[med-svn] [mne-python] branch upstream updated (21bf9c0 -> 3ceaf17)
Andreas Tille
tille at debian.org
Thu Nov 21 21:14:58 UTC 2013
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository mne-python.
from 21bf9c0 Imported Upstream version 0.6
new 3ceaf17 Imported Upstream version 0.7~rc1
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:
.travis.yml | 35 +
MANIFEST.in | 8 +-
Makefile | 22 +
README.rst | 8 +
bin/mne | 36 +
doc/Makefile | 5 +
doc/source/_static/logo.png | Bin 74269 -> 175727 bytes
doc/source/_templates/layout.html | 1 +
doc/source/cite.rst | 10 +
doc/source/contributing.rst | 127 +-
doc/source/getting_started.rst | 69 +-
doc/source/git_links.inc | 28 +-
doc/source/index.rst | 1 +
doc/source/mne-python.rst | 9 +-
doc/source/python_reference.rst | 59 +-
doc/source/python_tutorial.rst | 30 +-
doc/source/whats_new.rst | 89 +
doc/sphinxext/gen_rst.py | 8 +-
doc/upload_html.sh | 1 +
.../connectivity/plot_cwt_sensor_connectivity.py | 4 +-
.../plot_mne_inverse_coherence_epochs.py | 8 +-
.../plot_mne_inverse_connectivity_spectrum.py | 10 +-
.../plot_mne_inverse_label_connectivity.py | 8 +-
.../connectivity/plot_mne_inverse_psi_visual.py | 2 +-
examples/datasets/README.txt | 5 +
examples/datasets/plot_spm_faces_dataset.py | 118 +
examples/decoding/plot_decoding_csp_space.py | 106 +
examples/decoding/plot_decoding_sensors.py | 24 +-
.../plot_decoding_spatio_temporal_source.py | 2 +-
examples/export/plot_epochs_as_data_frame.py | 8 +-
examples/export/plot_epochs_to_nitime.py | 4 +-
examples/export/plot_evoked_to_nitime.py | 4 +-
examples/export/plot_raw_to_nitime.py | 14 +-
examples/inverse/plot_compute_mne_inverse.py | 12 +-
.../plot_compute_mne_inverse_epochs_in_label.py | 22 +-
.../plot_compute_mne_inverse_raw_in_label.py | 12 +-
.../inverse/plot_compute_mne_inverse_volume.py | 32 +-
examples/inverse/plot_dics_beamformer.py | 89 +
examples/inverse/plot_dics_source_power.py | 79 +
examples/inverse/plot_gamma_map_inverse.py | 9 +-
examples/inverse/plot_label_activation_from_stc.py | 24 +-
examples/inverse/plot_label_from_stc.py | 105 +
examples/inverse/plot_label_source_activations.py | 26 +-
examples/inverse/plot_lcmv_beamformer.py | 29 +-
examples/inverse/plot_lcmv_beamformer_volume.py | 31 +-
examples/inverse/plot_make_inverse_operator.py | 30 +-
examples/inverse/plot_mixed_norm_L21_inverse.py | 12 +-
examples/inverse/plot_morph_data.py | 16 +-
examples/inverse/plot_read_stc.py | 10 +-
examples/inverse/plot_tf_dics.py | 116 +
examples/inverse/plot_tf_lcmv.py | 130 +
.../plot_time_frequency_mixed_norm_inverse.py | 13 +-
examples/plot_channel_epochs_image.py | 10 +-
examples/plot_decimate_head_surface.py | 39 +
examples/plot_define_target_events.py | 20 +-
examples/plot_evoked_delayed_ssp.py | 12 +-
examples/plot_evoked_whitening.py | 3 +-
examples/plot_from_raw_to_epochs_to_evoked.py | 21 +-
.../plot_from_raw_to_multiple_epochs_to_evoked.py | 18 +-
