diff --git a/Pose2Sim/Demo/User/Config.toml b/Pose2Sim/Demo/S00_Demo_Session/Config.toml similarity index 59% rename from Pose2Sim/Demo/User/Config.toml rename to Pose2Sim/Demo/S00_Demo_Session/Config.toml index 37b064f..48b4eb5 100644 --- a/Pose2Sim/Demo/User/Config.toml +++ b/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_range = [] #For example [10,300], or [] for all frames -frame_rate = 60 #Hz - -rawImg_folder_name = 'raw' -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 +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] +# 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.opencap] # No parameters needed - [calibration.convert.easymocap] # No parameters needed - [calibration.convert.biocv] # No parameters needed + [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] - calculate_method = 'board' # 'board' or 'points' - - [calibration.calculate.board.intrinsics] # camera properties, only needs to be done once - intrinsics_board_type = 'checkerboard' # 'checkerboard' ('charucoboard' not supported yet) + # 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 - 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) diff --git a/Pose2Sim/Demo/calibration/Calib.qca.txt b/Pose2Sim/Demo/S00_Demo_Session/S00_Calibration/Calib.qca.txt similarity index 100% rename from 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b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/Config.toml similarity index 56% rename from Pose2Sim/Demo/User/test.toml rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/Config.toml index 1f80d6b..48b4eb5 100644 --- a/Pose2Sim/Demo/User/test.toml +++ b/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_range = [0,10] #For example [10,300], or [] for all frames -frame_rate = 60 #Hz - -rawImg_folder_name = 'raw' -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 +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] +# 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.opencap] # No parameters needed - [calibration.convert.easymocap] # No parameters needed - [calibration.convert.biocv] # No parameters needed + [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] - calculate_method = 'board' # 'board' or 'points' - - [calibration.calculate.board.intrinsics] # camera properties, only needs to be done once - intrinsics_board_type = 'checkerboard' # 'checkerboard' ('charucoboard' not supported yet) + # 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 - 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) diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/Config.toml b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T00_StaticTrial/Config.toml new file mode 100644 index 0000000..518b43f --- /dev/null +++ b/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" diff --git a/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/Config.toml b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/Config.toml new file mode 100644 index 0000000..6bd951d --- /dev/null +++ b/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" diff --git a/Pose2Sim/Demo/pose/cam1_json/cam01.0000.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam1_json/cam01.0000.json similarity index 100% rename from Pose2Sim/Demo/pose/cam1_json/cam01.0000.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam1_json/cam01.0000.json diff --git a/Pose2Sim/Demo/pose/cam1_json/cam01.0001.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam1_json/cam01.0001.json similarity index 100% rename from Pose2Sim/Demo/pose/cam1_json/cam01.0001.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam1_json/cam01.0001.json diff --git a/Pose2Sim/Demo/pose/cam1_json/cam01.0002.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam1_json/cam01.0002.json similarity index 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b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0095.json similarity index 100% rename from Pose2Sim/Demo/pose/cam4_json/cam04.0095.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0095.json diff --git a/Pose2Sim/Demo/pose/cam4_json/cam04.0096.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0096.json similarity index 100% rename from Pose2Sim/Demo/pose/cam4_json/cam04.0096.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0096.json diff --git a/Pose2Sim/Demo/pose/cam4_json/cam04.0097.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0097.json similarity index 100% rename from Pose2Sim/Demo/pose/cam4_json/cam04.0097.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0097.json diff --git a/Pose2Sim/Demo/pose/cam4_json/cam04.0098.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0098.json similarity index 100% rename from Pose2Sim/Demo/pose/cam4_json/cam04.0098.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0098.json diff --git a/Pose2Sim/Demo/pose/cam4_json/cam04.0099.json b/Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0099.json similarity index 100% rename from Pose2Sim/Demo/pose/cam4_json/cam04.0099.json rename to Pose2Sim/Demo/S00_Demo_Session/S00_P00_Participant/S00_P00_T01_BalancingTrial/pose/cam4_json/cam04.0099.json diff --git a/Pose2Sim/Demo/S00_Demo_Session/test.py b/Pose2Sim/Demo/S00_Demo_Session/test.py new file mode 100644 index 0000000..ad7d772 --- /dev/null +++ b/Pose2Sim/Demo/S00_Demo_Session/test.py @@ -0,0 +1,11 @@ +import os +import toml + +def test_workflow(): + from Pose2Sim import Pose2Sim + config_dict = toml.load(os.path.join('User', 'Config.toml')) + config_dict['filtering']['display_figures'] = False + Pose2Sim.calibration(config_dict) + Pose2Sim.personAssociation(config_dict) + Pose2Sim.triangulation(config_dict) + Pose2Sim.filtering(config_dict) diff --git a/Pose2Sim/Empty_project/User/Config.toml b/Pose2Sim/Demo/S01_Empty_Session/User/Config.toml similarity index 100% rename from Pose2Sim/Empty_project/User/Config.toml rename to Pose2Sim/Demo/S01_Empty_Session/User/Config.toml diff --git a/Pose2Sim/Empty_project/calibration/extrinsics/ext_cam1_img/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/calibration/extrinsics/ext_cam1_img/.gitkeep similarity index 100% rename from Pose2Sim/Empty_project/calibration/extrinsics/ext_cam1_img/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/calibration/extrinsics/ext_cam1_img/.gitkeep diff --git a/Pose2Sim/Empty_project/calibration/extrinsics/ext_cam2_img/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/calibration/extrinsics/ext_cam2_img/.gitkeep similarity index 100% rename from Pose2Sim/Empty_project/calibration/extrinsics/ext_cam2_img/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/calibration/extrinsics/ext_cam2_img/.gitkeep diff --git a/Pose2Sim/Empty_project/calibration/extrinsics/ext_cam3_img/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/calibration/extrinsics/ext_cam3_img/.gitkeep similarity index 100% rename from Pose2Sim/Empty_project/calibration/extrinsics/ext_cam3_img/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/calibration/extrinsics/ext_cam3_img/.gitkeep diff --git a/Pose2Sim/Empty_project/calibration/intrinsics/int_cam1_img/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/calibration/intrinsics/int_cam1_img/.gitkeep similarity index 100% rename from Pose2Sim/Empty_project/calibration/intrinsics/int_cam1_img/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/calibration/intrinsics/int_cam1_img/.gitkeep diff --git a/Pose2Sim/Empty_project/calibration/intrinsics/int_cam2_img/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/calibration/intrinsics/int_cam2_img/.gitkeep similarity index 100% rename from Pose2Sim/Empty_project/calibration/intrinsics/int_cam2_img/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/calibration/intrinsics/int_cam2_img/.gitkeep diff --git a/Pose2Sim/Empty_project/calibration/intrinsics/int_cam3_img/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/calibration/intrinsics/int_cam3_img/.gitkeep similarity index 100% rename from Pose2Sim/Empty_project/calibration/intrinsics/int_cam3_img/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/calibration/intrinsics/int_cam3_img/.gitkeep diff --git a/Pose2Sim/Empty_project/pose/pose_cam1_json/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/pose/pose_cam1_json/.gitkeep similarity index 100% rename from Pose2Sim/Empty_project/pose/pose_cam1_json/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/pose/pose_cam1_json/.gitkeep diff --git a/Pose2Sim/Empty_project/pose/pose_cam2_json/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/pose/pose_cam2_json/.gitkeep similarity index 100% rename from Pose2Sim/Empty_project/pose/pose_cam2_json/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/pose/pose_cam2_json/.gitkeep diff --git a/Pose2Sim/Empty_project/pose/pose_cam3_json/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/pose/pose_cam3_json/.gitkeep similarity index 100% rename from Pose2Sim/Empty_project/pose/pose_cam3_json/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/pose/pose_cam3_json/.gitkeep diff --git a/Pose2Sim/Empty_project/raw/.gitkeep b/Pose2Sim/Demo/S01_Empty_Session/videos/.gitkeep similarity index 100% rename from Pose2Sim/Empty_project/raw/.gitkeep rename to Pose2Sim/Demo/S01_Empty_Session/videos/.gitkeep diff --git a/Pose2Sim/Demo/calibration/Calib_qualisys.toml b/Pose2Sim/Demo/calibration/Calib_qualisys.toml deleted file mode 100644 index f291f73..0000000 --- a/Pose2Sim/Demo/calibration/Calib_qualisys.toml +++ /dev/null @@ -1,39 +0,0 @@ -[cam_01] -name = "cam_01" -size = [ 1088.0, 1920.0] -matrix = [ [ 1681.244873046875, 0.0, 532.97369384375], [ 0.0, 1681.075439453125, 948.137390140625], [ 0.0, 0.0, 1.0]] -distortions = [ -0.000721609375, 0.002187234375, 9.5e-06, 1.078125e-05] -rotation = [ 1.6882754799999993, 1.0483220499999997, -0.41955852000000016] -translation = [ 0.3211048899999996, 0.9563320600000009, 2.8907130499999996] -fisheye = false - -[cam_02] -name = "cam_02" -size = [ 1088.0, 1920.0] -matrix = [ [ 1673.729614265625, 0.0, 534.494567875], [ 0.0, 1673.79724121875, 963.225891109375], [ 0.0, 0.0, 1.0]] -distortions = [ -0.000747609375, 0.00213728125, 1.51875e-05, 4.546875e-06] -rotation = [ 1.34975875, 1.5963809099999993, -1.1983285799999999] -translation = [ -0.11152829000000017, 0.7766184800000001, 3.0675519599999994] -fisheye = false - -[cam_03] -name = "cam_03" -size = [ 1088.0, 1920.0] -matrix = [ [ 1681.598388671875, 0.0, 513.20837403125], [ 0.0, 1681.509887703125, 955.005126953125], [ 0.0, 0.0, 1.0]] -distortions = [ -0.000729765625, 0.00215034375, -8.46875e-06, -8.078125e-06] -rotation = [ 0.8109654899999995, -2.1972129299999996, 1.3760277799999996] -translation = [ -0.7934803899999996, 0.32283594000000126, 4.353514870000001] -fisheye = false - -[cam_04] -name = "cam_04" -size = [ 1088.0, 1920.0] -matrix = [ [ 1675.234985359375, 0.0, 540.106201171875], [ 0.0, 1675.204223640625, 964.0302734375], [ 0.0, 0.0, 1.0]] -distortions = [ -0.000744265625, 0.002104171875, 4.328125e-06, 