[med-svn] [python-mne] 326/376: DOC: better latex rendering of the doc
Yaroslav Halchenko
debian at onerussian.com
Fri Nov 27 17:23:16 UTC 2015
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yoh pushed a commit to annotated tag v0.1
in repository python-mne.
commit d6d60a79bdf5005b7ec17a9d092438fe69b1cf6e
Author: Alexandre Gramfort <alexandre.gramfort at inria.fr>
Date: Thu Jul 21 13:14:37 2011 -0400
DOC: better latex rendering of the doc
---
doc/source/_static/logo.png | Bin 77544 -> 74269 bytes
doc/source/_templates/layout.html | 7 +-
doc/source/command_line_tutorial.rst | 4 +-
doc/source/conf.py | 17 ++--
doc/source/config_doc.rst | 10 ---
doc/source/getting_started.rst | 18 +++--
doc/source/getting_started_at_martinos.rst | 2 +-
doc/source/index.rst | 31 +------
doc/source/manual/forward.rst | 12 +--
doc/source/manual/matlab.rst | 126 ++++++++++++++---------------
doc/source/manual/utilities.rst | 7 +-
doc/source/mne-python.rst | 2 +-
12 files changed, 105 insertions(+), 131 deletions(-)
diff --git a/doc/source/_static/logo.png b/doc/source/_static/logo.png
old mode 100755
new mode 100644
index 70ff8e5..4b86571
Binary files a/doc/source/_static/logo.png and b/doc/source/_static/logo.png differ
diff --git a/doc/source/_templates/layout.html b/doc/source/_templates/layout.html
index 846e4bc..1baaf89 100755
--- a/doc/source/_templates/layout.html
+++ b/doc/source/_templates/layout.html
@@ -1,15 +1,16 @@
{% extends "!layout.html" %}
+{% block relbar2 %}{% endblock %}
{% block rootrellink %}
<li><a href="{{ pathto('index') }}">Home</a> | </li>
- <li><a href="{{ pathto('contents') }}">Documentation</a> | </li>
- <li><a href="{{ pathto('search') }}">Search</a></li>
+ <li><a href="{{ pathto('manual') }}">Manual</a> | </li>
+ <li><a href="{{ pathto('mne-python') }}">Python</a> | </li>
+ <!-- <li><a href="{{ pathto('search') }}">Search</a></li> -->
{% endblock %}
{% block relbar1 %}
-
<div style="background-color: white; text-align: left; padding: 10px 10px 15px 15px">
<a href="{{ pathto('index') }}"><img src="{{
pathto("_static/logo.png", 1) }}" border="0" alt="py4sci"/></a>
diff --git a/doc/source/command_line_tutorial.rst b/doc/source/command_line_tutorial.rst
index b6448bf..c3be87a 100644
--- a/doc/source/command_line_tutorial.rst
+++ b/doc/source/command_line_tutorial.rst
@@ -1,4 +1,4 @@
-.. _example_command_line:
+.. _command_line_tutorial:
=====================================
Getting started with MNE command line
@@ -97,4 +97,4 @@ Produce stc files (activation files)::
And, we're done!
-You can now get started with the Python `examples <auto_examples/index.html>`_.
+You can now get started with the Python :ref:`examples-index`
diff --git a/doc/source/conf.py b/doc/source/conf.py
index 060f142..4c69d9d 100755
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -92,7 +92,7 @@ unused_docs = ['config_doc.rst']
# List of directories, relative to source directory, that shouldn't be searched
# for source files.
-exclude_trees = ['_build']
+exclude_trees = ['build']
# The reST default role (used for this markup: `text`) to use for all documents.
#default_role = None
@@ -121,20 +121,21 @@ modindex_common_prefix = ['mne.']
