def test_coreg_gui_pyvista_file_support(inst_path, tmp_path,
renderer_interactive_pyvistaqt):
"""Test reading supported files."""
from mne.gui import coregistration
if inst_path == 'gen_montage':
# generate a montage fig to use as inst.
tmp_info = read_info(raw_path)
eeg_chans = []
for pt in tmp_info['dig']:
if pt['kind'] == FIFF.FIFFV_POINT_EEG:
eeg_chans.append(f"EEG {pt['ident']:03d}")
dig = DigMontage(dig=tmp_info['dig'], ch_names=eeg_chans)
inst_path = tmp_path / 'tmp-dig.fif'
dig.save(inst_path)
if inst_path == ctf_raw_path:
ctx = pytest.warns(RuntimeWarning, match='MEG ref channel RMSP')
elif inst_path == snirf_nirsport2_raw_path: # TODO: This is maybe a bug?
ctx = pytest.warns(RuntimeWarning, match='assuming "head"')
else:
ctx = nullcontext()
with ctx:
coregistration(inst=inst_path,
subject='sample',
subjects_dir=subjects_dir)
def test_coreg_gui_pyvista_file_support(inst_path, tmp_path,
renderer_interactive_pyvistaqt):
"""Test reading supported files."""
from mne.gui import coregistration
if inst_path == 'gen_montage':
# generate a montage fig to use as inst.
tmp_info = read_info(raw_path)
eeg_chans = []
for pt in tmp_info['dig']:
if pt['kind'] == FIFF.FIFFV_POINT_EEG:
eeg_chans.append(f"EEG {pt['ident']:03d}")
dig = DigMontage(dig=tmp_info['dig'], ch_names=eeg_chans)
inst_path = tmp_path / 'tmp-dig.fif'
dig.save(inst_path)
# Suppressing warnings here is not ideal.
# However ctf_raw_path (catch-alp-good-f.ds) is poorly formed and causes
# mne.io.read_raw to issue warning.
# XXX consider replacing ctf_raw_path and removing warning ignore filter.
with warnings.catch_warnings():
warnings.simplefilter("ignore")
coregistration(inst=inst_path,
subject='sample',
subjects_dir=subjects_dir)
def test_coreg_gui_notebook(renderer_notebook, nbexec):
"""Test the coregistration UI in a notebook."""
import os
import mne
from mne.datasets import testing
from mne.gui import coregistration
mne.viz.set_3d_backend('notebook') # set the 3d backend
data_path = testing.data_path()
subjects_dir = os.path.join(data_path, 'subjects')
coregistration(subject='sample', subjects_dir=subjects_dir)
def test_coreg_gui_notebook(renderer_notebook, nbexec):
"""Test the coregistration UI in a notebook."""
import os
import mne
from mne.datasets import testing
from mne.gui import coregistration
mne.viz.set_3d_backend('notebook') # set the 3d backend
with mne.utils.modified_env(_MNE_FAKE_HOME_DIR=None):
data_path = testing.data_path(download=False)
subjects_dir = os.path.join(data_path, 'subjects')
coregistration(subject='sample', subjects_dir=subjects_dir)
def forward_pipeline(raw_fname, freesurfer_dir, subject,
trans_fname=None, fwd_fname=None, oct_fname=None,
bem_sol_fname=None, save_dir=None, overwrite=False):
import os.path as op
from jr.meg import check_freesurfer, mne_anatomy
# Setup paths
if save_dir is None:
save_dir = '/'.join(raw_fname.split('/')[:-1])
print('Save/read directory: %s' % save_dir)
if trans_fname is None:
trans_fname = op.join(save_dir, subject + '-trans.fif')
bem_sol_fname = op.join(freesurfer_dir, subject, 'bem',
subject + '-5120-bem-sol.fif')
oct_fname = op.join(freesurfer_dir, subject, 'bem',
subject + '-oct-6-src.fif')
fwd_fname = op.join(save_dir, subject + '-meg-fwd.fif')
# Checks Freesurfer segmentation and compute watershed bem
if check_freesurfer(subjects_dir=freesurfer_dir,
subject=subject):
mne_anatomy(subjects_dir=freesurfer_dir, subject=subject,
overwrite=overwrite)
# Manual coregisteration head markers with coils
if overwrite or not op.isfile(trans_fname):
from mne.gui import coregistration
coregistration(subject=subject, subjects_dir=freesurfer_dir,
inst=raw_fname)
# Forward solution
if overwrite or not op.exists(fwd_fname):
from mne import (make_forward_solution, convert_forward_solution,
write_forward_solution)
fwd = make_forward_solution(
raw_fname, trans_fname, oct_fname, bem_sol_fname,
fname=None, meg=True, eeg=False, mindist=5.0,
overwrite=True, ignore_ref=True)
# convert to surface orientation for better visualization
fwd = convert_forward_solution(fwd, surf_ori=True)
# save
write_forward_solution(fwd_fname, fwd, overwrite=True)
else:
from mne import read_forward_solution
fwd = read_forward_solution(fwd_fname, surf_ori=True)
return fwd
def test_coreg_gui_scraper(tmp_path, renderer_interactive_pyvistaqt):
"""Test the scrapper for the coregistration GUI."""
