def test_strict_stiminterval():
"""basic: Test strict_stiminterval"""
import efel
for strict, n_of_spikes in [(False, 5), (True, 3)]:
efel.reset()
efel.setIntSetting("strict_stiminterval", strict)
stim_start = 600.0
stim_end = 750.0
time = efel.io.load_fragment('%s#col=1' % meanfrequency1_url)
voltage = efel.io.load_fragment('%s#col=2' % meanfrequency1_url)
trace = {}
trace['T'] = time
trace['V'] = voltage
trace['stim_start'] = [stim_start]
trace['stim_end'] = [stim_end]
features = ['peak_indices', 'peak_time', 'Spikecount']
feature_values = \
efel.getFeatureValues(
[trace],
features, raise_warnings=False)
peak_indices = feature_values[0]['peak_indices']
peak_time = feature_values[0]['peak_time']
spikecount = feature_values[0]['Spikecount']
nt.assert_equal(len(peak_indices), n_of_spikes)
nt.assert_equal(len(peak_time), n_of_spikes)
nt.assert_equal(spikecount, n_of_spikes)
def _setup_efel(self):
"""Set up efel before extracting the feature"""
import efel
efel.reset()
if self.threshold is not None:
efel.setThreshold(self.threshold)
if self.stimulus_current is not None:
efel.setDoubleSetting('stimulus_current', self.stimulus_current)
if self.interp_step is not None:
efel.setDoubleSetting('interp_step', self.interp_step)
if self.double_settings is not None:
for setting_name, setting_value in self.double_settings.items():
efel.setDoubleSetting(setting_name, setting_value)
if self.int_settings is not None:
for setting_name, setting_value in self.int_settings.items():
efel.setIntSetting(setting_name, setting_value)
if self.string_settings is not None:
for setting_name, setting_value in self.string_settings.items():
efel.setStrSetting(setting_name, setting_value)
def test_unfinished_peak():
"""basic: Test if unfinished peak doesn't break Spikecount"""
import efel
efel.setIntSetting('strict_stiminterval', True)
dt = 0.1
v = numpy.zeros(int(100 / dt)) - 70.0
v[int(20 / dt):int(25 / dt)] = 20.
v[int(40 / dt):int(45 / dt)] = 20.
v[int(60 / dt):int(65 / dt)] = 20.
trace = {}
trace['T'] = numpy.arange(len(v)) * dt
trace['V'] = v
trace['stim_start'] = [10]
trace['stim_end'] = [70]
traces_results = efel.getFeatureValues([trace], ['Spikecount'])
spikecount = traces_results[0]['Spikecount'][0]
nt.assert_equal(spikecount, 3)
# When the signal at the end of the trace is larger than the threshold,
# Spikecount and possibly other features cannont be estimated.
v[int(80 / dt):] = -19
traces_results = efel.getFeatureValues([trace], ['Spikecount'])
spikecount = traces_results[0]['Spikecount'][0]
nt.assert_equal(spikecount, 3)
def test_min_AHP_indices_strict():
"""basic: Test min_AHP_indices with strict_stiminterval"""
import efel
for strict, n_of_ahp in [(False, 17), (True, 16)]:
efel.reset()
efel.setIntSetting('strict_stiminterval', strict)
stim_start = 700.0
stim_end = 2700.0
time = efel.io.load_fragment('%s#col=1' % ahptest1_url)
voltage = efel.io.load_fragment('%s#col=2' % ahptest1_url)
trace = {}
trace['T'] = time
trace['V'] = voltage
trace['stim_start'] = [stim_start]
trace['stim_end'] = [stim_end]
features = ['min_AHP_indices', 'AHP_time_from_peak', 'peak_time']
feature_values = \
efel.getFeatureValues(
[trace],
features, raise_warnings=False)
min_AHP_indices = feature_values[0]['min_AHP_indices']
AHP_time_from_peak = feature_values[0]['AHP_time_from_peak']
nt.assert_equal(len(min_AHP_indices), n_of_ahp)
nt.assert_equal(len(AHP_time_from_peak), n_of_ahp)
def test_strict_stiminterval():
"""basic: Test strict_stiminterval"""
import efel
for strict, n_of_spikes in [(False, 5), (True, 3)]:
efel.reset()
efel.setIntSetting("strict_stiminterval", strict)
stim_start = 600.0
stim_end = 750.0
time = efel.io.load_fragment('%s#col=1' % meanfrequency1_url)
voltage = efel.io.load_fragment('%s#col=2' % meanfrequency1_url)
trace = {}
trace['T'] = time
trace['V'] = voltage
trace['stim_start'] = [stim_start]
trace['stim_end'] = [stim_end]
