def test_make_scalp_surfaces():
"""Test mne make_scalp_surfaces"""
check_usage(mne_make_scalp_surfaces)
# Copy necessary files to avoid FreeSurfer call
tempdir = _TempDir()
surf_path = op.join(subjects_dir, 'sample', 'surf')
surf_path_new = op.join(tempdir, 'sample', 'surf')
os.mkdir(op.join(tempdir, 'sample'))
os.mkdir(surf_path_new)
os.mkdir(op.join(tempdir, 'sample', 'bem'))
shutil.copy(op.join(surf_path, 'lh.seghead'), surf_path_new)
orig_fs = os.getenv('FREESURFER_HOME', None)
orig_mne = os.getenv('MNE_ROOT')
if orig_fs is not None:
del os.environ['FREESURFER_HOME']
cmd = ('-s', 'sample', '--subjects-dir', tempdir)
os.environ['_MNE_TESTING_SCALP'] = 'true'
try:
with ArgvSetter(cmd, disable_stdout=False, disable_stderr=False):
assert_raises(RuntimeError, mne_make_scalp_surfaces.run)
os.environ['FREESURFER_HOME'] = tempdir # don't need it
del os.environ['MNE_ROOT']
assert_raises(RuntimeError, mne_make_scalp_surfaces.run)
os.environ['MNE_ROOT'] = orig_mne
mne_make_scalp_surfaces.run()
assert_raises(IOError, mne_make_scalp_surfaces.run) # no overwrite
finally:
if orig_fs is not None:
os.environ['FREESURFER_HOME'] = orig_fs
os.environ['MNE_ROOT'] = orig_mne
del os.environ['_MNE_TESTING_SCALP']
def test_make_scalp_surfaces():
"""Test mne make_scalp_surfaces"""
check_usage(mne_make_scalp_surfaces)
# Copy necessary files to avoid FreeSurfer call
tempdir = _TempDir()
surf_path = op.join(subjects_dir, 'sample', 'surf')
surf_path_new = op.join(tempdir, 'sample', 'surf')
os.mkdir(op.join(tempdir, 'sample'))
os.mkdir(surf_path_new)
subj_dir = op.join(tempdir, 'sample', 'bem')
os.mkdir(subj_dir)
shutil.copy(op.join(surf_path, 'lh.seghead'), surf_path_new)
orig_fs = os.getenv('FREESURFER_HOME', None)
orig_mne = os.getenv('MNE_ROOT')
if orig_fs is not None:
del os.environ['FREESURFER_HOME']
cmd = ('-s', 'sample', '--subjects-dir', tempdir)
os.environ['_MNE_TESTING_SCALP'] = 'true'
try:
with ArgvSetter(cmd, disable_stdout=False, disable_stderr=False):
assert_raises(RuntimeError, mne_make_scalp_surfaces.run)
os.environ['FREESURFER_HOME'] = tempdir # don't need it
del os.environ['MNE_ROOT']
assert_raises(RuntimeError, mne_make_scalp_surfaces.run)
os.environ['MNE_ROOT'] = orig_mne
mne_make_scalp_surfaces.run()
assert_true(op.isfile(op.join(subj_dir, 'sample-head-dense.fif')))
assert_true(op.isfile(op.join(subj_dir, 'sample-head-medium.fif')))
assert_raises(IOError, mne_make_scalp_surfaces.run) # no overwrite
finally:
if orig_fs is not None:
os.environ['FREESURFER_HOME'] = orig_fs
os.environ['MNE_ROOT'] = orig_mne
del os.environ['_MNE_TESTING_SCALP']
def test_make_scalp_surfaces():
"""Test mne make_scalp_surfaces"""
check_usage(mne_make_scalp_surfaces)
# Copy necessary files to avoid FreeSurfer call
tempdir = _TempDir()
surf_path = op.join(subjects_dir, "sample", "surf")
surf_path_new = op.join(tempdir, "sample", "surf")
os.mkdir(op.join(tempdir, "sample"))
os.mkdir(surf_path_new)
os.mkdir(op.join(tempdir, "sample", "bem"))
shutil.copy(op.join(surf_path, "lh.seghead"), surf_path_new)
orig_fs = os.getenv("FREESURFER_HOME", None)
orig_mne = os.getenv("MNE_ROOT")
if orig_fs is not None:
del os.environ["FREESURFER_HOME"]
cmd = ("-s", "sample", "--subjects-dir", tempdir)
os.environ["_MNE_TESTING_SCALP"] = "true"
try:
with ArgvSetter(cmd, disable_stdout=False, disable_stderr=False):
assert_raises(RuntimeError, mne_make_scalp_surfaces.run)
os.environ["FREESURFER_HOME"] = tempdir # don't need it
del os.environ["MNE_ROOT"]
assert_raises(RuntimeError, mne_make_scalp_surfaces.run)
os.environ["MNE_ROOT"] = orig_mne
mne_make_scalp_surfaces.run()
assert_raises(IOError, mne_make_scalp_surfaces.run) # no overwrite
finally:
if orig_fs is not None:
os.environ["FREESURFER_HOME"] = orig_fs
os.environ["MNE_ROOT"] = orig_mne
del os.environ["_MNE_TESTING_SCALP"]
def test_make_scalp_surfaces():
"""Test mne make_scalp_surfaces."""
