Python fiff.pick_types函数代码示例

def test_data():
    """Test reading raw kit files
    """
    raw_py = kit.read_raw_kit(input_fname=op.join(data_dir, 'test.sqd'),
                           mrk_fname=op.join(data_dir, 'test_mrk.sqd'),
                           elp_fname=op.join(data_dir, 'test_elp.txt'),
                           hsp_fname=op.join(data_dir, 'test_hsp.txt'),
                           sns_fname=op.join(data_dir, 'sns.txt'),
                           stim=range(167, 159, -1), stimthresh=1,
                           preload=True)
    # Binary file only stores the sensor channels
    py_picks = pick_types(raw_py.info, exclude='bads')
    raw_bin = op.join(data_dir, 'test_bin.fif')
    raw_bin = Raw(raw_bin, preload=True)
    bin_picks = pick_types(raw_bin.info, stim=True, exclude='bads')
    data_bin, _ = raw_bin[bin_picks]
    data_py, _ = raw_py[py_picks]

    # this .mat was generated using the Yokogawa MEG Reader
    data_Ykgw = op.join(data_dir, 'test_Ykgw.mat')
    data_Ykgw = scipy.io.loadmat(data_Ykgw)['data']
    data_Ykgw = data_Ykgw[py_picks]

    assert_array_almost_equal(data_py, data_Ykgw)

    py_picks = pick_types(raw_py.info, stim=True, exclude='bads')
    data_py, _ = raw_py[py_picks]
    assert_array_almost_equal(data_py, data_bin)

def test_data():
    """Test reading raw kit files
    """
    raw_py = read_raw_kit(sqd_path, mrk_path, elp_path, hsp_path,
                          stim=list(range(167, 159, -1)), slope='+',
                          stimthresh=1, preload=True)
    print(repr(raw_py))

    # Binary file only stores the sensor channels
    py_picks = pick_types(raw_py.info, exclude='bads')
    raw_bin = op.join(data_dir, 'test_bin.fif')
    raw_bin = Raw(raw_bin, preload=True)
    bin_picks = pick_types(raw_bin.info, stim=True, exclude='bads')
    data_bin, _ = raw_bin[bin_picks]
    data_py, _ = raw_py[py_picks]

    # this .mat was generated using the Yokogawa MEG Reader
    data_Ykgw = op.join(data_dir, 'test_Ykgw.mat')
    data_Ykgw = scipy.io.loadmat(data_Ykgw)['data']
    data_Ykgw = data_Ykgw[py_picks]

    assert_array_almost_equal(data_py, data_Ykgw)

    py_picks = pick_types(raw_py.info, stim=True, ref_meg=False,
                          exclude='bads')
    data_py, _ = raw_py[py_picks]
    assert_array_almost_equal(data_py, data_bin)

def test_compensation_mne():
    """Test comensation by comparing with MNE
    """
    def make_evoked(fname, comp):
        raw = Raw(fname, compensation=comp)
        picks = pick_types(raw.info, meg=True, ref_meg=True)
        events = np.array([[0, 0, 1]], dtype=np.int)
        evoked = Epochs(raw, events, 1, 0, 20e-3, picks=picks).average()
        return evoked

    def compensate_mne(fname, comp):
        tmp_fname = '%s-%d.fif' % (fname[:-4], comp)
        cmd = ['mne_compensate_data', '--in', fname,
               '--out', tmp_fname, '--grad', str(comp)]
        run_subprocess(cmd)
        return read_evokeds(tmp_fname)[0]

    # save evoked response with default compensation
    fname_default = op.join(tempdir, 'ctf_default-ave.fif')
    make_evoked(ctf_comp_fname, None).save(fname_default)

    for comp in [0, 1, 2, 3]:
        evoked_py = make_evoked(ctf_comp_fname, comp)
        evoked_c = compensate_mne(fname_default, comp)
        picks_py = pick_types(evoked_py.info, meg=True, ref_meg=True)
        picks_c = pick_types(evoked_c.info, meg=True, ref_meg=True)
        assert_allclose(evoked_py.data[picks_py], evoked_c.data[picks_c],
                        rtol=1e-3, atol=1e-17)

def test_set_eeg_reference():
    """ Test rereference eeg data"""
    raw = Raw(fif_fname, preload=True)

