def test_morph_data():
"""Test morphing of data
"""
subject_from = 'sample'
subject_to = 'fsaverage'
fname = op.join(data_path, 'MEG', 'sample', 'sample_audvis-meg')
stc_from = read_source_estimate(fname, subject='sample')
fname = op.join(data_path, 'MEG', 'sample', 'fsaverage_audvis-meg')
stc_to = read_source_estimate(fname)
# make sure we can specify grade
stc_from.crop(0.09, 0.1) # for faster computation
stc_to.crop(0.09, 0.1) # for faster computation
stc_to1 = stc_from.morph(subject_to, grade=3, smooth=12, buffer_size=1000)
stc_to1.save(op.join(tempdir, '%s_audvis-meg' % subject_to))
# make sure we can specify vertices
vertices_to = grade_to_vertices(subject_to, grade=3)
stc_to2 = morph_data(subject_from,
subject_to,
stc_from,
grade=vertices_to,
smooth=12,
buffer_size=1000)
# make sure we can use different buffer_size
stc_to3 = morph_data(subject_from,
subject_to,
stc_from,
grade=vertices_to,
smooth=12,
buffer_size=3)
# indexing silliness here due to mne_make_movie's indexing oddities
assert_array_almost_equal(stc_to.data, stc_to1.data, 5)
assert_array_almost_equal(stc_to1.data, stc_to2.data)
assert_array_almost_equal(stc_to1.data, stc_to3.data)
# make sure precomputed morph matrices work
morph_mat = compute_morph_matrix(subject_from,
subject_to,
stc_from.vertno,
vertices_to,
smooth=12)
stc_to3 = stc_from.morph_precomputed(subject_to, vertices_to, morph_mat)
assert_array_almost_equal(stc_to1.data, stc_to3.data)
mean_from = stc_from.data.mean(axis=0)
mean_to = stc_to1.data.mean(axis=0)
assert_true(np.corrcoef(mean_to, mean_from).min() > 0.999)
# make sure we can fill by morphing
stc_to5 = morph_data(subject_from,
subject_to,
stc_from,
grade=None,
smooth=12,
buffer_size=3)
assert_true(stc_to5.data.shape[0] == 163842 + 163842)
def test_morph_data():
"""Test morphing of data
"""
subject_from = 'sample'
subject_to = 'fsaverage'
fname = op.join(data_path, 'MEG', 'sample', 'sample_audvis-meg')
stc_from = read_source_estimate(fname)
stc_from.crop(0.09, 0.1) # for faster computation
# After running this:
# stc_from.save('%s_audvis-meg-cropped' % subject_from)
# this was run from a command line:
# mne_make_movie --stcin sample_audvis-meg-cropped-lh.stc
# --subject sample --morph fsaverage --smooth 12 --morphgrade 3
# --stc fsaverage_audvis-meg-cropped
# XXX These files should eventually be moved to the sample dataset and
# removed from mne/fiff/tests/data/
fname = op.join(op.dirname(__file__), '..', 'fiff', 'tests', 'data',
'fsaverage_audvis-meg-cropped')
stc_to = read_source_estimate(fname)
stc_to1 = morph_data(subject_from, subject_to, stc_from,
grade=3, smooth=12, buffer_size=1000)
stc_to1.save('%s_audvis-meg' % subject_to)
stc_to2 = morph_data(subject_from, subject_to, stc_from,
grade=3, smooth=12, buffer_size=3)
# indexing silliness here due to mne_make_movie's indexing oddities
assert_array_almost_equal(stc_to.data, stc_to1.data[:, 0][:, None], 5)
assert_array_almost_equal(stc_to1.data, stc_to2.data)
