File: test_field_interpolation.py

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from os import path as op

import numpy as np
from numpy.polynomial import legendre
from numpy.testing import (assert_allclose, assert_array_equal, assert_equal,
                           assert_array_almost_equal)
from scipy.interpolate import interp1d

import pytest

from mne.forward import _make_surface_mapping, make_field_map
from mne.forward._lead_dots import (_comp_sum_eeg, _comp_sums_meg,
                                    _get_legen_table, _do_cross_dots)
from mne.forward._make_forward import _create_meg_coils
from mne.forward._field_interpolation import _setup_dots
from mne.surface import get_meg_helmet_surf, get_head_surf
from mne.datasets import testing
from mne import read_evokeds, pick_types, make_fixed_length_events, Epochs
from mne.io import read_raw_fif
from mne.externals.six.moves import zip
from mne.utils import run_tests_if_main


base_dir = op.join(op.dirname(__file__), '..', '..', 'io', 'tests', 'data')
evoked_fname = op.join(base_dir, 'test-ave.fif')
raw_ctf_fname = op.join(base_dir, 'test_ctf_raw.fif')

data_path = testing.data_path(download=False)
trans_fname = op.join(data_path, 'MEG', 'sample',
                      'sample_audvis_trunc-trans.fif')
subjects_dir = op.join(data_path, 'subjects')


@testing.requires_testing_data
def test_field_map_ctf():
    """Test that field mapping can be done with CTF data."""
    raw = read_raw_fif(raw_ctf_fname).crop(0, 1)
    raw.apply_gradient_compensation(3)
    events = make_fixed_length_events(raw, duration=0.5)
    evoked = Epochs(raw, events).average()
    evoked.pick_channels(evoked.ch_names[:50])  # crappy mapping but faster
    # smoke test
    make_field_map(evoked, trans=trans_fname, subject='sample',
                   subjects_dir=subjects_dir)


def test_legendre_val():
    """Test Legendre polynomial (derivative) equivalence."""
    rng = np.random.RandomState(0)
    # check table equiv
    xs = np.linspace(-1., 1., 1000)
    n_terms = 100

    # True, numpy
    vals_np = legendre.legvander(xs, n_terms - 1)

    # Table approximation
    for nc, interp in zip([100, 50], ['nearest', 'linear']):
        lut, n_fact = _get_legen_table('eeg', n_coeff=nc, force_calc=True)
        lut_fun = interp1d(np.linspace(-1, 1, lut.shape[0]), lut, interp,
                           axis=0)
        vals_i = lut_fun(xs)
        # Need a "1:" here because we omit the first coefficient in our table!
        assert_allclose(vals_np[:, 1:vals_i.shape[1] + 1], vals_i,
                        rtol=1e-2, atol=5e-3)

        # Now let's look at our sums
        ctheta = rng.rand(20, 30) * 2.0 - 1.0
        beta = rng.rand(20, 30) * 0.8
        c1 = _comp_sum_eeg(beta.flatten(), ctheta.flatten(), lut_fun, n_fact)
        c1.shape = beta.shape

        # compare to numpy
        n = np.arange(1, n_terms, dtype=float)[:, np.newaxis, np.newaxis]
        coeffs = np.zeros((n_terms,) + beta.shape)
        coeffs[1:] = (np.cumprod([beta] * (n_terms - 1), axis=0) *
                      (2.0 * n + 1.0) * (2.0 * n + 1.0) / n)
        # can't use tensor=False here b/c it isn't in old numpy
        c2 = np.empty((20, 30))
        for ci1 in range(20):
            for ci2 in range(30):
                c2[ci1, ci2] = legendre.legval(ctheta[ci1, ci2],
                                               coeffs[:, ci1, ci2])
        assert_allclose(c1, c2, 1e-2, 1e-3)  # close enough...

