示例#1
0
def test_fit_matched_points():
    """Test fit_matched_points: fitting two matching sets of points."""
    tgt_pts = np.random.RandomState(42).uniform(size=(6, 3))

    # rotation only
    trans = rotation(2, 6, 3)
    src_pts = apply_trans(trans, tgt_pts)
    trans_est = fit_matched_points(src_pts, tgt_pts, translate=False,
                                   out='trans')
    est_pts = apply_trans(trans_est, src_pts)
    assert_array_almost_equal(tgt_pts, est_pts, 2, "fit_matched_points with "
                              "rotation")

    # rotation & translation
    trans = np.dot(translation(2, -6, 3), rotation(2, 6, 3))
    src_pts = apply_trans(trans, tgt_pts)
    trans_est = fit_matched_points(src_pts, tgt_pts, out='trans')
    est_pts = apply_trans(trans_est, src_pts)
    assert_array_almost_equal(tgt_pts, est_pts, 2, "fit_matched_points with "
                              "rotation and translation.")

    # rotation & translation & scaling
    trans = reduce(np.dot, (translation(2, -6, 3), rotation(1.5, .3, 1.4),
                            scaling(.5, .5, .5)))
    src_pts = apply_trans(trans, tgt_pts)
    trans_est = fit_matched_points(src_pts, tgt_pts, scale=1, out='trans')
    est_pts = apply_trans(trans_est, src_pts)
    assert_array_almost_equal(tgt_pts, est_pts, 2, "fit_matched_points with "
                              "rotation, translation and scaling.")

    # test exceeding tolerance
    tgt_pts[0, :] += 20
    pytest.raises(RuntimeError, fit_matched_points, tgt_pts, src_pts, tol=10)
示例#2
0
def test_fit_matched_points():
    """Test fit_matched_points: fitting two matching sets of points"""
    tgt_pts = np.random.RandomState(42).uniform(size=(6, 3))

    # rotation only
    trans = rotation(2, 6, 3)
    src_pts = apply_trans(trans, tgt_pts)
    trans_est = fit_matched_points(src_pts, tgt_pts, translate=False,
                                   out='trans')
    est_pts = apply_trans(trans_est, src_pts)
    assert_array_almost_equal(tgt_pts, est_pts, 2, "fit_matched_points with "
                              "rotation")

    # rotation & translation
    trans = np.dot(translation(2, -6, 3), rotation(2, 6, 3))
    src_pts = apply_trans(trans, tgt_pts)
    trans_est = fit_matched_points(src_pts, tgt_pts, out='trans')
    est_pts = apply_trans(trans_est, src_pts)
    assert_array_almost_equal(tgt_pts, est_pts, 2, "fit_matched_points with "
                              "rotation and translation.")

    # rotation & translation & scaling
    trans = reduce(np.dot, (translation(2, -6, 3), rotation(1.5, .3, 1.4),
                            scaling(.5, .5, .5)))
    src_pts = apply_trans(trans, tgt_pts)
    trans_est = fit_matched_points(src_pts, tgt_pts, scale=1, out='trans')
    est_pts = apply_trans(trans_est, src_pts)
    assert_array_almost_equal(tgt_pts, est_pts, 2, "fit_matched_points with "
                              "rotation, translation and scaling.")

    # test exceeding tolerance
    tgt_pts[0, :] += 20
    assert_raises(RuntimeError, fit_matched_points, tgt_pts, src_pts, tol=10)
示例#3
0
def _deface(t1w, mri_landmarks, deface, trans, raw):
    if not has_nibabel():  # pragma: no cover
        raise ImportError('This function requires nibabel.')
    import nibabel as nib

    inset, theta = (20, 35.)
    if isinstance(deface, dict):
        if 'inset' in deface:
            inset = deface['inset']
        if 'theta' in deface:
            theta = deface['theta']

    if not _is_numeric(inset):
        raise ValueError('inset must be numeric (float, int). '
                         'Got %s' % type(inset))

    if not _is_numeric(theta):
        raise ValueError('theta must be numeric (float, int). '
                         'Got %s' % type(theta))

    if inset < 0:
        raise ValueError('inset should be positive, ' 'Got %s' % inset)

    if not 0 < theta < 90:
        raise ValueError('theta should be between 0 and 90 '
                         'degrees. Got %s' % theta)

    # x: L/R L+, y: S/I I+, z: A/P A+
    t1w_data = t1w.get_data().copy()
    idxs_vox = np.meshgrid(np.arange(t1w_data.shape[0]),
                           np.arange(t1w_data.shape[1]),
                           np.arange(t1w_data.shape[2]),
                           indexing='ij')
    idxs_vox = np.array(idxs_vox)  # (3, *t1w_data.shape)
    idxs_vox = np.transpose(idxs_vox, [1, 2, 3, 0])  # (*t1w_data.shape, 3)
    idxs_vox = idxs_vox.reshape(-1, 3)  # (n_voxels, 3)

    mri_landmarks_ras = apply_trans(t1w.affine, mri_landmarks)
    ras_meg_t = \
        get_ras_to_neuromag_trans(*mri_landmarks_ras[[1, 0, 2]])

    idxs_ras = apply_trans(t1w.affine, idxs_vox)
    idxs_meg = apply_trans(ras_meg_t, idxs_ras)

    # now comes the actual defacing
    # 1. move center of voxels to (nasion - inset)
    # 2. rotate the head by theta from the normal to the plane passing
    # through anatomical coordinates
    trans_y = -mri_landmarks_ras[1, 1] + inset
    idxs_meg = apply_trans(translation(y=trans_y), idxs_meg)
    idxs_meg = apply_trans(rotation(x=-np.deg2rad(theta)), idxs_meg)
    coords = idxs_meg.reshape(t1w.shape + (3, ))  # (*t1w_data.shape, 3)
    mask = (coords[..., 2] < 0)  # z < 0

    t1w_data[mask] = 0.
    # smooth decided against for potential lack of anonymizaton
    # https://gist.github.com/alexrockhill/15043928b716a432db3a84a050b241ae

    t1w = nib.Nifti1Image(t1w_data, t1w.affine, t1w.header)
    return t1w
示例#4
0
def test_fit_point_cloud():
    """Test fit_point_cloud: fitting a set of points to a point cloud"""
    # evenly spaced target points on a sphere
    u = np.linspace(0, np.pi, 150)
    v = np.linspace(0, np.pi, 150)

    x = np.outer(np.cos(u), np.sin(v)).reshape((-1, 1))
    y = np.outer(np.sin(u), np.sin(v)).reshape((-1, 1))
    z = np.outer(np.ones(np.size(u)), np.cos(v)).reshape((-1, 1)) * 3

    tgt_pts = np.hstack((x, y, z))
    tgt_pts = _decimate_points(tgt_pts, .05)

    # pick some points to fit
    some_tgt_pts = tgt_pts[::362]

    # rotation only
    trans = rotation(1.5, .3, -0.4)
    src_pts = apply_trans(trans, some_tgt_pts)
    trans_est = fit_point_cloud(src_pts, tgt_pts, rotate=True, translate=False,
                                scale=0, out='trans')
    est_pts = apply_trans(trans_est, src_pts)
    err = _point_cloud_error(est_pts, tgt_pts)
    assert_array_less(err, .1, "fit_point_cloud with rotation.")

    # rotation and translation
    trans = np.dot(rotation(0.5, .3, -0.4), translation(.3, .2, -.2))
    src_pts = apply_trans(trans, some_tgt_pts)
    trans_est = fit_point_cloud(src_pts, tgt_pts, rotate=True, translate=True,
                                scale=0, out='trans')
    est_pts = apply_trans(trans_est, src_pts)
    err = _point_cloud_error(est_pts, tgt_pts)
    assert_array_less(err, .1, "fit_point_cloud with rotation and "
                      "translation.")

    # rotation and 1 scale parameter
    trans = np.dot(rotation(0.5, .3, -0.4), scaling(1.5, 1.5, 1.5))
    src_pts = apply_trans(trans, some_tgt_pts)
    trans_est = fit_point_cloud(src_pts, tgt_pts, rotate=True, translate=False,
                                scale=1, out='trans')
    est_pts = apply_trans(trans_est, src_pts)
    err = _point_cloud_error(est_pts, tgt_pts)
    assert_array_less(err, .1, "fit_point_cloud with rotation and 1 scaling "
                      "parameter.")

