Merge from trunk.

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/debian@1112 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 82a43e89115f09449d4f31ebfd9ff56170d8771f
author: glisse <glisse@636b058d-ea47-450e-bf9e-a15bfbe3eedb> 2016-04-08 16:19:20 +0000
committer: glisse <glisse@636b058d-ea47-450e-bf9e-a15bfbe3eedb> 2016-04-08 16:19:20 +0000
commit: a44155daa5ae4253a874dad4a22b6da4bd017fee (patch)
tree: dca668d3ada0f45329f80b3f7c49b74ea576523f /src/common
parent: 50327ad1f3fbf370fcdd3aa877b6e75644329662 (diff)
parent: baf1b5b39be90694b512fff9c79438bf362916f3 (diff)
18 files changed, 2182 insertions, 91 deletions
diff --git a/src/common/doc/Gudhi_banner.jpg b/src/common/doc/Gudhi_banner.jpg
deleted file mode 100644
index ebd3d8af..00000000
--- a/src/common/doc/Gudhi_banner.jpg
+++ /dev/null
diff --git a/src/common/doc/Gudhi_banner.png b/src/common/doc/Gudhi_banner.png
new file mode 100644
index 00000000..18e8a672
--- /dev/null
+++ b/src/common/doc/Gudhi_banner.png
diff --git a/src/common/doc/footer.html b/src/common/doc/footer.html
new file mode 100644
index 00000000..7b4cdc5c
--- /dev/null
+++ b/src/common/doc/footer.html
@@ -0,0 +1,29 @@
+<!-- HTML footer for doxygen 1.8.6-->
+<!-- start footer part -->
+<table style="width:100%">
+  <tr class="no-bullet shadow-black">
+      <td class="network-entypo">
+<!--BEGIN PROJECT_NAME--> $projectname
+<!--BEGIN PROJECT_NUMBER-->&#160;Version $projectnumber<!--END PROJECT_NUMBER-->
+<!--BEGIN PROJECT_BRIEF-->&#160;-&#160;$projectbrief<!--END PROJECT_BRIEF-->
+<!--END PROJECT_NAME-->
+      </td>
+      <td class="network-entypo">
+<!--BEGIN GENERATE_TREEVIEW-->
+        $generatedby
+        <a href="http://www.doxygen.org/index.html">
+        <img class="footer" src="$relpath^doxygen.png" alt="doxygen"/></a> $doxygenversion
+<!--END GENERATE_TREEVIEW-->
+      </td>
+  </tr>
+</table>
+
+<!--BEGIN !GENERATE_TREEVIEW-->
+<hr class="footer"/><address class="footer"><small> tralala
+$generatedby &#160;<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="$relpath^doxygen.png" alt="doxygen"/>
+</a> $doxygenversion
+</small></address>
+<!--END !GENERATE_TREEVIEW-->
+</body>
+</html>
diff --git a/src/common/doc/header.html b/src/common/doc/header.html
new file mode 100644
index 00000000..c958390c
--- /dev/null
+++ b/src/common/doc/header.html
@@ -0,0 +1,82 @@
+<!-- HTML header for doxygen 1.8.6-->
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!-- GUDHI website : class="no-js" lang="en" is necessary -->
+<html xmlns="http://www.w3.org/1999/xhtml" class="no-js" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen $doxygenversion"/>
+<!--BEGIN PROJECT_NAME--><title>$projectname: $title</title><!--END PROJECT_NAME-->
+<!--BEGIN !PROJECT_NAME--><title>$title</title><!--END !PROJECT_NAME-->
+<!-- GUDHI website css for header BEGIN -->
+<link rel="stylesheet" type="text/css" href="http://gudhi.gforge.inria.fr/assets/css/styles_feeling_responsive.css" />
+<!-- GUDHI website css for header END -->
+<link href="$relpath^tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="$relpath^jquery.js"></script>
+<script type="text/javascript" src="$relpath^dynsections.js"></script>
+$treeview
+$search
+$mathjax
+<link href="$relpath^$stylesheet" rel="stylesheet" type="text/css" />
+$extrastylesheet
+</head>
+<body>
+
+<!-- GUDHI website header BEGIN -->
+<div id="navigation" class="sticky">
+  <nav class="top-bar" role="navigation" data-topbar>
+    <section class="top-bar-section">
+      <ul class="right">
+              <li class="divider"></li>
+              <li><a href="http://gudhi.gforge.inria.fr/contact/">Contact</a></li>
+      </ul>
+      <ul class="left">
+              <li><a href="http://gudhi.gforge.inria.fr/"> <img src="http://gudhi.gforge.inria.fr/assets/img/home.png" alt="&nbsp;&nbsp;GUDHI">&nbsp;&nbsp;GUDHI </a></li>
+              <li class="divider"></li>
+              <li class="has-dropdown">
+                <a href="#">Project</a>
+                  <ul class="dropdown">
+                      <li><a href="http://gudhi.gforge.inria.fr/people/">People</a></li>
+                      <li><a href="http://gudhi.gforge.inria.fr/getinvolved/">Get involved</a></li>
+                      <li><a href="http://gudhi.gforge.inria.fr/partners/">Partners and Funding</a></li>
+                      <li><a href="http://gudhi.gforge.inria.fr/relatedprojects/">Related projects</a></li>
+                  </ul>
+              </li>
+              <li class="divider"></li>
+              <li class="has-dropdown">
+                <a href="#">Download</a>
+                  <ul class="dropdown">
+                      <li><a href="http://gudhi.gforge.inria.fr/licensing/">Licensing</a></li>
+                      <li><a href="https://gforge.inria.fr/frs/?group_id=3865" target="_blank">Get the sources</a></li>
+                      <li><a href="http://gudhi.gforge.inria.fr/doc/latest/installation.html">Installation manual</a></li>
+                  </ul>
+              </li>
+              <li class="divider"></li>
+              <li><a href="http://gudhi.gforge.inria.fr/doc/latest/modules.html">Documentation</a></li>
+              <li class="divider"></li>
+              <li><a href="http://gudhi.gforge.inria.fr/interfaces/">Interfaces</a></li>
+              <li class="divider"></li>
+      </ul>
+    </section>
+  </nav>
+</div><!-- /#navigation -->
+<!-- GUDHI website header BEGIN -->
+    
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+
+<!--BEGIN TITLEAREA-->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 30px;">
+  <!--BEGIN DISABLE_INDEX-->
+   <!--BEGIN SEARCHENGINE-->
+   <td>$searchbox</td>
+   <!--END SEARCHENGINE-->
+  <!--END DISABLE_INDEX-->
+ </tr>
+ </tbody>
+</table>
+</div>
+<!--END TITLEAREA-->
+<!-- end header part -->
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index 41b8ba1e..063e0a11 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -1,15 +1,14 @@
 /*! \mainpage
- * \image html "Gudhi_banner.jpg" "" width=20cm
+ *  \tableofcontents
+ * \image html "Gudhi_banner.png" "" width=20cm
  * 
  * \section Introduction Introduction
- * The Gudhi library (Geometric Understanding in Higher Dimensions) is a generic open source C++ library for
+ * The Gudhi library (Geometry Understanding in Higher Dimensions) is a generic open source C++ library for
  * Computational Topology and Topological Data Analysis
  * (<a class="el" target="_blank" href="https://en.wikipedia.org/wiki/Topological_data_analysis">TDA</a>).
- * The GUDHI library is developed as part of the
- * <a class="el" target="_blank" href="https://project.inria.fr/gudhi/">GUDHI project</a> supported by the European
- * Research Council. The GUDHI library intends  to help the development of new algorithmic solutions in TDA and their
- * transfer to applications. It provides robust, efficient, flexible and easy to use implementations of
- * state-of-the-art algorithms and data structures.
+ * The GUDHI library intends  to help the development of new algorithmic solutions in TDA and their transfer to
+ * applications. It provides robust, efficient, flexible and easy to use implementations of state-of-the-art
+ * algorithms and data structures.
