def main():
plt.close("all")
parser = argparse.ArgumentParser(description='CGM plotMAP')
parser.add_argument(
'-nd',
'--normativeData',
type=str,
help='normative Data set (Schwartz2008 or Pinzone2014)',
default="Schwartz2008")
parser.add_argument(
'-ndm',
'--normativeDataModality',
type=str,
help=
"if Schwartz2008 [VerySlow,SlowFree,Fast,VeryFast] - if Pinzone2014 [CentreOne,CentreTwo]",
default="Free")
parser.add_argument('-ps',
'--pointSuffix',
type=str,
help='suffix of model outputs')
args = parser.parse_args()
NEXUS = ViconNexus.ViconNexus()
NEXUS_PYTHON_CONNECTED = NEXUS.Client.IsConnected()
if not NEXUS_PYTHON_CONNECTED:
raise Exception("Vicon Nexus is not running")
#-----------------------SETTINGS---------------------------------------
pointSuffix = args.pointSuffix
#-----------------------SETTINGS---------------------------------------
normativeData = {
"Author": args.normativeData,
"Modality": args.normativeDataModality
}
if normativeData["Author"] == "Schwartz2008":
chosenModality = normativeData["Modality"]
elif normativeData["Author"] == "Pinzone2014":
chosenModality = normativeData["Modality"]
nds = normativeDatasets.NormativeData(normativeData["Author"],
chosenModality)
#--------------------------Data Location and subject-------------------------------------
if eclipse.getCurrentMarkedNodes() is not None:
LOGGER.logger.info(
"[pyCGM2] - Script worked with marked node of Vicon Eclipse")
# --- acquisition file and path----
DATA_PATH, modelledFilenames = eclipse.getCurrentMarkedNodes()
ECLIPSE_MODE = True
if not ECLIPSE_MODE:
LOGGER.logger.info(
"[pyCGM2] - Script works with the loaded c3d in vicon Nexus")
# --- acquisition file and path----
DATA_PATH, modelledFilenameNoExt = NEXUS.GetTrialName()
modelledFilename = modelledFilenameNoExt + ".c3d"
LOGGER.logger.info("data Path: " + DATA_PATH)
LOGGER.logger.info("file: " + modelledFilename)
# ----- Subject -----
# need subject to find input files
subject = nexusTools.getActiveSubject(NEXUS)
LOGGER.logger.info("Subject name : " + subject)
if not ECLIPSE_MODE:
# btkAcq builder
nacf = nexusFilters.NexusConstructAcquisitionFilter(
DATA_PATH, modelledFilenameNoExt, subject)
acq = nacf.build()
# --------------------------PROCESSING --------------------------------
analysisInstance = analysis.makeAnalysis(DATA_PATH, [modelledFilename],
type="Gait",
kineticLabelsDict=None,
emgChannels=None,
pointLabelSuffix=pointSuffix,
btkAcqs=[acq],
subjectInfo=None,
experimentalInfo=None,
modelInfo=None)
outputName = modelledFilename
else:
analysisInstance = analysis.makeAnalysis(DATA_PATH,
type="Gait",
kineticLabelsDict=None,
emgChannels=None,
pointLabelSuffix=pointSuffix,
subjectInfo=None,
experimentalInfo=None,
modelInfo=None)
outputName = "Eclipse-MAP"
plot.plot_MAP(DATA_PATH,
analysisInstance,
nds,
exportPdf=True,
outputName=outputName,
pointLabelSuffix=pointSuffix)
def main():
parser = argparse.ArgumentParser(description='CGM2.5 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_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"
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_5.translators")
if not translators: translators = settings["Translators"]
# btkAcq builder
nacf = nexusFilters.NexusConstructAcquisitionFilter(
DATA_PATH, calibrateFilenameLabelledNoExt, subject)
acq = nacf.build()
# --------------------------CONFIG ------------------------------------
model, finalAcqStatic, detectAnomaly = cgm2_5.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")
def main():
parser = argparse.ArgumentParser(description='EMG-plot_temporalEMG')
parser.add_argument('-bpf',
'--BandpassFrequencies',
nargs='+',
help='bandpass filter')
parser.add_argument('-ecf',
'--EnvelopLowpassFrequency',
type=int,
help='cutoff frequency for emg envelops')
parser.add_argument('-r',
'--raw',
action='store_true',
help='rectified data')
parser.add_argument('-ina',
'--ignoreNormalActivity',
action='store_true',
help='do not display normal activity')
args = parser.parse_args()
NEXUS = ViconNexus.ViconNexus()
NEXUS_PYTHON_CONNECTED = NEXUS.Client.IsConnected()
if NEXUS_PYTHON_CONNECTED: # run Operation