from mne.gui import coregistration
coreg = coregistration(subject='sample',
subjects_dir=subjects_dir,
trans=fname_trans)
(tmp_path / '_images').mkdir()
image_path = str(tmp_path / '_images' / 'temp.png')
gallery_conf = dict(builder_name='html', src_dir=str(tmp_path))
block_vars = dict(example_globals=dict(gui=coreg),
image_path_iterator=iter([image_path]))
assert not op.isfile(image_path)
assert not getattr(coreg, '_scraped', False)
mne.gui._GUIScraper()(None, block_vars, gallery_conf)
assert op.isfile(image_path)
assert coreg._scraped
def test_no_sparse_head(subjects_dir_tmp, renderer_interactive_pyvistaqt,
monkeypatch):
"""Test mne.gui.coregistration with no sparse head."""
from mne.gui import coregistration
subject = 'sample'
out_rr, out_tris = mne.read_surface(
op.join(subjects_dir_tmp, subject, 'bem', 'outer_skin.surf'))
for head in ('sample-head.fif', 'outer_skin.surf'):
os.remove(op.join(subjects_dir_tmp, subject, 'bem', head))
# Avoid actually doing the decimation (it's slow)
monkeypatch.setattr(mne.coreg, 'decimate_surface',
lambda rr, tris, n_triangles: (out_rr, out_tris))
with pytest.warns(RuntimeWarning, match='No low-resolution head found'):
coreg = coregistration(inst=raw_path,
subject=subject,
subjects_dir=subjects_dir_tmp)
coreg.close()
def test_coreg_gui_pyvista_basic(tmp_path, renderer_interactive_pyvistaqt,
monkeypatch):
"""Test that using CoregistrationUI matches mne coreg."""
from mne.gui import coregistration
config = get_config()
# the sample subject in testing has MRI fids
assert op.isfile(
op.join(subjects_dir, 'sample', 'bem', 'sample-fiducials.fif'))
coreg = coregistration(subject='sample',
subjects_dir=subjects_dir,
trans=fname_trans)
assert coreg._lock_fids
coreg._reset_fiducials()
coreg.close()
# make it always log the distances
monkeypatch.setattr(_3d.logger, 'info', _3d.logger.warning)
with catch_logging() as log:
coreg = coregistration(
inst=raw_path,
subject='sample',
head_high_res=False, # for speed
subjects_dir=subjects_dir,
verbose='debug')
log = log.getvalue()
assert 'Total 16/78 points inside the surface' in log
coreg._set_fiducials_file(fid_fname)
assert coreg._fiducials_file == fid_fname
# fitting (with scaling)
assert not coreg._mri_scale_modified
coreg._reset()
coreg._reset_fitting_parameters()
coreg._set_scale_mode("uniform")
coreg._fits_fiducials()
assert_allclose(coreg.coreg._scale,
np.array([97.46, 97.46, 97.46]) * 1e-2,
atol=1e-3)
shown_scale = [coreg._widgets[f's{x}'].get_value() for x in 'XYZ']
assert_allclose(shown_scale, coreg.coreg._scale * 100, atol=1e-2)
coreg._set_icp_fid_match("nearest")
coreg._set_scale_mode("3-axis")
coreg._fits_icp()
assert_allclose(coreg.coreg._scale,
np.array([104.43, 101.47, 125.78]) * 1e-2,
atol=1e-3)
shown_scale = [coreg._widgets[f's{x}'].get_value() for x in 'XYZ']
assert_allclose(shown_scale, coreg.coreg._scale * 100, atol=1e-2)
coreg._set_scale_mode("None")
coreg._set_icp_fid_match("matched")
assert coreg._mri_scale_modified
# unlock fiducials
assert coreg._lock_fids
coreg._set_lock_fids(False)
assert not coreg._lock_fids
# picking
assert not coreg._mri_fids_modified
vtk_picker = TstVTKPicker(coreg._surfaces['head'], 0, (0, 0))
coreg._on_mouse_move(vtk_picker, None)
coreg._on_button_press(vtk_picker, None)
coreg._on_pick(vtk_picker, None)
coreg._on_button_release(vtk_picker, None)
coreg._on_pick(vtk_picker, None) # also pick when locked
