few changes to the conversion to c3d

.gitignore

@@ -8,6 +8,7 @@ dist/
 # **/*.mp4
 **/*.trc
 **/*.sto
+**/*.c3d
 
 **/Calib_qualisys.toml
 **/pose-3d/

Pose2Sim/S00_Demo_BatchSession/Config.toml

@@ -164,6 +164,7 @@ make_c3d = false # also save triangulated data in c3d format
 ## Only works on BODY_25 and BODY_25B models
 participant_height = 1.72 # m # float if single person, list of float if multi-person (same order as the Static trials)
 participant_mass = 70.0 # kg
+make_c3d = false # save triangulated data in c3d format in addition to trc
 
 
 [opensim]

Pose2Sim/S00_Demo_BatchSession/S00_P00_SingleParticipant/Config.toml

@@ -163,10 +163,11 @@
 ## Only works on BODY_25 and BODY_25B models
 # participant_height = 1.72 # m # float if single person, list of float if multi-person (same order as the Static trials)
 # participant_mass = 70.0 # kg
+# make_c3d = false # save triangulated data in c3d format in addition to trc
 
 
 # [opensim]
-# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial']
+# static_trial = [# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial']
 #            # If this Config.toml file is at the Trial level, set to true or false (lowercase);
 #            # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial'];
 #            # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial']

Pose2Sim/S00_Demo_BatchSession/S00_P00_SingleParticipant/S00_P00_T00_StaticTrial/Config.toml

@@ -163,10 +163,11 @@
 ## Only works on BODY_25 and BODY_25B models
 # participant_height = 1.72 # m # float if single person, list of float if multi-person (same order as the Static trials)
 # participant_mass = 70.0 # kg
+# make_c3d = false # save triangulated data in c3d format in addition to trc
 
 
 # [opensim]
-# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial']
+# static_trial = [# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial']
 #            # If this Config.toml file is at the Trial level, set to true or false (lowercase);
 #            # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial'];
 #            # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial']

Pose2Sim/S00_Demo_BatchSession/S00_P00_SingleParticipant/S00_P00_T01_BalancingTrial/Config.toml

@@ -163,10 +163,11 @@ display_figures = false # true or false (lowercase)
 ## Only works on BODY_25 and BODY_25B models
 # participant_height = 1.72 # m # float if single person, list of float if multi-person (same order as the Static trials)
 # participant_mass = 70.0 # kg
+# make_c3d = false # save triangulated data in c3d format in addition to trc
 
 
 # [opensim]
-# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial']
+# static_trial = [# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial']
 #            # If this Config.toml file is at the Trial level, set to true or false (lowercase);
 #            # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial'];
 #            # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial']

Pose2Sim/S00_Demo_BatchSession/S00_P01_MultiParticipants/Config.toml

@@ -163,10 +163,12 @@
 ## Only works on BODY_25 and BODY_25B models
 # participant_height = 1.72 # m # float if single person, list of float if multi-person (same order as the Static trials)
 # participant_mass = 70.0 # kg
+# make_c3d = false # save triangulated data in c3d format in addition to trc
+# make_c3d = false # save triangulated data in c3d format in addition to trc
 
 
 # [opensim]
-# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial']
+# static_trial = [# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial']
 #            # If this Config.toml file is at the Trial level, set to true or false (lowercase);
 #            # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial'];
 #            # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial']

Pose2Sim/S00_Demo_BatchSession/S00_P01_MultiParticipants/S00_P01_T00_StaticTrialParticipant1/Config.toml

@@ -163,10 +163,11 @@
 ## Only works on BODY_25 and BODY_25B models
 participant_height = 1.21 # m # float if single person, list of float if multi-person (same order as the Static trials)
 participant_mass = 25.0 # kg
+# make_c3d = false # save triangulated data in c3d format in addition to trc
 
 
 # [opensim]
-# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial']
+# static_trial = [# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial']
 #            # If this Config.toml file is at the Trial level, set to true or false (lowercase);
 #            # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial'];
 #            # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial']

Pose2Sim/S00_Demo_BatchSession/S00_P01_MultiParticipants/S00_P01_T01_StaticTrialParticipant2/Config.toml

@@ -162,10 +162,11 @@
 ## Only works on BODY_25 and BODY_25B models
 participant_height = 1.72 # m # float if single person, list of float if multi-person (same order as the Static trials)
 participant_mass = 70.0 # kg
+# make_c3d = false # save triangulated data in c3d format in addition to trc
 