# make sure precomputed morph matrices work
vertices_to = grade_to_vertices(subject_to, grade=3)
morph_mat = compute_morph_matrix(subject_from, subject_to,
stc_from.vertno, vertices_to,
smooth=12)
stc_to3 = morph_data_precomputed(subject_from, subject_to,
stc_from, vertices_to, morph_mat)
assert_array_almost_equal(stc_to1.data, stc_to3.data)
mean_from = stc_from.data.mean(axis=0)
mean_to = stc_to1.data.mean(axis=0)
assert_true(np.corrcoef(mean_to, mean_from).min() > 0.999)
# test two types of morphing:
# 1) make sure we can fill by morphing
stc_to5 = morph_data(subject_from, subject_to, stc_from,
grade=None, smooth=12, buffer_size=3)
assert_true(stc_to5.data.shape[0] == 163842 + 163842)
# 2) make sure we can specify vertices
vertices_to = [np.arange(10242), np.arange(10242)]
stc_to3 = morph_data(subject_from, subject_to, stc_from,
grade=vertices_to, smooth=12, buffer_size=3)
stc_to4 = morph_data(subject_from, subject_to, stc_from,
grade=5, smooth=12, buffer_size=3)
assert_array_almost_equal(stc_to3.data, stc_to4.data)
def test_morph_data():
"""Test morphing of data
"""
subject_from = 'sample'
subject_to = 'fsaverage'
fname = op.join(data_path, 'MEG', 'sample', 'sample_audvis-meg')
stc_from = read_source_estimate(fname, subject='sample')
fname = op.join(data_path, 'MEG', 'sample', 'fsaverage_audvis-meg')
stc_to = read_source_estimate(fname)
# make sure we can specify grade
stc_from.crop(0.09, 0.1) # for faster computation
stc_to.crop(0.09, 0.1) # for faster computation
stc_to1 = stc_from.morph(subject_to, grade=3, smooth=12, buffer_size=1000,
subjects_dir=subjects_dir)
stc_to1.save(op.join(tempdir, '%s_audvis-meg' % subject_to))
# make sure we can specify vertices
vertices_to = grade_to_vertices(subject_to, grade=3)
stc_to2 = morph_data(subject_from, subject_to, stc_from,
grade=vertices_to, smooth=12, buffer_size=1000,
subjects_dir=subjects_dir)
# make sure we can use different buffer_size
stc_to3 = morph_data(subject_from, subject_to, stc_from,
grade=vertices_to, smooth=12, buffer_size=3,
subjects_dir=subjects_dir)
assert_array_almost_equal(stc_to.data, stc_to1.data, 5)
assert_array_almost_equal(stc_to1.data, stc_to2.data)
assert_array_almost_equal(stc_to1.data, stc_to3.data)
# make sure precomputed morph matrices work
morph_mat = compute_morph_matrix(subject_from, subject_to,
stc_from.vertno, vertices_to,
smooth=12, subjects_dir=subjects_dir)
stc_to3 = stc_from.morph_precomputed(subject_to, vertices_to, morph_mat)
assert_array_almost_equal(stc_to1.data, stc_to3.data)
mean_from = stc_from.data.mean(axis=0)
mean_to = stc_to1.data.mean(axis=0)
assert_true(np.corrcoef(mean_to, mean_from).min() > 0.999)
# make sure we can fill by morphing
stc_to5 = morph_data(subject_from, subject_to, stc_from, grade=None,
smooth=12, buffer_size=3, subjects_dir=subjects_dir)
assert_true(stc_to5.data.shape[0] == 163842 + 163842)
# test morphing to the same subject
stc_to6 = stc_from.morph(subject_from, grade=stc_from.vertno, smooth=1,
subjects_dir=subjects_dir)
mask = np.ones(stc_from.data.shape[0], dtype=np.bool)