check_usage(mne_make_scalp_surfaces)
# Copy necessary files to avoid FreeSurfer call
tempdir = _TempDir()
surf_path = op.join(subjects_dir, 'sample', 'surf')
surf_path_new = op.join(tempdir, 'sample', 'surf')
os.mkdir(op.join(tempdir, 'sample'))
os.mkdir(surf_path_new)
subj_dir = op.join(tempdir, 'sample', 'bem')
os.mkdir(subj_dir)
shutil.copy(op.join(surf_path, 'lh.seghead'), surf_path_new)
orig_fs = os.getenv('FREESURFER_HOME', None)
if orig_fs is not None:
del os.environ['FREESURFER_HOME']
cmd = ('-s', 'sample', '--subjects-dir', tempdir)
os.environ['_MNE_TESTING_SCALP'] = 'true'
dense_fname = op.join(subj_dir, 'sample-head-dense.fif')
medium_fname = op.join(subj_dir, 'sample-head-medium.fif')
try:
with ArgvSetter(cmd, disable_stdout=False, disable_stderr=False):
assert_raises(RuntimeError, mne_make_scalp_surfaces.run)
os.environ['FREESURFER_HOME'] = tempdir # don't actually use it
mne_make_scalp_surfaces.run()
assert_true(op.isfile(dense_fname))
assert_true(op.isfile(medium_fname))
assert_raises(IOError, mne_make_scalp_surfaces.run) # no overwrite
finally:
if orig_fs is not None:
os.environ['FREESURFER_HOME'] = orig_fs
else:
del os.environ['FREESURFER_HOME']
del os.environ['_MNE_TESTING_SCALP']
# actually check the outputs
head_py = read_bem_surfaces(dense_fname)
assert_equal(len(head_py), 1)
head_py = head_py[0]
head_c = read_bem_surfaces(
op.join(subjects_dir, 'sample', 'bem', 'sample-head-dense.fif'))[0]
assert_allclose(head_py['rr'], head_c['rr'])
def test_make_scalp_surfaces():
"""Test mne make_scalp_surfaces."""
check_usage(mne_make_scalp_surfaces)
# Copy necessary files to avoid FreeSurfer call
tempdir = _TempDir()
surf_path = op.join(subjects_dir, 'sample', 'surf')
surf_path_new = op.join(tempdir, 'sample', 'surf')
os.mkdir(op.join(tempdir, 'sample'))
os.mkdir(surf_path_new)
subj_dir = op.join(tempdir, 'sample', 'bem')
os.mkdir(subj_dir)
shutil.copy(op.join(surf_path, 'lh.seghead'), surf_path_new)
orig_fs = os.getenv('FREESURFER_HOME', None)
if orig_fs is not None:
del os.environ['FREESURFER_HOME']
cmd = ('-s', 'sample', '--subjects-dir', tempdir)
os.environ['_MNE_TESTING_SCALP'] = 'true'
dense_fname = op.join(subj_dir, 'sample-head-dense.fif')
medium_fname = op.join(subj_dir, 'sample-head-medium.fif')
try:
with ArgvSetter(cmd, disable_stdout=False, disable_stderr=False):
pytest.raises(RuntimeError, mne_make_scalp_surfaces.run)
os.environ['FREESURFER_HOME'] = tempdir # don't actually use it
mne_make_scalp_surfaces.run()
assert op.isfile(dense_fname)
assert op.isfile(medium_fname)
pytest.raises(IOError, mne_make_scalp_surfaces.run) # no overwrite
finally:
if orig_fs is not None:
os.environ['FREESURFER_HOME'] = orig_fs
else:
del os.environ['FREESURFER_HOME']
del os.environ['_MNE_TESTING_SCALP']
# actually check the outputs
head_py = read_bem_surfaces(dense_fname)
assert_equal(len(head_py), 1)
head_py = head_py[0]
head_c = read_bem_surfaces(op.join(subjects_dir, 'sample', 'bem',
'sample-head-dense.fif'))[0]
assert_allclose(head_py['rr'], head_c['rr'])
def test_make_scalp_surfaces():
"""Test mne make_scalp_surfaces."""