assert coreg._mri_fids_modified
# lock fiducials
coreg._set_lock_fids(True)
assert coreg._lock_fids
# fitting (no scaling)
assert coreg._nasion_weight == 10.
coreg._set_point_weight(11., 'nasion')
assert coreg._nasion_weight == 11.
coreg._fit_fiducials()
with catch_logging() as log:
coreg._redraw() # actually emit the log
log = log.getvalue()
assert 'Total 6/78 points inside the surface' in log
with catch_logging() as log:
coreg._fit_icp()
coreg._redraw()
log = log.getvalue()
assert 'Total 38/78 points inside the surface' in log
assert coreg.coreg._extra_points_filter is None
coreg._omit_hsp()
with catch_logging() as log:
coreg._redraw()
log = log.getvalue()
assert 'Total 29/53 points inside the surface' in log
assert coreg.coreg._extra_points_filter is not None
coreg._reset_omit_hsp_filter()
with catch_logging() as log:
coreg._redraw()
log = log.getvalue()
assert 'Total 38/78 points inside the surface' in log
assert coreg.coreg._extra_points_filter is None
assert coreg._grow_hair == 0
coreg._fit_fiducials() # go back to few inside to start
with catch_logging() as log:
coreg._redraw()
log = log.getvalue()
assert 'Total 6/78 points inside the surface' in log
norm = np.linalg.norm(coreg._head_geo['rr']) # what's used for inside
assert_allclose(norm, 5.949288, atol=1e-3)
coreg._set_grow_hair(20.0)
with catch_logging() as log:
coreg._redraw()
assert coreg._grow_hair == 20.0
norm = np.linalg.norm(coreg._head_geo['rr'])
assert_allclose(norm, 6.555220, atol=1e-3) # outward
log = log.getvalue()
assert 'Total 8/78 points inside the surface' in log # more outside now
# visualization
assert not coreg._helmet
coreg._set_helmet(True)
assert coreg._helmet
assert coreg._orient_glyphs
assert coreg._scale_by_distance
assert coreg._mark_inside
assert_allclose(coreg._head_opacity,
float(config.get('MNE_COREG_HEAD_OPACITY', '0.8')))
assert coreg._hpi_coils
assert coreg._eeg_channels
assert coreg._head_shape_points
assert coreg._scale_mode == 'None'
assert coreg._icp_fid_match == 'matched'
assert coreg._head_resolution is False
assert coreg._trans_modified
tmp_trans = tmp_path / 'tmp-trans.fif'
coreg._save_trans(tmp_trans)
assert not coreg._trans_modified
assert op.isfile(tmp_trans)
# first, disable auto cleanup
coreg._renderer._window_close_disconnect(after=True)
# test _close_callback()
coreg.close()
coreg._widgets['close_dialog'].trigger('Discard') # do not save
coreg._clean() # finally, cleanup internal structures
# Coregistration instance should survive
assert isinstance(coreg.coreg, Coregistration)
# Fullscreen mode
coreg = coregistration(subject='sample',
subjects_dir=subjects_dir,
fullscreen=True)
"""MRI <--> head coordinates coregistration"""
from argparse import ArgumentParser
from mne.gui import coregistration
from metacog import bp
from metacog.paths import dirs
parser = ArgumentParser(description=__doc__)
parser.add_argument("subject", help="subject id")
args = parser.parse_args()
subj = args.subject
info_src = bp.root.fpath(subject=subj, task="questions", run=1, session=None)
trans_path = bp.trans.fpath(subject=subj)
trans_path.parent.mkdir(exist_ok=True)
trans_path = trans_path if trans_path.exists() else None
coregistration(
subject=f"sub-{subj}",
subjects_dir=dirs.fsf_subjects,
inst=info_src,
trans=trans_path,
)
def test_coreg_gui_pyvista(tmp_path, renderer_interactive_pyvistaqt):
"""Test that using CoregistrationUI matches mne coreg."""
