Python inverse.prepare_inverse_operator函数代码示例

def test_io_inverse_operator():
    """Test IO of inverse_operator."""
    tempdir = _TempDir()
    inverse_operator = read_inverse_operator(fname_inv)
    x = repr(inverse_operator)
    assert (x)
    assert (isinstance(inverse_operator['noise_cov'], Covariance))
    # just do one example for .gz, as it should generalize
    _compare_io(inverse_operator, '.gz')

    # test warnings on bad filenames
    inv_badname = op.join(tempdir, 'test-bad-name.fif.gz')
    with pytest.warns(RuntimeWarning, match='-inv.fif'):
        write_inverse_operator(inv_badname, inverse_operator)
    with pytest.warns(RuntimeWarning, match='-inv.fif'):
        read_inverse_operator(inv_badname)

    # make sure we can write and read
    inv_fname = op.join(tempdir, 'test-inv.fif')
    args = (10, 1. / 9., 'dSPM')
    inv_prep = prepare_inverse_operator(inverse_operator, *args)
    write_inverse_operator(inv_fname, inv_prep)
    inv_read = read_inverse_operator(inv_fname)
    _compare(inverse_operator, inv_read)
    inv_read_prep = prepare_inverse_operator(inv_read, *args)
    _compare(inv_prep, inv_read_prep)
    inv_prep_prep = prepare_inverse_operator(inv_prep, *args)
    _compare(inv_prep, inv_prep_prep)

def test_io_inverse_operator():
    """Test IO of inverse_operator
    """
    tempdir = _TempDir()
    inverse_operator = read_inverse_operator(fname_inv)
    x = repr(inverse_operator)
    assert_true(x)
    assert_true(isinstance(inverse_operator['noise_cov'], Covariance))
    # just do one example for .gz, as it should generalize
    _compare_io(inverse_operator, '.gz')

    # test warnings on bad filenames
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter('always')
        inv_badname = op.join(tempdir, 'test-bad-name.fif.gz')
        write_inverse_operator(inv_badname, inverse_operator)
        read_inverse_operator(inv_badname)
    assert_naming(w, 'test_inverse.py', 2)

    # make sure we can write and read
    inv_fname = op.join(tempdir, 'test-inv.fif')
    args = (10, 1. / 9., 'dSPM')
    inv_prep = prepare_inverse_operator(inverse_operator, *args)
    write_inverse_operator(inv_fname, inv_prep)
    inv_read = read_inverse_operator(inv_fname)
    _compare(inverse_operator, inv_read)
    inv_read_prep = prepare_inverse_operator(inv_read, *args)
    _compare(inv_prep, inv_read_prep)
    inv_prep_prep = prepare_inverse_operator(inv_prep, *args)
    _compare(inv_prep, inv_prep_prep)

def test_apply_mne_inverse_raw():
    """Test MNE with precomputed inverse operator on Raw."""
    start = 3
    stop = 10
    raw = read_raw_fif(fname_raw)
    label_lh = read_label(fname_label % 'Aud-lh')
    _, times = raw[0, start:stop]
    inverse_operator = read_inverse_operator(fname_full)
    inverse_operator = prepare_inverse_operator(inverse_operator, nave=1,
                                                lambda2=lambda2, method="dSPM")
    for pick_ori in [None, "normal", "vector"]:
        stc = apply_inverse_raw(raw, inverse_operator, lambda2, "dSPM",
                                label=label_lh, start=start, stop=stop, nave=1,
                                pick_ori=pick_ori, buffer_size=None,
                                prepared=True)

        stc2 = apply_inverse_raw(raw, inverse_operator, lambda2, "dSPM",
                                 label=label_lh, start=start, stop=stop,
                                 nave=1, pick_ori=pick_ori,
                                 buffer_size=3, prepared=True)

        if pick_ori is None:
            assert_true(np.all(stc.data > 0))
            assert_true(np.all(stc2.data > 0))

        assert_true(stc.subject == 'sample')
        assert_true(stc2.subject == 'sample')
        assert_array_almost_equal(stc.times, times)
        assert_array_almost_equal(stc2.times, times)
        assert_array_almost_equal(stc.data, stc2.data)