check_usage(mne_make_scalp_surfaces)
# Copy necessary files to avoid FreeSurfer call
tempdir = _TempDir()
surf_path = op.join(subjects_dir, "sample", "surf")
surf_path_new = op.join(tempdir, "sample", "surf")
os.mkdir(op.join(tempdir, "sample"))
os.mkdir(surf_path_new)
subj_dir = op.join(tempdir, "sample", "bem")
os.mkdir(subj_dir)
shutil.copy(op.join(surf_path, "lh.seghead"), surf_path_new)
orig_fs = os.getenv("FREESURFER_HOME", None)
if orig_fs is not None:
del os.environ["FREESURFER_HOME"]
cmd = ("-s", "sample", "--subjects-dir", tempdir)
os.environ["_MNE_TESTING_SCALP"] = "true"
dense_fname = op.join(subj_dir, "sample-head-dense.fif")
medium_fname = op.join(subj_dir, "sample-head-medium.fif")
try:
with ArgvSetter(cmd, disable_stdout=False, disable_stderr=False):
assert_raises(RuntimeError, mne_make_scalp_surfaces.run)
os.environ["FREESURFER_HOME"] = tempdir # don't actually use it
mne_make_scalp_surfaces.run()
assert_true(op.isfile(dense_fname))
assert_true(op.isfile(medium_fname))
assert_raises(IOError, mne_make_scalp_surfaces.run) # no overwrite
finally:
if orig_fs is not None:
os.environ["FREESURFER_HOME"] = orig_fs
else:
del os.environ["FREESURFER_HOME"]
del os.environ["_MNE_TESTING_SCALP"]
# actually check the outputs
head_py = read_bem_surfaces(dense_fname)
assert_equal(len(head_py), 1)
head_py = head_py[0]
head_c = read_bem_surfaces(op.join(subjects_dir, "sample", "bem", "sample-head-dense.fif"))[0]
assert_allclose(head_py["rr"], head_c["rr"])
def test_make_scalp_surfaces(tmpdir):
"""Test mne make_scalp_surfaces."""
check_usage(mne_make_scalp_surfaces)
has = 'SUBJECTS_DIR' in os.environ
# Copy necessary files to avoid FreeSurfer call
tempdir = str(tmpdir)
surf_path = op.join(subjects_dir, 'sample', 'surf')
surf_path_new = op.join(tempdir, 'sample', 'surf')
os.mkdir(op.join(tempdir, 'sample'))
os.mkdir(surf_path_new)
subj_dir = op.join(tempdir, 'sample', 'bem')
os.mkdir(subj_dir)
shutil.copy(op.join(surf_path, 'lh.seghead'), surf_path_new)
cmd = ('-s', 'sample', '--subjects-dir', tempdir)
with modified_env(**{'_MNE_TESTING_SCALP': 'true'}):
dense_fname = op.join(subj_dir, 'sample-head-dense.fif')
medium_fname = op.join(subj_dir, 'sample-head-medium.fif')
with ArgvSetter(cmd, disable_stdout=False, disable_stderr=False):
with modified_env(FREESURFER_HOME=None):
pytest.raises(RuntimeError, mne_make_scalp_surfaces.run)
with modified_env(FREESURFER_HOME=tempdir):
mne_make_scalp_surfaces.run()
assert op.isfile(dense_fname)
assert op.isfile(medium_fname)
with pytest.raises(IOError, match='overwrite'):
mne_make_scalp_surfaces.run()
# actually check the outputs
head_py = read_bem_surfaces(dense_fname)
assert_equal(len(head_py), 1)
head_py = head_py[0]
head_c = read_bem_surfaces(op.join(subjects_dir, 'sample', 'bem',
'sample-head-dense.fif'))[0]
assert_allclose(head_py['rr'], head_c['rr'])
if not has:
assert 'SUBJECTS_DIR' not in os.environ
def test_make_scalp_surfaces(tmpdir):
"""Test mne make_scalp_surfaces."""
