devices = {
d: nwb['general']['devices'][d].value.decode('UTF-8')
for d in nwb['general']['devices']
}
# -- read data - intracellular_ephys
ie_filtering = nwb['general']['intracellular_ephys']['whole_cell'][
'filtering'].value
ie_location = nwb['general']['intracellular_ephys']['whole_cell'][
'location'].value
brain_region = re.split(',\s?', ie_location)[-1]
coord_ap_ml_dv = re.findall('\d+.\d+', ie_location)
# hemisphere: left-hemisphere is ipsi, so anything contra is right
brain_region, hemisphere = utilities.get_brain_hemisphere(brain_region)
brain_location = {
'brain_region': brain_region,
'brain_subregion': 'N/A',
'cortical_layer': 'N/A',
'hemisphere': hemisphere
}
# -- BrainLocation
if brain_location not in reference.BrainLocation.proj():
reference.BrainLocation.insert1(brain_location)
# -- ActionLocation
action_location = dict(brain_location,
coordinate_ref='bregma',
coordinate_ap=round(Decimal(coord_ap_ml_dv[0]), 2),
coordinate_ml=round(Decimal(coord_ap_ml_dv[1]), 2),
coordinate_dv=round(Decimal(coord_ap_ml_dv[2]), 2))
probe_placement_brain_loc = re.search("(?<=\[\')(.*)(?=\'\])", probe_placement_brain_loc).group()
# -- Probe
if {'probe_name': device_names[0], 'channel_counts': len(electrodes)} not in reference.Probe.proj():
reference.Probe.insert1(
{'probe_name': device_names[0],
'channel_counts': len(electrodes)})
reference.Probe.Channel.insert((
{'probe_name': device_names[0], 'channel_counts': len(electrodes), 'channel_id': electrode[0],
'channel_x_pos': electrode[1], 'channel_y_pos': electrode[2], 'channel_z_pos': electrode[3],
'shank_id' : int(re.search('\d+', electrode[-2].decode('UTF-8')).group())}
for electrode in electrodes))
# -- BrainLocation
# hemisphere: left-hemisphere is ipsi, so anything contra is right
brain_region, hemisphere = utilities.get_brain_hemisphere(probe_placement_brain_loc)
brain_location = {'brain_region': brain_region,
'brain_subregion': 'N/A',
'cortical_layer': 'N/A',
'hemisphere': hemisphere}
# -- BrainLocation
if brain_location not in reference.BrainLocation.proj():
reference.BrainLocation.insert1(brain_location)
# -- ActionLocation
ground_coordinates = nwb['general']['extracellular_ephys']['ground_coordinates'].value # using 'ground_coordinates' here as the x, y, z for where the probe is placed in the brain, TODO double check if this is correct
action_location = dict(brain_location,
coordinate_ref='bregma',
coordinate_ap=round(Decimal(str(ground_coordinates[0])), 2),
coordinate_ml=round(Decimal(str(ground_coordinates[1])), 2),
coordinate_dv=round(Decimal(str(ground_coordinates[2])), 2))
if action_location not in reference.ActionLocation.proj():