    # compare fast and slow for MEG
    ctheta = rng.rand(20 * 30) * 2.0 - 1.0
    beta = rng.rand(20 * 30) * 0.8
    lut, n_fact = _get_legen_table('meg', n_coeff=10, force_calc=True)
    fun = interp1d(np.linspace(-1, 1, lut.shape[0]), lut, 'nearest', axis=0)
    coeffs = _comp_sums_meg(beta, ctheta, fun, n_fact, False)
    lut, n_fact = _get_legen_table('meg', n_coeff=20, force_calc=True)
    fun = interp1d(np.linspace(-1, 1, lut.shape[0]), lut, 'linear', axis=0)
    coeffs = _comp_sums_meg(beta, ctheta, fun, n_fact, False)


def test_legendre_table():
    """Test Legendre table calculation."""
    # double-check our table generation
    n = 10
    for ch_type in ['eeg', 'meg']:
        lut1, n_fact1 = _get_legen_table(ch_type, n_coeff=25, force_calc=True)
        lut1 = lut1[:, :n - 1].copy()
        n_fact1 = n_fact1[:n - 1].copy()
        lut2, n_fact2 = _get_legen_table(ch_type, n_coeff=n, force_calc=True)
        assert_allclose(lut1, lut2)
        assert_allclose(n_fact1, n_fact2)


@testing.requires_testing_data
def test_make_field_map_eeg():
    """Test interpolation of EEG field onto head."""
    evoked = read_evokeds(evoked_fname, condition='Left Auditory')
    evoked.info['bads'] = ['MEG 2443', 'EEG 053']  # add some bads
    surf = get_head_surf('sample', subjects_dir=subjects_dir)
    # we must have trans if surface is in MRI coords
    pytest.raises(ValueError, _make_surface_mapping, evoked.info, surf, 'eeg')

    evoked.pick_types(meg=False, eeg=True)
    fmd = make_field_map(evoked, trans_fname,
                         subject='sample', subjects_dir=subjects_dir)

    # trans is necessary for EEG only
    pytest.raises(RuntimeError, make_field_map, evoked, None,
                  subject='sample', subjects_dir=subjects_dir)

    fmd = make_field_map(evoked, trans_fname,
                         subject='sample', subjects_dir=subjects_dir)
    assert len(fmd) == 1
    assert_array_equal(fmd[0]['data'].shape, (642, 59))  # maps data onto surf
    assert len(fmd[0]['ch_names']) == 59


@testing.requires_testing_data
@pytest.mark.slowtest
def test_make_field_map_meg():
    """Test interpolation of MEG field onto helmet | head."""
    evoked = read_evokeds(evoked_fname, condition='Left Auditory')
    info = evoked.info
    surf = get_meg_helmet_surf(info)
    # let's reduce the number of channels by a bunch to speed it up
    info['bads'] = info['ch_names'][:200]
    # bad ch_type
    pytest.raises(ValueError, _make_surface_mapping, info, surf, 'foo')
    # bad mode
    pytest.raises(ValueError, _make_surface_mapping, info, surf, 'meg',
                  mode='foo')
    # no picks
    evoked_eeg = evoked.copy().pick_types(meg=False, eeg=True)
    pytest.raises(RuntimeError, _make_surface_mapping, evoked_eeg.info,
                  surf, 'meg')
    # bad surface def
    nn = surf['nn']
    del surf['nn']
    pytest.raises(KeyError, _make_surface_mapping, info, surf, 'meg')
    surf['nn'] = nn
    cf = surf['coord_frame']
    del surf['coord_frame']
    pytest.raises(KeyError, _make_surface_mapping, info, surf, 'meg')
    surf['coord_frame'] = cf

    # now do it with make_field_map
    evoked.pick_types(meg=True, eeg=False)
    evoked.info.normalize_proj()  # avoid projection warnings
    fmd = make_field_map(evoked, None,
                         subject='sample', subjects_dir=subjects_dir)
    assert (len(fmd) == 1)
    assert_array_equal(fmd[0]['data'].shape, (304, 106))  # maps data onto surf
    assert len(fmd[0]['ch_names']) == 106

    pytest.raises(ValueError, make_field_map, evoked, ch_type='foobar')

    # now test the make_field_map on head surf for MEG
    evoked.pick_types(meg=True, eeg=False)
    evoked.info.normalize_proj()
    fmd = make_field_map(evoked, trans_fname, meg_surf='head',
                         subject='sample', subjects_dir=subjects_dir)
    assert len(fmd) == 1
    assert_array_equal(fmd[0]['data'].shape, (642, 106))  # maps data onto surf
    assert len(fmd[0]['ch_names']) == 106

    pytest.raises(ValueError, make_field_map, evoked, meg_surf='foobar',
                  subjects_dir=subjects_dir, trans=trans_fname)


