Python mne.Epochs类代码示例

def test_epochs_to_nitime():
    """Test test_to_nitime
    """
    raw, events, picks = _get_data()
    epochs = Epochs(raw, events[:5], event_id, tmin, tmax, picks=picks,
                    baseline=(None, 0), preload=True,
                    reject=reject, flat=flat)

    picks2 = [0, 3]

    epochs_ts = epochs.to_nitime(picks=None, epochs_idx=[0],
                                 collapse=True, copy=True)
    assert_true(epochs_ts.ch_names == epochs.ch_names)

    epochs_ts = epochs.to_nitime(picks=picks2, epochs_idx=None,
                                 collapse=True, copy=True)
    assert_true(epochs_ts.ch_names == [epochs.ch_names[k] for k in picks2])

    epochs_ts = epochs.to_nitime(picks=None, epochs_idx=[0],
                                 collapse=False, copy=False)
    assert_true(epochs_ts.ch_names == epochs.ch_names)

    epochs_ts = epochs.to_nitime(picks=picks2, epochs_idx=None,
                                 collapse=False, copy=False)
    assert_true(epochs_ts.ch_names == [epochs.ch_names[k] for k in picks2])

def test_drop_epochs():
    """Test dropping of epochs.
    """
    raw, events, picks = _get_data()
    epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
                    baseline=(None, 0))
    events1 = events[events[:, 2] == event_id]

    # Bound checks
    assert_raises(IndexError, epochs.drop_epochs, [len(epochs.events)])
    assert_raises(IndexError, epochs.drop_epochs, [-1])
    assert_raises(ValueError, epochs.drop_epochs, [[1, 2], [3, 4]])

    # Test selection attribute
    assert_array_equal(epochs.selection,
                       np.where(events[:, 2] == event_id)[0])
    assert_equal(len(epochs.drop_log), len(events))
    assert_true(all(epochs.drop_log[k] == ['IGNORED']
                for k in set(range(len(events))) - set(epochs.selection)))

    selection = epochs.selection.copy()
    n_events = len(epochs.events)
    epochs.drop_epochs([2, 4], reason='d')
    assert_equal(epochs.drop_log_stats(), 2. / n_events * 100)
    assert_equal(len(epochs.drop_log), len(events))
    assert_equal([epochs.drop_log[k]
                  for k in selection[[2, 4]]], [['d'], ['d']])
    assert_array_equal(events[epochs.selection], events1[[0, 1, 3, 5, 6]])
    assert_array_equal(events[epochs[3:].selection], events1[[5, 6]])
    assert_array_equal(events[epochs['1'].selection], events1[[0, 1, 3, 5, 6]])

def test_evoked_standard_error():
    """Test calculation and read/write of standard error
    """
    epochs = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks,
                    baseline=(None, 0))
    evoked = [epochs.average(), epochs.standard_error()]
    io.write_evokeds(op.join(tempdir, 'evoked.fif'), evoked)
    evoked2 = read_evokeds(op.join(tempdir, 'evoked.fif'), [0, 1])
    evoked3 = [read_evokeds(op.join(tempdir, 'evoked.fif'), 'Unknown'),
               read_evokeds(op.join(tempdir, 'evoked.fif'), 'Unknown',
                            kind='standard_error')]
    for evoked_new in [evoked2, evoked3]:
        assert_true(evoked_new[0]._aspect_kind ==
                    FIFF.FIFFV_ASPECT_AVERAGE)
        assert_true(evoked_new[0].kind == 'average')
        assert_true(evoked_new[1]._aspect_kind ==
                    FIFF.FIFFV_ASPECT_STD_ERR)
        assert_true(evoked_new[1].kind == 'standard_error')
        for ave, ave2 in zip(evoked, evoked_new):
            assert_array_almost_equal(ave.data, ave2.data)
            assert_array_almost_equal(ave.times, ave2.times)
            assert_equal(ave.nave, ave2.nave)
            assert_equal(ave._aspect_kind, ave2._aspect_kind)
            assert_equal(ave.kind, ave2.kind)
            assert_equal(ave.last, ave2.last)
            assert_equal(ave.first, ave2.first)

def test_xdawn_apply_transform():
    """Test Xdawn apply and transform."""
    # get data
    raw, events, picks = _get_data()
    epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
                    preload=True, baseline=None, verbose=False)
    n_components = 2
    # Fit Xdawn
    xd = Xdawn(n_components=n_components, correct_overlap='auto')
    xd.fit(epochs)