features = ['peak_indices', 'peak_time', 'Spikecount']
feature_values = \
efel.getFeatureValues(
[trace],
features, raise_warnings=False)
peak_indices = feature_values[0]['peak_indices']
peak_time = feature_values[0]['peak_time']
spikecount = feature_values[0]['Spikecount']
nt.assert_equal(len(peak_indices), n_of_spikes)
nt.assert_equal(len(peak_time), n_of_spikes)
nt.assert_equal(spikecount, n_of_spikes)
def test_min_AHP_indices_strict():
"""basic: Test min_AHP_indices with strict_stiminterval"""
import efel
for strict, n_of_ahp in [(False, 17), (True, 16)]:
efel.reset()
efel.setIntSetting('strict_stiminterval', strict)
stim_start = 700.0
stim_end = 2700.0
time = efel.io.load_fragment('%s#col=1' % ahptest1_url)
voltage = efel.io.load_fragment('%s#col=2' % ahptest1_url)
trace = {}
trace['T'] = time
trace['V'] = voltage
trace['stim_start'] = [stim_start]
trace['stim_end'] = [stim_end]
features = ['min_AHP_indices', 'AHP_time_from_peak', 'peak_time']
feature_values = \
efel.getFeatureValues(
[trace],
features, raise_warnings=False)
min_AHP_indices = feature_values[0]['min_AHP_indices']
AHP_time_from_peak = feature_values[0]['AHP_time_from_peak']
nt.assert_equal(len(min_AHP_indices), n_of_ahp)
nt.assert_equal(len(AHP_time_from_peak), n_of_ahp)
def test_unfinished_peak():
"""basic: Test if unfinished peak doesn't break Spikecount"""
import efel
efel.setIntSetting('strict_stiminterval', True)
dt = 0.1
v = numpy.zeros(int(100 / dt)) - 70.0
v[int(20 / dt):int(25 / dt)] = 20.
v[int(40 / dt):int(45 / dt)] = 20.
v[int(60 / dt):int(65 / dt)] = 20.
trace = {}
trace['T'] = numpy.arange(len(v)) * dt
trace['V'] = v
trace['stim_start'] = [10]
trace['stim_end'] = [70]
traces_results = efel.getFeatureValues([trace], ['Spikecount'])
spikecount = traces_results[0]['Spikecount'][0]
nt.assert_equal(spikecount, 3)
# When the signal at the end of the trace is larger than the threshold,
# Spikecount and possibly other features cannont be estimated.
v[int(80 / dt):] = -19
traces_results = efel.getFeatureValues([trace], ['Spikecount'])
spikecount = traces_results[0]['Spikecount'][0]
nt.assert_equal(spikecount, 3)
def test_derivwindow1():
"""basic: Test DerivativeWindow"""
import efel
efel.reset()
stim_start = 100.0
stim_end = 1000.0
time = efel.io.load_fragment('%s#col=1' % derivwindow1_url)
voltage = efel.io.load_fragment('%s#col=2' % derivwindow1_url)
trace = {}
trace['T'] = time
trace['V'] = voltage
trace['stim_start'] = [stim_start]
trace['stim_end'] = [stim_end]
features = ['AP_begin_voltage']
feature_values = \
efel.getFeatureValues(
[trace],
features)
AP_begin_voltage = feature_values[0]['AP_begin_voltage'][0]
nt.assert_almost_equal(AP_begin_voltage, -45.03627393790836)
efel.reset()
efel.setDoubleSetting('interp_step', 0.01)
feature_values = \
efel.getFeatureValues(
[trace],
features)
AP_begin_voltage = feature_values[0]['AP_begin_voltage'][0]
nt.assert_almost_equal(AP_begin_voltage, -83.57661997973835)
efel.reset()
efel.setDoubleSetting('interp_step', 0.01)
efel.setIntSetting('DerivativeWindow', 30)
feature_values = \
efel.getFeatureValues(
[trace],
features)
AP_begin_voltage = feature_values[0]['AP_begin_voltage'][0]
nt.assert_almost_equal(AP_begin_voltage, -45.505521563640386)
def _setup_efel(self):
"""Set up efel before extracting the feature"""
import efel
efel.reset()
if self.threshold is not None:
efel.setThreshold(self.threshold)
if self.stimulus_current is not None:
efel.setDoubleSetting('stimulus_current', self.stimulus_current)
if self.interp_step is not None:
efel.setDoubleSetting('interp_step', self.interp_step)
if self.double_settings is not None:
for setting_name, setting_value in self.double_settings.items():
efel.setDoubleSetting(setting_name, setting_value)
if self.int_settings is not None:
for setting_name, setting_value in self.int_settings.items():
efel.setIntSetting(setting_name, setting_value)
