def test_spike_later_than_hilbert(self):
# This is a spike clearly outside the bounds
st = SpikeTrain([1, 250],
units='s',
t_start=-1 * pq.s,
t_stop=300 * pq.s)
phases_noint, _, _ = elephant.phase_analysis.spike_triggered_phase(
elephant.signal_processing.hilbert(self.anasig0),
st,
interpolate=False)
self.assertEqual(len(phases_noint[0]), 1)
# This is a spike right on the border (length of the signal is 100s,
# spike sits at t=100s). However, by definition of intervals in
# Elephant (left borders inclusive, right borders exclusive), this
# spike is not to be considered.
st = SpikeTrain([1, 100],
units='s',
t_start=-1 * pq.s,
t_stop=200 * pq.s)
phases_noint, _, _ = elephant.phase_analysis.spike_triggered_phase(
elephant.signal_processing.hilbert(self.anasig0),
st,
interpolate=False)
self.assertEqual(len(phases_noint[0]), 1)
def default_data(block=None, n_chidx=1, n_units=1):
# generate new block if none provided, otherwise attach to provided block
if block is None:
block = Block()
for id in range(n_chidx):
sorting_hash = elephant.spike_sorting.SpikeSorter.get_sorting_hash({
'channel_index':
id,
'random annotation':
np.random.randint(0, 10**10)
})
chidx = ChannelIndex([], sorting_hash=sorting_hash)
chidx.block = block
block.channel_indexes.append(chidx)
for chidx in block.channel_indexes:
for id in range(n_units):
unit = Unit(unit_id=id)
chidx.units.append(unit)
unit.channel_index = chidx
for st_id in range(id):
st = SpikeTrain(np.random.uniform(0, st_id, 1) * pq.s,
t_start=0 * pq.s,
t_stop=st_id * pq.s,
spiketrain_id=st_id)
unit.spiketrains.append(st)
st.unit = unit
block.create_relationship()
return block
def test_write_read_single_spike(self):
block1 = Block()
seg = Segment('segment1')
spiketrain1 = SpikeTrain([1] * pq.s,
t_stop=10 * pq.s,
sampling_rate=1 * pq.Hz)
spiketrain1.annotate(yep='yop')
block1.segments.append(seg)
seg.spiketrains.append(spiketrain1)
# write block
filename = self.get_local_path('matlabiotestfile.mat')
io1 = self.ioclass(filename)
io1.write_block(block1)
# read block
io2 = self.ioclass(filename)
block2 = io2.read_block()
self.assertEqual(block1.segments[0].spiketrains[0],
block2.segments[0].spiketrains[0])
# test annotations
spiketrain2 = block2.segments[0].spiketrains[0]
assert 'yep' in spiketrain2.annotations
assert spiketrain2.annotations['yep'] == 'yop'
def setUp(self):
self.asiga0 = AnalogSignal(np.array(
[np.sin(np.arange(0, 20 * math.pi, 0.1))]).T,
units='mV',
sampling_rate=10 / ms)
self.asiga1 = AnalogSignal(np.array([
np.sin(np.arange(0, 20 * math.pi, 0.1)),
np.cos(np.arange(0, 20 * math.pi, 0.1))
]).T,
units='mV',
sampling_rate=10 / ms)
self.asiga2 = AnalogSignal(np.array([
np.sin(np.arange(0, 20 * math.pi, 0.1)),
np.cos(np.arange(0, 20 * math.pi, 0.1)),
np.tan(np.arange(0, 20 * math.pi, 0.1))
]).T,
units='mV',
sampling_rate=10 / ms)
self.st0 = SpikeTrain(
[9 * math.pi, 10 * math.pi, 11 * math.pi, 12 * math.pi],
units='ms',
t_stop=self.asiga0.t_stop)
self.lst = [
SpikeTrain([9 * math.pi, 10 * math.pi, 11 * math.pi, 12 * math.pi],
units='ms',
t_stop=self.asiga1.t_stop),
SpikeTrain([30, 35, 40], units='ms', t_stop=self.asiga1.t_stop)
]
def setUp(self):
# standard testsignals
tlen0 = 100 * pq.s
f0 = 20. * pq.Hz
fs0 = 1 * pq.ms
t0 = np.arange(
0, tlen0.rescale(pq.s).magnitude,
fs0.rescale(pq.s).magnitude) * pq.s
self.anasig0 = AnalogSignal(
np.sin(2 * np.pi * (f0 * t0).simplified.magnitude),
units=pq.mV, t_start=0 * pq.ms, sampling_period=fs0)
self.st0 = SpikeTrain(
np.arange(0, tlen0.rescale(pq.ms).magnitude, 50) * pq.ms,
t_start=0 * pq.ms, t_stop=tlen0)
self.bst0 = BinnedSpikeTrain(self.st0, binsize=fs0)
# shortened analogsignals
self.anasig1 = self.anasig0.time_slice(1 * pq.s, None)
self.anasig2 = self.anasig0.time_slice(None, 99 * pq.s)
# increased sampling frequency
fs1 = 0.1 * pq.ms
self.anasig3 = AnalogSignal(
np.sin(2 * np.pi * (f0 * t0).simplified.magnitude),
units=pq.mV, t_start=0 * pq.ms, sampling_period=fs1)
self.bst1 = BinnedSpikeTrain(
self.st0.time_slice(self.anasig3.t_start, self.anasig3.t_stop),
binsize=fs1)
# analogsignal containing multiple traces
self.anasig4 = AnalogSignal(
np.array([
np.sin(2 * np.pi * (f0 * t0).simplified.magnitude),
np.sin(4 * np.pi * (f0 * t0).simplified.magnitude)]).
transpose(),
units=pq.mV, t_start=0 * pq.ms, sampling_period=fs0)
# shortened spike train
self.st3 = SpikeTrain(
np.arange(
(tlen0.rescale(pq.ms).magnitude * .25),
(tlen0.rescale(pq.ms).magnitude * .75), 50) * pq.ms,
t_start=0 * pq.ms, t_stop=tlen0)
self.bst3 = BinnedSpikeTrain(self.st3, binsize=fs0)
self.st4 = SpikeTrain(np.arange(
(tlen0.rescale(pq.ms).magnitude * .25),
(tlen0.rescale(pq.ms).magnitude * .75), 50) * pq.ms,
t_start=5 * fs0, t_stop=tlen0 - 5 * fs0)
self.bst4 = BinnedSpikeTrain(self.st4, binsize=fs0)
# spike train with incompatible binsize
self.bst5 = BinnedSpikeTrain(self.st3, binsize=fs0 * 2.)
