sports2d 0.6.2__py3-none-any.whl → 0.7.0__py3-none-any.whl

Sports2D/Demo/Config_demo.toml

@@ -12,12 +12,16 @@
 
 
 [project]
-video_input = 'demo.mp4' # 'webcam' or '<video_path.ext>', or ['video1_path.mp4', 'video2_path.avi>', ...]
-                        # On Windows, replace '\' with '/'
-                        # Beware that images won't be saved if paths contain non ASCII characters.
-person_height = 1.70    # Height of the person in meters (for pixels -> meters conversion)
-load_trc = ''           # If you do not want to recalculate pose, load it from a trc file (in px, not in m)
-compare = false         # Not implemented yet
+video_input = 'demo.mp4'   # 'webcam' or '<video_path.ext>', or ['video1_path.mp4', 'video2_path.avi>', ...]
+                           # On Windows, replace '\' with '/'
+                           # Beware that images won't be saved if paths contain non ASCII characters.
+px_to_m_from_person_id = 2    # Person to use for pixels to meters conversion (not used if a calibration file is provided)
+px_to_m_person_height = 1.65  # Height of the reference person in meters (for pixels -> meters conversion). 
+visible_side = ['front', 'none', 'auto']  # Choose visible side among ['right', 'left', 'front', 'back', 'auto', 'none']. String or list of strings.
+                  # if 'auto', will be either 'left', 'right', or 'front' depending on the direction of the motion
+                  # if 'none', coordinates will be left in 2D rather than 3D
+load_trc_px = ''  # If you do not want to recalculate pose, load it from a trc file (in px, not in m)
+compare = false   # Not implemented yet
 
 # Video parameters
 time_range = []   # [] for the whole video, or [start_time, end_time] (in seconds), or [[start_time1, end_time1], [start_time2, end_time2], ...]
@@ -49,7 +53,16 @@ result_dir = '' # If empty, project dir is current dir
 slowmo_factor = 1       # 1 for normal speed. For a video recorded at 240 fps and exported to 30 fps, it would be 240/30 = 8
 
 # Pose detection parameters
-pose_model = 'Body_with_feet'  #With RTMLib: Body_with_feet (default HALPE_26 model), Whole_body (COCO_133: body + feet + hands), Body (COCO_17), CUSTOM (see example at the end of the file), or any from skeletons.py
+pose_model = 'Body_with_feet'  #With RTMLib: 
+                         # - Body_with_feet (default HALPE_26 model), 
+                         # - Whole_body_wrist (COCO_133_WRIST: body + feet + 2 hand_points), 
+                         # - Whole_body (COCO_133: body + feet + hands), 
+                         # - Body (COCO_17). Marker augmentation won't work, Kinematic analysis will work,
+                         # - Hand (HAND_21, only lightweight mode. Potentially better results with Whole_body), 
+                         # - Face (FACE_106), 
+                         # - Animal (ANIMAL2D_17)
+                         # /!\ Only RTMPose is natively embeded in Pose2Sim. For all other pose estimation methods, you will have to run them yourself, and then refer to the documentation to convert the output files if needed
+                         # /!\ For Face and Animal, use mode="""{dictionary}""", and find the corresponding .onnx model there https://github.com/open-mmlab/mmpose/tree/main/projects/rtmpose
 mode = 'balanced' # 'lightweight', 'balanced', 'performance', or """{dictionary}""" (see below)
 
 # A dictionary (WITHIN THREE DOUBLE QUOTES) allows you to manually select the person detection (if top_down approach) and/or pose estimation models (see https://github.com/Tau-J/rtmlib). 
@@ -67,15 +80,19 @@ mode = 'balanced' # 'lightweight', 'balanced', 'performance', or """{dictionary}
 # mode = """{'pose_class':'RTMO', 
 #          'pose_model':'https://download.openmmlab.com/mmpose/v1/projects/rtmo/onnx_sdk/rtmo-m_16xb16-600e_body7-640x640-39e78cc4_20231211.zip', 
 #          'pose_input_size':[640, 640]}"""
+# Example with animal pose estimation:
+# mode = """{'pose_class':'RTMPose',
+#          'pose_model':'https://download.openmmlab.com/mmpose/v1/projects/rtmposev1/onnx_sdk/rtmpose-m_simcc-ap10k_pt-aic-coco_210e-256x256-7a041aa1_20230206.zip',
+#          'pose_input_size':[256,256]}"""
 