    # apply on raw
    xd.apply(raw)
    # apply on epochs
    denoise = xd.apply(epochs)
    # apply on evoked
    xd.apply(epochs.average())
    # apply on other thing should raise an error
    assert_raises(ValueError, xd.apply, 42)

    # transform on epochs
    xd.transform(epochs)
    # transform on ndarray
    xd.transform(epochs._data)
    # transform on someting else
    assert_raises(ValueError, xd.transform, 42)

    # check numerical results with shuffled epochs
    idx = np.arange(len(epochs))
    np.random.shuffle(idx)
    xd.fit(epochs[idx])
    denoise_shfl = xd.apply(epochs)
    assert_array_equal(denoise['cond2']._data, denoise_shfl['cond2']._data)

def test_regularized_csp():
    """Test Common Spatial Patterns algorithm using regularized covariance."""
    raw = io.read_raw_fif(raw_fname)
    events = read_events(event_name)
    picks = pick_types(raw.info, meg=True, stim=False, ecg=False,
                       eog=False, exclude='bads')
    picks = picks[1:13:3]
    epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
                    baseline=(None, 0), preload=True)
    epochs_data = epochs.get_data()
    n_channels = epochs_data.shape[1]

    n_components = 3
    reg_cov = [None, 0.05, 'ledoit_wolf', 'oas']
    for reg in reg_cov:
        csp = CSP(n_components=n_components, reg=reg, norm_trace=False)
        csp.fit(epochs_data, epochs.events[:, -1])
        y = epochs.events[:, -1]
        X = csp.fit_transform(epochs_data, y)
        assert_true(csp.filters_.shape == (n_channels, n_channels))
        assert_true(csp.patterns_.shape == (n_channels, n_channels))
        assert_array_almost_equal(csp.fit(epochs_data, y).
                                  transform(epochs_data), X)

        # test init exception
        assert_raises(ValueError, csp.fit, epochs_data,
                      np.zeros_like(epochs.events))
        assert_raises(ValueError, csp.fit, epochs, y)
        assert_raises(ValueError, csp.transform, epochs)

        csp.n_components = n_components
        sources = csp.transform(epochs_data)
        assert_true(sources.shape[1] == n_components)

def test_scaler():
    """Test methods of Scaler
    """
    raw = fiff.Raw(raw_fname, preload=False)
    events = read_events(event_name)
    picks = fiff.pick_types(raw.info, meg=True, stim=False, ecg=False,
                            eog=False, exclude='bads')
    picks = picks[1:13:3]

    epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
                    baseline=(None, 0), preload=True)
    epochs_data = epochs.get_data()
    scaler = Scaler(epochs.info)
    y = epochs.events[:, -1]

    # np invalid divide value warnings
    with warnings.catch_warnings(record=True):
        X = scaler.fit_transform(epochs_data, y)
        assert_true(X.shape == epochs_data.shape)
        X2 = scaler.fit(epochs_data, y).transform(epochs_data)

    assert_array_equal(X2, X)

    # Test init exception
    assert_raises(ValueError, scaler.fit, epochs, y)
    assert_raises(ValueError, scaler.transform, epochs, y)

def test_xdawn_regularization():
    """Test Xdawn with regularization."""
    # Get data
    raw, events, picks = _get_data()
    epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
                    preload=True, baseline=None, verbose=False)

    # Test with overlapping events.
    # modify events to simulate one overlap
    events = epochs.events
    sel = np.where(events[:, 2] == 2)[0][:2]
    modified_event = events[sel[0]]
    modified_event[0] += 1
    epochs.events[sel[1]] = modified_event
    # Fit and check that overlap was found and applied
    xd = Xdawn(n_components=2, correct_overlap='auto', reg='oas')
    xd.fit(epochs)
    assert_equal(xd.correct_overlap_, True)
    evoked = epochs['cond2'].average()
    assert_true(np.sum(np.abs(evoked.data - xd.evokeds_['cond2'].data)))