# Sphinx are currently 'default' and 'sphinxdoc'.
html_theme = 'sphinxdoc'
html_style = 'navy.css'
+
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
# documentation.
#html_theme_options = {}
# Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
+# html_theme_path = ['themes']
# The name for this set of Sphinx documents. If None, it defaults to
# "<project> v<release> documentation".
-#html_title = None
+html_title = None
# A shorter title for the navigation bar. Default is the same as html_title.
-#html_short_title = None
+html_short_title = None
# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
@@ -166,16 +167,16 @@ html_last_updated_fmt = '%b %d, %Y'
#html_additional_pages = {}
# If false, no module index is generated.
-html_use_modindex = True
+html_use_modindex = False
# If false, no index is generated.
-html_use_index = True
+html_use_index = False
# If true, the index is split into individual pages for each letter.
#html_split_index = False
# If true, links to the reST sources are added to the pages.
-#html_show_sourcelink = True
+html_show_sourcelink = False
# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> tag referring to it. The value of this option must be the
@@ -210,7 +211,7 @@ latex_logo = "_static/logo.png"
# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
-#latex_use_parts = False
+latex_use_parts = True
# Additional stuff for the LaTeX preamble.
#latex_preamble = ''
diff --git a/doc/source/config_doc.rst b/doc/source/config_doc.rst
deleted file mode 100755
index e391493..0000000
--- a/doc/source/config_doc.rst
+++ /dev/null
@@ -1,10 +0,0 @@
-.. _config_doc:
-
-This is a skeleton config file for the MNE package.
-
-See the documentation at http://XXX
-
-Project Name
-------------
-
-projname : string -- project name
diff --git a/doc/source/getting_started.rst b/doc/source/getting_started.rst
index f558020..ab14ff7 100755
--- a/doc/source/getting_started.rst
+++ b/doc/source/getting_started.rst
@@ -6,7 +6,10 @@ Getting Started
Inside the Martinos Center
--------------------------
People within the MGH/MIT/HMS Martinos Center should follow
-:ref:`getting_started_martinos`.
+
+.. toctree::
+
+ ./getting_started_at_martinos
MNE is *already installed* on your system.
@@ -14,14 +17,19 @@ Outside the Martinos Center
---------------------------
MNE is written in pure Python making it easy to setup of
-any machine with Python >=2.4, Numpy >= 1.1 and Scipy >= 0.6.
+any machine with Python >=2.5, Numpy >= 1.4 and Scipy >= 0.6.
+
+For a free, fast and up to date scientific Python environment you
+can install EPD Free available at:
+
+http://www.enthought.com/products/epd_free.php
To test that everything works properly, open up IPython::
ipython
-
-Although all of the examples in this documentation are in the style
-of the standard Python interpreter, the use of IPython is highly
+
+Although all of the examples in this documentation are in the style
+of the standard Python interpreter, the use of IPython is highly
recommended. Then type::
>>> import mne
diff --git a/doc/source/getting_started_at_martinos.rst b/doc/source/getting_started_at_martinos.rst
index 9f42b49..9730190 100755
--- a/doc/source/getting_started_at_martinos.rst
+++ b/doc/source/getting_started_at_martinos.rst
@@ -27,5 +27,5 @@ recommended. Then type::
>>> import mne
If you get a new prompt with no error messages, you should be good to go.
-Start with the `examples <auto_examples/index.html>`_
+Start with the :ref:`examples-index`.
diff --git a/doc/source/index.rst b/doc/source/index.rst
index 9cd6dea..a791c0b 100755
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -1,6 +1,6 @@
-========
+###########
MNE Home
-========
+###########
MNE is a software package for processing magnetoencephalography data
(MEG) and electroencephalography (EEG). It includes python code
@@ -10,39 +10,14 @@ converted from other file formats.
* `Download <http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/MNE_register/index.php>`_ MNE
* Read the :ref:`manual`.
* Get started with :ref:`mne_python`
- * :ref:`example_command_line`
+ * :ref:`command_line_tutorial`
* Join the MNE `mailing list <http://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis>`_
* `Help/Feature Request/Bug Report <mailto:mne_support at nmr.mgh.harvard.edu>`_
* :ref:`ch_reading`
-Manual
-======
-
.. toctree::
:maxdepth: 2
manual
-
-MNE with Python
-===============
-
-.. toctree::
- :maxdepth: 2
-
mne-python
-Working with MNE Python's source code
-=====================================
-
-.. toctree::
- :maxdepth: 2
-
- gitwash/git_intro
- gitwash/git_install
- gitwash/following_latest
- gitwash/patching
- gitwash/git_development
- gitwash/git_resources
-
-* :ref:`search`
-
diff --git a/doc/source/manual/forward.rst b/doc/source/manual/forward.rst
index cc6eed0..4a0a5bb 100755
--- a/doc/source/manual/forward.rst
+++ b/doc/source/manual/forward.rst
@@ -173,7 +173,7 @@ and
.. note:: This section does not discuss the transformation between the MRI voxel indices and the different MRI coordinates. However, it is important to note that in FreeSurfer, MNE, as well as in Neuromag software an integer voxel coordinate corresponds to the location of the center of a voxel. Detailed information on the FreeSurfer MRI systems can be found at https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems.