# XXX: there is a bug somewhere that causes a difference at 2 vertices..
mask[6799] = False
mask[6800] = False
assert_array_almost_equal(stc_from.data[mask], stc_to6.data[mask], 5)
def test_morph_data():
"""Test morphing of data
"""
subject_from = 'sample'
subject_to = 'fsaverage'
fname = op.join(data_path, 'MEG', 'sample', 'sample_audvis-meg')
stc_from = read_source_estimate(fname, subject='sample')
fname = op.join(data_path, 'MEG', 'sample', 'fsaverage_audvis-meg')
stc_to = read_source_estimate(fname)
# make sure we can specify grade
stc_from.crop(0.09, 0.1) # for faster computation
stc_to.crop(0.09, 0.1) # for faster computation
stc_to1 = stc_from.morph(subject_to, grade=3, smooth=12, buffer_size=1000,
subjects_dir=subjects_dir)
stc_to1.save(op.join(tempdir, '%s_audvis-meg' % subject_to))
# make sure we can specify vertices
vertices_to = grade_to_vertices(subject_to, grade=3)
stc_to2 = morph_data(subject_from, subject_to, stc_from,
grade=vertices_to, smooth=12, buffer_size=1000,
subjects_dir=subjects_dir)
# make sure we can use different buffer_size
stc_to3 = morph_data(subject_from, subject_to, stc_from,
grade=vertices_to, smooth=12, buffer_size=3,
subjects_dir=subjects_dir)
# indexing silliness here due to mne_make_movie's indexing oddities
assert_array_almost_equal(stc_to.data, stc_to1.data, 5)
assert_array_almost_equal(stc_to1.data, stc_to2.data)
assert_array_almost_equal(stc_to1.data, stc_to3.data)
# make sure precomputed morph matrices work
morph_mat = compute_morph_matrix(subject_from, subject_to,
stc_from.vertno, vertices_to,
smooth=12, subjects_dir=subjects_dir)
stc_to3 = stc_from.morph_precomputed(subject_to, vertices_to, morph_mat)
assert_array_almost_equal(stc_to1.data, stc_to3.data)
mean_from = stc_from.data.mean(axis=0)
mean_to = stc_to1.data.mean(axis=0)
assert_true(np.corrcoef(mean_to, mean_from).min() > 0.999)
# make sure we can fill by morphing
stc_to5 = morph_data(subject_from, subject_to, stc_from, grade=None,
smooth=12, buffer_size=3, subjects_dir=subjects_dir)
assert_true(stc_to5.data.shape[0] == 163842 + 163842)
def test_morph_data():
"""Test morphing of data
"""
tempdir = _TempDir()
subject_from = 'sample'
subject_to = 'fsaverage'
stc_from = read_source_estimate(fname_smorph, subject='sample')
stc_to = read_source_estimate(fname_fmorph)
# make sure we can specify grade
stc_from.crop(0.09, 0.1) # for faster computation
stc_to.crop(0.09, 0.1) # for faster computation
stc_to1 = stc_from.morph(subject_to,
grade=3,
smooth=12,
buffer_size=1000,
subjects_dir=subjects_dir)
stc_to1.save(op.join(tempdir, '%s_audvis-meg' % subject_to))
# make sure we can specify vertices
vertices_to = grade_to_vertices(subject_to,
grade=3,
subjects_dir=subjects_dir)
stc_to2 = morph_data(subject_from,
subject_to,
stc_from,
grade=vertices_to,
smooth=12,
buffer_size=1000,
subjects_dir=subjects_dir)
# make sure we can use different buffer_size
stc_to3 = morph_data(subject_from,
subject_to,
stc_from,
grade=vertices_to,
smooth=12,
buffer_size=3,
subjects_dir=subjects_dir)
assert_array_almost_equal(stc_to.data, stc_to1.data, 5)
assert_array_almost_equal(stc_to1.data, stc_to2.data)
assert_array_almost_equal(stc_to1.data, stc_to3.data)
# make sure precomputed morph matrices work
morph_mat = compute_morph_matrix(subject_from,
subject_to,
stc_from.vertices,
vertices_to,
smooth=12,
subjects_dir=subjects_dir)
stc_to3 = stc_from.morph_precomputed(subject_to, vertices_to, morph_mat)
assert_array_almost_equal(stc_to1.data, stc_to3.data)
mean_from = stc_from.data.mean(axis=0)
mean_to = stc_to1.data.mean(axis=0)
assert_true(np.corrcoef(mean_to, mean_from).min() > 0.999)
# make sure we can fill by morphing
stc_to5 = morph_data(subject_from,
subject_to,
stc_from,
grade=None,
smooth=12,
buffer_size=3,
subjects_dir=subjects_dir)
assert_true(stc_to5.data.shape[0] == 163842 + 163842)
# Morph sparse data
# Make a sparse stc
stc_from.vertices[0] = stc_from.vertices[0][[100, 500]]
stc_from.vertices[1] = stc_from.vertices[1][[200]]
stc_from._data = stc_from._data[:3]
assert_raises(RuntimeError,
stc_from.morph,
subject_to,
sparse=True,
grade=5,
subjects_dir=subjects_dir)
stc_to_sparse = stc_from.morph(subject_to,
grade=None,
sparse=True,
subjects_dir=subjects_dir)
assert_array_almost_equal(np.sort(stc_from.data.sum(axis=1)),
np.sort(stc_to_sparse.data.sum(axis=1)))
assert_equal(len(stc_from.rh_vertno), len(stc_to_sparse.rh_vertno))
assert_equal(len(stc_from.lh_vertno), len(stc_to_sparse.lh_vertno))
assert_equal(stc_to_sparse.subject, subject_to)
assert_equal(stc_from.tmin, stc_from.tmin)
assert_equal(stc_from.tstep, stc_from.tstep)
stc_from.vertices[0] = np.array([], dtype=np.int64)
stc_from._data = stc_from._data[:1]
stc_to_sparse = stc_from.morph(subject_to,
grade=None,
sparse=True,
subjects_dir=subjects_dir)
assert_array_almost_equal(np.sort(stc_from.data.sum(axis=1)),
np.sort(stc_to_sparse.data.sum(axis=1)))
assert_equal(len(stc_from.rh_vertno), len(stc_to_sparse.rh_vertno))
assert_equal(len(stc_from.lh_vertno), len(stc_to_sparse.lh_vertno))
assert_equal(stc_to_sparse.subject, subject_to)
assert_equal(stc_from.tmin, stc_from.tmin)
assert_equal(stc_from.tstep, stc_from.tstep)
def test_morph_data():
"""Test morphing of data."""
