Python mne.pick_types函数代码示例

def _picks_by_type_old(info, meg_combined=False, ref_meg=False,
                       exclude='bads'):
    """Use the old, slower _picks_by_type code."""
    picks_list = []
    has = [_contains_ch_type(info, k) for k in _DATA_CH_TYPES_SPLIT]
    has = dict(zip(_DATA_CH_TYPES_SPLIT, has))
    if has['mag'] and (meg_combined is not True or not has['grad']):
        picks_list.append(
            ('mag', pick_types(info, meg='mag', eeg=False, stim=False,
                               ref_meg=ref_meg, exclude=exclude))
        )
    if has['grad'] and (meg_combined is not True or not has['mag']):
        picks_list.append(
            ('grad', pick_types(info, meg='grad', eeg=False, stim=False,
                                ref_meg=ref_meg, exclude=exclude))
        )
    if has['mag'] and has['grad'] and meg_combined is True:
        picks_list.append(
            ('meg', pick_types(info, meg=True, eeg=False, stim=False,
                               ref_meg=ref_meg, exclude=exclude))
        )
    for ch_type in _DATA_CH_TYPES_SPLIT:
        if ch_type in ['grad', 'mag']:  # exclude just MEG channels
            continue
        if has[ch_type]:
            picks_list.append(
                (ch_type, pick_types(info, meg=False, stim=False,
                                     ref_meg=ref_meg, exclude=exclude,
                                     **{ch_type: True}))
            )
    return picks_list

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]
    with warnings.catch_warnings(record=True):
        raw_ts = raw.to_nitime(picks=picks)
    assert_equal(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]
    with warnings.catch_warnings(record=True):
        raw_ts = raw.to_nitime(picks=picks)
    assert_equal(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]
    with warnings.catch_warnings(record=True):
        raw_ts = raw.to_nitime(picks=picks, copy=False)
    assert_equal(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]
    with warnings.catch_warnings(record=True):
        raw_ts = raw.to_nitime(picks=picks, copy=False)
    assert_equal(raw_ts.data.shape[0], len(picks))

def _load_data():
    """Helper function to load data."""
    # It is more memory efficient to load data in a separate
    # function so it's loaded on-demand
    raw = io.read_raw_fif(raw_fname, add_eeg_ref=False)
    events = read_events(event_name)
    picks_eeg = pick_types(raw.info, meg=False, eeg=True, exclude=[])
    # select every second channel for faster speed but compensate by using
    # mode='accurate'.
    picks_meg = pick_types(raw.info, meg=True, eeg=False, exclude=[])[1::2]
    picks = pick_types(raw.info, meg=True, eeg=True, exclude=[])

    with warnings.catch_warnings(record=True):  # proj
        epochs_eeg = Epochs(raw, events, event_id, tmin, tmax, picks=picks_eeg, preload=True, reject=dict(eeg=80e-6))
        epochs_meg = Epochs(
            raw, events, event_id, tmin, tmax, picks=picks_meg, preload=True, reject=dict(grad=1000e-12, mag=4e-12)
        )
        epochs = Epochs(
            raw,
            events,
            event_id,
            tmin,
            tmax,
            picks=picks,
            preload=True,
            reject=dict(eeg=80e-6, grad=1000e-12, mag=4e-12),
        )
    return raw, epochs, epochs_eeg, epochs_meg

def test_find_ecg():
    """Test find ECG peaks"""
    raw = Raw(raw_fname)

    # once with mag-trick
    # once with characteristic channel
    for ch_name in ['MEG 1531', None]:
        events, ch_ECG, average_pulse, ecg = find_ecg_events(
            raw, event_id=999, ch_name=None, return_ecg=True)
        assert_equal(len(raw.times), len(ecg))
        n_events = len(events)
        _, times = raw[0, :]
        assert_true(55 < average_pulse < 60)

    picks = pick_types(
        raw.info, meg='grad', eeg=False, stim=False,
        eog=False, ecg=True, emg=False, ref_meg=False,
        exclude='bads')

    raw.load_data()
    ecg_epochs = create_ecg_epochs(raw, picks=picks, keep_ecg=True)
    assert_equal(len(ecg_epochs.events), n_events)
    assert_true('ECG-SYN' not in raw.ch_names)
    assert_true('ECG-SYN' in ecg_epochs.ch_names)