-.. tabularcolumns:: |p{0.2\linewidth}|p{0.3\linewidth}||p{0.5\linewidth}|
+.. tabularcolumns:: |p{0.2\linewidth}|p{0.3\linewidth}|p{0.5\linewidth}|
.. _CHDJDEDJ:
.. table:: Coordinate transformations in FreeSurfer and MNE software packages. The symbols :math:`T_x` are defined in :ref:`CHDFFJIJ`. Note: mne_make_cor_set /mne_setup_mri prior to release 2.6 did not include transformations :math:`T_3`, :math:`T_4`, :math:`T_-`, and :math:`T_+` in the fif files produced.
@@ -719,9 +719,8 @@ geometry.
The output of each SQUID sensor is a weighted sum of the
magnetic fluxes threading the loops comprising the detection coil.
Since the flux threading a coil loop is an integral of the magnetic
-field component normal to the coil plane, the output of the *k*th
-MEG channel, :math:`b_k`, can be approximated
-by:
+field component normal to the coil plane, the output of the k :sup:`th`
+MEG channel, :math:`b_k` can be approximated by:
.. math:: b_k = \sum_{p = 1}^{N_k} {w_{kp} B(r_{kp}) \cdot n_{kp}}
@@ -852,7 +851,7 @@ The columns of the tables contain the following data:
| | diagonal gradients | | | |
+------+-------------------------+----+----------------------------------+----------------------+
-.. tabularcolumns:: |p{0.1\linewidth}|p{0.3\linewidth}|p{0.1\linewidth}|p{0.25\linewidth}|p{0.2\linewidth}|
+.. tabularcolumns:: |p{0.1\linewidth}|p{0.3\linewidth}|p{0.05\linewidth}|p{0.25\linewidth}|p{0.15\linewidth}|
.. _CHDBDFJE:
.. table:: Accurate coil descriptions
@@ -1227,8 +1226,9 @@ is then consulted to scale the model to the correct dimensions.
Even if the model setup file is not present, a model called Default is
always provided. This model has the structure given in :ref:`BABEBGDA`
-.. _BABEBGDA:
+.. tabularcolumns:: |p{0.1\linewidth}|p{0.25\linewidth}|p{0.2\linewidth}|
+.. _BABEBGDA:
.. table:: Structure of the default EEG model
======== ======================= =======================
diff --git a/doc/source/manual/matlab.rst b/doc/source/manual/matlab.rst
index 6c4fb19..1d50736 100755
--- a/doc/source/manual/matlab.rst
+++ b/doc/source/manual/matlab.rst
@@ -1127,12 +1127,12 @@ The documented structures are:
| mri_head_t | trans | Transformation from the MRI coordinate frame to the |
| | | (Neuromag) head coordinate frame. |
+-------------------------+-------------+----------------------------------------------------------+
- | src | surf(*) | he description of the source spaces. |
+ | src | surf(:) | The description of the source spaces. |
+-------------------------+-------------+----------------------------------------------------------+
| source_rr | double | The source locations. |
| | (nsource,3) | |
+-------------------------+-------------+----------------------------------------------------------+
- | source_nn | double(*,3) | The source orientations. Number of rows is either |
+ | source_nn | double(:,3) | The source orientations. Number of rows is either |
| | | nsource (fixed source orientations) or 3*nsource |
| | | (all source orientations). |
+-------------------------+-------------+----------------------------------------------------------+
@@ -1141,67 +1141,67 @@ The documented structures are:
.. tabularcolumns:: |p{0.2\linewidth}|p{0.2\linewidth}|p{0.55\linewidth}|
.. _BGBIEIJE:
-.. table:: The inv structure. Note: The fields proj , whitener , reginv , and noisenorm are filled in by the routine mne_prepare_inverse_operator.
