def test_make_field_map_eeg():
"""Test interpolation of EEG field onto head
"""
evoked = read_evokeds(evoked_fname, condition='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_make_field_map_meg():
"""Test interpolation of MEG field onto helmet | head
"""
evoked = read_evokeds(evoked_fname, condition='Left Auditory')
info = evoked.info
surf = get_meg_helmet_surf(info)
# let's reduce the number of channels by a bunch to speed it up
info['bads'] = info['ch_names'][:200]
# bad ch_type
assert_raises(ValueError, _make_surface_mapping, info, surf, 'foo')
# bad mode
assert_raises(ValueError,
_make_surface_mapping,
info,
surf,
'meg',
mode='foo')
# no picks
evoked_eeg = evoked.pick_types(meg=False, eeg=True, copy=True)
assert_raises(RuntimeError, _make_surface_mapping, evoked_eeg.info, surf,
'meg')
# bad surface def
nn = surf['nn']
del surf['nn']
assert_raises(KeyError, _make_surface_mapping, info, surf, 'meg')
surf['nn'] = nn
cf = surf['coord_frame']
del surf['coord_frame']
assert_raises(KeyError, _make_surface_mapping, info, surf, 'meg')
surf['coord_frame'] = cf
# now do it with make_field_map
evoked.pick_types(meg=True, eeg=False)
fmd = make_field_map(evoked,
None,
subject='sample',
subjects_dir=subjects_dir)
assert_true(len(fmd) == 1)
assert_array_equal(fmd[0]['data'].shape, (304, 106)) # maps data onto surf
assert_true(len(fmd[0]['ch_names']), 106)
assert_raises(ValueError, make_field_map, evoked, ch_type='foobar')
# now test the make_field_map on head surf for MEG
evoked.pick_types(meg=True, eeg=False)
fmd = make_field_map(evoked,
trans_fname,
meg_surf='head',
subject='sample',
subjects_dir=subjects_dir)
assert_true(len(fmd) == 1)
assert_array_equal(fmd[0]['data'].shape, (642, 106)) # maps data onto surf
assert_true(len(fmd[0]['ch_names']), 106)
assert_raises(ValueError,
make_field_map,
evoked,
meg_surf='foobar',
subjects_dir=subjects_dir,
trans=trans_fname)
def test_field_map_ctf():
"""Test that field mapping can be done with CTF data."""
raw = read_raw_fif(raw_ctf_fname).crop(0, 1)
raw.apply_gradient_compensation(3)
events = make_fixed_length_events(raw, duration=0.5)
evoked = Epochs(raw, events).average()
evoked.pick_channels(evoked.ch_names[:50]) # crappy mapping but faster
# smoke test
make_field_map(evoked, trans=trans_fname, subject='sample',
subjects_dir=subjects_dir)
def test_field_map_ctf():
"""Test that field mapping can be done with CTF data."""
raw = read_raw_fif(raw_ctf_fname).crop(0, 1)
raw.apply_gradient_compensation(3)
events = make_fixed_length_events(raw, duration=0.5)
evoked = Epochs(raw, events).average()
evoked.pick_channels(evoked.ch_names[:50]) # crappy mapping but faster
# smoke test
make_field_map(evoked,
trans=trans_fname,
subject='sample',
subjects_dir=subjects_dir)
def test_make_field_map_meg():
"""Test interpolation of MEG field onto helmet | head
"""
evoked = read_evokeds(evoked_fname, condition='Left Auditory')
info = evoked.info
surf = get_meg_helmet_surf(info)
# let's reduce the number of channels by a bunch to speed it up
info['bads'] = info['ch_names'][:200]
# bad ch_type
assert_raises(ValueError, _make_surface_mapping, info, surf, 'foo')
# bad mode
assert_raises(ValueError, _make_surface_mapping, info, surf, 'meg',
mode='foo')
# no picks
evoked_eeg = evoked.copy().pick_types(meg=False, eeg=True)
assert_raises(RuntimeError, _make_surface_mapping, evoked_eeg.info,
surf, 'meg')
# bad surface def
nn = surf['nn']
del surf['nn']
assert_raises(KeyError, _make_surface_mapping, info, surf, 'meg')
surf['nn'] = nn
cf = surf['coord_frame']
del surf['coord_frame']
assert_raises(KeyError, _make_surface_mapping, info, surf, 'meg')
surf['coord_frame'] = cf
# now do it with make_field_map
evoked.pick_types(meg=True, eeg=False)
evoked.info.normalize_proj() # avoid projection warnings
fmd = make_field_map(evoked, None,
subject='sample', subjects_dir=subjects_dir)
assert_true(len(fmd) == 1)
assert_array_equal(fmd[0]['data'].shape, (304, 106)) # maps data onto surf
assert_true(len(fmd[0]['ch_names']), 106)
assert_raises(ValueError, make_field_map, evoked, ch_type='foobar')
# now test the make_field_map on head surf for MEG
evoked.pick_types(meg=True, eeg=False)
evoked.info.normalize_proj()
fmd = make_field_map(evoked, trans_fname, meg_surf='head',
subject='sample', subjects_dir=subjects_dir)
assert_true(len(fmd) == 1)
assert_array_equal(fmd[0]['data'].shape, (642, 106)) # maps data onto surf
assert_true(len(fmd[0]['ch_names']), 106)
assert_raises(ValueError, make_field_map, evoked, meg_surf='foobar',
