def setUpContainer(self):
self.setUpElectrode()
return CurrentClampStimulusSeries(name="ccss",
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()
cCSS = CurrentClampStimulusSeries('test_cCSS', 'a hypothetical source', list(),
'unit', electrode_name, 1.0, timestamps=list())
self.assertEqual(cCSS.name, 'test_cCSS')
self.assertEqual(cCSS.source, 'a hypothetical source')
self.assertEqual(cCSS.unit, 'unit')
self.assertEqual(cCSS.electrode, electrode_name)
self.assertEqual(cCSS.gain, 1.0)
def setUpContainer(self):
self.setUpElectrode()
ccss = CurrentClampStimulusSeries(name="ccss",
source="command",
data=[1, 2, 3, 4, 5],
unit='A',
starting_time=123.6,
rate=10e3,
electrode=self.elec,
gain=0.126)
return ccss
def test_init(self):
electrode_name = GetElectrode()
cCSS = CurrentClampStimulusSeries('test_cCSS',
list(),
electrode_name,
1.0,
timestamps=list())
self.assertEqual(cCSS.name, 'test_cCSS')
self.assertEqual(cCSS.unit, 'amperes')
self.assertEqual(cCSS.electrode, electrode_name)
self.assertEqual(cCSS.gain, 1.0)
def test_unit_warning(self):
electrode_name = GetElectrode()
msg = (
"Unit for CurrentClampStimulusSeries 'test_cCSS' is ignored and will be set to 'amperes' as per NWB "
"2.1.0.")
with self.assertWarnsWith(UserWarning, msg):
cCSS = CurrentClampStimulusSeries('test_cCSS',
list(),
electrode_name,
1.0,
timestamps=list(),
unit='unit')
self.assertEqual(cCSS.unit, 'amperes')
def test_stimulus_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_stimulus_sweep",
"sweep_number": 4,
"unit": "amperes",
"gain": 32.0,
"resolution": 1.0,
"conversion": 1.0E-3,
"starting_time": 1.5,
"rate": 7000.0,
"stimulus_description": "STIMULUS_CODE"
}
time_series = CurrentClampStimulusSeries(data=data,
electrode=electrode,
**meta_data)
nwbfile.add_stimulus(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_stimulus(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
# Intracellular stimulus and response data are represented with subclasses of
# :py:class:`~pynwb.icephys.PatchClampSeries`. There are two classes for representing stimulus
# data--:py:class:`~pynwb.icephys.VoltageClampStimulusSeries` and
# :py:class:`~pynwb.icephys.CurrentClampStimulusSeries`--, and three classes for representing response
# data--:py:class:`~pynwb.icephys.VoltageClampSeries`,
# :py:class:`~pynwb.icephys.VoltageClampSeries`, :py:class:`~pynwb.icephys.CurrentClampSeries`, and
# :py:class:`~pynwb.icephys.IZeroClampSeries`.
#
# Here, we will use :py:class:`~pynwb.icephys.CurrentClampStimulusSeries` to store current clamp stimulus
# data and then add it to our NWBFile as stimulus data using the :py:class:`~pynwb.file.NWBFile` method
# :py:meth:`~pynwb.file.NWBFile.add_stimulus`.
from pynwb.icephys import CurrentClampStimulusSeries
ccss = CurrentClampStimulusSeries(
name="ccss", source="command", data=[1, 2, 3, 4, 5], unit='A',
starting_time=123.6, rate=10e3, electrode=elec, gain=0.02)
nwbfile.add_stimulus(ccss)
# Here, we will use :py:class:`~pynwb.icephys.VoltageClampSeries` to store voltage 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 VoltageClampSeries
vcs = VoltageClampSeries(
name='vcs', source="command", data=[0.1, 0.2, 0.3, 0.4, 0.5],
unit='A', conversion=1e-12, resolution=np.nan, starting_time=123.6, rate=20e3,
electrode=elec, gain=0.02, capacitance_slow=100e-12, resistance_comp_correction=70.0,
capacitance_fast=np.nan, resistance_comp_bandwidth=np.nan, resistance_comp_prediction=np.nan,
