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from itertools import product
import datetime
import os.path as op
import re
import numpy as np
from numpy.testing import (assert_array_equal, assert_equal, assert_allclose)
import pytest
import matplotlib.pyplot as plt
from scipy.signal import morlet2
import mne
from mne import (Epochs, read_events, pick_types, create_info, EpochsArray,
Info, Transform)
from mne.io import read_raw_fif
from mne.utils import (requires_version, requires_pandas, grand_average,
catch_logging)
from mne.time_frequency.tfr import (morlet, tfr_morlet, _make_dpss,
tfr_multitaper, AverageTFR, read_tfrs,
write_tfrs, combine_tfr, cwt, _compute_tfr,
EpochsTFR, fwhm)
from mne.time_frequency import tfr_array_multitaper, tfr_array_morlet
from mne.viz.utils import _fake_click, _fake_keypress, _fake_scroll
from mne.tests.test_epochs import assert_metadata_equal
data_path = op.join(op.dirname(__file__), '..', '..', 'io', 'tests', 'data')
raw_fname = op.join(data_path, 'test_raw.fif')
event_fname = op.join(data_path, 'test-eve.fif')
raw_ctf_fname = op.join(data_path, 'test_ctf_raw.fif')
def test_tfr_ctf():
"""Test that TFRs can be calculated on CTF data."""
raw = read_raw_fif(raw_ctf_fname).crop(0, 1)
raw.apply_gradient_compensation(3)
events = mne.make_fixed_length_events(raw, duration=0.5)
epochs = mne.Epochs(raw, events)
for method in (tfr_multitaper, tfr_morlet):
method(epochs, [10], 1) # smoke test
@pytest.mark.parametrize('sfreq', [1000., 100 + np.pi])
@pytest.mark.parametrize('freq', [10., np.pi])
@pytest.mark.parametrize('n_cycles', [7, 2])
def test_morlet(sfreq, freq, n_cycles):
"""Test morlet with and without zero mean."""
Wz = morlet(sfreq, freq, n_cycles, zero_mean=True)
W = morlet(sfreq, freq, n_cycles, zero_mean=False)
assert np.abs(np.mean(np.real(Wz))) < 1e-5
if n_cycles == 2:
assert np.abs(np.mean(np.real(W))) > 1e-3
else:
assert np.abs(np.mean(np.real(W))) < 1e-5
assert_allclose(np.linalg.norm(W), np.sqrt(2), atol=1e-6)
# Convert to SciPy nomenclature and compare
M = len(W)
w = n_cycles
s = w * sfreq / (2 * freq * np.pi) # from SciPy docs
Ws = morlet2(M, s, w) * np.sqrt(2)
assert_allclose(W, Ws)
# Check FWHM
fwhm_formula = fwhm(freq, n_cycles)
half_max = np.abs(W).max() / 2.
fwhm_empirical = (np.abs(W) >= half_max).sum() / sfreq
# Could be off by a few samples
assert_allclose(fwhm_formula, fwhm_empirical, atol=3 / sfreq)
def test_time_frequency():
"""Test time-frequency transform (PSD and ITC)."""
# Set parameters
event_id = 1
tmin = -0.2
tmax = 0.498 # Allows exhaustive decimation testing
# Setup for reading the raw data
raw = read_raw_fif(raw_fname)
events = read_events(event_fname)
include = []
exclude = raw.info['bads'] + ['MEG 2443', 'EEG 053'] # bads + 2 more
# picks MEG gradiometers
picks = pick_types(raw.info, meg='grad', eeg=False,
stim=False, include=include, exclude=exclude)
picks = picks[:2]
epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks)
data = epochs.get_data()
times = epochs.times
nave = len(data)
epochs_nopicks = Epochs(raw, events, event_id, tmin, tmax)
freqs = np.arange(6, 20, 5) # define frequencies of interest
n_cycles = freqs / 4.
# Test first with a single epoch
power, itc = tfr_morlet(epochs[0], freqs=freqs, n_cycles=n_cycles,
use_fft=True, return_itc=True)
# Now compute evoked
evoked = epochs.average()
pytest.raises(ValueError, tfr_morlet, evoked, freqs, 1., return_itc=True)
power, itc = tfr_morlet(epochs, freqs=freqs, n_cycles=n_cycles,
use_fft=True, return_itc=True)
power_, itc_ = tfr_morlet(epochs, freqs=freqs, n_cycles=n_cycles,
use_fft=True, return_itc=True, decim=slice(0, 2))
# Test picks argument and average parameter
pytest.raises(ValueError, tfr_morlet, epochs, freqs=freqs,
n_cycles=n_cycles, return_itc=True, average=False)
power_picks, itc_picks = \
tfr_morlet(epochs_nopicks,
freqs=freqs, n_cycles=n_cycles, use_fft=True,
return_itc=True, picks=picks, average=True)
epochs_power_picks = \
tfr_morlet(epochs_nopicks,
freqs=freqs, n_cycles=n_cycles, use_fft=True,
return_itc=False, picks=picks, average=False)
assert_allclose(
epochs_power_picks.data[0, 0, 0, 0], 9.130315e-23,
rtol=1e-4)
power_picks_avg = epochs_power_picks.average()
