draft for batch processing

Pose2Sim/Demo/S00_Demo_Session/Config.toml

@@ -2,34 +2,22 @@
 ## PROJECT PARAMETERS                                                        ##
 ###############################################################################
 
-# Configure your project parameters here
+
+# IMPORTANT: All configuration parameters specified at that level will 
+# overwrite the ones given in the subfolders. 
+# Example: A parameter given in the Config.toml file at the Session level 
+# will be ignored if it is also given at the Participant or Trial level.
+
 
 [project]
-project_dir = '' # BETWEEN SINGLE QUOTES! # If empty, project dir is current dir
+frame_rate = 60 # FPS
-frame_range = [] #For example [10,300], or [] for all frames
+frame_range = [] # For example [10,300], or [] for all frames
-frame_rate = 60 #Hz
+# N.B.: If you want a time range instead, use frame_range = time_range * frame_rate
-
+# For example if you want to analyze from 0.1 to 2 seconds with a 60 fps frame rate, 
-rawImg_folder_name = 'raw'
+# frame_range = [0.1, 2.0]*frame_rate = [6, 120]
-calib_folder_name = 'calibration'
-pose_folder_name = 'pose'
-pose_json_folder_extension = 'json'
-pose_img_folder_extension = 'img'
-poseAssociated_folder_name = 'pose-associated'
-pose3d_folder_name = 'pose-3d'
-opensim_folder_name = 'opensim'
-
-
-[pose]
-pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII. 
-						      #With mediapipe: BLAZEPOSE. 
-						      #With alphapose: HALPE_26, HALPE_68, HALPE_136, COCO_133. 
-						      #With deeplabcut: CUSTOM. See example at the end of the file.
-# What follows has not been implemented yet
-pose_framework = 'openpose' # 'openpose', 'mediapipe', 'alphapose', 'deeplabcut' 
-overwrite_pose = false
-openpose_path = '' # only checked if OpenPose is used
 
 
+# Take heart, calibration is not that complicated once you get the hang of it!
 [calibration]
 calibration_type = 'convert' # 'convert' or 'calculate'
 
@@ -38,52 +26,83 @@ calibration_type = 'convert' # 'convert' or 'calculate'
       [calibration.convert.qualisys]
       binning_factor = 1 # Usually 1, except when filming in 540p where it usually is 2
       [calibration.convert.optitrack]  # See readme for instructions
-      [calibration.convert.vicon]      # No parameters needed
+      [calibration.convert.vicon]      # No parameter needed
-      [calibration.convert.opencap]    # No parameters needed
+      [calibration.convert.opencap]    # No parameter needed
-      [calibration.convert.easymocap]    # No parameters needed
+      [calibration.convert.easymocap]  # No parameter needed
-      [calibration.convert.biocv]      # No parameters needed
+      [calibration.convert.biocv]      # No parameter needed
+      [calibration.convert.anipose]    # No parameter needed
+      [calibration.convert.freemocap]  # No parameter needed
   
 
    [calibration.calculate] 
-   calculate_method = 'board' # 'board' or 'points'
+      # Camera properties, theoretically need to be calculated only once in a camera lifetime
-      
+      [calibration.calculate.intrinsics]
-      [calibration.calculate.board.intrinsics] # camera properties, only needs to be done once
-      intrinsics_board_type = 'checkerboard' # 'checkerboard' ('charucoboard' not supported yet)
       overwrite_intrinsics = false # overwrite (or not) if they have already been calculated?
       show_detection_intrinsics = true # true or false (lowercase)
       intrinsics_extension = 'jpg' # any video or image extension
-
       extract_every_N_sec = 1 # if video, extract frames every N seconds (can be <1 )
       intrinsics_corners_nb = [4,7] 
       intrinsics_square_size = 60 # mm
-      intrinsics_marker_size = 40 # mm # only checked if charucoboard
-      intrinsics_aruco_dict = 'DICT_6X6_250' # only checked if charucoboard # see https://docs.opencv.org/3.4/dc/df7/dictionary_8hpp.html
-   
-      [calibration.calculate.board.extrinsics] # camera placement, needs to be done every time
-      extrinsics_board_type = 'scene' # 'checkerboard', 'scene'  ('charucoboard' not supported yet)
-      # 'board' should be large enough to be detected when laid on the floor. 
-      # 'scene' involves manually clicking any point of know coordinates on scene. Usually more accurate if points are spread out
-      moving_camera = false # Not implemented yet
-      calculate_extrinsics = true # true or false (lowercase) 
-      show_reprojection_error = true # true or false (lowercase)
-      extrinsics_extension = 'png' # any video or image extension
-      
-      # if extrinsics_board_type = 'checkerboard' or 'charucoboard'
-      extrinsics_corners_nb = [4,7] # [H,W] rather than [w,h]
-      extrinsics_square_size = 60 # mm # [h,w] if square is actually a rectangle
-      extrinsics_marker_size = 40 # mm # only checked if 'charucoboard' (not supported yet)
-      extrinsics_aruco_dict = 'DICT_6X6_250' # only checked if 'charucoboard' # see https://docs.opencv.org/3.4/dc/df7/dictionary_8hpp.html
-      
-      # if extrinsics_board_type = 'scene'
-      # list of 3D coordinates to be manually labelled on images. Can also be a 2 dimensional plane. # in m
-      object_coords_3d = [[-2.0,  0.3,  0.0], [-2.0 , 0.0,  0.0], [-2.0, 0.0,  0.05], [-2.0, -0.3 ,  0.0], [0.0,  0.3,  0.0], [0.0, 0.0,  0.0], [0.0, 0.0,  0.05], [0.0, -0.3,  0.0]] # in meters -> Not in mm! <-
-      
-  
-      [calibration.calculate.points]
-      calibration_points = 'wand' # 'wand' or 'keypoints'
-      # Not supported yet.
 
