def from_path(session_path, force=False, save=True):
"""
Extract a session from full ALF path (ex: '/scratch/witten/ibl_witten_01/2018-12-18/001')
:param force: (False) overwrite existing files
:param save: (True) boolean or list of ALF file names to extract
:return: None
"""
logger_.info('Extracting ' + str(session_path))
extractor_type = extractors_exist(session_path)
if is_extracted(session_path) and not force:
logger_.info(f"Session {session_path} already extracted.")
return
if extractor_type == 'training':
settings, data = raw.load_bpod(session_path)
logger_.info('training session on ' + settings['PYBPOD_BOARD'])
training_trials.extract_all(session_path, data=data, save=save)
training_wheel.extract_all(session_path, bp_data=data, save=save)
logger_.info('session extracted \n') # timing info in log
if extractor_type == 'biased':
settings, data = raw.load_bpod(session_path)
logger_.info('biased session on ' + settings['PYBPOD_BOARD'])
biased_trials.extract_all(session_path, data=data, save=save)
biased_wheel.extract_all(session_path, bp_data=data, save=save)
logger_.info('session extracted \n') # timing info in log
if extractor_type == 'ephys':
data = raw.load_data(session_path)
ephys_trials.extract_all(session_path, data=data, save=save)
ephys_fpga.extract_all(session_path, save=save)
def from_path(session_path, force=False, save=True):
"""
Extract a session from full ALF path (ex: '/scratch/witten/ibl_witten_01/2018-12-18/001')
:param force: (False) overwrite existing files
:param save: (True) boolean or list of ALF file names to extract
:return: None
"""
extractor_type = get_session_extractor_type(session_path)
logger_.info(f"Extracting {session_path} as {extractor_type}")
if is_extracted(session_path) and not force:
logger_.info(f"Session {session_path} already extracted.")
return
if extractor_type == 'training':
settings, data = rawio.load_bpod(session_path)
logger_.info('training session on ' + settings['PYBPOD_BOARD'])
training_trials.extract_all(session_path, data=data, save=save)
training_wheel.extract_all(session_path, bp_data=data, save=save)
logger_.info('session extracted \n') # timing info in log
if extractor_type == 'biased':
settings, data = rawio.load_bpod(session_path)
logger_.info('biased session on ' + settings['PYBPOD_BOARD'])
biased_trials.extract_all(session_path, data=data, save=save)
biased_wheel.extract_all(session_path, bp_data=data, save=save)
logger_.info('session extracted \n') # timing info in log
if extractor_type == 'ephys':
data = rawio.load_data(session_path)
logger_.info('extract BPOD for ephys session')
ephys_trials.extract_all(session_path, data=data, save=save)
logger_.info('extract FPGA information for ephys session')
tmax = data[-1]['behavior_data']['States timestamps']['exit_state'][0][-1] + 60
ephys_fpga.extract_all(session_path, save=save, tmax=tmax)
if extractor_type == 'sync_ephys':
ephys_fpga.extract_sync(session_path, save=save)