/usr/lib/python2.7/dist-packages/neo/test/test_irregularysampledsignal.py is in python-neo 0.3.3-2.
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"""
Tests of the neo.core.irregularlysampledsignal.IrregularySampledSignal class
"""
try:
import unittest2 as unittest
except ImportError:
import unittest
import numpy as np
import quantities as pq
from neo.core.irregularlysampledsignal import IrregularlySampledSignal
from neo.test.tools import (assert_arrays_almost_equal, assert_arrays_equal,
assert_neo_object_is_compliant,
assert_same_sub_schema)
class TestIrregularlySampledSignalConstruction(unittest.TestCase):
def test_IrregularlySampledSignal_creation_times_units_signal_units(self):
params = {'testarg2': 'yes', 'testarg3': True}
sig = IrregularlySampledSignal([1.1, 1.5, 1.7]*pq.ms,
signal=[20., 40., 60.]*pq.mV,
name='test', description='tester',
file_origin='test.file',
testarg1=1, **params)
sig.annotate(testarg1=1.1, testarg0=[1, 2, 3])
assert_neo_object_is_compliant(sig)
assert_arrays_equal(sig.times, [1.1, 1.5, 1.7]*pq.ms)
assert_arrays_equal(np.asarray(sig), np.array([20., 40., 60.]))
self.assertEqual(sig.units, pq.mV)
self.assertEqual(sig.name, 'test')
self.assertEqual(sig.description, 'tester')
self.assertEqual(sig.file_origin, 'test.file')
self.assertEqual(sig.annotations['testarg0'], [1, 2, 3])
self.assertEqual(sig.annotations['testarg1'], 1.1)
self.assertEqual(sig.annotations['testarg2'], 'yes')
self.assertTrue(sig.annotations['testarg3'])
def test_IrregularlySampledSignal_creation_units_arg(self):
params = {'testarg2': 'yes', 'testarg3': True}
sig = IrregularlySampledSignal([1.1, 1.5, 1.7],
signal=[20., 40., 60.],
units=pq.V, time_units=pq.s,
name='test', description='tester',
file_origin='test.file',
testarg1=1, **params)
sig.annotate(testarg1=1.1, testarg0=[1, 2, 3])
assert_neo_object_is_compliant(sig)
assert_arrays_equal(sig.times, [1.1, 1.5, 1.7]*pq.s)
assert_arrays_equal(np.asarray(sig), np.array([20., 40., 60.]))
self.assertEqual(sig.units, pq.V)
self.assertEqual(sig.name, 'test')
self.assertEqual(sig.description, 'tester')
self.assertEqual(sig.file_origin, 'test.file')
self.assertEqual(sig.annotations['testarg0'], [1, 2, 3])
self.assertEqual(sig.annotations['testarg1'], 1.1)
self.assertEqual(sig.annotations['testarg2'], 'yes')
self.assertTrue(sig.annotations['testarg3'])
def test_IrregularlySampledSignal_creation_units_rescale(self):
params = {'testarg2': 'yes', 'testarg3': True}
sig = IrregularlySampledSignal([1.1, 1.5, 1.7]*pq.s,
signal=[2., 4., 6.]*pq.V,
units=pq.mV, time_units=pq.ms,
name='test', description='tester',
file_origin='test.file',
testarg1=1, **params)
sig.annotate(testarg1=1.1, testarg0=[1, 2, 3])
assert_neo_object_is_compliant(sig)
assert_arrays_equal(sig.times, [1100, 1500, 1700]*pq.ms)
assert_arrays_equal(np.asarray(sig), np.array([2000., 4000., 6000.]))
self.assertEqual(sig.units, pq.mV)
self.assertEqual(sig.name, 'test')
self.assertEqual(sig.description, 'tester')
self.assertEqual(sig.file_origin, 'test.file')
self.assertEqual(sig.annotations['testarg0'], [1, 2, 3])
self.assertEqual(sig.annotations['testarg1'], 1.1)
self.assertEqual(sig.annotations['testarg2'], 'yes')
self.assertTrue(sig.annotations['testarg3'])
def test_IrregularlySampledSignal_different_lens_ValueError(self):
times = [1.1, 1.5, 1.7]*pq.ms
signal = [20., 40., 60., 70.]*pq.mV
self.assertRaises(ValueError, IrregularlySampledSignal, times, signal)
def test_IrregularlySampledSignal_no_signal_units_ValueError(self):
times = [1.1, 1.5, 1.7]*pq.ms
signal = [20., 40., 60.]