3.109375e-06] -rotation = [ 1.4045571699999995, -1.3887412699999993, 0.42535743000000026] -translation = [ 0.5030217200000007, 0.04894934000000083, 4.406564460000002] -fisheye = false - -[metadata] -adjusted = false -error = 0.0 diff --git a/Pose2Sim/Demo/opensim/Balancing_for_IK.trc b/Pose2Sim/Demo/opensim/Balancing_for_IK.trc deleted file mode 100644 index c5477a9..0000000 --- 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2721 2724 - - - - - diff --git a/Pose2Sim/Demo/opensim/IK_Setup_Pose2Sim_Body25b.xml b/Pose2Sim/Demo/opensim/IK_Setup_Pose2Sim_Body25b.xml deleted file mode 100644 index 63ea46d..0000000 --- a/Pose2Sim/Demo/opensim/IK_Setup_Pose2Sim_Body25b.xml +++ /dev/null @@ -1,167 +0,0 @@ - - - - - ./ - - Model_Pose2Sim_Body25b_scaled.osim - - Inf - - 1.0000000000000001e-05 - - 0.0166666666666666 1.6666666666666667 - - Balancing_for_IK.mot - - true - - - - - - true - - 0.10000000000000001 - - - - true - - 0.10000000000000001 - - - - true - - 0.20000000000000001 - - - - true - - 2 - - - - true - - 2 - - - - true - - 1 - - - - true - - 1 - - - - true - - 1 - - - - true - - 1 - - - - true - - 2 - - - - true - - 2 - - - - true - - 1 - - - - true - - 1 - - - - true - - 1 - - - - true - - 1 - - - - true - - 1 - - - - true - - 1 - - - - true - - 1 - - - - true - - 1 - - - - true - - 1 - - - - true - - 1 - - - - true - - 1 - - default_value - - 0 - - - - - - Balancing_for_IK.trc - - Unassigned - - false - - diff --git a/Pose2Sim/Demo/opensim/Model_Pose2Sim_Body25b.osim b/Pose2Sim/Demo/opensim/Model_Pose2Sim_Body25b.osim deleted file mode 100644 index 41d5046..0000000 --- a/Pose2Sim/Demo/opensim/Model_Pose2Sim_Body25b.osim +++ /dev/null @@ -1,6913 +0,0 @@ - - - - - - - - - .. - - 0.20000000000000001 0.20000000000000001 0.20000000000000001 - - - - - - - - - - - 0 -9.8066499999999994 0 - - Full-body model adapted from Beaucage-Gauvreau et al., with Rajagopal et al. knee angles. Openpose body_25b markers. No muscles included. Free pelvis translation, unlocked subtalar angle, added ball joint between head and torso, locked arm pronation/supination, clamped hip flexion to 150° instead of 120°. - - Pagnon, D., Domalain, M., Reveret, L. (2021). Pose2Sim: An End-to-End Workflow for 3D Markerless Sports Kinematics—Part 1: Robustness. 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Pose2Sim/Demo/opensim/Geometry/capitate_lvs.vtp rename to Pose2Sim/Opensim/Geometry/capitate_lvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/capitate_rvs.vtp b/Pose2Sim/Opensim/Geometry/capitate_rvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/capitate_rvs.vtp rename to Pose2Sim/Opensim/Geometry/capitate_rvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/cerv1sm.vtp b/Pose2Sim/Opensim/Geometry/cerv1sm.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/cerv1sm.vtp rename to Pose2Sim/Opensim/Geometry/cerv1sm.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/cerv2sm.vtp b/Pose2Sim/Opensim/Geometry/cerv2sm.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/cerv2sm.vtp rename to Pose2Sim/Opensim/Geometry/cerv2sm.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/cerv3sm.vtp b/Pose2Sim/Opensim/Geometry/cerv3sm.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/cerv3sm.vtp rename to Pose2Sim/Opensim/Geometry/cerv3sm.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/cerv4sm.vtp b/Pose2Sim/Opensim/Geometry/cerv4sm.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/cerv4sm.vtp rename to Pose2Sim/Opensim/Geometry/cerv4sm.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/cerv5sm.vtp b/Pose2Sim/Opensim/Geometry/cerv5sm.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/cerv5sm.vtp rename to Pose2Sim/Opensim/Geometry/cerv5sm.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/cerv6sm.vtp b/Pose2Sim/Opensim/Geometry/cerv6sm.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/cerv6sm.vtp rename to Pose2Sim/Opensim/Geometry/cerv6sm.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/cerv7.vtp b/Pose2Sim/Opensim/Geometry/cerv7.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/cerv7.vtp rename to Pose2Sim/Opensim/Geometry/cerv7.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/femur_l.vtp b/Pose2Sim/Opensim/Geometry/femur_l.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/femur_l.vtp rename to Pose2Sim/Opensim/Geometry/femur_l.vtp diff --git a/Pose2Sim/Empty_project/opensim/Geometry/femur_r.vtp b/Pose2Sim/Opensim/Geometry/femur_r.vtp similarity index 100% rename from Pose2Sim/Empty_project/opensim/Geometry/femur_r.vtp rename to Pose2Sim/Opensim/Geometry/femur_r.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/fibula_l.vtp b/Pose2Sim/Opensim/Geometry/fibula_l.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/fibula_l.vtp rename to Pose2Sim/Opensim/Geometry/fibula_l.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/fibula_r.vtp b/Pose2Sim/Opensim/Geometry/fibula_r.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/fibula_r.vtp rename to Pose2Sim/Opensim/Geometry/fibula_r.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/foot.vtp b/Pose2Sim/Opensim/Geometry/foot.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/foot.vtp rename to Pose2Sim/Opensim/Geometry/foot.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/hamate_lvs.vtp b/Pose2Sim/Opensim/Geometry/hamate_lvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/hamate_lvs.vtp rename to Pose2Sim/Opensim/Geometry/hamate_lvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/hamate_rvs.vtp b/Pose2Sim/Opensim/Geometry/hamate_rvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/hamate_rvs.vtp rename to Pose2Sim/Opensim/Geometry/hamate_rvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/hat_jaw.vtp b/Pose2Sim/Opensim/Geometry/hat_jaw.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/hat_jaw.vtp rename to Pose2Sim/Opensim/Geometry/hat_jaw.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/hat_ribs_scap.vtp b/Pose2Sim/Opensim/Geometry/hat_ribs_scap.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/hat_ribs_scap.vtp rename to Pose2Sim/Opensim/Geometry/hat_ribs_scap.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/hat_skull.vtp b/Pose2Sim/Opensim/Geometry/hat_skull.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/hat_skull.vtp rename to Pose2Sim/Opensim/Geometry/hat_skull.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/humerus_lv.vtp b/Pose2Sim/Opensim/Geometry/humerus_lv.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/humerus_lv.vtp rename to Pose2Sim/Opensim/Geometry/humerus_lv.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/humerus_rv.vtp b/Pose2Sim/Opensim/Geometry/humerus_rv.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/humerus_rv.vtp rename to Pose2Sim/Opensim/Geometry/humerus_rv.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/index_distal_lvs.vtp b/Pose2Sim/Opensim/Geometry/index_distal_lvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/index_distal_lvs.vtp rename to Pose2Sim/Opensim/Geometry/index_distal_lvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/index_distal_rvs.vtp b/Pose2Sim/Opensim/Geometry/index_distal_rvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/index_distal_rvs.vtp rename to Pose2Sim/Opensim/Geometry/index_distal_rvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/index_medial_lvs.vtp b/Pose2Sim/Opensim/Geometry/index_medial_lvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/index_medial_lvs.vtp rename to Pose2Sim/Opensim/Geometry/index_medial_lvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/index_medial_rvs.vtp b/Pose2Sim/Opensim/Geometry/index_medial_rvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/index_medial_rvs.vtp rename to Pose2Sim/Opensim/Geometry/index_medial_rvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/index_proximal_lvs.vtp b/Pose2Sim/Opensim/Geometry/index_proximal_lvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/index_proximal_lvs.vtp rename to Pose2Sim/Opensim/Geometry/index_proximal_lvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/index_proximal_rvs.vtp b/Pose2Sim/Opensim/Geometry/index_proximal_rvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/index_proximal_rvs.vtp rename to Pose2Sim/Opensim/Geometry/index_proximal_rvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/l_bofoot.vtp b/Pose2Sim/Opensim/Geometry/l_bofoot.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/l_bofoot.vtp rename to Pose2Sim/Opensim/Geometry/l_bofoot.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/l_foot.vtp b/Pose2Sim/Opensim/Geometry/l_foot.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/l_foot.vtp rename to Pose2Sim/Opensim/Geometry/l_foot.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/l_patella.vtp b/Pose2Sim/Opensim/Geometry/l_patella.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/l_patella.vtp rename to Pose2Sim/Opensim/Geometry/l_patella.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/l_pelvis.vtp b/Pose2Sim/Opensim/Geometry/l_pelvis.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/l_pelvis.vtp rename to Pose2Sim/Opensim/Geometry/l_pelvis.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/little_distal_lvs.vtp b/Pose2Sim/Opensim/Geometry/little_distal_lvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/little_distal_lvs.vtp rename to Pose2Sim/Opensim/Geometry/little_distal_lvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/little_distal_rvs.vtp b/Pose2Sim/Opensim/Geometry/little_distal_rvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/little_distal_rvs.vtp rename to Pose2Sim/Opensim/Geometry/little_distal_rvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/little_medial_lvs.vtp b/Pose2Sim/Opensim/Geometry/little_medial_lvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/little_medial_lvs.vtp rename to Pose2Sim/Opensim/Geometry/little_medial_lvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/little_medial_rvs.vtp b/Pose2Sim/Opensim/Geometry/little_medial_rvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/little_medial_rvs.vtp rename to Pose2Sim/Opensim/Geometry/little_medial_rvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/little_proximal_lvs.vtp b/Pose2Sim/Opensim/Geometry/little_proximal_lvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/little_proximal_lvs.vtp rename to Pose2Sim/Opensim/Geometry/little_proximal_lvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/little_proximal_rvs.vtp b/Pose2Sim/Opensim/Geometry/little_proximal_rvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/little_proximal_rvs.vtp rename to Pose2Sim/Opensim/Geometry/little_proximal_rvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/lumbar1.vtp b/Pose2Sim/Opensim/Geometry/lumbar1.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/lumbar1.vtp rename to Pose2Sim/Opensim/Geometry/lumbar1.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/lumbar2.vtp b/Pose2Sim/Opensim/Geometry/lumbar2.