650 lines
27 KiB
Python
650 lines
27 KiB
Python
#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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'''
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###########################################################################
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## POSE2SIM ##
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###########################################################################
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This repository offers a way to perform markerless kinematics, and gives an
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example workflow from an Openpose input to an OpenSim result.
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It offers tools for:
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- Cameras calibration,
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- 2D pose estimation,
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- Camera synchronization,
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- Tracking the person of interest,
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- Robust triangulation,
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- Filtration,
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- Marker augmentation,
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- OpenSim scaling and inverse kinematics
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It has been tested on Windows, Linux and MacOS, and works for any Python version >= 3.9
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Installation:
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# Open Anaconda prompt. Type:
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# - conda create -n Pose2Sim python=3.9
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# - conda activate Pose2Sim
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# - conda install -c opensim-org opensim -y
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# - pip install Pose2Sim
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Usage:
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# First run Pose estimation and organize your directories (see Readme.md)
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from Pose2Sim import Pose2Sim
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Pose2Sim.calibration()
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Pose2Sim.poseEstimation()
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Pose2Sim.synchronization()
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Pose2Sim.personAssociation()
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Pose2Sim.triangulation()
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Pose2Sim.filtering()
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Pose2Sim.markerAugmentation()
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Pose2Sim.kinematics()
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# Then run OpenSim (see Readme.md)
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'''
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## INIT
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import toml
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import os
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import time
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from copy import deepcopy
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import logging, logging.handlers
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from datetime import datetime
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## AUTHORSHIP INFORMATION
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__author__ = "David Pagnon"
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__copyright__ = "Copyright 2021, Pose2Sim"
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__credits__ = ["David Pagnon"]
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__license__ = "BSD 3-Clause License"
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__version__ = "0.9.4"
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__maintainer__ = "David Pagnon"
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__email__ = "contact@david-pagnon.com"
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__status__ = "Development"
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## FUNCTIONS
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def setup_logging(session_dir):
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'''
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Create logging file and stream handlers
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'''
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logging.basicConfig(format='%(message)s', level=logging.INFO,
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handlers = [logging.handlers.TimedRotatingFileHandler(os.path.join(session_dir, 'logs.txt'), when='D', interval=7), logging.StreamHandler()])
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def recursive_update(dict_to_update, dict_with_new_values):
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'''
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Update nested dictionaries without overwriting existing keys in any level of nesting
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Example:
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dict_to_update = {'key': {'key_1': 'val_1', 'key_2': 'val_2'}}
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dict_with_new_values = {'key': {'key_1': 'val_1_new'}}
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returns {'key': {'key_1': 'val_1_new', 'key_2': 'val_2'}}
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while dict_to_update.update(dict_with_new_values) would return {'key': {'key_1': 'val_1_new'}}
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'''
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for key, value in dict_with_new_values.items():
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if key in dict_to_update and isinstance(value, dict) and isinstance(dict_to_update[key], dict):
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# Recursively update nested dictionaries
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dict_to_update[key] = recursive_update(dict_to_update[key], value)
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else:
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# Update or add new key-value pairs
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dict_to_update[key] = value
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return dict_to_update
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def determine_level(config_dir):
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'''
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Determine the level at which the function is called.
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Level = 1: Trial folder
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Level = 2: Root folder
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'''
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len_paths = [len(root.split(os.sep)) for root,dirs,files in os.walk(config_dir) if 'Config.toml' in files]
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if len_paths == []:
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raise FileNotFoundError('You need a Config.toml file in each trial or root folder.')
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level = max(len_paths) - min(len_paths) + 1
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return level
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def read_config_files(config):
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'''
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Read Root and Trial configuration files,
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and output a dictionary with all the parameters.