    # With covariance regularization
    for reg in [.1, 0.1, 'ledoit_wolf', 'oas']:
        xd = Xdawn(n_components=2, correct_overlap=False,
                   signal_cov=np.eye(len(picks)), reg=reg)
        xd.fit(epochs)
    # With bad shrinkage
    xd = Xdawn(n_components=2, correct_overlap=False,
               signal_cov=np.eye(len(picks)), reg=2)
    assert_raises(ValueError, xd.fit, epochs)

def test_compute_proj_epochs():
    """Test SSP computation on epochs"""
    event_id, tmin, tmax = 1, -0.2, 0.3

    raw = Raw(raw_fname, preload=True)
    events = read_events(event_fname)
    bad_ch = 'MEG 2443'
    picks = pick_types(raw.info, meg=True, eeg=False, stim=False, eog=False,
                       exclude=[])
    epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
                    baseline=None, proj=False)

    evoked = epochs.average()
    projs = compute_proj_epochs(epochs, n_grad=1, n_mag=1, n_eeg=0, n_jobs=1)
    write_proj(op.join(tempdir, 'proj.fif.gz'), projs)
    for p_fname in [proj_fname, proj_gz_fname,
                    op.join(tempdir, 'proj.fif.gz')]:
        projs2 = read_proj(p_fname)

        assert_true(len(projs) == len(projs2))

        for p1, p2 in zip(projs, projs2):
            assert_true(p1['desc'] == p2['desc'])
            assert_true(p1['data']['col_names'] == p2['data']['col_names'])
            assert_true(p1['active'] == p2['active'])
            # compare with sign invariance
            p1_data = p1['data']['data'] * np.sign(p1['data']['data'][0, 0])
            p2_data = p2['data']['data'] * np.sign(p2['data']['data'][0, 0])
            if bad_ch in p1['data']['col_names']:
                bad = p1['data']['col_names'].index('MEG 2443')
                mask = np.ones(p1_data.size, dtype=np.bool)
                mask[bad] = False
                p1_data = p1_data[:, mask]
                p2_data = p2_data[:, mask]
            corr = np.corrcoef(p1_data, p2_data)[0, 1]
            assert_array_almost_equal(corr, 1.0, 5)

    # test that you can compute the projection matrix
    projs = activate_proj(projs)
    proj, nproj, U = make_projector(projs, epochs.ch_names, bads=[])

    assert_true(nproj == 2)
    assert_true(U.shape[1] == 2)

    # test that you can save them
    epochs.info['projs'] += projs
    evoked = epochs.average()
    evoked.save(op.join(tempdir, 'foo.fif'))

    projs = read_proj(proj_fname)

    projs_evoked = compute_proj_evoked(evoked, n_grad=1, n_mag=1, n_eeg=0)
    assert_true(len(projs_evoked) == 2)
    # XXX : test something

    # test parallelization
    projs = compute_proj_epochs(epochs, n_grad=1, n_mag=1, n_eeg=0, n_jobs=2)
    projs = activate_proj(projs)
    proj_par, _, _ = make_projector(projs, epochs.ch_names, bads=[])
    assert_allclose(proj, proj_par, rtol=1e-8, atol=1e-16)

def test_epochs_vector_inverse():
    """Test vector inverse consistency between evoked and epochs."""
    raw = read_raw_fif(fname_raw)
    events = find_events(raw, stim_channel='STI 014')[:2]
    reject = dict(grad=2000e-13, mag=4e-12, eog=150e-6)

    epochs = Epochs(raw, events, None, 0, 0.01, baseline=None,
                    reject=reject, preload=True)

    assert_equal(len(epochs), 2)

    evoked = epochs.average(picks=range(len(epochs.ch_names)))

    inv = read_inverse_operator(fname_inv)

    method = "MNE"
    snr = 3.
    lambda2 = 1. / snr ** 2

    stcs_epo = apply_inverse_epochs(epochs, inv, lambda2, method=method,
                                    pick_ori='vector', return_generator=False)
    stc_epo = np.mean(stcs_epo)