  * 
  * The current release of the GUDHI library includes:
  * 
@@ -20,24 +19,138 @@
  * All data-structures are generic and several of their aspects can be parameterized via template classes.
  * We refer to \cite gudhilibrary_ICMS14 for a detailed description of the design of the library.
  *
- * The library is available <a class="el" target="_blank" href="https://gforge.inria.fr/frs/?group_id=3865">here</a>
- * and the documentation is available at this <a class="el" href="http://gudhi.gforge.inria.fr/doc/latest/">
- * webpage</a>.
- * 
- * The library comes with data sets, \ref demos and \ref testsuites.
- * 
- * Gudhi is also accessible though the
- * <a class="el" target="_blank" href="https://cran.r-project.org/web/packages/TDA/index.html">R package TDA</a>
- * (Statistical Tools for Topological Data Analysis).
- * 
- * The development of the GUDHI library is steered by an Editorial Board composed of:
- * 
- * \li <a class="el" target="_blank" href="http://www-sop.inria.fr/members/Jean-Daniel.Boissonnat/">
- * Jean-Daniel Boissonnat</a> | INRIA Sophia Antipolis - Méditerranée
- * \li <a class="el" target="_blank" href="http://geometrica.saclay.inria.fr/team/Marc.Glisse/">Marc Glisse</a> | INRIA Saclay - Ile de France
- * \li Clément Jamin | INRIA Sophia Antipolis - Méditerranée
- * \li Vincent Rouvreau | INRIA Saclay - Ile de France
- * 
+ \section DataStructures Data structures
+ \subsection AlphaComplexDataStructure Alpha complex
+ \image html "alpha_complex_representation.png" "Alpha complex representation"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> Vincent Rouvreau<br>
+      <b>Introduced in:</b> GUDHI 1.3.0<br>
+      <b>Copyright:</b> GPL v3<br>
+    </td>
+    <td width="75%">
+    Alpha_complex is a simplicial complex constructed from the finite cells of a Delaunay Triangulation.<br>
+    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.<br>
+    <b>User manual:</b> \ref alpha_complex - <b>Reference manual:</b> Gudhi::alphacomplex::Alpha_complex
+    </td>
+ </tr>
+</table>
+ \subsection CubicalComplexDataStructure Cubical complex
+ \image html "Cubical_complex_representation.png" "Cubical complex representation"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> Pawel Dlotko<br>
+      <b>Introduced in:</b> GUDHI 1.3.0<br>
+      <b>Copyright:</b> GPL v3<br>
+    </td>
+    <td width="75%">
+    The cubical complex is an example of a structured complex useful in computational mathematics (specially
+    rigorous numerics) and image analysis.<br>
+    <b>User manual:</b> \ref cubical_complex - <b>Reference manual:</b> Gudhi::Cubical_complex::Bitmap_cubical_complex
+    </td>
+ </tr>
+</table>
+ \subsection SimplexTreeDataStructure Simplex tree
+ \image html "Simplex_tree_representation.png" "Simplex tree representation"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> Cl&eacute;ment Maria<br>
+      <b>Introduced in:</b> GUDHI 1.0.0<br>
+      <b>Copyright:</b> GPL v3<br>
+    </td>
+    <td width="75%">
+    The simplex tree is an efficient and flexible
+ data structure for representing general (filtered) simplicial complexes. The data structure
+ is described in \cite boissonnatmariasimplextreealgorithmica .<br>
+    <b>User manual:</b> \ref simplex_tree - <b>Reference manual:</b> Gudhi::Simplex_tree
+    </td>
+ </tr>
+</table>
+ \subsection SkeletonBlockerDataStructure Skeleton blocker
+ \image html "ds_representation.png" "Skeleton blocker representation"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> David Salinas<br>
+      <b>Introduced in:</b> GUDHI 1.1.0<br>
+      <b>Copyright:</b> GPL v3<br>
+    </td>
+    <td width="75%">
+    The Skeleton-Blocker data-structure proposes a light encoding for simplicial complexes by storing only an *implicit*
+    representation of its simplices \cite socg_blockers_2011,\cite blockers2012. Intuitively, it just stores the
+    1-skeleton of a simplicial complex with a graph and the set of its "missing faces" that is very small in practice.
+    This data-structure handles all simplicial complexes operations such as simplex enumeration or simplex removal but
+    operations that are particularly efficient are operations that do not require simplex enumeration such as edge
+    iteration, link computation or simplex contraction.<br>
+    <b>User manual:</b> \ref skbl - <b>Reference manual:</b> Gudhi::skbl::Skeleton_blocker_complex
+    </td>
+ </tr>
+</table>
+ \subsection WitnessComplexDataStructure Witness complex
+ \image html "Witness_complex_representation.png" "Witness complex representation"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> Siargey Kachanovich<br>
+      <b>Introduced in:</b> GUDHI 1.3.0<br>
+      <b>Copyright:</b> GPL v3<br>
+    </td>
+    <td width="75%">
+    Witness complex \f$ Wit(W,L) \f$  is a simplicial complex defined on two sets of points in \f$\mathbb{R}^D\f$.
+    The data structure is described in \cite boissonnatmariasimplextreealgorithmica .<br>
+    <b>User manual:</b> \ref witness_complex - <b>Reference manual:</b> Gudhi::witness_complex::SimplicialComplexForWitness
+    </td>
+ </tr>
+</table>
+ 
+ \section Toolbox Toolbox
+ \subsection ContractionToolbox Contraction
+ \image html "sphere_contraction_representation.png" "Sphere contraction example"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> David Salinas<br>
+      <b>Introduced in:</b> GUDHI 1.1.0<br>
+      <b>Copyright:</b> GPL v3<br>
+    </td>
+    <td width="75%">
+    The purpose of this package is to offer a user-friendly interface for edge contraction simplification of huge
+    simplicial complexes. It uses the \ref skbl data-structure whose size remains small  during simplification of most
+    used geometrical complexes of topological data analysis such as the Rips or the Delaunay complexes. In practice,
+    the size of this data-structure is even much lower than the total number of simplices.<br>
+    <b>User manual:</b> \ref contr
+    </td>
+ </tr>
+</table>
+ \subsection PersistentCohomologyToolbox Persistent Cohomology
+ \image html "3DTorus_poch.png" "Rips Persistent Cohomology on a 3D Torus"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> Cl&eacute;ment Maria<br>
+      <b>Introduced in:</b> GUDHI 1.0.0<br>
+      <b>Copyright:</b> GPL v3<br>
+    </td>
+    <td width="75%">
+    The theory of homology consists in attaching to a topological space a sequence of (homology) groups, capturing
+    global topological features like connected components, holes, cavities, etc. Persistent homology studies the
+    evolution -- birth, life and death -- of these features when the topological space is changing. Consequently, the
+    theory is essentially composed of three elements: topological spaces, their homology groups and an evolution
+    scheme.
+    Computation of persistent cohomology using the algorithm of \cite DBLP:journals/dcg/SilvaMV11 and
+    \cite DBLP:journals/corr/abs-1208-5018 and the Compressed Annotation Matrix implementation of
+    \cite DBLP:conf/esa/BoissonnatDM13 .<br>
+    <b>User manual:</b> \ref persistent_cohomology - <b>Reference manual:</b> Gudhi::persistent_cohomology::Persistent_cohomology
+    </td>
+ </tr>
+</table>
 */
 
