def main(): qtm_folder = os.getcwd() sessionXML = files.readXml(qtm_folder + "\\", "session.xml") # --------------------------MP ------------------------------------ required_mp, _ = qtmTools.SubjectMp(sessionXML) # --------------------------Check MP ---------------------------------- logging.info("--MP Checking--") inspectprocedure1 = inspectProcedures.AnthropometricDataQualityProcedure( required_mp) inspector = inspectFilters.QualityFilter(inspectprocedure1) inspector.run() # --------------------------FILES ----------------------- staticMeasurement = utils.find_static(sessionXML) staticFilename = qtmTools.getFilename(staticMeasurement) dynamicFilenames = [] dynamicMeasurements = qtmTools.findDynamic(sessionXML) for dynamicMeasurement in dynamicMeasurements: reconstructFilenameLabelled = qtmTools.getFilename(dynamicMeasurement) dynamicFilenames.append(reconstructFilenameLabelled) # --------------------------CHECKING ----------------------- # static is only in qtm folder and does not get processed runAllQualityProcedures(qtm_folder, [staticFilename]) runAllQualityProcedures(os.path.join(qtm_folder, "processed"), dynamicFilenames)
def prepare_folder_and_run_event_detection(sessionXML, work_folder, processed_folder): utils.create_directory_if_needed(processed_folder) staticMeasurement = utils.find_static(sessionXML) filename = qtmTools.getFilename(staticMeasurement) calibrated_file_path = os.path.join(processed_folder, filename) if not os.path.isfile(calibrated_file_path): shutil.copyfile(os.path.join(work_folder, filename), calibrated_file_path) logging.info( "qualisys exported c3d file [%s] copied to processed folder" % (filename)) dynamicMeasurements = qtmTools.findDynamic(sessionXML) for dynamicMeasurement in dynamicMeasurements: filename = qtmTools.getFilename(dynamicMeasurement) no_events_file_path = os.path.join(work_folder, filename) processed_file_path = os.path.join(processed_folder, filename) if not os.path.isfile(processed_file_path): shutil.copyfile(no_events_file_path, processed_file_path) logging.info( "qualisys exported c3d file [%s] copied to processed folder" % (filename)) acq = btkTools.smartReader(processed_file_path) if "5" in btkTools.smartGetMetadata(acq, "FORCE_PLATFORM", "TYPE"): forceplates.correctForcePlateType5(acq) acq, state = eventDetector.zeni(acq) btkTools.smartWriter(acq, processed_file_path)
def get_modelled_trials(session_xml, measurement_type): modelled_trials = [] dynamicMeasurements = qtmTools.findDynamic(session_xml) for dynamicMeasurement in dynamicMeasurements: if qtmTools.isType(dynamicMeasurement, measurement_type): filename = qtmTools.getFilename(dynamicMeasurement) modelled_trials.append(filename) return modelled_trials
def verify_events_in_mokka(sessionXML, processed_folder): dynamicMeasurements = qtmTools.findDynamic(sessionXML) for dynamicMeasurement in dynamicMeasurements: filename = qtmTools.getFilename(dynamicMeasurement) processed_file_path = os.path.join(processed_folder, filename) cmd = "Mokka.exe \"%s\"" % (processed_file_path) os.system(cmd)
def sessionReaderTest(cls): DATA_PATH = "C:\\Users\\HLS501\\Documents\\QUALISYS DATA\\pyCGM2-Data\\sessionXML\\" file = "sessionHUG.xml" soup = files.readXml(DATA_PATH, file) staticMeasurement = qtmTools.findStatic(soup) dynamicMeaurements = qtmTools.findDynamic(soup) qtmTools.SubjectMp(soup) types = qtmTools.detectMeasurementType(soup) mfpa = qtmTools.getForcePlateAssigment(dynamicMeaurements[0]) qtmTools.isType(dynamicMeaurements[0], "Gait")
def prepare_parser(testDataPath): # this code is mostly duplicate from the PAF modules template, possibly rework where the functionality goes session_xml_path = os.path.join(testDataPath, "session.xml") sessionXML = load_session_xml_soup(session_xml_path) sessionDate = utils.get_creation_date(sessionXML) session_type = qtmTools.detectMeasurementType(sessionXML)[ 0] # in this example there is only one modelledTrials = [] dynamicMeasurements = qtmTools.findDynamic(sessionXML) for dynamicMeasurement in dynamicMeasurements: if qtmTools.isType(dynamicMeasurement, session_type): filename = qtmTools.getFilename(dynamicMeasurement) modelledTrials.append(filename) subjectInfo = create_subject_metadata(sessionXML) # initiate parser uploader processedDir = os.path.join(testDataPath, "processed") reportJsonGenerator = ReportJsonGenerator(processedDir, configData["clientId"], modelledTrials, subjectInfo, sessionDate) return reportJsonGenerator
def main(): logging.info("------------------------------------------------") logging.info("------------QTM - pyCGM2 Workflow---------------") logging.info("------------------------------------------------") file = "session.xml" sessionXML = files.readXml(os.getcwd() + "\\", file) sessionDate = files.getFileCreationDate(os.getcwd() + "\\" + file) # --------------------------------------------------------------------------- # management of the Processed folder DATA_PATH = os.getcwd() + "\\" + "processed\\" files.createDir(DATA_PATH) staticMeasurement = utils.find_static(sessionXML) calibrateFilenameLabelled = qtmTools.getFilename(staticMeasurement) if not os.path.isfile(DATA_PATH + calibrateFilenameLabelled): shutil.copyfile(os.getcwd() + "\\" + calibrateFilenameLabelled, DATA_PATH + calibrateFilenameLabelled) logging.info( "qualisys