@testing.requires_testing_data
def test_make_field_map_meeg():
    """Test making a M/EEG field map onto helmet & head."""
    evoked = read_evokeds(evoked_fname, baseline=(-0.2, 0.0))[0]
    picks = pick_types(evoked.info, meg=True, eeg=True)
    picks = picks[::10]
    evoked.pick_channels([evoked.ch_names[p] for p in picks])
    evoked.info.normalize_proj()
    maps = make_field_map(evoked, trans_fname, subject='sample',
                          subjects_dir=subjects_dir, n_jobs=1, verbose='debug')
    assert_equal(maps[0]['data'].shape, (642, 6))  # EEG->Head
    assert_equal(maps[1]['data'].shape, (304, 31))  # MEG->Helmet
    # reasonable ranges
    maxs = (1.2, 2.0)  # before #4418, was (1.1, 2.0)
    mins = (-0.8, -1.3)  # before #4418, was (-0.6, -1.2)
    assert_equal(len(maxs), len(maps))
    for map_, max_, min_ in zip(maps, maxs, mins):
        assert_allclose(map_['data'].max(), max_, rtol=5e-2)
        assert_allclose(map_['data'].min(), min_, rtol=5e-2)
    # calculated from correct looking mapping on 2015/12/26
    assert_allclose(np.sqrt(np.sum(maps[0]['data'] ** 2)), 19.0903,  # 16.6088,
                    atol=1e-3, rtol=1e-3)
    assert_allclose(np.sqrt(np.sum(maps[1]['data'] ** 2)), 19.4748,  # 20.1245,
                    atol=1e-3, rtol=1e-3)


def _setup_args(info):
    """Configure args for test_as_meg_type_evoked."""
    coils = _create_meg_coils(info['chs'], 'normal', info['dev_head_t'])
    int_rad, noise, lut_fun, n_fact = _setup_dots('fast', coils, 'meg')
    my_origin = np.array([0., 0., 0.04])
    args_dict = dict(intrad=int_rad, volume=False, coils1=coils, r0=my_origin,
                     ch_type='meg', lut=lut_fun, n_fact=n_fact)
    return args_dict


@testing.requires_testing_data
def test_as_meg_type_evoked():
    """Test interpolation of data on to virtual channels."""
    # validation tests
    evoked = read_evokeds(evoked_fname, condition='Left Auditory')
    pytest.raises(ValueError, evoked.as_type, 'meg')
    pytest.raises(ValueError, evoked.copy().pick_types(meg='grad').as_type,
                  'meg')

    # channel names
    ch_names = evoked.info['ch_names']
    virt_evoked = evoked.copy().pick_channels(ch_names=ch_names[:10:1])
    virt_evoked.info.normalize_proj()
    virt_evoked = virt_evoked.as_type('mag')
    assert (all(ch.endswith('_v') for ch in virt_evoked.info['ch_names']))

    # pick from and to channels
    evoked_from = evoked.copy().pick_channels(ch_names=ch_names[2:10:3])
    evoked_to = evoked.copy().pick_channels(ch_names=ch_names[0:10:3])

    info_from, info_to = evoked_from.info, evoked_to.info

    # set up things
    args1, args2 = _setup_args(info_from), _setup_args(info_to)
    args1.update(coils2=args2['coils1'])
    args2.update(coils2=args1['coils1'])

    # test cross dots
    cross_dots1 = _do_cross_dots(**args1)
    cross_dots2 = _do_cross_dots(**args2)

    assert_array_almost_equal(cross_dots1, cross_dots2.T)

    # correlation test
    evoked = evoked.pick_channels(ch_names=ch_names[:10:]).copy()
    data1 = evoked.pick_types(meg='grad').data.ravel()
    data2 = evoked.as_type('grad').data.ravel()
    assert (np.corrcoef(data1, data2)[0, 1] > 0.95)


run_tests_if_main()