Documentation

Examples renaming


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1425 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 09bc66a795a4e4f5b2a484c607daa12b1e97b4de

12 files changed, 125 insertions, 48 deletions

diff --git a/src/cython/doc/source/alpha_complex_ref.rst b/src/cython/doc/source/alpha_complex_ref.rst
index ab81eee0..6a122b09 100644
--- a/src/cython/doc/source/alpha_complex_ref.rst
+++ b/src/cython/doc/source/alpha_complex_ref.rst
@@ -1,5 +1,6 @@
+==============================
 Alpha complex reference manual
-##############################
+==============================
 
 .. autoclass:: gudhi.AlphaComplex
    :members:
diff --git a/src/cython/doc/source/alpha_complex_sum.rst b/src/cython/doc/source/alpha_complex_sum.rst
new file mode 100644
index 00000000..b608050e
--- /dev/null
+++ b/src/cython/doc/source/alpha_complex_sum.rst
@@ -0,0 +1,21 @@
+=====================================  =====================================  =====================================
+:Author: Vincent Rouvreau              :Introduced in: GUDHI PYTHON 1.4.0     :Copyright: GPL v3
+=====================================  =====================================  =====================================
+
++-------------------------------------------+----------------------------------------------------------------------+
+| .. image::                                | Alpha_complex is a simplicial complex constructed from the finite    |
+|      img/alpha_complex_representation.png | cells of a Delaunay Triangulation.                                   |
+|                                           |                                                                      |
+|                                           | The filtration value of each simplex is computed as the square of the|
+|                                           | circumradius of the simplex if the circumsphere is empty (the simplex|
+|                                           | is then said to be Gabriel), and as the minimum of the filtration    |
+|                                           | values of the codimension 1 cofaces that make it not Gabriel         |
+|                                           | otherwise. All simplices that have a filtration value strictly       |
+|                                           | greater than a given alpha squared value are not inserted into the   |
+|                                           | complex.                                                             |
+|                                           |                                                                      |
+|                                           | This package requires having CGAL version 4.7 or higher (4.8.1 is    |
+|                                           | advised for better perfomances).                                     |
++-------------------------------------------+----------------------------------------------------------------------+
+| :doc:`alpha_complex_user`                 | :doc:`alpha_complex_ref`                                             |
++-------------------------------------------+----------------------------------------------------------------------+
diff --git a/src/cython/doc/source/alpha_complex_user.rst b/src/cython/doc/source/alpha_complex_user.rst
index 3b445d13..ba920fe3 100644
--- a/src/cython/doc/source/alpha_complex_user.rst
+++ b/src/cython/doc/source/alpha_complex_user.rst
@@ -1,8 +1,15 @@
+=========================
 Alpha complex user manual
-#########################
+=========================
+Definition
+----------
 
-blablabla
+.. include:: alpha_complex_sum.rst
 
-.. image:: img/alpha_complex_representation.png
-   :align: center
+Alpha_complex is constructing a Simplex_tree using Delaunay Triangulation from
+CGAL (the Computational Geometry Algorithms Library).
 
+The complex is a template class requiring an Epick_d dD Geometry Kernel [16] from CGAL as template parameter.
+
+Remarks
+    When Alpha_complex is constructed with an infinite value of alpha, the complex is a Delaunay complex.
\ No newline at end of file
diff --git a/src/cython/doc/source/cubical_complex_sum.rst b/src/cython/doc/source/cubical_complex_sum.rst
new file mode 100644
index 00000000..60b47f54
--- /dev/null
+++ b/src/cython/doc/source/cubical_complex_sum.rst
@@ -0,0 +1,11 @@
+=====================================  =====================================  =====================================
+:Author: Pawel Dlotko                  :Introduced in: GUDHI PYTHON 1.4.0     :Copyright: GPL v3
+=====================================  =====================================  =====================================
+
++---------------------------------------------+----------------------------------------------------------------------+
+| .. image::                                  | The cubical complex is an example of a structured complex useful in  |
+|      img/Cubical_complex_representation.png | computational mathematics (specially rigorous numerics) and image    |
+|                                             | analysis.                                                            |
++---------------------------------------------+----------------------------------------------------------------------+
+| :doc:`cubical_complex_user`                 | :doc:`cubical_complex_ref`                                           |
++---------------------------------------------+----------------------------------------------------------------------+
diff --git a/src/cython/doc/source/cubical_complex_user.rst b/src/cython/doc/source/cubical_complex_user.rst
index 7ade4b86..6ae67940 100644
--- a/src/cython/doc/source/cubical_complex_user.rst
+++ b/src/cython/doc/source/cubical_complex_user.rst
@@ -1,8 +1,8 @@
+=========================
 Cubical complex user manual
-###########################
+=========================
+Definition
+----------
 
