def test__time_slice__different_units(self):
self.signal2.t_start = 10.0 * pq.ms
assert_neo_object_is_compliant(self.signal2)
t_start = 2 * pq.s + 10.0 * pq.ms
t_stop = 4 * pq.s + 10.0 * pq.ms
result = self.signal2.time_slice(t_start, t_stop)
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.array([[2., 3.], [2., 3.]]).T,
t_start=t_start.rescale(pq.ms),
sampling_rate=1.0 * pq.Hz,
units='mV',
name='spam',
description='eggs',
file_origin='testfile.txt',
arg1='test')
assert_neo_object_is_compliant(result)
assert_neo_object_is_compliant(self.signal2)
self.assertEqual(self.signal2.t_start, 10.0 * pq.ms)
self.assertAlmostEqual(result.t_stop, t_stop, delta=1e-12 * pq.ms)
self.assertAlmostEqual(result.t_start, t_start, delta=1e-12 * pq.ms)
assert_arrays_almost_equal(result.times, targ.times, 1e-12 * pq.ms)
self.assertEqual(result.sampling_rate, targ.sampling_rate)
assert_arrays_equal(result, targ)
assert_same_sub_schema(result, targ)
def test__time_slice__different_units(self):
self.signal2.t_start = 10.0 * pq.ms
assert_neo_object_is_compliant(self.signal2)
t_start = 2 * pq.s + 10.0 * pq.ms
t_stop = 4 * pq.s + 10.0 * pq.ms
result = self.signal2.time_slice(t_start, t_stop)
self.assertIsInstance(result, AnalogSignalArray)
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 = AnalogSignalArray(np.array([[2, 3], [2, 3]]).T,
t_start=t_start.rescale(pq.ms),
sampling_rate=1.0*pq.Hz, units='mV',
name='spam', description='eggs',
file_origin='testfile.txt', arg1='test')
assert_neo_object_is_compliant(result)
assert_neo_object_is_compliant(self.signal2)
self.assertEqual(self.signal2.t_start, 10.0 * pq.ms)
self.assertAlmostEqual(result.t_stop, t_stop, delta=1e-12*pq.ms)
self.assertAlmostEqual(result.t_start, t_start, delta=1e-12*pq.ms)
assert_arrays_almost_equal(result.times, targ.times, 1e-12*pq.ms)
self.assertEqual(result.sampling_rate, targ.sampling_rate)
assert_arrays_equal(result, targ)
assert_same_sub_schema(result, targ)
def test_duplicate_with_new_data(self):
signal1 = self.event
new_data = np.sort(np.random.uniform(0, 100,
(self.event.size))) * pq.ms
signal1b = signal1.duplicate_with_new_data(new_data)
assert_arrays_almost_equal(np.asarray(signal1b), np.asarray(new_data),
1e-12)
def test__add_epoch(self):
proxy_event = EventProxy(rawio=self.reader,
event_channel_index=0,
block_index=0,
seg_index=0)
loaded_event = proxy_event.load()
regular_event = Event(times=loaded_event.times -
1 * loaded_event.units)
loaded_event.annotate(nix_name='neo.event.0')
regular_event.annotate(nix_name='neo.event.1')
seg = Segment()
seg.events = [regular_event, proxy_event]
# test cutting with two events one of which is a proxy
epoch = add_epoch(seg, regular_event, proxy_event)
assert_neo_object_is_compliant(epoch)
exp_annos = {
k: v
for k, v in regular_event.annotations.items() if k != 'nix_name'
}
self.assertDictEqual(epoch.annotations, exp_annos)
assert_arrays_almost_equal(epoch.times, regular_event.times, 1e-12)
assert_arrays_almost_equal(
epoch.durations,
np.ones(regular_event.shape) * loaded_event.units, 1e-12)
def test_AnalogSignalProxy(self):
