############################################################################### import numpy as np param_range = np.linspace(40e-6, 200e-6, 30) ############################################################################### # Next, we can use :class:`autoreject.GlobalAutoReject` to find global # (i.e., for all channels) peak-to-peak thresholds. It is a class which # follows a :mod:`scikit-learn`-like API. To compute the Root Mean Squared # (RMSE) values at the candidate thresholds, we will use the function # :func:`autoreject.validation_curve`. ############################################################################### from autoreject import GlobalAutoReject, validation_curve _, test_scores = validation_curve( GlobalAutoReject(), epochs, y=None, param_name="thresh", param_range=param_range, cv=5, n_jobs=1) test_scores = -test_scores.mean(axis=1) best_thresh = param_range[np.argmin(test_scores)] ############################################################################### # Now let us plot the RMSE values against the candidate thresholds. ############################################################################### import matplotlib.pyplot as plt from autoreject import set_matplotlib_defaults set_matplotlib_defaults(plt) human_thresh = 80e-6 unit = r'$\mu$V'
import numpy as np # noqa param_range = np.linspace(40e-6, 200e-6, 30) ############################################################################### # Next, we can use :func:`autoreject.validation_curve` to compute the Root Mean # Squared (RMSE) values at the candidate thresholds. Under the hood, this is # using :class:`autoreject._GlobalAutoReject` to find global (i.e., for all # channels) peak-to-peak thresholds. from autoreject import validation_curve # noqa from autoreject import get_rejection_threshold # noqa _, test_scores, param_range = validation_curve(epochs, param_range=param_range, cv=5, return_param_range=True, n_jobs=1) test_scores = -test_scores.mean(axis=1) best_thresh = param_range[np.argmin(test_scores)] ############################################################################### # We can also get the best threshold more efficiently using Bayesian # optimization reject2 = get_rejection_threshold(epochs, random_state=0, cv=5) ############################################################################### # Now let us plot the RMSE values against the candidate thresholds. import matplotlib.pyplot as plt # noqa
def test_autoreject(): """Test basic _AutoReject functionality.""" event_id = None tmin, tmax = -0.2, 0.5 events = mne.find_events(raw) ########################################################################## # picking epochs include = [u'EEG %03d' % i for i in range(1, 45, 3)] picks = mne.pick_types(raw.info, meg=False, eeg=False, stim=False, eog=True, include=include, exclude=[]) epochs = mne.Epochs(raw, events, event_id, tmin, tmax, picks=picks, baseline=(None, 0), decim=10, reject=None, preload=False)[:10] ar = _AutoReject() assert_raises(ValueError, ar.fit, epochs) epochs.load_data() ar.fit(epochs) assert_true(len(ar.picks_) == len(picks) - 1) # epochs with no picks. epochs = mne.Epochs(raw, events, event_id, tmin, tmax, baseline=(None, 0), decim=10, reject=None, preload=True)[:20] # let's drop some channels to speed up pre_picks = mne.pick_types(epochs.info, meg=True, eeg=True) pre_picks = np.r_[ mne.pick_types(epochs.info, meg='mag', eeg=False)[::15], mne.pick_types(epochs.info, meg='grad', eeg=False)[::60], mne.pick_types(epochs.info, meg=False, eeg=True)[::16], mne.pick_types(epochs.info, meg=False, eeg=False, eog=True)] pick_ch_names = [epochs.ch_names[pp] for pp in pre_picks] bad_ch_names = [ epochs.ch_names[ix] for ix in range(len(epochs.ch_names)) if ix not in pre_picks ] epochs_with_bads = epochs.copy() epochs_with_bads.info['bads'] = bad_ch_names