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__ = "contact@david-pagnon.com"
+__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, marker_coords
+    return marker_names, trc_data_np
 
-def create_c3d_file(trc_file, marker_names, marker_coords, frame_rate):
+
+def create_c3d_file(c3d_path, marker_names, trc_data_np):
+    '''
+    Create a c3d file from the data extracted from a trc file.
+
+    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)
+
+    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')
+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>    
+    '''
 
-    args = parser.parse_args()
+    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')
 
-    trc_file = args.trc_path
-    frame_rate = args.f
+    marker_names, trc_data_np = extract_marker_data(trc_path)
+    create_c3d_file(c3d_path, marker_names, trc_data_np)
 
-    if not os.path.isfile(trc_file):
-        print(f"Error: {trc_file} does not exist.")
-        return
-
-    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)

Pose2Sim/common.py

@@ -16,10 +16,8 @@ import json
 import numpy as np
 import re
 import cv2
-import os
-import pandas as pd
 import c3d
-import glob
+import sys
 
 import matplotlib as mpl
 mpl.use('qt5agg')
@@ -27,7 +25,8 @@ mpl.rc('figure', max_open_warning=0)
 from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
 from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar
 from PyQt5.QtWidgets import QMainWindow, QApplication, QWidget, QTabWidget, QVBoxLayout
-import sys
+import warnings
+warnings.filterwarnings("ignore", category=UserWarning, module="c3d")
 
 
 ## AUTHORSHIP INFORMATION
@@ -385,6 +384,83 @@ def zup2yup(Q):
     return Q
     
 
+def extract_trc_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]
+
+    # 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.
+
+    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)
+
+    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)
+    
+    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(0)
+    writer._set_last_frame(len(trc_data_np)-1)
+
+    with open(c3d_path, 'wb') as handle:
+        writer.write(handle)
+
+
+def convert_to_c3d(trc_path):
+    '''
+    Make Visual3D compatible c3d files from a trc path
+
+    INPUT:
+    - trc_path: string, trc file to convert
+
+    OUTPUT:
+    - c3d file
+    '''
+
+    c3d_path = trc_path.replace('.trc', '.c3d')
+    marker_names, trc_data_np = extract_trc_data(trc_path)
+    create_c3d_file(c3d_path, marker_names, trc_data_np)
+
+    return c3d_path
+
+
 ## CLASSES
 class plotWindow():
     '''
@@ -436,85 +512,3 @@ class plotWindow():
 