tempdir = _TempDir()
subject_from = 'sample'
subject_to = 'fsaverage'
stc_from = read_source_estimate(fname_smorph, subject='sample')
stc_to = read_source_estimate(fname_fmorph)
# make sure we can specify grade
stc_from.crop(0.09, 0.1) # for faster computation
stc_to.crop(0.09, 0.1) # for faster computation
assert_array_equal(stc_to.time_as_index([0.09, 0.1], use_rounding=True),
[0, len(stc_to.times) - 1])
pytest.raises(ValueError,
stc_from.morph,
subject_to,
grade=3,
smooth=-1,
subjects_dir=subjects_dir)
stc_to1 = stc_from.morph(subject_to,
grade=3,
smooth=12,
buffer_size=1000,
subjects_dir=subjects_dir)
stc_to1.save(op.join(tempdir, '%s_audvis-meg' % subject_to))
# Morphing to a density that is too high should raise an informative error
# (here we need to push to grade=6, but for some subjects even grade=5
# will break)
pytest.raises(ValueError,
stc_to1.morph,
subject_from,
grade=6,
subjects_dir=subjects_dir)
# make sure we can specify vertices
vertices_to = grade_to_vertices(subject_to,
grade=3,
subjects_dir=subjects_dir)
stc_to2 = morph_data(subject_from,
subject_to,
stc_from,
grade=vertices_to,
smooth=12,
buffer_size=1000,
subjects_dir=subjects_dir)
# make sure we can use different buffer_size
stc_to3 = morph_data(subject_from,
subject_to,
stc_from,
grade=vertices_to,
smooth=12,
buffer_size=3,
subjects_dir=subjects_dir)
# make sure we get a warning about # of steps
with pytest.warns(RuntimeWarning, match='consider increasing'):
morph_data(subject_from,
subject_to,
stc_from,
grade=vertices_to,
smooth=1,
buffer_size=3,
subjects_dir=subjects_dir)
assert_array_almost_equal(stc_to.data, stc_to1.data, 5)
assert_array_almost_equal(stc_to1.data, stc_to2.data)
assert_array_almost_equal(stc_to1.data, stc_to3.data)
# make sure precomputed morph matrices work
morph_mat = compute_morph_matrix(subject_from,
subject_to,
stc_from.vertices,
vertices_to,
smooth=12,
subjects_dir=subjects_dir)
stc_to3 = stc_from.morph_precomputed(subject_to, vertices_to, morph_mat)
assert_array_almost_equal(stc_to1.data, stc_to3.data)
pytest.raises(ValueError, stc_from.morph_precomputed, subject_to,
vertices_to, 'foo')
pytest.raises(ValueError, stc_from.morph_precomputed, subject_to,
[vertices_to[0]], morph_mat)
pytest.raises(ValueError, stc_from.morph_precomputed, subject_to,
[vertices_to[0][:-1], vertices_to[1]], morph_mat)
pytest.raises(ValueError,
stc_from.morph_precomputed,
subject_to,
vertices_to,
morph_mat,
subject_from='foo')
# steps warning
with pytest.warns(RuntimeWarning, match='steps'):
compute_morph_matrix(subject_from,
subject_to,
stc_from.vertices,
vertices_to,
smooth=1,
subjects_dir=subjects_dir)
mean_from = stc_from.data.mean(axis=0)
mean_to = stc_to1.data.mean(axis=0)
assert (np.corrcoef(mean_to, mean_from).min() > 0.999)
# make sure we can fill by morphing
stc_to5 = morph_data(subject_from,
subject_to,
stc_from,
grade=None,
smooth=12,
buffer_size=3,
subjects_dir=subjects_dir)
assert (stc_to5.data.shape[0] == 163842 + 163842)
# Morph sparse data
# Make a sparse stc
stc_from.vertices[0] = stc_from.vertices[0][[100, 500]]
stc_from.vertices[1] = stc_from.vertices[1][[200]]
stc_from._data = stc_from._data[:3]
pytest.raises(RuntimeError,
stc_from.morph,
subject_to,
sparse=True,
grade=5,
subjects_dir=subjects_dir)
stc_to_sparse = stc_from.morph(subject_to,
grade=None,
