コード例 #1
0
ファイル: test_dig.py プロジェクト: dominikwelke/mne-bids
def test_dig_io(tmp_path):
    """Test passing different coordinate frames give proper warnings."""
    bids_root = tmp_path / 'bids1'
    raw = _load_raw()
    for datatype in ('eeg', 'ieeg'):
        os.makedirs(op.join(bids_root, 'sub-01', 'ses-01', datatype))

    # test no coordinate frame in dig or in bids_path.space
    montage = raw.get_montage()
    montage.apply_trans(mne.transforms.Transform('head', 'unknown'))
    for datatype in ('eeg', 'ieeg'):
        bids_path = _bids_path.copy().update(root=bids_root,
                                             datatype=datatype,
                                             space=None)
        with pytest.warns(RuntimeWarning,
                          match='Coordinate frame could not be inferred'):
            _write_dig_bids(bids_path, raw, montage, acpc_aligned=True)

    # test coordinate frame-BIDSPath.space mismatch
    raw = _load_raw()
    montage = raw.get_montage()
    print(montage.get_positions()['coord_frame'])
    bids_path = _bids_path.copy().update(root=bids_root,
                                         datatype='eeg',
                                         space='fsaverage')
    with pytest.raises(ValueError,
                       match='Coordinates in the raw object '
                       'or montage are in the CapTrak '
                       'coordinate frame but '
                       'BIDSPath.space is fsaverage'):
        _write_dig_bids(bids_path, raw, montage)

    # test MEG space conflict fif (ElektaNeuromag) != CTF
    bids_path = _bids_path.copy().update(root=bids_root,
                                         datatype='meg',
                                         space='CTF')
    with pytest.raises(ValueError, match='conflicts'):
        write_raw_bids(raw, bids_path)
コード例 #2
0
ファイル: test_dig.py プロジェクト: aces/EEG2BIDS
def test_dig_pixels(tmp_path):
    """Test dig stored correctly for the Pixels coordinate frame."""
    bids_root = tmp_path / 'bids1'

    # test coordinates in pixels
    bids_path = _bids_path.copy().update(root=bids_root,
                                         datatype='ieeg',
                                         space='Pixels')
    os.makedirs(op.join(bids_root, 'sub-01', 'ses-01', bids_path.datatype),
                exist_ok=True)
    raw_test = raw.copy()
    raw_test.pick_types(eeg=True)
    raw_test.del_proj()
    raw_test.set_channel_types({ch: 'ecog' for ch in raw_test.ch_names})

    mnt = raw_test.get_montage()
    # fake transform to pixel coordinates
    mnt.apply_trans(mne.transforms.Transform('head', 'unknown'))
    _write_dig_bids(bids_path, raw_test, mnt)
    electrodes_path = bids_path.copy().update(task=None,
                                              run=None,
                                              suffix='electrodes',
                                              extension='.tsv')
    coordsystem_path = bids_path.copy().update(task=None,
                                               run=None,
                                               suffix='coordsystem',
                                               extension='.json')
    with pytest.warns(RuntimeWarning,
                      match='not an MNE-Python coordinate frame'):
        _read_dig_bids(electrodes_path, coordsystem_path, bids_path.datatype,
                       raw_test)
    mnt2 = raw_test.get_montage()
    assert mnt2.get_positions()['coord_frame'] == 'unknown'
    assert_almost_equal(
        np.array(list(mnt.get_positions()['ch_pos'].values())),
        np.array(list(mnt2.get_positions()['ch_pos'].values())))
コード例 #3
0
ファイル: test_dig.py プロジェクト: aces/EEG2BIDS
def test_dig_template(tmp_path):
    """Test that eeg and ieeg dig are stored properly."""
    bids_root = tmp_path / 'bids1'
    for datatype in ('eeg', 'ieeg'):
        (bids_root / 'sub-01' / 'ses-01' / datatype).mkdir(parents=True)

    raw_test = raw.copy().pick_types(eeg=True)

    for datatype in ('eeg', 'ieeg'):
        bids_path = _bids_path.copy().update(root=bids_root, datatype=datatype)
        for coord_frame in BIDS_STANDARD_TEMPLATE_COORDINATE_SYSTEMS:
            bids_path.update(space=coord_frame)
            mnt = montage.copy()
            pos = mnt.get_positions()
            mne_coord_frame = BIDS_TO_MNE_FRAMES.get(coord_frame, None)
            if mne_coord_frame is None:
                mnt.apply_trans(mne.transforms.Transform('head', 'unknown'))
            else:
                mnt.apply_trans(
                    mne.transforms.Transform('head', mne_coord_frame))
            _write_dig_bids(bids_path, raw_test, mnt, acpc_aligned=True)
            electrodes_path = bids_path.copy().update(task=None,
                                                      run=None,
                                                      suffix='electrodes',
                                                      extension='.tsv')
            coordsystem_path = bids_path.copy().update(task=None,
                                                       run=None,
                                                       suffix='coordsystem',
                                                       extension='.json')
            if mne_coord_frame is None:
                with pytest.warns(RuntimeWarning,
                                  match='not an MNE-Python coordinate frame'):
                    _read_dig_bids(electrodes_path, coordsystem_path, datatype,
                                   raw_test)
            else:
                if coord_frame == 'MNI305':  # saved to fsaverage, same
                    electrodes_path.update(space='fsaverage')
                    coordsystem_path.update(space='fsaverage')
                _read_dig_bids(electrodes_path, coordsystem_path, datatype,
                               raw_test)
            mnt2 = raw_test.get_montage()
            pos2 = mnt2.get_positions()
            np.testing.assert_array_almost_equal(
                np.array(list(pos['ch_pos'].values())),
                np.array(list(pos2['ch_pos'].values())))
            if mne_coord_frame is None:
                assert pos2['coord_frame'] == 'unknown'
            else:
                assert pos2['coord_frame'] == mne_coord_frame

    # test MEG
    raw_test = raw.copy()
    for coord_frame in BIDS_STANDARD_TEMPLATE_COORDINATE_SYSTEMS:
        bids_path = _bids_path.copy().update(root=bids_root,
                                             datatype='meg',
                                             space=coord_frame)
        write_raw_bids(raw_test, bids_path)
        raw_test2 = read_raw_bids(bids_path)
        for ch, ch2 in zip(raw.info['chs'], raw_test2.info['chs']):
            np.testing.assert_array_equal(ch['loc'], ch2['loc'])
            assert ch['coord_frame'] == ch2['coord_frame']