[med-svn] [python-mne] branch upstream updated (88d4b22 -> 4efa94e)
Andreas Tille
tille at debian.org
Wed Jan 25 08:58:43 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository python-mne.
from 88d4b22 Imported Upstream version 0.11+dfsg
new 4efa94e New upstream version 0.13.1+dfsg
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.coveragerc | 1 +
.gitignore | 9 +
.mailmap | 12 +
.travis.yml | 39 +-
LICENSE.txt | 4 +-
MANIFEST.in | 1 +
Makefile | 17 +-
README.rst | 111 +-
appveyor.yml | 31 +-
circle.yml | 141 ++
codecov.yml | 14 +
dictionary.txt | 273 ++-
doc/Makefile | 39 +-
doc/_static/style.css | 110 +-
doc/_templates/class.rst | 2 +-
doc/_templates/function.rst | 4 +
doc/advanced_setup.rst | 163 --
doc/cite.rst | 6 +-
doc/cited.rst | 112 ++
doc/conf.py | 181 +-
doc/contributing.rst | 368 ++--
doc/faq.rst | 184 +-
doc/getting_started.rst | 376 +----
doc/git_links.inc | 8 +-
doc/index.rst | 79 +-
doc/{getting_started.rst => install_mne_c.rst} | 173 +-
doc/install_mne_python.rst | 277 +++
doc/manual/appendix/bem_model.rst | 14 +-
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 | 20 +-
doc/manual/datasets_index.rst | 11 +-
doc/manual/decoding.rst | 7 +-
doc/manual/gui/analyze.rst | 2 +-
doc/manual/gui/browse.rst | 4 +-
doc/manual/index.rst | 93 +-
doc/manual/io.rst | 59 +-
doc/manual/matlab.rst | 11 +-
doc/manual/memory.rst | 9 +-
doc/manual/migrating.rst | 54 +
doc/manual/pitfalls.rst | 29 +-
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 | 119 +-
doc/references.rst | 14 +-
doc/sphinxext/cited_mne.py | 252 +++
doc/sphinxext/flow_diagram.py | 2 +-
doc/sphinxext/{commands.py => gen_commands.py} | 34 +-
doc/sphinxext/numpy_ext/docscrape.py | 512 ------
doc/sphinxext/numpy_ext/docscrape_sphinx.py | 240 ---
doc/sphinxext/numpy_ext/numpydoc.py | 192 ---
doc/this_project.inc | 6 +-
doc/tutorials.rst | 212 ++-
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 | 658 +++++++-
examples/README.txt | 5 +-
.../connectivity/plot_cwt_sensor_connectivity.py | 4 +-
.../plot_mne_inverse_coherence_epochs.py | 9 +-
.../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_megsim_data_single_trial.py | 4 +-
examples/datasets/plot_spm_faces_dataset.py | 37 +-
examples/decoding/plot_decoding_csp_eeg.py | 2 +-
examples/decoding/plot_decoding_csp_space.py | 14 +-
examples/decoding/plot_decoding_sensors.py | 62 -
.../plot_decoding_spatio_temporal_source.py | 10 +-
.../decoding/plot_decoding_time_generalization.py | 55 -
...plot_decoding_time_generalization_conditions.py | 10 +-
.../plot_decoding_unsupervised_spatial_filter.py | 67 +
examples/decoding/plot_decoding_xdawn_eeg.py | 6 +-
examples/decoding/plot_ems_filtering.py | 106 +-
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 | 4 +-
examples/inverse/plot_covariance_whitening_dspm.py | 116 +-
examples/inverse/plot_dics_beamformer.py | 17 +-
examples/inverse/plot_dics_source_power.py | 15 +-
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_morph_data.py | 1 -
examples/inverse/plot_tf_dics.py | 31 +-
examples/inverse/plot_tf_lcmv.py | 31 +-
.../plot_time_frequency_mixed_norm_inverse.py | 7 +-
examples/io/README.txt | 3 +-
