def test_io_trans():
"""Test reading and writing of trans files
"""
tempdir = _TempDir()
os.mkdir(op.join(tempdir, 'sample'))
assert_raises(RuntimeError, _find_trans, 'sample', subjects_dir=tempdir)
trans0 = read_trans(fname)
fname1 = op.join(tempdir, 'sample', 'test-trans.fif')
trans0.save(fname1)
assert_true(fname1 == _find_trans('sample', subjects_dir=tempdir))
trans1 = read_trans(fname1)
# check all properties
assert_true(trans0['from'] == trans1['from'])
assert_true(trans0['to'] == trans1['to'])
assert_array_equal(trans0['trans'], trans1['trans'])
# check reading non -trans.fif files
assert_raises(IOError, read_trans, fname_eve)
# check warning on bad filenames
with warnings.catch_warnings(record=True) as w:
fname2 = op.join(tempdir, 'trans-test-bad-name.fif')
write_trans(fname2, trans0)
assert_naming(w, 'test_transforms.py', 1)
def test_io_trans():
"""Test reading and writing of trans files
"""
tempdir = _TempDir()
os.mkdir(op.join(tempdir, "sample"))
assert_raises(RuntimeError, _find_trans, "sample", subjects_dir=tempdir)
trans0 = read_trans(fname)
fname1 = op.join(tempdir, "sample", "test-trans.fif")
write_trans(fname1, trans0)
assert_true(fname1 == _find_trans("sample", subjects_dir=tempdir))
trans1 = read_trans(fname1)
# check all properties
assert_true(trans0["from"] == trans1["from"])
assert_true(trans0["to"] == trans1["to"])
assert_array_equal(trans0["trans"], trans1["trans"])
# check reading non -trans.fif files
assert_raises(IOError, read_trans, fname_eve)
# check warning on bad filenames
with warnings.catch_warnings(record=True) as w:
fname2 = op.join(tempdir, "trans-test-bad-name.fif")
write_trans(fname2, trans0)
assert_true(len(w) >= 1)
def test_get_head_mri_trans_ctf():
"""Test getting a trans object from BIDS data in CTF."""
import nibabel as nib
ctf_data_path = op.join(testing.data_path(), 'CTF')
raw_ctf_fname = op.join(ctf_data_path, 'testdata_ctf.ds')
raw_ctf = _read_raw_ctf(raw_ctf_fname)
bids_root = _TempDir()
bids_path = _bids_path.copy().update(root=bids_root)
write_raw_bids(raw_ctf, bids_path, overwrite=False)
# Take a fake trans
trans = mne.read_trans(raw_fname.replace('_raw.fif', '-trans.fif'))
# Get the T1 weighted MRI data file ... test write_anat with a nibabel
# image instead of a file path
t1w_mgh = op.join(data_path, 'subjects', 'sample', 'mri', 'T1.mgz')
t1w_mgh = nib.load(t1w_mgh)
t1w_bids_path = BIDSPath(subject=subject_id,
session=session_id,
acquisition=acq,
root=bids_root)
write_anat(t1w_mgh, bids_path=t1w_bids_path, raw=raw_ctf, trans=trans)
# Try to get trans back through fitting points
estimated_trans = get_head_mri_trans(bids_path=bids_path)
assert_almost_equal(trans['trans'], estimated_trans['trans'])
def test_plot_dipole_mri_orthoview():
"""Test mpl dipole plotting."""
dipoles = read_dipole(dip_fname)
trans = read_trans(trans_fname)
for coord_frame, idx, show_all in zip(['head', 'mri'],
['gof', 'amplitude'], [True, False]):
fig = dipoles.plot_locations(trans,
'sample',
subjects_dir,
coord_frame=coord_frame,
idx=idx,
show_all=show_all,
mode='orthoview')
fig.canvas.scroll_event(0.5, 0.5, 1) # scroll up
fig.canvas.scroll_event(0.5, 0.5, -1) # scroll down
fig.canvas.key_press_event('up')
fig.canvas.key_press_event('down')
fig.canvas.key_press_event('a') # some other key
ax = plt.subplot(111)
pytest.raises(TypeError,
dipoles.plot_locations,
trans,
'sample',
subjects_dir,
ax=ax)
plt.close('all')
def test_plot_dipole_mri_orthoview(coord_frame, idx, show_all, title):
"""Test mpl dipole plotting."""
dipoles = read_dipole(dip_fname)
trans = read_trans(trans_fname)
fig = dipoles.plot_locations(trans=trans,
subject='sample',
subjects_dir=subjects_dir,
coord_frame=coord_frame,
idx=idx,
show_all=show_all,
title=title,
mode='orthoview')
fig.canvas.scroll_event(0.5, 0.5, 1) # scroll up
fig.canvas.scroll_event(0.5, 0.5, -1) # scroll down
fig.canvas.key_press_event('up')
fig.canvas.key_press_event('down')
fig.canvas.key_press_event('a') # some other key
ax = plt.subplot(111)
pytest.raises(TypeError,
dipoles.plot_locations,
trans,
'sample',
subjects_dir,
ax=ax)
plt.close('all')
def test_locate_scraper(_locate_ieeg, _fake_CT_coords, tmpdir):
"""Test sphinx-gallery scraping of the GUI."""
raw = mne.io.read_raw_fif(raw_path)
raw.pick_types(eeg=True)
ch_dict = {
'EEG 001': 'LAMY 1',
'EEG 002': 'LAMY 2',
'EEG 003': 'LSTN 1',
'EEG 004': 'LSTN 2'
}
raw.pick_channels(list(ch_dict.keys()))
raw.rename_channels(ch_dict)
raw.set_montage(None)
aligned_ct, _ = _fake_CT_coords
trans = mne.read_trans(fname_trans)
with pytest.warns(RuntimeWarning, match='`pial` surface not found'):
gui = _locate_ieeg(raw.info,
trans,
aligned_ct,
subject=subject,
subjects_dir=subjects_dir)
tmpdir.mkdir('_images')
image_path = str(tmpdir.join('_images', 'temp.png'))
gallery_conf = dict(builder_name='html', src_dir=str(tmpdir))
block_vars = dict(example_globals=dict(gui=gui),
image_path_iterator=iter([image_path]))
assert not op.isfile(image_path)
assert not getattr(gui, '_scraped', False)
mne.gui._LocateScraper()(None, block_vars, gallery_conf)
assert op.isfile(image_path)
assert gui._scraped
def plot_coregistration(subject, subjects_dir, hcp_path, recordings_path,
info_from=(('data_type', 'rest'), ('run_index', 0)),
view_init=(('azim', 0), ('elev', 0))):
"""A diagnostic plot to show the HCP coregistration
Parameters
----------
subject : str
The subject
subjects_dir : str
The path corresponding to MNE/freesurfer SUBJECTS_DIR (to be created)
hcp_path : str
The path where the HCP files can be found.
recordings_path : str
The path to converted data (including the head<->device transform).
info_from : tuple of tuples | dict
The reader info concerning the data from which sensor positions
should be read.
Must not be empty room as sensor positions are in head
coordinates for 4D systems, hence not available in that case.
Note that differences between the sensor positions across runs
are smaller than 12 digits, hence negligible.
view_init : tuple of tuples | dict
The initival view, defaults to azimuth and elevation of 0,
a simple lateral view
Returns
-------
fig : matplotlib.figure.Figure
The figure object.
"""
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D # noqa
if isinstance(info_from, tuple):
info_from = dict(info_from)
if isinstance(view_init, tuple):
view_init = dict(view_init)
head_mri_t = read_trans(
op.join(recordings_path, subject,
'{}-head_mri-trans.fif'.format(subject)))
info = read_info(subject=subject, hcp_path=hcp_path, **info_from)
info = pick_info(info, _pick_data_channels(info, with_ref_meg=False))
sens_pnts = np.array([c['loc'][:3] for c in info['chs']])
sens_pnts = apply_trans(head_mri_t, sens_pnts)
sens_pnts *= 1e3 # put in mm scale
pnts, tris = read_surface(
op.join(subjects_dir, subject, 'bem', 'inner_skull.surf'))
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
ax.scatter(*sens_pnts.T, color='purple', marker='o')
ax.scatter(*pnts.T, color='green', alpha=0.3)
ax.view_init(**view_init)
fig.tight_layout()
return fig
def test_plot_alignment_meg(renderer, system):
"""Test plotting of MEG sensors + helmet."""
