[med-svn] [python-mne] 02/07: Merge tag 'upstream/0.12+dfsg'
Yaroslav Halchenko
debian at onerussian.com
Sun Jul 10 22:22:46 UTC 2016
This is an automated email from the git hooks/post-receive script.
yoh pushed a commit to branch master
in repository python-mne.
commit eae569b0dd7b3bd6351b3a0bdc06d9e875bcf064
Merge: 4abda55 947cbfb
Author: Yaroslav Halchenko <debian at onerussian.com>
Date: Fri May 13 17:38:10 2016 -0400
Merge tag 'upstream/0.12+dfsg'
Upstream version 0.12+dfsg
* tag 'upstream/0.12+dfsg':
Imported Upstream version 0.12+dfsg
.gitignore | 9 +
.mailmap | 3 +
.travis.yml | 10 +-
LICENSE.txt | 4 +-
MANIFEST.in | 1 +
Makefile | 18 +-
README.rst | 27 +-
appveyor.yml | 1 +
circle.yml | 83 ++
dictionary.txt | 273 ++++++-
doc/Makefile | 34 +-
doc/_static/style.css | 107 ++-
doc/_templates/function.rst | 4 +
doc/advanced_setup.rst | 163 ----
doc/cite.rst | 4 +-
doc/cited.rst | 112 +++
doc/conf.py | 166 ++--
doc/contributing.rst | 22 +-
doc/faq.rst | 185 ++++-
doc/getting_started.rst | 376 +++------
doc/git_links.inc | 8 +-
doc/index.rst | 74 +-
doc/{getting_started.rst => install_mne_c.rst} | 173 ++--
doc/install_mne_python.rst | 277 +++++++
doc/manual/appendix/bem_model.rst | 4 +-
doc/manual/appendix/c_EULA.rst | 4 +-
doc/manual/appendix/c_release_notes.rst | 10 +-
doc/manual/c_reference.rst | 53 +-
doc/manual/channel_interpolation.rst | 75 ++
doc/manual/cookbook.rst | 18 +-
doc/manual/datasets_index.rst | 11 +-
doc/manual/decoding.rst | 3 +-
doc/manual/gui/analyze.rst | 2 +-
doc/manual/gui/browse.rst | 4 +-
doc/manual/index.rst | 93 ++-
doc/manual/io.rst | 35 +-
doc/manual/matlab.rst | 11 +-
doc/manual/memory.rst | 9 +-
doc/manual/migrating.rst | 54 ++
doc/manual/pitfalls.rst | 26 +-
doc/manual/preprocessing/maxwell.rst | 76 ++
doc/manual/preprocessing/ssp.rst | 21 +-
doc/manual/sample_dataset.rst | 9 +-
doc/manual/source_localization/covariance.rst | 5 -
doc/manual/source_localization/forward.rst | 12 +-
doc/manual/source_localization/inverse.rst | 84 +-
doc/manual/time_frequency.rst | 10 +-
doc/martinos.rst | 35 +
doc/mne_cpp.rst | 10 +-
doc/python_reference.rst | 85 +-
doc/references.rst | 14 +-
doc/sphinxext/cited_mne.py | 252 ++++++
doc/sphinxext/flow_diagram.py | 2 +-
doc/sphinxext/{commands.py => gen_commands.py} | 23 +-
doc/this_project.inc | 6 +-
doc/tutorials.rst | 196 +++--
doc/tutorials/command_line.rst | 26 +-
doc/tutorials/mne-report.png | Bin 172544 -> 159506 bytes
doc/tutorials/report.rst | 66 +-
doc/tutorials/seven_stories_about_mne.rst | 171 ++++
doc/whats_new.rst | 389 +++++++--
examples/README.txt | 5 +-
.../connectivity/plot_cwt_sensor_connectivity.py | 4 +-
.../plot_mne_inverse_coherence_epochs.py | 5 +-
.../plot_mne_inverse_connectivity_spectrum.py | 5 +-
.../plot_mne_inverse_label_connectivity.py | 5 +-
