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.pcs1 = PatchClampSeries(name="pcs1",
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))
self.pcs2a = PatchClampSeries(name="pcs2a",
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(4712))
self.pcs2b = PatchClampSeries(name="pcs2b",
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(4712))
# 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 setUpSweepTable(self):
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.pcs1 = PatchClampSeries(name="pcs1",
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)
self.pcs2a = PatchClampSeries(name="pcs2a",
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=4712)
self.pcs2b = PatchClampSeries(name="pcs2b",
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=4712)
self.sweep_table = SweepTable(name='sweep_table')
self.sweep_table.add_entry(self.pcs1)
self.sweep_table.add_entry(self.pcs2a)
self.sweep_table.add_entry(self.pcs2b)
def test_init(self):
electrode_name = GetElectrode()
pCS = PatchClampSeries('test_pCS', 'a hypothetical source', list(), 'unit',
electrode_name, 1.0, timestamps=list())
self.assertEqual(pCS.name, 'test_pCS')
self.assertEqual(pCS.source, 'a hypothetical source')
self.assertEqual(pCS.unit, 'unit')
self.assertEqual(pCS.electrode, electrode_name)
self.assertEqual(pCS.gain, 1.0)
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 setUpContainer(self):
self.setUpElectrode()
return 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)
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_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_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 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))
return SweepTable(name='sweep_table')
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])