-blablabla
-
-.. image:: img/Cubical_complex_representation.png
-   :align: center
+.. include:: cubical_complex_sum.rst
 
diff --git a/src/cython/doc/source/index.rst b/src/cython/doc/source/index.rst
index d08b465c..2b17464a 100644
--- a/src/cython/doc/source/index.rst
+++ b/src/cython/doc/source/index.rst
@@ -38,56 +38,22 @@ Data structures
 Alpha complex
 =============
 
-=====================================  =====================================  =====================================
-:Author: Vincent Rouvreau              :Introduced in: GUDHI PYTHON 1.4.0     :Copyright: GPL v3
-=====================================  =====================================  =====================================
-
-+-------------------------------------------+----------------------------------------------------------------------+
-| .. image::                                | Alpha_complex is a simplicial complex constructed from the finite    |
-|      img/alpha_complex_representation.png | cells of a Delaunay Triangulation.                                   |
-|                                           |                                                                      |
-|                                           | The filtration value of each simplex is computed as the square of the|
-|                                           | circumradius of the simplex if the circumsphere is empty (the simplex|
-|                                           | is then said to be Gabriel), and as the minimum of the filtration    |
-|                                           | values of the codimension 1 cofaces that make it not Gabriel         |
-|                                           | otherwise. All simplices that have a filtration value strictly       |
-|                                           | greater than a given alpha squared value are not inserted into the   |
-|                                           | complex.                                                             |
-|                                           |                                                                      |
-|                                           | This package requires having CGAL version 4.7 or higher (4.8.1 is    |
-|                                           | advised for better perfomances).                                     |
-+-------------------------------------------+----------------------------------------------------------------------+
-| :doc:`alpha_complex_user`                 | :doc:`alpha_complex_ref`                                             |
-+-------------------------------------------+----------------------------------------------------------------------+
+.. include:: alpha_complex_sum.rst
 
 Cubical complex
 ===============
 
-=====================================  =====================================  =====================================
-:Author: Pawel Dlotko                  :Introduced in: GUDHI PYTHON 1.4.0     :Copyright: GPL v3
-=====================================  =====================================  =====================================
-
-+---------------------------------------------+----------------------------------------------------------------------+
-| .. image::                                  | The cubical complex is an example of a structured complex useful in  |
-|      img/Cubical_complex_representation.png | computational mathematics (specially rigorous numerics) and image    |
-|                                             | analysis.                                                            |
-+---------------------------------------------+----------------------------------------------------------------------+
-| :doc:`cubical_complex_user`                 | :doc:`cubical_complex_ref`                                           |
-+---------------------------------------------+----------------------------------------------------------------------+
+.. include:: cubical_complex_sum.rst
 
 Simplex tree
 ============
 
-=====================================  =====================================  =====================================
-:Author: Clément Maria                 :Introduced in: GUDHI PYTHON 1.4.0     :Copyright: GPL v3
-=====================================  =====================================  =====================================
+.. include:: simplex_tree_sum.rst
 
 Witness complex
 ===============
 
-=====================================  =====================================  =====================================
-:Author: Siargey Kachanovich           :Introduced in: GUDHI PYTHON 1.4.0     :Copyright: GPL v3
-=====================================  =====================================  =====================================
+.. include:: witness_complex_sum.rst
 