# :py:class:`~pynwb.icephys.PatchClampSeries`. There are two classes for representing stimulus
# data--:py:class:`~pynwb.icephys.VoltageClampStimulusSeries` and
# :py:class:`~pynwb.icephys.CurrentClampStimulusSeries`--, and three classes for representing response
# data--:py:class:`~pynwb.icephys.VoltageClampSeries`, :py:class:`~pynwb.icephys.CurrentClampSeries`, and
# :py:class:`~pynwb.icephys.IZeroClampSeries`.
#
# Here, we will use :py:class:`~pynwb.icephys.CurrentClampStimulusSeries` to store current clamp stimulus
# data and then add it to our NWBFile as stimulus data using the :py:class:`~pynwb.file.NWBFile` method
# :py:meth:`~pynwb.file.NWBFile.add_stimulus`.
from pynwb.icephys import CurrentClampStimulusSeries
ccss = CurrentClampStimulusSeries(name="ccss",
data=[1, 2, 3, 4, 5],
unit='A',
starting_time=123.6,
rate=10e3,
electrode=elec,
gain=0.02,
sweep_number=15)
nwbfile.add_stimulus(ccss)
#######################
# Here, we will use :py:class:`~pynwb.icephys.VoltageClampSeries` to store voltage 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 VoltageClampSeries
vcs = VoltageClampSeries(name='vcs',
data=[0.1, 0.2, 0.3, 0.4, 0.5],
def nwbfile_to_test():
"""
Create a simple nwbfile for testing
Returns
-------
nwbfile
"""
nwbfile = pynwb.NWBFile(session_description="test nwb data",
identifier='test session',
session_start_time=datetime.datetime.now(),
file_create_date=datetime.datetime.now())
device = nwbfile.create_device(name='electrode_0')
electrode = nwbfile.create_icephys_electrode(name="electrode 0",
description='fancy electrode',
device=device)
stimulus_data = [0, 3, 3, 3, 0]
stimulus_meta_data = {
"name": "stimulus",
"sweep_number": 4,
"unit": "A",
"gain": 32.0,
"resolution": 1.0,
"conversion": 1.0E-3,
"starting_time": 1.5,
"rate": 7000.0,
"stimulus_description": "STIMULUS_CODE"
}
stimulus_series = CurrentClampStimulusSeries(data=stimulus_data,
electrode=electrode,
**stimulus_meta_data)
nwbfile.add_stimulus(stimulus_series)
response_data = [1, 2, 3, 4, 5]
response_meta_data = {
"name": "acquisition",
"sweep_number": 4,
"unit": "V",
"gain": 32.0,
"resolution": 1.0,
"conversion": 1.0E-3,
"bridge_balance": 500.0,
"bias_current": 100.0,
"starting_time": 1.5,
"rate": 7000.0,
"stimulus_description": "STIMULUS_CODE"
}
acquisition_series = CurrentClampSeries(data=response_data,
electrode=electrode,
**response_meta_data)
nwbfile.add_acquisition(acquisition_series)
return nwbfile
'DC': dc
}
# Access sweep data in the ABF files
abfFiles = glob.glob(dpath + '/*.abf')
abfFile = pyabf.ABF(abfFiles[i])
sweepADC = abfFile.sweepY
sweepDAC = abfFile.sweepC
# Create time series
stimulus = CurrentClampStimulusSeries(
name="ccss",
data=sweepADC,
unit='pA',
electrode=elec,
rate=10e4,
gain=float(metadata['Gain'][5:8]),
starting_time=0.0,
description='DC%s' % dc)
acquisition = CurrentClampSeries(
name='ccs',
data=sweepDAC,
electrode=elec,
unit='mV',
rate=10e4,
gain=0.00,
starting_time=0.0,
bias_current=np.nan,
bridge_balance=np.nan,