if system == 'Neuromag':
this_info = read_info(evoked_fname)
elif system == 'CTF':
this_info = read_raw_ctf(ctf_fname).info
elif system == 'BTi':
this_info = read_raw_bti(
pdf_fname, config_fname, hs_fname, convert=True,
preload=False).info
else:
assert system == 'KIT'
this_info = read_raw_kit(sqd_fname).info
meg = ['helmet', 'sensors']
if system == 'KIT':
meg.append('ref')
fig = plot_alignment(
this_info, read_trans(trans_fname), subject='sample',
subjects_dir=subjects_dir, meg=meg, eeg=False)
assert isinstance(fig, Figure3D)
# count the number of objects: should be n_meg_ch + 1 (helmet) + 1 (head)
use_info = pick_info(this_info, pick_types(
this_info, meg=True, eeg=False, ref_meg='ref' in meg, exclude=()))
n_actors = use_info['nchan'] + 2
_assert_n_actors(fig, renderer, n_actors)
def compute_forward_and_inverse_solutions(self, orientation = 'fixed'):
"""docstring for compute_forward_solution"""
info = self.grand_average_evoked.info
trans = mne.read_trans(op.join(self.processed_files, '%s-trans.fif' %self.subject))
src = glob.glob(op.join(self.subjects_dir, self.subject, 'bem', '*-ico-4-src.fif'))[0]
bem = glob.glob(op.join(self.subjects_dir, self.subject, 'bem', '*-bem-sol.fif'))[0]
fname = op.join(self.processed_files, '%s_forward.fif' %self.subject)
# check if fwd exists, if not, make it
if not op.exists(fname):
fwd = mne.make_forward_solution(info = info, trans = trans, src = src,
bem = bem, fname = fname, meg = True, eeg = False,
overwrite = True, ignore_ref = True)
self.add_preprocessing_notes("Forward solution generated and saved to %s" %fname)
if orientation == 'fixed':
force_fixed = True
else:
force_fixed = False
fwd = mne.read_forward_solution(fname,force_fixed=force_fixed)
self.forward_solution = fwd
inv = mne.minimum_norm.make_inverse_operator(info, self.forward_solution, self.cov_reg, loose = None, depth = None, fixed = force_fixed)
self.inverse_solution = inv
mne.minimum_norm.write_inverse_operator(op.join(self.processed_files, '%s_inv.fif' %self.subject), self.inverse_solution)
self.add_preprocessing_notes("Inverse solution generated and saved to %s" %op.join(self.processed_files, '%s_inv.fif' %self.subject))
return fwd, inv
def read_transformation(name, save_dir):
trans_name = name + '_dense-trans.fif'
trans_path = join(save_dir, trans_name)
trans = mne.read_trans(trans_path)
return trans
def test_io_trans():
"""Test reading and writing of trans files
"""
info0 = read_trans(fname)
fname1 = op.join(tempdir, 'test-trans.fif')
write_trans(fname1, info0)
info1 = read_trans(fname1)
# check all properties
assert_true(info0['from'] == info1['from'])
assert_true(info0['to'] == info1['to'])
assert_array_equal(info0['trans'], info1['trans'])
for d0, d1 in zip(info0['dig'], info1['dig']):
assert_array_equal(d0['r'], d1['r'])
for name in ['kind', 'ident', 'coord_frame']:
assert_true(d0[name] == d1[name])
def test_plot_dipole_locations():
"""Test plotting dipole locations."""
dipoles = read_dipole(dip_fname)
trans = read_trans(trans_fname)
dipoles.plot_locations(trans, 'sample', subjects_dir, fig_name='foo')
assert_raises(ValueError, dipoles.plot_locations, trans, 'sample',
subjects_dir, mode='foo')
def test_do_forward_solution():
"""Test wrapping forward solution from python
"""
mri = read_trans(fname_mri)
fname_fake = op.join(temp_dir, 'no_have.fif')
# ## Error checks
# bad subject
assert_raises(ValueError, do_forward_solution, 1, fname_raw,
subjects_dir=subjects_dir)
# bad meas
assert_raises(ValueError, do_forward_solution, 'sample', 1,
subjects_dir=subjects_dir)
# meas doesn't exist
assert_raises(IOError, do_forward_solution, 'sample', fname_fake,
subjects_dir=subjects_dir)
# don't specify trans and meas
assert_raises(ValueError, do_forward_solution, 'sample', fname_raw,
subjects_dir=subjects_dir)
# specify both trans and meas
assert_raises(ValueError, do_forward_solution, 'sample', fname_raw,
trans='me', mri='you', subjects_dir=subjects_dir)
# specify non-existent trans
assert_raises(IOError, do_forward_solution, 'sample', fname_raw,
trans=fname_fake, subjects_dir=subjects_dir)
# specify non-existent mri
assert_raises(IOError, do_forward_solution, 'sample', fname_raw,
mri=fname_fake, subjects_dir=subjects_dir)
# specify non-string mri
assert_raises(ValueError, do_forward_solution, 'sample', fname_raw,
mri=1, subjects_dir=subjects_dir)
# specify non-string trans
assert_raises(ValueError, do_forward_solution, 'sample', fname_raw,
trans=1, subjects_dir=subjects_dir)
# test specifying an actual trans in python space -- this should work but
# the transform I/O reduces our accuracy -- so we'll just hack a test here
# by making it bomb with eeg=False and meg=False
assert_raises(ValueError, do_forward_solution, 'sample', fname_raw,
mri=mri, eeg=False, meg=False, subjects_dir=subjects_dir)
# mindist as non-integer
assert_raises(TypeError, do_forward_solution, 'sample', fname_raw,
mri=fname_mri, mindist=dict(), subjects_dir=subjects_dir)
# mindist as string but not 'all'
assert_raises(ValueError, do_forward_solution, 'sample', fname_raw,
mri=fname_mri, eeg=False, mindist='yall',
subjects_dir=subjects_dir)
# src, spacing, and bem as non-str
assert_raises(ValueError, do_forward_solution, 'sample', fname_raw,
mri=fname_mri, src=1, subjects_dir=subjects_dir)
assert_raises(ValueError, do_forward_solution, 'sample', fname_raw,
mri=fname_mri, spacing=1, subjects_dir=subjects_dir)
assert_raises(ValueError, do_forward_solution, 'sample', fname_raw,
mri=fname_mri, bem=1, subjects_dir=subjects_dir)
# no overwrite flag
assert_raises(IOError, do_forward_solution, 'sample', fname_raw,
existing_file, mri=fname_mri, subjects_dir=subjects_dir)
# let's catch an MNE error, this time about trans being wrong
assert_raises(CalledProcessError, do_forward_solution, 'sample',
fname_raw, existing_file, trans=fname_mri, overwrite=True,
spacing='oct6', subjects_dir=subjects_dir)
def test_plot_alignment_surf(renderer):
"""Test plotting of a surface."""
info = read_info(evoked_fname)
fig = plot_alignment(
info, read_trans(trans_fname), subject='sample',
subjects_dir=subjects_dir, meg=False, eeg=False, dig=False,
surfaces=['white', 'head'])
_assert_n_actors(fig, renderer, 3) # left and right hemis plus head
def test_get_mri_head_t():
"""Test converting '-trans.txt' to '-trans.fif'"""
trans = read_trans(fname)
trans = invert_transform(trans) # starts out as head->MRI, so invert
trans_2 = _get_mri_head_t_from_trans_file(fname_trans)
assert_equal(trans["from"], trans_2["from"])
assert_equal(trans["to"], trans_2["to"])
assert_allclose(trans["trans"], trans_2["trans"], rtol=1e-5, atol=1e-5)
def test_get_trans():
"""Test converting '-trans.txt' to '-trans.fif'"""
trans = read_trans(fname)
trans = invert_transform(trans) # starts out as head->MRI, so invert
trans_2 = _get_trans(fname_trans)[0]
assert_equal(trans['from'], trans_2['from'])
assert_equal(trans['to'], trans_2['to'])
assert_allclose(trans['trans'], trans_2['trans'], rtol=1e-5, atol=1e-5)
def test_get_trans():
"""Test converting '-trans.txt' to '-trans.fif'"""
trans = read_trans(fname)
trans = invert_transform(trans) # starts out as head->MRI, so invert
trans_2 = _get_trans(fname_trans)[0]
assert_equal(trans['from'], trans_2['from'])
assert_equal(trans['to'], trans_2['to'])
assert_allclose(trans['trans'], trans_2['trans'], rtol=1e-5, atol=1e-5)
def test_plot_dipole_locations():
"""Test plotting dipole locations
"""
dipoles = read_dipole(dip_fname)
trans = read_trans(trans_fname)
dipoles.plot_locations(trans, 'sample', subjects_dir, fig_name='foo')
assert_raises(ValueError, dipoles.plot_locations, trans, 'sample',
subjects_dir, mode='foo')
def make_anony_fwd(subject,
dir_base,
subjects_dir,
conductivity=(0.3, 0.006, 0.3),
ico=4):
import os.path as op
from mne.io.constants import FIFF
from mne.bem import _surfaces_to_bem, _check_bem_size
import glob
import mayavi.mlab as mlab
for m in ['anonymi', 'defaced', 'mf']:
print('Preparing fwd - method: %s' % m)
bem_dir = op.join(dir_base, 'spatial', 'bems', m)
inner_skull = op.join(bem_dir,
'%s_%s_inner_skull_surface' % (subject, m))
outer_skull = op.join(bem_dir,
'%s_%s_outer_skull_surface' % (subject, m))
outer_skin = op.join(bem_dir,
'%s_%s_outer_skin_surface' % (subject, m))
surfaces = [inner_skull, outer_skull, outer_skin]
ids = [
FIFF.FIFFV_BEM_SURF_ID_BRAIN, FIFF.FIFFV_BEM_SURF_ID_SKULL,
FIFF.FIFFV_BEM_SURF_ID_HEAD
]
surfaces = _surfaces_to_bem(surfaces, ids, conductivity, ico)
_check_bem_size(surfaces)
bem = mne.make_bem_solution(surfaces)
bem_fname = op.join(dir_base, 'spatial', 'bems', m,