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'''
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if type(config)==dict:
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level = 2 # log_dir = os.getcwd()
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config_dicts = [config]
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if config_dicts[0].get('project').get('project_dir') == None:
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raise ValueError('Please specify the project directory in config_dict:\n \
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config_dict.get("project").update({"project_dir":"<YOUR_PROJECT_DIRECTORY>"})')
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else:
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# if launched without an argument, config == None, else it is the path to the config directory
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config_dir = ['.' if config == None else config][0]
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level = determine_level(config_dir)
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# Trial level
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if level == 1: # Trial
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try:
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# if batch
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session_config_dict = toml.load(os.path.join(config_dir, '..','Config.toml'))
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trial_config_dict = toml.load(os.path.join(config_dir, 'Config.toml'))
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session_config_dict = recursive_update(session_config_dict,trial_config_dict)
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except:
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# if single trial
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session_config_dict = toml.load(os.path.join(config_dir, 'Config.toml'))
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session_config_dict.get("project").update({"project_dir":config_dir})
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config_dicts = [session_config_dict]
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# Root level
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if level == 2:
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session_config_dict = toml.load(os.path.join(config_dir, 'Config.toml'))
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config_dicts = []
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# Create config dictionaries for all trials of the participant
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for (root,dirs,files) in os.walk(config_dir):
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if 'Config.toml' in files and root != config_dir:
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trial_config_dict = toml.load(os.path.join(root, files[0]))
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# deep copy, otherwise session_config_dict is modified at each iteration within the config_dicts list
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temp_dict = deepcopy(session_config_dict)
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temp_dict = recursive_update(temp_dict,trial_config_dict)
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temp_dict.get("project").update({"project_dir":os.path.join(config_dir, os.path.relpath(root))})
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if not os.path.basename(root) in temp_dict.get("project").get('exclude_from_batch'):
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config_dicts.append(temp_dict)
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return level, config_dicts
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def calibration(config=None):
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'''
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Cameras calibration from checkerboards or from qualisys files.
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config can be a dictionary,
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or a the directory path of a trial, participant, or session,
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or the function can be called without an argument, in which case it the config directory is the current one.
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'''
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from Pose2Sim.calibration import calibrate_cams_all
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level, config_dicts = read_config_files(config)
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config_dict = config_dicts[0]
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try:
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session_dir = os.path.realpath([os.getcwd() if level==2 else os.path.join(os.getcwd(), '..')][0])
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[os.path.join(session_dir, c) for c in os.listdir(session_dir) if 'calib' in c.lower() and not c.lower().endswith('.py')][0]
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except:
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session_dir = os.path.realpath(os.getcwd())
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config_dict.get("project").update({"project_dir":session_dir})
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# Set up logging
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setup_logging(session_dir)
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currentDateAndTime = datetime.now()
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# Run calibration
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calib_dir = [os.path.join(session_dir, c) for c in os.listdir(session_dir) if os.path.isdir(os.path.join(session_dir, c)) and 'calib' in c.lower()][0]
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logging.info("\n---------------------------------------------------------------------")
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logging.info("Camera calibration")
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logging.info(f"On {currentDateAndTime.strftime('%A %d. %B %Y, %H:%M:%S')}")
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logging.info(f"Calibration directory: {calib_dir}")
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logging.info("---------------------------------------------------------------------\n")
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start = time.time()
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try:
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calibrate_cams_all(config_dict)
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except Exception as e:
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logging.error(f"Error during calibration: {e}")
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return
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end = time.time()
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logging.info(f'\nCalibration took {end-start:.2f} s.\n')
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def poseEstimation(config=None):
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'''
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Estimate pose using RTMLib
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config can be a dictionary,
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or a the directory path of a trial, participant, or session,
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or the function can be called without an argument, in which case it the config directory is the current one.
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'''
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from Pose2Sim.poseEstimation import rtm_estimator # The name of the function might change
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level, config_dicts = read_config_files(config)
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if isinstance(config, dict):
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config_dict = config_dicts[0]
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if config_dict.get('project').get('project_dir') is None:
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raise ValueError('Please specify the project directory in config_dict:\n \
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config_dict.get("project").update({"project_dir":"<YOUR_TRIAL_DIRECTORY>"})')
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# Set up logging
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session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '..'))
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setup_logging(session_dir)
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# Batch process all trials
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for config_dict in config_dicts:
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start = time.time()
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currentDateAndTime = datetime.now()
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project_dir = os.path.realpath(config_dict.get('project').get('project_dir'))
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seq_name = os.path.basename(project_dir)
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frame_range = config_dict.get('project').get('frame_range')
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frames = ["all frames" if not frame_range else f"frames {frame_range[0]} to {frame_range[1]}"][0]
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logging.info("\n---------------------------------------------------------------------")
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logging.info(f"Pose estimation for {seq_name}, for {frames}.")
