[med-svn] [python-mne] 348/376: Merge branch 'master' into invop
Yaroslav Halchenko
debian at onerussian.com
Fri Nov 27 17:23:19 UTC 2015
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yoh pushed a commit to annotated tag v0.1
in repository python-mne.
commit 5e7e14a4064eceaa1b62a96ba0147600cc962308
Merge: 45600a4 906abbb
Author: Alexandre Gramfort <alexandre.gramfort at inria.fr>
Date: Tue Sep 13 16:46:59 2011 -0400
Merge branch 'master' into invop
Conflicts:
mne/minimum_norm/__init__.py
mne/minimum_norm/inverse.py
mne/minimum_norm/tests/test_inverse.py
.../plot_compute_mne_inverse_epochs_in_label.py | 65 +++++
mne/minimum_norm/inverse.py | 306 ++++++++++++---------
mne/minimum_norm/tests/test_inverse.py | 60 +++-
3 files changed, 296 insertions(+), 135 deletions(-)
diff --cc mne/minimum_norm/inverse.py
index 6183dcd,6930e94..787155a
--- a/mne/minimum_norm/inverse.py
+++ b/mne/minimum_norm/inverse.py
@@@ -15,11 -14,11 +15,11 @@@ from ..fiff.tag import find_ta
from ..fiff.matrix import _read_named_matrix, _transpose_named_matrix
from ..fiff.proj import read_proj, make_projector
from ..fiff.tree import dir_tree_find
- from ..fiff.pick import pick_channels_evoked, pick_channels
+ from ..fiff.pick import pick_channels
-from ..cov import read_cov
+from ..cov import read_cov, prepare_noise_cov
+from ..forward import compute_depth_prior
from ..source_space import read_source_spaces_from_tree, find_source_space_hemi
-from ..forward import _block_diag
from ..transforms import invert_transform, transform_source_space_to
from ..source_estimate import SourceEstimate
diff --cc mne/minimum_norm/tests/test_inverse.py
index bec08b9,d40f10f..07fdc6e
--- a/mne/minimum_norm/tests/test_inverse.py
+++ b/mne/minimum_norm/tests/test_inverse.py
@@@ -1,51 -1,94 +1,93 @@@
import os.path as op
import numpy as np
-# from numpy.testing import assert_array_almost_equal, assert_equal
+from numpy.testing import assert_array_almost_equal, assert_equal
from ...datasets import sample
+ from ...label import read_label
+ from ...event import read_events
+ from ...epochs import Epochs
from ... import fiff, Covariance, read_forward_solution
-from ..inverse import minimum_norm, apply_inverse, read_inverse_operator, \
- apply_inverse_raw, apply_inverse_epochs
-
+from ..inverse import apply_inverse, read_inverse_operator, \
++ apply_inverse_raw, apply_inverse_epochs, \
+ make_inverse_operator
-
examples_folder = op.join(op.dirname(__file__), '..', '..', '..', 'examples')
data_path = sample.data_path(examples_folder)
fname_inv = op.join(data_path, 'MEG', 'sample',
- 'sample_audvis-meg-oct-6-meg-inv.fif')
+ # 'sample_audvis-meg-eeg-oct-6-meg-eeg-inv.fif')
+ 'sample_audvis-meg-oct-6-meg-inv.fif')
fname_data = op.join(data_path, 'MEG', 'sample',
- 'sample_audvis-ave.fif')
+ 'sample_audvis-ave.fif')
fname_cov = op.join(data_path, 'MEG', 'sample',
- 'sample_audvis-cov.fif')
+ 'sample_audvis-cov.fif')
fname_fwd = op.join(data_path, 'MEG', 'sample',
- 'sample_audvis-meg-eeg-oct-6-fwd.fif')
+ 'sample_audvis-meg-oct-6-fwd.fif')
+ # 'sample_audvis-meg-eeg-oct-6-fwd.fif')
+ fname_raw = op.join(data_path, 'MEG', 'sample',
- 'sample_audvis_filt-0-40_raw.fif')
++ 'sample_audvis_filt-0-40_raw.fif')
+ fname_event = op.join(data_path, 'MEG', 'sample',
- 'sample_audvis_filt-0-40_raw-eve.fif')
++ 'sample_audvis_filt-0-40_raw-eve.fif')
+ label = 'Aud-lh'
+ fname_label = op.join(data_path, 'MEG', 'sample', 'labels', '%s.label' % label)
+ inverse_operator = read_inverse_operator(fname_inv)
+ label = read_label(fname_label)
+ raw = fiff.Raw(fname_raw)
+ snr = 3.0
+ lambda2 = 1.0 / snr ** 2
+ dSPM = True
+def test_inverse_operator():
- """Test MNE inverse computation with precomputed inverse operator."""
