[med-svn] [python-mne] tag 0.4 created (now 7a1b19d)
Yaroslav Halchenko
debian at onerussian.com
Fri Nov 27 17:24:22 UTC 2015
This is an automated email from the git hooks/post-receive script.
yoh pushed a change to tag 0.4
in repository python-mne.
at 7a1b19d (commit)
This tag includes the following new commits:
new d0b2b37 intial commit
new e334ccb first running version of read_evoked
new c3d0c6d first working version of read_evoked
new bcccd7c first working version of read_cov
new 621ae31 first working version of setup_read_raw
new 91dbc83 FIX : read raw
new 4f55842 working read_events
new 6529715 cleaning exaples
new 1f52ce4 bug fix in raw;py
new b91920b adding packaging info
new a480c5a first working example for reading forward solutions
new 8ce493a misc
new 588a6f6 adding first draft of doc
new 9072d39 reading stc files
new 2eea3ad starting readind code with cov (not working yet!)
new 3143ae5 first working version of writing covariance matrix + first test
new ee1585b forgot test file
new 69291b0 now writing evoked data
new 7b306cd example IO evoked
new 8435456 Reading BEM surfaces
new d514a11 writing events
new efed27f more tests + writing stc files
new fd29a5b starting to write functions doc + increasing coverage
new a173c05 speed improvement for sparse mult
new 3c98f6e more on doc
new a31f945 more more on doc + pep8
new 27f9ed0 adding makefile for easier clean + test cycle
new e785e6e writing raw files
new 5e8cb91 fix in raw + test raw write
new 05264df ENH : adding code to read epochs + debug in raw
new b475cbc ENH : now computing MNE solution
new 2da3802 splitting fif and MNE
new e80efbb fix
new 4da7024 better slicing for raw data
new 7738cc5 adding auto examples to doc
new 9c3e90b examples with new sample data + some docstrings
new ece7557 fix in doc + bsd license
new ce9c428 better example of reading evoked data
new e85622e more love to web page
new b2fff6f fix lambda2 in inverse computation
new 2b73715 better documentation
new 037e301 Edited the front page
new 6b4485a bug fix + doc on command line + baseline correction ...
new 66283d3 Merge branch 'master' of parsley:~/work/git/pyfiff
new 4fa2c3b BSD 3-clause licensing
new 7786a0f ENH: make MNE-dSPM computation work
new 81f317d fix tests + examples
new e9dc6af adding test for mne inverse computation
new f627fa2 fix bug to allow loading of any evoked data set
new 626003a adding Covariance object
new 5f24f9c better Covariance class
new f35a9ba adding way to estimate noise cov matrix in python
new f898d94 a bit of reorganization + pep8
new 839aa49 adding preprocessing.py (WIP)
new 4f67f88 ENH : pick by channel type ENH : data whitening with noise covariance matrix ENH : moving transform functions in transforms.py
new bccd977 fix test + import
new 60d472c updating logo + favicon
new 565bc76 update git infos
new f2fdbf9 update examples for doc
new ea771ff Added missing constants
new 4a38978 API : do not read bad channels from forward operator ENH : adding possibility to whiten forward solutions using noise covariance matrix.
new aa2ca95 adding example of forward field whitening
new 588aba1 adding sample test raw fif dataset updating corresponding tests
new 55b831b adding routines to compute simple time frequency analysis with morlet wavelet
new 82eb385 better tfr plot
new 54f9e47 ENH : new permutation t-test
new 0bd92c4 better docstring
new 71702c1 ENH : adding exact permutation test with all permutations + some tests and cosmits
new 611a97c partial previous commit
new ddb167c partial previous commit (again)
new dc7864b DOC : adding reference for perm stats
new 982d5dc Merge branch 'tfr'
new e2fa002 cosmit in permutations
new 4fb4c74 first attempt to be able to plot topographies
new 9a665e1 ENH : new stats on sensors + topography plots
new 4fd812d DOC : pretifying doc
new 81a34e9 ENH : better handling of sample dataset
new a5e5cef FIX : in handling of sample dataset
new 70fb56b ENH : new cluster level non-parametric statistic on 1D data
new 6d10f66 fix makefile
new 4d8055f fix doc
new 070e3fd Improved the scales in plot_read_evoked
new 2c0c2af Fixed plot scales in plot_read_epochs
new f49fefe The name of the inverse operator file was fixed
new 6913499 Fixed subplot placing
new 522cd32 Fixed formatting of diagnostic output
new 974205f Fixed the time scale
new 7b0b8a3 Fixed formatting of diagnostic output
new f9defd6 ENH : handling EEG layout files
new 5e744ee DOC : adding first version of converted mne manual WIP
new e2470f0 Merge branch 'master' of github.com:mne-tools/mne-python
new 208cd1b first attempt to extract signal in ROIs with label files
new 08c470e FIX : in TFR phase lock
new 004f196 FIX : fix in time interval
new 18444e2 updating axis scaling in tfr example
new aad71df updating copyright sign
new d9449a6 FIX : in cov whitening
new 528634d ENH : making reading source activations in one label file work
new 57bbf39 Merge branch 'label'
new e485bdc adding test for label handling
new 77b8287 adding test for time frequency transform
new fabc50b more on time-frequency (test + fix)
new 1804c0e ENH : allowing parallel computing in time frequency with joblib
new 47e17da ENH : refactoring time frequency for speed up in parallel settings
new 768dc2a cosmit
new 948cfad ENH : exposing epochs as an iterable object with lazy loading from disk
new dced7de ENH : adding averge() method in Epochs
