diff --git a/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/Config.toml b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/Config.toml new file mode 100644 index 0000000..30e44bd --- /dev/null +++ b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/Config.toml @@ -0,0 +1,254 @@ +############################################################################### +## PROJECT PARAMETERS ## +############################################################################### + + +# Configure your project parameters here. +# +# IMPORTANT: +# If a parameter is not found here, Pose2Sim will look for its value in the +# Config.toml file of the level above. This way, you can set global +# instructions for the Session and alter them for specific Participants or Trials. +# +# If you wish to overwrite a parameter for a specific trial or participant, +# edit its Config.toml file by uncommenting its key (e.g., [project]) +# and editing its value (e.g., frame_range = [10,300]). Or else, uncomment +# [filtering.butterworth] and set cut_off_frequency = 10, etc. + + + +[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 = [] # List of trials to be excluded from batch analysis, ['', 'etc']. +# e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P00_Participant/S00_P00_T01_BalancingTrial'] + +## Only taken into account if pose_model is 'BODY_25_AUGMENTED' # Coming soon! +participant_height = 1.7 # m +participant_mass = 70 # kg + + +# 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] + calculate_extrinsics = true # true or false (lowercase) + 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 + + [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, + # BODY_25_AUGMENTED # Coming soon! + #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 + +[BODY_25_AUGMENTED] +ModelName = "LSTM" +model = "v0.3" # now, 0.3 is lastest version +offset = true # default is ture + + +[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] +single_person = true # false for multi-person analysis (not supported yet), true for only triangulating the main person in scene. +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 +likelihood_threshold_association = 0.2 + + +[triangulation] +reproj_error_threshold_triangulation = 15 # px +likelihood_threshold_triangulation = 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 +handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower +undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low +make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon! + + +[filtering] +type = 'butterworth' # butterworth, kalman, gaussian, LOESS, median, butterworth_on_speed +display_figures = false # 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 = ['S00_P00_Participant/S00_P00_T00_StaticTrial'] +# # If this Config.toml file is at the Trial level, set to true or false (lowercase); +# # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial']; +# # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial'] +opensim_bin_path = 'C:\OpenSim 4.4\bin' + + + +# 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. +# +# Check your model hierarchy with: for pre, _, node in RenderTree(model): +# print(f'{pre}{node.name} id={node.id}') +[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/S01_Empty_Session/S01_P00_Participant0/S01_P00_T01_MotionTrial1/Config.toml b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T01_MotionTrial1/Config.toml new file mode 100644 index 0000000..30e44bd --- /dev/null +++ b/Pose2Sim/Demo/S01_Empty_Session/S01_P00_Participant0/S01_P00_T01_MotionTrial1/Config.toml @@ -0,0 +1,254 @@ +############################################################################### +## PROJECT PARAMETERS ## +############################################################################### + + +# Configure your project parameters here. +# +# IMPORTANT: +# If a parameter is not found here, Pose2Sim will look for its value in the +# Config.toml file of the level above. This way, you can set global +# instructions for the Session and alter them for specific Participants or Trials. +# +# If you wish to overwrite a parameter for a specific trial or participant, +# edit its Config.toml file by uncommenting its key (e.g., [project]) +# and editing its value (e.g., frame_range = [10,300]). Or else, uncomment +# [filtering.butterworth] and set cut_off_frequency = 10, etc. + + + +[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 = [] # List of trials to be excluded from batch analysis, ['', 'etc']. +# e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P00_Participant/S00_P00_T01_BalancingTrial'] + +## Only taken into account if pose_model is 'BODY_25_AUGMENTED' # Coming soon! +participant_height = 1.7 # m +participant_mass = 70 # kg + + +# 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] + calculate_extrinsics = true # true or false (lowercase) + 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 + + [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, + # BODY_25_AUGMENTED # Coming soon! + #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 + +[BODY_25_AUGMENTED] +ModelName = "LSTM" +model = "v0.3" # now, 0.3 is lastest version +offset = true # default is ture + + +[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] +single_person = true # false for multi-person analysis (not supported yet), true for only triangulating the main person in scene. +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 +likelihood_threshold_association = 0.2 + + +[triangulation] +reproj_error_threshold_triangulation = 15 # px +likelihood_threshold_triangulation = 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 +handle_LR_swap = true # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower +undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low +make_c3d = false # save triangulated data in c3d format in addition to trc # Coming soon! + + +[filtering] +type = 'butterworth' # butterworth, kalman, gaussian, LOESS, median, butterworth_on_speed +display_figures = false # 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 = ['S00_P00_Participant/S00_P00_T00_StaticTrial'] +# # If this Config.toml file is at the Trial level, set to true or false (lowercase); +# # At the Participant level, specify the name of the static trial folder name, e.g. ['S00_P00_T00_StaticTrial']; +# # At the Session level, add participant subdirectory, e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P01_Participant/S00_P00_T00_StaticTrial'] +opensim_bin_path = 'C:\OpenSim 4.4\bin' + + + +# 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. +# +# Check your model hierarchy with: for pre, _, node in RenderTree(model): +# print(f'{pre}{node.name} id={node.id}') +[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"