from mne.gui import coregistration
from mne.gui._coreg import CoregistrationUI
config = get_config(home_dir=os.environ.get('_MNE_FAKE_HOME_DIR'))
# the sample subject in testing has MRI fids
assert op.isfile(
op.join(subjects_dir, 'sample', 'bem', 'sample-fiducials.fif'))
deprecated_params = ['standalone', 'head_transparency', 'project_eeg']
for param in deprecated_params:
kwargs = {p: None for p in deprecated_params}
kwargs[param] = True
with pytest.warns(DeprecationWarning, match=f'{param} is deprecated'):
coreg = CoregistrationUI(info_file=None,
subject='sample',
subjects_dir=subjects_dir,
**kwargs)
coreg.close()
del kwargs
deprecated_params = ['project_eeg']
for param in deprecated_params:
kwargs = {p: None for p in deprecated_params}
kwargs[param] = True
with pytest.warns(DeprecationWarning, match=f'{param} is deprecated'):
coreg = coregistration(subject='sample',
subjects_dir=subjects_dir,
**kwargs)
coreg.close()
del kwargs
coreg = coregistration(subject='sample',
subjects_dir=subjects_dir,
trans=fname_trans)
assert coreg._lock_fids
coreg._reset_fiducials()
coreg.close()
coreg = coregistration(inst=raw_path,
subject='sample',
subjects_dir=subjects_dir)
coreg._set_fiducials_file(fid_fname)
assert coreg._fiducials_file == fid_fname
# fitting (with scaling)
assert not coreg._mri_scale_modified
coreg._reset()
coreg._reset_fitting_parameters()
coreg._set_scale_mode("uniform")
coreg._fits_fiducials()
assert_allclose(coreg.coreg._scale,
np.array([97.46, 97.46, 97.46]) * 1e-2,
atol=1e-3)
coreg._set_icp_fid_match("nearest")
coreg._set_scale_mode("3-axis")
coreg._fits_icp()
assert_allclose(coreg.coreg._scale,
np.array([104.43, 101.47, 125.78]) * 1e-2,
atol=1e-3)
coreg._set_scale_mode("None")
coreg._set_icp_fid_match("matched")
assert coreg._mri_scale_modified
# unlock fiducials
assert coreg._lock_fids
coreg._set_lock_fids(False)
assert not coreg._lock_fids
# picking
assert not coreg._mri_fids_modified
vtk_picker = TstVTKPicker(coreg._surfaces['head'], 0, (0, 0))
coreg._on_mouse_move(vtk_picker, None)
coreg._on_button_press(vtk_picker, None)
coreg._on_pick(vtk_picker, None)
coreg._on_button_release(vtk_picker, None)
coreg._on_pick(vtk_picker, None) # also pick when locked
assert coreg._mri_fids_modified
# lock fiducials
coreg._set_lock_fids(True)
assert coreg._lock_fids
# fitting (no scaling)
assert coreg._nasion_weight == 10.
coreg._set_point_weight(11., 'nasion')
assert coreg._nasion_weight == 11.