new fa1c2be adding Epochs.average() to test
new ab71920 starting manual editing of the manual
new c6570a2 more on doc
new 9628987 more on doc
new e123ba4 improve speed of cluster permutation WIP
new b9017b3 towards 2D permutation cluster stats WIP
new 3721652 Merge branch 'tfr4' into cluster
new 740f72b new example of TF cluster
new d281c2b create separate module for time freq analysis
new 0508abe ENH : Raw objects with IO capabilities
new affa3df new class Evoked to store an evoked dataset
new 5c7c993 bug fix due to new Evoked class + pyflakes
new 20e60b8 ENH : Epochs.average returns an Evoked object
new e26d6d2 API : mne.compute_inverse now takes as input an Evoked dataset + an inverse_operator
new 6dedaf9 FIX : due to latest API change
new 40becea ENH : reading events from a raw file
new 12b029a increasing coverage + bug fix in read_source_spaces when add_geom = True
new 41e2cd3 fix in plot_sensor_permutation_test.py
new 5bbbf0a pep8
new 26c2daf cosmit renaming
new dd5eca6 adding test for plot_topo
new 8147024 fix patch_info, commenting untested code, increase coverage
new 9f00678 increase coverage in cov.py + bug fix in read_forward_solution when surf_ori=True
new 55d8f06 pep8
new 33aa24c ENH : adding 1 sample cluster level stat
new 4b05bd9 cosmit
new 73713a8 bug fix in permutation_cluster_t_test with tail = -1
new 98d54e9 more bug fix in permutation_cluster_t_test
new 59b801f fix one more bug and make function _pval_from_histogram more readable
new 68a9473 cosmit
new 5761863 computing single_trial_power in parallel
new 5c32db9 tiny iteration on manual
new 0f489ab better induced power stat demo + addine baseline option in single_trial_power
new ffdce87 new plot_evoked function + nicer examples
new 15752b0 pep8
new efbbc25 using plot_evoked in plot_whitened_evoked_data.py
new 203cf5d pep8
new fc8276f fixing manual
new 38ae358 fixing manual
new 038454f fixing manual
new 90d5f92 fixing manual
new 961b087 fixing manual
new 604586b fixing manual
new 3e4d074 fixing manual
new 0f6c6ca fixing manual
new d496d3b adding __repr__ in Evoked, Raw and Epochs
new 85126db fix preload in Epochs
new 18c931c fixing manual
new 0c1e6d9 fixing manual
new 0c1a3da fixing manual
new f9bd5a8 fixing manual
new 9db7749 fixing manual
new 551a079 DOC : adding appendices to manual
new 1454b8f FIX : bug fix in reading of SSP vectors ENH : implementing minimum norm estimate WIP (todo: loose case + tests !)
new d1c4e60 mne WIP
new ce3505f ENH : reject epochs based on threshold + parsing of .ave + .cov files
new 758c90b adding epoch rejection everywhere
new 99ab29e Merge branch 'inverse'
new 860ef78 minor bug fix
new 75dc2c2 combining orients in source space
new 04adac5 minor bug fix in minimum_norm(...)
new 907410e handling loose case in minimum_norm
new a6a1818 fix epoch rejection
new 70c0639 bug fix in pick_types
new 2db8e0a fixing manual
new 2037e21 fixing manual
new a9cf2f7 fixing manual
new 25a16a7 ENH: refactoring covariance estimation. TODO: reject when cov estimation
new 0fd67ce API : changing epoch rejection API
new 419ae64 FIX : keeping only data channels when averaging
new 1e52640 Merge branch 'manual' of github.com:mne-tools/mne-python
new d2bb290 fixing manual
new 243a144 fixing manual
new 700c4bd fixing manual
new ccd178e ENH : finish artefact rejection in cov estimation
new bdbc36a ENH : can drop channels from Epochs
new 62e89f5 fixing manual
new f9ce0df fixing manual
new a56d71d Merge branch 'master' of https://github.com/emilyruzich/mne-python
new 95f5699 fixing manual
new 850d2da fixing manual
new 3fd3d06 Merge branch 'master' of https://github.com/emilyruzich/mne-python
new 1185fff FIX : in makefile for doc
new eb67b7a API: refactoring inverse pb to pass whitener to solver and not covariance
new 19097ed ENH : refactoring IO of evoked, API : new crop method for evoked
new e193348 API : change access to raw data to hide the first_samp mess API : rename cov estimation methods FIX : write of raw data FIX : some tests
new 2459381 adding show kw to plot_evoked
new 018c573 fixing manual
new 879debc MISC : s/from_/from/g + some pep8
new 189ebab Merge branch 'master' of https://github.com/emilyruzich/mne-python
new bd1860e pep8
new 945bf97 misc in tf cluster example
new fe4fbec pep8
new f21fedb pyflakes
new 6b0d529 ENH : faster complete_source_space_info
new 49c4df6 ENH : rm some XXX for speed
new 3fd04c0 FIX : rejecting cropped epochs
new 581ad27 ENH : making permutation_cluster_1samp_test more generic with stat_fun
new 70c16aa Merge branch 'master' of github.com:mne-tools/mne-python
new 1838855 Merge branch 'master' of github.com:mne-tools/mne-python
new 35c7ba1 ENH : source_induced_power and SourceEstimate class + viz source WIP
new 7bccdfc ENH : source_induced_power and SourceEstimate + 3D source viewer
new 8502ef8 ENH : adding the possibility to morph source estimates FIX : some fix to read sparse data in fif FIX : fix failing stats test
new aef45e3 refactoring stc.py to source_space.py
new f095c6d pep8
new 10088c6 numpy trick
new 00a3aad renaming bem_surfaces.py to surface.py + merge surfer.py and surface.py
new 097c812 ENH : speed improvement e.g. in source_induced_power
new bb22095 ENH : allowing source_induced_power to run in parallel
new 30e0ee1 new setup instructions for martinos
new 278b76b misc
new 93313fd adding ch_names property in Raw