def test_tfr_with_inverse_operator():
    """Test time freq with MNE inverse computation"""

    tmin, tmax, event_id = -0.2, 0.5, 1

    # Setup for reading the raw data
    raw = io.Raw(fname_data)
    events = find_events(raw, stim_channel='STI 014')
    inverse_operator = read_inverse_operator(fname_inv)
    inv = prepare_inverse_operator(inverse_operator, nave=1,
                                   lambda2=1. / 9., method="dSPM")

    raw.info['bads'] += ['MEG 2443', 'EEG 053']  # bads + 2 more

    # picks MEG gradiometers
    picks = pick_types(raw.info, meg=True, eeg=False, eog=True,
                       stim=False, exclude='bads')

    # Load condition 1
    event_id = 1
    events3 = events[:3]  # take 3 events to keep the computation time low
    epochs = Epochs(raw, events3, event_id, tmin, tmax, picks=picks,
                    baseline=(None, 0), reject=dict(grad=4000e-13, eog=150e-6),
                    preload=True)

    # Compute a source estimate per frequency band
    bands = dict(alpha=[10, 10])
    label = read_label(fname_label)

    stcs = source_band_induced_power(epochs, inv, bands,
                                     n_cycles=2, use_fft=False, pca=True,
                                     label=label, prepared=True)

    stc = stcs['alpha']
    assert_true(len(stcs) == len(list(bands.keys())))
    assert_true(np.all(stc.data > 0))
    assert_array_almost_equal(stc.times, epochs.times)

    stcs_no_pca = source_band_induced_power(epochs, inv, bands,
                                            n_cycles=2, use_fft=False,
                                            pca=False, label=label,
                                            prepared=True)

    assert_array_almost_equal(stcs['alpha'].data, stcs_no_pca['alpha'].data)

    # Compute a source estimate per frequency band
    epochs = Epochs(raw, events[:10], event_id, tmin, tmax, picks=picks,
                    baseline=(None, 0), reject=dict(grad=4000e-13, eog=150e-6),
                    preload=True)

    frequencies = np.arange(7, 30, 2)  # define frequencies of interest
    power, phase_lock = source_induced_power(epochs, inv,
                                             frequencies, label,
                                             baseline=(-0.1, 0),
                                             baseline_mode='percent',
                                             n_cycles=2, n_jobs=1,
                                             prepared=True)
    assert_true(np.all(phase_lock > 0))
    assert_true(np.all(phase_lock <= 1))
    assert_true(np.max(power) > 10)

def test_apply_inverse_operator():
    """Test MNE inverse application
    """
    inverse_operator = read_inverse_operator(fname_full)
    evoked = _get_evoked()

    # Inverse has 306 channels - 4 proj = 302
    assert_true(compute_rank_inverse(inverse_operator) == 302)

    # Inverse has 306 channels - 4 proj = 302
    assert_true(compute_rank_inverse(inverse_operator) == 302)

    stc = apply_inverse(evoked, inverse_operator, lambda2, "MNE")
    assert_true(stc.subject == 'sample')
    assert_true(stc.data.min() > 0)
    assert_true(stc.data.max() < 10e-9)
    assert_true(stc.data.mean() > 1e-11)

    # test if using prepared and not prepared inverse operator give the same
    # result
    inv_op = prepare_inverse_operator(inverse_operator, nave=evoked.nave,
                                      lambda2=lambda2, method="MNE")
    stc2 = apply_inverse(evoked, inv_op, lambda2, "MNE")
    assert_array_almost_equal(stc.data, stc2.data)
    assert_array_almost_equal(stc.times, stc2.times)

    stc = apply_inverse(evoked, inverse_operator, lambda2, "sLORETA")
    assert_true(stc.subject == 'sample')
    assert_true(stc.data.min() > 0)
    assert_true(stc.data.max() < 10.0)
    assert_true(stc.data.mean() > 0.1)

    stc = apply_inverse(evoked, inverse_operator, lambda2, "dSPM")
    assert_true(stc.subject == 'sample')
    assert_true(stc.data.min() > 0)
    assert_true(stc.data.max() < 35)
    assert_true(stc.data.mean() > 0.1)