    picks = pick_types(
        ecg_epochs.info, meg=False, eeg=False, stim=False,
        eog=False, ecg=True, emg=False, ref_meg=False,
        exclude='bads')
    assert_true(len(picks) == 1)

def test_check_compensation_consistency():
    """Test check picks compensation."""
    raw = read_raw_ctf(ctf_fname, preload=False)
    events = make_fixed_length_events(raw, 99999)
    picks = pick_types(raw.info, meg=True, exclude=[], ref_meg=True)
    pick_ch_names = [raw.info['ch_names'][idx] for idx in picks]
    for (comp, expected_result) in zip([0, 1], [False, False]):
        raw.apply_gradient_compensation(comp)
        ret, missing = _bad_chans_comp(raw.info, pick_ch_names)
        assert ret == expected_result
        assert len(missing) == 0
        Epochs(raw, events, None, -0.2, 0.2, preload=False, picks=picks)

    picks = pick_types(raw.info, meg=True, exclude=[], ref_meg=False)
    pick_ch_names = [raw.info['ch_names'][idx] for idx in picks]

    for (comp, expected_result) in zip([0, 1], [False, True]):
        raw.apply_gradient_compensation(comp)
        ret, missing = _bad_chans_comp(raw.info, pick_ch_names)
        assert ret == expected_result
        assert len(missing) == 17
        with catch_logging() as log:
            Epochs(raw, events, None, -0.2, 0.2, preload=False,
                   picks=picks, verbose=True)
            assert'Removing 5 compensators' in log.getvalue()

def test_simulate_raw_chpi():
    """Test simulation of raw data with cHPI"""
    with warnings.catch_warnings(record=True):  # MaxShield
        raw = Raw(raw_chpi_fname, allow_maxshield=True)
    sphere = make_sphere_model('auto', 'auto', raw.info)
    # make sparse spherical source space
    sphere_vol = tuple(sphere['r0'] * 1000.) + (sphere.radius * 1000.,)
    src = setup_volume_source_space('sample', sphere=sphere_vol, pos=70.)
    stc = _make_stc(raw, src)
    # simulate data with cHPI on
    raw_sim = simulate_raw(raw, stc, None, src, sphere, cov=None, chpi=False)
    raw_chpi = simulate_raw(raw, stc, None, src, sphere, cov=None, chpi=True)
    # XXX we need to test that the cHPI signals are actually in the correct
    # place, but that should be a subsequent enhancement (not trivial to do so)
    psd_sim, freqs_sim = compute_raw_psd(raw_sim)
    psd_chpi, freqs_chpi = compute_raw_psd(raw_chpi)
    assert_array_equal(freqs_sim, freqs_chpi)
    hpi_freqs = np.array([x['custom_ref'][0]
                          for x in raw.info['hpi_meas'][0]['hpi_coils']])
    freq_idx = np.sort([np.argmin(np.abs(freqs_sim - f)) for f in hpi_freqs])
    picks_meg = pick_types(raw.info, meg=True, eeg=False)
    picks_eeg = pick_types(raw.info, meg=False, eeg=True)
    assert_allclose(psd_sim[picks_eeg], psd_chpi[picks_eeg])
    assert_true((psd_chpi[picks_meg][:, freq_idx] >
                 100 * psd_sim[picks_meg][:, freq_idx]).all())

def test_brainvision_data():
    """Test reading raw Brain Vision files
    """
    assert_raises(IOError, read_raw_brainvision, vmrk_path)
    assert_raises(ValueError, read_raw_brainvision, vhdr_path, montage,
                  preload=True, scale="foo")
    raw_py = _test_raw_reader(read_raw_brainvision, test_preloading=True,
                              vhdr_fname=vhdr_path, montage=montage, eog=eog)

    assert_true('RawBrainVision' in repr(raw_py))

    assert_equal(raw_py.info['highpass'], 0.)
    assert_equal(raw_py.info['lowpass'], 250.)

    picks = pick_types(raw_py.info, meg=False, eeg=True, exclude='bads')
    data_py, times_py = raw_py[picks]

    # 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
    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'] == 'STI 014':
            assert_equal(ch['kind'], FIFF.FIFFV_STIM_CH)
        elif ch['ch_name'] in raw_py.info['ch_names']:
            assert_equal(ch['kind'], FIFF.FIFFV_EEG_CH)
        else:
            raise RuntimeError("Unknown Channel: %s" % ch['ch_name'])

def test_ransac():
    """Some basic tests for ransac."""