 det_frequency = 4       # Run person detection only every N frames, and inbetween track previously detected bounding boxes (keypoint detection is still run on all frames). 
                         # Equal to or greater than 1, can be as high as you want in simple uncrowded cases. Much faster, but might be less accurate. 
 device = 'auto' # 'auto', 'CPU', 'CUDA', 'MPS', 'ROCM'
 backend = 'auto' # 'auto', 'openvino', 'onnxruntime', 'opencv'
 tracking_mode = 'sports2d' # 'sports2d' or 'deepsort'. 'deepsort' is slower but more robust in difficult configurations
-deepsort_params = """{'max_age':30, 'n_init':3, 'nms_max_overlap':0.8, 'max_cosine_distance':0.3, 'nn_budget':200, 'max_iou_distance':0.8, 'embedder_gpu': True}""" # """{dictionary between 3 double quotes}"""
-                  # More robust in crowded scenes but Can be tricky to parametrize. More information there: https://github.com/levan92/deep_sort_realtime/blob/master/deep_sort_realtime/deepsort_tracker.py#L51
-                  # Note: For even more robust tracking, use 'embedder':'torchreid', which runs osnet_ain_x1_0 by default. Install additional dependencies with: `pip install torchreid gdown tensorboard`
+# deepsort_params = """{'max_age':30, 'n_init':3, 'max_cosine_distance':0.3, 'max_iou_distance':0.8, 'embedder_gpu': True, embedder':'torchreid'}""" # """{dictionary between 3 double quotes}"""
+                  # More robust in crowded scenes but tricky to parametrize. More information there: https://github.com/levan92/deep_sort_realtime/blob/master/deep_sort_realtime/deepsort_tracker.py#L51
+                  # Requires `pip install torch torchvision torchreid gdown tensorboard`
 
 
 # Processing parameters
@@ -87,18 +104,15 @@ keypoint_number_threshold = 0.3     # Person will be ignored if the number of go
 [px_to_meters_conversion]
 # Pixel to meters conversion
 to_meters = true
-# If conversion from a calibration file
-calib_file = ''         # Calibration in the Pose2Sim format. 'calib_demo.toml', or '' if not available
-# If conversion from person_height
-calib_on_person_id = 0  # Person to use for calibration
+make_c3d = true
+save_calib = true # Coming soon!
+
+# If conversion from px_to_m_person_height
 floor_angle = 'auto'    # 'auto' or a value in degrees, eg 2.3. If 'auto', estimated from the line formed by the toes when they are on the ground (where speed = 0)
 xy_origin = ['auto']    # ['auto'] or [px_x,px_y]. N.B.: px_y points downwards. If ['auto'], direction estimated from the start to the end of the line formed by the toes when they are on the ground
-save_calib = true
 
-fastest_frames_to_remove_percent = 0.1 # Frames with high speed are considered as outliers
-close_to_zero_speed_px = 50 # Sum for all keypoints: about 50 px/frame or 0.2 m/frame
-large_hip_knee_angles = 45 # Hip and knee angles below this value are considered as imprecise
-trimmed_extrema_percent = 0.5 # Proportion of the most extreme segment values to remove before calculating their mean)
+# If conversion from a calibration file
+calib_file = ''         # Calibration in the Pose2Sim format. 'calib_demo.toml', or '' if not available
 
 
 [angles]
@@ -136,15 +150,22 @@ filter_type = 'butterworth'   # butterworth, gaussian, LOESS, median
    kernel_size = 3
 
