def test_glob_ephys(self):
def dict_equals(d1, d2):
return all([x in d1 for x in d2]) and all([x in d2 for x in d1])
ef3b = spikeglx.glob_ephys_files(self.dir3b)
ef3a = spikeglx.glob_ephys_files(self.dir3a)
ef3b_ch = spikeglx.glob_ephys_files(self.dir3b, ext='ch')
# test glob
self.assertTrue(dict_equals(self.dict3a, ef3a))
self.assertTrue(dict_equals(self.dict3b, ef3b))
self.assertTrue(dict_equals(self.dict3b_ch, ef3b_ch))
# test the version from glob
self.assertTrue(
spikeglx.get_neuropixel_version_from_files(ef3a) == '3A')
self.assertTrue(
spikeglx.get_neuropixel_version_from_files(ef3b) == '3B')
# test the version from paths
self.assertTrue(
spikeglx.get_neuropixel_version_from_folder(self.dir3a) == '3A')
self.assertTrue(
spikeglx.get_neuropixel_version_from_folder(self.dir3b) == '3B')
self.dir3b.joinpath('imec1',
'sync_testing_g0_t0.imec1.ap.bin').unlink()
self.assertEqual(
spikeglx.glob_ephys_files(self.dir3b.joinpath('imec1')), [])
def sync(ses_path, **kwargs):
"""
Wrapper for sync_probes.version3A and sync_probes.version3B that automatically determines
the version
:param ses_path:
:return: bool True on a a successful sync
"""
version = spikeglx.get_neuropixel_version_from_folder(ses_path)
if version == '3A':
return version3A(ses_path, **kwargs)
elif version == '3B':
return version3B(ses_path, **kwargs)
def create_alyx_probe_insertions(session_path: str,
force: bool = False,
one: object = None,
model: str = None,
labels: list = None):
if one is None:
one = ONE()
if is_uuid_string(session_path):
eid = session_path
else:
eid = one.eid_from_path(session_path)
if eid is None:
print(
'Session not found on Alyx: please create session before creating insertions'
)
if model is None:
probe_model = spikeglx.get_neuropixel_version_from_folder(session_path)
pmodel = '3B2' if probe_model == '3B' else probe_model
else:
pmodel = model
raw_ephys_data_path = Path(session_path) / 'raw_ephys_data'
if labels is None:
probe_labels = [
x.name for x in Path(raw_ephys_data_path).glob('*')
if x.is_dir() and ('00' in x.name or '01' in x.name)
]
else:
probe_labels = labels
# create the dictionary
for plabel in probe_labels:
insdict = {'session': eid, 'name': plabel, 'model': pmodel}
# search for the corresponding insertion in Alyx
alyx_insertion = one.alyx.rest('insertions',
'list',
session=insdict['session'],
name=insdict['name'])
# if it doesn't exist, create it
if len(alyx_insertion) == 0:
alyx_insertion = one.alyx.rest('insertions',
'create',
data=insdict)
else:
iid = alyx_insertion[0]['id']
if force:
alyx_insertion = one.alyx.rest('insertions',
'update',
id=iid,
data=insdict)
else:
alyx_insertion = alyx_insertion[0]
def create_alyx_probe_insertions(
session_path: str,
force: bool = False,
one: object = None,
model: str = None,
labels: list = None,
):
if one is None:
one = ONE()
if is_uuid_string(session_path):
eid = session_path
else:
eid = one.eid_from_path(session_path)
if eid is None:
print(
"Session not found on Alyx: please create session before creating insertions"
)
if model is None:
probe_model = spikeglx.get_neuropixel_version_from_folder(session_path)
pmodel = "3B2" if probe_model == "3B" else probe_model
else:
pmodel = model
raw_ephys_data_path = Path(session_path) / "raw_ephys_data"
if labels is None:
probe_labels = [
x.name for x in Path(raw_ephys_data_path).glob("*")
if x.is_dir() and ("00" in x.name or "01" in x.name)
]
else:
probe_labels = labels
# create the qc fields in the json field
qc_dict = {}
qc_dict.update({"qc": "NOT_SET"})
qc_dict.update({"extended_qc": {}})
# create the dictionary
for plabel in probe_labels:
insdict = {
"session": eid,
"name": plabel,
"model": pmodel,
"json": qc_dict
}
# search for the corresponding insertion in Alyx
alyx_insertion = one.alyx.rest("insertions",
"list",
session=insdict["session"],
name=insdict["name"])
# if it doesn't exist, create it
if len(alyx_insertion) == 0:
alyx_insertion = one.alyx.rest("insertions",
"create",
data=insdict)
else:
iid = alyx_insertion[0]["id"]
if force:
alyx_insertion = one.alyx.rest("insertions",
"update",
id=iid,
data=insdict)
else:
alyx_insertion = alyx_insertion[0]
