pose2sim/Pose2Sim/Pose2Sim.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-


'''
###########################################################################
## POSE2SIM                                                              ##
###########################################################################

This repository offers a way to perform markerless kinematics, and gives an
example workflow from an Openpose input to an OpenSim result.

It offers tools for:
- Cameras calibration,
- 2D pose estimation,
- Camera synchronization,
- Tracking the person of interest,
- Robust triangulation,
- Filtration,
- Marker augmentation,
- OpenSim scaling and inverse kinematics

It has been tested on Windows, Linux and MacOS, and works for any Python version >= 3.9

Installation:
# Open Anaconda prompt. Type:
# - conda create -n Pose2Sim python=3.9
# - conda activate Pose2Sim
# - conda install -c opensim-org opensim -y
# - pip install Pose2Sim

Usage:
# First run Pose estimation and organize your directories (see Readme.md)
from Pose2Sim import Pose2Sim
Pose2Sim.calibration()
Pose2Sim.poseEstimation()
Pose2Sim.synchronization()
Pose2Sim.personAssociation()
Pose2Sim.triangulation()
Pose2Sim.filtering()
Pose2Sim.markerAugmentation()
Pose2Sim.kinematics()
# Then run OpenSim (see Readme.md)
'''


## INIT
import toml
import os
import time
from copy import deepcopy
import logging, logging.handlers
from datetime import datetime


## AUTHORSHIP INFORMATION
__author__ = "David Pagnon"
__copyright__ = "Copyright 2021, Pose2Sim"
__credits__ = ["David Pagnon"]
__license__ = "BSD 3-Clause License"
__version__ = "0.9.4"
__maintainer__ = "David Pagnon"
__email__ = "contact@david-pagnon.com"
__status__ = "Development"


## FUNCTIONS
def setup_logging(session_dir):
    '''
    Create logging file and stream handlers
    '''

    logging.basicConfig(format='%(message)s', level=logging.INFO,
        handlers = [logging.handlers.TimedRotatingFileHandler(os.path.join(session_dir, 'logs.txt'), when='D', interval=7), logging.StreamHandler()])


def recursive_update(dict_to_update, dict_with_new_values):
    '''
    Update nested dictionaries without overwriting existing keys in any level of nesting

    Example:
    dict_to_update = {'key': {'key_1': 'val_1', 'key_2': 'val_2'}}
    dict_with_new_values = {'key': {'key_1': 'val_1_new'}}
    returns {'key': {'key_1': 'val_1_new', 'key_2': 'val_2'}}
    while dict_to_update.update(dict_with_new_values) would return {'key': {'key_1': 'val_1_new'}}
    '''

    for key, value in dict_with_new_values.items():
        if key in dict_to_update and isinstance(value, dict) and isinstance(dict_to_update[key], dict):
            # Recursively update nested dictionaries
            dict_to_update[key] = recursive_update(dict_to_update[key], value)
        else:
            # Update or add new key-value pairs
            dict_to_update[key] = value

    return dict_to_update


def determine_level(config_dir):
    '''
    Determine the level at which the function is called.
    Level = 1: Trial folder
    Level = 2: Root folder
    '''

    len_paths = [len(root.split(os.sep)) for root,dirs,files in os.walk(config_dir) if 'Config.toml' in files]
    if len_paths == []:
        raise FileNotFoundError('You need a Config.toml file in each trial or root folder.')
    level = max(len_paths) - min(len_paths) + 1
    return level


def read_config_files(config):
    '''
    Read Root and Trial configuration files,
    and output a dictionary with all the parameters.
    '''

    if type(config)==dict:
        level = 2 # log_dir = os.getcwd()
        config_dicts = [config]
        if config_dicts[0].get('project').get('project_dir') == None:
            raise ValueError('Please specify the project directory in config_dict:\n \
                             config_dict.get("project").update({"project_dir":"<YOUR_PROJECT_DIRECTORY>"})')
    else:
        # if launched without an argument, config == None, else it is the path to the config directory
        config_dir = ['.' if config == None else config][0]
        level = determine_level(config_dir)

        # Trial level
        if level == 1: # Trial
            try:
                # if batch
                session_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,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]

        # Root level
        if level == 2:
            session_config_dict = toml.load(os.path.join(config_dir, 'Config.toml'))
            config_dicts = []
            # Create config dictionaries for all trials of the participant
            for (root,dirs,files) in os.walk(config_dir):
                if 'Config.toml' in files and root != config_dir:
                    trial_config_dict = toml.load(os.path.join(root, files[0]))
                    # deep copy, otherwise session_config_dict is modified at each iteration within the config_dicts list
                    temp_dict = deepcopy(session_config_dict)
                    temp_dict = recursive_update(temp_dict,trial_config_dict)
                    temp_dict.get("project").update({"project_dir":os.path.join(config_dir, os.path.relpath(root))})
                    if not os.path.basename(root) in temp_dict.get("project").get('exclude_from_batch'):
                        config_dicts.append(temp_dict)

    return level, config_dicts


def calibration(config=None):
    '''
    Cameras calibration from checkerboards or from qualisys files.