examples/plot_make_forward.py | 54 +
examples/plot_megsim_data.py | 6 +-
examples/plot_megsim_data_single_trial.py | 1 -
examples/plot_read_forward.py | 26 +-
examples/plot_read_noise_covariance_matrix.py | 8 +-
examples/plot_shift_evoked.py | 4 +-
examples/plot_simulate_evoked_data.py | 10 +-
examples/plot_ssp_projs_sensitivity_map.py | 10 +-
examples/plot_ssp_projs_topomaps.py | 4 +-
examples/plot_topo_channel_epochs_image.py | 4 +-
examples/plot_topo_compare_conditions.py | 6 +-
examples/plot_topography.py | 4 +-
examples/preprocessing/plot_find_ecg_artifacts.py | 12 +-
examples/preprocessing/plot_find_eog_artifacts.py | 10 +-
examples/preprocessing/plot_ica_from_epochs.py | 78 +-
examples/preprocessing/plot_ica_from_raw.py | 111 +-
examples/realtime/README.txt | 5 +
examples/realtime/plot_compute_rt_average.py | 64 +
examples/realtime/plot_compute_rt_decoder.py | 111 +
examples/realtime/rt_feedback_client.py | 116 +
examples/realtime/rt_feedback_server.py | 144 +
.../plot_cluster_1samp_test_time_frequency.py | 50 +-
examples/stats/plot_cluster_methods_tutorial.py | 18 +-
examples/stats/plot_cluster_stats_evoked.py | 35 +-
.../stats/plot_cluster_stats_spatio_temporal.py | 28 +-
.../plot_cluster_stats_spatio_temporal_2samp.py | 20 +-
...tats_spatio_temporal_repeated_measures_anova.py | 63 +-
.../stats/plot_cluster_stats_time_frequency.py | 44 +-
...stats_time_frequency_repeated_measures_anova.py | 80 +-
examples/stats/plot_fdr_stats_evoked.py | 28 +-
examples/stats/plot_sensor_permutation_test.py | 22 +-
.../plot_compute_raw_data_spectrum.py | 61 +-
.../plot_compute_source_psd_epochs.py | 12 +-
.../time_frequency/plot_single_trial_spectra.py | 84 +
.../plot_source_label_time_frequency.py | 96 +-
.../time_frequency/plot_source_power_spectrum.py | 14 +-
.../plot_source_space_time_frequency.py | 16 +-
examples/time_frequency/plot_temporal_whitening.py | 26 +-
examples/time_frequency/plot_tfr_topography.py | 6 +-
examples/time_frequency/plot_time_frequency.py | 58 +-
mne/__init__.py | 75 +-
mne/baseline.py | 10 +-
mne/beamformer/__init__.py | 3 +-
mne/beamformer/_dics.py | 587 ++
mne/beamformer/_lcmv.py | 444 +-
mne/beamformer/tests/test_dics.py | 296 +
mne/beamformer/tests/test_lcmv.py | 357 +-
mne/{transforms/tests => commands}/__init__.py | 0
{bin => mne/commands}/mne_browse_raw.py | 23 +-
{bin => mne/commands}/mne_bti2fiff.py | 33 +-
{bin => mne/commands}/mne_clean_eog_ecg.py | 13 +-
{bin => mne/commands}/mne_compute_proj_ecg.py | 141 +-
{bin => mne/commands}/mne_compute_proj_eog.py | 15 +-
{bin => mne/commands}/mne_flash_bem_model.py | 7 +-
{bin => mne/commands}/mne_kit2fiff.py | 32 +-
mne/commands/mne_make_scalp_surfaces.py | 129 +
{bin => mne/commands}/mne_maxfilter.py | 9 +-
{bin => mne/commands}/mne_surf2bem.py | 21 +-
mne/commands/utils.py | 39 +
mne/connectivity/effective.py | 4 +-
mne/connectivity/spectral.py | 21 +-