self.assertRaises(ValueError, IrregularlySampledSignal, times, signal)
def test_IrregularlySampledSignal_no_time_units_ValueError(self):
times = [1.1, 1.5, 1.7]
signal = [20., 40., 60.]*pq.mV
self.assertRaises(ValueError, IrregularlySampledSignal, times, signal)
class TestIrregularlySampledSignalProperties(unittest.TestCase):
def setUp(self):
self.times = [np.arange(10.0)*pq.s,
np.arange(-100.0, 100.0, 10.0)*pq.ms,
np.arange(100)*pq.ns]
self.data = [np.arange(10.0)*pq.nA,
np.arange(-100.0, 100.0, 10.0)*pq.mV,
np.random.uniform(size=100)*pq.uV]
self.signals = [IrregularlySampledSignal(t, signal=D,
testattr='test')
for D, t in zip(self.data, self.times)]
def test__compliant(self):
for signal in self.signals:
assert_neo_object_is_compliant(signal)
def test__t_start_getter(self):
for signal, times in zip(self.signals, self.times):
self.assertAlmostEqual(signal.t_start,
times[0],
delta=1e-15)
def test__t_stop_getter(self):
for signal, times in zip(self.signals, self.times):
self.assertAlmostEqual(signal.t_stop,
times[-1],
delta=1e-15)
def test__duration_getter(self):
for signal, times in zip(self.signals, self.times):
self.assertAlmostEqual(signal.duration,
times[-1] - times[0],
delta=1e-15)
def test__sampling_intervals_getter(self):
for signal, times in zip(self.signals, self.times):
assert_arrays_almost_equal(signal.sampling_intervals,
np.diff(times),
threshold=1e-15)
def test_IrregularlySampledSignal_repr(self):
sig = IrregularlySampledSignal([1.1, 1.5, 1.7]*pq.s,
signal=[2., 4., 6.]*pq.V,
name='test', description='tester',
file_origin='test.file',
testarg1=1)
assert_neo_object_is_compliant(sig)
targ = ('<IrregularlySampledSignal(array([ 2., 4., 6.]) * V ' +
'at times [ 1.1 1.5 1.7] s)>')
res = repr(sig)
self.assertEqual(targ, res)
class TestIrregularlySampledSignalArrayMethods(unittest.TestCase):
def setUp(self):
self.data1 = np.arange(10.0)
self.data1quant = self.data1 * pq.mV
self.time1 = np.logspace(1, 5, 10)
self.time1quant = self.time1*pq.ms
self.signal1 = IrregularlySampledSignal(self.time1quant,
signal=self.data1quant,
name='spam',
description='eggs',
file_origin='testfile.txt',
arg1='test')
def test__compliant(self):
assert_neo_object_is_compliant(self.signal1)
self.assertEqual(self.signal1.name, 'spam')
self.assertEqual(self.signal1.description, 'eggs')
self.assertEqual(self.signal1.file_origin, 'testfile.txt')
self.assertEqual(self.signal1.annotations, {'arg1': 'test'})
def test__slice_should_return_IrregularlySampledSignal(self):
result = self.signal1[3:8]
self.assertIsInstance(result, IrregularlySampledSignal)
assert_neo_object_is_compliant(result)
self.assertEqual(result.name, 'spam')
self.assertEqual(result.description, 'eggs')
self.assertEqual(result.file_origin, 'testfile.txt')
self.assertEqual(result.annotations, {'arg1': 'test'})
self.assertEqual(result.size, 5)
self.assertEqual(result.t_start, self.time1quant[3])
self.assertEqual(result.t_stop, self.time1quant[7])
assert_arrays_equal(self.time1quant[3:8], result.times)
assert_arrays_equal(self.data1[3:8], result)
# Test other attributes were copied over (in this case, defaults)
self.assertEqual(result.file_origin, self.signal1.file_origin)
self.assertEqual(result.name, self.signal1.name)
self.assertEqual(result.description, self.signal1.description)
self.assertEqual(result.annotations, self.signal1.annotations)
def test__getitem_should_return_single_quantity(self):
self.assertEqual(self.signal1[0], 0*pq.mV)
self.assertEqual(self.signal1[9], 9*pq.mV)
self.assertRaises(IndexError, self.signal1.__getitem__, 10)
def test__getitem_out_of_bounds_IndexError(self):
self.assertRaises(IndexError, self.signal1.__getitem__, 10)
def test_comparison_operators(self):
assert_arrays_equal(self.signal1 >= 5*pq.mV,
np.array([False, False, False, False, False,
True, True, True, True, True]))