'%s_%s-bem.fif' % (subject, m))
mne.write_bem_solution(bem_fname, bem)
files_epochs = glob.glob(
op.join(dir_base, 'data', 'fif', '%s*' % subject))
epo = mne.read_epochs(files_epochs[0])
trans_fname = op.join(dir_base, 'spatial', 'fwd',
'%s-trans.fif' % subject)
src_fname = op.join(dir_base, 'spatial', 'fwd', '%s-src.fif' % subject)
fwd = mne.make_forward_solution(epo.info, trans_fname, src_fname,
bem_fname)
trans = mne.read_trans(trans_fname)
mne.viz.plot_alignment(epo.info,
trans,
subject=subject,
surfaces=['head', 'brain'],
bem=bem,
subjects_dir=subjects_dir)
mlab.show()
mne.write_forward_solution(
op.join(dir_base, 'spatial', 'bems', m,
'%s_%s-fwd.fif' % (subject, m)), fwd)
def test_combine():
"""Test combining transforms
"""
trans = read_trans(fname)
inv = invert_transform(trans)
combine_transforms(trans, inv, trans["from"], trans["from"])
assert_raises(RuntimeError, combine_transforms, trans, inv, trans["to"], trans["from"])
assert_raises(RuntimeError, combine_transforms, trans, inv, trans["from"], trans["to"])
assert_raises(RuntimeError, combine_transforms, trans, trans, trans["from"], trans["to"])
def coreg_head2mri(subjects_dir, subject, native_fid, raw_path, raw_NosePtsOut, trans_dst, flag_fid=False):
import scipy.io
import numpy as np
from mne.gui._coreg_gui import CoregModel
model = CoregModel()
model.mri.subjects_dir = subjects_dir
model.mri.subject = subject
# Remove Polhemus points around the nose (y>0, z<0)
model.hsp.file = raw_path
head_pts = model.hsp.points
raw = read_raw_fif(raw_path, preload=True)
pos = np.where((head_pts[:,1] <= 0) | (head_pts[:,2] >= 0))
dig = raw.info['dig']
dig2 = dig[0:8]
dig3 = [dig[p+7] for p in pos[0]]
dig_yeah = dig2+dig3
raw.info['dig'] = dig_yeah
raw.save(raw_NosePtsOut, overwrite=True)
model.hsp.file = raw_NosePtsOut
# Load CamCAN fiducials from matlab file
if flag_fid:
fid = scipy.io.loadmat(native_fid, struct_as_record=False, squeeze_me=True)
fid = fid['fid']
model.mri.lpa = np.reshape(fid.native.mm.lpa*0.001,(1,3))
model.mri.nasion = np.reshape(fid.native.mm.nas*0.001,(1,3))
model.mri.rpa = np.reshape(fid.native.mm.rpa*0.001,(1,3))
assert (model.mri.fid_ok)
lpa_distance = model.lpa_distance
nasion_distance = model.nasion_distance
rpa_distance = model.rpa_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
avg_point_distance = np.mean(model.point_distance)
while True:
model.fit_icp(0)
new_dist = np.mean(model.point_distance)
assert new_dist < avg_point_distance
if model.status_text.endswith('converged)'):
break
model.save_trans(trans_dst)
trans = mne.read_trans(trans_dst)
np.testing.assert_allclose(trans['trans'], model.head_mri_t)
def test_eeg_field_interpolation():
"""Test interpolation of EEG field onto head
"""
trans = read_trans(trans_fname)
info = read_info(evoked_fname)
surf = get_head_surface('sample', subjects_dir=subjects_dir)
# we must have trans if surface is in MRI coords
assert_raises(ValueError, make_surface_mapping, info, surf, 'eeg')
data = make_surface_mapping(info, surf, 'eeg', trans, mode='accurate')
assert_array_equal(data.shape, (2562, 60)) # maps data onto surf
def test_plot_dipole_orientations(renderer):
"""Test dipole plotting in 3d."""
dipoles = read_dipole(dip_fname)
trans = read_trans(trans_fname)
for coord_frame, mode in zip(['head', 'mri'],
['arrow', 'sphere']):
dipoles.plot_locations(trans=trans, subject='sample',
subjects_dir=subjects_dir,
mode=mode, coord_frame=coord_frame)
renderer._close_all()
def make_forward_solution(experiment,
subject,
spacing,
process_slug=DEFAULT_PROC):
struct = sub_to_struct[experiment][subject]
if struct == 'NA':
raise IOError(
'Freesurfer Reconstruction has not yet been done for this subject. See the Freesurfer Recommended Reconstruction page.')
trans_fname = TRANS_FNAME.format(experiment=experiment, subject=subject, struct=struct)
if not os.path.isfile(trans_fname):
raise IOError(
'Coregistration has not yet been done for this subject. Use mne_analyze on big-brain and follow MNE handbook chapter 7.')
trans = mne.read_trans(trans_fname)
fwd_path = FWD_PATH.format(experiment=experiment, subject=subject)
if not os.path.exists(fwd_path):
try:
os.mkdir(fwd_path)
except:
os.mkdir(FWD_PATH.format(experiment=experiment, subject=''))
os.mkdir(fwd_path)
fwd_fname = FWD_FNAME.format(fwd_path=fwd_path, subject=subject, experiment=experiment, process_slug=process_slug,
struct=struct, spacing=spacing)
raw = mne.io.Raw(PROC_FNAME.format(experiment=experiment, subject=subject, process_slug=process_slug))
bem_path = [fn for fn in os.listdir(BEM_PATH.format(struct=struct)) if fnmatch.fnmatch(fn, '*-bem-sol.fif')]
if len(bem_path) == 0:
raise IOError('BEM has not yet been done for this subject. See MNE_pipeline_2018.sh')
bem_fname = pjoin(BEM_PATH.format(struct=struct), bem_path[0])
src_file = SRC_FNAME.format(struct=struct, spacing=spacing)
mne.set_config('SUBJECTS_DIR', SUBJ_DIR)
# Not sure how to make sure this runs effectively
if os.path.isfile(src_file):
src = mne.read_source_spaces(src_file)
else:
src = mne.setup_source_space(struct, spacing='oct6')
mne.write_source_spaces(src_file, src)
fwd = mne.make_forward_solution(raw.info, trans,
src=src,
bem=bem_fname)
mne.write_forward_solution(fwd_fname, fwd)
return fwd
def _get_bem_src_trans(p, info, subj, struc):
subjects_dir = get_subjects_dir(p.subjects_dir, raise_error=True)
assert isinstance(subjects_dir, str)
if struc is None: # spherical case
bem, src, trans = _spherical_conductor(info, subj, p.src_pos)
bem_type = 'spherical-model'
else:
from mne.transforms import _ensure_trans
trans = op.join(p.work_dir, subj, p.trans_dir, subj + '-trans.fif')
if not op.isfile(trans):
old = trans
trans = op.join(p.work_dir, subj, p.trans_dir,
subj + '-trans_head2mri.txt')
if not op.isfile(trans):
raise IOError('Unable to find head<->MRI trans files in:\n'
'%s\n%s' % (old, trans))
trans = read_trans(trans)
trans = _ensure_trans(trans, 'mri', 'head')
this_src = _handle_dict(p.src, subj)
assert isinstance(this_src, str)
if this_src.startswith('oct'):
kind = 'oct'
elif this_src.startswith('vol'):
kind = 'vol'
else:
raise RuntimeError('Unknown source space type %s, must be '
'oct or vol' % (this_src, ))
num = int(this_src.split(kind)[-1].split('-')[-1])
bem = op.join(subjects_dir, struc, 'bem',
'%s-%s-bem-sol.fif' % (struc, p.bem_type))
for mid in ('', '-'):
src_space_file = op.join(
subjects_dir, struc, 'bem',
'%s-%s%s%s-src.fif' % (struc, kind, mid, num))
if op.isfile(src_space_file):
break
else: # if neither exists, use last filename
print(' Creating %s%s source space for %s...' %
(kind, num, subj))
if kind == 'oct':
src = setup_source_space(struc,
spacing='%s%s' % (kind, num),
subjects_dir=p.subjects_dir,
n_jobs=p.n_jobs)
else:
assert kind == 'vol'
src = setup_volume_source_space(struc,
pos=num,
bem=bem,
subjects_dir=p.subjects_dir)
write_source_spaces(src_space_file, src)
src = read_source_spaces(src_space_file)
bem = read_bem_solution(bem, verbose=False)
bem_type = ('%s-layer BEM' % len(bem['surfs']))
return bem, src, trans, bem_type
def make_forward_solution(info,
trans_fname,
src,
bem_model,
meg=True,
eeg=True,
mindist=0.0,
ignore_ref=False,
n_jobs=1,
verbose=None):
assert not meg # XXX for now
coord_frame = 'head'
trans = mne.read_trans(trans_fname)
head_trans, meg_trans, mri_trans = _prepare_trans(info, trans, coord_frame)
dipoles = _get_dipoles(src, mri_trans, head_trans)
eeg_electrodes, ch_names = _get_sensors(info, head_trans)
geom = _get_geom_files(bem_model, mri_trans, head_trans)
assert geom.is_nested()
assert geom.selfCheck()
# OpenMEEG
gauss_order = 3
use_adaptive_integration = True
# dipole_in_cortex = True
hm = om.HeadMat(geom, gauss_order)
hm.invert()
hminv = hm
dsm = om.DipSourceMat(geom, dipoles, gauss_order, use_adaptive_integration,
"Brain")
# For EEG
eeg_picks = mne.pick_types(info, meg=False, eeg=True)
# meg_picks = mne.pick_types(info, meg=True, eeg=False)
# seeg_picks = mne.pick_types(info, meg=False, seeg=True)
if eeg and len(eeg_picks) > 0:
h2em = om.Head2EEGMat(geom, eeg_electrodes)
eeg_leadfield = om.GainEEG(hminv, dsm, h2em)
eegfwd = _make_forward(eeg_leadfield, ch_names, info, src, trans_fname)
# if meg and len(meg_picks) > 0:
# h2em = om.Head2EEGMat(geom, eeg_electrodes)
# eeg_leadfield = om.GainEEG(hminv, dsm, h2em)
# megfwd = _make_forward(eeg_leadfield, ch_names, info, src, trans_fname)
# # merge forwards
# fwd = _merge_meg_eeg_fwds(_to_forward_dict(megfwd, megnames),
# _to_forward_dict(eegfwd, eegnames),
# verbose=False)
return eegfwd
def test_combine():
"""Test combining transforms."""