# the actual data arrays here are equivalent, too...
assert_allclose(power.data, power_picks.data)
assert_allclose(power.data, power_picks_avg.data)
assert_allclose(itc.data, itc_picks.data)
# test on evoked
power_evoked = tfr_morlet(evoked, freqs, n_cycles, use_fft=True,
return_itc=False)
# 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)
with pytest.raises(AssertionError, match='Not equal to tolerance'):
assert_allclose(power.data, power_evoked.data)
# complex output
with pytest.raises(ValueError, match='must be "power" if average=True'):
tfr_morlet(epochs, freqs, n_cycles, return_itc=False, average=True,
output='complex')
with pytest.raises(ValueError, match='Inter-trial coher.*average=False'):
tfr_morlet(epochs, freqs, n_cycles, return_itc=True, average=False,
output='complex')
epochs_power_complex = tfr_morlet(
epochs, freqs, n_cycles, return_itc=False, average=False,
output='complex')
epochs_amplitude_2 = abs(epochs_power_complex)
epochs_amplitude_3 = epochs_amplitude_2.copy()
epochs_amplitude_3.data[:] = np.inf # test that it's actually copied
# test that the power computed via `complex` is equivalent to power
# computed within the method.
assert_allclose(epochs_amplitude_2.data**2, epochs_power_picks.data)
# test that averaging power across tapers when multitaper with
# output='complex' gives the same as output='power'
epoch_data = epochs.get_data()
multitaper_power = tfr_array_multitaper(
epoch_data, epochs.info['sfreq'], freqs, n_cycles,
output="power")
multitaper_complex = tfr_array_multitaper(
epoch_data, epochs.info['sfreq'], freqs, n_cycles,
output="complex")
taper_dim = 2
power_from_complex = (multitaper_complex * multitaper_complex.conj()
).real.mean(axis=taper_dim)
assert_allclose(power_from_complex, multitaper_power)
print(itc) # test repr
print(itc.ch_names) # test property
itc += power # test add
itc -= power # test sub
ret = itc * 23 # test mult
itc = ret / 23 # test dic
power = power.apply_baseline(baseline=(-0.1, 0), mode='logratio')
assert power.baseline == (-0.1, 0)
assert 'meg' in power
assert 'grad' in power
assert 'mag' not in power
assert 'eeg' not in power
assert power.nave == nave
assert itc.nave == nave
assert (power.data.shape == (len(picks), len(freqs), len(times)))
assert (power.data.shape == itc.data.shape)
assert (power_.data.shape == (len(picks), len(freqs), 2))
assert (power_.data.shape == itc_.data.shape)
assert (np.sum(itc.data >= 1) == 0)
assert (np.sum(itc.data <= 0) == 0)
# grand average
itc2 = itc.copy()
itc2.info['bads'] = [itc2.ch_names[0]] # test channel drop
gave = grand_average([itc2, itc])
assert gave.data.shape == (itc2.data.shape[0] - 1,
itc2.data.shape[1],
itc2.data.shape[2])
assert itc2.ch_names[1:] == gave.ch_names
assert gave.nave == 2
itc2.drop_channels(itc2.info["bads"])
assert_allclose(gave.data, itc2.data)
itc2.data = np.ones(itc2.data.shape)
itc.data = np.zeros(itc.data.shape)
itc2.nave = 2
itc.nave = 1
itc.drop_channels([itc.ch_names[0]])
combined_itc = combine_tfr([itc2, itc])
assert_allclose(combined_itc.data,
np.ones(combined_itc.data.shape) * 2 / 3)
# more tests
power, itc = tfr_morlet(epochs, freqs=freqs, n_cycles=2, use_fft=False,
return_itc=True)
assert (power.data.shape == (len(picks), len(freqs), len(times)))
assert (power.data.shape == itc.data.shape)
assert (np.sum(itc.data >= 1) == 0)
assert (np.sum(itc.data <= 0) == 0)
tfr = tfr_morlet(epochs[0], freqs, use_fft=True, n_cycles=2, average=False,
return_itc=False)
tfr_data = tfr.data[0]
assert (tfr_data.shape == (len(picks), len(freqs), len(times)))
tfr2 = tfr_morlet(epochs[0], freqs, use_fft=True, n_cycles=2,
decim=slice(0, 2), average=False,
return_itc=False).data[0]
assert (tfr2.shape == (len(picks), len(freqs), 2))
single_power = tfr_morlet(epochs, freqs, 2, average=False,
return_itc=False).data
single_power2 = tfr_morlet(epochs, freqs, 2, decim=slice(0, 2),
average=False, return_itc=False).data
single_power3 = tfr_morlet(epochs, freqs, 2, decim=slice(1, 3),
average=False, return_itc=False).data
single_power4 = tfr_morlet(epochs, freqs, 2, decim=slice(2, 4),
average=False, return_itc=False).data
assert_allclose(np.mean(single_power, axis=0), power.data)
assert_allclose(np.mean(single_power2, axis=0), power.data[:, :, :2])
assert_allclose(np.mean(single_power3, axis=0), power.data[:, :, 1:3])
assert_allclose(np.mean(single_power4, axis=0), power.data[:, :, 2:4])
power_pick = power.pick_channels(power.ch_names[:10:2])
assert_equal(len(power_pick.ch_names), len(power.ch_names[:10:2]))
assert_equal(power_pick.data.shape[0], len(power.ch_names[:10:2]))
power_drop = power.drop_channels(power.ch_names[1:10:2])
assert_equal(power_drop.ch_names, power_pick.ch_names)
assert_equal(power_pick.data.shape[0], len(power_drop.ch_names))
power_pick, power_drop = mne.equalize_channels([power_pick, power_drop])
assert_equal(power_pick.ch_names, power_drop.ch_names)
assert_equal(power_pick.data.shape, power_drop.data.shape)
# Test decimation:
# 2: multiple of len(times) even
# 3: multiple odd
# 8: not multiple, even
# 9: not multiple, odd
for decim in [2, 3, 8, 9]:
for use_fft in [True, False]:
power, itc = tfr_morlet(epochs, freqs=freqs, n_cycles=2,
use_fft=use_fft, return_itc=True,
decim=decim)
assert_equal(power.data.shape[2],
np.ceil(float(len(times)) / decim))
freqs = list(range(50, 55))
decim = 2
_, n_chan, n_time = data.shape
tfr = tfr_morlet(epochs[0], freqs, 2., decim=decim, average=False,
return_itc=False).data[0]
assert_equal(tfr.shape, (n_chan, len(freqs), n_time // decim))
# Test cwt modes
Ws = morlet(512, [10, 20], n_cycles=2)
pytest.raises(ValueError, cwt, data[0, :, :], Ws, mode='foo')
for use_fft in [True, False]:
for mode in ['same', 'valid', 'full']:
cwt(data[0], Ws, use_fft=use_fft, mode=mode)
# Test invalid frequency arguments
with pytest.raises(ValueError, match=" 'freqs' must be greater than 0"):
tfr_morlet(epochs, freqs=np.arange(0, 3), n_cycles=7)
with pytest.raises(ValueError, match=" 'freqs' must be greater than 0"):
tfr_morlet(epochs, freqs=np.arange(-4, -1), n_cycles=7)
# Test decim parameter checks
pytest.raises(TypeError, tfr_morlet, epochs, freqs=freqs,
n_cycles=n_cycles, use_fft=True, return_itc=True,
decim='decim')
# When convolving in time, wavelets must not be longer than the data
pytest.raises(ValueError, cwt, data[0, :, :Ws[0].size - 1], Ws,
use_fft=False)
with pytest.warns(UserWarning, match='one of the wavelets.*is longer'):
cwt(data[0, :, :Ws[0].size - 1], Ws, use_fft=True)
# Check for off-by-one errors when using wavelets with an even number of
# samples
psd = cwt(data[0], [Ws[0][:-1]], use_fft=False, mode='full')
assert_equal(psd.shape, (2, 1, 420))
def test_dpsswavelet():
"""Test DPSS tapers."""