.../connectivity/plot_mne_inverse_psi_visual.py | 3 +-
examples/connectivity/plot_sensor_connectivity.py | 4 +-
examples/datasets/plot_brainstorm_data.py | 16 +-
examples/datasets/plot_megsim_data.py | 4 +-
examples/datasets/plot_spm_faces_dataset.py | 28 +-
examples/decoding/plot_decoding_csp_eeg.py | 2 +-
examples/decoding/plot_decoding_csp_space.py | 14 +-
.../plot_decoding_spatio_temporal_source.py | 5 +-
.../decoding/plot_decoding_time_generalization.py | 55 --
...plot_decoding_time_generalization_conditions.py | 2 +-
examples/decoding/plot_decoding_xdawn_eeg.py | 2 +-
examples/decoding/plot_ems_filtering.py | 2 +-
examples/decoding/plot_linear_model_patterns.py | 6 +-
examples/forward/plot_bem_contour_mri.py | 27 -
examples/forward/plot_coregistration_transform.py | 33 -
...forward.py => plot_forward_sensitivity_maps.py} | 27 +-
examples/forward/plot_read_forward.py | 67 --
.../plot_compute_mne_inverse_epochs_in_label.py | 5 +-
.../plot_compute_mne_inverse_raw_in_label.py | 3 +-
examples/inverse/plot_covariance_whitening_dspm.py | 116 ++-
examples/inverse/plot_dics_beamformer.py | 3 +-
examples/inverse/plot_dics_source_power.py | 3 +-
examples/inverse/plot_dipole_fit.py | 43 -
examples/inverse/plot_lcmv_beamformer.py | 24 +-
examples/inverse/plot_lcmv_beamformer_volume.py | 16 +-
examples/inverse/plot_make_inverse_operator.py | 84 --
examples/inverse/plot_tf_dics.py | 21 +-
examples/inverse/plot_tf_lcmv.py | 31 +-
examples/io/README.txt | 3 +-
examples/io/plot_objects_from_arrays.py | 15 +-
examples/io/plot_read_and_write_raw_data.py | 2 +-
examples/io/plot_read_epochs.py | 2 +-
examples/io/plot_read_evoked.py | 5 +
examples/plot_compute_mne_inverse.py | 60 --
examples/plot_extract_events_from_raw.py | 41 -
examples/plot_from_raw_to_epochs_to_evoked.py | 77 --
examples/preprocessing/plot_corrmap_detection.py | 76 --
.../preprocessing/plot_define_target_events.py | 2 +-
.../preprocessing/plot_eog_artifact_histogram.py | 2 +-
.../plot_estimate_covariance_matrix_baseline.py | 55 --
.../plot_estimate_covariance_matrix_raw.py | 38 -
examples/preprocessing/plot_find_ecg_artifacts.py | 2 +-
examples/preprocessing/plot_find_eog_artifacts.py | 2 +-
.../preprocessing/plot_movement_compensation.py | 53 ++
examples/preprocessing/plot_rereference_eeg.py | 2 +-
examples/preprocessing/plot_resample.py | 16 +-
examples/preprocessing/plot_run_ica.py | 3 +-
examples/preprocessing/plot_xdawn_denoising.py | 2 +-
examples/realtime/ftclient_rt_compute_psd.py | 4 +-
examples/realtime/plot_compute_rt_average.py | 3 +-
examples/realtime/plot_compute_rt_decoder.py | 2 +-
examples/realtime/rt_feedback_server.py | 2 +-
examples/simulation/plot_simulate_evoked_data.py | 20 +-
examples/simulation/plot_simulate_raw_data.py | 7 +-
examples/stats/plot_cluster_stats_evoked.py | 4 +-
