def test_serialize():
"""ephys.locations: Test serialize functionality"""
from bluepyopt.ephys.locations import (
NrnSeclistCompLocation,
NrnSeclistLocation,
NrnSeclistSecLocation,
NrnSomaDistanceCompLocation)
seclist_name, sec_index, comp_x, soma_distance = 'somatic', 0, 0.5, 800
locations = (
NrnSeclistCompLocation('NrnSeclistCompLocation',
seclist_name, sec_index, comp_x),
NrnSeclistLocation(
'NrnSeclistLocation', seclist_name),
NrnSeclistSecLocation(
'NrnSeclistSecLocation', seclist_name, sec_index),
NrnSomaDistanceCompLocation(
'NrnSomaDistanceCompLocation', soma_distance, seclist_name),)
for loc in locations:
serialized = loc.to_dict()
assert isinstance(json.dumps(serialized), str)
deserialized = instantiator(serialized)
assert isinstance(deserialized, loc.__class__)
assert deserialized.seclist_name == seclist_name
assert deserialized.name == loc.__class__.__name__
def test_mechanism_serialize():
"""ephys.mechanisms: Testing serialize"""
mech = utils.make_mech()
serialized = mech.to_dict()
nt.ok_(isinstance(json.dumps(serialized), str))
deserialized = instantiator(serialized)
nt.ok_(isinstance(deserialized, ephys.mechanisms.NrnMODMechanism))
def test_mechanism_serialize():
"""ephys.mechanisms: Testing serialize"""
mech = utils.make_mech()
serialized = mech.to_dict()
nt.assert_true(isinstance(json.dumps(serialized), str))
deserialized = instantiator(serialized)
nt.assert_true(isinstance(deserialized, ephys.mechanisms.NrnMODMechanism))
def test_serialize():
"""ephys.locations: Test serialize functionality"""
from bluepyopt.ephys.locations import (
NrnSeclistCompLocation,
NrnSeclistLocation,
NrnSeclistSecLocation,
NrnSomaDistanceCompLocation)
seclist_name, sec_index, comp_x, soma_distance = 'somatic', 0, 0.5, 800
locations = (
NrnSeclistCompLocation('NrnSeclistCompLocation',
seclist_name, sec_index, comp_x),
NrnSeclistLocation(
'NrnSeclistLocation', seclist_name),
NrnSeclistSecLocation(
'NrnSeclistSecLocation', seclist_name, sec_index),
NrnSomaDistanceCompLocation(
'NrnSomaDistanceCompLocation', soma_distance, seclist_name),)
for loc in locations:
serialized = loc.to_dict()
nt.ok_(isinstance(json.dumps(serialized), str))
deserialized = instantiator(serialized)
nt.ok_(isinstance(deserialized, loc.__class__))
nt.eq_(deserialized.seclist_name, seclist_name)
nt.eq_(deserialized.name, loc.__class__.__name__)
def test_serialize():
"""ephys.locations: Test serialize functionality"""
from bluepyopt.ephys.locations import (
NrnSeclistCompLocation,
NrnSeclistLocation,
NrnSeclistSecLocation,
NrnSomaDistanceCompLocation,
)
seclist_name, sec_index, comp_x, soma_distance = "somatic", 0, 0.5, 800
locations = (
NrnSeclistCompLocation("NrnSeclistCompLocation", seclist_name,
sec_index, comp_x),
NrnSeclistLocation("NrnSeclistLocation", seclist_name),
NrnSeclistSecLocation("NrnSeclistSecLocation", seclist_name,
sec_index),
NrnSomaDistanceCompLocation("NrnSomaDistanceCompLocation",
soma_distance, seclist_name),
)
for loc in locations:
serialized = loc.to_dict()
nt.ok_(isinstance(json.dumps(serialized), str))
deserialized = instantiator(serialized)
nt.ok_(isinstance(deserialized, loc.__class__))
nt.eq_(deserialized.seclist_name, seclist_name)
nt.eq_(deserialized.name, loc.__class__.__name__)
def test_mechanism_serialize():
basal = ephys.locations.NrnSeclistLocation('basal', seclist_name='basal')
apical = ephys.locations.NrnSeclistLocation('apical', seclist_name='apical')
mech = ephys.mechanisms.NrnMODMechanism('Ih', prefix='Ih', locations=[basal, apical, ])
serialized = mech.to_dict()
nt.ok_(isinstance(json.dumps(serialized), str))
deserialized = instantiator(serialized)
nt.ok_(isinstance(deserialized, ephys.mechanisms.NrnMODMechanism))
def test_serialize():
"""ephys.morphology: testing serialization"""
morph = ephys.morphologies.NrnFileMorphology(simpleswc_morphpath)
serialized = morph.to_dict()
nt.ok_(isinstance(json.dumps(serialized), str))
deserialized = instantiator(serialized)
nt.ok_(isinstance(deserialized, ephys.morphologies.NrnFileMorphology))
nt.eq_(deserialized.morphology_path, simpleswc_morphpath)
def test_serialize():
"""ephys.morphology: testing serialization"""
morph = ephys.morphologies.NrnFileMorphology(simpleswc_morphpath)
serialized = morph.to_dict()
nt.ok_(isinstance(json.dumps(serialized), str))
deserialized = instantiator(serialized)
nt.ok_(isinstance(deserialized, ephys.morphologies.NrnFileMorphology))
nt.eq_(deserialized.morphology_path, simpleswc_morphpath)
def test_serialize():
parameters = utils.make_parameters()
for param in parameters:
serialized = param.to_dict()
nt.ok_(isinstance(json.dumps(serialized), str))
deserialized = instantiator(serialized)
nt.ok_(isinstance(deserialized, param.__class__))
