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commit 907acd7850721843f08256adea6a837016f834ea Author: Andreas Tille <[email protected]> Date: Tue Nov 26 19:35:20 2013 +0100 Imported Upstream version 0.7 --- .mailmap | 18 +++++-- .../_images/plot_read_and_write_raw_data.png | Bin 61418 -> 238712 bytes doc/source/_images/plot_read_epochs.png | Bin 186065 -> 124444 bytes doc/source/cite.rst | 2 +- doc/source/python_reference.rst | 52 ++++++++++++++++++++- doc/source/python_tutorial.rst | 3 +- doc/source/whats_new.rst | 22 +++++---- examples/plot_simulate_evoked_data.py | 1 - mne/__init__.py | 2 +- mne/datasets/spm_face/__init__.py | 2 +- mne/fiff/pick.py | 19 ++++---- mne/fiff/raw.py | 6 +++ 12 files changed, 100 insertions(+), 27 deletions(-) diff --git a/.mailmap b/.mailmap index ef644f0..8b0f8a7 100644 --- a/.mailmap +++ b/.mailmap @@ -1,6 +1,7 @@ -Alexandre Gramfort <[email protected]> Alexandre Gramfort <[email protected]> -Alexandre Gramfort <[email protected]> Alexandre Gramfort <[email protected]> -Alexandre Gramfort <[email protected]> Alexandre Gramfort <gramfort@localhost.(none)> +Alexandre Gramfort <[email protected]> Alexandre Gramfort <[email protected]> +Alexandre Gramfort <[email protected]> Alexandre Gramfort <[email protected]> +Alexandre Gramfort <[email protected]> Alexandre Gramfort <[email protected]> +Alexandre Gramfort <[email protected]> Alexandre Gramfort <gramfort@localhost.(none)> Martin Luessi <[email protected]> [email protected] <[email protected]> Martin Luessi <[email protected]> martin <[email protected]> Martin Luessi <[email protected]> martin <martin@think.(none)> @@ -10,14 +11,25 @@ Louis Thibault <[email protected]> = <[email protected]> Louis Thibault <[email protected]> Louis Thibault <louist@ltpc.(none)> Eric Larson <[email protected]> Eric Larson <[email protected]> Eric Larson <[email protected]> Eric89GXL <[email protected]> +Eric Larson <[email protected]> Eric Larson <[email protected]> +Eric Larson <[email protected]> Eric89GXL <[email protected]> Denis A. Engemann <[email protected]> dengemann <[email protected]> Denis A. Engemann <[email protected]> denis <[email protected]> +Denis A. Engemann <[email protected]> dengemann <[email protected]> +Denis A. Engemann <[email protected]> Denis Engemann <[email protected]> +Denis A. Engemann <[email protected]> Denis A. Engemann <[email protected]> +Denis A. Engemann <[email protected]> Denis Engemann <[email protected]> Daniel Strohmeier <[email protected]> joewalter <[email protected]> Dan G. Wakeman <[email protected]> Teon Brooks <[email protected]> +Teon Brooks <[email protected]> Teon <[email protected]> +Teon Brooks <[email protected]> Teon Brooks <[email protected]> Romain Trachel <[email protected]> Roman Goj <[email protected]> Andrew Dykstra <[email protected]> Yousra BEKHTI <[email protected]> Yoursa BEKHTI <[email protected]> Yousra BEKHTI <[email protected]> Yoursa BEKHTI <[email protected]> Mainak Jas <[email protected]> Mainak <[email protected]> +Alan Leggitt <[email protected]> leggitta <[email protected]> +Praveen Sripad <[email protected]> prav <[email protected]> +Praveen Sripad <[email protected]> prav <prav@prav-dell.(none)> diff --git a/doc/source/_images/plot_read_and_write_raw_data.png b/doc/source/_images/plot_read_and_write_raw_data.png index 4b63526..bdc5a88 100644 Binary files a/doc/source/_images/plot_read_and_write_raw_data.png and b/doc/source/_images/plot_read_and_write_raw_data.png differ diff --git a/doc/source/_images/plot_read_epochs.png b/doc/source/_images/plot_read_epochs.png index 6484722..c409439 100644 Binary files a/doc/source/_images/plot_read_epochs.png and b/doc/source/_images/plot_read_epochs.png differ diff --git a/doc/source/cite.rst b/doc/source/cite.rst index 7ca0308..e4c3734 100644 --- a/doc/source/cite.rst +++ b/doc/source/cite.rst @@ -5,6 +5,6 @@ Cite MNE and MNE-Python If you use in your research the implementations provided by the MNE software you should cite: - - [1] A. Gramfort, M. Luessi, E. Larson, D. Engemann, D. Strohmeier, C. Brodbeck, L. Parkkonen, M. Hämäläinen, `MNE software for processing MEG and EEG data <http://www.ncbi.nlm.nih.gov/pubmed/24161808>`_, NeuroImage, 2013, ISSN 