From 9dff5d73be28fc3b0cdc5221cc4769fbf3659a83 Mon Sep 17 00:00:00 2001 From: davidpagnon Date: Sat, 9 Dec 2023 22:06:57 +0100 Subject: [PATCH] config can be dict, dir, None (from current dir) --- Pose2Sim/Pose2Sim.py | 142 +++++++++--------- Pose2Sim/Utilities/opensim.log | 107 -------------- Pose2Sim/Utilities/reproj_from_trc_calib.py | 156 ++++++++++++++++++++ 3 files changed, 229 insertions(+), 176 deletions(-) delete mode 100644 Pose2Sim/Utilities/opensim.log create mode 100644 Pose2Sim/Utilities/reproj_from_trc_calib.py diff --git a/Pose2Sim/Pose2Sim.py b/Pose2Sim/Pose2Sim.py index 41d63f5..55f0173 100644 --- a/Pose2Sim/Pose2Sim.py +++ b/Pose2Sim/Pose2Sim.py @@ -68,18 +68,6 @@ def setup_logging(session_dir): handlers = [logging.handlers.TimedRotatingFileHandler(os.path.join(session_dir, 'logs.txt'), when='D', interval=7), logging.StreamHandler()]) -def determine_level(): - ''' - Determine the level at which the function is called. - Level = 1: called from a Trial folder - Level = 2: called from a Participant folder - Level = 3: called from a Session folder - ''' - - level = max([len(root.split(os.sep)) for root,dirs,files in os.walk('.') if 'Config.toml' in files]) - return level - - def recursive_update(dict_to_update, dict_with_new_values): ''' Update nested dictionaries without overwriting existing keys in any level of nesting @@ -102,62 +90,86 @@ def recursive_update(dict_to_update, dict_with_new_values): return dict_to_update -def read_config_files(level): +def determine_level(config_dir): + ''' + Determine the level at which the function is called. + Level = 1: Trial folder + Level = 2: Participant folder + Level = 3: Session folder + ''' + + len_paths = [len(root.split(os.sep)) for root,dirs,files in os.walk(config_dir) if 'Config.toml' in files] + level = max(len_paths) - min(len_paths) + 1 + return level + + +def read_config_files(config): ''' Read Session, Participant, and Trial configuration files, and output a dictionary with all the parameters. ''' - # Trial level - if level == 1: - session_config_dict = toml.load(os.path.join('..','..','Config.toml')) - participant_config_dict = toml.load(os.path.join('..','Config.toml')) - trial_config_dict = toml.load('Config.toml') - - session_config_dict = recursive_update(session_config_dict,participant_config_dict) - session_config_dict = recursive_update(session_config_dict,trial_config_dict) - session_config_dict.get("project").update({"project_dir":os.getcwd()}) - config_dicts = [session_config_dict] - - # Participant level - if level == 2: - session_config_dict = toml.load(os.path.join('..','Config.toml')) - participant_config_dict = toml.load('Config.toml') - config_dicts = [] - # Create config dictionaries for all trials of the participant - for (root,dirs,files) in os.walk('.'): - if 'Config.toml' in files and root != '.': - trial_config_dict = toml.load(os.path.join(root, files[0])) - # deep copy, otherwise session_config_dict is modified at each iteration within the config_dicts list - temp_dict = deepcopy(session_config_dict) - temp_dict = recursive_update(temp_dict,participant_config_dict) - temp_dict = recursive_update(temp_dict,trial_config_dict) - temp_dict.get("project").update({"project_dir":os.path.join(os.getcwd(), os.path.relpath(root))}) - if not os.path.basename(root) in temp_dict.get("project").get('exclude_from_batch'): - config_dicts.append(temp_dict) - - # Session level - if level == 3: - session_config_dict = toml.load('Config.toml') - config_dicts = [] - # Create config dictionaries for all trials of all participants of the session - for (root,dirs,files) in os.walk('.'): - if 'Config.toml' in files and root != '.': - # participant - if len(root.split(os.sep)) == 2: - participant_config_dict = toml.load(os.path.join(root, files[0])) - # trial - elif len(root.split(os.sep)) == 3: + if type(config)==dict: + level = 3 # log_dir = os.getcwd() + config_dicts = [config] + if config_dicts[0].get('project').get('project_dir') == None: + raise ValueError('Please specify the project directory in config_dict:\n \ + config_dict.get("project").update({"project_dir":""})') + else: + # if launched without an argument, config == None, else it is the path to the config directory + config_dir = ['.' if config == None else config][0] + level = determine_level(config_dir) + + # Trial level + if level == 1: + session_config_dict = toml.load(os.path.join(config_dir, '..','..','Config.toml')) + participant_config_dict = toml.load(os.path.join(config_dir, '..','Config.toml')) + trial_config_dict = toml.load(os.path.join(config_dir, 'Config.toml')) + + session_config_dict = recursive_update(session_config_dict,participant_config_dict) + session_config_dict = recursive_update(session_config_dict,trial_config_dict) + session_config_dict.get("project").update({"project_dir":config_dir}) + config_dicts = [session_config_dict] + + # Participant level + if level == 2: + session_config_dict = toml.load(os.path.join(config_dir, '..','Config.toml')) + participant_config_dict = toml.load(os.path.join(config_dir, 'Config.toml')) + config_dicts = [] + # Create config dictionaries for all trials of the participant + for (root,dirs,files) in os.walk(config_dir): + if 'Config.toml' in files and root != config_dir: trial_config_dict = toml.load(os.path.join(root, files[0])) # deep copy, otherwise session_config_dict is modified at each iteration within the config_dicts list temp_dict = deepcopy(session_config_dict) temp_dict = recursive_update(temp_dict,participant_config_dict) temp_dict = recursive_update(temp_dict,trial_config_dict) - temp_dict.get("project").update({"project_dir":os.path.join(os.getcwd(), os.path.relpath(root))}) - if not os.path.relpath(root) in [os.path.relpath(p) for p in temp_dict.get("project").get('exclude_from_batch')]: + temp_dict.get("project").update({"project_dir":os.path.join(config_dir, os.path.relpath(root))}) + if not os.path.basename(root) in temp_dict.get("project").get('exclude_from_batch'): config_dicts.append(temp_dict) - return config_dicts + # Session level + if level == 3: + session_config_dict = toml.load(os.path.join(config_dir, 'Config.toml')) + config_dicts = [] + # Create config dictionaries for all trials of all participants of the session + for (root,dirs,files) in os.walk(config_dir): + if 'Config.toml' in files and root != config_dir: + # participant + if determine_level(root) == 2: + participant_config_dict = toml.load(os.path.join(root, files[0])) + # trial + elif determine_level(root) == 1: + trial_config_dict = toml.load(os.path.join(root, files[0])) + # deep copy, otherwise session_config_dict is modified at each iteration within the config_dicts list + temp_dict = deepcopy(session_config_dict) + temp_dict = recursive_update(temp_dict,participant_config_dict) + temp_dict = recursive_update(temp_dict,trial_config_dict) + temp_dict.get("project").update({"project_dir":os.path.join(config_dir, os.path.relpath(root))}) + if not os.path.relpath(root) in [os.path.relpath(p) for p in temp_dict.get("project").get('exclude_from_batch')]: + config_dicts.append(temp_dict) + + return level, config_dicts def base_params(config_dict, level): @@ -182,23 +194,15 @@ def calibration(config=None): ''' Cameras calibration from checkerboards or from qualisys files. - config is usually deduced from the path the function is called from - (see read_config_files(level) function) but it can also be a dictionary + config can be a dictionary, + or a trial, participant, or session directory path, + or the function can be called without