examples/io/plot_elekta_epochs.py | 68 +
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 | 23 +-
examples/preprocessing/plot_xdawn_denoising.py | 7 +-
examples/realtime/ftclient_rt_average.py | 3 +-
examples/realtime/ftclient_rt_compute_psd.py | 4 +-
examples/realtime/plot_compute_rt_average.py | 5 +-
examples/realtime/plot_compute_rt_decoder.py | 6 +-
examples/realtime/rt_feedback_server.py | 8 +-
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 +-
examples/time_frequency/README.txt | 3 +-
.../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 | 12 +-
.../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 -
make/install_python.ps1 | 93 --
mne/__init__.py | 25 +-
mne/annotations.py | 132 ++
mne/baseline.py | 133 +-
mne/beamformer/_dics.py | 26 +-
mne/beamformer/_lcmv.py | 32 +-
mne/beamformer/tests/test_dics.py | 51 +-
mne/beamformer/tests/test_lcmv.py | 101 +-
mne/bem.py | 335 +++-
mne/channels/channels.py | 354 +++-
mne/channels/data/layouts/KIT-UMD-3.lout | 158 ++
.../data/layouts/Vectorview-grad_norm.lout | 103 ++
mne/channels/data/neighbors/KIT-UMD-1_neighb.mat | Bin 0 -> 4750 bytes
mne/channels/data/neighbors/KIT-UMD-2_neighb.mat | Bin 0 -> 4832 bytes
mne/channels/data/neighbors/KIT-UMD-3_neighb.mat | Bin 0 -> 4794 bytes
mne/channels/data/neighbors/__init__.py | 3 +
mne/channels/interpolation.py | 49 +-
mne/channels/layout.py | 163 +-
mne/channels/montage.py | 315 +++-
mne/channels/tests/test_channels.py | 67 +-
mne/channels/tests/test_interpolation.py | 33 +-
mne/channels/tests/test_layout.py | 161 +-
mne/channels/tests/test_montage.py | 164 +-
mne/chpi.py | 750 +++++----
mne/commands/mne_browse_raw.py | 15 +-
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 | 22 +-
mne/commands/mne_flash_bem.py | 6 +-
mne/commands/mne_freeview_bem_surfaces.py | 2 +-
mne/commands/mne_kit2fiff.py | 8 +-
mne/commands/mne_make_scalp_surfaces.py | 23 +-
mne/commands/mne_maxfilter.py | 2 +-
mne/commands/mne_show_fiff.py | 6 +
mne/commands/mne_show_info.py | 34 +
mne/commands/mne_surf2bem.py | 2 +-
mne/commands/tests/test_commands.py | 54 +-
mne/connectivity/spectral.py | 22 +-
mne/connectivity/tests/test_spectral.py | 51 +-
mne/coreg.py | 168 +-
mne/cov.py | 576 ++++---
mne/cuda.py | 77 +-
mne/data/coil_def.dat | 44 +-
mne/data/mne_analyze.sel | 8 +-
mne/datasets/__init__.py | 9 +-
mne/datasets/brainstorm/__init__.py | 3 +-
mne/datasets/brainstorm/bst_auditory.py | 5 +-
.../{bst_resting.py => bst_phantom_ctf.py} | 19 +-
.../{bst_resting.py => bst_phantom_elekta.py} | 20 +-
mne/datasets/brainstorm/bst_raw.py | 5 +-
mne/datasets/brainstorm/bst_resting.py | 5 +-
mne/datasets/megsim/megsim.py | 2 +-
mne/datasets/megsim/urls.py | 9 +-
mne/datasets/misc/__init__.py | 4 +
mne/datasets/misc/_misc.py | 18 +
mne/datasets/multimodal/__init__.py | 4 +
.../{somato/somato.py => multimodal/multimodal.py} | 15 +-
mne/datasets/sample/sample.py | 3 +-
mne/datasets/somato/somato.py | 3 +-
mne/datasets/spm_face/__init__.py | 2 +-
mne/datasets/spm_face/spm_data.py | 17 +-
mne/datasets/testing/__init__.py | 2 +-
mne/datasets/testing/_testing.py | 3 +-
