def test_get_iblrig_data_folder(self):
df = ph.get_iblrig_data_folder(subjects=False)
self.assertTrue(isinstance(df, str))
self.assertTrue("iblrig_data" in df)
self.assertTrue("Subjects" not in df)
dfs = ph.get_iblrig_data_folder(subjects=True)
self.assertTrue(isinstance(dfs, str))
self.assertTrue("iblrig_data" in dfs)
self.assertTrue("Subjects" in dfs)
def check_delete_empty_folders(path, rglob_pattern='*', dry=True):
data_path = Path(ph.get_iblrig_data_folder())
all_dirs = {p for p in data_path.rglob(rglob_pattern) if p.is_dir()}
empty_dirs = {p for p in all_dirs if not list(p.glob('*'))}
for d in empty_dirs:
if dry:
print('Found empty folder:', d)
elif not dry:
print('Deleting empty folder: ', d)
d.rmdir()
else:
if dry:
print(f'Empty folders: {len(empty_dirs)}')
elif not dry:
print(f'Deleted folders: {len(empty_dirs)}')
def update_param_key_values(param_key):
if param_key == "NAME":
return get_pybpod_board_name()
elif param_key == "IBLRIG_VERSION":
return get_iblrig_version()
elif param_key == "COM_BPOD":
return get_pybpod_board_comport()
elif param_key == "SCREEN_FREQ_TARGET":
return 60
elif param_key == "DATA_FOLDER_LOCAL":
return ph.get_iblrig_data_folder(subjects=False)
elif param_key == "DATA_FOLDER_REMOTE":
return ph.get_iblserver_data_folder(subjects=False)
else:
return None
return names
def get_mice(session_list):
names = {s.parts[-3] for s in session_list}
return names
def get_dates(session_list):
names = {s.parts[-2] for s in session_list}
return names
# Load
def load_session_settings(path_list):
path_list = [Path(path) for path in path_list]
settings = []
for s in path_list:
settings.append(raw.load_settings(s))
return settings
if __name__ == "__main__":
data_path = Path(ph.get_iblrig_data_folder())
check_delete_empty_files(data_path, 'taskSettings')
check_delete_empty_folders(data_path)
sessions_with_settings = find_sessions(data_path,
rglob_pattern='*taskSettings*')
sessions_with_data = find_sessions(data_path, rglob_pattern='*taskData*')
settings = load_session_settings(sessions_with_settings)
import iblrig.bonsai as bonsai
import iblrig.frame2TTL
import iblrig.params as params
import iblrig.path_helper as ph
import user_settings
sys.stdout.flush()
log = logging.getLogger('iblrig')
log.setLevel(logging.INFO)
PARAMS = params.load_params()
subj = '_iblrig_test_mouse'
datetime = parser.parse(user_settings.PYBPOD_SESSION).isoformat().replace(
':', '_')
folder = Path(ph.get_iblrig_data_folder()) / subj / datetime
folder.mkdir()
bpod_data_file = folder / 'bpod_ts_data.jsonable'
bpod_data_lengths_file = folder / 'bpod_ts_data_lengths.jsonable'
bonsai_data_file = folder / 'bonsai_ts_data.jsonable'
bonsai_data_lengths_file = folder / 'bonsai_ts_data_lengths.jsonable'
def softcode_handler(data):
if data:
# Launch the workflow
bonsai.start_frame2ttl_test(bonsai_data_file, bonsai_data_lengths_file)
return
# Set the thresholds for Frame2TTL
#!/usr/bin/env python
# -*- coding:utf-8 -*-
# @Author: Niccolò Bonacchi
# @Date: Monday, December 2nd 2019, 4:52:40 pm
from pathlib import Path
import ibllib.io.raw_data_loaders as raw
import ibllib.pipes.misc as misc
import iblrig.path_helper as ph
import logging
log = logging.getLogger("iblrig")
IBLRIG_DATA_PATH = Path(ph.get_iblrig_data_folder())
def main():
passive_sessions = IBLRIG_DATA_PATH.rglob("passive_data_for_ephys.flag")
# For each passive session found look into passiveSettings to find ephysSession name
# search for the ephys session session in the rglobbed ephys sessions
# If you find it just rename and move the folder raw_behavior_data -> raw_passive_data,
# If no find search specifically for that session from the metadata and try to copy the folder
# If folder exists throw an error
for ps in passive_sessions:
sett = raw.load_settings(str(ps.parent))
esess = sett["CORRESPONDING_EPHYS_SESSION"]
if not esess or esess is None:
log.warning(
"Corresponding ephys session NOT FOUND in settings - data not moved"
)