-	  
+      # Camera placements, need to be done before every session
+      [calibration.calculate.extrinsics]
+      extrinsics_method = 'scene' # 'board', 'scene', 'keypoints'
+      # 'board' should be large enough to be detected when laid on the floor. Not recommended.
+      # 'scene' involves manually clicking any point of know coordinates on scene. Usually more accurate if points are spread out.
+      # 'keypoints' uses automatic pose estimation of a person freely walking and waving arms in the scene. Slighlty less accurate, requires synchronized cameras.
+
+      moving_cameras = false # Not implemented yet
+      calculate_extrinsics = true # true or false (lowercase) 
+
+         [calibration.calculate.extrinsics.board]
+         show_reprojection_error = true # true or false (lowercase)
+         extrinsics_extension = 'png' # any video or image extension
+         extrinsics_corners_nb = [4,7] # [H,W] rather than [w,h]
+         extrinsics_square_size = 60 # mm # [h,w] if square is actually a rectangle
+
+         [calibration.calculate.extrinsics.scene]
+         show_reprojection_error = true # true or false (lowercase)
+         extrinsics_extension = 'png' # any video or image extension
+         # list of 3D coordinates to be manually labelled on images. Can also be a 2 dimensional plane. 
+         # in m -> unlike for intrinsics, NOT in mm!
+         object_coords_3d =   [[-2.0,  0.3,  0.0], 
+                              [-2.0 , 0.0,  0.0], 
+                              [-2.0, 0.0,  0.05], 
+                              [-2.0, -0.3 ,  0.0], 
+                              [0.0,  0.3,  0.0], 
+                              [0.0, 0.0,  0.0], 
+                              [0.0, 0.0,  0.05], 
+                              [0.0, -0.3,  0.0]]
+        
+         [calibration.calculate.extrinsics.keypoints]
+         # Coming soon!
+
+
+[pose]
+pose_framework = 'openpose' # 'openpose', 'mediapipe', 'alphapose', 'deeplabcut' 
+pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII. 
+						      #With mediapipe: BLAZEPOSE. 
+						      #With alphapose: HALPE_26, HALPE_68, HALPE_136, COCO_133. 
+						      #With deeplabcut: CUSTOM. See example at the end of the file.
+# What follows has not been implemented yet
+overwrite_pose = false
+openpose_path = '' # only checked if OpenPose is used
+
+
+[synchronization]
+# COMING SOON! 
+reset_sync = true # Recalculate synchronization even if already done
+frames = [2850,3490] # Frames to use for synchronization, should point to a moment with fast motion.
+cut_off_frequency = 10 # cut-off frequency for a 4th order low-pass Butterworth filter
+# Vertical speeds (on X, Y, or Z axis, or 2D speeds)
+speed_kind = 'y' # 'x', 'y', 'z', or '2D'
+vmax = 20 # px/s
+cam1_nb = 4
+cam2_nb = 3
+id_kpt = [9,10] # Pour plus tard aller chercher numéro depuis keypoint name dans skeleton.py. 'RWrist' BLAZEPOSE 16, BODY_25B 10, BODY_25 4 ; 'LWrist' BLAZEPOSE 15, BODY_25B 9, BODY_25 7
+weights_kpt = [1,1] # Pris en compte uniquement si on a plusieurs keypoints
+
+
 [personAssociation]
 tracked_keypoint = 'Neck' # If the neck is not detected by the pose_model, check skeleton.py 
 # and choose a stable point for tracking the person of interest (e.g., 'right_shoulder' with BLAZEPOSE)
@@ -122,6 +141,10 @@ display_figures = true # true or false (lowercase)
    kernel_size = 9
 
 [opensim]
+static_trial = 'yes' # 'yes' or 'no' at the Trial level;
+                     # folder name at the Participant level, e.g. 'S00_P00_T00_StaticTrial';
+                     # list of folder names at the Session level, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01/S00_P01_T00', 'S00_P02/S00_P02_T00']
+
 
 
 # CUSTOM skeleton, for DeepLabCut for example (others are in skeletons.py)

Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/Config.toml

@@ -2,34 +2,22 @@
 ## PROJECT PARAMETERS                                                        ##
 ###############################################################################
 