trans = read_trans(fname)
inv = invert_transform(trans)
combine_transforms(trans, inv, trans['from'], trans['from'])
pytest.raises(RuntimeError, combine_transforms, trans, inv, trans['to'],
trans['from'])
pytest.raises(RuntimeError, combine_transforms, trans, inv, trans['from'],
trans['to'])
pytest.raises(RuntimeError, combine_transforms, trans, trans,
trans['from'], trans['to'])
def test_get_head_mri_trans():
"""Test getting a trans object from BIDS data."""
import nibabel as nib
event_id = {'Auditory/Left': 1, 'Auditory/Right': 2, 'Visual/Left': 3,
'Visual/Right': 4, 'Smiley': 5, 'Button': 32}
events_fname = op.join(data_path, 'MEG', 'sample',
'sample_audvis_trunc_raw-eve.fif')
# Drop unknown events.
events = mne.read_events(events_fname)
events = events[events[:, 2] != 0]
# Write it to BIDS
raw = _read_raw_fif(raw_fname)
bids_root = _TempDir()
bids_path = _bids_path.copy().update(root=bids_root)
write_raw_bids(raw, bids_path, events_data=events, event_id=event_id,
overwrite=False)
# We cannot recover trans, if no MRI has yet been written
with pytest.raises(RuntimeError):
estimated_trans = get_head_mri_trans(bids_path=bids_path)
# Write some MRI data and supply a `trans` so that a sidecar gets written
trans = mne.read_trans(raw_fname.replace('_raw.fif', '-trans.fif'))
# Get the T1 weighted MRI data file ... test write_anat with a nibabel
# image instead of a file path
t1w_mgh = op.join(data_path, 'subjects', 'sample', 'mri', 'T1.mgz')
t1w_mgh = nib.load(t1w_mgh)
t1w_bidspath = BIDSPath(subject=subject_id, session=session_id,
acquisition=acq, root=bids_root)
t1w_bidspath = write_anat(t1w_mgh, bids_path=t1w_bidspath,
raw=raw, trans=trans, verbose=True)
anat_dir = t1w_bidspath.directory
# Try to get trans back through fitting points
estimated_trans = get_head_mri_trans(bids_path=bids_path)
assert trans['from'] == estimated_trans['from']
assert trans['to'] == estimated_trans['to']
assert_almost_equal(trans['trans'], estimated_trans['trans'])
print(trans)
print(estimated_trans)
# provoke an error by introducing NaNs into MEG coords
with pytest.raises(RuntimeError, match='AnatomicalLandmarkCoordinates'):
raw.info['dig'][0]['r'] = np.ones(3) * np.nan
sh.rmtree(anat_dir)
bids_path = write_anat(t1w_mgh, bids_path=t1w_bidspath,
raw=raw, trans=trans, verbose=True)
estimated_trans = get_head_mri_trans(bids_path=bids_path)
def test_combine():
"""Test combining transforms."""
trans = read_trans(fname)
inv = invert_transform(trans)
combine_transforms(trans, inv, trans['from'], trans['from'])
pytest.raises(RuntimeError, combine_transforms, trans, inv,
trans['to'], trans['from'])
pytest.raises(RuntimeError, combine_transforms, trans, inv,
trans['from'], trans['to'])
pytest.raises(RuntimeError, combine_transforms, trans, trans,
trans['from'], trans['to'])
def compute_forward_and_inverse_solutions(self, orientation='fixed'):
"""docstring for compute_forward_solution"""
info = self.grand_average_evoked.info
trans = mne.read_trans(
op.join(self.processed_files, '%s-trans.fif' % self.subject))
src = glob.glob(
op.join(self.subjects_dir, self.subject, 'bem',
'*-ico-4-src.fif'))[0]
bem = glob.glob(
op.join(self.subjects_dir, self.subject, 'bem',
'*-bem-sol.fif'))[0]
fname = op.join(self.processed_files, '%s_forward.fif' % self.subject)
# check if fwd exists, if not, make it
if not op.exists(fname):
fwd = mne.make_forward_solution(info=info,
trans=trans,
src=src,
bem=bem,
fname=fname,
meg=True,
eeg=False,
overwrite=True,
ignore_ref=True)
self.add_preprocessing_notes(
"Forward solution generated and saved to %s" % fname)
if orientation == 'fixed':
force_fixed = True
else:
force_fixed = False
fwd = mne.read_forward_solution(fname, force_fixed=force_fixed)
self.forward_solution = fwd
inv = mne.minimum_norm.make_inverse_operator(info,
self.forward_solution,
self.cov_reg,
loose=None,
depth=None,
fixed=force_fixed)
self.inverse_solution = inv
mne.minimum_norm.write_inverse_operator(
op.join(self.processed_files, '%s_inv.fif' % self.subject),
self.inverse_solution)
self.add_preprocessing_notes(
"Inverse solution generated and saved to %s" %
op.join(self.processed_files, '%s_inv.fif' % self.subject))
return fwd, inv
def test_io_trans():
"""Test reading and writing of trans files
"""
trans0 = read_trans(fname)
fname1 = op.join(tempdir, 'test-trans.fif')
write_trans(fname1, trans0)
trans1 = read_trans(fname1)
# check all properties
assert_true(trans0['from'] == trans1['from'])
assert_true(trans0['to'] == trans1['to'])
assert_array_equal(trans0['trans'], trans1['trans'])
# check reading non -trans.fif files
assert_raises(IOError, read_trans, fname_eve)
# check warning on bad filenames
with warnings.catch_warnings(record=True) as w:
fname2 = op.join(tempdir, 'trans-test-bad-name.fif')
write_trans(fname2, trans0)
assert_true(len(w) >= 1)
def test_io_trans():
"""Test reading and writing of trans files."""
tempdir = _TempDir()
os.mkdir(op.join(tempdir, 'sample'))
pytest.raises(RuntimeError, _find_trans, 'sample', subjects_dir=tempdir)
trans0 = read_trans(fname)
fname1 = op.join(tempdir, 'sample', 'test-trans.fif')
trans0.save(fname1)
assert fname1 == _find_trans('sample', subjects_dir=tempdir)
trans1 = read_trans(fname1)
# check all properties
assert trans0 == trans1
# check reading non -trans.fif files
pytest.raises(IOError, read_trans, fname_eve)
# check warning on bad filenames
fname2 = op.join(tempdir, 'trans-test-bad-name.fif')
with pytest.warns(RuntimeWarning, match='-trans.fif'):
write_trans(fname2, trans0)
def test_io_trans():
"""Test reading and writing of trans files."""
tempdir = _TempDir()
os.mkdir(op.join(tempdir, 'sample'))
pytest.raises(RuntimeError, _find_trans, 'sample', subjects_dir=tempdir)
trans0 = read_trans(fname)
fname1 = op.join(tempdir, 'sample', 'test-trans.fif')
trans0.save(fname1)
assert fname1 == _find_trans('sample', subjects_dir=tempdir)
trans1 = read_trans(fname1)
# check all properties
assert trans0 == trans1
# check reading non -trans.fif files
pytest.raises(IOError, read_trans, fname_eve)
# check warning on bad filenames
fname2 = op.join(tempdir, 'trans-test-bad-name.fif')
with pytest.warns(RuntimeWarning, match='-trans.fif'):
write_trans(fname2, trans0)
def test_io_trans():
"""Test reading and writing of trans files."""
tempdir = _TempDir()
os.mkdir(op.join(tempdir, 'sample'))
pytest.raises(RuntimeError, _find_trans, 'sample', subjects_dir=tempdir)
trans0 = read_trans(fname)
fname1 = op.join(tempdir, 'sample', 'test-trans.fif')
trans0.save(fname1)
assert fname1 == _find_trans('sample', subjects_dir=tempdir)
trans1 = read_trans(fname1)
# check all properties
assert trans0 == trans1
# check reading non -trans.fif files
pytest.raises(IOError, read_trans, fname_eve)
# check warning on bad filenames
with warnings.catch_warnings(record=True) as w:
fname2 = op.join(tempdir, 'trans-test-bad-name.fif')
write_trans(fname2, trans0)
assert_naming(w, 'test_transforms.py', 1)
def _make_forward(eeg_leadfield, ch_names, info, src, trans_fname):
fwd = eeg_leadfield.array().astype(np.float32).T
fwd = _to_forward_dict(fwd, ch_names)
picks = mne.pick_channels(info['ch_names'], ch_names)
fwd['info'] = mne.pick_info(info, picks)
fwd['info']['mri_file'] = trans_fname
fwd['info']['mri_id'] = fwd['info']['file_id']
fwd['mri_head_t'] = invert_transform(mne.read_trans(trans_fname))
fwd['info']['mri_head_t'] = fwd['mri_head_t']
fwd['info']['meas_file'] = ""
fwd['src'] = src
fwd['surf_ori'] = False
return fwd
def test_compute_distance_to_sensors(picks, limits):
"""Test computation of distances between vertices and sensors."""