check_usage(mne_make_scalp_surfaces)
has = 'SUBJECTS_DIR' in os.environ
# Copy necessary files to avoid FreeSurfer call
tempdir = str(tmpdir)
surf_path = op.join(subjects_dir, 'sample', 'surf')
surf_path_new = op.join(tempdir, 'sample', 'surf')
os.mkdir(op.join(tempdir, 'sample'))
os.mkdir(surf_path_new)
subj_dir = op.join(tempdir, 'sample', 'bem')
os.mkdir(subj_dir)
shutil.copy(op.join(surf_path, 'lh.seghead'), surf_path_new)
cmd = ('-s', 'sample', '--subjects-dir', tempdir)
with modified_env(**{'_MNE_TESTING_SCALP': 'true'}):
dense_fname = op.join(subj_dir, 'sample-head-dense.fif')
medium_fname = op.join(subj_dir, 'sample-head-medium.fif')
with ArgvSetter(cmd, disable_stdout=False, disable_stderr=False):
with modified_env(FREESURFER_HOME=None):
pytest.raises(RuntimeError, mne_make_scalp_surfaces.run)
with modified_env(FREESURFER_HOME=tempdir):
mne_make_scalp_surfaces.run()
assert op.isfile(dense_fname)
assert op.isfile(medium_fname)
with pytest.raises(IOError, match='overwrite'):
mne_make_scalp_surfaces.run()
# actually check the outputs
head_py = read_bem_surfaces(dense_fname)
assert_equal(len(head_py), 1)
head_py = head_py[0]
head_c = read_bem_surfaces(op.join(subjects_dir, 'sample', 'bem',
'sample-head-dense.fif'))[0]
assert_allclose(head_py['rr'], head_c['rr'])
if not has:
assert 'SUBJECTS_DIR' not in os.environ
def test_make_scalp_surfaces(tmp_path, monkeypatch):
"""Test mne make_scalp_surfaces."""
pytest.importorskip('nibabel')
pytest.importorskip('pyvista')
check_usage(mne_make_scalp_surfaces)
has = 'SUBJECTS_DIR' in os.environ
# Copy necessary files to avoid FreeSurfer call
tempdir = str(tmp_path)
surf_path = op.join(subjects_dir, 'sample', 'surf')
surf_path_new = op.join(tempdir, 'sample', 'surf')
os.mkdir(op.join(tempdir, 'sample'))
os.mkdir(surf_path_new)
subj_dir = op.join(tempdir, 'sample', 'bem')
os.mkdir(subj_dir)
cmd = ('-s', 'sample', '--subjects-dir', tempdir)
monkeypatch.setattr(
mne.bem, 'decimate_surface', lambda points, triangles, n_triangles:
(points, triangles))
dense_fname = op.join(subj_dir, 'sample-head-dense.fif')
medium_fname = op.join(subj_dir, 'sample-head-medium.fif')
with ArgvSetter(cmd, disable_stdout=False, disable_stderr=False):
monkeypatch.delenv('FREESURFER_HOME', None)
with pytest.raises(RuntimeError, match='The FreeSurfer environ'):
mne_make_scalp_surfaces.run()
shutil.copy(op.join(surf_path, 'lh.seghead'), surf_path_new)
monkeypatch.setenv('FREESURFER_HOME', tempdir)
mne_make_scalp_surfaces.run()
assert op.isfile(dense_fname)
assert op.isfile(medium_fname)
with pytest.raises(IOError, match='overwrite'):
mne_make_scalp_surfaces.run()
# actually check the outputs
head_py = read_bem_surfaces(dense_fname)
assert_equal(len(head_py), 1)
head_py = head_py[0]
head_c = read_bem_surfaces(
op.join(subjects_dir, 'sample', 'bem', 'sample-head-dense.fif'))[0]
assert_allclose(head_py['rr'], head_c['rr'])
if not has:
assert 'SUBJECTS_DIR' not in os.environ