 
-[inverse-kinematics]
-do_ik = false # Do scaling and inverse kinematics?
-person_orientation = ['front', 'none', 'left'] # Choose among 'auto', 'none', 'front', 'back', 'left', 'right'
-                     # if 'none', no IK will be performed on the corresponding person
-                     # if 'auto', will be either 'left' or 'right' depending on the direction of the motion
-                     # Example with one person on one video: ['front']
-                     # Or ['front', 'none', 'left'] with 3 persons on one video
-osim_setup_path = '../OpenSim_setup' # Path to the OpenSim setup folder
-close_to_zero_speed_m = 0.2 # Sum for all keypoints: about 50 px/frame or 0.2 m/frame 
+[kinematics]
+do_ik = true # Do scaling and inverse kinematics?
+use_augmentation = true  # true or false (lowercase) # Set to true if you want to use the model with augmented markers
+use_contacts_muscles = true # true or false (lowercase) # If true, contact spheres and muscles are added to the model
+participant_mass = [67.0, 55.0] # kg # defaults to 70 if not provided. No influence on kinematics (motion), only on kinetics (forces)
+right_left_symmetry = true # true or false (lowercase) # Set to false only if you have good reasons to think the participant is not symmetrical (e.g. prosthetic limb)
+
+# Choosing best frames to scale the model
+default_height = 1.7 # meters # If automatic height calculation did not work, this value is used to scale the model
+fastest_frames_to_remove_percent = 0.1 # Frames with high speed are considered as outliers
+close_to_zero_speed_px = 50 # Sum for all keypoints: about 50 px/frame
+close_to_zero_speed_m = 0.2 # Sum for all keypoints: 0.2 m/frame
+large_hip_knee_angles = 45 # Hip and knee angles below this value are considered as imprecise
+trimmed_extrema_percent = 0.5 # Proportion of the most extreme segment values to remove before calculating their mean)
+remove_individual_scaling_setup = true # true or false (lowercase) # If true, the individual scaling setup files are removed to avoid cluttering
+remove_individual_ik_setup = true # true or false (lowercase) # If true, the individual IK setup files are removed to avoid cluttering
 
 
 [logging]

Sports2D/Sports2D.py

@@ -122,8 +122,10 @@ from Sports2D import Sports2D
 
 ## CONSTANTS
 DEFAULT_CONFIG =   {'project': {'video_input': ['demo.mp4'],
-                                'person_height': 1.70,
-                                'load_trc': '',
+                                'px_to_m_from_person_id': 2,
+                                'px_to_m_person_height': 1.65,
+                                'visible_side': ['front', 'none', 'auto'],
+                                'load_trc_px': '',
                                 'compare': False,
                                 'time_range': [],
                                 'video_dir': '',
@@ -153,15 +155,11 @@ DEFAULT_CONFIG =   {'project': {'video_input': ['demo.mp4'],
                                 },
                     'px_to_meters_conversion': {
                                 'to_meters': True,
+                                'make_c3d': True,
                                 'calib_file': '',
-                                'calib_on_person_id': 0,
                                 'floor_angle': 'auto',
                                 'xy_origin': ['auto'],
-                                'save_calib': True,
-                                'fastest_frames_to_remove_percent': 0.1,
-                                'close_to_zero_speed_px': 50,
-                                'large_hip_knee_angles': 45,
-                                'trimmed_extrema_percent': 0.5
+                                'save_calib': True
                                 },
                     'angles':   {'display_angle_values_on': ['body', 'list'],
                                 'fontSize': 0.3,
@@ -205,18 +203,29 @@ DEFAULT_CONFIG =   {'project': {'video_input': ['demo.mp4'],
                                         'loess': {'nb_values_used': 5},
                                         'median': {'kernel_size': 3}
                                         },
-                    'inverse-kinematics':{'do_ik': False,
-                                          'person_orientation': ['front', '', 'left'],
-                                          'osim_setup_path': '../OpenSim_setup',
-                                          'close_to_zero_speed_m': 0.2
+                    'kinematics':{'do_ik': False,
+                                          'use_augmentation': False,
+                                          'use_contacts_muscles': True,
+                                          'participant_mass': [67.0, 55.0], 
+                                          'right_left_symmetry': True,
+                                          'default_height': 1.70,
+                                          'remove_individual_scaling_setup': True,
+                                          'remove_individual_ik_setup': True,
+                                          'fastest_frames_to_remove_percent': 0.1,
+                                          'close_to_zero_speed_px': 50,
+                                          'close_to_zero_speed_m': 0.2,
+                                          'large_hip_knee_angles': 45,
+                                          'trimmed_extrema_percent': 0.5,
+                                          'osim_setup_path': '../OpenSim_setup'
                                           },
                     'logging': {'use_custom_logging': False}
                     }
 
