[med-svn] [python-mne] 344/353: DOC : update reference + fix some docstrings
Yaroslav Halchenko
debian at onerussian.com
Fri Nov 27 17:25:29 UTC 2015
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yoh pushed a commit to tag 0.4
in repository python-mne.
commit 1b0ca56c7d94bcc01d6370b3efa57bcbed2dd217
Author: Alexandre Gramfort <alexandre.gramfort at inria.fr>
Date: Sun Aug 5 15:18:19 2012 +0200
DOC : update reference + fix some docstrings
---
doc/source/python_reference.rst | 57 +++++++++++++++++++++++++++++++++++++++--
mne/beamformer/__init__.py | 2 +-
mne/cov.py | 4 +--
mne/label.py | 14 +++++-----
mne/preprocessing/maxfilter.py | 4 +--
mne/source_estimate.py | 8 +++---
mne/time_frequency/psd.py | 4 +--
mne/transforms.py | 4 +--
8 files changed, 75 insertions(+), 22 deletions(-)
diff --git a/doc/source/python_reference.rst b/doc/source/python_reference.rst
index cf48135..e24d4b8 100644
--- a/doc/source/python_reference.rst
+++ b/doc/source/python_reference.rst
@@ -32,11 +32,14 @@ Functions reference
read_cov
write_cov
+ compute_covariance
+ compute_raw_data_covariance
label_time_courses
read_label
label_sign_flip
write_label
stc_to_label
+ grow_labels
read_bem_surfaces
read_surface
write_bem_surface
@@ -47,12 +50,18 @@ Functions reference
write_stc
read_w
write_w
+ read_proj
+ write_proj
+ compute_proj_epochs
+ compute_proj_evoked
+ read_selection
fiff.pick_types
fiff.pick_channels
fiff.pick_types_evoked
fiff.pick_channels_regexp
fiff.pick_channels_forward
fiff.pick_types_forward
+ fiff.pick_channels_cov
.. automodule:: mne.minimum_norm
:no-members:
@@ -65,14 +74,40 @@ Functions reference
:template: function.rst
read_inverse_operator
+ write_inverse_operator
+ make_inverse_operator
apply_inverse
apply_inverse_raw
apply_inverse_epochs
- make_inverse_operator
- write_inverse_operator
source_band_induced_power
source_induced_power
+.. automodule:: mne.mixed_norm
+ :no-members:
+ :no-inherited-members:
+
+.. currentmodule:: mne.mixed_norm
+
+.. autosummary::
+ :toctree: generated/
+ :template: function.rst
+
+ mixed_norm
+
+.. automodule:: mne.beamformer
+ :no-members:
+ :no-inherited-members:
+
+.. currentmodule:: mne.beamformer
+
+.. autosummary::
+ :toctree: generated/
+ :template: function.rst
+
+ lcmv
+ lcmv_epochs
+ lcmv_raw
+
.. automodule:: mne.stats
:no-members:
:no-inherited-members:
@@ -115,3 +150,21 @@ Functions reference
induced_power
single_trial_power
compute_raw_psd
+ morlet
+ yule_walker
+ ar_raw
+ iir_filter_raw
+
+.. automodule:: mne.simulation
+ :no-members:
+ :no-inherited-members:
+
+.. currentmodule:: mne.simulation
+
+.. autosummary::
+ :toctree: generated/
+ :template: function.rst
+
+ generate_evoked
+ select_source_in_label
+ generate_sparse_stc
diff --git a/mne/beamformer/__init__.py b/mne/beamformer/__init__.py
index b24e865..b6c1ad7 100644
--- a/mne/beamformer/__init__.py
+++ b/mne/beamformer/__init__.py
@@ -1,4 +1,4 @@
-"""Artifacts finding/correction related functions
+"""Beamformers for source localization
"""
from ._lcmv import lcmv, lcmv_epochs, lcmv_raw
diff --git a/mne/cov.py b/mne/cov.py
index 518a403..6b1a362 100644
--- a/mne/cov.py
+++ b/mne/cov.py
@@ -470,8 +470,8 @@ def regularize(cov, info, mag=0.1, grad=0.1, eeg=0.1, exclude=None,
proj: bool
Apply or not projections to keep rank of data.