mne/connectivity/tests/test_effective.py | 25 +-
mne/connectivity/tests/test_spectral.py | 39 +-
mne/coreg.py | 1041 +++
mne/cov.py | 57 +-
mne/cuda.py | 10 +-
mne/data/coil_def.dat | 416 +
mne/datasets/__init__.py | 1 +
mne/datasets/megsim/megsim.py | 7 +-
mne/datasets/sample/__init__.py | 2 +-
mne/datasets/sample/sample.py | 156 +-
mne/datasets/spm_face/__init__.py | 4 +
mne/datasets/spm_face/spm_data.py | 30 +
mne/datasets/{sample/sample.py => utils.py} | 134 +-
mne/decoding/__init__.py | 4 +
mne/decoding/classifier.py | 425 +
mne/decoding/csp.py | 205 +
mne/decoding/mixin.py | 30 +
.../numpy_ext => mne/decoding/tests}/__init__.py | 0
mne/decoding/tests/test_classifier.py | 127 +
mne/decoding/tests/test_csp.py | 97 +
mne/dipole.py | 4 +-
mne/epochs.py | 718 +-
mne/event.py | 218 +-
mne/fiff/__init__.py | 15 +-
mne/fiff/brainvision/__init__.py | 7 +
mne/fiff/brainvision/brainvision.py | 518 ++
mne/fiff/brainvision/tests/__init__.py | 1 +
mne/fiff/brainvision/tests/data/test.eeg | Bin 0 -> 505600 bytes
mne/fiff/brainvision/tests/data/test.vhdr | 142 +
mne/fiff/brainvision/tests/data/test.vmrk | 22 +
mne/fiff/brainvision/tests/data/test_bin_raw.fif | Bin 0 -> 526560 bytes
mne/fiff/brainvision/tests/data/test_elp.txt | 45 +
mne/fiff/brainvision/tests/test_brainvision.py | 75 +
mne/fiff/bti/raw.py | 50 +-
mne/fiff/bti/read.py | 3 -
mne/fiff/bti/tests/test_bti.py | 13 +-
mne/fiff/compensator.py | 15 +-
mne/fiff/constants.py | 88 +-
mne/fiff/cov.py | 14 +-
mne/fiff/ctf.py | 5 +-
mne/fiff/diff.py | 5 +-
mne/fiff/edf/__init__.py | 7 +
mne/fiff/edf/edf.py | 594 ++
.../numpy_ext => mne/fiff/edf/tests}/__init__.py | 0
mne/fiff/edf/tests/data/biosemi.hpts | 82 +
mne/fiff/edf/tests/data/test.bdf | 3222 +++++++
mne/fiff/edf/tests/data/test.edf | 9591 ++++++++++++++++++++
mne/fiff/edf/tests/data/test_bdf_eeglab.mat | Bin 0 -> 447053 bytes
mne/fiff/edf/tests/data/test_edf_eeglab.mat | Bin 0 -> 799941 bytes
mne/fiff/edf/tests/data/test_eeglab.mat | Bin 0 -> 447053 bytes
mne/fiff/edf/tests/test_edf.py | 87 +
mne/fiff/evoked.py | 57 +-
mne/fiff/kit/__init__.py | 1 +
mne/fiff/kit/constants.py | 22 +-
mne/fiff/kit/coreg.py | 306 +-
mne/fiff/kit/kit.py | 390 +-
mne/fiff/kit/tests/data/trans-sample.fif | Bin 0 -> 420 bytes
mne/fiff/kit/tests/test_coreg.py | 75 +
mne/fiff/kit/tests/test_kit.py | 91 +-
mne/fiff/matrix.py | 9 +-
mne/fiff/meas_info.py | 162 +-
mne/fiff/open.py | 4 +-
mne/fiff/pick.py | 88 +-
mne/fiff/proj.py | 56 +-
mne/fiff/raw.py | 328 +-
mne/fiff/tag.py | 21 +-
mne/fiff/tests/data/fsaverage-fiducials.fif | Bin 0 -> 260 bytes
mne/fiff/tests/data/sample-audvis-raw-trans.txt | 4 +
mne/fiff/tests/data/test-lh.label | 101 +
mne/fiff/tests/data/test-rh.label | 102 +
mne/fiff/tests/data/test_chpi_raw_hp.txt | 5 +
mne/fiff/tests/data/test_chpi_raw_sss.fif | Bin 0 -> 13071083 bytes
mne/fiff/tests/test_compensator.py | 2 +
mne/fiff/tests/test_evoked.py | 4 +-