new 8bd01b8 ENH : adding option to subtract_evoked in source_induced_power
new 8cf0a1a bug fix
new 39582d5 ENH : better handling of SSP projection in Epochs and Evoked
new 0b8c43f making permutation_t_test parallel
new 9dc791a fix docstring of permutation_t_test
new 4100ab9 ENH : adding the possibility to compute MNE on raw data + restriction to 1 label
new 0ccd0bd DOC : clean before build
new a63f8b1 ENH : speeding up source_induced_power using true data dimension
new 962fd2d fix write_events
new 88fc40a DOC : some cleanup in index page
new 0ef5163 DOC : fix many warnings in doc generation + more conversion
new c3bad67 running reindent on all files
new 1c9ef2e inplace square computation
new a5fab20 DOC : adding gitwash to the doc
new f8a385e basic band pass filter based on firwin2
new 8565be6 ENH : basic EOG + ECG artifacts detectors
new d2fdbff reindent
new 83f5066 TEST : better test in artifacts
new 6a94339 DOC : docstring in find_eog_events
new e36c38c ENH : adding time_func in apply_inverse_raw
new a3d1ccb fixing manual
new 25ad2d2 Merge branch 'manual' of git://github.com/mne-tools/mne-python
new 722ad1f adding low and high pass filters
new 401cf7a fixing manual
new 73f428e avoiding underflows in norm computation
new aa4bf20 fixing manual
new b59e350 ENH : setup.py + packaging
new 31ac536 Merge branch 'master' of https://github.com/emilyruzich/mne-python
new e9c20fc fixing manual
new f4c285f fixing manual
new 3bdfe3c fixing manual
new c55c582 fixing manual
new c02493a fixing manual
new 64d641e Merge branch 'master' of https://github.com/emilyruzich/mne-python
new f66609f fixing manual
new 49b0fe0 ENH : can crop SourceEstimate
new c713757 changing file permissions
new de57d29 fixing manual
new c1d9ad3 better docstring
new c71e160 ENH : adding alpha version of script to remove EOG + ECG artifacts from data
new d173657 ENH : adding script to generate BEM models from flash sequences (mne_flash_bem_model.py)
new 480062b fix in path setup at MGH
new 46c6144 DOC: reorganizing examples
new f9f03d5 Merge branch 'master' of https://github.com/emilyruzich/mne-python
new 3bdf465 DOC : fix some paths
new 811c2db cleanup manual + some examples
new ff70699 DOC : fixing manual (refs + links)
new 593a321 update README.rst
new bd3f1e5 update README.rst
new 8d7bed5 update README.rst
new b8eefc4 ENH : adding support for quad surf files API : no need to pass source space to mne.morph_data
new 3079d56 var naming
new e455879 fixing manual
new 2d65617 fixing manual
new f28ba25 FIX : None bug in copy_tree
new 9c5d3e7 FIX : bug with pca in source_induced_power
new afeb01d TEST : for pca in source_induced_power
new 4844e51 Merge branch 'master' of github.com:mne-tools/mne-python
new 328ad44 fixing manual
new 693e686 Merge branch 'master' of https://github.com/emilyruzich/mne-python
new 2faca7a fix manual indentation
new 1b8342b fixing manual
new 6f1c7d6 ENH : adding cluster level stats with connectivity matrix (for mesh)
new acf298d Merge branch 'master' of https://github.com/emilyruzich/mne-python
new f0d3912 more on manual
new 3c8860b fixing manual
new 466d646 fixing manual
new 81fc4ed DOC : more fix on manual (done)
new da8526e FIX : bug fix in cluster_level with connectivity + FIX in pval computation
new 49b5fe9 ENH : adding option for nb smoothing iter in morphing
new 2d492f5 MISC : cleaning cluster level with connectivity
new 7d4a8c0 ENH : factoring code for baseline correction
new 33b7045 ENH: adding tools to generate source space connectivity
new bfad910 adding verbose option
new bda9bd5 factoring joblib parallel code
new 7b19fca ENH : can pass seed in cluster level stats
new c970a54 misc in manual
new 11a4ecf fix
new d32cb2b FIX: reading old evoked file
new 2377d9c FIX : in Evoked.crop
new 929a53c ENH : store sfreq and nchan as float and int in Evoked
new d7aaed6 FIX: getting rid of Bunch object which was error prone with deepcopy
new ef97d51 ENH : first support for CTF data
new 5e61e34 FIX : misuse of is to compare strings
new 96f01a6 FIX : some is istead of == and some speed improvement
new 1390376 misc in MNE
new 37b7360 doc fix
new 0bf4b4a fix preload inconsistency due to bad epochs
new 17d1dfe ENH : better support for CTF data + tests
new c36a91a ENH : adding EEG ssp in Epochs FIX : Evoked.times now match C code TEST : better test with C code between Epochs.average and Evoked NOTE : cov estimation + SSP estimation still needs to be fixed
new b498ec7 FIX : fix cov estimation with events (not 100 pct sure yet)
new 404f762 API: compute_covariance now takes as input Epochs
new 398b4c8 ENH : make SSP computation work + adding tests
new 43636df FIX : adding missing fif proj file for tests
new a76551d TEST: test find ECG peaks
new 6ddb6fa TEST: test find EOG peaks
new eb4d68e FIX : fix reject param in cov estimation example
new 2cd1df9 FIX : fix text in cov estimation example
new a3920a5 ENH : using local imports in tests
new 46e1291 ENH : using local imports in tests
new 31a64f7 DOC: capturing mayavi for doc generation
new bc6dace DOC: capturing mayavi for doc generation for real
new 868b5bd some doc string
new 3124bf4 some doc string
new 240886c DOC: better latex doc
new 8d16d66 DOC : better doc upload procedure with rsync
new d6d60a7 DOC: better latex rendering of the doc
new d9613ce DOC: misc title formatting