sparse=True,
subjects_dir=subjects_dir)
assert_array_almost_equal(np.sort(stc_from.data.sum(axis=1)),
np.sort(stc_to_sparse.data.sum(axis=1)))
assert_equal(len(stc_from.rh_vertno), len(stc_to_sparse.rh_vertno))
assert_equal(len(stc_from.lh_vertno), len(stc_to_sparse.lh_vertno))
assert_equal(stc_to_sparse.subject, subject_to)
assert_equal(stc_from.tmin, stc_from.tmin)
assert_equal(stc_from.tstep, stc_from.tstep)
stc_from.vertices[0] = np.array([], dtype=np.int64)
stc_from._data = stc_from._data[:1]
stc_to_sparse = stc_from.morph(subject_to,
grade=None,
sparse=True,
subjects_dir=subjects_dir)
assert_array_almost_equal(np.sort(stc_from.data.sum(axis=1)),
np.sort(stc_to_sparse.data.sum(axis=1)))
assert_equal(len(stc_from.rh_vertno), len(stc_to_sparse.rh_vertno))
assert_equal(len(stc_from.lh_vertno), len(stc_to_sparse.lh_vertno))
assert_equal(stc_to_sparse.subject, subject_to)
assert_equal(stc_from.tmin, stc_from.tmin)
assert_equal(stc_from.tstep, stc_from.tstep)
# Morph vector data
stc_vec = _real_vec_stc()
# Ignore warnings about number of steps
stc_vec_to1 = stc_vec.morph(subject_to,
grade=3,
smooth=12,
buffer_size=1000,
subjects_dir=subjects_dir)
stc_vec_to2 = stc_vec.morph_precomputed(subject_to, vertices_to, morph_mat)
assert_array_almost_equal(stc_vec_to1.data, stc_vec_to2.data)
def test_morph_data():
"""Test morphing of data
"""
subject_from = 'sample'
subject_to = 'fsaverage'
fname = op.join(data_path, 'MEG', 'sample', 'sample_audvis-meg')
stc_from = read_source_estimate(fname, subject='sample')
fname = op.join(data_path, 'MEG', 'sample', 'fsaverage_audvis-meg')
stc_to = read_source_estimate(fname)
# make sure we can specify grade
stc_from.crop(0.09, 0.1) # for faster computation
stc_to.crop(0.09, 0.1) # for faster computation
stc_to1 = stc_from.morph(subject_to,
grade=3,
smooth=12,
buffer_size=1000,
subjects_dir=subjects_dir)
stc_to1.save(op.join(tempdir, '%s_audvis-meg' % subject_to))
# make sure we can specify vertices
vertices_to = grade_to_vertices(subject_to, grade=3)
stc_to2 = morph_data(subject_from,
subject_to,
stc_from,
grade=vertices_to,
smooth=12,
buffer_size=1000,
subjects_dir=subjects_dir)
# make sure we can use different buffer_size
stc_to3 = morph_data(subject_from,
subject_to,
stc_from,
grade=vertices_to,
smooth=12,
buffer_size=3,
subjects_dir=subjects_dir)
assert_array_almost_equal(stc_to.data, stc_to1.data, 5)
assert_array_almost_equal(stc_to1.data, stc_to2.data)
assert_array_almost_equal(stc_to1.data, stc_to3.data)
# make sure precomputed morph matrices work
morph_mat = compute_morph_matrix(subject_from,
subject_to,
stc_from.vertno,
vertices_to,
smooth=12,
subjects_dir=subjects_dir)
stc_to3 = stc_from.morph_precomputed(subject_to, vertices_to, morph_mat)
assert_array_almost_equal(stc_to1.data, stc_to3.data)
mean_from = stc_from.data.mean(axis=0)
mean_to = stc_to1.data.mean(axis=0)
assert_true(np.corrcoef(mean_to, mean_from).min() > 0.999)
# make sure we can fill by morphing
stc_to5 = morph_data(subject_from,
subject_to,
stc_from,
grade=None,
smooth=12,
buffer_size=3,
subjects_dir=subjects_dir)
assert_true(stc_to5.data.shape[0] == 163842 + 163842)
# test morphing to the same subject
stc_to6 = stc_from.morph(subject_from,
grade=stc_from.vertno,
smooth=1,
subjects_dir=subjects_dir)
mask = np.ones(stc_from.data.shape[0], dtype=np.bool)