    # rotation and 3 scale parameter
    trans = np.dot(rotation(0.5, .3, -0.4), scaling(1.5, 1.7, 1.1))
    src_pts = apply_trans(trans, some_tgt_pts)
    trans_est = fit_point_cloud(src_pts, tgt_pts, rotate=True, translate=False,
                                scale=3, out='trans')
    est_pts = apply_trans(trans_est, src_pts)
    err = _point_cloud_error(est_pts, tgt_pts)
    assert_array_less(err, .1, "fit_point_cloud with rotation and 3 scaling "
                      "parameters.")
def test_fit_point_cloud():
    """Test fit_point_cloud: fitting a set of points to a point cloud"""
    # evenly spaced target points on a sphere
    u = np.linspace(0, np.pi, 150)
    v = np.linspace(0, np.pi, 150)

    x = np.outer(np.cos(u), np.sin(v)).reshape((-1, 1))
    y = np.outer(np.sin(u), np.sin(v)).reshape((-1, 1))
    z = np.outer(np.ones(np.size(u)), np.cos(v)).reshape((-1, 1)) * 3

    tgt_pts = np.hstack((x, y, z))
    tgt_pts = _decimate_points(tgt_pts, .05)

    # pick some points to fit
    some_tgt_pts = tgt_pts[::362]

    # rotation only
    trans = rotation(1.5, .3, -0.4)
    src_pts = apply_trans(trans, some_tgt_pts)
    trans_est = fit_point_cloud(src_pts, tgt_pts, rotate=True, translate=False,
                                scale=0, out='trans')
    est_pts = apply_trans(trans_est, src_pts)
    err = _point_cloud_error(est_pts, tgt_pts)
    assert_array_less(err, .1, "fit_point_cloud with rotation.")

    # rotation and translation
    trans = np.dot(rotation(0.5, .3, -0.4), translation(.3, .2, -.2))
    src_pts = apply_trans(trans, some_tgt_pts)
    trans_est = fit_point_cloud(src_pts, tgt_pts, rotate=True, translate=True,
                                scale=0, out='trans')
    est_pts = apply_trans(trans_est, src_pts)
    err = _point_cloud_error(est_pts, tgt_pts)
    assert_array_less(err, .1, "fit_point_cloud with rotation and "
                      "translation.")

    # rotation and 1 scale parameter
    trans = np.dot(rotation(0.5, .3, -0.4), scaling(1.5, 1.5, 1.5))
    src_pts = apply_trans(trans, some_tgt_pts)
    trans_est = fit_point_cloud(src_pts, tgt_pts, rotate=True, translate=False,
                                scale=1, out='trans')
    est_pts = apply_trans(trans_est, src_pts)
    err = _point_cloud_error(est_pts, tgt_pts)
    assert_array_less(err, .1, "fit_point_cloud with rotation and 1 scaling "
                      "parameter.")

    # rotation and 3 scale parameter
    trans = np.dot(rotation(0.5, .3, -0.4), scaling(1.5, 1.7, 1.1))
    src_pts = apply_trans(trans, some_tgt_pts)
    trans_est = fit_point_cloud(src_pts, tgt_pts, rotate=True, translate=False,
                                scale=3, out='trans')
    est_pts = apply_trans(trans_est, src_pts)
    err = _point_cloud_error(est_pts, tgt_pts)
    assert_array_less(err, .1, "fit_point_cloud with rotation and 3 scaling "
                      "parameters.")
示例#6
0
def test_get_ras_to_neuromag_trans():
    """Test the coordinate transformation from ras to neuromag"""
    # create model points in neuromag-like space
    anterior = [0, 1, 0]
    left = [-1, 0, 0]
    right = [.8, 0, 0]
    up = [0, 0, 1]
    rand_pts = np.random.uniform(-1, 1, (3, 3))
    pts = np.vstack((anterior, left, right, up, rand_pts))

    # change coord system
    rx, ry, rz, tx, ty, tz = np.random.uniform(-2 * np.pi, 2 * np.pi, 6)
    trans = np.dot(translation(tx, ty, tz), rotation(rx, ry, rz))
    pts_changed = apply_trans(trans, pts)

    # transform back into original space
    nas, lpa, rpa = pts_changed[:3]
    hsp_trans = get_ras_to_neuromag_trans(nas, lpa, rpa)
    pts_restored = apply_trans(hsp_trans, pts_changed)

    err = "Neuromag transformation failed"
    assert_array_almost_equal(pts_restored, pts, 6, err)
示例#7
0
def test_get_ras_to_neuromag_trans():
    """Test the coordinate transformation from ras to neuromag"""
    # create model points in neuromag-like space
    anterior = [0, 1, 0]
    left = [-1, 0, 0]
    right = [0.8, 0, 0]
    up = [0, 0, 1]
    rand_pts = np.random.uniform(-1, 1, (3, 3))
    pts = np.vstack((anterior, left, right, up, rand_pts))

    # change coord system
    rx, ry, rz, tx, ty, tz = np.random.uniform(-2 * np.pi, 2 * np.pi, 6)
    trans = np.dot(translation(tx, ty, tz), rotation(rx, ry, rz))
    pts_changed = apply_trans(trans, pts)

    # transform back into original space
    nas, lpa, rpa = pts_changed[:3]
    hsp_trans = get_ras_to_neuromag_trans(nas, lpa, rpa)
    pts_restored = apply_trans(hsp_trans, pts_changed)

    err = "Neuromag transformation failed"
    assert_array_almost_equal(pts_restored, pts, 6, err)
示例#8
0
def test_coregister_fiducials():
    """Test coreg.coregister_fiducials()."""
    # prepare head and MRI fiducials
    trans = Transform('head', 'mri',
                      rotation(.4, .1, 0).dot(translation(.1, -.1, .1)))
    coords_orig = np.array([[-0.08061612, -0.02908875, -0.04131077],
                            [0.00146763, 0.08506715, -0.03483611],
                            [0.08436285, -0.02850276, -0.04127743]])
    coords_trans = apply_trans(trans, coords_orig)

    def make_dig(coords, cf):
        return ({'coord_frame': cf, 'ident': 1, 'kind': 1, 'r': coords[0]},
                {'coord_frame': cf, 'ident': 2, 'kind': 1, 'r': coords[1]},
                {'coord_frame': cf, 'ident': 3, 'kind': 1, 'r': coords[2]})

    mri_fiducials = make_dig(coords_trans, FIFF.FIFFV_COORD_MRI)
    info = {'dig': make_dig(coords_orig, FIFF.FIFFV_COORD_HEAD)}

    # test coregister_fiducials()
    trans_est = coregister_fiducials(info, mri_fiducials)
    assert trans_est.from_str == trans.from_str
    assert trans_est.to_str == trans.to_str
    assert_array_almost_equal(trans_est['trans'], trans['trans'])
示例#9
0
def test_coregister_fiducials():
    """Test coreg.coregister_fiducials()"""
    # prepare head and MRI fiducials
    trans = Transform('head', 'mri',
                      rotation(.4, .1, 0).dot(translation(.1, -.1, .1)))
    coords_orig = np.array([[-0.08061612, -0.02908875, -0.04131077],
                            [0.00146763, 0.08506715, -0.03483611],
                            [0.08436285, -0.02850276, -0.04127743]])
    coords_trans = apply_trans(trans, coords_orig)

    def make_dig(coords, cf):
        return ({'coord_frame': cf, 'ident': 1, 'kind': 1, 'r': coords[0]},
                {'coord_frame': cf, 'ident': 2, 'kind': 1, 'r': coords[1]},
                {'coord_frame': cf, 'ident': 3, 'kind': 1, 'r': coords[2]})

    mri_fiducials = make_dig(coords_trans, FIFF.FIFFV_COORD_MRI)
    info = {'dig': make_dig(coords_orig, FIFF.FIFFV_COORD_HEAD)}