mne/datasets/tests/test_datasets.py | 10 +
mne/datasets/utils.py | 203 ++-
mne/decoding/__init__.py | 6 +-
mne/decoding/base.py | 124 +-
mne/decoding/csp.py | 395 +++--
mne/decoding/ems.py | 140 +-
mne/decoding/search_light.py | 629 +++++++
mne/decoding/tests/test_csp.py | 141 +-
mne/decoding/tests/test_ems.py | 50 +-
mne/decoding/tests/test_search_light.py | 170 ++
mne/decoding/tests/test_time_frequency.py | 41 +
mne/decoding/tests/test_time_gen.py | 266 ++-
mne/decoding/tests/test_transformer.py | 141 +-
mne/decoding/time_frequency.py | 152 ++
mne/decoding/time_gen.py | 887 ++++++----
mne/decoding/transformer.py | 397 ++++-
mne/defaults.py | 40 +-
mne/dipole.py | 733 ++++++--
mne/epochs.py | 1193 ++++++-------
mne/event.py | 681 +++++++-
mne/evoked.py | 1103 ++++++------
mne/externals/h5io/_h5io.py | 186 ++-
mne/externals/tempita/__init__.py | 1305 +--------------
mne/externals/tempita/{__init__.py => _tempita.py} | 369 ++--
mne/externals/tempita/compat3.py | 20 +-
mne/filter.py | 1741 +++++++++++++------
mne/fixes.py | 1182 ++++---------
mne/forward/__init__.py | 9 +-
mne/forward/_compute_forward.py | 30 +-
mne/forward/_field_interpolation.py | 32 +-
mne/forward/_lead_dots.py | 60 +-
mne/forward/_make_forward.py | 224 ++-
mne/forward/forward.py | 175 +-
mne/forward/tests/test_field_interpolation.py | 59 +-
mne/forward/tests/test_forward.py | 34 +-
mne/forward/tests/test_make_forward.py | 265 +--
mne/gui/__init__.py | 21 +-
mne/gui/_backend.py | 27 +
mne/gui/_coreg_gui.py | 214 ++-
mne/gui/_fiducials_gui.py | 53 +-
mne/gui/_file_traits.py | 97 +-
mne/gui/_kit2fiff_gui.py | 277 ++-
mne/gui/help/kit2fiff.json | 5 +-
mne/gui/tests/test_coreg_gui.py | 73 +-
mne/gui/tests/test_fiducials_gui.py | 2 +-
mne/gui/tests/test_file_traits.py | 6 +-
mne/gui/tests/test_kit2fiff_gui.py | 18 +-
mne/inverse_sparse/_gamma_map.py | 7 +-
mne/inverse_sparse/mxne_inverse.py | 2 +-
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 | 9 +-
mne/io/array/array.py | 15 +-
mne/io/array/tests/test_array.py | 54 +-
mne/io/base.py | 1254 +++++++-------
mne/io/brainvision/brainvision.py | 418 +++--
mne/io/brainvision/tests/data/test.vhdr | 24 +-
.../{test_highpass.vhdr => test_highpass_hz.vhdr} | 41 +-
.../{test_highpass.vhdr => test_lowpass_s.vhdr} | 105 +-
...test_highpass.vhdr => test_mixed_highpass.vhdr} | 41 +-
...t_highpass.vhdr => test_mixed_highpass_hz.vhdr} | 43 +-
...{test_highpass.vhdr => test_mixed_lowpass.vhdr} | 41 +-
...est_highpass.vhdr => test_mixed_lowpass_s.vhdr} | 105 +-
.../test_old_layout_latin1_software_filter.eeg | Bin 0 -> 29116 bytes
.../test_old_layout_latin1_software_filter.vhdr | 156 ++
.../test_old_layout_latin1_software_filter.vmrk | 14 +
...vhdr => test_partially_disabled_hw_filter.vhdr} | 63 +-
mne/io/brainvision/tests/test_brainvision.py | 354 +++-
mne/io/bti/bti.py | 136 +-
mne/io/bti/read.py | 12 -
mne/io/bti/tests/test_bti.py | 84 +-
mne/io/cnt/__init__.py | 1 +
mne/io/cnt/cnt.py | 419 +++++
.../numpy_ext => mne/io/cnt/tests}/__init__.py | 0
mne/io/cnt/tests/test_cnt.py | 35 +
mne/io/compensator.py | 40 +-
mne/io/constants.py | 153 +-
mne/io/ctf/ctf.py | 14 +-
mne/io/ctf/eeg.py | 48 +-