    # test without using a label (so delayed computation is used)
    label = read_label(fname_label % 'Aud-lh')
    stc = apply_inverse(evoked, inv_op, lambda2, "MNE")
    stc_label = apply_inverse(evoked, inv_op, lambda2, "MNE",
                              label=label)
    assert_equal(stc_label.subject, 'sample')
    label_stc = stc.in_label(label)
    assert_true(label_stc.subject == 'sample')
    assert_array_almost_equal(stc_label.data, label_stc.data)

    # Test we get errors when using custom ref or no average proj is present
    evoked.info['custom_ref_applied'] = True
    assert_raises(ValueError, apply_inverse, evoked, inv_op, lambda2, "MNE")
    evoked.info['custom_ref_applied'] = False
    evoked.info['projs'] = []  # remove EEG proj
    assert_raises(ValueError, apply_inverse, evoked, inv_op, lambda2, "MNE")

def _apply_inverse_evoked_list(evoked_list, inverse_operator, lambda2, method="MNE",
                              labels=None, nave=1, pick_ori=None,
                              verbose=None, pick_normal=None):
    """ Utility function for applying the inverse solution to a list of evoked object
        Assume that the info for each evoked object in the list is the same
        Input:
            evoked_list, 
            inverse_operator,
            lambda2, 
            method,
            labels, list of label objects
            nave = 1,
            pick_ori = None,
            verbos = none,
            pick_normal = None
        Output: stc_Data, [n_sources_labels, n_times, n_trials]
    """
    info = evoked_list[0].info
    method = _check_method(method)
    pick_ori = _check_ori(pick_ori, pick_normal)
    _check_ch_names(inverse_operator, info)
    inv = prepare_inverse_operator(inverse_operator, nave, lambda2, method)
    sel = _pick_channels_inverse_operator(info['ch_names'], inv)
    labels_union = None
    if labels is not None:
        labels_union = labels[0]
        if len(labels) > 1:
            for i in range(1,len(labels)):
                labels_union += labels[i]
    K, noise_norm, vertno = _assemble_kernel(inv, labels_union, method, pick_ori)
    is_free_ori = (inverse_operator['source_ori'] == FIFF.FIFFV_MNE_FREE_ORI
                   and pick_ori is None)
    if not is_free_ori and noise_norm is not None:
        # premultiply kernel with noise normalization
        K *= noise_norm
    n_channels = len(sel)
    n_times = len(evoked_list[0].times)
    n_trials = len(evoked_list)
    n_sources = K.shape[0]
    stc_Data = np.zeros([n_sources,n_times, n_trials])
    for i in range(n_trials):
        if is_free_ori:
            # Compute solution and combine current components (non-linear)
            sol = np.dot(K, evoked_list[i].data)  # apply imaging kernel
            if is_free_ori:
                sol = combine_xyz(sol)
                if noise_norm is not None:
                    sol *= noise_norm
        else:
            # Linear inverse: do computation here or delayed
            sol = np.dot(K, evoked_list[i].data)
        stc_Data[:,:,i] = sol
    return stc_Data

def test_apply_mne_inverse_fixed_raw():
    """Test MNE with fixed-orientation inverse operator on Raw."""
    raw = read_raw_fif(fname_raw)
    start = 3
    stop = 10
    _, times = raw[0, start:stop]
    label_lh = read_label(fname_label % 'Aud-lh')

    # create a fixed-orientation inverse operator
    fwd = read_forward_solution_meg(fname_fwd, force_fixed=False,
                                    surf_ori=True)
    noise_cov = read_cov(fname_cov)
    assert_raises(ValueError, make_inverse_operator,
                  raw.info, fwd, noise_cov, loose=1., fixed=True)
    inv_op = make_inverse_operator(raw.info, fwd, noise_cov,
                                   fixed=True, use_cps=True)

    inv_op2 = prepare_inverse_operator(inv_op, nave=1,
                                       lambda2=lambda2, method="dSPM")
    stc = apply_inverse_raw(raw, inv_op2, lambda2, "dSPM",
                            label=label_lh, start=start, stop=stop, nave=1,
                            pick_ori=None, buffer_size=None, prepared=True)

    stc2 = apply_inverse_raw(raw, inv_op2, lambda2, "dSPM",
                             label=label_lh, start=start, stop=stop, nave=1,
                             pick_ori=None, buffer_size=3, prepared=True)