 /*! \page installation Gudhi installation
@@ -47,7 +160,7 @@
  * 
  * \section compiling Compiling
  * The library uses c++11 and requires <a target="_blank" href="http://www.boost.org/">Boost</a> with version 1.48.0 or
- * more recent. It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2013.
+ * more recent. It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015.
  * 
  * \subsection gmp GMP:
  * The multi-field persistent homology algorithm requires GMP which is a free library for arbitrary-precision
@@ -55,29 +168,114 @@
  * 
  * The following example requires the <a target="_blank" href="http://gmplib.org/">GNU Multiple Precision Arithmetic
  * Library</a> (GMP) and will not be built if GMP is not installed:
- * \li Persistent_cohomology/rips_multifield_persistence
+ * \li <a href="_persistent_cohomology_2alpha_shapes_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_shapes_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2performance_rips_persistence_8cpp-example.html">
+ * Persistent_cohomology/performance_rips_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html">
+ * Persistent_cohomology/rips_multifield_persistence.cpp</a>
+ * \li <a href="_simplex_tree_2simplex_tree_from_alpha_shapes_3_8cpp-example.html">
+ * Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp</a>
  *
  * Having GMP version 4.2 or higher installed is recommended.
  * 
  * \subsection cgal CGAL:
  * CGAL is a C++ library which provides easy access to efficient and reliable geometric algorithms.
  * 
- * The following examples require the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms
- * Library</a> (CGAL) and will not be built if CGAL is not installed:
- * \li GudhUI
- * \li Persistent_cohomology/alpha_shapes_persistence
- * \li Simplex_tree/simplex_tree_from_alpha_shapes_3
- * 
  * Having CGAL version 4.4 or higher installed is recommended. The procedure to install this library according to
  * your operating system is detailed here http://doc.cgal.org/latest/Manual/installation.html
  * 
+ * The following examples require the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms
+ * Library</a> (CGAL \cite cgal:eb-15b) and will not be built if CGAL is not installed:
+ * \li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_complex_persistence.cpp</a>
+ * \li <a href="_simplex_tree_2simplex_tree_from_alpha_shapes_3_8cpp-example.html">
+ * Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp</a>
+ * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html">
+ *  Alpha_complex/Alpha_complex_from_off.cpp</a>
+ * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
+ *  Alpha_complex/Alpha_complex_from_points.cpp</a>
+ * 
+ * The following example requires CGAL version &ge; 4.6:
+ * \li <a href="_witness_complex_2witness_complex_sphere_8cpp-example.html">
+ * Witness_complex/witness_complex_sphere.cpp</a>
+ * 
+ * The following example requires CGAL version &ge; 4.7:
+ * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html">
+ * Alpha_complex/Alpha_complex_from_off.cpp</a>
+ * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
+ * Alpha_complex/Alpha_complex_from_points.cpp</a>
+ * \li <a href="common_2_c_g_a_l_points_off_reader_8cpp-example.html">
+ * common/CGAL_points_off_reader.cpp</a>
+ * 
+ * \subsection eigen3 Eigen3:
+ * <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen3</a> is a C++ template library for linear algebra:
+ * matrices, vectors, numerical solvers, and related algorithms.
+ * 
+ * The following example requires the <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen3</a> and will not be
+ * built if Eigen3 is not installed:
+ * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html">
+ * Alpha_complex/Alpha_complex_from_off.cpp</a> (requires also Eigen3)
+ * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
+ * Alpha_complex/Alpha_complex_from_points.cpp</a> (requires also Eigen3)
+ * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_complex_persistence.cpp</a>
+ * 
+ * \subsection tbb Threading Building Blocks:
+ * <a target="_blank" href="https://www.threadingbuildingblocks.org/">Intel&reg; TBB</a> lets you easily write parallel
+ * C++ programs that take full advantage of multicore performance, that are portable and composable, and that have
+ * future-proof scalability.
+ * 
+ * Having Intel&reg; TBB installed is recommended to parallelize and accelerate some GUDHI computations.
+ * 
+ * The following examples are using Intel&reg; TBB if installed:
+ * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html">
+ * Alpha_complex/Alpha_complex_from_off.cpp</a>
+ * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
+ * Alpha_complex/Alpha_complex_from_points.cpp</a>
+ * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_8cpp-example.html">
+ * Bitmap_cubical_complex/Bitmap_cubical_complex.cpp</a>
+ * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_periodic_boundary_conditions_8cpp-example.html">
+ * Bitmap_cubical_complex/Bitmap_cubical_complex_periodic_boundary_conditions.cpp</a>
+ * \li <a href="_bitmap_cubical_complex_2_random_bitmap_cubical_complex_8cpp-example.html">
+ * Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp</a>
+ * \li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_complex_persistence.cpp</a>
+ * \li <a href="_simplex_tree_2simple_simplex_tree_8cpp-example.html">
+ * Simplex_tree/simple_simplex_tree.cpp</a>
+ * \li <a href="_simplex_tree_2simplex_tree_from_alpha_shapes_3_8cpp-example.html">
+ * Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp</a>
+ * \li <a href="_simplex_tree_2simplex_tree_from_cliques_of_graph_8cpp-example.html">
+ * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp</a>
+ * \li <a href="_persistent_cohomology_2alpha_shapes_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_shapes_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2parallel_rips_persistence_8cpp-example.html">
+ * Persistent_cohomology/parallel_rips_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2performance_rips_persistence_8cpp-example.html">
+ * Persistent_cohomology/performance_rips_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2persistence_from_file_8cpp-example.html">
+ * Persistent_cohomology/persistence_from_file.cpp</a>
+ * \li <a href="_persistent_cohomology_2persistence_from_simple_simplex_tree_8cpp-example.html">
+ * Persistent_cohomology/persistence_from_simple_simplex_tree.cpp</a>
+ * \li <a href="_persistent_cohomology_2plain_homology_8cpp-example.html">
+ * Persistent_cohomology/plain_homology.cpp</a>
+ * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html">
+ * Persistent_cohomology/rips_multifield_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2rips_persistence_8cpp-example.html">
+ * Persistent_cohomology/rips_persistence.cpp</a>
+ * 
  * \subsection demos Demos and examples
- * To build the demos and libraries, run the following commands in a terminal:
+ * To build the demos and examples, run the following commands in a terminal:
 \verbatim  cd /path-to-gudhi/
 mkdir build
 cd build/
 cmake ..
 make \endverbatim
+ * A list of examples is available <a href="examples.html">here</a>.
  * 
  * \subsection testsuites Test suites
  * To test your build, run the following command in a terminal:
@@ -91,17 +289,6 @@ make \endverbatim
  * 
 */
 
