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_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():
NEXUS = ViconNexus.ViconNexus()
NEXUS_PYTHON_CONNECTED = NEXUS.Client.IsConnected()
parser = argparse.ArgumentParser(description='CGM1 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()
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)
markerDiameter = argsManager.getMarkerDiameter()
pointSuffix = argsManager.getPointSuffix("cgm1")
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 != "CGM1.0":
raise Exception(
"%s-pyCGM2.model file was not calibrated from the CGM1.0 calibration pipeline"
% model.version)
# --------------------------SESSION INFOS ------------------------------------
# translators management
translators = files.getTranslators(DATA_PATH, "CGM1.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 = cgm1.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"])
else:
raise Exception("NO Nexus connection. Turn on Nexus")
def main():
parser = argparse.ArgumentParser(description='CGM1 Calibration')
parser.add_argument('-l',
'--leftFlatFoot',
type=int,
help='left flat foot option')
parser.add_argument('-r',
'--rightFlatFoot',
type=int,
help='right flat foot option')
parser.add_argument('-hf', '--headFlat', type=int, help='head flat option')
parser.add_argument('-md',
'--markerDiameter',
type=float,
help='marker diameter')
parser.add_argument('-ps',
'--pointSuffix',
type=str,
help='suffix of model outputs')
parser.add_argument('--check',
action='store_true',
help='force model output suffix')
parser.add_argument('--resetMP',
action='store_true',
help='reset optional mass parameters')
parser.add_argument('-ae',
'--anomalyException',
action='store_true',
help='stop if anomaly detected ')
args = parser.parse_args()
NEXUS = ViconNexus.ViconNexus()
NEXUS_PYTHON_CONNECTED = NEXUS.Client.IsConnected()
if NEXUS_PYTHON_CONNECTED: # run Operation
# --------------------------GLOBAL SETTINGS ------------------------------------
# global setting ( in user/AppData)
if os.path.isfile(pyCGM2.PYCGM2_APPDATA_PATH + "CGM1-pyCGM2.settings"):
settings = files.openFile(pyCGM2.PYCGM2_APPDATA_PATH,
"CGM1-pyCGM2.settings")
else:
settings = files.openFile(pyCGM2.PYCGM2_SETTINGS_FOLDER,
"CGM1-pyCGM2.settings")
# --------------------------CONFIG ------------------------------------
argsManager = CgmArgsManager.argsManager_cgm1(settings, args)
leftFlatFoot = argsManager.getLeftFlatFoot()
rightFlatFoot = argsManager.getRightFlatFoot()
headFlat = argsManager.getHeadFlat()
markerDiameter = argsManager.getMarkerDiameter()
pointSuffix = argsManager.getPointSuffix("cgm1")
DATA_PATH, calibrateFilenameLabelledNoExt = NEXUS.GetTrialName()
calibrateFilenameLabelled = calibrateFilenameLabelledNoExt + ".c3d"
LOGGER.logger.info("data Path: " + DATA_PATH)
LOGGER.set_file_handler(DATA_PATH + "pyCGM2-Calibration.log")
LOGGER.logger.info("calibration file: " + calibrateFilenameLabelled)
# --------------------------SUBJECT ------------------------------------
subjects = NEXUS.GetSubjectNames()
subject = nexusTools.getActiveSubject(
NEXUS) #checkActivatedSubject(NEXUS,subjects)
Parameters = NEXUS.GetSubjectParamNames(subject)
required_mp, optional_mp = nexusUtils.getNexusSubjectMp(
NEXUS, subject, resetFlag=args.resetMP)
# -------------------------- INFOS ------------------------------------
mpInfo, mpFilename = files.getMpFileContent(DATA_PATH, "mp.pyCGM2",
subject)
# translators management
translators = files.getTranslators(DATA_PATH, "CGM1.translators")
if not translators: translators = settings["Translators"]
# btkAcq builder
nacf = nexusFilters.NexusConstructAcquisitionFilter(
DATA_PATH, calibrateFilenameLabelledNoExt, subject)
acq = nacf.build()
# --------------------------MODELLING PROCESSING -----------------------
model, acqStatic, detectAnomaly = cgm1.calibrate(
DATA_PATH,
calibrateFilenameLabelled,
translators,
required_mp,
optional_mp,
leftFlatFoot,
rightFlatFoot,
headFlat,
markerDiameter,
pointSuffix,
forceBtkAcq=acq,
anomalyException=args.anomalyException)
# ----------------------SAVE-------------------------------------------
#pyCGM2.model
files.saveModel(model, DATA_PATH, subject)
# save mp
files.saveMp(mpInfo, model, DATA_PATH, mpFilename)
# ----------------------DISPLAY ON VICON-------------------------------
nexusUtils.updateNexusSubjectMp(NEXUS, model, subject)
nexusFilters.NexusModelFilter(NEXUS,
model,
acqStatic,
subject,
pointSuffix,
staticProcessing=True).run()