com.py

# -*- coding: utf-8 -*-
import os.path as op
import numpy as np
import mne


def select_center_vertex_in_label(src, label):
    """ Select vertex closest (in Euclidean distance) to the center of mass of
        the given label.

    Parameters
    ----------
    src : list of dict
        The source space
    label : Label
        the label (read with mne.read_label)

    Returns
    -------
    center_vert : int
        index of central vertex
    """
    pos = label.pos
    mean_pos = np.mean(pos, axis=0)
    dists = np.sqrt(np.sum((pos - mean_pos)**2, axis=1))

    hemi_to_ind = {'lh': 0, 'rh': 1}
    src_sel = np.intersect1d(src[hemi_to_ind[label.hemi]]['vertno'],
                             label.vertices)
    idx_sel = np.searchsorted(label.vertices, src_sel)
    center_vertex = idx_sel[np.argmin(dists[idx_sel])]
    return center_vertex

subject = 'sample'
subjects_dir = mne.get_config('SUBJECTS_DIR')
rrs = [mne.read_surface(op.join(subjects_dir, subject, 'surf',
                                '%s.white' % hemi))[0]
       for hemi in ['lh', 'rh']]
src = mne.read_source_spaces(op.join(mne.datasets.sample.data_path(),
                                     'subjects', 'sample', 'bem',
                                     'sample-oct-6-src.fif'))
for label in mne.read_labels_from_annot(subject):
    label.values.fill(1.)
    idx = 0 if label.hemi == 'lh' else 1
    # Verify positions
    # Three reasonable choices for restrictions:
    restrict_vertices = np.intersect1d(src[idx]['vertno'], label.vertices)  # works!
    # restrict_vertices = label.vertices  # AssertionError
    # restrict_vertices = True  # AssertionError (equiv to above)
    # restrict_vertices = False  # AssertionError
    mne_vert = label.center_of_mass(restrict_vertices=restrict_vertices,
                                    surf='white')
    nick_vert = select_center_vertex_in_label(src, label)
    nick_vert = label.vertices[nick_vert]
    assert np.allclose(rrs[idx][label.vertices] / 1000., label.pos)
    assert mne_vert == nick_vert