new eb91264 API : s/source_induced_power/source_band_induced_power ENH : new source_induced_power to computer power and phase lock in a label
new 30f576f FIX: bug fix in reading of dig points
new 747ed2c DOC : adding tutorials on Python
new 31eb147 FIX: Isotrak does not throw an Exception when not found
new 317db4d FIX : one more fix on isotrak
new 62582ee DOC : tiny fix to getting started page
new 15aefd3 ENH : adding pick_normal option in MNE estimates
new 5b3d1ae ENH : adding multi tapper PSD computation
new e7284e5 Added more information about the software
new 36133fc FIX : less code duplication in write of meas info between raw and evoked (WIP)
new ff5b2ef API: do not copy the digitization points from original raw data but read it from info dict
new 83c9b08 FIX : fix writing of meas info for maxfilter
new 9caac93 ENH: adding transform_coordinates
new 26a5f9b ENH: adding drop_small_buffer to Raw.save for maxfilter
new c7c38b7 API: removing support for fMRI prior
new 906abbb ENH : new apply_inverse_epochs and refactoring of minimum_norm.inverse + tests
new 2912534 Fix time units (s->ms)
new 5656994 ENH : improve Makefile
new 63cf54c FIX : fix scikit-learn renaming compat
new 45600a4 ENH : adding support to assemble inverse operator in Python and removing old version
new 5e7e14a Merge branch 'master' into invop
new 6550839 FIX : removing old test_whitening_cov
new bbbd7bf Merge pull request #2 from agramfort/invop
new c71e096 Merge pull request #1 from KuperbergLab/master
new 2b8c40c STY : misc
new ecb5fae trailing spaces
new 234b9d9 ENH : using nose.tools.assert_true instead of assert
new 1d4a117 Merge branch 'master' into label_tfr
new 11d22fd ENH : using pick_normal for PLV in source space + cleanup
new 3569d70 ENH : fix for new sample dataset
new e7d0874 DOC: using scipy-lectures as tuto
new 4c0e1a9 Merge branch 'master' into label_tfr
new 87c0dff prettify example + adding test for source_induced_power
new abac1f6 ENH: misc extra line
new b8e6f91 Merge pull request #3 from agramfort/label_tfr
new eff54af FIX : fix svd without full_matrices=False
new f1ca553 add info to example
new a1862f1 Merge pull request #4 from mluessi/doc_fixes
new 8e30d92 typo
new 4c3f8b8 typo in example comment
new 9215d22 Merge branch 'master' of github.com:mne-tools/mne-python
new c577258 typo
new f45a9b5 Merge branch 'master' of github.com:mne-tools/mne-python
new 2e624ce preparing 0.1 release
new 756067e Merge branch 'master' of github.com:mne-tools/mne-python
new 768d149 updating README
new d902b34 BF: fixing executable flags for all docs/scripts/images
new a98e2d9 Merge pull request #5 from neurodebian/master
new b5d6768 fix copyrights and authors
new 44a5ef5 DOC: few typos spotted while browsing the docs
new 866d33d Merge pull request #6 from neurodebian/master
new f9ced9b typo
new 8660408 added indexing and slicing operations for epoch
new 71daef7 use warnings module, cosmetic changes
new a27f900 ENH : avoid allocating memory for all epochs (even bads)
new 382c164 Merge branch 'master' of github.com:mne-tools/mne-python
new 42feb3c use __get_item__ instead of __get_slice__, support pythonic indexing, small fixes based on Alex' comments
new 6799065 Multiple fixes: - indexing and slicing now always returns Epochs object - fixed bugs that occurs when Epochs only has one event (len(self.events) is 3 for single event) - still using shallow copy to avoid copying raw
new 2e58b78 removed debug stuff
new 51a953b indentation was meesed up
new 361b2eb Merge branch 'master' into epoch_indexing
new a23fb11 lemoved len() function, use len(self.events) instead of len(self)
new 20a4119 fixed bug that could occur if only one good event
new ce83e7a remnoved unused variables
new 468735e better way of constructing 3D array. this should be the last commit (hopefully)
new b63a138 ENH : adding decimation factor to reduce computation time source time frequency
new 5700564 Merge pull request #7 from mluessi/epoch_indexing
new d432365 Merge branch 'master' of github.com:mne-tools/mne-python
new a54ebbd STY: misc
new 7c23f79 ENH : adding temporal decimation factor to induced_power
new af719ff adding test-profile target in Makefile
new f84a054 ENH : adding numeric interface to SourceEstimate class
new e438eb0 Merge pull request #8 from agramfort/stc_array
new d4b38ce FIX : bug fix with stc.times in apply_inverse_raw
new f2fb34d ENH : first start on volume based source estimates
new c4fd097 ENH : first working support for volume source spaces
new b498e21 ENH : read volume source space info from fif
new aef0cd7 ENH : adding mne.read_proj and adding __repr__ to projection vectors
new efb9400 ENH : adding support for nifti output + nice example
new ccb9c17 wip on overlap add
new 109a9c5 ENH : allowing export of volume stc to full MRI resolution
new e3a2b8a zero phase, not yet working correctly
new 5e2766f zero-phase using overlap-add working, code needs cleanup
new 45cd849 Merge pull request #9 from agramfort/volume
new b91de33 ENH : adding pick_types_evoked function
new 2d02924 FIX : fix apply inverse with dSPM=False
new 02baee5 All filters using overlap-add
new 4deab5f ENH: overlap-add filtering for long signals
new 60a8797 TEST : adding test for MNE values around 1 nAm
new aa0ef52 ENH : raise exception when channels in inv op and data do not match
new f60e6ce ENH : nicer covariance example
new 5252c42 First commit of my branch with my fixes.