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/lumbar2.vtp rename to Pose2Sim/Opensim/Geometry/lumbar2.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/lumbar3.vtp b/Pose2Sim/Opensim/Geometry/lumbar3.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/lumbar3.vtp rename to Pose2Sim/Opensim/Geometry/lumbar3.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/lumbar4.vtp b/Pose2Sim/Opensim/Geometry/lumbar4.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/lumbar4.vtp rename to Pose2Sim/Opensim/Geometry/lumbar4.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/lumbar5.vtp b/Pose2Sim/Opensim/Geometry/lumbar5.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/lumbar5.vtp rename to Pose2Sim/Opensim/Geometry/lumbar5.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/lunate_lvs.vtp b/Pose2Sim/Opensim/Geometry/lunate_lvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/lunate_lvs.vtp rename to Pose2Sim/Opensim/Geometry/lunate_lvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/lunate_rvs.vtp b/Pose2Sim/Opensim/Geometry/lunate_rvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/lunate_rvs.vtp rename to Pose2Sim/Opensim/Geometry/lunate_rvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/metacarpal1_lvs.vtp b/Pose2Sim/Opensim/Geometry/metacarpal1_lvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/metacarpal1_lvs.vtp rename to Pose2Sim/Opensim/Geometry/metacarpal1_lvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/metacarpal1_rvs.vtp b/Pose2Sim/Opensim/Geometry/metacarpal1_rvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/metacarpal1_rvs.vtp rename to Pose2Sim/Opensim/Geometry/metacarpal1_rvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/metacarpal2_lvs.vtp b/Pose2Sim/Opensim/Geometry/metacarpal2_lvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/metacarpal2_lvs.vtp rename to Pose2Sim/Opensim/Geometry/metacarpal2_lvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/metacarpal2_rvs.vtp b/Pose2Sim/Opensim/Geometry/metacarpal2_rvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/metacarpal2_rvs.vtp rename to Pose2Sim/Opensim/Geometry/metacarpal2_rvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/metacarpal3_lvs.vtp b/Pose2Sim/Opensim/Geometry/metacarpal3_lvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/metacarpal3_lvs.vtp rename to Pose2Sim/Opensim/Geometry/metacarpal3_lvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/metacarpal3_rvs.vtp b/Pose2Sim/Opensim/Geometry/metacarpal3_rvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/metacarpal3_rvs.vtp rename to Pose2Sim/Opensim/Geometry/metacarpal3_rvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/metacarpal4_lvs.vtp b/Pose2Sim/Opensim/Geometry/metacarpal4_lvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/metacarpal4_lvs.vtp rename to Pose2Sim/Opensim/Geometry/metacarpal4_lvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/metacarpal4_rvs.vtp b/Pose2Sim/Opensim/Geometry/metacarpal4_rvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/metacarpal4_rvs.vtp rename to Pose2Sim/Opensim/Geometry/metacarpal4_rvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/metacarpal5_lvs.vtp b/Pose2Sim/Opensim/Geometry/metacarpal5_lvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/metacarpal5_lvs.vtp rename to Pose2Sim/Opensim/Geometry/metacarpal5_lvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/metacarpal5_rvs.vtp b/Pose2Sim/Opensim/Geometry/metacarpal5_rvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/metacarpal5_rvs.vtp rename to Pose2Sim/Opensim/Geometry/metacarpal5_rvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/middle_distal_lvs.vtp b/Pose2Sim/Opensim/Geometry/middle_distal_lvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/middle_distal_lvs.vtp rename to Pose2Sim/Opensim/Geometry/middle_distal_lvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/middle_distal_rvs.vtp b/Pose2Sim/Opensim/Geometry/middle_distal_rvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/middle_distal_rvs.vtp rename to Pose2Sim/Opensim/Geometry/middle_distal_rvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/middle_medial_lvs.vtp b/Pose2Sim/Opensim/Geometry/middle_medial_lvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/middle_medial_lvs.vtp rename to Pose2Sim/Opensim/Geometry/middle_medial_lvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/middle_medial_rvs.vtp b/Pose2Sim/Opensim/Geometry/middle_medial_rvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/middle_medial_rvs.vtp rename to Pose2Sim/Opensim/Geometry/middle_medial_rvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/middle_proximal_lvs.vtp b/Pose2Sim/Opensim/Geometry/middle_proximal_lvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/middle_proximal_lvs.vtp rename to Pose2Sim/Opensim/Geometry/middle_proximal_lvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/middle_proximal_rvs.vtp b/Pose2Sim/Opensim/Geometry/middle_proximal_rvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/middle_proximal_rvs.vtp rename to Pose2Sim/Opensim/Geometry/middle_proximal_rvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/pisiform_lvs.vtp b/Pose2Sim/Opensim/Geometry/pisiform_lvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/pisiform_lvs.vtp rename to Pose2Sim/Opensim/Geometry/pisiform_lvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/pisiform_rvs.vtp b/Pose2Sim/Opensim/Geometry/pisiform_rvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/pisiform_rvs.vtp rename to Pose2Sim/Opensim/Geometry/pisiform_rvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/r_patella.vtp b/Pose2Sim/Opensim/Geometry/r_patella.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/r_patella.vtp rename to Pose2Sim/Opensim/Geometry/r_patella.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/r_pelvis.vtp b/Pose2Sim/Opensim/Geometry/r_pelvis.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/r_pelvis.vtp rename to Pose2Sim/Opensim/Geometry/r_pelvis.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/radius_lv.vtp b/Pose2Sim/Opensim/Geometry/radius_lv.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/radius_lv.vtp rename to Pose2Sim/Opensim/Geometry/radius_lv.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/radius_rv.vtp b/Pose2Sim/Opensim/Geometry/radius_rv.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/radius_rv.vtp rename to Pose2Sim/Opensim/Geometry/radius_rv.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/ring_distal_lvs.vtp b/Pose2Sim/Opensim/Geometry/ring_distal_lvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/ring_distal_lvs.vtp rename to Pose2Sim/Opensim/Geometry/ring_distal_lvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/ring_distal_rvs.vtp b/Pose2Sim/Opensim/Geometry/ring_distal_rvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/ring_distal_rvs.vtp rename to Pose2Sim/Opensim/Geometry/ring_distal_rvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/ring_medial_lvs.vtp b/Pose2Sim/Opensim/Geometry/ring_medial_lvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/ring_medial_lvs.vtp rename to Pose2Sim/Opensim/Geometry/ring_medial_lvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/ring_medial_rvs.vtp b/Pose2Sim/Opensim/Geometry/ring_medial_rvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/ring_medial_rvs.vtp rename to Pose2Sim/Opensim/Geometry/ring_medial_rvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/ring_proximal_lvs.vtp b/Pose2Sim/Opensim/Geometry/ring_proximal_lvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/ring_proximal_lvs.vtp rename to Pose2Sim/Opensim/Geometry/ring_proximal_lvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/ring_proximal_rvs.vtp b/Pose2Sim/Opensim/Geometry/ring_proximal_rvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/ring_proximal_rvs.vtp rename to Pose2Sim/Opensim/Geometry/ring_proximal_rvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/sacrum.vtp b/Pose2Sim/Opensim/Geometry/sacrum.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/sacrum.vtp rename to Pose2Sim/Opensim/Geometry/sacrum.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/scaphoid_lvs.vtp b/Pose2Sim/Opensim/Geometry/scaphoid_lvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/scaphoid_lvs.vtp rename to Pose2Sim/Opensim/Geometry/scaphoid_lvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/scaphoid_rvs.vtp b/Pose2Sim/Opensim/Geometry/scaphoid_rvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/scaphoid_rvs.vtp rename to Pose2Sim/Opensim/Geometry/scaphoid_rvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/talus_lv.vtp b/Pose2Sim/Opensim/Geometry/talus_lv.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/talus_lv.vtp rename to Pose2Sim/Opensim/Geometry/talus_lv.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/talus_rv.vtp b/Pose2Sim/Opensim/Geometry/talus_rv.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/talus_rv.vtp rename to Pose2Sim/Opensim/Geometry/talus_rv.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/thoracic10_s.vtp b/Pose2Sim/Opensim/Geometry/thoracic10_s.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/thoracic10_s.vtp rename to Pose2Sim/Opensim/Geometry/thoracic10_s.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/thoracic11_s.vtp b/Pose2Sim/Opensim/Geometry/thoracic11_s.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/thoracic11_s.vtp rename to Pose2Sim/Opensim/Geometry/thoracic11_s.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/thoracic12_s.vtp b/Pose2Sim/Opensim/Geometry/thoracic12_s.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/thoracic12_s.vtp rename to Pose2Sim/Opensim/Geometry/thoracic12_s.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/thoracic1_s.vtp b/Pose2Sim/Opensim/Geometry/thoracic1_s.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/thoracic1_s.vtp rename to Pose2Sim/Opensim/Geometry/thoracic1_s.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/thoracic2_s.vtp b/Pose2Sim/Opensim/Geometry/thoracic2_s.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/thoracic2_s.vtp rename to Pose2Sim/Opensim/Geometry/thoracic2_s.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/thoracic3_s.vtp b/Pose2Sim/Opensim/Geometry/thoracic3_s.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/thoracic3_s.vtp rename to Pose2Sim/Opensim/Geometry/thoracic3_s.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/thoracic4_s.vtp b/Pose2Sim/Opensim/Geometry/thoracic4_s.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/thoracic4_s.vtp rename to Pose2Sim/Opensim/Geometry/thoracic4_s.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/thoracic5_s.vtp b/Pose2Sim/Opensim/Geometry/thoracic5_s.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/thoracic5_s.vtp rename to Pose2Sim/Opensim/Geometry/thoracic5_s.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/thoracic6_s.vtp b/Pose2Sim/Opensim/Geometry/thoracic6_s.