def test__comparison_with_inconsistent_units_should_raise_Exception(self):
self.assertRaises(ValueError, self.signal1.__gt__, 5*pq.nA)
def test_simple_statistics(self):
targmean = self.signal1[:-1]*np.diff(self.time1quant)
targmean = targmean.sum()/(self.time1quant[-1]-self.time1quant[0])
self.assertEqual(self.signal1.max(), 9*pq.mV)
self.assertEqual(self.signal1.min(), 0*pq.mV)
self.assertEqual(self.signal1.mean(), targmean)
def test_mean_interpolation_NotImplementedError(self):
self.assertRaises(NotImplementedError, self.signal1.mean, True)
def test_resample_NotImplementedError(self):
self.assertRaises(NotImplementedError, self.signal1.resample, True)
def test__rescale_same(self):
result = self.signal1.copy()
result = result.rescale(pq.mV)
self.assertIsInstance(result, IrregularlySampledSignal)
assert_neo_object_is_compliant(result)
self.assertEqual(result.name, 'spam')
self.assertEqual(result.description, 'eggs')
self.assertEqual(result.file_origin, 'testfile.txt')
self.assertEqual(result.annotations, {'arg1': 'test'})
self.assertEqual(result.units, 1*pq.mV)
assert_arrays_equal(result, self.data1)
assert_arrays_equal(result.times, self.time1quant)
assert_same_sub_schema(result, self.signal1)
def test__rescale_new(self):
result = self.signal1.copy()
result = result.rescale(pq.uV)
self.assertIsInstance(result, IrregularlySampledSignal)
assert_neo_object_is_compliant(result)
self.assertEqual(result.name, 'spam')
self.assertEqual(result.description, 'eggs')
self.assertEqual(result.file_origin, 'testfile.txt')
self.assertEqual(result.annotations, {'arg1': 'test'})
self.assertEqual(result.units, 1*pq.uV)
assert_arrays_almost_equal(np.array(result), self.data1*1000., 1e-10)
assert_arrays_equal(result.times, self.time1quant)
def test__rescale_new_incompatible_ValueError(self):
self.assertRaises(ValueError, self.signal1.rescale, pq.nA)
class TestIrregularlySampledSignalCombination(unittest.TestCase):
def setUp(self):
self.data1 = np.arange(10.0)
self.data1quant = self.data1 * pq.mV
self.time1 = np.logspace(1, 5, 10)
self.time1quant = self.time1*pq.ms
self.signal1 = IrregularlySampledSignal(self.time1quant,
signal=self.data1quant,
name='spam',
description='eggs',
file_origin='testfile.txt',
arg1='test')
def test__compliant(self):
assert_neo_object_is_compliant(self.signal1)
self.assertEqual(self.signal1.name, 'spam')
self.assertEqual(self.signal1.description, 'eggs')
self.assertEqual(self.signal1.file_origin, 'testfile.txt')
self.assertEqual(self.signal1.annotations, {'arg1': 'test'})
def test__add_const_quantity_should_preserve_data_complement(self):
result = self.signal1 + 0.065*pq.V
self.assertIsInstance(result, IrregularlySampledSignal)
assert_neo_object_is_compliant(result)
self.assertEqual(result.name, 'spam')
self.assertEqual(result.description, 'eggs')
self.assertEqual(result.file_origin, 'testfile.txt')
self.assertEqual(result.annotations, {'arg1': 'test'})
assert_arrays_equal(result, self.data1 + 65)
assert_arrays_equal(result.times, self.time1quant)
self.assertEqual(self.signal1[9], 9*pq.mV)
self.assertEqual(result[9], 74*pq.mV)
def test__add_two_consistent_signals_should_preserve_data_complement(self):
data2 = np.arange(10.0, 20.0)
data2quant = data2*pq.mV
signal2 = IrregularlySampledSignal(self.time1quant, signal=data2quant)
assert_neo_object_is_compliant(signal2)
result = self.signal1 + signal2
self.assertIsInstance(result, IrregularlySampledSignal)
assert_neo_object_is_compliant(result)
self.assertEqual(result.name, 'spam')
self.assertEqual(result.description, 'eggs')
self.assertEqual(result.file_origin, 'testfile.txt')
self.assertEqual(result.annotations, {'arg1': 'test'})
targ = IrregularlySampledSignal(self.time1quant,
signal=np.arange(10.0, 30.0, 2.0),
units="mV",
name='spam', description='eggs',
file_origin='testfile.txt',
arg1='test')
assert_neo_object_is_compliant(targ)
