An NWB:N extension for storing bipolar referencing schema
Project description
ndx-bipolar-referencing Extension for NWB:N
Structure for storing the bipolar schema of a recording in an NWB file.
python installation
$ pip install ndx-bipolar-referencing
python usage
from pynwb import NWBHDF5IO, NWBFile
from pynwb.file import DynamicTable, DynamicTableRegion
from datetime import datetime
from ndx_bipolar_referencing import EcephysExt
from pynwb.ecephys import ElectricalSeries
import numpy as np
nwbfile = NWBFile('description', 'id', datetime.now().astimezone())
device = nwbfile.create_device('device_name')
electrode_group = nwbfile.create_electrode_group('electrode_group',
'desc', 'loc', device=device)
for _ in range(20):
nwbfile.add_electrode(np.nan, np.nan, np.nan, np.nan, 'loc', 'filt',
electrode_group)
positive_electrodes = DynamicTableRegion('positive_electrodes',
np.arange(0, 20, 2),
'desc',
nwbfile.electrodes)
negative_electrodes = DynamicTableRegion('negative_electrodes',
np.arange(1, 20, 2),
'desc',
nwbfile.electrodes)
bipolar_reference_scheme = DynamicTable(name='bipolar_reference_scheme',
description='desc',
columns=[positive_electrodes,
negative_electrodes])
ecephys_ext = EcephysExt(bipolar_reference_scheme=bipolar_reference_scheme)
nwbfile.add_lab_meta_data(ecephys_ext)
bipolar_scheme = DynamicTableRegion(
name='electrodes',
data=np.arange(0, 10),
description='desc',
table=nwbfile.lab_meta_data['extracellular_electrophysiology_extensions'].bipolar_reference_scheme)
ec_series = ElectricalSeries(name='test_ec_series',
description='desc',
data=np.random.rand(100, 10),
rate=1000.,
electrodes=bipolar_scheme)
nwbfile.add_acquisition(ec_series)
with NWBHDF5IO('test_nwb.nwb', 'w') as io:
io.write(nwbfile)
with NWBHDF5IO('test_nwb.nwb', 'r', load_namespaces=True) as io:
nwbfile = io.read()
print(nwbfile.acquisition['test_ec_series'].electrodes.table['positive_electrodes'].data)
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