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/thoracic6_s.vtp rename to Pose2Sim/Opensim/Geometry/thoracic6_s.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/thoracic7_s.vtp b/Pose2Sim/Opensim/Geometry/thoracic7_s.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/thoracic7_s.vtp rename to Pose2Sim/Opensim/Geometry/thoracic7_s.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/thoracic8_s.vtp b/Pose2Sim/Opensim/Geometry/thoracic8_s.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/thoracic8_s.vtp rename to Pose2Sim/Opensim/Geometry/thoracic8_s.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/thoracic9_s.vtp b/Pose2Sim/Opensim/Geometry/thoracic9_s.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/thoracic9_s.vtp rename to Pose2Sim/Opensim/Geometry/thoracic9_s.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/thumb_distal_lvs.vtp b/Pose2Sim/Opensim/Geometry/thumb_distal_lvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/thumb_distal_lvs.vtp rename to Pose2Sim/Opensim/Geometry/thumb_distal_lvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/thumb_distal_rvs.vtp b/Pose2Sim/Opensim/Geometry/thumb_distal_rvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/thumb_distal_rvs.vtp rename to Pose2Sim/Opensim/Geometry/thumb_distal_rvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/thumb_proximal_lvs.vtp b/Pose2Sim/Opensim/Geometry/thumb_proximal_lvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/thumb_proximal_lvs.vtp rename to Pose2Sim/Opensim/Geometry/thumb_proximal_lvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/thumb_proximal_rvs.vtp b/Pose2Sim/Opensim/Geometry/thumb_proximal_rvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/thumb_proximal_rvs.vtp rename to Pose2Sim/Opensim/Geometry/thumb_proximal_rvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/tibia_l.vtp b/Pose2Sim/Opensim/Geometry/tibia_l.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/tibia_l.vtp rename to Pose2Sim/Opensim/Geometry/tibia_l.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/tibia_r.vtp b/Pose2Sim/Opensim/Geometry/tibia_r.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/tibia_r.vtp rename to Pose2Sim/Opensim/Geometry/tibia_r.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/trapezium_lvs.vtp b/Pose2Sim/Opensim/Geometry/trapezium_lvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/trapezium_lvs.vtp rename to Pose2Sim/Opensim/Geometry/trapezium_lvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/trapezium_rvs.vtp b/Pose2Sim/Opensim/Geometry/trapezium_rvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/trapezium_rvs.vtp rename to Pose2Sim/Opensim/Geometry/trapezium_rvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/trapezoid_lvs.vtp b/Pose2Sim/Opensim/Geometry/trapezoid_lvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/trapezoid_lvs.vtp rename to Pose2Sim/Opensim/Geometry/trapezoid_lvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/trapezoid_rvs.vtp b/Pose2Sim/Opensim/Geometry/trapezoid_rvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/trapezoid_rvs.vtp rename to Pose2Sim/Opensim/Geometry/trapezoid_rvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/triquetrum_lvs.vtp b/Pose2Sim/Opensim/Geometry/triquetrum_lvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/triquetrum_lvs.vtp rename to Pose2Sim/Opensim/Geometry/triquetrum_lvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/triquetrum_rvs.vtp b/Pose2Sim/Opensim/Geometry/triquetrum_rvs.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/triquetrum_rvs.vtp rename to Pose2Sim/Opensim/Geometry/triquetrum_rvs.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/ulna_lv.vtp b/Pose2Sim/Opensim/Geometry/ulna_lv.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/ulna_lv.vtp rename to Pose2Sim/Opensim/Geometry/ulna_lv.vtp diff --git a/Pose2Sim/Demo/opensim/Geometry/ulna_rv.vtp b/Pose2Sim/Opensim/Geometry/ulna_rv.vtp similarity index 100% rename from Pose2Sim/Demo/opensim/Geometry/ulna_rv.vtp rename to Pose2Sim/Opensim/Geometry/ulna_rv.vtp diff --git a/Pose2Sim/Empty_project/opensim/IK_Setup_Pose2Sim_Blazepose.xml b/Pose2Sim/Opensim/IK_Setup_Pose2Sim_Blazepose.xml similarity index 100% rename from Pose2Sim/Empty_project/opensim/IK_Setup_Pose2Sim_Blazepose.xml rename to Pose2Sim/Opensim/IK_Setup_Pose2Sim_Blazepose.xml diff --git a/Pose2Sim/Empty_project/opensim/IK_Setup_Pose2Sim_Body135.xml b/Pose2Sim/Opensim/IK_Setup_Pose2Sim_Body135.xml similarity index 100% rename from Pose2Sim/Empty_project/opensim/IK_Setup_Pose2Sim_Body135.xml rename to Pose2Sim/Opensim/IK_Setup_Pose2Sim_Body135.xml diff --git a/Pose2Sim/Empty_project/opensim/IK_Setup_Pose2Sim_Body25.xml b/Pose2Sim/Opensim/IK_Setup_Pose2Sim_Body25.xml similarity index 100% rename from Pose2Sim/Empty_project/opensim/IK_Setup_Pose2Sim_Body25.xml rename to Pose2Sim/Opensim/IK_Setup_Pose2Sim_Body25.xml diff --git a/Pose2Sim/Empty_project/opensim/IK_Setup_Pose2Sim_Body25b.xml b/Pose2Sim/Opensim/IK_Setup_Pose2Sim_Body25b.xml similarity index 100% rename from Pose2Sim/Empty_project/opensim/IK_Setup_Pose2Sim_Body25b.xml rename to Pose2Sim/Opensim/IK_Setup_Pose2Sim_Body25b.xml diff --git a/Pose2Sim/Empty_project/opensim/IK_Setup_Pose2Sim_Coco133.xml b/Pose2Sim/Opensim/IK_Setup_Pose2Sim_Coco133.xml similarity index 100% rename from Pose2Sim/Empty_project/opensim/IK_Setup_Pose2Sim_Coco133.xml rename to Pose2Sim/Opensim/IK_Setup_Pose2Sim_Coco133.xml diff --git a/Pose2Sim/Empty_project/opensim/IK_Setup_Pose2Sim_Coco18.xml b/Pose2Sim/Opensim/IK_Setup_Pose2Sim_Coco18.xml similarity index 100% rename from Pose2Sim/Empty_project/opensim/IK_Setup_Pose2Sim_Coco18.xml rename to Pose2Sim/Opensim/IK_Setup_Pose2Sim_Coco18.xml diff --git a/Pose2Sim/Empty_project/opensim/IK_Setup_Pose2Sim_Halpe26.xml b/Pose2Sim/Opensim/IK_Setup_Pose2Sim_Halpe26.xml similarity index 100% rename from Pose2Sim/Empty_project/opensim/IK_Setup_Pose2Sim_Halpe26.xml rename to Pose2Sim/Opensim/IK_Setup_Pose2Sim_Halpe26.xml diff --git a/Pose2Sim/Empty_project/opensim/IK_Setup_Pose2Sim_Halpe68_136.xml b/Pose2Sim/Opensim/IK_Setup_Pose2Sim_Halpe68_136.xml similarity index 100% rename from Pose2Sim/Empty_project/opensim/IK_Setup_Pose2Sim_Halpe68_136.xml rename to Pose2Sim/Opensim/IK_Setup_Pose2Sim_Halpe68_136.xml diff --git a/Pose2Sim/Empty_project/opensim/Model_Pose2Sim_BlazePose.osim b/Pose2Sim/Opensim/Model_Pose2Sim_BlazePose.osim similarity index 100% rename from Pose2Sim/Empty_project/opensim/Model_Pose2Sim_BlazePose.osim rename to Pose2Sim/Opensim/Model_Pose2Sim_BlazePose.osim diff --git a/Pose2Sim/Empty_project/opensim/Model_Pose2Sim_Body135.osim b/Pose2Sim/Opensim/Model_Pose2Sim_Body135.osim similarity index 100% rename from Pose2Sim/Empty_project/opensim/Model_Pose2Sim_Body135.osim rename to Pose2Sim/Opensim/Model_Pose2Sim_Body135.osim diff --git a/Pose2Sim/Empty_project/opensim/Model_Pose2Sim_Body25.osim b/Pose2Sim/Opensim/Model_Pose2Sim_Body25.osim similarity index 100% rename from Pose2Sim/Empty_project/opensim/Model_Pose2Sim_Body25.osim rename to Pose2Sim/Opensim/Model_Pose2Sim_Body25.osim diff --git a/Pose2Sim/Empty_project/opensim/Model_Pose2Sim_Body25b.osim b/Pose2Sim/Opensim/Model_Pose2Sim_Body25b.osim similarity index 100% rename from Pose2Sim/Empty_project/opensim/Model_Pose2Sim_Body25b.osim rename to Pose2Sim/Opensim/Model_Pose2Sim_Body25b.osim diff --git a/Pose2Sim/Empty_project/opensim/Model_Pose2Sim_Body25b_contacts_muscles.osim b/Pose2Sim/Opensim/Model_Pose2Sim_Body25b_contacts_muscles.osim similarity index 100% rename from Pose2Sim/Empty_project/opensim/Model_Pose2Sim_Body25b_contacts_muscles.osim rename to Pose2Sim/Opensim/Model_Pose2Sim_Body25b_contacts_muscles.osim diff --git a/Pose2Sim/Empty_project/opensim/Model_Pose2Sim_Coco133.osim b/Pose2Sim/Opensim/Model_Pose2Sim_Coco133.osim similarity index 100% rename from Pose2Sim/Empty_project/opensim/Model_Pose2Sim_Coco133.osim rename to Pose2Sim/Opensim/Model_Pose2Sim_Coco133.osim diff --git a/Pose2Sim/Empty_project/opensim/Model_Pose2Sim_Coco18.osim b/Pose2Sim/Opensim/Model_Pose2Sim_Coco18.osim similarity index 100% rename from Pose2Sim/Empty_project/opensim/Model_Pose2Sim_Coco18.osim rename to Pose2Sim/Opensim/Model_Pose2Sim_Coco18.osim diff --git a/Pose2Sim/Empty_project/opensim/Model_Pose2Sim_Halpe26.osim b/Pose2Sim/Opensim/Model_Pose2Sim_Halpe26.osim similarity index 100% rename from Pose2Sim/Empty_project/opensim/Model_Pose2Sim_Halpe26.osim rename to Pose2Sim/Opensim/Model_Pose2Sim_Halpe26.osim diff --git a/Pose2Sim/Empty_project/opensim/Model_Pose2Sim_Halpe68_136.osim b/Pose2Sim/Opensim/Model_Pose2Sim_Halpe68_136.osim similarity index 100% rename from Pose2Sim/Empty_project/opensim/Model_Pose2Sim_Halpe68_136.osim rename to Pose2Sim/Opensim/Model_Pose2Sim_Halpe68_136.osim diff --git a/Pose2Sim/Empty_project/opensim/Scaling_Setup_Pose2Sim_Blazepose.xml b/Pose2Sim/Opensim/Scaling_Setup_Pose2Sim_Blazepose.xml similarity index 100% rename from Pose2Sim/Empty_project/opensim/Scaling_Setup_Pose2Sim_Blazepose.xml rename to Pose2Sim/Opensim/Scaling_Setup_Pose2Sim_Blazepose.xml diff --git a/Pose2Sim/Empty_project/opensim/Scaling_Setup_Pose2Sim_Body135.xml b/Pose2Sim/Opensim/Scaling_Setup_Pose2Sim_Body135.xml similarity index 100% rename from Pose2Sim/Empty_project/opensim/Scaling_Setup_Pose2Sim_Body135.xml rename to Pose2Sim/Opensim/Scaling_Setup_Pose2Sim_Body135.xml diff --git a/Pose2Sim/Empty_project/opensim/Scaling_Setup_Pose2Sim_Body25.xml b/Pose2Sim/Opensim/Scaling_Setup_Pose2Sim_Body25.xml similarity index 100% rename from Pose2Sim/Empty_project/opensim/Scaling_Setup_Pose2Sim_Body25.xml rename to Pose2Sim/Opensim/Scaling_Setup_Pose2Sim_Body25.xml diff --git a/Pose2Sim/Empty_project/opensim/Scaling_Setup_Pose2Sim_Body25b.xml b/Pose2Sim/Opensim/Scaling_Setup_Pose2Sim_Body25b.xml similarity index 100% rename from Pose2Sim/Empty_project/opensim/Scaling_Setup_Pose2Sim_Body25b.xml rename to Pose2Sim/Opensim/Scaling_Setup_Pose2Sim_Body25b.xml diff --git a/Pose2Sim/Empty_project/opensim/Scaling_Setup_Pose2Sim_Coco133.xml b/Pose2Sim/Opensim/Scaling_Setup_Pose2Sim_Coco133.xml similarity index 100% rename from Pose2Sim/Empty_project/opensim/Scaling_Setup_Pose2Sim_Coco133.xml rename to Pose2Sim/Opensim/Scaling_Setup_Pose2Sim_Coco133.xml diff --git a/Pose2Sim/Empty_project/opensim/Scaling_Setup_Pose2Sim_Coco18.xml b/Pose2Sim/Opensim/Scaling_Setup_Pose2Sim_Coco18.xml similarity index 100% rename from Pose2Sim/Empty_project/opensim/Scaling_Setup_Pose2Sim_Coco18.xml rename to Pose2Sim/Opensim/Scaling_Setup_Pose2Sim_Coco18.xml diff --git a/Pose2Sim/Empty_project/opensim/Scaling_Setup_Pose2Sim_Halpe26.xml b/Pose2Sim/Opensim/Scaling_Setup_Pose2Sim_Halpe26.xml similarity index 100% rename from Pose2Sim/Empty_project/opensim/Scaling_Setup_Pose2Sim_Halpe26.xml rename to Pose2Sim/Opensim/Scaling_Setup_Pose2Sim_Halpe26.xml diff --git a/Pose2Sim/Empty_project/opensim/Scaling_Setup_Pose2Sim_Halpe68_136.xml b/Pose2Sim/Opensim/Scaling_Setup_Pose2Sim_Halpe68_136.xml