    event_id = {'Visual/Left': 3}
    tmin, tmax = -0.2, 0.5

    events = mne.find_events(raw)
    epochs = mne.Epochs(raw, events, event_id, tmin, tmax,
                        baseline=(None, 0), decim=8,
                        reject=None, preload=True)
    # normal case
    picks = mne.pick_types(epochs.info, meg='mag', eeg=False, stim=False,
                           eog=False, exclude=[])

    ransac = Ransac(picks=picks)
    epochs_clean = ransac.fit_transform(epochs)
    assert_true(len(epochs_clean) == len(epochs))
    # Pass numpy instead of epochs
    X = epochs.get_data()
    assert_raises(AttributeError, ransac.fit, X)
    #
    # should not contain both channel types
    picks = mne.pick_types(epochs.info, meg=True, eeg=False, stim=False,
                           eog=False, exclude=[])
    ransac = Ransac(picks=picks)
    assert_raises(ValueError, ransac.fit, epochs)
    #
    # should not contain other channel types.
    picks = mne.pick_types(raw.info, meg=False, eeg=True, stim=True,
                           eog=False, exclude=[])
    ransac = Ransac(picks=picks)
    assert_raises(ValueError, ransac.fit, epochs)

def test_clean_info_bads():
    """Test cleaning info['bads'] when bad_channels are excluded """

    raw_file = op.join(op.dirname(__file__), "io", "tests", "data", "test_raw.fif")
    raw = Raw(raw_file)

    # select eeg channels
    picks_eeg = pick_types(raw.info, meg=False, eeg=True)

    # select 3 eeg channels as bads
    idx_eeg_bad_ch = picks_eeg[[1, 5, 14]]
    eeg_bad_ch = [raw.info["ch_names"][k] for k in idx_eeg_bad_ch]

    # select meg channels
    picks_meg = pick_types(raw.info, meg=True, eeg=False)

    # select randomly 3 meg channels as bads
    idx_meg_bad_ch = picks_meg[[0, 15, 34]]
    meg_bad_ch = [raw.info["ch_names"][k] for k in idx_meg_bad_ch]

    # simulate the bad channels
    raw.info["bads"] = eeg_bad_ch + meg_bad_ch

    # simulate the call to pick_info excluding the bad eeg channels
    info_eeg = pick_info(raw.info, picks_eeg)

    # simulate the call to pick_info excluding the bad meg channels
    info_meg = pick_info(raw.info, picks_meg)

    assert_equal(info_eeg["bads"], eeg_bad_ch)
    assert_equal(info_meg["bads"], meg_bad_ch)

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_load_fiff_from_raw():
    "Test loading data from a fiff raw file"
    ds = load.fiff.events(raw_path)

    # test separate events
    ds_evt = load.fiff.events(events=evt_path)
    ds_evt.name = ds.name
    assert_dataobj_equal(ds_evt, ds)

    # add epochs as ndvar
    ds = ds.sub('trigger == 32')
    ds_ndvar = load.fiff.add_epochs(ds, -0.1, 0.3, decim=10, data='mag',
                                    proj=False, reject=2e-12)
    meg = ds_ndvar['meg']
    eq_(meg.ndim, 3)
    data = meg.get_data(('case', 'sensor', 'time'))
    eq_(data.shape, (14, 102, 6))

    # compare with mne epochs
    ds_mne = load.fiff.add_mne_epochs(ds, -0.1, 0.3, decim=10, proj=False,
                                      reject={'mag': 2e-12})
    epochs = ds_mne['epochs']
    picks = pick_types(epochs.info, meg='mag')
    mne_data = epochs.get_data()[:, picks]
    eq_(meg.sensor.names, [epochs.info['ch_names'][i] for i in picks])
    assert_array_equal(data, mne_data)

    # with proj
    meg = load.fiff.epochs(ds, -0.1, 0.3, decim=10, data='mag', proj=True,
                           reject=2e-12)
    epochs = load.fiff.mne_epochs(ds, -0.1, 0.3, decim=10, proj=True,
                                  reject={'mag': 2e-12})
    picks = pick_types(epochs.info, meg='mag')
    mne_data = epochs.get_data()[:, picks]
    assert_array_almost_equal(meg.x, mne_data, 10)

