def eid_from_path(self, path_obj):
"""
From a local path, gets the experiment id
:param path_obj: local path or list of local paths
:return: eid or list of eids
"""
# If path_obj is a list recurse through it and return a list
if isinstance(path_obj, list):
path_obj = [Path(x) for x in path_obj]
eid_list = []
for p in path_obj:
eid_list.append(self.eid_from_path(p))
return eid_list
# else ensure the path ends with mouse,date, number
path_obj = Path(path_obj)
session_path = alfio.get_session_path(path_obj)
# if path does not have a date and a number, or cache is empty return None
if session_path is None or self._cache.size == 0:
return None
# fetch eid from cache
ind = ((self._cache['subject'] == session_path.parts[-3]) &
(self._cache['start_time'].apply(
lambda x: x.isoformat()[:10] == session_path.parts[-2])) &
(self._cache['number']) == int(session_path.parts[-1]))
ind = np.where(ind.to_numpy())[0]
if ind.size > 0:
return parquet.np2str(self._cache[['eid_0', 'eid_1']].iloc[ind[0]])
def eid_from_path(self,
path_obj: Union[str, Path],
use_cache: bool = True) -> Listable(Path):
"""
From a local path, gets the experiment id
:param path_obj: local path or list of local paths
:param use_cache: if set to False, will force database connection
:return: eid or list of eids
"""
# If path_obj is a list recurse through it and return a list
if isinstance(path_obj, list):
path_obj = [Path(x) for x in path_obj]
eid_list = []
for p in path_obj:
eid_list.append(self.eid_from_path(p))
return eid_list
# else ensure the path ends with mouse,date, number
path_obj = Path(path_obj)
session_path = alfio.get_session_path(path_obj)
# if path does not have a date and a number return None
if session_path is None:
return None
# try the cached info to possibly avoid hitting database
cache_eid = super().eid_from_path(path_obj)
if cache_eid:
return cache_eid
# if not search for subj, date, number XXX: hits the DB
uuid = self.search(subjects=session_path.parts[-3],
date_range=session_path.parts[-2],
number=session_path.parts[-1])
# Return the uuid if any
return uuid[0] if uuid else None
def get_task_extractor_type(task_name):
"""
Splits the task name according to naming convention:
- ignores everything
_iblrig_tasks_biasedChoiceWorld3.7.0 returns "biased"
_iblrig_tasks_trainingChoiceWorld3.6.0 returns "training'
:param task_name:
:return: one of ['biased', 'habituation', 'training', 'ephys', 'mock_ephys', 'sync_ephys']
"""
if isinstance(task_name, Path):
try:
settings = rawio.load_settings(get_session_path(task_name))
except json.decoder.JSONDecodeError:
return
if settings:
task_name = settings.get('PYBPOD_PROTOCOL', None)
else:
return
if '_biasedChoiceWorld' in task_name:
return 'biased'
elif 'biasedScanningChoiceWorld' in task_name:
return 'biased'
elif 'biasedVisOffChoiceWorld' in task_name:
return 'biased'
elif '_habituationChoiceWorld' in task_name:
return 'habituation'
elif '_trainingChoiceWorld' in task_name:
return 'training'
elif 'ephysChoiceWorld' in task_name:
return 'ephys'
elif 'ephysMockChoiceWorld' in task_name:
return 'mock_ephys'
elif task_name and task_name.startswith('_iblrig_tasks_ephys_certification'):
return 'sync_ephys'
def get_task_extractor_type(task_name):
"""
Returns the task type string from the full pybpod task name:
_iblrig_tasks_biasedChoiceWorld3.7.0 returns "biased"
_iblrig_tasks_trainingChoiceWorld3.6.0 returns "training'
:param task_name:
:return: one of ['biased', 'habituation', 'training', 'ephys', 'mock_ephys', 'sync_ephys']
"""
if isinstance(task_name, Path):
try:
settings = load_settings(get_session_path(task_name))
except json.decoder.JSONDecodeError:
return
if settings:
task_name = settings.get('PYBPOD_PROTOCOL', None)
else:
return
task_types = _get_task_types_json_config()
return next((task_types[tt] for tt in task_types if tt in task_name), None)
def eid_from_path(self, path_obj):
# If path_obj is a list recurse through it and return a list
if isinstance(path_obj, list):
path_obj = [Path(x) for x in path_obj]
eid_list = []
for p in path_obj:
eid_list.append(self.eid_from_path(p))
return eid_list
# else ensure the path ends with mouse,date, number
path_obj = Path(path_obj)
session_path = get_session_path(path_obj)
# if path does not have a date and a number return None
if session_path is None:
return None
# search for subj, date, number XXX: hits the DB
uuid = self.search(subjects=session_path.parts[-3],
date_range=session_path.parts[-2],
number=session_path.parts[-1])
# Return the uuid if any
return uuid[0] if uuid else None
def eid_from_path(self, path_obj, use_cache=True):
"""
From a local path, gets the experiment id
:param path_obj: local path or list of local paths
:param use_cache: if set to False, will force database connection
:return: eid or list of eids
"""
# If path_obj is a list recurse through it and return a list
if isinstance(path_obj, list):
path_obj = [Path(x) for x in path_obj]
eid_list = []
for p in path_obj:
eid_list.append(self.eid_from_path(p))
return eid_list
# else ensure the path ends with mouse,date, number
path_obj = Path(path_obj)
session_path = alfio.get_session_path(path_obj)
# if path does not have a date and a number return None
if session_path is None:
return None
# try the cached info to possibly avoid hitting database
if self._cache.size > 0 and use_cache:
ind = ((self._cache['subject'] == session_path.parts[-3]) &
(self._cache['start_time'].apply(
lambda x: x.isoformat()[:10] == session_path.parts[-2]))
& (self._cache['number']) == int(session_path.parts[-1]))
ind = np.where(ind.to_numpy())[0]
if ind.size > 0:
return parquet.np2str(self._cache[['eid_0',
'eid_1']].iloc[ind[0]])
# if not search for subj, date, number XXX: hits the DB
uuid = self.search(subjects=session_path.parts[-3],
date_range=session_path.parts[-2],
number=session_path.parts[-1])
# Return the uuid if any
return uuid[0] if uuid else None
def path_from_eid(self, eid: str, grep_str=None) -> Path:
# If eid is a list of eIDs recurse through list and return the results
if isinstance(eid, list):
path_list = []
for p in eid:
path_list.append(self.path_from_eid(p, grep_str=grep_str))
return path_list
# If not valid return None
if not is_uuid_string(eid):
print(eid, " is not a valid eID/UUID string")
return
# Load data, if no data present on disk return None
data = self._load(eid, download_only=True, offline=True)
if not data.local_path:
return None
# If user defined a grep list of specific files return paths to files
if grep_str is not None:
files = [x for x in data.local_path if grep_str in str(x)]
return files
# If none of the above happen return the session path of the first file you find
session_path = get_session_path(data.local_path[0])
return session_path