mne/io/ctf/info.py | 85 +-
mne/io/ctf/tests/test_ctf.py | 61 +-
mne/io/edf/edf.py | 53 +-
mne/io/edf/tests/test_edf.py | 63 +-
mne/io/eeglab/eeglab.py | 308 +++-
mne/io/eeglab/tests/test_eeglab.py | 92 +-
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 | 221 ++-
mne/io/fiff/tests/test_raw_fiff.py | 847 ++++++----
mne/io/kit/constants.py | 63 +-
mne/io/kit/coreg.py | 7 +-
mne/io/kit/kit.py | 232 +--
mne/io/kit/tests/data/test.elp | 37 +
mne/io/kit/tests/data/test.hsp | 514 ++++++
mne/io/kit/tests/data/test_umd-raw.sqd | Bin 0 -> 99692 bytes
mne/io/kit/tests/test_coreg.py | 15 +
mne/io/kit/tests/test_kit.py | 88 +-
mne/io/matrix.py | 15 +-
mne/io/meas_info.py | 343 +++-
mne/io/nicolet/nicolet.py | 36 +-
mne/io/open.py | 20 +-
mne/io/pick.py | 139 +-
mne/io/proc_history.py | 4 +-
mne/io/proj.py | 119 +-
mne/io/reference.py | 81 +-
mne/io/tag.py | 552 +++---
mne/io/tests/data/test-ave-2.log | 6 +-
mne/io/tests/data/test-ave.log | 3 +-
mne/io/tests/test_compensator.py | 56 +-
mne/io/tests/test_meas_info.py | 201 ++-
mne/io/tests/test_pick.py | 121 +-
mne/io/tests/test_proc_history.py | 15 +-
mne/io/tests/test_raw.py | 22 +-
mne/io/tests/test_reference.py | 137 +-
mne/io/utils.py | 80 +-
mne/io/write.py | 17 +-
mne/label.py | 279 +++-
mne/minimum_norm/inverse.py | 38 +-
mne/minimum_norm/tests/test_inverse.py | 46 +-
mne/minimum_norm/tests/test_time_frequency.py | 31 +-
mne/minimum_norm/time_frequency.py | 38 +-
mne/parallel.py | 11 +-
mne/preprocessing/__init__.py | 2 +-
mne/preprocessing/_fine_cal.py | 84 +
mne/preprocessing/ecg.py | 79 +-
mne/preprocessing/eog.py | 22 +-
mne/preprocessing/ica.py | 637 ++++---
mne/preprocessing/infomax_.py | 131 +-
mne/preprocessing/maxfilter.py | 9 +-
mne/preprocessing/maxwell.py | 1054 ++++++++----
mne/preprocessing/ssp.py | 13 +-
mne/preprocessing/stim.py | 11 +-
mne/preprocessing/tests/test_ctps.py | 9 +-
mne/preprocessing/tests/test_ecg.py | 24 +-
mne/preprocessing/tests/test_eeglab_infomax.py | 285 ++--
mne/preprocessing/tests/test_eog.py | 6 +-
mne/preprocessing/tests/test_fine_cal.py | 40 +
mne/preprocessing/tests/test_ica.py | 192 ++-
mne/preprocessing/tests/test_infomax.py | 40 +-
mne/preprocessing/tests/test_maxwell.py | 550 ++++--
mne/preprocessing/tests/test_ssp.py | 28 +-
mne/preprocessing/tests/test_stim.py | 13 +-
mne/preprocessing/tests/test_xdawn.py | 203 ++-
mne/preprocessing/xdawn.py | 647 ++++---
mne/proj.py | 26 +-
mne/realtime/epochs.py | 19 +-
mne/realtime/fieldtrip_client.py | 25 +-
mne/realtime/stim_server_client.py | 8 +-
mne/realtime/tests/test_fieldtrip_client.py | 3 +
mne/realtime/tests/test_mockclient.py | 24 +-
mne/realtime/tests/test_stim_client_server.py | 4 +-
mne/report.py | 70 +-
mne/selection.py | 191 ++-
mne/simulation/evoked.py | 27 +-
mne/simulation/raw.py | 55 +-
mne/simulation/source.py | 153 +-
mne/simulation/tests/test_evoked.py | 28 +-
mne/simulation/tests/test_raw.py | 118 +-
mne/simulation/tests/test_source.py | 59 +-
mne/source_estimate.py | 292 ++--
mne/source_space.py | 145 +-
mne/stats/cluster_level.py | 37 +-
mne/stats/parametric.py | 22 +-
mne/stats/regression.py | 124 +-
