128 lines
4.9 KiB
Python
128 lines
4.9 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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## Convert c3d files to trc ##
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##################################################
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Converts c3d files to trc files.
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Beware that it only allows you to retrieve 3D points, you won't get analog data nor computed data such as angles or powers with this code.
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N.B.: First install c3d: `pip install c3d`
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Usage:
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from Pose2Sim.Utilities import c3d_to_trc; c3d_to_trc.c3d_to_trc_func(r'<input_c3d_file>')
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python -m c3d_to_trc -i input_c3d_file
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python -m c3d_to_trc -i input_c3d_file -o output_c3d_file
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'''
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## INIT
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import c3d
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import numpy as np
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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__ = '0.6'
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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 c3d_to_trc_func(*args):
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'''
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Convert c3d to trc
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/!\ Only point data are retrieved. Analog data (force plates, emg) and
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computed data (angles, powers, etc) will be lost.
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Usage:
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import c3d_to_trc; c3d_to_trc.c3d_to_trc_func(r'<input_c3d_file>')
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c3d_to_trc -i input_c3d_file
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c3d_to_trc -i input_c3d_file -o output_c3d_file
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'''
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try:
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c3d_path = args[0]['input'] # invoked with argparse
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if args[0]['output'] == None:
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trc_path = c3d_path.replace('.c3d', '.trc')
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else:
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trc_path = args[0]['output']
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except:
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c3d_path = args[0] # invoked as a function
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trc_path = c3d_path.replace('.c3d', '.trc')
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# c3d header
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reader = c3d.Reader(open(c3d_path, 'rb'))
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items_header = str(reader.header).split('\n')
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items_header_list = [item.strip().split(': ') for item in items_header]
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label_item = [item[0] for item in items_header_list]
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value_item = [item[1] for item in items_header_list]
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header_c3d = dict(zip(label_item, value_item))
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# unit
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for k1 in reader.group_items():
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if k1[0]=='POINT':
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for k2 in k1[1].param_items():
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if k2[0]=='UNITS':
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if 'mm' in k2[1].bytes[:].decode('utf-8'):
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unit = 'mm'
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unit_scale= 0.001
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else:
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unit = 'm'
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unit_scale= 1 # mm
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# c3d data: reads 3D points (no analog data) and takes off computed data
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labels = reader.point_labels
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index_labels_markers = [i for i, s in enumerate(labels) if 'Angle' not in s and 'Power' not in s and 'Force' not in s and 'Moment' not in s and 'GRF' not in s]
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labels_markers = [labels[ind] for ind in index_labels_markers]
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# trc header
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header0_str = 'PathFileType\t4\t(X/Y/Z)\t' + trc_path
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header1 = {}
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header1['DataRate'] = str(int(float(header_c3d['frame_rate'])))
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header1['CameraRate'] = header1['DataRate']
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header1['NumFrames'] = str(int(header_c3d['last_frame']) - int(header_c3d['first_frame']) + 1)
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header1['NumMarkers'] = str(len(labels_markers))
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header1['Units'] = unit
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header1['OrigDataRate'] = header1['DataRate']
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header1['OrigDataStartFrame'] = header_c3d['first_frame']
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header1['OrigNumFrames'] = header1['NumFrames']
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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([item.strip() for item in labels_markers]) + '\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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with open(trc_path, 'w') as trc_o:
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trc_o.write(header_trc+'\n')
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# trc data
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index_data_markers = np.sort(np.concatenate([np.array(index_labels_markers)*3, np.array(index_labels_markers)*3+1, np.array(index_labels_markers)*3+2]))
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t0 = int(float(header_c3d['first_frame'])) / int(float(header_c3d['frame_rate']))
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tf = int(float(header_c3d['last_frame'])) / int(float(header_c3d['frame_rate']))
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trc_time = np.linspace(t0, tf, num=(int(header_c3d['last_frame']) - int(header_c3d['first_frame']) + 1))
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for n, (i, points, _) in enumerate(list(reader.read_frames())):
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c3d_line = np.concatenate([item[:3] for item in points])*unit_scale
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c3d_line_markers = c3d_line[index_data_markers]
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trc_line = '{i}\t{t}\t'.format(i=i, t=trc_time[n]) + '\t'.join(map(str,c3d_line_markers))
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trc_o.write(trc_line+'\n')
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if __name__ == '__main__':
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parser = argparse.ArgumentParser()
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parser.add_argument('-i', '--input', required = True, help='c3d input file name')
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parser.add_argument('-o', '--output', required=False, help='trc output file name')
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args = vars(parser.parse_args())
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c3d_to_trc_func(args)
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