- setno = 0
- snr = 3.0
- lambda2 = 1.0 / snr ** 2
- dSPM = True
-
- evoked = fiff.Evoked(fname_data, setno=setno, baseline=(None, 0))
- inverse_operator = read_inverse_operator(fname_inv)
++ """Test MNE inverse computation
-def test_apply_mne_inverse():
- """Test MNE with precomputed inverse operator on Evoked
++ With and without precomputed inverse operator.
+ """
- setno = 0
+ evoked = fiff.Evoked(fname_data, setno=0, baseline=(None, 0))
stc = apply_inverse(evoked, inverse_operator, lambda2, dSPM)
assert np.all(stc.data > 0)
assert np.all(stc.data < 35)
+ # Test MNE inverse computation starting from forward operator
+ noise_cov = Covariance(fname_cov)
+ evoked = fiff.Evoked(fname_data, setno=0, baseline=(None, 0))
+ fwd_op = read_forward_solution(fname_fwd, surf_ori=True)
+ my_inv_op = make_inverse_operator(evoked.info, fwd_op, noise_cov,
+ loose=0.2, depth=0.8)
+
+ my_stc = apply_inverse(evoked, my_inv_op, lambda2, dSPM)
+
+ assert_equal(stc.times, my_stc.times)
+ assert_array_almost_equal(stc.data, my_stc.data, 2)
++
+
+ def test_apply_mne_inverse_raw():
+ """Test MNE with precomputed inverse operator on Raw
+ """
+ stc = apply_inverse_raw(raw, inverse_operator, lambda2, dSPM=True,
+ label=label, start=0, stop=10, nave=1,
+ pick_normal=False)
+ assert np.all(stc.data > 0)
+
+
+ def test_apply_mne_inverse_epochs():
+ """Test MNE with precomputed inverse operator on Epochs
+ """
+ event_id, tmin, tmax = 1, -0.2, 0.5
+
+ picks = fiff.pick_types(raw.info, meg=True, eeg=False, stim=True,
+ ecg=True, eog=True, include=['STI 014'])
+ reject = dict(grad=4000e-13, mag=4e-12, eog=150e-6)
+ flat = dict(grad=1e-15, mag=1e-15)
+
+ events = read_events(fname_event)[:3]
+ epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
+ baseline=(None, 0), reject=reject, flat=flat)
+ stcs = apply_inverse_epochs(epochs, inverse_operator, lambda2, dSPM,
+ label=label)
+
+ assert len(stcs) == 1
+ assert np.all(stcs[0].data > 0)
+ assert np.all(stcs[0].data < 42)
+
-
-def test_compute_minimum_norm():
- """Test MNE inverse computation starting from forward operator
- """
- setno = 0
- noise_cov = Covariance(fname_cov)
- forward = read_forward_solution(fname_fwd)
- evoked = fiff.Evoked(fname_data, setno=setno, baseline=(None, 0))
- whitener = noise_cov.get_whitener(evoked.info, mag_reg=0.1,
- grad_reg=0.1, eeg_reg=0.1, pca=True)
- stc = minimum_norm(evoked, forward, whitener,
- orientation='loose', method='dspm', snr=3, loose=0.2)
-
- assert np.all(stc.data > 0)
- # XXX : test something
--
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