Python mne.setup_volume_source_space函数代码示例

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_volume_source_space():
    """Test setting up volume source spaces
    """
    fname_vol = op.join(data_path, "subjects", "sample", "bem", "volume-7mm-src.fif")
    src = read_source_spaces(fname_vol)
    temp_name = op.join(tempdir, "temp-src.fif")
    try:
        # The one in the sample dataset (uses bem as bounds)
        src_new = setup_volume_source_space(
            "sample", temp_name, pos=7.0, bem=fname_bem, mri=fname_mri, subjects_dir=subjects_dir
        )
        _compare_source_spaces(src, src_new, mode="approx")
        src_new = read_source_spaces(temp_name)
        _compare_source_spaces(src, src_new, mode="approx")

        # let's try the spherical one (no bem or surf supplied)
        run_subprocess(["mne_volume_source_space", "--grid", "15.0", "--src", temp_name, "--mri", fname_mri])
        src = read_source_spaces(temp_name)
        src_new = setup_volume_source_space("sample", temp_name, pos=15.0, mri=fname_mri, subjects_dir=subjects_dir)
        _compare_source_spaces(src, src_new, mode="approx")

        # now without MRI argument, it should give an error when we try
        # to read it
        run_subprocess(["mne_volume_source_space", "--grid", "15.0", "--src", temp_name])
        assert_raises(ValueError, read_source_spaces, temp_name)
    finally:
        if op.isfile(temp_name):
            os.remove(temp_name)

def test_volume_source_space():
    """Test setting up volume source spaces
    """
    fname_vol = op.join(data_path, 'subjects', 'sample', 'bem',
                        'volume-7mm-src.fif')
    src = read_source_spaces(fname_vol)
    temp_name = op.join(tempdir, 'temp-src.fif')
    try:
        # The one in the sample dataset (uses bem as bounds)
        src_new = setup_volume_source_space('sample', temp_name, pos=7.0,
                                            bem=fname_bem, mri=fname_mri,
                                            subjects_dir=subjects_dir)
        _compare_source_spaces(src, src_new, mode='approx')
        src_new = read_source_spaces(temp_name)
        _compare_source_spaces(src, src_new, mode='approx')

        # let's try the spherical one (no bem or surf supplied)
        run_subprocess(['mne_volume_source_space',
                        '--grid',  '15.0',
                        '--src', temp_name,
                        '--mri', fname_mri])
        src = read_source_spaces(temp_name)
        src_new = setup_volume_source_space('sample', temp_name, pos=15.0,
                                            mri=fname_mri,
                                            subjects_dir=subjects_dir)
        _compare_source_spaces(src, src_new, mode='approx')
    finally:
        if op.isfile(temp_name):
            os.remove(temp_name)

def test_forward_mixed_source_space():
    """Test making the forward solution for a mixed source space
    """
    # get bem file
    fname_bem = op.join(subjects_dir, 'sample', 'bem',
                        'sample-5120-5120-5120-bem-sol.fif')
    # get the aseg file
    fname_aseg = op.join(subjects_dir, 'sample', 'mri', 'aseg.mgz')

    # get the surface source space
    surf = setup_source_space('sample', fname=None, spacing='ico2')

    # setup two volume source spaces
    label_names = get_volume_labels_from_aseg(fname_aseg)
    vol_labels = [label_names[int(np.random.rand() * len(label_names))]
                  for _ in range(2)]
    vol1 = setup_volume_source_space('sample', fname=None, pos=20.,
                                     mri=fname_aseg,
                                     volume_label=vol_labels[0])
    vol2 = setup_volume_source_space('sample', fname=None, pos=20.,
                                     mri=fname_aseg,
                                     volume_label=vol_labels[1])

    # merge surfaces and volume
    src = surf + vol1 + vol2

    # calculate forward solution
    fwd = make_forward_solution(fname_raw, mri=fname_mri, src=src,
                                bem=fname_bem, fname=None)