src = read_source_spaces(fname_src)
fwd = mne.read_forward_solution(fname_fwd)
info = fwd['info']
trans = read_trans(trans_fname)
# trans = fwd['info']['mri_head_t']
if isinstance(picks, str):
kwargs = dict()
kwargs[picks] = True
if picks == 'eeg':
info['dev_head_t'] = None # should not break anything
use_picks = pick_types(info, **kwargs, exclude=())
else:
use_picks = picks
n_picks = len(_picks_to_idx(info, use_picks, 'data', exclude=()))
# Make sure same vertices are used in src and fwd
src[0]['inuse'] = fwd['src'][0]['inuse']
src[1]['inuse'] = fwd['src'][1]['inuse']
src[0]['nuse'] = fwd['src'][0]['nuse']
src[1]['nuse'] = fwd['src'][1]['nuse']
n_verts = src[0]['nuse'] + src[1]['nuse']
# minimum distances between vertices and sensors
depths = compute_distance_to_sensors(src,
info=info,
picks=use_picks,
trans=trans)
assert depths.shape == (n_verts, n_picks)
assert limits[0] * 5 > depths.min() # meaningful choice of limits
assert_array_less(limits[0], depths)
assert_array_less(depths, limits[1])
# If source space from Forward Solution and trans=None (i.e. identity) then
# depths2 should be the same as depth.
depths2 = compute_distance_to_sensors(src=fwd['src'],
info=info,
picks=use_picks,
trans=None)
assert_allclose(depths, depths2, rtol=1e-5)
if picks != 'eeg':
# this should break things
info['dev_head_t'] = None
with pytest.raises(ValueError, match='Transform between meg<->head'):
compute_distance_to_sensors(src, info, use_picks, trans)
def plotAlignment(subjectName):
"""
Usage example:
-----------------------------
from uhClass import Forward
subjectName = 'xS9017'
Forward.plotAlignment(subjectName)
"""
import glob, os
# mainDir = 'C:\\uhdata\\freesurfer'
mainDir = Forward.mainDir
path = os.path.join(mainDir, subjectName)
os.chdir(path)
trans = glob.glob('*-trans.fif')
# bemsol = glob.glob('*-bemsol.fif')
src = glob.glob('*-src.fif')
epo = glob.glob('*-epo.fif')
info = mne.io.read_info(epo[0])
# read source space
stc = mne.source_space.read_source_spaces(os.path.join(path, src[0]))
# read bem solution
# bem_path = os.path.join(path, bemsol)
# bem = mne.read_bem_solution(bem_path)
# read transformation matrix
trans_path = os.path.join(path, trans[0])
trans = mne.read_trans(trans_path)
# Here we look at the dense head, which isn't used for BEM computations but
# is useful for coregistration.
mne.viz.plot_alignment(info, trans=trans,
subject=subjectName,
subjects_dir=mainDir,
surfaces=['head'], coord_frame='head', meg=None,
eeg='original', dig=True, ecog=False,
src=stc, mri_fiducials=False, bem=None,
seeg=False, show_axes=False, fig=None,
interaction ='trackball', verbose=None)
def run(args=None, config=None):
parser = AnalysisParser('config')
args = parser.parse_analysis_args(args)
config = args.config
print(__doc__)
data_path = sample.data_path()
subjects_dir = op.join(data_path, 'subjects')
raw_fname = op.join(data_path, 'MEG', 'sample', 'sample_audvis_raw.fif')
trans_fname = op.join(data_path, 'MEG', 'sample',
'sample_audvis_raw-trans.fif')
raw = mne.io.read_raw_fif(raw_fname)
trans = mne.read_trans(trans_fname)
src = mne.read_source_spaces(op.join(subjects_dir, 'sample', 'bem',
'sample-oct-6-src.fif'))
def dip_source_loc(evoked, cov, fs_subj, study_path, plot=False):
evo_crop = evoked.copy().crop(-0.003, 0.003)
subj = fs_subj.strip('_an') if fs_subj.find('_an') > 0 else fs_subj
img_type = 'anony' if fs_subj.find('_an') > 0 else 'orig'
trans_fname = op.join(study_path, 'source_stim', subj, 'source_files', img_type, '%s_fid-trans.fif' % fs_subj)
bem_fname = op.join(subjects_dir, fs_subj, 'bem', '%s-bem-sol.fif' % fs_subj)
cond = evoked.info['description']
stim_coords = find_stim_coords(cond, subj, study_path)
dip, res = mne.fit_dipole(evo_crop, cov, bem_fname, trans_fname, min_dist=10, n_jobs=3)
import mne.transforms as tra
from scipy import linalg
trans = mne.read_trans(trans_fname)
stim_point = stim_coords['surf'] # get point for plot in mm
#dip.pos[np.argmax(dip.gof)] = tra.apply_trans(surf_to_head, stim_coords['surf_ori']/1e3) # check stim loc (apply affine in m)
dip_surf = tra.apply_trans(trans['trans'], dip.pos[np.argmax(dip.gof)]) * 1e3 # transform from head to surface
dist_surf = euclidean(dip_surf, stim_point) # compute distance in surface space
print(dist_surf)
if plot:
# Plot the result in 3D brain with the MRI image.
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
dip.plot_locations(trans_fname, fs_subj, subjects_dir, mode='orthoview', coord_frame='mri', ax=ax, show_all=True,
idx='gof')
ax.scatter(stim_point[0], stim_point[1], stim_point[2])
ax.plot([stim_point[0], -128], [stim_point[1], stim_point[1]], [stim_point[2], stim_point[2]], color='g')
ax.plot([stim_point[0], stim_point[0]], [stim_point[1], -128], [stim_point[2], stim_point[2]], color='g')
ax.plot([stim_point[0], stim_point[0]], [stim_point[1], stim_point[1]], [stim_point[2], -128], color='g')
ax.text2D(0.05, 0.90, 'distance: %i mm \nstim coords = %0.1f %0.1f %0.1f' % (dist_surf, stim_point[0], stim_point[1], stim_point[2]),
transform=ax.transAxes)
red_patch = mpatches.Patch(color='red')
green_patch = mpatches.Patch(color='green')
fig.legend(handles=[red_patch, green_patch], labels=['dipole', 'electrode'])
fig.savefig(op.join(study_path, 'source_stim', subj, 'figures', 'dipole', '%s_dip_15mm.png' % cond))
plt.close()
plot_dipole_amplitudes(dip)
plot_dipole_locations(dip, trans, subj, subjects_dir=subjects_dir)
return dist_surf
def _get_data():
"""Helper to get some starting data"""
# raw with ECG channel
raw = Raw(raw_fname).crop(0.0, 5.0).load_data()
data_picks = pick_types(raw.info, meg=True, eeg=True)
other_picks = pick_types(raw.info, meg=False, stim=True, eog=True)
picks = np.sort(np.concatenate((data_picks[::16], other_picks)))
raw = raw.pick_channels([raw.ch_names[p] for p in picks])
ecg = RawArray(np.zeros((1, len(raw.times))), create_info(["ECG 063"], raw.info["sfreq"], "ecg"))
for key in ("dev_head_t", "buffer_size_sec", "highpass", "lowpass", "filename", "dig"):
ecg.info[key] = raw.info[key]
raw.add_channels([ecg])
src = read_source_spaces(src_fname)
trans = read_trans(trans_fname)
sphere = make_sphere_model("auto", "auto", raw.info)
stc = _make_stc(raw, src)
return raw, src, stc, trans, sphere
def test_plot_dipole_mri_orthoview():
"""Test mpl dipole plotting."""
dipoles = read_dipole(dip_fname)
trans = read_trans(trans_fname)
for coord_frame, idx, show_all in zip(['head', 'mri'],
['gof', 'amplitude'], [True, False]):
fig = dipoles.plot_locations(trans, 'sample', subjects_dir,
coord_frame=coord_frame, idx=idx,
show_all=show_all, mode='orthoview')
fig.canvas.scroll_event(0.5, 0.5, 1) # scroll up
fig.canvas.scroll_event(0.5, 0.5, -1) # scroll down
fig.canvas.key_press_event('up')
fig.canvas.key_press_event('down')
fig.canvas.key_press_event('a') # some other key
ax = plt.subplot(111)
pytest.raises(TypeError, dipoles.plot_locations, trans, 'sample',
subjects_dir, ax=ax)
plt.close('all')
def _get_data():
"""Helper to get some starting data."""
# raw with ECG channel
raw = read_raw_fif(raw_fname).crop(0., 5.0).load_data()
data_picks = pick_types(raw.info, meg=True, eeg=True)
other_picks = pick_types(raw.info, meg=False, stim=True, eog=True)
picks = np.sort(np.concatenate((data_picks[::16], other_picks)))
raw = raw.pick_channels([raw.ch_names[p] for p in picks])
raw.info.normalize_proj()
ecg = RawArray(np.zeros((1, len(raw.times))),
create_info(['ECG 063'], raw.info['sfreq'], 'ecg'))
for key in ('dev_head_t', 'buffer_size_sec', 'highpass', 'lowpass', 'dig'):
ecg.info[key] = raw.info[key]
raw.add_channels([ecg])
src = read_source_spaces(src_fname)
trans = read_trans(trans_fname)
sphere = make_sphere_model('auto', 'auto', raw.info)
stc = _make_stc(raw, src)
return raw, src, stc, trans, sphere
def raw_data():
"""Get some starting data."""
# raw with ECG channel
raw = read_raw_fif(raw_fname).crop(0., 5.0).load_data()
data_picks = pick_types(raw.info, meg=True, eeg=True)
other_picks = pick_types(raw.info, meg=False, stim=True, eog=True)
picks = np.sort(np.concatenate((data_picks[::16], other_picks)))
raw = raw.pick_channels([raw.ch_names[p] for p in picks])
raw.info.normalize_proj()
ecg = RawArray(np.zeros((1, len(raw.times))),
create_info(['ECG 063'], raw.info['sfreq'], 'ecg'))
for key in ('dev_head_t', 'highpass', 'lowpass', 'dig'):
ecg.info[key] = raw.info[key]
raw.add_channels([ecg])
src = read_source_spaces(src_fname)
trans = read_trans(trans_fname)
sphere = make_sphere_model('auto', 'auto', raw.info)
stc = _make_stc(raw, src)
return raw, src, stc, trans, sphere
def test_head_to_mni():
"""Test conversion of aseg vertices to MNI coordinates."""