# --- acquisition file and path----
DATA_PATH, inputFileNoExt = NEXUS.GetTrialName()
inputFile = inputFileNoExt + ".c3d"
#--------------------------settings-------------------------------------
if os.path.isfile(DATA_PATH + "emg.settings"):
emgSettings = files.openFile(DATA_PATH, "emg.settings")
LOGGER.logger.warning(
"[pyCGM2]: emg.settings detected in the data folder")
else:
emgSettings = None
manager = EmgManager.EmgConfigManager(
None, localInternalSettings=emgSettings)
manager.contruct()
# ----------------------INPUTS-------------------------------------------
bandPassFilterFrequencies = manager.BandpassFrequencies #emgSettings["Processing"]["BandpassFrequencies"]
if args.BandpassFrequencies is not None:
if len(args.BandpassFrequencies) != 2:
raise Exception(
"[pyCGM2] - bad configuration of the bandpass frequencies ... set 2 frequencies only"
)
else:
bandPassFilterFrequencies = [
float(args.BandpassFrequencies[0]),
float(args.BandpassFrequencies[1])
]
LOGGER.logger.info(
"Band pass frequency set to %i - %i instead of 20-200Hz",
bandPassFilterFrequencies[0], bandPassFilterFrequencies[1])
envelopCutOffFrequency = manager.EnvelopLowpassFrequency #emgSettings["Processing"]["EnvelopLowpassFrequency"]
if args.EnvelopLowpassFrequency is not None:
envelopCutOffFrequency = args.EnvelopLowpassFrequency
LOGGER.logger.info("Cut-off frequency set to %i instead of 6Hz ",
envelopCutOffFrequency)
rectifyBool = False if args.raw else True
# --------------------------SUBJECT ------------------------------------
subjects = NEXUS.GetSubjectNames()
subject = nexusTools.getActiveSubject(NEXUS)
# btk Acquisition
nacf = nexusFilters.NexusConstructAcquisitionFilter(
DATA_PATH, inputFileNoExt, subject)
acq = nacf.build()
# --------------emg Processing--------------
EMG_LABELS, EMG_MUSCLES, EMG_CONTEXT, NORMAL_ACTIVITIES = manager.getEmgConfiguration(
)
emg.processEMG_fromBtkAcq(
acq,
EMG_LABELS,
highPassFrequencies=bandPassFilterFrequencies,
envelopFrequency=envelopCutOffFrequency
) # high pass then low pass for all c3ds
plot.plotTemporalEMG(DATA_PATH,
inputFile,
EMG_LABELS,
EMG_MUSCLES,
EMG_CONTEXT,
NORMAL_ACTIVITIES,
exportPdf=True,
rectify=rectifyBool,
btkAcq=acq,
ignoreNormalActivity=args.ignoreNormalActivity)
else:
raise Exception("NO Nexus connection. Turn on Nexus")
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')
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"
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='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():
parser = argparse.ArgumentParser(description='2Dof Knee Calibration')
parser.add_argument('-s','--side', type=str, help="Side : Left or Right")
parser.add_argument('-b','--beginFrame', type=int, help="begin frame")
parser.add_argument('-e','--endFrame', type=int, help="end frame")
args = parser.parse_args()
NEXUS = ViconNexus.ViconNexus()
NEXUS_PYTHON_CONNECTED = NEXUS.Client.IsConnected()
if NEXUS_PYTHON_CONNECTED: # run Operation
DATA_PATH, reconstructedFilenameLabelledNoExt = NEXUS.GetTrialName()
reconstructFilenameLabelled = reconstructedFilenameLabelledNoExt+".c3d"
LOGGER.logger.info( "data Path: "+ DATA_PATH )
LOGGER.logger.info( "reconstructed 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 - INIT ------------------------------
model = files.loadModel(DATA_PATH,subject)
LOGGER.logger.info("loaded model : %s" %(model.version ))
if model.version == "CGM1.0":
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")
elif model.version == "CGM1.1":
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")
elif model.version == "CGM2.1":
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")
elif model.version == "CGM2.2":
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")
elif model.version == "CGM2.3":
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")
elif model.version in ["CGM2.4"]:
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")
elif model.version in ["CGM2.5"]:
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")
else:
raise Exception ("model version not found [contact admin]")