mne/stats/tests/test_cluster_level.py | 27 +-
mne/stats/tests/test_regression.py | 32 +-
mne/surface.py | 177 +-
mne/tests/common.py | 93 +-
mne/tests/test_annotations.py | 67 +
mne/tests/test_bem.py | 170 +-
mne/tests/test_chpi.py | 222 ++-
mne/tests/test_cov.py | 223 ++-
mne/tests/test_dipole.py | 215 ++-
mne/tests/test_docstring_parameters.py | 25 +-
mne/tests/test_epochs.py | 925 ++++++----
mne/tests/test_event.py | 244 ++-
mne/tests/test_evoked.py | 227 ++-
mne/tests/test_filter.py | 393 +++--
mne/tests/test_fixes.py | 184 +-
mne/tests/test_import_nesting.py | 5 +-
mne/tests/test_label.py | 158 +-
mne/tests/test_line_endings.py | 8 +-
mne/tests/test_proj.py | 77 +-
mne/tests/test_report.py | 39 +-
mne/tests/test_selection.py | 31 +-
mne/tests/test_source_estimate.py | 25 +-
mne/tests/test_source_space.py | 22 +-
mne/tests/test_surface.py | 47 +-
mne/tests/test_transforms.py | 70 +-
mne/tests/test_utils.py | 330 +++-
mne/time_frequency/__init__.py | 10 +-
mne/time_frequency/_stockwell.py | 19 +-
mne/time_frequency/csd.py | 301 +++-
mne/time_frequency/multitaper.py | 121 +-
mne/time_frequency/psd.py | 326 ++--
mne/time_frequency/tests/test_ar.py | 8 +-
mne/time_frequency/tests/test_csd.py | 301 +++-
mne/time_frequency/tests/test_multitaper.py | 17 +-
mne/time_frequency/tests/test_psd.py | 212 +--
mne/time_frequency/tests/test_stockwell.py | 67 +-
mne/time_frequency/tests/test_tfr.py | 307 +++-
mne/time_frequency/tfr.py | 1758 ++++++++++++--------
mne/transforms.py | 139 +-
mne/utils.py | 829 +++++++--
mne/viz/_3d.py | 311 +++-
mne/viz/__init__.py | 11 +-
mne/viz/circle.py | 11 +-
mne/viz/decoding.py | 12 +-
mne/viz/epochs.py | 255 ++-
mne/viz/evoked.py | 944 ++++++++++-
mne/viz/ica.py | 395 +++--
mne/viz/misc.py | 133 +-
mne/viz/raw.py | 412 +++--
mne/viz/tests/test_3d.py | 65 +-
mne/viz/tests/test_decoding.py | 9 +-
mne/viz/tests/test_epochs.py | 48 +-
mne/viz/tests/test_evoked.py | 77 +-
mne/viz/tests/test_ica.py | 141 +-
mne/viz/tests/test_misc.py | 34 +-
mne/viz/tests/test_raw.py | 111 +-
mne/viz/tests/test_topo.py | 69 +-
mne/viz/tests/test_topomap.py | 84 +-
mne/viz/tests/test_utils.py | 61 +-
mne/viz/topo.py | 514 ++++--
mne/viz/topomap.py | 845 ++++++++--
mne/viz/utils.py | 821 ++++++++-
setup.cfg | 5 +-
setup.py | 6 +-
tutorials/plot_artifacts_correction_filtering.py | 131 ++
tutorials/plot_artifacts_correction_ica.py | 257 +++
.../plot_artifacts_correction_maxwell_filtering.py | 28 +-
tutorials/plot_artifacts_correction_rejection.py | 199 +++
tutorials/plot_artifacts_correction_ssp.py | 89 +
tutorials/plot_artifacts_detection.py | 134 ++
tutorials/plot_background_filtering.py | 951 +++++++++++
tutorials/plot_brainstorm_auditory.py | 360 ++++
tutorials/plot_brainstorm_phantom_ctf.py | 112 ++
tutorials/plot_brainstorm_phantom_elekta.py | 106 ++
tutorials/plot_compute_covariance.py | 139 ++
tutorials/plot_creating_data_structures.py | 19 +-
tutorials/plot_dipole_fit.py | 85 +
tutorials/plot_eeg_erp.py | 199 +++
tutorials/plot_epoching_and_averaging.py | 159 ++
tutorials/plot_epochs_to_data_frame.py | 14 +-
tutorials/plot_forward.py | 189 +++
tutorials/plot_ica_from_raw.py | 8 +-
