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import numpy as np
from pynwb.icephys import (
PatchClampSeries,
CurrentClampSeries,
IZeroClampSeries,
CurrentClampStimulusSeries,
VoltageClampSeries,
VoltageClampStimulusSeries,
IntracellularElectrode,
SweepTable,
)
from pynwb.device import Device
from pynwb.testing import TestCase
from pynwb.file import NWBFile # Needed to test icephys functionality defined on NWBFile
from datetime import datetime
from dateutil.tz import tzlocal
def GetElectrode():
device = Device(name='device_name')
elec = IntracellularElectrode(
name='test_iS',
device=device,
description='description',
slice='slice',
seal='seal',
location='location',
resistance='resistance',
filtering='filtering',
initial_access_resistance='initial_access_resistance',
cell_id='this_cell',
)
return elec
class NWBFileICEphys(TestCase):
"""Test ICEphys-specific functionality on NWBFile"""
def setUp(self):
self.icephys_electrode = GetElectrode()
def test_sweep_table_depractation_warn(self):
msg = ("Use of SweepTable is deprecated. Use the IntracellularRecordingsTable "
"instead. See also the NWBFile.add_intracellular_recordings function.")
with self.assertWarnsWith(DeprecationWarning, msg):
_ = NWBFile(
session_description='NWBFile icephys test',
identifier='NWB123', # required
session_start_time=datetime(2017, 4, 3, 11, tzinfo=tzlocal()),
ic_electrodes=[self.icephys_electrode, ],
sweep_table=SweepTable())
def test_ic_electrodes_parameter_deprecation(self):
# Make sure we warn when using the ic_electrodes parameter on NWBFile
msg = "Use of the ic_electrodes parameter is deprecated. Use the icephys_electrodes parameter instead"
with self.assertWarnsWith(DeprecationWarning, msg):
_ = NWBFile(
session_description='NWBFile icephys test',
identifier='NWB123', # required
session_start_time=datetime(2017, 4, 3, 11, tzinfo=tzlocal()),
ic_electrodes=[self.icephys_electrode, ])
def test_icephys_electrodes_parameter(self):
nwbfile = NWBFile(
session_description='NWBFile icephys test',
identifier='NWB123', # required
session_start_time=datetime(2017, 4, 3, 11, tzinfo=tzlocal()),
icephys_electrodes=[self.icephys_electrode, ])
self.assertEqual(nwbfile.get_icephys_electrode('test_iS'), self.icephys_electrode)
def test_add_ic_electrode_deprecation(self):
# Make sure we warn when using the add_ic_electrodes parameter on NWBFile
nwbfile = NWBFile(
session_description='NWBFile icephys test',
identifier='NWB123', # required
session_start_time=datetime(2017, 4, 3, 11, tzinfo=tzlocal()))
msg = "NWBFile.add_ic_electrode has been replaced by NWBFile.add_icephys_electrode."
with self.assertWarnsWith(DeprecationWarning, msg):
nwbfile.add_ic_electrode(self.icephys_electrode)
def test_ic_electrodes_attribute_deprecation(self):
nwbfile = NWBFile(
session_description='NWBFile icephys test',
identifier='NWB123', # required
session_start_time=datetime(2017, 4, 3, 11, tzinfo=tzlocal()),
icephys_electrodes=[self.icephys_electrode, ])
# make sure NWBFile.ic_electrodes property warns
msg = "NWBFile.ic_electrodes has been replaced by NWBFile.icephys_electrodes."
with self.assertWarnsWith(DeprecationWarning, msg):
nwbfile.ic_electrodes
# make sure NWBFile.get_ic_electrode warns
msg = "NWBFile.get_ic_electrode has been replaced by NWBFile.get_icephys_electrode."
with self.assertWarnsWith(DeprecationWarning, msg):
nwbfile.get_ic_electrode(self.icephys_electrode.name)
def test_create_ic_electrode_deprecation(self):
nwbfile = NWBFile(
session_description='NWBFile icephys test',
identifier='NWB123', # required
session_start_time=datetime(2017, 4, 3, 11, tzinfo=tzlocal()))
device = Device(name='device_name')
msg = "NWBFile.create_ic_electrode has been replaced by NWBFile.create_icephys_electrode."