# obtained using freeview
coords = np.array([[22.52, 11.24, 17.72], [22.52, 5.46, 21.58],
[16.10, 5.46, 22.23], [21.24, 8.36, 22.23]])
xfm = _read_talxfm('sample', subjects_dir)
coords_MNI = apply_trans(xfm['trans'], coords)
trans = read_trans(trans_fname) # head->MRI (surface RAS)
mri_head_t = invert_transform(trans) # MRI (surface RAS)->head matrix
# obtained from sample_audvis-meg-oct-6-mixed-fwd.fif
coo_right_amygdala = np.array([[0.01745682, 0.02665809, 0.03281873],
[0.01014125, 0.02496262, 0.04233755],
[0.01713642, 0.02505193, 0.04258181],
[0.01720631, 0.03073877, 0.03850075]])
coords_MNI_2 = head_to_mni(coo_right_amygdala, 'sample', mri_head_t,
subjects_dir)
# less than 1mm error
assert_allclose(coords_MNI, coords_MNI_2, atol=10.0)
def test_head_to_mni():
"""Test conversion of aseg vertices to MNI coordinates."""
# obtained using freeview
coords = np.array([[22.52, 11.24, 17.72], [22.52, 5.46, 21.58],
[16.10, 5.46, 22.23], [21.24, 8.36, 22.23]])
xfm = _read_talxfm('sample', subjects_dir)
coords_MNI = apply_trans(xfm['trans'], coords)
trans = read_trans(trans_fname) # head->MRI (surface RAS)
mri_head_t = invert_transform(trans) # MRI (surface RAS)->head matrix
# obtained from sample_audvis-meg-oct-6-mixed-fwd.fif
coo_right_amygdala = np.array([[0.01745682, 0.02665809, 0.03281873],
[0.01014125, 0.02496262, 0.04233755],
[0.01713642, 0.02505193, 0.04258181],
[0.01720631, 0.03073877, 0.03850075]])
coords_MNI_2 = head_to_mni(coo_right_amygdala, 'sample', mri_head_t,
subjects_dir)
# less than 1mm error
assert_allclose(coords_MNI, coords_MNI_2, atol=10.0)
def test_get_head_mri_trans_ctf(fname, tmpdir):
"""Test getting a trans object from BIDS data in CTF."""
import nibabel as nib
ctf_data_path = op.join(testing.data_path(), 'CTF')
raw_ctf_fname = op.join(ctf_data_path, fname)
raw_ctf = _read_raw_ctf(raw_ctf_fname, clean_names=True)
bids_path = _bids_path.copy().update(root=tmpdir)
write_raw_bids(raw_ctf, bids_path, overwrite=False)
# Take a fake trans
trans = mne.read_trans(raw_fname.replace('_raw.fif', '-trans.fif'))
# Get the T1 weighted MRI data file ... test write_anat with a nibabel
# image instead of a file path
t1w_mgh = op.join(data_path, 'subjects', 'sample', 'mri', 'T1.mgz')
t1w_mgh = nib.load(t1w_mgh)
t1w_bids_path = BIDSPath(subject=subject_id,
session=session_id,
acquisition=acq,
root=tmpdir)
landmarks = get_anat_landmarks(t1w_mgh,
raw_ctf.info,
trans,
fs_subject='sample',
fs_subjects_dir=op.join(
data_path, 'subjects'))
write_anat(t1w_mgh, bids_path=t1w_bids_path, landmarks=landmarks)
# Try to get trans back through fitting points
estimated_trans = get_head_mri_trans(bids_path=bids_path,
extra_params=dict(clean_names=True),
fs_subject='sample',
fs_subjects_dir=op.join(
data_path, 'subjects'))
assert_almost_equal(trans['trans'], estimated_trans['trans'])
def test_plot_dipole_mri_outlines(surf, coord_frame, ax, title):
"""Test mpl dipole plotting."""
dipoles = read_dipole(dip_fname)
trans = read_trans(trans_fname)
if ax is not None:
assert isinstance(ax, str) and ax == 'mpl', ax
_, ax = plt.subplots(3, 1)
ax = list(ax)
with pytest.raises(ValueError, match='but the length is 2'):
dipoles.plot_locations(trans,
'sample',
subjects_dir,
ax=ax[:2],
mode='outlines')
fig = dipoles.plot_locations(trans=trans,
subject='sample',
subjects_dir=subjects_dir,
mode='outlines',
coord_frame=coord_frame,
surf=surf,
ax=ax,
title=title)
assert isinstance(fig, Figure)
def test_make_field_map_eeg():
"""Test interpolation of EEG field onto head
"""
trans = read_trans(trans_fname)
evoked = read_evoked(evoked_fname, setno='Left Auditory')
evoked.info['bads'] = ['MEG 2443', 'EEG 053'] # add some bads
surf = get_head_surf('sample', subjects_dir=subjects_dir)
# we must have trans if surface is in MRI coords
assert_raises(ValueError, _make_surface_mapping, evoked.info, surf, 'eeg')
evoked = pick_types_evoked(evoked, meg=False, eeg=True)
fmd = make_field_map(evoked, trans_fname=trans_fname,
subject='sample', subjects_dir=subjects_dir)
# trans is necessary for EEG only
assert_raises(RuntimeError, make_field_map, evoked, trans_fname=None,
subject='sample', subjects_dir=subjects_dir)
fmd = make_field_map(evoked, trans_fname=trans_fname,
subject='sample', subjects_dir=subjects_dir)
assert_true(len(fmd) == 1)
assert_array_equal(fmd[0]['data'].shape, (2562, 59)) # maps data onto surf
assert_true(len(fmd[0]['ch_names']), 59)
def test_get_trans():
"""Test converting '-trans.txt' to '-trans.fif'"""
trans = read_trans(fname)
trans = invert_transform(trans) # starts out as head->MRI, so invert
trans_2 = _get_trans(fname_trans)[0]
assert trans.__eq__(trans_2, atol=1e-5)
###############################################################################
# Source estimation.
# We compute the noise covariance matrix from the empty room measurement
# and use it for the other runs.
reject = dict(mag=4e-12)
cov = mne.compute_raw_covariance(raw_erm, reject=reject)
cov.plot(raw_erm.info)
del raw_erm
###############################################################################
# The transformation is read from a file. More information about coregistering
# the data, see :ref:`ch_interactive_analysis` or
# :func:`mne.gui.coregistration`.
trans_fname = op.join(data_path, 'MEG', 'bst_auditory',
'bst_auditory-trans.fif')
trans = mne.read_trans(trans_fname)
###############################################################################
# To save time and memory, the forward solution is read from a file. Set
# ``use_precomputed=False`` in the beginning of this script to build the
# forward solution from scratch. The head surfaces for constructing a BEM
# solution are read from a file. Since the data only contains MEG channels, we
# only need the inner skull surface for making the forward solution. For more
# information: :ref:`CHDBBCEJ`, :func:`mne.setup_source_space`,
# :ref:`create_bem_model`, :func:`mne.bem.make_watershed_bem`.
if use_precomputed:
fwd_fname = op.join(data_path, 'MEG', 'bst_auditory',
'bst_auditory-meg-oct-6-fwd.fif')
fwd = mne.read_forward_solution(fwd_fname)
else:
src = mne.setup_source_space(subject, spacing='ico4',
def compute_forward_stack(subjects_dir,
subject,
recordings_path,
info_from=(('data_type', 'rest'), ('run_index', 0)),
fwd_params=None, src_params=None,
hcp_path=op.curdir, n_jobs=1, verbose=None):
"""
Convenience function for conducting standard MNE analyses.
.. note::
this function computes bem solutions, source spaces and forward models
optimized for connectivity computation, i.e., the fsaverage space
is morphed onto the subject's space.
Parameters
----------
subject : str
The subject name.
hcp_path : str
The directory containing the HCP data.
recordings_path : str
The path where MEG data and transformations are stored.
subjects_dir : str
The directory containing the extracted HCP subject data.
info_from : tuple of tuples | dict
The reader info concerning the data from which sensor positions
should be read.
Must not be empty room as sensor positions are in head
coordinates for 4D systems, hence not available in that case.
Note that differences between the sensor positions across runs
are smaller than 12 digits, hence negligible.
fwd_params : None | dict
The forward parameters
src_params : None | dict
The src params. Defaults to:
dict(subject='fsaverage', fname=None, spacing='oct6', n_jobs=2,
surface='white', subjects_dir=subjects_dir, add_dist=True)
hcp_path : str
The prefix of the path of the HCP data.
n_jobs : int
The number of jobs to use in parallel.
verbose : bool, str, int, or None
If not None, override default verbose level (see mne.verbose)
Returns
-------
out : dict
A dictionary with the following keys:
fwd : instance of mne.Forward
The forward solution.
src_subject : instance of mne.SourceSpace
The source model on the subject's surface
src_fsaverage : instance of mne.SourceSpace
The source model on fsaverage's surface
bem_sol : dict
The BEM.
info : instance of mne.io.meas_info.Info
The actual measurement info used.