new f1f9e28 ENH : adding keep_only_data_channels option to Epochs.average
new 379aae8 FIX : allow morphing on data only defined on one hemisphere
new d8d9caa ENH : improve API for ECG detection and fix broken test
new c17966a ENH : adding support for FDR and Bonferonni p-value correction
new 4389232 Merge pull request #13 from agramfort/fdr
new 683de5c ENH : add support for ND-array in FDR + Bonferroni
new 9154cb2 Merge pull request #12 from agramfort/fix
new 422ee50 ENH : adding what's new page
new c3dde30 ENH : adding what's new page
new 9db7c13 bump version number
new ab65aa3 FIX : hot fix in plot_find_ecg_artifacts.py
new 3b02ae3 bump version number to 0.2.git
new 11ca75b ENH : Sign flip computation for robust label average of signed values
new 67922cd ENH: added filter_length parameter, improved test, cleaned up code
new 44593b8 ENH : adding write_label function + function that converts an stc to a label
new c890cbd FIX : in stc_to_label
new a2b6389 MISC: remove auto_examples with make clean in doc
new 9b95b6b cosmit
new bcef766 Merge branch 'overlap_add'
new c15907c ENH : raise warning with n_fft is not a power of 2
new 559a4c2 ENH : handle FS labels starting with lh. or rh.
new e1bc357 fixed typo
new a04eb1f FIX: ignore additional outputs of find_ecg_events
new 7befeb0 ENH: support loading of .w files for SourceEstimate
new bd2f6ff ENH: better reading of w, writing of w, unit test
new efe18eb update python system requirements
new 37b2b8f Merge branch 'master' of github.com:mne-tools/mne-python
new 1171603 ENH : more informative error message in read vol iop
new 7f4ea3a Added docstring
new 745b7c7 Merge pull request #14 from mluessi/w_file_suport
new 66d0174 FIX: mistake in documentation
new 4b09231 adding @mluessi to file header
new 18fb4c4 fix test docstring + pyflakes
new e7abf60 Update changelog
new 2ff43d2 ENH: preload and setitem for raw
new 538c87f BF: save correct first_samp time in raw file
new 1fa2b7a HACK: prevent proliferation of image files in documentation build
new 201a17b ENH: setitem for raw
new d2155cc ENH: test for raw
new bcc7e42 ENH: correct first_samp when tmin is not None
new bb71018 tmin default param 0 instead of None
new 58e8c0d ENH: preload keyword in init, support memmapped-file, moved test
new 9f5576a Merge branch 'raw_preload_setitem' of github.com:mluessi/mne-python into raw_preload_setitem
new 6bed834 Correct whats_new
new 05d10d7 Fix: wrong default argument
new 89d4ab9 ENH : update sklearn import path + fix heisen test by fixing the seed
new 7fff5eb ENH : Raw no longer derive from dict by just object + simply getitem and setitem + adding test
new adab8a9 MISC : updating what's new
new 44f835f Merge branch 'raw_preload_setitem'
new 3b273f6 ENH : adding pick_events function
new 941f3ef ENH : making Epochs.bad_dropped hidden
new d1351e6 ENH : allowing event_id == None in Epochs
new 900bd2f DOC: fix for doc math issue
new d57ec0c FIX : hard coding stime channel in mne.find_events
new 1446e94 FIX : missing pick of FIFFV_MISC_CH
new 4b8d486 ENH : allowing multiple stim channels in mne.find_events
new 89fd09f Merge pull request #16 from agramfort/simple_events
new 369e43a Merge branch 'master' of github.com:mne-tools/mne-python
new 5b9793d ENH : raise Exception with inverse operator was computed with bad channels
new 5603114 ENH : add possible to pick channel using regular expression
new 2d6a2f2 ENH: conserve_memory option for apply_inverse_raw
new 868f268 Changed conserve_memory to buffer_size
new 92f36a1 ENH: better tests for apply_inverse_raw
new f352dc7 create fixed orientation inverse operator correctly
new 25b75f8 FIX : fix make_inverse using fixed orientation forward
new 8400c67 cosmit
new de324e3 ENH : first attempt to make make_inverse_operator work with fixed orientation (small diff with C code to investigate)
new a3160e3 Merge branch 'inv_raw_lessmem'
new 04bfc74 ENH : allow the merge of evoked data obtain for example on different raw files
new 7d9e1ee ENH : support for arithmetic of Evoked objects (used for contrasts)
new ef9d5f4 update what's new
new 9e8732b Merge pull request #18 from agramfort/merge_evoked
new aa342f2 ENH: include pick_normal into _assemble_kernel to avoid computation of non-normal components when pick_normal=True
new 598355e Merge pull request #19 from mluessi/pick_normal_opt
new eb50e4d DOC: adding mne-python-intro tutorial to main doc
new 9a72ede Merge pull request #20 from agramfort/tuto
new 37d6f8e ENH: adding function applY_forward() (not finished)
new 9592210 ENH: apply_forward, finished implementation, added test
new 9d9e595 use small raw file for test
new f119671 ENH : ignore loose param with fixed orient forward
new 6267e6f apply_forward returns Evoked, cleaned up code
new ffda002 rem. include, exclude from apply_forward functions, added pick_types_forward
new 57708a3 Merge pull request #21 from mluessi/apply_forward
new f3f71d8 COSMIT: polish test_forward.py
new b991e7d FIX: pass subjects_dir to read_morph_map
new 29fd866 ENH: morph_data optimization
new 8270c58 Merge pull request #22 from mluessi/morph_data_opt
new cbd49da FIX: use float64 for sing. val in inverse to prevent underflow in square
new dd0f0fd Merge pull request #23 from mluessi/inv_sing_double
new 01d2845 ENH : more permissive test for evoked algebra
new 958e5af DOC : docstring formatting
new d2ebbdf DOC : docstring formatting