# XXX: there is a bug somewhere that causes a difference at 2 vertices..
mask[6799] = False
mask[6800] = False
assert_array_almost_equal(stc_from.data[mask], stc_to6.data[mask], 5)
def test_morph_data():
"""Test morphing of data
"""
tempdir = _TempDir()
subject_from = 'sample'
subject_to = 'fsaverage'
stc_from = read_source_estimate(fname_smorph, subject='sample')
stc_to = read_source_estimate(fname_fmorph)
# make sure we can specify grade
stc_from.crop(0.09, 0.1) # for faster computation
stc_to.crop(0.09, 0.1) # for faster computation
assert_array_equal(stc_to.time_as_index([0.09, 0.1], use_rounding=True),
[0, len(stc_to.times) - 1])
assert_raises(ValueError, stc_from.morph, subject_to, grade=3, smooth=-1,
subjects_dir=subjects_dir)
stc_to1 = stc_from.morph(subject_to, grade=3, smooth=12, buffer_size=1000,
subjects_dir=subjects_dir)
stc_to1.save(op.join(tempdir, '%s_audvis-meg' % subject_to))
# Morphing to a density that is too high should raise an informative error
# (here we need to push to grade=6, but for some subjects even grade=5
# will break)
assert_raises(ValueError, stc_to1.morph, subject_from, grade=6,
subjects_dir=subjects_dir)
# make sure we can specify vertices
vertices_to = grade_to_vertices(subject_to, grade=3,
subjects_dir=subjects_dir)
stc_to2 = morph_data(subject_from, subject_to, stc_from,
grade=vertices_to, smooth=12, buffer_size=1000,
subjects_dir=subjects_dir)
# make sure we can use different buffer_size
stc_to3 = morph_data(subject_from, subject_to, stc_from,
grade=vertices_to, smooth=12, buffer_size=3,
subjects_dir=subjects_dir)
# make sure we get a warning about # of steps
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
morph_data(subject_from, subject_to, stc_from,
grade=vertices_to, smooth=1, buffer_size=3,
subjects_dir=subjects_dir)
assert_equal(len(w), 2)
assert_array_almost_equal(stc_to.data, stc_to1.data, 5)
assert_array_almost_equal(stc_to1.data, stc_to2.data)
assert_array_almost_equal(stc_to1.data, stc_to3.data)
# make sure precomputed morph matrices work
morph_mat = compute_morph_matrix(subject_from, subject_to,
stc_from.vertices, vertices_to,
smooth=12, subjects_dir=subjects_dir)
stc_to3 = stc_from.morph_precomputed(subject_to, vertices_to, morph_mat)
assert_array_almost_equal(stc_to1.data, stc_to3.data)
assert_raises(ValueError, stc_from.morph_precomputed,
subject_to, vertices_to, 'foo')
assert_raises(ValueError, stc_from.morph_precomputed,
subject_to, [vertices_to[0]], morph_mat)
assert_raises(ValueError, stc_from.morph_precomputed,
subject_to, [vertices_to[0][:-1], vertices_to[1]], morph_mat)
assert_raises(ValueError, stc_from.morph_precomputed, subject_to,
vertices_to, morph_mat, subject_from='foo')
# steps warning
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
compute_morph_matrix(subject_from, subject_to,
stc_from.vertices, vertices_to,
smooth=1, subjects_dir=subjects_dir)
assert_equal(len(w), 2)
mean_from = stc_from.data.mean(axis=0)
mean_to = stc_to1.data.mean(axis=0)
assert_true(np.corrcoef(mean_to, mean_from).min() > 0.999)
# make sure we can fill by morphing
stc_to5 = morph_data(subject_from, subject_to, stc_from, grade=None,
smooth=12, buffer_size=3, subjects_dir=subjects_dir)
assert_true(stc_to5.data.shape[0] == 163842 + 163842)