tutorials/plot_info.py | 24 +-
tutorials/plot_introduction.py | 85 +-
tutorials/plot_mne_dspm_source_localization.py | 138 ++
tutorials/plot_modifying_data_inplace.py | 28 +-
...lot_epochs_objects.py => plot_object_epochs.py} | 73 +-
tutorials/plot_object_evoked.py | 74 +
.../{plot_raw_objects.py => plot_object_raw.py} | 85 +-
tutorials/plot_point_spread.py | 171 ++
tutorials/plot_python_intro.py | 46 +
tutorials/plot_sensors_decoding.py | 116 ++
tutorials/plot_sensors_time_frequency.py | 133 ++
tutorials/plot_source_localization_basics.py | 98 --
...lot_stats_cluster_1samp_test_time_frequency.py} | 76 +-
...s_tutorial.py => plot_stats_cluster_methods.py} | 38 +-
...al.py => plot_stats_cluster_spatio_temporal.py} | 64 +-
...=> plot_stats_cluster_spatio_temporal_2samp.py} | 18 +-
...ter_spatio_temporal_repeated_measures_anova.py} | 98 +-
...ncy.py => plot_stats_cluster_time_frequency.py} | 89 +-
...ster_time_frequency_repeated_measures_anova.py} | 146 +-
... plot_stats_spatio_temporal_cluster_sensors.py} | 42 +-
tutorials/plot_visualize_epochs.py | 60 +
tutorials/plot_visualize_evoked.py | 185 ++
tutorials/plot_visualize_raw.py | 112 ++
500 files changed, 40159 insertions(+), 20143 deletions(-)
create mode 100644 circle.yml
create mode 100644 codecov.yml
delete mode 100644 doc/advanced_setup.rst
create mode 100644 doc/cited.rst
copy doc/{getting_started.rst => install_mne_c.rst} (64%)
create mode 100644 doc/install_mne_python.rst
create mode 100644 doc/manual/channel_interpolation.rst
create mode 100644 doc/manual/migrating.rst
create mode 100644 doc/manual/preprocessing/maxwell.rst
delete mode 100644 doc/manual/source_localization/covariance.rst
create mode 100644 doc/martinos.rst
create mode 100644 doc/sphinxext/cited_mne.py
rename doc/sphinxext/{commands.py => gen_commands.py} (69%)
delete mode 100644 doc/sphinxext/numpy_ext/docscrape.py
delete mode 100644 doc/sphinxext/numpy_ext/docscrape_sphinx.py
delete mode 100644 doc/sphinxext/numpy_ext/numpydoc.py
create mode 100644 doc/tutorials/seven_stories_about_mne.rst
delete mode 100644 examples/decoding/plot_decoding_sensors.py
delete mode 100644 examples/decoding/plot_decoding_time_generalization.py
create mode 100644 examples/decoding/plot_decoding_unsupervised_spatial_filter.py
delete mode 100644 examples/forward/plot_bem_contour_mri.py
delete mode 100644 examples/forward/plot_coregistration_transform.py
rename examples/forward/{plot_make_forward.py => plot_forward_sensitivity_maps.py} (72%)
delete mode 100644 examples/forward/plot_read_forward.py
delete mode 100644 examples/inverse/plot_dipole_fit.py
delete mode 100644 examples/inverse/plot_make_inverse_operator.py
create mode 100644 examples/io/plot_elekta_epochs.py
delete mode 100644 examples/plot_compute_mne_inverse.py
delete mode 100644 examples/plot_extract_events_from_raw.py
delete mode 100644 examples/plot_from_raw_to_epochs_to_evoked.py
delete mode 100644 examples/preprocessing/plot_corrmap_detection.py
delete mode 100644 examples/preprocessing/plot_estimate_covariance_matrix_baseline.py
delete mode 100644 examples/preprocessing/plot_estimate_covariance_matrix_raw.py