    stc3 = apply_inverse_raw(raw, inv_op, lambda2, "dSPM",
                             label=label_lh, start=start, stop=stop, nave=1,
                             pick_ori=None, buffer_size=None)

    assert_true(stc.subject == 'sample')
    assert_true(stc2.subject == 'sample')
    assert_array_almost_equal(stc.times, times)
    assert_array_almost_equal(stc2.times, times)
    assert_array_almost_equal(stc3.times, times)
    assert_array_almost_equal(stc.data, stc2.data)
    assert_array_almost_equal(stc.data, stc3.data)

def test_apply_inverse_operator():
    """Test MNE inverse application
    """
    inverse_operator = read_inverse_operator(fname_full)
    evoked = _get_evoked()

    # Inverse has 306 channels - 4 proj = 302
    assert_true(compute_rank_inverse(inverse_operator) == 302)

    # Inverse has 306 channels - 4 proj = 302
    assert_true(compute_rank_inverse(inverse_operator) == 302)

    stc = apply_inverse(evoked, inverse_operator, lambda2, "MNE")
    assert_true(stc.subject == 'sample')
    assert_true(stc.data.min() > 0)
    assert_true(stc.data.max() < 10e-9)
    assert_true(stc.data.mean() > 1e-11)

    # test if using prepared and not prepared inverse operator give the same
    # result
    inv_op = prepare_inverse_operator(inverse_operator, nave=evoked.nave,
                                      lambda2=lambda2, method="MNE")
    stc2 = apply_inverse(evoked, inv_op, lambda2, "MNE")
    assert_array_almost_equal(stc.data, stc2.data)
    assert_array_almost_equal(stc.times, stc2.times)

    stc = apply_inverse(evoked, inverse_operator, lambda2, "sLORETA")
    assert_true(stc.subject == 'sample')
    assert_true(stc.data.min() > 0)
    assert_true(stc.data.max() < 10.0)
    assert_true(stc.data.mean() > 0.1)

    stc = apply_inverse(evoked, inverse_operator, lambda2, "dSPM")
    assert_true(stc.subject == 'sample')
    assert_true(stc.data.min() > 0)
    assert_true(stc.data.max() < 35)
    assert_true(stc.data.mean() > 0.1)

def test_apply_mne_inverse_epochs():
    """Test MNE with precomputed inverse operator on Epochs."""
    inverse_operator = read_inverse_operator(fname_full)
    label_lh = read_label(fname_label % 'Aud-lh')
    label_rh = read_label(fname_label % 'Aud-rh')
    event_id, tmin, tmax = 1, -0.2, 0.5
    raw = read_raw_fif(fname_raw)

    picks = pick_types(raw.info, meg=True, eeg=False, stim=True, ecg=True,
                       eog=True, include=['STI 014'], exclude='bads')
    reject = dict(grad=4000e-13, mag=4e-12, eog=150e-6)
    flat = dict(grad=1e-15, mag=1e-15)

    events = read_events(fname_event)[:15]
    epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
                    baseline=(None, 0), reject=reject, flat=flat)

    inverse_operator = prepare_inverse_operator(inverse_operator, nave=1,
                                                lambda2=lambda2,
                                                method="dSPM")
    for pick_ori in [None, "normal", "vector"]:
        stcs = apply_inverse_epochs(epochs, inverse_operator, lambda2, "dSPM",
                                    label=label_lh, pick_ori=pick_ori)
        stcs2 = apply_inverse_epochs(epochs, inverse_operator, lambda2, "dSPM",
                                     label=label_lh, pick_ori=pick_ori,
                                     prepared=True)
        # test if using prepared and not prepared inverse operator give the
        # same result
        assert_array_almost_equal(stcs[0].data, stcs2[0].data)
        assert_array_almost_equal(stcs[0].times, stcs2[0].times)

        assert_true(len(stcs) == 2)
        assert_true(3 < stcs[0].data.max() < 10)
        assert_true(stcs[0].subject == 'sample')
    inverse_operator = read_inverse_operator(fname_full)

    stcs = apply_inverse_epochs(epochs, inverse_operator, lambda2, "dSPM",
                                label=label_lh, pick_ori='normal')
    data = sum(stc.data for stc in stcs) / len(stcs)
    flip = label_sign_flip(label_lh, inverse_operator['src'])

    label_mean = np.mean(data, axis=0)
    label_mean_flip = np.mean(flip[:, np.newaxis] * data, axis=0)

    assert_true(label_mean.max() < label_mean_flip.max())

