129 lines
4.9 KiB
Python
129 lines
4.9 KiB
Python
#! /usr/bin/env python
|
|
# -*- coding: utf-8 -*-
|
|
|
|
|
|
'''
|
|
##################################################
|
|
## Convert c3d files to trc ##
|
|
##################################################
|
|
|
|
Converts c3d files to trc files.
|
|
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.
|
|
|
|
Usage:
|
|
from Pose2Sim.Utilities import c3d_to_trc; c3d_to_trc.c3d_to_trc_func(r'<input_c3d_file>')
|
|
python -m c3d_to_trc -i input_c3d_file
|
|
python -m c3d_to_trc -i input_c3d_file -o output_c3d_file
|
|
'''
|
|
|
|
|
|
## INIT
|
|
import c3d
|
|
import numpy as np
|
|
import argparse
|
|
|
|
|
|
## AUTHORSHIP INFORMATION
|
|
__author__ = "David Pagnon"
|
|
__copyright__ = "Copyright 2021, Pose2Sim"
|
|
__credits__ = ["David Pagnon"]
|
|
__license__ = "BSD 3-Clause License"
|
|
__version__ = "0.8.2"
|
|
__maintainer__ = "David Pagnon"
|
|
__email__ = "contact@david-pagnon.com"
|
|
__status__ = "Development"
|
|
|
|
|
|
## FUNCTIONS
|
|
def c3d_to_trc_func(*args):
|
|
'''
|
|
Convert c3d to trc
|
|
/!\ Only point data are retrieved. Analog data (force plates, emg) and
|
|
computed data (angles, powers, etc) will be lost.
|
|
|
|
Usage:
|
|
import c3d_to_trc; c3d_to_trc.c3d_to_trc_func(r'<input_c3d_file>')
|
|
c3d_to_trc -i input_c3d_file
|
|
c3d_to_trc -i input_c3d_file -o output_c3d_file
|
|
'''
|
|
|
|
try:
|
|
c3d_path = args[0]['input'] # invoked with argparse
|
|
if args[0]['output'] == None:
|
|
trc_path = c3d_path.replace('.c3d', '.trc')
|
|
else:
|
|
trc_path = args[0]['output']
|
|
except:
|
|
c3d_path = args[0] # invoked as a function
|
|
trc_path = c3d_path.replace('.c3d', '.trc')
|
|
|
|
# c3d header
|
|
reader = c3d.Reader(open(c3d_path, 'rb'))
|
|
items_header = str(reader.header).split('\n')
|
|
items_header_list = [item.strip().split(': ') for item in items_header]
|
|
label_item = [item[0] for item in items_header_list]
|
|
value_item = [item[1] for item in items_header_list]
|
|
header_c3d = dict(zip(label_item, value_item))
|
|
|
|
# unit
|
|
for k1 in reader.group_items():
|
|
if k1[0]=='POINT':
|
|
for k2 in k1[1].param_items():
|
|
if k2[0]=='UNITS':
|
|
if 'mm' in k2[1].bytes[:].decode('utf-8'):
|
|
unit = 'mm'
|
|
unit_scale= 0.001
|
|
else:
|
|
unit = 'm'
|
|
unit_scale= 1 # mm
|
|
|
|
# c3d data: reads 3D points (no analog data) and takes off computed data
|
|
labels = reader.point_labels
|
|
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]
|
|
labels_markers = [labels[ind] for ind in index_labels_markers]
|
|
|
|
# trc header
|
|
header0_str = 'PathFileType\t4\t(X/Y/Z)\t' + trc_path
|
|
|
|
header1 = {}
|
|
header1['DataRate'] = str(int(float(header_c3d['frame_rate'])))
|
|
header1['CameraRate'] = header1['DataRate']
|
|
header1['NumFrames'] = str(int(header_c3d['last_frame']) - int(header_c3d['first_frame']) + 1)
|
|
header1['NumMarkers'] = str(len(labels_markers))
|
|
header1['Units'] = unit
|
|
header1['OrigDataRate'] = header1['DataRate']
|
|
header1['OrigDataStartFrame'] = header_c3d['first_frame']
|
|
header1['OrigNumFrames'] = header1['NumFrames']
|
|
header1_str1 = '\t'.join(header1.keys())
|
|
header1_str2 = '\t'.join(header1.values())
|
|
|
|
header2_str1 = 'Frame#\tTime\t' + '\t\t\t'.join([item.strip() for item in labels_markers]) + '\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])
|
|
|
|
with open(trc_path, 'w') as trc_o:
|
|
trc_o.write(header_trc+'\n')
|
|
|
|
# trc data
|
|
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]))
|
|
t0 = int(float(header_c3d['first_frame'])) / int(float(header_c3d['frame_rate']))
|
|
tf = int(float(header_c3d['last_frame'])) / int(float(header_c3d['frame_rate']))
|
|
trc_time = np.linspace(t0, tf, num=(int(header_c3d['last_frame']) - int(header_c3d['first_frame']) + 1))
|
|
for n, (i, points, _) in enumerate(list(reader.read_frames())):
|
|
c3d_line = np.concatenate([item[:3] for item in points])*unit_scale
|
|
c3d_line_markers = c3d_line[index_data_markers]
|
|
trc_line = '{i}\t{t}\t'.format(i=i, t=trc_time[n]) + '\t'.join(map(str,c3d_line_markers))
|
|
trc_o.write(trc_line+'\n')
|
|
|
|
print(f'Converted c3d file to {trc_path}')
|
|
|
|
|
|
if __name__ == '__main__':
|
|
parser = argparse.ArgumentParser()
|
|
parser.add_argument('-i', '--input', required = True, help='c3d input file name')
|
|
parser.add_argument('-o', '--output', required=False, help='trc output file name')
|
|
args = vars(parser.parse_args())
|
|
|
|
c3d_to_trc_func(args)
|