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# Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
#
# License: BSD (3-clause)
import os
import os.path as op
import re
import shutil
import sys
from unittest import SkipTest
import numpy as np
from numpy.testing import (assert_allclose, assert_equal,
assert_array_almost_equal)
import pytest
import mne
from mne.datasets import testing
from mne.io.kit.tests import data_dir as kit_data_dir
from mne.transforms import invert_transform
from mne.utils import _TempDir, run_tests_if_main, requires_mayavi, traits_test
from mne.externals.six import string_types
# backend needs to be set early
try:
from traits.etsconfig.api import ETSConfig
except ImportError:
pass
else:
ETSConfig.toolkit = 'qt4'
data_path = testing.data_path(download=False)
raw_path = op.join(data_path, 'MEG', 'sample', 'sample_audvis_trunc_raw.fif')
fname_trans = op.join(data_path, 'MEG', 'sample',
'sample_audvis_trunc-trans.fif')
kit_raw_path = op.join(kit_data_dir, 'test_bin_raw.fif')
subjects_dir = op.join(data_path, 'subjects')
@testing.requires_testing_data
@requires_mayavi
@traits_test
def test_coreg_model_decimation():
"""Test CoregModel decimation of high-res to low-res head."""
from mne.gui._coreg_gui import CoregModel
tempdir = _TempDir()
subject_dir = op.join(tempdir, 'sample')
shutil.copytree(op.join(subjects_dir, 'sample'), subject_dir)
# This makes the test much faster
shutil.move(op.join(subject_dir, 'bem', 'outer_skin.surf'),
op.join(subject_dir, 'surf', 'lh.seghead'))
for fname in ('sample-head.fif', 'sample-head-dense.fif'):
os.remove(op.join(subject_dir, 'bem', fname))
model = CoregModel(guess_mri_subject=False)
with pytest.warns(RuntimeWarning, match='No low-resolution'):
model.mri.subjects_dir = tempdir
assert model.mri.subject == 'sample' # already set by setting subjects_dir
assert model.mri.bem_low_res.file == ''
assert len(model.mri.bem_low_res.surf.rr) == 2562
assert len(model.mri.bem_high_res.surf.rr) == 2562 # because we moved it
@testing.requires_testing_data
@requires_mayavi
@traits_test
def test_coreg_model():
"""Test CoregModel."""
from mne.gui._coreg_gui import CoregModel
tempdir = _TempDir()
trans_dst = op.join(tempdir, 'test-trans.fif')
model = CoregModel()
pytest.raises(RuntimeError, model.save_trans, 'blah.fif')
model.mri.subjects_dir = subjects_dir
model.mri.subject = 'sample'
assert not model.mri.fid_ok
model.mri.lpa = [[-0.06, 0, 0]]
model.mri.nasion = [[0, 0.05, 0]]
model.mri.rpa = [[0.08, 0, 0]]
assert (model.mri.fid_ok)
model.hsp.file = raw_path
assert_allclose(model.hsp.lpa, [[-7.137e-2, 0, 5.122e-9]], 1e-4)
assert_allclose(model.hsp.rpa, [[+7.527e-2, 0, 5.588e-9]], 1e-4)
assert_allclose(model.hsp.nasion, [[+3.725e-9, 1.026e-1, 4.191e-9]], 1e-4)
assert model.has_lpa_data
assert model.has_nasion_data
assert model.has_rpa_data
assert len(model.hsp.eeg_points) > 1
assert len(model.mri.bem_low_res.surf.rr) == 2562
assert len(model.mri.bem_high_res.surf.rr) == 267122
lpa_distance = model.lpa_distance
nasion_distance = model.nasion_distance
rpa_distance = model.rpa_distance
avg_point_distance = np.mean(model.point_distance)
model.nasion_weight = 1.