    # Rereference raw data by creating a copy of original data
    reref, ref_data = set_eeg_reference(raw, ['EEG 001', 'EEG 002'], copy=True)

    # Separate EEG channels from other channel types
    picks_eeg = pick_types(raw.info, meg=False, eeg=True, exclude='bads')
    picks_other = pick_types(raw.info, meg=True, eeg=False, eog=True,
                             stim=True, exclude='bads')

    # Get the raw EEG data and other channel data
    raw_eeg_data = raw[picks_eeg][0]
    raw_other_data = raw[picks_other][0]

    # Get the rereferenced EEG data and channel other
    reref_eeg_data = reref[picks_eeg][0]
    unref_eeg_data = reref_eeg_data + ref_data
    # Undo rereferencing of EEG channels
    reref_other_data = reref[picks_other][0]

    # Check that both EEG data and other data is the same
    assert_array_equal(raw_eeg_data, unref_eeg_data)
    assert_array_equal(raw_other_data, reref_other_data)

    # Test that data is modified in place when copy=False
    reref, ref_data = set_eeg_reference(raw, ['EEG 001', 'EEG 002'],
                                        copy=False)
    assert_true(raw is reref)

def test_raw_to_nitime():
    """ Test nitime export """
    raw = Raw(fif_fname, preload=True)
    picks_meg = pick_types(raw.info, meg=True, exclude='bads')
    picks = picks_meg[:4]
    raw_ts = raw.to_nitime(picks=picks)
    assert_true(raw_ts.data.shape[0] == len(picks))

    raw = Raw(fif_fname, preload=False)
    picks_meg = pick_types(raw.info, meg=True, exclude='bads')
    picks = picks_meg[:4]
    raw_ts = raw.to_nitime(picks=picks)
    assert_true(raw_ts.data.shape[0] == len(picks))

    raw = Raw(fif_fname, preload=True)
    picks_meg = pick_types(raw.info, meg=True, exclude='bads')
    picks = picks_meg[:4]
    raw_ts = raw.to_nitime(picks=picks, copy=False)
    assert_true(raw_ts.data.shape[0] == len(picks))

    raw = Raw(fif_fname, preload=False)
    picks_meg = pick_types(raw.info, meg=True, exclude='bads')
    picks = picks_meg[:4]
    raw_ts = raw.to_nitime(picks=picks, copy=False)
    assert_true(raw_ts.data.shape[0] == len(picks))

def test_brainvision_data():
    """Test reading raw Brain Vision files
    """
    raw_py = read_raw_brainvision(vhdr_path, elp_path, elp_names, preload=True)
    picks = pick_types(raw_py.info, meg=False, eeg=True, exclude='bads')
    data_py, times_py = raw_py[picks]

    print(raw_py)  # to test repr
    print(raw_py.info)  # to test Info repr

    # compare with a file that was generated using MNE-C
    raw_bin = Raw(eeg_bin, preload=True)
    picks = pick_types(raw_py.info, meg=False, eeg=True, exclude='bads')
    data_bin, times_bin = raw_bin[picks]

    assert_array_almost_equal(data_py, data_bin)
    assert_array_almost_equal(times_py, times_bin)