examples/stats/plot_fdr_stats_evoked.py | 2 +-
examples/stats/plot_linear_regression_raw.py | 51 +-
examples/stats/plot_sensor_permutation_test.py | 4 +-
examples/stats/plot_sensor_regression.py | 2 +-
.../plot_compute_raw_data_spectrum.py | 42 +-
.../plot_compute_source_psd_epochs.py | 3 +-
examples/time_frequency/plot_epochs_spectra.py | 45 --
.../plot_source_label_time_frequency.py | 2 +-
.../time_frequency/plot_source_power_spectrum.py | 2 +-
.../plot_source_space_time_frequency.py | 2 +-
examples/time_frequency/plot_stockwell.py | 50 --
examples/time_frequency/plot_temporal_whitening.py | 4 +-
.../plot_time_frequency_multitaper_sensors.py | 55 --
.../time_frequency/plot_time_frequency_sensors.py | 66 --
.../visualization/plot_channel_epochs_image.py | 2 +-
examples/visualization/plot_clickable_image.py | 2 +-
examples/visualization/plot_evoked_delayed_ssp.py | 95 ---
examples/visualization/plot_evoked_erf_erp.py | 51 --
examples/visualization/plot_evoked_topomap.py | 3 +
.../plot_evoked_topomap_delayed_ssp.py | 62 --
examples/visualization/plot_evoked_whitening.py | 2 +-
examples/visualization/plot_meg_eeg_fields_3d.py | 46 --
examples/visualization/plot_meg_sensors.py | 42 +
.../plot_ssp_projs_sensitivity_map.py | 5 +-
examples/visualization/plot_ssp_projs_topomaps.py | 29 -
.../plot_topo_channel_epochs_image.py | 55 --
.../visualization/plot_topo_compare_conditions.py | 3 +-
examples/visualization/plot_topo_customized.py | 8 +-
examples/visualization/plot_topography.py | 31 -
mne/__init__.py | 16 +-
mne/annotations.py | 113 +++
mne/baseline.py | 99 +--
mne/beamformer/_dics.py | 10 +-
mne/beamformer/_lcmv.py | 30 +-
mne/beamformer/tests/test_dics.py | 5 +-
mne/beamformer/tests/test_lcmv.py | 93 +--
mne/bem.py | 211 +++--
mne/channels/channels.py | 181 +++--
.../data/layouts/Vectorview-grad_norm.lout | 103 +++
mne/channels/interpolation.py | 42 +-
mne/channels/layout.py | 93 ++-
mne/channels/montage.py | 151 +++-
mne/channels/tests/test_channels.py | 37 +-
mne/channels/tests/test_interpolation.py | 23 +-
mne/channels/tests/test_layout.py | 78 +-
mne/channels/tests/test_montage.py | 63 +-
mne/chpi.py | 659 ++++++++++------
mne/commands/mne_browse_raw.py | 5 +-
mne/commands/mne_bti2fiff.py | 3 +-
mne/commands/mne_clean_eog_ecg.py | 2 +-
mne/commands/mne_compute_proj_ecg.py | 15 +-
mne/commands/mne_compute_proj_eog.py | 4 +-
mne/commands/mne_coreg.py | 2 +-
mne/commands/mne_freeview_bem_surfaces.py | 2 +-
mne/commands/mne_kit2fiff.py | 2 +-
mne/commands/mne_make_scalp_surfaces.py | 3 +-
mne/commands/mne_maxfilter.py | 2 +-
mne/commands/mne_show_info.py | 34 +
mne/commands/mne_surf2bem.py | 2 +-
mne/commands/tests/test_commands.py | 12 +-
mne/connectivity/spectral.py | 9 +-
mne/cov.py | 389 +++++----
mne/cuda.py | 74 +-
mne/data/coil_def.dat | 29 +-