 CONFIG_HELP =   {'config': ["C", "path to a toml configuration file"],
                 'video_input': ["i", "webcam, or video_path.mp4, or video1_path.avi video2_path.mp4 ... Beware that images won't be saved if paths contain non ASCII characters"],
-                'person_height': ["H", "height of the person in meters. 1.70 if not specified"],
-                'load_trc': ["", "load trc file to avaid running pose estimation again. false if not specified"],
+                'px_to_m_person_height': ["H", "height of the person in meters. 1.70 if not specified"],
+                'visible_side': ["", "front, back, left, right, auto, or none. 'front none auto' if not specified. If 'auto', will be either left or right depending on the direction of the motion. If 'none', no IK for this person"],
+                'load_trc_px': ["", "load trc file to avaid running pose estimation again. false if not specified"],
                 'compare': ["", "visually compare motion with trc file. false if not specified"],
                 'webcam_id': ["w", "webcam ID. 0 if not specified"],
                 'time_range': ["t", "start_time end_time. In seconds. Whole video if not specified. start_time1 end_time1 start_time2 end_time2 ... if multiple videos with different time ranges"],
@@ -240,27 +249,26 @@ CONFIG_HELP =   {'config': ["C", "path to a toml configuration file"],
                 'backend': ["", "Backend for pose estimation can be 'auto', 'cpu', 'cuda', 'mps' (for MacOS), or 'rocm' (for AMD GPUs)"],
                 'device': ["", "Device for pose estimatino can be 'auto', 'openvino', 'onnxruntime', 'opencv'"],
                 'to_meters': ["M", "convert pixels to meters. true if not specified"],
-                'calib_on_person_id': ["", "person ID to calibrate on. 0 if not specified"],
+                'make_c3d': ["", "Convert trc to c3d file. true if not specified"],
+                'px_to_m_from_person_id': ["", "person ID to calibrate on. 0 if not specified"],
                 'floor_angle': ["", "angle of the floor. 'auto' if not specified"],
                 'xy_origin': ["", "origin of the xy plane. 'auto' if not specified"],
                 'calib_file': ["", "path to calibration file. '' if not specified, eg no calibration file"],
                 'save_calib': ["", "save calibration file. true if not specified"],
                 'do_ik': ["", "do inverse kinematics. false if not specified"],
-                'osim_setup_path': ["", "path to OpenSim setup. '../OpenSim_setup' if not specified"],
-                'person_orientation': ["", "front, back, left, right, auto, or none. 'front none left' if not specified. If 'auto', will be either left or right depending on the direction of the motion."],
+                'use_augmentation': ["", "Use LSTM marker augmentation. false if not specified"],
+                'use_contacts_muscles': ["", "Use model with contact spheres and muscles. false if not specified"],
+                'participant_mass': ["", "mass of the participant in kg or none. Defaults to 70 if not provided. No influence on kinematics (motion), only on kinetics (forces)"],
                 'close_to_zero_speed_m': ["","Sum for all keypoints: about 50 px/frame or 0.2 m/frame"], 
                 'multiperson': ["", "multiperson involves tracking: will be faster if set to false. true if not specified"],
                 'tracking_mode': ["", "sports2d or rtmlib. sports2d is generally much more accurate and comparable in speed. sports2d if not specified"],
                 'deepsort_params': ["", 'Deepsort tracking parameters: """{dictionary between 3 double quotes}""". \n\
-                                    More information there: https://github.com/levan92/deep_sort_realtime/blob/master/deep_sort_realtime/deepsort_tracker.py#L51'],                 # 
+                                    Default: max_age:30, n_init:3, nms_max_overlap:0.8, max_cosine_distance:0.3, nn_budget:200, max_iou_distance:0.8, embedder_gpu: True\n\
+                                    More information there: https://github.com/levan92/deep_sort_realtime/blob/master/deep_sort_realtime/deepsort_tracker.py#L51'],
                 'input_size': ["", "width, height. 1280, 720 if not specified. Lower resolution will be faster but less precise"],
                 'keypoint_likelihood_threshold': ["", "detected keypoints are not retained if likelihood is below this threshold. 0.3 if not specified"],
                 'average_likelihood_threshold': ["", "detected persons are not retained if average keypoint likelihood is below this threshold. 0.5 if not specified"],
                 'keypoint_number_threshold': ["", "detected persons are not retained if number of detected keypoints is below this threshold. 0.3 if not specified, i.e., i.e., 30 percent"],
-                'fastest_frames_to_remove_percent': ["", "Frames with high speed are considered as outliers. Defaults to 0.1"],
-                'close_to_zero_speed_px': ["", "Sum for all keypoints: about 50 px/frame or 0.2 m/frame. Defaults to 50"],
-                'large_hip_knee_angles': ["", "Hip and knee angles below this value are considered as imprecise. Defaults to 45"],
-                'trimmed_extrema_percent': ["", "Proportion of the most extreme segment values to remove before calculating their mean. Defaults to 50"],
                 'fontSize': ["", "font size for angle values. 0.3 if not specified"],
                 'flip_left_right': ["", "true or false. true to get consistent angles with people facing both left and right sides. Set it to false if you want timeseries to be continuous even when the participent switches their stance. true if not specified"],
                 'correct_segment_angles_with_floor_angle': ["", "true or false. If the camera is tilted, corrects segment angles as regards to the floor angle. Set to false is the floor is tilted instead. True if not specified"],
@@ -274,6 +282,16 @@ CONFIG_HELP =   {'config': ["C", "path to a toml configuration file"],
                 'sigma_kernel': ["", "sigma of the gaussian filter. 1 if not specified"],
                 'nb_values_used': ["", "number of values used for the loess filter. 5 if not specified"],
                 'kernel_size': ["", "kernel size of the median filter. 3 if not specified"],
+                'osim_setup_path': ["", "path to OpenSim setup. '../OpenSim_setup' if not specified"],
+                'right_left_symmetry': ["", "right left symmetry. true if not specified"],
+                'default_height': ["", "default height for scaling. 1.70 if not specified"],
+                'remove_individual_scaling_setup': ["", "remove individual scaling setup files generated during scaling. true if not specified"],
+                'remove_individual_ik_setup': ["", "remove individual IK setup files generated during IK. true if not specified"],
+                'fastest_frames_to_remove_percent': ["", "Frames with high speed are considered as outliers. Defaults to 0.1"],
+                'close_to_zero_speed_m': ["","Sum for all keypoints: about 0.2 m/frame. Defaults to 0.2"],
+                'close_to_zero_speed_px': ["", "Sum for all keypoints: about 50 px/frame. Defaults to 50"],
+                'large_hip_knee_angles': ["", "Hip and knee angles below this value are considered as imprecise and ignored. Defaults to 45"],
+                'trimmed_extrema_percent': ["", "Proportion of the most extreme segment values to remove before calculating their mean. Defaults to 50"],
                 'use_custom_logging': ["", "use custom logging. false if not specified"]
                 }
 