freqs = np.arange(5, 25, 3)
Ws = _make_dpss(1000, freqs=freqs, n_cycles=freqs / 2., time_bandwidth=4.0,
zero_mean=True)
assert (len(Ws) == 3) # 3 tapers expected
# Check that zero mean is true
assert (np.abs(np.mean(np.real(Ws[0][0]))) < 1e-5)
assert (len(Ws[0]) == len(freqs)) # As many wavelets as asked for
@pytest.mark.slowtest
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.float64) / 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.float64)
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_allclose(power.data, power_picks.data)
assert_allclose(power.data, power_averaged.data)
assert_allclose(power.times, power_epochs.times)
assert_allclose(power.times, power_averaged.times)
assert_equal(power.nave, power_averaged.nave)
assert_equal(power_epochs.data.shape, (3, 2, 7, 200))
assert_allclose(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_allclose,
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_crop():
"""Test TFR cropping."""
data = np.zeros((3, 4, 5))
times = np.array([.1, .2, .3, .4, .5])
freqs = np.array([.10, .20, .30, .40])
info = mne.create_info(['MEG 001', 'MEG 002', 'MEG 003'], 1000.,
['mag', 'mag', 'mag'])
tfr = AverageTFR(info, data=data, times=times, freqs=freqs,
nave=20, comment='test', method='crazy-tfr')
tfr.crop(tmin=0.2)
assert_array_equal(tfr.times, [0.2, 0.3, 0.4, 0.5])
assert tfr.data.ndim == 3
assert tfr.data.shape[-1] == 4
tfr.crop(fmax=0.3)
assert_array_equal(tfr.freqs, [0.1, 0.2, 0.3])
assert tfr.data.ndim == 3
assert tfr.data.shape[-2] == 3
tfr.crop(tmin=0.3, tmax=0.4, fmin=0.1, fmax=0.2)
assert_array_equal(tfr.times, [0.3, 0.4])
assert tfr.data.ndim == 3
assert tfr.data.shape[-1] == 2
assert_array_equal(tfr.freqs, [0.1, 0.2])
assert tfr.data.shape[-2] == 2
def test_decim():
"""Test TFR decimation."""
data = np.zeros((3, 3, 3, 1000))
times = np.linspace(0, 1, 1000)
freqs = np.array([.10, .20, .30])
info = mne.create_info(['MEG 001', 'MEG 002', 'MEG 003'], 1000.,
['mag', 'mag', 'mag'])
with info._unlock():
info['lowpass'] = 100
tfr = EpochsTFR(info, data=data, times=times, freqs=freqs)
tfr.decimate(3)
assert tfr.times.size == 1000 // 3 + 1
assert tfr.data.shape == ((3, 3, 3, 1000 // 3 + 1))
@requires_version('h5io')
@requires_pandas
def test_io(tmp_path):
"""Test TFR IO capacities."""
from pandas import DataFrame
tempdir = str(tmp_path)
fname = op.join(tempdir, 'test-tfr.h5')
data = np.zeros((3, 2, 3))
times = np.array([.1, .2, .3])
freqs = np.array([.10, .20])
info = mne.create_info(['MEG 001', 'MEG 002', 'MEG 003'], 1000.,
['mag', 'mag', 'mag'])
with info._unlock(check_after=True):
info['meas_date'] = datetime.datetime(year=2020, month=2, day=5,
tzinfo=datetime.timezone.utc)
tfr = AverageTFR(info, data=data, times=times, freqs=freqs,
nave=20, comment='test', method='crazy-tfr')
tfr.save(fname)
tfr2 = read_tfrs(fname, condition='test')
assert isinstance(tfr2.info, Info)
assert isinstance(tfr2.info['dev_head_t'], Transform)
assert_array_equal(tfr.data, tfr2.data)
assert_array_equal(tfr.times, tfr2.times)
assert_array_equal(tfr.freqs, tfr2.freqs)
assert_equal(tfr.comment, tfr2.comment)
assert_equal(tfr.nave, tfr2.nave)
pytest.raises(IOError, tfr.save, fname)
tfr.comment = None
# test old meas_date
with info._unlock():
info['meas_date'] = (1, 2)
tfr.save(fname, overwrite=True)
assert_equal(read_tfrs(fname, condition=0).comment, tfr.comment)
tfr.comment = 'test-A'
tfr2.comment = 'test-B'
fname = op.join(tempdir, 'test2-tfr.h5')
write_tfrs(fname, [tfr, tfr2])
tfr3 = read_tfrs(fname, condition='test-A')
assert_equal(tfr.comment, tfr3.comment)
assert (isinstance(tfr.info, mne.Info))
tfrs = read_tfrs(fname, condition=None)
assert_equal(len(tfrs), 2)
tfr4 = tfrs[1]
assert_equal(tfr2.comment, tfr4.comment)
pytest.raises(ValueError, read_tfrs, fname, condition='nonono')