# --------------------------SESSION INFOS ------------------------------------
mpInfo,mpFilename = files.getMpFileContent(DATA_PATH,"mp.pyCGM2",subject)
# translators management
if model.version in ["CGM1.0"]:
translators = files.getTranslators(DATA_PATH,"CGM1.translators")
elif model.version in ["CGM1.1"]:
translators = files.getTranslators(DATA_PATH,"CGM1_1.translators")
elif model.version in ["CGM2.1"]:
translators = files.getTranslators(DATA_PATH,"CGM2_1.translators")
elif model.version in ["CGM2.2"]:
translators = files.getTranslators(DATA_PATH,"CGM2_2.translators")
elif model.version in ["CGM2.3"]:
translators = files.getTranslators(DATA_PATH,"CGM2_3.translators")
elif model.version in ["CGM2.4"]:
translators = files.getTranslators(DATA_PATH,"CGM2_4.translators")
elif model.version in ["CGM2.5"]:
translators = files.getTranslators(DATA_PATH,"CGM2_5.translators")
if not translators:
translators = settings["Translators"]
# btkAcq builder
nacf = nexusFilters.NexusConstructAcquisitionFilter(DATA_PATH,reconstructedFilenameLabelledNoExt,subject)
acq = nacf.build()
# --------------------------MODEL PROCESSING----------------------------
model,acqFunc,side = kneeCalibration.calibration2Dof(model,
DATA_PATH,reconstructFilenameLabelled,translators,
args.side,args.beginFrame,args.endFrame,None,forceBtkAcq=acq)
# ----------------------SAVE-------------------------------------------
files.saveModel(model,DATA_PATH,subject)
LOGGER.logger.warning("model updated with a %s knee calibrated with 2Dof method" %(side))
# save mp
files.saveMp(mpInfo,model,DATA_PATH,mpFilename)
# ----------------------VICON INTERFACE-------------------------------------------
#--- update mp
nexusUtils.updateNexusSubjectMp(NEXUS,model,subject)
if side == "Left":
nexusTools.appendBones(NEXUS,subject,acqFunc,"LFE0", model.getSegment("Left Thigh"),OriginValues = acqFunc.GetPoint("LKJC").GetValues() )
elif side == "Right":
nexusTools.appendBones(NEXUS,subject,acqFunc,"RFE0", model.getSegment("Right Thigh"),OriginValues = acqFunc.GetPoint("RKJC").GetValues() )
# --------------------------NEW MOTION FILTER - DISPLAY BONES---------
scp=modelFilters.StaticCalibrationProcedure(model)
if model.version in ["CGM1.0","CGM1.1","CGM2.1","CGM2.2"]:
modMotion=modelFilters.ModelMotionFilter(scp,acqFunc,model,enums.motionMethod.Determinist)
modMotion.compute()
elif model.version in ["CGM2.3","CGM2.4"]:
proximalSegmentLabel=str(side+" Thigh")
distalSegmentLabel=str(side+" Shank")
# Motion
modMotion=modelFilters.ModelMotionFilter(scp,acqFunc,model,enums.motionMethod.Sodervisk)
modMotion.segmentalCompute([proximalSegmentLabel,distalSegmentLabel])
# -- add nexus Bones
if side == "Left":
nexusTools.appendBones(NEXUS,subject,acqFunc,"LFE1", model.getSegment("Left Thigh"),OriginValues = acqFunc.GetPoint("LKJC").GetValues() )
LOGGER.logger.warning("offset %s" %(str(model.mp_computed["LeftKneeFuncCalibrationOffset"] )))
elif side == "Right":
nexusTools.appendBones(NEXUS,subject,acqFunc,"RFE1", model.getSegment("Right Thigh"),OriginValues = acqFunc.GetPoint("RKJC").GetValues() )
LOGGER.logger.warning("offset %s" %(str(model.mp_computed["RightKneeFuncCalibrationOffset"] )))
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")
def main(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(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()
def main():
parser = argparse.ArgumentParser(description='CGM2-2 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('-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_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()
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 ------------------------------------
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]
# check model
LOGGER.logger.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, detectAnomaly = cgm2_2.fitting(
model,
DATA_PATH,
reconstructFilenameLabelled,
translators,
settings,
markerDiameter,
pointSuffix,
mfpa,
momentProjection,
forceBtkAcq=acq,
ikAccuracy=ikAccuracy,
anomalyException=args.anomalyException,
frameInit=args.frameInit,
frameEnd=args.frameEnd)
# ----------------------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")