Sports2D/Utilities/common.py

@@ -22,6 +22,7 @@ import subprocess
 from pathlib import Path
 import itertools as it
 import logging
+from collections import defaultdict
 from anytree import PreOrderIter
 
 import numpy as np
@@ -29,11 +30,12 @@ import pandas as pd
 from scipy import interpolate
 import imageio_ffmpeg as ffmpeg
 import cv2
+import c3d
 
 import matplotlib.pyplot as plt
-from PyQt5.QtWidgets import QMainWindow, QApplication, QWidget, QTabWidget, QVBoxLayout
 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
 
 
 ## AUTHORSHIP INFORMATION
@@ -63,7 +65,7 @@ angle_dict = { # lowercase!
     'right elbow': [['RWrist', 'RElbow', 'RShoulder'], 'flexion', 180, -1],
     'left elbow': [['LWrist', 'LElbow', 'LShoulder'], 'flexion', 180, -1],
     'right wrist': [['RElbow', 'RWrist', 'RIndex'], 'flexion', -180, 1],
-    'left wrist': [['LElbow', 'LIndex', 'LWrist'], 'flexion', -180, 1],
+    'left wrist': [['LElbow', 'LWrist', 'LIndex'], 'flexion', -180, 1],
 
     # segment angles
     'right foot': [['RBigToe', 'RHeel'], 'horizontal', 0, -1],
@@ -84,6 +86,32 @@ angle_dict = { # lowercase!
     'left hand': [['LIndex', 'LWrist'], 'horizontal', 0, -1]
     }
 