an argument, in which case it is the current directory. ''' from Pose2Sim.calibration import calibrate_cams_all - - if type(config)==dict: - level = 3 # log_dir = os.getcwd() - config_dict = config - if config_dict.get('project').get('project_dir') == None: - raise ValueError('Please specify the project directory in config_dict:\n \ - config_dict.get("project").update({"project_dir":""})') - else: - # Determine the level at which the function is called (session:3, participant:2, trial:1) - level = determine_level() - config_dict = read_config_files(level)[0] + level, config_dicts = read_config_files(config) + config_dict = config_dicts[0] session_dir = os.path.realpath([os.getcwd() if level==3 else os.path.join(os.getcwd(), '..') if level==2 else os.path.join(os.getcwd(), '..', '..')][0]) config_dict.get("project").update({"project_dir":session_dir}) diff --git a/Pose2Sim/Utilities/opensim.log b/Pose2Sim/Utilities/opensim.log deleted file mode 100644 index 9522f12..0000000 --- a/Pose2Sim/Utilities/opensim.log +++ /dev/null @@ -1,107 +0,0 @@ -[2023-12-08 12:52:35.337] [info] Loaded model model from file D:\softs\github_david\Openpose-to-Opensim\Pose_from_simu_draft\Model_Pose2Sim_Body25b_scaled.osim -[2023-12-08 12:52:35.338] [warning] Couldn't find file 'r_pelvis.vtp'. -[2023-12-08 12:52:35.338] [warning] Couldn't find file 'l_pelvis.vtp'. -[2023-12-08 12:52:35.339] [warning] Couldn't find file 'sacrum.vtp'. -[2023-12-08 12:52:35.339] [warning] Couldn't find file 'femur_r.vtp'. -[2023-12-08 12:52:35.339] [warning] Couldn't find file 'r_patella.vtp'. -[2023-12-08 12:52:35.339] [warning] Couldn't find file 'tibia_r.vtp'. -[2023-12-08 12:52:35.339] [warning] Couldn't find file 'fibula_r.vtp'. -[2023-12-08 12:52:35.340] [warning] Couldn't find file 'talus_rv.vtp'. -[2023-12-08 12:52:35.341] [warning] Couldn't find file 'foot.vtp'. -[2023-12-08 12:52:35.341] [warning] Couldn't find file 'bofoot.vtp'. -[2023-12-08 12:52:35.341] [warning] Couldn't find file 'femur_l.vtp'. -[2023-12-08 12:52:35.341] [warning] Couldn't find file 'l_patella.vtp'. -[2023-12-08 12:52:35.342] [warning] Couldn't find file 'tibia_l.vtp'. -[2023-12-08 12:52:35.342] [warning] Couldn't find file 'fibula_l.vtp'. -[2023-12-08 12:52:35.342] [warning] Couldn't find file 'talus_lv.vtp'. -[2023-12-08 12:52:35.342] [warning] Couldn't find file 'l_foot.vtp'. -[2023-12-08 12:52:35.343] [warning] Couldn't find file 'l_bofoot.vtp'. -[2023-12-08 12:52:35.343] [warning] Couldn't find file 'lumbar5.vtp'. -[2023-12-08 12:52:35.343] [warning] Couldn't find file 'lumbar4.vtp'. -[2023-12-08 12:52:35.343] [warning] Couldn't find file 'lumbar3.vtp'. -[2023-12-08 12:52:35.343] [warning] Couldn't find file 'lumbar2.vtp'. -[2023-12-08 12:52:35.344] [warning] Couldn't find file 'lumbar1.vtp'. -[2023-12-08 12:52:35.344] [warning] Couldn't find file 'cerv1sm.vtp'. -[2023-12-08 12:52:35.344] [warning] Couldn't find file 'cerv2sm.vtp'. -[2023-12-08 12:52:35.344] [warning] Couldn't find file 'cerv3sm.vtp'. -[2023-12-08 12:52:35.344] [warning] Couldn't find file 'cerv4sm.vtp'. -[2023-12-08 12:52:35.345] [warning] Couldn't find file 'cerv5sm.vtp'. -[2023-12-08 12:52:35.345] [warning] Couldn't find file 'cerv6sm.vtp'. -[2023-12-08 12:52:35.345] [warning] Couldn't find file 'cerv7.vtp'. -[2023-12-08 12:52:35.345] [warning] Couldn't find file 'thoracic12_s.vtp'. -[2023-12-08 12:52:35.345] [warning] Couldn't find file 'thoracic11_s.vtp'. -[2023-12-08 12:52:35.345] [warning] Couldn't find file 'thoracic10_s.vtp'. -[2023-12-08 12:52:35.346] [warning] Couldn't find file 'thoracic9_s.vtp'. -[2023-12-08 12:52:35.346] [warning] Couldn't find file 'thoracic8_s.vtp'. -[2023-12-08 12:52:35.346] [warning] Couldn't find file 'thoracic7_s.vtp'. -[2023-12-08 12:52:35.346] [warning] Couldn't