def test_show_single_sweep_sequence():
device = Device(name='Axon Patch-Clamp')
electrode = IntracellularElectrode(name='Patch Clamp',
device=device,
description='whole-cell')
stimulus_data = np.random.rand(160, 2)
stimulus = TimeSeries(name='test_timeseries',
data=stimulus_data,
unit='m',
starting_time=0.0,
rate=1.0)
response_data = np.random.rand(160, 2)
response = TimeSeries(name='test_timeseries',
data=response_data,
unit='m',
starting_time=0.0,
rate=1.0)
icr = IntracellularRecordings()
icr.add_recording(electrode=electrode,
stimulus_start_index=0,
stimulus_index_count=100,
stimulus=stimulus,
response_start_index=0,
response_index_count=100,
response=response)
sweeps_table = Sweeps(intracellular_recordings_table=icr)
assert isinstance(show_single_sweep_sequence(sweeps_table), plt.Figure)
def setUpContainer(self):
""" Return the test SweepTable to read/write """
self.device = Device(name='device_name')
self.elec = IntracellularElectrode(
name="elec0",
slice='tissue slice',
resistance='something measured in ohms',
seal='sealing method',
description='a fake electrode object',
location='Springfield Elementary School',
filtering='a meaningless free-form text field',
initial_access_resistance='I guess this changes',
device=self.device)
self.pcs = PatchClampSeries(name="pcs",
data=[1, 2, 3, 4, 5],
unit='A',
starting_time=123.6,
rate=10e3,
electrode=self.elec,
gain=0.126,
stimulus_description="gotcha ya!",
sweep_number=np.uint(4711))
# Create the SweepTable but ignore the DeprecationWarning
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('ignore', DeprecationWarning)
sweeptable = SweepTable(name='sweep_table')
# Reissue any other warnings that may have occured
for i in w:
warnings.warn(i.message, i.category)
return sweeptable
def addContainer(self, nwbfile):
device = Device(name='device_name')
nwbfile.add_device(device)
elec = IntracellularElectrode(
name="elec0",
slice='tissue slice',
resistance='something measured in ohms',
seal='sealing method',
description='a fake electrode object',
location='Springfield Elementary School',
filtering='a meaningless free-form text field',
initial_access_resistance='I guess this changes',
device=device)
nwbfile.add_ic_electrode(elec)
pcs = PatchClampSeries(name="pcs",
data=[1, 2, 3, 4, 5],
unit='A',
starting_time=123.6,
rate=10e3,
electrode=elec,
gain=0.126,
stimulus_description="gotcha ya!",
sweep_number=4711)
nwbfile.add_acquisition(pcs)
self.container = nwbfile.sweep_table
self.assertEqual(len(self.container['series'].data), 1)
self.assertEqual(self.container.id[0], 0)
self.assertEqual(self.container['sweep_number'].data[0], 4711)
def _createElectrodes(self, device):
"""
Create pynwb ic_electrodes objects from the ABF file contents.
