lab.activate(db_prefix + "lab")
subject.activate(db_prefix + "subject", linking_module=__name__)
Session = session.Session
Experimenter = lab.User
session.activate(db_prefix + "session", linking_module=__name__)
# Activate "event" and "trial" schema ---------------------------------
trial.activate(db_prefix + "trial",
db_prefix + "event",
linking_module=__name__)
# ------------- Declare table Equipment for use in element_calcium_imaging -------------
@lab.schema
class Equipment(dj.Manual):
definition = """
scanner: varchar(32)
"""
# ------------- Activate "imaging" schema -------------
imaging.activate(db_prefix + "imaging",
db_prefix + "scan",
linking_module=__name__)
from .paths import (get_imaging_root_data_dir, get_scan_image_files,
get_scan_box_files)
if 'custom' not in dj.config:
dj.config['custom'] = {}
db_prefix = dj.config['custom'].get('database.prefix', '')
# ------------- Activate "lab", "subject", "session" schema -------------
lab.activate(db_prefix + 'lab')
subject.activate(db_prefix + 'subject', linking_module=__name__)
session.activate(db_prefix + 'session', linking_module=__name__)
# ------------- Declare table Equipment for use in element_calcium_imaging -------------
@lab.schema
class Equipment(dj.Manual):
definition = """
scanner: varchar(32)
"""
# ------------- Activate "imaging" schema -------------
imaging.activate(db_prefix + 'imaging',
db_prefix + 'scan',
linking_module=__name__)
bucket_scan_dir = (imaging.FieldOfView & sess_key & {
'fov': processing_task_key['scan_id']
}).fetch1('relative_fov_directory')
if bucket_scan_dir[0] == '/':
bucket_scan_dir = bucket_scan_dir[1:]
data_dir = get_imaging_root_data_dir()
sess_dir = data_dir / bucket_scan_dir / 'suite2p'
relative_suite2p_dir = (pathlib.Path(bucket_scan_dir) /
'suite2p').as_posix()
# Check if suite2p dir exists
if not sess_dir.exists():
raise FileNotFoundError(f'Session directory not found ({scan_dir})')
# Check if ops.npy is inside suite2pdir
suite2p_dirs = set([fp.parent.parent for fp in sess_dir.rglob('*ops.npy')])
if len(suite2p_dirs) != 1:
raise FileNotFoundError(
f'Error searching for Suite2p output directory in {scan_dir} - Found {suite2p_dirs}'
)
return relative_suite2p_dir
# ------------- Activate "imaging" schema -------------
imaging_element.activate(imaging_schema_name,
scan_schema_name,
linking_module=__name__)