Python mne.compute_covariance函数代码示例

def _get_data():
    """Read in data used in tests."""
    # read forward model
    forward = mne.read_forward_solution(fname_fwd)
    # read data
    raw = mne.io.read_raw_fif(fname_raw, preload=True)
    events = mne.read_events(fname_event)
    event_id, tmin, tmax = 1, -0.1, 0.15

    # decimate for speed
    left_temporal_channels = mne.read_selection('Left-temporal')
    picks = mne.pick_types(raw.info, selection=left_temporal_channels)
    picks = picks[::2]
    raw.pick_channels([raw.ch_names[ii] for ii in picks])
    del picks

    raw.info.normalize_proj()  # avoid projection warnings

    epochs = mne.Epochs(raw, events, event_id, tmin, tmax, proj=True,
                        baseline=(None, 0.), preload=True, reject=reject)

    noise_cov = mne.compute_covariance(epochs, tmin=None, tmax=0.)

    data_cov = mne.compute_covariance(epochs, tmin=0.01, tmax=0.15)

    return epochs, data_cov, noise_cov, forward

def test_cov_ctf():
    """Test basic cov computation on ctf data with/without compensation."""
    raw = read_raw_ctf(ctf_fname).crop(0., 2.).load_data()
    events = make_fixed_length_events(raw, 99999)
    assert len(events) == 2
    ch_names = [raw.info['ch_names'][pick]
                for pick in pick_types(raw.info, meg=True, eeg=False,
                                       ref_meg=False)]

    for comp in [0, 1]:
        raw.apply_gradient_compensation(comp)
        epochs = Epochs(raw, events, None, -0.2, 0.2, preload=True)
        with pytest.warns(RuntimeWarning, match='Too few samples'):
            noise_cov = compute_covariance(epochs, tmax=0.,
                                           method=['empirical'])
        prepare_noise_cov(noise_cov, raw.info, ch_names)

    raw.apply_gradient_compensation(0)
    epochs = Epochs(raw, events, None, -0.2, 0.2, preload=True)
    with pytest.warns(RuntimeWarning, match='Too few samples'):
        noise_cov = compute_covariance(epochs, tmax=0., method=['empirical'])
    raw.apply_gradient_compensation(1)

    # TODO This next call in principle should fail.
    prepare_noise_cov(noise_cov, raw.info, ch_names)

    # make sure comps matrices was not removed from raw
    assert raw.info['comps'], 'Comps matrices removed'

def test_compute_covariance_auto_reg():
    """Test automated regularization"""

    raw = Raw(raw_fname, preload=False)
    events = find_events(raw, stim_channel='STI 014')
    event_ids = [1, 2, 3, 4]
    reject = dict(mag=4e-12)

    # cov with merged events and keep_sample_mean=True
    events_merged = merge_events(events, event_ids, 1234)
    picks = pick_types(raw.info, meg='mag', eeg=False)
    epochs = Epochs(raw, events_merged, 1234, tmin=-0.2, tmax=0,
                    picks=picks[:5], baseline=(-0.2, -0.1), proj=True,
                    reject=reject, preload=True)
    epochs.crop(None, 0)[:10]

    method_params = dict(factor_analysis=dict(iter_n_components=[30]),
                         pca=dict(iter_n_components=[30]))

    with warnings.catch_warnings(record=True) as w:
        covs = compute_covariance(epochs, method='auto',
                                  method_params=method_params,
                                  projs=True,
                                  return_estimators=True)
        warnings.simplefilter('always')
        assert_equal(len(w), 1)

    logliks = [c['loglik'] for c in covs]
    assert_true(np.diff(logliks).max() <= 0)  # descending order

    methods = ['empirical',
               'factor_analysis',
               'ledoit_wolf',
               # 'pca',  XXX FAILS
               ]
    with warnings.catch_warnings(record=True) as w:
        cov3 = compute_covariance(epochs, method=methods,
                                  method_params=method_params, projs=False,
                                  return_estimators=True)
        warnings.simplefilter('always')
        assert_equal(len(w), 1)

    assert_equal(set([c['method'] for c in cov3]),
                 set(methods))

    # projs not allowed with FA or PCA
    assert_raises(ValueError, compute_covariance, epochs, method='pca',
                  projs=True)

    # invalid prespecified method
    assert_raises(ValueError, compute_covariance, epochs, method='pizza')

    # invalid scalings
    assert_raises(ValueError, compute_covariance, epochs, method='shrunk',
                  scalings=dict(misc=123))

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
        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, 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_cov_estimation_with_triggers():
    """Estimate raw with triggers
    """
    raw = Raw(raw_fname)
    events = find_events(raw)
    event_ids = [1, 2, 3, 4]
    reject = dict(grad=10000e-13, mag=4e-12, eeg=80e-6, eog=150e-6)

