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")
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(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 test_getMpFileContent(self): mp = files.getMpFileContent( pyCGM2.TEST_DATA_PATH + "\\LowLevel\\IO\\Hanibal_files\\", "mp.pyCGM2", "Nick") assert mp != False
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 + "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()