def main():
parser = argparse.ArgumentParser(description='CGM2-3 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('--noIk',
action='store_true',
help='cancel inverse kinematic')
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('-a',
'--accuracy',
type=float,
help='Inverse Kinematics accuracy')
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 +
"CGM2_3-pyCGM2.settings"):
settings = files.openFile(pyCGM2.PYCGM2_APPDATA_PATH,
"CGM2_3-pyCGM2.settings")
else:
settings = files.openFile(pyCGM2.PYCGM2_SETTINGS_FOLDER,
"CGM2_3-pyCGM2.settings")
# --------------------------CONFIG ------------------------------------
argsManager = CgmArgsManager.argsManager_cgm(settings, args)
markerDiameter = argsManager.getMarkerDiameter()
pointSuffix = argsManager.getPointSuffix("cgm2.3")
momentProjection = argsManager.getMomentProjection()
ik_flag = argsManager.enableIKflag
ikAccuracy = argsManager.getIkAccuracy()
# ----------------------LOADING-------------------------------------------
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
LOGGER.logger.info("loaded model : %s" % (model.version))
if model.version != "CGM2.3":
raise Exception(
"%s-pyCGM2.model file was not calibrated from the CGM2.3 calibration pipeline"
% subject)
# --------------------------SESSION INFOS ------------------------------------
# translators management
translators = files.getTranslators(DATA_PATH, "CGM2_3.translators")
if not translators: translators = settings["Translators"]
# ikweight
ikWeight = files.getIKweightSet(DATA_PATH, "CGM2_3.ikw")
if not ikWeight: ikWeight = settings["Fitting"]["Weight"]
#force plate assignement from Nexus
mfpa = nexusTools.getForcePlateAssignment(NEXUS)
# btkAcquisition
nacf = nexusFilters.NexusConstructAcquisitionFilter(
DATA_PATH, reconstructFilenameLabelledNoExt, subject)
acq = nacf.build()
# --------------------------MODELLING PROCESSING -----------------------
finalAcqGait, detectAnomaly = cgm2_3.fitting(
model,
DATA_PATH,
reconstructFilenameLabelled,
translators,
settings,
ik_flag,
markerDiameter,
pointSuffix,
mfpa,
momentProjection,
forceBtkAcq=acq,
ikAccuracy=ikAccuracy,
anomalyException=args.anomalyException,
frameInit=args.frameInit,
frameEnd=args.frameEnd)
# ----------------------DISPLAY ON VICON-------------------------------
nexusFilters.NexusModelFilter(NEXUS, model, finalAcqGait, subject,
pointSuffix).run()
nexusTools.createGeneralEvents(NEXUS, subject, finalAcqGait,
["Left-FP", "Right-FP"])
# ========END of the nexus OPERATION if run from Nexus =========
else:
raise Exception("NO Nexus connection. Turn on Nexus")
# configEnf.read(enfFile)
#
#
# indexFP=1
# for letter in mappedForcePlate:
#
# if letter =="L": configEnf["TRIAL_INFO"]["FP"+str(indexFP)]="Left"
# if letter =="R": configEnf["TRIAL_INFO"]["FP"+str(indexFP)]="Right"
# if letter =="X": configEnf["TRIAL_INFO"]["FP"+str(indexFP)]="Invalid"
#
# indexFP+=1
#
# tmpFile =str(DATA_PATH+reconstructFilenameLabelledNoExt+".Trial.enf-tmp")
# with open(tmpFile, 'w') as configfile:
# configEnf.write(configfile)
#
# os.remove(enfFile)
# os.rename(tmpFile,enfFile)
# logging.warning("Enf file updated with Force plate assignement")
# ----------------------DISPLAY ON VICON-------------------------------
nexusTools.createGeneralEvents(NEXUS, subject, acqGait,
["Left-FP", "Right-FP"])
# ========END of the nexus OPERATION if run from Nexus =========
if DEBUG:
NEXUS.SaveTrial(30)
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_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():
parser = argparse.ArgumentParser(description='CGM2-1 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')
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 +
"CGM2_1-pyCGM2.settings"):
settings = files.openFile(pyCGM2.PYCGM2_APPDATA_PATH,
"CGM2_1-pyCGM2.settings")
else:
settings = files.openFile(pyCGM2.PYCGM2_SETTINGS_FOLDER,
"CGM2_1-pyCGM2.settings")
# --------------------------CONFIG ------------------------------------
argsManager = CgmArgsManager.argsManager_cgm(settings, args)