mne/datasets/__init__.py | 8 +-
mne/datasets/brainstorm/bst_auditory.py | 2 +-
mne/datasets/brainstorm/bst_raw.py | 2 +-
mne/datasets/brainstorm/bst_resting.py | 2 +-
mne/datasets/megsim/megsim.py | 2 +-
mne/datasets/megsim/urls.py | 7 +
mne/datasets/misc/__init__.py | 4 +
mne/datasets/misc/_misc.py | 18 +
mne/datasets/spm_face/__init__.py | 2 +-
mne/datasets/spm_face/spm_data.py | 14 +-
mne/datasets/testing/__init__.py | 2 +-
mne/datasets/utils.py | 181 +++--
mne/decoding/base.py | 10 +-
mne/decoding/csp.py | 10 +-
mne/decoding/ems.py | 19 +-
mne/decoding/tests/test_csp.py | 17 +-
mne/decoding/tests/test_ems.py | 6 +-
mne/decoding/tests/test_time_gen.py | 251 ++++--
mne/decoding/tests/test_transformer.py | 8 +-
mne/decoding/time_gen.py | 868 +++++++++++++--------
mne/decoding/transformer.py | 34 +-
mne/defaults.py | 23 +-
mne/dipole.py | 517 +++++++++---
mne/epochs.py | 665 +++++++++++-----
mne/event.py | 129 ++-
mne/evoked.py | 650 +++++++++------
mne/filter.py | 97 ++-
mne/fixes.py | 95 ++-
mne/forward/__init__.py | 7 +-
mne/forward/_compute_forward.py | 28 +-
mne/forward/_field_interpolation.py | 27 +-
mne/forward/_lead_dots.py | 60 +-
mne/forward/_make_forward.py | 225 +++++-
mne/forward/forward.py | 211 +++--
mne/forward/tests/test_field_interpolation.py | 45 +-
mne/forward/tests/test_forward.py | 29 +-
mne/forward/tests/test_make_forward.py | 260 +++---
mne/gui/__init__.py | 19 +-
mne/gui/_backend.py | 27 +
mne/inverse_sparse/_gamma_map.py | 7 +-
mne/inverse_sparse/mxne_optim.py | 17 +-
mne/inverse_sparse/tests/test_gamma_map.py | 53 +-
mne/inverse_sparse/tests/test_mxne_inverse.py | 2 +-
mne/io/__init__.py | 8 +-
mne/io/array/array.py | 15 +-
mne/io/array/tests/test_array.py | 12 +-
mne/io/base.py | 576 ++++++++------
mne/io/brainvision/brainvision.py | 171 ++--
mne/io/brainvision/tests/test_brainvision.py | 160 ++--
mne/io/bti/bti.py | 137 ++--
mne/io/bti/read.py | 12 -
mne/io/bti/tests/test_bti.py | 88 ++-
mne/io/cnt/__init__.py | 1 +
mne/io/cnt/cnt.py | 371 +++++++++
mne/io/cnt/tests/__init__.py | 0
mne/io/cnt/tests/test_cnt.py | 34 +
mne/io/compensator.py | 3 +-
mne/io/constants.py | 44 +-
mne/io/ctf/ctf.py | 14 +-
mne/io/ctf/eeg.py | 48 +-
mne/io/ctf/info.py | 65 +-
mne/io/ctf/tests/test_ctf.py | 60 +-
mne/io/edf/edf.py | 36 +-
mne/io/edf/tests/test_edf.py | 15 +
mne/io/eeglab/eeglab.py | 240 ++++--
mne/io/eeglab/tests/test_eeglab.py | 53 +-
mne/io/egi/egi.py | 74 +-
mne/io/egi/tests/test_egi.py | 7 +-
mne/io/fiff/__init__.py | 2 +-
mne/io/fiff/raw.py | 77 +-
mne/io/fiff/tests/test_raw_fiff.py | 322 +++++---
mne/io/kit/constants.py | 2 +-
mne/io/kit/kit.py | 138 ++--
mne/io/matrix.py | 15 +-
mne/io/meas_info.py | 226 ++++--
mne/io/nicolet/nicolet.py | 36 +-
mne/io/pick.py | 110 ++-
mne/io/proc_history.py | 4 +-
mne/io/proj.py | 98 ++-
