def _read_settings_json_compatibility_enforced(json_file):
with open(json_file) as js:
md = json.load(js)
if 'IBLRIG_VERSION_TAG' not in md.keys():
md['IBLRIG_VERSION_TAG'] = '3.2.3'
if not md['IBLRIG_VERSION_TAG']:
logger_.warning("You appear to be on an untagged version...")
return md
# 2018-12-05 Version 3.2.3 fixes (permanent fixes in IBL_RIG from 3.2.4 on)
if version.le(md['IBLRIG_VERSION_TAG'], '3.2.3'):
if 'LAST_TRIAL_DATA' in md.keys():
md.pop('LAST_TRIAL_DATA')
if 'weighings' in md['PYBPOD_SUBJECT_EXTRA'].keys():
md['PYBPOD_SUBJECT_EXTRA'].pop('weighings')
if 'water_administration' in md['PYBPOD_SUBJECT_EXTRA'].keys():
md['PYBPOD_SUBJECT_EXTRA'].pop('water_administration')
if 'IBLRIG_COMMIT_HASH' not in md.keys():
md['IBLRIG_COMMIT_HASH'] = 'f9d8905647dbafe1f9bdf78f73b286197ae2647b'
# parse the date format to Django supported ISO
dt = dateparser.parse(md['SESSION_DATETIME'])
md['SESSION_DATETIME'] = ibllib.time.date2isostr(dt)
# add the weight key if it doesn't already exists
if 'SUBJECT_WEIGHT' not in md.keys():
md['SUBJECT_WEIGHT'] = None
return md
def rename_files_compatibility(ses_path, version_tag):
if version.le(version_tag, '3.2.3'):
task_code = ses_path.glob('**/_ibl_trials.iti_duration.npy')
for fn in task_code:
fn.replace(fn.parent.joinpath('_ibl_trials.itiDuration.npy'))
task_code = ses_path.glob('**/_iblrig_taskCodeFiles.raw.zip')
for fn in task_code:
fn.replace(fn.parent.joinpath('_iblrig_codeFiles.raw.zip'))
def extract_all(session_path, save=True, bpod_trials=None, settings=None):
"""
Extracts a training session from its path. NB: Wheel must be extracted first in order to
extract trials.firstMovement_times.
:param session_path: the path to the session to be extracted
:param save: if true a subset of the extracted data are saved as ALF
:param bpod_trials: list of Bpod trial data
:param settings: the Bpod session settings
:return: trials: Bunch/dict of trials
:return: wheel: Bunch/dict of wheel positions
:return: out_Files: list of output files
"""
extractor_type = ibllib.io.extractors.base.get_session_extractor_type(
session_path)
_logger.info(f"Extracting {session_path} as {extractor_type}")
bpod_trials = bpod_trials or rawio.load_data(session_path)
settings = settings or rawio.load_settings(session_path)
if extractor_type == 'training':
_logger.info('training session on ' + settings['PYBPOD_BOARD'])
wheel, files_wheel = training_wheel.extract_all(
session_path,
bpod_trials=bpod_trials,
settings=settings,
save=save)
trials, files_trials = training_trials.extract_all(
session_path,
bpod_trials=bpod_trials,
settings=settings,
save=save)
elif extractor_type == 'biased' or extractor_type == 'ephys':
_logger.info('biased session on ' + settings['PYBPOD_BOARD'])
wheel, files_wheel = training_wheel.extract_all(
session_path,
bpod_trials=bpod_trials,
settings=settings,
save=save)
trials, files_trials = biased_trials.extract_all(
session_path,
bpod_trials=bpod_trials,
settings=settings,
save=save)
elif extractor_type == 'habituation':
from ibllib.misc import version
_logger.info('habituation session on ' + settings['PYBPOD_BOARD'])
if version.le(settings['IBLRIG_VERSION_TAG'], '5.0.0'):
_logger.warning("No extraction of legacy habituation sessions")
return None, None, None
trials, files_trials = habituation_trials.extract_all(
session_path,
bpod_trials=bpod_trials,
settings=settings,
save=save)
wheel = None
files_wheel = []
else:
raise ValueError(f"No extractor for task {extractor_type}")
_logger.info('session extracted \n') # timing info in log
return trials, wheel, (files_trials + files_wheel) if save else None
def extract_all(session_path, save=True, bpod_trials=None, settings=None):
"""
Extracts a training session from its path. NB: Wheel must be extracted first in order to
extract trials.firstMovement_times.