+marker_Z_positions = {'right':
+                        {"RHip": 0.105, "RKnee": 0.0886, "RAnkle": 0.0972, "RBigToe":0.0766, "RHeel":0.0883, "RSmallToe": 0.1200, 
+                        "RShoulder": 0.2016, "RElbow": 0.1613, "RWrist": 0.120, "RThumb": 0.1625, "RIndex": 0.1735, "RPinky": 0.1740, "REye": 0.0311, 
+                        "LHip": -0.105, "LKnee": -0.0886, "LAnkle": -0.0972, "LBigToe": -0.0766, "LHeel": -0.0883, "LSmallToe": -0.1200, 
+                        "LShoulder": -0.2016, "LElbow": -0.1613, "LWrist": -0.120, "LThumb": -0.1625, "LIndex": -0.1735, "LPinky": -0.1740, "LEye": -0.0311, 
+                        "Hip": 0.0, "Neck": 0.0, "Head":0.0, "Nose": 0.0},
+                    'left':
+                        {"RHip": -0.105, "RKnee": -0.0886, "RAnkle": -0.0972, "RBigToe": -0.0766, "RHeel": -0.0883, "RSmallToe": -0.1200, 
+                        "RShoulder": -0.2016, "RElbow": -0.1613, "RWrist": -0.120, "RThumb": -0.1625, "RIndex": -0.1735, "RPinky": -0.1740, "REye": -0.0311, 
+                        "LHip": 0.105, "LKnee": 0.0886, "LAnkle": 0.0972, "LBigToe":0.0766, "LHeel":0.0883, "LSmallToe": 0.1200, 
+                        "LShoulder": 0.2016, "LElbow": 0.1613, "LWrist": 0.120, "LThumb": 0.1625, "LIndex": 0.1735, "LPinky": 0.1740, "LEye": 0.0311, 
+                        "Hip": 0.0, "Neck": 0.0, "Head":0.0, "Nose": 0.0},
+                    'front': # original knee:0.0179
+                        {"RHip": 0.0301, "RKnee": 0.129, "RAnkle": 0.0230, "RBigToe": 0.2179, "RHeel": -0.0119, "RSmallToe": 0.1804, 
+                        "RShoulder": -0.01275, "RElbow": 0.0702, "RWrist": 0.1076, "RThumb": 0.0106, "RIndex": -0.0004, "RPinky": -0.0009, "REye": 0.0702, 
+                        "LHip": 0.0301, "LKnee": 0.129, "LAnkle": 0.0230, "LBigToe": 0.2179, "LHeel": -0.0119, "LSmallToe": 0.1804, 
+                        "LShoulder": -0.01275, "LElbow": 0.0702, "LWrist": 0.1076, "LThumb": 0.0106, "LIndex": -0.0004, "LPinky": -0.0009, "LEye": 0.0702, 
+                        "Hip": 0.0301, "Neck": 0.0008, "Head": 0.0655, "Nose": 0.1076},
+                    'back':
+                        {"RHip": -0.0301, "RKnee": -0.129, "RAnkle": -0.0230, "RBigToe": -0.2179, "RHeel": 0.0119, "RSmallToe": -0.1804, 
+                        "RShoulder": 0.01275, "RElbow": 0.0702, "RWrist": -1076.0002, "RThumb": -0.0106, "RIndex": 0.0004, "RPinky": 0.0009, "REye": -0.0702, 
+                        "LHip": -0.0301, "LKnee": -0.129, "LAnkle": -0.0230, "LBigToe": -0.2179, "LHeel": 0.0119, "LSmallToe": -0.1804, 
+                        "LShoulder": 0.01275, "LElbow": 0.0702, "LWrist": -0.1076, "LThumb": -0.0106, "LIndex": 0.0004, "LPinky": 0.0009, "LEye": -0.0702, 
+                        "Hip": -0.0301, "Neck": -0.0008, "Head": -0.0655, "Nose": -0.1076},
+            }
+
 colors = [(255, 0, 0), (0, 0, 255), (255, 255, 0), (255, 0, 255), (0, 255, 255), (0, 0, 0), (255, 255, 255),
             (125, 0, 0), (0, 125, 0), (0, 0, 125), (125, 125, 0), (125, 0, 125), (0, 125, 125), 
             (255, 125, 125), (125, 255, 125), (125, 125, 255), (255, 255, 125), (255, 125, 255), (125, 255, 255), (125, 125, 125),
@@ -143,6 +171,15 @@ class plotWindow():
         self.app.exec_()
         
 ## FUNCTIONS
+def to_dict(d):
+    '''
+    Convert a defaultdict to a dict.
+    '''
+    if isinstance(d, defaultdict):
+        return {k: to_dict(v) for k, v in d.items()}
+    return d
+
+
 def read_trc(trc_path):
     '''
     Read a TRC file and extract its contents.
@@ -172,6 +209,85 @@ def read_trc(trc_path):
         raise ValueError(f"Error reading TRC file at {trc_path}: {e}")
 
 
+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)
+    writer.set_screen_axis(X='+Z', Y='+Y')
+    
+    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
+    '''
+
+    trc_path = str(trc_path)
+    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
+
+
 def interpolate_zeros_nans(col, *args):
     '''
     Interpolate missing points (of value zero),
@@ -469,7 +585,7 @@ def add_neck_hip_coords(kpt_name, p_X, p_Y, p_scores, kpt_ids, kpt_names):
     return p_X, p_Y, p_scores
 