-# Configure your project parameters here
+
+# IMPORTANT: All configuration parameters specified at that level will 
+# overwrite the ones given in the subfolders. 
+# Example: A parameter given in the Config.toml file at the Session level 
+# will be ignored if it is also given at the Participant or Trial level.
+
 
 [project]
-project_dir = '' # BETWEEN SINGLE QUOTES! # If empty, project dir is current dir
+frame_rate = 60 # FPS
-frame_range = [0,10] #For example [10,300], or [] for all frames
+frame_range = [] # For example [10,300], or [] for all frames
-frame_rate = 60 #Hz
+# N.B.: If you want a time range instead, use frame_range = time_range * frame_rate
-
+# For example if you want to analyze from 0.1 to 2 seconds with a 60 fps frame rate, 
-rawImg_folder_name = 'raw'
+# frame_range = [0.1, 2.0]*frame_rate = [6, 120]
-calib_folder_name = 'calibration'
-pose_folder_name = 'pose'
-pose_json_folder_extension = 'json'
-pose_img_folder_extension = 'img'
-poseAssociated_folder_name = 'pose-associated'
-pose3d_folder_name = 'pose-3d'
-opensim_folder_name = 'opensim'
-
-
-[pose]
-pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII. 
-						      #With mediapipe: BLAZEPOSE. 
-                        #With alphapose: HALPE_26, HALPE_68, HALPE_136, COCO_133. 
-                        #With deeplabcut: CUSTOM. See example at the end of the file.
-# What follows has not been implemented yet
-pose_framework = 'openpose' # 'openpose', 'mediapipe', 'alphapose', 'deeplabcut' 
-overwrite_pose = false
-openpose_path = '' # only checked if OpenPose is used
 
 
+# Take heart, calibration is not that complicated once you get the hang of it!
 [calibration]
 calibration_type = 'convert' # 'convert' or 'calculate'
 
@@ -38,52 +26,83 @@ calibration_type = 'convert' # 'convert' or 'calculate'
       [calibration.convert.qualisys]
       binning_factor = 1 # Usually 1, except when filming in 540p where it usually is 2
       [calibration.convert.optitrack]  # See readme for instructions
-      [calibration.convert.vicon]      # No parameters needed
+      [calibration.convert.vicon]      # No parameter needed
-      [calibration.convert.opencap]    # No parameters needed
+      [calibration.convert.opencap]    # No parameter needed
-      [calibration.convert.easymocap]    # No parameters needed
+      [calibration.convert.easymocap]  # No parameter needed
-      [calibration.convert.biocv]      # No parameters needed
+      [calibration.convert.biocv]      # No parameter needed
+      [calibration.convert.anipose]    # No parameter needed
+      [calibration.convert.freemocap]  # No parameter needed
   
 
    [calibration.calculate] 
-   calculate_method = 'board' # 'board' or 'points'
+      # Camera properties, theoretically need to be calculated only once in a camera lifetime
-      
+      [calibration.calculate.intrinsics]
-      [calibration.calculate.board.intrinsics] # camera properties, only needs to be done once
-      intrinsics_board_type = 'checkerboard' # 'checkerboard' ('charucoboard' not supported yet)
       overwrite_intrinsics = false # overwrite (or not) if they have already been calculated?
       show_detection_intrinsics = true # true or false (lowercase)
       intrinsics_extension = 'jpg' # any video or image extension
-
       extract_every_N_sec = 1 # if video, extract frames every N seconds (can be <1 )
       intrinsics_corners_nb = [4,7] 
       intrinsics_square_size = 60 # mm
-      intrinsics_marker_size = 40 # mm # only checked if charucoboard
-      intrinsics_aruco_dict = 'DICT_6X6_250' # only checked if charucoboard # see https://docs.opencv.org/3.4/dc/df7/dictionary_8hpp.html
-   
-      [calibration.calculate.board.extrinsics] # camera placement, needs to be done every time
-      extrinsics_board_type = 'scene' # 'checkerboard', 'scene'  ('charucoboard' not supported yet)
-      # 'board' should be large enough to be detected when laid on the floor. 
-      # 'scene' involves manually clicking any point of know coordinates on scene. Usually more accurate if points are spread out
-      moving_camera = false # Not implemented yet
-      calculate_extrinsics = true # true or false (lowercase)
-      show_reprojection_error = true # true or false (lowercase)
-      extrinsics_extension = 'png' # any video or image extension
-      
-      # if extrinsics_board_type = 'checkerboard' or 'charucoboard'
-      extrinsics_corners_nb = [4,7] # [H,W] rather than [w,h]
-      extrinsics_square_size = 60 # mm # [h,w] if square is actually a rectangle
-      extrinsics_marker_size = 40 # mm # only checked if 'charucoboard' (not supported yet)
-      extrinsics_aruco_dict = 'DICT_6X6_250' # only checked if 'charucoboard' # see https://docs.opencv.org/3.4/dc/df7/dictionary_8hpp.html
-      
-      # if extrinsics_board_type = 'scene'
-      # list of 3D coordinates to be manually labelled on images. Can also be a 2 dimensional plane. # in m
-      object_coords_3d = [[-2.0,  0.3,  0.0], [-2.0 , 0.0,  0.0], [-2.0, 0.0,  0.05], [-2.0, -0.3 ,  0.0], [0.0,  0.3,  0.0], [0.0, 0.0,  0.0], [0.0, 0.0,  0.05], [0.0, -0.3,  0.0]] # in meters -> Not in mm! <-
-      
-  
-      [calibration.calculate.points]
-      calibration_points = 'wand' # 'wand' or 'keypoints'
-      # Not supported yet.
 