model.fit_fiducials(0)
old_x = lpa_distance ** 2 + rpa_distance ** 2 + nasion_distance ** 2
new_x = (model.lpa_distance ** 2 + model.rpa_distance ** 2 +
model.nasion_distance ** 2)
assert new_x < old_x
model.fit_icp(0)
new_dist = np.mean(model.point_distance)
assert new_dist < avg_point_distance
model.save_trans(trans_dst)
trans = mne.read_trans(trans_dst)
assert_allclose(trans['trans'], model.head_mri_t)
# test restoring trans
x, y, z = 100, 200, 50
rot_x, rot_y, rot_z = np.rad2deg([1.5, 0.1, -1.2])
model.trans_x = x
model.trans_y = y
model.trans_z = z
model.rot_x = rot_x
model.rot_y = rot_y
model.rot_z = rot_z
trans = model.mri_head_t
model.reset_traits(["trans_x", "trans_y", "trans_z", "rot_x", "rot_y",
"rot_z"])
assert_equal(model.trans_x, 0)
model.set_trans(trans)
assert_array_almost_equal(model.trans_x, x)
assert_array_almost_equal(model.trans_y, y)
assert_array_almost_equal(model.trans_z, z)
assert_array_almost_equal(model.rot_x, rot_x)
assert_array_almost_equal(model.rot_y, rot_y)
assert_array_almost_equal(model.rot_z, rot_z)
# info
assert (isinstance(model.fid_eval_str, string_types))
assert (isinstance(model.points_eval_str, string_types))
# scaling job
assert not model.can_prepare_bem_model
model.n_scale_params = 1
assert (model.can_prepare_bem_model)
model.prepare_bem_model = True
sdir, sfrom, sto, scale, skip_fiducials, labels, annot, bemsol = \
model.get_scaling_job('sample2', False)
assert_equal(sdir, subjects_dir)
assert_equal(sfrom, 'sample')
assert_equal(sto, 'sample2')
assert_allclose(scale, model.parameters[6:9])
assert_equal(skip_fiducials, False)
# find BEM files
bems = set()
for fname in os.listdir(op.join(subjects_dir, 'sample', 'bem')):
match = re.match(r'sample-(.+-bem)\.fif', fname)
if match:
bems.add(match.group(1))
assert_equal(set(bemsol), bems)
model.prepare_bem_model = False
sdir, sfrom, sto, scale, skip_fiducials, labels, annot, bemsol = \
model.get_scaling_job('sample2', True)
assert_equal(bemsol, [])
assert (skip_fiducials)
model.load_trans(fname_trans)
model.save_trans(trans_dst)
trans = mne.read_trans(trans_dst)
assert_allclose(trans['trans'], model.head_mri_t)
assert_allclose(invert_transform(trans)['trans'][:3, 3] * 1000.,
[model.trans_x, model.trans_y, model.trans_z])
def _check_ci():
if os.getenv('TRAVIS', 'false').lower() == 'true' and \
sys.platform == 'darwin':
raise SkipTest('Skipping GUI tests on Travis OSX')
@testing.requires_testing_data
@requires_mayavi
@traits_test
def test_coreg_gui():
"""Test CoregFrame."""
_check_ci()
home_dir = _TempDir()
os.environ['_MNE_GUI_TESTING_MODE'] = 'true'
os.environ['_MNE_FAKE_HOME_DIR'] = home_dir
try:
pytest.raises(ValueError, mne.gui.coregistration, subject='Elvis',
subjects_dir=subjects_dir)
from pyface.api import GUI
from tvtk.api import tvtk
gui = GUI()
# avoid modal dialog if SUBJECTS_DIR is set to a directory that
# does not contain valid subjects
ui, frame = mne.gui.coregistration(subjects_dir='')
frame.model.mri.subjects_dir = subjects_dir
frame.model.mri.subject = 'sample'
assert not frame.model.mri.fid_ok
frame.model.mri.lpa = [[-0.06, 0, 0]]
frame.model.mri.nasion = [[0, 0.05, 0]]
frame.model.mri.rpa = [[0.08, 0, 0]]
assert (frame.model.mri.fid_ok)
frame.data_panel.raw_src.file = raw_path
assert isinstance(frame.eeg_obj.glyph.glyph.glyph_source.glyph_source,
tvtk.SphereSource)
frame.data_panel.view_options_panel.eeg_obj.project_to_surface = True
assert isinstance(frame.eeg_obj.glyph.glyph.glyph_source.glyph_source,
tvtk.CylinderSource)
# grow hair (faster for low-res)
assert frame.data_panel.view_options_panel.head_high_res
frame.data_panel.view_options_panel.head_high_res = False
frame.model.grow_hair = 40.
