[med-svn] [python-mne] 355/376: Merge branch 'master' into label_tfr

[Yaroslav Halchenko]

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yoh pushed a commit to annotated tag v0.1
in repository python-mne.

commit 1d4a117a74487348df81b07fcc8fcd30d02dbe42
Merge: eb91264 234b9d9
Author: Alexandre Gramfort <alexandre.gramfort at inria.fr>
Date:   Thu Sep 15 16:51:59 2011 -0400

    Merge branch 'master' into label_tfr
    
    Conflicts:
    	mne/minimum_norm/__init__.py
    	mne/minimum_norm/inverse.py
    	mne/minimum_norm/tests/test_time_frequency.py

 Makefile                                           |   5 +-
 doc/source/getting_started.rst                     |  47 +-
 doc/source/getting_started_at_martinos.rst         |  31 --
 doc/source/gitwash/index.rst                       |   6 +-
 doc/source/index.rst                               |  33 +-
 examples/inverse/plot_compute_mne_inverse.py       |   2 +-
 .../plot_compute_mne_inverse_epochs_in_label.py    |  65 +++
 .../plot_compute_mne_inverse_raw_in_label.py       |   2 +-
 examples/inverse/plot_label_source_activations.py  |   2 +-
 examples/inverse/plot_make_inverse_operator.py     |  53 ++
 .../plot_compute_raw_data_spectrum.py              |  55 ++
 mne/__init__.py                                    |   1 +
 mne/artifacts/tests/test_ecg.py                    |   3 +-
 mne/artifacts/tests/test_eog.py                    |   3 +-
 mne/cov.py                                         | 237 +++-----
 mne/fiff/meas_info.py                              |  84 ++-
 mne/fiff/raw.py                                    | 142 ++---
 mne/fiff/tag.py                                    |   2 +-
 mne/fiff/tests/test_proj.py                        |   9 +-
 mne/fiff/tests/test_raw.py                         |  16 +
 mne/fiff/write.py                                  |   2 +-
 mne/forward.py                                     | 101 ++--
 mne/minimum_norm/__init__.py                       |   4 +-
 mne/minimum_norm/inverse.py                        | 594 +++++++++++----------
 mne/minimum_norm/tests/test_inverse.py             | 104 ++--
 mne/minimum_norm/tests/test_time_frequency.py      |  15 +-
 mne/source_estimate.py                             |   1 -
 mne/stats/cluster_level.py                         |   6 +-
 mne/stats/tests/test_cluster_level.py              |   5 +-
 mne/tests/test_cov.py                              |  38 +-
 mne/tests/test_epochs.py                           |   9 +-
 mne/tests/test_label.py                            |   5 +-
 mne/tests/test_misc.py                             |   3 +-
 mne/tests/test_source_estimate.py                  |   3 +-
 mne/tests/test_source_space.py                     |  17 +-
 mne/time_frequency/__init__.py                     |   1 +
 mne/time_frequency/psd.py                          |  70 +++
 mne/time_frequency/tests/test_psd.py               |  34 ++
 mne/time_frequency/tests/test_tfr.py               |  19 +-
 mne/transforms.py                                  | 109 +++-
 40 files changed, 1148 insertions(+), 790 deletions(-)

diff --cc mne/minimum_norm/__init__.py
index dbf8766,fe3d453..e9dbf7e
--- a/mne/minimum_norm/__init__.py
+++ b/mne/minimum_norm/__init__.py
@@@ -1,3 -1,3 +1,3 @@@
- from .inverse import read_inverse_operator, apply_inverse, minimum_norm, \
-                      apply_inverse_raw
+ from .inverse import read_inverse_operator, apply_inverse, \
+                      apply_inverse_raw, make_inverse_operator
 -from .time_frequency import source_induced_power
 +from .time_frequency import source_band_induced_power, source_induced_power
diff --cc mne/minimum_norm/tests/test_time_frequency.py
index 3059af8,b5fd78f..550e494
--- a/mne/minimum_norm/tests/test_time_frequency.py
+++ b/mne/minimum_norm/tests/test_time_frequency.py
@@@ -1,7 -1,8 +1,8 @@@
  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
+ from nose.tools import assert_true
  
  from ...datasets import sample
  from ... import fiff, find_events, Epochs
@@@ -34,28 -33,27 +35,28 @@@ def test_tfr_with_inverse_operator()
  
      # picks MEG gradiometers
      picks = fiff.pick_types(raw.info, meg=True, eeg=False, eog=True,
--                                    stim=False, include=include, exclude=exclude)
++                                stim=False, include=include, exclude=exclude)
  
      # Load condition 1
      event_id = 1
      events = events[:3]  # take 3 events to keep the computation time low
      epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
--                        baseline=(None, 0), reject=dict(grad=4000e-13, eog=150e-6),
--                        preload=True)
++                    baseline=(None, 0), reject=dict(grad=4000e-13, eog=150e-6),
++                    preload=True)
  
      # Compute a source estimate per frequency band
      bands = dict(alpha=[10, 10])
 +    label = read_label(fname_label)
  
-     stcs = source_band_induced_power(epochs, inverse_operator, bands, n_cycles=2,
-                                 use_fft=False, pca=True, label=label)
 -    stcs = source_induced_power(epochs, inverse_operator, bands, n_cycles=2,
 -                                use_fft=False, pca=True)
++    stcs = source_band_induced_power(epochs, inverse_operator, bands,
++                            n_cycles=2, use_fft=False, pca=True, label=label)
  
      stc = stcs['alpha']
-     assert len(stcs) == len(bands.keys())
-     assert np.all(stc.data > 0)
+     assert_true(len(stcs) == len(bands.keys()))
+     assert_true(np.all(stc.data > 0))
      assert_array_almost_equal(stc.times, epochs.times)
  
 -    stcs_no_pca = source_induced_power(epochs, inverse_operator, bands, n_cycles=2,
 -                                use_fft=False, pca=False)
 +    stcs_no_pca = source_band_induced_power(epochs, inverse_operator, bands,
 +                            n_cycles=2, use_fft=False, pca=False, label=label)
  
      assert_array_almost_equal(stcs['alpha'].data, stcs_no_pca['alpha'].data)

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