# spike train with same binsize as the analog signal, but with
# bin edges not aligned to the time axis of the analog signal
self.bst6 = BinnedSpikeTrain(
self.st3, binsize=fs0, t_start=4.5 * fs0, t_stop=tlen0 - 4.5 * fs0)
def test_one_spiketrain_empty(self):
'''Test for one empty SpikeTrain, but existing spikes in other'''
st = [SpikeTrain(
[9 * math.pi, 10 * math.pi, 11 * math.pi, 12 * math.pi],
units='ms', t_stop=self.asiga1.t_stop),
SpikeTrain([], units='ms', t_stop=self.asiga1.t_stop)]
STA = sta.spike_triggered_average(self.asiga1, st, (-1 * ms, 1 * ms))
cmp_array = AnalogSignalArray(np.array([np.zeros(20, dtype=float)]).T,
units='mV', sampling_rate=10 / ms)
cmp_array = cmp_array / 0.
cmp_array.t_start = -1 * ms
assert_array_equal(STA[:, 1], cmp_array[:, 0])
def __init__(self, spk_trains, t_starts=None, t_stops=None):
"""Create a Spikes instance."""
# Create empty instance.
self.spk_trains = None
self.t_starts = None
self.t_stops = None
# Init t_starts and t_stops.
# Below deals with single values, including None.
n_trs = len(spk_trains)
if not util.is_iterable(t_starts):
t_starts = n_trs * [t_starts]
if not util.is_iterable(t_stops):
t_stops = n_trs * [t_stops]
# Convert into Pandas Series for speed and more functionality.
self.t_starts = pd.Series(t_starts)
self.t_stops = pd.Series(t_stops)
# Create list of Neo SpikeTrain objects.
self.spk_trains = pd.Series(index=np.arange(n_trs), dtype=object)
for i in self.spk_trains.index:
# Remove spikes outside of time window.
t_start, t_stop = self.t_starts[i], self.t_stops[i]
spk_tr = util.values_in_window(spk_trains[i], t_start, t_stop)
self.spk_trains[i] = SpikeTrain(spk_tr,
t_start=t_start,
t_stop=t_stop)
def test_one_spiketrain_empty(self):
"""Test for one empty SpikeTrain, but existing spikes in other"""
st = [SpikeTrain(
[9 * math.pi, 10 * math.pi, 11 * math.pi, 12 * math.pi],
units='ms', t_stop=self.asiga1.t_stop),
SpikeTrain([], units='ms', t_stop=self.asiga1.t_stop)]
with warnings.catch_warnings():
warnings.simplefilter("ignore")
"""
Ignore the RuntimeWarning: invalid value encountered in true_divide
new_signal = f(other, *args) for the empty SpikeTrain.
"""
STA = sta.spike_triggered_average(self.asiga1,
spiketrains=st,
window=(-1 * ms, 1 * ms))
assert np.isnan(STA.magnitude[:, 1]).all()
def test_spike_earlier_than_analogsignal(self):
st = SpikeTrain([-1 * math.pi, 2 * math.pi],
units='ms',
t_start=-2 * math.pi,
t_stop=20 * math.pi)
self.assertRaises(ValueError, sta.spike_triggered_average, self.asiga0,
st, (-2 * ms, 2 * ms))
def test_usage_of_spikes(self):
st = SpikeTrain([16.5 * math.pi, 17.5 * math.pi,
18.5 * math.pi, 19.5 * math.pi], units='ms', t_stop=20 * math.pi)
STA = sta.spike_triggered_average(
self.asiga0, st, (-math.pi * ms, math.pi * ms))
self.assertEqual(STA.annotations['used_spikes'], 3)
self.assertEqual(STA.annotations['unused_spikes'], 1)
def _pool_spiketrains(trains, extremes='inner'):
"""
Pool spikes from any number of spike trains into a unique spike train.
Parameters
----------
trains: list
list of spike trains to merge
extremes: str, optional
Only spikes of a and b in the specified extremes are considered.
* 'inner': pool all spikes from min(a.t_start b.t_start) to
max(a.t_stop, b.t_stop)
* 'outer': pool all spikes from max(a.tstart_ b.t_start) to
min(a.t_stop, b.t_stop)
Default: 'inner'
Output
------
neo.SpikeTrain containing all spikes in trains falling in the
specified extremes
"""
merge_trains = trains[0]
for t in trains[1:]:
merge_trains = _pool_two_spiketrains(
merge_trains, t, extremes=extremes)
t_start, t_stop = merge_trains.t_start, merge_trains.t_stop
merge_trains = sorted(merge_trains)
merge_trains = np.squeeze(merge_trains)
merge_trains = SpikeTrain(
merge_trains, t_stop=t_stop, t_start=t_start, units=trains[0].units)
return merge_trains
def setUp(self):
tlen0 = 100 * pq.s
f0 = 20. * pq.Hz
fs0 = 1 * pq.ms
t0 = np.arange(
0, tlen0.rescale(pq.s).magnitude,
fs0.rescale(pq.s).magnitude) * pq.s
self.anasig0 = AnalogSignal(
np.sin(2 * np.pi * (f0 * t0).simplified.magnitude),
units=pq.mV, t_start=0 * pq.ms, sampling_period=fs0)
self.st0 = SpikeTrain(
np.arange(50, tlen0.rescale(pq.ms).magnitude - 50, 50) * pq.ms,
t_start=0 * pq.ms, t_stop=tlen0)
self.st1 = SpikeTrain(
[100., 100.1, 100.2, 100.3, 100.9, 101.] * pq.ms,
t_start=0 * pq.ms, t_stop=tlen0)
def _cpp_hom_stat(A, t_stop, rate, t_start=0 * ms):
"""
Generate a Compound Poisson Process (CPP) with amplitude distribution
A and heterogeneous firing rates r=r[0], r[1], ..., r[-1].