    # cov with merged events and keep_sample_mean=True
    events_merged = merge_events(events, event_ids, 1234)
    epochs = Epochs(raw, events_merged, 1234, tmin=-0.2, tmax=0,
                    baseline=(-0.2, -0.1), proj=True,
                    reject=reject, preload=True)

    cov = compute_covariance(epochs, keep_sample_mean=True)
    cov_mne = read_cov(cov_km_fname)
    assert_true(cov_mne.ch_names == cov.ch_names)
    assert_true((linalg.norm(cov.data - cov_mne.data, ord='fro')
            / linalg.norm(cov.data, ord='fro')) < 0.005)

    # Test with tmin and tmax (different but not too much)
    cov_tmin_tmax = compute_covariance(epochs, tmin=-0.19, tmax=-0.01)
    assert_true(np.all(cov.data != cov_tmin_tmax.data))
    assert_true((linalg.norm(cov.data - cov_tmin_tmax.data, ord='fro')
            / linalg.norm(cov_tmin_tmax.data, ord='fro')) < 0.05)

    # cov using a list of epochs and keep_sample_mean=True
    epochs = [Epochs(raw, events, ev_id, tmin=-0.2, tmax=0,
              baseline=(-0.2, -0.1), proj=True, reject=reject)
              for ev_id in event_ids]

    cov2 = compute_covariance(epochs, keep_sample_mean=True)
    assert_array_almost_equal(cov.data, cov2.data)
    assert_true(cov.ch_names == cov2.ch_names)

    # cov with keep_sample_mean=False using a list of epochs
    cov = compute_covariance(epochs, keep_sample_mean=False)
    cov_mne = read_cov(cov_fname)
    assert_true(cov_mne.ch_names == cov.ch_names)
    assert_true((linalg.norm(cov.data - cov_mne.data, ord='fro')
            / linalg.norm(cov.data, ord='fro')) < 0.005)

    # test IO when computation done in Python
    cov.save('test-cov.fif')  # test saving
    cov_read = read_cov('test-cov.fif')
    assert_true(cov_read.ch_names == cov.ch_names)
    assert_true(cov_read.nfree == cov.nfree)
    assert_true((linalg.norm(cov.data - cov_read.data, ord='fro')
            / linalg.norm(cov.data, ord='fro')) < 1e-5)

def test_compute_covariance_auto_reg():
    """Test automated regularization"""

    raw = read_raw_fif(raw_fname, preload=True)
    raw.resample(100, npad='auto')  # much faster estimation
    events = find_events(raw, stim_channel='STI 014')
    event_ids = [1, 2, 3, 4]
    reject = dict(mag=4e-12)

    # cov with merged events and keep_sample_mean=True
    events_merged = merge_events(events, event_ids, 1234)
    # we need a few channels for numerical reasons in PCA/FA
    picks = pick_types(raw.info, meg='mag', eeg=False)[:10]
    raw.pick_channels([raw.ch_names[pick] for pick in picks])
    raw.info.normalize_proj()
    epochs = Epochs(
        raw, events_merged, 1234, tmin=-0.2, tmax=0,
        baseline=(-0.2, -0.1), proj=True, reject=reject, preload=True)
    epochs = epochs.crop(None, 0)[:10]

    method_params = dict(factor_analysis=dict(iter_n_components=[3]),
                         pca=dict(iter_n_components=[3]))

    covs = compute_covariance(epochs, method='auto',
                              method_params=method_params,
                              projs=True,
                              return_estimators=True)

    logliks = [c['loglik'] for c in covs]
    assert_true(np.diff(logliks).max() <= 0)  # descending order

    methods = ['empirical',
               'factor_analysis',
               'ledoit_wolf',
               'pca']
    cov3 = compute_covariance(epochs, method=methods,
                              method_params=method_params, projs=None,
                              return_estimators=True)

    assert_equal(set([c['method'] for c in cov3]),
                 set(methods))

    # invalid prespecified method
    assert_raises(ValueError, compute_covariance, epochs, method='pizza')

    # invalid scalings
    assert_raises(ValueError, compute_covariance, epochs, method='shrunk',
                  scalings=dict(misc=123))

def run_evoked(subject_id):
    subject = "sub%03d" % subject_id
    print("processing subject: %s" % subject)

    data_path = op.join(meg_dir, subject)
    epochs = mne.read_epochs(op.join(data_path, '%s-epo.fif' % subject),
                             preload=False)

    evoked_famous = epochs['face/famous'].average()
    evoked_scrambled = epochs['scrambled'].average()
    evoked_unfamiliar = epochs['face/unfamiliar'].average()