# Morph sparse data
# Make a sparse stc
stc_from.vertices[0] = stc_from.vertices[0][[100, 500]]
stc_from.vertices[1] = stc_from.vertices[1][[200]]
stc_from._data = stc_from._data[:3]
assert_raises(RuntimeError, stc_from.morph, subject_to, sparse=True,
grade=5, subjects_dir=subjects_dir)
stc_to_sparse = stc_from.morph(subject_to, grade=None, sparse=True,
subjects_dir=subjects_dir)
assert_array_almost_equal(np.sort(stc_from.data.sum(axis=1)),
np.sort(stc_to_sparse.data.sum(axis=1)))
assert_equal(len(stc_from.rh_vertno), len(stc_to_sparse.rh_vertno))
assert_equal(len(stc_from.lh_vertno), len(stc_to_sparse.lh_vertno))
assert_equal(stc_to_sparse.subject, subject_to)
assert_equal(stc_from.tmin, stc_from.tmin)
assert_equal(stc_from.tstep, stc_from.tstep)
stc_from.vertices[0] = np.array([], dtype=np.int64)
stc_from._data = stc_from._data[:1]
stc_to_sparse = stc_from.morph(subject_to, grade=None, sparse=True,
subjects_dir=subjects_dir)
assert_array_almost_equal(np.sort(stc_from.data.sum(axis=1)),
np.sort(stc_to_sparse.data.sum(axis=1)))
assert_equal(len(stc_from.rh_vertno), len(stc_to_sparse.rh_vertno))
assert_equal(len(stc_from.lh_vertno), len(stc_to_sparse.lh_vertno))
assert_equal(stc_to_sparse.subject, subject_to)
assert_equal(stc_from.tmin, stc_from.tmin)
assert_equal(stc_from.tstep, stc_from.tstep)
def test_morph_data():
"""Test morphing of data
"""
tempdir = _TempDir()
subject_from = 'sample'
subject_to = 'fsaverage'
stc_from = read_source_estimate(fname_smorph, subject='sample')
stc_to = read_source_estimate(fname_fmorph)
# make sure we can specify grade
stc_from.crop(0.09, 0.1) # for faster computation
stc_to.crop(0.09, 0.1) # for faster computation
stc_to1 = stc_from.morph(subject_to, grade=3, smooth=12, buffer_size=1000,
subjects_dir=subjects_dir)
stc_to1.save(op.join(tempdir, '%s_audvis-meg' % subject_to))
# make sure we can specify vertices
vertices_to = grade_to_vertices(subject_to, grade=3,
subjects_dir=subjects_dir)
stc_to2 = morph_data(subject_from, subject_to, stc_from,
grade=vertices_to, smooth=12, buffer_size=1000,
subjects_dir=subjects_dir)
# make sure we can use different buffer_size
stc_to3 = morph_data(subject_from, subject_to, stc_from,
grade=vertices_to, smooth=12, buffer_size=3,
subjects_dir=subjects_dir)
assert_array_almost_equal(stc_to.data, stc_to1.data, 5)
assert_array_almost_equal(stc_to1.data, stc_to2.data)
assert_array_almost_equal(stc_to1.data, stc_to3.data)
# make sure precomputed morph matrices work
morph_mat = compute_morph_matrix(subject_from, subject_to,
stc_from.vertices, vertices_to,
smooth=12, subjects_dir=subjects_dir)
stc_to3 = stc_from.morph_precomputed(subject_to, vertices_to, morph_mat)
assert_array_almost_equal(stc_to1.data, stc_to3.data)
mean_from = stc_from.data.mean(axis=0)
mean_to = stc_to1.data.mean(axis=0)
assert_true(np.corrcoef(mean_to, mean_from).min() > 0.999)
# make sure we can fill by morphing
stc_to5 = morph_data(subject_from, subject_to, stc_from, grade=None,
smooth=12, buffer_size=3, subjects_dir=subjects_dir)
assert_true(stc_to5.data.shape[0] == 163842 + 163842)
# Morph sparse data
# Make a sparse stc
stc_from.vertices[0] = stc_from.vertices[0][[100, 500]]
stc_from.vertices[1] = stc_from.vertices[1][[200]]
stc_from._data = stc_from._data[:3]
assert_raises(RuntimeError, stc_from.morph, subject_to, sparse=True,