Parameters
----------
A : numpy.ndarray
Amplitude distribution. A[j] represents the probability of a
synchronous event of size j.
The sum over all entries of A must be equal to one.
t_stop : quantities.Quantity
The end time of the output spike trains
rate : quantities.Quantity
Average rate of each spike train generated
t_start : quantities.Quantity, optional
The start time of the output spike trains
Default: 0 ms
Output
------
List of n neo.SpikeTrains, having average firing rate r and correlated
such to form a CPP with amplitude distribution a
"""
# Generate mother process and associated spike labels
mother = _mother_proc_cpp_stat(
A=A, t_stop=t_stop, rate=rate, t_start=t_start)
labels = _sample_int_from_pdf(A, len(mother))
N = len(A) - 1 # Number of trains in output
try: # Faster but more memory-consuming approach
M = len(mother) # number of spikes in the mother process
spike_matrix = np.zeros((N, M), dtype=bool)
# for each spike, take its label l
for spike_id, l in enumerate(labels):
# choose l random trains
train_ids = random.sample(range(N), l)
# and set the spike matrix for that train
for train_id in train_ids:
spike_matrix[train_id, spike_id] = True # and spike to True
times = [[] for i in range(N)]
for train_id, row in enumerate(spike_matrix):
times[train_id] = mother[row].view(Quantity)
except MemoryError: # Slower (~2x) but less memory-consuming approach
print('memory case')
times = [[] for i in range(N)]
for t, l in zip(mother, labels):
train_ids = random.sample(range(N), l)
for train_id in train_ids:
times[train_id].append(t)
trains = [SpikeTrain(
times=t, t_start=t_start, t_stop=t_stop) for t in times]
return trains
def setUp(self):
# standard testsignals
tlen0 = 100 * pq.s
f0 = 20. * pq.Hz
fs0 = 1 * pq.ms
t0 = np.arange(
0, tlen0.rescale(pq.s).magnitude,
fs0.rescale(pq.s).magnitude) * pq.s
self.anasig0 = AnalogSignal(
np.sin(2 * np.pi * (f0 * t0).simplified.magnitude),
units=pq.mV, t_start=0 * pq.ms, sampling_period=fs0)
self.st0 = SpikeTrain(
np.arange(0, tlen0.rescale(pq.ms).magnitude, 50) * pq.ms,
t_start=0 * pq.ms, t_stop=tlen0)
self.bst0 = BinnedSpikeTrain(self.st0, binsize=fs0)
# shortened analogsignals
self.anasig1 = self.anasig0.time_slice(1 * pq.s, None)
self.anasig2 = self.anasig0.time_slice(None, 99 * pq.s)
# increased sampling frequency
fs1 = 0.1 * pq.ms
self.anasig3 = AnalogSignal(
np.sin(2 * np.pi * (f0 * t0).simplified.magnitude),
units=pq.mV, t_start=0 * pq.ms, sampling_period=fs1)
self.bst1 = BinnedSpikeTrain(
self.st0.time_slice(self.anasig3.t_start, self.anasig3.t_stop),
binsize=fs1)
# analogsignal containing multiple traces
self.anasig4 = AnalogSignal(
np.array([
np.sin(2 * np.pi * (f0 * t0).simplified.magnitude),
np.sin(4 * np.pi * (f0 * t0).simplified.magnitude)]).
transpose(),
units=pq.mV, t_start=0 * pq.ms, sampling_period=fs0)
# shortened spike train
self.st3 = SpikeTrain(
np.arange(
(tlen0.rescale(pq.ms).magnitude * .25),
(tlen0.rescale(pq.ms).magnitude * .75), 50) * pq.ms,
t_start=0 * pq.ms, t_stop=tlen0)
self.bst3 = BinnedSpikeTrain(self.st3, binsize=fs0)
self.st4 = SpikeTrain(np.arange(
(tlen0.rescale(pq.ms).magnitude * .25),
(tlen0.rescale(pq.ms).magnitude * .75), 50) * pq.ms,
t_start=5 * fs0, t_stop=tlen0 - 5 * fs0)
self.bst4 = BinnedSpikeTrain(self.st4, binsize=fs0)
# spike train with incompatible binsize
self.bst5 = BinnedSpikeTrain(self.st3, binsize=fs0 * 2.)
# spike train with same binsize as the analog signal, but with
# bin edges not aligned to the time axis of the analog signal
self.bst6 = BinnedSpikeTrain(
self.st3, binsize=fs0, t_start=4.5 * fs0, t_stop=tlen0 - 4.5 * fs0)
def get_instantaneous_FR(spiketrain,
sampling_period,
t_start=0.,
t_stop=5000.):
from elephant.statistics import instantaneous_rate as ir_fnc
from neo import SpikeTrain
from quantities import ms
spiketrain = SpikeTrain(spiketrain, t_stop, units='ms', t_start=t_start)
return ir_fnc(spiketrain, sampling_period * ms, kernel='auto')
def threshold_detection(signal, threshold=0.0 * mV, sign='above'):
"""
Returns the times when the analog signal crosses a threshold.
