works both for single trial and batch
@ -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)
|
||||
|
@ -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)
|
||||
|
254
Pose2Sim/S01_Demo_SingleTrial/Config.toml
Normal file
@ -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
|
38
Pose2Sim/S01_Demo_SingleTrial/calibration/Calib.qca.txt
Normal file
@ -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"/>
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