def test_watershed_bem(tmpdir):
"""Test mne watershed bem."""
check_usage(mne_watershed_bem)
# Copy necessary files to tempdir
tempdir = str(tmpdir)
mridata_path = op.join(subjects_dir, 'sample', 'mri')
subject_path_new = op.join(tempdir, 'sample')
mridata_path_new = op.join(subject_path_new, 'mri')
os.mkdir(op.join(tempdir, 'sample'))
os.mkdir(mridata_path_new)
if op.exists(op.join(mridata_path, 'T1')):
shutil.copytree(op.join(mridata_path, 'T1'), op.join(mridata_path_new,
'T1'))
if op.exists(op.join(mridata_path, 'T1.mgz')):
shutil.copyfile(op.join(mridata_path, 'T1.mgz'),
op.join(mridata_path_new, 'T1.mgz'))
out_fnames = list()
for kind in ('outer_skin', 'outer_skull', 'inner_skull'):
out_fnames.append(op.join(subject_path_new, 'bem', 'inner_skull.surf'))
assert not any(op.isfile(out_fname) for out_fname in out_fnames)
with ArgvSetter(('-d', tempdir, '-s', 'sample', '-o'),
disable_stdout=False, disable_stderr=False):
mne_watershed_bem.run()
for out_fname in out_fnames:
_, tris = read_surface(out_fname)
assert len(tris) == 20480
def test_watershed_bem():
"""Test mne watershed bem."""
check_usage(mne_watershed_bem)
# Copy necessary files to tempdir
tempdir = _TempDir()
mridata_path = op.join(subjects_dir, 'sample', 'mri')
subject_path_new = op.join(tempdir, 'sample')
mridata_path_new = op.join(subject_path_new, 'mri')
os.mkdir(op.join(tempdir, 'sample'))
os.mkdir(mridata_path_new)
if op.exists(op.join(mridata_path, 'T1')):
shutil.copytree(op.join(mridata_path, 'T1'), op.join(mridata_path_new,
'T1'))
if op.exists(op.join(mridata_path, 'T1.mgz')):
shutil.copyfile(op.join(mridata_path, 'T1.mgz'),
op.join(mridata_path_new, 'T1.mgz'))
out_fnames = list()
for kind in ('outer_skin', 'outer_skull', 'inner_skull'):
out_fnames.append(op.join(subject_path_new, 'bem', 'inner_skull.surf'))
assert not any(op.isfile(out_fname) for out_fname in out_fnames)
with ArgvSetter(('-d', tempdir, '-s', 'sample', '-o'),
disable_stdout=False, disable_stderr=False):
mne_watershed_bem.run()
for out_fname in out_fnames:
_, tris = read_surface(out_fname)
assert len(tris) == 20480
def test_watershed_bem(tmpdir):
"""Test mne watershed bem."""
check_usage(mne_watershed_bem)
# Copy necessary files to tempdir
tempdir = str(tmpdir)
mridata_path = op.join(subjects_dir, 'sample', 'mri')
subject_path_new = op.join(tempdir, 'sample')
mridata_path_new = op.join(subject_path_new, 'mri')
os.makedirs(mridata_path_new)
new_fname = op.join(mridata_path_new, 'T1.mgz')
shutil.copyfile(op.join(mridata_path, 'T1.mgz'), new_fname)
old_mode = os.stat(new_fname).st_mode
os.chmod(new_fname, 0)
args = ('-d', tempdir, '-s', 'sample', '-o')
with pytest.raises(PermissionError, match=r'read permissions.*T1\.mgz'):
with ArgvSetter(args):
mne_watershed_bem.run()
os.chmod(new_fname, old_mode)
out_fnames = list()
for kind in ('outer_skin', 'outer_skull', 'inner_skull'):
out_fnames.append(op.join(subject_path_new, 'bem', 'inner_skull.surf'))
assert not any(op.isfile(out_fname) for out_fname in out_fnames)
with ArgvSetter(args):
mne_watershed_bem.run()
for out_fname in out_fnames:
_, tris = read_surface(out_fname)
assert len(tris) == 20480
def test_watershed_bem():
"""Test mne watershed bem."""