Usually used for extracting spike times from a membrane potential.
Adapted from version in NeuroTools.
Parameters
----------
signal : neo AnalogSignal object
'signal' is an analog signal.
threshold : A quantity, e.g. in mV
'threshold' contains a value that must be reached
for an event to be detected. Default: 0.0 * mV.
sign : 'above' or 'below'
'sign' determines whether to count thresholding crossings
that cross above or below the threshold.
format : None or 'raw'
Whether to return as SpikeTrain (None)
or as a plain array of times ('raw').
Returns
-------
result_st : neo SpikeTrain object
'result_st' contains the spike times of each of the events (spikes)
extracted from the signal.
"""
assert threshold is not None, "A threshold must be provided"
if sign is 'above':
cutout = np.where(signal > threshold)[0]
elif sign in 'below':
cutout = np.where(signal < threshold)[0]
if len(cutout) <= 0:
events_base = np.zeros(0)
else:
take = np.where(np.diff(cutout) > 1)[0] + 1
take = np.append(0, take)
time = signal.times
events = time[cutout][take]
events_base = events.magnitude
if events_base is None:
# This occurs in some Python 3 builds due to some
# bug in quantities.
events_base = np.array([event.magnitude
for event in events]) # Workaround
result_st = SpikeTrain(events_base,
units=signal.times.units,
t_start=signal.t_start,
t_stop=signal.t_stop)
return result_st
def test_regression_269(self):
# This is a spike train on a 30KHz sampling, one spike at 1s, one just
# before the end of the signal
cu = pq.CompoundUnit("1/30000.*s")
st = SpikeTrain(
[30000., (self.anasig0.t_stop - 1 * pq.s).rescale(cu).magnitude],
units=pq.CompoundUnit("1/30000.*s"),
t_start=-1 * pq.s, t_stop=300 * pq.s)
phases_noint, _, _ = elephant.phase_analysis.spike_triggered_phase(
elephant.signal_processing.hilbert(self.anasig0),
st,
interpolate=False)
self.assertEqual(len(phases_noint[0]), 2)
def test_victor_purpura_matlab_comparison_int(self):
repo_path =\
r"unittest/spike_train_dissimilarity/victor_purpura_distance/data"
files_to_download = [
("times_int.npy", "aa1411c04da3f58d8b8913ae2f935057"),
("matlab_results_int.npy", "7edd32e50edde12dc1ef4aa5f57f70fb")
]
for filename, checksum in files_to_download:
download_datasets(repo_path=f"{repo_path}/{filename}",
checksum=checksum)
times_int = np.load(ELEPHANT_TMP_DIR / 'times_int.npy')
mat_res_int = np.load(ELEPHANT_TMP_DIR / 'matlab_results_int.npy')
r_int = SpikeTrain(times_int[0],
units='ms',
t_start=0,
t_stop=1000 * ms)
s_int = SpikeTrain(times_int[1],
units='ms',
t_start=0,
t_stop=1000 * ms)
t_int = SpikeTrain(times_int[2],
units='ms',
t_start=0,
t_stop=1000 * ms)
vic_pur_result_int = stds.victor_purpura_distance(
[r_int, s_int, t_int],
cost_factor=1.0 / ms,
kernel=None,
sort=True,
algorithm='intuitive')
assert_array_equal(vic_pur_result_int, mat_res_int)
def test_victor_purpura_matlab_comparison_float(self):
repo_path =\
r"unittest/spike_train_dissimilarity/victor_purpura_distance/data"
files_to_download = [
("times_float.npy", "ed1ff4d2c0eeed4a2b50a456803656be"),
("matlab_results_float.npy", "a17f049e7ad0ddf7ca812e86fdb92646")
]
for filename, checksum in files_to_download:
download_datasets(repo_path=f"{repo_path}/{filename}",
checksum=checksum)
times_float = np.load(ELEPHANT_TMP_DIR / 'times_float.npy')
mat_res_float = np.load(ELEPHANT_TMP_DIR / 'matlab_results_float.npy')
r_float = SpikeTrain(times_float[0],
units='ms',
t_start=0,
t_stop=1000 * ms)
s_float = SpikeTrain(times_float[1],
units='ms',
t_start=0,
t_stop=1000 * ms)
t_float = SpikeTrain(times_float[2],
units='ms',
t_start=0,
t_stop=1000 * ms)
vic_pur_result_float = stds.victor_purpura_distance(
[r_float, s_float, t_float],
cost_factor=1.0 / ms,
kernel=None,
sort=True,
algorithm='intuitive')
assert_array_almost_equal(vic_pur_result_float, mat_res_float)
def test_all_spiketrains_empty(self):
st = SpikeTrain([], units='ms', t_stop=self.asiga1.t_stop)
