This is an automated email from the git hooks/post-receive script. yoh pushed a commit to tag 0.4 in repository python-mne.
commit 4002002ef2b1eb3a1d731337fab3ccaabd277494 Author: Alexandre Gramfort <[email protected]> Date: Wed Mar 21 18:53:11 2012 +0100 DOC : improve reference + some doc fixes --- .../_images/plot_read_and_write_raw_data.png | Bin 0 -> 61418 bytes doc/source/_images/plot_read_epochs.png | Bin 0 -> 186065 bytes doc/source/_images/plot_time_frequency.png | Bin 0 -> 151383 bytes doc/source/mne-python.rst | 2 +- doc/source/python_reference.rst | 38 ++++++++++++--------- mne/__init__.py | 11 +++--- mne/fiff/__init__.py | 2 ++ mne/fiff/pick.py | 4 +-- mne/minimum_norm/__init__.py | 2 ++ mne/source_estimate.py | 9 +++++ mne/stats/__init__.py | 2 ++ mne/viz.py | 6 +++- 12 files changed, 51 insertions(+), 25 deletions(-) diff --git a/doc/source/_images/plot_read_and_write_raw_data.png b/doc/source/_images/plot_read_and_write_raw_data.png new file mode 100644 index 0000000..4b63526 Binary files /dev/null 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 new file mode 100644 index 0000000..6484722 Binary files /dev/null and b/doc/source/_images/plot_read_epochs.png differ diff --git a/doc/source/_images/plot_time_frequency.png b/doc/source/_images/plot_time_frequency.png new file mode 100644 index 0000000..da7456b Binary files /dev/null and b/doc/source/_images/plot_time_frequency.png differ diff --git a/doc/source/mne-python.rst b/doc/source/mne-python.rst index 5199eca..c9c386c 100644 --- a/doc/source/mne-python.rst +++ b/doc/source/mne-python.rst @@ -8,9 +8,9 @@ MNE with Python :maxdepth: 1 getting_started.rst + auto_examples/index.rst python_tutorial.rst python_reference.rst - auto_examples/index.rst whats_new.rst gitwash/index.rst diff --git a/doc/source/python_reference.rst b/doc/source/python_reference.rst index 8b73446..2807742 100644 --- a/doc/source/python_reference.rst +++ b/doc/source/python_reference.rst @@ -4,7 +4,7 @@ Reference This is the classes and functions reference of mne-python. -.. _mne_ref: +.. currentmodule:: mne.fiff .. automodule:: mne :no-members: @@ -13,17 +13,15 @@ This is the classes and functions reference of mne-python. Classes reference ================= -.. currentmodule:: mne - .. autosummary:: :toctree: generated/ :template: class.rst - fiff.Raw - fiff.Evoked - Epochs - Covariance - SourceEstimate + mne.fiff.Raw + mne.fiff.Evoked + mne.Epochs + mne.Covariance + mne.SourceEstimate Functions reference =================== @@ -34,23 +32,17 @@ Functions reference read_cov write_cov - label_time_courses read_label label_sign_flip write_label stc_to_label - read_bem_surfaces read_surface write_bem_surface - read_source_spaces - save_stc_as_volume - morph_data - read_stc write_stc read_w @@ -59,8 +51,8 @@ Functions reference .. currentmodule:: mne.fiff .. autosummary:: - :toctree: generated/ - :template: function.rst + :toctree: generated/ + :template: function.rst pick_types pick_channels @@ -78,8 +70,20 @@ Functions reference read_inverse_operator apply_inverse apply_inverse_raw - make_inverse_operator apply_inverse_epochs + make_inverse_operator write_inverse_operator source_band_induced_power source_induced_power + +.. currentmodule:: mne.stats + +.. autosummary:: + :toctree: generated/ + :template: function.rst + + permutation_t_test + permutation_cluster_test + permutation_cluster_1samp_test + fdr_correction + bonferroni_correction diff --git a/mne/__init__.py b/mne/__init__.py index 8044dcc..652aa62 100644 --- a/mne/__init__.py +++ b/mne/__init__.py @@ -1,3 +1,6 @@ +"""MNE for MEG and EEG data analysis +""" + __version__ = '0.2.git' from .cov import read_cov, write_cov, Covariance, \ @@ -18,7 +21,7 @@ from .label import label_time_courses, read_label, label_sign_flip, \ from .misc import parse_config, read_reject_parameters from .transforms import transform_coordinates from .proj import read_proj -import fiff -import artifacts -import stats -import viz +from . import fiff +from . import artifacts +from . import stats +from . import viz diff --git a/mne/fiff/__init__.py b/mne/fiff/__init__.py index da57656..fda05f2 100644 --- a/mne/fiff/__init__.py +++ b/mne/fiff/__init__.py @@ -1,3 +1,5 @@ +"""FIF module for IO with .fif files""" + # Authors: Alexandre Gramfort <[email protected]> # Matti Hamalainen <[email protected]> # diff --git a/mne/fiff/pick.py b/mne/fiff/pick.py index d911ca3..9912c79 100644 --- a/mne/fiff/pick.py +++ b/mne/fiff/pick.py @@ -98,8 +98,8 @@ def pick_channels_regexp(ch_names, regexp): sel : array of int Indices of good channels. - Example - ------- + Examples + -------- >>> pick_channels_regexp(['MEG 2331', 'MEG 2332', 'MEG 2333'], 'MEG ...1') [0] >>> pick_channels_regexp(['MEG 2331', 'MEG 2332', 'MEG 2333'], 'MEG *') diff --git a/mne/minimum_norm/__init__.py b/mne/minimum_norm/__init__.py index 5fbf009..06a815a 100644 --- a/mne/minimum_norm/__init__.py +++ b/mne/minimum_norm/__init__.py @@ -1,3 +1,5 @@ +"""Linear inverse solvers based on L2 Minimum Norm Estimates (MNE)""" + from .inverse import read_inverse_operator, apply_inverse, \ apply_inverse_raw, make_inverse_operator, \ apply_inverse_epochs, write_inverse_operator diff --git a/mne/source_estimate.py b/mne/source_estimate.py index 38c3162..865fb67 100644 --- a/mne/source_estimate.py +++ b/mne/source_estimate.py @@ -328,6 +328,15 @@ class SourceEstimate(object): return "SourceEstimate (%s)" % s def crop(self, tmin=None, tmax=None): + """Restrict SourceEstimate to a time interval + + Parameters + ---------- + tmin : float or None + The first time point in seconds. It None the first present is used. + tmax : float or None + The last time point in seconds. It None the last present is used. + """ mask = np.ones(len(self.times), dtype=np.bool) if tmin is not None: mask = mask & (self.times >= tmin) diff --git a/mne/stats/__init__.py b/mne/stats/__init__.py index 4211030..38aa10f 100644 --- a/mne/stats/__init__.py +++ b/mne/stats/__init__.py @@ -1,3 +1,5 @@ +"""Functions for statistical analysis""" + from .permutations import permutation_t_test from .cluster_level import permutation_cluster_test, \ permutation_cluster_1samp_test diff --git a/mne/viz.py b/mne/viz.py index a750f78..260302a 100644 --- a/mne/viz.py +++ b/mne/viz.py @@ -7,7 +7,8 @@ import copy import numpy as np -import pylab as pl + +# XXX : don't import pylab here or you will break the doc from .fiff.pick import channel_type, pick_types from .fiff.proj import make_projector @@ -20,6 +21,7 @@ def plot_topo(evoked, layout): times = evoked.times data = evoked.data + import pylab as pl pl.rcParams['axes.edgecolor'] = 'w' pl.figure(facecolor='k') for name in layout.names: @@ -47,6 +49,7 @@ def plot_evoked(evoked, picks=None, unit=True, show=True): show : bool Call pylab.show() as the end or not. """ + import pylab as pl pl.clf() if picks is None: picks = range(evoked.info['nchan']) @@ -131,6 +134,7 @@ def plot_cov(cov, info, exclude=None, colorbar=True, proj=False, show=True): else: print ' The projection vectors do not apply to these channels.' + import pylab as pl pl.figure(figsize=(2.5 * len(idx_names), 2.7)) for k, (idx, name) in enumerate(idx_names): pl.subplot(1, len(idx_names), k + 1) -- Alioth's /usr/local/bin/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