"""
if isinstance(info_from, tuple):
info_from = dict(info_from)
head_mri_t = mne.read_trans(
op.join(recordings_path, subject, '{}-head_mri-trans.fif'.format(
subject)))
src_defaults = dict(subject='fsaverage', spacing='oct6', n_jobs=n_jobs,
surface='white', subjects_dir=subjects_dir, add_dist=True)
if 'fname' in mne.fixes._get_args(mne.setup_source_space):
# needed for mne-0.14 and below
src_defaults.update(dict(fname=None))
else:
# remove 'fname' argument (if necessary) when using mne-0.15+
if 'fname' in src_params:
del src_params['fname']
src_params = _update_dict_defaults(src_params, src_defaults)
add_source_space_distances = False
if src_params['add_dist']: # we want the distances on the morphed space
src_params['add_dist'] = False
add_source_space_distances = True
src_fsaverage = mne.setup_source_space(**src_params)
src_subject = mne.morph_source_spaces(
src_fsaverage, subject, subjects_dir=subjects_dir)
if add_source_space_distances: # and here we compute them post hoc.
src_subject = mne.add_source_space_distances(
src_subject, n_jobs=n_jobs)
bems = mne.make_bem_model(subject, conductivity=(0.3,),
subjects_dir=subjects_dir,
ico=None) # ico = None for morphed SP.
bem_sol = mne.make_bem_solution(bems)
bem_sol['surfs'][0]['coord_frame'] = 5
info = read_info(subject=subject, hcp_path=hcp_path, **info_from)
picks = _pick_data_channels(info, with_ref_meg=False)
info = pick_info(info, picks)
# here we assume that as a result of our MNE-HCP processing
# all other transforms in info are identity
for trans in ['dev_head_t', 'ctf_head_t']:
# 'dev_ctf_t' is not identity
assert np.sum(info[trans]['trans'] - np.eye(4)) == 0
fwd = mne.make_forward_solution(
info, trans=head_mri_t, bem=bem_sol, src=src_subject,
n_jobs=n_jobs)
return dict(fwd=fwd, src_subject=src_subject,
src_fsaverage=src_fsaverage,
bem_sol=bem_sol, info=info)
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, str))
assert (isinstance(model.points_eval_str, str))
# 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])
Plotting EEG sensors on the scalp
=================================
In this example, digitized EEG sensor locations are shown on the scalp.
"""
# Author: Eric Larson <*****@*****.**>
#
# License: BSD (3-clause)
import mne
from mne.viz import plot_trans
from mayavi import mlab
print(__doc__)
data_path = mne.datasets.sample.data_path()
subjects_dir = data_path + "/subjects"
trans = mne.read_trans(data_path + "/MEG/sample/sample_audvis_raw-trans.fif")
raw = mne.io.read_raw_fif(data_path + "/MEG/sample/sample_audvis_raw.fif")
fig = plot_trans(
raw.info,
trans,
subject="sample",
dig=False,
eeg_sensors=["original", "projected"],
meg_sensors=[],
coord_frame="head",
subjects_dir=subjects_dir,
)
mlab.view(135, 80)
def test_do_forward_solution():
"""Test wrapping forward solution from python
"""
raw = Raw(fname_raw)
mri = read_trans(fname_mri)
fname_fake = op.join(temp_dir, 'no_have.fif')
# ## Error checks
# bad subject
assert_raises(ValueError, do_forward_solution, 1, fname_raw,
subjects_dir=subjects_dir)
# bad meas
assert_raises(ValueError, do_forward_solution, 'sample', 1,
subjects_dir=subjects_dir)
# meas doesn't exist
assert_raises(IOError, do_forward_solution, 'sample', fname_fake,
subjects_dir=subjects_dir)
# don't specify trans and meas
assert_raises(ValueError, do_forward_solution, 'sample', fname_raw,
subjects_dir=subjects_dir)
# specify both trans and meas
assert_raises(ValueError, do_forward_solution, 'sample', fname_raw,
trans='me', mri='you', subjects_dir=subjects_dir)
# specify non-existent trans
assert_raises(IOError, do_forward_solution, 'sample', fname_raw,
trans=fname_fake, subjects_dir=subjects_dir)
# specify non-existent mri
assert_raises(IOError, do_forward_solution, 'sample', fname_raw,
mri=fname_fake, subjects_dir=subjects_dir)
# specify non-string mri
assert_raises(ValueError, do_forward_solution, 'sample', fname_raw,
mri=1, subjects_dir=subjects_dir)
# specify non-string trans
assert_raises(ValueError, do_forward_solution, 'sample', fname_raw,
trans=1, subjects_dir=subjects_dir)
# test specifying an actual trans in python space -- this should work but
# the transform I/O reduces our accuracy -- so we'll just hack a test here
# by making it bomb with eeg=False and meg=False
assert_raises(ValueError, do_forward_solution, 'sample', fname_raw,
mri=mri, eeg=False, meg=False, subjects_dir=subjects_dir)
# mindist as non-integer
assert_raises(TypeError, do_forward_solution, 'sample', fname_raw,
mri=fname_mri, mindist=dict(), subjects_dir=subjects_dir)
# mindist as string but not 'all'
assert_raises(ValueError, do_forward_solution, 'sample', fname_raw,
mri=fname_mri, eeg=False, mindist='yall',
subjects_dir=subjects_dir)
# src, spacing, and bem as non-str
assert_raises(ValueError, do_forward_solution, 'sample', fname_raw,
mri=fname_mri, src=1, subjects_dir=subjects_dir)
assert_raises(ValueError, do_forward_solution, 'sample', fname_raw,
mri=fname_mri, spacing=1, subjects_dir=subjects_dir)
assert_raises(ValueError, do_forward_solution, 'sample', fname_raw,
mri=fname_mri, bem=1, subjects_dir=subjects_dir)
# no overwrite flag
assert_raises(IOError, do_forward_solution, 'sample', fname_raw,
existing_file, mri=fname_mri, subjects_dir=subjects_dir)
# let's catch an MNE error, this time about trans being wrong
assert_raises(CalledProcessError, do_forward_solution, 'sample',
fname_raw, existing_file, trans=fname_mri, overwrite=True,
spacing='oct-6', subjects_dir=subjects_dir)
# ## Actually calculate one and check
# make a meas from raw (tests all steps in creating evoked),
# don't do EEG or 5120-5120-5120 BEM because they're ~3x slower
fwd_py = do_forward_solution('sample', raw, mindist=5, spacing='oct-6',
bem='sample-5120', mri=fname_mri, eeg=False,
subjects_dir=subjects_dir)
fwd = read_forward_solution(fname)
assert_allclose(fwd['sol']['data'], fwd_py['sol']['data'],
rtol=1e-5, atol=1e-8)
assert_equal(fwd_py['sol']['data'].shape, (306, 22494))
assert_equal(len(fwd['sol']['row_names']), 306)
def test_coreg_model():
"""Test CoregModel"""
from mne.gui._coreg_gui import CoregModel
tempdir = _TempDir()
trans_dst = os.path.join(tempdir, 'test-trans.fif')
model = CoregModel()
assert_raises(RuntimeError, model.save_trans, 'blah.fif')
model.mri.use_high_res_head = False
model.mri.subjects_dir = subjects_dir
model.mri.subject = 'sample'
assert_false(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_true(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_true(model.has_fid_data)
lpa_distance = model.lpa_distance
nasion_distance = model.nasion_distance
rpa_distance = model.rpa_distance
avg_point_distance = np.mean(model.point_distance)
model.fit_auricular_points()
old_x = lpa_distance ** 2 + rpa_distance ** 2
new_x = model.lpa_distance ** 2 + model.rpa_distance ** 2
assert_true(new_x < old_x)
model.fit_fiducials()
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_true(new_x < old_x)
model.fit_hsp_points()
assert_true(np.mean(model.point_distance) < avg_point_distance)
model.save_trans(trans_dst)
trans = mne.read_trans(trans_dst)
assert_allclose(trans['trans'], model.head_mri_trans)
# test restoring trans
x, y, z, rot_x, rot_y, rot_z = .1, .2, .05, 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.head_mri_trans
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_almost_equal(model.trans_x, x)
assert_almost_equal(model.trans_y, y)
assert_almost_equal(model.trans_z, z)
assert_almost_equal(model.rot_x, rot_x)
assert_almost_equal(model.rot_y, rot_y)
assert_almost_equal(model.rot_z, rot_z)
# info
assert_true(isinstance(model.fid_eval_str, string_types))
assert_true(isinstance(model.points_eval_str, string_types))
# scaling job
sdir, sfrom, sto, scale, skip_fiducials, bemsol = \
model.get_scaling_job('sample2', False, True)
assert_equal(sdir, subjects_dir)
assert_equal(sfrom, 'sample')
assert_equal(sto, 'sample2')
assert_equal(scale, model.scale)
assert_equal(skip_fiducials, False)
# find BEM files
bems = set()
for fname in os.listdir(os.path.join(subjects_dir, 'sample', 'bem')):
match = re.match('sample-(.+-bem)\.fif', fname)
if match:
bems.add(match.group(1))
assert_equal(set(bemsol), bems)
sdir, sfrom, sto, scale, skip_fiducials, bemsol = \
model.get_scaling_job('sample2', True, False)
assert_equal(bemsol, [])
assert_true(skip_fiducials)
model.load_trans(fname_trans)
from mne.gui._coreg_gui import CoregFrame
x = CoregFrame(raw_path, 'sample', subjects_dir)
os.environ['_MNE_GUI_TESTING_MODE'] = 'true'
try:
with warnings.catch_warnings(record=True): # traits spews warnings
warnings.simplefilter('always')
x._init_plot()
finally:
del os.environ['_MNE_GUI_TESTING_MODE']
def __init__(self, raw, mrk, bem='head', trans=None, subject=None,
subjects_dir=None):
"""
Parameters
----------
raw : mne.fiff.Raw | str(path)
MNE Raw object, or path to a raw file.
mrk : load.kit.MarkerFile | str(path) | array, shape = (5, 3)
MarkerFile object, or path to a marker file, or marker points.
bem : None | str(path)
Name of the bem model to load (optional, only for visualization
purposes).
trans : None | dict | str(path)
MRI-Head transform (optional).