find file 'thoracic6_s.vtp'. -[2023-12-08 12:52:35.346] [warning] Couldn't find file 'thoracic5_s.vtp'. -[2023-12-08 12:52:35.346] [warning] Couldn't find file 'thoracic4_s.vtp'. -[2023-12-08 12:52:35.346] [warning] Couldn't find file 'thoracic3_s.vtp'. -[2023-12-08 12:52:35.347] [warning] Couldn't find file 'thoracic2_s.vtp'. -[2023-12-08 12:52:35.347] [warning] Couldn't find file 'thoracic1_s.vtp'. -[2023-12-08 12:52:35.347] [warning] Couldn't find file 'hat_ribs_scap.vtp'. -[2023-12-08 12:52:35.347] [warning] Couldn't find file 'hat_jaw.vtp'. -[2023-12-08 12:52:35.347] [warning] Couldn't find file 'hat_skull.vtp'. -[2023-12-08 12:52:35.347] [warning] Couldn't find file 'humerus_rv.vtp'. -[2023-12-08 12:52:35.348] [warning] Couldn't find file 'ulna_rv.vtp'. -[2023-12-08 12:52:35.348] [warning] Couldn't find file 'radius_rv.vtp'. -[2023-12-08 12:52:35.348] [warning] Couldn't find file 'pisiform_rvs.vtp'. -[2023-12-08 12:52:35.348] [warning] Couldn't find file 'lunate_rvs.vtp'. -[2023-12-08 12:52:35.348] [warning] Couldn't find file 'scaphoid_rvs.vtp'. -[2023-12-08 12:52:35.348] [warning] Couldn't find file 'triquetrum_rvs.vtp'. -[2023-12-08 12:52:35.348] [warning] Couldn't find file 'hamate_rvs.vtp'. -[2023-12-08 12:52:35.348] [warning] Couldn't find file 'capitate_rvs.vtp'. -[2023-12-08 12:52:35.348] [warning] Couldn't find file 'trapezoid_rvs.vtp'. -[2023-12-08 12:52:35.349] [warning] Couldn't find file 'trapezium_rvs.vtp'. -[2023-12-08 12:52:35.349] [warning] Couldn't find file 'metacarpal2_rvs.vtp'. -[2023-12-08 12:52:35.349] [warning] Couldn't find file 'index_proximal_rvs.vtp'. -[2023-12-08 12:52:35.349] [warning] Couldn't find file 'index_medial_rvs.vtp'. -[2023-12-08 12:52:35.349] [warning] Couldn't find file 'index_distal_rvs.vtp'. -[2023-12-08 12:52:35.349] [warning] Couldn't find file 'metacarpal3_rvs.vtp'. -[2023-12-08 12:52:35.349] [warning] Couldn't find file 'middle_proximal_rvs.vtp'. -[2023-12-08 12:52:35.349] [warning] Couldn't find file 'middle_medial_rvs.vtp'. -[2023-12-08 12:52:35.349] [warning] Couldn't find file 'middle_distal_rvs.vtp'. -[2023-12-08 12:52:35.350] [warning] Couldn't find file 'metacarpal4_rvs.vtp'. -[2023-12-08 12:52:35.350] [warning] Couldn't find file 'ring_proximal_rvs.vtp'. -[2023-12-08 12:52:35.350] [warning] Couldn't find file 'ring_medial_rvs.vtp'. -[2023-12-08 12:52:35.350] [warning] Couldn't find file 'ring_distal_rvs.vtp'. -[2023-12-08 12:52:35.350] [warning] Couldn't find file 'metacarpal5_rvs.vtp'. -[2023-12-08 12:52:35.350] [warning] Couldn't find file 'little_proximal_rvs.vtp'. -[2023-12-08 12:52:35.350] [warning] Couldn't find file 'little_medial_rvs.vtp'. -[2023-12-08 12:52:35.351] [warning] Couldn't find file 'little_distal_rvs.vtp'. -[2023-12-08 12:52:35.351] [warning] Couldn't find file 'metacarpal1_rvs.vtp'. -[2023-12-08 12:52:35.351] [warning] Couldn't find file 'thumb_proximal_rvs.vtp'. -[2023-12-08 12:52:35.351] [warning] Couldn't find file 'thumb_distal_rvs.vtp'. -[2023-12-08 12:52:35.351] [warning] Couldn't find file 'humerus_lv.vtp'. -[2023-12-08 12:52:35.352] [warning] Couldn't find file 'ulna_lv.vtp'. -[2023-12-08 12:52:35.352] [warning] Couldn't find file 'radius_lv.vtp'. -[2023-12-08 12:52:35.352] [warning] Couldn't find file 'pisiform_lvs.vtp'. -[2023-12-08 12:52:35.352] [warning] Couldn't find file 'lunate_lvs.vtp'. -[2023-12-08 12:52:35.352] [warning] Couldn't find file 'scaphoid_lvs.vtp'. -[2023-12-08 12:52:35.352] [warning] Couldn't find file 'triquetrum_lvs.vtp'. -[2023-12-08 12:52:35.353] [warning] Couldn't find file 'hamate_lvs.vtp'. -[2023-12-08 12:52:35.353] [warning] Couldn't find file 'capitate_lvs.vtp'. -[2023-12-08 12:52:35.353] [warning] Couldn't find file 'trapezoid_lvs.vtp'. -[2023-12-08 12:52:35.353] [warning] Couldn't