# Test save of EpochsTFR.
n_events = 5
data = np.zeros((n_events, 3, 2, 3))
# create fake metadata
rng = np.random.RandomState(42)
rt = np.round(rng.uniform(size=(n_events,)), 3)
trialtypes = np.array(['face', 'place'])
trial = trialtypes[(rng.uniform(size=(n_events,)) > .5).astype(int)]
meta = DataFrame(dict(RT=rt, Trial=trial))
# fake events and event_id
events = np.zeros([n_events, 3])
events[:, 0] = np.arange(n_events)
events[:, 2] = np.ones(n_events)
event_id = {'a/b': 1}
# fake selection
n_dropped_epochs = 3
selection = np.arange(n_events + n_dropped_epochs)[n_dropped_epochs:]
drop_log = tuple([('IGNORED',) for i in range(n_dropped_epochs)] +
[() for i in range(n_events)])
tfr = EpochsTFR(info, data=data, times=times, freqs=freqs,
comment='test', method='crazy-tfr', events=events,
event_id=event_id, selection=selection, drop_log=drop_log,
metadata=meta)
fname_save = fname
tfr.save(fname_save, True)
fname_write = op.join(tempdir, 'test3-tfr.h5')
write_tfrs(fname_write, tfr, overwrite=True)
for fname in [fname_save, fname_write]:
read_tfr = read_tfrs(fname)[0]
assert_array_equal(tfr.data, read_tfr.data)
assert_metadata_equal(tfr.metadata, read_tfr.metadata)
assert_array_equal(tfr.events, read_tfr.events)
assert tfr.event_id == read_tfr.event_id
assert_array_equal(tfr.selection, read_tfr.selection)
assert tfr.drop_log == read_tfr.drop_log
with pytest.raises(NotImplementedError, match='condition not supported'):
tfr = read_tfrs(fname, condition='a')
def test_init_EpochsTFR():
"""Test __init__ for EpochsTFR."""
# Create fake data:
data = np.zeros((3, 3, 3, 3))
times = np.array([.1, .2, .3])
freqs = np.array([.10, .20, .30])
info = mne.create_info(['MEG 001', 'MEG 002', 'MEG 003'], 1000.,
['mag', 'mag', 'mag'])
data_x = data[:, :, :, 0]
with pytest.raises(ValueError, match='data should be 4d. Got 3'):
tfr = EpochsTFR(info, data=data_x, times=times, freqs=freqs)
data_x = data[:, :-1, :, :]
with pytest.raises(ValueError, match="channels and data size don't"):
tfr = EpochsTFR(info, data=data_x, times=times, freqs=freqs)
times_x = times[:-1]
with pytest.raises(ValueError, match="times and data size don't match"):
tfr = EpochsTFR(info, data=data, times=times_x, freqs=freqs)
freqs_x = freqs[:-1]
with pytest.raises(ValueError, match="frequencies and data size don't"):
tfr = EpochsTFR(info, data=data, times=times_x, freqs=freqs_x)
del tfr
def test_dB_computation():
"""Test dB computation in plot methods (gh 11091)."""
ampl = 2.
data = np.full((3, 2, 3), ampl ** 2) # already power
complex_data = np.full((3, 2, 3), ampl + 0j) # ampl → power when plotting
times = np.array([.1, .2, .3])
freqs = np.array([.10, .20])
info = mne.create_info(['MEG 001', 'MEG 002', 'MEG 003'], 1000.,
['mag', 'mag', 'mag'])
kwargs = dict(times=times, freqs=freqs, nave=20, comment='test',
method='crazy-tfr')
tfr = AverageTFR(info, data=data, **kwargs)
complex_tfr = AverageTFR(info, data=complex_data, **kwargs)
plot_kwargs = dict(dB=True, combine='mean', vmin=0, vmax=7)
fig1 = tfr.plot(**plot_kwargs)[0]
fig2 = complex_tfr.plot(**plot_kwargs)[0]
# since we're fixing vmin/vmax, equal colors should mean ~equal input data
quadmesh1 = fig1.axes[0].collections[0]
quadmesh2 = fig2.axes[0].collections[0]
if hasattr(quadmesh1, '_mapped_colors'): # fails on compat/old
assert_array_equal(quadmesh1._mapped_colors, quadmesh2._mapped_colors)
def test_plot():
"""Test TFR plotting."""