- Return
- ------
+ Returns
+ -------
reg_cov : Covariance
The regularized covariance matrix.
"""
diff --git a/mne/label.py b/mne/label.py
index 40d470c..2408728 100644
--- a/mne/label.py
+++ b/mne/label.py
@@ -234,8 +234,8 @@ def stc_to_label(stc, src, smooth=5):
def _verts_within_dist(graph, source, max_dist):
"""Find all vertices wihin a maximum geodesic distance from source
- Parameters:
- -----------
+ Parameters
+ ----------
graph : scipy.sparse.csr_matrix
Sparse matrix with distances between adjacent vertices
source : int
@@ -243,8 +243,8 @@ def _verts_within_dist(graph, source, max_dist):
max_dist: float
Maximum geodesic distance
- Returns:
- --------
+ Returns
+ -------
verts : array
Vertices within max_dist
dist : array
@@ -292,7 +292,7 @@ def grow_labels(subject, seeds, extents, hemis, subjects_dir=None):
label, or integers, in which case the same extent and hemisphere is
used for each label.
- Parameters:
+ Parameters
----------
subject : string
Name of the subject as in SUBJECTS_DIR
@@ -305,8 +305,8 @@ def grow_labels(subject, seeds, extents, hemis, subjects_dir=None):
subjects_dir : string
Path to SUBJECTS_DIR if not set in the environment
- Returns:
- --------
+ Returns
+ -------
labels : list
List with lables. Each label is a dictionary with keys:
comment Comment with seed vertex and extent
diff --git a/mne/preprocessing/maxfilter.py b/mne/preprocessing/maxfilter.py
index e9bb121..b8f1368 100644
--- a/mne/preprocessing/maxfilter.py
+++ b/mne/preprocessing/maxfilter.py
@@ -96,8 +96,8 @@ def apply_maxfilter(in_fname, out_fname, origin=None, frame='device',
Needs Maxfilter license, maxfilter has to be in PATH
- Parameters:
- -----------
+ Parameters
+ ----------
in_fname: string
Input file name
diff --git a/mne/source_estimate.py b/mne/source_estimate.py
index 4bf741f..67c3bb7 100644
--- a/mne/source_estimate.py
+++ b/mne/source_estimate.py
@@ -559,15 +559,15 @@ def mesh_dist(tris, vert):
It generates an adjacency matrix where the entries are the distances
between neighboring vertices.
- Parameters:
- -----------
+ Parameters
+ ----------
tris : array (n_tris x 3)
Mesh triangulation
vert : array (n_vert x 3)
Vertex locations
- Returns:
- --------
+ Returns
+ -------
dist_matrix : scipy.sparse.csr_matrix
Sparse matrix with distances between adjacent vertices
"""
diff --git a/mne/time_frequency/psd.py b/mne/time_frequency/psd.py
index 5443759..956e591 100644
--- a/mne/time_frequency/psd.py
+++ b/mne/time_frequency/psd.py
@@ -48,8 +48,8 @@ def compute_raw_psd(raw, tmin=0, tmax=np.inf, picks=None,
proj : bool
Apply SSP projection vectors
- Return
- ------
+ Returns
+ -------
psd: array of float
The PSD for all channels
diff --git a/mne/transforms.py b/mne/transforms.py
index 4d3a6d0..a594079 100644
--- a/mne/transforms.py
+++ b/mne/transforms.py
@@ -74,8 +74,8 @@ def transform_coordinates(filename, pos, orig, dest):
'mni_tal' is MNI Talairach
'fs_tal' is FreeSurfer Talairach
- Return
- ------
+ Returns
+ -------
trans_pos: array of shape N x 3
The transformed locations
--
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