    # Make sure EOG channels are marked correctly
    raw_py = read_raw_brainvision(vhdr_path, elp_path, elp_names, eog=eog,
                                  preload=True)
    for ch in raw_py.info['chs']:
        if ch['ch_name'] in eog:
            assert_equal(ch['kind'], FIFF.FIFFV_EOG_CH)
        elif ch['ch_name'] in elp_names:
            assert_equal(ch['kind'], FIFF.FIFFV_EEG_CH)
        elif ch['ch_name'] == 'STI 014':
            assert_equal(ch['kind'], FIFF.FIFFV_STIM_CH)
        else:
            raise RuntimeError("Unknown Channel: %s" % ch['ch_name'])

def test_rank_estimation():
    """Test raw rank estimation
    """
    raw = Raw(fif_fname)
    n_meg = len(pick_types(raw.info, meg=True, eeg=False, exclude="bads"))
    n_eeg = len(pick_types(raw.info, meg=False, eeg=True, exclude="bads"))
    raw = Raw(fif_fname, preload=True)
    assert_array_equal(raw.estimate_rank(), n_meg + n_eeg)
    raw = Raw(fif_fname, preload=False)
    raw.apply_proj()
    n_proj = len(raw.info["projs"])
    assert_array_equal(raw.estimate_rank(tstart=10, tstop=20), n_meg + n_eeg - n_proj)

def test_filter():
    """ Test filtering and Raw.apply_function interface """

    raw = Raw(fif_fname, preload=True)
    picks_meg = pick_types(raw.info, meg=True)
    picks = picks_meg[:4]

    raw_lp = deepcopy(raw)
    raw_lp.filter(0.0, 4.0, picks=picks, n_jobs=2)

    raw_hp = deepcopy(raw)
    raw_lp.filter(8.0, None, picks=picks, n_jobs=2)

    raw_bp = deepcopy(raw)
    raw_bp.filter(4.0, 8.0, picks=picks)

    data, _ = raw[picks, :]

    lp_data, _ = raw_lp[picks, :]
    hp_data, _ = raw_hp[picks, :]
    bp_data, _ = raw_bp[picks, :]

    assert_array_almost_equal(data, lp_data + hp_data + bp_data)

    # make sure we didn't touch other channels
    data, _ = raw[picks_meg[4:], :]
    bp_data, _ = raw_bp[picks_meg[4:], :]

    assert_array_equal(data, bp_data)

def test_detrend():
    """Test detrending of epochs
    """
    # test first-order
    epochs_1 = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks,
                      baseline=None, detrend=1)
    epochs_2 = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks,
                      baseline=None, detrend=None)
    data_picks = fiff.pick_types(epochs_1.info, meg=True, eeg=True,
                                 exclude='bads')
    evoked_1 = epochs_1.average()
    evoked_2 = epochs_2.average()
    evoked_2.detrend(1)
    # Due to roundoff these won't be exactly equal, but they should be close
    assert_true(np.allclose(evoked_1.data, evoked_2.data,
                            rtol=1e-8, atol=1e-20))

    # test zeroth-order case
    for preload in [True, False]:
        epochs_1 = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks,
                          baseline=(None, None), preload=preload)
        epochs_2 = Epochs(raw, events[:4], event_id, tmin, tmax, picks=picks,
                          baseline=None, preload=preload, detrend=0)
        a = epochs_1.get_data()
        b = epochs_2.get_data()
        # All data channels should be almost equal
        assert_true(np.allclose(a[:, data_picks, :], b[:, data_picks, :],
                                rtol=1e-16, atol=1e-20))
        # There are non-M/EEG channels that should not be equal:
        assert_true(not np.allclose(a, b))

def test_preload_modify():
    """ Test preloading and modifying data
    """
    for preload in [False, True, "memmap.dat"]:
        raw = Raw(fif_fname, preload=preload)

        nsamp = raw.last_samp - raw.first_samp + 1
        picks = pick_types(raw.info, meg="grad", exclude="bads")

        data = np.random.randn(len(picks), nsamp / 2)

        try:
            raw[picks, : nsamp / 2] = data
        except RuntimeError as err:
            if not preload:
                continue
            else:
                raise err

        tmp_fname = op.join(tempdir, "raw.fif")
        raw.save(tmp_fname, overwrite=True)

        raw_new = Raw(tmp_fname)
        data_new, _ = raw_new[picks, : nsamp / 2]

        assert_allclose(data, data_new)

def test_psd():
    """Test PSD estimation
    """
    raw = fiff.Raw(raw_fname)

