def test_tfr_multitaper():
"""Test tfr_multitaper"""
sfreq = 200.0
ch_names = ['SIM0001', 'SIM0002', 'SIM0003']
ch_types = ['grad', 'grad', 'grad']
info = create_info(ch_names=ch_names, sfreq=sfreq, ch_types=ch_types)
n_times = int(sfreq) # Second long epochs
n_epochs = 3
seed = 42
rng = np.random.RandomState(seed)
noise = 0.1 * rng.randn(n_epochs, len(ch_names), n_times)
t = np.arange(n_times, dtype=np.float) / sfreq
signal = np.sin(np.pi * 2. * 50. * t) # 50 Hz sinusoid signal
signal[np.logical_or(t < 0.45, t > 0.55)] = 0. # Hard windowing
on_time = np.logical_and(t >= 0.45, t <= 0.55)
signal[on_time] *= np.hanning(on_time.sum()) # Ramping
dat = noise + signal
reject = dict(grad=4000.)
events = np.empty((n_epochs, 3), int)
first_event_sample = 100
event_id = dict(sin50hz=1)
for k in range(n_epochs):
events[k, :] = first_event_sample + k * n_times, 0, event_id['sin50hz']
epochs = EpochsArray(data=dat, info=info, events=events, event_id=event_id,
reject=reject)
freqs = np.arange(5, 100, 3, dtype=np.float)
power, itc = tfr_multitaper(epochs, freqs=freqs, n_cycles=freqs / 2.,
time_bandwidth=4.0)
picks = np.arange(len(ch_names))
power_picks, itc_picks = tfr_multitaper(epochs, freqs=freqs,
n_cycles=freqs / 2.,
time_bandwidth=4.0, picks=picks)
power_evoked = tfr_multitaper(epochs.average(), freqs=freqs,
n_cycles=freqs / 2., time_bandwidth=4.0,
return_itc=False)
# test picks argument
assert_array_almost_equal(power.data, power_picks.data)
assert_array_almost_equal(itc.data, itc_picks.data)
# one is squared magnitude of the average (evoked) and
# the other is average of the squared magnitudes (epochs PSD)
# so values shouldn't match, but shapes should
assert_array_equal(power.data.shape, power_evoked.data.shape)
assert_raises(AssertionError, assert_array_almost_equal,
power.data, power_evoked.data)
tmax = t[np.argmax(itc.data[0, freqs == 50, :])]
fmax = freqs[np.argmax(power.data[1, :, t == 0.5])]
assert_true(tmax > 0.3 and tmax < 0.7)
assert_false(np.any(itc.data < 0.))
assert_true(fmax > 40 and fmax < 60)
def test_getitem_epochsTFR():
"""Test GetEpochsMixin in the context of EpochsTFR."""
from pandas import DataFrame
# Setup for reading the raw data and select a few trials
raw = read_raw_fif(raw_fname)
events = read_events(event_fname)
n_events = 10
# create fake metadata
rng = np.random.RandomState(42)
rt = rng.uniform(size=(n_events,))
trialtypes = np.array(['face', 'place'])
trial = trialtypes[(rng.uniform(size=(n_events,)) > .5).astype(int)]
meta = DataFrame(dict(RT=rt, Trial=trial))
event_id = dict(a=1, b=2, c=3, d=4)
epochs = Epochs(raw, events[:n_events], event_id=event_id, metadata=meta,
decim=1)
freqs = np.arange(12., 17., 2.) # define frequencies of interest
n_cycles = freqs / 2. # 0.5 second time windows for all frequencies
# Choose time x (full) bandwidth product
time_bandwidth = 4.0 # With 0.5 s time windows, this gives 8 Hz smoothing
power = tfr_multitaper(epochs, freqs=freqs, n_cycles=n_cycles,
use_fft=True, time_bandwidth=time_bandwidth,
return_itc=False, average=False, n_jobs=1)