-	  
+      # Camera placements, need to be done before every session
+      [calibration.calculate.extrinsics]
+      extrinsics_method = 'scene' # 'board', 'scene', 'keypoints'
+      # 'board' should be large enough to be detected when laid on the floor. Not recommended.
+      # 'scene' involves manually clicking any point of know coordinates on scene. Usually more accurate if points are spread out.
+      # 'keypoints' uses automatic pose estimation of a person freely walking and waving arms in the scene. Slighlty less accurate, requires synchronized cameras.
+
+      moving_cameras = false # Not implemented yet
+      calculate_extrinsics = true # true or false (lowercase) 
+
+         [calibration.calculate.extrinsics.board]
+         show_reprojection_error = true # true or false (lowercase)
+         extrinsics_extension = 'png' # any video or image extension
+         extrinsics_corners_nb = [4,7] # [H,W] rather than [w,h]
+         extrinsics_square_size = 60 # mm # [h,w] if square is actually a rectangle
+
+         [calibration.calculate.extrinsics.scene]
+         show_reprojection_error = true # true or false (lowercase)
+         extrinsics_extension = 'png' # any video or image extension
+         # list of 3D coordinates to be manually labelled on images. Can also be a 2 dimensional plane. 
+         # in m -> unlike for intrinsics, NOT in mm!
+         object_coords_3d =   [[-2.0,  0.3,  0.0], 
+                              [-2.0 , 0.0,  0.0], 
+                              [-2.0, 0.0,  0.05], 
+                              [-2.0, -0.3 ,  0.0], 
+                              [0.0,  0.3,  0.0], 
+                              [0.0, 0.0,  0.0], 
+                              [0.0, 0.0,  0.05], 
+                              [0.0, -0.3,  0.0]]
+        
+         [calibration.calculate.extrinsics.keypoints]
+         # Coming soon!
+
+
+[pose]
+pose_framework = 'openpose' # 'openpose', 'mediapipe', 'alphapose', 'deeplabcut' 
+pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII. 
+						      #With mediapipe: BLAZEPOSE. 
+						      #With alphapose: HALPE_26, HALPE_68, HALPE_136, COCO_133. 
+						      #With deeplabcut: CUSTOM. See example at the end of the file.
+# What follows has not been implemented yet
+overwrite_pose = false
+openpose_path = '' # only checked if OpenPose is used
+
+
+[synchronization]
+# COMING SOON! 
+reset_sync = true # Recalculate synchronization even if already done
+frames = [2850,3490] # Frames to use for synchronization, should point to a moment with fast motion.
+cut_off_frequency = 10 # cut-off frequency for a 4th order low-pass Butterworth filter
+# Vertical speeds (on X, Y, or Z axis, or 2D speeds)
+speed_kind = 'y' # 'x', 'y', 'z', or '2D'
+vmax = 20 # px/s
+cam1_nb = 4
+cam2_nb = 3
+id_kpt = [9,10] # Pour plus tard aller chercher numéro depuis keypoint name dans skeleton.py. 'RWrist' BLAZEPOSE 16, BODY_25B 10, BODY_25 4 ; 'LWrist' BLAZEPOSE 15, BODY_25B 9, BODY_25 7
+weights_kpt = [1,1] # Pris en compte uniquement si on a plusieurs keypoints
+
+
 [personAssociation]
 tracked_keypoint = 'Neck' # If the neck is not detected by the pose_model, check skeleton.py 
 # and choose a stable point for tracking the person of interest (e.g., 'right_shoulder' with BLAZEPOSE)
@@ -102,7 +121,7 @@ show_interp_indices = true # true or false (lowercase). For each keypoint, retur
 
 [filtering]
 type = 'butterworth' # butterworth, kalman, gaussian, LOESS, median, butterworth_on_speed
-display_figures = false # true or false (lowercase)
+display_figures = true # true or false (lowercase)
 
    [filtering.butterworth]
    order = 4 
@@ -122,6 +141,10 @@ display_figures = false # true or false (lowercase)
    kernel_size = 9
 
 [opensim]
+static_trial = 'yes' # 'yes' or 'no' at the Trial level;
+                     # folder name at the Participant level, e.g. 'S00_P00_T00_StaticTrial';
+                     # list of folder names at the Session level, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01/S00_P01_T00', 'S00_P02/S00_P02_T00']
+
 