epochs.pick_channels(pick_ch_names) epochs_fit = epochs[:12] # make sure to use different size of epochs epochs_new = epochs[12:] epochs_with_bads_fit = epochs_with_bads[:12] X = epochs_fit.get_data() n_epochs, n_channels, n_times = X.shape X = X.reshape(n_epochs, -1) ar = _GlobalAutoReject() assert_raises(ValueError, ar.fit, X) ar = _GlobalAutoReject(n_channels=n_channels) assert_raises(ValueError, ar.fit, X) ar = _GlobalAutoReject(n_times=n_times) assert_raises(ValueError, ar.fit, X) ar_global = _GlobalAutoReject(n_channels=n_channels, n_times=n_times, thresh=40e-6) ar_global.fit(X) param_range = np.linspace(40e-6, 200e-6, 10) train_scores, test_scores = \ validation_curve(epochs_fit, param_range=param_range) assert len(train_scores) == len(test_scores) train_scores, test_scores, param_range = \ validation_curve(epochs_fit, return_param_range=True) assert len(train_scores) == len(test_scores) == len(param_range) assert_raises(ValueError, validation_curve, X, param_range=param_range) ########################################################################## # picking AutoReject picks = mne.pick_types(epochs.info, meg='mag', eeg=True, stim=False, eog=False, include=[], exclude=[]) non_picks = mne.pick_types(epochs.info, meg='grad', eeg=False, stim=False, eog=False, include=[], exclude=[]) ch_types = ['mag', 'eeg'] ar = _AutoReject(picks=picks) # XXX : why do we need this?? ar = AutoReject(cv=3, picks=picks, random_state=42, n_interpolate=[1, 2], consensus=[0.5, 1]) assert_raises(AttributeError, ar.fit, X) assert_raises(ValueError, ar.transform, X) assert_raises(ValueError, ar.transform, epochs) epochs_nochs = epochs_fit.copy() for ch in epochs_nochs.info['chs']: ch['loc'] = np.zeros(9) assert_raises(RuntimeError, ar.fit, epochs_nochs) ar2 = AutoReject(cv=3, picks=picks, random_state=42, n_interpolate=[1, 2], consensus=[0.5, 1], verbose='blah') assert_raises(ValueError, ar2.fit, epochs_fit) ar.fit(epochs_fit) reject_log = ar.get_reject_log(epochs_fit) for ch_type in ch_types: # test that kappa & rho are selected assert_true(ar.n_interpolate_[ch_type] in ar.n_interpolate) assert_true(ar.consensus_[ch_type] in ar.consensus) assert_true(ar.n_interpolate_[ch_type] == ar.local_reject_[ch_type].n_interpolate_[ch_type]) assert_true(ar.consensus_[ch_type] == ar.local_reject_[ch_type].consensus_[ch_type]) # test complementarity of goods and bads assert_array_equal(len(reject_log.bad_epochs), len(epochs_fit)) # test that transform does not change state of ar epochs_clean = ar.transform(epochs_fit) # apply same data assert_true(repr(ar)) assert_true(repr(ar.local_reject_)) reject_log2 = ar.get_reject_log(epochs_fit) assert_array_equal(reject_log.labels, reject_log2.labels) assert_array_equal(reject_log.bad_epochs, reject_log2.bad_epochs) assert_array_equal(reject_log.ch_names, reject_log2.ch_names) epochs_new_clean = ar.transform(epochs_new) # apply to new data reject_log_new = ar.get_reject_log(epochs_new) assert_array_equal(len(reject_log_new.bad_epochs), len(epochs_new)) assert_true(len(reject_log_new.bad_epochs) != len(reject_log.bad_epochs)) picks_by_type = _get_picks_by_type(epochs.info, ar.picks) # test correct entries in fix log assert_true(np.isnan(reject_log_new.labels[:, non_picks]).sum() > 0) assert_true(np.isnan(reject_log_new.labels[:, picks]).sum() == 0) assert_equal(reject_log_new.labels.shape, (len(epochs_new), len(epochs_new.ch_names))) # test correct interpolations by type for ch_type, this_picks in picks_by_type: interp_counts = np.sum(reject_log_new.labels[:, this_picks] == 2, axis=1) labels = reject_log_new.labels.copy() not_this_picks = np.setdiff1d(np.arange(labels.shape[1]), this_picks) labels[:, not_this_picks] = np.nan interp_channels = _get_interp_chs(labels, reject_log.ch_names, this_picks) assert_array_equal(interp_counts, [len(cc) for