# Check that power and epochs metadata is the same
assert_metadata_equal(epochs.metadata, power.metadata)
assert_metadata_equal(epochs[::2].metadata, power[::2].metadata)
assert_metadata_equal(epochs['RT < .5'].metadata,
power['RT < .5'].metadata)
# Check that get power is functioning
assert_array_equal(power[3:6].data, power.data[3:6])
assert_array_equal(power[3:6].events, power.events[3:6])
indx_check = (power.metadata['Trial'] == 'face').nonzero()
assert_array_equal(power['Trial == "face"'].events,
power.events[indx_check])
assert_array_equal(power['Trial == "face"'].data,
power.data[indx_check])
# Check that the wrong Key generates a Key Error for Metadata search
with pytest.raises(KeyError):
power['Trialz == "place"']
# Test length function
assert len(power) == n_events
assert len(power[3:6]) == 3
# Test iteration function
for ind, power_ep in enumerate(power):
assert_array_equal(power_ep, power.data[ind])
if ind == 5:
break
# Test that current state is maintained
assert_array_equal(power.next(), power.data[ind + 1])
def test_tfr_multitaper():
""" Some tests for tfr_multitaper() """
sfreq = 200.0
ch_names = ['SIM0001', 'SIM0002', 'SIM0003']
ch_types = ['grad', 'grad', 'grad']
info = create_info(ch_names=ch_names, sfreq=sfreq, ch_types=ch_types)
n_times = int(sfreq) # Second long epochs
n_epochs = 3
seed = 42
rng = np.random.RandomState(seed)
noise = 0.1 * rng.randn(n_epochs, len(ch_names), n_times)
t = np.arange(n_times, dtype=np.float) / sfreq
signal = np.sin(np.pi * 2. * 50. * t) # 50 Hz sinusoid signal
signal[np.logical_or(t < 0.45, t > 0.55)] = 0. # Hard windowing
on_time = np.logical_and(t >= 0.45, t <= 0.55)
signal[on_time] *= np.hanning(on_time.sum()) # Ramping
dat = noise + signal
reject = dict(grad=4000.)
events = np.empty((n_epochs, 3))
first_event_sample = 100
event_id = dict(sin50hz=1)
for k in range(n_epochs):
events[k, :] = first_event_sample + k * n_times, 0, event_id['sin50hz']
epochs = EpochsArray(data=dat, info=info, events=events, event_id=event_id,
reject=reject)
freqs = np.arange(5, 100, 3, dtype=np.float)
power, itc = tfr_multitaper(epochs, freqs=freqs, n_cycles=freqs / 2.,
time_bandwidth=4.0)
tmax = t[np.argmax(itc.data[0, freqs == 50, :])]
fmax = freqs[np.argmax(power.data[1, :, t == 0.5])]
assert_true(tmax > 0.3 and tmax < 0.7)
assert_false(np.any(itc.data < 0.))
assert_true(fmax > 40 and fmax < 60)
def test_tfr_multitaper():
"""Test tfr_multitaper."""
sfreq = 200.0
ch_names = ['SIM0001', 'SIM0002']
ch_types = ['grad', 'grad']
info = create_info(ch_names=ch_names, sfreq=sfreq, ch_types=ch_types)
n_times = int(sfreq) # Second long epochs
n_epochs = 3
seed = 42
rng = np.random.RandomState(seed)
noise = 0.1 * rng.randn(n_epochs, len(ch_names), n_times)
t = np.arange(n_times, dtype=np.float) / sfreq
signal = np.sin(np.pi * 2. * 50. * t) # 50 Hz sinusoid signal
signal[np.logical_or(t < 0.45, t > 0.55)] = 0. # Hard windowing
on_time = np.logical_and(t >= 0.45, t <= 0.55)
signal[on_time] *= np.hanning(on_time.sum()) # Ramping
dat = noise + signal
reject = dict(grad=4000.)