similarity index 100% rename from Pose2Sim/Empty_project/opensim/Scaling_Setup_Pose2Sim_Halpe68_136.xml rename to Pose2Sim/Opensim/Scaling_Setup_Pose2Sim_Halpe68_136.xml diff --git a/Pose2Sim/Pose2Sim.py b/Pose2Sim/Pose2Sim.py index 0088ac9..dd32851 100644 --- a/Pose2Sim/Pose2Sim.py +++ b/Pose2Sim/Pose2Sim.py @@ -60,11 +60,18 @@ __status__ = "Development" ## FUNCTIONS def read_config_file(config): ''' - Read configation file. + Read Session configuration file, and overwrite it with Participant and Trial + configuration dicts if exist. ''' - config_dict = toml.load(config) - return config_dict + trial_config_dict = toml.load(config) + participant_config_dict = toml.load('BLa') + session_config_dict = toml.load(config) + + session_config_dict.update(participant_config_dict) + session_config_dict.update(trial_config_dict) + + return session_config_dict def base_params(config_dict): @@ -72,8 +79,7 @@ def base_params(config_dict): Retrieve sequence name and frames to be analyzed. ''' - project_dir = config_dict.get('project').get('project_dir') - if project_dir == '': project_dir = os.getcwd() + project_dir = os.getcwd() frame_range = config_dict.get('project').get('frame_range') seq_name = os.path.basename(project_dir) frames = ["all frames" if frame_range == [] else f"frames {frame_range[0]} to {frame_range[1]}"][0] @@ -86,7 +92,40 @@ def base_params(config_dict): return project_dir, seq_name, frames -def poseEstimation(config=os.path.join('User', 'Config.toml')): +def calibration(config='Config.toml'): + ''' + Cameras calibration from checkerboards or from qualisys files. + + config can either be a path or a dictionary (for batch processing) + ''' + + from Pose2Sim.calibration import calibrate_cams_all + + if type(config)==dict: + config_dict = config + else: + config_dict = read_config_file(config) + + ## Rechercher dans sublevels jusqu'à ce qu'on n'ait plus de config.toml + # Créer une boucle avec un config_dict différent pour chaque trial + # Exclure from batch analysis + + + project_dir, seq_name, frames = base_params(config_dict) + + logging.info("\n\n---------------------------------------------------------------------") + logging.info("Camera calibration") + logging.info("---------------------------------------------------------------------") + logging.info(f"\nProject directory: {project_dir}") + start = time.time() + + calibrate_cams_all(config_dict) + + end = time.time() + logging.info(f'Calibration took {end-start:.2f} s.') + + +def poseEstimation(config='Config.toml'): ''' Estimate pose using BlazePose, OpenPose, AlphaPose, or DeepLabCut. @@ -114,36 +153,9 @@ def poseEstimation(config=os.path.join('User', 'Config.toml')): end = time.time() logging.info(f'Pose estimation took {end-start:.2f} s.') - - -def calibration(config=os.path.join('User', 'Config.toml')): - ''' - Cameras calibration from checkerboards or from qualisys files. - - config can either be a path or a dictionary (for batch processing) - ''' - - from Pose2Sim.calibration import calibrate_cams_all - - if type(config)==dict: - config_dict = config - else: - config_dict = read_config_file(config) - project_dir, seq_name, frames = base_params(config_dict) - - logging.info("\n\n---------------------------------------------------------------------") - logging.info("Camera calibration") - logging.info("---------------------------------------------------------------------") - logging.info(f"\nProject directory: {project_dir}") - start = time.time() - - calibrate_cams_all(config_dict) - - end = time.time() - logging.info(f'Calibration took {end-start:.2f} s.') -def synchronization(config=os.path.join('User', 'Config.toml')): +def synchronization(config='Config.toml'): ''' Synchronize cameras if needed. @@ -173,7 +185,7 @@ def synchronization(config=os.path.join('User', 'Config.toml')): logging.info(f'Synchronization took {end-start:.2f} s.') -def personAssociation(config=os.path.join('User', 'Config.toml')): +def personAssociation(config='Config.toml'): ''' Tracking of the person of interest in case of multiple persons detection. Needs a calibration file. @@ -201,7 +213,7 @@ def personAssociation(config=os.path.join('User', 'Config.toml')): logging.info(f'Tracking took {end-start:.2f} s.') -def triangulation(config=os.path.join('User', 'Config.toml')): +def triangulation(config='Config.toml'): ''' Robust triangulation of 2D points coordinates. @@ -228,7 +240,7 @@ def triangulation(config=os.path.join('User', 'Config.toml')): logging.info(f'Triangulation took {end-start:.2f} s.') -def filtering(config=os.path.join('User', 'Config.toml')): +def filtering(config='Config.toml'): ''' Filter trc 3D coordinates. @@ -251,7 +263,7 @@ def filtering(config=os.path.join('User', 'Config.toml')): filter_all(config_dict) -def scalingModel(config=os.path.join('User', 'Config.toml')): +def scalingModel(config='Config.toml'): ''' Uses OpenSim to scale a model based on a static 3D pose. @@ -281,7 +293,7 @@ def scalingModel(config=os.path.join('User', 'Config.toml')): logging.info(f'Model scaling took {end-start:.2f} s.') -def inverseKinematics(config=os.path.join('User', 'Config.toml')): +def inverseKinematics(config='Config.toml'): ''' Uses OpenSim to perform inverse kinematics. diff --git a/Pose2Sim/Utilities/synchronize_cams_draft.py b/Pose2Sim/Utilities/synchronize_cams_draft.py index 228f98c..f5d5a56 100644 --- a/Pose2Sim/Utilities/synchronize_cams_draft.py +++ b/Pose2Sim/Utilities/synchronize_cams_draft.py @@ -37,7 +37,7 @@ cut_off_frequency = 10 # cut-off frequency for a 4th order low-pass Butterworth # Vertical speeds (on X, Y, or Z axis, or 2D speeds) speed_kind = 'y' # 'x', 'y', 'z', or '2D' -vmax = 20 # pxs +vmax = 20 # px/s cam1_nb = 4 cam2_nb = 3 diff --git a/Pose2Sim/calibration.py b/Pose2Sim/calibration.py index 144941f..a70e8de 100644 --- a/Pose2Sim/calibration.py +++ b/Pose2Sim/calibration.py @@ -467,8 +467,8 @@ def calib_board_fun(calib_dir, intrinsics_config_dict, extrinsics_config_dict): INPUTS: - calib_dir: directory containing intrinsic and extrinsic folders, each populated with camera directories - - intrinsics_config_dict: dictionary of intrinsics parameters (intrinsics_board_type, overwrite_intrinsics, show_detection_intrinsics, intrinsics_extension, extract_every_N_sec, intrinsics_corners_nb, intrinsics_square_size, intrinsics_marker_size, intrinsics_aruco_dict) - - extrinsics_config_dict: dictionary of extrinsics parameters (extrinsics_board_type, calculate_extrinsics, show_detection_extrinsics, extrinsics_extension, extrinsics_corners_nb, extrinsics_square_size, extrinsics_marker_size, extrinsics_aruco_dict, object_coords_3d) + - intrinsics_config_dict: dictionary of intrinsics parameters (overwrite_intrinsics, show_detection_intrinsics, intrinsics_extension, extract_every_N_sec, intrinsics_corners_nb, intrinsics_square_size, intrinsics_marker_size, intrinsics_aruco_dict) + - extrinsics_config_dict: dictionary of extrinsics parameters (calculate_extrinsics, show_detection_extrinsics, extrinsics_extension, extrinsics_corners_nb, extrinsics_square_size, extrinsics_marker_size, extrinsics_aruco_dict, object_coords_3d) OUTPUTS: - ret: residual reprojection error in _px_: list of floats @@ -528,7 +528,7 @@ def calibrate_intrinsics(calib_dir, intrinsics_config_dict): INPUTS: - calib_dir: directory containing intrinsic and extrinsic folders, each populated with camera directories - - intrinsics_config_dict: dictionary of intrinsics parameters (intrinsics_board_type, overwrite_intrinsics, show_detection_intrinsics, intrinsics_extension, extract_every_N_sec, intrinsics_corners_nb, intrinsics_square_size, intrinsics_marker_size, intrinsics_aruco_dict) + - intrinsics_config_dict: dictionary of intrinsics parameters (overwrite_intrinsics, show_detection_intrinsics, intrinsics_extension, extract_every_N_sec, intrinsics_corners_nb, intrinsics_square_size, intrinsics_marker_size, intrinsics_aruco_dict) OUTPUTS: - D: distorsion: list of arrays of floats @@ -1201,8 +1201,7 @@ def calibrate_cams_all(config): # Read config project_dir = config.get('project').get('project_dir') if project_dir == '': project_dir = os.getcwd() - calib_folder_name = config.get('project').get('calib_folder_name') - calib_dir = os.path.join(project_dir, calib_folder_name) + calib_dir = os.path.join(project_dir, 'Calibration') calib_type = config.get('calibration').get('calibration_type') if calib_type=='convert': @@ -1233,6 +1232,9 @@ def calibrate_cams_all(config): list_dir_noext = [os.path.splitext(f)[0] for f in list_dir if os.path.splitext(f)[1]==''] file_to_convert_path = [os.path.join(calib_dir,f) for f in list_dir_noext if os.path.isfile(os.path.join(calib_dir, f))] binning_factor = 1 + elif convert_filetype=='biocv' or convert_filetype=='biocv': # no conversion needed, skips this stage + logging.info(f'\n--> No conversion needed from AniPose nor from FreeMocap. Calibration skipped.\n') + return else: convert_ext = '???' file_to_convert_path = [''] @@ -1249,11 +1251,10 @@ def calibrate_cams_all(config): elif calib_type=='calculate': calculate_method = config.get('calibration').get('calculate').get('calculate_method') if calculate_method=='board': - intrinsics_board_type = config.get('calibration').get('calculate').get('board').get('intrinsics').get('intrinsics_board_type') intrinsics_config_dict = config.get('calibration').get('calculate').get('board').get('intrinsics') extrinsics_board_type = config.get('calibration').get('calculate').get('board').get('extrinsics').get('extrinsics_board_type') extrinsics_config_dict = config.get('calibration').get('calculate').get('board').get('extrinsics') - calib_output_path = os.path.join(calib_dir, f'Calib_int{intrinsics_board_type}_ext{extrinsics_board_type}.toml') + calib_output_path = os.path.join(calib_dir, f'Calib_{extrinsics_board_type}.toml') calib_full_type = '_'.join([calib_type, calculate_method]) args_calib_fun = [calib_dir, intrinsics_config_dict, extrinsics_config_dict] diff --git a/Pose2Sim/filtering.py b/Pose2Sim/filtering.py index 5d2c9f0..1709bdd 100644 --- a/Pose2Sim/filtering.py +++ b/Pose2Sim/filtering.py @@ -445,25 +445,21 @@ def filter_all(config): # Read config project_dir = config.get('project').get('project_dir') if project_dir == '': project_dir = os.getcwd() - pose_tracked_folder_name = config.get('project').get('poseAssociated_folder_name') - pose_folder_name = config.get('project').get('pose_folder_name') try: - pose_tracked_dir = os.path.join(project_dir, pose_tracked_folder_name) + pose_tracked_dir = os.path.join(project_dir, 'pose-associated') os.listdir(pose_tracked_dir) pose_dir = pose_tracked_dir except: - pose_dir = os.path.join(project_dir, pose_folder_name) - json_folder_extension = config.get('project').get('pose_json_folder_extension') + pose_dir = os.path.join(project_dir, 'pose') frame_range = config.get('project').get('frame_range') seq_name = os.path.basename(project_dir) - pose3d_folder_name = config.get('project').get('pose3d_folder_name') - pose3d_dir = os.path.join(project_dir, pose3d_folder_name) + pose3d_dir = os.path.join(project_dir, 'pose-3d') display_figures = config.get('filtering').get('display_figures') filter_type = config.get('filtering').get('type') # Frames range pose_listdirs_names = next(os.walk(pose_dir))[1] - json_dirs_names = [k for k in pose_listdirs_names if json_folder_extension in k] + json_dirs_names = [k for k in pose_listdirs_names if 'json' in k] json_files_names = [fnmatch.filter(os.listdir(os.path.join(pose_dir, js_dir)), '*.json') for js_dir in json_dirs_names] f_range = [[0,min([len(j) for j in json_files_names])] if frame_range==[] else frame_range][0] diff --git a/Pose2Sim/personAssociation.py b/Pose2Sim/personAssociation.py index 784cd11..799d723 100644 --- a/Pose2Sim/personAssociation.py +++ b/Pose2Sim/personAssociation.py @@ -194,12 +194,10 @@ def recap_tracking(config, error, nb_cams_excluded): # Read config project_dir = config.get('project').get('project_dir') if project_dir == '': project_dir = os.getcwd() - poseTracked_folder_name = config.get('project').get('poseAssociated_folder_name') - calib_folder_name = config.get('project').get('calib_folder_name') tracked_keypoint = config.get('personAssociation').get('tracked_keypoint') error_threshold_tracking = config.get('personAssociation').get('error_threshold_tracking') - poseTracked_dir = os.path.join(project_dir, poseTracked_folder_name) - calib_dir = os.path.join(project_dir, calib_folder_name) + poseTracked_dir = os.path.join(project_dir, 'pose-associated') + calib_dir = os.path.join(project_dir, 'Calibration') calib_file = glob.glob(os.path.join(calib_dir, '*.toml'))[0] # Error @@ -243,18 +241,14 @@ def track_2d_all(config): # Read config project_dir = config.get('project').get('project_dir') if project_dir == '': project_dir = os.getcwd() - calib_folder_name = config.get('project').get('calib_folder_name') - poseTracked_folder_name = config.get('project').get('poseAssociated_folder_name') - pose_folder_name = config.get('project').get('pose_folder_name') pose_model = config.get('pose').get('pose_model') tracked_keypoint = config.get('personAssociation').get('tracked_keypoint') - json_folder_extension = config.get('project').get('pose_json_folder_extension') frame_range = config.get('project').get('frame_range') - calib_dir = os.path.join(project_dir, calib_folder_name) + calib_dir = os.path.join(project_dir, 'Calibration') calib_file = glob.glob(os.path.join(calib_dir, '*.toml'))[0] - pose_dir = os.path.join(project_dir, pose_folder_name) - poseTracked_dir = os.path.join(project_dir, poseTracked_folder_name) + pose_dir = os.path.join(project_dir, 'pose') + poseTracked_dir = os.path.join(project_dir, 'pose-associated') # projection matrix from toml calibration file P = computeP(calib_file) @@ -274,7 +268,7 @@ def track_2d_all(config): # 2d-pose files selection pose_listdirs_names = next(os.walk(pose_dir))[1] pose_listdirs_names = natural_sort(pose_listdirs_names) - json_dirs_names = [k for k in pose_listdirs_names if json_folder_extension in k] + json_dirs_names = [k for k in pose_listdirs_names if 'json' in k] json_files_names = [fnmatch.filter(os.listdir(os.path.join(pose_dir, js_dir)), '*.json') for js_dir in json_dirs_names] json_files_names = [natural_sort(j) for j in json_files_names] json_files = [[os.path.join(pose_dir, j_dir, j_file) for j_file in json_files_names[j]] for j, j_dir in enumerate(json_dirs_names)] diff --git a/Pose2Sim/triangulation.py b/Pose2Sim/triangulation.py index 6cecf54..242b279 100644 --- a/Pose2Sim/triangulation.py +++ b/Pose2Sim/triangulation.py @@ -145,8 +145,7 @@ def make_trc(config, Q, keypoints_names, f_range): if project_dir == '': project_dir = os.getcwd() frame_rate = config.get('project').get('frame_rate') seq_name = os.path.basename(project_dir) - pose3d_folder_name = config.get('project').get('pose3d_folder_name') - pose3d_dir = os.path.join(project_dir, pose3d_folder_name) + pose3d_dir = os.path.join(project_dir, 'pose-3d') trc_f = f'{seq_name}_{f_range[0]}-{f_range[1]}.trc' @@ -196,8 +195,7 @@ def recap_triangulate(config, error, nb_cams_excluded, keypoints_names, cam_excl # Read config project_dir = config.get('project').get('project_dir') if project_dir == '': project_dir = os.getcwd() - calib_folder_name = config.get('project').get('calib_folder_name') - calib_dir = os.path.join(project_dir, calib_folder_name) + calib_dir = os.path.join(project_dir, 'Calibration') calib_file = glob.glob(os.path.join(calib_dir, '*.toml'))[0] calib = toml.load(calib_file) cam_names = np.array([calib[c].get('name') for c in list(calib.keys())]) @@ -408,20 +406,16 @@ def triangulate_all(config): # Read config project_dir = config.get('project').get('project_dir') if project_dir == '': project_dir = os.getcwd() - calib_folder_name = config.get('project').get('calib_folder_name') pose_model = config.get('pose').get('pose_model') - pose_folder_name = config.get('project').get('pose_folder_name') - json_folder_extension = config.get('project').get('pose_json_folder_extension') frame_range = config.get('project').get('frame_range') likelihood_threshold = config.get('triangulation').get('likelihood_threshold') interpolation_kind = config.get('triangulation').get('interpolation') interp_gap_smaller_than = config.get('triangulation').get('interp_if_gap_smaller_than') show_interp_indices = config.get('triangulation').get('show_interp_indices') - pose_dir = os.path.join(project_dir, pose_folder_name) - poseTracked_folder_name = config.get('project').get('poseAssociated_folder_name') - calib_dir = os.path.join(project_dir, calib_folder_name) + pose_dir = os.path.join(project_dir, 'pose') + calib_dir = os.path.join(project_dir, 'Calibration') calib_file = glob.glob(os.path.join(calib_dir, '*.toml'))[0] - poseTracked_dir = os.path.join(project_dir, poseTracked_folder_name) + poseTracked_dir = os.path.join(project_dir, 'pose-associated') # Projection matrix from toml calibration file P = computeP(calib_file) @@ -444,7 +438,7 @@ def triangulate_all(config): # 2d-pose files selection pose_listdirs_names = next(os.walk(pose_dir))[1] pose_listdirs_names = natural_sort(pose_listdirs_names) - json_dirs_names = [k for k in pose_listdirs_names if json_folder_extension in k] + json_dirs_names = [k for k in pose_listdirs_names if 'json' in k] try: json_files_names = [fnmatch.filter(os.listdir(os.path.join(poseTracked_dir, js_dir)), '*.json') for js_dir in json_dirs_names] json_files_names = [natural_sort(j) for j in json_files_names] diff --git a/README.md b/README.md index 9f7b9d0..8ee9173 100644 --- a/README.md +++ b/README.md @@ -13,9 +13,9 @@ # Pose2Sim -> **_News_: Version 0.4 released:** \ -**Calibration used to be the main stumbling block for users: it should be easier and better now!**\ -To upgrade, type `pip install pose2sim --upgrade`. You will need to update your [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file.\ +> **_News_: Version 0.5 released:** \ +**New folder structure to allow batch processing!**\ +To upgrade, type `pip install pose2sim --upgrade`.\ *N.B.:* As always, I am more than happy to welcome contributors (see [How to contribute](#how-to-contribute)). `Pose2Sim` provides a workflow for 3D markerless kinematics, as an alternative to the more usual marker-based motion capture methods. It aims to provide a free tool to obtain research-grade results from consumer-grade equipment. Any combination of phone, webcam, gopro, etc can be used. @@ -35,15 +35,16 @@ If you can only use one single camera and don't mind losing some accuracy, pleas 2. [Demonstration Part-1: Build 3D TRC file on Python](#demonstration-part-1-build-3d-trc-file-on-python) 3. [Demonstration Part-2: Obtain 3D joint angles with OpenSim](#demonstration-part-2-obtain-3d-joint-angles-with-opensim) 2. [Use on your own data](#use-on-your-own-data) - 1. [Prepare for running on your own data](#prepare-for-running-on-your-own-data) - 2. [2D pose estimation](#2d-pose-estimation) + 1. [Folder structure](#folder-structure) + 2. [Camera calibration](#camera-calibration) + 1. [Convert from Qualisys, Optitrack, Vicon, OpenCap, EasyMocap, or bioCV](#convert-from-qualisys-optitrack-vicon-opencap-easymocap-or-biocv) + 2. [Calculate from scratch](#calculate-from-scratch) + 1. + 3. [2D pose estimation](#2d-pose-estimation) 1. [With OpenPose](#with-openpose) 2. [With Mediapipe](#with-mediapipe) 3. [With DeepLabCut](#with-deeplabcut) 4. [With AlphaPose](#with-alphapose) - 3. [Camera calibration](#camera-calibration) - 1. [Convert from Qualisys, Optitrack, Vicon, OpenCap, EasyMocap, or bioCV](#convert-from-qualisys-optitrack-vicon-opencap-easymocap-or-biocv) - 2. [Calculate from scratch](#calculate-from-scratch) 4. [Camera synchronization](#camera-synchronization) 5. [Tracking, Triangulating, Filtering](#tracking-triangulating-filtering) 1. [Associate persons across cameras](#associate-persons-across-cameras) @@ -90,7 +91,7 @@ If you don't use Anaconda, type `python -V` in terminal to make sure python>=3.8 > _**This demonstration provides an example experiment of a person balancing on a beam, filmed with 4 calibrated cameras processed with OpenPose.**_ Open a terminal, enter `pip show pose2sim`, report package location. \ -Copy this path and go to the Demo folder with `cd \pose2sim\Demo`. \ +Copy this path and go to the Demo folder with `cd \pose2sim\Demo\S00_Demo_Session`. \ Type `ipython`, and test the following code: ``` python from Pose2Sim import Pose2Sim @@ -122,14 +123,16 @@ Results are stored as .trc files in the `Demo/pose-3d` directory. # Use on your own data -> _**Deeper explanations and instructions are given below.**_ +> _**Deeper explanations and instructions are given below.**_ \ +> N.B.: If a step is not relevant for your use case (synchronization, person association, etc), you can skip it. -## Prepare for running on your own data +## Folder structure > _**Get ready.**_ - 1. Find your `Pose2Sim\Empty_project`, copy-paste it where you like and give it the name of your choice. + 1. Open a terminal, enter `pip show pose2sim`, report package location. \ + Copy this path and go to the Demo folder with `cd \pose2sim\Demo\S01_Empty_Session`. 2. Edit the [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file as needed, **especially regarding the path to your project**. - 3. Populate the `raw-2d`folder with your videos. + 3. Populate the `videos` folder with your videos.
        Project
@@ -140,7 +143,7 @@ Results are stored as .trc files in the `Demo/pose-3d` directory.
        │    ├──Scaling_Setup_Pose2Sim_Body25b.xml
        │    └──IK_Setup_Pose2Sim_Body25b.xml
        │        
-       ├── raw
+       ├── videos
        │    ├──vid_cam1.mp4 (or other extension)
        │    ├──...
        │    └──vid_camN.mp4
@@ -149,6 +152,139 @@ Results are stored as .trc files in the `Demo/pose-3d` directory.