     def show(self):
         self.app.exec_() 
-
-# Save c3d
-def trc_to_c3d(project_dir, frame_rate, called_from):
-    '''
-    Converts.trc files to.c3d files
-    INPUT:
-    - project_dir: path to project folder
-    - frame_rate: frame rate of the video
-    - called_from: string that determines which.trc files to convert.
-        'triangulation' for.trc files from triangulation step
-        'filtering' for.trc files from filtering step
-        
-    '''
-    # Determine the 3D pose folder
-    pose3d_dir = os.path.join(project_dir, 'pose-3d')
-
-    # Determine the .trc file name to read
-    trc_files = []
-    if called_from == 'triangulation':
-        trc_pattern = "*.trc"
-        trc_files = [os.path.basename(f) for f in glob.glob(os.path.join(pose3d_dir, trc_pattern)) if 'filt' not in f]
-    elif called_from == 'filtering':
-        trc_pattern = "*_filt_*.trc"
-        trc_files = [os.path.basename(f) for f in glob.glob(os.path.join(pose3d_dir, trc_pattern))]
-    else:
-        print("Invalid called_from value.")
-
-    for trc_file in trc_files:
-        # Extract marker names from the 4th row of the TRC file
-        with open(os.path.join(pose3d_dir, trc_file), 'r') as file:
-            lines = file.readlines()
-            marker_names_line = lines[3]
-            marker_names = marker_names_line.strip().split('\t')[2::3]
-
-        # Read the data frame (skiprows=5)
-        trc_data = pd.read_csv(os.path.join(pose3d_dir, trc_file), sep='\t', skiprows=5)
-
-        # Extract marker coordinates
-        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)
-
-        scale_factor = 1000
-        marker_coords = marker_coords * scale_factor
-
-        # Create a C3D writer
-        writer = c3d.Writer(point_rate=frame_rate, analog_rate=0, point_scale=1.0, point_units='mm', gen_scale=-1.0)
-
-        # Add marker parameters
-        writer.set_point_labels(marker_names)
-
-        # # Add marker descriptions (optional)
-        # marker_descriptions = [''] * len(marker_names)
-        # writer.point_group.add_param('DESCRIPTIONS', desc='Marker descriptions', 
-        #                             bytes_per_element=-1, dimensions=[len(marker_names)], 
-        #                             bytes=np.array(marker_descriptions, dtype=object))
-        
-        # # Set the data start parameter
-        # data_start = writer.header.data_block
-        # writer.point_group.add_param('DATA_START', desc='Data start parameter',
-        #                             bytes_per_element=2, dimensions=[], bytes=struct.pack('<H', data_start))
-        
-        # Create a C3D group for markers
-        markers_group = writer.point_group
-
-        # Add frame data
-        for frame in marker_coords:
-            # Add residual and camera columns
-            residuals = np.full((frame.shape[0], 1), 0.0)  # Set residuals to 0.0
-            cameras = np.zeros((frame.shape[0], 1))  # Set cameras to 0
-            points = np.hstack((frame, residuals, cameras))
-            writer.add_frames([(points, np.array([]))])
-
-        # Set the trial start and end frames
-        writer.set_start_frame(1)
-        writer._set_last_frame(len(marker_coords))
-
-        # Write the C3D file
-        c3d_file_path = trc_file.replace('.trc', '.c3d')
-        with open(os.path.join(pose3d_dir, c3d_file_path), 'wb') as handle:
-            writer.write(handle)
-        
-        print(f"-->c3d file saved: {c3d_file_path}")

Pose2Sim/filtering.py

@@ -37,7 +37,7 @@ from filterpy.kalman import KalmanFilter, rts_smoother
 from filterpy.common import Q_discrete_white_noise
 
 from Pose2Sim.common import plotWindow
-from Pose2Sim.common import trc_to_c3d
+from Pose2Sim.common import convert_to_c3d
 
 ## AUTHORSHIP INFORMATION
 __author__ = "David Pagnon"
@@ -416,6 +416,7 @@ def recap_filter3d(config, trc_path):
     gaussian_filter_sigma_kernel = int(config.get('filtering').get('gaussian').get('sigma_kernel'))
     loess_filter_nb_values = config.get('filtering').get('LOESS').get('nb_values_used')
     median_filter_kernel_size = config.get('filtering').get('median').get('kernel_size')
+    make_c3d = config.get('filtering').get('make_c3d')
     
     # Recap
     filter_mapping_recap = {
@@ -428,6 +429,8 @@ def recap_filter3d(config, trc_path):
     }
     logging.info(filter_mapping_recap[filter_type])
     logging.info(f'Filtered 3D coordinates are stored at {trc_path}.\n')
+    if make_c3d:
+        logging.info('All filtered trc files have been converted to c3d.')
 
 
 def filter_all(config):
@@ -497,10 +500,11 @@ def filter_all(config):
             # Q_filt = Q_filt.fillna(' ')
             Q_filt.to_csv(trc_o, sep='\t', index=False, header=None, lineterminator='\n')
 
+        # Save c3d
+        if make_c3d:
+            convert_to_c3d(t_out)
+
         # Recap
         recap_filter3d(config, t_out)
 
-        # Save c3d
-        if make_c3d == True:
-            trc_to_c3d(project_dir, frame_rate, called_from='filtering')
 

Pose2Sim/markerAugmentation.py

@@ -23,14 +23,15 @@ OUTPUT:
 ## INIT
 import os
 import numpy as np
-from Pose2Sim.MarkerAugmenter import utilsDataman
 import copy
 import tensorflow as tf
-from Pose2Sim.MarkerAugmenter.utils import TRC2numpy
-import json
 import glob
 import logging
 