    # test extracting a BiHemiLabel
    inverse_operator = prepare_inverse_operator(inverse_operator, nave=1,
                                                lambda2=lambda2,
                                                method="dSPM")
    stcs_rh = apply_inverse_epochs(epochs, inverse_operator, lambda2, "dSPM",
                                   label=label_rh, pick_ori="normal",
                                   prepared=True)
    stcs_bh = apply_inverse_epochs(epochs, inverse_operator, lambda2, "dSPM",
                                   label=label_lh + label_rh,
                                   pick_ori="normal",
                                   prepared=True)

    n_lh = len(stcs[0].data)
    assert_array_almost_equal(stcs[0].data, stcs_bh[0].data[:n_lh])
    assert_array_almost_equal(stcs_rh[0].data, stcs_bh[0].data[n_lh:])

    # test without using a label (so delayed computation is used)
    stcs = apply_inverse_epochs(epochs, inverse_operator, lambda2, "dSPM",
                                pick_ori="normal", prepared=True)
    assert_true(stcs[0].subject == 'sample')
    label_stc = stcs[0].in_label(label_rh)
    assert_true(label_stc.subject == 'sample')
    assert_array_almost_equal(stcs_rh[0].data, label_stc.data)

def test_apply_inverse_operator():
    """Test MNE inverse application."""
    inverse_operator = read_inverse_operator(fname_full)
    evoked = _get_evoked()

    # Inverse has 306 channels - 4 proj = 302
    assert_true(compute_rank_inverse(inverse_operator) == 302)

    # Inverse has 306 channels - 4 proj = 302
    assert_true(compute_rank_inverse(inverse_operator) == 302)

    stc = apply_inverse(evoked, inverse_operator, lambda2, "MNE")
    assert_true(stc.subject == 'sample')
    assert_true(stc.data.min() > 0)
    assert_true(stc.data.max() < 10e-9)
    assert_true(stc.data.mean() > 1e-11)

    # test if using prepared and not prepared inverse operator give the same
    # result
    inv_op = prepare_inverse_operator(inverse_operator, nave=evoked.nave,
                                      lambda2=lambda2, method="MNE")
    stc2 = apply_inverse(evoked, inv_op, lambda2, "MNE")
    assert_array_almost_equal(stc.data, stc2.data)
    assert_array_almost_equal(stc.times, stc2.times)

    stc = apply_inverse(evoked, inverse_operator, lambda2, "sLORETA")
    assert_true(stc.subject == 'sample')
    assert_true(stc.data.min() > 0)
    assert_true(stc.data.max() < 10.0)
    assert_true(stc.data.mean() > 0.1)

    stc = apply_inverse(evoked, inverse_operator, lambda2, "dSPM")
    assert_true(stc.subject == 'sample')
    assert_true(stc.data.min() > 0)
    assert_true(stc.data.max() < 35)
    assert_true(stc.data.mean() > 0.1)

    # test without using a label (so delayed computation is used)
    label = read_label(fname_label % 'Aud-lh')
    stc = apply_inverse(evoked, inv_op, lambda2, "MNE")
    stc_label = apply_inverse(evoked, inv_op, lambda2, "MNE",
                              label=label)
    assert_equal(stc_label.subject, 'sample')
    label_stc = stc.in_label(label)
    assert_true(label_stc.subject == 'sample')
    assert_allclose(stc_label.data, label_stc.data)

    # Test that no errors are raised with loose inverse ops and picking normals
    noise_cov = read_cov(fname_cov)
    fwd = read_forward_solution_meg(fname_fwd)
    inv_op2 = make_inverse_operator(evoked.info, fwd, noise_cov, loose=1,
                                    fixed='auto', depth=None)
    apply_inverse(evoked, inv_op2, 1 / 9., method='MNE',
                  pick_ori='normal')