-/*! \page Upcoming Upcoming
- *
- * The library is under active development. New packages to be released next include:
- * \li Alpha complex.
- * \li Bottleneck distance.
- * \li Zig zag persistence.
- * \li Witness complex.
- * \li Tangential complex.
- * \li Clustering.
-*/
-
 /*! \page Citation Acknowledging the GUDHI library
  * We kindly ask users to cite the GUDHI library as appropriately as possible in their papers, and to mention the use
  * of the GUDHI library on the web pages of their projects using GUDHI and provide us with links to these web pages.
@@ -113,3 +300,33 @@ make \endverbatim
  * \verbinclude  biblio/how_to_cite_gudhi.bib
 */
 
+// List of Gudhi examples - Doxygen needs at least a file tag to analyse comments
+/*! @file Examples
+ * @example Alpha_complex/Alpha_complex_from_off.cpp
+ * @example Alpha_complex/Alpha_complex_from_points.cpp
+ * @example Bitmap_cubical_complex/Bitmap_cubical_complex.cpp
+ * @example Bitmap_cubical_complex/Bitmap_cubical_complex_periodic_boundary_conditions.cpp
+ * @example Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp
+ * @example common/CGAL_points_off_reader.cpp
+ * @example Contraction/Garland_heckbert.cpp
+ * @example Contraction/Rips_contraction.cpp
+ * @example Persistent_cohomology/alpha_complex_3d_persistence.cpp
+ * @example Persistent_cohomology/alpha_complex_persistence.cpp
+ * @example Persistent_cohomology/parallel_rips_persistence.cpp
+ * @example Persistent_cohomology/performance_rips_persistence.cpp
+ * @example Persistent_cohomology/persistence_from_file.cpp
+ * @example Persistent_cohomology/persistence_from_simple_simplex_tree.cpp
+ * @example Persistent_cohomology/plain_homology.cpp
+ * @example Persistent_cohomology/rips_multifield_persistence.cpp
+ * @example Persistent_cohomology/rips_persistence.cpp
+ * @example Simplex_tree/mini_simplex_tree.cpp
+ * @example Simplex_tree/simple_simplex_tree.cpp
+ * @example Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp
+ * @example Simplex_tree/simplex_tree_from_cliques_of_graph.cpp
+ * @example Skeleton_blocker/Skeleton_blocker_from_simplices.cpp
+ * @example Skeleton_blocker/Skeleton_blocker_iteration.cpp
+ * @example Skeleton_blocker/Skeleton_blocker_link.cpp
+ * @example Witness_complex/witness_complex_from_file.cpp
+ * @example Witness_complex/witness_complex_sphere.cpp
+ */
+
diff --git a/src/common/doc/stylesheet.css b/src/common/doc/stylesheet.css
new file mode 100644
index 00000000..1df177a4
--- /dev/null
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@@ -0,0 +1,1367 @@
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+        padding: 3px 7px 2px;
+}
+
+.fieldtable td.fieldtype, .fieldtable td.fieldname {
+        white-space: nowrap;
+        border-right: 1px solid #A8B8D9;
+        border-bottom: 1px solid #A8B8D9;
+        vertical-align: top;
+}
+
+.fieldtable td.fieldname {
+        padding-top: 3px;
+}
+
+.fieldtable td.fielddoc {
+        border-bottom: 1px solid #A8B8D9;
+        /*width: 100%;*/
+}
+
+.fieldtable td.fielddoc p:first-child {
+        margin-top: 0px;
+}       
+        
+.fieldtable td.fielddoc p:last-child {
+        margin-bottom: 2px;
+}
+
+.fieldtable tr:last-child td {
+        border-bottom: none;
+}
+
+.fieldtable th {
+        background-image:url('nav_f.png');
+        background-repeat:repeat-x;
+        background-color: #E2E8F2;
+        font-size: 90%;
+        color: #253555;
+        padding-bottom: 4px;
+        padding-top: 5px;
+        text-align:left;
+        -moz-border-radius-topleft: 4px;
+        -moz-border-radius-topright: 4px;
+        -webkit-border-top-left-radius: 4px;
+        -webkit-border-top-right-radius: 4px;
+        border-top-left-radius: 4px;
+        border-top-right-radius: 4px;
+        border-bottom: 1px solid #A8B8D9;
+}
+
+
+.tabsearch {
+	top: 0px;
+	left: 10px;
+	height: 36px;
+	background-image: url('tab_b.png');
+	z-index: 101;
+	overflow: hidden;
+	font-size: 13px;
+}
+
+.navpath ul
+{
+	font-size: 11px;
+	background-image:url('tab_b.png');
+	background-repeat:repeat-x;
+	background-position: 0 -5px;
+	height:30px;
+	line-height:30px;
+	color:#8AA0CC;
+	border:solid 1px #C2CDE4;
+	overflow:hidden;
+	margin:0px;
+	padding:0px;
+}
+
+.navpath li
+{
+	list-style-type:none;
+	float:left;
+	padding-left:10px;
+	padding-right:15px;
+	background-image:url('bc_s.png');
+	background-repeat:no-repeat;
+	background-position:right;
+	color:#364D7C;
+}
+
+.navpath li.navelem a
+{
+	height:32px;
+	display:block;
+	text-decoration: none;
+	outline: none;
+	color: #283A5D;
+	font-family: 'Lucida Grande',Geneva,Helvetica,Arial,sans-serif;
+	text-shadow: 0px 1px 1px rgba(255, 255, 255, 0.9);
+	text-decoration: none;        
+}
+
+.navpath li.navelem a:hover
+{
+	color:#6884BD;
+}
+
+.navpath li.footer
+{
+        list-style-type:none;
+        float:right;
+        padding-left:10px;
+        padding-right:15px;
+        background-image:none;
+        background-repeat:no-repeat;
+        background-position:right;
+        color:#364D7C;
+        font-size: 8pt;
+}
+
+
+div.summary
+{
+	float: right;
+	font-size: 8pt;
+	padding-right: 5px;
+	width: 50%;
+	text-align: right;
+}       
+
+div.summary a
+{
+	white-space: nowrap;
+}
+
+div.ingroups
+{
+	font-size: 8pt;
+	width: 50%;
+	text-align: left;
+}
+
+div.ingroups a
+{
+	white-space: nowrap;
+}
+
+div.header
+{
+        background-image:url('nav_h.png');
+        background-repeat:repeat-x;
+	background-color: #F9FAFC;
+	margin:  0px;
+	border-bottom: 1px solid #C4CFE5;
+}
+
+div.headertitle
+{
+	padding: 5px 5px 5px 10px;
+}
+
+dl
+{
+        padding: 0 0 0 10px;
+}
+
+/* dl.note, dl.warning, dl.attention, dl.pre, dl.post, dl.invariant, dl.deprecated, dl.todo, dl.test, dl.bug */
+dl.section
+{
+	margin-left: 0px;
+	padding-left: 0px;
+}
+
+dl.note
+{
+        margin-left:-7px;
+        padding-left: 3px;
+        border-left:4px solid;
+        border-color: #D0C000;
+}
+
+dl.warning, dl.attention
+{
+        margin-left:-7px;
+        padding-left: 3px;
+        border-left:4px solid;
+        border-color: #FF0000;
+}
+
+dl.pre, dl.post, dl.invariant
+{
+        margin-left:-7px;
+        padding-left: 3px;
+        border-left:4px solid;
+        border-color: #00D000;
+}
+
+dl.deprecated
+{
+        margin-left:-7px;
+        padding-left: 3px;
+        border-left:4px solid;
+        border-color: #505050;
+}
+
+dl.todo
+{
+        margin-left:-7px;
+        padding-left: 3px;
+        border-left:4px solid;
+        border-color: #00C0E0;
+}
+
+dl.test
+{
+        margin-left:-7px;
+        padding-left: 3px;
+        border-left:4px solid;
+        border-color: #3030E0;
+}
+
+dl.bug
+{
+        margin-left:-7px;
+        padding-left: 3px;
+        border-left:4px solid;
+        border-color: #C08050;
+}
+
+dl.section dd {
+	margin-bottom: 6px;
+}
+
+
+#projectlogo
+{
+	text-align: center;
+	vertical-align: bottom;
+	border-collapse: separate;
+}
+ 
+#projectlogo img
+{ 
+	border: 0px none;
+}
+ 
+#projectname
+{
+	border: 0px none;
+	font: 300% Tahoma, Arial,sans-serif;
+	margin: 0px;
+	padding: 2px 0px;
+}
+    
+#projectbrief
+{
+	font: 60% Tahoma, Arial,sans-serif;
+	margin: 0px;
+	padding: 0px;
+}
+
+#projectnumber
+{
+	font: 80% Tahoma, Arial,sans-serif;
+	margin: 0px;
+	padding: 0px;
+}
+
+#titlearea
+{
+	padding: 0px;
+	margin: 0px;
+	width: 100%;
+	border-bottom: 1px solid #5373B4;
+}
+
+.image
+{
+        text-align: center;
+}
+
+.dotgraph
+{
+        text-align: center;
+}
+
+.mscgraph
+{
+        text-align: center;
+}
+
+.diagraph
+{
+        text-align: center;
+}
+
+.caption
+{
+	font-weight: bold;
+}
+
+div.zoom
+{
+	border: 1px solid #90A5CE;
+}
+
+dl.citelist {
+        margin-bottom:50px;
+}
+
+dl.citelist dt {
+        color:#334975;
+        float:left;
+        font-weight:bold;
+        margin-right:10px;
+        padding:5px;
+}
+
+dl.citelist dd {
+        margin:2px 0;
+        padding:5px 0;
+}
+
+div.toc {
+        padding: 14px 25px;
+        background-color: #F4F6FA;
+        border: 1px solid #D8DFEE;
+        border-radius: 7px 7px 7px 7px;
+        float: right;
+        height: auto;
+        margin: 0 20px 10px 10px;
+        width: 200px;
+}
+
+div.toc li {
+        background: url("bdwn.png") no-repeat scroll 0 5px transparent;
