Python mne.make_sphere_model函数代码示例

def test_make_sphere_model():
    """Test making a sphere model."""
    info = read_info(fname_raw)
    pytest.raises(ValueError, make_sphere_model, 'foo', 'auto', info)
    pytest.raises(ValueError, make_sphere_model, 'auto', 'auto', None)
    pytest.raises(ValueError, make_sphere_model, 'auto', 'auto', info,
                  relative_radii=(), sigmas=())
    pytest.raises(ValueError, make_sphere_model, 'auto', 'auto', info,
                  relative_radii=(1,))  # wrong number of radii
    # here we just make sure it works -- the functionality is actually
    # tested more extensively e.g. in the forward and dipole code
    with catch_logging() as log:
        bem = make_sphere_model('auto', 'auto', info, verbose=True)
    log = log.getvalue()
    assert ' RV = ' in log
    for line in log.split('\n'):
        if ' RV = ' in line:
            val = float(line.split()[-2])
            assert val < 0.01  # actually decent fitting
            break
    assert '3 layers' in repr(bem)
    assert 'Sphere ' in repr(bem)
    assert ' mm' in repr(bem)
    bem = make_sphere_model('auto', None, info)
    assert 'no layers' in repr(bem)
    assert 'Sphere ' in repr(bem)
    pytest.raises(ValueError, make_sphere_model, sigmas=(0.33,),
                  relative_radii=(1.0,))

def test_volume_source_space():
    """Test setting up volume source spaces."""
    tempdir = _TempDir()
    src = read_source_spaces(fname_vol)
    temp_name = op.join(tempdir, 'temp-src.fif')
    surf = read_bem_surfaces(fname_bem, s_id=FIFF.FIFFV_BEM_SURF_ID_BRAIN)
    surf['rr'] *= 1e3  # convert to mm
    # The one in the testing dataset (uses bem as bounds)
    for bem, surf in zip((fname_bem, None), (None, surf)):
        src_new = setup_volume_source_space(
            'sample', pos=7.0, bem=bem, surface=surf, mri='T1.mgz',
            subjects_dir=subjects_dir)
        write_source_spaces(temp_name, src_new, overwrite=True)
        src[0]['subject_his_id'] = 'sample'  # XXX: to make comparison pass
        _compare_source_spaces(src, src_new, mode='approx')
        del src_new
        src_new = read_source_spaces(temp_name)
        _compare_source_spaces(src, src_new, mode='approx')
    pytest.raises(IOError, setup_volume_source_space, 'sample',
                  pos=7.0, bem=None, surface='foo',  # bad surf
                  mri=fname_mri, subjects_dir=subjects_dir)
    assert repr(src) == repr(src_new)
    assert src.kind == 'volume'
    # Spheres
    sphere = make_sphere_model(r0=(0., 0., 0.), head_radius=0.1,
                               relative_radii=(0.9, 1.0), sigmas=(0.33, 1.0))
    src = setup_volume_source_space(pos=10)
    src_new = setup_volume_source_space(pos=10, sphere=sphere)
    _compare_source_spaces(src, src_new, mode='exact')
    pytest.raises(ValueError, setup_volume_source_space, sphere='foo')
    # Need a radius
    sphere = make_sphere_model(head_radius=None)
    pytest.raises(ValueError, setup_volume_source_space, sphere=sphere)

def test_make_sphere_model():
    """Test making a sphere model"""
    info = read_info(fname_raw)
    assert_raises(ValueError, make_sphere_model, 'foo', 'auto', info)
    assert_raises(ValueError, make_sphere_model, 'auto', 'auto', None)
    # here we just make sure it works -- the functionality is actually
    # tested more extensively e.g. in the forward and dipole code
    make_sphere_model('auto', 'auto', info)