    # test coregister_fiducials()
    trans_est = coregister_fiducials(info, mri_fiducials)
    assert_equal(trans_est.from_str, trans.from_str)
    assert_equal(trans_est.to_str, trans.to_str)
    assert_array_almost_equal(trans_est['trans'], trans['trans'])
示例#10
0
def test_fit_sphere_to_headshape():
    """Test fitting a sphere to digitization points"""
    # Create points of various kinds
    rad = 90.0  # mm
    big_rad = 120.0
    center = np.array([0.5, -10.0, 40.0])  # mm
    dev_trans = np.array([0.0, -0.005, -10.0])
    dev_center = center - dev_trans
    dig = [
        # Left auricular
        {
            "coord_frame": FIFF.FIFFV_COORD_HEAD,
            "ident": FIFF.FIFFV_POINT_LPA,
            "kind": FIFF.FIFFV_POINT_CARDINAL,
            "r": np.array([-1.0, 0.0, 0.0]),
        },
        # Nasion
        {
            "coord_frame": FIFF.FIFFV_COORD_HEAD,
            "ident": FIFF.FIFFV_POINT_NASION,
            "kind": FIFF.FIFFV_POINT_CARDINAL,
            "r": np.array([0.0, 1.0, 0.0]),
        },
        # Right auricular
        {
            "coord_frame": FIFF.FIFFV_COORD_HEAD,
            "ident": FIFF.FIFFV_POINT_RPA,
            "kind": FIFF.FIFFV_POINT_CARDINAL,
            "r": np.array([1.0, 0.0, 0.0]),
        },
        # Top of the head (extra point)
        {"coord_frame": FIFF.FIFFV_COORD_HEAD, "kind": FIFF.FIFFV_POINT_EXTRA, "r": np.array([0.0, 0.0, 1.0])},
        # EEG points
        # Fz
        {"coord_frame": FIFF.FIFFV_COORD_HEAD, "kind": FIFF.FIFFV_POINT_EEG, "r": np.array([0, 0.72, 0.69])},
        # F3
        {"coord_frame": FIFF.FIFFV_COORD_HEAD, "kind": FIFF.FIFFV_POINT_EEG, "r": np.array([-0.55, 0.67, 0.50])},
        # F4
        {"coord_frame": FIFF.FIFFV_COORD_HEAD, "kind": FIFF.FIFFV_POINT_EEG, "r": np.array([0.55, 0.67, 0.50])},
        # Cz
        {"coord_frame": FIFF.FIFFV_COORD_HEAD, "kind": FIFF.FIFFV_POINT_EEG, "r": np.array([0.0, 0.0, 1.0])},
        # Pz
        {"coord_frame": FIFF.FIFFV_COORD_HEAD, "kind": FIFF.FIFFV_POINT_EEG, "r": np.array([0, -0.72, 0.69])},
    ]
    for d in dig:
        d["r"] *= rad / 1000.0
        d["r"] += center / 1000.0

    # Device to head transformation (rotate .2 rad over X-axis)
    dev_head_t = Transform("meg", "head", translation(*(dev_trans / 1000.0)))

    info = {"dig": dig, "dev_head_t": dev_head_t}

    # Degenerate conditions
    assert_raises(ValueError, fit_sphere_to_headshape, info, dig_kinds=(FIFF.FIFFV_POINT_HPI,))
    info["dig"][0]["coord_frame"] = FIFF.FIFFV_COORD_DEVICE
    assert_raises(RuntimeError, fit_sphere_to_headshape, info)
    info["dig"][0]["coord_frame"] = FIFF.FIFFV_COORD_HEAD

    #  # Test with 4 points that match a perfect sphere
    dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
    r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
    kwargs = dict(rtol=1e-3, atol=1e-2)  # in mm
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, dev_center, **kwargs)

    # Test with all points
    dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA, FIFF.FIFFV_POINT_EEG)
    kwargs = dict(rtol=1e-3, atol=1.0)  # in mm
    r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, dev_center, **kwargs)

    # Test with some noisy EEG points only.
    dig_kinds = (FIFF.FIFFV_POINT_EEG,)
    r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
    kwargs = dict(rtol=1e-3, atol=10.0)  # in mm
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, center, **kwargs)

    # Test big size
    dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
    info_big = deepcopy(info)
    for d in info_big["dig"]:
        d["r"] -= center / 1000.0
        d["r"] *= big_rad / rad
        d["r"] += center / 1000.0
    with warnings.catch_warnings(record=True):  # fit
        with catch_logging() as log_file:
            r, oh, od = fit_sphere_to_headshape(info_big, dig_kinds=dig_kinds, verbose="warning")
    log_file = log_file.getvalue().strip()
    assert_equal(len(log_file.split("\n")), 1)
    assert_true(log_file.startswith("Estimated head size"))
    assert_allclose(oh, center, atol=1e-3)
    assert_allclose(r, big_rad, atol=1e-3)
    del info_big

    # Test offcenter
    dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
    info_shift = deepcopy(info)
    shift_center = np.array([0.0, -30, 0.0])
    for d in info_shift["dig"]:
        d["r"] -= center / 1000.0
        d["r"] += shift_center / 1000.0
    with warnings.catch_warnings(record=True):
        with catch_logging() as log_file:
            r, oh, od = fit_sphere_to_headshape(info_shift, dig_kinds=dig_kinds, verbose="warning")
    log_file = log_file.getvalue().strip()
    assert_equal(len(log_file.split("\n")), 1)
    assert_true("from head frame origin" in log_file)
    assert_allclose(oh, shift_center, atol=1e-3)
    assert_allclose(r, rad, atol=1e-3)
示例#11
0
def test_fit_sphere_to_headshape():
    """Test fitting a sphere to digitization points."""
    # Create points of various kinds
    rad = 0.09
    big_rad = 0.12
    center = np.array([0.0005, -0.01, 0.04])
    dev_trans = np.array([0., -0.005, -0.01])
    dev_center = center - dev_trans
    dig = [
        # Left auricular
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'ident': FIFF.FIFFV_POINT_LPA,
         'kind': FIFF.FIFFV_POINT_CARDINAL,
         'r': np.array([-1.0, 0.0, 0.0])},
        # Nasion
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'ident': FIFF.FIFFV_POINT_NASION,
         'kind': FIFF.FIFFV_POINT_CARDINAL,
         'r': np.array([0.0, 1.0, 0.0])},
        # Right auricular
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'ident': FIFF.FIFFV_POINT_RPA,
         'kind': FIFF.FIFFV_POINT_CARDINAL,
         'r': np.array([1.0, 0.0, 0.0])},

        # Top of the head (extra point)
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EXTRA,
         'ident': 0,
         'r': np.array([0.0, 0.0, 1.0])},

        # EEG points
        # Fz
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'ident': 0,
         'r': np.array([0, .72, .69])},
        # F3
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'ident': 1,
         'r': np.array([-.55, .67, .50])},
        # F4
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'ident': 2,
         'r': np.array([.55, .67, .50])},
        # Cz
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'ident': 3,
         'r': np.array([0.0, 0.0, 1.0])},
        # Pz
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'ident': 4,
         'r': np.array([0, -.72, .69])},
    ]
    for d in dig:
        d['r'] *= rad
        d['r'] += center

    # Device to head transformation (rotate .2 rad over X-axis)
    dev_head_t = Transform('meg', 'head', translation(*(dev_trans)))
    info = Info(dig=dig, dev_head_t=dev_head_t)

    # Degenerate conditions
    pytest.raises(ValueError, fit_sphere_to_headshape, info,
                  dig_kinds=(FIFF.FIFFV_POINT_HPI,))
    pytest.raises(ValueError, fit_sphere_to_headshape, info,
                  dig_kinds='foo', units='m')
    info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_DEVICE
    pytest.raises(RuntimeError, fit_sphere_to_headshape, info, units='m')
    info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_HEAD

    #  # Test with 4 points that match a perfect sphere
    dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
    with pytest.warns(RuntimeWarning, match='Only .* head digitization'):
        r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds,
                                            units='m')
    kwargs = dict(rtol=1e-3, atol=1e-5)
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, dev_center, **kwargs)