markerDiameter = argsManager.getMarkerDiameter()
pointSuffix = argsManager.getPointSuffix("cgm2.1")
momentProjection = argsManager.getMomentProjection()
# --------------------------LOADING ------------------------------------
DATA_PATH, reconstructFilenameLabelledNoExt = NEXUS.GetTrialName()
reconstructFilenameLabelled = reconstructFilenameLabelledNoExt + ".c3d"
logging.info("data Path: " + DATA_PATH)
logging.info("calibration file: " + reconstructFilenameLabelled)
# --------------------------SUBJECT ------------------------------------
subjects = NEXUS.GetSubjectNames()
subject = nexusTools.checkActivatedSubject(NEXUS, subjects)
logging.info("Subject name : " + subject)
# --------------------pyCGM2 MODEL ------------------------------
model = files.loadModel(DATA_PATH, subject)
# check model
logging.info("loaded model : %s" % (model.version))
if model.version != "CGM2.1":
raise Exception(
"%s-pyCGM2.model file was not calibrated from the CGM2.1 calibration pipeline"
% subject)
# --------------------------SESSION INFOS ------------------------------------
# translators management
translators = files.getTranslators(DATA_PATH, "CGM2_1.translators")
if not translators: translators = settings["Translators"]
#force plate assignement from Nexus
mfpa = nexusTools.getForcePlateAssignment(NEXUS)
# btkAcq builder
nacf = nexusFilters.NexusConstructAcquisitionFilter(
DATA_PATH, reconstructFilenameLabelledNoExt, subject)
acq = nacf.build()
# --------------------------MODELLING PROCESSING -----------------------
acqGait = cgm2_1.fitting(model,
DATA_PATH,
reconstructFilenameLabelled,
translators,
markerDiameter,
pointSuffix,
mfpa,
momentProjection,
forceBtkAcq=acq)
# ----------------------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):
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 + "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")
# --------------------------CONFIG ------------------------------------
argsManager = CgmArgsManager.argsManager_cgm(settings,args)
markerDiameter = argsManager.getMarkerDiameter()
pointSuffix = argsManager.getPointSuffix("cgm2.2")
momentProjection = argsManager.getMomentProjection()
# --------------------------LOADING ------------------------------------
DATA_PATH, reconstructFilenameLabelledNoExt = NEXUS.GetTrialName()
reconstructFilenameLabelled = reconstructFilenameLabelledNoExt+".c3d"
logging.info( "data Path: "+ DATA_PATH )
logging.info( "calibration file: "+ reconstructFilenameLabelled)
# --------------------------SUBJECT ------------------------------------
subjects = NEXUS.GetSubjectNames()
subject = nexusTools.checkActivatedSubject(NEXUS,subjects)
logging.info( "Subject name : " + subject )
# --------------------pyCGM2 MODEL ------------------------------
model = files.loadModel(DATA_PATH,subject)
# check model
logging.info("loaded model : %s" %(model.version))
if model.version != "CGM2.2":
raise Exception ("%s-pyCGM2.model file was not calibrated from the CGM2.2 calibration pipeline"%subject)
# --------------------------SESSION INFOS ------------------------------------
translators = files.getTranslators(DATA_PATH,"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"]
#force plate assignement from Nexus
mfpa = nexusTools.getForcePlateAssignment(NEXUS)
nacf = nexusFilters.NexusConstructAcquisitionFilter(DATA_PATH,reconstructFilenameLabelledNoExt,subject)
acq = nacf.build()
# --------------------------MODELLING PROCESSING -----------------------
acqIK = cgm2_2.fitting(model,DATA_PATH, reconstructFilenameLabelled,
translators,settings,
markerDiameter,
pointSuffix,
mfpa,
momentProjection,
forceBtkAcq=acq)
# ----------------------DISPLAY ON VICON-------------------------------
nexusFilters.NexusModelFilter(NEXUS,model,acqIK,subject,pointSuffix).run()
nexusTools.createGeneralEvents(NEXUS,subject,acqIK,["Left-FP","Right-FP"])
# ========END of the nexus OPERATION if run from Nexus =========
else:
raise Exception("NO Nexus connection. Turn on Nexus")