 
-def best_coords_for_measurements(Q_coords, keypoints_names, fastest_frames_to_remove_percent=0.2, close_to_zero_speed=0.2, large_hip_knee_angles=45):
+def best_coords_for_measurements(Q_coords, keypoints_names, beginning_frames_to_remove_percent=0.2, end_frames_to_remove_percent=0.2, fastest_frames_to_remove_percent=0.2, close_to_zero_speed=0.2, large_hip_knee_angles=45):
     '''
     Compute the best coordinates for measurements, after removing:
     - 20% fastest frames (may be outliers)
@@ -479,6 +595,8 @@ def best_coords_for_measurements(Q_coords, keypoints_names, fastest_frames_to_re
     INPUTS:
     - Q_coords: pd.DataFrame. The XYZ coordinates of each marker
     - keypoints_names: list. The list of marker names
+    - beginning_frames_to_remove_percent: float
+    - end_frames_to_remove_percent: float
     - fastest_frames_to_remove_percent: float
     - close_to_zero_speed: float (sum for all keypoints: about 50 px/frame or 0.2 m/frame)
     - large_hip_knee_angles: int
@@ -501,6 +619,9 @@ def best_coords_for_measurements(Q_coords, keypoints_names, fastest_frames_to_re
         Q_coords = pd.concat((Q_coords.reset_index(drop=True), df_Hip), axis=1)
     n_markers = len(keypoints_names)
 
+    # Removing first and last frames
+    # Q_coords = Q_coords.iloc[int(len(Q_coords) * beginning_frames_to_remove_percent):int(len(Q_coords) * (1-end_frames_to_remove_percent))]
+
     # Using 80% slowest frames
     sum_speeds = pd.Series(np.nansum([np.linalg.norm(Q_coords.iloc[:,kpt:kpt+3].diff(), axis=1) for kpt in range(n_markers)], axis=0))
     sum_speeds = sum_speeds[sum_speeds>close_to_zero_speed] # Removing when speeds close to zero (out of frame)

Sports2D/Utilities/skeletons.py

@@ -85,10 +85,10 @@ HALPE_26 = Node("Hip", id=19, children=[
 ])
 
 
-'''COCO_133_wrist (full-body with hands and face, from AlphaPose, MMPose, etc.)
+'''COCO_133_WRIST (full-body with hands and face, from AlphaPose, MMPose, etc.)
 https://github.com/MVIG-SJTU/AlphaPose/blob/master/docs/MODEL_ZOO.md
 https://github.com/open-mmlab/mmpose/tree/main/projects/rtmpose'''
-COCO_133_wrist = Node("CHip", id=None, children=[
+COCO_133_WRIST = Node("Hip", id=None, children=[
     Node("RHip", id=12, children=[
         Node("RKnee", id=14, children=[
             Node("RAnkle", id=16, children=[
@@ -139,7 +139,7 @@ COCO_133_wrist = Node("CHip", id=None, children=[
 '''COCO_133 (full-body with hands and face, from AlphaPose, MMPose, etc.)
 https://github.com/MVIG-SJTU/AlphaPose/blob/master/docs/MODEL_ZOO.md
 https://github.com/open-mmlab/mmpose/tree/main/projects/rtmpose'''
-COCO_133 = Node("CHip", id=None, children=[
+COCO_133 = Node("Hip", id=None, children=[
     Node("RHip", id=12, children=[
         Node("RKnee", id=14, children=[
             Node("RAnkle", id=16, children=[
@@ -359,9 +359,7 @@ COCO_133 = Node("CHip", id=None, children=[
                                                                         Node("Mouth17", id=87, children=[
                                                                             Node("Mouth18", id=88, children=[
                                                                                 Node("Mouth19", id=89, children=[
-                                                                                    Node("Mouth20", id=90, children=[
-                                                                                        Node("Mouth21", id=91)
-                                                                                    ]),
+                                                                                    Node("Mouth20", id=90)
                                                                                 ]),
                                                                             ]),
                                                                         ]),
@@ -387,7 +385,7 @@ COCO_133 = Node("CHip", id=None, children=[
 
