An NWB extension for storing bipolar scheme
Project description
ndx-bipolar-scheme Extension for NWB
Structure for storing the bipolar schema of a recording in an NWB file.
python installation
$ pip install ndx-bipolar-scheme
python usage
from pynwb import NWBHDF5IO, NWBFile
from pynwb.file import DynamicTableRegion
from datetime import datetime
from ndx_bipolar_scheme import BipolarSchemeTable, 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 i in np.arange(20.):
nwbfile.add_electrode(i, i, i, np.nan, 'loc', 'filt', electrode_group)
bipolar_scheme_table = BipolarSchemeTable(name='bipolar_scheme_table',
description='desc')
bipolar_scheme_table.add_row(anodes=[0], cathodes=[1])
bipolar_scheme_table.add_row(anodes=[0, 1], cathodes=[2, 3])
bipolar_scheme_table.add_row(anodes=[0, 1], cathodes=[2])
bipolar_scheme_table.anodes.table = nwbfile.electrodes
bipolar_scheme_table.cathodes.table = nwbfile.electrodes
bipolar_scheme_region = DynamicTableRegion(
name='electrodes',
data=np.arange(0, 3),
description='desc',
table=bipolar_scheme_table)
ec_series = ElectricalSeries(name='test_ec_series',
description='desc',
data=np.random.rand(100, 3),
rate=1000.,
electrodes=bipolar_scheme_region)
nwbfile.add_acquisition(ec_series)
ecephys_ext = EcephysExt(name='ecephys_ext')
ecephys_ext.bipolar_scheme_table = bipolar_scheme_table
nwbfile.add_lab_meta_data(ecephys_ext)
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['anodes'][2]['x'])
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