events = np.empty((n_epochs, 3), int)
first_event_sample = 100
event_id = dict(sin50hz=1)
for k in range(n_epochs):
events[k, :] = first_event_sample + k * n_times, 0, event_id['sin50hz']
epochs = EpochsArray(data=dat, info=info, events=events, event_id=event_id,
reject=reject)
freqs = np.arange(35, 70, 5, dtype=np.float)
power, itc = tfr_multitaper(epochs, freqs=freqs, n_cycles=freqs / 2.,
time_bandwidth=4.0)
power2, itc2 = tfr_multitaper(epochs, freqs=freqs, n_cycles=freqs / 2.,
time_bandwidth=4.0, decim=slice(0, 2))
picks = np.arange(len(ch_names))
power_picks, itc_picks = tfr_multitaper(epochs, freqs=freqs,
n_cycles=freqs / 2.,
time_bandwidth=4.0, picks=picks)
power_epochs = tfr_multitaper(epochs, freqs=freqs,
n_cycles=freqs / 2., time_bandwidth=4.0,
return_itc=False, average=False)
power_averaged = power_epochs.average()
power_evoked = tfr_multitaper(epochs.average(), freqs=freqs,
n_cycles=freqs / 2., time_bandwidth=4.0,
return_itc=False, average=False).average()
print(power_evoked) # test repr for EpochsTFR
# Test channel picking
power_epochs_picked = power_epochs.copy().drop_channels(['SIM0002'])
assert_equal(power_epochs_picked.data.shape, (3, 1, 7, 200))
assert_equal(power_epochs_picked.ch_names, ['SIM0001'])
pytest.raises(ValueError, tfr_multitaper, epochs,
freqs=freqs, n_cycles=freqs / 2.,
return_itc=True, average=False)
# test picks argument
assert_array_almost_equal(power.data, power_picks.data)
assert_array_almost_equal(power.data, power_averaged.data)
assert_array_almost_equal(power.times, power_epochs.times)
assert_array_almost_equal(power.times, power_averaged.times)
assert_equal(power.nave, power_averaged.nave)
assert_equal(power_epochs.data.shape, (3, 2, 7, 200))
assert_array_almost_equal(itc.data, itc_picks.data)
# one is squared magnitude of the average (evoked) and
# the other is average of the squared magnitudes (epochs PSD)
# so values shouldn't match, but shapes should
assert_array_equal(power.data.shape, power_evoked.data.shape)
pytest.raises(AssertionError, assert_array_almost_equal,
power.data, power_evoked.data)
tmax = t[np.argmax(itc.data[0, freqs == 50, :])]
fmax = freqs[np.argmax(power.data[1, :, t == 0.5])]
assert (tmax > 0.3 and tmax < 0.7)
assert not np.any(itc.data < 0.)
assert (fmax > 40 and fmax < 60)
assert (power2.data.shape == (len(picks), len(freqs), 2))
assert (power2.data.shape == itc2.data.shape)
# Test decim parameter checks and compatibility between wavelets length
# and instance length in the time dimension.
pytest.raises(TypeError, tfr_multitaper, epochs, freqs=freqs,
n_cycles=freqs / 2., time_bandwidth=4.0, decim=(1,))
pytest.raises(ValueError, tfr_multitaper, epochs, freqs=freqs,
n_cycles=1000, time_bandwidth=4.0)
def test_getitem_epochsTFR():
"""Test GetEpochsMixin in the context of EpochsTFR."""
from pandas import DataFrame
# Setup for reading the raw data and select a few trials
raw = read_raw_fif(raw_fname)
events = read_events(event_fname)
n_events = 10
# create fake metadata
rng = np.random.RandomState(42)
rt = rng.uniform(size=(n_events, ))
trialtypes = np.array(['face', 'place'])
trial = trialtypes[(rng.uniform(size=(n_events, )) > .5).astype(int)]
meta = DataFrame(dict(RT=rt, Trial=trial))
event_id = dict(a=1, b=2, c=3, d=4)
epochs = Epochs(raw,
events[:n_events],
event_id=event_id,
metadata=meta,
decim=1)
freqs = np.arange(12., 17., 2.) # define frequencies of interest
n_cycles = freqs / 2. # 0.5 second time windows for all frequencies
# Choose time x (full) bandwidth product
time_bandwidth = 4.0 # With 0.5 s time windows, this gives 8 Hz smoothing
kwargs = dict(freqs=freqs,
n_cycles=n_cycles,
use_fft=True,
time_bandwidth=time_bandwidth,
return_itc=False,
average=False,
n_jobs=1)
power = tfr_multitaper(epochs, **kwargs)
# Check decim affects sfreq
power_decim = tfr_multitaper(epochs, decim=2, **kwargs)
assert power.info['sfreq'] / 2. == power_decim.info['sfreq']
# Check that power and epochs metadata is the same
assert_metadata_equal(epochs.metadata, power.metadata)
assert_metadata_equal(epochs[::2].metadata, power[::2].metadata)
assert_metadata_equal(epochs['RT < .5'].metadata,
power['RT < .5'].metadata)
# Check that get power is functioning
assert_array_equal(power[3:6].data, power.data[3:6])
assert_array_equal(power[3:6].events, power.events[3:6])
indx_check = (power.metadata['Trial'] == 'face')
try:
indx_check = indx_check.to_numpy()
except Exception:
pass # older Pandas
indx_check = indx_check.nonzero()
assert_array_equal(power['Trial == "face"'].events,
power.events[indx_check])
assert_array_equal(power['Trial == "face"'].data, power.data[indx_check])
# Check that the wrong Key generates a Key Error for Metadata search
with pytest.raises(KeyError):
power['Trialz == "place"']
# Test length function
assert len(power) == n_events
assert len(power[3:6]) == 3
# Test iteration function
for ind, power_ep in enumerate(power):
assert_array_equal(power_ep, power.data[ind])
if ind == 5:
break
# Test that current state is maintained
assert_array_equal(power.next(), power.data[ind + 1])
def test_tfr_multitaper():
"""Test tfr_multitaper."""