proxy_anasig = AnalogSignalProxy(rawio=self.reader, global_channel_indexes=None,
block_index=0, seg_index=0,)
assert proxy_anasig.sampling_rate == 10 * pq.kHz
assert proxy_anasig.t_start == 0 * pq.s
assert proxy_anasig.t_stop == 10 * pq.s
assert proxy_anasig.duration == 10 * pq.s
assert proxy_anasig.file_origin == 'my_filename.fake'
# full load
full_anasig = proxy_anasig.load(time_slice=None)
assert isinstance(full_anasig, AnalogSignal)
assert_same_attributes(proxy_anasig, full_anasig)
# slice time
anasig = proxy_anasig.load(time_slice=(2. * pq.s, 5 * pq.s))
assert anasig.t_start == 2. * pq.s
assert anasig.duration == 3. * pq.s
assert anasig.shape == (30000, 16)
assert_same_attributes(proxy_anasig.time_slice(2. * pq.s, 5 * pq.s), anasig)
# ceil next sample when slicing
anasig = proxy_anasig.load(time_slice=(1.99999 * pq.s, 5.000001 * pq.s))
assert anasig.t_start == 2. * pq.s
assert anasig.duration == 3. * pq.s
assert anasig.shape == (30000, 16)
# buggy time slice
with self.assertRaises(AssertionError):
anasig = proxy_anasig.load(time_slice=(2. * pq.s, 15 * pq.s))
anasig = proxy_anasig.load(time_slice=(2. * pq.s, 15 * pq.s), strict_slicing=False)
assert proxy_anasig.t_stop == 10 * pq.s
# select channels
anasig = proxy_anasig.load(channel_indexes=[3, 4, 9])
assert anasig.shape[1] == 3
# select channels and slice times
anasig = proxy_anasig.load(time_slice=(2. * pq.s, 5 * pq.s), channel_indexes=[3, 4, 9])
assert anasig.shape == (30000, 3)
# magnitude mode rescaled
anasig_float = proxy_anasig.load(magnitude_mode='rescaled')
assert anasig_float.dtype == 'float32'
assert anasig_float.units == pq.uV
assert anasig_float.units == proxy_anasig.units
# magnitude mode raw
anasig_int = proxy_anasig.load(magnitude_mode='raw')
assert anasig_int.dtype == 'int16'
assert anasig_int.units == pq.CompoundUnit('0.0152587890625*uV')
assert_arrays_almost_equal(anasig_float, anasig_int.rescale('uV'), 1e-9)
# test array_annotations
assert 'info' in proxy_anasig.array_annotations
assert proxy_anasig.array_annotations['info'].size == 16
assert 'info' in anasig_float.array_annotations
assert anasig_float.array_annotations['info'].size == 16
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 / 1000.0), 1e-12)
self.assertEqual(signal1b.t_start, signal1.t_start)
self.assertEqual(signal1b.sampling_rate, signal1.sampling_rate)
def test_duplicate_with_new_data(self):
signal1 = self.epoch
new_data = np.sort(np.random.uniform(0, 100, (self.epoch))) * pq.ms
signal1b = signal1.duplicate_with_new_data(new_data)
assert_arrays_almost_equal(np.asarray(signal1b),
np.asarray(new_data), 1e-12)
assert_arrays_almost_equal(np.asarray(signal1b.durations),
np.asarray(signal1.durations), 1e-12)
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)
def test_duplicate_with_new_data(self):
signal1 = self.event
new_times = np.sort(np.random.uniform(0, 100, (self.event.size))) * pq.ms
new_labels = np.array(list("zyxwvutsrqponmlkjihgfedcba"[:self.event.size]))
signal1b = signal1.duplicate_with_new_data(new_times, new_labels)
assert_arrays_almost_equal(np.asarray(signal1b), np.asarray(new_times), 1e-12)
