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commit 3569d70e3baaccbf49cfdcaa1c7aa0ab3ba49862 Author: Alexandre Gramfort <[email protected]> Date: Fri Sep 16 16:21:56 2011 -0400 ENH : fix for new sample dataset --- examples/inverse/plot_morph_data.py | 6 ++-- examples/plot_whitened_evoked_data.py | 61 ----------------------------------- mne/minimum_norm/__init__.py | 3 +- mne/tests/test_source_estimate.py | 3 +- mne/tests/test_source_space.py | 2 +- 5 files changed, 7 insertions(+), 68 deletions(-) diff --git a/examples/inverse/plot_morph_data.py b/examples/inverse/plot_morph_data.py index 63f9f67..749018f 100644 --- a/examples/inverse/plot_morph_data.py +++ b/examples/inverse/plot_morph_data.py @@ -4,8 +4,8 @@ Morph source estimates from one subject to another subject ========================================================== A source estimate from a given subject 'sample' is morphed -to the anatomy of another subject 'morph'. The output -is a source estimate defined on the anatomy of 'morph' +to the anatomy of another subject 'fsaverage'. The output +is a source estimate defined on the anatomy of 'fsaverage' """ # Author: Alexandre Gramfort <[email protected]> @@ -20,7 +20,7 @@ from mne.datasets import sample data_path = sample.data_path('..') subject_from = 'sample' -subject_to = 'morph' +subject_to = 'fsaverage' fname = data_path + '/MEG/sample/sample_audvis-meg' src_fname = data_path + '/MEG/sample/sample_audvis-meg-oct-6-fwd.fif' diff --git a/examples/plot_whitened_evoked_data.py b/examples/plot_whitened_evoked_data.py deleted file mode 100644 index dff4394..0000000 --- a/examples/plot_whitened_evoked_data.py +++ /dev/null @@ -1,61 +0,0 @@ -""" -================================================== -Whiten evoked data using a noise covariance matrix -================================================== - -""" -# Author: Alexandre Gramfort <[email protected]> -# -# License: BSD (3-clause) - -print __doc__ - -import numpy as np -import mne -from mne import fiff -from mne.datasets import sample - -data_path = sample.data_path('.') -raw_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw.fif' -# raw_fname = data_path + '/MEG/sample/sample_audvis_raw.fif' -cov_fname = data_path + '/MEG/sample/sample_audvis-cov.fif' - -############################################################################### -# Set epochs parameters -event_id = 1 -tmin = -0.2 -tmax = 0.5 - -############################################################################### -# Create evoked data - -# Setup for reading the raw data -raw = fiff.Raw(raw_fname) -events = mne.find_events(raw) - -# pick EEG channels - bad channels (modify to your needs) -exclude = raw.info['bads'] + ['EEG 053'] # bads + 1 more -picks = fiff.pick_types(raw.info, meg=False, eeg=True, stim=False, eog=True, - exclude=exclude) -epochs = mne.Epochs(raw, events, event_id, tmin, tmax, picks=picks, - baseline=(None, 0), reject=dict(eeg=80e-6, eog=150e-6)) -evoked = epochs.average() # average epochs and get an Evoked dataset. - -cov = mne.Covariance(cov_fname) - -# Whiten data -whitener = cov.get_whitener(evoked.info, pca=False) # get whitening matrix -sel = mne.fiff.pick_channels(evoked.ch_names, include=whitener.ch_names) -whitened_data = np.dot(whitener.W, evoked.data[sel]) # apply whitening - -############################################################################### -# Show result -times = 1e3 * epochs.times # in ms -import pylab as pl -pl.clf() -pl.plot(times, whitened_data.T) -pl.xlim([times[0], times[-1]]) -pl.xlabel('time (ms)') -pl.ylabel('data (NA)') -pl.title('Whitened EEG data') -pl.show() diff --git a/mne/minimum_norm/__init__.py b/mne/minimum_norm/__init__.py index fe3d453..6a22998 100644 --- a/mne/minimum_norm/__init__.py +++ b/mne/minimum_norm/__init__.py @@ -1,3 +1,4 @@ from .inverse import read_inverse_operator, apply_inverse, \ - apply_inverse_raw, make_inverse_operator + apply_inverse_raw, make_inverse_operator, \ + apply_inverse_epochs from .time_frequency import source_induced_power diff --git a/mne/tests/test_source_estimate.py b/mne/tests/test_source_estimate.py index 46e7623..e24eed0 100644 --- a/mne/tests/test_source_estimate.py +++ b/mne/tests/test_source_estimate.py @@ -35,7 +35,7 @@ def test_morph_data(): """Test morphing of data """ subject_from = 'sample' - subject_to = 'morph' + subject_to = 'fsaverage' fname = op.join(data_path, 'MEG', 'sample', 'sample_audvis-meg') stc_from = SourceEstimate(fname) stc_to = morph_data(subject_from, subject_to, stc_from, @@ -67,4 +67,3 @@ def test_spatio_temporal_src_connectivity(): src[1]['use_tris'] = np.array([[0, 1, 2]]) connectivity2 = spatio_temporal_src_connectivity(src, 2) assert_array_equal(connectivity.todense(), connectivity2.todense()) - diff --git a/mne/tests/test_source_space.py b/mne/tests/test_source_space.py index 1213352..7f51e88 100644 --- a/mne/tests/test_source_space.py +++ b/mne/tests/test_source_space.py @@ -29,4 +29,4 @@ def test_read_source_spaces(): assert_true(rh_faces.min() == 0) assert_true(rh_faces.max() == rh_points.shape[0] - 1) assert_true(rh_use_faces.min() >= 0) - assert_true(rh_use_faces.max() <= lh_points.shape[0] - 1) + assert_true(rh_use_faces.max() <= rh_points.shape[0] - 1) -- 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