 '''COCO_17 (full-body without hands and feet, from OpenPose, AlphaPose, OpenPifPaf, YOLO-pose, MMPose, etc.)
 https://github.com/open-mmlab/mmpose/tree/main/projects/rtmpose'''
-COCO_17 = Node("CHip", id=None, children=[
+COCO_17 = Node("Hip", id=None, children=[
     Node("RHip", id=12, children=[
         Node("RKnee", id=14, children=[
             Node("RAnkle", id=16),
@@ -647,7 +645,7 @@ FACE_106 = Node("root", id=None, children=[
 
 '''ANIMAL2D_17 (full-body animal)
 https://github.com/AlexTheBad/AP-10K/'''
-ANIMAL2D_17 = Node("CHip", id=4, children=[
+ANIMAL2D_17 = Node("Hip", id=4, children=[
     Node("RHip", id=14, children=[
         Node("RKnee", id=15, children=[
             Node("RAnkle", id=16),

Sports2D/Utilities/tests.py

@@ -56,15 +56,24 @@ def test_workflow():
 
     # Default
     demo_cmd = ["sports2d", "--show_realtime_results", "False", "--show_graphs", "False"]
-    subprocess.run(demo_cmd, check=True, capture_output=True, text=True)
+    subprocess.run(demo_cmd, check=True, capture_output=True, text=True, encoding='utf-8')
 
     # With no pixels to meters conversion, no multiperson, lightweight mode, detection frequency, time range and slowmo factor
-    demo_cmd2 = ["sports2d", "--to_meters", "False", "--multiperson", "False", "--mode", "lightweight", "--det_frequency", "50", "--time_range", "1.2", "2.7",  "--slowmo_factor", "4", "--show_realtime_results", "False", "--show_graphs", "False"]
-    subprocess.run(demo_cmd2, check=True, capture_output=True, text=True)
+    demo_cmd2 = ["sports2d", "--show_realtime_results", "False", "--show_graphs", "False", 
+                 "--to_meters", "False", 
+                 "--multiperson", "False", 
+                 "--mode", "lightweight", "--det_frequency", "50", 
+                 "--time_range", "1.2", "2.7",  "--slowmo_factor", "4"]
+    subprocess.run(demo_cmd2, check=True, capture_output=True, text=True, encoding='utf-8')
     
-    # With inverse kinematics, body pose_model and custom RTMO mode
-    # demo_cmd3 = ["sports2d", "--do_ik", "--person_orientation", "front none left", "--pose_model", "body", "--mode", "{'pose_class':'RTMO', 'pose_model':'https://download.openmmlab.com/mmpose/v1/projects/rtmo/onnx_sdk/rtmo-m_16xb16-600e_body7-640x640-39e78cc4_20231211.zip', 'pose_input_size':[640, 640]}", "--show_realtime_results", "False", "--show_graphs", "False"]
-    # subprocess.run(demo_cmd3, check=True, capture_output=True, text=True)
+    # With a time range, inverse kinematics, marker augmentation, body pose_model and custom RTMO mode
+    demo_cmd3 = ["sports2d", "--show_realtime_results", "False", "--show_graphs", "False",
+                 "--time_range", "1.2", "2.7",
+                 "--do_ik", "True", "--use_augmentation", "True", 
+                 "--px_to_m_from_person_id", "1", "--px_to_m_person_height", "1.65",
+                 "--visible_side", "left", "front", "--participant_mass", "55.0", "67.0",
+                 "--pose_model", "body", "--mode", """{'pose_class':'RTMO', 'pose_model':'https://download.openmmlab.com/mmpose/v1/projects/rtmo/onnx_sdk/rtmo-m_16xb16-600e_body7-640x640-39e78cc4_20231211.zip', 'pose_input_size':[640, 640]}"""]
+    subprocess.run(demo_cmd3, check=True, capture_output=True, text=True)
     
     # From config file
     cli_config_path = Path(__file__).resolve().parent.parent / 'Demo' / 'Config_demo.toml'
@@ -72,6 +81,5 @@ def test_workflow():
     cli_video_dir = Path(__file__).resolve().parent.parent / 'Demo'
     config_dict.get("project").update({"video_dir": str(cli_video_dir)})
     with open(cli_config_path, 'w') as f: toml.dump(config_dict, f)
-
     demo_cmd4 = ["sports2d", "--config", str(cli_config_path), "--show_realtime_results", "False", "--show_graphs", "False"]
-    subprocess.run(demo_cmd4, check=True, capture_output=True, text=True)
+    subprocess.run(demo_cmd4, check=True, capture_output=True, text=True, encoding='utf-8')