works both for single trial and batch

This commit is contained in:
davidpagnon 2024-04-13 18:42:30 +02:00
parent db676146c9
commit bd9bbb68ab
453 changed files with 1505 additions and 676 deletions

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@ -125,12 +125,16 @@ def read_config_files(config):
# Trial level
if level == 1:
session_config_dict = toml.load(os.path.join(config_dir, '..','..','Config.toml'))
participant_config_dict = toml.load(os.path.join(config_dir, '..','Config.toml'))
trial_config_dict = toml.load(os.path.join(config_dir, 'Config.toml'))
session_config_dict = recursive_update(session_config_dict,participant_config_dict)
session_config_dict = recursive_update(session_config_dict,trial_config_dict)
try:
# if batch
session_config_dict = toml.load(os.path.join(config_dir, '..','..','Config.toml'))
participant_config_dict = toml.load(os.path.join(config_dir, '..','Config.toml'))
session_config_dict = recursive_update(session_config_dict,participant_config_dict)
trial_config_dict = toml.load(os.path.join(config_dir, 'Config.toml'))
session_config_dict = recursive_update(session_config_dict,trial_config_dict)
except:
# if single trial
session_config_dict = toml.load(os.path.join(config_dir, 'Config.toml'))
session_config_dict.get("project").update({"project_dir":config_dir})
config_dicts = [session_config_dict]
@ -267,7 +271,7 @@ def synchronization(config=None):
'''
# Import the function
from Pose2Sim.synchronize_cams import synchronize_cams_all
from Pose2Sim.synchronization import synchronize_cams_all
# Determine the level at which the function is called (session:3, participant:2, trial:1)
level, config_dicts = read_config_files(config)

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@ -43,7 +43,7 @@ openpose_path = '' # only checked if OpenPose is used
[synchronization]
display_corr = true # true or false (lowercase)
display_sync_plots = true # true or false (lowercase)
keypoints_to_consider = 'all' # 'all' if all points should be considered (default)
# ['RWrist', 'RElbow'] list of keypoint names if you want to specify the keypoints to consider
approx_time_maxspeed = 'auto' # 'auto' if you want to consider the whole capture (default, slower if long sequences)

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@ -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]
# multi_person = false # true for trials with multiple participants. If false, only the main person in scene is analyzed (and it run much faster).
nb_persons_to_detect = 2 # checked only if multi_person is selected
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, ['<participant_dir/trial_dir>', 'etc'].
# e.g. ['S00_P00_Participant/S00_P00_T00_StaticTrial', 'S00_P00_Participant/S00_P00_T01_BalancingTrial']
# Take heart, calibration is not that complicated once you get the hang of it!
[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]
display_sync_plots = true # true or false (lowercase)
keypoints_to_consider = 'all' # 'all' if all points should be considered (default)
# ['RWrist', 'RElbow'] list of keypoint names if you want to specify the keypoints to consider
approx_time_maxspeed = 'auto' # 'auto' if you want to consider the whole capture (default, slower if long sequences)
# [1.0, 0.2, 0.8, 1.1] list of times in seconds, one value per camera if you want to specify an approximate time where to search for synchronization.
# Best times: only one person is in the scene, who performs a sharp vertical movement (with keypoints_to_consider).
reset_sync = false # Revert to state before synchronization. Won't attempt to synchronize unless set to false.
[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 # # set to false if you don't want to recalculate intrinsic parameters
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!
[personAssociation]
likelihood_threshold_association = 0.3
[personAssociation.single_person]
reproj_error_threshold_association = 20 # px
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)
[personAssociation.multi_person]
reconstruction_error_threshold = 0.1 # 0.1 = 10 cm
min_affinity = 0.2 # affinity below which a correspondence is ignored
[triangulation]
reorder_trc = false # only checked if multi_person analysis
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 = false # Better if few cameras (eg less than 4) with risk of limb swapping (eg camera facing sagittal plane), otherwise slightly less accurate and slower
undistort_points = false # Better if distorted image (parallel lines curvy on the edge or at least one param > 10^-2), but unnecessary (and slightly slower) if distortions are low
make_c3d = false # save triangulated data in c3d format in addition to trc # 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
[markerAugmentation]
## Only works on BODY_25 and BODY_25B models
participant_height = 1.72 # m # float if single person, list of float if multi-person (same order as the Static trials)
participant_mass = 70.0 # kg
[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]]
name = "RHip"
id = 12
[[pose.CUSTOM.children.children]]
name = "RKnee"
id = 14
[[pose.CUSTOM.children.children.children]]
name = "RAnkle"
id = 16
[[pose.CUSTOM.children.children.children.children]]
name = "RBigToe"
id = 22
[[pose.CUSTOM.children.children.children.children.children]]
name = "RSmallToe"
id = 23
[[pose.CUSTOM.children.children.children.children]]
name = "RHeel"
id = 24
[[pose.CUSTOM.children]]
name = "LHip"
id = 11
[[pose.CUSTOM.children.children]]
name = "LKnee"
id = 13
[[pose.CUSTOM.children.children.children]]
name = "LAnkle"
id = 15
[[pose.CUSTOM.children.children.children.children]]
name = "LBigToe"
id = 19
[[pose.CUSTOM.children.children.children.children.children]]
name = "LSmallToe"
id = 20
[[pose.CUSTOM.children.children.children.children]]
name = "LHeel"
id = 21
[[pose.CUSTOM.children]]
name = "Neck"
id = 17
[[pose.CUSTOM.children.children]]
name = "Head"
id = 18
[[pose.CUSTOM.children.children.children]]
name = "Nose"
id = 0
[[pose.CUSTOM.children.children]]
name = "RShoulder"
id = 6
[[pose.CUSTOM.children.children.children]]
name = "RElbow"
id = 8
[[pose.CUSTOM.children.children.children.children]]
name = "RWrist"
id = 10
[[pose.CUSTOM.children.children]]
name = "LShoulder"
id = 5
[[pose.CUSTOM.children.children.children]]
name = "LElbow"
id = 7
[[pose.CUSTOM.children.children.children.children]]
name = "LWrist"
id = 9