    # extract source spaces
    src_from_fwd = fwd['src']

    # get the coordinate frame of each source space
    coord_frames = np.array([s['coord_frame'] for s in src_from_fwd])

    # assert that all source spaces are in head coordinates
    assert_true((coord_frames == FIFF.FIFFV_COORD_HEAD).all())

    # run tests for SourceSpaces.export_volume
    fname_img = op.join(temp_dir, 'temp-image.mgz')

    # head coordinates and mri_resolution, but trans file
    assert_raises(ValueError, src_from_fwd.export_volume, fname_img,
                  mri_resolution=True, trans=None)

    # head coordinates and mri_resolution, but wrong trans file
    vox_mri_t = vol1[0]['vox_mri_t']
    assert_raises(RuntimeError, src_from_fwd.export_volume, fname_img,
                  mri_resolution=True, trans=vox_mri_t)

def create_mixed_source_space(sbj_dir, sbj_id, spacing, labels, src):
    import os.path as op
    from mne import setup_volume_source_space

    bem_dir = op.join(sbj_dir, sbj_id, 'bem')

#    src_aseg_fname = op.join(bem_dir, '%s-%s-aseg-src.fif' %(sbj_id, spacing))
    aseg_fname = op.join(sbj_dir, sbj_id, 'mri/aseg.mgz')

    if spacing == 'oct-6':
        pos = 5.0
    elif spacing == 'ico-5':
        pos = 3.0

    model_fname = op.join(bem_dir, '%s-5120-bem.fif' % sbj_id)
    for l in labels:
        print l
        vol_label = setup_volume_source_space(sbj_id, mri=aseg_fname,
                                              pos=pos,
                                              bem=model_fname,
                                              volume_label=l,
                                              subjects_dir=sbj_dir)
        src += vol_label

#    write_source_spaces(src_aseg_fname, src)

    # Export source positions to nift file
    nii_fname = op.join(bem_dir, '%s-%s-aseg-src.nii' % (sbj_id, spacing))

    # Combine the source spaces
    src.export_volume(nii_fname, mri_resolution=True)

    return src

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_discrete_source_space():
    """Test setting up (and reading/writing) discrete source spaces
    """
    src = read_source_spaces(fname)
    v = src[0]["vertno"]

    # let's make a discrete version with the C code, and with ours
    temp_name = op.join(tempdir, "temp-src.fif")
    try:
        # save
        temp_pos = op.join(tempdir, "temp-pos.txt")
        np.savetxt(temp_pos, np.c_[src[0]["rr"][v], src[0]["nn"][v]])
        # let's try the spherical one (no bem or surf supplied)
        run_subprocess(["mne_volume_source_space", "--meters", "--pos", temp_pos, "--src", temp_name])
        src_c = read_source_spaces(temp_name)
        pos_dict = dict(rr=src[0]["rr"][v], nn=src[0]["nn"][v])
        src_new = setup_volume_source_space("sample", None, pos=pos_dict, subjects_dir=subjects_dir)
        _compare_source_spaces(src_c, src_new, mode="approx")
        assert_allclose(src[0]["rr"][v], src_new[0]["rr"], rtol=1e-3, atol=1e-6)
        assert_allclose(src[0]["nn"][v], src_new[0]["nn"], rtol=1e-3, atol=1e-6)

        # now do writing
        write_source_spaces(temp_name, src_c)
        src_c2 = read_source_spaces(temp_name)
        _compare_source_spaces(src_c, src_c2)

        # now do MRI
        assert_raises(ValueError, setup_volume_source_space, "sample", pos=pos_dict, mri=fname_mri)
    finally:
        if op.isfile(temp_name):
            os.remove(temp_name)

def _mne_source_space(subject, src_tag, subjects_dir):
    """Load mne source space

