/usr/lib/python2.7/dist-packages/neo/test/test_analogsignal.py is in python-neo 0.3.3-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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"""
Tests of the neo.core.analogsignal.AnalogSignal class and related functions
"""
# needed for python 3 compatibility
from __future__ import division
import os
import pickle
from pprint import pformat
try:
import unittest2 as unittest
except ImportError:
import unittest
import numpy as np
import quantities as pq
from neo.core.analogsignal import AnalogSignal, _get_sampling_rate
from neo.test.tools import (assert_arrays_almost_equal, assert_arrays_equal,
assert_neo_object_is_compliant,
assert_same_sub_schema)
class TestAnalogSignalConstructor(unittest.TestCase):
def test__create_from_list(self):
data = range(10)
rate = 1000*pq.Hz
signal = AnalogSignal(data, sampling_rate=rate, units="mV")
assert_neo_object_is_compliant(signal)
self.assertEqual(signal.t_start, 0*pq.ms)
self.assertEqual(signal.t_stop, len(data)/rate)
self.assertEqual(signal[9], 9000*pq.uV)
def test__create_from_np_array(self):
data = np.arange(10.0)
rate = 1*pq.kHz
signal = AnalogSignal(data, sampling_rate=rate, units="uV")
assert_neo_object_is_compliant(signal)
self.assertEqual(signal.t_start, 0*pq.ms)
self.assertEqual(signal.t_stop, data.size/rate)
self.assertEqual(signal[9], 0.009*pq.mV)
def test__create_from_quantities_array(self):
data = np.arange(10.0) * pq.mV
rate = 5000*pq.Hz
signal = AnalogSignal(data, sampling_rate=rate)
assert_neo_object_is_compliant(signal)
self.assertEqual(signal.t_start, 0*pq.ms)
self.assertEqual(signal.t_stop, data.size/rate)
self.assertEqual(signal[9], 0.009*pq.V)
def test__create_from_array_no_units_ValueError(self):
data = np.arange(10.0)
self.assertRaises(ValueError, AnalogSignal, data,
sampling_rate=1 * pq.kHz)
def test__create_from_quantities_array_inconsistent_units_ValueError(self):
data = np.arange(10.0) * pq.mV
self.assertRaises(ValueError, AnalogSignal, data,
sampling_rate=1 * pq.kHz, units="nA")
def test__create_without_sampling_rate_or_period_ValueError(self):
data = np.arange(10.0) * pq.mV
self.assertRaises(ValueError, AnalogSignal, data)
def test__create_with_None_sampling_rate_should_raise_ValueError(self):
data = np.arange(10.0) * pq.mV
self.assertRaises(ValueError, AnalogSignal, data, sampling_rate=None)
def test__create_with_None_t_start_should_raise_ValueError(self):
data = np.arange(10.0) * pq.mV
rate = 5000 * pq.Hz
self.assertRaises(ValueError, AnalogSignal, data,
sampling_rate=rate, t_start=None)
def test__create_inconsistent_sampling_rate_and_period_ValueError(self):
data = np.arange(10.0) * pq.mV
self.assertRaises(ValueError, AnalogSignal, data,
sampling_rate=1 * pq.kHz, sampling_period=5 * pq.s)
def test__create_with_copy_true_should_return_copy(self):
data = np.arange(10.0) * pq.mV
rate = 5000*pq.Hz
signal = AnalogSignal(data, copy=True, sampling_rate=rate)
data[3] = 99*pq.mV
assert_neo_object_is_compliant(signal)
self.assertNotEqual(signal[3], 99*pq.mV)
def test__create_with_copy_false_should_return_view(self):
data = np.arange(10.0) * pq.mV
rate = 5000*pq.Hz
signal = AnalogSignal(data, copy=False, sampling_rate=rate)
data[3] = 99*pq.mV
assert_neo_object_is_compliant(signal)
self.assertEqual(signal[3], 99*pq.mV)
def test__create_with_additional_argument(self):
signal = AnalogSignal([1, 2, 3], units="mV", sampling_rate=1*pq.kHz,
file_origin='crack.txt', ratname='Nicolas')
assert_neo_object_is_compliant(signal)
self.assertEqual(signal.annotations, {'ratname': 'Nicolas'})
# This one is universally recommended and handled by BaseNeo
self.assertEqual(signal.file_origin, 'crack.txt')
# signal must be 1D - should raise Exception if not 1D
class TestAnalogSignalProperties(unittest.TestCase):
def setUp(self):
self.t_start = [0.0*pq.ms, 100*pq.ms, -200*pq.ms]
self.rates = [1*pq.kHz, 420*pq.Hz, 999*pq.Hz]
self.rates2 = [2*pq.kHz, 290*pq.Hz, 1111*pq.Hz]
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 = [AnalogSignal(D, sampling_rate=r, t_start=t,
testattr='test')
for r, D, t in zip(self.rates,
self.data,
self.t_start)]
def test__compliant(self):
for signal in self.signals:
assert_neo_object_is_compliant(signal)