data = np.zeros((3, 2, 3))
times = np.array([.1, .2, .3])
freqs = np.array([.10, .20])
info = mne.create_info(['MEG 001', 'MEG 002', 'MEG 003'], 1000.,
['mag', 'mag', 'mag'])
tfr = AverageTFR(info, data=data, times=times, freqs=freqs,
nave=20, comment='test', method='crazy-tfr')
# test title=auto, combine=None, and correct length of figure list
picks = [1, 2]
figs = tfr.plot(picks, title='auto', colorbar=False,
mask=np.ones(tfr.data.shape[1:], bool))
assert len(figs) == len(picks)
assert 'MEG' in figs[0].texts[0].get_text()
plt.close('all')
# test combine and title keyword
figs = tfr.plot(picks, title='title', colorbar=False, combine='rms',
mask=np.ones(tfr.data.shape[1:], bool))
assert len(figs) == 1
assert figs[0].texts[0].get_text() == 'title'
figs = tfr.plot(picks, title='auto', colorbar=False, combine='mean',
mask=np.ones(tfr.data.shape[1:], bool))
assert len(figs) == 1
assert figs[0].texts[0].get_text() == 'Mean of 2 sensors'
figs = tfr.plot(
picks,
title='auto',
colorbar=False,
combine=lambda x: x.mean(axis=0),
mask=np.ones(tfr.data.shape[1:], bool),
)
assert len(figs) == 1
with pytest.raises(ValueError, match="Invalid value for the 'combine'"):
tfr.plot(picks, colorbar=False, combine='something',
mask=np.ones(tfr.data.shape[1:], bool))
with pytest.raises(RuntimeError, match="must operate on a single"):
tfr.plot(picks, combine=lambda x, y: x.mean(axis=0))
with pytest.raises(
RuntimeError,
match=re.escape("of shape (n_freqs, n_times).")
):
tfr.plot(picks, combine=lambda x: x.mean(axis=0, keepdims=True))
with pytest.raises(
RuntimeError,
match=re.escape("return a numpy array of shape (n_freqs, n_times).")
):
tfr.plot(picks, combine=lambda x: 101)
plt.close('all')
# test axes argument - first with list of axes
ax = plt.subplot2grid((2, 2), (0, 0))
ax2 = plt.subplot2grid((2, 2), (0, 1))
ax3 = plt.subplot2grid((2, 2), (1, 0))
figs = tfr.plot(picks=[0, 1, 2], axes=[ax, ax2, ax3])
assert len(figs) == len([ax, ax2, ax3])
# and as a single axes
figs = tfr.plot(picks=[0], axes=ax)
assert len(figs) == 1
plt.close('all')
# and invalid inputs
with pytest.raises(ValueError, match='axes must be None'):
tfr.plot(picks, colorbar=False, axes={},
mask=np.ones(tfr.data.shape[1:], bool))
# different number of axes and picks should throw a RuntimeError
with pytest.raises(RuntimeError, match='There must be an axes'):
tfr.plot(picks=[0], colorbar=False, axes=[ax, ax2],
mask=np.ones(tfr.data.shape[1:], bool))
tfr.plot_topo(picks=[1, 2])
plt.close('all')
# interactive mode on by default
fig = tfr.plot(picks=[1], cmap='RdBu_r')[0]
_fake_keypress(fig, 'up')
_fake_keypress(fig, ' ')
_fake_keypress(fig, 'down')
_fake_keypress(fig, ' ')
_fake_keypress(fig, '+')
_fake_keypress(fig, ' ')
_fake_keypress(fig, '-')
_fake_keypress(fig, ' ')
_fake_keypress(fig, 'pageup')
_fake_keypress(fig, ' ')
_fake_keypress(fig, 'pagedown')
cbar = fig.get_axes()[0].CB # Fake dragging with mouse.
ax = cbar.cbar.ax
_fake_click(fig, ax, (0.1, 0.1))
_fake_click(fig, ax, (0.1, 0.2), kind='motion')
_fake_click(fig, ax, (0.1, 0.3), kind='release')
_fake_click(fig, ax, (0.1, 0.1), button=3)
_fake_click(fig, ax, (0.1, 0.2), button=3, kind='motion')
_fake_click(fig, ax, (0.1, 0.3), kind='release')
_fake_scroll(fig, 0.5, 0.5, -0.5) # scroll down
_fake_scroll(fig, 0.5, 0.5, 0.5) # scroll up
plt.close('all')
def test_plot_joint():
"""Test TFR joint plotting."""
raw = read_raw_fif(raw_fname)
times = np.linspace(-0.1, 0.1, 200)
n_freqs = 3
nave = 1
rng = np.random.RandomState(42)
data = rng.randn(len(raw.ch_names), n_freqs, len(times))
tfr = AverageTFR(raw.info, data, times, np.arange(n_freqs), nave)
topomap_args = {'res': 8, 'contours': 0, 'sensors': False}
for combine in ('mean', 'rms', lambda x: x.mean(axis=0)):
with catch_logging() as log:
tfr.plot_joint(title='auto', colorbar=True,
combine=combine, topomap_args=topomap_args,
verbose='debug')
plt.close('all')
log = log.getvalue()
assert 'Plotting topomap for grad data' in log
# check various timefreqs
for timefreqs in (
{(tfr.times[0], tfr.freqs[1]): (0.1, 0.5),
(tfr.times[-1], tfr.freqs[-1]): (0.2, 0.6)},
[(tfr.times[1], tfr.freqs[1])]):
tfr.plot_joint(timefreqs=timefreqs, topomap_args=topomap_args)
plt.close('all')
# test bad timefreqs
timefreqs = ([(-100, 1)], tfr.times[1], [1],
[(tfr.times[1], tfr.freqs[1], tfr.freqs[1])])
for these_timefreqs in timefreqs:
pytest.raises(ValueError, tfr.plot_joint, these_timefreqs)
# test that the object is not internally modified
tfr_orig = tfr.copy()
tfr.plot_joint(baseline=(0, None), exclude=[tfr.ch_names[0]],
topomap_args=topomap_args)
plt.close('all')
assert_array_equal(tfr.data, tfr_orig.data)
assert set(tfr.ch_names) == set(tfr_orig.ch_names)
assert set(tfr.times) == set(tfr_orig.times)
# test tfr with picked channels
tfr.pick_channels(tfr.ch_names[:-1])
tfr.plot_joint(title='auto', colorbar=True, topomap_args=topomap_args)
def test_add_channels():
"""Test tfr splitting / re-appending channel types."""