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
# Trigger warnings.
STA = sta.spike_triggered_average(
self.asiga1, st, (-1 * ms, 1 * ms))
self.assertEqual("No spike at all was either found or used "
"for averaging", str(w[-1].message))
nan_array = np.empty(20)
nan_array.fill(np.nan)
cmp_array = AnalogSignal(np.array([nan_array, nan_array]).T,
units='mV', sampling_rate=10 / ms)
assert_array_equal(STA.magnitude, cmp_array.magnitude)
def test_spike_triggered_average_with_n_spikes_on_constant_function(self):
"""Signal should average to the input"""
const = 13.8
x = const * np.ones(201)
asiga = AnalogSignal(
np.array([x]).T, units='mV', sampling_rate=10 / ms)
st = SpikeTrain([3, 5.6, 7, 7.1, 16, 16.3], units='ms', t_stop=20)
window_starttime = -2 * ms
window_endtime = 2 * ms
STA = sta.spike_triggered_average(
asiga, st, (window_starttime, window_endtime))
a = int(((window_endtime - window_starttime) *
asiga.sampling_rate).simplified)
cutout = asiga[0: a]
cutout.t_start = window_starttime
assert_array_almost_equal(STA, cutout, 12)
def test_only_one_spike(self):
"""The output should be the same as the input"""
x = np.arange(0, 20, 0.1)
y = x**2
sr = 10 / ms
z = AnalogSignal(np.array([y]).T, units='mV', sampling_rate=sr)
spiketime = 8 * ms
spiketime_in_ms = int((spiketime / ms).simplified)
st = SpikeTrain([spiketime_in_ms], units='ms', t_stop=20)
window_starttime = -3 * ms
window_endtime = 5 * ms
STA = sta.spike_triggered_average(
z, st, (window_starttime, window_endtime))
cutout = z[int(((spiketime + window_starttime) * sr).simplified):
int(((spiketime + window_endtime) * sr).simplified)]
cutout.t_start = window_starttime
assert_array_equal(STA, cutout)
def _pool_two_spiketrains(a, b, extremes='inner'):
"""
Pool the spikes of two spike trains a and b into a unique spike train.
Parameters
----------
a, b : neo.SpikeTrains
Spike trains to be pooled
extremes: str, optional
Only spikes of a and b in the specified extremes are considered.
* 'inner': pool all spikes from max(a.tstart_ b.t_start) to
min(a.t_stop, b.t_stop)
* 'outer': pool all spikes from min(a.tstart_ b.t_start) to
max(a.t_stop, b.t_stop)
Default: 'inner'
Output
------
neo.SpikeTrain containing all spikes in a and b falling in the
specified extremes
"""
unit = a.units
times_a_dimless = list(a.view(Quantity).magnitude)
times_b_dimless = list(b.rescale(unit).view(Quantity).magnitude)
times = (times_a_dimless + times_b_dimless) * unit
if extremes == 'outer':
t_start = min(a.t_start, b.t_start)
t_stop = max(a.t_stop, b.t_stop)
elif extremes == 'inner':
t_start = max(a.t_start, b.t_start)
t_stop = min(a.t_stop, b.t_stop)
times = times[times > t_start]
times = times[times < t_stop]
else:
raise ValueError('extremes (%s) can only be "inner" or "outer"' %
extremes)
pooled_train = SpikeTrain(times=sorted(times.magnitude),
units=unit,
t_start=t_start,
t_stop=t_stop)
return pooled_train
def test_write_read_single_spike(self):
block1 = Block()
seg = Segment('segment1')
spiketrain = SpikeTrain([1] * pq.s, t_stop=10 * pq.s, sampling_rate=1 * pq.Hz)
block1.segments.append(seg)
seg.spiketrains.append(spiketrain)
# write block
filename = BaseTestIO.get_filename_path(self, 'matlabiotestfile.mat')
io1 = self.ioclass(filename)
io1.write_block(block1)
# read block
io2 = self.ioclass(filename)
block2 = io2.read_block()
self.assertEqual(block1.segments[0].spiketrains[0],
block2.segments[0].spiketrains[0])
def setUp(self):
# standard testsignals
tlen0 = 100 * pq.s
f0 = 20. * pq.Hz
fs0 = 1 * pq.ms
t0 = np.arange(
0, tlen0.rescale(pq.s).magnitude,
fs0.rescale(pq.s).magnitude) * pq.s
self.anasig0 = AnalogSignal(
np.sin(2 * np.pi * (f0 * t0).simplified.magnitude),
units=pq.mV, t_start=0 * pq.ms, sampling_period=fs0)
self.st0 = SpikeTrain(
np.arange(0, tlen0.rescale(pq.ms).magnitude, 50) * pq.ms,
t_start=0 * pq.ms, t_stop=tlen0)
self.bst0 = BinnedSpikeTrain(self.st0, bin_size=fs0)
def test_old_scipy_version(self):
self.assertRaises(AttributeError, sta.spike_field_coherence,
self.anasig0, self.bst0)
def _homogeneous_process(interval_generator, args, mean_rate, t_start, t_stop,
as_array):
"""
Returns a spike train whose spikes are a realization of a random process
generated by the function `interval_generator` with the given rate,
starting at time `t_start` and stopping `time t_stop`.
"""
def rescale(x):
return (x / mean_rate.units).rescale(t_stop.units)
n = int(((t_stop - t_start) * mean_rate).simplified)
number = np.ceil(n + 3 * np.sqrt(n))
if number < 100:
number = min(5 + np.ceil(2 * n), 100)
assert number > 4 # if positive, number cannot be less than 5
isi = rescale(interval_generator(*args, size=int(number)))
spikes = np.cumsum(isi)
spikes += t_start
i = spikes.searchsorted(t_stop)
if i == len(spikes):
# ISI buffer overrun
extra_spikes = []
t_last = spikes[-1] + rescale(interval_generator(*args, size=1))[0]
while t_last < t_stop:
extra_spikes.append(t_last)
t_last = t_last + rescale(interval_generator(*args, size=1))[0]
# np.concatenate does not conserve units
spikes = Quantity(np.concatenate((spikes, extra_spikes)).magnitude,
units=spikes.units)
else:
spikes = spikes[:i]
if as_array:
spikes = spikes.magnitude
else:
spikes = SpikeTrain(spikes,
t_start=t_start,
t_stop=t_stop,
units=spikes.units)
return spikes
def get_spikes(self, trs=None, t1s=None, t2s=None, ref_ts=None):
"""Return spike times of given trials within time windows."""
