def test_datasets_basic(tmpdir):
"""Test simple dataset functions."""
# XXX 'hf_sef' and 'misc' do not conform to these standards
for dname in ('sample', 'somato', 'spm_face', 'testing', 'opm',
'bst_raw', 'bst_auditory', 'bst_resting', 'multimodal',
'bst_phantom_ctf', 'bst_phantom_elekta', 'kiloword',
'mtrf', 'phantom_4dbti',
'visual_92_categories', 'fieldtrip_cmc'):
if dname.startswith('bst'):
dataset = getattr(datasets.brainstorm, dname)
check_name = 'brainstorm.%s' % (dname,)
else:
dataset = getattr(datasets, dname)
check_name = dname
if dataset.data_path(download=False) != '':
assert isinstance(dataset.get_version(), str)
assert datasets.utils.has_dataset(check_name)
else:
assert dataset.get_version() is None
assert not datasets.utils.has_dataset(check_name)
print('%s: %s' % (dname, datasets.utils.has_dataset(check_name)))
tempdir = str(tmpdir)
# don't let it read from the config file to get the directory,
# force it to look for the default
with modified_env(**{'_MNE_FAKE_HOME_DIR': tempdir, 'SUBJECTS_DIR': None}):
assert (datasets.utils._get_path(None, 'foo', 'bar') ==
op.join(tempdir, 'mne_data'))
assert get_subjects_dir(None) is None
_set_montage_coreg_path()
sd = get_subjects_dir()
assert sd.endswith('MNE-fsaverage-data')
def test_make_scalp_surfaces(tmpdir):
"""Test mne make_scalp_surfaces."""
check_usage(mne_make_scalp_surfaces)
has = 'SUBJECTS_DIR' in os.environ
# Copy necessary files to avoid FreeSurfer call
tempdir = str(tmpdir)
surf_path = op.join(subjects_dir, 'sample', 'surf')
surf_path_new = op.join(tempdir, 'sample', 'surf')
os.mkdir(op.join(tempdir, 'sample'))
os.mkdir(surf_path_new)
subj_dir = op.join(tempdir, 'sample', 'bem')
os.mkdir(subj_dir)
shutil.copy(op.join(surf_path, 'lh.seghead'), surf_path_new)
cmd = ('-s', 'sample', '--subjects-dir', tempdir)
with modified_env(**{'_MNE_TESTING_SCALP': 'true'}):
dense_fname = op.join(subj_dir, 'sample-head-dense.fif')
medium_fname = op.join(subj_dir, 'sample-head-medium.fif')
with ArgvSetter(cmd, disable_stdout=False, disable_stderr=False):
with modified_env(FREESURFER_HOME=None):
pytest.raises(RuntimeError, mne_make_scalp_surfaces.run)
with modified_env(FREESURFER_HOME=tempdir):
mne_make_scalp_surfaces.run()
assert op.isfile(dense_fname)
assert op.isfile(medium_fname)
with pytest.raises(IOError, match='overwrite'):
mne_make_scalp_surfaces.run()
# actually check the outputs
head_py = read_bem_surfaces(dense_fname)
assert_equal(len(head_py), 1)
head_py = head_py[0]
head_c = read_bem_surfaces(op.join(subjects_dir, 'sample', 'bem',
'sample-head-dense.fif'))[0]
assert_allclose(head_py['rr'], head_c['rr'])
if not has:
assert 'SUBJECTS_DIR' not in os.environ
def test_setup_source_space_spacing(tmpdir, spacing):
"""Test setting up surface source spaces using a given spacing."""
tempdir = str(tmpdir)
copytree(op.join(subjects_dir, 'sample'), op.join(tempdir, 'sample'))
args = [] if spacing == 7 else ['--spacing', str(spacing)]
with modified_env(SUBJECTS_DIR=tempdir, SUBJECT='sample'):
run_subprocess(['mne_setup_source_space'] + args)
src = read_source_spaces(op.join(tempdir, 'sample', 'bem',
'sample-%d-src.fif' % spacing))
src_new = setup_source_space('sample', spacing=spacing, add_dist=False,
subjects_dir=subjects_dir)
_compare_source_spaces(src, src_new, mode='approx', nearest=True)
# Degenerate conditions
with pytest.raises(TypeError, match='spacing must be.*got.*float.*'):
setup_source_space('sample', 7., subjects_dir=subjects_dir)
with pytest.raises(ValueError, match='spacing must be >= 2, got 1'):
setup_source_space('sample', 1, subjects_dir=subjects_dir)
def test_setup_source_space_spacing(tmpdir, spacing):
"""Test setting up surface source spaces using a given spacing."""
copytree(op.join(subjects_dir, 'sample'), str(tmpdir.join('sample')))
args = [] if spacing == 7 else ['--spacing', str(spacing)]
with modified_env(SUBJECTS_DIR=str(tmpdir), SUBJECT='sample'):
run_subprocess(['mne_setup_source_space'] + args)
src = read_source_spaces(
tmpdir.join('sample', 'bem', 'sample-%d-src.fif' % spacing))
src_new = setup_source_space('sample',
spacing=spacing,
add_dist=False,
subjects_dir=subjects_dir)
_compare_source_spaces(src, src_new, mode='approx', nearest=True)
# Degenerate conditions
with pytest.raises(TypeError, match='spacing must be.*got.*float.*'):
setup_source_space('sample', 7., subjects_dir=subjects_dir)
with pytest.raises(ValueError, match='spacing must be >= 2, got 1'):
setup_source_space('sample', 1, subjects_dir=subjects_dir)
def test_kit2fiff_gui(check_gui_ci, tmpdir):
"""Test Kit2Fiff GUI."""
home_dir = str(tmpdir)
with modified_env(_MNE_GUI_TESTING_MODE='true',
_MNE_FAKE_HOME_DIR=home_dir):
from pyface.api import GUI
gui = GUI()
gui.process_events()
ui, frame = mne.gui.kit2fiff()
assert not frame.model.can_save
assert frame.model.stim_threshold == 1.
frame.model.stim_threshold = 10.
frame.model.stim_chs = 'save this!'
frame.save_config(home_dir)
ui.dispose()
gui.process_events()
# test setting persistence
ui, frame = mne.gui.kit2fiff()
assert frame.model.stim_threshold == 10.
assert frame.model.stim_chs == 'save this!'