data = np.zeros((6, 2, 3))
times = np.array([.1, .2, .3])
freqs = np.array([.10, .20])
info = mne.create_info(
['MEG 001', 'MEG 002', 'MEG 003', 'EEG 001', 'EEG 002', 'STIM 001'],
1000., ['mag', 'mag', 'mag', 'eeg', 'eeg', 'stim'])
tfr = AverageTFR(info, data=data, times=times, freqs=freqs,
nave=20, comment='test', method='crazy-tfr')
tfr_eeg = tfr.copy().pick_types(meg=False, eeg=True)
tfr_meg = tfr.copy().pick_types(meg=True)
tfr_stim = tfr.copy().pick_types(meg=False, stim=True)
tfr_eeg_meg = tfr.copy().pick_types(meg=True, eeg=True)
tfr_new = tfr_meg.copy().add_channels([tfr_eeg, tfr_stim])
assert all(ch in tfr_new.ch_names
for ch in tfr_stim.ch_names + tfr_meg.ch_names)
tfr_new = tfr_meg.copy().add_channels([tfr_eeg])
have_all = all(ch in tfr_new.ch_names
for ch in tfr.ch_names if ch != 'STIM 001')
assert have_all
assert_array_equal(tfr_new.data, tfr_eeg_meg.data)
assert all(ch not in tfr_new.ch_names for ch in tfr_stim.ch_names)
# Now test errors
tfr_badsf = tfr_eeg.copy()
with tfr_badsf.info._unlock():
tfr_badsf.info['sfreq'] = 3.1415927
tfr_eeg = tfr_eeg.crop(.1, .1)
pytest.raises(RuntimeError, tfr_meg.add_channels, [tfr_badsf])
pytest.raises(ValueError, tfr_meg.add_channels, [tfr_eeg])
pytest.raises(ValueError, tfr_meg.add_channels, [tfr_meg])
pytest.raises(TypeError, tfr_meg.add_channels, tfr_badsf)
def test_compute_tfr():
"""Test _compute_tfr function."""
# Set parameters
event_id = 1
tmin = -0.2
tmax = 0.498 # Allows exhaustive decimation testing
# Setup for reading the raw data
raw = read_raw_fif(raw_fname)
events = read_events(event_fname)
exclude = raw.info['bads'] + ['MEG 2443', 'EEG 053'] # bads + 2 more
# picks MEG gradiometers
picks = pick_types(raw.info, meg='grad', eeg=False,
stim=False, include=[], exclude=exclude)
picks = picks[:2]
epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks)
data = epochs.get_data()
sfreq = epochs.info['sfreq']
freqs = np.arange(10, 20, 3).astype(float)
# Check all combination of options
for func, use_fft, zero_mean, output in product(
(tfr_array_multitaper, tfr_array_morlet), (False, True), (False, True),
('complex', 'power', 'phase',
'avg_power_itc', 'avg_power', 'itc')):
# Check runs
out = func(data, sfreq=sfreq, freqs=freqs, use_fft=use_fft,
zero_mean=zero_mean, n_cycles=2., output=output)
# Check shapes
if func == tfr_array_multitaper and output in ['complex', 'phase']:
n_tapers = 3
shape = np.r_[data.shape[:2], n_tapers, len(freqs), data.shape[2]]
else:
shape = np.r_[data.shape[:2], len(freqs), data.shape[2]]
if ('avg' in output) or ('itc' in output):
assert_array_equal(shape[1:], out.shape)
else:
assert_array_equal(shape, out.shape)
# Check types
if output in ('complex', 'avg_power_itc'):
assert_equal(np.complex128, out.dtype)
else:
assert_equal(np.float64, out.dtype)
assert (np.all(np.isfinite(out)))
# Check errors params
for _data in (None, 'foo', data[0]):
pytest.raises(ValueError, _compute_tfr, _data, freqs, sfreq)
for _freqs in (None, 'foo', [[0]]):
pytest.raises(ValueError, _compute_tfr, data, _freqs, sfreq)
for _sfreq in (None, 'foo'):
pytest.raises(ValueError, _compute_tfr, data, freqs, _sfreq)
for key in ('output', 'method', 'use_fft', 'decim', 'n_jobs'):
for value in (None, 'foo'):
kwargs = {key: value} # FIXME pep8
pytest.raises(ValueError, _compute_tfr, data, freqs, sfreq,
**kwargs)
with pytest.raises(ValueError, match='above Nyquist'):
_compute_tfr(data, [sfreq], sfreq)
# No time_bandwidth param in morlet
pytest.raises(ValueError, _compute_tfr, data, freqs, sfreq,
method='morlet', time_bandwidth=1)
# Inter-trial coherence tests
out = _compute_tfr(data, freqs, sfreq, output='itc', n_cycles=2.)
assert np.sum(out >= 1) == 0
assert np.sum(out <= 0) == 0
# Check decim shapes
# 2: multiple of len(times) even
# 3: multiple odd
# 8: not multiple, even
# 9: not multiple, odd
for decim in (2, 3, 8, 9, slice(0, 2), slice(1, 3), slice(2, 4)):
_decim = slice(None, None, decim) if isinstance(decim, int) else decim
n_time = len(np.arange(data.shape[2])[_decim])
shape = np.r_[data.shape[:2], len(freqs), n_time]
for method in ('multitaper', 'morlet'):
# Single trials
out = _compute_tfr(data, freqs, sfreq, method=method, decim=decim,
output='power', n_cycles=2.)
assert_array_equal(shape, out.shape)
# Averages
out = _compute_tfr(data, freqs, sfreq, method=method, decim=decim,
output='avg_power', n_cycles=2.)
assert_array_equal(shape[1:], out.shape)
@pytest.mark.parametrize('method', ('multitaper', 'morlet'))
@pytest.mark.parametrize('decim', (1, slice(1, None, 2), 3))
def test_compute_tfr_correct(method, decim):
"""Test that TFR actually gets us our freq back."""
sfreq = 1000.
t = np.arange(1000) / sfreq
f = 50.
data = np.sin(2 * np.pi * f * t)
data *= np.hanning(data.size)
data = data[np.newaxis, np.newaxis]
freqs = np.arange(10, 111, 4)
assert f in freqs
# previous n_cycles=2 gives weird results for multitaper
n_cycles = freqs * 0.25
tfr = _compute_tfr(data, freqs, sfreq, method=method, decim=decim,
n_cycles=n_cycles, output='power')[0, 0]
assert freqs[np.argmax(tfr.mean(-1))] == f
def test_averaging_epochsTFR():
"""Test that EpochsTFR averaging methods work."""