sfreq = 200.0
ch_names = ['SIM0001', 'SIM0002']
ch_types = ['grad', 'grad']
info = create_info(ch_names=ch_names, sfreq=sfreq, ch_types=ch_types)
n_times = int(sfreq) # Second long epochs
n_epochs = 3
seed = 42
rng = np.random.RandomState(seed)
noise = 0.1 * rng.randn(n_epochs, len(ch_names), n_times)
t = np.arange(n_times, dtype=np.float) / sfreq
signal = np.sin(np.pi * 2. * 50. * t) # 50 Hz sinusoid signal
signal[np.logical_or(t < 0.45, t > 0.55)] = 0. # Hard windowing
on_time = np.logical_and(t >= 0.45, t <= 0.55)
signal[on_time] *= np.hanning(on_time.sum()) # Ramping
dat = noise + signal
reject = dict(grad=4000.)
events = np.empty((n_epochs, 3), int)
first_event_sample = 100
event_id = dict(sin50hz=1)
for k in range(n_epochs):
events[k, :] = first_event_sample + k * n_times, 0, event_id['sin50hz']
epochs = EpochsArray(data=dat,
info=info,
events=events,
event_id=event_id,
reject=reject)
freqs = np.arange(35, 70, 5, dtype=np.float)
power, itc = tfr_multitaper(epochs,
freqs=freqs,
n_cycles=freqs / 2.,
time_bandwidth=4.0)
power2, itc2 = tfr_multitaper(epochs,
freqs=freqs,
n_cycles=freqs / 2.,
time_bandwidth=4.0,
decim=slice(0, 2))
picks = np.arange(len(ch_names))
power_picks, itc_picks = tfr_multitaper(epochs,
freqs=freqs,
n_cycles=freqs / 2.,
time_bandwidth=4.0,
picks=picks)
power_epochs = tfr_multitaper(epochs,
freqs=freqs,
n_cycles=freqs / 2.,
time_bandwidth=4.0,
return_itc=False,
average=False)
power_averaged = power_epochs.average()
power_evoked = tfr_multitaper(epochs.average(),
freqs=freqs,
n_cycles=freqs / 2.,
time_bandwidth=4.0,
return_itc=False,
average=False).average()
print(power_evoked) # test repr for EpochsTFR
# Test channel picking
power_epochs_picked = power_epochs.copy().drop_channels(['SIM0002'])
assert_equal(power_epochs_picked.data.shape, (3, 1, 7, 200))
assert_equal(power_epochs_picked.ch_names, ['SIM0001'])
pytest.raises(ValueError,
tfr_multitaper,
epochs,
freqs=freqs,
n_cycles=freqs / 2.,
return_itc=True,
average=False)
# test picks argument
assert_array_almost_equal(power.data, power_picks.data)
assert_array_almost_equal(power.data, power_averaged.data)
assert_array_almost_equal(power.times, power_epochs.times)
assert_array_almost_equal(power.times, power_averaged.times)
assert_equal(power.nave, power_averaged.nave)
assert_equal(power_epochs.data.shape, (3, 2, 7, 200))
assert_array_almost_equal(itc.data, itc_picks.data)
# one is squared magnitude of the average (evoked) and
# the other is average of the squared magnitudes (epochs PSD)
# so values shouldn't match, but shapes should
assert_array_equal(power.data.shape, power_evoked.data.shape)
pytest.raises(AssertionError, assert_array_almost_equal, power.data,
power_evoked.data)
tmax = t[np.argmax(itc.data[0, freqs == 50, :])]
fmax = freqs[np.argmax(power.data[1, :, t == 0.5])]
assert (tmax > 0.3 and tmax < 0.7)
assert not np.any(itc.data < 0.)