+        font: 10px/1.2 Verdana,DejaVu Sans,Geneva,sans-serif;
+        margin-top: 5px;
+        padding-left: 10px;
+        padding-top: 2px;
+}
+
+div.toc h3 {
+        font: bold 12px/1.2 Arial,FreeSans,sans-serif;
+	color: #4665A2;
+        border-bottom: 0 none;
+        margin: 0;
+}
+
+div.toc ul {
+        list-style: none outside none;
+        border: medium none;
+        padding: 0px;
+}       
+
+div.toc li.level1 {
+        margin-left: 0px;
+}
+
+div.toc li.level2 {
+        margin-left: 15px;
+}
+
+div.toc li.level3 {
+        margin-left: 30px;
+}
+
+div.toc li.level4 {
+        margin-left: 45px;
+}
+
+.inherit_header {
+        font-weight: bold;
+        color: gray;
+        cursor: pointer;
+	-webkit-touch-callout: none;
+	-webkit-user-select: none;
+	-khtml-user-select: none;
+	-moz-user-select: none;
+	-ms-user-select: none;
+	user-select: none;
+}
+
+.inherit_header td {
+        padding: 6px 0px 2px 5px;
+}
+
+.inherit {
+        display: none;
+}
+
+tr.heading h2 {
+        margin-top: 12px;
+        margin-bottom: 4px;
+}
+
+/* tooltip related style info */
+
+.ttc {
+        position: absolute;
+        display: none;
+}
+
+#powerTip {
+	cursor: default;
+	white-space: nowrap;
+	background-color: white;
+	border: 1px solid gray;
+	border-radius: 4px 4px 4px 4px;
+	box-shadow: 1px 1px 7px gray;
+	display: none;
+	font-size: smaller;
+	max-width: 80%;
+	opacity: 0.9;
+	padding: 1ex 1em 1em;
+	position: absolute;
+	z-index: 2147483647;
+}
+
+#powerTip div.ttdoc {
+        color: grey;
+	font-style: italic;
+}
+
+#powerTip div.ttname a {
+        font-weight: bold;
+}
+
+#powerTip div.ttname {
+        font-weight: bold;
+}
+
+#powerTip div.ttdeci {
+        color: #006318;
+}
+
+#powerTip div {
+        margin: 0px;
+        padding: 0px;
+        font: 12px/16px Roboto,sans-serif;
+}
+
+#powerTip:before, #powerTip:after {
+	content: "";
+	position: absolute;
+	margin: 0px;
+}
+
+#powerTip.n:after,  #powerTip.n:before,
+#powerTip.s:after,  #powerTip.s:before,
+#powerTip.w:after,  #powerTip.w:before,
+#powerTip.e:after,  #powerTip.e:before,
+#powerTip.ne:after, #powerTip.ne:before,
+#powerTip.se:after, #powerTip.se:before,
+#powerTip.nw:after, #powerTip.nw:before,
+#powerTip.sw:after, #powerTip.sw:before {
+	border: solid transparent;
+	content: " ";
+	height: 0;
+	width: 0;
+	position: absolute;
+}
+
+#powerTip.n:after,  #powerTip.s:after,
+#powerTip.w:after,  #powerTip.e:after,
+#powerTip.nw:after, #powerTip.ne:after,
+#powerTip.sw:after, #powerTip.se:after {
+	border-color: rgba(255, 255, 255, 0);
+}
+
+#powerTip.n:before,  #powerTip.s:before,
+#powerTip.w:before,  #powerTip.e:before,
+#powerTip.nw:before, #powerTip.ne:before,
+#powerTip.sw:before, #powerTip.se:before {
+	border-color: rgba(128, 128, 128, 0);
+}
+
+#powerTip.n:after,  #powerTip.n:before,
+#powerTip.ne:after, #powerTip.ne:before,
+#powerTip.nw:after, #powerTip.nw:before {
+	top: 100%;
+}
+
+#powerTip.n:after, #powerTip.ne:after, #powerTip.nw:after {
+	border-top-color: #ffffff;
+	border-width: 10px;
+	margin: 0px -10px;
+}
+#powerTip.n:before {
+	border-top-color: #808080;
+	border-width: 11px;
+	margin: 0px -11px;
+}
+#powerTip.n:after, #powerTip.n:before {
+	left: 50%;
+}
+
+#powerTip.nw:after, #powerTip.nw:before {
+	right: 14px;
+}
+
+#powerTip.ne:after, #powerTip.ne:before {
+	left: 14px;
+}
+
+#powerTip.s:after,  #powerTip.s:before,
+#powerTip.se:after, #powerTip.se:before,
+#powerTip.sw:after, #powerTip.sw:before {
+	bottom: 100%;
+}
+
+#powerTip.s:after, #powerTip.se:after, #powerTip.sw:after {
+	border-bottom-color: #ffffff;
+	border-width: 10px;
+	margin: 0px -10px;
+}
+
+#powerTip.s:before, #powerTip.se:before, #powerTip.sw:before {
+	border-bottom-color: #808080;
+	border-width: 11px;
+	margin: 0px -11px;
+}
+
+#powerTip.s:after, #powerTip.s:before {
+	left: 50%;
+}
+
+#powerTip.sw:after, #powerTip.sw:before {
+	right: 14px;
+}
+
+#powerTip.se:after, #powerTip.se:before {
+	left: 14px;
+}
+
+#powerTip.e:after, #powerTip.e:before {
+	left: 100%;
+}
+#powerTip.e:after {
+	border-left-color: #ffffff;
+	border-width: 10px;
+	top: 50%;
+	margin-top: -10px;
+}
+#powerTip.e:before {
+	border-left-color: #808080;
+	border-width: 11px;
+	top: 50%;
+	margin-top: -11px;
+}
+
+#powerTip.w:after, #powerTip.w:before {
+	right: 100%;
+}
+#powerTip.w:after {
+	border-right-color: #ffffff;
+	border-width: 10px;
+	top: 50%;
+	margin-top: -10px;
+}
+#powerTip.w:before {
+	border-right-color: #808080;
+	border-width: 11px;
+	top: 50%;
+	margin-top: -11px;
+}
+
+@media print
+{
+  #top { display: none; }
+  #side-nav { display: none; }
+  #nav-path { display: none; }
+  body { overflow:visible; }
+  h1, h2, h3, h4, h5, h6 { page-break-after: avoid; }
+  .summary { display: none; }
+  .memitem { page-break-inside: avoid; }
+  #doc-content
+  {
+    margin-left:0 !important;
+    height:auto !important;
+    width:auto !important;
+    overflow:inherit;
+    display:inline;
+  }
+}
+
diff --git a/src/common/example/CGAL_points_off_reader.cpp b/src/common/example/CGAL_points_off_reader.cpp
new file mode 100644
index 00000000..45e9f1e6
--- /dev/null
+++ b/src/common/example/CGAL_points_off_reader.cpp
@@ -0,0 +1,44 @@
+#include <gudhi/Points_off_io.h>
+
+// For CGAL points type in dimension d
+// cf. http://doc.cgal.org/latest/Kernel_d/classCGAL_1_1Point__d.html
+#include <CGAL/Epick_d.h>
+
+#include <iostream>
+#include <string>
+#include <vector>
+
+typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel;
+typedef typename Kernel::Point_d Point_d;
+
+void usage(int argc, char * const progName) {
+  std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl;
+  std::cerr << "Usage: " << progName << " inputFile.off" << std::endl;
+  exit(-1);
+}
+
+int main(int argc, char **argv) {
+  if (argc != 2) usage(argc, (argv[0] - 1));
+
+  std::string offInputFile(argv[1]);
+  // Read the OFF file (input file name given as parameter) and triangulate points
+  Gudhi::Points_off_reader<Point_d> off_reader(offInputFile);
+  // Check the read operation was correct
+  if (!off_reader.is_valid()) {
+    std::cerr << "Unable to read file " << offInputFile << std::endl;
+    exit(-1);
+  }
+
+  // Retrieve the triangulation
+  std::vector<Point_d> point_cloud = off_reader.get_point_cloud();
+
+  int n = 0;
+  for (auto point : point_cloud) {
+    std::cout << "Point[" << n << "] = ";
+    for (int i = 0; i < point.dimension(); i++)
+      std::cout << point[i] << " ";
+    std::cout << "\n";
+    ++n;
+  }
+  return 0;
+}
diff --git a/src/common/example/CMakeLists.txt b/src/common/example/CMakeLists.txt
new file mode 100644
index 00000000..5aeaa8c6
--- /dev/null
+++ b/src/common/example/CMakeLists.txt
@@ -0,0 +1,22 @@
+cmake_minimum_required(VERSION 2.6)
+project(GUDHIDelaunayTriangulationOffFileReadWrite)
+
+# need CGAL 4.7
+if(CGAL_FOUND)
+  if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+    find_package(Eigen3 3.1.0)
+    if (EIGEN3_FOUND)
+      message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
+      include( ${EIGEN3_USE_FILE} )
+      
+      add_executable ( cgaloffreader CGAL_points_off_reader.cpp )
+      target_link_libraries(cgaloffreader  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+      add_test(cgaloffreader ${CMAKE_CURRENT_BINARY_DIR}/cgaloffreader ${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off)
+
+    else()
+      message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.")
+    endif()
+  else()
+    message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.")
+  endif ()
+endif()
diff --git a/src/common/example/cgaloffreader_result.txt b/src/common/example/cgaloffreader_result.txt
new file mode 100644
index 00000000..1deb8dbd
--- /dev/null
+++ b/src/common/example/cgaloffreader_result.txt
@@ -0,0 +1,7 @@
+Point[0] = 1 1 
+Point[1] = 7 0 
+Point[2] = 4 6 
+Point[3] = 9 6 
+Point[4] = 0 14 
+Point[5] = 2 19 
+Point[6] = 9 17 
diff --git a/src/common/include/gudhi/Utils.h b/src/common/include/gudhi/Debug_utils.h
index 43916f11..7573a9db 100644
--- a/src/common/include/gudhi/Utils.h
+++ b/src/common/include/gudhi/Debug_utils.h
@@ -19,28 +19,37 @@
  *    You should have received a copy of the GNU General Public License
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
-#ifndef UTILS_H_
-#define UTILS_H_
+#ifndef DEBUG_UTILS_H_
+#define DEBUG_UTILS_H_
 