    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.calibration import calibrate_cams_all

    level, config_dicts = read_config_files(config)
    config_dict = config_dicts[0]
    try:
        session_dir = os.path.realpath([os.getcwd() if level==2 else os.path.join(os.getcwd(), '..')][0])
        [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]
    except:
        session_dir = os.path.realpath(os.getcwd())
    config_dict.get("project").update({"project_dir":session_dir})

    # Set up logging
    setup_logging(session_dir)
    currentDateAndTime = datetime.now()

    # Run calibration
    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]
    logging.info("\n---------------------------------------------------------------------")
    logging.info("Camera calibration")
    logging.info(f"On {currentDateAndTime.strftime('%A %d. %B %Y, %H:%M:%S')}")
    logging.info(f"Calibration directory: {calib_dir}")
    logging.info("---------------------------------------------------------------------\n")
    start = time.time()

    calibrate_cams_all(config_dict)

    end = time.time()
    logging.info(f'\nCalibration took {end-start:.2f} s.\n')


def poseEstimation(config=None):
    '''
    Estimate pose using RTMLib

    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.poseEstimation import rtm_estimator # The name of the function might change

    level, config_dicts = read_config_files(config)

    if isinstance(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>"})')

    # Set up logging
    session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '.'))
    setup_logging(session_dir)

    # Batch process all trials
    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 not frame_range else f"frames {frame_range[0]} to {frame_range[1]}"][0]

        logging.info("\n---------------------------------------------------------------------")
        logging.info(f"Pose estimation 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")

        rtm_estimator(config_dict)
        
        end = time.time()
        elapsed = end - start
        logging.info(f'\nPose estimation took {time.strftime("%Hh%Mm%Ss", time.gmtime(elapsed))}.\n')


def synchronization(config=None):
    '''
    Synchronize cameras if needed.

    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.
    '''

    # Import the function
    from Pose2Sim.synchronization import synchronize_cams_all

    # Determine the level at which the function is called (root:2, trial:1)
    level, config_dicts = read_config_files(config)

    if type(config)==dict:
        config_dict = config_dicts[0]
        if config_dict.get('project').get('project_dir') == None:
            raise ValueError('Please specify the project directory in config_dict:\n \
                             config_dict.get("project").update({"project_dir":"<YOUR_TRIAL_DIRECTORY>"})')

    # Set up logging
    session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '.'))
    setup_logging(session_dir)

    # Batch process all trials
    for config_dict in config_dicts:
        start = time.time()
        currentDateAndTime = datetime.now()
        project_dir = os.path.realpath(config_dict.get('project').get('project_dir'))

        logging.info("\n---------------------------------------------------------------------")
        logging.info("Camera synchronization")
        logging.info(f"On {currentDateAndTime.strftime('%A %d. %B %Y, %H:%M:%S')}")
        logging.info(f"Project directory: {project_dir}")
        logging.info("---------------------------------------------------------------------\n")

        synchronize_cams_all(config_dict)
        
        end = time.time()
        elapsed = end-start
        logging.info(f'\nSynchronization took {time.strftime("%Hh%Mm%Ss", time.gmtime(elapsed))}.\n')


def personAssociation(config=None):
    '''
    Tracking one or several persons of interest.
    Needs a calibration file.

    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.personAssociation import associate_all

    # Determine the level at which the function is called (root:2, trial:1)
    level, config_dicts = read_config_files(config)

    if type(config)==dict:
        config_dict = config_dicts[0]
        if config_dict.get('project').get('project_dir') == None:
            raise ValueError('Please specify the project directory in config_dict:\n \
                             config_dict.get("project").update({"project_dir":"<YOUR_TRIAL_DIRECTORY>"})')

    # Set up logging
    session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '.'))
    setup_logging(session_dir)

    # Batch process all trials
    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"Associating persons 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")

        associate_all(config_dict)
        
        end = time.time()
        elapsed = end-start
        logging.info(f'\nAssociating persons took {time.strftime("%Hh%Mm%Ss", time.gmtime(elapsed))}.\n')


def triangulation(config=None):
    '''
    Robust triangulation of 2D points coordinates.

    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.triangulation import triangulate_all

    # Determine the level at which the function is called (root:2, trial:1)
    level, config_dicts = read_config_files(config)

    if type(config)==dict:
        config_dict = config_dicts[0]
        if config_dict.get('project').get('project_dir') == None:
            raise ValueError('Please specify the project directory in config_dict:\n \
                             config_dict.get("project").update({"project_dir":"<YOUR_TRIAL_DIRECTORY>"})')

    # Set up logging
    session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '.'))
    setup_logging(session_dir)

    # Batch process all trials
    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"Triangulation of 2D points 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")

        triangulate_all(config_dict)
        
        end = time.time()
        elapsed = end-start
        logging.info(f'\nTriangulation took {time.strftime("%Hh%Mm%Ss", time.gmtime(elapsed))}.\n')


def filtering(config=None):
    '''
    Filter trc 3D coordinates.

    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.filtering import filter_all

    # Determine the level at which the function is called (root:2, trial:1)
    level, config_dicts = read_config_files(config)

    if type(config)==dict:
        config_dict = config_dicts[0]
        if config_dict.get('project').get('project_dir') == None:
            raise ValueError('Please specify the project directory in config_dict:\n \
                             config_dict.get("project").update({"project_dir":"<YOUR_TRIAL_DIRECTORY>"})')

    # Set up logging
    session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '.'))
    setup_logging(session_dir)

    # Batch process all trials
    for config_dict in config_dicts:
        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"Filtering 3D coordinates 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}\n")
        logging.info("---------------------------------------------------------------------\n")

        filter_all(config_dict)
        
        logging.info('\n')


def markerAugmentation(config=None):
    '''
    Augment trc 3D coordinates.
    Estimate the position of 43 additional markers.

    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.markerAugmentation import augmentTRC
    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)

    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")

        augmentTRC(config_dict)
        
        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")

        kinematics(config_dict)
        
        end = time.time()
        elapsed = end - start
        logging.info(f'OpenSim 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')