    # Test with all points
    dig_kinds = ('cardinal', FIFF.FIFFV_POINT_EXTRA, 'eeg')
    kwargs = dict(rtol=1e-3, atol=1e-3)
    with pytest.warns(RuntimeWarning, match='Only .* head digitization'):
        r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds,
                                            units='m')
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, dev_center, **kwargs)

    # Test with some noisy EEG points only.
    dig_kinds = 'eeg'
    with pytest.warns(RuntimeWarning, match='Only .* head digitization'):
        r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds,
                                            units='m')
    kwargs = dict(rtol=1e-3, atol=1e-2)
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, center, **kwargs)

    # Test big size
    dig_kinds = ('cardinal', 'extra')
    info_big = deepcopy(info)
    for d in info_big['dig']:
        d['r'] -= center
        d['r'] *= big_rad / rad
        d['r'] += center
    with pytest.warns(RuntimeWarning, match='Estimated head size'):
        r, oh, od = fit_sphere_to_headshape(info_big, dig_kinds=dig_kinds,
                                            units='mm')
    assert_allclose(oh, center * 1000, atol=1e-3)
    assert_allclose(r, big_rad * 1000, atol=1e-3)
    del info_big

    # Test offcenter
    dig_kinds = ('cardinal', 'extra')
    info_shift = deepcopy(info)
    shift_center = np.array([0., -0.03, 0.])
    for d in info_shift['dig']:
        d['r'] -= center
        d['r'] += shift_center
    with pytest.warns(RuntimeWarning, match='from head frame origin'):
        r, oh, od = fit_sphere_to_headshape(
            info_shift, dig_kinds=dig_kinds, units='m')
    assert_allclose(oh, shift_center, atol=1e-6)
    assert_allclose(r, rad, atol=1e-6)

    # Test "auto" mode (default)
    # Should try "extra", fail, and go on to EEG
    with pytest.warns(RuntimeWarning, match='Only .* head digitization'):
        r, oh, od = fit_sphere_to_headshape(info, units='m')
    kwargs = dict(rtol=1e-3, atol=1e-3)
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, dev_center, **kwargs)
    with pytest.warns(RuntimeWarning, match='Only .* head digitization'):
        r2, oh2, od2 = fit_sphere_to_headshape(info, units='m')
    assert_allclose(r, r2, atol=1e-7)
    assert_allclose(oh, oh2, atol=1e-7)
    assert_allclose(od, od2, atol=1e-7)
    # this one should pass, 1 EXTRA point and 3 EEG (but the fit is terrible)
    info = Info(dig=dig[:7], dev_head_t=dev_head_t)
    with pytest.warns(RuntimeWarning, match='Only .* head digitization'):
        r, oh, od = fit_sphere_to_headshape(info, units='m')
    # this one should fail, 1 EXTRA point and 3 EEG (but the fit is terrible)
    info = Info(dig=dig[:6], dev_head_t=dev_head_t)
    pytest.raises(ValueError, fit_sphere_to_headshape, info, units='m')
    pytest.raises(TypeError, fit_sphere_to_headshape, 1, units='m')
示例#12
0
def test_fit_sphere_to_headshape():
    """Test fitting a sphere to digitization points."""
    # Create points of various kinds
    rad = 0.09
    big_rad = 0.12
    center = np.array([0.0005, -0.01, 0.04])
    dev_trans = np.array([0., -0.005, -0.01])
    dev_center = center - dev_trans
    dig = [
        # Left auricular
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'ident': FIFF.FIFFV_POINT_LPA,
         'kind': FIFF.FIFFV_POINT_CARDINAL,
         'r': np.array([-1.0, 0.0, 0.0])},
        # Nasion
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'ident': FIFF.FIFFV_POINT_NASION,
         'kind': FIFF.FIFFV_POINT_CARDINAL,
         'r': np.array([0.0, 1.0, 0.0])},
        # Right auricular
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'ident': FIFF.FIFFV_POINT_RPA,
         'kind': FIFF.FIFFV_POINT_CARDINAL,
         'r': np.array([1.0, 0.0, 0.0])},

        # Top of the head (extra point)
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EXTRA,
         'r': np.array([0.0, 0.0, 1.0])},

        # EEG points
        # Fz
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'r': np.array([0, .72, .69])},
        # F3
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'r': np.array([-.55, .67, .50])},
        # F4
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'r': np.array([.55, .67, .50])},
        # Cz
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'r': np.array([0.0, 0.0, 1.0])},
        # Pz
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'r': np.array([0, -.72, .69])},
    ]
    for d in dig:
        d['r'] *= rad
        d['r'] += center

    # Device to head transformation (rotate .2 rad over X-axis)
    dev_head_t = Transform('meg', 'head', translation(*(dev_trans)))
    info = Info(dig=dig, dev_head_t=dev_head_t)

    # Degenerate conditions
    pytest.raises(ValueError, fit_sphere_to_headshape, info,
                  dig_kinds=(FIFF.FIFFV_POINT_HPI,))
    pytest.raises(ValueError, fit_sphere_to_headshape, info,
                  dig_kinds='foo', units='m')
    info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_DEVICE
    pytest.raises(RuntimeError, fit_sphere_to_headshape, info, units='m')
    info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_HEAD

    #  # Test with 4 points that match a perfect sphere
    dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
    with pytest.warns(RuntimeWarning, match='Only .* head digitization'):
        r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds,
                                            units='m')
    kwargs = dict(rtol=1e-3, atol=1e-5)
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, dev_center, **kwargs)

    # Test with all points
    dig_kinds = ('cardinal', FIFF.FIFFV_POINT_EXTRA, 'eeg')
    kwargs = dict(rtol=1e-3, atol=1e-3)
    with pytest.warns(RuntimeWarning, match='Only .* head digitization'):
        r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds,
                                            units='m')
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, dev_center, **kwargs)

    # Test with some noisy EEG points only.
    dig_kinds = 'eeg'
    with pytest.warns(RuntimeWarning, match='Only .* head digitization'):
        r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds,
                                            units='m')
    kwargs = dict(rtol=1e-3, atol=1e-2)
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, center, **kwargs)

    # Test big size
    dig_kinds = ('cardinal', 'extra')
    info_big = deepcopy(info)
    for d in info_big['dig']:
        d['r'] -= center
        d['r'] *= big_rad / rad
        d['r'] += center
    with pytest.warns(RuntimeWarning, match='Estimated head size'):
        r, oh, od = fit_sphere_to_headshape(info_big, dig_kinds=dig_kinds,
                                            units='mm')
    assert_allclose(oh, center * 1000, atol=1e-3)
    assert_allclose(r, big_rad * 1000, atol=1e-3)
    del info_big

    # Test offcenter
    dig_kinds = ('cardinal', 'extra')
    info_shift = deepcopy(info)
    shift_center = np.array([0., -0.03, 0.])
    for d in info_shift['dig']:
        d['r'] -= center
        d['r'] += shift_center
    with pytest.warns(RuntimeWarning, match='from head frame origin'):
        r, oh, od = fit_sphere_to_headshape(
            info_shift, dig_kinds=dig_kinds, units='m')
    assert_allclose(oh, shift_center, atol=1e-6)
    assert_allclose(r, rad, atol=1e-6)

