daily commit

This commit is contained in:
davidpagnon 2023-12-08 09:39:34 +01:00
parent b0d89e08b3
commit 96b1d59351
2 changed files with 31 additions and 47 deletions

View File

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

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@ -1192,7 +1192,7 @@ def calibrate_cams_all(config):
Prints recap. Prints recap.
INPUTS: INPUTS:
- a Config.toml file - a config dictionary
OUTPUT: OUTPUT:
- a .toml camera calibration file - a .toml camera calibration file
@ -1200,8 +1200,7 @@ def calibrate_cams_all(config):
# Read config # Read config
project_dir = config.get('project').get('project_dir') project_dir = config.get('project').get('project_dir')
if project_dir == '': project_dir = os.getcwd() calib_dir = [os.path.join(session_dir, c) for c in os.listdir(session_dir) if ('Calib' or 'calib') in c][0]
calib_dir = os.path.join(project_dir, 'Calibration')
calib_type = config.get('calibration').get('calibration_type') calib_type = config.get('calibration').get('calibration_type')
if calib_type=='convert': if calib_type=='convert':