def addContainer(self, file):
table = ElectrodeTable('electrodes')
dev1 = Device('dev1', 'a test source')
group = ElectrodeGroup('tetrode1', 'a test source',
'tetrode description', 'tetrode location', dev1)
table.add_row(1, 1.0, 2.0, 3.0, -1.0, 'CA1', 'none',
'first channel of tetrode', group)
table.add_row(2, 1.0, 2.0, 3.0, -2.0, 'CA1', 'none',
'second channel of tetrode', group)
table.add_row(3, 1.0, 2.0, 3.0, -3.0, 'CA1', 'none',
'third channel of tetrode', group)
table.add_row(4, 1.0, 2.0, 3.0, -4.0, 'CA1', 'none',
'fourth channel of tetrode', group)
file.set_device(dev1)
file.set_electrode_group(group)
file.set_electrode_table(table)
region = ElectrodeTableRegion(
table, [0, 2], 'the first and third electrodes') # noqa: F405
data = list(zip(range(10), range(10, 20)))
timestamps = list(range(10))
es = ElectricalSeries('test_eS',
'a hypothetical source',
data,
region,
timestamps=timestamps)
file.add_acquisition(es)
return es
def addContainer(self, file):
dev1 = Device('dev1', 'a test source')
file.set_device(dev1)
eg = ElectrodeGroup('elec1', 'a test source', 'a test ElectrodeGroup',
'a nonexistent place', dev1)
file.set_electrode_group(eg)
return eg
def setUp(self) -> None:
data1 = np.array([1, 2, 2, 3, 1, 1, 3, 2, 3])
data2 = np.array([3, 4, 2, 4, 3, 2, 2, 4, 4])
device = Device(name="device")
eg_1 = ElectrodeGroup(name="electrodegroup1",
description="desc",
location="brain",
device=device)
eg_2 = ElectrodeGroup(name="electrodegroup2",
description="desc",
location="brain",
device=device)
data3 = [eg_1, eg_2, eg_1, eg_1, eg_1, eg_1, eg_1, eg_1, eg_1]
vd1 = VectorData("Data1",
"vector data for creating a DynamicTable",
data=data1)
vd2 = VectorData("Data2",
"vector data for creating a DynamicTable",
data=data2)
vd3 = VectorData("ElectrodeGroup",
"vector data for creating a DynamicTable",
data=data3)
vd = [vd1, vd2, vd3]
self.dynamic_table = DynamicTable(
name="test table",
description="This is a test table",
columns=vd,
colnames=["Data1", "Data2", "ElectrodeGroup"],
)
def test_create_electrode_group(self):
name = 'example_electrode_group'
desc = 'An example electrode'
loc = 'an example location'
d = Device('a fake device', 'a fake source')
elecgrp = self.nwbfile.create_electrode_group(name, 'a fake source', desc, loc, d)
self.assertEqual(elecgrp.description, desc)
self.assertEqual(elecgrp.location, loc)
self.assertIs(elecgrp.device, d)
def test_init(self):
device = Device('name')
oS = OptogeneticStimulusSite('site1', device, 'description', 300., 'location')
self.assertEqual(oS.name, 'site1')
self.assertEqual(oS.device, device)
self.assertEqual(oS.description, 'description')
self.assertEqual(oS.excitation_lambda, 300.)
self.assertEqual(oS.location, 'location')
iS = OptogeneticSeries('test_iS', list(), oS, timestamps=list())
self.assertEqual(iS.name, 'test_iS')
self.assertEqual(iS.unit, 'watts')
self.assertEqual(iS.site, oS)
def test_init(self):
device = Device('name')
oS = OptogeneticStimulusSite(name='site1',
device=device,
description='description',
excitation_lambda=300.,
location='location')
self.assertEqual(oS.name, 'site1')
self.assertEqual(oS.device, device)
self.assertEqual(oS.description, 'description')
self.assertEqual(oS.excitation_lambda, 300.)
self.assertEqual(oS.location, 'location')
iS = OptogeneticSeries(name='test_iS',
data=[1, 2, 3],
site=oS,
timestamps=[0.1, 0.2, 0.3])
self.assertEqual(iS.name, 'test_iS')
self.assertEqual(iS.unit, 'watts')
self.assertEqual(iS.site, oS)
def test_init(self):
device = Device('name', 'source')
oS = OptogeneticStimulusSite('site1', 'a test source', device,
'description', 'excitation_lambda',
'location')
self.assertEqual(oS.name, 'site1')
self.assertEqual(oS.device, device)
self.assertEqual(oS.description, 'description')
self.assertEqual(oS.excitation_lambda, 'excitation_lambda')
self.assertEqual(oS.location, 'location')
iS = OptogeneticSeries('test_iS',
'a hypothetical source',
list(),
oS,
timestamps=list())
self.assertEqual(iS.name, 'test_iS')
self.assertEqual(iS.source, 'a hypothetical source')
self.assertEqual(iS.unit, 'Watt')
self.assertEqual(iS.site, oS)