+#include <iostream>
+
+#ifndef NDEBUG
+  // GUDHI_DEBUG is the Gudhi official flag for debug mode.
+  #define GUDHI_DEBUG
+#endif
+
+// GUDHI_CHECK throw an exception if expression is false in debug mode, but does nothing in release mode
+// Could assert in release mode, but cmake sets NDEBUG (for "NO DEBUG") in this mode, means assert does nothing.
+#ifdef GUDHI_DEBUG
+  #define GUDHI_CHECK(expression, excpt) if ((expression) == 0) throw excpt
+#else
+  #define GUDHI_CHECK(expression, excpt) (void) 0
+#endif
 
 #define PRINT(a) std::cerr << #a << ": " << (a) << " (DISP)" << std::endl
 
 // #define DBG_VERBOSE
 #ifdef DBG_VERBOSE
-#define DBG(a) std::cerr << "DBG: " << (a) << std::endl
-#define DBGMSG(a, b) std::cerr << "DBG: " << a << b << std::endl
-#define DBGVALUE(a) std::cerr << "DBG: " <<  #a << ": " << a << std::endl
-#define DBGCONT(a) std::cerr << "DBG: container " << #a << " -> "; for (auto x : a) std::cerr << x << ","; std::cerr <<
-std::endl
+  #define DBG(a) std::cout << "DBG: " << (a) << std::endl
+  #define DBGMSG(a, b) std::cout << "DBG: " << a << b << std::endl
+  #define DBGVALUE(a) std::cout << "DBG: " <<  #a << ": " << a << std::endl
+  #define DBGCONT(a) std::cout << "DBG: container " << #a << " -> "; for (auto x : a) std::cout << x << ","; std::cout << std::endl
 #else
-// #define DBG(a) a
-// #define DBGMSG(a,b) b
-// #define DBGVALUE(a) a
-// #define DBGCONT(a) a
-#define DBG(a)
-#define DBGMSG(a, b)
-#define DBGVALUE(a)
-#define DBGCONT(a)
+  #define DBG(a) (void) 0
+  #define DBGMSG(a, b) (void) 0
+  #define DBGVALUE(a) (void) 0
+  #define DBGCONT(a) (void) 0
 #endif
 
-#endif  // UTILS_H_
+#endif  // DEBUG_UTILS_H_
diff --git a/src/common/include/gudhi/Off_reader.h b/src/common/include/gudhi/Off_reader.h
index 81b9e634..4fcd2af2 100644
--- a/src/common/include/gudhi/Off_reader.h
+++ b/src/common/include/gudhi/Off_reader.h
@@ -31,40 +31,35 @@
 #include <iterator>
 #include <string>
 #include <vector>
+#include <fstream>
 
 namespace Gudhi {
 
-/**
- * Read an off file and calls a visitor methods while reading it.
- * An off file must have its first/snd line in this format :
- * OFF
- * num_vert num_faces num_edges
- *
- * A noff file must have its first/snd line in this format :
- * nOFF
- * dim num_vert num_faces num_edges
- *
- * The number of edges num_edges is optional and can be left to zero.
+/** \brief OFF file reader top class visitor. 
+ * 
+ * OFF file must be conform to format described here : 
+ * http://www.geomview.org/docs/html/OFF.html
  */
 class Off_reader {
  public:
   Off_reader(std::ifstream& stream) : stream_(stream) { }
-  // Off_reader(const std::string& name):stream_(name){
-  //   if(!stream_.is_open())
-  //   std::cerr <<"could not open file \n";
-  // }
 