cc in interp_channels]) is_same = epochs_new_clean.get_data() == epochs_new.get_data() if not np.isscalar(is_same): is_same = np.isscalar(is_same) assert_true(not is_same) # test that transform ignores bad channels epochs_with_bads_fit.pick_types(meg='mag', eeg=True, eog=True, exclude=[]) ar_bads = AutoReject(cv=3, random_state=42, n_interpolate=[1, 2], consensus=[0.5, 1]) ar_bads.fit(epochs_with_bads_fit) epochs_with_bads_clean = ar_bads.transform(epochs_with_bads_fit) good_w_bads_ix = mne.pick_types(epochs_with_bads_clean.info, meg='mag', eeg=True, eog=True, exclude='bads') good_wo_bads_ix = mne.pick_types(epochs_clean.info, meg='mag', eeg=True, eog=True, exclude='bads') assert_array_equal(epochs_with_bads_clean.get_data()[:, good_w_bads_ix, :], epochs_clean.get_data()[:, good_wo_bads_ix, :]) bad_ix = [ epochs_with_bads_clean.ch_names.index(ch) for ch in epochs_with_bads_clean.info['bads'] ] epo_ix = ~ar_bads.get_reject_log(epochs_with_bads_fit).bad_epochs assert_array_equal( epochs_with_bads_clean.get_data()[:, bad_ix, :], epochs_with_bads_fit.get_data()[epo_ix, :, :][:, bad_ix, :]) assert_equal(epochs_clean.ch_names, epochs_fit.ch_names) assert_true(isinstance(ar.threshes_, dict)) assert_true(len(ar.picks) == len(picks)) assert_true(len(ar.threshes_.keys()) == len(ar.picks)) pick_eog = mne.pick_types(epochs.info, meg=False, eeg=False, eog=True)[0] assert_true(epochs.ch_names[pick_eog] not in ar.threshes_.keys()) assert_raises( IndexError, ar.transform, epochs.copy().pick_channels([epochs.ch_names[pp] for pp in picks[:3]])) epochs.load_data() assert_raises(ValueError, compute_thresholds, epochs, 'dfdfdf') index, ch_names = zip(*[(ii, epochs_fit.ch_names[pp]) for ii, pp in enumerate(picks)]) threshes_a = compute_thresholds(epochs_fit, picks=picks, method='random_search') assert_equal(set(threshes_a.keys()), set(ch_names)) threshes_b = compute_thresholds(epochs_fit, picks=picks, method='bayesian_optimization') assert_equal(set(threshes_b.keys()), set(ch_names))
picks=picks, baseline=(None, 0), reject=None, verbose=False, detrend=True) param_range = np.linspace(400e-7, 200e-6, 30) human_thresh = 80e-6 unit = r'$\mu$V' scaling = 1e6 _, test_scores = validation_curve(GlobalAutoReject(), epochs, y=None, param_name="thresh", param_range=param_range, cv=5, n_jobs=1) test_scores = -test_scores.mean(axis=1) best_thresh = param_range[np.argmin(test_scores)] matplotlib.style.use('ggplot') fontsize = 17 params = { 'axes.labelsize': fontsize + 2, 'text.fontsize': fontsize, 'legend.fontsize': fontsize, 'xtick.labelsize': fontsize, 'ytick.labelsize': fontsize
# Let us define a range of candidate thresholds which we would like to try. # In this particular case, we try from :math:`40{\mu}V` to :math:`200{\mu}V` import numpy as np # noqa param_range = np.linspace(40e-6, 200e-6, 30) ############################################################################### # Next, we can use :class:`autoreject.GlobalAutoReject` to find global # (i.e., for all channels) peak-to-peak thresholds. It is a class which # follows a :mod:`scikit-learn`-like API. To compute the Root Mean Squared # (RMSE) values at the candidate thresholds, we will use the function # :func:`autoreject.validation_curve`. from autoreject import validation_curve # noqa _, test_scores = validation_curve( epochs, y=None, param_name="thresh", param_range=param_range, cv=5) test_scores = -test_scores.mean(axis=1) best_thresh = param_range[np.argmin(test_scores)] ############################################################################### # Now let us plot the RMSE values against the candidate thresholds. import matplotlib.pyplot as plt # noqa from autoreject import set_matplotlib_defaults # noqa set_matplotlib_defaults(plt) human_thresh = 80e-6 unit = r'$\mu$V' scaling = 1e6