def test__t_stop_getter(self):
for i, signal in enumerate(self.signals):
self.assertEqual(signal.t_stop,
self.t_start[i] + self.data[i].size/self.rates[i])
def test__duration_getter(self):
for signal in self.signals:
self.assertAlmostEqual(signal.duration,
signal.t_stop - signal.t_start,
delta=1e-15)
def test__sampling_rate_getter(self):
for signal, rate in zip(self.signals, self.rates):
self.assertEqual(signal.sampling_rate, rate)
def test__sampling_period_getter(self):
for signal, rate in zip(self.signals, self.rates):
self.assertEqual(signal.sampling_period, 1 / rate)
def test__sampling_rate_setter(self):
for signal, rate in zip(self.signals, self.rates2):
signal.sampling_rate = rate
assert_neo_object_is_compliant(signal)
self.assertEqual(signal.sampling_rate, rate)
self.assertEqual(signal.sampling_period, 1 / rate)
def test__sampling_period_setter(self):
for signal, rate in zip(self.signals, self.rates2):
signal.sampling_period = 1 / rate
assert_neo_object_is_compliant(signal)
self.assertEqual(signal.sampling_rate, rate)
self.assertEqual(signal.sampling_period, 1 / rate)
def test__sampling_rate_setter_None_ValueError(self):
self.assertRaises(ValueError, setattr, self.signals[0],
'sampling_rate', None)
def test__sampling_rate_setter_not_quantity_ValueError(self):
self.assertRaises(ValueError, setattr, self.signals[0],
'sampling_rate', 5.5)
def test__sampling_period_setter_None_ValueError(self):
signal = self.signals[0]
assert_neo_object_is_compliant(signal)
self.assertRaises(ValueError, setattr, signal, 'sampling_period', None)
def test__sampling_period_setter_not_quantity_ValueError(self):
self.assertRaises(ValueError, setattr, self.signals[0],
'sampling_period', 5.5)
def test__t_start_setter_None_ValueError(self):
signal = self.signals[0]
assert_neo_object_is_compliant(signal)
self.assertRaises(ValueError, setattr, signal, 't_start', None)
def test__times_getter(self):
for i, signal in enumerate(self.signals):
targ = np.arange(self.data[i].size)
targ = targ/self.rates[i] + self.t_start[i]
assert_neo_object_is_compliant(signal)
assert_arrays_almost_equal(signal.times, targ, 1e-12*pq.ms)
def test__pprint(self):
for i, signal in enumerate(self.signals):
prepr = pformat(signal)
targ = '<AnalogSignal(%s, [%s, %s], sampling rate: %s)>' % \
(pformat(self.data[i]),
self.t_start[i],
self.t_start[i] + len(self.data[i])/self.rates[i],
self.rates[i])
self.assertEqual(prepr, targ)
def test__duplicate_with_new_array(self):
signal1 = self.signals[1]
signal2 = self.signals[2]
data2 = self.data[2]
signal1b = signal1.duplicate_with_new_array(data2)
assert_arrays_almost_equal(np.asarray(signal1b),
np.asarray(signal2/1000.), 1e-12)
self.assertEqual(signal1b.t_start, signal1.t_start)
self.assertEqual(signal1b.sampling_rate, signal1.sampling_rate)
class TestAnalogSignalArrayMethods(unittest.TestCase):
def setUp(self):
self.data1 = np.arange(10.0)
self.data1quant = self.data1 * pq.nA
self.signal1 = AnalogSignal(self.data1quant, sampling_rate=1*pq.kHz,
name='spam', description='eggs',
file_origin='testfile.txt', arg1='test')
def test__compliant(self):
assert_neo_object_is_compliant(self.signal1)
def test__slice_should_return_AnalogSignal(self):
# slice
result = self.signal1[3:8]
self.assertIsInstance(result, AnalogSignal)
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.sampling_period, self.signal1.sampling_period)
self.assertEqual(result.sampling_rate, self.signal1.sampling_rate)
self.assertEqual(result.t_start,
self.signal1.t_start+3*result.sampling_period)
self.assertEqual(result.t_stop,
result.t_start + 5*result.sampling_period)
assert_arrays_equal(result, self.data1[3:8])
# 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__slice_should_change_sampling_period(self):
result1 = self.signal1[:2]
result2 = self.signal1[::2]
result3 = self.signal1[1:7:2]
self.assertIsInstance(result1, AnalogSignal)
assert_neo_object_is_compliant(result1)
self.assertEqual(result1.name, 'spam')
self.assertEqual(result1.description, 'eggs')
self.assertEqual(result1.file_origin, 'testfile.txt')
self.assertEqual(result1.annotations, {'arg1': 'test'})
self.assertIsInstance(result2, AnalogSignal)
assert_neo_object_is_compliant(result2)
self.assertEqual(result2.name, 'spam')