assert_arrays_equal(signal1b.labels, new_labels)
# After duplicating, array annotations should always be empty,
# because different length of data would cause inconsistencies
self.assertTrue('index' not in signal1b.array_annotations)
self.assertTrue('test' not in signal1b.array_annotations)
self.assertIsInstance(signal1b.array_annotations, ArrayDict)
def test_AnalogSignalProxy(self):
proxy_anasig = AnalogSignalProxy(rawio=self.reader, global_channel_indexes=None,
block_index=0, seg_index=0,)
assert proxy_anasig.sampling_rate == 10 * pq.kHz
assert proxy_anasig.t_start == 0 * pq.s
assert proxy_anasig.t_stop == 10 * pq.s
assert proxy_anasig.duration == 10 * pq.s
assert proxy_anasig.file_origin == 'my_filename.fake'
# full load
full_anasig = proxy_anasig.load(time_slice=None)
assert isinstance(full_anasig, AnalogSignal)
assert_same_attributes(proxy_anasig, full_anasig)
# slice time
anasig = proxy_anasig.load(time_slice=(2. * pq.s, 5 * pq.s))
assert anasig.t_start == 2. * pq.s
assert anasig.duration == 3. * pq.s
assert anasig.shape == (30000, 16)
# ceil next sample when slicing
anasig = proxy_anasig.load(time_slice=(1.99999 * pq.s, 5.000001 * pq.s))
assert anasig.t_start == 2. * pq.s
assert anasig.duration == 3. * pq.s
assert anasig.shape == (30000, 16)
# buggy time slice
with self.assertRaises(AssertionError):
anasig = proxy_anasig.load(time_slice=(2. * pq.s, 15 * pq.s))
anasig = proxy_anasig.load(time_slice=(2. * pq.s, 15 * pq.s), strict_slicing=False)
assert proxy_anasig.t_stop == 10 * pq.s
# select channels
anasig = proxy_anasig.load(channel_indexes=[3, 4, 9])
assert anasig.shape[1] == 3
# select channels and slice times
anasig = proxy_anasig.load(time_slice=(2. * pq.s, 5 * pq.s), channel_indexes=[3, 4, 9])
assert anasig.shape == (30000, 3)
# magnitude mode rescaled
anasig_float = proxy_anasig.load(magnitude_mode='rescaled')
assert anasig_float.dtype == 'float32'
assert anasig_float.units == pq.uV
assert anasig_float.units == proxy_anasig.units
# magnitude mode raw
anasig_int = proxy_anasig.load(magnitude_mode='raw')
assert anasig_int.dtype == 'int16'
assert anasig_int.units == pq.CompoundUnit('0.0152587890625*uV')
assert_arrays_almost_equal(anasig_float, anasig_int.rescale('uV'), 1e-9)
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(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__duplicate_with_new_data(self):
signal1 = self.signals[1]
signal2 = self.signals[2]
data2 = self.data[2]
signal1.array_annotate(ann=np.arange(signal1.shape[-1]))
signal1b = signal1.duplicate_with_new_data(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)
# After duplicating, array annotations should always be empty,
# because different length of data would cause inconsistencies
self.assertEqual(signal1b.array_annotations, {})
self.assertIsInstance(signal1b.array_annotations, ArrayDict)
def test_duplicate_with_new_data(self):
signal1 = self.event
new_data = np.sort(np.random.uniform(0, 100, (self.event.size))) * pq.ms
signal1b = signal1.duplicate_with_new_data(new_data)
assert_arrays_almost_equal(np.asarray(signal1b), np.asarray(new_data), 1e-12)