+from Pose2Sim.MarkerAugmenter import utilsDataman
+from Pose2Sim.MarkerAugmenter.utils import TRC2numpy
+from Pose2Sim.common import convert_to_c3d
+
 
 ## AUTHORSHIP INFORMATION
 __author__ = "Antoine Falisse, adapted by HunMin Kim"
@@ -65,7 +66,6 @@ def augmentTRC(config_dict):
     project_dir = config_dict.get('project').get('project_dir')
     pathInputTRCFile = os.path.realpath(os.path.join(project_dir, 'pose-3d'))
     pathOutputTRCFile = os.path.realpath(os.path.join(project_dir, 'pose-3d'))
-    pose_model = config_dict.get('pose').get('pose_model')
     subject_height = config_dict.get('markerAugmentation').get('participant_height')
     if subject_height is None or subject_height == 0 or subject_height==0:
         raise ValueError("Subject height is not set or invalid in the config file.")
@@ -73,6 +73,7 @@ def augmentTRC(config_dict):
     if not type(subject_height) == list:
         subject_height = [subject_height]
         subject_mass = [subject_mass]
+    make_c3d = config_dict.get('markerAugmentation').get('make_c3d')
     augmenterDir = os.path.dirname(utilsDataman.__file__)
     augmenterModelName = 'LSTM'
     augmenter_model = 'v0.3'
@@ -151,8 +152,6 @@ def augmentTRC(config_dict):
             trc_data_data = trc_data[:,1:]
 
             # Step 2: Normalize with reference marker position.
-            with open(os.path.join(augmenterModelDir, "metadata.json"), 'r') as f:
-                metadata = json.load(f)
             referenceMarker_data = midhip_data  # instead of trc_file.marker(referenceMarker) # change by HunMin
             norm_trc_data_data = np.zeros((trc_data_data.shape[0],
                                         trc_data_data.shape[1]))
@@ -245,7 +244,15 @@ def augmentTRC(config_dict):
         # %% Return augmented .trc file   
         trc_file.write(pathOutputTRCFile)
 
-        logging.info(f'Augmented marker coordinates are stored at {pathOutputTRCFile}.\n')
+        logging.info(f'Augmented marker coordinates are stored at {pathOutputTRCFile}.')
+
+        # Save c3d
+        if make_c3d:
+            print(pathOutputTRCFile)
+            convert_to_c3d(pathOutputTRCFile)
+            logging.info(f'Augmented trc files have been converted to c3d.')
+        
+        logging.info('\n')
     
     return min_y_pos
 

Pose2Sim/triangulation.py

@@ -50,8 +50,7 @@ from anytree.importer import DictImporter
 import logging
 
 from Pose2Sim.common import retrieve_calib_params, computeP, weighted_triangulation, \
-    reprojection, euclidean_distance, sort_stringlist_by_last_number, zup2yup
-from Pose2Sim.common import trc_to_c3d
+    reprojection, euclidean_distance, sort_stringlist_by_last_number, zup2yup, convert_to_c3d
 from Pose2Sim.skeletons import *
 
 
@@ -312,7 +311,7 @@ def recap_triangulate(config, error, nb_cams_excluded, keypoints_names, cam_excl
     # if batch
     session_dir = os.path.realpath(os.path.join(project_dir, '..', '..'))
     # if single trial
-    session_dir = os.getcwd() if not 'Config.toml' in session_dir else session_dir
+    session_dir = os.getcwd() if not 'Config.toml' in os.listdir(session_dir) else session_dir
     calib_dir = [os.path.join(session_dir, c) for c in os.listdir(session_dir) if 'calib' in c.lower()][0]
     calib_file = glob.glob(os.path.join(calib_dir, '*.toml'))[0] # lastly created calibration file
     calib = toml.load(calib_file)
@@ -322,6 +321,7 @@ def recap_triangulate(config, error, nb_cams_excluded, keypoints_names, cam_excl
     likelihood_threshold = config.get('triangulation').get('likelihood_threshold_triangulation')
     show_interp_indices = config.get('triangulation').get('show_interp_indices')
     interpolation_kind = config.get('triangulation').get('interpolation')
+    make_c3d = config.get('triangulation').get('make_c3d')
     handle_LR_swap = config.get('triangulation').get('handle_LR_swap')
     undistort_points = config.get('triangulation').get('undistort_points')
     
