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Update to permit multiple root dirs #41

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Update to permit multiple root dirs #41

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17 changes: 11 additions & 6 deletions element_array_ephys/ephys.py
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Original file line number Diff line number Diff line change
Expand Up @@ -141,20 +141,22 @@ class EphysFile(dj.Part):

def make(self, key):
sess_dir = pathlib.Path(get_session_directory(key))
sess_dir_full = find_full_path(get_ephys_root_data_dir(), sess_dir)

inserted_probe_serial_number = (ProbeInsertion * probe.Probe & key).fetch1('probe')

# search session dir and determine acquisition software
for ephys_pattern, ephys_acq_type in zip(['*.ap.meta', '*.oebin'],
['SpikeGLX', 'Open Ephys']):
ephys_meta_filepaths = [fp for fp in sess_dir.rglob(ephys_pattern)]
ephys_meta_filepaths = [fp for fp in sess_dir_full.rglob(ephys_pattern)]
if ephys_meta_filepaths:
acq_software = ephys_acq_type
break
else:
raise FileNotFoundError(
f'Ephys recording data not found!'
f' Neither SpikeGLX nor Open Ephys recording files found')
f' Neither SpikeGLX nor Open Ephys recording files found'
f' in {sess_dir}')

if acq_software == 'SpikeGLX':
for meta_filepath in ephys_meta_filepaths:
Expand Down Expand Up @@ -192,7 +194,7 @@ def make(self, key):
**key,
'file_path': meta_filepath.relative_to(root_dir).as_posix()})
elif acq_software == 'Open Ephys':
dataset = openephys.OpenEphys(sess_dir)
dataset = openephys.OpenEphys(sess_dir_full)
for serial_number, probe_data in dataset.probes.items():
if str(serial_number) == inserted_probe_serial_number:
break
Expand Down Expand Up @@ -291,7 +293,8 @@ def make(self, key):
electrode_keys.append(probe_electrodes[(shank, shank_col, shank_row)])
elif acq_software == 'Open Ephys':
sess_dir = pathlib.Path(get_session_directory(key))
loaded_oe = openephys.OpenEphys(sess_dir)
sess_dir_full = find_full_path(get_ephys_root_data_dir(), sess_dir)
loaded_oe = openephys.OpenEphys(sess_dir_full)
oe_probe = loaded_oe.probes[probe_sn]

lfp_channel_ind = np.arange(
Expand Down Expand Up @@ -614,7 +617,8 @@ def yield_unit_waveforms():
neuropixels_recording = spikeglx.SpikeGLX(spikeglx_meta_filepath.parent)
elif acq_software == 'Open Ephys':
sess_dir = pathlib.Path(get_session_directory(key))
openephys_dataset = openephys.OpenEphys(sess_dir)
sess_dir_full = find_full_path(get_ephys_root_data_dir(), sess_dir)
openephys_dataset = openephys.OpenEphys(sess_dir_full)
neuropixels_recording = openephys_dataset.probes[probe_serial_number]

def yield_unit_waveforms():
Expand Down Expand Up @@ -697,7 +701,8 @@ def get_neuropixels_channel2electrode_map(ephys_recording_key, acq_software):
spikeglx_meta.shankmap['data'])}
elif acq_software == 'Open Ephys':
sess_dir = pathlib.Path(get_session_directory(ephys_recording_key))
openephys_dataset = openephys.OpenEphys(sess_dir)
sess_dir_full = find_full_path(get_ephys_root_data_dir(), sess_dir)
openephys_dataset = openephys.OpenEphys(sess_dir_full)
probe_serial_number = (ProbeInsertion & ephys_recording_key).fetch1('probe')
probe_dataset = openephys_dataset.probes[probe_serial_number]

Expand Down