clearer error when empty pose directories

Pose2Sim/Pose2Sim.py

@@ -99,8 +99,7 @@ def determine_level(config_dir):
  '''
  Determine the level at which the function is called.
  Level = 1: Trial folder
- Level = 2: Participant folder
- Level = 3: Session 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]
@@ -112,12 +111,12 @@ def determine_level(config_dir):
 
 def read_config_files(config):
  '''
- Read Session, Participant, and Trial configuration files, 
+ Read Root and Trial configuration files, 
  and output a dictionary with all the parameters.
  '''
 
  if type(config)==dict:
- level = 3 # log_dir = os.getcwd()
+ 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 \
@@ -128,12 +127,10 @@ def read_config_files(config):
  level = determine_level(config_dir)
 
  # Trial level
- if level == 1: 
+ if level == 1: # Trial
  try:
  # if batch
- session_config_dict = toml.load(os.path.join(config_dir, '..','..','Config.toml'))
- participant_config_dict = toml.load(os.path.join(config_dir, '..','Config.toml'))
- session_config_dict = recursive_update(session_config_dict,participant_config_dict)
+ 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:
@@ -142,44 +139,21 @@ def read_config_files(config):
  session_config_dict.get("project").update({"project_dir":config_dir})
  config_dicts = [session_config_dict]
 
- # Participant level
+ # Root level
  if level == 2:
- session_config_dict = toml.load(os.path.join(config_dir, '..','Config.toml'))
- participant_config_dict = toml.load(os.path.join(config_dir, 'Config.toml'))
+ 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,participant_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)
 
- # Session level
- if level == 3:
- session_config_dict = toml.load(os.path.join(config_dir, 'Config.toml'))
- config_dicts = []
- # Create config dictionaries for all trials of all participants of the session
- for (root,dirs,files) in os.walk(config_dir):
- if 'Config.toml' in files and root != config_dir:
- # participant
- if determine_level(root) == 2:
- participant_config_dict = toml.load(os.path.join(root, files[0]))
- # trial 
- elif determine_level(root) == 1: 
- 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,participant_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.relpath(root) in [os.path.relpath(p) for p in temp_dict.get("project").get('exclude_from_batch')]:
- config_dicts.append(temp_dict)
-
  return level, config_dicts
 
 
@@ -197,7 +171,7 @@ def calibration(config=None):
  level, config_dicts = read_config_files(config)
  config_dict = config_dicts[0]
  try:
- 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_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() ][0]
  except:
  session_dir = os.path.realpath(os.getcwd())
@@ -242,7 +216,7 @@ def poseEstimation(config=None):
  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'), '..', '..'))
+ session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '..'))
  setup_logging(session_dir)
 
  # Batch process all trials
@@ -289,7 +263,7 @@ def synchronization(config=None):
  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'), '..', '..'))
+ session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '..'))
  setup_logging(session_dir) 
 
  # Batch process all trials
@@ -333,7 +307,7 @@ def personAssociation(config=None):
  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'), '..', '..'))
+ session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '..'))
  setup_logging(session_dir) 
 
  # Batch process all trials
@@ -379,7 +353,7 @@ def triangulation(config=None):
  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'), '..', '..'))
+ session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '..'))
  setup_logging(session_dir) 
 
  # Batch process all trials
@@ -425,13 +399,9 @@ def filtering(config=None):
  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'), '..', '..'))
+ session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '..'))
  setup_logging(session_dir)
 
- # 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()
@@ -468,7 +438,7 @@ def markerAugmentation(config=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'), '..', '..'))
+ 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:
@@ -517,7 +487,7 @@ def opensimProcessing(config=None):
  # 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'), '..', '..'))
+ # session_dir = os.path.realpath(os.path.join(config_dicts[0].get('project').get('project_dir'), '..'))
  # setup_logging(session_dir) 
 
  # # Batch process all trials
@@ -547,3 +517,89 @@ def opensimProcessing(config=None):
  # # else:
  # # logging.info(f'Inverse kinematics took {time.strftime("%Hh%Mm%Ss", time.gmtime(elapsed))}.')
 
+
+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_opensimProcessing=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.
+ '''
+
+ # Determine the level at which the function is called (session:3, participant: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\n=====================================================================")
+ logging.info(f"RUNNING ALL FOR {seq_name}, FOR {frames}.")
+ logging.info(f"On {currentDateAndTime.strftime('%A %d. %B %Y, %H:%M:%S')}")
+ logging.info("=====================================================================")
+ logging.info(f"\nProject directory: {project_dir}\n")
+
+ if do_calibration:
+ logging.info('\nRUNNING CALIBRATION...')
+ calibration(config)
+ else: 
+ logging.info('\nSKIPPING CALIBRATION.')
+
+ if do_poseEstimation:
+ logging.info('\nRUNNING POSE ESTIMATION...')
+ poseEstimation(config)
+ else:
+ logging.info('\nSKIPPING POSE ESTIMATION.')
+
+ if do_synchronization:
+ logging.info('\nRUNNING SYNCHRONIZATION...')
+ synchronization(config)
+ else:
+ logging.info('\nSKIPPING SYNCHRONIZATION.')
+
+ if do_personAssociation:
+ logging.info('\nRUNNING PERSON ASSOCIATION...')
+ personAssociation(config)
+ else:
+ logging.info('\nSKIPPING PERSON ASSOCIATION.')
+
+ if do_triangulation:
+ logging.info('\nRUNNING TRIANGULATION...')
+ triangulation(config)
+ else:
+ logging.info('\nSKIPPING TRIANGULATION.')
+
+ if do_filtering:
+ logging.info('\nRUNNING FILTERING...')
+ filtering(config)
+ else:
+ logging.info('\nSKIPPING FILTERING.')
+
+ if do_markerAugmentation:
+ logging.info('\nRUNNING MARKER AUGMENTATION.')
+ markerAugmentation(config)
+ else:
+ logging.info('\nSKIPPING MARKER AUGMENTATION.')
+
+ # if do_opensimProcessing:
+ # logging.info('\nRUNNING OPENSIM PROCESSING.')
+ # opensimProcessing(config)
+ # else:
+ # logging.info('\nSKIPPING OPENSIM PROCESSING.')
+
+ end = time.time()
+ elapsed = end-start 
+ logging.info(f'\nRUNNING ALL FUNCTIONS TOOK {time.strftime("%Hh%Mm%Ss", time.gmtime(elapsed))}.')