 
 # [opensim]
-# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial']
+# static_trial = [# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial']
 #            # If this Config.toml file is at the Trial level, set to true or false (lowercase);
 #            # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial'];
 #            # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial']

Pose2Sim/S00_Demo_BatchSession/S00_P01_MultiParticipants/S00_P01_T02_Participants1-2/Config.toml

@@ -129,13 +129,13 @@ reorder_trc = true # only checked if multi_person analysis
 # show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
 # handle_LR_swap = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
 # undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
-# make_c3d = false # save triangulated data in c3d format in addition to trc
+make_c3d = true # save triangulated data in c3d format in addition to trc
 
 
-# [filtering]
+[filtering]
 # type = 'butterworth' # butterworth, kalman, gaussian, LOESS, median, butterworth_on_speed
 # display_figures = false # true or false (lowercase)
-# make_c3d = false # save triangulated data in c3d format in addition to trc
+make_c3d = true # save triangulated data in c3d format in addition to trc
 
    # [filtering.butterworth]
    # order = 4 
@@ -159,10 +159,11 @@ reorder_trc = true # only checked if multi_person analysis
 ## Only works on BODY_25 and BODY_25B models
 participant_height = [1.21, 1.72] # m # float if single person, list of float if multi-person (same order as the Static trials)
 participant_mass = [25.0, 70.0] # kg
+make_c3d = true # save triangulated data in c3d format in addition to trc
 
 
 # [opensim]
-# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial']
+# static_trial = [# static_trial = ['S00_P00_Participant/S00_P00_T00_StaticTrial']
 #              # If this Config.toml file is at the Trial level, set to true or false (lowercase);
 #              # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial'];
 #              # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial']

Pose2Sim/S01_Demo_SingleTrial/Config.toml

@@ -164,6 +164,7 @@ make_c3d = false # save triangulated data in c3d format in addition to trc
 ## Only works on BODY_25 and BODY_25B models
 participant_height = 1.72 # m # float if single person, list of float if multi-person (same order as the Static trials)
 participant_mass = 70.0 # kg
+make_c3d = false # save triangulated data in c3d format in addition to trc
 
 
 [opensim]

Pose2Sim/Utilities/c3d_to_trc.py

@@ -10,8 +10,6 @@
     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. 
     
-    N.B.: First install c3d: `pip install c3d`
-    
     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

Pose2Sim/Utilities/trc_to_c3d.py

@@ -1,73 +1,126 @@
-"""
-Extracts marker data from a TRC file and creates a corresponding C3D file.
+#! /usr/bin/env python
+# -*- coding: utf-8 -*-
 
-Usage:
-    python trc_to_c3d.py --trc_path <path_to_trc_file> --f <frame_rate>
 
---trc_path: Path to the TRC file.
---f: Frame rate of the 3D data.
-c3d file will be saved in the same directory as the TRC file with the same name.
+'''
+    ##################################################
+    ## Convert trc files to c3d                     ##
+    ##################################################
+    
+    Converts trc files to c3d files.
+    
+    Usage: 
+    from Pose2Sim.Utilities import trc_to_c3d; trc_to_c3d.trc_to_c3d_func(r'<input_trc_file>')
+    python -m trc_to_c3d -t <path_to_trc_path>
+    python -m trc_to_c3d --trc_path <path_to_trc_path> --c3d_path <output_c3d_file>
+'''
 
-"""
 
-import os
+## INIT
 import argparse
 import numpy as np
-import pandas as pd
 import c3d
 
-def extract_marker_data(trc_file):
-    with open(trc_file, 'r') as file:
+
+## AUTHORSHIP INFORMATION
+__author__ = "HunMin Kim, David Pagnon"
+__copyright__ = "Copyright 2021, Pose2Sim"
+__credits__ = ["HuMin Kim, David Pagnon"]
+__license__ = "BSD 3-Clause License"
+__version__ = '0.8'
+__maintainer__ = "David Pagnon"
+__email__ = "[email protected]"
+__status__ = "Development"
+
+
+## FUNCTIONS
+def extract_marker_data(trc_path):
+    '''
+    Extract marker names and coordinates from a trc file.
+
+    INPUTS:
+    - trc_path: Path to the trc file
+
+    OUTPUTS:
+    - marker_names: List of marker names
+    - marker_coords: Array of marker coordinates (n_frames, t+3*n_markers)
+    '''
+
+    # marker names
+    with open(trc_path, 'r') as file:
         lines = file.readlines()
         marker_names_line = lines[3]
         marker_names = marker_names_line.strip().split('\t')[2::3]
 
-    trc_data = pd.read_csv(trc_file, sep='\t', skiprows=5)
-    marker_coords = trc_data.iloc[:, 2:].to_numpy().reshape(-1, len(marker_names), 3)
-    # marker_coords = np.nan_to_num(marker_coords, nan=0.0)
-    marker_coords *= 1000  # Convert from meters to millimeters
+    # time and marker coordinates
+    trc_data_np = np.genfromtxt(trc_path, skip_header=5, delimiter = '\t')[:,1:] 
+
+    return marker_names, trc_data_np
+
+
+def create_c3d_file(c3d_path, marker_names, trc_data_np):
+    '''
+    Create a c3d file from the data extracted from a trc file.
 