 
 Toolbox
diff --git a/src/cython/doc/source/simplex_tree_ref.rst b/src/cython/doc/source/simplex_tree_ref.rst
new file mode 100644
index 00000000..6d196843
--- /dev/null
+++ b/src/cython/doc/source/simplex_tree_ref.rst
@@ -0,0 +1,10 @@
+=============================
+Simplex tree reference manual
+=============================
+
+.. autoclass:: gudhi.SimplexTree
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+   .. automethod:: gudhi.SimplexTree.__init__
diff --git a/src/cython/doc/source/simplex_tree_sum.rst b/src/cython/doc/source/simplex_tree_sum.rst
new file mode 100644
index 00000000..cc02ccc2
--- /dev/null
+++ b/src/cython/doc/source/simplex_tree_sum.rst
@@ -0,0 +1,14 @@
+=====================================  =====================================  =====================================
+:Author: Clément Maria                 :Introduced in: GUDHI PYTHON 1.4.0     :Copyright: GPL v3
+=====================================  =====================================  =====================================
+
++-------------------------------------------+----------------------------------------------------------------------+
+| .. image::                                | The simplex tree is an efficient and flexible data structure for     |
+|      img/Simplex_tree_representation.png  | representing general (filtered) simplicial complexes.                |
+|                                           |                                                                      |
+|                                           | The data structure is described in                                   |
+|                                           | `this document <http://dx.doi.org/10.1007/s00453-014-9887-3>`_       |
++-------------------------------------------+----------------------------------------------------------------------+
+| :doc:`simplex_tree_user`                  | :doc:`simplex_tree_ref`                                              |
++-------------------------------------------+----------------------------------------------------------------------+
+ 
\ No newline at end of file
diff --git a/src/cython/doc/source/simplex_tree_user.rst b/src/cython/doc/source/simplex_tree_user.rst
new file mode 100644
index 00000000..e1f6e93d
--- /dev/null
+++ b/src/cython/doc/source/simplex_tree_user.rst
@@ -0,0 +1,8 @@
+========================
+Simplex tree user manual
+========================
+Definition
+----------
+
+.. include:: simplex_tree_sum.rst
+
diff --git a/src/cython/doc/source/witness_complex_ref.rst b/src/cython/doc/source/witness_complex_ref.rst
new file mode 100644
index 00000000..79e39739
--- /dev/null
+++ b/src/cython/doc/source/witness_complex_ref.rst
@@ -0,0 +1,10 @@
+===============================
+Witness complex reference manual
+===============================
+
+.. autoclass:: gudhi.WitnessComplex
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+   .. automethod:: gudhi.WitnessComplex.__init__
diff --git a/src/cython/doc/source/witness_complex_sum.rst b/src/cython/doc/source/witness_complex_sum.rst
new file mode 100644
index 00000000..a91ff01b
--- /dev/null
+++ b/src/cython/doc/source/witness_complex_sum.rst
@@ -0,0 +1,21 @@
+=====================================  =====================================  =====================================
+:Author: Siargey Kachanovich           :Introduced in: GUDHI PYTHON 1.4.0     :Copyright: GPL v3
+=====================================  =====================================  =====================================
+
++---------------------------------------------+----------------------------------------------------------------------+
+| .. image::                                  | Alpha_complex is a simplicial complex constructed from the finite    |
+|      img/Witness_complex_representation.png | cells of a Delaunay Triangulation.                                   |
+|                                             |                                                                      |
+|                                             | The filtration value of each simplex is computed as the square of the|
+|                                             | circumradius of the simplex if the circumsphere is empty (the simplex|
+|                                             | is then said to be Gabriel), and as the minimum of the filtration    |
+|                                             | values of the codimension 1 cofaces that make it not Gabriel         |
+|                                             | otherwise. All simplices that have a filtration value strictly       |
+|                                             | greater than a given alpha squared value are not inserted into the   |
+|                                             | complex.                                                             |
+|                                             |                                                                      |
+|                                             | This package requires having CGAL version 4.7 or higher (4.8.1 is    |
+|                                             | advised for better perfomances).                                     |
++---------------------------------------------+----------------------------------------------------------------------+
+| :doc:`witness_complex_user`                 | :doc:`witness_complex_ref`                                           |
++---------------------------------------------+----------------------------------------------------------------------+
diff --git a/src/cython/doc/source/witness_complex_user.rst b/src/cython/doc/source/witness_complex_user.rst
new file mode 100644
index 00000000..3b4c3891
--- /dev/null
+++ b/src/cython/doc/source/witness_complex_user.rst
@@ -0,0 +1,8 @@
+==========================
+Witness complex user manual
+==========================
+Definition
+----------
+
+.. include:: witness_complex_sum.rst
+