    # Simplify comment
    evoked_famous.comment = 'famous'
    evoked_scrambled.comment = 'scrambled'
    evoked_unfamiliar.comment = 'unfamiliar'

    contrast = mne.combine_evoked([evoked_famous, evoked_unfamiliar,
                                   evoked_scrambled], weights=[0.5, 0.5, -1.])
    contrast.comment = 'contrast'
    faces = mne.combine_evoked([evoked_famous, evoked_unfamiliar], 'nave')
    faces.comment = 'faces'

    mne.evoked.write_evokeds(op.join(data_path, '%s-ave.fif' % subject),
                             [evoked_famous, evoked_scrambled,
                              evoked_unfamiliar, contrast, faces])

    # take care of noise cov
    cov = mne.compute_covariance(epochs, tmax=0, method='shrunk')
    cov.save(op.join(data_path, '%s-cov.fif' % subject))

def test_low_rank_methods(rank, raw_epochs_events):
    """Test low-rank covariance matrix estimation."""
    epochs = raw_epochs_events[1]
    sss_proj_rank = 139  # 80 MEG + 60 EEG - 1 proj
    n_ch = 366
    methods = ('empirical', 'diagonal_fixed', 'oas')
    bounds = {
        'None': dict(empirical=(-15000, -5000),
                     diagonal_fixed=(-1500, -500),
                     oas=(-700, -600)),
        'full': dict(empirical=(-18000, -8000),
                     diagonal_fixed=(-2000, -1600),
                     oas=(-1600, -1000)),
        'info': dict(empirical=(-15000, -5000),
                     diagonal_fixed=(-700, -600),
                     oas=(-700, -600)),
    }
    with pytest.warns(RuntimeWarning, match='Too few samples'):
        covs = compute_covariance(
            epochs, method=methods, return_estimators=True, rank=rank,
            verbose=True)
    for cov in covs:
        method = cov['method']
        these_bounds = bounds[str(rank)][method]
        this_rank = _cov_rank(cov, epochs.info, proj=(rank != 'full'))
        if rank == 'full' and method != 'empirical':
            assert this_rank == n_ch
        else:
            assert this_rank == sss_proj_rank
        assert these_bounds[0] < cov['loglik'] < these_bounds[1], \
            (rank, method)

def test_lcmv_reg_proj(proj):
    """Test LCMV with and without proj."""
    raw = mne.io.read_raw_fif(fname_raw, preload=True)
    events = mne.find_events(raw)
    raw.pick_types()
    assert len(raw.ch_names) == 305
    epochs = mne.Epochs(raw, events, None, preload=True, proj=proj)
    with pytest.warns(RuntimeWarning, match='Too few samples'):
        noise_cov = mne.compute_covariance(epochs, tmax=0)
        data_cov = mne.compute_covariance(epochs, tmin=0.04, tmax=0.15)
    forward = mne.read_forward_solution(fname_fwd)
    filters = make_lcmv(epochs.info, forward, data_cov, reg=0.05,
                        noise_cov=noise_cov, pick_ori='max-power',
                        weight_norm='nai', rank=None, verbose=True)
    want_rank = 302  # 305 good channels - 3 MEG projs
    assert filters['rank'] == want_rank

def test_lcmv():
    """Test LCMV
    """
    event_id, tmin, tmax = 1, -0.2, 0.2

    # Setup for reading the raw data
    raw.info['bads'] = ['MEG 2443', 'EEG 053']  # 2 bads channels

    # Set up pick list: EEG + MEG - bad channels (modify to your needs)
    left_temporal_channels = mne.read_selection('Left-temporal')
    picks = mne.fiff.pick_types(raw.info, meg=True, eeg=False, stim=True, eog=True,
                       exclude=raw.info['bads'], selection=left_temporal_channels)

    # Read epochs
    epochs = mne.Epochs(raw, events, event_id, tmin, tmax, proj=True,
                        picks=picks, baseline=(None, 0), preload=True,
                        reject=dict(grad=4000e-13, mag=4e-12, eog=150e-6))
    evoked = epochs.average()

    noise_cov = mne.read_cov(fname_cov)
    noise_cov = mne.cov.regularize(noise_cov, evoked.info,
                                   mag=0.05, grad=0.05, eeg=0.1, proj=True)

    data_cov = mne.compute_covariance(epochs, tmin=0.04, tmax=0.15)
    stc = lcmv(evoked, forward, noise_cov, data_cov, reg=0.01)

    stc_pow = np.sum(stc.data, axis=1)
    idx = np.argmax(stc_pow)
    max_stc = stc.data[idx]
    tmax = stc.times[np.argmax(max_stc)]

    assert_true(0.09 < tmax < 0.1)
    assert_true(2. < np.max(max_stc) < 3.)