    # Test "auto" mode (default)
    # Should try "extra", fail, and go on to EEG
    with pytest.warns(RuntimeWarning, match='Only .* head digitization'):
        r, oh, od = fit_sphere_to_headshape(info, units='m')
    kwargs = dict(rtol=1e-3, atol=1e-3)
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, dev_center, **kwargs)
    with pytest.warns(RuntimeWarning, match='Only .* head digitization'):
        r2, oh2, od2 = fit_sphere_to_headshape(info, units='m')
    assert_allclose(r, r2, atol=1e-7)
    assert_allclose(oh, oh2, atol=1e-7)
    assert_allclose(od, od2, atol=1e-7)
    # this one should pass, 1 EXTRA point and 3 EEG (but the fit is terrible)
    info = Info(dig=dig[:7], dev_head_t=dev_head_t)
    with pytest.warns(RuntimeWarning, match='Only .* head digitization'):
        r, oh, od = fit_sphere_to_headshape(info, units='m')
    # this one should fail, 1 EXTRA point and 3 EEG (but the fit is terrible)
    info = Info(dig=dig[:6], dev_head_t=dev_head_t)
    pytest.raises(ValueError, fit_sphere_to_headshape, info, units='m')
    pytest.raises(TypeError, fit_sphere_to_headshape, 1, units='m')
示例#13
0
def test_fit_sphere_to_headshape():
    """Test fitting a sphere to digitization points"""
    # Create points of various kinds
    rad = 0.09
    big_rad = 0.12
    center = np.array([0.0005, -0.01, 0.04])
    dev_trans = np.array([0., -0.005, -0.01])
    dev_center = center - dev_trans
    dig = [
        # Left auricular
        {
            'coord_frame': FIFF.FIFFV_COORD_HEAD,
            'ident': FIFF.FIFFV_POINT_LPA,
            'kind': FIFF.FIFFV_POINT_CARDINAL,
            'r': np.array([-1.0, 0.0, 0.0])
        },
        # Nasion
        {
            'coord_frame': FIFF.FIFFV_COORD_HEAD,
            'ident': FIFF.FIFFV_POINT_NASION,
            'kind': FIFF.FIFFV_POINT_CARDINAL,
            'r': np.array([0.0, 1.0, 0.0])
        },
        # Right auricular
        {
            'coord_frame': FIFF.FIFFV_COORD_HEAD,
            'ident': FIFF.FIFFV_POINT_RPA,
            'kind': FIFF.FIFFV_POINT_CARDINAL,
            'r': np.array([1.0, 0.0, 0.0])
        },

        # Top of the head (extra point)
        {
            'coord_frame': FIFF.FIFFV_COORD_HEAD,
            'kind': FIFF.FIFFV_POINT_EXTRA,
            'r': np.array([0.0, 0.0, 1.0])
        },

        # EEG points
        # Fz
        {
            'coord_frame': FIFF.FIFFV_COORD_HEAD,
            'kind': FIFF.FIFFV_POINT_EEG,
            'r': np.array([0, .72, .69])
        },
        # F3
        {
            'coord_frame': FIFF.FIFFV_COORD_HEAD,
            'kind': FIFF.FIFFV_POINT_EEG,
            'r': np.array([-.55, .67, .50])
        },
        # F4
        {
            'coord_frame': FIFF.FIFFV_COORD_HEAD,
            'kind': FIFF.FIFFV_POINT_EEG,
            'r': np.array([.55, .67, .50])
        },
        # Cz
        {
            'coord_frame': FIFF.FIFFV_COORD_HEAD,
            'kind': FIFF.FIFFV_POINT_EEG,
            'r': np.array([0.0, 0.0, 1.0])
        },
        # Pz
        {
            'coord_frame': FIFF.FIFFV_COORD_HEAD,
            'kind': FIFF.FIFFV_POINT_EEG,
            'r': np.array([0, -.72, .69])
        },
    ]
    for d in dig:
        d['r'] *= rad
        d['r'] += center

    # Device to head transformation (rotate .2 rad over X-axis)
    dev_head_t = Transform('meg', 'head', translation(*(dev_trans)))
    info = {'dig': dig, 'dev_head_t': dev_head_t}

    # Degenerate conditions
    with warnings.catch_warnings(record=True) as w:
        assert_raises(ValueError,
                      fit_sphere_to_headshape,
                      info,
                      dig_kinds=(FIFF.FIFFV_POINT_HPI, ))
    assert_equal(len(w), 1)
    assert_true(w[0].category == DeprecationWarning)
    assert_raises(ValueError,
                  fit_sphere_to_headshape,
                  info,
                  dig_kinds='foo',
                  units='m')
    info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_DEVICE
    assert_raises(RuntimeError, fit_sphere_to_headshape, info, units='m')
    info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_HEAD

    #  # Test with 4 points that match a perfect sphere
    dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
    with warnings.catch_warnings(record=True):  # not enough points
        r, oh, od = fit_sphere_to_headshape(info,
                                            dig_kinds=dig_kinds,
                                            units='m')
    kwargs = dict(rtol=1e-3, atol=1e-5)
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, dev_center, **kwargs)

    # Test with all points
    dig_kinds = ('cardinal', FIFF.FIFFV_POINT_EXTRA, 'eeg')
    kwargs = dict(rtol=1e-3, atol=1e-3)
    with warnings.catch_warnings(record=True):  # not enough points
        r, oh, od = fit_sphere_to_headshape(info,
                                            dig_kinds=dig_kinds,
                                            units='m')
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, dev_center, **kwargs)

    # Test with some noisy EEG points only.
    dig_kinds = 'eeg'
    with warnings.catch_warnings(record=True):  # not enough points
        r, oh, od = fit_sphere_to_headshape(info,
                                            dig_kinds=dig_kinds,
                                            units='m')
    kwargs = dict(rtol=1e-3, atol=1e-2)
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, center, **kwargs)

    # Test big size
    dig_kinds = ('cardinal', 'extra')
    info_big = deepcopy(info)
    for d in info_big['dig']:
        d['r'] -= center
        d['r'] *= big_rad / rad
        d['r'] += center
    with warnings.catch_warnings(record=True):  # fit
        with catch_logging() as log_file:
            r, oh, od = fit_sphere_to_headshape(info_big,
                                                dig_kinds=dig_kinds,
                                                verbose='warning',
                                                units='mm')
    log_file = log_file.getvalue().strip()
    assert_equal(len(log_file.split('\n')), 2)
    assert_true('Estimated head size' in log_file)
    assert_allclose(oh, center * 1000, atol=1e-3)
    assert_allclose(r, big_rad * 1000, atol=1e-3)
    del info_big

    # Test offcenter
    dig_kinds = ('cardinal', 'extra')
    info_shift = deepcopy(info)
    shift_center = np.array([0., -0.03, 0.])
    for d in info_shift['dig']:
        d['r'] -= center
        d['r'] += shift_center
    with warnings.catch_warnings(record=True):
        with catch_logging() as log_file:
            r, oh, od = fit_sphere_to_headshape(info_shift,
                                                dig_kinds=dig_kinds,
                                                verbose='warning',
                                                units='m')
    log_file = log_file.getvalue().strip()
    assert_equal(len(log_file.split('\n')), 2)
    assert_true('from head frame origin' in log_file)
    assert_allclose(oh, shift_center, atol=1e-6)
    assert_allclose(r, rad, atol=1e-6)

    # Test "auto" mode (default)
    # Should try "extra", fail, and go on to EEG
    with warnings.catch_warnings(record=True):  # not enough points
        r, oh, od = fit_sphere_to_headshape(info, units='m')
    kwargs = dict(rtol=1e-3, atol=1e-3)
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, dev_center, **kwargs)
    with warnings.catch_warnings(record=True):  # not enough points
        r2, oh2, od2 = fit_sphere_to_headshape(info, units='m')
    assert_allclose(r, r2, atol=1e-7)
    assert_allclose(oh, oh2, atol=1e-7)
    assert_allclose(od, od2, atol=1e-7)
    # this one should pass, 1 EXTRA point and 3 EEG (but the fit is terrible)
    info = {'dig': dig[:7], 'dev_head_t': dev_head_t}
    with warnings.catch_warnings(record=True):  # bad fit
        r, oh, od = fit_sphere_to_headshape(info, units='m')
    # this one should fail, 1 EXTRA point and 3 EEG (but the fit is terrible)
    info = {'dig': dig[:6], 'dev_head_t': dev_head_t}
    assert_raises(ValueError, fit_sphere_to_headshape, info, units='m')
示例#14
0
def test_fit_sphere_to_headshape():
    """Test fitting a sphere to digitization points"""
    # Create points of various kinds
    rad = 90.  # mm
    big_rad = 120.
    center = np.array([0.5, -10., 40.])  # mm
    dev_trans = np.array([0., -0.005, -10.])
    dev_center = center - dev_trans
    dig = [
        # Left auricular
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'ident': FIFF.FIFFV_POINT_LPA,
         'kind': FIFF.FIFFV_POINT_CARDINAL,
         'r': np.array([-1.0, 0.0, 0.0])},
        # Nasion
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'ident': FIFF.FIFFV_POINT_NASION,
         'kind': FIFF.FIFFV_POINT_CARDINAL,
         'r': np.array([0.0, 1.0, 0.0])},
        # Right auricular
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'ident': FIFF.FIFFV_POINT_RPA,
         'kind': FIFF.FIFFV_POINT_CARDINAL,
         'r': np.array([1.0, 0.0, 0.0])},

        # Top of the head (extra point)
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EXTRA,
         'r': np.array([0.0, 0.0, 1.0])},

        # EEG points
        # Fz
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'r': np.array([0, .72, .69])},
        # F3
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'r': np.array([-.55, .67, .50])},
        # F4
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'r': np.array([.55, .67, .50])},
        # Cz
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'r': np.array([0.0, 0.0, 1.0])},
        # Pz
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'r': np.array([0, -.72, .69])},
    ]
    for d in dig:
        d['r'] *= rad / 1000.
        d['r'] += center / 1000.