grade=5, subjects_dir=subjects_dir)
stc_to_sparse = stc_from.morph(subject_to, grade=None, sparse=True,
subjects_dir=subjects_dir)
assert_array_almost_equal(np.sort(stc_from.data.sum(axis=1)),
np.sort(stc_to_sparse.data.sum(axis=1)))
assert_equal(len(stc_from.rh_vertno), len(stc_to_sparse.rh_vertno))
assert_equal(len(stc_from.lh_vertno), len(stc_to_sparse.lh_vertno))
assert_equal(stc_to_sparse.subject, subject_to)
assert_equal(stc_from.tmin, stc_from.tmin)
assert_equal(stc_from.tstep, stc_from.tstep)
stc_from.vertices[0] = np.array([], dtype=np.int64)
stc_from._data = stc_from._data[:1]
stc_to_sparse = stc_from.morph(subject_to, grade=None, sparse=True,
subjects_dir=subjects_dir)
assert_array_almost_equal(np.sort(stc_from.data.sum(axis=1)),
np.sort(stc_to_sparse.data.sum(axis=1)))
assert_equal(len(stc_from.rh_vertno), len(stc_to_sparse.rh_vertno))
assert_equal(len(stc_from.lh_vertno), len(stc_to_sparse.lh_vertno))
assert_equal(stc_to_sparse.subject, subject_to)
assert_equal(stc_from.tmin, stc_from.tmin)
assert_equal(stc_from.tstep, stc_from.tstep)
def test_morph_data():
"""Test morphing of data
"""
subject_from = 'sample'
subject_to = 'fsaverage'
fname = op.join(data_path, 'MEG', 'sample', 'sample_audvis-meg')
stc_from = read_source_estimate(fname)
stc_from.crop(0.09, 0.1) # for faster computation
# After running this:
# stc_from.save('%s_audvis-meg-cropped' % subject_from)
# this was run from a command line:
# mne_make_movie --stcin sample_audvis-meg-cropped-lh.stc
# --subject sample --morph fsaverage --smooth 12 --morphgrade 3
# --stc fsaverage_audvis-meg-cropped
# XXX These files should eventually be moved to the sample dataset and
# removed from mne/fiff/tests/data/
fname = op.join(op.dirname(__file__), '..', 'fiff', 'tests', 'data',
'fsaverage_audvis-meg-cropped')
stc_to = read_source_estimate(fname)
stc_to1 = morph_data(subject_from,
subject_to,
stc_from,
grade=3,
smooth=12,
buffer_size=1000)
stc_to1.save('%s_audvis-meg' % subject_to)
stc_to2 = morph_data(subject_from,
subject_to,
stc_from,
grade=3,
smooth=12,
buffer_size=3)
# indexing silliness here due to mne_make_movie's indexing oddities
assert_array_almost_equal(stc_to.data, stc_to1.data[:, 0][:, None], 5)
assert_array_almost_equal(stc_to1.data, stc_to2.data)
# make sure precomputed morph matrices work
vertices_to = grade_to_vertices(subject_to, grade=3)
morph_mat = compute_morph_matrix(subject_from,
subject_to,
stc_from.vertno,
vertices_to,
smooth=12)
stc_to3 = morph_data_precomputed(subject_from, subject_to, stc_from,
vertices_to, morph_mat)
assert_array_almost_equal(stc_to1.data, stc_to3.data)
mean_from = stc_from.data.mean(axis=0)
mean_to = stc_to1.data.mean(axis=0)
assert_true(np.corrcoef(mean_to, mean_from).min() > 0.999)
# test two types of morphing:
# 1) make sure we can fill by morphing
stc_to5 = morph_data(subject_from,
subject_to,
stc_from,
grade=None,
smooth=12,
buffer_size=3)
assert_true(stc_to5.data.shape[0] == 163842 + 163842)
# 2) make sure we can specify vertices
vertices_to = [np.arange(10242), np.arange(10242)]
stc_to3 = morph_data(subject_from,
subject_to,
stc_from,
grade=vertices_to,
smooth=12,
buffer_size=3)
stc_to4 = morph_data(subject_from,
subject_to,
stc_from,
grade=5,
smooth=12,
buffer_size=3)
assert_array_almost_equal(stc_to3.data, stc_to4.data)