exported c3d file [%s] copied to processed folder" % (calibrateFilenameLabelled)) dynamicMeasurements = qtmTools.findDynamic(sessionXML) for dynamicMeasurement in dynamicMeasurements: reconstructFilenameLabelled = qtmTools.getFilename(dynamicMeasurement) if not os.path.isfile(DATA_PATH + reconstructFilenameLabelled): shutil.copyfile(os.getcwd() + "\\" + reconstructFilenameLabelled, DATA_PATH + reconstructFilenameLabelled) logging.info( "qualisys exported c3d file [%s] copied to processed folder" % (reconstructFilenameLabelled)) acq = btkTools.smartReader( str(DATA_PATH + reconstructFilenameLabelled)) if btkTools.checkForcePlateExist(acq): if "5" in btkTools.smartGetMetadata(acq, "FORCE_PLATFORM", "TYPE"): forceplates.correctForcePlateType5(acq) acq, zeniState = eventDetector.zeni(acq) if zeniState: btkTools.smartWriter( acq, str(DATA_PATH + reconstructFilenameLabelled)) cmd = "Mokka.exe \"%s\"" % (str(DATA_PATH + reconstructFilenameLabelled)) os.system(cmd) # --------------------------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") # --------------------------MP ------------------------------------ required_mp, optional_mp = qtmTools.SubjectMp(sessionXML) # --Check MP inspectprocedure = inspectProcedures.AnthropometricDataQualityProcedure( required_mp) inspector = inspectFilters.QualityFilter(inspectprocedure) inspector.run() # translators management translators = files.getTranslators(os.getcwd() + "\\", "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"] # --------------------------MODEL CALIBRATION ----------------------- logging.info( "--------------------------MODEL CALIBRATION -----------------------") staticMeasurement = utils.find_static(sessionXML) calibrateFilenameLabelled = qtmTools.getFilename(staticMeasurement) logging.info("----- CALIBRATION- static file [%s]--" % (calibrateFilenameLabelled)) leftFlatFoot = toBool( staticMeasurement.Left_foot_normalised_to_static_trial.text) rightFlatFoot = toBool( staticMeasurement.Right_foot_normalised_to_static_trial.text) headFlat = toBool(staticMeasurement.Head_normalised_to_static_trial.text) markerDiameter = float(staticMeasurement.Marker_diameter.text) * 1000.0 hjcMethod = settings["Calibration"]["HJC"] pointSuffix = None # Calibration checking # -------------------- acqStatic = btkTools.smartReader(DATA_PATH + calibrateFilenameLabelled) for key in MARKERSETS.keys(): logging.info("[pyCGM2] Checking of the %s" % (key)) # presence ip_presence = inspectProcedures.MarkerPresenceQualityProcedure( acqStatic, markers=MARKERSETS[key]) inspector = inspectFilters.QualityFilter(ip_presence) inspector.run() if ip_presence.markersIn != []: ip_gap = inspectProcedures.GapQualityProcedure( acqStatic, markers=ip_presence.markersIn) inspector = inspectFilters.QualityFilter(ip_gap) inspector.run() ip_swap = inspectProcedures.SwappingMarkerQualityProcedure( acqStatic, markers=ip_presence.markersIn) inspector = inspectFilters.QualityFilter(ip_swap) inspector.run() ip_pos = inspectProcedures.MarkerPositionQualityProcedure( acqStatic, markers=ip_presence.markersIn) inspector = inspectFilters.QualityFilter(ip_pos) # Calibration operation # -------------------- logging.info("[pyCGM2] --- calibration operation ---") model, acqStatic = cgm2_2.calibrate(DATA_PATH, calibrateFilenameLabelled, translators, settings, required_mp, optional_mp, False, leftFlatFoot, rightFlatFoot, headFlat, markerDiameter, hjcMethod, pointSuffix) logging.info("----- CALIBRATION- static file [%s]-----> DONE" % (calibrateFilenameLabelled)) # --------------------------MODEL FITTING ---------------------------------- logging.info( "--------------------------MODEL FITTING ----------------------------------" ) dynamicMeasurements = qtmTools.findDynamic(sessionXML) modelledC3ds = list() eventInspectorStates = list() for dynamicMeasurement in dynamicMeasurements: reconstructFilenameLabelled = qtmTools.getFilename(dynamicMeasurement) logging.info("----Processing of [%s]-----" % (reconstructFilenameLabelled)) mfpa = qtmTools.getForcePlateAssigment(dynamicMeasurement) momentProjection_text = dynamicMeasurement.Moment_Projection.text if momentProjection_text == "Default": momentProjection_text = settings["Fitting"]["Moment Projection"] if momentProjection_text == "Distal": momentProjection = enums.MomentProjection.Distal elif momentProjection_text == "Proximal": momentProjection = enums.MomentProjection.Proximal elif momentProjection_text == "Global": momentProjection = enums.MomentProjection.Global elif momentProjection_text == "JCS": momentProjection = enums.MomentProjection.JCS acq = btkTools.smartReader(DATA_PATH + reconstructFilenameLabelled) # Fitting checking # -------------------- for key in MARKERSETS.keys(): if key != "Calibration markers": logging.info("[pyCGM2] Checking of the %s" % (key)) # presence ip_presence = inspectProcedures.MarkerPresenceQualityProcedure( acq, markers=MARKERSETS[key]) inspector = inspectFilters.QualityFilter(ip_presence) inspector.run() if ip_presence.markersIn != []: ip_gap = inspectProcedures.GapQualityProcedure( acq, markers=ip_presence.markersIn) inspector = inspectFilters.QualityFilter(ip_gap) inspector.run() ip_swap = inspectProcedures.SwappingMarkerQualityProcedure( acq, markers=ip_presence.markersIn) inspector = inspectFilters.QualityFilter(ip_swap) inspector.run() ip_pos = inspectProcedures.MarkerPositionQualityProcedure( acq, markers=ip_presence.markersIn) inspector = inspectFilters.QualityFilter(ip_pos) # filtering # ----------------------- # marker order = int(float(dynamicMeasurement.Marker_lowpass_filter_order.text)) fc = float(dynamicMeasurement.Marker_lowpass_filter_frequency.text) signal_processing.markerFiltering(acq, order=order, fc=fc) # management of force plate type 5 and force plate filtering order = int( float(dynamicMeasurement.Forceplate_lowpass_filter_order.text)) fc = float(dynamicMeasurement.Forceplate_lowpass_filter_frequency.text) if order != 0 and fc != 0: acq = btkTools.smartReader(DATA_PATH + reconstructFilenameLabelled) if btkTools.checkForcePlateExist(acq): if "5" in btkTools.smartGetMetadata(acq, "FORCE_PLATFORM", "TYPE"): forceplates.correctForcePlateType5(acq) signal_processing.markerFiltering(acq, order=order, fc=fc) else: if btkTools.checkForcePlateExist(acq): if "5" in btkTools.smartGetMetadata(acq, "FORCE_PLATFORM", "TYPE"): forceplates.correctForcePlateType5(acq) btkTools.smartWriter(acq, DATA_PATH + reconstructFilenameLabelled) # event checking # ----------------------- inspectprocedureEvents = inspectProcedures.GaitEventQualityProcedure( acq) inspector = inspectFilters.QualityFilter(inspectprocedureEvents) inspector.run() eventInspectorStates.append(inspectprocedureEvents.state) # fitting operation # ----------------------- logging.info("[pyCGM2] --- Fitting operation ---") acqGait = cgm2_2.fitting(model, DATA_PATH, reconstructFilenameLabelled, translators, settings, markerDiameter, pointSuffix, mfpa, momentProjection) outFilename = reconstructFilenameLabelled # [:-4] + "_CGM1.c3d" btkTools.smartWriter(acqGait, str(DATA_PATH + outFilename)) modelledC3ds.append(outFilename) logging.info("----Processing of [%s]-----> DONE" % (reconstructFilenameLabelled)) # --------------------------GAIT PROCESSING ----------------------- if not all(eventInspectorStates): raise Exception( "[pyCGM2] Impossible to run Gait processing. Badly gait event detection. check the log file" ) logging.info( "---------------------GAIT PROCESSING -----------------------") return model
def main(sessionFilename, createPDFReport=True, checkEventsInMokka=True, anomalyException=False): detectAnomaly = False LOGGER.set_file_handler("pyCGM2-QTM-Workflow.log") LOGGER.logger.info("------------QTM - pyCGM2 Workflow---------------") sessionXML = files.readXml(os.getcwd() + "\\", sessionFilename) sessionDate = files.getFileCreationDate(os.getcwd() + "\\" + sessionFilename) #--------------------------------------------------------------------------- #management of the Processed folder DATA_PATH = os.getcwd() + "\\" + "processed\\" files.createDir(DATA_PATH) staticMeasurement = qtmTools.findStatic(sessionXML) calibrateFilenameLabelled = qtmTools.getFilename(staticMeasurement) if not os.path.isfile(DATA_PATH + calibrateFilenameLabelled): shutil.copyfile(os.getcwd() + "\\" + calibrateFilenameLabelled, DATA_PATH + calibrateFilenameLabelled) LOGGER.logger.info( "qualisys exported c3d file [%s] copied to processed folder" % (calibrateFilenameLabelled)) if qtmTools.findKneeCalibration( sessionXML, "Left") is not None or qtmTools.findKneeCalibration( sessionXML, "Right") is not None: LOGGER.logger.info( " the %s not accept functional knee calibration !!" % (MODEL)) dynamicMeasurements = qtmTools.findDynamic(sessionXML) for dynamicMeasurement in dynamicMeasurements: reconstructFilenameLabelled = qtmTools.getFilename(dynamicMeasurement) # marker order_marker = int( float(dynamicMeasurement.Marker_lowpass_filter_order.text)) fc_marker = float( dynamicMeasurement.Marker_lowpass_filter_frequency.text) if not os.path.isfile(DATA_PATH + reconstructFilenameLabelled): shutil.copyfile(os.getcwd() + "\\" + reconstructFilenameLabelled, DATA_PATH + reconstructFilenameLabelled) LOGGER.logger.info( "qualisys exported c3d file [%s] copied to processed folder" % (reconstructFilenameLabelled)) acq = btkTools.smartReader( str(DATA_PATH + reconstructFilenameLabelled)) acq, zeniState = eventDetector.zeni( acq, fc_lowPass_marker=fc_marker, order_lowPass_marker=order_marker) if zeniState: btkTools.smartWriter( acq, str(DATA_PATH + reconstructFilenameLabelled)) if checkEventsInMokka: cmd = "Mokka.exe \"%s\"" % ( str(DATA_PATH + reconstructFilenameLabelled)) os.system(cmd) # --------------------------GLOBAL SETTINGS ------------------------------------ # global setting ( 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") # --------------------------MP ------------------------------------ required_mp, optional_mp = qtmTools.SubjectMp(sessionXML) # translators management translators = files.getTranslators(os.getcwd() + "\\", "CGM2_5.translators") if not translators: translators = settings["Translators"] # ikweight ikWeight = files.getIKweightSet(DATA_PATH, "CGM2_5.ikw") if not ikWeight: ikWeight = settings["Fitting"]["Weight"] # --------------------------MODEL CALIBRATION ----------------------- LOGGER.logger.info( "--------------------------MODEL CALIBRATION -----------------------") staticMeasurement = qtmTools.findStatic(sessionXML) calibrateFilenameLabelled = qtmTools.getFilename(staticMeasurement) LOGGER.logger.info("----- CALIBRATION- static file [%s]--" % (calibrateFilenameLabelled)) leftFlatFoot = utils.toBool( sessionXML.Left_foot_normalised_to_static_trial.text) rightFlatFoot = utils.toBool( sessionXML.Right_foot_normalised_to_static_trial.text) headFlat = utils.toBool(sessionXML.Head_normalised_to_static_trial.text) markerDiameter = float(sessionXML.Marker_diameter.text) * 1000.0 hjcMethod = settings["Calibration"]["HJC"] pointSuffix = None # Calibration checking # -------------------- acqStatic = btkTools.smartReader(DATA_PATH + calibrateFilenameLabelled) # Calibration operation # -------------------- model, acqStatic, detectAnomaly = cgm2_5.calibrate( DATA_PATH, calibrateFilenameLabelled, translators, settings, required_mp, optional_mp, False, leftFlatFoot, rightFlatFoot, headFlat, markerDiameter, hjcMethod, pointSuffix, anomalyException=anomalyException) LOGGER.logger.info("----- CALIBRATION- static file [%s]-----> DONE" % (calibrateFilenameLabelled)) # --------------------------MODEL FITTING ---------------------------------- LOGGER.logger.info( "--------------------------MODEL FITTING ----------------------------------" ) dynamicMeasurements = qtmTools.findDynamic(sessionXML) ik_flag = True modelledC3ds = list() eventInspectorStates = list() for dynamicMeasurement in dynamicMeasurements: reconstructFilenameLabelled = qtmTools.getFilename(dynamicMeasurement) LOGGER.logger.info("----Processing of [%s]-----" % (reconstructFilenameLabelled)) mfpa = qtmTools.getForcePlateAssigment(dynamicMeasurement) momentProjection_text = sessionXML.Moment_Projection.text if momentProjection_text == "Default": momentProjection_text = settings["Fitting"]["Moment Projection"] if momentProjection_text == "Distal": momentProjection = enums.MomentProjection.Distal elif momentProjection_text == "Proximal": momentProjection = enums.MomentProjection.Proximal elif momentProjection_text == "Global": momentProjection = enums.MomentProjection.Global elif momentProjection_text == "JCS": momentProjection = enums.MomentProjection.JCS acq = btkTools.smartReader(DATA_PATH + reconstructFilenameLabelled) # filtering # ----------------------- # marker order_marker = int( float(dynamicMeasurement.Marker_lowpass_filter_order.text)) fc_marker = float( dynamicMeasurement.Marker_lowpass_filter_frequency.text) # force plate order_fp = int( float(dynamicMeasurement.Forceplate_lowpass_filter_order.text)) fc_fp = float( dynamicMeasurement.Forceplate_lowpass_filter_frequency.text) # ik accuracy ikAccuracy = float(dynamicMeasurement.IkAccuracy.text) if dynamicMeasurement.First_frame_to_process.text != "": vff = int(dynamicMeasurement.First_frame_to_process.text) else: vff = None if dynamicMeasurement.Last_frame_to_process.text != "": vlf = int(dynamicMeasurement.Last_frame_to_process.text) else: vlf = None # fitting operation # ----------------------- LOGGER.logger.info("[pyCGM2] --- Fitting operation ---") acqGait, detectAnomaly = cgm2_5.fitting( model, DATA_PATH, reconstructFilenameLabelled, translators, settings, ik_flag, markerDiameter, pointSuffix, mfpa, momentProjection, fc_lowPass_marker=fc_marker, order_lowPass_marker=order_marker, fc_lowPass_forcePlate=fc_fp, order_lowPass_forcePlate=order_fp, anomalyException=anomalyException, ikAccuracy=ikAccuracy, frameInit=vff, frameEnd=vlf) outFilename = reconstructFilenameLabelled btkTools.smartWriter(acqGait, str(DATA_PATH + outFilename)) modelledC3ds.append(outFilename) LOGGER.logger.info("----Processing of [%s]-----> DONE" % (reconstructFilenameLabelled)) LOGGER.logger.info( "---------------------GAIT PROCESSING -----------------------") if createPDFReport: nds = normativeDatasets.NormativeData("Schwartz2008", "Free") types = qtmTools.detectMeasurementType(sessionXML) for type in types: modelledTrials = list() for dynamicMeasurement in dynamicMeasurements: if qtmTools.isType(dynamicMeasurement, type): filename = qtmTools.getFilename(dynamicMeasurement) # event checking # ----------------------- acq = btkTools.smartReader(DATA_PATH + filename) geap = AnomalyDetectionProcedure.GaitEventAnomalyProcedure( ) adf = AnomalyFilter.AnomalyDetectionFilter( acq, filename, geap) anomaly_events = adf.run() if anomaly_events["ErrorState"]: detectAnomaly = True LOGGER.logger.warning( "file [%s] not used for generating the gait report. bad gait event detected" % (filename)) else: modelledTrials.append(filename) try: report.pdfGaitReport(DATA_PATH, model, modelledTrials, nds, pointSuffix, title=type) LOGGER.logger.error("Generation of Gait report complete") except: LOGGER.logger.error("Generation of Gait report failed") LOGGER.logger.info( "-------------------------------------------------------") if detectAnomaly: LOGGER.logger.error( "Anomalies has been detected - Find Error messages, then check warning message in the log file" ) else: LOGGER.logger.info("workflow return with no detected anomalies")