mne/fiff/tests/test_meas_info.py | 66 +
mne/fiff/tests/test_raw.py | 180 +-
mne/fiff/tree.py | 5 +-
mne/fiff/write.py | 42 +-
mne/filter.py | 28 +-
mne/fixes.py | 26 +
mne/forward/__init__.py | 12 +
mne/forward/_compute_forward.py | 346 +
mne/forward/_make_forward.py | 494 +
mne/{ => forward}/forward.py | 327 +-
.../numpy_ext => mne/forward/tests}/__init__.py | 0
mne/{ => forward}/tests/test_forward.py | 153 +-
mne/forward/tests/test_make_forward.py | 227 +
mne/inverse_sparse/_gamma_map.py | 5 +-
mne/inverse_sparse/mxne_debiasing.py | 6 +-
mne/inverse_sparse/mxne_inverse.py | 5 +-
mne/inverse_sparse/mxne_optim.py | 14 +-
mne/inverse_sparse/tests/test_gamma_map.py | 18 +-
mne/inverse_sparse/tests/test_mxne_debiasing.py | 2 +-
mne/inverse_sparse/tests/test_mxne_inverse.py | 71 +-
mne/inverse_sparse/tests/test_mxne_optim.py | 10 +-
mne/label.py | 410 +-
mne/layouts/layout.py | 10 +-
mne/minimum_norm/__init__.py | 12 +-
mne/minimum_norm/inverse.py | 257 +-
mne/minimum_norm/tests/test_inverse.py | 97 +-
mne/minimum_norm/tests/test_time_frequency.py | 28 +-
mne/minimum_norm/time_frequency.py | 97 +-
mne/parallel.py | 72 +-
mne/preprocessing/__init__.py | 4 +-
mne/preprocessing/ecg.py | 122 +-
mne/preprocessing/eog.py | 25 +-
mne/preprocessing/ica.py | 660 +-
mne/preprocessing/maxfilter.py | 27 +-
mne/preprocessing/peak_finder.py | 10 +-
mne/preprocessing/ssp.py | 104 +-
mne/preprocessing/stim.py | 15 +-
mne/preprocessing/tests/test_ica.py | 261 +-
mne/preprocessing/tests/test_ssp.py | 51 +-
mne/preprocessing/tests/test_stim.py | 54 +-
mne/proj.py | 59 +-
mne/realtime/__init__.py | 13 +
mne/realtime/client.py | 370 +
mne/realtime/epochs.py | 398 +
mne/realtime/mockclient.py | 175 +
mne/realtime/stim_server_client.py | 289 +
.../numpy_ext => mne/realtime/tests}/__init__.py | 0
mne/realtime/tests/test_mockclient.py | 58 +
mne/realtime/tests/test_stim_client_server.py | 63 +
mne/selection.py | 5 +-
mne/simulation/__init__.py | 4 +-
mne/simulation/tests/test_evoked.py | 5 +-
mne/simulation/tests/test_source.py | 42 +-
mne/source_estimate.py | 1152 +--
mne/source_space.py | 968 +-
mne/stats/__init__.py | 14 +-
mne/stats/cluster_level.py | 172 +-
mne/stats/parametric.py | 19 +-
mne/stats/tests/test_cluster_level.py | 223 +-
mne/stats/tests/test_parametric.py | 4 +-
mne/surface.py | 961 +-
mne/tests/__init__.py | 3 +
mne/tests/test_coreg.py | 154 +
mne/tests/test_cov.py | 20 +-
mne/tests/test_dipole.py | 4 +-
mne/tests/test_epochs.py | 84 +-
mne/tests/test_event.py | 44 +-
mne/tests/test_filter.py | 17 +-
mne/tests/test_label.py | 126 +-
mne/tests/test_misc.py | 2 +-
mne/tests/test_proj.py | 11 +-
mne/tests/test_source_estimate.py | 207 +-
mne/tests/test_source_space.py | 368 +-
mne/tests/test_surface.py | 84 +-
mne/tests/test_transforms.py | 62 +
mne/tests/test_utils.py | 53 +-
mne/tests/test_viz.py | 187 +-
mne/time_frequency/__init__.py | 3 +-
mne/time_frequency/csd.py | 258 +