with self.assertWarnsWith(DeprecationWarning, msg):
nwbfile.create_ic_electrode(
name='test_iS',
device=device,
description='description',
slice='slice',
seal='seal',
location='location',
resistance='resistance',
filtering='filtering',
initial_access_resistance='initial_access_resistance')
class IntracellularElectrodeConstructor(TestCase):
def test_constructor(self):
device = Device(name='device_name')
elec = IntracellularElectrode('test_iS',
device,
'description',
'slice',
'seal',
'location',
'resistance',
'filtering',
'initial_access_resistance',
'this_cell')
self.assertEqual(elec.name, 'test_iS')
self.assertEqual(elec.device, device)
self.assertEqual(elec.description, 'description')
self.assertEqual(elec.slice, 'slice')
self.assertEqual(elec.seal, 'seal')
self.assertEqual(elec.location, 'location')
self.assertEqual(elec.resistance, 'resistance')
self.assertEqual(elec.filtering, 'filtering')
self.assertEqual(elec.initial_access_resistance, 'initial_access_resistance')
self.assertEqual(elec.cell_id, 'this_cell')
class PatchClampSeriesConstructor(TestCase):
def test_default(self):
electrode_name = GetElectrode()
pCS = PatchClampSeries('test_pCS', list(), 'unit',
electrode_name, 1.0, timestamps=list())
self.assertEqual(pCS.name, 'test_pCS')
self.assertEqual(pCS.unit, 'unit')
self.assertEqual(pCS.electrode, electrode_name)
self.assertEqual(pCS.gain, 1.0)
def test_sweepNumber_valid(self):
electrode_name = GetElectrode()
pCS = PatchClampSeries('test_pCS', list(), 'unit',
electrode_name, 1.0, timestamps=list(), sweep_number=4711)
self.assertEqual(pCS.name, 'test_pCS')
self.assertEqual(pCS.unit, 'unit')
self.assertEqual(pCS.electrode, electrode_name)
self.assertEqual(pCS.gain, 1.0)
self.assertEqual(pCS.sweep_number, 4711)
def test_sweepNumber_valid_np(self):
electrode_name = GetElectrode()
pCS = PatchClampSeries('test_pCS', list(), 'unit',
electrode_name, 1.0, timestamps=list(), sweep_number=1)
self.assertEqual(pCS.name, 'test_pCS')
self.assertEqual(pCS.unit, 'unit')
self.assertEqual(pCS.electrode, electrode_name)
self.assertEqual(pCS.gain, 1.0)
self.assertEqual(pCS.sweep_number, np.uint32(1))
def test_sweepNumber_large_and_valid(self):
electrode_name = GetElectrode()
pCS = PatchClampSeries('test_pCS', list(), 'unit',
electrode_name, 1.0, timestamps=list(), sweep_number=np.uint64(2**63-1))
self.assertEqual(pCS.name, 'test_pCS')
self.assertEqual(pCS.unit, 'unit')
self.assertEqual(pCS.electrode, electrode_name)
self.assertEqual(pCS.gain, 1.0)
self.assertEqual(pCS.sweep_number, 2**63-1)
def test_sweepNumber_throws_with_negative(self):
electrode_name = GetElectrode()
with self.assertRaises(ValueError):
PatchClampSeries('test_pCS', list(), 'unit',
electrode_name, 1.0, timestamps=list(), sweep_number=-1)
def test_sweepNumber_throws_with_NaN(self):
electrode_name = GetElectrode()
with self.assertRaises(TypeError):
PatchClampSeries('test_pCS', list(), 'unit',
electrode_name, 1.0, timestamps=list(), sweep_number=float('nan'))
def test_sweepNumber_throws_with_Float(self):
electrode_name = GetElectrode()
with self.assertRaises(TypeError):
PatchClampSeries('test_pCS', list(), 'unit',
electrode_name, 1.0, timestamps=list(), sweep_number=1.5)
def test_data_shape(self):
electrode_name = GetElectrode()
with self.assertRaises(ValueError):
PatchClampSeries(
name="test_pCS",
data=np.ones((30, 2)),
unit="unit",
electrode=electrode_name,
gain=1.0,
rate=100_000.,
)
class CurrentClampSeriesConstructor(TestCase):
def test_init(self):
electrode_name = GetElectrode()
cCS = CurrentClampSeries('test_cCS', list(), electrode_name, 1.0, "stimset", 2.0, 3.0, 4.0,
timestamps=list())
self.assertEqual(cCS.name, 'test_cCS')
self.assertEqual(cCS.unit, 'volts')
self.assertEqual(cCS.electrode, electrode_name)
self.assertEqual(cCS.stimulus_description, "stimset")
self.assertEqual(cCS.gain, 1.0)
self.assertEqual(cCS.bias_current, 2.0)
self.assertEqual(cCS.bridge_balance, 3.0)
self.assertEqual(cCS.capacitance_compensation, 4.0)
def test_unit_warning(self):
electrode_name = GetElectrode()
msg = "Unit 'unit' for CurrentClampSeries 'test_cCS' is ignored and will be set to 'volts' as per NWB 2.1.0."