def test_make_sphere_model():
    """Test making a sphere model"""
    info = read_info(fname_raw)
    assert_raises(ValueError, make_sphere_model, "foo", "auto", info)
    assert_raises(ValueError, make_sphere_model, "auto", "auto", None)
    # here we just make sure it works -- the functionality is actually
    # tested more extensively e.g. in the forward and dipole code
    bem = make_sphere_model("auto", "auto", info)
    assert_true("3 layers" in repr(bem))
    assert_true("Sphere " in repr(bem))
    assert_true(" mm" in repr(bem))
    bem = make_sphere_model("auto", None, info)
    assert_true("no layers" in repr(bem))
    assert_true("Sphere " in repr(bem))

def test_make_forward_solution_sphere():
    """Test making a forward solution with a sphere model"""
    temp_dir = _TempDir()
    fname_src_small = op.join(temp_dir, "sample-oct-2-src.fif")
    src = setup_source_space("sample", fname_src_small, "oct2", subjects_dir=subjects_dir, add_dist=False)
    out_name = op.join(temp_dir, "tmp-fwd.fif")
    run_subprocess(
        [
            "mne_forward_solution",
            "--meg",
            "--eeg",
            "--meas",
            fname_raw,
            "--src",
            fname_src_small,
            "--mri",
            fname_trans,
            "--fwd",
            out_name,
        ]
    )
    fwd = read_forward_solution(out_name)
    sphere = make_sphere_model(verbose=True)
    fwd_py = make_forward_solution(fname_raw, fname_trans, src, sphere, meg=True, eeg=True, verbose=True)
    _compare_forwards(fwd, fwd_py, 366, 108, meg_rtol=5e-1, meg_atol=1e-6, eeg_rtol=5e-1, eeg_atol=5e-1)
    # Since the above is pretty lax, let's check a different way
    for meg, eeg in zip([True, False], [False, True]):
        fwd_ = pick_types_forward(fwd, meg=meg, eeg=eeg)
        fwd_py_ = pick_types_forward(fwd, meg=meg, eeg=eeg)
        assert_allclose(np.corrcoef(fwd_["sol"]["data"].ravel(), fwd_py_["sol"]["data"].ravel())[0, 1], 1.0, rtol=1e-3)

def make_montage(info, kind, check=False):
    from . import _reorder
    assert kind in ('mgh60', 'mgh70', 'uw_70', 'uw_60')
    picks = mne.pick_types(info, meg=False, eeg=True, exclude=())
    if kind in ('mgh60', 'mgh70'):
        ch_names = mne.utils._clean_names(
            [info['ch_names'][pick] for pick in picks], remove_whitespace=True)
        if kind == 'mgh60':
            assert len(ch_names) in (59, 60)
        else:
            assert len(ch_names) in (70,)
        montage = mne.channels.read_montage(kind, ch_names=ch_names)
    else:
        ch_names = getattr(_reorder, 'ch_names_' + kind)
        ch_names = ch_names
        montage = mne.channels.read_montage('standard_1020', ch_names=ch_names)
        assert len(montage.ch_names) == len(ch_names)
        montage.ch_names = ['EEG%03d' % ii for ii in range(1, 61)]
    sphere = mne.make_sphere_model('auto', 'auto', info)
    montage.pos /= np.linalg.norm(montage.pos, axis=-1, keepdims=True)
    montage.pos *= sphere.radius
    montage.pos += sphere['r0']
    info = mne.pick_info(info, picks)
    eeg_pos = np.array([ch['loc'][:3] for ch in info['chs']])
    assert len(eeg_pos) == len(montage.pos), (len(eeg_pos), len(montage.pos))
    if check:
        from mayavi import mlab
        mlab.figure(size=(800, 800))
        mlab.points3d(*sphere['r0'], scale_factor=2 * sphere.radius,
                      color=(0., 0., 1.), opacity=0.1, mode='sphere')
        mlab.points3d(*montage.pos.T, scale_factor=0.01,
                      color=(1, 0, 0), mode='sphere', opacity=0.5)
        mlab.points3d(*eeg_pos.T, scale_factor=0.005, color=(1, 1, 1),
                      mode='sphere', opacity=1)
    return montage, sphere