self.assertEqual(result2.description, 'eggs')
self.assertEqual(result2.file_origin, 'testfile.txt')
self.assertEqual(result2.annotations, {'arg1': 'test'})
self.assertIsInstance(result3, AnalogSignal)
assert_neo_object_is_compliant(result3)
self.assertEqual(result3.name, 'spam')
self.assertEqual(result3.description, 'eggs')
self.assertEqual(result3.file_origin, 'testfile.txt')
self.assertEqual(result3.annotations, {'arg1': 'test'})
self.assertEqual(result1.sampling_period, self.signal1.sampling_period)
self.assertEqual(result2.sampling_period,
self.signal1.sampling_period * 2)
self.assertEqual(result3.sampling_period,
self.signal1.sampling_period * 2)
assert_arrays_equal(result1, self.data1[:2])
assert_arrays_equal(result2, self.data1[::2])
assert_arrays_equal(result3, self.data1[1:7:2])
def test__getitem_should_return_single_quantity(self):
result1 = self.signal1[0]
result2 = self.signal1[9]
self.assertIsInstance(result1, pq.Quantity)
self.assertFalse(hasattr(result1, 'name'))
self.assertFalse(hasattr(result1, 'description'))
self.assertFalse(hasattr(result1, 'file_origin'))
self.assertFalse(hasattr(result1, 'annotations'))
self.assertIsInstance(result2, pq.Quantity)
self.assertFalse(hasattr(result2, 'name'))
self.assertFalse(hasattr(result2, 'description'))
self.assertFalse(hasattr(result2, 'file_origin'))
self.assertFalse(hasattr(result2, 'annotations'))
self.assertEqual(result1, 0*pq.nA)
self.assertEqual(result2, 9*pq.nA)
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.nA,
np.array([False, False, False, False, False,
True, True, True, True, True]))
assert_arrays_equal(self.signal1 >= 5*pq.pA,
np.array([False, True, True, True, True,
True, True, True, True, True]))
def test__comparison_with_inconsistent_units_should_raise_Exception(self):
self.assertRaises(ValueError, self.signal1.__gt__, 5*pq.mV)
def test__simple_statistics(self):
self.assertEqual(self.signal1.max(), 9*pq.nA)
self.assertEqual(self.signal1.min(), 0*pq.nA)
self.assertEqual(self.signal1.mean(), 4.5*pq.nA)
def test__rescale_same(self):
result = self.signal1.copy()
result = result.rescale(pq.nA)
self.assertIsInstance(result, AnalogSignal)
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.nA)
assert_arrays_equal(result, self.data1)
assert_same_sub_schema(result, self.signal1)
def test__rescale_new(self):
result = self.signal1.copy()
result = result.rescale(pq.pA)
self.assertIsInstance(result, AnalogSignal)
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.pA)
assert_arrays_almost_equal(np.array(result), self.data1*1000., 1e-10)
def test__rescale_new_incompatible_ValueError(self):
self.assertRaises(ValueError, self.signal1.rescale, pq.mV)
class TestAnalogSignalEquality(unittest.TestCase):
def test__signals_with_different_data_complement_should_be_not_equal(self):
signal1 = AnalogSignal(np.arange(10.0), units="mV",
sampling_rate=1*pq.kHz)
signal2 = AnalogSignal(np.arange(10.0), units="mV",
sampling_rate=2*pq.kHz)
assert_neo_object_is_compliant(signal1)
assert_neo_object_is_compliant(signal2)
self.assertNotEqual(signal1, signal2)
class TestAnalogSignalCombination(unittest.TestCase):
def setUp(self):
self.data1 = np.arange(10.0)
self.data1quant = self.data1 * pq.mV
self.signal1 = AnalogSignal(self.data1quant,
sampling_rate=1*pq.kHz,
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, AnalogSignal)
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)
self.assertEqual(self.signal1[9], 9*pq.mV)
self.assertEqual(result[9], 74*pq.mV)
self.assertEqual(self.signal1.t_start, result.t_start)
self.assertEqual(self.signal1.sampling_rate, result.sampling_rate)
def test__add_quantity_should_preserve_data_complement(self):
data2 = np.arange(10.0, 20.0)
data2quant = data2*pq.mV
result = self.signal1 + data2quant
self.assertIsInstance(result, AnalogSignal)
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 = AnalogSignal(np.arange(10.0, 30.0, 2.0), units="mV",
sampling_rate=1*pq.kHz,
name='spam', description='eggs',
file_origin='testfile.txt', arg1='test')
assert_neo_object_is_compliant(targ)
assert_arrays_equal(result, targ)
assert_same_sub_schema(result, targ)
def test__add_two_consistent_signals_should_preserve_data_complement(self):