with self.assertWarnsWith(UserWarning, msg):
cCS = CurrentClampSeries('test_cCS', list(), electrode_name, 1.0, "stimset", 2.0, 3.0, 4.0,
timestamps=list(), unit='unit')
self.assertEqual(cCS.unit, 'volts')
class IZeroClampSeriesConstructor(TestCase):
def test_init(self):
electrode_name = GetElectrode()
iZCS = IZeroClampSeries('test_iZCS', list(), electrode_name, 1.0, timestamps=list())
self.assertEqual(iZCS.name, 'test_iZCS')
self.assertEqual(iZCS.unit, 'volts')
self.assertEqual(iZCS.electrode, electrode_name)
self.assertEqual(iZCS.gain, 1.0)
self.assertEqual(iZCS.bias_current, 0.0)
self.assertEqual(iZCS.bridge_balance, 0.0)
self.assertEqual(iZCS.capacitance_compensation, 0.0)
self.assertEqual(iZCS.stimulus_description, 'N/A')
def test_unit_warning(self):
electrode_name = GetElectrode()
msg = "Unit 'unit' for IZeroClampSeries 'test_iZCS' is ignored and will be set to 'volts' as per NWB 2.1.0."
with self.assertWarnsWith(UserWarning, msg):
iZCS = IZeroClampSeries('test_iZCS', list(), electrode_name, 1.0, timestamps=list(), unit='unit')
self.assertEqual(iZCS.unit, 'volts')
def test_stim_desc_warning(self):
electrode_name = GetElectrode()
msg = ("Stimulus description 'desc' for IZeroClampSeries 'test_iZCS' is ignored and will be set to 'N/A' "
"as per NWB 2.3.0.")
with self.assertWarnsWith(UserWarning, msg):
iZCS = IZeroClampSeries('test_iZCS', list(), electrode_name, 1.0, timestamps=list(),
stimulus_description='desc')
self.assertEqual(iZCS.stimulus_description, 'N/A')
class CurrentClampStimulusSeriesConstructor(TestCase):
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 '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')
class VoltageClampSeriesConstructor(TestCase):
def test_init(self):
electrode_name = GetElectrode()
vCS = VoltageClampSeries('test_vCS', list(), electrode_name,
1.0, "stimset", 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, timestamps=list())
self.assertEqual(vCS.name, 'test_vCS')
self.assertEqual(vCS.unit, 'amperes')
self.assertEqual(vCS.electrode, electrode_name)
self.assertEqual(vCS.stimulus_description, "stimset")
self.assertEqual(vCS.gain, 1.0)
self.assertEqual(vCS.capacitance_fast, 2.0)
self.assertEqual(vCS.capacitance_slow, 3.0)
self.assertEqual(vCS.resistance_comp_bandwidth, 4.0)
self.assertEqual(vCS.resistance_comp_correction, 5.0)
self.assertEqual(vCS.resistance_comp_prediction, 6.0)
self.assertEqual(vCS.whole_cell_capacitance_comp, 7.0)
self.assertEqual(vCS.whole_cell_series_resistance_comp, 8.0)
def test_unit_warning(self):
electrode_name = GetElectrode()
msg = "Unit 'unit' for VoltageClampSeries 'test_vCS' is ignored and will be set " \
"to 'amperes' as per NWB 2.1.0."
with self.assertWarnsWith(UserWarning, msg):
vCS = VoltageClampSeries('test_vCS', list(), electrode_name,
1.0, "stimset", 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, timestamps=list(), unit='unit')
self.assertEqual(vCS.unit, 'amperes')
class VoltageClampStimulusSeriesConstructor(TestCase):
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 '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')
|