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@ -0,0 +1,38 @@
<?xml version='1.0' encoding='ASCII'?>
<calibration created="sometimes ago" longArmEnd="none" longArmMiddle="none" maximumFrames="none" qtm-version="none" shortArmEnd="none" source="calibration_qca_rotated.qca.txt" type="regular" wandLength="none">
<results min-max-diff="0." std-dev="0."/>
<cameras>
<camera active="1" avg-residual="0.402000" model="none" point-count="999999999" serial="cam_01" viewrotation="0">
<fov_marker bottom="1919" left="0" right="1087" top="0"/>
<fov_marker_max bottom="1919" left="0" right="1087" top="0"/>
<fov_video bottom="1919" left="0" right="1087" top="0"/>
<fov_video_max bottom="1919" left="0" right="1087" top="0"/>
<transform r11="0.5536380477336265" r12="0.8046719867383512" r13="0.2144479094331626" r21="-0.4345300743838753" r22="0.05946489349975602" r23="0.8986921279821063" r31="0.7104002579937896" r32="-0.5907342212870501" r33="0.3825762057979294" x="1460.2323709212087" y="-1909.1590482454608" z="1896.5058524092062"/>
<intrinsic centerPointU="34110.316406" centerPointV="60680.792969" focalLengthU="107599.671875" focalLengthV="107588.828125" focallength="9.314096596679686" radialDistortion1="-0.046183" radialDistortion2="0.139983" radialDistortion3="0.000000" sensorMaxU="69568" sensorMaxV="122816" sensorMinU="0.000000" sensorMinV="0.000000" skew="0.000000" tangentalDistortion1="0.000608" tangentalDistortion2="0.00069"/>
</camera>
<camera active="1" avg-residual="0.444749" model="none" point-count="999999999" serial="cam_02" viewrotation="0">
<fov_marker bottom="1919" left="0" right="1087" top="0"/>
<fov_marker_max bottom="1919" left="0" right="1087" top="0"/>
<fov_video bottom="1919" left="0" right="1087" top="0"/>
<fov_video_max bottom="1919" left="0" right="1087" top="0"/>
<transform r11="-0.1966832217091926" r12="0.979523227309506" r13="-0.043011131806342306" r21="-0.31478107085300017" r22="-0.02153908797812718" r23="0.9489198834051846" r31="0.9285626460991909" r32="0.20017570994064315" r33="0.3125717476340885" x="2582.0136248568124" y="706.5662881637625" z="1690.9818366061595"/>
<intrinsic centerPointU="34207.652344" centerPointV="61646.457031" focalLengthU="107118.695313" focalLengthV="107123.023438" focallength="9.272462063031563" radialDistortion1="-0.047847" radialDistortion2="0.136786" radialDistortion3="0.000000" sensorMaxU="69568" sensorMaxV="122816" sensorMinU="0.000000" sensorMinV="0.000000" skew="0.000000" tangentalDistortion1="0.000972" tangentalDistortion2="0.000291"/>
</camera>
<camera active="1" avg-residual="0.450323" model="none" point-count="999999999" serial="cam_03" viewrotation="0">
<fov_marker bottom="1919" left="0" right="1087" top="0"/>
<fov_marker_max bottom="1919" left="0" right="1087" top="0"/>
<fov_video bottom="1919" left="0" right="1087" top="0"/>
<fov_video_max bottom="1919" left="0" right="1087" top="0"/>
<transform r11="-0.740641130147863" r12="-0.6704153360235378" r13="-0.044654154988568895" r21="0.25251118212268814" r22="-0.3393170985114385" r23="0.9061467925015139" r31="-0.6226466246887545" r32="0.6598539110153292" r33="0.4205995683324882" x="-3216.86586729648" y="2231.1786368869416" z="2088.19103027083"/>
<intrinsic centerPointU="32845.335938" centerPointV="61120.328125" focalLengthU="107622.296875" focalLengthV="107616.632813" focallength="9.316055073242188" radialDistortion1="-0.046705" radialDistortion2="0.137622" radialDistortion3="0.000000" sensorMaxU="69568" sensorMaxV="122816" sensorMinU="0.000000" sensorMinV="0.000000" skew="0.000000" tangentalDistortion1="-0.000542" tangentalDistortion2="-0.000517"/>
</camera>
<camera active="1" avg-residual="0.504772" model="none" point-count="999999999" serial="cam_04" viewrotation="0">
<fov_marker bottom="1919" left="0" right="1087" top="0"/>
<fov_marker_max bottom="1919" left="0" right="1087" top="0"/>
<fov_video bottom="1919" left="0" right="1087" top="0"/>
<fov_video_max bottom="1919" left="0" right="1087" top="0"/>
<transform r11="0.2586331447643361" r12="-0.875095795920923" r13="-0.40904308378315923" r21="0.49590579729377593" r22="-0.24310718522469382" r23="0.8336524076031634" r31="-0.8289670298870364" r32="-0.4184569804097585" r33="0.3710895025551282" x="-3758.720480260634" y="-1415.6654017496533" z="1881.7941041388026"/>
<intrinsic centerPointU="34566.796875" centerPointV="61697.9375" focalLengthU="107215.039063" focalLengthV="107213.070313" focallength="9.280801818890938" radialDistortion1="-0.047633" radialDistortion2="0.134667" radialDistortion3="0.000000" sensorMaxU="69568" sensorMaxV="122816" sensorMinU="0.000000" sensorMinV="0.000000" skew="0.000000" tangentalDistortion1="0.000277" tangentalDistortion2="0.000199"/>
</camera>
</cameras>
</calibration>