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logging.info(f"On {currentDateAndTime.strftime('%A %d. %B %Y, %H:%M:%S')}")
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logging.info(f"Project directory: {project_dir}")
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logging.info("---------------------------------------------------------------------\n")
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try:
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rtm_estimator(config_dict)
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except Exception as e:
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logging.error(f"Error during pose estimation: {e}")
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continue
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end = time.time()
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elapsed = end - start
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logging.info(f'\nPose estimation took {time.strftime("%Hh%Mm%Ss", time.gmtime(elapsed))}.\n')
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def synchronization(config=None):
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'''
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Synchronize cameras if needed.
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config can be a dictionary,
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or a the directory path of a trial, participant, or session,
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or the function can be called without an argument, in which case it the config directory is the current one.
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'''
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# Import the function
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from Pose2Sim.synchronization import synchronize_cams_all
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# Determine the level at which the function is called (root:2, trial:1)
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level, config_dicts = read_config_files(config)
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if type(config)==dict:
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config_dict = config_dicts[0]
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if config_dict.get('project').get('project_dir') == None:
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raise ValueError('Please specify the project directory in config_dict:\n \
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config_dict.get("project").update({"project_dir":"<YOUR_TRIAL_DIRECTORY>"})')
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# Set up logging
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session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '..'))
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setup_logging(session_dir)
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# Batch process all trials
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for config_dict in config_dicts:
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start = time.time()
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currentDateAndTime = datetime.now()
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project_dir = os.path.realpath(config_dict.get('project').get('project_dir'))
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logging.info("\n---------------------------------------------------------------------")
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logging.info("Camera synchronization")
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logging.info(f"On {currentDateAndTime.strftime('%A %d. %B %Y, %H:%M:%S')}")
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logging.info(f"Project directory: {project_dir}")
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logging.info("---------------------------------------------------------------------\n")
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try:
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synchronize_cams_all(config_dict)
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except Exception as e:
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logging.error(f"Error during synchronization: {e}")
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continue
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end = time.time()
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elapsed = end-start
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logging.info(f'\nSynchronization took {time.strftime("%Hh%Mm%Ss", time.gmtime(elapsed))}.\n')
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def personAssociation(config=None):
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'''
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Tracking one or several persons of interest.
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Needs a calibration file.
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config can be a dictionary,
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or a the directory path of a trial, participant, or session,
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or the function can be called without an argument, in which case it the config directory is the current one.
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'''
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from Pose2Sim.personAssociation import track_2d_all
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# Determine the level at which the function is called (root:2, trial:1)
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level, config_dicts = read_config_files(config)
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if type(config)==dict:
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config_dict = config_dicts[0]
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if config_dict.get('project').get('project_dir') == None:
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raise ValueError('Please specify the project directory in config_dict:\n \
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config_dict.get("project").update({"project_dir":"<YOUR_TRIAL_DIRECTORY>"})')
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# Set up logging
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session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '..'))
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setup_logging(session_dir)
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# Batch process all trials
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for config_dict in config_dicts:
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start = time.time()
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currentDateAndTime = datetime.now()
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project_dir = os.path.realpath(config_dict.get('project').get('project_dir'))
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seq_name = os.path.basename(project_dir)
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frame_range = config_dict.get('project').get('frame_range')
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frames = ["all frames" if frame_range == [] else f"frames {frame_range[0]} to {frame_range[1]}"][0]
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logging.info("\n---------------------------------------------------------------------")
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logging.info(f"Associating persons for {seq_name}, for {frames}.")
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logging.info(f"On {currentDateAndTime.strftime('%A %d. %B %Y, %H:%M:%S')}")
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logging.info(f"Project directory: {project_dir}")
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logging.info("---------------------------------------------------------------------\n")
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try:
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track_2d_all(config_dict)
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except Exception as e:
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logging.error(f"Error during person association: {e}")
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continue
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end = time.time()
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elapsed = end-start
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logging.info(f'\nAssociating persons took {time.strftime("%Hh%Mm%Ss", time.gmtime(elapsed))}.\n')
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def triangulation(config=None):
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'''
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Robust triangulation of 2D points coordinates.
