def phy2alf_conversion(session_path, ks2_path, alf_path, probe_label):
try:
# Find spikeglx meta data files associated with the session and probe
files = spikeglx.glob_ephys_files(session_path, ext='meta')
ap_files = [(ef.get("ap"), ef.get("label")) for ef in files
if "ap" in ef.keys()]
meta_file = next(ap[0] for ap in ap_files if ap[1] == probe_label)
# The .cbin file doesn't always still exist on server so point to it from meta
ap_file = meta_file.with_suffix('.cbin')
# Convert to alf format
spikes.ks2_to_alf(
ks2_path,
bin_path=meta_file.parent,
out_path=alf_path,
bin_file=None,
ampfactor=SpikeSorting_KS2_Matlab._sample2v(ap_file))
# Sync the probes
out_files, _ = spikes.sync_spike_sorting(ap_file=ap_file,
out_path=alf_path)
return 0, out_files, None
except BaseException as err:
_logger.error(
f'{session_path} and {probe_label} errored with message: {err}'
)
return -1, None, err
def _run(self, overwrite=False):
"""
Multiple steps. For each probe:
- Runs ks2 (skips if it already ran)
- synchronize the spike sorting
- output the probe description files
:param overwrite:
:return: list of files to be registered on database
"""
efiles = spikeglx.glob_ephys_files(self.session_path)
ap_files = [(ef.get('ap'), ef.get('label')) for ef in efiles
if 'ap' in ef.keys()]
out_files = []
for ap_file, label in ap_files:
try:
ks2_dir = self._run_ks2(
ap_file) # runs ks2, skips if it already ran
probe_out_path = self.session_path.joinpath('alf', label)
probe_out_path.mkdir(parents=True, exist_ok=True)
spikes.ks2_to_alf(ks2_dir,
bin_path=ap_file.parent,
out_path=probe_out_path,
bin_file=ap_file,
ampfactor=self._sample2v(ap_file))
out, _ = spikes.sync_spike_sorting(ap_file=ap_file,
out_path=probe_out_path)
out_files.extend(out)
except BaseException as err:
_logger.error(err)
self.status = -1
continue
probe_files = spikes.probes_description(self.session_path,
one=self.one)
return out_files + probe_files
def sorting_sync_and_alf(session_path, overwrite=False):
"""
Multiple steps. For each probe:
- Runs ks2 (skips if it already ran)
- synchronize the spike sorting
- output the probe description files
:param overwrite:
:return: list of files to be registered on database
"""
efiles = spikeglx.glob_ephys_files(session_path)
ap_files = [(ef.get("ap"), ef.get("label")) for ef in efiles
if "ap" in ef.keys()]
out_files = []
for ap_file, label in ap_files:
ks2_dir = session_path.joinpath("spike_sorters", "ks2_matlab", label)
probe_out_path = session_path.joinpath("alf", label)
probe_out_path.mkdir(parents=True, exist_ok=True)
spikes.ks2_to_alf(
ks2_dir,
bin_path=ap_file.parent,
out_path=probe_out_path,
bin_file=ap_file,
ampfactor=_sample2v(ap_file),
)
out, _ = spikes.sync_spike_sorting(ap_file=ap_file,
out_path=probe_out_path)
out_files.extend(out)
# convert ks2_output into tar file and also register
# Make this in case spike sorting is in old raw_ephys_data folders, for new
# sessions it should already exist
tar_dir = session_path.joinpath('spike_sorters', 'ks2_matlab', label)
tar_dir.mkdir(parents=True, exist_ok=True)
out = spikes.ks2_to_tar(ks2_dir, tar_dir)
out_files.extend(out)
def _run(self, overwrite=False):
"""
Multiple steps. For each probe:
- Runs ks2 (skips if it already ran)
- synchronize the spike sorting
- output the probe description files
:param overwrite:
:return: list of files to be registered on database
"""
efiles = spikeglx.glob_ephys_files(self.session_path)
ap_files = [(ef.get("ap"), ef.get("label")) for ef in efiles
if "ap" in ef.keys()]
out_files = []
for ap_file, label in ap_files:
try:
ks2_dir = self._run_ks2(
ap_file) # runs ks2, skips if it already ran
probe_out_path = self.session_path.joinpath("alf", label)
probe_out_path.mkdir(parents=True, exist_ok=True)
spikes.ks2_to_alf(
ks2_dir,
bin_path=ap_file.parent,
out_path=probe_out_path,
bin_file=ap_file,
ampfactor=self._sample2v(ap_file),
)
out, _ = spikes.sync_spike_sorting(ap_file=ap_file,
out_path=probe_out_path)
out_files.extend(out)
# convert ks2_output into tar file and also register
# Make this in case spike sorting is in old raw_ephys_data folders, for new
# sessions it should already exist
tar_dir = self.session_path.joinpath('spike_sorters',
'ks2_matlab', label)
tar_dir.mkdir(parents=True, exist_ok=True)
out = spikes.ks2_to_tar(ks2_dir, tar_dir)
out_files.extend(out)
except BaseException:
_logger.error(traceback.format_exc())
self.status = -1
continue
probe_files = spikes.probes_description(self.session_path,
one=self.one)
return out_files + probe_files