subjects_dir=subjects_dir, trans=trans_fname)
def test_make_field_map_meeg():
"""Test making a M/EEG field map onto helmet & head"""
evoked = read_evokeds(evoked_fname, baseline=(-0.2, 0.0))[0]
picks = pick_types(evoked.info, meg=True, eeg=True)
picks = picks[::10]
evoked.pick_channels([evoked.ch_names[p] for p in picks])
maps = make_field_map(evoked,
trans_fname,
subject='sample',
subjects_dir=subjects_dir,
n_jobs=1)
assert_equal(maps[0]['data'].shape, (642, 6)) # EEG->Head
assert_equal(maps[1]['data'].shape, (304, 31)) # MEG->Helmet
# reasonable ranges
for map_ in maps:
assert_true(0.5 < map_['data'].max() < 2)
assert_true(-2 < map_['data'].min() < -0.5)
# calculated from correct looking mapping on 2015/12/26
assert_allclose(np.sqrt(np.sum(maps[0]['data']**2)),
16.6088,
atol=1e-3,
rtol=1e-3)
assert_allclose(np.sqrt(np.sum(maps[1]['data']**2)),
20.1245,
atol=1e-3,
rtol=1e-3)
def test_make_field_map_meeg():
"""Test making a M/EEG field map onto helmet & head."""
evoked = read_evokeds(evoked_fname, baseline=(-0.2, 0.0))[0]
picks = pick_types(evoked.info, meg=True, eeg=True)
picks = picks[::10]
evoked.pick_channels([evoked.ch_names[p] for p in picks])
evoked.info.normalize_proj()
maps = make_field_map(evoked,
trans_fname,
subject='sample',
subjects_dir=subjects_dir,
n_jobs=1,
verbose='debug')
assert_equal(maps[0]['data'].shape, (642, 6)) # EEG->Head
assert_equal(maps[1]['data'].shape, (304, 31)) # MEG->Helmet
# reasonable ranges
maxs = (1.2, 2.0) # before #4418, was (1.1, 2.0)
mins = (-0.8, -1.3) # before #4418, was (-0.6, -1.2)
assert_equal(len(maxs), len(maps))
for map_, max_, min_ in zip(maps, maxs, mins):
assert_allclose(map_['data'].max(), max_, rtol=5e-2)
assert_allclose(map_['data'].min(), min_, rtol=5e-2)
# calculated from correct looking mapping on 2015/12/26
assert_allclose(
np.sqrt(np.sum(maps[0]['data']**2)),
19.0903, # 16.6088,
atol=1e-3,
rtol=1e-3)
assert_allclose(
np.sqrt(np.sum(maps[1]['data']**2)),
19.4748, # 20.1245,
atol=1e-3,
rtol=1e-3)
def test_make_field_map_eeg():
"""Test interpolation of EEG field onto head
"""
evoked = read_evokeds(evoked_fname, condition="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(meg=False, eeg=True)
fmd = make_field_map(evoked, trans_fname, subject="sample", subjects_dir=subjects_dir)
# trans is necessary for EEG only
assert_raises(RuntimeError, make_field_map, evoked, None, subject="sample", subjects_dir=subjects_dir)
fmd = make_field_map(evoked, trans_fname, subject="sample", subjects_dir=subjects_dir)
assert_true(len(fmd) == 1)
assert_array_equal(fmd[0]["data"].shape, (642, 59)) # maps data onto surf
assert_true(len(fmd[0]["ch_names"]), 59)
def test_make_field_map_meg():
"""Test interpolation of MEG field onto helmet | head
"""
evoked = read_evokeds(evoked_fname, condition="Left Auditory")
info = evoked.info
surf = get_meg_helmet_surf(info)
# let's reduce the number of channels by a bunch to speed it up
info["bads"] = info["ch_names"][:200]
# bad ch_type
assert_raises(ValueError, _make_surface_mapping, info, surf, "foo")
# bad mode
assert_raises(ValueError, _make_surface_mapping, info, surf, "meg", mode="foo")
# no picks
evoked_eeg = evoked.pick_types(meg=False, eeg=True, copy=True)
assert_raises(RuntimeError, _make_surface_mapping, evoked_eeg.info, surf, "meg")
# bad surface def
nn = surf["nn"]
del surf["nn"]
assert_raises(KeyError, _make_surface_mapping, info, surf, "meg")
surf["nn"] = nn
cf = surf["coord_frame"]
del surf["coord_frame"]
assert_raises(KeyError, _make_surface_mapping, info, surf, "meg")
surf["coord_frame"] = cf
# now do it with make_field_map
evoked.pick_types(meg=True, eeg=False)
fmd = make_field_map(evoked, None, subject="sample", subjects_dir=subjects_dir)
assert_true(len(fmd) == 1)
assert_array_equal(fmd[0]["data"].shape, (304, 106)) # maps data onto surf
assert_true(len(fmd[0]["ch_names"]), 106)
assert_raises(ValueError, make_field_map, evoked, ch_type="foobar")
# now test the make_field_map on head surf for MEG
evoked.pick_types(meg=True, eeg=False)
fmd = make_field_map(evoked, trans_fname, meg_surf="head", subject="sample", subjects_dir=subjects_dir)
assert_true(len(fmd) == 1)
assert_array_equal(fmd[0]["data"].shape, (642, 106)) # maps data onto surf
assert_true(len(fmd[0]["ch_names"]), 106)
assert_raises(ValueError, make_field_map, evoked, meg_surf="foobar", subjects_dir=subjects_dir, trans=trans_fname)
def test_make_field_map_eeg():
"""Test interpolation of EEG field onto head."""
