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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.")
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