            └──Config.toml
        
     
+
+## Camera calibration
+> _**Calculate camera intrinsic properties and extrinsic locations and positions.\
+> Convert a preexisting calibration file, or calculate intrinsic and extrinsic parameters from scratch.**_ \
+> _**N.B.:**_ You can visualize camera calibration in 3D with my (experimental) [Maya-Mocap tool](https://github.com/davidpagnon/Maya-Mocap). 
+
+Open an Anaconda prompt or a terminal, type `ipython`.\
+By default, `calibration()` will look for `Config.toml` in the `User` folder of your current directory. If you want to store it somewhere else (e.g. in your data directory), specify this path as an argument: `Pose2Sim.calibration(r'path_to_config.toml')`.
+
+``` python
+from Pose2Sim import Pose2Sim
+Pose2Sim.calibration()
+```
+
+Output:\
+
+
+
+### Convert from Qualisys, Optitrack, Vicon, OpenCap, EasyMocap, or bioCV
+
+If you already have a calibration file, set `calibration_type` type to `convert` in your [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file.
+- **From [Qualisys](https://www.qualisys.com):**
+  - Export calibration to `.qca.txt` within QTM.
+  - Copy it in the `calibration` Pose2Sim folder.
+  - set `convert_from` to 'qualisys' in your [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file. Change `binning_factor` to 2 if you film in 540p.
+- **From [Optitrack](https://optitrack.com/):** Exporting calibration will be available in Motive 3.2. In the meantime:
+  - Calculate intrinsics with a board (see next section).
+  - Use their C++ API [to retrieve extrinsic properties](https://docs.optitrack.com/developer-tools/motive-api/motive-api-function-reference#tt_cameraxlocation). Translation can be copied as is in your `Calib.toml` file, but TT_CameraOrientationMatrix first needs to be [converted to a Rodrigues vector](https://docs.opencv.org/3.4/d9/d0c/group__calib3d.html#ga61585db663d9da06b68e70cfbf6a1eac) with OpenCV. See instructions [here](https://github.com/perfanalytics/pose2sim/issues/28).
+  - Use the `Calib.toml` file as is and do not run Pose2Sim.calibration()
+- **From [Vicon](http://www.vicon.com/Software/Nexus):**  
+  - Copy your `.xcp` Vicon calibration file to the Pose2Sim `Calibration` folder.
+  - set `convert_from` to 'vicon' in your [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file. No other setting is needed.
+- **From [OpenCap](https://www.opencap.ai/):**  
+  - Copy your `.pickle` OpenCap calibration files to the Pose2Sim `Calibration` folder.
+  - set `convert_from` to 'opencap' in your [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file. No other setting is needed.
+- **From [EasyMocap](https://github.com/zju3dv/EasyMocap/):**  
+  - Copy your `intri.yml` and `extri.yml` files to the Pose2Sim `Calibration` folder.
+  - set `convert_from` to 'easymocap' in your [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file. No other setting is needed.
+- **From [bioCV](https://github.com/camera-mc-dev/.github/blob/main/profile/mocapPipe.md):**  
+  - Copy your bioCV calibration files (no extension) to the Pose2Sim `Calibration` folder.
+  - set `convert_from` to 'biocv' in your [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file. No other setting is needed.
+- **From [AniPose](https://github.com/lambdaloop/anipose) or [FreeMocap](https://github.com/freemocap/freemocap):**  
+  - Copy your `.toml` calibration file to the Pose2Sim `Calibration` folder.
+  - Calibration can be skipped since Pose2Sim uses the same [Aniposelib](https://anipose.readthedocs.io/en/latest/aniposelibtutorial.html) format.
+
+
+### Calculate from scratch
+
+> _**Calculate calibration parameters with a checkerboard, with measurements on the scene, or automatically with detected keypoints.**_\
+> Take heart, it is not that complicated once you get the hang of it!
+
+  > *N.B.:* Try the calibration tool on the Demo by changing `calibration_type` to `calculate` in [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml).\
+  For the sake of practicality, there are voluntarily few board images for intrinsic calibration, and few points to click for extrinsic calibration. In spite of this, your reprojection error should be under 1-2 cm, which [does not hinder the quality of kinematic results in practice](https://www.mdpi.com/1424-8220/21/19/6530/htm#:~:text=Angle%20results%20were,Table%203).).
+  
+  - **Calculate intrinsic parameters with a checkerboard:**
+
+    > *N.B.:* _Intrinsic parameters:_ camera properties (focal length, optical center, distortion), usually need to be calculated only once in their lifetime. In theory, cameras with same model and same settings will have identical intrinsic parameters.\
+    > *N.B.:* If you already calculated intrinsic parameters earlier, you can skip this step. Copy your intrinsic parameters (`size`, `mat`, and `dist`) in a new `Calib*.toml` file, and set `overwrite_intrinsics` to false. Run Demo to obtain an example `Calib.toml` file.
+
+    - Create a folder for each camera in your `calibration\intrinsics` folder.
+    - For each camera, film a checkerboard or a charucoboard. Either the board or the camera can be moved.
+    - Adjust parameters in the [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file.
+    - Make sure that the board:
+      - is filmed from different angles, covers a large part of the video frame, and is in focus.
+      - is flat, without reflections, surrounded by a white border, and is not rotationally invariant (Nrows ≠ Ncols, and Nrows odd if Ncols even).
+    - A common error is to specify the external, instead of the internal number of corners. This may be one less than you would intuitively think. 
+    
+    
+
+    ***Intrinsic calibration error should be below 0.5 px.***
+        
+- **Calculate extrinsic parameters:** 
+
+  > *N.B.:* _Extrinsic parameters:_ camera placement in space (position and orientation), need to be calculated every time a camera is moved. Can be calculated from a board, or from points in the scene with known coordinates.
+
+  - Create a folder for each camera in your `calibration\extrinsics` folder.
+  - Once your cameras are in place, shortly film either a board laid on the floor, or the raw scene\
+  (only one frame is needed, but do not just take a photo unless you are sure it does not change the image format).
+  - Adjust parameters in the [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file.
+  - Then,
+    - **With a checkerboard:**\
+      Make sure that it is seen by all cameras. \
+      It should preferably be larger than the one used for intrinsics, as results will not be very accurate out of the covered zone.
+    - **With scene measurements** (more flexible and potentially more accurate if points are spread out):\
+      Manually measure the 3D coordinates of 10 or more points in the scene (tiles, lines on wall, boxes, treadmill dimensions, etc). These points should be as spread out as possible.\
+      Then you will click on the corresponding image points for each view.
+    - **With keypoints:**\
+      For a more automatic calibration, OpenPose keypoints could also be used for calibration.\
+      **COMING SOON!**
+
+  
+  
+  ***Extrinsic calibration error should be below 1 cm, but depending on your application, results will still be potentially acceptable up to 2.5 cm.***
+
+
+
+ The project hierarchy becomes: (CLICK TO SHOW) +
+   Project
+   │
+   ├──calibration
+   │   ├──intrinsics
+   │   │  ├──int_cam1_img
+   │   │  ├──...
+   │   │  └──int_camN_img
+   │   ├──extrinsics
+   │   │  ├──ext_cam1_img
+   │   │  ├──...
+   │   │  └──ext_camN_img
+   │   └──Calib.toml
+   │
+   ├──opensim
+   │    ├──Geometry
+   │    ├──Model_Pose2Sim_Body25b.osim
+   │    ├──Scaling_Setup_Pose2Sim_Body25b.xml
+   │    └──IK_Setup_Pose2Sim_Body25b.xml
+   │
+   ├──pose-2d
+   │    ├──pose_cam1_json
+   │    ├──...
+   │    └──pose_camN_json
+   │        
+   ├── videos
+   │    ├──vid_cam1.mp4
+   │    ├──...
+   │    └──vid_camN.mp4
+   │
+   └──User
+       └──Config.toml
+   
+
+ + ## 2D pose estimation > _**Estimate 2D pose from images with Openpose or another pose estimation solution.**_ \ N.B.: First film a short static pose that will be used for scaling the OpenSim model (A-pose for example), and then film your motions of interest.\ @@ -157,9 +293,9 @@ N.B.: Note that the names of your camera folders must follow the same order as i ### With OpenPose: The accuracy and robustness of Pose2Sim have been thoroughly assessed only with OpenPose, and especially with the BODY_25B model. Consequently, we recommend using this 2D pose estimation solution. See [OpenPose repository](https://github.com/CMU-Perceptual-Computing-Lab/openpose) for installation and running. * Open a command prompt in your **OpenPose** directory. \ - Launch OpenPose for each raw image folder: + Launch OpenPose for each `videos` folder: ``` cmd - bin\OpenPoseDemo.exe --model_pose BODY_25B --video \raw-2d\vid_cam1.mp4 --write_json \pose-2d\pose_cam1_json + bin\OpenPoseDemo.exe --model_pose BODY_25B --video \videos\vid_cam1.mp4 --write_json \pose\pose_cam1_json ``` * The [BODY_25B model](https://github.com/CMU-Perceptual-Computing-Lab/openpose_train/tree/master/experimental_models) has more accurate results than the standard BODY_25 one and has been extensively tested for Pose2Sim. \ You can also use the [BODY_135 model](https://github.com/CMU-Perceptual-Computing-Lab/openpose_train/tree/master/experimental_models), which allows for the evaluation of pronation/supination, wrist flexion, and wrist deviation.\ @@ -227,139 +363,7 @@ All AlphaPose models are supported (HALPE_26, HALPE_68, HALPE_136, COCO_133, COC │ ├──... │ └──pose_camN_json │ - ├── raw-2d - │ ├──vid_cam1.mp4 - │ ├──... - │ └──vid_camN.mp4 - │ - └──User - └──Config.toml -
