def test_eFELFeature_force_max_score():
"""ephys.efeatures: Testing eFELFeature force_max_score option"""
recording_names = {'': 'square_pulse_step1.soma.v'}
response = TimeVoltageResponse('mock_response')
testdata_dir = joinp(os.path.dirname(os.path.abspath(__file__)),
'testdata')
response.read_csv(joinp(testdata_dir, 'TimeVoltageResponse.csv'))
responses = {
'square_pulse_step1.soma.v': response,
}
efeature_normal = 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=.001)
score_normal = efeature_normal.calculate_score(responses)
nt.assert_true(score_normal > 250)
efeature_force = 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=.001,
force_max_score=True)
score_force = efeature_force.calculate_score(responses)
nt.assert_almost_equal(score_force, 250)
def test_eFELFeature_double_settings():
"""ephys.efeatures: Testing eFELFeature double_settings"""
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)
efeature_ds = efeatures.eFELFeature(
name='test_eFELFeature_other_perc',
efel_feature_name='voltage_base',
recording_names=recording_names,
stim_start=700,
stim_end=2700,
exp_mean=1,
exp_std=1,
double_settings={'voltage_base_start_perc': 0.01})
response = TimeVoltageResponse('mock_response')
testdata_dir = joinp(os.path.dirname(os.path.abspath(__file__)),
'testdata')
response.read_csv(joinp(testdata_dir, 'TimeVoltageResponse.csv'))
responses = {
'square_pulse_step1.soma.v': response,
}
vb_other_perc = efeature_ds.calculate_feature(responses,
raise_warnings=True)
vb = efeature.calculate_feature(responses, raise_warnings=True)
nt.assert_true(vb_other_perc != vb)
def test_eFELFeature_max_score():
"""ephys.efeatures: Testing eFELFeature max_score option"""
recording_names = {'': 'square_pulse_step1.soma.v'}
response = TimeVoltageResponse('mock_response')
testdata_dir = joinp(os.path.dirname(os.path.abspath(__file__)),
'testdata')
response.read_csv(joinp(testdata_dir, 'TimeVoltageResponse.csv'))
responses = {
'square_pulse_step1.soma.v': response,
}
efeature_normal = efeatures.eFELFeature(name='test_eFELFeature',
efel_feature_name='AP_amplitude',
recording_names=recording_names,
stim_start=600,
stim_end=700,
exp_mean=1,
exp_std=1)
score_normal = efeature_normal.calculate_score(responses)
nt.assert_almost_equal(score_normal, 250)
efeature_150 = efeatures.eFELFeature(name='test_eFELFeature',
efel_feature_name='AP_amplitude',
recording_names=recording_names,
stim_start=600,
stim_end=700,
exp_mean=1,
exp_std=1,
max_score=150)
score_150 = efeature_150.calculate_score(responses)
nt.assert_almost_equal(score_150, 150)
def test_eFELFeature_int_settings():
"""ephys.efeatures: Testing eFELFeature int_settings"""
recording_names = {'': 'square_pulse_step1.soma.v'}
efeature = efeatures.eFELFeature(name='test_eFELFeature',
efel_feature_name='Spikecount',
recording_names=recording_names,
stim_start=1200,
stim_end=2000,
exp_mean=1,
exp_std=1)
efeature_strict = efeatures.eFELFeature(
name='test_eFELFeature_strict',
efel_feature_name='Spikecount',
recording_names=recording_names,
stim_start=1200,
stim_end=2000,
exp_mean=1,
exp_std=1,
int_settings={'strict_stiminterval': True})
response = TimeVoltageResponse('mock_response')
testdata_dir = joinp(os.path.dirname(os.path.abspath(__file__)),
'testdata')
response.read_csv(joinp(testdata_dir, 'TimeVoltageResponse.csv'))
responses = {
'square_pulse_step1.soma.v': response,
}
spikecount = efeature.calculate_feature(responses)
spikecount_strict = efeature_strict.calculate_feature(responses)
nt.assert_true(spikecount_strict != spikecount)
def test_eFELFeature_string_settings():
"""ephys.efeatures: Testing eFELFeature string_settings"""
recording_names = {'': 'square_pulse_step1.soma.v'}
efeature = efeatures.eFELFeature(name='test_eFELFeature_vb_default',
efel_feature_name='voltage_base',
recording_names=recording_names,
stim_start=700,
stim_end=2700)
efeature_median = efeatures.eFELFeature(
name='test_eFELFeature_vb_median',
efel_feature_name='voltage_base',
recording_names=recording_names,
stim_start=700,
stim_end=2700,
string_settings={
'voltage_base_mode': "median"})
response = TimeVoltageResponse('mock_response')
testdata_dir = joinp(
os.path.dirname(
os.path.abspath(__file__)),
'testdata')
response.read_csv(joinp(testdata_dir, 'TimeVoltageResponse.csv'))
responses = {'square_pulse_step1.soma.v': response, }
vb_median = efeature_median.calculate_feature(
responses,
raise_warnings=True)
vb_default = efeature.calculate_feature(responses, raise_warnings=True)
assert vb_median != vb_default
def test_eFELFeature_int_settings():
"""ephys.efeatures: Testing eFELFeature int_settings"""
recording_names = {"": "square_pulse_step1.soma.v"}
efeature = efeatures.eFELFeature(
name="test_eFELFeature",
efel_feature_name="Spikecount",
recording_names=recording_names,
stim_start=1200,
stim_end=2000,
exp_mean=1,
exp_std=1,
)
efeature_strict = efeatures.eFELFeature(
name="test_eFELFeature_strict",
efel_feature_name="Spikecount",
recording_names=recording_names,
stim_start=1200,