    # Test we get errors when using custom ref or no average proj is present
    evoked.info['custom_ref_applied'] = True
    assert_raises(ValueError, apply_inverse, evoked, inv_op, lambda2, "MNE")
    evoked.info['custom_ref_applied'] = False
    evoked.info['projs'] = []  # remove EEG proj
    assert_raises(ValueError, apply_inverse, evoked, inv_op, lambda2, "MNE")

def test_source_psd_epochs():
    """Test multi-taper source PSD computation in label from epochs."""
    raw = read_raw_fif(fname_data)
    inverse_operator = read_inverse_operator(fname_inv)
    label = read_label(fname_label)

    event_id, tmin, tmax = 1, -0.2, 0.5
    lambda2, method = 1. / 9., 'dSPM'
    bandwidth = 8.
    fmin, fmax = 0, 100

    picks = pick_types(raw.info, meg=True, eeg=False, stim=True,
                       ecg=True, eog=True, include=['STI 014'],
                       exclude='bads')
    reject = dict(grad=4000e-13, mag=4e-12, eog=150e-6)

    events = find_events(raw, stim_channel='STI 014')
    epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
                    baseline=(None, 0), reject=reject)

    # only look at one epoch
    epochs.drop_bad()
    one_epochs = epochs[:1]

    inv = prepare_inverse_operator(inverse_operator, nave=1,
                                   lambda2=1. / 9., method="dSPM")
    # return list
    stc_psd = compute_source_psd_epochs(one_epochs, inv,
                                        lambda2=lambda2, method=method,
                                        pick_ori="normal", label=label,
                                        bandwidth=bandwidth,
                                        fmin=fmin, fmax=fmax,
                                        prepared=True)[0]

    # return generator
    stcs = compute_source_psd_epochs(one_epochs, inv,
                                     lambda2=lambda2, method=method,
                                     pick_ori="normal", label=label,
                                     bandwidth=bandwidth,
                                     fmin=fmin, fmax=fmax,
                                     return_generator=True,
                                     prepared=True)

    for stc in stcs:
        stc_psd_gen = stc

    assert_array_almost_equal(stc_psd.data, stc_psd_gen.data)

    # compare with direct computation
    stc = apply_inverse_epochs(one_epochs, inv,
                               lambda2=lambda2, method=method,
                               pick_ori="normal", label=label,
                               prepared=True)[0]

    sfreq = epochs.info['sfreq']
    psd, freqs = _psd_multitaper(stc.data, sfreq=sfreq, bandwidth=bandwidth,
                                 fmin=fmin, fmax=fmax)

    assert_array_almost_equal(psd, stc_psd.data)
    assert_array_almost_equal(freqs, stc_psd.times)

    # Check corner cases caused by tiny bandwidth
    with warnings.catch_warnings(record=True) as w:
        warnings.simplefilter('always')
        compute_source_psd_epochs(one_epochs, inv,
                                  lambda2=lambda2, method=method,
                                  pick_ori="normal", label=label,
                                  bandwidth=0.01, low_bias=True,
                                  fmin=fmin, fmax=fmax,
                                  return_generator=False,
                                  prepared=True)
        compute_source_psd_epochs(one_epochs, inv,
                                  lambda2=lambda2, method=method,
                                  pick_ori="normal", label=label,
                                  bandwidth=0.01, low_bias=False,
                                  fmin=fmin, fmax=fmax,
                                  return_generator=False,
                                  prepared=True)
    assert_true(len(w) >= 2)
    assert_true(any('not properly use' in str(ww.message) for ww in w))
    assert_true(any('Bandwidth too small' in str(ww.message) for ww in w))

def test_apply_inverse_operator():
    """Test MNE inverse application."""
    # use fname_inv as it will be faster than fname_full (fewer verts and chs)
    inverse_operator = read_inverse_operator(fname_inv)
    evoked = _get_evoked()

    # Inverse has 306 channels - 4 proj = 302
    assert (compute_rank_inverse(inverse_operator) == 302)

    # Inverse has 306 channels - 4 proj = 302
    assert (compute_rank_inverse(inverse_operator) == 302)

    stc = apply_inverse(evoked, inverse_operator, lambda2, "MNE")
    assert stc.subject == 'sample'
    assert stc.data.min() > 0
    assert stc.data.max() < 13e-9
    assert stc.data.mean() > 1e-11