mne/io/reference.py | 30 +-
mne/io/tag.py | 552 ++++++-------
mne/io/tests/test_meas_info.py | 124 ++-
mne/io/tests/test_pick.py | 98 ++-
mne/io/tests/test_proc_history.py | 4 +-
mne/io/tests/test_raw.py | 10 +-
mne/io/tests/test_reference.py | 25 +-
mne/io/utils.py | 80 +-
mne/io/write.py | 4 +-
mne/label.py | 208 +++--
mne/minimum_norm/inverse.py | 38 +-
mne/minimum_norm/tests/test_inverse.py | 16 +-
mne/minimum_norm/tests/test_time_frequency.py | 14 +-
mne/minimum_norm/time_frequency.py | 30 +-
mne/parallel.py | 11 +-
mne/preprocessing/ecg.py | 21 +-
mne/preprocessing/eog.py | 7 +-
mne/preprocessing/ica.py | 252 +++---
mne/preprocessing/infomax_.py | 8 +-
mne/preprocessing/maxfilter.py | 5 +-
mne/preprocessing/maxwell.py | 833 ++++++++++++++------
mne/preprocessing/ssp.py | 6 +-
mne/preprocessing/stim.py | 11 +-
mne/preprocessing/tests/test_ctps.py | 9 +-
mne/preprocessing/tests/test_eeglab_infomax.py | 4 +-
mne/preprocessing/tests/test_ica.py | 52 +-
mne/preprocessing/tests/test_maxwell.py | 318 ++++++--
mne/preprocessing/tests/test_ssp.py | 6 +-
mne/preprocessing/tests/test_xdawn.py | 3 +-
mne/preprocessing/xdawn.py | 6 +-
mne/proj.py | 22 +-
mne/realtime/epochs.py | 4 +-
mne/realtime/fieldtrip_client.py | 23 +-
mne/realtime/tests/test_mockclient.py | 6 +-
mne/report.py | 32 +-
mne/selection.py | 117 +--
mne/simulation/evoked.py | 2 +-
mne/simulation/raw.py | 47 +-
mne/simulation/source.py | 8 +-
mne/simulation/tests/test_raw.py | 54 +-
mne/source_estimate.py | 54 +-
mne/source_space.py | 76 +-
mne/stats/cluster_level.py | 20 +-
mne/stats/parametric.py | 7 +-
mne/stats/regression.py | 121 ++-
mne/stats/tests/test_cluster_level.py | 19 +-
mne/stats/tests/test_regression.py | 21 +-
mne/surface.py | 18 +-
mne/tests/common.py | 93 ++-
mne/tests/test_annotations.py | 58 ++
mne/tests/test_bem.py | 124 ++-
mne/tests/test_chpi.py | 165 ++--
mne/tests/test_cov.py | 133 +++-
mne/tests/test_dipole.py | 173 ++--
mne/tests/test_docstring_parameters.py | 1 +
mne/tests/test_epochs.py | 348 ++++++---
mne/tests/test_event.py | 125 ++-
mne/tests/test_evoked.py | 60 +-
mne/tests/test_filter.py | 17 +-
mne/tests/test_label.py | 85 +-
mne/tests/test_proj.py | 48 +-
mne/tests/test_selection.py | 31 +-
mne/tests/test_source_estimate.py | 7 +-
mne/tests/test_source_space.py | 17 +-
mne/tests/test_surface.py | 8 +-
mne/tests/test_transforms.py | 68 +-
mne/tests/test_utils.py | 125 ++-
mne/time_frequency/__init__.py | 2 +-
mne/time_frequency/_stockwell.py | 9 +-
mne/time_frequency/csd.py | 13 +-
mne/time_frequency/multitaper.py | 175 +++--
mne/time_frequency/psd.py | 283 ++++++-
mne/time_frequency/tests/test_ar.py | 2 +-
mne/time_frequency/tests/test_multitaper.py | 17 +-
mne/time_frequency/tests/test_psd.py | 217 +++---
mne/time_frequency/tests/test_stockwell.py | 18 +-