-    return marker_names, marker_coords
+    INPUTS:
+    - c3d_path: Path to the c3d file
+    - marker_names: List of marker names
+    - trc_data_np: Array of marker coordinates (n_frames, t+3*n_markers)
 
-def create_c3d_file(trc_file, marker_names, marker_coords, frame_rate):
+    OUTPUTS:
+    - c3d file
+    '''
+
+    # retrieve frame rate
+    times = trc_data_np[:,0]
+    frame_rate = round((len(times)-1) / (times[-1] - times[0]))
+
+    # write c3d file
     writer = c3d.Writer(point_rate=frame_rate, analog_rate=0, point_scale=1.0, point_units='mm', gen_scale=-1.0)
     writer.set_point_labels(marker_names)
 
-    markers_group = writer.point_group
-
-    for frame in marker_coords:
-        residuals = np.full((frame.shape[0], 1), 0.0)
-        cameras = np.zeros((frame.shape[0], 1))
-        points = np.hstack((frame, residuals, cameras))
+    for frame in trc_data_np:
+        residuals = np.full((len(marker_names), 1), 0.0)
+        cameras = np.zeros((len(marker_names), 1))
+        coords = frame[1:].reshape(-1,3)*1000
+        points = np.hstack((coords, residuals, cameras))
         writer.add_frames([(points, np.array([]))])
 
-    writer.set_start_frame(1)
-    writer._set_last_frame(len(marker_coords))
+    writer.set_start_frame(0)
+    writer._set_last_frame(len(trc_data_np)-1)
 
-    c3d_file_path = trc_file.replace('.trc', '.c3d')
-    with open(c3d_file_path, 'wb') as handle:
+    with open(c3d_path, 'wb') as handle:
         writer.write(handle)
-    print(f"Successfully created c3d file.")
-
-def trc_to_c3d(trc_file, frame_rate):
-    marker_names, marker_coords = extract_marker_data(trc_file)
-    create_c3d_file(trc_file, marker_names, marker_coords, frame_rate)
-
-def main():
-    parser = argparse.ArgumentParser(description='Convert TRC files to C3D files.')
-    parser.add_argument('--trc_path', type=str, required=True, help='Path to the TRC file')
-    parser.add_argument('--f', type=int, required=True, help='Frame rate')
-
-    args = parser.parse_args()
 
-    trc_file = args.trc_path
-    frame_rate = args.f
 
-    if not os.path.isfile(trc_file):
-        print(f"Error: {trc_file} does not exist.")
-        return
+def trc_to_c3d_func(*args):
+    '''
+    Converts trc files to c3d files.
+    
+    Usage: 
+    from Pose2Sim.Utilities import trc_to_c3d; trc_to_c3d.trc_to_c3d_func(r'<input_trc_file>')
+    python -m trc_to_c3d -t <path_to_trc_path>
+    python -m trc_to_c3d --trc_path <path_to_trc_path> --c3d_path <output_c3d_file>    
+    '''
+
+    try:
+        trc_path = args[0]['trc_path'] # invoked with argparse
+        if args[0]['c3d_path'] == None:
+            c3d_path = trc_path.replace('.trc', '.c3d')
+        else:
+            c3d_path = args[0]['c3d_path']
+    except:
+        trc_path = args[0] # invoked as a function
+        c3d_path = trc_path.replace('.trc', '.c3d')
+
+    marker_names, trc_data_np = extract_marker_data(trc_path)
+    create_c3d_file(c3d_path, marker_names, trc_data_np)
 
-    trc_to_c3d(trc_file, frame_rate)
 
 if __name__ == '__main__':
-    main()
+    parser = argparse.ArgumentParser(description='Convert TRC files to C3D files.')
+    parser.add_argument('-t', '--trc_path', type=str, required=True, help='trc input file path')
+    parser.add_argument('-c', '--c3d_path', type=str, required=False, help='c3d output file path')
+    args = vars(parser.parse_args())
+
+    trc_to_c3d_func(args)