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Custom model def in Config.toml, not skeletons.py

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davidpagnon 2023-11-01 15:56:37 +01:00
parent ad26885c69
commit b970c86d1d
7 changed files with 252 additions and 32 deletions
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80
Pose2Sim/Demo/User/Config.toml
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@ -21,10 +21,9 @@ 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 Pose2Sim\skeleton.py for their skeleton hierarchy
#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
@ -123,3 +122,76 @@ display_figures = true # true or false (lowercase)
kernel_size = 9
[opensim]
# 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 the file and replace CUSTOM by the name of your choice.
# Make sure the node ids correspond to the column numbers, 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"

79
Pose2Sim/Demo/User/test.toml
View File

@ -21,10 +21,9 @@ 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 Pose2Sim\skeleton.py for their skeleton hierarchy
#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
@ -124,3 +123,75 @@ display_figures = false # true or false (lowercase)
[opensim]
# 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 the file and replace CUSTOM by the name of your choice.
# Make sure the node ids correspond to the column numbers, 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"

81
Pose2Sim/Empty_project/User/Config.toml
View File

@ -21,10 +21,9 @@ 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 Pose2Sim\skeleton.py for their skeleton hierarchy
#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
@ -84,7 +83,7 @@ calibration_type = 'convert' # 'convert' or 'calculate'
calibration_points = 'wand' # 'wand' or 'keypoints'
# Not supported yet.
[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)
@ -124,3 +123,75 @@ display_figures = true # true or false (lowercase)
[opensim]
# 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 the file and replace CUSTOM by the name of your choice.
# Make sure the node ids correspond to the column numbers, 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"

12
Pose2Sim/personAssociation.py
View File

@ -34,6 +34,8 @@ import json
import itertools as it
import toml
from tqdm import tqdm
from anytree import RenderTree
from anytree.importer import DictImporter
import logging
from Pose2Sim.common import computeP, weighted_triangulation, reprojection, \
@ -258,7 +260,15 @@ def track_2d_all(config):
P = computeP(calib_file)
# selection of tracked keypoint id
model = eval(pose_model)
try: # from skeletons.py
model = eval(pose_model)
except:
try: # from Config.toml
model = DictImporter().import_(config.get('pose').get(pose_model))
if model.id == 'None':
model.id = None
except:
raise NameError('Model not found in skeletons.py nor in Config.toml')
tracked_keypoint_id = [node.id for _, _, node in RenderTree(model) if node.name==tracked_keypoint][0]
# 2d-pose files selection

18
Pose2Sim/skeletons.py
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@ -8,11 +8,11 @@
###########################################################################
The definition and hierarchy of the following skeletons are available:
- CUSTOM (e.g.., from DeepLabCut),
- OpenPose BODY_25B, BODY_25, BODY_135, COCO, MPII
- Mediapipe BLAZEPOSE
- AlphaPose HALPE_26, HALPE_68, HALPE_136, COCO_133, COCO, MPII
(for COCO and MPII, AlphaPose must be run with the flag "--format cmu")
- DeepLabCut CUSTOM: the skeleton will be defined in Config.toml
N.B.: Not all face and hand keypoints are reported in the skeleton architecture,
since some are redundant for the orientation of some bodies.
@ -20,17 +20,10 @@
N.B.: The corresponding OpenSim model files are provided in the "Pose2Sim\Empty project" folder.
If you wish to use any other, you will need to adjust the markerset in the .osim model file,
as well as in the scaling and IK setup files.
N.B.: In case you built a custom skeleton, you can check its structure by typing:
from anytree import Node, RenderTree
for pre, _, node in RenderTree(CUSTOM):
print(f'{pre}{node.name} id={node.id}')
If you build it from a DeepLabCut model, make sure the node ids
correspond to the column numbers, starting from zero.
'''
## INIT
from anytree import Node, RenderTree
from anytree import Node
## AUTHORSHIP INFORMATION
@ -44,13 +37,6 @@ __email__ = "contact@david-pagnon.com"
__status__ = "Development"
'''CUSTOM SKELETON (e.g., from DeepLabCut detection)'''
CUSTOM = Node("Root", id=0, children=[
Node("Child1", id=1),
Node("Child2", id=2),
])
'''BODY_25B (full-body without hands, experimental, from OpenPose)
https://github.com/CMU-Perceptual-Computing-Lab/openpose_train/blob/master/experimental_models/README.md'''
BODY_25B = Node("CHip", id=None, children=[

12
Pose2Sim/triangulation.py
View File

@ -41,6 +41,8 @@ import toml
from tqdm import tqdm
from scipy import interpolate
from collections import Counter
from anytree import RenderTree
from anytree.importer import DictImporter
import logging
from Pose2Sim.common import computeP, weighted_triangulation, reprojection, \
@ -425,7 +427,15 @@ def triangulate_all(config):
P = computeP(calib_file)
# Retrieve keypoints from model
model = eval(pose_model)
try: # from skeletons.py
model = eval(pose_model)
except:
try: # from Config.toml
model = DictImporter().import_(config.get('pose').get(pose_model))
if model.id == 'None':
model.id = None
except:
raise NameError('Model not found in skeletons.py nor in Config.toml')
keypoints_ids = [node.id for _, _, node in RenderTree(model) if node.id!=None]
keypoints_names = [node.name for _, _, node in RenderTree(model) if node.id!=None]
keypoints_idx = list(range(len(keypoints_ids)))

2
setup.cfg
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@ -1,6 +1,6 @@
[metadata]
name = pose2sim
version = 0.4.7
version = 0.4.8
author = David Pagnon
author_email = contact@david-pagnon.com
description = Perform a markerless kinematic analysis from multiple calibrated views as a unified workflow from an OpenPose input to an OpenSim result.