stim_end=2000,
exp_mean=1,
exp_std=1,
int_settings={"strict_stiminterval": True},
)
response = TimeVoltageResponse("mock_response")
testdata_dir = joinp(os.path.dirname(os.path.abspath(__file__)),
"testdata")
response.read_csv(joinp(testdata_dir, "TimeVoltageResponse.csv"))
responses = {
"square_pulse_step1.soma.v": response,
}
spikecount = efeature.calculate_feature(responses)
spikecount_strict = efeature_strict.calculate_feature(responses)
nt.assert_true(spikecount_strict != spikecount)
def test_eFELFeature_double_settings():
"""ephys.efeatures: Testing eFELFeature double_settings"""
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)
efeature_ds = efeatures.eFELFeature(
name='test_eFELFeature_other_perc',
efel_feature_name='voltage_base',
recording_names=recording_names,
stim_start=700,
stim_end=2700,
exp_mean=1,
exp_std=1,
double_settings={
'voltage_base_start_perc': 0.01})
response = TimeVoltageResponse('mock_response')
testdata_dir = joinp(os.path.dirname(os.path.abspath(__file__)), 'testdata')
response.read_csv(joinp(testdata_dir, 'TimeVoltageResponse.csv'))
responses = {'square_pulse_step1.soma.v': response, }
vb_other_perc = efeature_ds.calculate_feature(
responses,
raise_warnings=True)
vb = efeature.calculate_feature(responses, raise_warnings=True)
nt.assert_true(vb_other_perc != vb)
def test_eFELFeature():
"""ephys.efeatures: Testing eFELFeature creation"""
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)
response = TimeVoltageResponse('mock_response')
testdata_dir = joinp(os.path.dirname(os.path.abspath(__file__)),
'testdata')
response.read_csv(joinp(testdata_dir, 'TimeVoltageResponse.csv'))
responses = {
'square_pulse_step1.soma.v': response,
}
ret = efeature.calculate_feature(responses, raise_warnings=True)
nt.assert_almost_equal(ret, -72.0575843859)
score = efeature.calculate_score(responses)
nt.assert_almost_equal(score, 73.05758438592171)
nt.eq_(efeature.name, 'test_eFELFeature')
nt.ok_('voltage_base' in str(efeature))
def test_eFELFeature():
"""ephys.efeatures: Testing eFELFeature creation"""
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,
)
response = TimeVoltageResponse("mock_response")
testdata_dir = joinp(os.path.dirname(os.path.abspath(__file__)),
"testdata")
response.read_csv(joinp(testdata_dir, "TimeVoltageResponse.csv"))
responses = {
"square_pulse_step1.soma.v": response,
}
ret = efeature.calculate_feature(responses, raise_warnings=True)
nt.assert_almost_equal(ret, -72.0576124731685)
score = efeature.calculate_score(responses)
nt.assert_almost_equal(score, 73.05761247316)
nt.eq_(efeature.name, "test_eFELFeature")
nt.ok_("voltage_base" in str(efeature))
def test_eFELFeature_force_max_score():
"""ephys.efeatures: Testing eFELFeature force_max_score option"""
recording_names = {"": "square_pulse_step1.soma.v"}
response = TimeVoltageResponse("mock_response")
testdata_dir = joinp(os.path.dirname(os.path.abspath(__file__)),
"testdata")
response.read_csv(joinp(testdata_dir, "TimeVoltageResponse.csv"))
responses = {
"square_pulse_step1.soma.v": response,
}
efeature_normal = 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=0.001,
)
score_normal = efeature_normal.calculate_score(responses)
nt.assert_true(score_normal > 250)
efeature_force = 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=0.001,
force_max_score=True,
)
score_force = efeature_force.calculate_score(responses)
nt.assert_almost_equal(score_force, 250)
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_double_settings():
"""ephys.efeatures: Testing eFELFeature double_settings"""
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,
)
efeature_ds = efeatures.eFELFeature(
name="test_eFELFeature_other_perc",
efel_feature_name="voltage_base",
recording_names=recording_names,
stim_start=700,
stim_end=2700,
exp_mean=1,
exp_std=1,
double_settings={"voltage_base_start_perc": 0.01},
)
response = TimeVoltageResponse("mock_response")
testdata_dir = joinp(os.path.dirname(os.path.abspath(__file__)),
"testdata")
response.read_csv(joinp(testdata_dir, "TimeVoltageResponse.csv"))
responses = {
"square_pulse_step1.soma.v": response,
}
vb_other_perc = efeature_ds.calculate_feature(responses,
raise_warnings=True)
vb = efeature.calculate_feature(responses, raise_warnings=True)
nt.assert_true(vb_other_perc != vb)
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_eFELFeature():
"""ephys.efeatures: Testing eFELFeature creation"""
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)
response = TimeVoltageResponse('mock_response')
testdata_dir = joinp(os.path.dirname(os.path.abspath(__file__)), 'testdata')
response.read_csv(joinp(testdata_dir, 'TimeVoltageResponse.csv'))
responses = {'square_pulse_step1.soma.v': response, }
ret = efeature.calculate_feature(responses, raise_warnings=True)
nt.assert_almost_equal(ret, -72.069487699766668)
score = efeature.calculate_score(responses)
nt.assert_almost_equal(score, 73.06948769976667)
nt.eq_(efeature.name, 'test_eFELFeature')
nt.ok_('voltage_base' in str(efeature))