def _check_session_sync(ses_path, channel):
"""
Resync the original cam pulses
:param ses_path:
:return:
"""
efiles = spikeglx.glob_ephys_files(ses_path, bin_exists=False)
tprobe = []
tinterp = []
for ef in efiles:
if not ef.get('ap'):
continue
sync_events = alf.io.load_object(ef.ap.parent, 'sync', short_keys=True)
# the first step is to construct list arrays with probe sync
sync_file = ef.ap.parent.joinpath(ef.ap.name.replace(
'.ap.', '.sync.')).with_suffix('.npy')
t = sync_events.times[sync_events.channels == channel]
tsync = sync_probes.apply_sync(sync_file, t, forward=True)
tprobe.append(t)
tinterp.append(tsync)
# the second step is to make sure sample / time_ref files match time / time_ref files
ts_file = ef.ap.parent.joinpath(
ef.ap.name.replace('.ap.', '.timestamps.')).with_suffix('.npy')
fs = spikeglx._get_fs_from_meta(
spikeglx.read_meta_data(ef.ap.with_suffix('.meta')))
tstamp = sync_probes.apply_sync(ts_file, t * fs, forward=True)
assert (np.all(tstamp - tsync < 1e-12))
return tinterp[0] - tinterp[1]
def phy_model_from_ks2_path(ks2_path):
params_file = ks2_path.joinpath('params.py')
if params_file.exists():
m = model.load_model(params_file)
else:
meta_file = next(ks2_path.rglob('*.ap.meta'), None)
if meta_file and meta_file.exists():
meta = spikeglx.read_meta_data(meta_file)
fs = spikeglx._get_fs_from_meta(meta)
nch = (spikeglx._get_nchannels_from_meta(meta) -
len(spikeglx._get_sync_trace_indices_from_meta(meta)))
else:
fs = 30000
nch = 384
m = model.TemplateModel(dir_path=ks2_path,
dat_path=[],
sample_rate=fs,
n_channels_dat=nch)
return m
def phy_model_from_ks2_path(ks2_path, bin_path, bin_file=None):
if not bin_file:
bin_file = next(bin_path.rglob('*.ap.*bin'), None)
meta_file = next(bin_path.rglob('*.ap.meta'), None)
if meta_file and meta_file.exists():
meta = spikeglx.read_meta_data(meta_file)
fs = spikeglx._get_fs_from_meta(meta)
nch = (spikeglx._get_nchannels_from_meta(meta) -
len(spikeglx._get_sync_trace_indices_from_meta(meta)))
else:
fs = 30000
nch = 384
m = model.TemplateModel(dir_path=ks2_path,
dat_path=bin_file, # this assumes the raw data is in the same folder
sample_rate=fs,
n_channels_dat=nch,
n_closest_channels=NCH_WAVEFORMS)
m.depths = m.get_depths()
return m
def _get_sr(ephys_file):
meta = spikeglx.read_meta_data(ephys_file.ap.with_suffix('.meta'))
return spikeglx._get_fs_from_meta(meta)
def _sr(ap_file):
md = spikeglx.read_meta_data(ap_file.with_suffix('.meta'))
return spikeglx._get_fs_from_meta(md)
def _sr(ap_file):
# gets sampling rate from data
md = spikeglx.read_meta_data(ap_file.with_suffix('.meta'))
return spikeglx._get_fs_from_meta(md)
