def setUpContainer(self):
self.setUpElectrode()
return VoltageClampStimulusSeries(name="vcss",
data=[1, 2, 3, 4, 5],
starting_time=123.6,
rate=10e3,
electrode=self.elec,
gain=0.126)
def test_init(self):
electrode_name = GetElectrode()
vCSS = VoltageClampStimulusSeries('test_vCSS', 'a hypothetical source', list(),
'unit', electrode_name, 1.0, timestamps=list())
self.assertEqual(vCSS.name, 'test_vCSS')
self.assertEqual(vCSS.source, 'a hypothetical source')
self.assertEqual(vCSS.unit, 'unit')
self.assertEqual(vCSS.electrode, electrode_name)
def test_init(self):
electrode_name = GetElectrode()
vCSS = VoltageClampStimulusSeries('test_vCSS',
list(),
electrode_name,
1.0,
timestamps=list())
self.assertEqual(vCSS.name, 'test_vCSS')
self.assertEqual(vCSS.unit, 'volts')
self.assertEqual(vCSS.electrode, electrode_name)
def test_unit_warning(self):
electrode_name = GetElectrode()
msg = "Unit for VoltageClampStimulusSeries 'test_vCSS' is ignored and will be set to 'volts' as per NWB 2.1.0."
with self.assertWarnsWith(UserWarning, msg):
vCSS = VoltageClampStimulusSeries('test_vCSS',
list(),
electrode_name,
1.0,
timestamps=list(),
unit='unit')
self.assertEqual(vCSS.unit, 'volts')
def create_icephys_stimulus_and_response(sweep_number, electrode,
randomize_data):
"""
Internal helper function to construct a dummy stimulus and response pair representing an
intracellular recording:
:param sweep_number: Integer sweep number of the recording
:type sweep_number: int
:param electrode: Intracellular electrode used
:type electrode: pynwb.icephys.IntracellularElectrode
:param randomize_data: Randomize data values in the stimulus and response
:type randomize_data: bool
:returns: Tuple of VoltageClampStimulusSeries with the stimulus and VoltageClampSeries with the response.
"""
stimulus = VoltageClampStimulusSeries(
name="ccss_" + str(sweep_number),
data=[1, 2, 3, 4, 5] if not randomize_data else np.random.rand(10),
starting_time=123.6 if not randomize_data else
(np.random.rand() * 100),
rate=10e3
if not randomize_data else int(np.random.rand() * 10) * 1000 + 1000.,
electrode=electrode,
gain=0.1 if not randomize_data else np.random.rand(),
sweep_number=sweep_number)
# Create and ic-response
response = VoltageClampSeries(
name='vcs_' + str(sweep_number),
data=[0.1, 0.2, 0.3, 0.4, 0.5]
if not randomize_data else np.random.rand(10),
conversion=1e-12,
resolution=np.nan,
starting_time=123.6 if not randomize_data else
(np.random.rand() * 100),
rate=20e3
if not randomize_data else int(np.random.rand() * 20) * 1000. + 1000.,
electrode=electrode,
gain=0.02 if not randomize_data else np.random.rand(),
capacitance_slow=100e-12,
resistance_comp_correction=70.0 if not randomize_data else 70.0 +
np.random.rand(),
sweep_number=sweep_number)
return stimulus, response
def test_acquisition_round_trip(nwb_filename):
nwbfile = NWBFile(session_description='test ephys',
identifier='session_uuid',
session_start_time=datetime.datetime.now(),
file_create_date=datetime.datetime.now())
device = nwbfile.create_device(name='electrode_0')
electrode = nwbfile.create_ic_electrode(
name="elec0", description=' some kind of electrode', device=device)
data = np.array([1., 3.76, 0., 67, -2.89])
meta_data = {
"name": "test_acquisition_sweep",
"sweep_number": 4,
"unit": "volts",
"gain": 32.0,
"resolution": 1.0,
"conversion": 1.0E-3,
"starting_time": 1.5,
"rate": 7000.0,
"stimulus_description": "STIMULUS_CODE"
}
time_series = VoltageClampStimulusSeries(data=data,
electrode=electrode,
**meta_data)
nwbfile.add_acquisition(time_series)
with NWBHDF5IO(nwb_filename, mode='w') as io:
io.write(nwbfile)
nwbfile_in = NWBHDF5IO(nwb_filename, mode='r').read()
time_series_in = nwbfile_in.get_acquisition(meta_data["name"])
assert np.allclose(data, time_series_in.data)
for k, v in meta_data.items():
assert getattr(time_series_in, k) == v
electrode=elec,
gain=0.02,
sweep_number=0)
nwbfile.add_stimulus(ccss)
#######################
# We now add another stimulus series but from a different sweep. TimeSeries
# having the same starting time belong to the same sweep.
from pynwb.icephys import VoltageClampStimulusSeries
vcss = VoltageClampStimulusSeries(name="vcss",
data=[2, 3, 4, 5, 6],
starting_time=234.5,
rate=10e3,
electrode=elec,
gain=0.03,
sweep_number=1)
nwbfile.add_stimulus(vcss)
#######################
# Here, we will use :py:class:`~pynwb.icephys.CurrentClampSeries` to store current clamp
# data and then add it to our NWBFile as acquired data using the :py:class:`~pynwb.file.NWBFile` method
# :py:meth:`~pynwb.file.NWBFile.add_acquisition`.
from pynwb.icephys import CurrentClampSeries
ccs = CurrentClampSeries(name="ccs",
data=[0.1, 0.2, 0.3, 0.4, 0.5],
identifier='EXAMPLE_ID',
session_start_time=datetime.now(tzlocal()))
# Add a device
ex_device = ex_nwbfile.create_device(name='Heka ITC-1600')
# Add an intracellular electrode
ex_electrode = ex_nwbfile.create_icephys_electrode(
name="elec0",
description='a mock intracellular electrode',
device=ex_device)
# Create an ic-ephys stimulus
ex_stimulus = VoltageClampStimulusSeries(name="stimulus",
data=[1, 2, 3, 4, 5],
starting_time=123.6,
rate=10e3,
electrode=ex_electrode,
gain=0.02)
# Create an ic-response
ex_response = VoltageClampSeries(name='response',
data=[0.1, 0.2, 0.3, 0.4, 0.5],
conversion=1e-12,
resolution=np.nan,
starting_time=123.6,
rate=20e3,
electrode=ex_electrode,
gain=0.02,
capacitance_slow=100e-12,
resistance_comp_correction=70.0)