   ~Off_reader() {
     stream_.close();
   }
 
-  /**
-   * read an off file and calls the following methods :
-   * void init(int dim,int num_vertices,int num_faces,int num_edges); //num_edges may not be set
-   * void point(const std::vector<double>& point);
-   * void maximal_face(const std::list<int>& face);
-   * void done();
-   * of the visitor when reading a point or a maximal face.
+  /** \brief
+   * Read an OFF file and calls the following methods :
+   * 
+   * <CODE>void init(int dim,int num_vertices,int num_faces,int num_edges);  // from file header - num_edges may not be set
+   * 
+   * void point(const std::vector<double>& point);  // for each point read
+   * 
+   * void maximal_face(const std::list<int>& face);  // for each face read
+   * 
+   * void done();  // upon file read is finished</CODE>
+   * 
+   * of the visitor when reading a point or a maximal face. Edges are not taken into account.
    */
   template<typename OffVisitor>
   bool read(OffVisitor& off_visitor) {
@@ -118,7 +113,7 @@ class Off_reader {
 
     if (!goto_next_uncomment_line(line)) return false;
     std::istringstream iss(line);
-    if (is_off_file) {
+    if ((is_off_file) && (!is_noff_file)) {
       off_info_.dim = 3;
       if (!(iss >> off_info_.num_vertices >> off_info_.num_faces >> off_info_.num_edges)) {
         std::cerr << "incorrect number of vertices/faces/edges\n";
@@ -126,8 +121,8 @@ class Off_reader {
       }
     } else {
       if (!(iss >> off_info_.dim >> off_info_.num_vertices >> off_info_.num_faces >> off_info_.num_edges)) {
-        std::cerr << "incorrect number of vertices/faces/edges\n";
-        return false;
+      std::cerr << "incorrect number of vertices/faces/edges\n";
+      return false;
       }
     }
     off_visitor.init(off_info_.dim, off_info_.num_vertices, off_info_.num_faces, off_info_.num_edges);
@@ -138,7 +133,7 @@ class Off_reader {
   bool goto_next_uncomment_line(std::string& uncomment_line) {
     uncomment_line.clear();
     do
-      std::getline(stream_, uncomment_line); while (uncomment_line[0] == '%');  // || uncomment_line.empty());
+      std::getline(stream_, uncomment_line); while (uncomment_line[0] == '%');
     return (uncomment_line.size() > 0 && uncomment_line[0] != '%');
   }
 
@@ -166,7 +161,7 @@ class Off_reader {
       iss >> num_face_vertices;
       std::vector<int> face;
       face.assign(std::istream_iterator<int>(iss), std::istream_iterator<int>());
-      if (face.size() != off_info_.dim) return false;
+      // if (face.size() != (off_info_.dim + 1)) return false;
       visitor.maximal_face(face);
     }
     return true;
diff --git a/src/common/include/gudhi/Points_off_io.h b/src/common/include/gudhi/Points_off_io.h
new file mode 100644
index 00000000..77f36be2
--- /dev/null
+++ b/src/common/include/gudhi/Points_off_io.h
@@ -0,0 +1,177 @@
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2015  INRIA Saclay (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+#ifndef POINTS_OFF_IO_H_
+#define POINTS_OFF_IO_H_
+
+#include <gudhi/Off_reader.h>
+
+#include <string>
+#include <vector>
+#include <fstream>
+#include <map>
+
+namespace Gudhi {
+
+/** 
+ * \brief OFF file visitor implementation according to Off_reader in order to read points from an OFF file.
+ */
+template<typename Point_d>
+class Points_off_visitor_reader {
+ private:
+  std::vector<Point_d> point_cloud;
+
+ public:
+  /** \brief Off_reader visitor init implementation. 
+   * 
+   * The init parameters are set from OFF file header.
+   * Dimension value is required in order to construct Alpha complex.
+   *
+   * @param[in] dim space dimension of vertices.
+   * @param[in] num_vertices number of vertices in the OFF file (not used).
+   * @param[in] num_faces number of faces in the OFF file (not used).
+   * @param[in] num_edges number of edges in the OFF file (not used).
+   */
+  void init(int dim, int num_vertices, int num_faces, int num_edges) {
+#ifdef DEBUG_TRACES
+    std::cout << "Points_off_visitor_reader::init - dim=" << dim << " - num_vertices=" <<
+        num_vertices << " - num_faces=" << num_faces << " - num_edges=" << num_edges << std::endl;
+#endif  // DEBUG_TRACES
+    if (num_faces > 0) {
+      std::cerr << "Points_off_visitor_reader::init faces are not taken into account from OFF file for Points.\n";
+    }
+    if (num_edges > 0) {
+      std::cerr << "Points_off_visitor_reader::init edges are not taken into account from OFF file for Points.\n";
+    }
+  }
+
+  /** \brief Off_reader visitor point implementation. 
+   * 
+   * The point function is called on each vertex line from OFF file.
+   * This function inserts the vertex in the Alpha complex.
+   *
+   * @param[in] point vector of vertex coordinates.
+   */
+  void point(const std::vector<double>& point) {
+#ifdef DEBUG_TRACES
+    std::cout << "Points_off_visitor_reader::point ";
+    for (auto coordinate : point) {
+      std::cout << coordinate << " | ";
+    }
+    std::cout << std::endl;
+#endif  // DEBUG_TRACES
+    // Fill the point cloud
+    point_cloud.push_back(Point_d(point.size(), point.begin(), point.end()));
+  }
+
+  // Off_reader visitor maximal_face implementation - Only points are read
+  void maximal_face(const std::vector<int>& face) { }
+
+  // Off_reader visitor done implementation - Only points are read
+  void done() { }
+
+  /** \brief Point cloud getter.
+   *
+   * @return point_cloud.
+   */
+  const std::vector<Point_d>& get_point_cloud() const {
+    return point_cloud;
+  }
+};
+
+/** 
+ * \brief OFF file reader implementation in order to read points from an OFF file.
+ * 
+ * This class is using the Points_off_visitor_reader to visit the OFF file according to Off_reader.
+ * 
+ * Point_d must have a constructor with the following form:
+ * 
+ * \code template<class InputIterator > Point_d::Point_d(int d, InputIterator first, InputIterator last) \endcode
+ * 
+ * where d is the point dimension. 		
+ * 
+ * \section Example
+ *
+ * This example loads points from an OFF file and builds a vector of CGAL points in dimension d.
+ * Then, it is asked to display the points.
+ * 
+ * \include common/CGAL_points_off_reader.cpp
+ * 
+ * When launching:
+ * 
+ * \code $> ./cgaloffreader ../../data/points/alphacomplexdoc.off
+ * \endcode
+ *
+ * the program output is:
+ * 
+ * \include common/cgaloffreader_result.txt
+ */
+template<typename Point_d>
+class Points_off_reader {
+ public:
+  /** \brief Reads the OFF file and constructs the Alpha complex from the points
+   * that are in the OFF file.
+   *
+   * @param[in] name_file OFF file to read.
+   * 
+   * \post Check with is_valid() function to see if read operation was successful.
+   */
+  Points_off_reader(const std::string& name_file)
+  : valid_(false) {
+    std::ifstream stream(name_file);
+    if (stream.is_open()) {
+      Off_reader off_reader(stream);
+      Points_off_visitor_reader<Point_d> off_visitor;
+      valid_ = off_reader.read(off_visitor);
+      if (valid_) {
+        point_cloud = off_visitor.get_point_cloud();
+      }
+    } else {
+      std::cerr << "Points_off_reader::Points_off_reader could not open file " << name_file << "\n";
+    }
+  }
+
+  /** \brief Returns if the OFF file read operation was successful or not.
+   *
+   * @return OFF file read status.
+   */
+  bool is_valid() const {
+    return valid_;
+  }
+
+   /** \brief Point cloud getter.
+   *
+   * @return point_cloud.
+   */
+  const std::vector<Point_d>& get_point_cloud() const {
+    return point_cloud;
+  }
+
+ private:
+  /** \brief point_cloud.*/
+  std::vector<Point_d> point_cloud;
+  /** \brief OFF file read status.*/
+  bool valid_;
+};
+
+}  // namespace Gudhi
+
+#endif  // POINTS_OFF_IO_H_
diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h
index e5c79ded..cd518581 100644
--- a/src/common/include/gudhi/distance_functions.h
+++ b/src/common/include/gudhi/distance_functions.h
@@ -23,6 +23,8 @@
 #ifndef DISTANCE_FUNCTIONS_H_
 #define DISTANCE_FUNCTIONS_H_
 