1053-8119, `[DOI] <http://dx.doi.org/10.1016/j.neuroimage.2013.10.027>`_ + [1] A. Gramfort, M. Luessi, E. Larson, D. Engemann, D. Strohmeier, C. Brodbeck, L. Parkkonen, M. Hämäläinen, `MNE software for processing MEG and EEG data <http://www.ncbi.nlm.nih.gov/pubmed/24161808>`_, NeuroImage, 2013, ISSN 1053-8119, `[DOI] <http://dx.doi.org/10.1016/j.neuroimage.2013.10.027>`_ You should as well cite the related method papers, some of which are listed in :ref:`ch_reading`. diff --git a/doc/source/python_reference.rst b/doc/source/python_reference.rst index 0fef8d9..2c2561e 100644 --- a/doc/source/python_reference.rst +++ b/doc/source/python_reference.rst @@ -29,7 +29,6 @@ Classes Label BiHemiLabel preprocessing.ICA - decoding.TransformerMixin decoding.CSP decoding.Scaler decoding.ConcatenateChannels @@ -91,7 +90,7 @@ Functions: :template: function.rst parse_config - decimate_surfaces + decimate_surface read_bem_solution read_bem_surfaces read_cov @@ -131,6 +130,41 @@ Functions: read_raw_bti +.. currentmodule:: mne.fiff.kit + +:py:mod:`mne.fiff.kit`: + +.. autosummary:: + :toctree: generated/ + :template: function.rst + + read_raw_kit + read_elp + read_hsp + read_mrk + write_hsp + write_mrk + +.. currentmodule:: mne.fiff.edf + +:py:mod:`mne.fiff.edf`: + +.. autosummary:: + :toctree: generated/ + :template: function.rst + + read_raw_edf + +.. currentmodule:: mne.fiff.brainvision + +:py:mod:`mne.fiff.brainvision`: + +.. autosummary:: + :toctree: generated/ + :template: function.rst + + read_raw_brainvision + :py:mod:`mne.datasets.sample`: .. automodule:: mne.datasets.sample @@ -145,6 +179,20 @@ Functions: data_path +:py:mod:`mne.datasets.spm_face`: + +.. automodule:: mne.datasets.spm_face + :no-members: + :no-inherited-members: + +.. currentmodule:: mne.datasets.spm_face + +.. autosummary:: + :toctree: generated/ + :template: function.rst + + data_path + :py:mod:`mne.datasets.megsim`: .. automodule:: mne.datasets.megsim diff --git a/doc/source/python_tutorial.rst b/doc/source/python_tutorial.rst index 039c098..12abf40 100644 --- a/doc/source/python_tutorial.rst +++ b/doc/source/python_tutorial.rst @@ -158,9 +158,10 @@ Read and plot a segment of raw data (376, 2252) >>> print times.shape (2252,) - >>> data, times = raw[2:20:3, start:stop] # take some Magnetometers + >>> data, times = raw[2:20:3, start:stop] # access underlying data Reading 15015 ... 17266 = 99.998 ... 114.989 secs... [done] + >>> raw.plot() # doctest: +SKIP .. figure:: _images/plot_read_and_write_raw_data.png :alt: Raw data diff --git a/doc/source/whats_new.rst b/doc/source/whats_new.rst index 66fbc32..0853e0c 100644 --- a/doc/source/whats_new.rst +++ b/doc/source/whats_new.rst @@ -3,8 +3,8 @@ What's new .. _changes_0_7: -Current -------- +Version 0.7 +----------- Changelog ~~~~~~~~~ @@ -13,7 +13,7 @@ Changelog - New decoding module for MEG analysis containing sklearn compatible transformers by `Mainak Jas`_ and `Alex Gramfort`_ - - New realtime module containing RtEpochs, RtClient and MockRtClient class by `Martin Luessi`_, Christopher Dinh, `Alex Gramfort`_, `Denis Engemann`_ and `Mainak Jas`_ + - New realtime module containing RtEpochs, RtClient and MockRtClient class by `Martin Luessi`_, `Christopher Dinh`_, `Alex Gramfort`_, `Denis Engemann`_ and `Mainak Jas`_ - Allow picking normal orientation in LCMV beamformers by `Roman Goj`_, `Alex Gramfort`_, `Denis Engemann`_ and `Martin Luessi`_ @@ -76,9 +76,9 @@ Changelog - Add SPM face data set by `Denis Engemann`_ `Martin Luessi`_ and `Alex Gramfort`_ - Support reading of EDF+,BDF data by `Teon Brooks`_ - - - Tools for scaling MRIs (mne.scale_mri) by `Christian Brodbeck`_ - + + - Tools for scaling MRIs (mne.scale_mri) by `Christian Brodbeck`_ + - GUI for head-MRI coregistration (mne.gui.coregistration) by `Christian Brodbeck`_ - GUI for ki2fiff conversion (mne.gui.kit2fiff) by `Christian Brodbeck`_ @@ -86,11 +86,15 @@ Changelog - Support reading of EEG BrainVision data by `Teon Brooks`_ - Improve CTF compensation handling by `Martin Luessi`_ and `Eric Larson`_ - + - Improve and extend automated layout guessing by `Denis Engemann`_ - Add Continuum Analytics Anaconda support by `Denis Engemann`_ + - Add `subtract evoked` option to beamformers by `Andrew Dykstra`_ + + - Add new `transform` method to SourceEstimate(s) by `Andrew Dykstra`_ + API ~~~ @@ -103,7 +107,7 @@ API - Removed deprecated read/write_stc/w, use SourceEstimate methods instead - The `chs` argument in `mne.layouts.find_layout` is deprecated and will be removed in MNE-Python 0.9. Use `info` instead. - + - `plot_evoked` and `Epochs.plot` now open a new figure by default. To plot on an existing figure please specify the `axes` parameter. .. _changes_0_6: @@ -549,3 +553,5 @@ of commits): .. _Andrew Dykstra: https://github.com/adykstra .. _Romain Trachel: http://www-sop.inria.fr/athena/Site/RomainTrachel + +.. _Christopher Dinh: https://github.com/chdinh diff --git a/examples/plot_simulate_evoked_data.py b/examples/plot_simulate_evoked_data.py index 8c954c9..a0cc632 100644 --- a/examples/plot_simulate_evoked_data.py +++ b/examples/plot_simulate_evoked_data.py @@ -81,5 +81,4 @@ plot_sparse_source_estimates(fwd['src'], stc, bgcolor=(1, 1, 1), plt.figure() plt.psd(evoked.data[0]) -plt.figure() plot_evoked(evoked) diff --git a/mne/__init__.py b/mne/__init__.py index 3948289..b95152e 100644 --- a/mne/__init__.py +++ b/mne/__init__.py @@ -1,7 +1,7 @@ """MNE for MEG and EEG data analysis """ -__version__ = '0.7.git' +__version__ = '0.7' # have to import verbose first since it's needed by many things from .utils import (set_log_level, set_log_file, verbose, set_config, diff --git a/mne/datasets/spm_face/__init__.py b/mne/datasets/spm_face/__init__.py index 3a44b6e..f151c52 100644 --- a/mne/datasets/spm_face/__init__.py +++ b/mne/datasets/spm_face/__init__.py @@ -1,4 +1,4 @@ -"""MNE sample dataset +"""SPM face dataset """ from .spm_data import data_path, has_spm_data, requires_spm_data diff --git a/mne/fiff/pick.py b/mne/fiff/pick.py index 5e8f45e..9c2b6ae 100644 --- a/mne/fiff/pick.py +++ b/mne/fiff/pick.py @@ -305,9 +305,9 @@ def pick_channels_evoked(orig, include=[], exclude='bads'): One evoked dataset. include : list of string, (optional) List of channels to include (if empty, include all available). - exclude : list of string, (optional) + exclude : list of string, (optional) | 'bads' Channels to exclude (if empty, do not exclude any). - + Defaults to 'bads'. Returns ------- res : instance of Evoked @@ -397,17 +397,18 @@ def pick_types_evoked(orig, meg=True, eeg=False, stim=False, eog=False, @verbose -def pick_channels_forward(orig, include=[], exclude='bads', verbose=None): +def pick_channels_forward(orig, include=[], exclude=[], verbose=None): """Pick channels from forward operator Parameters ---------- orig : dict A forward solution. - include : list of string (optional) - List of channels to include (if empty, include all available). - exclude : list of string (optional) - Channels to exclude (if empty, do not exclude any). + include : list of string (optional) | None + List of channels to include (if empty, include all available). Defaults + auto None. + exclude : list of string (optional) | None + Channels to exclude (if empty, do not exclude any). Defaults to None. verbose : bool, str, int, or None If not None, override default verbose level (see mne.verbose). @@ -515,8 +516,8 @@ def pick_channels_cov(orig, include=[], exclude='bads'): A covariance. include : list of string, (optional) List of channels to include (if empty, include all available). - exclude : list of string, (optional) - Channels to exclude (if empty, do not exclude any). + exclude : list of string, (optional) | 'bads' + Channels to exclude (if empty, do not exclude any). Defaults to 'bads'. Returns ------- diff --git a/mne/fiff/raw.py b/mne/fiff/raw.py index f39bc80..18c00da 100644 --- a/mne/fiff/raw.py +++ b/mne/fiff/raw.py @@ -1954,6 +1954,12 @@ def write_raw_buffer(fid, buf, cals, format, inv_comp): write_function(fid, FIFF.FIFF_DATA_BUFFER, buf) + # make sure we didn't go over the 2GB file size limit + pos = fid.tell() + if pos >= 2147483647: # np.iinfo(np.int32).max + raise IOError('2GB file size limit reached. Support for larger ' + 'raw files will be added in the future.') + def finish_writing_raw(fid): """Finish writing raw FIF file -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/python-mne.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