mne/time_frequency/multitaper.py | 28 +-
mne/time_frequency/psd.py | 101 +-
mne/time_frequency/stft.py | 5 +-
mne/time_frequency/tests/test_csd.py | 163 +
mne/time_frequency/tests/test_psd.py | 54 +-
mne/time_frequency/tfr.py | 11 +-
mne/{transforms => }/transforms.py | 176 +-
mne/transforms/__init__.py | 2 -
mne/transforms/coreg.py | 67 -
mne/transforms/tests/test_coreg.py | 20 -
mne/transforms/tests/test_transforms.py | 31 -
mne/utils.py | 225 +-
mne/viz.py | 1436 ++-
setup.py | 50 +-
287 files changed, 34137 insertions(+), 5036 deletions(-)
create mode 100644 .travis.yml
create mode 100755 bin/mne
create mode 100644 doc/source/cite.rst
create mode 100644 examples/datasets/README.txt
create mode 100644 examples/datasets/plot_spm_faces_dataset.py
create mode 100644 examples/decoding/plot_decoding_csp_space.py
create mode 100644 examples/inverse/plot_dics_beamformer.py
create mode 100644 examples/inverse/plot_dics_source_power.py
create mode 100644 examples/inverse/plot_label_from_stc.py
create mode 100644 examples/inverse/plot_tf_dics.py
create mode 100644 examples/inverse/plot_tf_lcmv.py
create mode 100644 examples/plot_decimate_head_surface.py
create mode 100644 examples/plot_make_forward.py
create mode 100644 examples/realtime/README.txt
create mode 100644 examples/realtime/plot_compute_rt_average.py
create mode 100644 examples/realtime/plot_compute_rt_decoder.py
create mode 100644 examples/realtime/rt_feedback_client.py
create mode 100644 examples/realtime/rt_feedback_server.py
create mode 100644 examples/time_frequency/plot_single_trial_spectra.py
create mode 100644 mne/beamformer/_dics.py
create mode 100644 mne/beamformer/tests/test_dics.py
rename mne/{transforms/tests => commands}/__init__.py (100%)
rename {bin => mne/commands}/mne_browse_raw.py (81%)
rename {bin => mne/commands}/mne_bti2fiff.py (94%)
rename {bin => mne/commands}/mne_clean_eog_ecg.py (95%)
rename {bin => mne/commands}/mne_compute_proj_ecg.py (50%)
rename {bin => mne/commands}/mne_compute_proj_eog.py (93%)
rename {bin => mne/commands}/mne_flash_bem_model.py (97%)
rename {bin => mne/commands}/mne_kit2fiff.py (62%)
create mode 100755 mne/commands/mne_make_scalp_surfaces.py
rename {bin => mne/commands}/mne_maxfilter.py (97%)
rename {bin => mne/commands}/mne_surf2bem.py (67%)
create mode 100644 mne/commands/utils.py
create mode 100644 mne/coreg.py
create mode 100644 mne/data/coil_def.dat
create mode 100644 mne/datasets/spm_face/__init__.py
create mode 100644 mne/datasets/spm_face/spm_data.py
copy mne/datasets/{sample/sample.py => utils.py} (53%)
create mode 100644 mne/decoding/__init__.py
create mode 100644 mne/decoding/classifier.py
create mode 100644 mne/decoding/csp.py
create mode 100644 mne/decoding/mixin.py
copy {doc/sphinxext/numpy_ext => mne/decoding/tests}/__init__.py (100%)
create mode 100644 mne/decoding/tests/test_classifier.py
create mode 100644 mne/decoding/tests/test_csp.py