    stc_evo = apply_inverse(evoked, inv, lambda2, method=method,
                            pick_ori='vector')

    assert_allclose(stc_epo.data, stc_evo.data, rtol=1e-9, atol=0)

def test_psdestimator():
    """Test methods of PSDEstimator
    """
    raw = io.Raw(raw_fname, preload=False)
    events = read_events(event_name)
    picks = pick_types(
        raw.info, meg=True, stim=False, ecg=False, eog=False, exclude='bads')
    picks = picks[1:13:3]
    epochs = Epochs(
        raw,
        events,
        event_id,
        tmin,
        tmax,
        picks=picks,
        baseline=(None, 0),
        preload=True)
    epochs_data = epochs.get_data()
    psd = PSDEstimator(2 * np.pi, 0, np.inf)
    y = epochs.events[:, -1]
    X = psd.fit_transform(epochs_data, y)

    assert_true(X.shape[0] == epochs_data.shape[0])
    assert_array_equal(psd.fit(epochs_data, y).transform(epochs_data), X)

    # Test init exception
    assert_raises(ValueError, psd.fit, epochs, y)
    assert_raises(ValueError, psd.transform, epochs, y)

def test_pick_seeg_ecog():
    """Test picking with sEEG and ECoG
    """
    names = 'A1 A2 Fz O OTp1 OTp2 E1 OTp3 E2 E3'.split()
    types = 'mag mag eeg eeg seeg seeg ecog seeg ecog ecog'.split()
    info = create_info(names, 1024., types)
    idx = channel_indices_by_type(info)
    assert_array_equal(idx['mag'], [0, 1])
    assert_array_equal(idx['eeg'], [2, 3])
    assert_array_equal(idx['seeg'], [4, 5, 7])
    assert_array_equal(idx['ecog'], [6, 8, 9])
    assert_array_equal(pick_types(info, meg=False, seeg=True), [4, 5, 7])
    for i, t in enumerate(types):
        assert_equal(channel_type(info, i), types[i])
    raw = RawArray(np.zeros((len(names), 10)), info)
    events = np.array([[1, 0, 0], [2, 0, 0]])
    epochs = Epochs(raw, events, {'event': 0}, -1e-5, 1e-5, add_eeg_ref=False)
    evoked = epochs.average(pick_types(epochs.info, meg=True, seeg=True))
    e_seeg = evoked.copy().pick_types(meg=False, seeg=True)
    for l, r in zip(e_seeg.ch_names, [names[4], names[5], names[7]]):
        assert_equal(l, r)
    # Deal with constant debacle
    raw = read_raw_fif(op.join(io_dir, 'tests', 'data',
                               'test_chpi_raw_sss.fif'), add_eeg_ref=False)
    assert_equal(len(pick_types(raw.info, meg=False, seeg=True, ecog=True)), 0)

def test_cov_mismatch():
    """Test estimation with MEG<->Head mismatch."""
    raw = read_raw_fif(raw_fname, add_eeg_ref=False).crop(0, 5).load_data()
    events = find_events(raw, stim_channel="STI 014")
    raw.pick_channels(raw.ch_names[:5])
    raw.add_proj([], remove_existing=True)
    epochs = Epochs(raw, events, None, tmin=-0.2, tmax=0.0, preload=True, add_eeg_ref=False)
    for kind in ("shift", "None"):
        epochs_2 = epochs.copy()
        # This should be fine
        with warnings.catch_warnings(record=True) as w:
            compute_covariance([epochs, epochs_2])
            assert_equal(len(w), 0)
            if kind == "shift":
                epochs_2.info["dev_head_t"]["trans"][:3, 3] += 0.001
            else:  # None
                epochs_2.info["dev_head_t"] = None
            assert_raises(ValueError, compute_covariance, [epochs, epochs_2])
            assert_equal(len(w), 0)
            compute_covariance([epochs, epochs_2], on_mismatch="ignore")
            assert_equal(len(w), 0)
            compute_covariance([epochs, epochs_2], on_mismatch="warn")
            assert_raises(ValueError, compute_covariance, epochs, on_mismatch="x")
        assert_true(any("transform mismatch" in str(ww.message) for ww in w))
    # This should work
    epochs.info["dev_head_t"] = None
    epochs_2.info["dev_head_t"] = None
    compute_covariance([epochs, epochs_2], method=None)

