"model updated with a %s knee calibrated with SARA method" %
(side))
# save mp
files.saveMp(mpInfo, model, DATA_PATH, mpFilename)
# ----------------------VICON INTERFACE-------------------------------------------
#--- update mp
nexusUtils.updateNexusSubjectMp(NEXUS, model, subject)
# -- add nexus Bones
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())
proximalSegmentLabel = str(side + " Thigh")
distalSegmentLabel = str(side + " Shank")
def main(args):
NEXUS = ViconNexus.ViconNexus()
NEXUS_PYTHON_CONNECTED = NEXUS.Client.IsConnected()
if NEXUS_PYTHON_CONNECTED: # run Operation
# --------------------------PATH + FILE ------------------------------------
DATA_PATH, reconstructedFilenameLabelledNoExt = NEXUS.GetTrialName()
reconstructFilenameLabelled = reconstructedFilenameLabelledNoExt + ".c3d"
logging.info("data Path: " + DATA_PATH)
logging.info("reconstructed 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)
logging.info("loaded model : %s" % (model.version))
# --------------------------CONFIG ------------------------------------
# --------------------CHECKING ------------------------------
if model.version in ["CGM1.0", "CGM1.1", "CGM2.1", "CGM2.2"]:
raise Exception(
"Can t use SARA method with your model %s [minimal version : CGM2.3]"
% (model.version))
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 ["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.sara(
model,
DATA_PATH,
reconstructFilenameLabelled,
translators,
args.side,
args.beginFrame,
args.endFrame,
forceBtkAcq=acq)
# ----------------------SAVE-------------------------------------------
files.saveModel(model, DATA_PATH, subject)
logging.warning(
"model updated with a %s knee calibrated with SARA method" %
(side))
# save mp
files.saveMp(mpInfo, model, DATA_PATH, mpFilename)
# ----------------------VICON INTERFACE-------------------------------------------
#--- update mp
nexusUtils.updateNexusSubjectMp(NEXUS, model, subject)
# -- add nexus Bones
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())
proximalSegmentLabel = str(side + " Thigh")
distalSegmentLabel = str(side + " Shank")
# add modelled markers
meanOr_inThigh = model.getSegment(proximalSegmentLabel).getReferential(
"TF").getNodeTrajectory("KJC_Sara")
meanAxis_inThigh = model.getSegment(
proximalSegmentLabel).getReferential("TF").getNodeTrajectory(
"KJC_SaraAxis")
btkTools.smartAppendPoint(acqFunc, side + "_KJC_Sara", meanOr_inThigh)
btkTools.smartAppendPoint(acqFunc, side + "_KJC_SaraAxis",
meanAxis_inThigh)
nexusTools.appendModelledMarkerFromAcq(NEXUS, subject,
side + "_KJC_Sara", acqFunc)
nexusTools.appendModelledMarkerFromAcq(NEXUS, subject,
side + "_KJC_SaraAxis", acqFunc)
#---Second model motion filter
# consider new anatomical frame
scp = modelFilters.StaticCalibrationProcedure(model)
modMotion = modelFilters.ModelMotionFilter(
scp, acqFunc, model, enums.motionMethod.Sodervisk)
modMotion.segmentalCompute([proximalSegmentLabel, distalSegmentLabel])
# projection of the Sara axis in the transversale plane
# -- add nexus Bones
if side == "Left":
nexusTools.appendBones(
NEXUS,
subject,
acqFunc,
"LFE1",
model.getSegment("Left Thigh"),
OriginValues=acqFunc.GetPoint("LKJC").GetValues())
print model.mp_computed["LeftKneeFuncCalibrationOffset"]
logging.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())
logging.warning(
"offset %s" %
(str(model.mp_computed["RightKneeFuncCalibrationOffset"])))
print model.mp_computed["RightKneeFuncCalibrationOffset"]
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")