def test_volume_labels_morph(tmpdir):
    """Test generating a source space from volume label."""
    # see gh-5224
    evoked = mne.read_evokeds(fname_evoked)[0].crop(0, 0)
    evoked.pick_channels(evoked.ch_names[:306:8])
    evoked.info.normalize_proj()
    n_ch = len(evoked.ch_names)
    aseg_fname = op.join(subjects_dir, 'sample', 'mri', 'aseg.mgz')
    label_names = get_volume_labels_from_aseg(aseg_fname)
    src = setup_volume_source_space(
        'sample', subjects_dir=subjects_dir, volume_label=label_names[:2],
        mri=aseg_fname)
    assert len(src) == 2
    assert src.kind == 'volume'
    n_src = sum(s['nuse'] for s in src)
    sphere = make_sphere_model('auto', 'auto', evoked.info)
    fwd = make_forward_solution(evoked.info, fname_trans, src, sphere)
    assert fwd['sol']['data'].shape == (n_ch, n_src * 3)
    inv = make_inverse_operator(evoked.info, fwd, make_ad_hoc_cov(evoked.info),
                                loose=1.)
    stc = apply_inverse(evoked, inv)
    assert stc.data.shape == (n_src, 1)
    img = stc.as_volume(src, mri_resolution=True)
    n_on = np.array(img.dataobj).astype(bool).sum()
    assert n_on == 291  # was 291 on `master` before gh-5590
    img = stc.as_volume(src, mri_resolution=False)
    n_on = np.array(img.dataobj).astype(bool).sum()
    assert n_on == 44  # was 20 on `master` before gh-5590

def test_gamma_map_vol_sphere():
    """Gamma MAP with a sphere forward and volumic source space"""
    evoked = read_evokeds(fname_evoked, condition=0, baseline=(None, 0),
                          proj=False)
    evoked.resample(50, npad=100)
    evoked.crop(tmin=0.1, tmax=0.16)  # crop to window around peak

    cov = read_cov(fname_cov)
    cov = regularize(cov, evoked.info)

    info = evoked.info
    sphere = mne.make_sphere_model(r0=(0., 0., 0.), head_radius=0.080)
    src = mne.setup_volume_source_space(subject=None, pos=15., mri=None,
                                        sphere=(0.0, 0.0, 0.0, 80.0),
                                        bem=None, mindist=5.0,
                                        exclude=2.0)
    fwd = mne.make_forward_solution(info, trans=None, src=src, bem=sphere,
                                    eeg=False, meg=True)

    alpha = 0.5
    assert_raises(ValueError, gamma_map, evoked, fwd, cov, alpha,
                  loose=0, return_residual=False)

    assert_raises(ValueError, gamma_map, evoked, fwd, cov, alpha,
                  loose=0.2, return_residual=False)

    stc = gamma_map(evoked, fwd, cov, alpha, tol=1e-4,
                    xyz_same_gamma=False, update_mode=2,
                    return_residual=False)

    assert_array_almost_equal(stc.times, evoked.times, 5)

def test_make_forward_solution_sphere():
    """Test making a forward solution with a sphere model."""
    temp_dir = _TempDir()
    fname_src_small = op.join(temp_dir, 'sample-oct-2-src.fif')
    src = setup_source_space('sample', 'oct2', subjects_dir=subjects_dir,
                             add_dist=False)
    write_source_spaces(fname_src_small, src)  # to enable working with MNE-C
    out_name = op.join(temp_dir, 'tmp-fwd.fif')
    run_subprocess(['mne_forward_solution', '--meg', '--eeg',
                    '--meas', fname_raw, '--src', fname_src_small,
                    '--mri', fname_trans, '--fwd', out_name])
    fwd = read_forward_solution(out_name)
    sphere = make_sphere_model(verbose=True)
    fwd_py = make_forward_solution(fname_raw, fname_trans, src, sphere,
                                   meg=True, eeg=True, verbose=True)
    _compare_forwards(fwd, fwd_py, 366, 108,
                      meg_rtol=5e-1, meg_atol=1e-6,
                      eeg_rtol=5e-1, eeg_atol=5e-1)
    # Since the above is pretty lax, let's check a different way
    for meg, eeg in zip([True, False], [False, True]):
        fwd_ = pick_types_forward(fwd, meg=meg, eeg=eeg)
        fwd_py_ = pick_types_forward(fwd, meg=meg, eeg=eeg)
        assert_allclose(np.corrcoef(fwd_['sol']['data'].ravel(),
                                    fwd_py_['sol']['data'].ravel())[0, 1],
                        1.0, rtol=1e-3)