# Note: Labels and Durations are NOT copied any more!!!
# After duplicating, array annotations should always be empty,
# because different length of data would cause inconsistencies
# Only labels and durations should be available
assert_arrays_equal(signal1b.labels, np.ndarray((0,), dtype='S'))
self.assertTrue('index' not in signal1b.array_annotations)
self.assertTrue('test' not in signal1b.array_annotations)
self.assertIsInstance(signal1b.array_annotations, ArrayDict)
def test__duplicate_with_new_data(self):
signal1 = self.signals[1]
signal2 = self.signals[2]
data2 = self.data[2]
signal1.array_annotate(ann=np.arange(signal1.shape[-1]))
signal1b = signal1.duplicate_with_new_data(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)
# After duplicating, array annotations should always be empty,
# because different length of data would cause inconsistencies
self.assertEqual(signal1b.array_annotations, {})
self.assertIsInstance(signal1b.array_annotations, ArrayDict)
def test2(self):
"""Read data into two segments instead of just one"""
full_range = 8192 * pq.mV
bio = neo.io.BlackrockIO(filename=self.fn, full_range=full_range)
block = bio.read_block(n_starts=[0, 3], n_stops=[2, 6])
self.assertEqual(bio.header.Channel_Count, 2)
self.assertEqual(bio.header.n_samples, 6)
# Everything in two segments
self.assertEqual(len(block.segments), 2)
# Test first seg
seg = block.segments[0]
self.assertEqual(len(seg.analogsignals), 2)
assert_arrays_almost_equal(seg.analogsignals[0],
[3., 4.] * pq.mV, .0001)
assert_arrays_almost_equal(seg.analogsignals[1],
[6., -4.] * pq.mV, .0001)
# Test second seg
seg = block.segments[1]
self.assertEqual(len(seg.analogsignals), 2)
assert_arrays_almost_equal(seg.analogsignals[0],
[-3., -4., -5.] * pq.mV, .0001)
assert_arrays_almost_equal(seg.analogsignals[1],
[-6., 4., 5.] * pq.mV, .0001)
def test_time_slice_different_units(self):
#import numpy
av = AnalogSignalArray(numpy.array([[0,1,2,3,4,5],[0,1,2,3,4,5]]).T, t_start = 10.0 * pq.ms,sampling_rate=1.0*pq.Hz, units='mV')
t_start = 2 * pq.s + 10.0 * pq.ms
t_stop = 4 * pq.s + 10.0 * pq.ms
av2 = av.time_slice(t_start,t_stop)
correct = AnalogSignalArray(numpy.array([[2,3],[2,3]]).T, t_start = t_start,sampling_rate=1.0*pq.Hz, units='mV')
self.assertIsInstance(av2, AnalogSignalArray)
self.assertAlmostEqual(av2.t_stop,t_stop,delta=1e-12*ms)
self.assertAlmostEqual(av2.t_start,t_start,delta=1e-12*ms)
assert_arrays_almost_equal(av2.times,correct.times,1e-12*ms)
self.assertEqual(av2.sampling_rate, correct.sampling_rate)
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.reshape(-1, 1)*1000., 1e-10)
assert_array_equal(result.times, self.time1quant)
def test__add_epoch(self):
starts = Event(times=[0.5, 10.0, 25.2] * pq.s)
starts.annotate(event_type='trial start')
starts.array_annotate(trial_id=[1, 2, 3])
stops = Event(times=[5.5, 14.9, 30.1] * pq.s)
stops.annotate(event_type='trial stop')
stops.array_annotate(trial_id=[1, 2, 3])
seg = Segment()
seg.events = [starts, stops]
# test cutting with one event only
ep_starts = add_epoch(seg, starts, pre=-300 * pq.ms, post=250 * pq.ms)
assert_neo_object_is_compliant(ep_starts)
assert_same_annotations(ep_starts, starts)
assert_arrays_almost_equal(ep_starts.times, starts.times - 300 * pq.ms,