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config can be a dictionary,
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or a the directory path of a trial, participant, or session,
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or the function can be called without an argument, in which case it the config directory is the current one.
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'''
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from Pose2Sim.triangulation import triangulate_all
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# Determine the level at which the function is called (root:2, trial:1)
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level, config_dicts = read_config_files(config)
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if type(config)==dict:
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config_dict = config_dicts[0]
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if config_dict.get('project').get('project_dir') == None:
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raise ValueError('Please specify the project directory in config_dict:\n \
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config_dict.get("project").update({"project_dir":"<YOUR_TRIAL_DIRECTORY>"})')
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# Set up logging
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session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '..'))
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setup_logging(session_dir)
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# Batch process all trials
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for config_dict in config_dicts:
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start = time.time()
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currentDateAndTime = datetime.now()
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project_dir = os.path.realpath(config_dict.get('project').get('project_dir'))
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seq_name = os.path.basename(project_dir)
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frame_range = config_dict.get('project').get('frame_range')
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frames = ["all frames" if frame_range == [] else f"frames {frame_range[0]} to {frame_range[1]}"][0]
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logging.info("\n---------------------------------------------------------------------")
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logging.info(f"Triangulation of 2D points for {seq_name}, for {frames}.")
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logging.info(f"On {currentDateAndTime.strftime('%A %d. %B %Y, %H:%M:%S')}")
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logging.info(f"Project directory: {project_dir}")
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logging.info("---------------------------------------------------------------------\n")
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try:
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triangulate_all(config_dict)
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except Exception as e:
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logging.error(f"Error during triangulation: {e}")
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continue
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end = time.time()
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elapsed = end-start
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logging.info(f'\nTriangulation took {time.strftime("%Hh%Mm%Ss", time.gmtime(elapsed))}.\n')
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def filtering(config=None):
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'''
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Filter trc 3D coordinates.
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config can be a dictionary,
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or a the directory path of a trial, participant, or session,
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or the function can be called without an argument, in which case it the config directory is the current one.
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'''
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from Pose2Sim.filtering import filter_all
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# Determine the level at which the function is called (root:2, trial:1)
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level, config_dicts = read_config_files(config)
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if type(config)==dict:
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config_dict = config_dicts[0]
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if config_dict.get('project').get('project_dir') == None:
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raise ValueError('Please specify the project directory in config_dict:\n \
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config_dict.get("project").update({"project_dir":"<YOUR_TRIAL_DIRECTORY>"})')
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# Set up logging
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session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '..'))
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setup_logging(session_dir)
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# Batch process all trials
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for config_dict in config_dicts:
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currentDateAndTime = datetime.now()
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project_dir = os.path.realpath(config_dict.get('project').get('project_dir'))
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seq_name = os.path.basename(project_dir)
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frame_range = config_dict.get('project').get('frame_range')
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frames = ["all frames" if frame_range == [] else f"frames {frame_range[0]} to {frame_range[1]}"][0]
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logging.info("\n---------------------------------------------------------------------")
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logging.info(f"Filtering 3D coordinates for {seq_name}, for {frames}.")
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logging.info(f"On {currentDateAndTime.strftime('%A %d. %B %Y, %H:%M:%S')}")
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logging.info(f"Project directory: {project_dir}\n")
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logging.info("---------------------------------------------------------------------\n")
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try:
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filter_all(config_dict)
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except Exception as e:
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logging.error(f"Error during filtering: {e}")
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continue
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logging.info('\n')
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def markerAugmentation(config=None):
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'''
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Augment trc 3D coordinates.
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Estimate the position of 43 additional markers.
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config can be a dictionary,
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or a the directory path of a trial, participant, or session,
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or the function can be called without an argument, in which case it the config directory is the current one.