coreg._fit_fiducials()
coreg._fit_icp()
assert coreg.coreg._extra_points_filter is None
coreg._omit_hsp()
assert coreg.coreg._extra_points_filter is not None
coreg._reset_omit_hsp_filter()
assert coreg.coreg._extra_points_filter is None
assert coreg._grow_hair == 0
coreg._set_grow_hair(0.1)
assert coreg._grow_hair == 0.1
# visualization
assert not coreg._helmet
coreg._set_helmet(True)
assert coreg._helmet
assert coreg._orient_glyphs
assert coreg._scale_by_distance
assert coreg._mark_inside
assert_allclose(coreg._head_opacity,
float(config.get('MNE_COREG_HEAD_OPACITY', '0.8')))
assert coreg._hpi_coils
assert coreg._eeg_channels
assert coreg._head_shape_points
assert coreg._scale_mode == 'None'
assert coreg._icp_fid_match == 'matched'
assert coreg._head_resolution == \
(config.get('MNE_COREG_HEAD_HIGH_RES', 'true') == 'true')
assert coreg._trans_modified
tmp_trans = tmp_path / 'tmp-trans.fif'
coreg._save_trans(tmp_trans)
assert not coreg._trans_modified
assert op.isfile(tmp_trans)
# first, disable auto cleanup
coreg._renderer._window_close_disconnect(after=True)
# test _close_callback()
coreg.close()
coreg._widgets['close_dialog'].trigger('Discard') # do not save
coreg._clean() # finally, cleanup internal structures
# Coregistration instance should survive
assert isinstance(coreg.coreg, Coregistration)
def forward_pipeline(raw_fname,
freesurfer_dir,
subject,
trans_fname=None,
fwd_fname=None,
oct_fname=None,
bem_sol_fname=None,
save_dir=None,
overwrite=False):
import os.path as op
from jr.meg import check_freesurfer, mne_anatomy
# Setup paths
if save_dir is None:
save_dir = '/'.join(raw_fname.split('/')[:-1])
print('Save/read directory: %s' % save_dir)
if trans_fname is None:
trans_fname = op.join(save_dir, subject + '-trans.fif')
bem_sol_fname = op.join(freesurfer_dir, subject, 'bem',
subject + '-5120-bem-sol.fif')
oct_fname = op.join(freesurfer_dir, subject, 'bem',
subject + '-oct-6-src.fif')
fwd_fname = op.join(save_dir, subject + '-meg-fwd.fif')
# Checks Freesurfer segmentation and compute watershed bem
if check_freesurfer(subjects_dir=freesurfer_dir, subject=subject):
mne_anatomy(subjects_dir=freesurfer_dir,
subject=subject,
overwrite=overwrite)
# Manual coregisteration head markers with coils
if overwrite or not op.isfile(trans_fname):
from mne.gui import coregistration
coregistration(subject=subject,
subjects_dir=freesurfer_dir,
inst=raw_fname)
# Forward solution
if overwrite or not op.exists(fwd_fname):
from mne import (make_forward_solution, convert_forward_solution,
write_forward_solution)
fwd = make_forward_solution(raw_fname,
trans_fname,
oct_fname,
bem_sol_fname,
fname=None,
meg=True,
eeg=False,
mindist=5.0,
overwrite=True,
ignore_ref=True)
# convert to surface orientation for better visualization
fwd = convert_forward_solution(fwd, surf_ori=True)
# save
write_forward_solution(fwd_fname, fwd, overwrite=True)
else:
from mne import read_forward_solution
fwd = read_forward_solution(fwd_fname, surf_ori=True)
return fwd
def test_coreg_gui_pyvista(tmp_path, renderer_interactive_pyvistaqt):
"""Test that using CoregistrationUI matches mne coreg."""
from mne.gui import coregistration
config = get_config(home_dir=os.environ.get('_MNE_FAKE_HOME_DIR'))
tmp_trans = tmp_path / 'tmp-trans.fif'
# the sample subject in testing has MRI fids
assert op.isfile(
op.join(subjects_dir, 'sample', 'bem', 'sample-fiducials.fif'))
coreg = coregistration(subject='sample',
subjects_dir=subjects_dir,
trans=fname_trans)
assert coreg._lock_fids
coreg._reset_fiducials()
coreg.close()
coreg = coregistration(inst=raw_path,
subject='sample',
subjects_dir=subjects_dir)
coreg._set_fiducials_file(fid_fname)
assert coreg._fiducials_file == fid_fname
# unlock fiducials
assert coreg._lock_fids
coreg._set_lock_fids(False)
assert not coreg._lock_fids
# picking
vtk_picker = TstVTKPicker(coreg._surfaces['head'], 0, (0, 0))
coreg._on_mouse_move(vtk_picker, None)
coreg._on_button_press(vtk_picker, None)
coreg._on_pick(vtk_picker, None)
coreg._on_button_release(vtk_picker, None)
coreg._on_pick(vtk_picker, None) # also pick when locked
# lock fiducials
coreg._set_lock_fids(True)
assert coreg._lock_fids
# fitting
assert coreg._nasion_weight == 10.