create mode 100644 examples/preprocessing/plot_movement_compensation.py
delete mode 100644 examples/time_frequency/plot_epochs_spectra.py
delete mode 100644 examples/time_frequency/plot_stockwell.py
delete mode 100644 examples/time_frequency/plot_time_frequency_multitaper_sensors.py
delete mode 100644 examples/time_frequency/plot_time_frequency_sensors.py
delete mode 100644 examples/visualization/plot_evoked_delayed_ssp.py
delete mode 100644 examples/visualization/plot_evoked_erf_erp.py
delete mode 100644 examples/visualization/plot_evoked_topomap_delayed_ssp.py
delete mode 100644 examples/visualization/plot_meg_eeg_fields_3d.py
create mode 100644 examples/visualization/plot_meg_sensors.py
delete mode 100644 examples/visualization/plot_ssp_projs_topomaps.py
delete mode 100644 examples/visualization/plot_topo_channel_epochs_image.py
delete mode 100644 examples/visualization/plot_topography.py
delete mode 100644 make/install_python.ps1
create mode 100644 mne/annotations.py
create mode 100644 mne/channels/data/layouts/KIT-UMD-3.lout
create mode 100644 mne/channels/data/layouts/Vectorview-grad_norm.lout
create mode 100644 mne/channels/data/neighbors/KIT-UMD-1_neighb.mat
create mode 100644 mne/channels/data/neighbors/KIT-UMD-2_neighb.mat
create mode 100644 mne/channels/data/neighbors/KIT-UMD-3_neighb.mat
create mode 100644 mne/commands/mne_show_info.py
copy mne/datasets/brainstorm/{bst_resting.py => bst_phantom_ctf.py} (71%)
copy mne/datasets/brainstorm/{bst_resting.py => bst_phantom_elekta.py} (71%)
create mode 100644 mne/datasets/misc/__init__.py
create mode 100644 mne/datasets/misc/_misc.py
create mode 100644 mne/datasets/multimodal/__init__.py
copy mne/datasets/{somato/somato.py => multimodal/multimodal.py} (59%)
create mode 100644 mne/decoding/search_light.py
create mode 100644 mne/decoding/tests/test_search_light.py
create mode 100644 mne/decoding/tests/test_time_frequency.py
create mode 100644 mne/decoding/time_frequency.py
copy mne/externals/tempita/{__init__.py => _tempita.py} (79%)
create mode 100644 mne/gui/_backend.py
copy mne/io/brainvision/tests/data/{test_highpass.vhdr => test_highpass_hz.vhdr} (84%)
mode change 100755 => 100644
copy mne/io/brainvision/tests/data/{test_highpass.vhdr => test_lowpass_s.vhdr} (60%)
copy mne/io/brainvision/tests/data/{test_highpass.vhdr => test_mixed_highpass.vhdr} (85%)
copy mne/io/brainvision/tests/data/{test_highpass.vhdr => test_mixed_highpass_hz.vhdr} (83%)
mode change 100755 => 100644
copy mne/io/brainvision/tests/data/{test_highpass.vhdr => test_mixed_lowpass.vhdr} (85%)
mode change 100755 => 100644
copy mne/io/brainvision/tests/data/{test_highpass.vhdr => test_mixed_lowpass_s.vhdr} (60%)
mode change 100755 => 100644
create mode 100644 mne/io/brainvision/tests/data/test_old_layout_latin1_software_filter.eeg
create mode 100644 mne/io/brainvision/tests/data/test_old_layout_latin1_software_filter.vhdr
create mode 100644 mne/io/brainvision/tests/data/test_old_layout_latin1_software_filter.vmrk
copy mne/io/brainvision/tests/data/{test.vhdr => test_partially_disabled_hw_filter.vhdr} (74%)