Pose2Sim/personAssociation.py

@@ -669,12 +669,19 @@ def track_2d_all(config_dict):
 
  # 2d-pose files selection
  pose_listdirs_names = next(os.walk(pose_dir))[1]
- pose_listdirs_names = sort_stringlist_by_last_number(pose_listdirs_names)
+ try:
+ pose_listdirs_names = sort_stringlist_by_last_number(pose_listdirs_names)
+ os.listdir(os.path.join(pose_dir, pose_listdirs_names[0]))[0]
+ except:
+ raise ValueError(f'No json files found in {pose_dir} subdirectories. Make sure you run Pose2Sim.poseEstimation() first.')
  json_dirs_names = [k for k in pose_listdirs_names if 'json' in k]
  try: 
  json_files_names = [fnmatch.filter(os.listdir(os.path.join(poseSync_dir, js_dir)), '*.json') for js_dir in json_dirs_names]
  except:
- json_files_names = [fnmatch.filter(os.listdir(os.path.join(pose_dir, js_dir)), '*.json') for js_dir in json_dirs_names]
+ try:
+ json_files_names = [fnmatch.filter(os.listdir(os.path.join(pose_dir, js_dir)), '*.json') for js_dir in json_dirs_names]
+ except:
+ raise ValueError(f'No json files found in {pose_dir} nor {poseSync_dir} subdirectories. Make sure you run Pose2Sim.poseEstimation() first.')
  json_files_names = [sort_stringlist_by_last_number(j) for j in json_files_names]
 
  # 2d-pose-associated files creation

Pose2Sim/synchronization.py

@@ -290,8 +290,9 @@ def synchronize_cams_all(config_dict):
  # List json files
  try:
  pose_listdirs_names = next(os.walk(pose_dir))[1]
+ os.listdir(os.path.join(pose_dir, pose_listdirs_names[0]))[0]
  except:
- raise ValueError(f'No json files found in {pose_dir}. Make sure you run Pose2Sim.poseEstimation() first.')
+ raise ValueError(f'No json files found in {pose_dir} subdirectories. Make sure you run Pose2Sim.poseEstimation() first.')
  pose_listdirs_names = sort_stringlist_by_last_number(pose_listdirs_names)
  json_dirs_names = [k for k in pose_listdirs_names if 'json' in k]
  json_dirs = [os.path.join(pose_dir, j_d) for j_d in json_dirs_names] # list of json directories in pose_dir

Pose2Sim/triangulation.py

@@ -778,7 +778,11 @@ def triangulate_all(config_dict):
  keypoints_idx_swapped = [keypoints_names.index(keypoint_name_swapped) for keypoint_name_swapped in keypoints_names_swapped] # find index of new keypoint_name
 
  # 2d-pose files selection
- pose_listdirs_names = next(os.walk(pose_dir))[1]
+ try:
+ pose_listdirs_names = next(os.walk(pose_dir))[1]
+ os.listdir(os.path.join(pose_dir, pose_listdirs_names[0]))[0]
+ except:
+ raise ValueError(f'No json files found in {pose_dir} subdirectories. Make sure you run Pose2Sim.poseEstimation() first.')
  pose_listdirs_names = sort_stringlist_by_last_number(pose_listdirs_names)
  json_dirs_names = [k for k in pose_listdirs_names if 'json' in k]
  n_cams = len(json_dirs_names)
@@ -790,7 +794,10 @@ def triangulate_all(config_dict):
  json_files_names = [fnmatch.filter(os.listdir(os.path.join(poseSync_dir, js_dir)), '*.json') for js_dir in json_dirs_names]
  pose_dir = poseSync_dir
  except:
- json_files_names = [fnmatch.filter(os.listdir(os.path.join(pose_dir, js_dir)), '*.json') for js_dir in json_dirs_names]
+ try:
+ json_files_names = [fnmatch.filter(os.listdir(os.path.join(pose_dir, js_dir)), '*.json') for js_dir in json_dirs_names]
+ except:
+ raise Exception(f'No json files found in {pose_dir}, {poseSync_dir}, nor {poseTracked_dir} subdirectories. Make sure you run Pose2Sim.poseEstimation() first.')
  json_files_names = [sort_stringlist_by_last_number(js) for js in json_files_names] 
 
  # frame range selection