Can be None if the file is located in the raw directory and named
"{subject}-trans.fif"
subject : None | str
Name of the mri subject.
Can be None if the raw file-name starts with "{subject}_".
"""
subjects_dir = get_subjects_dir(subjects_dir)
# interpret mrk
if isinstance(mrk, basestring):
mrk = load.kit.MarkerFile(mrk)
if isinstance(mrk, load.kit.MarkerFile):
mrk = mrk.points
# interpret raw
if isinstance(raw, basestring):
raw_fname = raw
raw = load.fiff.Raw(raw)
else:
raw_fname = raw.info['filename']
self._raw_fname = raw_fname
self.raw = raw
# subject
if subject is None:
_, tail = os.path.split(raw_fname)
subject = tail.split('_')[0]
self.subject = subject
# bem (mri-head-trans)
if bem is None:
self.MRI = None
else:
# trans
if trans is None:
head, _ = os.path.split(raw_fname)
trans = os.path.join(head, subject + '-trans.fif')
if isinstance(trans, basestring):
head_mri_t = mne.read_trans(trans)
# mri_dev_t
self.mri_head_t = np.matrix(head_mri_t['trans']).I
fname = os.path.join(subjects_dir, subject, 'bem',
'%s-%s.fif' % (subject, bem))
self.MRI = geom_bem(fname, unit='m')
self.MRI.set_T(self.mri_head_t)
# sensors
pts = filter(lambda d: d['kind'] == FIFF.FIFFV_MEG_CH, raw.info['chs'])
pts = np.array([d['loc'][:3] for d in pts])
self.sensors = geom(pts)
# marker points
pts = mrk / 1000
pts = pts[:, [1, 0, 2]]
pts[:, 0] *= -1
self.mrk = geom(pts)
# head shape
pts = filter(lambda d: d['kind'] == FIFF.FIFFV_POINT_EXTRA, raw.info['dig'])
pts = np.array([d['r'] for d in pts])
self.headshape = geom(pts)
# HPI points
pts = filter(lambda d: d['kind'] == FIFF.FIFFV_POINT_HPI, raw.info['dig'])
assert [d['ident'] for d in pts] == range(1, 6)
pts = np.array([d['r'] for d in pts])
self.HPI = geom(pts)
# T head-to-device
trans = raw.info['dev_head_t']['trans']
self.T_head2dev = np.matrix(trans).I
self.reset()
self._HPI_flipped = False
def __init__(self, raw, subject=None, head_mri_t=None, mri='head',
hs='wireframe', subjects_dir=None, fig=None):
"""
Parameters
----------
raw : str(path) | Raw
Path to raw fiff file, or the mne.fiff.Raw instance.
subject : None | str
Name of the mri subject. Can be None if the raw file-name starts
with "{subject}_".
head_mri_t : None | str(path)
Path to the trans file for head-mri coregistration. Can be None if
the file is located in the raw directory and named
"{subject}-trans.fif"
mri : str
Name of the mri model to load (default is 'head')
hs : None | 'wireframe' | 'surface' | 'points' | 'balls'
How to display the digitizer head-shape stored in the raw file.
"""
subjects_dir = get_subjects_dir(subjects_dir)
if fig is None:
fig = mlab.figure()
self.fig = fig
# raw
if isinstance(raw, basestring):
raw_fname = raw
raw = load.fiff.Raw(raw_fname)
else:
raw_fname = raw.info['filename']
# subject
if subject is None:
_, tail = os.path.split(raw_fname)
subject = tail.split('_')[0]
# mri_head_t
if head_mri_t is None:
head, _ = os.path.split(raw_fname)
head_mri_t = os.path.join(head, subject + '-trans.fif')
if isinstance(head_mri_t, basestring):
head_mri_t = mne.read_trans(head_mri_t)
# mri_dev_t
mri_head_t = np.matrix(head_mri_t['trans']).I
head_dev_t = np.matrix(raw.info['dev_head_t']['trans']).I
mri_dev_t = head_dev_t * mri_head_t
# sensors
pts = filter(lambda d: d['kind'] == FIFF.FIFFV_MEG_CH, raw.info['chs'])
pts = np.array([d['loc'][:3] for d in pts])
self.sensors = geom(pts)
self.sensors.plot_points(fig, scale=0.005, color=(0, 0, 1))
# mri
bemdir = os.path.join(subjects_dir, subject, 'bem')
bem = os.path.join(bemdir, '%s-%s.fif' % (subject, mri))
self.mri = geom_bem(bem, unit='m')
self.mri.set_T(mri_dev_t)
self.mri.plot_solid(fig, color=(.8, .6, .5))
# head-shape
if hs:
self.hs = geom_dig_hs(raw.info['dig'], unit='m')
self.hs.set_T(head_dev_t)
if hs in ['surface', 'wireframe', 'points']:
self.hs.plot_solid(fig, opacity=1, rep=hs, color=(1, .5, 0))
elif hs == 'balls':
self.hs.plot_points(fig, 0.01, opacity=0.5, color=(1, .5, 0))
else:
raise ValueError('hs kwarg can not be %r' % hs)
self.hs.plot_solid(fig, opacity=1, rep='points', color=(1, .5, 0))
# Fiducials
fname = os.path.join(bemdir, subject + '-fiducials.fif')
if os.path.exists(fname):
dig, _ = read_fiducials(fname)
self.mri_fid = geom_fid(dig, unit='m')
self.mri_fid.set_T(mri_dev_t)
self.mri_fid.plot_points(fig, scale=0.005)
self.dig_fid = geom_fid(raw.info['dig'], unit='m')
self.dig_fid.set_T(head_dev_t)
self.dig_fid.plot_points(fig, scale=0.04, opacity=.25,
color=(.5, .5, 1))
self.view()
def test_coreg_model():
"""Test CoregModel"""
from mne.gui._coreg_gui import CoregModel
tempdir = _TempDir()
trans_dst = os.path.join(tempdir, 'test-trans.fif')
model = CoregModel()
assert_raises(RuntimeError, model.save_trans, 'blah.fif')
model.mri.subjects_dir = subjects_dir
model.mri.subject = 'sample'
assert_false(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_true(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_true(model.has_fid_data)
lpa_distance = model.lpa_distance
nasion_distance = model.nasion_distance
rpa_distance = model.rpa_distance
avg_point_distance = np.mean(model.point_distance)
model.fit_auricular_points()
old_x = lpa_distance ** 2 + rpa_distance ** 2
new_x = model.lpa_distance ** 2 + model.rpa_distance ** 2
assert_true(new_x < old_x)
model.fit_fiducials()
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_true(new_x < old_x)
model.fit_hsp_points()
assert_true(np.mean(model.point_distance) < avg_point_distance)
model.save_trans(trans_dst)
trans = mne.read_trans(trans_dst)
assert_allclose(trans['trans'], model.head_mri_trans)
# test restoring trans
x, y, z, rot_x, rot_y, rot_z = .1, .2, .05, 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.head_mri_trans
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_almost_equal(model.trans_x, x)
assert_almost_equal(model.trans_y, y)
assert_almost_equal(model.trans_z, z)
assert_almost_equal(model.rot_x, rot_x)
assert_almost_equal(model.rot_y, rot_y)
assert_almost_equal(model.rot_z, rot_z)
# info
assert_true(isinstance(model.fid_eval_str, string_types))
assert_true(isinstance(model.points_eval_str, string_types))
model.get_prepare_bem_model_job('sample')
model.load_trans(fname_trans)
from mne.gui._coreg_gui import CoregFrame
x = CoregFrame(raw_path, 'sample', subjects_dir)
os.environ['_MNE_GUI_TESTING_MODE'] = 'true'
try:
with warnings.catch_warnings(record=True): # traits spews warnings
warnings.simplefilter('always')
x._init_plot()
finally:
del os.environ['_MNE_GUI_TESTING_MODE']
hcp_path = op.join(storage_dir, 'HCP')
recordings_path = op.join(storage_dir, 'hcp-meg')
subjects_dir = op.join(storage_dir, 'hcp-subjects')
subject = '105923' # our test subject
##############################################################################
# and we assume to have the downloaded data, the MNE/freesurfer style
# anatomy directory, and the MNE style MEG directory.
# these can be obtained from :func:`make_mne_anatomy`.
# See also :ref:`tut_make_anatomy`.
##############################################################################
# first we read the coregistration.
head_mri_t = mne.read_trans(
op.join(recordings_path, subject, '{}-head_mri-trans.fif'.format(
subject)))
##############################################################################
# Now we can setup our source model.
# Note that spacing has to be set to 'all' since no common MNE resampling
# scheme has been employed in the HCP pipelines.
# Since this will take very long time to compute and at this point no other
# decimation scheme is available inside MNE, we will compute the source
# space on fsaverage, the freesurfer average brain, and morph it onto
# the subject's native space. With `oct6` we have ~8000 dipole locations.
src_fsaverage = mne.setup_source_space(
subject='fsaverage', subjects_dir=subjects_dir, add_dist=False,
spacing='oct6', overwrite=True)