def get_calibration_arguments_and_model_manager(model_type, data_path, session_xml, point_suffix): settings = get_settings(model_type) translators = settings["Translators"] required_mp, optional_mp = qtmTools.SubjectMp(session_xml) static_session_xml_soup = utils.find_static(session_xml) calibration_filename = qtmTools.getFilename(static_session_xml_soup) leftFlatFoot = toBool(static_session_xml_soup.Left_foot_flat) rightFlatFoot = toBool(static_session_xml_soup.Right_foot_flat) headFlat = toBool(static_session_xml_soup.Head_flat) markerDiameter = float( static_session_xml_soup.Marker_diameter.text) * 1000.0 dynamic_measurements = qtmTools.findDynamic(session_xml) user_settings = { "Calibration": { "Left flat foot": leftFlatFoot, "Right flat foot": rightFlatFoot, "Head flat": headFlat, "StaticTrial": calibration_filename }, "Global": { "Marker diameter": markerDiameter, "Point suffix": point_suffix }, "MP": { "Required": required_mp, "Optional": optional_mp }, "Fitting": { "Trials": dynamic_measurements } } if model_type == "CGM1": model_manager = ModelManager.CGM1ConfigManager( user_settings, localInternalSettings=settings, localTranslators={"Translators": translators}) model_manager.contruct() calibration_arguments = ( data_path + "\\", model_manager.staticTrial, model_manager.translators, model_manager.requiredMp, model_manager.optionalMp, model_manager.leftFlatFoot, model_manager.rightFlatFoot, model_manager.headFlat, model_manager.markerDiameter, model_manager.pointSuffix, ) elif model_type == "CGM2_3": model_manager = ModelManager.CGM2_3ConfigManager( user_settings, localInternalSettings=settings, localTranslators={"Translators": translators}) model_manager.contruct() finalSettings = model_manager.getFinalSettings() calibration_arguments = ( data_path + "\\", model_manager.staticTrial, model_manager.translators, finalSettings, model_manager.requiredMp, model_manager.optionalMp, model_manager.enableIK, model_manager.leftFlatFoot, model_manager.rightFlatFoot, model_manager.headFlat, model_manager.markerDiameter, model_manager.hjcMethod, model_manager.pointSuffix, ) else: raise Exception( "Processing for model_type={} is not implemented".format( model_type)) return calibration_arguments, model_manager
def main(): logging.info("------------------------------------------------") logging.info("------------QTM - pyCGM2 Workflow---------------") logging.info("------------------------------------------------") file = "session.xml" sessionXML = files.readXml(os.getcwd() + "\\", file) sessionDate = files.getFileCreationDate(os.getcwd() + "\\" + file) #--------------------------------------------------------------------------- #management of the Processed folder DATA_PATH = os.getcwd() + "\\" + "processed\\" files.createDir(DATA_PATH) staticMeasurement = qtmTools.findStatic(sessionXML) calibrateFilenameLabelled = qtmTools.getFilename(staticMeasurement) if not os.path.isfile(DATA_PATH + calibrateFilenameLabelled): shutil.copyfile(os.getcwd() + "\\" + calibrateFilenameLabelled, DATA_PATH + calibrateFilenameLabelled) logging.info( "qualisys exported c3d file [%s] copied to processed folder" % (calibrateFilenameLabelled)) dynamicMeasurements = qtmTools.findDynamic(sessionXML) for dynamicMeasurement in dynamicMeasurements: reconstructFilenameLabelled = qtmTools.getFilename(dynamicMeasurement) if not os.path.isfile(DATA_PATH + reconstructFilenameLabelled): shutil.copyfile(os.getcwd() + "\\" + reconstructFilenameLabelled, DATA_PATH + reconstructFilenameLabelled) logging.info( "qualisys exported c3d file [%s] copied to processed folder" % (reconstructFilenameLabelled)) acq = btkTools.smartReader( str(DATA_PATH + reconstructFilenameLabelled)) if btkTools.checkForcePlateExist(acq): if "5" in btkTools.smartGetMetadata(acq, "FORCE_PLATFORM", "TYPE"): forceplates.correctForcePlateType5(acq) acq, zeniState = eventDetector.zeni(acq) if zeniState: btkTools.smartWriter( acq, str(DATA_PATH + reconstructFilenameLabelled)) cmd = "Mokka.exe \"%s\"" % (str(DATA_PATH + reconstructFilenameLabelled)) os.system(cmd) # --------------------------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") # --------------------------MP ------------------------------------ required_mp, optional_mp = qtmTools.SubjectMp(sessionXML) # --Check MP inspectprocedure = inspectProcedures.AnthropometricDataQualityProcedure( required_mp) inspector = inspectFilters.QualityFilter(inspectprocedure) inspector.run() # translators management translators = files.getTranslators(os.getcwd() + "\\", "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"] # --------------------------MODEL CALIBRATION ----------------------- logging.info( "--------------------------MODEL CALIBRATION -----------------------") staticMeasurement = qtmTools.findStatic(sessionXML) calibrateFilenameLabelled = qtmTools.getFilename(staticMeasurement) logging.info("----- CALIBRATION- static file [%s]--" % (calibrateFilenameLabelled)) leftFlatFoot = toBool( staticMeasurement.Left_foot_normalised_to_static_trial.text) rightFlatFoot = toBool( staticMeasurement.Right_foot_normalised_to_static_trial.text) headFlat = toBool(staticMeasurement.Head_normalised_to_static_trial.text) markerDiameter = float(staticMeasurement.Marker_diameter.text) * 1000.0 hjcMethod = settings["Calibration"]["HJC"] pointSuffix = None # Calibration checking # -------------------- acqStatic = btkTools.smartReader(DATA_PATH + calibrateFilenameLabelled) for key in MARKERSETS.keys(): logging.info("[pyCGM2] Checking of the %s" % (key)) # presence ip_presence = inspectProcedures.MarkerPresenceQualityProcedure( acqStatic, markers=MARKERSETS[key]) inspector = inspectFilters.QualityFilter(ip_presence) inspector.run() if ip_presence.markersIn != []: ip_gap = inspectProcedures.GapQualityProcedure( acqStatic, markers=ip_presence.markersIn) inspector = inspectFilters.QualityFilter(ip_gap) inspector.run() ip_swap = inspectProcedures.SwappingMarkerQualityProcedure( acqStatic, markers=ip_presence.markersIn) inspector = inspectFilters.QualityFilter(ip_swap) inspector.run() ip_pos = inspectProcedures.MarkerPositionQualityProcedure( acqStatic, markers=ip_presence.markersIn) inspector = inspectFilters.QualityFilter(ip_pos) # Calibration operation # -------------------- logging.info("[pyCGM2] --- calibration operation ---") model, acqStatic = cgm2_2.calibrate(DATA_PATH, calibrateFilenameLabelled, translators, settings, required_mp, optional_mp, False, leftFlatFoot, rightFlatFoot, headFlat, markerDiameter, hjcMethod, pointSuffix) logging.info("----- CALIBRATION- static file [%s]-----> DONE" % (calibrateFilenameLabelled)) # --------------------------MODEL FITTING ---------------------------------- logging.info( "--------------------------MODEL FITTING ----------------------------------" ) dynamicMeasurements = qtmTools.findDynamic(sessionXML) modelledC3ds = list() eventInspectorStates = list() for dynamicMeasurement in dynamicMeasurements: reconstructFilenameLabelled = qtmTools.getFilename(dynamicMeasurement) logging.info("----Processing of [%s]-----" % (reconstructFilenameLabelled)) mfpa = qtmTools.getForcePlateAssigment(dynamicMeasurement) momentProjection_text = dynamicMeasurement.Moment_Projection.text if momentProjection_text == "Default": momentProjection_text = settings["Fitting"]["Moment Projection"] if momentProjection_text == "Distal": momentProjection = enums.MomentProjection.Distal elif momentProjection_text == "Proximal": momentProjection = enums.MomentProjection.Proximal elif momentProjection_text == "Global": momentProjection = enums.MomentProjection.Global elif momentProjection_text == "JCS": momentProjection = enums.MomentProjection.JCS acq = btkTools.smartReader(DATA_PATH + reconstructFilenameLabelled) # Fitting checking # -------------------- for key in MARKERSETS.keys(): if key != "Calibration markers": logging.info("[pyCGM2] Checking of the %s" % (key)) # presence ip_presence = inspectProcedures.MarkerPresenceQualityProcedure( acq, markers=MARKERSETS[key]) inspector = inspectFilters.QualityFilter(ip_presence) inspector.run() if ip_presence.markersIn != []: ip_gap = inspectProcedures.GapQualityProcedure( acq, markers=ip_presence.markersIn) inspector = inspectFilters.QualityFilter(ip_gap) inspector.run() ip_swap = inspectProcedures.SwappingMarkerQualityProcedure( acq, markers=ip_presence.markersIn) inspector = inspectFilters.QualityFilter(ip_swap) inspector.run() ip_pos = inspectProcedures.MarkerPositionQualityProcedure( acq, markers=ip_presence.markersIn) inspector = inspectFilters.QualityFilter(ip_pos) # filtering # ----------------------- # marker order = int(float(dynamicMeasurement.Marker_lowpass_filter_order.text)) fc = float(dynamicMeasurement.Marker_lowpass_filter_frequency.text) signal_processing.markerFiltering(acq, order=order, fc=fc) # management of force plate type 5 and force plate filtering order = int( float(dynamicMeasurement.Forceplate_lowpass_filter_order.text)) fc = float(dynamicMeasurement.Forceplate_lowpass_filter_frequency.text) if order != 0 and fc != 0: acq = btkTools.smartReader(DATA_PATH + reconstructFilenameLabelled) if btkTools.checkForcePlateExist(acq): if "5" in btkTools.smartGetMetadata(acq, "FORCE_PLATFORM", "TYPE"): forceplates.correctForcePlateType5(acq) signal_processing.markerFiltering(acq, order=order, fc=fc) else: if btkTools.checkForcePlateExist(acq): if "5" in btkTools.smartGetMetadata(acq, "FORCE_PLATFORM", "TYPE"): forceplates.correctForcePlateType5(acq) btkTools.smartWriter(acq, DATA_PATH + reconstructFilenameLabelled) # event checking # ----------------------- inspectprocedureEvents = inspectProcedures.GaitEventQualityProcedure( acq) inspector = inspectFilters.QualityFilter(inspectprocedureEvents) inspector.run() eventInspectorStates.append(inspectprocedureEvents.state) # fitting operation # ----------------------- logging.info("[pyCGM2] --- Fitting operation ---") acqGait = cgm2_2.fitting(model, DATA_PATH, reconstructFilenameLabelled, translators, settings, markerDiameter, pointSuffix, mfpa, momentProjection) outFilename = reconstructFilenameLabelled #[:-4] + "_CGM1.c3d" btkTools.smartWriter(acqGait, str(DATA_PATH + outFilename)) modelledC3ds.append(outFilename) logging.info("----Processing of [%s]-----> DONE" % (reconstructFilenameLabelled)) # --------------------------GAIT PROCESSING ----------------------- if not all(eventInspectorStates): raise Exception( "[pyCGM2] Impossible to run Gait processing. Badly gait event detection. check the log file" ) logging.info( "---------------------GAIT PROCESSING -----------------------") nds = normativeDatasets.Schwartz2008("Free") types = qtmTools.detectMeasurementType(sessionXML) for type in types: modelledTrials = list() for dynamicMeasurement in dynamicMeasurements: if qtmTools.isType(dynamicMeasurement, type): filename = qtmTools.getFilename(dynamicMeasurement) modelledTrials.append(filename) #.replace(".c3d","_CGM1.c3d")) subjectMd = { "patientName": sessionXML.find("Last_name").text + " " + sessionXML.find("First_name").text, "bodyHeight": sessionXML.find("Height").text, "bodyWeight": sessionXML.find("Weight").text, "diagnosis": sessionXML.find("Diagnosis").text, "dob": sessionXML.find("Date_of_birth").text, "sex": sessionXML.find("Sex").text, "test condition": type, "gmfcs": sessionXML.find("Gross_Motor_Function_Classification").text, "fms": sessionXML.find("Functional_Mobility_Scale").text } analysisInstance = analysis.makeAnalysis(DATA_PATH, modelledTrials, subjectInfo=None, experimentalInfo=None, modelInfo=None, pointLabelSuffix=None) title = type # spatiotemporal plot.plot_spatioTemporal(DATA_PATH, analysisInstance, exportPdf=True, outputName=title, show=None, title=title) #Kinematics if model.m_bodypart in [ enums.BodyPart.LowerLimb, enums.BodyPart.LowerLimbTrunk, enums.BodyPart.FullBody ]: plot.plot_DescriptiveKinematic(DATA_PATH, analysisInstance, "LowerLimb", nds, exportPdf=True, outputName=title, pointLabelSuffix=pointSuffix, show=False, title=title) plot.plot_ConsistencyKinematic(DATA_PATH, analysisInstance, "LowerLimb", nds, exportPdf=True, outputName=title, pointLabelSuffix=pointSuffix, show=False, title=title) if model.m_bodypart in [ enums.BodyPart.LowerLimbTrunk, enums.BodyPart.FullBody ]: plot.plot_DescriptiveKinematic(DATA_PATH, analysisInstance, "Trunk", nds, exportPdf=True, outputName=title, pointLabelSuffix=pointSuffix, show=False, title=title) plot.plot_ConsistencyKinematic(DATA_PATH, analysisInstance, "Trunk", nds, exportPdf=True, outputName=title, pointLabelSuffix=pointSuffix, show=False, title=title) if model.m_bodypart in [ enums.BodyPart.UpperLimb, enums.BodyPart.FullBody ]: pass # TODO plot upperlimb panel #Kinetics if model.m_bodypart in [ enums.BodyPart.LowerLimb, enums.BodyPart.LowerLimbTrunk, enums.BodyPart.FullBody ]: plot.plot_DescriptiveKinetic(DATA_PATH, analysisInstance, "LowerLimb", nds, exportPdf=True, outputName=title, pointLabelSuffix=pointSuffix, show=False, title=title) plot.plot_ConsistencyKinetic(DATA_PATH, analysisInstance, "LowerLimb", nds, exportPdf=True, outputName=title, pointLabelSuffix=pointSuffix, show=False, title=title) #MAP plot.plot_MAP(DATA_PATH, analysisInstance, nds, exportPdf=True, outputName=title, pointLabelSuffix=pointSuffix, show=False, title=title) plt.show(False) logging.info("----- Gait Processing -----> DONE")
def main(sessionFilename, createPDFReport=True): logging.info("------------------------------------------------") logging.info("------------QTM - pyCGM2 Workflow---------------") logging.info("------------------------------------------------") sessionXML = files.readXml(os.getcwd() + "\\", sessionFilename) sessionDate = files.getFileCreationDate(os.getcwd() + "\\" + sessionFilename) #--------------------------------------------------------------------------- #management of the Processed folder DATA_PATH = os.getcwd() + "\\" + "processed\\" files.createDir(DATA_PATH) staticMeasurement = qtmTools.findStatic(sessionXML) calibrateFilenameLabelled = qtmTools.getFilename(staticMeasurement) if not os.path.isfile(DATA_PATH + calibrateFilenameLabelled): shutil.copyfile(os.getcwd() + "\\" + calibrateFilenameLabelled, DATA_PATH + calibrateFilenameLabelled) logging.info( "qualisys exported c3d file [%s] copied to processed folder" % (calibrateFilenameLabelled)) dynamicMeasurements = qtmTools.findDynamic(sessionXML) for dynamicMeasurement in dynamicMeasurements: reconstructFilenameLabelled = qtmTools.getFilename(dynamicMeasurement) if not os.path.isfile(DATA_PATH + reconstructFilenameLabelled): shutil.copyfile(os.getcwd() + "\\" + reconstructFilenameLabelled, DATA_PATH + reconstructFilenameLabelled) logging.info( "qualisys exported c3d file [%s] copied to processed folder" % (reconstructFilenameLabelled)) acq = btkTools.smartReader( str(DATA_PATH + reconstructFilenameLabelled)) acq, zeniState = eventDetector.zeni(acq) if zeniState: btkTools.smartWriter( acq, str(DATA_PATH + reconstructFilenameLabelled)) cmd = "Mokka.exe \"%s\"" % (str(DATA_PATH + reconstructFilenameLabelled)) os.system(cmd) # --------------------------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") # --------------------------MP ------------------------------------ required_mp, optional_mp = qtmTools.SubjectMp(sessionXML) # --Check MP inspectprocedure = inspectProcedures.AnthropometricDataQualityProcedure( required_mp) inspector = inspectFilters.QualityFilter(inspectprocedure) inspector.run() # translators management translators = files.getTranslators(os.getcwd() + "\\", "CGM1_1.translators") if not translators: translators = settings["Translators"] # --------------------------MODEL CALIBRATION ----------------------- logging.info( "--------------------------MODEL CALIBRATION -----------------------") staticMeasurement = qtmTools.findStatic(sessionXML) calibrateFilenameLabelled = qtmTools.getFilename(staticMeasurement) logging.info("----- CALIBRATION- static file [%s]--" % (calibrateFilenameLabelled)) leftFlatFoot = utils.toBool( sessionXML.Left_foot_normalised_to_static_trial.text) rightFlatFoot = utils.toBool( sessionXML.Right_foot_normalised_to_static_trial.text) headFlat = utils.toBool(sessionXML.Head_normalised_to_static_trial.text) markerDiameter = float(sessionXML.Marker_diameter.text) * 1000.0 pointSuffix = None # Calibration checking # -------------------- acqStatic = btkTools.smartReader(DATA_PATH + calibrateFilenameLabelled) for key in MARKERSETS.keys(): logging.info("[pyCGM2] Checking of the %s" % (key)) # presence ip_presence = inspectProcedures.MarkerPresenceQualityProcedure( acqStatic, markers=MARKERSETS[key]) inspector = inspectFilters.QualityFilter(ip_presence) inspector.run() if ip_presence.markersIn != []: ip_gap = inspectProcedures.GapQualityProcedure( acqStatic, markers=ip_presence.markersIn) inspector = inspectFilters.QualityFilter(ip_gap) inspector.run() ip_swap = inspectProcedures.SwappingMarkerQualityProcedure( acqStatic, markers=ip_presence.markersIn) inspector = inspectFilters.QualityFilter(ip_swap) inspector.run() ip_pos = inspectProcedures.MarkerPositionQualityProcedure( acqStatic, markers=ip_presence.markersIn) inspector = inspectFilters.QualityFilter(ip_pos) # Calibration operation # -------------------- logging.info("[pyCGM2] --- calibration operation ---") model, acqStatic = cgm1_1.calibrate(DATA_PATH, calibrateFilenameLabelled, translators, required_mp, optional_mp, leftFlatFoot, rightFlatFoot, headFlat, markerDiameter, pointSuffix) logging.info("----- CALIBRATION- static file [%s]-----> DONE" % (calibrateFilenameLabelled)) # --------------------------MODEL FITTING ---------------------------------- logging.info( "--------------------------MODEL FITTING ----------------------------------" ) dynamicMeasurements = qtmTools.findDynamic(sessionXML) modelledC3ds = list() eventInspectorStates = list() for dynamicMeasurement in dynamicMeasurements: reconstructFilenameLabelled = qtmTools.getFilename(dynamicMeasurement) logging.info("----Processing of [%s]-----" % (reconstructFilenameLabelled)) mfpa = qtmTools.getForcePlateAssigment(dynamicMeasurement) momentProjection_text = sessionXML.Moment_Projection.text if momentProjection_text == "Default": momentProjection_text = settings["Fitting"]["Moment Projection"] if momentProjection_text == "Distal": momentProjection = enums.MomentProjection.Distal elif momentProjection_text == "Proximal": momentProjection = enums.MomentProjection.Proximal elif momentProjection_text == "Global": momentProjection = enums.MomentProjection.Global elif momentProjection_text == "JCS": momentProjection = enums.MomentProjection.JCS acq = btkTools.smartReader(DATA_PATH + reconstructFilenameLabelled) # Fitting checking # -------------------- for key in MARKERSETS.keys(): if key != "Calibration markers": logging.info("[pyCGM2] Checking of the %s" % (key)) # presence ip_presence = inspectProcedures.MarkerPresenceQualityProcedure( acq, markers=MARKERSETS[key]) inspector = inspectFilters.QualityFilter(ip_presence) inspector.run() if ip_presence.markersIn != []: ip_gap = inspectProcedures.GapQualityProcedure( acq, markers=ip_presence.markersIn) inspector = inspectFilters.QualityFilter(ip_gap) inspector.run() ip_swap = inspectProcedures.SwappingMarkerQualityProcedure( acq, markers=ip_presence.markersIn) inspector = inspectFilters.QualityFilter(ip_swap) inspector.run() ip_pos = inspectProcedures.MarkerPositionQualityProcedure( acq, markers=ip_presence.markersIn) inspector = inspectFilters.QualityFilter(ip_pos) # filtering # ----------------------- # marker order_marker = int( float(dynamicMeasurement.Marker_lowpass_filter_order.text)) fc_marker = float( dynamicMeasurement.Marker_lowpass_filter_frequency.text) # force plate order_fp = int( float(dynamicMeasurement.Forceplate_lowpass_filter_order.text)) fc_fp = float( dynamicMeasurement.Forceplate_lowpass_filter_frequency.text) # event checking # ----------------------- inspectprocedureEvents = inspectProcedures.GaitEventQualityProcedure( acq) inspector = inspectFilters.QualityFilter(inspectprocedureEvents) inspector.run() eventInspectorStates.append(inspectprocedureEvents.state) # fitting operation # ----------------------- logging.info("[pyCGM2] --- Fitting operation ---") acqGait = cgm1_1.fitting(model, DATA_PATH, reconstructFilenameLabelled, translators, markerDiameter, pointSuffix, mfpa, momentProjection, fc_lowPass_marker=fc_marker, order_lowPass_marker=order_marker, fc_lowPass_forcePlate=fc_fp, order_lowPass_forcePlate=order_fp) outFilename = reconstructFilenameLabelled btkTools.smartWriter(acqGait, str(DATA_PATH + outFilename)) modelledC3ds.append(outFilename) logging.info("----Processing of [%s]-----> DONE" % (reconstructFilenameLabelled)) # --------------------------GAIT PROCESSING ----------------------- if not all(eventInspectorStates): raise Exception( "[pyCGM2] Impossible to run Gait processing. Badly gait event detection. check the log file" ) logging.info( "---------------------GAIT PROCESSING -----------------------") if createPDFReport: nds = normativeDatasets.Schwartz2008("Free") types = qtmTools.detectMeasurementType(sessionXML) for type in types: modelledTrials = list() for dynamicMeasurement in dynamicMeasurements: if qtmTools.isType(dynamicMeasurement, type): filename = qtmTools.getFilename(dynamicMeasurement) modelledTrials.append(filename) report.pdfGaitReport(DATA_PATH, model, modelledTrials, nds, pointSuffix, title=type) logging.info("----- Gait Processing -----> DONE")