1e-12)
assert_arrays_almost_equal(
ep_starts.durations,
(550 * pq.ms).rescale(ep_starts.durations.units) * np.ones(
(len(starts))), 1e-12)
# test cutting with two events
ep_trials = add_epoch(seg, starts, stops)
assert_neo_object_is_compliant(ep_trials)
assert_same_annotations(ep_trials, starts)
assert_arrays_almost_equal(ep_trials.times, starts.times, 1e-12)
assert_arrays_almost_equal(ep_trials.durations, stops - starts, 1e-12)
def test2(self):
"""Read data into two segments instead of just one"""
full_range = 8192 * pq.mV
bio = neo.io.BlackrockIO(filename=self.fn, full_range=full_range)
block = bio.read_block(n_starts=[0, 3], n_stops=[2, 6])
self.assertEqual(bio.header.Channel_Count, 2)
self.assertEqual(bio.header.n_samples, 6)
# Everything in two segments
self.assertEqual(len(block.segments), 2)
# Test first seg
seg = block.segments[0]
self.assertEqual(len(seg.analogsignals), 2)
assert_arrays_almost_equal(seg.analogsignals[0], [3., 4.] * pq.mV,
.0001)
assert_arrays_almost_equal(seg.analogsignals[1], [6., -4.] * pq.mV,
.0001)
# Test second seg
seg = block.segments[1]
self.assertEqual(len(seg.analogsignals), 2)
assert_arrays_almost_equal(seg.analogsignals[0],
[-3., -4., -5.] * pq.mV, .0001)
assert_arrays_almost_equal(seg.analogsignals[1], [-6., 4., 5.] * pq.mV,
.0001)
def test__time_slice__no_explicit_time(self):
self.signal2.t_start = 10.0 * pq.ms
assert_neo_object_is_compliant(self.signal2)
t1 = 2 * pq.s + 10.0 * pq.ms
t2 = 4 * pq.s + 10.0 * pq.ms
for t_start, t_stop in [(t1, None), (None, None), (None, t2)]:
t_start_targ = t1 if t_start is not None else self.signal2.t_start
t_stop_targ = t2 if t_stop is not None else self.signal2.t_stop
result = self.signal2.time_slice(t_start, t_stop)
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.array_annotations['anno1'],
np.array([10, 11]))
assert_arrays_equal(result.array_annotations['anno2'],
np.array(['k', 'l']))
self.assertIsInstance(result.array_annotations, ArrayDict)
targ_ind = np.where((self.signal2.times >= t_start_targ)
& (self.signal2.times < t_stop_targ))
targ_array = self.signal2.magnitude[targ_ind]
targ = AnalogSignal(targ_array,
t_start=t_start_targ.rescale(pq.ms),
sampling_rate=1.0 * pq.Hz,
units='mV',
name='spam',
description='eggs',
file_origin='testfile.txt',
arg1='test')
assert_neo_object_is_compliant(result)
assert_neo_object_is_compliant(self.signal2)
self.assertEqual(self.signal2.t_start, 10.0 * pq.ms)
self.assertAlmostEqual(result.t_stop,
t_stop_targ,
delta=1e-12 * pq.ms)
self.assertAlmostEqual(result.t_start,
t_start_targ,
delta=1e-12 * pq.ms)
assert_arrays_almost_equal(result.times, targ.times, 1e-12 * pq.ms)
self.assertEqual(result.sampling_rate, targ.sampling_rate)
assert_array_equal(result.magnitude, targ.magnitude)
assert_same_sub_schema(result, targ)
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.reshape(-1, 1) * 1000., 1e-10)
assert_array_equal(result.times, self.time1quant)
def test_duplicate_with_new_data(self):
signal1 = self.event
new_data = np.sort(np.random.uniform(0, 100,
(self.event.size))) * pq.ms
signal1b = signal1.duplicate_with_new_data(new_data)
assert_arrays_almost_equal(np.asarray(signal1b), np.asarray(new_data),
1e-12)