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 interpolate_bads(inst, picks, dots=None, reset_bads=True, mode='accurate'):
    """Interpolate bad MEG and EEG channels."""
    import mne
    # to prevent cobyla printf error
    # XXX putting to critical for now unless better solution
    # emerges
    verbose = mne.set_log_level('CRITICAL', return_old_level=True)

    eeg_picks = set(pick_types(inst.info, meg=False, eeg=True, exclude=[]))
    eeg_picks_interp = [p for p in picks if p in eeg_picks]
    if len(eeg_picks_interp) > 0:
        _interpolate_bads_eeg(inst, picks=eeg_picks_interp)

    meg_picks = set(pick_types(inst.info, meg=True, eeg=False, exclude=[]))
    meg_picks_interp = [p for p in picks if p in meg_picks]
    if len(meg_picks_interp) > 0:
        _interpolate_bads_meg_fast(inst, picks=meg_picks_interp,
                                   dots=dots, mode=mode)

    if reset_bads is True:
        inst.info['bads'] = []

    mne.set_log_level(verbose)

    return inst

def test_epochs_proj():
    """Test handling projection (apply proj in Raw or in Epochs)
    """
    exclude = raw.info["bads"] + ["MEG 2443", "EEG 053"]  # bads + 2 more
    this_picks = pick_types(raw.info, meg=True, eeg=False, stim=True, eog=True, exclude=exclude)
    epochs = Epochs(raw, events[:4], event_id, tmin, tmax, picks=this_picks, baseline=(None, 0), proj=True)
    assert_true(all(p["active"] is True for p in epochs.info["projs"]))
    evoked = epochs.average()
    assert_true(all(p["active"] is True for p in evoked.info["projs"]))
    data = epochs.get_data()

    raw_proj = io.Raw(raw_fname, proj=True)
    epochs_no_proj = Epochs(
        raw_proj, events[:4], event_id, tmin, tmax, picks=this_picks, baseline=(None, 0), proj=False
    )

    data_no_proj = epochs_no_proj.get_data()
    assert_true(all(p["active"] is True for p in epochs_no_proj.info["projs"]))
    evoked_no_proj = epochs_no_proj.average()
    assert_true(all(p["active"] is True for p in evoked_no_proj.info["projs"]))
    assert_true(epochs_no_proj.proj is True)  # as projs are active from Raw

    assert_array_almost_equal(data, data_no_proj, decimal=8)

    # make sure we can exclude avg ref
    this_picks = pick_types(raw.info, meg=True, eeg=True, stim=True, eog=True, exclude=exclude)
    epochs = Epochs(
        raw, events[:4], event_id, tmin, tmax, picks=this_picks, baseline=(None, 0), proj=True, add_eeg_ref=True
    )
    assert_true(_has_eeg_average_ref_proj(epochs.info["projs"]))
    epochs = Epochs(
        raw, events[:4], event_id, tmin, tmax, picks=this_picks, baseline=(None, 0), proj=True, add_eeg_ref=False
    )
    assert_true(not _has_eeg_average_ref_proj(epochs.info["projs"]))

def get_data_picks(inst, meg_combined=False):
    """Get data channel indices as separate list of tuples

    Parameters
    ----------
    inst : instance of mne.measuerment_info.Info
        The info
    meg_combined : bool
        Whether to return combined picks for grad and mag.

    Returns
    -------
    picks_list : list of tuples
        The list of tuples of picks and the type string.
    """
    info = inst.info
    picks_list = []
    has_mag, has_grad, has_eeg = [k in inst for k in ('mag', 'grad', 'eeg')]
    if has_mag and (meg_combined is not True or not has_grad):
        picks_list.append(
            (pick_types(info, meg='mag', eeg=False, stim=False), 'mag')
        )
    if has_grad and (meg_combined is not True or not has_mag):
        picks_list.append(
            (pick_types(info, meg='grad', eeg=False, stim=False), 'grad')
        )
    if has_mag and has_grad and meg_combined is True:
        picks_list.append(
            (pick_types(info, meg=True, eeg=False, stim=False), 'meg')
        )
    if has_eeg:
        picks_list.append(
            (pick_types(info, meg=False, eeg=True, stim=False), 'eeg')
        )
    return picks_list