daily commit
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davidpagnon
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b0d89e08b3
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96b1d59351
@ -123,7 +123,7 @@ def read_config_files(level):
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temp_dict = deepcopy(session_config_dict)
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temp_dict = recursive_update(temp_dict,participant_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(os.getcwd(), os.path.basename(root))})
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temp_dict.get("project").update({"project_dir":os.path.join(os.getcwd(), 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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@ -144,14 +144,14 @@ def read_config_files(level):
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temp_dict = deepcopy(session_config_dict)
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temp_dict = recursive_update(temp_dict,participant_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(os.getcwd(), root)})
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temp_dict.get("project").update({"project_dir":os.path.join(os.getcwd(), os.path.relpath(root))})
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if not os.path.relpath(root) in [os.path.relpath(p) for p in temp_dict.get("project").get('exclude_from_batch')]:
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config_dicts.append(temp_dict)
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return config_dicts
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def base_params(config_dict):
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def base_params(config_dict, level):
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'''
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Retrieve sequence name and frames to be analyzed.
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'''
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@ -161,64 +161,49 @@ def base_params(config_dict):
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seq_name = os.path.basename(project_dir)
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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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if not os.path.exists('User'): os.mkdir('User')
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with open(os.path.join(project_dir, 'User', 'logs.txt'), 'a+') as log_f: pass
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log_dir = os.path.realpath([os.getcwd() if level==3 else os.path.join(os.getcwd(), '..') if level==2 else os.path.join(os.getcwd(), '..', '..')][0])
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with open(os.path.join(log_dir, 'logs.txt'), 'a+') as log_f: pass
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logging.basicConfig(format='%(message)s', level=logging.INFO,
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handlers = [logging.handlers.TimedRotatingFileHandler(os.path.join(project_dir, 'User', 'logs.txt'), when='D', interval=7), logging.StreamHandler()])
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handlers = [logging.handlers.TimedRotatingFileHandler(os.path.join(log_dir, 'logs.txt'), when='D', interval=7), logging.StreamHandler()])
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return project_dir, seq_name, frames
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def calibration(config='Config.toml'):
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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 either be a path or a dictionary (for batch processing)
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config is usually deduced from the path the function is called from
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(see read_config_files(level) function) but it can also be a dictionary
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'''
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from Pose2Sim.calibration import calibrate_cams_all
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if type(config)==dict:
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config_dict = config # which project?
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level = 3 # log_dir = os.getcwd()
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config_dict = config
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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_PROJECT_DIRECTORY>"})')
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else:
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# Determine the level at which the function is called (session:3, participant:2, trial:1)
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level = determine_level()
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config_dict = read_config_files(level)[0]
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if level == 1: # trial
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session_config_dict = toml.load(os.path.join('..','..','Config.toml'))
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participant_config_dict = toml.load(os.path.join('..','Config.toml'))
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trial_config_dict = toml.load('Config.toml')
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session_config_dict.update(participant_config_dict)
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session_config_dict.update(trial_config_dict)
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session_config_dict.get("project").update({"project_dir":os.path.join('..','..',os.getcwd())})
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if level == 2: # participant
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session_config_dict = toml.load(os.path.join('..','Config.toml'))
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participant_config_dict = toml.load('Config.toml')
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session_config_dict.update(participant_config_dict)
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session_config_dict.get("project").update({"project_dir":os.path.join('..',os.getcwd())})
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if level == 3: # session
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session_config_dict = toml.load('Config.toml')
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session_config_dict.get("project").update({"project_dir":os.getcwd()})
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config_dict = session_config_dict
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session_dir = os.path.realpath([os.getcwd() if level==3 else os.path.join(os.getcwd(), '..') if level==2 else os.path.join(os.getcwd(), '..', '..')][0])
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config_dict.get("project").update({"project_dir":session_dir})
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# Set up logging
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with open(os.path.join(session_dir, 'logs.txt'), 'a+') as log_f: pass
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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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# config_dicts = read_config_files(level)
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#LANCER LA CALIBRATION
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project_dir, seq_name, frames = base_params(config_dict)
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# Path to the calibration directory
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calib_dir = [os.path.join(session_dir, c) for c in os.listdir(session_dir) if ('Calib' or 'calib') in c][0]
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logging.info("\n\n---------------------------------------------------------------------")
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logging.info("Camera calibration")
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logging.info("---------------------------------------------------------------------")
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logging.info(f"\nProject directory: {project_dir}")
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logging.info(f"\nCalibration directory: {calib_dir}")
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start = time.time()
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calibrate_cams_all(config_dict)
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@ -227,7 +212,7 @@ def calibration(config='Config.toml'):
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logging.info(f'Calibration took {end-start:.2f} s.')
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def poseEstimation(config='Config.toml'):
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def poseEstimation(config=None):
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'''
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Estimate pose using BlazePose, OpenPose, AlphaPose, or DeepLabCut.
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@ -257,7 +242,7 @@ def poseEstimation(config='Config.toml'):
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logging.info(f'Pose estimation took {end-start:.2f} s.')
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def synchronization(config='Config.toml'):
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def synchronization(config=None):
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'''
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Synchronize cameras if needed.
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@ -287,7 +272,7 @@ def synchronization(config='Config.toml'):
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logging.info(f'Synchronization took {end-start:.2f} s.')
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def personAssociation(config='Config.toml'):
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def personAssociation(config=None):
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'''
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Tracking of the person of interest in case of multiple persons detection.
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Needs a calibration file.
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@ -315,7 +300,7 @@ def personAssociation(config='Config.toml'):
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logging.info(f'Tracking took {end-start:.2f} s.')
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def triangulation(config='Config.toml'):
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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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@ -342,7 +327,7 @@ def triangulation(config='Config.toml'):
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logging.info(f'Triangulation took {end-start:.2f} s.')
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def filtering(config='Config.toml'):
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def filtering(config=None):
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'''
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Filter trc 3D coordinates.
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@ -365,7 +350,7 @@ def filtering(config='Config.toml'):
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filter_all(config_dict)
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def scalingModel(config='Config.toml'):
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def scalingModel(config=None):
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'''
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Uses OpenSim to scale a model based on a static 3D pose.
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@ -395,7 +380,7 @@ def scalingModel(config='Config.toml'):
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logging.info(f'Model scaling took {end-start:.2f} s.')
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def inverseKinematics(config='Config.toml'):
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def inverseKinematics(config=None):
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'''
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Uses OpenSim to perform inverse kinematics.
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@ -1192,7 +1192,7 @@ def calibrate_cams_all(config):
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Prints recap.
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INPUTS:
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- a Config.toml file
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- a config dictionary
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OUTPUT:
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- a .toml camera calibration file
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@ -1200,8 +1200,7 @@ def calibrate_cams_all(config):
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# Read config
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project_dir = config.get('project').get('project_dir')
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if project_dir == '': project_dir = os.getcwd()
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calib_dir = os.path.join(project_dir, 'Calibration')
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calib_dir = [os.path.join(session_dir, c) for c in os.listdir(session_dir) if ('Calib' or 'calib') in c][0]
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calib_type = config.get('calibration').get('calibration_type')
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if calib_type=='convert':
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