new 9292090 DOC : docstring formatting
new 0c22e60 ENH : support algebra of covariance matrices + fix writing when cov is computed in python
new 46dd988 ENH : more permissive test for evoked algebra
new cc76c08 FIX : fix stupid mistake in averaging cov
new 52863c6 Merge pull request #24 from agramfort/cov_algebra
new 37d9fb4 ENH : add support to write BEM surfaces in fif file
new a180543 fix docstring
new 3380d9f Merge pull request #25 from agramfort/write_bem_surface
new 5f33313 ENH : new mne_surf2bem.py that mimics mne_surf2bem without crashing when surface is not clean
new d74ca2c Merge pull request #26 from agramfort/mne_surf2bem
new f6cd0f3 ENH: filtering and apply_function for Raw
new decb721 ENH: support complex data, analytic signal, conditional data type conversion
new 08fbe22 Save memory if n_jobs=1 and dtype stays the same
new adfe663 added envelope parameter, renamed vars, more comments
new be3a06a Merge pull request #27 from mluessi/raw_apply
new ec73fec ENH : add support to write inverse_operators (surf + volume)
new 88e70a1 ENH : add plot_cov function to display noise cov with and without SSPs
new 7d7ab1c ENH : avoid FIFF constants duplication
new e2661ea typos
new fb6491e update what's new
new a8707f6 Merge pull request #29 from agramfort/write_inv_op
new 57d54eb typo
new 603022f Merge pull request #30 from agramfort/plot_cov
new 989e855 API: read cov now form .fif with mne.read_cov and mne.fiff.read_cov is used to read from file id
new ced9b64 API : cleanup Covariance which now restricted to noise cov
new 590e90a Merge pull request #31 from agramfort/mv_read_cov
new 74bce0d removed unused keep_sample_mean paramter
new 7b9583f Merge pull request #32 from mluessi/cov_typos
new 5352e2b FIX: wrong dimension in sample_mean computation
new 0e93b02 cov was still wrong
new a61c248 compute sample mean over epochs, can only handle single event type
new 2e287f4 FIX: cov comp. for multiple event types if keep_sample_mean=False
new 593095a Merge pull request #33 from mluessi/cov_sample_mean
new a3af68d updated whats_new
new 03805ab typo
new 7d2c6a3 removing old __version__ number
new 786ef32 Merge branch 'master' of github.com:mne-tools/mne-python
new 0ce34a2 ENH : first attemps to add class/function refence to the doc
new 46faf7f FIX : cluster problem with ndimage on some version of scipy
new 4002002 DOC : improve reference + some doc fixes
new 2e50625 update dependency list
new 6e3c479 DOC : fix doc reference page
new 3fc9397 Merge pull request #34 from agramfort/doc_reference
new 905f579 fix doctest
new d3a2824 bump version number
new 8fe9b9b bump version to 0.4.git
new 93074a1 ENH : refactor proj/SSP/PCA computation and adding support for computation on evoked data
new aab969b fix permissions
new bc1bdbd ENH : add support for ECG channel name
new 30376eb Merge pull request #35 from agramfort/proj_refactor
new 517749c factorize activate_proj function
new bfc488f FIX : fix proj['active'] mess
new 1d2961a ENH : add reject parameters in mne_compute_proj_ecg.py
new 9d1c2e1 ENH : append existing projections to generated proj in mne_compute_proj_ecg.py
new 70fc89b ENH : add average ref to mne_compute_proj_ecg.py and support for manual bad channels
new 77c7e89 update usage
new 3888322 Merge pull request #36 from agramfort/refactor_proj2
new 4158f69 ENH: warning for large currents
new 49322b7 Merge pull request #37 from mluessi/cur_warning
new d7da4ad API : clean up options in mne_compute_proj_ecg.py
new 8d5025f Merge branch 'master' of github.com:mne-tools/mne-python
new ac79afd ENH : add plot for noise covariance eigenvalues decay
new c356aed fix std not var
new 5d21b3b Merge pull request #38 from agramfort/cov_svd_vals
new e0f61f3 API : make Covariance inherit from dict
new 8786d8a ENH : new pick_channels_cov function
new 39dd68e ENH : add new function to regularize noise covariance
new 5a66d43 DOC: add mne.cov.regularize to an example
new 4cf4209 update waht's new
new 0a6fea3 Merge pull request #39 from agramfort/reg_cov
new b15d6f4 DOC : update install doc
new 504d484 FIX : fix negative triggers due to old neuromag system
new 46c676d preproc: ecg_proj rework
new f9fc4ac added missing files
new 13c2aa8 FIX : fix writing of inv op obtained with make_inverse_operator
new 7981d00 Merge pull request #41 from agramfort/fix_make_inv_methods
new 3b776ce EXG proj
new cdffe53 EXG proj
new f23fd8a maffilter wip
new 602fc1d FIX : fix writing of inv op for mne_analyze + refactoring
new 3025cf1 Merge pull request #42 from agramfort/fix_write_made_inv_op
new 6c85101 maxfilter, EOG SSP computation
new 41f3d55 code cleanup
new 6c191df added tests
new 8f7ca56 typos and cosmetics
new e403e1b ENH : changing filtering default parameters + adding option to pass ECG proj in mne_compute_proj_eog.py + adding EXG name to SSPs
new bf56288 Merge pull request #1 from agramfort/preproc_refact
new 676354b Merge pull request #40 from mluessi/preproc_refact
new 669b2c8 update what's new
new df0f197 adding neurospin path to sample data
new 7d8f88c Added mne_maxfilter.py, proj argument in proj_ecg script, setup.py
new bf1f614 updated whats_new
new b55fac5 added comment
new a769da3 Merge pull request #43 from mluessi/preproc_fixes
new da11aac define option types
new c066d3f Merge pull request #44 from mluessi/opt_types
new c1893aa opt. to use dif. file for event det.