find file 'trapezium_lvs.vtp'. -[2023-12-08 12:52:35.353] [warning] Couldn't find file 'metacarpal2_lvs.vtp'. -[2023-12-08 12:52:35.353] [warning] Couldn't find file 'index_proximal_lvs.vtp'. -[2023-12-08 12:52:35.353] [warning] Couldn't find file 'index_medial_lvs.vtp'. -[2023-12-08 12:52:35.353] [warning] Couldn't find file 'index_distal_lvs.vtp'. -[2023-12-08 12:52:35.353] [warning] Couldn't find file 'metacarpal3_lvs.vtp'. -[2023-12-08 12:52:35.354] [warning] Couldn't find file 'middle_proximal_lvs.vtp'. -[2023-12-08 12:52:35.354] [warning] Couldn't find file 'middle_medial_lvs.vtp'. -[2023-12-08 12:52:35.354] [warning] Couldn't find file 'middle_distal_lvs.vtp'. -[2023-12-08 12:52:35.354] [warning] Couldn't find file 'metacarpal4_lvs.vtp'. -[2023-12-08 12:52:35.354] [warning] Couldn't find file 'ring_proximal_lvs.vtp'. -[2023-12-08 12:52:35.354] [warning] Couldn't find file 'ring_medial_lvs.vtp'. -[2023-12-08 12:52:35.354] [warning] Couldn't find file 'ring_distal_lvs.vtp'. -[2023-12-08 12:52:35.355] [warning] Couldn't find file 'metacarpal5_lvs.vtp'. -[2023-12-08 12:52:35.355] [warning] Couldn't find file 'little_proximal_lvs.vtp'. -[2023-12-08 12:52:35.355] [warning] Couldn't find file 'little_medial_lvs.vtp'. -[2023-12-08 12:52:35.355] [warning] Couldn't find file 'little_distal_lvs.vtp'. -[2023-12-08 12:52:35.355] [warning] Couldn't find file 'metacarpal1_lvs.vtp'. -[2023-12-08 12:52:35.355] [warning] Couldn't find file 'thumb_proximal_lvs.vtp'. -[2023-12-08 12:52:35.355] [warning] Couldn't find file 'thumb_distal_lvs.vtp'. -[2023-12-08 12:52:35.680] [warning] Coordinate.setValue: coordinate pro_sup_r is locked. Unable to change its value. -[2023-12-08 12:52:35.758] [warning] Coordinate.setValue: coordinate pro_sup_l is locked. Unable to change its value. diff --git a/Pose2Sim/Utilities/reproj_from_trc_calib.py b/Pose2Sim/Utilities/reproj_from_trc_calib.py new file mode 100644 index 0000000..f2fc379 --- /dev/null +++ b/Pose2Sim/Utilities/reproj_from_trc_calib.py @@ -0,0 +1,156 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + + +''' + ################################################## + ## Reproject 3D points on camera planes ## + ################################################## + + Build a trc file which stores all real and virtual markers + calculated from a .mot motion file and a .osim model file. + + Default: DeepLabCut + + Usage: + from Pose2Sim.Utilities import reproj_from_trc_calib; reproj_from_trc_calib.reproj_from_trc_calib_func(r'', r'', r'') + python -m reproj_from_trc_calib -t input_trc_file -c input_calib_file + python -m reproj_from_trc_calib -t input_trc_file -c input_calib_file -o 'openpose' +''' + + +## INIT +import os +import pandas as pd +import numpy as np +import opensim as osim +import argparse + + +## AUTHORSHIP INFORMATION +__author__ = "David Pagnon" +__copyright__ = "Copyright 2021, Pose2Sim" +__credits__ = ["David Pagnon"] +__license__ = "BSD 3-Clause License" +__version__ = "0.5" +__maintainer__ = "David Pagnon" +__email__ = "contact@david-pagnon.com" +__status__ = "Development" + + +## FUNCTIONS +def get_marker_positions(motion_data, model): + ''' + Get dataframe of marker positions + + INPUTS: + - motion_data: .mot file opened with osim.TimeSeriesTable + - model: .osim file opened with osim.Model + + OUTPUT: + - marker_positions_pd: DataFrame of marker positions + ''' + + # Markerset + marker_set = model.getMarkerSet() + marker_set_names = [mk.getName() for mk in list(marker_set)] + marker_set_names_xyz = np.array([[m+'_x', m+'_y', m+'_z'] for m in marker_set_names]).flatten() + + # Data + times = motion_data.getIndependentColumn() + joint_angle_set_names = motion_data.getColumnLabels() # or [c.getName() for c in model.getCoordinateSet()] + joint_angle_set_names = [j for j in joint_angle_set_names if not j.endswith('activation')] + motion_data_pd = pd.DataFrame(motion_data.getMatrix().to_numpy()[:,:len(joint_angle_set_names)], columns=joint_angle_set_names) + + # Get marker positions at each state + state = model.initSystem() + marker_positions = [] + for n,t in enumerate(times): + # put the model in the right position + for coord in joint_angle_set_names: + if not coord.endswith('_tx') and not coord.endswith('_ty') and not coord.endswith('_tz'): + value = motion_data_pd.loc[n,coord]*np.pi/180 + else: + value = motion_data_pd.loc[n,coord] + model.getCoordinateSet().get(coord).setValue(state,value) + # get marker positions + marker_positions += [np.array([marker_set.get(mk_name).findLocationInFrame(state, model.getGround()).to_numpy() for mk_name in marker_set_names]).flatten()] + marker_positions_pd = pd.DataFrame(marker_positions, columns=marker_set_names_xyz) + marker_positions_pd.insert(0, 'time', times) + marker_positions_pd.insert(0, 'frame', np.arange(len(times))) + + return marker_positions_pd + + +def trc_from_mot_osim_func(*args): + ''' + Build a trc file which stores all real and virtual markers + calculated from a .mot motion file and a .osim model file. + + Usage: + from Pose2Sim.Utilities import trc_from_mot_osim; trc_from_mot_osim.trc_from_mot_osim_func(r'', r'', r'') + python -m trc_from_mot_osim -m input_mot_file -o input_osim_file + python -m trc_from_mot_osim -m input_mot_file -o input_osim_file -t trc_output_file + ''' + + try: + motion_path = args[0]['input_mot_file'] # invoked with argparse + osim_path = args[0]['input_osim_file'] + if args[0]['trc_output_file'] == None: + trc_path = motion_path.replace('.mot', '.trc') + else: + trc_path = args[0]['trc_output_file'] + except: + motion_path = args[0] # invoked as a function + osim_path = args[1] + try: + trc_path = args[2] + except: + trc_path = motion_path.replace('.mot', '.trc') + + # Create dataframe with marker positions + model = osim.Model(osim_path) + motion_data = osim.TimeSeriesTable(motion_path) + marker_positions_pd = get_marker_positions(motion_data, model) + + # Trc header + times = motion_data.getIndependentColumn() + marker_set = model.getMarkerSet() + marker_set_names = [mk.getName() for mk in list(marker_set)] + + fps = str(int( 1/ (times[1]-times[0]) / (len(times)-1) )) + nb_frames = str(len(times)) + nb_markers = str(len(marker_set_names)) + header0_str = 'PathFileType\t4\t(X/Y/Z)\t' + os.path.basename(trc_path) + + header1 = {} + header1['DataRate'] = fps + header1['CameraRate'] = fps + header1['NumFrames'] = nb_frames + header1['NumMarkers'] = nb_markers + header1['Units'] = 'm' + header1['OrigDataRate'] = fps + header1['OrigDataStartFrame'] = '0' + header1['OrigNumFrames'] = nb_frames + header1_str1 = '\t'.join(header1.keys()) + header1_str2 = '\t'.join(header1.values()) + + header2_str1 = 'Frame#\tTime\t' + '\t\t\t'.join([mk.strip() for mk in marker_set_names]) + '\t\t' + header2_str2 = '\t\t'+'\t'.join(['X{i}\tY{i}\tZ{i}'.format(i=i+1) for i in range(int(header1['NumMarkers']))]) + + header_trc = '\n'.join([header0_str, header1_str1, header1_str2, header2_str1, header2_str2]) + + # write data + with open(trc_path, 'w') as trc_o: + trc_o.write(header_trc+'\n') + marker_positions_pd.to_csv(trc_path, header=False, sep = '\t', mode='a', index=False) + + +if __name__ == '__main__': + parser = argparse.ArgumentParser() + parser.add_argument('-m', '--input_mot_file', required = True, help='input mot file') + parser.add_argument('-o', '--input_osim_file', required = True, help='input osim file') + parser.add_argument('-t', '--trc_output_file', required=False, help='trc output file') + args = vars(parser.parse_args()) + + trc_from_mot_osim_func(args) \ No newline at end of file