# Setup for reading the raw data
event_id = 1
tmin = -0.2
tmax = 0.498 # Allows exhaustive decimation testing
freqs = np.arange(6, 20, 5) # define frequencies of interest
n_cycles = freqs / 4.
raw = read_raw_fif(raw_fname)
# only pick a few events for speed
events = read_events(event_fname)[:4]
include = []
exclude = raw.info['bads'] + ['MEG 2443', 'EEG 053'] # bads + 2 more
# picks MEG gradiometers
picks = pick_types(raw.info, meg='grad', eeg=False,
stim=False, include=include, exclude=exclude)
picks = picks[:2]
epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks)
# Obtain EpochsTFR
power = tfr_morlet(epochs, freqs=freqs, n_cycles=n_cycles,
average=False, use_fft=True,
return_itc=False)
# Test average methods
for func, method in zip(
[np.mean, np.median, np.mean],
['mean', 'median', lambda x: np.mean(x, axis=0)]):
avgpower = power.average(method=method)
assert_array_equal(func(power.data, axis=0), avgpower.data)
with pytest.raises(RuntimeError, match='You passed a function that '
'resulted in data'):
power.average(method=np.mean)
@pytest.mark.parametrize('copy', [True, False])
def test_averaging_freqsandtimes_epochsTFR(copy):
"""Test that EpochsTFR averaging freqs methods work."""
# Setup for reading the raw data
event_id = 1
tmin = -0.2
tmax = 0.498 # Allows exhaustive decimation testing
freqs = np.arange(6, 20, 5) # define frequencies of interest
n_cycles = freqs / 4.
raw = read_raw_fif(raw_fname)
# only pick a few events for speed
events = read_events(event_fname)[:4]
include = []
exclude = raw.info['bads'] + ['MEG 2443', 'EEG 053'] # bads + 2 more
# picks MEG gradiometers
picks = pick_types(raw.info, meg='grad', eeg=False,
stim=False, include=include, exclude=exclude)
picks = picks[:2]
epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks)
# Obtain EpochsTFR
power = tfr_morlet(epochs, freqs=freqs, n_cycles=n_cycles,
average=False, use_fft=True,
return_itc=False)
# Test average methods for freqs and times
for idx, (func, method) in enumerate(zip(
[np.mean, np.median, np.mean, np.mean],
['mean', 'median', lambda x: np.mean(x, axis=2),
lambda x: np.mean(x, axis=3)])):
if idx == 3:
with pytest.raises(RuntimeError, match='You passed a function'):
avgpower = power.copy().average(method=method, dim='freqs',
copy=copy)
continue
avgpower = power.copy().average(method=method, dim='freqs', copy=copy)
assert_array_equal(func(power.data, axis=2, keepdims=True),
avgpower.data)
assert avgpower.freqs == np.mean(power.freqs)
assert isinstance(avgpower, EpochsTFR)
# average over epochs
avgpower = avgpower.average()
assert isinstance(avgpower, AverageTFR)
# Test average methods for freqs and times
for idx, (func, method) in enumerate(zip(
[np.mean, np.median, np.mean, np.mean],
['mean', 'median', lambda x: np.mean(x, axis=3),
lambda x: np.mean(x, axis=2)])):
if idx == 3:
with pytest.raises(RuntimeError, match='You passed a function'):
avgpower = power.copy().average(method=method, dim='times',
copy=copy)
continue
avgpower = power.copy().average(method=method, dim='times', copy=copy)
assert_array_equal(func(power.data, axis=-1, keepdims=True),
avgpower.data)
assert avgpower.times == np.mean(power.times)
assert isinstance(avgpower, EpochsTFR)
# average over epochs
avgpower = avgpower.average()
assert isinstance(avgpower, AverageTFR)
@requires_pandas
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)
# create fake data, test with and without dropping epochs
for n_drop_epochs in [0, 2]:
n_events = 12
# 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)
epochs.drop(np.arange(n_drop_epochs))
n_events -= n_drop_epochs
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=None)
power = tfr_multitaper(epochs, **kwargs)
# 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)
assert_array_equal(epochs.selection, power.selection)
assert epochs.drop_log == power.drop_log
# 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])
assert_array_equal(epochs.selection[3:6], power.selection[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])
# Check decim affects sfreq
power_decim = tfr_multitaper(epochs, decim=2, **kwargs)
assert power.info['sfreq'] / 2. == power_decim.info['sfreq']
@requires_pandas
def test_to_data_frame():
"""Test EpochsTFR Pandas exporter."""