assert_arrays_equal(result, targ)
assert_arrays_equal(self.time1quant, targ.times)
assert_arrays_equal(result.times, targ.times)
assert_same_sub_schema(result, targ)
def test__add_signals_with_inconsistent_times_AssertionError(self):
signal2 = IrregularlySampledSignal(self.time1quant*2.,
signal=np.arange(10.0), units="mV")
assert_neo_object_is_compliant(signal2)
self.assertRaises(ValueError, self.signal1.__add__, signal2)
def test__add_signals_with_inconsistent_dimension_ValueError(self):
signal2 = np.arange(20).reshape(2, 10)
self.assertRaises(ValueError, self.signal1.__add__, signal2)
def test__subtract_const_should_preserve_data_complement(self):
result = self.signal1 - 65*pq.mV
self.assertIsInstance(result, IrregularlySampledSignal)
assert_neo_object_is_compliant(result)
self.assertEqual(result.name, 'spam')
self.assertEqual(result.description, 'eggs')
self.assertEqual(result.file_origin, 'testfile.txt')
self.assertEqual(result.annotations, {'arg1': 'test'})
self.assertEqual(self.signal1[9], 9*pq.mV)
self.assertEqual(result[9], -56*pq.mV)
assert_arrays_equal(result, self.data1 - 65)
assert_arrays_equal(result.times, self.time1quant)
def test__subtract_from_const_should_return_signal(self):
result = 10*pq.mV - self.signal1
self.assertIsInstance(result, IrregularlySampledSignal)
assert_neo_object_is_compliant(result)
self.assertEqual(result.name, 'spam')
self.assertEqual(result.description, 'eggs')
self.assertEqual(result.file_origin, 'testfile.txt')
self.assertEqual(result.annotations, {'arg1': 'test'})
self.assertEqual(self.signal1[9], 9*pq.mV)
self.assertEqual(result[9], 1*pq.mV)
assert_arrays_equal(result, 10 - self.data1)
assert_arrays_equal(result.times, self.time1quant)
def test__mult_signal_by_const_float_should_preserve_data_complement(self):
result = self.signal1*2.
self.assertIsInstance(result, IrregularlySampledSignal)
assert_neo_object_is_compliant(result)
self.assertEqual(result.name, 'spam')
self.assertEqual(result.description, 'eggs')
self.assertEqual(result.file_origin, 'testfile.txt')
self.assertEqual(result.annotations, {'arg1': 'test'})
self.assertEqual(self.signal1[9], 9*pq.mV)
self.assertEqual(result[9], 18*pq.mV)
assert_arrays_equal(result, self.data1*2)
assert_arrays_equal(result.times, self.time1quant)
def test__mult_signal_by_const_array_should_preserve_data_complement(self):
result = self.signal1*np.array(2.)
self.assertIsInstance(result, IrregularlySampledSignal)
assert_neo_object_is_compliant(result)
self.assertEqual(result.name, 'spam')
self.assertEqual(result.description, 'eggs')
self.assertEqual(result.file_origin, 'testfile.txt')
self.assertEqual(result.annotations, {'arg1': 'test'})
self.assertEqual(self.signal1[9], 9*pq.mV)
self.assertEqual(result[9], 18*pq.mV)
assert_arrays_equal(result, self.data1*2)
assert_arrays_equal(result.times, self.time1quant)
def test__divide_signal_by_const_should_preserve_data_complement(self):
result = self.signal1/0.5
self.assertIsInstance(result, IrregularlySampledSignal)
assert_neo_object_is_compliant(result)
self.assertEqual(result.name, 'spam')
self.assertEqual(result.description, 'eggs')
self.assertEqual(result.file_origin, 'testfile.txt')
self.assertEqual(result.annotations, {'arg1': 'test'})
self.assertEqual(self.signal1[9], 9*pq.mV)
self.assertEqual(result[9], 18*pq.mV)
assert_arrays_equal(result, self.data1/0.5)
assert_arrays_equal(result.times, self.time1quant)
class TestIrregularlySampledSignalEquality(unittest.TestCase):
def test__signals_with_different_times_should_be_not_equal(self):
signal1 = IrregularlySampledSignal(np.arange(10.0)/100*pq.s,
np.arange(10.0), units="mV")
signal2 = IrregularlySampledSignal(np.arange(10.0)/100*pq.ms,
np.arange(10.0), units="mV")
self.assertNotEqual(signal1, signal2)
if __name__ == "__main__":
unittest.main()
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