-
- +---------------------------+-----------+----------------------------------------------------------+
- | Field | Data Type | Description |
- +===========================+===========+==========================================================+
- | methods | int32 | Has the solution been computed using MEG data (1), EEG |
- | | | data (2), or both (3). |
- +---------------------------+-----------+----------------------------------------------------------+
- | source_ori | int32 | Has the solution been computed for the current component |
- | | | normal to the cortex only (1) or all three source |
- | | | orientations (2). |
- +---------------------------+-----------+----------------------------------------------------------+
- | nsource | int32 | Total number of source space points. |
- +---------------------------+-----------+----------------------------------------------------------+
- | nchan | int32 | Number of channels. |
- +---------------------------+-----------+----------------------------------------------------------+
- | coord_frame | int32 | Coordinate frame in which the locations and orientations |
- | | | are expressed. |
- +---------------------------+-----------+----------------------------------------------------------+
- | source_nn |double(*,3)| The source orientations. Number of rows is either |
- | | | nsource (fixed source orientations) or 3*nsource (all |
- | | | source orientations). |
- +---------------------------+-----------+----------------------------------------------------------+
- | sing | double | The singular values, *i.e.*, the diagonal values of |
- | | (nchan) | :math:`\Lambda`, see :ref:`CHDBEHBC`. |
- +---------------------------+-----------+----------------------------------------------------------+
- | eigen_leads | double | The matrix :math:`V`, see :ref:`CHDBEHBC`. |
- | | (*,nchan) | |
- +---------------------------+-----------+----------------------------------------------------------+
- | eigen_fields | double | The matrix :math:`U^T`, see :ref:`CHDBEHBC`. |
- | | (nchan, | |
- | | nchan) | |
- +---------------------------+-----------+----------------------------------------------------------+
- | noise_cov | cov | The noise covariance matrix :math:`C`. |
- +---------------------------+-----------+----------------------------------------------------------+
- | source_cov | cov | The source covariance matrix :math:`R`. |
- +---------------------------+-----------+----------------------------------------------------------+
- | src | surf(*) | The description of the source spaces. |
- +---------------------------+-----------+----------------------------------------------------------+
- | mri_head_t | trans | Transformation from the MRI coordinate frame to the |
- | | | (Neuromag) head coordinate frame. |
- +---------------------------+-----------+----------------------------------------------------------+
- | nave | double | The number of averages. |
- +---------------------------+-----------+----------------------------------------------------------+
- | projs | proj(*) | The SSP vectors which were active when the decomposition |
- | | | was computed. |
- +---------------------------+-----------+----------------------------------------------------------+
- | proj | double | The projection operator computed using projs. |
- | | (nchan) | |
- +---------------------------+-----------+----------------------------------------------------------+
- | whitener | | A sparse matrix containing the noise normalization |
- | | | factors. Dimension is either nsource (fixed source |
- | | | orientations) or 3*nsource (all source orientations). |
- +---------------------------+-----------+----------------------------------------------------------+
- | reginv | double | The diagonal matrix :math:`\Gamma`, see :ref:`CHDBEHBC`. |
- | | (nchan) | |
- +---------------------------+-----------+----------------------------------------------------------+
- | noisenorm | double(*) | A sparse matrix containing the noise normalization |
- | | | factors. Dimension is either nsource (fixed source |
- | | | orientations) or 3*nsource (all source orientations). |
- +---------------------------+-----------+----------------------------------------------------------+
+.. table:: The inv structure. Note: The fields proj, whitener, reginv, and noisenorm are filled in by the routine mne_prepare_inverse_operator.