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@ -0,0 +1 @@
{"version":1.3,"people":[{"person_id":[-1],"pose_keypoints_2d":[505.232,431.63,0.664216,515.849,410.613,0.60741,489.417,405.32,0.668967,521.069,405.425,0.133121,452.648,400.017,0.679661,521.038,494.789,0.71398,384.303,478.904,0.666443,542.041,610.29,0.659144,300.143,594.661,0.690961,568.227,720.712,0.674367,268.58,715.519,0.707265,478.869,736.483,0.675958,389.456,725.953,0.649799,457.99,920.553,0.640835,368.557,899.416,0.664056,421.056,1078.38,0.6676,331.681,1010.01,0.658113,463.158,463.215,0.64987,515.746,342.25,0.685157,431.649,1146.64,0.676574,447.471,1141.34,0.700625,400.105,1094.02,0.645542,326.456,1062.48,0.627354,310.734,1046.81,0.626106,331.792,1025.62,0.555979],"face_keypoints_2d":[],"hand_left_keypoints_2d":[],"hand_right_keypoints_2d":[],"pose_keypoints_3d":[],"face_keypoints_3d":[],"hand_left_keypoints_3d":[],"hand_right_keypoints_3d":[]},{"person_id":[-1],"pose_keypoints_2d":[79.3784,331.803,0.451137,89.9826,326.423,0.438317,74.0443,321.232,0.440268,105.512,331.734,0.380456,58.4093,321.252,0.315967,116.171,394.615,0.518987,0,0,0,110.915,452.698,0.51267,16.1649,442.076,0.396311,74.0335,405.465,0.474693,13.577,484.198,0.280037,89.8712,515.834,0.530878,0,0,0,74.0298,620.871,0.488649,13.5983,615.692,0.49765,63.6432,720.772,0.481855,13.5832,705.086,0.461627,79.4497,363.346,0.453015,89.8711,279.267,0.458461,58.2763,741.769,0.372975,68.8046,741.858,0.400318,68.8799,731.295,0.445516,13.6271,736.484,0.268078,13.6527,731.235,0.279725,0,0,0],"face_keypoints_2d":[],"hand_left_keypoints_2d":[],"hand_right_keypoints_2d":[],"pose_keypoints_3d":[],"face_keypoints_3d":[],"hand_left_keypoints_3d":[],"hand_right_keypoints_3d":[]}]}

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