    # test if using prepared and not prepared inverse operator give the same
    # result
    inv_op = prepare_inverse_operator(inverse_operator, nave=evoked.nave,
                                      lambda2=lambda2, method="MNE")
    stc2 = apply_inverse(evoked, inv_op, lambda2, "MNE")
    assert_array_almost_equal(stc.data, stc2.data)
    assert_array_almost_equal(stc.times, stc2.times)

    # This is little more than a smoke test...
    stc = apply_inverse(evoked, inverse_operator, lambda2, "sLORETA")
    assert stc.subject == 'sample'
    assert stc.data.min() > 0
    assert stc.data.max() < 10.0
    assert stc.data.mean() > 0.1

    stc = apply_inverse(evoked, inverse_operator, lambda2, "eLORETA")
    assert stc.subject == 'sample'
    assert stc.data.min() > 0
    assert stc.data.max() < 3.0
    assert stc.data.mean() > 0.1

    stc = apply_inverse(evoked, inverse_operator, lambda2, "dSPM")
    assert stc.subject == 'sample'
    assert stc.data.min() > 0
    assert stc.data.max() < 35
    assert stc.data.mean() > 0.1

    # test without using a label (so delayed computation is used)
    label = read_label(fname_label % 'Aud-lh')
    stc = apply_inverse(evoked, inv_op, lambda2, "MNE")
    stc_label = apply_inverse(evoked, inv_op, lambda2, "MNE",
                              label=label)
    assert_equal(stc_label.subject, 'sample')
    label_stc = stc.in_label(label)
    assert label_stc.subject == 'sample'
    assert_allclose(stc_label.data, label_stc.data)

    # Test that no errors are raised with loose inverse ops and picking normals
    noise_cov = read_cov(fname_cov)
    fwd = read_forward_solution_meg(fname_fwd)
    inv_op_meg = make_inverse_operator(evoked.info, fwd, noise_cov, loose=1,
                                       fixed='auto', depth=None)
    apply_inverse(evoked, inv_op_meg, 1 / 9., method='MNE', pick_ori='normal')

    # Test we get errors when using custom ref or no average proj is present
    evoked.info['custom_ref_applied'] = True
    pytest.raises(ValueError, apply_inverse, evoked, inv_op, lambda2, "MNE")
    evoked.info['custom_ref_applied'] = False
    evoked.info['projs'] = []  # remove EEG proj
    pytest.raises(ValueError, apply_inverse, evoked, inv_op, lambda2, "MNE")

    # But test that we do not get EEG-related errors on MEG-only inv (gh-4650)
    apply_inverse(evoked, inv_op_meg, 1. / 9.)

def test_apply_inverse_operator():
    """Test MNE inverse computation (precomputed and non-precomputed)
    """
    inverse_operator = read_inverse_operator(fname_inv)
    evoked = _get_evoked()
    noise_cov = read_cov(fname_cov)

    # Test old version of inverse computation starting from forward operator
    fwd_op = read_forward_solution(fname_fwd, surf_ori=True)
    my_inv_op = make_inverse_operator(evoked.info, fwd_op, noise_cov,
                                      loose=0.2, depth=0.8,
                                      limit_depth_chs=False)
    _compare_io(my_inv_op)
    assert_true(inverse_operator['units'] == 'Am')
    _compare_inverses_approx(my_inv_op, inverse_operator, evoked, 2,
                             check_depth=False)
    # Inverse has 306 channels - 4 proj = 302
    assert_true(compute_rank_inverse(inverse_operator) == 302)

    # Test MNE inverse computation starting from forward operator
    my_inv_op = make_inverse_operator(evoked.info, fwd_op, noise_cov,
                                      loose=0.2, depth=0.8)
    _compare_io(my_inv_op)
    _compare_inverses_approx(my_inv_op, inverse_operator, evoked, 2)
    # Inverse has 306 channels - 4 proj = 302
    assert_true(compute_rank_inverse(inverse_operator) == 302)

    stc = apply_inverse(evoked, inverse_operator, lambda2, "MNE")
    assert_true(stc.subject == 'sample')
    assert_true(stc.data.min() > 0)
    assert_true(stc.data.max() < 10e-10)
    assert_true(stc.data.mean() > 1e-11)

