def move_ephys_files(session_folder: str) -> None:
"""move_ephys_files is system agnostic (3A, 3B1, 3B2).
Moves all properly named ephys files to appropriate locations for transfer.
Use rename_ephys_files function before this one.
:param session_folder: Session folder path
:type session_folder: str
:return: None - Moves files on filesystem
:rtype: None
"""
session_path = Path(session_folder)
raw_ephys_data_path = session_path / "raw_ephys_data"
imec_files = session_path.rglob("*.imec*")
for imf in imec_files:
# For 3B system probe0x == imecx
probe_number = re.match(r'_spikeglx_ephysData_g\d_t\d.imec(\d+).*',
imf.name)
if not probe_number:
# For 3A system imec files must be in a 'probexx' folder
probe_label = re.search(r'probe\d+', str(imf))
assert probe_label, f'Cannot assign probe number to file {imf}'
probe_label = probe_label.group()
else:
probe_number, = probe_number.groups()
probe_label = f'probe{probe_number.zfill(2)}'
raw_ephys_data_path.joinpath(probe_label).mkdir(exist_ok=True)
shutil.move(imf, raw_ephys_data_path.joinpath(probe_label, imf.name))
# NIDAq files (3B system only)
nidq_files = session_path.rglob("*.nidq.*")
for nidqf in nidq_files:
shutil.move(str(nidqf), str(raw_ephys_data_path / nidqf.name))
# Delete all empty folders recursively
delete_empty_folders(raw_ephys_data_path, dry=False, recursive=True)
def move_ephys_files(session_folder: str) -> None:
"""move_ephys_files is system agnostic (3A, 3B1, 3B2).
Moves all properly named ephys files to appropriate locations for transfer.
Use rename_ephys_files function before this one.
:param session_folder: Session folder path
:type session_folder: str
:return: None - Moves files on filesystem
:rtype: None
"""
session_path = Path(session_folder)
raw_ephys_data_path = session_path / "raw_ephys_data"
probe00_path = raw_ephys_data_path / "probe00"
probe01_path = raw_ephys_data_path / "probe01"
# 3A system imec only
imec_files = session_path.rglob("*.imec.*")
for imf in imec_files:
if "probe00" in str(imf):
shutil.move(str(imf), str(probe00_path / imf.name))
elif "probe01" in str(imf):
shutil.move(str(imf), str(probe01_path / imf.name))
# 3B system
imec0_files = session_path.rglob("*.imec0.*")
imec1_files = session_path.rglob("*.imec1.*")
nidq_files = session_path.rglob("*.nidq.*")
# All imec 0 in probe00 folder
for i0f in imec0_files:
shutil.move(str(i0f), str(probe00_path / i0f.name))
# All imec 1 in probe01 folder
for i1f in imec1_files:
shutil.move(str(i1f), str(probe01_path / i1f.name))
# NIDAq files
nidq_files = session_path.rglob("*.nidq.*")
for nidqf in nidq_files:
shutil.move(str(nidqf), str(raw_ephys_data_path / nidqf.name))
# Delete all empty folders recursively
from ibllib.io.misc import delete_empty_folders
delete_empty_folders(raw_ephys_data_path, dry=False, recursive=True)
def test_delete_empty_folders(self):
pre = [x.exists() for x in self.subdirs]
pre_expected = [True, True, True, True]
self.assertTrue(all([x == y for x, y in zip(pre, pre_expected)]))
# Test dry run
pos_expected = None
pos = misc.delete_empty_folders(self.tempdir)
self.assertTrue(pos == pos_expected)
# Test dry=False, non recursive
pos_expected = [True, False, False, True]
misc.delete_empty_folders(self.tempdir, dry=False)
pos = [x.exists() for x in self.subdirs]
self.assertTrue(all([x == y for x, y in zip(pos, pos_expected)]))
self._resetup_folders()
# Test recursive
pos_expected = [False, False, False, True]
misc.delete_empty_folders(self.tempdir, dry=False, recursive=True)
pos = [x.exists() for x in self.subdirs]
self.assertTrue(all([x == y for x, y in zip(pos, pos_expected)]))