data2 = np.arange(10.0, 20.0)
data2quant = data2*pq.mV
signal2 = AnalogSignal(data2quant, sampling_rate=1*pq.kHz)
assert_neo_object_is_compliant(signal2)
result = self.signal1 + signal2
self.assertIsInstance(result, AnalogSignal)
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 = AnalogSignal(np.arange(10.0, 30.0, 2.0), units="mV",
sampling_rate=1*pq.kHz,
name='spam', description='eggs',
file_origin='testfile.txt', arg1='test')
assert_neo_object_is_compliant(targ)
assert_arrays_equal(result, targ)
assert_same_sub_schema(result, targ)
def test__add_signals_with_inconsistent_data_complement_ValueError(self):
self.signal1.t_start = 0.0*pq.ms
assert_neo_object_is_compliant(self.signal1)
signal2 = AnalogSignal(np.arange(10.0), units="mV",
t_start=100.0*pq.ms, sampling_rate=0.5*pq.kHz)
assert_neo_object_is_compliant(signal2)
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, AnalogSignal)
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)
self.assertEqual(self.signal1.sampling_rate, result.sampling_rate)
def test__subtract_from_const_should_return_signal(self):
result = 10*pq.mV - self.signal1
self.assertIsInstance(result, AnalogSignal)
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)
self.assertEqual(self.signal1.sampling_rate, result.sampling_rate)
def test__mult_by_const_float_should_preserve_data_complement(self):
result = self.signal1*2
self.assertIsInstance(result, AnalogSignal)
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)
self.assertEqual(self.signal1.sampling_rate, result.sampling_rate)
def test__divide_by_const_should_preserve_data_complement(self):
result = self.signal1/0.5
self.assertIsInstance(result, AnalogSignal)
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)
self.assertEqual(self.signal1.sampling_rate, result.sampling_rate)
def test__merge_NotImplementedError(self):
self.assertRaises(NotImplementedError,
self.signal1.merge, self.signal1)
class TestAnalogSignalFunctions(unittest.TestCase):
def test__pickle(self):
signal1 = AnalogSignal([1, 2, 3, 4], sampling_period=1*pq.ms,
units=pq.S, channel_index=42)
signal1.annotations['index'] = 2
fobj = open('./pickle', 'wb')
pickle.dump(signal1, fobj)
fobj.close()
fobj = open('./pickle', 'rb')
try:
signal2 = pickle.load(fobj)
except ValueError:
signal2 = None
assert_arrays_equal(signal1, signal2)
self.assertEqual(signal1.channel_index, signal2.channel_index, 42)
fobj.close()
os.remove('./pickle')
class TestAnalogSignalSampling(unittest.TestCase):
def test___get_sampling_rate__period_none_rate_none_ValueError(self):
sampling_rate = None
sampling_period = None
self.assertRaises(ValueError, _get_sampling_rate,
sampling_rate, sampling_period)
def test___get_sampling_rate__period_quant_rate_none(self):
sampling_rate = None
sampling_period = pq.Quantity(10., units=pq.s)
targ_rate = 1/sampling_period
out_rate = _get_sampling_rate(sampling_rate, sampling_period)
self.assertEqual(targ_rate, out_rate)
def test___get_sampling_rate__period_none_rate_quant(self):
sampling_rate = pq.Quantity(10., units=pq.Hz)
sampling_period = None
targ_rate = sampling_rate
out_rate = _get_sampling_rate(sampling_rate, sampling_period)
self.assertEqual(targ_rate, out_rate)
def test___get_sampling_rate__period_rate_equivalent(self):
sampling_rate = pq.Quantity(10., units=pq.Hz)
sampling_period = pq.Quantity(0.1, units=pq.s)
targ_rate = sampling_rate
out_rate = _get_sampling_rate(sampling_rate, sampling_period)
self.assertEqual(targ_rate, out_rate)
def test___get_sampling_rate__period_rate_not_equivalent_ValueError(self):
sampling_rate = pq.Quantity(10., units=pq.Hz)
sampling_period = pq.Quantity(10, units=pq.s)
self.assertRaises(ValueError, _get_sampling_rate,
sampling_rate, sampling_period)
def test___get_sampling_rate__period_none_rate_float_TypeError(self):
sampling_rate = 10.
sampling_period = None
self.assertRaises(TypeError, _get_sampling_rate,
sampling_rate, sampling_period)
def test___get_sampling_rate__period_array_rate_none_TypeError(self):
sampling_rate = None
sampling_period = np.array(10.)
self.assertRaises(TypeError, _get_sampling_rate,
sampling_rate, sampling_period)
if __name__ == "__main__":
unittest.main()
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