    # Device to head transformation (rotate .2 rad over X-axis)
    dev_head_t = Transform('meg', 'head', translation(*(dev_trans / 1000.)))

    info = {'dig': dig, 'dev_head_t': dev_head_t}

    # Degenerate conditions
    assert_raises(ValueError, fit_sphere_to_headshape, info,
                  dig_kinds=(FIFF.FIFFV_POINT_HPI,))
    info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_DEVICE
    assert_raises(RuntimeError, fit_sphere_to_headshape, info)
    info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_HEAD

    #  # Test with 4 points that match a perfect sphere
    dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
    r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
    kwargs = dict(rtol=1e-3, atol=1e-2)  # in mm
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, dev_center, **kwargs)

    # Test with all points
    dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA,
                 FIFF.FIFFV_POINT_EEG)
    kwargs = dict(rtol=1e-3, atol=1.)  # in mm
    r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, dev_center, **kwargs)

    # Test with some noisy EEG points only.
    dig_kinds = (FIFF.FIFFV_POINT_EEG,)
    r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
    kwargs = dict(rtol=1e-3, atol=10.)  # in mm
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, center, **kwargs)

    # Test big size
    dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
    info_big = deepcopy(info)
    for d in info_big['dig']:
        d['r'] -= center / 1000.
        d['r'] *= big_rad / rad
        d['r'] += center / 1000.
    with warnings.catch_warnings(record=True):  # fit
        with catch_logging() as log_file:
            r, oh, od = fit_sphere_to_headshape(info_big, dig_kinds=dig_kinds,
                                                verbose='warning')
    log_file = log_file.getvalue().strip()
    assert_equal(len(log_file.split('\n')), 1)
    assert_true(log_file.startswith('Estimated head size'))
    assert_allclose(oh, center, atol=1e-3)
    assert_allclose(r, big_rad, atol=1e-3)
    del info_big

    # Test offcenter
    dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
    info_shift = deepcopy(info)
    shift_center = np.array([0., -30, 0.])
    for d in info_shift['dig']:
        d['r'] -= center / 1000.
        d['r'] += shift_center / 1000.
    with warnings.catch_warnings(record=True):
        with catch_logging() as log_file:
            r, oh, od = fit_sphere_to_headshape(
                info_shift, dig_kinds=dig_kinds, verbose='warning')
    log_file = log_file.getvalue().strip()
    assert_equal(len(log_file.split('\n')), 1)
    assert_true('from head frame origin' in log_file)
    assert_allclose(oh, shift_center, atol=1e-3)
    assert_allclose(r, rad, atol=1e-3)
def test_fit_sphere_to_headshape():
    """Test fitting a sphere to digitization points"""
    # Create points of various kinds
    rad = 90.  # mm
    center = np.array([0.5, -10., 40.])  # mm
    dev_trans = np.array([0., -0.005, -10.])
    dev_center = center - dev_trans
    dig = [
        # Left auricular
        {
            'coord_frame': FIFF.FIFFV_COORD_HEAD,
            'ident': FIFF.FIFFV_POINT_LPA,
            'kind': FIFF.FIFFV_POINT_CARDINAL,
            'r': np.array([-1.0, 0.0, 0.0])
        },
        # Nasion
        {
            'coord_frame': FIFF.FIFFV_COORD_HEAD,
            'ident': FIFF.FIFFV_POINT_NASION,
            'kind': FIFF.FIFFV_POINT_CARDINAL,
            'r': np.array([0.0, 1.0, 0.0])
        },
        # Right auricular
        {
            'coord_frame': FIFF.FIFFV_COORD_HEAD,
            'ident': FIFF.FIFFV_POINT_RPA,
            'kind': FIFF.FIFFV_POINT_CARDINAL,
            'r': np.array([1.0, 0.0, 0.0])
        },

        # Top of the head (extra point)
        {
            'coord_frame': FIFF.FIFFV_COORD_HEAD,
            'kind': FIFF.FIFFV_POINT_EXTRA,
            'r': np.array([0.0, 0.0, 1.0])
        },

        # EEG points
        # Fz
        {
            'coord_frame': FIFF.FIFFV_COORD_HEAD,
            'kind': FIFF.FIFFV_POINT_EEG,
            'r': np.array([0, .72, .69])
        },
        # F3
        {
            'coord_frame': FIFF.FIFFV_COORD_HEAD,
            'kind': FIFF.FIFFV_POINT_EEG,
            'r': np.array([-.55, .67, .50])
        },
        # F4
        {
            'coord_frame': FIFF.FIFFV_COORD_HEAD,
            'kind': FIFF.FIFFV_POINT_EEG,
            'r': np.array([.55, .67, .50])
        },
        # Cz
        {
            'coord_frame': FIFF.FIFFV_COORD_HEAD,
            'kind': FIFF.FIFFV_POINT_EEG,
            'r': np.array([0.0, 0.0, 1.0])
        },
        # Pz
        {
            'coord_frame': FIFF.FIFFV_COORD_HEAD,
            'kind': FIFF.FIFFV_POINT_EEG,
            'r': np.array([0, -.72, .69])
        },
    ]
    for d in dig:
        d['r'] *= rad / 1000.
        d['r'] += center / 1000.

    # Device to head transformation (rotate .2 rad over X-axis)
    dev_head_t = Transform('meg', 'head', translation(*(dev_trans / 1000.)))

    info = {'dig': dig, 'dev_head_t': dev_head_t}

    # Degenerate conditions
    assert_raises(ValueError,
                  fit_sphere_to_headshape,
                  info,
                  dig_kinds=(FIFF.FIFFV_POINT_HPI, ))
    info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_DEVICE
    assert_raises(RuntimeError, fit_sphere_to_headshape, info)
    info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_HEAD

    #  # Test with 4 points that match a perfect sphere
    dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
    r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
    kwargs = dict(rtol=1e-3, atol=1e-2)  # in mm
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, dev_center, **kwargs)

    # Test with all points
    dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA,
                 FIFF.FIFFV_POINT_EXTRA)
    r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, dev_center, **kwargs)

    # Test with some noisy EEG points only.
    dig_kinds = (FIFF.FIFFV_POINT_EEG, )
    r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
    kwargs = dict(rtol=1e-3, atol=10.)  # in mm
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, center, **kwargs)

    dig = [dict(coord_frame=FIFF.FIFFV_COORD_DEVICE, )]
示例#16
0
def test_fit_sphere_to_headshape():
    """Test fitting a sphere to digitization points"""
    # Create points of various kinds
    rad = 0.09
    big_rad = 0.12
    center = np.array([0.0005, -0.01, 0.04])
    dev_trans = np.array([0., -0.005, -0.01])
    dev_center = center - dev_trans
    dig = [
        # Left auricular
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'ident': FIFF.FIFFV_POINT_LPA,
         'kind': FIFF.FIFFV_POINT_CARDINAL,
         'r': np.array([-1.0, 0.0, 0.0])},
        # Nasion
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'ident': FIFF.FIFFV_POINT_NASION,
         'kind': FIFF.FIFFV_POINT_CARDINAL,
         'r': np.array([0.0, 1.0, 0.0])},
        # Right auricular
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'ident': FIFF.FIFFV_POINT_RPA,
         'kind': FIFF.FIFFV_POINT_CARDINAL,
         'r': np.array([1.0, 0.0, 0.0])},