 
 # CUSTOM skeleton, for DeepLabCut for example (others are in skeletons.py)

Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/Config.toml

@@ -0,0 +1,225 @@
+###############################################################################
+## PROJECT PARAMETERS                                                        ##
+###############################################################################
+
+# Configure your project parameters here. 
+# 
+# IMPORTANT:
+# All configuration parameters specified at that level will be overwritten by 
+# the ones given in sublevels. Thus a parameters given at the Trial level will 
+# prevail over those given at the Participant or Session level. 
+# This way, you can set global instructions for the Session and alter them
+# for specific Participants or Trials.
+
+
+[project]
+frame_range = [] # For example [10,300], or [] for all frames
+frame_rate = 60 # fps
+
+exclude_from_batch = [] # [] if this Config.toml file is at the Trial level; 
+                        # folder name at the Participant level, e.g. 'S00_P00_T00_StaticTrial';
+                        # list of folder names at the Session level, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01/S00_P01_T00', 'S00_P02/S00_P02_T00']
+
+
+# Take heart, calibration is not that complicated once you get the hang of it!
+[calibration]
+calibration_type = 'convert' # 'convert' or 'calculate'
+
+   [calibration.convert]
+   convert_from = 'qualisys' # 'qualisys', 'optitrack', vicon', 'opencap', 'easymocap', 'biocv', 'anipose', or 'freemocap'
+      [calibration.convert.qualisys]
+      binning_factor = 1 # Usually 1, except when filming in 540p where it usually is 2
+      [calibration.convert.optitrack]  # See readme for instructions
+      [calibration.convert.vicon]      # No parameter needed
+      [calibration.convert.opencap]    # No parameter needed
+      [calibration.convert.easymocap]  # No parameter needed
+      [calibration.convert.biocv]      # No parameter needed
+      [calibration.convert.anipose]    # No parameter needed
+      [calibration.convert.freemocap]  # No parameter needed
+  
+
+   [calibration.calculate] 
+      # Camera properties, theoretically need to be calculated only once in a camera lifetime
+      [calibration.calculate.intrinsics]
+      overwrite_intrinsics = false # overwrite (or not) if they have already been calculated?
+      show_detection_intrinsics = true # true or false (lowercase)
+      intrinsics_extension = 'jpg' # any video or image extension
+      extract_every_N_sec = 1 # if video, extract frames every N seconds (can be <1 )
+      intrinsics_corners_nb = [4,7] 
+      intrinsics_square_size = 60 # mm
+
+      # Camera placements, need to be done before every session
+      [calibration.calculate.extrinsics]
+      extrinsics_method = 'scene' # 'board', 'scene', 'keypoints'
+      # 'board' should be large enough to be detected when laid on the floor. Not recommended.
+      # 'scene' involves manually clicking any point of know coordinates on scene. Usually more accurate if points are spread out.
+      # 'keypoints' uses automatic pose estimation of a person freely walking and waving arms in the scene. Slighlty less accurate, requires synchronized cameras.
+
+      moving_cameras = false # Not implemented yet
+      calculate_extrinsics = true # true or false (lowercase) 
+
+         [calibration.calculate.extrinsics.board]
+         show_reprojection_error = true # true or false (lowercase)
+         extrinsics_extension = 'png' # any video or image extension
+         extrinsics_corners_nb = [4,7] # [H,W] rather than [w,h]
+         extrinsics_square_size = 60 # mm # [h,w] if square is actually a rectangle
+
+         [calibration.calculate.extrinsics.scene]
+         show_reprojection_error = true # true or false (lowercase)
+         extrinsics_extension = 'png' # any video or image extension
+         # list of 3D coordinates to be manually labelled on images. Can also be a 2 dimensional plane. 
+         # in m -> unlike for intrinsics, NOT in mm!
+         object_coords_3d =   [[-2.0,  0.3,  0.0], 
+                              [-2.0 , 0.0,  0.0], 
+                              [-2.0, 0.0,  0.05], 
+                              [-2.0, -0.3 ,  0.0], 
+                              [0.0,  0.3,  0.0], 
+                              [0.0, 0.0,  0.0], 
+                              [0.0, 0.0,  0.05], 
+                              [0.0, -0.3,  0.0]]
+        
+         [calibration.calculate.extrinsics.keypoints]
+         # Coming soon!
+
+
+[pose]
+pose_framework = 'openpose' # 'openpose', 'mediapipe', 'alphapose', 'deeplabcut' 
+pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII. 
+						      #With mediapipe: BLAZEPOSE. 
+						      #With alphapose: HALPE_26, HALPE_68, HALPE_136, COCO_133. 
+						      #With deeplabcut: CUSTOM. See example at the end of the file.
+# What follows has not been implemented yet
+overwrite_pose = false
+openpose_path = '' # only checked if OpenPose is used
+
+
+[synchronization]