+
+ +---------------------+-------------+----------------------------------------------------------+
+ | Field | Data Type | Description |
+ +=====================+=============+==========================================================+
+ | methods | int32 | Has the solution been computed using MEG data (1), EEG |
+ | | | data (2), or both (3). |
+ +---------------------+-------------+----------------------------------------------------------+
+ | source_ori | int32 | Has the solution been computed for the current component |
+ | | | normal to the cortex only (1) or all three source |
+ | | | orientations (2). |
+ +---------------------+-------------+----------------------------------------------------------+
+ | nsource | int32 | Total number of source space points. |
+ +---------------------+-------------+----------------------------------------------------------+
+ | nchan | int32 | Number of channels. |
+ +---------------------+-------------+----------------------------------------------------------+
+ | coord_frame | int32 | Coordinate frame in which the locations and orientations |
+ | | | are expressed. |
+ +---------------------+-------------+----------------------------------------------------------+
+ | source_nn | double(:,3) | The source orientations. Number of rows is either |
+ | | | nsource (fixed source orientations) or 3*nsource (all |
+ | | | source orientations). |
+ +---------------------+-------------+----------------------------------------------------------+
+ | sing | double | The singular values, *i.e.*, the diagonal values of |
+ | | (nchan) | :math:`\Lambda`, see :ref:`CHDBEHBC`. |
+ +---------------------+-------------+----------------------------------------------------------+
+ | eigen_leads | double | The matrix :math:`V`, see :ref:`CHDBEHBC`. |
+ | | (:,nchan) | |
+ +---------------------+-------------+----------------------------------------------------------+
+ | eigen_fields | double | The matrix :math:`U^T`, see :ref:`CHDBEHBC`. |
+ | | (nchan, | |
+ | | nchan) | |
+ +---------------------+-------------+----------------------------------------------------------+
+ | noise_cov | cov | The noise covariance matrix :math:`C`. |
+ +---------------------+-------------+----------------------------------------------------------+
+ | source_cov | cov | The source covariance matrix :math:`R`. |
+ +---------------------+-------------+----------------------------------------------------------+
+ | src | surf(:) | The description of the source spaces. |
+ +---------------------+-------------+----------------------------------------------------------+
+ | mri_head_t | trans | Transformation from the MRI coordinate frame to the |
+ | | | (Neuromag) head coordinate frame. |
+ +---------------------+-------------+----------------------------------------------------------+
+ | nave | double | The number of averages. |
+ +---------------------+-------------+----------------------------------------------------------+
+ | projs | proj(:) | The SSP vectors which were active when the decomposition |
+ | | | was computed. |
+ +---------------------+-------------+----------------------------------------------------------+
+ | proj | double | The projection operator computed using projs. |
+ | | (nchan) | |
+ +---------------------+-------------+----------------------------------------------------------+
+ | whitener | | A sparse matrix containing the noise normalization |
+ | | | factors. Dimension is either nsource (fixed source |
+ | | | orientations) or 3*nsource (all source orientations). |
+ +---------------------+-------------+----------------------------------------------------------+
+ | reginv | double | The diagonal matrix :math:`\Gamma`, see :ref:`CHDBEHBC`. |
+ | | (nchan) | |
+ +---------------------+-------------+----------------------------------------------------------+
+ | noisenorm | double(:) | A sparse matrix containing the noise normalization |
+ | | | factors. Dimension is either nsource (fixed source |
+ | | | orientations) or 3*nsource (all source orientations). |
+ +---------------------+-------------+----------------------------------------------------------+
On-line documentation for individual routines
diff --git a/doc/source/manual/utilities.rst b/doc/source/manual/utilities.rst
index 82a6ba1..69c1ad5 100755
--- a/doc/source/manual/utilities.rst
+++ b/doc/source/manual/utilities.rst
@@ -1276,12 +1276,11 @@ The arithmetic expressions can use usual arithmetic operations
as well as mathematical functions listed in :ref:`CHDJIBHA`.
The arguments can be vectors or scalar numbers. In addition, standard
relational operators ( <, >, ==, <=, >=) and their textual
-equivalents (lt, gt, eq, le, ge) are available. Table :ref:`CHDDJEHH` gives some useful examples of source waveform
-expressions.
-
-.. _CHDJIBHA:
+equivalents (lt, gt, eq, le, ge) are available. Table :ref:`CHDDJEHH` gives some
+useful examples of source waveform expressions.
.. tabularcolumns:: |p{0.2\linewidth}|p{0.6\linewidth}|
+.. _CHDJIBHA:
.. table:: Mathematical functions available for source waveform expressions
+-----------------------+---------------------------------------------------------------+
diff --git a/doc/source/mne-python.rst b/doc/source/mne-python.rst
index ca0b269..5115e60 100755
--- a/doc/source/mne-python.rst
+++ b/doc/source/mne-python.rst
@@ -8,6 +8,6 @@ MNE with Python
:maxdepth: 2
getting_started.rst
- getting_started_at_martinos.rst
auto_examples/index.rst
+ gitwash/index.rst
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