def test_cov_mismatch():
    """Test estimation with MEG<->Head mismatch."""
    raw = read_raw_fif(raw_fname).crop(0, 5).load_data()
    events = find_events(raw, stim_channel='STI 014')
    raw.pick_channels(raw.ch_names[:5])
    raw.add_proj([], remove_existing=True)
    epochs = Epochs(raw, events, None, tmin=-0.2, tmax=0., preload=True)
    for kind in ('shift', 'None'):
        epochs_2 = epochs.copy()
        # This should be fine
        compute_covariance([epochs, epochs_2])
        if kind == 'shift':
            epochs_2.info['dev_head_t']['trans'][:3, 3] += 0.001
        else:  # None
            epochs_2.info['dev_head_t'] = None
        pytest.raises(ValueError, compute_covariance, [epochs, epochs_2])
        compute_covariance([epochs, epochs_2], on_mismatch='ignore')
        with pytest.raises(RuntimeWarning, match='transform mismatch'):
            compute_covariance([epochs, epochs_2], on_mismatch='warn')
        pytest.raises(ValueError, compute_covariance, epochs,
                      on_mismatch='x')
    # This should work
    epochs.info['dev_head_t'] = None
    epochs_2.info['dev_head_t'] = None
    compute_covariance([epochs, epochs_2], method=None)

def test_scaler():
    """Test methods of Scaler."""
    raw = io.read_raw_fif(raw_fname)
    events = read_events(event_name)
    picks = pick_types(raw.info, meg=True, stim=False, ecg=False,
                       eog=False, exclude='bads')
    picks = picks[1:13:3]

    epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
                    baseline=(None, 0), preload=True)
    epochs_data = epochs.get_data()
    scaler = Scaler(epochs.info)
    y = epochs.events[:, -1]

    # np invalid divide value warnings
    with warnings.catch_warnings(record=True):
        X = scaler.fit_transform(epochs_data, y)
        assert_true(X.shape == epochs_data.shape)
        X2 = scaler.fit(epochs_data, y).transform(epochs_data)

    assert_array_equal(X2, X)

    # Test inverse_transform
    with warnings.catch_warnings(record=True):  # invalid value in mult
        Xi = scaler.inverse_transform(X, y)
    assert_array_almost_equal(epochs_data, Xi)

    for kwargs in [{'with_mean': False}, {'with_std': False}]:
        scaler = Scaler(epochs.info, **kwargs)
        scaler.fit(epochs_data, y)
        assert_array_almost_equal(
            X, scaler.inverse_transform(scaler.transform(X)))
    # Test init exception
    assert_raises(ValueError, scaler.fit, epochs, y)
    assert_raises(ValueError, scaler.transform, epochs, y)

def test_xdawn_apply_transform():
    """Test Xdawn apply and transform."""
    # Get data
    raw, events, picks = _get_data()
    raw.pick_types(eeg=True, meg=False)
    epochs = Epochs(raw, events, event_id, tmin, tmax, proj=False,
                    preload=True, baseline=None,
                    verbose=False)
    n_components = 2
    # Fit Xdawn
    xd = Xdawn(n_components=n_components, correct_overlap=False)
    xd.fit(epochs)

    # Apply on different types of instances
    for inst in [raw, epochs.average(), epochs]:
        denoise = xd.apply(inst)
    # Apply on other thing should raise an error
    assert_raises(ValueError, xd.apply, 42)

    # Transform on epochs
    xd.transform(epochs)
    # Transform on ndarray
    xd.transform(epochs._data)
    # Transform on someting else
    assert_raises(ValueError, xd.transform, 42)

    # Check numerical results with shuffled epochs
    np.random.seed(0)  # random makes unstable linalg
    idx = np.arange(len(epochs))
    np.random.shuffle(idx)
    xd.fit(epochs[idx])
    denoise_shfl = xd.apply(epochs)
    assert_array_almost_equal(denoise['cond2']._data,
                              denoise_shfl['cond2']._data)