new 449f0bb Merge pull request #45 from mluessi/raw_event
new 2440bc8 add warning in ecg.py
new b216df9 Merge branch 'master' of github.com:mne-tools/mne-python
new fc767b8 ENH : expose qrs_detector params in mne_compute_ecg_proj.py (add --tstart option)
new c8941dd clean up
new f34a4b9 Merge pull request #46 from agramfort/ecg_detect
new 3b90fef FIX : fix hemisphere identification with full path in read_label
new 0dd43ea FIX : fix filter with low high pass freq
new 7a2b200 FIX : fix Epochs with reject=None and epoch at the end of file
new de823d0 ENH : nicer plot of PSD in examples
new fd939de ENH : new Raw.filter method to simply filtering
new 9e079fb ENH : add tmin = tmax to compute_covariance
new a1ed363 DOC : improve example docstring
new 99e8c0b ENH + API : add support for sLORETA to apply_inverse, apply_inverse_raw, apply_inverse_epochs
new 7c57b93 Merge pull request #48 from agramfort/filter
new b5a724b merge conflict resolved
new 6e00213 typos
new 4f7d7e6 Merge pull request #50 from agramfort/sloreta
new d17d730 ENH: pick using named selection
new 91a2ef9 selection file added
new 0b62f1e Merge pull request #51 from mluessi/pick_selection
new 16832eb ENH: rework of selection
new 72bd4ec added selection.py
new cf818c8 typo, beautification
new 9b0aadd whats new
new 4e5ed0b Merge pull request #52 from mluessi/pick_selection_rework
new 2923459 ENH : add implementation of LCMV
new 5cf2e7d DOC : better lcmv docstring
new a11e228 FIX : Backporting scipy.signal.firwin2
new 6c25cd8 Merge pull request #53 from agramfort/lcmv
new 13a83e6 TST : adding test in firwin2
new 587ee2b Merge branch 'master' of github.com:mne-tools/mne-python
new aa194a2 use built-in set
new 8d7e0de Merge branch 'master' of github.com:mne-tools/mne-python
new 5c6205b ENH : speedup + reduce memory of morphing
new 8056436 Merge pull request #55 from agramfort/morph_buffer
new c656aa8 ENH: filter trans bw, warning
new 60d61a8 low and high trans_bandwidth
new b1a56f6 Merge pull request #56 from mluessi/filter_enh
new 68acde5 FIX: do not use parallel if n_jobs==1
new c8bb5ab Merge pull request #57 from mluessi/tfr_parallel_fix
new 46ba514 ENH : add support for n_cycles varying with frequency
new 2e193c6 FIX: bug in print output
new 34add6f ENH: proj support in compute_raw_psd
new e915ad0 ENH : add basic support for temporal whitening with AR model
new 567538e Merge pull request #58 from agramfort/tfr_improvement
new 80d2dad ENH: warning if sample dataset old
new d4cfece new size of sample data
new ab71896 lazy import comment
new 74e9718 Merge pull request #61 from mluessi/sample_version
new fd0d62b ENH: raw.add_proj, updated example
new 9814673 bump version number
new 7565056 correct freq. range
new 7962858 proj idle/active handling
new bc5af6a use include_active
new 726c4ca Merge pull request #59 from mluessi/compute_raw_psd_proj
new 6792b09 FIX: wrong number of proj
new 8bab411 Merge pull request #62 from mluessi/proj_fix
new 61f688a doctest fix
new 4b74e63 Merge branch 'master' of github.com:mne-tools/mne-python
new 4e948cf ENH : new option to have morlet be zero mean (relevant for low number of cycles)
new 691bec2 Decreased verbosity when reading events from Raw objects.
new 6d40f6d verbose flag defaults to True np.abs now properly called in mne/fiff/raw.py
new 3e4e5a4 TST: add test on morlet
new 6a0aa9d Merge pull request #63 from agramfort/zero_mean_morlet
new c7a878e Added docstring entries for verbosity flag.
new 4ab6fff Fixed accidental editing of docstring for write_events in mne/events.py (sorry!)
