[med-svn] [python-mne] 02/04: Imported Upstream version 0.7
Andreas Tille
tille at debian.org
Tue Nov 26 19:09:14 UTC 2013
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository python-mne.
commit 907acd7850721843f08256adea6a837016f834ea
Author: Andreas Tille <tille at debian.org>
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 <alexandre.gramfort at inria.fr> Alexandre Gramfort <alexandre.gramfort at gmail.com>
-Alexandre Gramfort <alexandre.gramfort at inria.fr> Alexandre Gramfort <alexandre.gramfort at m4x.org>
-Alexandre Gramfort <alexandre.gramfort at inria.fr> Alexandre Gramfort <gramfort at localhost.(none)>
+Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr> Alexandre Gramfort <alexandre.gramfort at inria.fr>
+Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr> Alexandre Gramfort <alexandre.gramfort at gmail.com>
+Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr> Alexandre Gramfort <alexandre.gramfort at m4x.org>
+Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr> Alexandre Gramfort <gramfort at localhost.(none)>
Martin Luessi <mluessi at nmr.mgh.harvard.edu> mluessi at nmr.mgh.harvard.edu <mluessi at nmr.mgh.harvard.edu>
Martin Luessi <mluessi at nmr.mgh.harvard.edu> martin <martin at think.hsd1.ma.comcast.net>
Martin Luessi <mluessi at nmr.mgh.harvard.edu> martin <martin at think.(none)>
@@ -10,14 +11,25 @@ Louis Thibault <louist87 at gmail.com> = <louist87 at gmail.com>
Louis Thibault <louist87 at gmail.com> Louis Thibault <louist at ltpc.(none)>
Eric Larson <larson.eric.d at gmail.com> Eric Larson <larson.eric.d at gmail.com>
Eric Larson <larson.eric.d at gmail.com> Eric89GXL <larson.eric.d at gmail.com>
+Eric Larson <larson.eric.d at gmail.com> Eric Larson <larsoner at uw.edu>
+Eric Larson <larson.eric.d at gmail.com> Eric89GXL <larsoner at uw.edu>
Denis A. Engemann <denis.engemann at gmail.com> dengemann <denis.engemann at gmail.com>
Denis A. Engemann <denis.engemann at gmail.com> denis <denis.engemann at gmail.com>
+Denis A. Engemann <denis.engemann at gmail.com> dengemann <d.engemann at fz-juelich.de>
+Denis A. Engemann <denis.engemann at gmail.com> Denis Engemann <dengemann at Deniss-MacBook-Pro.local>
+Denis A. Engemann <denis.engemann at gmail.com> Denis A. Engemann <d.engemann at fz-juelich.de>
+Denis A. Engemann <denis.engemann at gmail.com> Denis Engemann <dengemann at pool-186-21-zam037.wlan.kfa-juelich.de>
Daniel Strohmeier <daniel.strohmeier at googlemail.com> joewalter <daniel.strohmeier at googlemail.com>
Dan G. Wakeman <dgwakeman at gmail.com>
Teon Brooks <teon.brooks at gmail.com>
+Teon Brooks <teon.brooks at gmail.com> Teon <teon at nyu.edu>
+Teon Brooks <teon.brooks at gmail.com> Teon Brooks <teon at nyu.edu>
Romain Trachel <romain.trachel at inria.fr>
Roman Goj <roman.goj at gmail.com>
Andrew Dykstra <andrew.r.dykstra at gmail.com>
Yousra BEKHTI <yousra.bekhti at gmail.com> Yoursa BEKHTI <ybekhti at is222485.intra.cea.fr>
Yousra BEKHTI <yousra.bekhti at gmail.com> Yoursa BEKHTI <yousra.bekhti at gmail.com>
Mainak Jas <mainakjas at gmail.com> Mainak <mainakjas at gmail.com>
+Alan Leggitt <leggitta3 at gmail.com> leggitta <leggitta3 at gmail.com>
+Praveen Sripad <pravsripad at gmail.com> prav <pravsripad at gmail.com>
+Praveen Sripad <pravsripad at gmail.com> prav <prav at 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
--
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