mne/time_frequency/tests/test_tfr.py | 92 ++-
mne/time_frequency/tfr.py | 323 ++++----
mne/transforms.py | 127 +++
mne/utils.py | 388 +++++++--
mne/viz/_3d.py | 189 +++--
mne/viz/__init__.py | 7 +-
mne/viz/circle.py | 4 +-
mne/viz/decoding.py | 12 +-
mne/viz/epochs.py | 163 ++--
mne/viz/evoked.py | 398 ++++++++--
mne/viz/ica.py | 30 +-
mne/viz/misc.py | 17 +-
mne/viz/raw.py | 177 +++--
mne/viz/tests/test_3d.py | 53 +-
mne/viz/tests/test_decoding.py | 3 +-
mne/viz/tests/test_epochs.py | 30 +-
mne/viz/tests/test_evoked.py | 14 +-
mne/viz/tests/test_ica.py | 32 +-
mne/viz/tests/test_misc.py | 5 +-
mne/viz/tests/test_raw.py | 39 +-
mne/viz/tests/test_topo.py | 39 +-
mne/viz/tests/test_topomap.py | 29 +-
mne/viz/tests/test_utils.py | 34 +-
mne/viz/topo.py | 479 ++++++++----
mne/viz/topomap.py | 595 ++++++++++----
mne/viz/utils.py | 295 ++++++-
setup.cfg | 2 +-
setup.py | 4 +
tutorials/plot_artifacts_correction_filtering.py | 98 +++
tutorials/plot_artifacts_correction_ica.py | 201 +++++
.../plot_artifacts_correction_maxwell_filtering.py | 28 +-
tutorials/plot_artifacts_correction_rejection.py | 197 +++++
tutorials/plot_artifacts_correction_ssp.py | 88 +++
tutorials/plot_artifacts_detection.py | 134 ++++
tutorials/plot_brainstorm_auditory.py | 357 +++++++++
tutorials/plot_compute_covariance.py | 138 ++++
tutorials/plot_creating_data_structures.py | 19 +-
tutorials/plot_dipole_fit.py | 85 ++
tutorials/plot_eeg_erp.py | 191 +++++
tutorials/plot_epoching_and_averaging.py | 158 ++++
tutorials/plot_epochs_to_data_frame.py | 8 +-
tutorials/plot_forward.py | 181 +++++
tutorials/plot_ica_from_raw.py | 7 +-
tutorials/plot_info.py | 22 +-
tutorials/plot_introduction.py | 38 +-
...ics.py => plot_mne_dspm_source_localization.py} | 73 +-
tutorials/plot_modifying_data_inplace.py | 2 +-
...lot_epochs_objects.py => plot_object_epochs.py} | 68 +-
tutorials/plot_object_evoked.py | 74 ++
.../{plot_raw_objects.py => plot_object_raw.py} | 43 +-
tutorials/plot_python_intro.py | 46 ++
.../plot_sensors_decoding.py | 60 +-
tutorials/plot_sensors_time_frequency.py | 133 ++++
...lot_stats_cluster_1samp_test_time_frequency.py} | 5 +-
...s_tutorial.py => plot_stats_cluster_methods.py} | 35 +-
...al.py => plot_stats_cluster_spatio_temporal.py} | 58 +-
...=> plot_stats_cluster_spatio_temporal_2samp.py} | 13 +-
...ter_spatio_temporal_repeated_measures_anova.py} | 94 ++-
...ncy.py => plot_stats_cluster_time_frequency.py} | 4 +-
...ster_time_frequency_repeated_measures_anova.py} | 84 +-
... plot_stats_spatio_temporal_cluster_sensors.py} | 39 +-
tutorials/plot_visualize_epochs.py | 54 ++
tutorials/plot_visualize_evoked.py | 158 ++++
tutorials/plot_visualize_raw.py | 92 +++
404 files changed, 20096 insertions(+), 8931 deletions(-)
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