+# COMING SOON! 
+reset_sync = true # Recalculate synchronization even if already done
+frames = [2850,3490] # Frames to use for synchronization, should point to a moment with fast motion.
+cut_off_frequency = 10 # cut-off frequency for a 4th order low-pass Butterworth filter
+# Vertical speeds (on X, Y, or Z axis, or 2D speeds)
+speed_kind = 'y' # 'x', 'y', 'z', or '2D'
+vmax = 20 # px/s
+cam1_nb = 4
+cam2_nb = 3
+id_kpt = [9,10] # Pour plus tard aller chercher numéro depuis keypoint name dans skeleton.py. 'RWrist' BLAZEPOSE 16, BODY_25B 10, BODY_25 4 ; 'LWrist' BLAZEPOSE 15, BODY_25B 9, BODY_25 7
+weights_kpt = [1,1] # Pris en compte uniquement si on a plusieurs keypoints
+
+
+[personAssociation]
+tracked_keypoint = 'Neck' # If the neck is not detected by the pose_model, check skeleton.py 
+# and choose a stable point for tracking the person of interest (e.g., 'right_shoulder' with BLAZEPOSE)
+reproj_error_threshold_association = 20 # px
+
+
+[triangulation]
+reproj_error_threshold_triangulation = 15 # px
+likelihood_threshold = 0.3
+min_cameras_for_triangulation = 2
+interpolation = 'cubic' #linear, slinear, quadratic, cubic, or none
+# 'none' if you don't want to interpolate missing points
+interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
+show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
+
+
+[filtering]
+type = 'butterworth' # butterworth, kalman, gaussian, LOESS, median, butterworth_on_speed
+display_figures = true # true or false (lowercase)
+
+   [filtering.butterworth]
+   order = 4 
+   cut_off_frequency = 6 # Hz
+   [filtering.kalman]
+   # How much more do you trust triangulation results (measurements), than previous data (process assuming constant acceleration)?
+   trust_ratio = 100 # = measurement_trust/process_trust ~= process_noise/measurement_noise
+   smooth = true # should be true, unless you need real-time filtering
+   [filtering.butterworth_on_speed]
+   order = 4 
+   cut_off_frequency = 10 # Hz
+   [filtering.gaussian]
+   sigma_kernel = 2 #px
+   [filtering.LOESS]
+   nb_values_used = 30 # = fraction of data used * nb frames
+   [filtering.median]
+   kernel_size = 9
+
+[opensim]
+static_trial = 'yes' # 'yes' or 'no' if this Config.toml file is at the Trial level;
+                     # folder name at the Participant level, e.g. 'S00_P00_T00_StaticTrial';
+                     # list of folder names at the Session level, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01/S00_P01_T00', 'S00_P02/S00_P02_T00']
+
+
+
+# CUSTOM skeleton, if you trained your own DeepLabCut model for example. 
+# Make sure the node ids correspond to the column numbers of the 2D pose file, starting from zero.
+# If you want to perform inverse kinematics, you will also need to create an OpenSim model
+# and add to its markerset the location where you expect the triangulated keypoints to be detected.
+# In this example, CUSTOM reproduces the BODY_25B skeleton  (default skeletons are stored in skeletons.py).
+# You can create as many custom skeletons as you want, just add them further down and rename them.
+[pose.CUSTOM]
+name = "CHip"
+id = "None"
+  [[pose.CUSTOM.children]]
+  id = 12
+  name = "RHip"
+     [[pose.CUSTOM.children.children]]
+     id = 14
+     name = "RKnee"
+        [[pose.CUSTOM.children.children.children]]
+        id = 16
+        name = "RAnkle"
+           [[pose.CUSTOM.children.children.children.children]]
+           id = 22
+           name = "RBigToe"
+              [[pose.CUSTOM.children.children.children.children.children]]
+              id = 23
+              name = "RSmallToe"
+           [[pose.CUSTOM.children.children.children.children]]
+           id = 24
+           name = "RHeel"
+  [[pose.CUSTOM.children]]
+  id = 11
+  name = "LHip"
+     [[pose.CUSTOM.children.children]]
+     id = 13
+     name = "LKnee"
+        [[pose.CUSTOM.children.children.children]]
+        id = 15
+        name = "LAnkle"
+           [[pose.CUSTOM.children.children.children.children]]
+           id = 19
+           name = "LBigToe"
+              [[pose.CUSTOM.children.children.children.children.children]]
+              id = 20
+              name = "LSmallToe"
+           [[pose.CUSTOM.children.children.children.children]]
+           id = 21
+           name = "LHeel"
+  [[pose.CUSTOM.children]]
+  id = 17
+  name = "Neck"
+     [[pose.CUSTOM.children.children]]
+     id = 18
+     name = "Head"
+        [[pose.CUSTOM.children.children.children]]
+        id = 0
+        name = "Nose"
+     [[pose.CUSTOM.children.children]]
+     id = 6
+     name = "RShoulder"
+        [[pose.CUSTOM.children.children.children]]
+        id = 8
+        name = "RElbow"
+           [[pose.CUSTOM.children.children.children.children]]
+           id = 10
+           name = "RWrist"
+     [[pose.CUSTOM.children.children]]
+     id = 5
+     name = "LShoulder"
+        [[pose.CUSTOM.children.children.children]]
+        id = 7
+        name = "LElbow"
+           [[pose.CUSTOM.children.children.children.children]]
+           id = 9
+           name = "LWrist"

Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/Config.toml

@@ -0,0 +1,225 @@
+###############################################################################
+## PROJECT PARAMETERS                                                        ##
+###############################################################################
+
+# Configure your project parameters here. 
+# 
+# IMPORTANT:
+# All configuration parameters specified at that level will be overwritten by 
+# the ones given in sublevels. Thus a parameters given at the Trial level will 
+# prevail over those given at the Participant or Session level. 
+# This way, you can set global instructions for the Session and alter them
+# for specific Participants or Trials.
+
+
+[project]
+frame_rate = 60 # FPS
+frame_range = [] # For example [10,300], or [] for all frames
+# N.B.: If you want a time range instead, use frame_range = time_range * frame_rate
+# For example if you want to analyze from 0.1 to 2 seconds with a 60 fps frame rate, 
+# frame_range = [0.1, 2.0]*frame_rate = [6, 120]
+
+exclude_from_batch = 
+
+
+
+# Take heart, calibration is not that complicated once you get the hang of it!
+[calibration]
+calibration_type = 'convert' # 'convert' or 'calculate'
+
+   [calibration.convert]
+   convert_from = 'qualisys' # 'qualisys', 'optitrack', vicon', 'opencap', 'easymocap', or 'biocv'
+      [calibration.convert.qualisys]
+      binning_factor = 1 # Usually 1, except when filming in 540p where it usually is 2
+      [calibration.convert.optitrack]  # See readme for instructions
+      [calibration.convert.vicon]      # No parameter needed
+      [calibration.convert.opencap]    # No parameter needed
+      [calibration.convert.easymocap]  # No parameter needed
+      [calibration.convert.biocv]      # No parameter needed
+      [calibration.convert.anipose]    # No parameter needed
+      [calibration.convert.freemocap]  # No parameter needed
+  
+
+   [calibration.calculate] 
+      # Camera properties, theoretically need to be calculated only once in a camera lifetime
+      [calibration.calculate.intrinsics]
+      overwrite_intrinsics = false # overwrite (or not) if they have already been calculated?
+      show_detection_intrinsics = true # true or false (lowercase)
+      intrinsics_extension = 'jpg' # any video or image extension
+      extract_every_N_sec = 1 # if video, extract frames every N seconds (can be <1 )
+      intrinsics_corners_nb = [4,7] 
+      intrinsics_square_size = 60 # mm
+
+      # Camera placements, need to be done before every session
+      [calibration.calculate.extrinsics]
+      extrinsics_method = 'scene' # 'board', 'scene', 'keypoints'
+      # 'board' should be large enough to be detected when laid on the floor. Not recommended.
+      # 'scene' involves manually clicking any point of know coordinates on scene. Usually more accurate if points are spread out.
+      # 'keypoints' uses automatic pose estimation of a person freely walking and waving arms in the scene. Slighlty less accurate, requires synchronized cameras.
+
+      moving_cameras = false # Not implemented yet
+      calculate_extrinsics = true # true or false (lowercase) 
+
+         [calibration.calculate.extrinsics.board]
+         show_reprojection_error = true # true or false (lowercase)
+         extrinsics_extension = 'png' # any video or image extension
+         extrinsics_corners_nb = [4,7] # [H,W] rather than [w,h]
+         extrinsics_square_size = 60 # mm # [h,w] if square is actually a rectangle
+
+         [calibration.calculate.extrinsics.scene]
+         show_reprojection_error = true # true or false (lowercase)
+         extrinsics_extension = 'png' # any video or image extension
+         # list of 3D coordinates to be manually labelled on images. Can also be a 2 dimensional plane. 
+         # in m -> unlike for intrinsics, NOT in mm!
+         object_coords_3d =   [[-2.0,  0.3,  0.0], 
+                              [-2.0 , 0.0,  0.0], 
+                              [-2.0, 0.0,  0.05], 
+                              [-2.0, -0.3 ,  0.0], 
+                              [0.0,  0.3,  0.0], 
+                              [0.0, 0.0,  0.0], 
+                              [0.0, 0.0,  0.05], 
+                              [0.0, -0.3,  0.0]]
+        
+         [calibration.calculate.extrinsics.keypoints]
+         # Coming soon!
+
+
+[pose]
+pose_framework = 'openpose' # 'openpose', 'mediapipe', 'alphapose', 'deeplabcut' 
+pose_model = 'BODY_25B' #With openpose: BODY_25B, BODY_25, BODY_135, COCO, MPII. 
+						      #With mediapipe: BLAZEPOSE. 
+						      #With alphapose: HALPE_26, HALPE_68, HALPE_136, COCO_133. 
+						      #With deeplabcut: CUSTOM. See example at the end of the file.
+# What follows has not been implemented yet
+overwrite_pose = false
+openpose_path = '' # only checked if OpenPose is used
+
+