:param session_path: the path to the session to be extracted
:param save: if true a subset of the extracted data are saved as ALF
:param bpod_trials: list of Bpod trial data
:param settings: the Bpod session settings
:return: trials: Bunch/dict of trials
:return: wheel: Bunch/dict of wheel positions
:return: out_Files: list of output files
"""
extractor_type = ibllib.io.extractors.base.get_session_extractor_type(session_path)
_logger.info(f"Extracting {session_path} as {extractor_type}")
bpod_trials = bpod_trials or rawio.load_data(session_path)
settings = settings or rawio.load_settings(session_path)
_logger.info(f'{extractor_type} session on {settings["PYBPOD_BOARD"]}')
# Determine which additional extractors are required
extra = []
if extractor_type == 'ephys': # Should exclude 'ephys_biased'
_logger.debug('Engaging biased TrialsTableEphys')
extra.append(biased_trials.TrialsTableEphys)
if extractor_type in ['biased_opto', 'ephys_biased_opto']:
_logger.debug('Engaging opto_trials LaserBool')
extra.append(opto_trials.LaserBool)
# Determine base extraction
if extractor_type in ['training', 'ephys_training']:
trials, files_trials = training_trials.extract_all(
session_path, bpod_trials=bpod_trials, settings=settings, save=save)
# This is hacky but avoids extracting the wheel twice.
# files_trials should contain wheel files at the end.
files_wheel = []
wheel = OrderedDict({k: trials.pop(k) for k in tuple(trials.keys()) if 'wheel' in k})
elif 'biased' in extractor_type or 'ephys' in extractor_type:
trials, files_trials = biased_trials.extract_all(
session_path, bpod_trials=bpod_trials, settings=settings, save=save, extra_classes=extra)
files_wheel = []
wheel = OrderedDict({k: trials.pop(k) for k in tuple(trials.keys()) if 'wheel' in k})
elif extractor_type == 'habituation':
if settings['IBLRIG_VERSION_TAG'] and version.le(settings['IBLRIG_VERSION_TAG'], '5.0.0'):
_logger.warning("No extraction of legacy habituation sessions")
return None, None, None
trials, files_trials = habituation_trials.extract_all(
session_path, bpod_trials=bpod_trials, settings=settings, save=save)
wheel = None
files_wheel = []
else:
raise ValueError(f"No extractor for task {extractor_type}")
_logger.info('session extracted \n') # timing info in log
return trials, wheel, (files_trials + files_wheel) if save else None
def _read_settings_json_compatibility_enforced(json_file):
with open(json_file) as js:
md = json.load(js)
if 'IBLRIG_VERSION_TAG' not in md.keys():
md['IBLRIG_VERSION_TAG'] = '3.2.3'
# 2018-12-05 Version 3.2.3 fixes (permanent fixes in IBL_RIG from 3.2.4 on)
if version.le(md['IBLRIG_VERSION_TAG'], '3.2.3'):
if 'LAST_TRIAL_DATA' in md.keys():
md.pop('LAST_TRIAL_DATA')
if 'weighings' in md['PYBPOD_SUBJECT_EXTRA'].keys():
md['PYBPOD_SUBJECT_EXTRA'].pop('weighings')
if 'water_administration' in md['PYBPOD_SUBJECT_EXTRA'].keys():
md['PYBPOD_SUBJECT_EXTRA'].pop('water_administration')
if 'IBLRIG_COMMIT_HASH' not in md.keys():
md['IBLRIG_COMMIT_HASH'] = 'f9d8905647dbafe1f9bdf78f73b286197ae2647b'
# change the date format to proper ISO
dt = datetime.datetime.strptime(md['SESSION_DATETIME'], '%Y-%m-%d %H:%M:%S.%f')
md['SESSION_DATETIME'] = ibllib.time.date2isostr(dt)
if 'SUBJECT_WEIGHT' not in md.keys():
md['SUBJECT_WEIGHT'] = None
return md
def assert_g(self, v0, v_):
self.assertFalse(version.eq(v0, v_))
self.assertTrue(version.ge(v0, v_))
self.assertFalse(version.le(v0, v_))
self.assertTrue(version.gt(v0, v_))
self.assertFalse(version.lt(v0, v_))