# Create fake EpochsTFR data:
n_epos = 3
ch_names = ['EEG 001', 'EEG 002', 'EEG 003', 'EEG 004']
n_picks = len(ch_names)
ch_types = ['eeg'] * n_picks
n_freqs = 5
n_times = 6
data = np.random.rand(n_epos, n_picks, n_freqs, n_times)
times = np.arange(6)
srate = 1000.
freqs = np.arange(5)
events = np.zeros((n_epos, 3), dtype=int)
events[:, 0] = np.arange(n_epos)
events[:, 2] = np.arange(5, 5 + n_epos)
event_id = {k: v for v, k in zip(events[:, 2], ['ha', 'he', 'hu'])}
info = mne.create_info(ch_names, srate, ch_types)
tfr = mne.time_frequency.EpochsTFR(info, data, times, freqs,
events=events, event_id=event_id)
# test index checking
with pytest.raises(ValueError, match='options. Valid index options are'):
tfr.to_data_frame(index=['foo', 'bar'])
with pytest.raises(ValueError, match='"qux" is not a valid option'):
tfr.to_data_frame(index='qux')
with pytest.raises(TypeError, match='index must be `None` or a string '):
tfr.to_data_frame(index=np.arange(400))
# test wide format
df_wide = tfr.to_data_frame()
assert all(np.in1d(tfr.ch_names, df_wide.columns))
assert all(np.in1d(['time', 'condition', 'freq', 'epoch'],
df_wide.columns))
# test long format
df_long = tfr.to_data_frame(long_format=True)
expected = ('condition', 'epoch', 'freq', 'time', 'channel', 'ch_type',
'value')
assert set(expected) == set(df_long.columns)
assert set(tfr.ch_names) == set(df_long['channel'])
assert len(df_long) == tfr.data.size
# test long format w/ index
df_long = tfr.to_data_frame(long_format=True, index=['freq'])
del df_wide, df_long
# test whether data is in correct shape
df = tfr.to_data_frame(index=['condition', 'epoch', 'freq', 'time'])
data = tfr.data
assert_array_equal(df.values[:, 0],
data[:, 0, :, :].reshape(1, -1).squeeze())
# compare arbitrary observation:
assert (df.loc[('he', slice(None), freqs[1], times[2]), ch_names[3]].iat[0]
== data[1, 3, 1, 2])
# Check also for AverageTFR:
tfr = tfr.average()
with pytest.raises(ValueError, match='options. Valid index options are'):
tfr.to_data_frame(index=['epoch', 'condition'])
with pytest.raises(ValueError, match='"epoch" is not a valid option'):
tfr.to_data_frame(index='epoch')
with pytest.raises(TypeError, match='index must be `None` or a string '):
tfr.to_data_frame(index=np.arange(400))
# test wide format
df_wide = tfr.to_data_frame()
assert all(np.in1d(tfr.ch_names, df_wide.columns))
assert all(np.in1d(['time', 'freq'], df_wide.columns))
# test long format
df_long = tfr.to_data_frame(long_format=True)
expected = ('freq', 'time', 'channel', 'ch_type', 'value')
assert set(expected) == set(df_long.columns)
assert set(tfr.ch_names) == set(df_long['channel'])
assert len(df_long) == tfr.data.size
# test long format w/ index
df_long = tfr.to_data_frame(long_format=True, index=['freq'])
del df_wide, df_long
# test whether data is in correct shape
df = tfr.to_data_frame(index=['freq', 'time'])
data = tfr.data
assert_array_equal(df.values[:, 0],
data[0, :, :].reshape(1, -1).squeeze())
# compare arbitrary observation:
assert df.loc[(freqs[1], times[2]), ch_names[3]] == data[3, 1, 2]
@requires_pandas
@pytest.mark.parametrize('index', ('time', ['condition', 'time', 'freq'],
['freq', 'time'], ['time', 'freq'], None))
def test_to_data_frame_index(index):
"""Test index creation in epochs Pandas exporter."""
# Create fake EpochsTFR data:
n_epos = 3
ch_names = ['EEG 001', 'EEG 002', 'EEG 003', 'EEG 004']
n_picks = len(ch_names)
ch_types = ['eeg'] * n_picks
n_freqs = 5
n_times = 6
data = np.random.rand(n_epos, n_picks, n_freqs, n_times)
times = np.arange(6)
freqs = np.arange(5)
events = np.zeros((n_epos, 3), dtype=int)
events[:, 0] = np.arange(n_epos)
events[:, 2] = np.arange(5, 8)
event_id = {k: v for v, k in zip(events[:, 2], ['ha', 'he', 'hu'])}
info = mne.create_info(ch_names, 1000., ch_types)
tfr = mne.time_frequency.EpochsTFR(info, data, times, freqs,
events=events, event_id=event_id)
df = tfr.to_data_frame(picks=[0, 2, 3], index=index)
# test index order/hierarchy preservation
if not isinstance(index, list):
index = [index]
assert (df.index.names == index)
# test that non-indexed data were present as columns
non_index = list(set(['condition', 'time', 'freq', 'epoch']) - set(index))
if len(non_index):
assert all(np.in1d(non_index, df.columns))
@requires_pandas
@pytest.mark.parametrize('time_format', (None, 'ms', 'timedelta'))
def test_to_data_frame_time_format(time_format):
"""Test time conversion in epochs Pandas exporter."""
from pandas import Timedelta
n_epos = 3
ch_names = ['EEG 001', 'EEG 002', 'EEG 003', 'EEG 004']
n_picks = len(ch_names)
ch_types = ['eeg'] * n_picks
n_freqs = 5
n_times = 6
data = np.random.rand(n_epos, n_picks, n_freqs, n_times)
times = np.arange(6)
freqs = np.arange(5)
events = np.zeros((n_epos, 3), dtype=int)
events[:, 0] = np.arange(n_epos)
events[:, 2] = np.arange(5, 8)
event_id = {k: v for v, k in zip(events[:, 2], ['ha', 'he', 'hu'])}
info = mne.create_info(ch_names, 1000., ch_types)
tfr = mne.time_frequency.EpochsTFR(info, data, times, freqs,
events=events, event_id=event_id)
# test time_format
df = tfr.to_data_frame(time_format=time_format)
dtypes = {None: np.float64, 'ms': np.int64, 'timedelta': Timedelta}
assert isinstance(df['time'].iloc[0], dtypes[time_format])
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