# Note: Labels and Durations are NOT copied any more!!!
# After duplicating, array annotations should always be empty,
# because different length of data would cause inconsistencies
# Only labels and durations should be available
assert_arrays_equal(signal1b.labels, np.ndarray((0, ), dtype='S'))
self.assertTrue('index' not in signal1b.array_annotations)
self.assertTrue('test' not in signal1b.array_annotations)
self.assertIsInstance(signal1b.array_annotations, ArrayDict)
def test1(self):
"""Read data into one big segment (default)"""
full_range = 8192 * pq.mV
bio = neo.io.BlackrockIO(filename=self.fn, full_range=full_range)
block = bio.read_block(n_starts=[0], n_stops=[6])
self.assertEqual(bio.header.Channel_Count, 2)
self.assertEqual(bio.header.n_samples, 6)
# Everything put in one segment
self.assertEqual(len(block.segments), 1)
seg = block.segments[0]
self.assertEqual(len(seg.analogsignals), 2)
assert_arrays_almost_equal(seg.analogsignals[0],
[3., 4., 5., -3., -4., -5.] * pq.mV, .0001)
assert_arrays_almost_equal(seg.analogsignals[1],
[6., -4., -5., -6., 4., 5.] * pq.mV, .0001)
def test1(self):
"""Read data into one big segment (default)"""
full_range = 8192 * pq.mV
bio = neo.io.BlackrockIO(filename=self.fn, full_range=full_range)
block = bio.read_block(n_starts=[0], n_stops=[6])
self.assertEqual(bio.header.Channel_Count, 2)
self.assertEqual(bio.header.n_samples, 6)
# Everything put in one segment
self.assertEqual(len(block.segments), 1)
seg = block.segments[0]
self.assertEqual(len(seg.analogsignals), 2)
assert_arrays_almost_equal(seg.analogsignals[0],
[3., 4., 5., -3., -4., -5.] * pq.mV, .0001)
assert_arrays_almost_equal(seg.analogsignals[1],
[6., -4., -5., -6., 4., 5.] * pq.mV, .0001)
def test__add_epoch(self):
proxy_event = EventProxy(rawio=self.reader, event_channel_index=0,
block_index=0, seg_index=0)
loaded_event = proxy_event.load()
regular_event = Event(times=loaded_event.times - 1 * loaded_event.units)
seg = Segment()
seg.events = [regular_event, proxy_event]
# test cutting with two events one of which is a proxy
epoch = add_epoch(seg, regular_event, proxy_event)
assert_neo_object_is_compliant(epoch)
assert_same_annotations(epoch, regular_event)
assert_arrays_almost_equal(epoch.times, regular_event.times, 1e-12)
assert_arrays_almost_equal(epoch.durations,
np.ones(regular_event.shape) * loaded_event.units, 1e-12)
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.array_annotations, {'anno1': [23], 'anno2': ['A']})
self.assertIsInstance(result.array_annotations, ArrayDict)
self.assertEqual(result.units, 1 * pq.pA)
assert_arrays_almost_equal(np.array(result), self.data1.reshape(-1, 1) * 1000., 1e-10)
self.assertIsInstance(result.channel_index, ChannelIndex)
self.assertIsInstance(result.segment, Segment)
self.assertIs(result.channel_index, self.signal1.channel_index)
self.assertIs(result.segment, self.signal1.segment)
def test_rescale(self):
times = [2, 3, 4, 5]
labels = ["A", "B", "C", "D"]
arr_ann = {'index': np.arange(4), 'test': ['a', 'b', 'c', 'd']}
evt = Event(times * pq.ms, labels=labels, array_annotations=arr_ann)
result = evt.rescale(pq.us)
self.assertIsInstance(result, Event)
assert_neo_object_is_compliant(result)
assert_arrays_equal(result.array_annotations['index'], np.arange(4))
assert_arrays_equal(result.array_annotations['test'],
np.array(['a', 'b', 'c', 'd']))
self.assertIsInstance(result.array_annotations, ArrayDict)
self.assertEqual(result.units, 1 * pq.us)
assert_array_equal(evt.labels, result.labels)
assert_arrays_almost_equal(result.times,
[2000, 3000, 4000, 5000] * pq.us, 1e-9)