evoked = read_evokeds(evoked_fname, condition='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
pytest.raises(ValueError, _make_surface_mapping, evoked.info, surf, 'eeg')
evoked.pick_types(meg=False, eeg=True)
fmd = make_field_map(evoked, trans_fname,
subject='sample', subjects_dir=subjects_dir)
# trans is necessary for EEG only
pytest.raises(RuntimeError, make_field_map, evoked, None,
subject='sample', subjects_dir=subjects_dir)
fmd = make_field_map(evoked, trans_fname,
subject='sample', subjects_dir=subjects_dir)
assert len(fmd) == 1
assert_array_equal(fmd[0]['data'].shape, (642, 59)) # maps data onto surf
assert len(fmd[0]['ch_names']) == 59
def test_make_field_map_meeg():
"""Test making a M/EEG field map onto helmet & head"""
evoked = read_evokeds(evoked_fname, baseline=(-0.2, 0.0))[0]
picks = pick_types(evoked.info, meg=True, eeg=True)
picks = picks[::10]
evoked.pick_channels([evoked.ch_names[p] for p in picks])
maps = make_field_map(evoked, trans_fname, subject='sample',
subjects_dir=subjects_dir, n_jobs=1)
assert_equal(maps[0]['data'].shape, (642, 6)) # EEG->Head
assert_equal(maps[1]['data'].shape, (304, 31)) # MEG->Helmet
# reasonable ranges
for map_ in maps:
assert_true(0.5 < map_['data'].max() < 2)
assert_true(-2 < map_['data'].min() < -0.5)
# calculated from correct looking mapping on 2015/12/26
assert_allclose(np.sqrt(np.sum(maps[0]['data'] ** 2)), 16.6088,
atol=1e-3, rtol=1e-3)
assert_allclose(np.sqrt(np.sum(maps[1]['data'] ** 2)), 20.1245,
atol=1e-3, rtol=1e-3)
def test_make_field_map_meeg():
"""Test making a M/EEG field map onto helmet & head."""
evoked = read_evokeds(evoked_fname, baseline=(-0.2, 0.0))[0]
picks = pick_types(evoked.info, meg=True, eeg=True)
picks = picks[::10]
evoked.pick_channels([evoked.ch_names[p] for p in picks])
evoked.info.normalize_proj()
maps = make_field_map(evoked, trans_fname, subject='sample',
subjects_dir=subjects_dir, n_jobs=1, verbose='debug')
assert_equal(maps[0]['data'].shape, (642, 6)) # EEG->Head
assert_equal(maps[1]['data'].shape, (304, 31)) # MEG->Helmet
# reasonable ranges
maxs = (1.2, 2.0) # before #4418, was (1.1, 2.0)
mins = (-0.8, -1.3) # before #4418, was (-0.6, -1.2)
assert_equal(len(maxs), len(maps))
for map_, max_, min_ in zip(maps, maxs, mins):
assert_allclose(map_['data'].max(), max_, rtol=5e-2)
assert_allclose(map_['data'].min(), min_, rtol=5e-2)
# calculated from correct looking mapping on 2015/12/26
assert_allclose(np.sqrt(np.sum(maps[0]['data'] ** 2)), 19.0903, # 16.6088,
atol=1e-3, rtol=1e-3)
assert_allclose(np.sqrt(np.sum(maps[1]['data'] ** 2)), 19.4748, # 20.1245,
atol=1e-3, rtol=1e-3)