def get_window(master: EpochsArray, config, start):
fps = config['fps']
end = start + config['window_duration'] - 1. / fps
window = master.copy().crop(start, end)
return window
def test_decim():
"""Test evoked decimation."""
rng = np.random.RandomState(0)
n_epochs, n_channels, n_times = 5, 10, 20
dec_1, dec_2 = 2, 3
decim = dec_1 * dec_2
sfreq = 1000.
sfreq_new = sfreq / decim
data = rng.randn(n_epochs, n_channels, n_times)
events = np.array([np.arange(n_epochs), [0] * n_epochs, [1] * n_epochs]).T
info = create_info(n_channels, sfreq, 'eeg')
info['lowpass'] = sfreq_new / float(decim)
epochs = EpochsArray(data, info, events)
data_epochs = epochs.copy().decimate(decim).get_data()
data_epochs_2 = epochs.copy().decimate(decim, offset=1).get_data()
data_epochs_3 = epochs.decimate(dec_1).decimate(dec_2).get_data()
assert_array_equal(data_epochs, data[:, :, ::decim])
assert_array_equal(data_epochs_2, data[:, :, 1::decim])
assert_array_equal(data_epochs, data_epochs_3)
# Now let's do it with some real data
raw = read_raw_fif(raw_fname, add_eeg_ref=False)
events = read_events(event_name)
sfreq_new = raw.info['sfreq'] / decim
raw.info['lowpass'] = sfreq_new / 4. # suppress aliasing warnings
picks = pick_types(raw.info, meg=True, eeg=True, exclude=())
epochs = Epochs(raw, events, 1, -0.2, 0.5, picks=picks, preload=True,
add_eeg_ref=False)
for offset in (0, 1):
ev_ep_decim = epochs.copy().decimate(decim, offset).average()
ev_decim = epochs.average().decimate(decim, offset)
expected_times = epochs.times[offset::decim]
assert_allclose(ev_decim.times, expected_times)
assert_allclose(ev_ep_decim.times, expected_times)
expected_data = epochs.get_data()[:, :, offset::decim].mean(axis=0)
assert_allclose(ev_decim.data, expected_data)
assert_allclose(ev_ep_decim.data, expected_data)
assert_equal(ev_decim.info['sfreq'], sfreq_new)
assert_array_equal(ev_decim.times, expected_times)
def _compute_fold(metric_fx,
targets,
train,
test,
epoch,
cv_normalize_noise=None,
mean_groups=False,
time_diag_only=False):
"""
Computes pairwise metric across time for one fold
Arguments
---------
metric_fx : either an allowed string (e.g., 'correlation') or an object
with attributes 'fit' and 'score' (similar to scikit-learn estimators)
targets : array (n_trials,)
target (condition) for each trials; they must be integers
train : array-like of int
indices of the training data
test : array-like of int
indices of the testing data
epoch : instance of mne.Epoch
cv_normalize_noise : str | None (default None)
Multivariately normalize the trials before applying the metric
(distance or classification). Normalization is performed with
cross-validation, that is the covariance matrix is estimated in the
training set, and then applied to the test set. Normalization is
always performed on single trials, thus before averaging within each
class if `mean_groups` is set to True.
Valid values for `cv_normalize_noise` are 'epoch' | 'baseline' | None:
- 'epoch' computes the covariance matrix on the entire epoch;
- 'baseline' uses only the baseline condition; it requires `epoch`
to have a valid baseline (i.e., to have performed baseline
correction)
mean_groups : bool (default False)
Whether the trials belonging to each target should be averaged prior
to running the metric. This is useful if the metric is a distance
metric. Should be set to False for classification.
time_diag_only : bool (default False)
Whether to run only for the diagonal in time,
e.g. for train_time == test_time
Returns
-------
rdms: array (n_pairwise_targets, n_pairwise_times)
the cross-validated RDM over time
targets_pairs : list of len n_pairwise_targets
the labels corresponding to each element in rdms
"""
targets = np.asarray(targets)
if targets.dtype != np.dtype('int64'):
raise ValueError("targets must be integers, "
"not {0}".format(targets.dtype))
# impose conditions in epoch as targets, so that covariance
# matrix is computed within each target
events_ = epoch.events.copy()
events_[:, 2] = targets
epoch_ = EpochsArray(epoch.get_data(),
info=epoch.info,
events=events_,
tmin=epoch.times[0])
epoch_.baseline = epoch.baseline
# get training and testing data
epoch_train = epoch_.copy()[train]
targets_train = targets[train]
assert (len(epoch_train) == len(targets_train))
epoch_test = epoch_.copy()[test]
targets_test = targets[test]
assert (len(epoch_test) == len(targets_test))
# perform multi variate noise normalization
epoch_train, epoch_test = _multiv_normalize(epoch_train, epoch_test,
cv_normalize_noise)
if mean_groups:
# average within train and test for each target
epoch_train, targets_train = mean_group(epoch_train, targets_train)
epoch_test, targets_test = mean_group(epoch_test, targets_test)
# the targets should be the same in both training and testing
# set or else we are correlating weird things together
assert_array_equal(targets_train, targets_test)
rdms = _run_metric(metric_fx,
epoch_train,
targets_train,
epoch_test,
targets_test,
time_diag_only=time_diag_only)
# return also the pairs labels. since we are taking triu, we loop first
# across rows
unique_targets = _get_unique_targets(targets_train, targets_test)
targets_pairs = []
for tr_lbl, te_lbl in _get_combinations_triu(unique_targets):
targets_pairs.append('+'.join(map(str, [tr_lbl, te_lbl])))
return rdms, targets_pairs