    Parameters
    ----------
    subject : str
        Subejct
    src_tag : str
        Spacing (e.g., 'ico-4').
    """
    src_file = os.path.join(subjects_dir, subject, "bem", "%s-%s-src.fif" % (subject, src_tag))
    src, spacing = src_tag.split("-")
    if os.path.exists(src_file):
        return mne.read_source_spaces(src_file, False)
    elif src == "ico":
        return mne.setup_source_space(subject, src_file, src + spacing, subjects_dir=subjects_dir, add_dist=True)
    elif src == "vol":
        mri_file = os.path.join(subjects_dir, subject, "mri", "orig.mgz")
        bem_file = os.path.join(subjects_dir, subject, "bem", "sample-5120-5120-5120-bem-sol.fif")
        return mne.setup_volume_source_space(
            subject,
            src_file,
            float(spacing),
            mri=mri_file,
            bem=bem_file,
            mindist=0.0,
            exclude=0.0,
            subjects_dir=subjects_dir,
        )
    else:
        raise ValueError("src_tag=%s" % repr(src_tag))

def test_source_space_from_label():
    """Test generating a source space from volume label."""
    tempdir = _TempDir()
    aseg_fname = op.join(subjects_dir, 'sample', 'mri', 'aseg.mgz')
    label_names = get_volume_labels_from_aseg(aseg_fname)
    volume_label = label_names[int(np.random.rand() * len(label_names))]

    # Test pos as dict
    pos = dict()
    pytest.raises(ValueError, setup_volume_source_space, 'sample', pos=pos,
                  volume_label=volume_label, mri=aseg_fname)

    # Test no mri provided
    pytest.raises(RuntimeError, setup_volume_source_space, 'sample', mri=None,
                  volume_label=volume_label)

    # Test invalid volume label
    pytest.raises(ValueError, setup_volume_source_space, 'sample',
                  volume_label='Hello World!', mri=aseg_fname)

    src = setup_volume_source_space('sample', subjects_dir=subjects_dir,
                                    volume_label=volume_label, mri=aseg_fname,
                                    add_interpolator=False)
    assert_equal(volume_label, src[0]['seg_name'])

    # test reading and writing
    out_name = op.join(tempdir, 'temp-src.fif')
    write_source_spaces(out_name, src)
    src_from_file = read_source_spaces(out_name)
    _compare_source_spaces(src, src_from_file, mode='approx')

def test_other_volume_source_spaces():
    """Test setting up other volume source spaces"""
    # these are split off because they require the MNE tools, and
    # Travis doesn't seem to like them

    # let's try the spherical one (no bem or surf supplied)
    tempdir = _TempDir()
    temp_name = op.join(tempdir, 'temp-src.fif')
    run_subprocess(['mne_volume_source_space',
                    '--grid', '7.0',
                    '--src', temp_name,
                    '--mri', fname_mri])
    src = read_source_spaces(temp_name)
    src_new = setup_volume_source_space('sample', temp_name, pos=7.0,
                                        mri=fname_mri,
                                        subjects_dir=subjects_dir)
    _compare_source_spaces(src, src_new, mode='approx')
    del src
    del src_new
    assert_raises(ValueError, setup_volume_source_space, 'sample', temp_name,
                  pos=7.0, sphere=[1., 1.], mri=fname_mri,  # bad sphere
                  subjects_dir=subjects_dir)

    # now without MRI argument, it should give an error when we try
    # to read it
    run_subprocess(['mne_volume_source_space',
                    '--grid', '7.0',
                    '--src', temp_name])
    assert_raises(ValueError, read_source_spaces, temp_name)

def test_read_volume_from_src():
    """Test reading volumes from a mixed source space."""
    aseg_fname = op.join(subjects_dir, 'sample', 'mri', 'aseg.mgz')
    labels_vol = ['Left-Amygdala',
                  'Brain-Stem',
                  'Right-Amygdala']

    src = read_source_spaces(fname)