create mode 100644 mne/io/cnt/__init__.py
create mode 100644 mne/io/cnt/cnt.py
rename {doc/sphinxext/numpy_ext => mne/io/cnt/tests}/__init__.py (100%)
create mode 100644 mne/io/cnt/tests/test_cnt.py
create mode 100644 mne/io/kit/tests/data/test.elp
create mode 100644 mne/io/kit/tests/data/test.hsp
create mode 100644 mne/io/kit/tests/data/test_umd-raw.sqd
create mode 100644 mne/preprocessing/_fine_cal.py
create mode 100644 mne/preprocessing/tests/test_fine_cal.py
create mode 100644 mne/tests/test_annotations.py
create mode 100644 tutorials/plot_artifacts_correction_filtering.py
create mode 100644 tutorials/plot_artifacts_correction_ica.py
rename examples/preprocessing/plot_maxwell_filter.py => tutorials/plot_artifacts_correction_maxwell_filtering.py (63%)
create mode 100644 tutorials/plot_artifacts_correction_rejection.py
create mode 100644 tutorials/plot_artifacts_correction_ssp.py
create mode 100644 tutorials/plot_artifacts_detection.py
create mode 100644 tutorials/plot_background_filtering.py
create mode 100644 tutorials/plot_brainstorm_auditory.py
create mode 100644 tutorials/plot_brainstorm_phantom_ctf.py
create mode 100644 tutorials/plot_brainstorm_phantom_elekta.py
create mode 100644 tutorials/plot_compute_covariance.py
create mode 100644 tutorials/plot_dipole_fit.py
create mode 100644 tutorials/plot_eeg_erp.py
create mode 100644 tutorials/plot_epoching_and_averaging.py
create mode 100644 tutorials/plot_forward.py
create mode 100644 tutorials/plot_mne_dspm_source_localization.py
rename tutorials/{plot_epochs_objects.py => plot_object_epochs.py} (50%)
create mode 100644 tutorials/plot_object_evoked.py
rename tutorials/{plot_raw_objects.py => plot_object_raw.py} (58%)
create mode 100644 tutorials/plot_point_spread.py
create mode 100644 tutorials/plot_python_intro.py
create mode 100644 tutorials/plot_sensors_decoding.py
create mode 100644 tutorials/plot_sensors_time_frequency.py
delete mode 100644 tutorials/plot_source_localization_basics.py
rename tutorials/{plot_cluster_1samp_test_time_frequency.py => plot_stats_cluster_1samp_test_time_frequency.py} (64%)
rename tutorials/{plot_cluster_methods_tutorial.py => plot_stats_cluster_methods.py} (89%)
rename tutorials/{plot_cluster_stats_spatio_temporal.py => plot_stats_cluster_spatio_temporal.py} (76%)
rename tutorials/{plot_cluster_stats_spatio_temporal_2samp.py => plot_stats_cluster_spatio_temporal_2samp.py} (92%)
rename tutorials/{plot_cluster_stats_spatio_temporal_repeated_measures_anova.py => plot_stats_cluster_spatio_temporal_repeated_measures_anova.py} (78%)
rename tutorials/{plot_cluster_stats_time_frequency.py => plot_stats_cluster_time_frequency.py} (60%)
rename tutorials/{plot_cluster_stats_time_frequency_repeated_measures_anova.py => plot_stats_cluster_time_frequency_repeated_measures_anova.py} (65%)
rename tutorials/{plot_spatio_temporal_cluster_stats_sensor.py => plot_stats_spatio_temporal_cluster_sensors.py} (86%)
create mode 100644 tutorials/plot_visualize_epochs.py
create mode 100644 tutorials/plot_visualize_evoked.py
create mode 100644 tutorials/plot_visualize_raw.py
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