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'''
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from Pose2Sim.markerAugmentation import augmentTRC
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level, config_dicts = read_config_files(config)
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if type(config) == dict:
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config_dict = config_dicts[0]
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if config_dict.get('project').get('project_dir') is None:
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raise ValueError('Please specify the project directory in config_dict:\n \
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config_dict.get("project").update({"project_dir":"<YOUR_TRIAL_DIRECTORY>"})')
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session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '..'))
|
|
setup_logging(session_dir)
|
|
|
|
for config_dict in config_dicts:
|
|
start = time.time()
|
|
currentDateAndTime = datetime.now()
|
|
project_dir = os.path.realpath(config_dict.get('project').get('project_dir'))
|
|
seq_name = os.path.basename(project_dir)
|
|
frame_range = config_dict.get('project').get('frame_range')
|
|
frames = ["all frames" if frame_range == [] else f"frames {frame_range[0]} to {frame_range[1]}"][0]
|
|
|
|
logging.info("\n---------------------------------------------------------------------")
|
|
logging.info(f"Augmentation process for {seq_name}, for {frames}.")
|
|
logging.info(f"On {currentDateAndTime.strftime('%A %d. %B %Y, %H:%M:%S')}")
|
|
logging.info(f"Project directory: {project_dir}")
|
|
logging.info("---------------------------------------------------------------------\n")
|
|
|
|
try:
|
|
augmentTRC(config_dict)
|
|
except Exception as e:
|
|
logging.error(f"Error during marker augmentation: {e}")
|
|
continue
|
|
|
|
end = time.time()
|
|
elapsed = end-start
|
|
logging.info(f'\nMarker augmentation took {time.strftime("%Hh%Mm%Ss", time.gmtime(elapsed))}.\n')
|
|
|
|
|
|
def kinematics(config=None):
|
|
'''
|
|
Performing OpenSim scaling and inverse kinematics.
|
|
Select the 10% slowest frames from trc for scaling
|
|
Save scaled model as .osim and output motion as .mot
|
|
|
|
config can be a dictionary,
|
|
or a the directory path of a trial, participant, or session,
|
|
or the function can be called without an argument, in which case it the config directory is the current one.
|
|
'''
|
|
|
|
from Pose2Sim.kinematics import kinematics
|
|
level, config_dicts = read_config_files(config)
|
|
|
|
if type(config) == dict:
|
|
config_dict = config_dicts[0]
|
|
if config_dict.get('project').get('project_dir') is None:
|
|
raise ValueError('Please specify the project directory in config_dict:\n \
|
|
config_dict.get("project").update({"project_dir":"<YOUR_TRIAL_DIRECTORY>"})')
|
|
|
|
session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '..'))
|
|
setup_logging(session_dir)
|
|
|
|
# Process each configuration dictionary
|
|
for config_dict in config_dicts:
|
|
start = time.time()
|
|
currentDateAndTime = datetime.now()
|
|
project_dir = os.path.realpath(config_dict.get('project').get('project_dir'))
|
|
seq_name = os.path.basename(project_dir)
|
|
frame_range = config_dict.get('project').get('frame_range')
|
|
frames = ["all frames" if frame_range == [] else f"frames {frame_range[0]} to {frame_range[1]}"][0]
|
|
|
|
logging.info("\n---------------------------------------------------------------------")
|
|
logging.info(f"OpenSim scaling and inverse kinematics for {seq_name}, for {frames}.")
|
|
logging.info(f"On {currentDateAndTime.strftime('%A %d. %B %Y, %H:%M:%S')}")
|
|
logging.info(f"Project directory: {project_dir}")
|
|
logging.info("---------------------------------------------------------------------\n")
|
|
|
|
try:
|
|
kinematics(config_dict)
|
|
except Exception as e:
|
|
logging.error(f"Error during OpenSim processing: {e}")
|
|
continue
|
|
|
|
end = time.time()
|
|
elapsed = end - start
|
|
logging.info(f'\nOpenSim scaling and inverse kinematics took {time.strftime("%Hh%Mm%Ss", time.gmtime(elapsed))}.\n')
|
|
|
|
|
|
def runAll(config=None, do_calibration=True, do_poseEstimation=True, do_synchronization=True, do_personAssociation=True, do_triangulation=True, do_filtering=True, do_markerAugmentation=True, do_kinematics=True):
|
|
'''
|
|
Run all functions at once. Beware that Synchronization, personAssociation, and markerAugmentation are not always necessary,
|
|
and may even lead to worse results. Think carefully before running all.