# set and reset marker file
points = [[-0.084612, 0.021582, -0.056144],
[0.080425, 0.021995, -0.061171],
[-0.000787, 0.105530, 0.014168],
[-0.047943, 0.091835, 0.010240],
[0.042976, 0.094380, 0.010807]]
assert_array_equal(frame.marker_panel.mrk1_obj.points, 0)
assert_array_equal(frame.marker_panel.mrk3_obj.points, 0)
frame.model.markers.mrk1.file = mrk_pre_path
assert_allclose(frame.marker_panel.mrk1_obj.points, points, atol=1e-6)
assert_allclose(frame.marker_panel.mrk3_obj.points, points, atol=1e-6)
frame.marker_panel.mrk1_obj.label = True
frame.marker_panel.mrk1_obj.label = False
frame.kit2fiff_panel.clear_all = True
assert_array_equal(frame.marker_panel.mrk1_obj.points, 0)
assert_array_equal(frame.marker_panel.mrk3_obj.points, 0)
ui.dispose()
gui.process_events()
def few_surfaces():
"""Set the _MNE_FEW_SURFACES env var."""
with modified_env(_MNE_FEW_SURFACES='true'):
yield
def test_coreg_gui_display(tmpdir):
"""Test CoregFrame."""
_check_ci()
from mayavi import mlab
from tvtk.api import tvtk
home_dir = str(tmpdir)
with modified_env(**{'_MNE_GUI_TESTING_MODE': 'true',
'_MNE_FAKE_HOME_DIR': home_dir}):
with pytest.raises(ValueError, match='not a valid subject'):
mne.gui.coregistration(subject='Elvis', subjects_dir=subjects_dir)
# avoid modal dialog if SUBJECTS_DIR is set to a directory that
# does not contain valid subjects
ui, frame = mne.gui.coregistration(subjects_dir='')
mlab.process_ui_events()
ui.dispose()
mlab.process_ui_events()
ui, frame = mne.gui.coregistration(subjects_dir=subjects_dir,
subject='sample')
mlab.process_ui_events()
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)
mlab.process_ui_events()
# 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()
mlab.process_ui_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()
mlab.process_ui_events()
def test_combine_markers_panel(check_gui_ci):
"""Test CombineMarkersPanel."""
from mne.gui._marker_gui import CombineMarkersPanel
with modified_env(_MNE_GUI_TESTING_MODE='true'):
CombineMarkersPanel()
def test_coreg_gui_display(tmpdir):
"""Test CoregFrame."""
_check_ci()
from mayavi import mlab
from tvtk.api import tvtk
home_dir = str(tmpdir)
with modified_env(**{
'_MNE_GUI_TESTING_MODE': 'true',
'_MNE_FAKE_HOME_DIR': home_dir
}):
with pytest.raises(ValueError, match='not a valid subject'):
mne.gui.coregistration(subject='Elvis', subjects_dir=subjects_dir)
# avoid modal dialog if SUBJECTS_DIR is set to a directory that
# does not contain valid subjects
ui, frame = mne.gui.coregistration(subjects_dir='')
mlab.process_ui_events()
ui.dispose()
mlab.process_ui_events()
ui, frame = mne.gui.coregistration(subjects_dir=subjects_dir,
subject='sample')
mlab.process_ui_events()
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)
mlab.process_ui_events()
# 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()
mlab.process_ui_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()
mlab.process_ui_events()
def test_coreg_gui_display(subjects_dir_tmp, check_gui_ci):
"""Test CoregFrame."""
from mayavi import mlab
from tvtk.api import tvtk
home_dir = subjects_dir_tmp
# Remove the two files that will make the fiducials okay via MNI estimation
os.remove(
op.join(subjects_dir_tmp, 'sample', 'bem', 'sample-fiducials.fif'))
os.remove(
op.join(subjects_dir_tmp, 'sample', 'mri', 'transforms',
'talairach.xfm'))
with modified_env(_MNE_GUI_TESTING_MODE='true',
_MNE_FAKE_HOME_DIR=home_dir):
with pytest.raises(ValueError, match='not a valid subject'):
mne.gui.coregistration(subject='Elvis',
subjects_dir=subjects_dir_tmp)
# avoid modal dialog if SUBJECTS_DIR is set to a directory that
# does not contain valid subjects
ui, frame = mne.gui.coregistration(subjects_dir='')
mlab.process_ui_events()
ui.dispose()
mlab.process_ui_events()
ui, frame = mne.gui.coregistration(subjects_dir=subjects_dir_tmp,
subject='sample')
mlab.process_ui_events()
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)
mlab.process_ui_events()
# 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 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()
mlab.process_ui_events()
ui, frame = mne.gui.coregistration(subjects_dir=subjects_dir_tmp)
assert not frame.model.prepare_bem_model
assert not frame.data_panel.view_options_panel.head_high_res
ui.dispose()
mlab.process_ui_events()