+[synchronization]
+# COMING SOON! 
+reset_sync = true # Recalculate synchronization even if already done
+frames = [2850,3490] # Frames to use for synchronization, should point to a moment with fast motion.
+cut_off_frequency = 10 # cut-off frequency for a 4th order low-pass Butterworth filter
+# Vertical speeds (on X, Y, or Z axis, or 2D speeds)
+speed_kind = 'y' # 'x', 'y', 'z', or '2D'
+vmax = 20 # px/s
+cam1_nb = 4
+cam2_nb = 3
+id_kpt = [9,10] # Pour plus tard aller chercher numéro depuis keypoint name dans skeleton.py. 'RWrist' BLAZEPOSE 16, BODY_25B 10, BODY_25 4 ; 'LWrist' BLAZEPOSE 15, BODY_25B 9, BODY_25 7
+weights_kpt = [1,1] # Pris en compte uniquement si on a plusieurs keypoints
+
+
+[personAssociation]
+tracked_keypoint = 'Neck' # If the neck is not detected by the pose_model, check skeleton.py 
+# and choose a stable point for tracking the person of interest (e.g., 'right_shoulder' with BLAZEPOSE)
+reproj_error_threshold_association = 20 # px
+
+
+[triangulation]
+reproj_error_threshold_triangulation = 15 # px
+likelihood_threshold = 0.3
+min_cameras_for_triangulation = 2
+interpolation = 'cubic' #linear, slinear, quadratic, cubic, or none
+# 'none' if you don't want to interpolate missing points
+interp_if_gap_smaller_than = 10 # do not interpolate bigger gaps
+show_interp_indices = true # true or false (lowercase). For each keypoint, return the frames that need to be interpolated
+
+
+[filtering]
+type = 'butterworth' # butterworth, kalman, gaussian, LOESS, median, butterworth_on_speed
+display_figures = true # true or false (lowercase)
+
+   [filtering.butterworth]
+   order = 4 
+   cut_off_frequency = 6 # Hz
+   [filtering.kalman]
+   # How much more do you trust triangulation results (measurements), than previous data (process assuming constant acceleration)?
+   trust_ratio = 100 # = measurement_trust/process_trust ~= process_noise/measurement_noise
+   smooth = true # should be true, unless you need real-time filtering
+   [filtering.butterworth_on_speed]
+   order = 4 
+   cut_off_frequency = 10 # Hz
+   [filtering.gaussian]
+   sigma_kernel = 2 #px
+   [filtering.LOESS]
+   nb_values_used = 30 # = fraction of data used * nb frames
+   [filtering.median]
+   kernel_size = 9
+
+[opensim]
+static_trial = 'yes' # 'yes' or 'no' at the Trial level;
+                     # folder name at the Participant level, e.g. 'S00_P00_T00_StaticTrial';
+                     # list of folder names at the Session level, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01/S00_P01_T00', 'S00_P02/S00_P02_T00']
+
+
+
+# CUSTOM skeleton, for DeepLabCut for example (others are in skeletons.py)
+# In this example, CUSTOM reproduces the BODY_25B skeleton.
+# You can create as many custom skeletons as you want, just add them further down and rename them.
+# Make sure the node ids correspond to the column numbers of the 2D pose file, starting from zero.
+[pose.CUSTOM]
+name = "CHip"
+id = "None"
+  [[pose.CUSTOM.children]]
+  id = 12
+  name = "RHip"
+     [[pose.CUSTOM.children.children]]
+     id = 14
+     name = "RKnee"
+        [[pose.CUSTOM.children.children.children]]
+        id = 16
+        name = "RAnkle"
+           [[pose.CUSTOM.children.children.children.children]]
+           id = 22
+           name = "RBigToe"
+              [[pose.CUSTOM.children.children.children.children.children]]
+              id = 23
+              name = "RSmallToe"
+           [[pose.CUSTOM.children.children.children.children]]
+           id = 24
+           name = "RHeel"
+  [[pose.CUSTOM.children]]
+  id = 11
+  name = "LHip"
+     [[pose.CUSTOM.children.children]]
+     id = 13
+     name = "LKnee"
+        [[pose.CUSTOM.children.children.children]]
+        id = 15
+        name = "LAnkle"
+           [[pose.CUSTOM.children.children.children.children]]
+           id = 19
+           name = "LBigToe"
+              [[pose.CUSTOM.children.children.children.children.children]]
+              id = 20
+              name = "LSmallToe"
+           [[pose.CUSTOM.children.children.children.children]]
+           id = 21
+           name = "LHeel"
+  [[pose.CUSTOM.children]]
+  id = 17
+  name = "Neck"
+     [[pose.CUSTOM.children.children]]
+     id = 18
+     name = "Head"
+        [[pose.CUSTOM.children.children.children]]
+        id = 0
+        name = "Nose"
+     [[pose.CUSTOM.children.children]]
+     id = 6
+     name = "RShoulder"
+        [[pose.CUSTOM.children.children.children]]
+        id = 8
+        name = "RElbow"
+           [[pose.CUSTOM.children.children.children.children]]
+           id = 10
+           name = "RWrist"
+     [[pose.CUSTOM.children.children]]
+     id = 5
+     name = "LShoulder"
+        [[pose.CUSTOM.children.children.children]]
+        id = 7
+        name = "LElbow"
+           [[pose.CUSTOM.children.children.children.children]]
+           id = 9
+           name = "LWrist"