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 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_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 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')
class TestSweepTableRoundTripComplicated(base.TestMapRoundTrip):
_required_tests = ('test_container', 'test_build', 'test_construct',
'test_roundtrip')
def setUpContainer(self):
self.setUpSweepTable()
return self.sweep_table
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 addContainer(self, nwbfile):
''' Should take an NWBFile object and add the SweepTable container to it '''
nwbfile.add_device(self.device)
nwbfile.add_ic_electrode(self.elec)
nwbfile.add_acquisition(self.pcs1)
nwbfile.add_stimulus_template(self.pcs2a)
nwbfile.add_stimulus(self.pcs2b)
def test_container(self):
description = 'a file to test writing and reading a %s' % self.container_type
identifier = 'TEST_%s' % self.container_type
nwbfile = NWBFile(description,
identifier,
self.start_time,
file_create_date=self.create_date)
self.addContainer(nwbfile)
sweep_table = self.getContainer(nwbfile)
self.assertEqual(len(sweep_table['series'].data), 3)
self.assertEqual(sweep_table['sweep_number'].data[0], 4711)
self.assertEqual(sweep_table['sweep_number'].data[1], 4712)
self.assertEqual(sweep_table['sweep_number'].data[2], 4712)
series = sweep_table.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 = sweep_table.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])
def getContainer(self, nwbfile):
return nwbfile.sweep_table
def setUpBuilder(self):
device = GroupBuilder('device_name',
attributes={
'neurodata_type': 'Device',
'help': 'A recording device e.g. amplifier',
'namespace': 'core',
})
datasets = [
DatasetBuilder('slice', data=u'tissue slice'),
DatasetBuilder('resistance', data=u'something measured in ohms'),
DatasetBuilder('seal', data=u'sealing method'),
DatasetBuilder('description', data=u'a fake electrode object'),
DatasetBuilder('location', data=u'Springfield Elementary School'),
DatasetBuilder('filtering',
data=u'a meaningless free-form text field'),
DatasetBuilder('initial_access_resistance',
data=u'I guess this changes'),
]
elec = GroupBuilder('elec0',
attributes={
'help':
'Metadata about an intracellular electrode',
'namespace': 'core',
'neurodata_type': 'IntracellularElectrode',
},
datasets={d.name: d
for d in datasets},
links={'device': LinkBuilder(device, 'device')})
datasets = [
DatasetBuilder(
'gain',
data=0.126,
attributes={},
),
DatasetBuilder('data',
data=[1, 2, 3, 4, 5],
attributes={
'conversion': 1.0,
'resolution': 0.0,
'unit': u'A',
}),
DatasetBuilder('starting_time',
data=123.6,
attributes={
'rate': 10000.0,
'unit': 'Seconds',
}),
]
attributes = {
'neurodata_type': 'PatchClampSeries',
'namespace': 'core',
'comments': u'no comments',
'help': 'Superclass definition for patch-clamp data',
'description': u'no description',
'stimulus_description': u'gotcha ya!',
}
attributes['sweep_number'] = 4711
pcs1 = GroupBuilder(
'pcs1',
attributes=attributes,
links={'electrode': LinkBuilder(elec, 'electrode')},
datasets={d.name: d
for d in datasets},
)
attributes['sweep_number'] = 4712
pcs2a = GroupBuilder(
'pcs2a',
attributes=attributes,
links={'electrode': LinkBuilder(elec, 'electrode')},
datasets={d.name: d
for d in datasets},
)
pcs2b = GroupBuilder(
'pcs2b',
attributes=attributes,
links={'electrode': LinkBuilder(elec, 'electrode')},
datasets={d.name: d
for d in datasets},
)
column_id = DatasetBuilder(
'id', [0, 1, 2],
attributes={
'neurodata_type': 'ElementIdentifiers',
'namespace': 'core',
'help': 'unique identifiers for a list of elements',
})
column_series = DatasetBuilder(
'series',
attributes={
'neurodata_type': 'VectorData',
'namespace': 'core',
'help': 'Values for a list of elements',
'description': u'PatchClampSeries with the same sweep number',
},
data=[LinkBuilder(pcs) for pcs in (pcs1, pcs2a, pcs2b)])
column_index = DatasetBuilder(
'series_index',
[1, 2, 3],
attributes={
'neurodata_type': 'VectorIndex',
'namespace': 'core',
'help': 'indexes into a list of values for a list of elements',
'target': ReferenceBuilder(column_series),
},
)
column_sweep_number = DatasetBuilder(
'sweep_number',
data=[4711, 4712, 4712],
attributes={
'neurodata_type': 'VectorData',
'namespace': 'core',
'help': 'Values for a list of elements',
'description': u'Sweep number of the entries in that row',
})
columns = [column_id, column_series, column_index, column_sweep_number]
sweep_table = GroupBuilder(
'sweep_table',
datasets={c.name: c
for c in columns},
attributes={
'neurodata_type':
'SweepTable',
'namespace':
'core',
'colnames': (b'series', b'sweep_number'),
'help':
'The table which groups different PatchClampSeries together',
'description':
u'A sweep table groups different PatchClampSeries together.',
},
)
return sweep_table