# Init trials and time limits.
trs = self.init_trials(trs)
t1s, t2s, ref_ts = self.init_time_limits(t1s, t2s, ref_ts)
# Assamble time-windowed spike trains.
spk_trains = pd.Series(index=trs, dtype=object)
for itr in trs:
# Select spikes between t1 and t2 during selected trials, and
# convert them into new SpikeTrain list, with time limits set.
t1, t2, tr = t1s[itr], t2s[itr], ref_ts[itr]
spk_tr = util.values_in_window(self.spk_trains[itr], t1, t2)
spk_tr, t1, t2 = spk_tr - tr, t1 - tr, t2 - tr # align to reference time
# Need to check range once again to deal with rounding errors.
spk_tr = util.values_in_window(spk_tr, t1, t2)
spk_trains[itr] = SpikeTrain(spk_tr, t_start=t1, t_stop=t2)
return spk_trains
def calc_corellation(spike_times, spike_ids, num, duration, bin_x=None):
# Create randomly shuffled indices
neuron_indices = np.arange(num)
np.random.shuffle(neuron_indices)
# Loop through indices
spike_trains = []
for n in neuron_indices:
# Extract spike times
neuron_spike_times = spike_times[spike_ids == n]
# If there are any spikes
if len(neuron_spike_times) > 0:
# Add neo SpikeTrain object
spike_trains.append(
SpikeTrain(neuron_spike_times * ms,
t_start=1 * s,
t_stop=10 * s))
# If we have found our 200 spike trains, stop
if len(spike_trains) == 200:
break
# Check that 200 spike trains containing spikes could be found
assert len(spike_trains) == 200
# Bin spikes using bins corresponding to 2ms refractory period
binned_spike_trains = BinnedSpikeTrain(spike_trains, binsize=2.0 * ms)
# Calculate correlation matrix
correlation = corrcoef(binned_spike_trains)
# Take lower triangle of matrix (minus diagonal)
correlation_non_disjoint = correlation[np.tril_indices_from(correlation,
k=-1)]
# Calculate histogram
return calc_histogram(correlation_non_disjoint, 0.002, bin_x)
event = Event(name="Seg {} :: Event".format(idx),
times=event_times,
labels=["A", "B", "C", "D", "E"])
seg.events.append(event)
epoch_times = tstart + np.cumsum(np.array([0,1,2])) * pq.ms
epoch = Epoch(name="Seg {} :: Epoch".format(idx),
times=epoch_times,
durations=np.array([0,1,2])*pq.ms,
labels=["A+", "B+", "C+"])
seg.epochs.append(epoch)
tstart = 10 *pq.s
st_times = tstart + np.cumsum(np.arange(0,1,0.1)) * pq.s
tstop = max(event_times[-1], epoch_times[-1], st_times[-1]) + 1 * pq.s
st = SpikeTrain(name="Seg {} :: SpikeTrain".format(idx),
times=st_times, t_start=tstart, t_stop=tstop)
wf = np.random.random((len(st_times), nchannels, 30)) * pq.mV
st.waveforms = wf
st.sampling_rate = sampling_rate
seg.spiketrains.append(st)
unit = Unit(name="unit-{}".format(idx))
print(unit)
unit.spiketrains.append(st)
chx.units.append(unit)
# Write the Block to file using the NixIO
# Any existing file will be overwritten
fname = "test_case.nix"
io = NixIO(fname, "ow")
io.write_block(block1)
class sfc_TestCase_new_scipy(unittest.TestCase):
def setUp(self):
# standard testsignals
tlen0 = 100 * pq.s
f0 = 20. * pq.Hz
fs0 = 1 * pq.ms
t0 = np.arange(
0, tlen0.rescale(pq.s).magnitude,
fs0.rescale(pq.s).magnitude) * pq.s
self.anasig0 = AnalogSignal(
np.sin(2 * np.pi * (f0 * t0).simplified.magnitude),
units=pq.mV, t_start=0 * pq.ms, sampling_period=fs0)
self.st0 = SpikeTrain(
np.arange(0, tlen0.rescale(pq.ms).magnitude, 50) * pq.ms,
t_start=0 * pq.ms, t_stop=tlen0)
self.bst0 = BinnedSpikeTrain(self.st0, binsize=fs0)
# shortened analogsignals
self.anasig1 = self.anasig0.time_slice(1 * pq.s, None)
self.anasig2 = self.anasig0.time_slice(None, 99 * pq.s)
# increased sampling frequency
fs1 = 0.1 * pq.ms
self.anasig3 = AnalogSignal(
np.sin(2 * np.pi * (f0 * t0).simplified.magnitude),
units=pq.mV, t_start=0 * pq.ms, sampling_period=fs1)
self.bst1 = BinnedSpikeTrain(
self.st0.time_slice(self.anasig3.t_start, self.anasig3.t_stop),
binsize=fs1)
# analogsignal containing multiple traces
self.anasig4 = AnalogSignal(
np.array([
np.sin(2 * np.pi * (f0 * t0).simplified.magnitude),
np.sin(4 * np.pi * (f0 * t0).simplified.magnitude)]).
transpose(),
units=pq.mV, t_start=0 * pq.ms, sampling_period=fs0)
# shortened spike train
self.st3 = SpikeTrain(
np.arange(
(tlen0.rescale(pq.ms).magnitude * .25),
(tlen0.rescale(pq.ms).magnitude * .75), 50) * pq.ms,
t_start=0 * pq.ms, t_stop=tlen0)
self.bst3 = BinnedSpikeTrain(self.st3, binsize=fs0)
self.st4 = SpikeTrain(np.arange(
(tlen0.rescale(pq.ms).magnitude * .25),
(tlen0.rescale(pq.ms).magnitude * .75), 50) * pq.ms,
t_start=5 * fs0, t_stop=tlen0 - 5 * fs0)
self.bst4 = BinnedSpikeTrain(self.st4, binsize=fs0)
# spike train with incompatible binsize
self.bst5 = BinnedSpikeTrain(self.st3, binsize=fs0 * 2.)