def _get_bf_data(save_fieldtrip=False):
    raw, epochs, evoked, data_cov, _, _, _, _, _, fwd = _get_data(proj=False)

    if save_fieldtrip is True:
        # raw needs to be saved with all channels and picked in FieldTrip
        raw.save(op.join(ft_data_path, 'raw.fif'), overwrite=True)

        # src (tris are not available in fwd['src'] once imported into MATLAB)
        src = fwd['src'].copy()
        mne.write_source_spaces(op.join(ft_data_path, 'src.fif'), src)

    # pick gradiometers only:
    epochs.pick_types(meg='grad')
    evoked.pick_types(meg='grad')

    # compute covariance matrix
    data_cov = mne.compute_covariance(epochs, tmin=0.04, tmax=0.145,
                                      method='empirical')

    if save_fieldtrip is True:
        # if the covariance matrix and epochs need resaving:
        # data covariance:
        cov_savepath = op.join(ft_data_path, 'sample_cov')
        sample_cov = {'sample_cov': data_cov['data']}
        savemat(cov_savepath, sample_cov)
        # evoked data:
        ev_savepath = op.join(ft_data_path, 'sample_evoked')
        data_ev = {'sample_evoked': evoked.data}
        savemat(ev_savepath, data_ev)

    return evoked, data_cov, fwd

def _get_data(tmin=-0.1, tmax=0.15, all_forward=True, epochs=True,
              epochs_preload=True, data_cov=True):
    """Read in data used in tests."""
    label = mne.read_label(fname_label)
    events = mne.read_events(fname_event)
    raw = mne.io.read_raw_fif(fname_raw, preload=True)
    forward = mne.read_forward_solution(fname_fwd)
    if all_forward:
        forward_surf_ori = _read_forward_solution_meg(
            fname_fwd, surf_ori=True)
        forward_fixed = _read_forward_solution_meg(
            fname_fwd, force_fixed=True, surf_ori=True, use_cps=False)
        forward_vol = _read_forward_solution_meg(fname_fwd_vol)
    else:
        forward_surf_ori = None
        forward_fixed = None
        forward_vol = None

    event_id, tmin, tmax = 1, tmin, tmax

    # Setup for reading the raw data
    raw.info['bads'] = ['MEG 2443', 'EEG 053']  # 2 bad channels
    # Set up pick list: MEG - bad channels
    left_temporal_channels = mne.read_selection('Left-temporal')
    picks = mne.pick_types(raw.info, meg=True, eeg=False, stim=True,
                           eog=True, ref_meg=False, exclude='bads',
                           selection=left_temporal_channels)
    raw.pick_channels([raw.ch_names[ii] for ii in picks])
    raw.info.normalize_proj()  # avoid projection warnings

    if epochs:
        # Read epochs
        epochs = mne.Epochs(
            raw, events, event_id, tmin, tmax, proj=True,
            baseline=(None, 0), preload=epochs_preload,
            reject=dict(grad=4000e-13, mag=4e-12, eog=150e-6))
        if epochs_preload:
            epochs.resample(200, npad=0, n_jobs=2)
        epochs.crop(0, None)
        evoked = epochs.average()
        info = evoked.info
    else:
        epochs = None
        evoked = None
        info = raw.info

    noise_cov = mne.read_cov(fname_cov)
    noise_cov['projs'] = []  # avoid warning
    with warnings.catch_warnings(record=True):  # bad proj
        noise_cov = mne.cov.regularize(noise_cov, info, mag=0.05, grad=0.05,
                                       eeg=0.1, proj=True)
    if data_cov:
        with warnings.catch_warnings(record=True):  # too few samples
            data_cov = mne.compute_covariance(epochs, tmin=0.04, tmax=0.145)
    else:
        data_cov = None

    return raw, epochs, evoked, data_cov, noise_cov, label, forward,\
        forward_surf_ori, forward_fixed, forward_vol

def calc_inverse_operator(events_id, epochs_fn, fwd_sub_fn, inv_fn, min_crop_t=None, max_crop_t=0):
    for cond in events_id.keys():
        epochs = mne.read_epochs(epochs_fn.format(cond=cond))
        noise_cov = mne.compute_covariance(epochs.crop(min_crop_t, max_crop_t, copy=True))
        forward_sub = mne.read_forward_solution(fwd_sub_fn.format(cond=cond))
        inverse_operator_sub = make_inverse_operator(epochs.info, forward_sub, noise_cov,
            loose=None, depth=None)
        write_inverse_operator(inv_fn.format(cond=cond), inverse_operator_sub)