Writing Intracellular Ephys data (for Bart Jongbloets)

jongbloets_icephys.py

""" import the pynwb packages"""
from pynwb import NWBFile, TimeSeries, get_manager
from pynwb.form.backends.hdf5 import HDF5IO
from pynwb.icephys import CurrentClampSeries
from pynwb.icephys import VoltageClampSeries
import datetime
import numpy as np
import os

experimentID = 'BJ5523'#folderPath.split('/')[-1]
nwbFile = NWBFile(session_description= 'NaN',
                      identifier='NaN',
                      session_start_time=datetime.datetime(2017, 2, 17, 13, 26, 23),
                      file_create_date='Tue Dec  5 17:33:51 2017',
                      experimenter='NaN',
                      experiment_description='NaN',
                      session_id='NaN',
                      institution='NaN',
                      lab='NaN',
                      source='Ephus (Janelia Farm) software generated files')

Amp1_VoltData = np.arange(1,1000)
Amp2_VoltData = np.arange(10,1010)
Amp1_AmpData = np.arange(20,1020)
Amp2_AmpData = np.arange(30,1030)

amp1 = nwbFile.create_intracellular_electrode(name = 'Amp1',
                                       source = 'Amp_700B_1',
                                       slice = 'Horizontal mouse slice 300um',
                                       seal = '2000',
                                       description = 'whole-cell',
                                       location ='locX',
                                       resistance = '10',
                                       filtering = '2.2 Hz Bessel',
                                       initial_access_resistance = '110',
                                       device = 'Multiclamp 700B')
amp2 = nwbFile.create_intracellular_electrode(name = 'Amp2',
                                       source = 'Amp_700B_2',
                                       slice = 'Horizontal mouse slice 300um',
                                       seal = '3000',
                                       description = 'whole-cell',
                                       location ='locX',
                                       resistance = '15',
                                       filtering = '2.2 Hz Bessel',
                                       initial_access_resistance = '165',
                                       device = 'Multiclamp 700B')

amp1Volt_ts = VoltageClampSeries(name = 'Amp1VoltClamp',
                                 source = 'Multiclamp 700B',
                                 data = Amp1_AmpData,
                                 unit = 'picoAmpere',
                                 electrode = amp1, # This is where it requires type:'IntracellularElectrode', which I though is the object amp1 or 2
                                 gain = 10.0,
                                 capacitance_fast = 0.0,
                                 capacitance_slow = 0.0,
                                 resistance_comp_bandwidth = 0.0,
                                 resistance_comp_correction = 0.0,
                                 resistance_comp_prediction = 0.0,
                                 whole_cell_capacitance_comp = 0.0,
                                 whole_cell_series_resistance_comp = 0.0,
                                 resolution = 0.001,
                                 conversion = 1000000000.0,
                                 timestamps = np.arange(1,len(Amp1_AmpData)),
                                 starting_time = 0.0,
                                 rate = 10000.0)

amp1Amp_ts = CurrentClampSeries(name = 'Amp1CurrentClamp',
                                 source = 'Multiclamp 700B',
                                 data = Amp1_VoltData,
                                 unit = 'milliVolt',
                                 electrode = amp1,
                                 gain = 10.0,
                                 bias_current = 0.0,
                                 bridge_balance = 0.0,
                                 capacitance_compensation = 0.0,
                                 resolution = 0.001,
                                 conversion = 1000.0,
                                 timestamps = np.arange(1,len(Amp1_VoltData)),
                                 starting_time = 0.0,
                                 rate = 10000.0)

amp2Volt_ts = VoltageClampSeries(name = 'Amp2VoltClamp',
                                 source = 'Multiclamp 700B',
                                 data = Amp2_AmpData,
                                 unit = 'picoAmpere',
                                 electrode = amp2, # This is where it requires type:'IntracellularElectrode', which I though is the object amp1 or 2
                                 gain = 10.0,
                                 capacitance_fast = 0.0,
                                 capacitance_slow = 0.0,
                                 resistance_comp_bandwidth = 0.0,
                                 resistance_comp_correction = 0.0,
                                 resistance_comp_prediction = 0.0,
                                 whole_cell_capacitance_comp = 0.0,
                                 whole_cell_series_resistance_comp = 0.0,
                                 resolution = 0.001,
                                 conversion = 1000000000.0,
                                 timestamps = np.arange(1,len(Amp2_AmpData)),
                                 starting_time = 0.0,
                                 rate = 10000.0)

amp2Amp_ts = CurrentClampSeries(name = 'Amp2CurrentClamp',
                                 source = 'Multiclamp 700B',
                                 data = Amp2_VoltData,
                                 unit = 'milliVolt',
                                 electrode = amp2,
                                 gain = 10.0,
                                 bias_current = 0.0,
                                 bridge_balance = 0.0,
                                 capacitance_compensation = 0.0,
                                 resolution = 0.001,
                                 conversion = 1000.0,
                                 timestamps = np.arange(1,len(Amp2_VoltData)),
                                 starting_time = 0.0,
                                 rate = 10000.0)

nwbFile.add_acquisition(amp1Volt_ts)
nwbFile.add_acquisition(amp2Volt_ts)
nwbFile.add_acquisition(amp1Amp_ts)
nwbFile.add_acquisition(amp2Amp_ts)

saveFileName = experimentID+'.nwb'

if os.path.exists(saveFileName):
    os.remove(saveFileName)

manager = get_manager()
io = HDF5IO(saveFileName, manager)
io.write(nwbFile)
nwbfile = io.read(saveFileName)
print('Found the following acquisition timeseries')
for icets in nwbfile.acquisition:
    print(icets.name)

print('Found the following intracellular electrodes')
for ice in nwbfile.ic_electrodes:
    print(ice.name)