# spike train with same binsize as the analog signal, but with
# bin edges not aligned to the time axis of the analog signal
self.bst6 = BinnedSpikeTrain(
self.st3, binsize=fs0, t_start=4.5 * fs0, t_stop=tlen0 - 4.5 * fs0)
# =========================================================================
# Tests for correct input handling
# =========================================================================
def test_wrong_input_type(self):
self.assertRaises(TypeError,
sta.spike_field_coherence,
np.array([1, 2, 3]), self.bst0)
self.assertRaises(TypeError,
sta.spike_field_coherence,
self.anasig0, [1, 2, 3])
self.assertRaises(ValueError,
sta.spike_field_coherence,
self.anasig0.duplicate_with_new_array([]), self.bst0)
def test_start_stop_times_out_of_range(self):
self.assertRaises(ValueError,
sta.spike_field_coherence,
self.anasig1, self.bst0)
self.assertRaises(ValueError,
sta.spike_field_coherence,
self.anasig2, self.bst0)
def test_non_matching_input_binning(self):
self.assertRaises(ValueError,
sta.spike_field_coherence,
self.anasig0, self.bst1)
def test_incompatible_spiketrain_analogsignal(self):
# These spike trains have incompatible binning (binsize or alignment to
# time axis of analog signal)
self.assertRaises(ValueError,
sta.spike_field_coherence,
self.anasig0, self.bst5)
self.assertRaises(ValueError,
sta.spike_field_coherence,
self.anasig0, self.bst6)
def test_signal_dimensions(self):
# single analogsignal trace and single spike train
s_single, f_single = sta.spike_field_coherence(self.anasig0, self.bst0)
self.assertEqual(len(f_single.shape), 1)
self.assertEqual(len(s_single.shape), 2)
# multiple analogsignal traces and single spike train
s_multi, f_multi = sta.spike_field_coherence(self.anasig4, self.bst0)
self.assertEqual(len(f_multi.shape), 1)
self.assertEqual(len(s_multi.shape), 2)
# frequencies are identical since same sampling frequency was used
# in both cases and data length is the same
assert_array_equal(f_single, f_multi)
# coherences of s_single and first signal in s_multi are identical,
# since first analogsignal trace in anasig4 is same as in anasig0
assert_array_equal(s_single[:, 0], s_multi[:, 0])
def test_non_binned_spiketrain_input(self):
s, f = sta.spike_field_coherence(self.anasig0, self.st0)
f_ind = np.where(f >= 19.)[0][0]
max_ind = np.argmax(s[1:]) + 1
self.assertEqual(f_ind, max_ind)
self.assertAlmostEqual(s[f_ind], 1., delta=0.01)
# =========================================================================
# Tests for correct return values
# =========================================================================
def test_spike_field_coherence_perfect_coherence(self):
# check for detection of 20Hz peak in anasig0/bst0
s, f = sta.spike_field_coherence(
self.anasig0, self.bst0, window='boxcar')
f_ind = np.where(f >= 19.)[0][0]
max_ind = np.argmax(s[1:]) + 1
self.assertEqual(f_ind, max_ind)
self.assertAlmostEqual(s[f_ind], 1., delta=0.01)
def test_output_frequencies(self):
nfft = 256
_, f = sta.spike_field_coherence(self.anasig3, self.bst1, nfft=nfft)
# check number of frequency samples
self.assertEqual(len(f), nfft / 2 + 1)
# check values of frequency samples
assert_array_almost_equal(
f, np.linspace(
0, self.anasig3.sampling_rate.rescale('Hz').magnitude / 2,
nfft / 2 + 1) * pq.Hz)
def test_short_spiketrain(self):
# this spike train has the same length as anasig0
s1, f1 = sta.spike_field_coherence(
self.anasig0, self.bst3, window='boxcar')
# this spike train has the same spikes as above, but is shorter than
# anasig0
s2, f2 = sta.spike_field_coherence(
self.anasig0, self.bst4, window='boxcar')
# the results above should be the same, nevertheless
assert_array_equal(s1.magnitude, s2.magnitude)
assert_array_equal(f1.magnitude, f2.magnitude)
class sfc_TestCase_new_scipy(unittest.TestCase):
def setUp(self):
# standard testsignals
tlen0 = 100 * pq.s
f0 = 20. * pq.Hz
fs0 = 1 * pq.ms
t0 = np.arange(0,
tlen0.rescale(pq.s).magnitude,
fs0.rescale(pq.s).magnitude) * pq.s
self.anasig0 = AnalogSignal(np.sin(2 * np.pi *
(f0 * t0).simplified.magnitude),
units=pq.mV,
t_start=0 * pq.ms,
sampling_period=fs0)
self.st0 = SpikeTrain(np.arange(0,
tlen0.rescale(pq.ms).magnitude, 50) *
pq.ms,
t_start=0 * pq.ms,
t_stop=tlen0)
self.bst0 = BinnedSpikeTrain(self.st0, bin_size=fs0)
# shortened analogsignals
self.anasig1 = self.anasig0.time_slice(1 * pq.s, None)
self.anasig2 = self.anasig0.time_slice(None, 99 * pq.s)
# increased sampling frequency
fs1 = 0.1 * pq.ms
self.anasig3 = AnalogSignal(np.sin(2 * np.pi *
(f0 * t0).simplified.magnitude),
units=pq.mV,
t_start=0 * pq.ms,
sampling_period=fs1)
self.bst1 = BinnedSpikeTrain(self.st0.time_slice(
self.anasig3.t_start, self.anasig3.t_stop),
bin_size=fs1)
# analogsignal containing multiple traces
self.anasig4 = AnalogSignal(np.array([
np.sin(2 * np.pi * (f0 * t0).simplified.magnitude),
np.sin(4 * np.pi * (f0 * t0).simplified.magnitude)
]).transpose(),
units=pq.mV,
t_start=0 * pq.ms,
sampling_period=fs0)
# shortened spike train
self.st3 = SpikeTrain(np.arange(
(tlen0.rescale(pq.ms).magnitude * .25),
(tlen0.rescale(pq.ms).magnitude * .75), 50) * pq.ms,
t_start=0 * pq.ms,
t_stop=tlen0)
self.bst3 = BinnedSpikeTrain(self.st3, bin_size=fs0)
self.st4 = SpikeTrain(np.arange(
(tlen0.rescale(pq.ms).magnitude * .25),
(tlen0.rescale(pq.ms).magnitude * .75), 50) * pq.ms,
t_start=5 * fs0,
t_stop=tlen0 - 5 * fs0)
self.bst4 = BinnedSpikeTrain(self.st4, bin_size=fs0)
# spike train with incompatible bin_size
self.bst5 = BinnedSpikeTrain(self.st3, bin_size=fs0 * 2.)