- - -## Camera calibration -> _**Calculate camera intrinsic properties and extrinsic locations and positions.\ -> Convert a preexisting calibration file, or calculate intrinsic and extrinsic parameters from scratch.**_ \ -> _**N.B.:**_ You can visualize camera calibration in 3D with my (experimental) [Maya-Mocap tool](https://github.com/davidpagnon/Maya-Mocap). - -Open an Anaconda prompt or a terminal, type `ipython`.\ -By default, `calibration()` will look for `Config.toml` in the `User` folder of your current directory. If you want to store it somewhere else (e.g. in your data directory), specify this path as an argument: `Pose2Sim.calibration(r'path_to_config.toml')`. - -``` python -from Pose2Sim import Pose2Sim -Pose2Sim.calibration() -``` - -Output:\ - - - -### Convert from Qualisys, Optitrack, Vicon, OpenCap, EasyMocap, or bioCV - -> N.B.: Since Pose2Sim uses the [Aniposelib](https://anipose.readthedocs.io/en/latest/aniposelibtutorial.html) format, calibration does not need to be run if you already have an [AniPose](https://github.com/lambdaloop/anipose) or [FreeMocap](https://github.com/freemocap/freemocap) calibration .toml file. - -If you already have a calibration file, set `calibration_type` type to `convert` in your [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file. -- **From [Qualisys](https://www.qualisys.com):** - - Export calibration to `.qca.txt` within QTM. - - Copy it in the `calibration` Pose2Sim folder. - - set `convert_from` to 'qualisys' in your [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file. Change `binning_factor` to 2 if you film in 540p. -- **From [Optitrack](https://optitrack.com/):** Exporting calibration will be available in Motive 3.2. In the meantime: - - Calculate intrinsics with a board (see next section). - - Use their C++ API [to retrieve extrinsic properties](https://docs.optitrack.com/developer-tools/motive-api/motive-api-function-reference#tt_cameraxlocation). Translation can be copied as is in your `Calib.toml` file, but TT_CameraOrientationMatrix first needs to be [converted to a Rodrigues vector](https://docs.opencv.org/3.4/d9/d0c/group__calib3d.html#ga61585db663d9da06b68e70cfbf6a1eac) with OpenCV. See instructions [here](https://github.com/perfanalytics/pose2sim/issues/28). - - Use the `Calib.toml` file as is and do not run Pose2Sim.calibration() -- **From [Vicon](http://www.vicon.com/Software/Nexus):** - - Copy your `.xcp` Vicon calibration file to the Pose2Sim `calibration` folder. - - set `convert_from` to 'vicon' in your [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file. No other setting is needed. -- **From [OpenCap](https://www.opencap.ai/):** - - Copy your `.pickle` OpenCap calibration files to the Pose2Sim `calibration` folder. - - set `convert_from` to 'opencap' in your [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file. No other setting is needed. -- **From [EasyMocap](https://github.com/zju3dv/EasyMocap/):** - - Copy your `intri.yml` and `extri.yml` files to the Pose2Sim `calibration` folder. - - set `convert_from` to 'easymocap' in your [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file. No other setting is needed. -- **From [bioCV](https://github.com/camera-mc-dev/.github/blob/main/profile/mocapPipe.md):** - - Copy your bioCV calibration files (no extension) to the Pose2Sim `calibration` folder. - - set `convert_from` to 'biocv' in your [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file. No other setting is needed. - - -### Calculate from scratch - -> Calculate calibration parameters with a board, or with points (such as detected on a wand or a human body). - -- **With a board:** - > *N.B.:* Try the calibration tool on the Demo by changing `calibration_type` to `calculate` in [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml).\ - For the sake of practicality, there are voluntarily few board images for intrinsic calibration, and few points to click for extrinsic calibration. In spite of this, your reprojection error should be under 1-2 cm, which [does not hinder the quality of kinematic results in practice](https://www.mdpi.com/1424-8220/21/19/6530/htm#:~:text=Angle%20results%20were,Table%203).). - - - **Calculate intrinsic parameters:** - - > *N.B.:* _Intrinsic parameters:_ camera properties (focal length, optical center, distortion), usually need to be calculated only once in their lifetime. In theory, cameras with same model and same settings will have identical intrinsic parameters.\ - > *N.B.:* If you already calculated intrinsic parameters earlier, you can skip this step. Copy your intrinsic parameters (`size`, `mat`, and `dist`) in a new `Calib*.toml` file, and set `overwrite_intrinsics` to false. Run Demo to obtain an example `Calib.toml` file. - - - Create a folder for each camera in your `calibration\intrinsics` folder. - - For each camera, film a checkerboard or a charucoboard. Either the board or the camera can be moved. - - Adjust parameters in the [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file. - - Make sure that the board: - - is filmed from different angles, covers a large part of the video frame, and is in focus. - - is flat, without reflections, surrounded by a white border, and is not rotationally invariant (Nrows ≠ Ncols, and Nrows odd if Ncols even). - - A common error is to specify the external, instead of the internal number of corners. This may be one less than you would intuitively think. - - - - ***Intrinsic calibration error should be below 0.5 px.*** - - - **Calculate extrinsic parameters:** - - > *N.B.:* _Extrinsic parameters:_ camera placement in space (position and orientation), need to be calculated every time a camera is moved. Can be calculated from a board, or from points in the scene with known coordinates. - - - Create a folder for each camera in your `calibration\extrinsics` folder. - - Once your cameras are in place, shortly film either a board laid on the floor, or the raw scene\ - (only one frame is needed, but do not just take a photo unless you are sure it does not change the image format). - - Adjust parameters in the [User\Config.toml](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Empty_project/User/Config.toml) file. - - Then, - - **If you film a board:**\ - Make sure that it is seen by all cameras. \ - It should preferably be larger than the one used for intrinsics, as results will not be very accurate out of the covered zone. - - **If you film the raw scene** (more flexible and potentially more accurate if points are spread out):\ - Manually measure the 3D coordinates of 10 or more points in the scene (tiles, lines on wall, boxes, treadmill dimensions, etc). These points should be as spread out as possible.\ - Then you will click on the corresponding image points for each view. - - - - ***Extrinsic calibration error should be below 1 cm, but depending on your application, results will still be potentially acceptable up to 2.5 cm.*** - -- **With points:** - - Points can be detected from a wand.\ - [Want to contribute?](#how-to-contribute) - - For a more automatic calibration, OpenPose keypoints could also be used for calibration.\ - [Want to contribute?](#how-to-contribute) - -
- The project hierarchy becomes: (CLICK TO SHOW) -
-   Project
-   │
-   ├──calibration
-   │   ├──intrinsics
-   │   │  ├──int_cam1_img
-   │   │  ├──...
-   │   │  └──int_camN_img
-   │   ├──extrinsics
-   │   │  ├──ext_cam1_img
-   │   │  ├──...
-   │   │  └──ext_camN_img
-   │   └──Calib.toml
-   │
-   ├──opensim
-   │    ├──Geometry
-   │    ├──Model_Pose2Sim_Body25b.osim
-   │    ├──Scaling_Setup_Pose2Sim_Body25b.xml
-   │    └──IK_Setup_Pose2Sim_Body25b.xml
-   │
-   ├──pose-2d
-   │    ├──pose_cam1_json
-   │    ├──...
-   │    └──pose_camN_json
-   │        
-   ├── raw-2d
+   ├── videos
    │    ├──vid_cam1.mp4
    │    ├──...
    │    └──vid_camN.mp4
@@ -376,7 +380,7 @@ If you already have a calibration file, set `calibration_type` type to `convert`
 *N.B.: Skip this step if your cameras are already synchronized.*
 
 If your cameras are not natively synchronized, you can use [this script](https://github.com/perfanalytics/pose2sim/blob/main/Pose2Sim/Utilities/synchronize_cams_draft.py). This is still a draft, and will be updated in the future.\
-Alternatively, use a clap, a flash, or a beep noise to synchronize them.
+Alternatively, use a flashlight or a clap to synchronize them. GoPro cameras can also be synchronized with a timecode, by GPS (outdoors) or with a remote control (slightly less reliable).
 
 
 ## Tracking, Triangulating, Filtering
@@ -432,7 +436,7 @@ Output:\
    │   ├──...
    │   └──tracked_camN_json
    │        
-   ├── raw-2d
+   ├── videos
    │    ├──vid_cam1.mp4
    │    ├──...
    │    └──vid_camN.mp4
@@ -497,7 +501,7 @@ Output:\
    ├──pose-3d
        └──Pose-3d.trc>
    │        
-   ├── raw-2d
+   ├── videos
    │    ├──vid_cam1.mp4
    │    ├──...
    │    └──vid_camN.mp4
@@ -564,7 +568,7 @@ Output:\
    │   ├──Pose-3d.trc
    │   └──Pose-3d-filtered.trc
    │        
-   ├── raw-2d
+   ├── videos
    │    ├──vid_cam1.mp4
    │    ├──...
    │    └──vid_camN.mp4
@@ -666,7 +670,7 @@ Make sure to replace `py38np120` with your Python version (3.8 in this case) and
    │   ├──triangulation.trc
    │   └──triangulation-filtered.trc
    │        
-   ├── raw
+   ├── videos
    │    ├──vid_cam1.mp4
    │    ├──...
    │    └──vid_camN.mp4
@@ -831,7 +835,8 @@ If you use this code or data, please cite [Pagnon et al., 2022b](https://doi.org
 ### How to contribute and to-do list
 
 I would happily welcome any proposal for new features, code improvement, and more!\
-If you want to contribute to Pose2Sim, please follow [this guide](https://docs.github.com/en/get-started/quickstart/contributing-to-projects) on how to fork, modify and push code, and submit a pull request. I would appreciate it if you provided as much useful information as possible about how you modified the code, and a rationale for why you're making this pull request. Please also specify on which operating system and on which Python version you have tested the code.
+If you want to contribute to Pose2Sim, please see [this issue](https://github.com/perfanalytics/pose2sim/issues/40).\
+You will be proposed a to-do list, but please feel absolutely free to propose your own ideas and improvements.
 
 
@@ -842,7 +847,7 @@ If you want to contribute to Pose2Sim, please follow [this guide](https://docs.g - Self-calibration based on keypoint detection
- Detailed to-do list (CLICK TO SHOW) + Detailed GOT-DONE and TO-DO list (CLICK TO SHOW)
        
 ✔ **Pose:** Support OpenPose [body_25b](https://github.com/CMU-Perceptual-Computing-Lab/openpose_train/tree/master/experimental_models#body_25b-model---option-2-recommended) for more accuracy, [body_135](https://github.com/CMU-Perceptual-Computing-Lab/openpose_train/tree/master/experimental_models#single-network-whole-body-pose-estimation-model) for pronation/supination.
@@ -930,7 +935,7 @@ If you want to contribute to Pose2Sim, please follow [this guide](https://docs.g
 - Supervised my PhD: [@lreveret](https://github.com/lreveret) (INRIA, Université Grenoble Alpes), and [@mdomalai](https://github.com/mdomalai) (Université de Poitiers).
 - Provided the Demo data: [@aaiaueil](https://github.com/aaiaueil) from Université Gustave Eiffel.
 - Tested the code and provided feedback: [@simonozan](https://github.com/simonozan), [@daeyongyang](https://github.com/daeyongyang), [@ANaaim](https://github.com/ANaaim), [@rlagnsals](https://github.com/rlagnsals)
-- Submitted merged pull requests: [@ANaaim](https://github.com/ANaaim)
+- Submitted various accepted pull requests: [@ANaaim](https://github.com/ANaaim)
 - Provided a code snippet for Optitrack calibration: [@claraaudap](https://github.com/claraaudap) (Université Bretagne Sud).
 - Issued MPP2SOS, a (non-free) Blender extension based on Pose2Sim: [@carlosedubarreto](https://github.com/carlosedubarreto)
 
@@ -940,8 +945,10 @@ If you want to contribute to Pose2Sim, please follow [this guide](https://docs.g
 - [x] v0.1: Published online
 - [x] v0.2: Published associated paper
 - [x] v0.3: Supported other pose estimation algorithms
-- [x] v0.4: New calibration tool
-- [ ] v0.5: Supports multi-person analysis
-- [ ] v0.6: New synchronization tool
-- [ ] v0.7: Graphical User Interface
+- [x] v0.4: New calibration tool based on scene measurements
+- [ ] v0.5: Batch processing
+- [ ] v0.6: Calibration based on keypoint detection
+- [ ] v0.7: Supports multi-person analysis
+- [ ] v0.8: New synchronization tool
+- [ ] v0.9: Graphical User Interface
 - [ ] v1.0: First accomplished release
diff --git a/setup.cfg b/setup.cfg
index 09020f6..b3e4b83 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -49,4 +49,4 @@ install_requires =
 packages = find_namespace:
 
 [options.package_data]
-* = Demo/**, Empty_project/**, Empty_project/**/.*, Empty_project/**/**/.*, Empty_project/**/**/**/.*, Empty_project/**/**/**/**/.*
+* = OpenSim/**, Demo/**, Demo/**/.*, Demo/**/**/.*, Demo/**/**/**/.*, Demo/**/**/**/**/.*