+#include <cmath>  // for std::sqrt
+
 /* Compute the Euclidean distance between two Points given
  * by a range of coordinates. The points are assumed to have 
  * the same dimension. */
@@ -35,7 +37,7 @@ double euclidean_distance(Point &p1, Point &p2) {
     double tmp = *it1 - *it2;
     dist += tmp*tmp;
   }
-  return sqrt(dist);
+  return std::sqrt(dist);
 }
 
 #endif  // DISTANCE_FUNCTIONS_H_
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index e05714c7..899f9df6 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -58,7 +58,9 @@ inline void read_points(std::string file_name, std::vector< std::vector< double
     while (iss >> x) {
       point.push_back(x);
     }
-    points.push_back(point);
+    // Check for empty lines
+    if (!point.empty())
+      points.push_back(point);
   }
   in_file.close();
 }
@@ -159,7 +161,7 @@ bool read_simplex(std::istream & in_, std::vector< Vertex_handle > & simplex, Fi
     simplex.push_back(v);
   }
   in_ >> fil;
-  in_.ignore((std::numeric_limits<std::streamsize>::max)(), '\n'); // ignore until the carriage return
+  in_.ignore((std::numeric_limits<std::streamsize>::max)(), '\n');  // ignore until the carriage return
   return true;
 }
 
diff --git a/src/common/test/CMakeLists.txt b/src/common/test/CMakeLists.txt
new file mode 100644
index 00000000..789546ae
--- /dev/null
+++ b/src/common/test/CMakeLists.txt
@@ -0,0 +1,39 @@
+cmake_minimum_required(VERSION 2.6)
+project(GUDHIDelaunayTriangulationOffFileReadWriteUT)
+
+if (GCOVR_PATH)
+  # for gcovr to make coverage reports - Corbera Jenkins plugin
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
+endif()
+if (GPROF_PATH)
+  # for gprof to make coverage reports - Jenkins
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
+endif()
+
+# need CGAL 4.7
+if(CGAL_FOUND)
+  if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+    find_package(Eigen3 3.1.0)
+    if (EIGEN3_FOUND)
+      message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
+      include( ${EIGEN3_USE_FILE} )
+      
+      add_executable ( poffreader_UT points_off_reader_unit_test.cpp )
+      target_link_libraries(poffreader_UT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+
+      # Do not forget to copy test files in current binary dir
+      file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+
+      # Unitary tests
+      add_test(poffreader_UT ${CMAKE_CURRENT_BINARY_DIR}/poffreader_UT
+      # XML format for Jenkins xUnit plugin 
+      --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/poffreader_UT.xml --log_level=test_suite --report_level=no)
+
+    else()
+      message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.")
+    endif()
+  else()
+    message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.")
+  endif ()
+endif()
+
diff --git a/src/common/test/README b/src/common/test/README
new file mode 100644
index 00000000..f2a7eb5a
--- /dev/null
+++ b/src/common/test/README
@@ -0,0 +1,14 @@
+To compile:
+***********
+
+cmake .
+make
+
+To launch with details:
+***********************
+
+./dtoffrw_UT --report_level=detailed --log_level=all 
+
+   ==> echo $? returns 0 in case of success (non-zero otherwise)
+
+
diff --git a/src/common/test/dtoffrw_alphashapedoc_result.off b/src/common/test/dtoffrw_alphashapedoc_result.off
new file mode 100644
index 00000000..1deb8dbd
--- /dev/null
+++ b/src/common/test/dtoffrw_alphashapedoc_result.off
@@ -0,0 +1,7 @@
+Point[0] = 1 1 
+Point[1] = 7 0 
+Point[2] = 4 6 
+Point[3] = 9 6 
+Point[4] = 0 14 
+Point[5] = 2 19 
+Point[6] = 9 17 
diff --git a/src/common/test/points_off_reader_unit_test.cpp b/src/common/test/points_off_reader_unit_test.cpp
new file mode 100644
index 00000000..73e19cbc
--- /dev/null
+++ b/src/common/test/points_off_reader_unit_test.cpp
@@ -0,0 +1,78 @@
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2015  INRIA Saclay (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <gudhi/Points_off_io.h>
+
+// For CGAL points type in dimension d
+// cf. http://doc.cgal.org/latest/Kernel_d/classCGAL_1_1Point__d.html
+#include <CGAL/Epick_d.h>
+
+#include <iostream>
+#include <string>
+#include <vector>
+
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "points_off_read_write"
+#include <boost/test/unit_test.hpp>
+
+typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel;
+typedef typename Kernel::Point_d Point_d;
+
+BOOST_AUTO_TEST_CASE( points_doc_test )
+{
+  // Read the OFF file (input file name given as parameter) and triangulates points
+  Gudhi::Points_off_reader<Point_d> off_reader("alphacomplexdoc.off");
+  // Check the read operation was correct
+  BOOST_CHECK(off_reader.is_valid());
+  
+  // Retrieve the triangulation
+  std::vector<Point_d> point_cloud = off_reader.get_point_cloud();
+  BOOST_CHECK(point_cloud.size() == 7);
+
+  std::vector<Point_d> expected_points;
+  std::vector<double> point = {1.0, 1.0};
+  expected_points.push_back(Point_d(2, point.begin(), point.end()));
+  point = {7.0, 0.0};
+  expected_points.push_back(Point_d(2, point.begin(), point.end()));
+  point = {4.0, 6.0};
+  expected_points.push_back(Point_d(2, point.begin(), point.end()));
+  point = {9.0, 6.0};
+  expected_points.push_back(Point_d(2, point.begin(), point.end()));
+  point = {0.0, 14.0};
+  expected_points.push_back(Point_d(2, point.begin(), point.end()));
+  point = {2.0, 19.0};
+  expected_points.push_back(Point_d(2, point.begin(), point.end()));
+  point = {9.0, 17.0};
+  expected_points.push_back(Point_d(2, point.begin(), point.end()));
+
+  BOOST_CHECK(point_cloud == expected_points);
+}
+
+BOOST_AUTO_TEST_CASE( Delaunay_triangulation_unexisting_file_read_test )
+{
+  Gudhi::Points_off_reader<Point_d> off_reader("some_impossible_weird_file_name.off");
+  // Check the read operation was correct
+  BOOST_CHECK(!off_reader.is_valid());
+  
+  std::vector<Point_d> point_cloud = off_reader.get_point_cloud();
+  BOOST_CHECK(point_cloud.size() == 0);
+}
author	glisse <glisse@636b058d-ea47-450e-bf9e-a15bfbe3eedb>	2016-04-08 16:19:20 +0000
committer	glisse <glisse@636b058d-ea47-450e-bf9e-a15bfbe3eedb>	2016-04-08 16:19:20 +0000
commit	a44155daa5ae4253a874dad4a22b6da4bd017fee (patch)
tree	dca668d3ada0f45329f80b3f7c49b74ea576523f /src/common
parent	50327ad1f3fbf370fcdd3aa877b6e75644329662 (diff)
parent	baf1b5b39be90694b512fff9c79438bf362916f3 (diff)