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_apply_inverse_sphere():
    """Test applying an inverse with a sphere model (rank-deficient)."""
    evoked = _get_evoked()
    evoked.pick_channels(evoked.ch_names[:306:8])
    evoked.info['projs'] = []
    cov = make_ad_hoc_cov(evoked.info)
    sphere = make_sphere_model('auto', 'auto', evoked.info)
    fwd = read_forward_solution(fname_fwd)
    vertices = [fwd['src'][0]['vertno'][::5],
                fwd['src'][1]['vertno'][::5]]
    stc = SourceEstimate(np.zeros((sum(len(v) for v in vertices), 1)),
                         vertices, 0., 1.)
    fwd = restrict_forward_to_stc(fwd, stc)
    fwd = make_forward_solution(evoked.info, fwd['mri_head_t'], fwd['src'],
                                sphere, mindist=5.)
    evoked = EvokedArray(fwd['sol']['data'].copy(), evoked.info)
    assert fwd['sol']['nrow'] == 39
    assert fwd['nsource'] == 101
    assert fwd['sol']['ncol'] == 303
    tempdir = _TempDir()
    temp_fname = op.join(tempdir, 'temp-inv.fif')
    inv = make_inverse_operator(evoked.info, fwd, cov, loose=1.)
    # This forces everything to be float32
    write_inverse_operator(temp_fname, inv)
    inv = read_inverse_operator(temp_fname)
    stc = apply_inverse(evoked, inv, method='eLORETA',
                        method_params=dict(eps=1e-2))
    # assert zero localization bias
    assert_array_equal(np.argmax(stc.data, axis=0),
                       np.repeat(np.arange(101), 3))

def test_make_sphere_model():
    """Test making a sphere model"""
    info = read_info(fname_raw)
    assert_raises(ValueError, make_sphere_model, 'foo', 'auto', info)
    assert_raises(ValueError, make_sphere_model, 'auto', 'auto', None)
    assert_raises(ValueError, make_sphere_model, 'auto', 'auto', info,
                  relative_radii=(), sigmas=())
    assert_raises(ValueError, make_sphere_model, 'auto', 'auto', info,
                  relative_radii=(1,))  # wrong number of radii
    # here we just make sure it works -- the functionality is actually
    # tested more extensively e.g. in the forward and dipole code
    bem = make_sphere_model('auto', 'auto', info)
    assert_true('3 layers' in repr(bem))
    assert_true('Sphere ' in repr(bem))
    assert_true(' mm' in repr(bem))
    bem = make_sphere_model('auto', None, info)
    assert_true('no layers' in repr(bem))
    assert_true('Sphere ' in repr(bem))