check_usage(mne_watershed_bem)
# Copy necessary files to tempdir
tempdir = _TempDir()
mridata_path = op.join(subjects_dir, "sample", "mri")
mridata_path_new = op.join(tempdir, "sample", "mri")
os.mkdir(op.join(tempdir, "sample"))
os.mkdir(mridata_path_new)
if op.exists(op.join(mridata_path, "T1")):
shutil.copytree(op.join(mridata_path, "T1"), op.join(mridata_path_new, "T1"))
if op.exists(op.join(mridata_path, "T1.mgz")):
shutil.copyfile(op.join(mridata_path, "T1.mgz"), op.join(mridata_path_new, "T1.mgz"))
with ArgvSetter(("-d", tempdir, "-s", "sample", "-o"), disable_stdout=False, disable_stderr=False):
mne_watershed_bem.run()
def test_watershed_bem():
"""Test mne watershed bem."""
check_usage(mne_watershed_bem)
# Copy necessary files to tempdir
tempdir = _TempDir()
mridata_path = op.join(subjects_dir, 'sample', 'mri')
mridata_path_new = op.join(tempdir, 'sample', 'mri')
os.mkdir(op.join(tempdir, 'sample'))
os.mkdir(mridata_path_new)
if op.exists(op.join(mridata_path, 'T1')):
shutil.copytree(op.join(mridata_path, 'T1'), op.join(mridata_path_new,
'T1'))
if op.exists(op.join(mridata_path, 'T1.mgz')):
shutil.copyfile(op.join(mridata_path, 'T1.mgz'),
op.join(mridata_path_new, 'T1.mgz'))
with ArgvSetter(('-d', tempdir, '-s', 'sample', '-o'),
disable_stdout=False, disable_stderr=False):
mne_watershed_bem.run()
def test_watershed_bem():
"""Test mne watershed bem"""
check_usage(mne_watershed_bem)
# Copy necessary files to tempdir
tempdir = _TempDir()
mridata_path = op.join(subjects_dir, 'sample', 'mri')
mridata_path_new = op.join(tempdir, 'sample', 'mri')
os.mkdir(op.join(tempdir, 'sample'))
os.mkdir(mridata_path_new)
if op.exists(op.join(mridata_path, 'T1')):
shutil.copytree(op.join(mridata_path, 'T1'), op.join(mridata_path_new,
'T1'))
if op.exists(op.join(mridata_path, 'T1.mgz')):
shutil.copyfile(op.join(mridata_path, 'T1.mgz'),
op.join(mridata_path_new, 'T1.mgz'))
with ArgvSetter(('-d', tempdir, '-s', 'sample', '-o'),
disable_stdout=False, disable_stderr=False):
mne_watershed_bem.run()
def test_watershed_bem(tmp_path):
"""Test mne watershed bem."""
check_usage(mne_watershed_bem)
# from T1.mgz
Mdc = np.array([[-1, 0, 0], [0, 0, -1], [0, 1, 0]])
Pxyz_c = np.array([-5.273613, 9.039085, -27.287964])
# Copy necessary files to tempdir
tempdir = str(tmp_path)
mridata_path = op.join(subjects_dir, 'sample', 'mri')
subject_path_new = op.join(tempdir, 'sample')
mridata_path_new = op.join(subject_path_new, 'mri')
os.makedirs(mridata_path_new)
new_fname = op.join(mridata_path_new, 'T1.mgz')
shutil.copyfile(op.join(mridata_path, 'T1.mgz'), new_fname)
old_mode = os.stat(new_fname).st_mode
os.chmod(new_fname, 0)
args = ('-d', tempdir, '-s', 'sample', '-o')
with pytest.raises(PermissionError, match=r'read permissions.*T1\.mgz'):
with ArgvSetter(args):
mne_watershed_bem.run()
os.chmod(new_fname, old_mode)
for s in ('outer_skin', 'outer_skull', 'inner_skull'):
assert not op.isfile(op.join(subject_path_new, 'bem', '%s.surf' % s))
with ArgvSetter(args):
mne_watershed_bem.run()
kwargs = dict(rtol=1e-5, atol=1e-5)
for s in ('outer_skin', 'outer_skull', 'inner_skull'):
rr, tris, vol_info = read_surface(op.join(subject_path_new, 'bem',
'%s.surf' % s),
read_metadata=True)
assert_equal(len(tris), 20480)
assert_equal(tris.min(), 0)
assert_equal(rr.shape[0], tris.max() + 1)
# compare the volume info to the mgz header
assert_allclose(vol_info['xras'], Mdc[0], **kwargs)
assert_allclose(vol_info['yras'], Mdc[1], **kwargs)
assert_allclose(vol_info['zras'], Mdc[2], **kwargs)
assert_allclose(vol_info['cras'], Pxyz_c, **kwargs)
