172 lines
7.0 KiB
Python
172 lines
7.0 KiB
Python
#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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'''
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##################################################
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## Build trc from mot and osim files ##
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##################################################
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Build a trc file which stores real and virtual markers
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calculated from a .mot motion file and a .osim model file.
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If no marker list is specified, all markers are included.
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Usage:
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from Pose2Sim.Utilities import trc_from_mot_osim; trc_from_mot_osim.trc_from_mot_osim_func(input_mot_file=r'<input_mot_file>', input_osim_file=r'<output_osim_file>', trc_output_file=r'<trc_output_file>', marker_list=['_rknee', 'r_hip'])
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python -m trc_from_mot_osim -m input_mot_file -o input_osim_file
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python -m trc_from_mot_osim -m input_mot_file -o input_osim_file -t trc_output_file -l r_knee r_hip
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'''
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## INIT
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import os
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import pandas as pd
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import numpy as np
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import opensim as osim
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import argparse
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## AUTHORSHIP INFORMATION
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__author__ = "David Pagnon"
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__copyright__ = "Copyright 2021, Pose2Sim"
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__credits__ = ["David Pagnon"]
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__license__ = "BSD 3-Clause License"
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__version__ = "0.9.4"
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__maintainer__ = "David Pagnon"
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__email__ = "contact@david-pagnon.com"
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__status__ = "Development"
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## FUNCTIONS
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def get_marker_positions(motion_data, model, in_degrees=True, marker_list=[]):
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'''
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Get dataframe of marker positions
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INPUTS:
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- motion_data: .mot file opened with osim.TimeSeriesTable
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- model: .osim file opened with osim.Model
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- in_degrees: True if the motion data is in degrees, False if in radians
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- marker_list: list of marker names to include in the trc file. All if not specified
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OUTPUT:
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- marker_positions_pd: DataFrame of marker positions
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'''
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# Markerset
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marker_set = model.getMarkerSet()
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marker_set_names = [mk.getName() for mk in list(marker_set)]
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if len(marker_list)>0:
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marker_set_names = [marker for marker in marker_list if marker in marker_set_names]
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absent_markers = [marker for marker in marker_list if marker not in marker_set_names]
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if len(absent_markers)>0:
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print(f'The following markers were not found in the model: {absent_markers}')
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marker_set_names_xyz = np.array([[m+'_x', m+'_y', m+'_z'] for m in marker_set_names]).flatten()
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# Data
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times = motion_data.getIndependentColumn()
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joint_angle_set_names = motion_data.getColumnLabels() # or [c.getName() for c in model.getCoordinateSet()]
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joint_angle_set_names = [j for j in joint_angle_set_names if not j.endswith('activation')]
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motion_data_pd = pd.DataFrame(motion_data.getMatrix().to_numpy()[:,:len(joint_angle_set_names)], columns=joint_angle_set_names)
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# Get marker positions at each state
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state = model.initSystem()
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marker_positions = []
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print('Time frame:')
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for n,t in enumerate(times):
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print('t = ', t, 's')
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# put the model in the right position
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for coord in joint_angle_set_names:
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if in_degrees and not coord.endswith('_tx') and not coord.endswith('_ty') and not coord.endswith('_tz'):
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value = motion_data_pd.loc[n,coord]*np.pi/180
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else:
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value = motion_data_pd.loc[n,coord]
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model.getCoordinateSet().get(coord).setValue(state,value, enforceContraints=False)
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model.assemble(state)
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# get marker positions
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marker_positions += [np.array([marker_set.get(mk_name).findLocationInFrame(state, model.getGround()).to_numpy() for mk_name in marker_set_names]).flatten()]
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marker_positions_pd = pd.DataFrame(marker_positions, columns=marker_set_names_xyz)
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marker_positions_pd.insert(0, 'time', times)
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marker_positions_pd.insert(0, 'frame', np.arange(len(times))+1)
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return marker_positions_pd, marker_set_names
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def trc_from_mot_osim_func(**args):
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'''
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Build a trc file which stores real and virtual markers
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calculated from a .mot motion file and a .osim model file.
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If no marker list is specified, all markers are included.
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Usage:
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from Pose2Sim.Utilities import trc_from_mot_osim; trc_from_mot_osim.trc_from_mot_osim_func(input_mot_file=r'<input_mot_file>', input_osim_file=r'<output_osim_file>', trc_output_file=r'<trc_output_file>', marker_list=['_rknee', 'r_hip'])
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python -m trc_from_mot_osim -m input_mot_file -o input_osim_file
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python -m trc_from_mot_osim -m input_mot_file -o input_osim_file -t trc_output_file -l r_knee r_hip
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'''
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motion_path = args.get('input_mot_file') # invoked with argparse
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osim_path = args.get('input_osim_file')
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trc_path = args.get('trc_output_file')
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if trc_path == None:
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trc_path = motion_path.replace('.mot', '.trc')
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marker_list = args.get('marker_list')
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if marker_list == None:
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marker_list = []
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# Create dataframe with marker positions
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model = osim.Model(osim_path)
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motion_data = osim.TimeSeriesTable(motion_path)
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# In degrees or radians
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with open(motion_path) as m_p:
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while True:
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line = m_p.readline()
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if 'inDegrees' in line:
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break
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if 'yes' in line:
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in_degrees = True
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else:
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in_degrees = False
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marker_positions_pd, marker_set_names = get_marker_positions(motion_data, model, in_degrees=in_degrees, marker_list=marker_list)
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# Trc header
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times = motion_data.getIndependentColumn()
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fps = str( int(1/ ((times[-1]-times[0]) / (len(times)-1))))
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nb_frames = str(len(times))
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nb_markers = str(len(marker_set_names))
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header0_str = 'PathFileType\t4\t(X/Y/Z)\t' + os.path.basename(trc_path)
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header1 = {}
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header1['DataRate'] = fps
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header1['CameraRate'] = fps
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header1['NumFrames'] = nb_frames
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header1['NumMarkers'] = nb_markers
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header1['Units'] = 'm'
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header1['OrigDataRate'] = fps
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header1['OrigDataStartFrame'] = '0'
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header1['OrigNumFrames'] = nb_frames
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header1_str1 = '\t'.join(header1.keys())
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header1_str2 = '\t'.join(header1.values())
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header2_str1 = 'Frame#\tTime\t' + '\t\t\t'.join([mk.strip() for mk in marker_set_names]) + '\t\t'
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header2_str2 = '\t\t'+'\t'.join(['X{i}\tY{i}\tZ{i}'.format(i=i+1) for i in range(int(header1['NumMarkers']))])
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header_trc = '\n'.join([header0_str, header1_str1, header1_str2, header2_str1, header2_str2])
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# write data
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with open(trc_path, 'w') as trc_o:
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trc_o.write(header_trc+'\n')
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marker_positions_pd.to_csv(trc_path, header=False, sep = '\t', mode='a', index=False)
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print(f'trc file successfully saved as {trc_path}')
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if __name__ == '__main__':
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parser = argparse.ArgumentParser()
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parser.add_argument('-m', '--input_mot_file', required = True, help='input mot file')
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parser.add_argument('-o', '--input_osim_file', required = True, help='input osim file')
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parser.add_argument('-t', '--trc_output_file', required=False, help='trc output file')
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parser.add_argument('-l', '--marker_list', required=False, nargs='+', default=[], help='list of markers to include in the trc file. All if not specified')
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args = vars(parser.parse_args())
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trc_from_mot_osim_func(**args)
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