        # Top of the head (extra point)
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EXTRA,
         'r': np.array([0.0, 0.0, 1.0])},

        # EEG points
        # Fz
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'r': np.array([0, .72, .69])},
        # F3
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'r': np.array([-.55, .67, .50])},
        # F4
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'r': np.array([.55, .67, .50])},
        # Cz
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'r': np.array([0.0, 0.0, 1.0])},
        # Pz
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'r': np.array([0, -.72, .69])},
    ]
    for d in dig:
        d['r'] *= rad
        d['r'] += center

    # Device to head transformation (rotate .2 rad over X-axis)
    dev_head_t = Transform('meg', 'head', translation(*(dev_trans)))
    info = {'dig': dig, 'dev_head_t': dev_head_t}

    # Degenerate conditions
    with warnings.catch_warnings(record=True) as w:
        assert_raises(ValueError, fit_sphere_to_headshape, info,
                      dig_kinds=(FIFF.FIFFV_POINT_HPI,))
    assert_equal(len(w), 1)
    assert_true(w[0].category == DeprecationWarning)
    assert_raises(ValueError, fit_sphere_to_headshape, info,
                  dig_kinds='foo', units='m')
    info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_DEVICE
    assert_raises(RuntimeError, fit_sphere_to_headshape, info, units='m')
    info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_HEAD

    #  # Test with 4 points that match a perfect sphere
    dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
    with warnings.catch_warnings(record=True):  # not enough points
        r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds,
                                            units='m')
    kwargs = dict(rtol=1e-3, atol=1e-5)
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, dev_center, **kwargs)

    # Test with all points
    dig_kinds = ('cardinal', FIFF.FIFFV_POINT_EXTRA, 'eeg')
    kwargs = dict(rtol=1e-3, atol=1e-3)
    with warnings.catch_warnings(record=True):  # not enough points
        r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds,
                                            units='m')
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, dev_center, **kwargs)

    # Test with some noisy EEG points only.
    dig_kinds = 'eeg'
    with warnings.catch_warnings(record=True):  # not enough points
        r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds,
                                            units='m')
    kwargs = dict(rtol=1e-3, atol=1e-2)
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, center, **kwargs)

    # Test big size
    dig_kinds = ('cardinal', 'extra')
    info_big = deepcopy(info)
    for d in info_big['dig']:
        d['r'] -= center
        d['r'] *= big_rad / rad
        d['r'] += center
    with warnings.catch_warnings(record=True):  # fit
        with catch_logging() as log_file:
            r, oh, od = fit_sphere_to_headshape(info_big, dig_kinds=dig_kinds,
                                                verbose='warning', units='mm')
    log_file = log_file.getvalue().strip()
    assert_equal(len(log_file.split('\n')), 2)
    assert_true('Estimated head size' in log_file)
    assert_allclose(oh, center * 1000, atol=1e-3)
    assert_allclose(r, big_rad * 1000, atol=1e-3)
    del info_big

    # Test offcenter
    dig_kinds = ('cardinal', 'extra')
    info_shift = deepcopy(info)
    shift_center = np.array([0., -0.03, 0.])
    for d in info_shift['dig']:
        d['r'] -= center
        d['r'] += shift_center
    with warnings.catch_warnings(record=True):
        with catch_logging() as log_file:
            r, oh, od = fit_sphere_to_headshape(
                info_shift, dig_kinds=dig_kinds, verbose='warning', units='m')
    log_file = log_file.getvalue().strip()
    assert_equal(len(log_file.split('\n')), 2)
    assert_true('from head frame origin' in log_file)
    assert_allclose(oh, shift_center, atol=1e-6)
    assert_allclose(r, rad, atol=1e-6)

    # Test "auto" mode (default)
    # Should try "extra", fail, and go on to EEG
    with warnings.catch_warnings(record=True):  # not enough points
        r, oh, od = fit_sphere_to_headshape(info, units='m')
    kwargs = dict(rtol=1e-3, atol=1e-3)
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, dev_center, **kwargs)
    with warnings.catch_warnings(record=True):  # not enough points
        r2, oh2, od2 = fit_sphere_to_headshape(info, units='m')
    assert_allclose(r, r2, atol=1e-7)
    assert_allclose(oh, oh2, atol=1e-7)
    assert_allclose(od, od2, atol=1e-7)
    # this one should pass, 1 EXTRA point and 3 EEG (but the fit is terrible)
    info = {'dig': dig[:7], 'dev_head_t': dev_head_t}
    with warnings.catch_warnings(record=True):  # bad fit
        r, oh, od = fit_sphere_to_headshape(info, units='m')
    # this one should fail, 1 EXTRA point and 3 EEG (but the fit is terrible)
    info = {'dig': dig[:6], 'dev_head_t': dev_head_t}
    assert_raises(ValueError, fit_sphere_to_headshape, info, units='m')
示例#17
0
def test_scale_mri_xfm(tmp_path, few_surfaces, subjects_dir_tmp_few):
    """Test scale_mri transforms and MRI scaling."""
    # scale fsaverage
    tempdir = str(subjects_dir_tmp_few)
    sample_dir = subjects_dir_tmp_few / 'sample'
    subject_to = 'flachkopf'
    spacing = 'oct2'
    for subject_from in ('fsaverage', 'sample'):
        if subject_from == 'fsaverage':
            scale = 1.  # single dim
        else:
            scale = [0.9, 2, .8]  # separate
        src_from_fname = op.join(tempdir, subject_from, 'bem',
                                 '%s-%s-src.fif' % (subject_from, spacing))
        src_from = mne.setup_source_space(subject_from,
                                          spacing,
                                          subjects_dir=tempdir,
                                          add_dist=False)
        write_source_spaces(src_from_fname, src_from)
        vertices_from = np.concatenate([s['vertno'] for s in src_from])
        assert len(vertices_from) == 36
        hemis = ([0] * len(src_from[0]['vertno']) +
                 [1] * len(src_from[0]['vertno']))
        mni_from = mne.vertex_to_mni(vertices_from,
                                     hemis,
                                     subject_from,
                                     subjects_dir=tempdir)
        if subject_from == 'fsaverage':  # identity transform
            source_rr = np.concatenate(
                [s['rr'][s['vertno']] for s in src_from]) * 1e3
            assert_allclose(mni_from, source_rr)
        if subject_from == 'fsaverage':
            overwrite = skip_fiducials = False
        else:
            with pytest.raises(IOError, match='No fiducials file'):
                scale_mri(subject_from,
                          subject_to,
                          scale,
                          subjects_dir=tempdir)
            skip_fiducials = True
            with pytest.raises(IOError, match='already exists'):
                scale_mri(subject_from,
                          subject_to,
                          scale,
                          subjects_dir=tempdir,
                          skip_fiducials=skip_fiducials)
            overwrite = True
        if subject_from == 'sample':  # support for not needing all surf files
            os.remove(op.join(sample_dir, 'surf', 'lh.curv'))
        scale_mri(subject_from,
                  subject_to,
                  scale,
                  subjects_dir=tempdir,
                  verbose='debug',
                  overwrite=overwrite,
                  skip_fiducials=skip_fiducials)
        if subject_from == 'fsaverage':
            assert _is_mri_subject(subject_to, tempdir), "Scaling failed"
        src_to_fname = op.join(tempdir, subject_to, 'bem',
                               '%s-%s-src.fif' % (subject_to, spacing))
        assert op.exists(src_to_fname), "Source space was not scaled"
        # Check MRI scaling
        fname_mri = op.join(tempdir, subject_to, 'mri', 'T1.mgz')
        assert op.exists(fname_mri), "MRI was not scaled"
        # Check MNI transform
        src = mne.read_source_spaces(src_to_fname)
        vertices = np.concatenate([s['vertno'] for s in src])
        assert_array_equal(vertices, vertices_from)
        mni = mne.vertex_to_mni(vertices,
                                hemis,
                                subject_to,
                                subjects_dir=tempdir)
        assert_allclose(mni, mni_from, atol=1e-3)  # 0.001 mm
        # Check head_to_mni (the `trans` here does not really matter)
        trans = rotation(0.001, 0.002, 0.003) @ translation(0.01, 0.02, 0.03)
        trans = Transform('head', 'mri', trans)
        pos_head_from = np.random.RandomState(0).randn(4, 3)
        pos_mni_from = mne.head_to_mni(pos_head_from, subject_from, trans,
                                       tempdir)
        pos_mri_from = apply_trans(trans, pos_head_from)
        pos_mri = pos_mri_from * scale
        pos_head = apply_trans(invert_transform(trans), pos_mri)
        pos_mni = mne.head_to_mni(pos_head, subject_to, trans, tempdir)
        assert_allclose(pos_mni, pos_mni_from, atol=1e-3)
示例#18
0
def test_fit_sphere_to_headshape():
    """Test fitting a sphere to digitization points"""
    # Create points of various kinds
    rad = 90.  # mm
    big_rad = 120.
    center = np.array([0.5, -10., 40.])  # mm
    dev_trans = np.array([0., -0.005, -10.])
    dev_center = center - dev_trans
    dig = [
        # Left auricular
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'ident': FIFF.FIFFV_POINT_LPA,
         'kind': FIFF.FIFFV_POINT_CARDINAL,
         'r': np.array([-1.0, 0.0, 0.0])},
        # Nasion
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'ident': FIFF.FIFFV_POINT_NASION,
         'kind': FIFF.FIFFV_POINT_CARDINAL,
         'r': np.array([0.0, 1.0, 0.0])},
        # Right auricular
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'ident': FIFF.FIFFV_POINT_RPA,
         'kind': FIFF.FIFFV_POINT_CARDINAL,
         'r': np.array([1.0, 0.0, 0.0])},