coreg._set_point_weight(11., 'nasion')
assert coreg._nasion_weight == 11.
coreg._fit_fiducials()
coreg._fit_icp()
assert coreg._coreg._extra_points_filter is None
coreg._omit_hsp()
assert coreg._coreg._extra_points_filter is not None
coreg._reset_omit_hsp_filter()
assert coreg._coreg._extra_points_filter is None
assert coreg._grow_hair == 0
coreg._set_grow_hair(0.1)
assert coreg._grow_hair == 0.1
# visualization
assert coreg._orient_glyphs == \
(config.get('MNE_COREG_ORIENT_TO_SURFACE', '') == 'true')
assert coreg._hpi_coils
assert coreg._eeg_channels
assert coreg._head_shape_points
assert coreg._scale_mode == 'None'
assert coreg._icp_fid_match == 'nearest'
assert coreg._head_resolution == \
(config.get('MNE_COREG_HEAD_HIGH_RES', 'true') == 'true')
assert not coreg._head_transparency
coreg._set_head_transparency(True)
assert coreg._head_transparency
coreg._save_trans(tmp_trans)
assert op.isfile(tmp_trans)
coreg.close()
from mne.viz import plot_trans
from mne.gui import coregistration
if True:
for meg_subject, subject in zip(range(1, 21), subjects_id):
if subject in missing_mri + bad_mri:
continue
raw_fname = paths('sss', subject=meg_subject, block=1)
trans_fname = paths('trans', subject=meg_subject)
# XXX for one subject the HPI were adequately triangulated before the
# first block
if subject == 'ps120458':
raw_fname.split('1-sss.fif')[0] + '2-sss.fif'
# Manual coregistration
print(subject, meg_subject)
coregistration(subject=subject,
subjects_dir=subjects_dir,
inst=raw_fname)
# Plot
info = read_info(raw_fname)
plot_trans(info,
trans_fname,
subject=subject,
dig=True,
meg_sensors=True)
def _copy_from_fsaverage(subject, subjects_dir, overwrite=False):
"""Copy fsaverage files for subjects with missing MRI"""
for this_dir in ['bem', 'surf']:
bem_dir = os.path.join(subjects_dir, subject, this_dir)
if not os.path.exists(bem_dir):
# Manual Coregistration -------------------------------------------------------
from mne.viz import plot_trans
from mne.gui import coregistration
if True:
for meg_subject, subject in zip(range(1, 21), subjects_id):
if subject in missing_mri + bad_mri:
continue
raw_fname = paths('sss', subject=meg_subject, block=1)
trans_fname = paths('trans', subject=meg_subject)
# XXX for one subject the HPI were adequately triangulated before the
# first block
if subject == 'ps120458':
raw_fname.split('1-sss.fif')[0] + '2-sss.fif'
# Manual coregistration
print(subject, meg_subject)
coregistration(subject=subject, subjects_dir=subjects_dir,
inst=raw_fname)
# Plot
info = read_info(raw_fname)
plot_trans(info, trans_fname, subject=subject, dig=True,
meg_sensors=True)
def _copy_from_fsaverage(subject, subjects_dir, overwrite=False):
"""Copy fsaverage files for subjects with missing MRI"""
for this_dir in ['bem', 'surf']:
bem_dir = os.path.join(subjects_dir, subject, this_dir)
if not os.path.exists(bem_dir):
os.makedirs(bem_dir)
f_from = os.path.join(subjects_dir, 'fsaverage', 'bem',
'fsaverage-5120-bem.fif')
f_to = os.path.join(subjects_dir, subject, 'bem',