assert_arrays_almost_equal(result.times.magnitude,
np.array([2000, 3000, 4000, 5000]), 1e-9)
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.array_annotations, {'anno1': [23], 'anno2': ['A']})
self.assertIsInstance(result.array_annotations, ArrayDict)
self.assertEqual(result.units, 1 * pq.pA)
assert_arrays_almost_equal(np.array(result), self.data1.reshape(-1, 1) * 1000., 1e-10)
self.assertIsInstance(result.channel_index, ChannelIndex)
self.assertIsInstance(result.segment, Segment)
self.assertIs(result.channel_index, self.signal1.channel_index)
self.assertIs(result.segment, self.signal1.segment)
def test_time_slice_different_units(self):
#import numpy
av = AnalogSignalArray(numpy.array([[0, 1, 2, 3, 4, 5],
[0, 1, 2, 3, 4, 5]]).T,
t_start=10.0 * pq.ms,
sampling_rate=1.0 * pq.Hz,
units='mV')
t_start = 2 * pq.s + 10.0 * pq.ms
t_stop = 4 * pq.s + 10.0 * pq.ms
av2 = av.time_slice(t_start, t_stop)
correct = AnalogSignalArray(numpy.array([[2, 3], [2, 3]]).T,
t_start=t_start,
sampling_rate=1.0 * pq.Hz,
units='mV')
self.assertIsInstance(av2, AnalogSignalArray)
self.assertAlmostEqual(av2.t_stop, t_stop, delta=1e-12 * ms)
self.assertAlmostEqual(av2.t_start, t_start, delta=1e-12 * ms)
assert_arrays_almost_equal(av2.times, correct.times, 1e-12 * ms)
self.assertEqual(av2.sampling_rate, correct.sampling_rate)
def test__time_slice__no_explicit_time(self):
self.signal2.t_start = 10.0 * pq.ms
assert_neo_object_is_compliant(self.signal2)
t1 = 2 * pq.s + 10.0 * pq.ms
t2 = 4 * pq.s + 10.0 * pq.ms
for t_start,t_stop in [(t1,None),(None,None),(None,t2)]:
t_start_targ = t1 if t_start!=None else self.signal2.t_start
t_stop_targ = t2 if t_stop!=None else self.signal2.t_stop
result = self.signal2.time_slice(t_start, t_stop)
self.assertIsInstance(result, AnalogSignalArray)
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_ind = np.where((self.signal2.times >= t_start_targ) &
(self.signal2.times < t_stop_targ))
targ_array = self.signal2.magnitude[targ_ind]
targ = AnalogSignalArray(targ_array,
t_start=t_start_targ.rescale(pq.ms),
sampling_rate=1.0*pq.Hz, units='mV',
name='spam', description='eggs',
file_origin='testfile.txt', arg1='test')
assert_neo_object_is_compliant(result)
assert_neo_object_is_compliant(self.signal2)
self.assertEqual(self.signal2.t_start, 10.0 * pq.ms)
self.assertAlmostEqual(result.t_stop, t_stop_targ, delta=1e-12*pq.ms)
self.assertAlmostEqual(result.t_start, t_start_targ, delta=1e-12*pq.ms)
assert_arrays_almost_equal(result.times, targ.times, 1e-12*pq.ms)
self.assertEqual(result.sampling_rate, targ.sampling_rate)
assert_arrays_equal(result, targ)
assert_same_sub_schema(result, targ)
def test1(self):
"""Create clu and fet files based on spiketrains in a block.
Checks that
Files are created
Converted to samples correctly
Missing sampling rate are taken from IO reader default
Spiketrains without cluster info are assigned to cluster 0
Spiketrains across segments are concatenated
"""
block = neo.Block()
segment = neo.Segment()
segment2 = neo.Segment()
block.segments.append(segment)
block.segments.append(segment2)
# Fake spiketrain 1
st1 = neo.SpikeTrain(times=[.002, .004, .006], units='s', t_stop=1.)
st1.annotations['cluster'] = 0
st1.annotations['group'] = 0
wff = np.array([[11.3, 0.2], [-0.3, 12.3], [3.0, -2.5]])
st1.annotations['waveform_features'] = wff
segment.spiketrains.append(st1)
# Create empty directory for writing
if not os.path.exists(self.dirname):
os.mkdir(self.dirname)
delete_test_session(self.dirname)
# Create writer
kio = KlustaKwikIO(filename=os.path.join(self.dirname, 'base2'),
sampling_rate=1000.)
