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(): 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(): """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__)