new fe401b9 add *.pyo to gitignore
new 52fb2f0 FIX Epochs.average(): use correct n_events when preload==False
new 4afa43d TST : add test for n_events average fix with no preload
new 6088e97 Merge pull request #64 from louist87/master
new 879baac fix tutorial doctest
new 7accfa6 ENH : clean up the raw.verbose option
new 9ae6870 Merge pull request #1 from agramfort/cmb-epochs-average-fix
new 775e897 Merge pull request #65 from christianmbrodbeck/cmb-epochs-average-fix
new 4676d83 ENH : stft with tight frame and sine window
new 8f985c1 ENH : new stim artifact rejection function
new a3d41d4 TST : better tests in stim artifact
new 37256a2 ENH : pass sfreq to stftfreq
new 488f368 fix doctest
new 6acb9de added Alex's comments
new 4a3696f removed duplicated code
new d3cfc4f added check if preloaded is true
new 0a3d400 modified changelog in whats_new
new 5250dbf deleted empty line
new d9e2bfa Merge pull request #66 from agramfort/stft
new 55fb036 changed array to tuple in call to interp1d
new a7c064d Merge pull request #60 from agramfort/time_whiten
new c339669 ENH : new simulator (WIP)
new eea3d62 ENH : big cleanup of simulation code + new plot function for sparse stc
new 0a4c44b ENH : cleanup and remove duplicated gabor atoms code
new 0793fb0 ENH : simplify evoked data generate + some docstring updaes
new 436efac ENH: generate circular labels
new 8a3accd ENH: also retrun distance
new 53480e5 API : rename to generate_sparse_stc
new a075c40 rename sim_evoked.py
new 48d2bfa merged branch mluessi/simulation
new 02dc8ec typo
new 8dc0042 evoked in separate file
new 5e66a38 added generate_stc
new 247916e Merge pull request #1 from mluessi/simulator
new 4c12dd9 ENH : simulation code refactoring
new dd42b2d fix tests + pep8
new 111bee4 Merge pull request #67 from joewalter/stim_artifact
new 88fdc49 style on stim artifact
new 47ab928 FIX: data order, whats_new, test
new 8593614 Merge pull request #2 from mluessi/simulator
new 77b480c Merge pull request #68 from agramfort/simulator
new bf7fa34 added bootstrap and crop function to epochs
new f03d078 made return of idx in bootstrap optional
new 8ba89d5 fixed idx in test_bootstrap
new a7331a3 added comments on the pull request
new 5f0e95b added atleast_1d support
new f64cf2c corrected bad doc string
new e3ddc42 Merge pull request #69 from joewalter/bootstrap_epochs
new 095f2f0 ENH : implement MxNE with L21 prior
new 395fafc ENH : better plot_evoked with ylim and tight_layout
new 4014c12 ENH : add MxNE example of sample data
new 903a20c ENH : add better debiasing as suggested by Daniel
new b9c5690 ENH : factorize _prepare_inverse function
new 3acb855 ENH : factorize is_fixed_orient and compute_orient_prior
new 86331de update changelog
new 822a8eb ENH : add refs + cleanup in MxNE
new e311952 Merge pull request #70 from agramfort/mxne
new 4e71fba added sim, mixed_norm to setup.py
new 4e40701 FIX : missing random_state passed to generate_noise_evoked
new 0293347 DOC : document python setup.py install --user
new 3ab7ace FIX : fix doc with nested import of pylab in psd.py
new e012e4c MISC cleanup old coverage info in Makefile
new cb42641 ENH : add example of LCMV on volume grid
new f5f8981 Merge pull request #72 from agramfort/lcmv_volume
new 8a76a63 tiny change in LCMV volume example
new e420093 FIX: fir->iir, time index bug
new e16fc1b iir->fir
new 4a2d23c Merge pull request #73 from mluessi/ar_fixes
new 6c72874 ENH : add function to compute source PSD from raw file
new fc2dd0e pep8
new 5bb1822 update what's new
new 91b6cd8 Import joblib directly if sklearn not installed
new fa39acb Merge pull request #74 from agramfort/psd_stc
new bda8a2d Fixed indentation error
new c91b329 Merge pull request #75 from bburan/joblib_import
new db09465 ENH: LCMV for raw data
new 1e73c0d FIX: reg. if cov. is subset of channels
new de08911 FIX: don't use index() in loop
new df4b1e5 whats new
new 8966cfe DOC: note on brain_vision2fiff
new fd35c30 code cleanup
new 86e834f Merge pull request #77 from christianmbrodbeck/cmb-doc
new 3cf4266 ENH: lcmv_epochs()
new 5546ab4 not heavily tested
new 073c7c2 rem. nested fun
new c12da25 Merge pull request #76 from mluessi/lcmv_raw
new 0d0bf8c ENH : new stft_norm2 to compute stft norm taking into account negative freqs
new 576f1ac ENH : no relative imports in tests (check proper install)
new d3c80dc pyflakes + pep8
new 29523ca DOC : misc
new d22cbb8 FIX : error due to incmplete renaming
new 792952b ENH : new sphinx extension for example gallery
new 52a67fb ENH : plot something in plot_lcmv_beamformer_volume.py
new 1b0ca56 DOC : update reference + fix some docstrings
new 6f1b184 Merge pull request #80 from agramfort/no_relative_import_in_test
new 7068159 Merge pull request #81 from agramfort/better_example_gallery
new f7789ed API: make sfreq, lowpass, highpass float attributes (not np.array)
new 6073ba1 Merge pull request #82 from agramfort/sfreq_as_float
new 173b67a typo
new eff9ace typo
new 550e026 TST : add test for evoked simulation
new 07a86d6 Merge pull request #83 from agramfort/add_test_simu
new 7a1b19d bump version number to 0.4
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