    # test if using prepared and not prepared inverse operator give the same
    # result
    inv_op = prepare_inverse_operator(inverse_operator, nave=evoked.nave,
                                      lambda2=lambda2, method="MNE")
    stc2 = apply_inverse(evoked, inv_op, lambda2, "MNE")
    assert_array_almost_equal(stc.data, stc2.data)
    assert_array_almost_equal(stc.times, stc2.times)

    stc = apply_inverse(evoked, inverse_operator, lambda2, "sLORETA")
    assert_true(stc.subject == 'sample')
    assert_true(stc.data.min() > 0)
    assert_true(stc.data.max() < 10.0)
    assert_true(stc.data.mean() > 0.1)

    stc = apply_inverse(evoked, inverse_operator, lambda2, "dSPM")
    assert_true(stc.subject == 'sample')
    assert_true(stc.data.min() > 0)
    assert_true(stc.data.max() < 35)
    assert_true(stc.data.mean() > 0.1)

    my_stc = apply_inverse(evoked, my_inv_op, lambda2, "dSPM")

    assert_true('dev_head_t' in my_inv_op['info'])
    assert_true('mri_head_t' in my_inv_op)

    assert_true(my_stc.subject == 'sample')
    assert_equal(stc.times, my_stc.times)
    assert_array_almost_equal(stc.data, my_stc.data, 2)

def test_source_psd_epochs():
    """Test multi-taper source PSD computation in label from epochs."""
    raw = read_raw_fif(fname_data)
    inverse_operator = read_inverse_operator(fname_inv)
    label = read_label(fname_label)

    event_id, tmin, tmax = 1, -0.2, 0.5
    lambda2, method = 1. / 9., 'dSPM'
    bandwidth = 8.
    fmin, fmax = 0, 100

    picks = pick_types(raw.info, meg=True, eeg=False, stim=True,
                       ecg=True, eog=True, include=['STI 014'],
                       exclude='bads')
    reject = dict(grad=4000e-13, mag=4e-12, eog=150e-6)

    events = find_events(raw, stim_channel='STI 014')
    epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
                    baseline=(None, 0), reject=reject)

    # only look at one epoch
    epochs.drop_bad()
    one_epochs = epochs[:1]

    inv = prepare_inverse_operator(inverse_operator, nave=1,
                                   lambda2=1. / 9., method="dSPM")
    # return list
    stc_psd = compute_source_psd_epochs(one_epochs, inv,
                                        lambda2=lambda2, method=method,
                                        pick_ori="normal", label=label,
                                        bandwidth=bandwidth,
                                        fmin=fmin, fmax=fmax,
                                        prepared=True)[0]

    # return generator
    stcs = compute_source_psd_epochs(one_epochs, inv,
                                     lambda2=lambda2, method=method,
                                     pick_ori="normal", label=label,
                                     bandwidth=bandwidth,
                                     fmin=fmin, fmax=fmax,
                                     return_generator=True,
                                     prepared=True)

    for stc in stcs:
        stc_psd_gen = stc

    assert_allclose(stc_psd.data, stc_psd_gen.data, atol=1e-7)

    # compare with direct computation
    stc = apply_inverse_epochs(one_epochs, inv,
                               lambda2=lambda2, method=method,
                               pick_ori="normal", label=label,
                               prepared=True)[0]

    sfreq = epochs.info['sfreq']
    psd, freqs = psd_array_multitaper(stc.data, sfreq=sfreq,
                                      bandwidth=bandwidth, fmin=fmin,
                                      fmax=fmax)

    assert_allclose(psd, stc_psd.data, atol=1e-7)
    assert_allclose(freqs, stc_psd.times)

    # Check corner cases caused by tiny bandwidth
    with pytest.raises(ValueError, match='use a value of at least'):
        compute_source_psd_epochs(
            one_epochs, inv, lambda2=lambda2, method=method,
            pick_ori="normal", label=label, bandwidth=0.01, low_bias=True,
            fmin=fmin, fmax=fmax, return_generator=False, prepared=True)