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commit 49b5fe94b367827896ec537b1edfa3e1f6637fdb Author: Alexandre Gramfort <[email protected]> Date: Mon Jun 6 09:51:09 2011 -0400 ENH : adding option for nb smoothing iter in morphing --- mne/source_estimate.py | 20 ++++++++++++++------ mne/tests/test_source_estimate.py | 3 ++- 2 files changed, 16 insertions(+), 7 deletions(-) diff --git a/mne/source_estimate.py b/mne/source_estimate.py index ef52ccd..02e61ad 100644 --- a/mne/source_estimate.py +++ b/mne/source_estimate.py @@ -274,7 +274,7 @@ def mesh_edges(tris): return edges -def morph_data(subject_from, subject_to, stc_from, grade=5, +def morph_data(subject_from, subject_to, stc_from, grade=5, smooth=None, subjects_dir=None): """Morph a source estimate from one subject to another @@ -290,6 +290,10 @@ def morph_data(subject_from, subject_to, stc_from, grade=5, Source estimates for subject "from" to morph grade : int Resolution of the icosahedral mesh (typically 5) + smooth : int or None + Number of iterations for the smoothing of the surface data. + If None, smooth is automatically defined to fill the surface + with non-zero values. subjects_dir : string Path to SUBJECTS_DIR is not set in the environment @@ -336,13 +340,17 @@ def morph_data(subject_from, subject_to, stc_from, grade=5, data1 = e_use * np.ones(len(idx_use)) data[hemi] = e_use * data[hemi] idx_use = np.where(data1)[0] - if (k == (n_iter - 1)) or (len(idx_use) >= n_vertices): - data[hemi][idx_use, :] /= data1[idx_use][:, None] + if smooth is None: + if ((k == (n_iter - 1)) or (len(idx_use) >= n_vertices)): + # stop when source space in filled with non-zeros + break + elif k == (smooth - 1): break - else: - data[hemi] = data[hemi][idx_use, :] / data1[idx_use][:, None] + data[hemi] = data[hemi][idx_use, :] / data1[idx_use][:, None] - print '\t%d smooth iterations done.' % k + data[hemi][idx_use, :] /= data1[idx_use][:, None] + + print '\t%d smooth iterations done.' % (k + 1) dmap[hemi] = maps[hemi] * data[hemi] ico_file_name = os.path.join(os.environ['MNE_ROOT'], 'share', 'mne', diff --git a/mne/tests/test_source_estimate.py b/mne/tests/test_source_estimate.py index 586f04b..a84eb30 100644 --- a/mne/tests/test_source_estimate.py +++ b/mne/tests/test_source_estimate.py @@ -34,7 +34,8 @@ def test_morph_data(): subject_to = 'morph' fname = op.join(data_path, 'MEG', 'sample', 'sample_audvis-meg') stc_from = mne.SourceEstimate(fname) - stc_to = mne.morph_data(subject_from, subject_to, stc_from, 3) + stc_to = mne.morph_data(subject_from, subject_to, stc_from, + grade=3, smooth=12) stc_to.save('%s_audvis-meg' % subject_to) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-mne.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