nt.eq_(deserialized.name, param.__class__.__name__)
def test_serialize():
"""ephys.parameters: Test serialize"""
parameters = utils.make_parameters()
for param in parameters:
serialized = param.to_dict()
assert isinstance(json.dumps(serialized), str)
deserialized = instantiator(serialized)
assert isinstance(deserialized, param.__class__)
assert deserialized.name == param.__class__.__name__
def test_serialize():
multiplier, offset, distribution = 12.12, 3.58, '1 + {distance}'
paramscalers = (
NrnSegmentLinearScaler('NrnSegmentLinearScaler', multiplier, offset),
NrnSegmentSomaDistanceScaler('NrnSegmentSomaDistanceScaler', distribution),)
for ps in paramscalers:
serialized = ps.to_dict()
nt.ok_(isinstance(json.dumps(serialized), str))
deserialized = instantiator(serialized)
nt.ok_(isinstance(deserialized, ps.__class__))
nt.eq_(deserialized.name, ps.__class__.__name__)
def test_mechanism_serialize():
basal = ephys.locations.NrnSeclistLocation('basal', seclist_name='basal')
apical = ephys.locations.NrnSeclistLocation('apical',
seclist_name='apical')
mech = ephys.mechanisms.NrnMODMechanism('Ih',
prefix='Ih',
locations=[
basal,
apical,
])
serialized = mech.to_dict()
nt.ok_(isinstance(json.dumps(serialized), str))
deserialized = instantiator(serialized)
nt.ok_(isinstance(deserialized, ephys.mechanisms.NrnMODMechanism))
def test_eFELFeature_serialize():
recording_names = {'': 'square_pulse_step1.soma.v'}
efeature = efeatures.eFELFeature(name='test_eFELFeature',
efel_feature_name='voltage_base',
recording_names=recording_names,
stim_start=700,
stim_end=2700,
exp_mean=1,
exp_std=1)
serialized = efeature.to_dict()
deserialized = instantiator(serialized)
nt.ok_(isinstance(deserialized, efeatures.eFELFeature))
nt.eq_(deserialized.stim_start, 700)
nt.eq_(deserialized.recording_names, recording_names)
def test_eFELFeature_serialize():
recording_names = {'': 'square_pulse_step1.soma.v'}
efeature = efeatures.eFELFeature(name='test_eFELFeature',
efel_feature_name='voltage_base',
recording_names=recording_names,
stim_start=700,
stim_end=2700,
exp_mean=1,
exp_std=1)
serialized = efeature.to_dict()
deserialized = instantiator(serialized)
nt.ok_(isinstance(deserialized, efeatures.eFELFeature))
nt.eq_(deserialized.stim_start, 700)
nt.eq_(deserialized.recording_names, recording_names)
def test_eFELFeature_serialize():
"""ephys.efeatures: Testing eFELFeature serialization"""
recording_names = {'': 'square_pulse_step1.soma.v'}
efeature = efeatures.eFELFeature(name='test_eFELFeature',
efel_feature_name='voltage_base',
recording_names=recording_names,
stim_start=700,
stim_end=2700,
exp_mean=1,
exp_std=1)
serialized = efeature.to_dict()
deserialized = instantiator(serialized)
assert isinstance(deserialized, efeatures.eFELFeature)
assert deserialized.stim_start == 700
assert deserialized.recording_names == recording_names
def test_eFELFeature_serialize():
"""ephys.efeatures: Testing eFELFeature serialization"""
recording_names = {"": "square_pulse_step1.soma.v"}
efeature = efeatures.eFELFeature(
name="test_eFELFeature",
efel_feature_name="voltage_base",
recording_names=recording_names,
stim_start=700,
stim_end=2700,
exp_mean=1,
exp_std=1,
)
serialized = efeature.to_dict()
deserialized = instantiator(serialized)
nt.ok_(isinstance(deserialized, efeatures.eFELFeature))
nt.eq_(deserialized.stim_start, 700)
nt.eq_(deserialized.recording_names, recording_names)
def test_serialize():
"""ephys.parameterscalers: test serialization"""
multiplier, offset, distribution = 12.12, 3.58, '1 + {distance}'
paramscalers = (
NrnSegmentLinearScaler(
'NrnSegmentLinearScaler',
multiplier,
offset),
NrnSegmentSomaDistanceScaler(
'NrnSegmentSomaDistanceScaler',
distribution),
)
for ps in paramscalers:
serialized = ps.to_dict()
assert isinstance(json.dumps(serialized), str)
deserialized = instantiator(serialized)
assert isinstance(deserialized, ps.__class__)
assert deserialized.name == ps.__class__.__name__
def test_serialize():
value, frozen, bounds, param_name = 65, False, [0, 100.0], 'gSKv3_1bar_SKv3_1'
value_scaler = ephys.parameterscalers.NrnSegmentLinearScaler()
locations = (NrnSeclistLocation('Location0', 'somatic'),
NrnSeclistLocation('Location1', 'apical'),
)
parameters = (
NrnGlobalParameter('NrnGlobalParameter', value, frozen, bounds, param_name),
NrnSectionParameter(
'NrnSectionParameter', value, frozen, bounds, param_name, value_scaler, locations ),
NrnRangeParameter(
'NrnRangeParameter', value, frozen, bounds, param_name, value_scaler, locations),
)
for param in parameters:
serialized = param.to_dict()
nt.ok_(isinstance(json.dumps(serialized), str))
deserialized = instantiator(serialized)
nt.ok_(isinstance(deserialized, param.__class__))
nt.eq_(deserialized.name, param.__class__.__name__)