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

    # picks MEG gradiometers
    picks = fiff.pick_types(raw.info, meg='mag', eeg=False, stim=False,
                            exclude=exclude)

    picks = picks[:2]

    tmin, tmax = 0, 10  # use the first 60s of data
    fmin, fmax = 2, 70  # look at frequencies between 5 and 70Hz
    NFFT = 124  # the FFT size (NFFT). Ideally a power of 2
    psds, freqs = compute_raw_psd(raw, tmin=tmin, tmax=tmax, picks=picks,
                                  fmin=fmin, fmax=fmax, NFFT=NFFT, n_jobs=1,
                                  proj=False)
    psds_proj, freqs = compute_raw_psd(raw, tmin=tmin, tmax=tmax, picks=picks,
                                       fmin=fmin, fmax=fmax, NFFT=NFFT,
                                       n_jobs=1, proj=True)

    assert_array_almost_equal(psds, psds_proj)
    assert_true(psds.shape == (len(picks), len(freqs)))
    assert_true(np.sum(freqs < 0) == 0)
    assert_true(np.sum(psds < 0) == 0)

def test_apply_mne_inverse_epochs():
    """Test MNE with precomputed inverse operator on Epochs
    """
    event_id, tmin, tmax = 1, -0.2, 0.5

    picks = fiff.pick_types(raw.info, meg=True, eeg=False, stim=True,
                            ecg=True, eog=True, include=['STI 014'])
    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)
    stcs = apply_inverse_epochs(epochs, inverse_operator, lambda2, "dSPM",
                                label=label, pick_normal=True)

    assert_true(len(stcs) == 4)
    assert_true(3 < stcs[0].data.max() < 10)

    data = sum(stc.data for stc in stcs) / len(stcs)
    flip = label_sign_flip(label, 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())

def test_ems():
    """Test event-matched spatial filters"""
    raw = fiff.Raw(raw_fname, preload=False)

    # create unequal number of events
    events = read_events(event_name)
    events[-2, 2] = 3
    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)
    assert_raises(ValueError, compute_ems, epochs, ['aud_l', 'vis_l'])
    epochs.equalize_event_counts(epochs.event_id, copy=False)

    assert_raises(KeyError, compute_ems, epochs, ['blah', 'hahah'])
    surrogates, filters, conditions = compute_ems(epochs)
    assert_equal(list(set(conditions)), [1, 3])

    events = read_events(event_name)
    event_id2 = dict(aud_l=1, aud_r=2, vis_l=3)
    epochs = Epochs(raw, events, event_id2, tmin, tmax, picks=picks,
                    baseline=(None, 0), preload=True)
    epochs.equalize_event_counts(epochs.event_id, copy=False)

    n_expected = sum([len(epochs[k]) for k in ['aud_l', 'vis_l']])

    assert_raises(ValueError, compute_ems, epochs)
    surrogates, filters, conditions = compute_ems(epochs, ['aud_r', 'vis_l'])
    assert_equal(n_expected, len(surrogates))
    assert_equal(n_expected, len(conditions))
    assert_equal(list(set(conditions)), [2, 3])
    raw.close()

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_preload_modify():
    """ Test preloading and modifying data
    """
    for preload in [False, True, 'memmap.dat']:
        raw = Raw(fif_fname, preload=preload)

        nsamp = raw.last_samp - raw.first_samp + 1
        picks = pick_types(raw.info, meg='grad', exclude='bads')

        data = np.random.randn(len(picks), nsamp / 2)

        try:
            raw[picks, :nsamp / 2] = data
        except RuntimeError as err:
            if not preload:
                continue
            else:
                raise err

        tmp_fname = op.join(tempdir, 'raw.fif')
        raw.save(tmp_fname)

        raw_new = Raw(tmp_fname)
        data_new, _ = raw_new[picks, :nsamp / 2]

        assert_array_almost_equal(data, data_new)