"""
return [IntracellularElectrode(f"Electrode {x:d}",
device,
description=PLACEHOLDER)
for x in self.refabf.channelList]
def setUpElectrode(self):
""" Set up the test IntracellularElectrode """
self.device = Device(name='device_name')
self.elec = IntracellularElectrode(name="elec0", slice='tissue slice',
resistance='something measured in ohms',
seal='sealing method', description='a fake electrode object',
location='Springfield Elementary School',
filtering='a meaningless free-form text field',
initial_access_resistance='I guess this changes',
device=self.device)
def setUpElectrode(self):
self.elec = IntracellularElectrode(name="elec0",
source='',
slice='',
resistance='',
seal='',
description='',
location='',
filtering='',
initial_access_resistance='',
device='')
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')
return elec
def GetElectrode():
device = Device(name='device_name', source='device_source')
elec = IntracellularElectrode('test_iS',
device,
'a test source',
'slice',
'seal',
'description',
'location',
'resistance',
'filtering',
'initial_access_resistance')
return elec
def GetElectrode(self):
device = Device(name='device_name', source='device_source')
elec = IntracellularElectrode('slice', 'seal', 'description', 'location', 'resistance',
'filtering', 'initial_access_resistance',
device)
self.assertEqual(elec.slice, 'slice')
self.assertEqual(elec.seal, 'seal')
self.assertEqual(elec.description, 'description')
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.device, device)
def setUpContainer(self):
elec = IntracellularElectrode(
name="elec0",
source='ice source',
slice='tissue slice',
resistance='something measured in ohms',
seal='sealing method',
description='a fake electrode object',
location='Springfield Elementary School',
filtering='a meaningless free-form text field',
initial_access_resistance='I guess this changes',
device='I should be a Device object, but just a name will do')
return elec
def setUpContainer(self):
""" Return the test SweepTable to read/write """
self.device = Device(name='device_name')
self.elec = IntracellularElectrode(name="elec0", slice='tissue slice',
resistance='something measured in ohms',
seal='sealing method', description='a fake electrode object',
location='Springfield Elementary School',
filtering='a meaningless free-form text field',
initial_access_resistance='I guess this changes',
device=self.device)
self.pcs = PatchClampSeries(name="pcs", data=[1, 2, 3, 4, 5], unit='A',
starting_time=123.6, rate=10e3, electrode=self.elec, gain=0.126,
stimulus_description="gotcha ya!", sweep_number=4711)
return SweepTable(name='sweep_table')
def test_constructor(self):
device = Device(name='device_name')
elec = IntracellularElectrode('test_iS', device, 'description',
'slice', 'seal', 'location',
'resistance', 'filtering',
'initial_access_resistance')
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')
def _createElectrodes(self, device):
"""
Create pynwb ic_electrodes objects from the DAT file contents.
Parameters
----------
pynwb.Device
Returns
-------
pynwb.IntracellularElectrode
"""
return [
IntracellularElectrode(f"Electrode {x:d}",
device,
description=PLACEHOLDER)
for x in self.electrodeDict.values()
]
def addContainer(self, nwbfile):
device = Device(name='device_name')
nwbfile.add_device(device)
elec = IntracellularElectrode(
name="elec0",
slice='tissue slice',
resistance='something measured in ohms',
seal='sealing method',
description='a fake electrode object',
location='Springfield Elementary School',
filtering='a meaningless free-form text field',
initial_access_resistance='I guess this changes',
device=device)
nwbfile.add_ic_electrode(elec)
self.pcs1 = PatchClampSeries(name="pcs1",
data=[1, 2, 3, 4, 5],
unit='A',
starting_time=123.6,
rate=10e3,
electrode=elec,
gain=0.126,
stimulus_description="gotcha ya!",
sweep_number=4711)
nwbfile.add_acquisition(self.pcs1)
self.pcs2a = PatchClampSeries(name="pcs2a",
data=[1, 2, 3, 4, 5],
unit='A',
starting_time=123.6,
rate=10e3,
electrode=elec,
gain=0.126,
stimulus_description="gotcha ya!",
sweep_number=4712)
nwbfile.add_stimulus_template(self.pcs2a)
self.pcs2b = PatchClampSeries(name="pcs2b",
data=[1, 2, 3, 4, 5],
unit='A',
starting_time=123.6,
rate=10e3,
electrode=elec,
gain=0.126,
stimulus_description="gotcha ya!",
sweep_number=4712)
nwbfile.add_stimulus(self.pcs2b)
self.container = nwbfile.sweep_table
self.assertEqual(len(self.container['series'].data), 3)
self.assertEqual(self.container['sweep_number'].data[0], 4711)
self.assertEqual(self.container['sweep_number'].data[1], 4712)
self.assertEqual(self.container['sweep_number'].data[2], 4712)
series = self.container.get_series(4711)
self.assertEqual(len(series), 1)
names = [elem.name for elem in series]
self.assertEqual(names, ["pcs1"])
sweep_numbers = [elem.sweep_number for elem in series]
self.assertEqual(sweep_numbers, [4711])
series = self.container.get_series(4712)
self.assertEqual(len(series), 2)
names = [elem.name for elem in series]
self.assertEqual(names, ["pcs2a", "pcs2b"])
sweep_numbers = [elem.sweep_number for elem in series]
self.assertEqual(sweep_numbers, [4712, 4712])