def test_dipole_fitting_fixed():
    """Test dipole fitting with a fixed position."""
    import matplotlib.pyplot as plt
    tpeak = 0.073
    sphere = make_sphere_model(head_radius=0.1)
    evoked = read_evokeds(fname_evo, baseline=(None, 0))[0]
    evoked.pick_types(meg=True)
    t_idx = np.argmin(np.abs(tpeak - evoked.times))
    evoked_crop = evoked.copy().crop(tpeak, tpeak)
    assert_equal(len(evoked_crop.times), 1)
    cov = read_cov(fname_cov)
    dip_seq, resid = fit_dipole(evoked_crop, cov, sphere)
    assert isinstance(dip_seq, Dipole)
    assert isinstance(resid, Evoked)
    assert_equal(len(dip_seq.times), 1)
    pos, ori, gof = dip_seq.pos[0], dip_seq.ori[0], dip_seq.gof[0]
    amp = dip_seq.amplitude[0]
    # Fix position, allow orientation to change
    dip_free, resid_free = fit_dipole(evoked, cov, sphere, pos=pos)
    assert isinstance(dip_free, Dipole)
    assert isinstance(resid_free, Evoked)
    assert_allclose(dip_free.times, evoked.times)
    assert_allclose(np.tile(pos[np.newaxis], (len(evoked.times), 1)),
                    dip_free.pos)
    assert_allclose(ori, dip_free.ori[t_idx])  # should find same ori
    assert (np.dot(dip_free.ori, ori).mean() < 0.9)  # but few the same
    assert_allclose(gof, dip_free.gof[t_idx])  # ... same gof
    assert_allclose(amp, dip_free.amplitude[t_idx])  # and same amp
    assert_allclose(resid.data, resid_free.data[:, [t_idx]])
    # Fix position and orientation
    dip_fixed, resid_fixed = fit_dipole(evoked, cov, sphere, pos=pos, ori=ori)
    assert (isinstance(dip_fixed, DipoleFixed))
    assert_allclose(dip_fixed.times, evoked.times)
    assert_allclose(dip_fixed.info['chs'][0]['loc'][:3], pos)
    assert_allclose(dip_fixed.info['chs'][0]['loc'][3:6], ori)
    assert_allclose(dip_fixed.data[1, t_idx], gof)
    assert_allclose(resid.data, resid_fixed.data[:, [t_idx]])
    _check_roundtrip_fixed(dip_fixed)
    # bad resetting
    evoked.info['bads'] = [evoked.ch_names[3]]
    dip_fixed, resid_fixed = fit_dipole(evoked, cov, sphere, pos=pos, ori=ori)
    # Degenerate conditions
    evoked_nan = evoked.copy().crop(0, 0)
    evoked_nan.data[0, 0] = None
    pytest.raises(ValueError, fit_dipole, evoked_nan, cov, sphere)
    pytest.raises(ValueError, fit_dipole, evoked, cov, sphere, ori=[1, 0, 0])
    pytest.raises(ValueError, fit_dipole, evoked, cov, sphere, pos=[0, 0, 0],
                  ori=[2, 0, 0])
    pytest.raises(ValueError, fit_dipole, evoked, cov, sphere, pos=[0.1, 0, 0])
    # copying
    dip_fixed_2 = dip_fixed.copy()
    dip_fixed_2.data[:] = 0.
    assert not np.isclose(dip_fixed.data, 0., atol=1e-20).any()
    # plotting
    plt.close('all')
    dip_fixed.plot()
    plt.close('all')

def test_make_forward_solution_discrete():
    """Test making and converting a forward solution with discrete src."""
    # smoke test for depth weighting and discrete source spaces
    src = read_source_spaces(fname_src)[0]
    src = SourceSpaces([src] + setup_volume_source_space(
        pos=dict(rr=src['rr'][src['vertno'][:3]].copy(),
                 nn=src['nn'][src['vertno'][:3]].copy())))
    sphere = make_sphere_model()
    fwd = make_forward_solution(fname_raw, fname_trans, src, sphere,
                                meg=True, eeg=False)
    convert_forward_solution(fwd, surf_ori=True)

def test_dipole_fitting_ctf():
    """Test dipole fitting with CTF data."""
    raw_ctf = read_raw_ctf(fname_ctf).set_eeg_reference()
    events = make_fixed_length_events(raw_ctf, 1)
    evoked = Epochs(raw_ctf, events, 1, 0, 0, baseline=None).average()
    cov = make_ad_hoc_cov(evoked.info)
    sphere = make_sphere_model((0., 0., 0.))
    # XXX Eventually we should do some better checks about accuracy, but
    # for now our CTF phantom fitting tutorials will have to do
    # (otherwise we need to add that to the testing dataset, which is
    # a bit too big)
    fit_dipole(evoked, cov, sphere)