# scale
frame.coreg_panel.n_scale_params = 3
frame.coreg_panel.scale_x_inc = True
assert frame.model.scale_x == 101.
frame.coreg_panel.scale_y_dec = True
assert frame.model.scale_y == 99.
# reset parameters
frame.coreg_panel.reset_params = True
assert_equal(frame.model.grow_hair, 0)
assert not frame.data_panel.view_options_panel.head_high_res
# configuration persistence
assert (frame.model.prepare_bem_model)
frame.model.prepare_bem_model = False
frame.save_config(home_dir)
ui.dispose()
gui.process_events()
ui, frame = mne.gui.coregistration(subjects_dir=subjects_dir)
assert not frame.model.prepare_bem_model
assert not frame.data_panel.view_options_panel.head_high_res
ui.dispose()
gui.process_events()
finally:
del os.environ['_MNE_GUI_TESTING_MODE']
del os.environ['_MNE_FAKE_HOME_DIR']
@testing.requires_testing_data
@requires_mayavi
@traits_test
def test_coreg_model_with_fsaverage():
"""Test CoregModel with the fsaverage brain data."""
tempdir = _TempDir()
from mne.gui._coreg_gui import CoregModel
mne.create_default_subject(subjects_dir=tempdir,
fs_home=op.join(subjects_dir, '..'))
model = CoregModel()
model.mri.subjects_dir = tempdir
model.mri.subject = 'fsaverage'
assert (model.mri.fid_ok)
model.hsp.file = raw_path
lpa_distance = model.lpa_distance
nasion_distance = model.nasion_distance
rpa_distance = model.rpa_distance
avg_point_distance = np.mean(model.point_distance)
# test hsp point omission
model.nasion_weight = 1.
model.trans_y = -0.008
model.fit_fiducials(0)
model.omit_hsp_points(0.02)
assert model.hsp.n_omitted == 1
model.omit_hsp_points(np.inf)
assert model.hsp.n_omitted == 0
model.omit_hsp_points(0.02)
assert model.hsp.n_omitted == 1
model.omit_hsp_points(0.01)
assert model.hsp.n_omitted == 4
model.omit_hsp_points(0.005)
assert model.hsp.n_omitted == 40
model.omit_hsp_points(0.01)
assert model.hsp.n_omitted == 4
model.omit_hsp_points(0.02)
assert model.hsp.n_omitted == 1
# scale with 1 parameter
model.n_scale_params = 1
model.fit_fiducials(1)
old_x = lpa_distance ** 2 + rpa_distance ** 2 + nasion_distance ** 2
new_x = (model.lpa_distance ** 2 + model.rpa_distance ** 2 +
model.nasion_distance ** 2)
assert (new_x < old_x)
model.fit_icp(1)
avg_point_distance_1param = np.mean(model.point_distance)
assert (avg_point_distance_1param < avg_point_distance)
# scaling job
sdir, sfrom, sto, scale, skip_fiducials, labels, annot, bemsol = \
model.get_scaling_job('scaled', False)
assert_equal(sdir, tempdir)
assert_equal(sfrom, 'fsaverage')
assert_equal(sto, 'scaled')
assert_allclose(scale, model.parameters[6:9])
assert_equal(set(bemsol), set(('inner_skull-bem',)))
model.prepare_bem_model = False
sdir, sfrom, sto, scale, skip_fiducials, labels, annot, bemsol = \
model.get_scaling_job('scaled', False)
assert_equal(bemsol, [])
# scale with 3 parameters
model.n_scale_params = 3
model.fit_icp(3)
assert (np.mean(model.point_distance) < avg_point_distance_1param)
# test switching raw disables point omission
assert_equal(model.hsp.n_omitted, 1)
model.hsp.file = kit_raw_path
assert_equal(model.hsp.n_omitted, 0)
run_tests_if_main()
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