create mode 100644 mne/fiff/brainvision/__init__.py
create mode 100644 mne/fiff/brainvision/brainvision.py
create mode 100644 mne/fiff/brainvision/tests/__init__.py
create mode 100755 mne/fiff/brainvision/tests/data/test.eeg
create mode 100755 mne/fiff/brainvision/tests/data/test.vhdr
create mode 100755 mne/fiff/brainvision/tests/data/test.vmrk
create mode 100644 mne/fiff/brainvision/tests/data/test_bin_raw.fif
create mode 100644 mne/fiff/brainvision/tests/data/test_elp.txt
create mode 100644 mne/fiff/brainvision/tests/test_brainvision.py
create mode 100644 mne/fiff/edf/__init__.py
create mode 100644 mne/fiff/edf/edf.py
copy {doc/sphinxext/numpy_ext => mne/fiff/edf/tests}/__init__.py (100%)
create mode 100644 mne/fiff/edf/tests/data/biosemi.hpts
create mode 100644 mne/fiff/edf/tests/data/test.bdf
create mode 100644 mne/fiff/edf/tests/data/test.edf
create mode 100644 mne/fiff/edf/tests/data/test_bdf_eeglab.mat
create mode 100644 mne/fiff/edf/tests/data/test_edf_eeglab.mat
create mode 100644 mne/fiff/edf/tests/data/test_eeglab.mat
create mode 100644 mne/fiff/edf/tests/test_edf.py
create mode 100644 mne/fiff/kit/tests/data/trans-sample.fif
create mode 100644 mne/fiff/kit/tests/test_coreg.py
create mode 100644 mne/fiff/tests/data/fsaverage-fiducials.fif
create mode 100644 mne/fiff/tests/data/sample-audvis-raw-trans.txt
create mode 100644 mne/fiff/tests/data/test-lh.label
create mode 100644 mne/fiff/tests/data/test-rh.label
create mode 100644 mne/fiff/tests/data/test_chpi_raw_hp.txt
create mode 100644 mne/fiff/tests/data/test_chpi_raw_sss.fif
create mode 100644 mne/fiff/tests/test_meas_info.py
create mode 100644 mne/forward/__init__.py
create mode 100644 mne/forward/_compute_forward.py
create mode 100644 mne/forward/_make_forward.py
rename mne/{ => forward}/forward.py (84%)
copy {doc/sphinxext/numpy_ext => mne/forward/tests}/__init__.py (100%)
rename mne/{ => forward}/tests/test_forward.py (65%)
create mode 100644 mne/forward/tests/test_make_forward.py
create mode 100644 mne/realtime/__init__.py
create mode 100644 mne/realtime/client.py
create mode 100644 mne/realtime/epochs.py
create mode 100644 mne/realtime/mockclient.py
create mode 100644 mne/realtime/stim_server_client.py
copy {doc/sphinxext/numpy_ext => mne/realtime/tests}/__init__.py (100%)
create mode 100644 mne/realtime/tests/test_mockclient.py
create mode 100644 mne/realtime/tests/test_stim_client_server.py
create mode 100644 mne/tests/test_coreg.py
create mode 100644 mne/tests/test_transforms.py
create mode 100644 mne/time_frequency/csd.py
create mode 100644 mne/time_frequency/tests/test_csd.py
rename mne/{transforms => }/transforms.py (67%)
delete mode 100644 mne/transforms/__init__.py
delete mode 100644 mne/transforms/coreg.py
delete mode 100644 mne/transforms/tests/test_coreg.py
delete mode 100644 mne/transforms/tests/test_transforms.py
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