# spike train with same bin_size as the analog signal, but with
# bin edges not aligned to the time axis of the analog signal
self.bst6 = BinnedSpikeTrain(self.st3,
bin_size=fs0,
t_start=4.5 * fs0,
t_stop=tlen0 - 4.5 * fs0)
# =========================================================================
# Tests for correct input handling
# =========================================================================
def test_wrong_input_type(self):
self.assertRaises(TypeError, sta.spike_field_coherence,
np.array([1, 2, 3]), self.bst0)
self.assertRaises(TypeError, sta.spike_field_coherence, self.anasig0,
[1, 2, 3])
self.assertRaises(ValueError, sta.spike_field_coherence,
self.anasig0.duplicate_with_new_data([]), self.bst0)
def test_start_stop_times_out_of_range(self):
self.assertRaises(ValueError, sta.spike_field_coherence, self.anasig1,
self.bst0)
self.assertRaises(ValueError, sta.spike_field_coherence, self.anasig2,
self.bst0)
def test_non_matching_input_binning(self):
self.assertRaises(ValueError, sta.spike_field_coherence, self.anasig0,
self.bst1)
def test_incompatible_spiketrain_analogsignal(self):
# These spike trains have incompatible binning (bin_size or alignment
# to time axis of analog signal)
self.assertRaises(ValueError, sta.spike_field_coherence, self.anasig0,
self.bst5)
self.assertRaises(ValueError, sta.spike_field_coherence, self.anasig0,
self.bst6)
def test_signal_dimensions(self):
# single analogsignal trace and single spike train
s_single, f_single = sta.spike_field_coherence(self.anasig0, self.bst0)
self.assertEqual(len(f_single.shape), 1)
self.assertEqual(len(s_single.shape), 2)
# multiple analogsignal traces and single spike train
s_multi, f_multi = sta.spike_field_coherence(self.anasig4, self.bst0)
self.assertEqual(len(f_multi.shape), 1)
self.assertEqual(len(s_multi.shape), 2)
# frequencies are identical since same sampling frequency was used
# in both cases and data length is the same
assert_array_equal(f_single, f_multi)
# coherences of s_single and first signal in s_multi are identical,
# since first analogsignal trace in anasig4 is same as in anasig0
assert_array_equal(s_single[:, 0], s_multi[:, 0])
def test_non_binned_spiketrain_input(self):
s, f = sta.spike_field_coherence(self.anasig0, self.st0)
f_ind = np.where(f >= 19.)[0][0]
max_ind = np.argmax(s[1:]) + 1
self.assertEqual(f_ind, max_ind)
self.assertAlmostEqual(s[f_ind], 1., delta=0.01)
# =========================================================================
# Tests for correct return values
# =========================================================================
def test_spike_field_coherence_perfect_coherence(self):
# check for detection of 20Hz peak in anasig0/bst0
with warnings.catch_warnings():
warnings.simplefilter("ignore")
"""
When the spiketrain is a vector with zero values, ignore the
warning RuntimeWarning: invalid value encountered in true_divide
Cxy = np.abs(Pxy)**2 / Pxx / Pyy.
"""
s, f = sta.spike_field_coherence(self.anasig0,
self.bst0,
window='boxcar')
f_ind = np.where(f >= 19.)[0][0]
max_ind = np.argmax(s[1:]) + 1
self.assertEqual(f_ind, max_ind)
self.assertAlmostEqual(s[f_ind], 1., delta=0.01)
def test_output_frequencies(self):
nfft = 256
_, f = sta.spike_field_coherence(self.anasig3, self.bst1, nfft=nfft)
# check number of frequency samples
self.assertEqual(len(f), nfft / 2 + 1)
f_max = self.anasig3.sampling_rate.rescale('Hz').magnitude / 2
f_ground_truth = np.linspace(start=0, stop=f_max,
num=nfft // 2 + 1) * pq.Hz
# check values of frequency samples
assert_array_almost_equal(f, f_ground_truth)
def test_short_spiketrain(self):
# this spike train has the same length as anasig0
with warnings.catch_warnings():
warnings.simplefilter("ignore")
"""
When the spiketrain is a vector with zero values, ignore the
warning RuntimeWarning: invalid value encountered in true_divide
Cxy = np.abs(Pxy)**2 / Pxx / Pyy.
"""
s1, f1 = sta.spike_field_coherence(self.anasig0,
self.bst3,
window='boxcar')
# this spike train has the same spikes as above,
# but it's shorter than anasig0
s2, f2 = sta.spike_field_coherence(self.anasig0,
self.bst4,
window='boxcar')
# the results above should be the same, nevertheless
assert_array_equal(s1.magnitude, s2.magnitude)
assert_array_equal(f1.magnitude, f2.magnitude)
def test_empty_analogsignal(self):
asiga = AnalogSignal([], units='mV', sampling_rate=10 / ms)
st = SpikeTrain([5], units='ms', t_stop=10)
self.assertRaises(ValueError, sta.spike_triggered_average, asiga, st,
(-1 * ms, 1 * ms))