    # Setup a volume source space
    vol_src = setup_volume_source_space('sample', mri=aseg_fname,
                                        pos=5.0,
                                        bem=fname_bem,
                                        volume_label=labels_vol,
                                        subjects_dir=subjects_dir)
    # Generate the mixed source space
    src += vol_src

    volume_src = get_volume_labels_from_src(src, 'sample', subjects_dir)
    volume_label = volume_src[0].name
    volume_label = 'Left-' + volume_label.replace('-lh', '')

    # Test
    assert_equal(volume_label, src[2]['seg_name'])

    assert_equal(src[2]['type'], 'vol')

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_discrete_source_space():
    """Test setting up (and reading/writing) discrete source spaces
    """
    src = read_source_spaces(fname)
    v = src[0]['vertno']

    # let's make a discrete version with the C code, and with ours
    temp_name = op.join(tempdir, 'temp-src.fif')
    try:
        # save
        temp_pos = op.join(tempdir, 'temp-pos.txt')
        np.savetxt(temp_pos, np.c_[src[0]['rr'][v], src[0]['nn'][v]])
        # let's try the spherical one (no bem or surf supplied)
        run_subprocess(['mne_volume_source_space', '--meters',
                        '--pos',  temp_pos, '--src', temp_name])
        src_c = read_source_spaces(temp_name)
        src_new = setup_volume_source_space('sample', None,
                                            pos=dict(rr=src[0]['rr'][v],
                                                     nn=src[0]['nn'][v]),
                                            subjects_dir=subjects_dir)
        _compare_source_spaces(src_c, src_new, mode='approx')
        assert_allclose(src[0]['rr'][v], src_new[0]['rr'],
                        rtol=1e-3, atol=1e-6)
        assert_allclose(src[0]['nn'][v], src_new[0]['nn'],
                        rtol=1e-3, atol=1e-6)

        # now do writing
        write_source_spaces(temp_name, src_c)
        src_c2 = read_source_spaces(temp_name)
        _compare_source_spaces(src_c, src_c2)
    finally:
        if op.isfile(temp_name):
            os.remove(temp_name)

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_forward_mixed_source_space():
    """Test making the forward solution for a mixed source space
    """
    temp_dir = _TempDir()
    # get the surface source space
    surf = read_source_spaces(fname_src)

    # setup two volume source spaces
    label_names = get_volume_labels_from_aseg(fname_aseg)
    vol_labels = [label_names[int(np.random.rand() * len(label_names))]
                  for _ in range(2)]
    vol1 = setup_volume_source_space('sample', fname=None, pos=20.,
                                     mri=fname_aseg,
                                     volume_label=vol_labels[0],
                                     add_interpolator=False)
    vol2 = setup_volume_source_space('sample', fname=None, pos=20.,
                                     mri=fname_aseg,
                                     volume_label=vol_labels[1],
                                     add_interpolator=False)

    # merge surfaces and volume
    src = surf + vol1 + vol2

    # calculate forward solution
    fwd = make_forward_solution(fname_raw, fname_trans, src, fname_bem, None)
    assert_true(repr(fwd))

    # extract source spaces
    src_from_fwd = fwd['src']

    # get the coordinate frame of each source space
    coord_frames = np.array([s['coord_frame'] for s in src_from_fwd])

    # assert that all source spaces are in head coordinates
    assert_true((coord_frames == FIFF.FIFFV_COORD_HEAD).all())

    # run tests for SourceSpaces.export_volume
    fname_img = op.join(temp_dir, 'temp-image.mgz')

    # head coordinates and mri_resolution, but trans file
    assert_raises(ValueError, src_from_fwd.export_volume, fname_img,
                  mri_resolution=True, trans=None)

    # head coordinates and mri_resolution, but wrong trans file
    vox_mri_t = vol1[0]['vox_mri_t']
    assert_raises(ValueError, src_from_fwd.export_volume, fname_img,
                  mri_resolution=True, trans=vox_mri_t)