assert (fmax > 40 and fmax < 60)
assert (power2.data.shape == (len(picks), len(freqs), 2))
assert (power2.data.shape == itc2.data.shape)
# Test decim parameter checks and compatibility between wavelets length
# and instance length in the time dimension.
pytest.raises(TypeError,
tfr_multitaper,
epochs,
freqs=freqs,
n_cycles=freqs / 2.,
time_bandwidth=4.0,
decim=(1, ))
pytest.raises(ValueError,
tfr_multitaper,
epochs,
freqs=freqs,
n_cycles=1000,
time_bandwidth=4.0)
# Test invalid frequency arguments
with pytest.raises(ValueError, match=" 'freqs' must be greater than 0"):
tfr_multitaper(epochs, freqs=np.arange(0, 3), n_cycles=7)
with pytest.raises(ValueError, match=" 'freqs' must be greater than 0"):
tfr_multitaper(epochs, freqs=np.arange(-4, -1), n_cycles=7)
def test_tfr_multitaper():
"""Test tfr_multitaper"""
sfreq = 200.0
ch_names = ['SIM0001', 'SIM0002', 'SIM0003']
ch_types = ['grad', 'grad', 'grad']
info = create_info(ch_names=ch_names, sfreq=sfreq, ch_types=ch_types)
n_times = int(sfreq) # Second long epochs
n_epochs = 3
seed = 42
rng = np.random.RandomState(seed)
noise = 0.1 * rng.randn(n_epochs, len(ch_names), n_times)
t = np.arange(n_times, dtype=np.float) / sfreq
signal = np.sin(np.pi * 2. * 50. * t) # 50 Hz sinusoid signal
signal[np.logical_or(t < 0.45, t > 0.55)] = 0. # Hard windowing
on_time = np.logical_and(t >= 0.45, t <= 0.55)
signal[on_time] *= np.hanning(on_time.sum()) # Ramping
dat = noise + signal
reject = dict(grad=4000.)
events = np.empty((n_epochs, 3), int)
first_event_sample = 100
event_id = dict(sin50hz=1)
for k in range(n_epochs):
events[k, :] = first_event_sample + k * n_times, 0, event_id['sin50hz']
epochs = EpochsArray(data=dat,
info=info,
events=events,
event_id=event_id,
reject=reject)
freqs = np.arange(5, 100, 3, dtype=np.float)
power, itc = tfr_multitaper(epochs,
freqs=freqs,
n_cycles=freqs / 2.,
time_bandwidth=4.0)
picks = np.arange(len(ch_names))
power_picks, itc_picks = tfr_multitaper(epochs,
freqs=freqs,
n_cycles=freqs / 2.,
time_bandwidth=4.0,
picks=picks)
power_evoked = tfr_multitaper(epochs.average(),
freqs=freqs,
n_cycles=freqs / 2.,
time_bandwidth=4.0,
return_itc=False)
# test picks argument
assert_array_almost_equal(power.data, power_picks.data)
assert_array_almost_equal(itc.data, itc_picks.data)
# one is squared magnitude of the average (evoked) and
# the other is average of the squared magnitudes (epochs PSD)
# so values shouldn't match, but shapes should
assert_array_equal(power.data.shape, power_evoked.data.shape)
assert_raises(AssertionError, assert_array_almost_equal, power.data,
power_evoked.data)
tmax = t[np.argmax(itc.data[0, freqs == 50, :])]
fmax = freqs[np.argmax(power.data[1, :, t == 0.5])]
assert_true(tmax > 0.3 and tmax < 0.7)
assert_false(np.any(itc.data < 0.))
assert_true(fmax > 40 and fmax < 60)