        # Top of the head (extra point)
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EXTRA,
         'r': np.array([0.0, 0.0, 1.0])},

        # EEG points
        # Fz
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'r': np.array([0, .72, .69])},
        # F3
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'r': np.array([-.55, .67, .50])},
        # F4
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'r': np.array([.55, .67, .50])},
        # Cz
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'r': np.array([0.0, 0.0, 1.0])},
        # Pz
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'r': np.array([0, -.72, .69])},
    ]
    for d in dig:
        d['r'] *= rad / 1000.
        d['r'] += center / 1000.

    # Device to head transformation (rotate .2 rad over X-axis)
    dev_head_t = Transform('meg', 'head', translation(*(dev_trans / 1000.)))

    info = {'dig': dig, 'dev_head_t': dev_head_t}

    # Degenerate conditions
    assert_raises(ValueError, fit_sphere_to_headshape, info,
                  dig_kinds=(FIFF.FIFFV_POINT_HPI,))
    info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_DEVICE
    assert_raises(RuntimeError, fit_sphere_to_headshape, info)
    info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_HEAD

    #  # Test with 4 points that match a perfect sphere
    dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
    r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
    kwargs = dict(rtol=1e-3, atol=1e-2)  # in mm
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, dev_center, **kwargs)

    # Test with all points
    dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA,
                 FIFF.FIFFV_POINT_EEG)
    kwargs = dict(rtol=1e-3, atol=1.)  # in mm
    r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, dev_center, **kwargs)

    # Test with some noisy EEG points only.
    dig_kinds = (FIFF.FIFFV_POINT_EEG,)
    r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
    kwargs = dict(rtol=1e-3, atol=10.)  # in mm
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, center, **kwargs)

    # Test big size
    dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
    info_big = deepcopy(info)
    for d in info_big['dig']:
        d['r'] -= center / 1000.
        d['r'] *= big_rad / rad
        d['r'] += center / 1000.
    with catch_logging() as log_file:
        r, oh, od = fit_sphere_to_headshape(info_big, dig_kinds=dig_kinds,
                                            verbose='warning')
    log_file = log_file.getvalue().strip()
    assert_equal(len(log_file.split('\n')), 1)
    assert_true(log_file.startswith('Estimated head size'))
    assert_allclose(oh, center, atol=1e-3)
    assert_allclose(r, big_rad, atol=1e-3)
    del info_big

    # Test offcenter
    dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
    info_shift = deepcopy(info)
    shift_center = np.array([0., -30, 0.])
    for d in info_shift['dig']:
        d['r'] -= center / 1000.
        d['r'] += shift_center / 1000.
    with catch_logging() as log_file:
        r, oh, od = fit_sphere_to_headshape(info_shift, dig_kinds=dig_kinds,
                                            verbose='warning')
    log_file = log_file.getvalue().strip()
    assert_equal(len(log_file.split('\n')), 1)
    assert_true('from head frame origin' in log_file)
    assert_allclose(oh, shift_center, atol=1e-3)
    assert_allclose(r, rad, atol=1e-3)
示例#19
0
def test_fit_sphere_to_headshape():
    """Test fitting a sphere to digitization points"""
    # Create points of various kinds
    rad = 90.  # mm
    center = np.array([0.5, -10., 40.])  # mm
    dev_trans = np.array([0., -0.005, -10.])
    dev_center = center - dev_trans
    dig = [
        # Left auricular
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'ident': FIFF.FIFFV_POINT_LPA,
         'kind': FIFF.FIFFV_POINT_CARDINAL,
         'r': np.array([-1.0, 0.0, 0.0])},
        # Nasion
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'ident': FIFF.FIFFV_POINT_NASION,
         'kind': FIFF.FIFFV_POINT_CARDINAL,
         'r': np.array([0.0, 1.0, 0.0])},
        # Right auricular
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'ident': FIFF.FIFFV_POINT_RPA,
         'kind': FIFF.FIFFV_POINT_CARDINAL,
         'r': np.array([1.0, 0.0, 0.0])},

        # Top of the head (extra point)
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EXTRA,
         'r': np.array([0.0, 0.0, 1.0])},

        # EEG points
        # Fz
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'r': np.array([0, .72, .69])},
        # F3
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'r': np.array([-.55, .67, .50])},
        # F4
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'r': np.array([.55, .67, .50])},
        # Cz
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'r': np.array([0.0, 0.0, 1.0])},
        # Pz
        {'coord_frame': FIFF.FIFFV_COORD_HEAD,
         'kind': FIFF.FIFFV_POINT_EEG,
         'r': np.array([0, -.72, .69])},
    ]
    for d in dig:
        d['r'] *= rad / 1000.
        d['r'] += center / 1000.

    # Device to head transformation (rotate .2 rad over X-axis)
    dev_head_t = Transform('meg', 'head', translation(*(dev_trans / 1000.)))

    info = {'dig': dig, 'dev_head_t': dev_head_t}

    # Degenerate conditions
    assert_raises(ValueError, fit_sphere_to_headshape, info,
                  dig_kinds=(FIFF.FIFFV_POINT_HPI,))
    info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_DEVICE
    assert_raises(RuntimeError, fit_sphere_to_headshape, info)
    info['dig'][0]['coord_frame'] = FIFF.FIFFV_COORD_HEAD

    #  # Test with 4 points that match a perfect sphere
    dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA)
    r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
    kwargs = dict(rtol=1e-3, atol=1e-2)  # in mm
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, dev_center, **kwargs)

    # Test with all points
    dig_kinds = (FIFF.FIFFV_POINT_CARDINAL, FIFF.FIFFV_POINT_EXTRA,
                 FIFF.FIFFV_POINT_EXTRA)
    r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, dev_center, **kwargs)

    # Test with some noisy EEG points only.
    dig_kinds = (FIFF.FIFFV_POINT_EEG,)
    r, oh, od = fit_sphere_to_headshape(info, dig_kinds=dig_kinds)
    kwargs = dict(rtol=1e-3, atol=10.)  # in mm
    assert_allclose(r, rad, **kwargs)
    assert_allclose(oh, center, **kwargs)
    assert_allclose(od, center, **kwargs)

    dig = [dict(coord_frame=FIFF.FIFFV_COORD_DEVICE, )]