PROCESSING -----------------------
model, acqStatic = cgm2_1.calibrate(DATA_PATH,
calibrateFilenameLabelled,
translators, required_mp,
optional_mp, leftFlatFoot,
rightFlatFoot, markerDiameter,
def main():
parser = argparse.ArgumentParser(description='CGM1.1 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')
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_cgm1(settings, args)
leftFlatFoot = argsManager.getLeftFlatFoot()
rightFlatFoot = argsManager.getRightFlatFoot()
headFlat = argsManager.getHeadFlat()
markerDiameter = argsManager.getMarkerDiameter()
pointSuffix = argsManager.getPointSuffix("cgm1_1")
# --------------------------LOADING ------------------------------------
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_1.translators")
if not translators: translators = settings["Translators"]
# btkAcq builder
nacf = nexusFilters.NexusConstructAcquisitionFilter(
DATA_PATH, calibrateFilenameLabelledNoExt, subject)
acq = nacf.build()
# --------------------------MODELLING PROCESSING -----------------------
model, acqStatic = cgm1_1.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()
# ========END of the nexus OPERATION if run from Nexus =========
else:
raise Exception("NO Nexus connection. Turn on Nexus")
def main(args):
NEXUS = ViconNexus.ViconNexus()
NEXUS_PYTHON_CONNECTED = NEXUS.Client.IsConnected()
if NEXUS_PYTHON_CONNECTED: # run Operation
# --------------------GLOBAL SETTINGS ------------------------------
# ( in user/AppData)
if os.path.isfile(pyCGM2.PYCGM2_APPDATA_PATH +
"CGM2_5-pyCGM2.settings"):
settings = files.openFile(pyCGM2.PYCGM2_APPDATA_PATH,
"CGM2_5-pyCGM2.settings")
else:
settings = files.openFile(pyCGM2.PYCGM2_SETTINGS_FOLDER,
"CGM2_5-pyCGM2.settings")
argsManager = CgmArgsManager.argsManager_cgm(settings, args)
leftFlatFoot = argsManager.getLeftFlatFoot()
rightFlatFoot = argsManager.getRightFlatFoot()
headFlat = argsManager.getHeadFlat()
markerDiameter = argsManager.getMarkerDiameter()
pointSuffix = argsManager.getPointSuffix("cgm2.5")
ik_flag = argsManager.enableIKflag()
hjcMethod = settings["Calibration"]["HJC"]
lhjc = argsManager.forceHjc("left")
rhjc = argsManager.forceHjc("right")
if lhjc is not None:
hjcMethod["Left"] = lhjc
if rhjc is not None:
hjcMethod["Right"] = rhjc
# --------------------------LOADING------------------------------
DATA_PATH, calibrateFilenameLabelledNoExt = NEXUS.GetTrialName()
calibrateFilenameLabelled = calibrateFilenameLabelledNoExt + ".c3d"
logging.info("data Path: " + DATA_PATH)
logging.info("calibration file: " + calibrateFilenameLabelled)
# --------------------------SUBJECT -----------------------------------
# Notice : Work with ONE subject by session
subjects = NEXUS.GetSubjectNames()
subject = nexusTools.checkActivatedSubject(NEXUS, subjects)
Parameters = NEXUS.GetSubjectParamNames(subject)
required_mp, optional_mp = nexusUtils.getNexusSubjectMp(
NEXUS, subject, resetFlag=args.resetMP)
# --------------------------SESSION INFOS -----------------------------
# --------------------------SESSIONS INFOS -----------------------------------
mpInfo, mpFilename = files.getMpFileContent(DATA_PATH, "mp.pyCGM2",
subject)
# translators management
translators = files.getTranslators(DATA_PATH, "CGM2_5.translators")
if not translators: translators = settings["Translators"]
# btkAcq builder
nacf = nexusFilters.NexusConstructAcquisitionFilter(
DATA_PATH, calibrateFilenameLabelledNoExt, subject)
acq = nacf.build()
# --------------------------CONFIG ------------------------------------
model, finalAcqStatic = cgm2_5.calibrate(DATA_PATH,
calibrateFilenameLabelled,
translators,
settings,
required_mp,
optional_mp,
ik_flag,
leftFlatFoot,
rightFlatFoot,
headFlat,
markerDiameter,
hjcMethod,
pointSuffix,
forceBtkAcq=acq)
# ----------------------SAVE-------------------------------------------
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,
finalAcqStatic,
subject,
pointSuffix,
staticProcessing=True).run()
# ========END of the nexus OPERATION if run from Nexus =========
else:
raise Exception("NO Nexus connection. Turn on Nexus")
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()