@@ -374,8 +374,11 @@ def recap_triangulate(config, error, nb_cams_excluded, keypoints_names, cam_excl
                 str_cam_excluded_count += f'Camera {k}: {int(np.round(v*100))}%, '
         logging.info(str_cam_excluded_count)
         logging.info(f'\n3D coordinates are stored at {trc_path[n]}.')
-    
-    logging.info(f'\n\nLimb swapping was {"handled" if handle_LR_swap else "not handled"}.')
+        
+    logging.info('\n\n')
+    if make_c3d:
+        logging.info('All trc files have been converted to c3d.')
+    logging.info(f'Limb swapping was {"handled" if handle_LR_swap else "not handled"}.')
     logging.info(f'Lens distortions were {"taken into account" if undistort_points else "not taken into account"}.')
 
 
@@ -693,7 +696,7 @@ def triangulate_all(config):
     # if batch
     session_dir = os.path.realpath(os.path.join(project_dir, '..', '..'))
     # if single trial
-    session_dir = os.getcwd() if not 'Config.toml' in session_dir else session_dir
+    session_dir = os.getcwd() if not 'Config.toml' in os.listdir(session_dir) else session_dir
     multi_person = config.get('project').get('multi_person')
     pose_model = config.get('pose').get('pose_model')
     frame_range = config.get('project').get('frame_range')
@@ -705,7 +708,7 @@ def triangulate_all(config):
     undistort_points = config.get('triangulation').get('undistort_points')
     make_c3d = config.get('triangulation').get('make_c3d')
     frame_rate = config.get('project').get('frame_rate')
-
+    
     calib_dir = [os.path.join(session_dir, c) for c in os.listdir(session_dir) if 'calib' in c.lower()][0]
     try:
         calib_file = glob.glob(os.path.join(calib_dir, '*.toml'))[0] # lastly created calibration file
@@ -909,23 +912,25 @@ def triangulate_all(config):
     
     # Create TRC file
     trc_paths = [make_trc(config, Q_tot[n], keypoints_names, f_range, id_person=n) for n in range(len(Q_tot))]
-
+    if make_c3d:
+        c3d_paths = [convert_to_c3d(t) for t in trc_paths]
+        
     # Reorder TRC files
     if multi_person and reorder_trc and len(trc_paths)>1:
         trc_id = retrieve_right_trc_order(trc_paths)
         [os.rename(t, t+'.old') for t in trc_paths]
         [os.rename(t+'.old', trc_paths[i]) for i, t in zip(trc_id,trc_paths)]
+        if make_c3d:
+            [os.rename(c, c+'.old') for c in c3d_paths]
+            [os.rename(c+'.old', c3d_paths[i]) for i, c in zip(trc_id,c3d_paths)]
         error_tot = [error_tot[i] for i in trc_id]
         nb_cams_excluded_tot = [nb_cams_excluded_tot[i] for i in trc_id]
         cam_excluded_count = [cam_excluded_count[i] for i in trc_id]
         interp_frames = [interp_frames[i] for i in trc_id]
         non_interp_frames = [non_interp_frames[i] for i in trc_id]
         
-        logging.info('\nThe trc files have been renamed to match the order of the static sequences.')
-    
+        logging.info('\nThe trc and c3d files have been renamed to match the order of the static sequences.')
+
+
     # Recap message
     recap_triangulate(config, error_tot, nb_cams_excluded_tot, keypoints_names, cam_excluded_count, interp_frames, non_interp_frames, trc_paths)
-
-    # Save c3d
-    if make_c3d == True:
-            trc_to_c3d(project_dir, frame_rate, called_from='triangulation')