|
|
'''
|
|
|
|
|
|
# Set up logging
|
|
level, config_dicts = read_config_files(config)
|
|
session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '..'))
|
|
setup_logging(session_dir)
|
|
|
|
currentDateAndTime = datetime.now()
|
|
start = time.time()
|
|
|
|
logging.info("\n\n=====================================================================")
|
|
logging.info(f"RUNNING ALL.")
|
|
logging.info(f"On {currentDateAndTime.strftime('%A %d. %B %Y, %H:%M:%S')}")
|
|
logging.info(f"Project directory: {session_dir}\n")
|
|
logging.info("=====================================================================")
|
|
|
|
if do_calibration:
|
|
logging.info("\n\n=====================================================================")
|
|
logging.info('Running calibration...')
|
|
logging.info("=====================================================================")
|
|
calibration(config)
|
|
else:
|
|
logging.info("\n\n=====================================================================")
|
|
logging.info('Skipping calibration.')
|
|
logging.info("=====================================================================")
|
|
|
|
if do_poseEstimation:
|
|
logging.info("\n\n=====================================================================")
|
|
logging.info('Running pose estimation...')
|
|
logging.info("=====================================================================")
|
|
poseEstimation(config)
|
|
else:
|
|
logging.info("\n\n=====================================================================")
|
|
logging.info('Skipping pose estimation.')
|
|
logging.info("=====================================================================")
|
|
|
|
if do_synchronization:
|
|
logging.info("\n\n=====================================================================")
|
|
logging.info('Running synchronization...')
|
|
logging.info("=====================================================================")
|
|
synchronization(config)
|
|
else:
|
|
logging.info("\n\n=====================================================================")
|
|
logging.info('Skipping synchronization.')
|
|
logging.info("=====================================================================")
|
|
|
|
if do_personAssociation:
|
|
logging.info("\n\n=====================================================================")
|
|
logging.info('Running person association...')
|
|
logging.info("=====================================================================")
|
|
personAssociation(config)
|
|
else:
|
|
logging.info("\n\n=====================================================================")
|
|
logging.info('Skipping person association.')
|
|
logging.info("=====================================================================")
|
|
|
|
if do_triangulation:
|
|
logging.info("\n\n=====================================================================")
|
|
logging.info('Running triangulation...')
|
|
logging.info("=====================================================================")
|
|
triangulation(config)
|
|
else:
|
|
logging.info("\n\n=====================================================================")
|
|
logging.info('Skipping triangulation.')
|
|
logging.info("=====================================================================")
|
|
|
|
if do_filtering:
|
|
logging.info("\n\n=====================================================================")
|
|
logging.info('Running filtering...')
|
|
logging.info("=====================================================================")
|
|
filtering(config)
|
|
else:
|
|
logging.info("\n\n=====================================================================")
|
|
logging.info('Skipping filtering.')
|
|
logging.info("=====================================================================")
|
|
|
|
if do_markerAugmentation:
|
|
logging.info("\n\n=====================================================================")
|
|
logging.info('Running marker augmentation.')
|
|
logging.info("=====================================================================")
|
|
markerAugmentation(config)
|
|
else:
|
|
logging.info("\n\n=====================================================================")
|
|
logging.info('Skipping marker augmentation.')
|
|
logging.info("\n\n=====================================================================")
|
|
|
|
if do_kinematics:
|
|
logging.info("\n\n=====================================================================")
|
|
logging.info("Running OpenSim processing.")
|
|
logging.info("=====================================================================")
|
|
kinematics(config)
|
|
else:
|
|
logging.info("\n\n=====================================================================")
|
|
logging.info('Skipping OpenSim processing.')
|
|
logging.info("\n\n=====================================================================")
|
|
|
|
logging.info("Pose2Sim pipeline completed.")
|
|
end = time.time()
|
|
elapsed = end-start
|
|
logging.info(f'\nRUNNING ALL FUNCTIONS TOOK {time.strftime("%Hh%Mm%Ss", time.gmtime(elapsed))}.\n')
|