import os from nose.tools import assert_raises, assert_true, assert_equal import numpy as np from numpy.testing import (assert_array_equal, assert_array_almost_equal, assert_array_less) from mne.transforms import apply_trans, rotation, translation, scaling from mne.coreg import (fit_matched_points, fit_point_cloud, _point_cloud_error, _decimate_points, create_default_subject, scale_mri, _is_mri_subject, scale_labels, scale_source_space, read_elp) from mne.io.kit.tests import data_dir as kit_data_dir from mne.utils import requires_mne_fs_in_env, _TempDir, run_subprocess from functools import reduce tempdir = _TempDir() def test_read_elp(): """Test reading an ELP file""" path = os.path.join(kit_data_dir, 'test_elp.txt') points = read_elp(path) assert_equal(points.shape, (8, 3)) assert_array_equal(points[0], [1.3930, 13.1613, -4.6967]) @requires_mne_fs_in_env def test_scale_mri(): """Test creating fsaverage and scaling it""" # create fsaverage create_default_subject(subjects_dir=tempdir) is_mri = _is_mri_subject('fsaverage', tempdir) assert_true(is_mri, "Creating fsaverage failed") fid_path = os.path.join(tempdir, 'fsaverage', 'bem', 'fsaverage-fiducials.fif') os.remove(fid_path) create_default_subject(update=True, subjects_dir=tempdir) assert_true(os.path.exists(fid_path), "Updating fsaverage") # create source space path = os.path.join(tempdir, 'fsaverage', 'bem', 'fsaverage-ico-6-src.fif') if not os.path.exists(path): cmd = ['mne_setup_source_space', '--subject', 'fsaverage', '--ico', '6'] env = os.environ.copy() env['SUBJECTS_DIR'] = tempdir run_subprocess(cmd, env=env) # scale fsaverage scale_mri('fsaverage', 'flachkopf', [1, .2, .8], True, subjects_dir=tempdir) is_mri = _is_mri_subject('flachkopf', tempdir) assert_true(is_mri, "Scaling fsaverage failed") src_path = os.path.join(tempdir, 'flachkopf', 'bem', 'flachkopf-ico-6-src.fif') assert_true(os.path.exists(src_path), "Source space was not scaled") scale_labels('flachkopf', subjects_dir=tempdir) # scale source space separately os.remove(src_path) scale_source_space('flachkopf', 'ico-6', subjects_dir=tempdir) assert_true(os.path.exists(src_path), "Source space was not scaled") def test_fit_matched_points(): """Test fit_matched_points: fitting two matching sets of points""" tgt_pts = np.random.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 & scaling trans = np.dot(rotation(2, 6, 3), scaling(.5, .5, .5)) src_pts = apply_trans(trans, tgt_pts) trans_est = fit_matched_points(src_pts, tgt_pts, translate=False, 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 and scaling.") # 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) 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.")