kio.write_block(block)
# Check files were created
for fn in ['.fet.0', '.clu.0']:
self.assertTrue(
os.path.exists(os.path.join(self.dirname, 'base2' + fn)))
# Check files contain correct content
fi = file(os.path.join(self.dirname, 'base2.fet.0'))
# first line is nbFeatures
self.assertEqual(fi.readline(), '2\n')
# Now check waveforms and times are same
data = fi.readlines()
new_wff = []
new_times = []
for line in data:
line_split = line.split()
new_wff.append([float(val) for val in line_split[:-1]])
new_times.append(int(line_split[-1]))
self.assertEqual(new_times, [2, 4, 6])
assert_arrays_almost_equal(wff, np.array(new_wff), .00001)
# Clusters on group 0
data = file(os.path.join(self.dirname, 'base2.clu.0')).readlines()
data = [int(d) for d in data]
self.assertEqual(data, [1, 0, 0, 0])
# Now read the features and test same
block = kio.read_block()
train = block.segments[0].spiketrains[0]
assert_arrays_almost_equal(wff, train.annotations['waveform_features'],
.00001)
# Empty out test session again
delete_test_session(self.dirname)
def test__times(self):
for i in range(3):
assert_arrays_almost_equal(
self.signals[i].times,
numpy.arange(self.data[i].size) / self.rates[i] +
self.t_start[i], 1e-12 * ms)
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 test1(self):
"""Create clu and fet files based on spiketrains in a block.
Checks that
Files are created
Converted to samples correctly
Missing sampling rate are taken from IO reader default
Spiketrains without cluster info are assigned to cluster 0
Spiketrains across segments are concatenated
"""
block = neo.Block()
segment = neo.Segment()
segment2 = neo.Segment()
block.segments.append(segment)
block.segments.append(segment2)
# Fake spiketrain 1
st1 = neo.SpikeTrain(times=[.002, .004, .006], units='s', t_stop=1.)
st1.annotations['cluster'] = 0
st1.annotations['group'] = 0
wff = np.array([
[11.3, 0.2],
[-0.3, 12.3],
[3.0, -2.5]])
st1.annotations['waveform_features'] = wff
segment.spiketrains.append(st1)
# Create empty directory for writing
if not os.path.exists(self.dirname):
os.mkdir(self.dirname)
delete_test_session(self.dirname)
# Create writer
kio = KlustaKwikIO(filename=os.path.join(self.dirname, 'base2'),
sampling_rate=1000.)
kio.write_block(block)
# Check files were created
for fn in ['.fet.0', '.clu.0']:
self.assertTrue(os.path.exists(os.path.join(self.dirname,
'base2' + fn)))
# Check files contain correct content
fi = file(os.path.join(self.dirname, 'base2.fet.0'))
# first line is nbFeatures
self.assertEqual(fi.readline(), '2\n')
# Now check waveforms and times are same
data = fi.readlines()
new_wff = []
new_times = []
for line in data:
line_split = line.split()
new_wff.append([float(val) for val in line_split[:-1]])
new_times.append(int(line_split[-1]))
self.assertEqual(new_times, [2, 4, 6])
assert_arrays_almost_equal(wff, np.array(new_wff), .00001)
# Clusters on group 0
data = file(os.path.join(self.dirname, 'base2.clu.0')).readlines()
data = [int(d) for d in data]
self.assertEqual(data, [1, 0, 0, 0])
# Now read the features and test same
block = kio.read_block()
train = block.segments[0].spiketrains[0]
assert_arrays_almost_equal(wff, train.annotations['waveform_features'],
.00001)
# Empty out test session again
delete_test_session(self.dirname)
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__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__times(self):
for i, signal in enumerate(self.signals):
targ = np.arange(self.data[i].shape[0])
targ = targ/self.rates[i] + self.t_start[i]
assert_arrays_almost_equal(signal.times, targ, 1e-12*pq.ms)
def test__times(self):
for i in range(3):
assert_arrays_almost_equal(self.signals[i].times,
numpy.arange(self.data[i].shape[0])/self.rates[i] + self.t_start[i],
1e-12*ms)
def test__times(self):
for i, signal in enumerate(self.signals):
targ = np.arange(self.data[i].shape[0])
targ = targ / self.rates[i] + self.t_start[i]
assert_arrays_almost_equal(signal.times, targ, 1e-12 * pq.ms)