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 _get_all_probes_sync(session_path, bin_exists=True):
# round-up of all bin ephys files in the session, infer revision and get sync map
ephys_files = spikeglx.glob_ephys_files(session_path, bin_exists=bin_exists)
version = spikeglx.get_neuropixel_version_from_files(ephys_files)
# attach the sync information to each binary file found
for ef in ephys_files:
ef['sync'] = alfio.load_object(ef.path, 'sync', namespace='spikeglx', short_keys=True)
ef['sync_map'] = get_ibl_sync_map(ef, version)
return ephys_files
def _get_all_probes_sync(session_path):
# round-up of all bin ephys files in the session, infer revision and get sync map
ephys_files = glob_ephys_files(session_path)
version = get_neuropixel_version_from_files(ephys_files)
extract_sync(session_path, save=True)
# attach the sync information to each binary file found
for ef in ephys_files:
ef['sync'] = alf.io.load_object(ef.path,
'_spikeglx_sync',
short_keys=True)
ef['sync_map'] = get_ibl_sync_map(ef, version)
return ephys_files
def _get_main_probe_sync(session_path, bin_exists=True):
"""
From 3A or 3B multiprobe session, returns the main probe (3A) or nidq sync pulses
with the attached channel map (default chmap if none)
:param session_path:
:return:
"""
ephys_files = _get_all_probes_sync(session_path, bin_exists=bin_exists)
if not ephys_files:
raise FileNotFoundError(f"No ephys files found in {session_path}")
version = get_neuropixel_version_from_files(ephys_files)
if version == '3A':
# the sync master is the probe with the most sync pulses
sync_box_ind = np.argmax([ef.sync.times.size for ef in ephys_files])
elif version == '3B':
# the sync master is the nidq breakout box
sync_box_ind = np.argmax([1 if ef.get('nidq') else 0 for ef in ephys_files])
sync = ephys_files[sync_box_ind].sync
sync_chmap = ephys_files[sync_box_ind].sync_map
return sync, sync_chmap
