Merge last trunk modifications

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/python_nerve_gic_vincent@3656 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 1f02e2f3b3e716d6578be49437e7d0b33fa99e5b

16 files changed, 75 insertions, 77 deletions

diff --git a/src/Alpha_complex/concept/SimplicialComplexForAlpha.h b/src/Alpha_complex/concept/SimplicialComplexForAlpha.h
index 2b8bff94..a51df127 100644
--- a/src/Alpha_complex/concept/SimplicialComplexForAlpha.h
+++ b/src/Alpha_complex/concept/SimplicialComplexForAlpha.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2016  INRIA
+ *    Copyright (C) 2016 Inria
  *
  *    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
diff --git a/src/Alpha_complex/doc/COPYRIGHT b/src/Alpha_complex/doc/COPYRIGHT
index dbad2380..5f1d97cc 100644
--- a/src/Alpha_complex/doc/COPYRIGHT
+++ b/src/Alpha_complex/doc/COPYRIGHT
@@ -4,7 +4,7 @@ computational topology.
 
 Author(s):       Vincent Rouvreau
 
-Copyright (C) 2015  INRIA
+Copyright (C) 2015 Inria
 
 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
diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h
index a08663ca..7a375c9f 100644
--- a/src/Alpha_complex/doc/Intro_alpha_complex.h
+++ b/src/Alpha_complex/doc/Intro_alpha_complex.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2015  INRIA
+ *    Copyright (C) 2015 Inria
  *
  *    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
@@ -57,9 +57,13 @@ namespace alpha_complex {
  * href="http://doc.cgal.org/latest/Kernel_d/index.html#Chapter_dD_Geometry_Kernel">dD Geometry Kernel</a>
  * \cite cgal:s-gkd-15b from CGAL as template parameter.
  * 
- * \remark When the simplicial complex is constructed with an infinite value of alpha, the complex is a Delaunay
+ * \remark
+ * - When the simplicial complex is constructed with an infinite value of alpha, the complex is a Delaunay
  * complex.
- * 
+ * - For people only interested in the topology of the \ref alpha_complex (for instance persistence),
+ * \ref alpha_complex is equivalent to the \ref cech_complex and much smaller if you do not bound the radii.
+ * \ref cech_complex can still make sense in higher dimension precisely because you can bound the radii.
+ *
  * \section pointsexample Example from points
  * 
  * This example builds the Delaunay triangulation from the given points in a 2D static kernel, and creates a
@@ -89,63 +93,29 @@ namespace alpha_complex {
  * \image html "alpha_complex_doc.png" "Simplicial complex structure construction example"
  *
  * \subsection filtrationcomputation Filtration value computation algorithm
- *
- *
- *
- * <ul>
- *   <li style="list-style-type: none;">\f$ \textbf{for } i : dimension \rightarrow 0 \textbf{ do} \f$
- *     <ul>
- *       <li style="list-style-type: none;">\f$\textbf{for all } \sigma of dimension i \f$
- *         <ul>
- *           <li style="list-style-type: none;">\f$\textbf{if } filtration( \sigma ) is NaN \textbf{ then} \f$
- *             <ul>
- *               <li style="list-style-type: none;">\f$ filtration( \sigma ) = \alpha^2( \sigma ) \f$
- *               </li>
- *             </ul>
- *           </li>
- *           <li style="list-style-type: none;">\f$\textbf{end if}\f$
- *           </li>
- *           <li style="list-style-type: none;">\f$\textbf{for all } \tau face of \sigma \textbf{ do} \f$
- *             &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;// propagate alpha filtration value
- *             <ul>
- *               <li style="list-style-type: none;">\f$\textbf{if } filtration( \tau ) is not NaN \textbf{ then} \f$
- *                 <ul>
- *                   <li style="list-style-type: none;">\f$ filtration( \tau ) = min ( filtration( \tau ), filtration( \sigma ) ) \f$
- *                   </li>
- *                 </ul>
- *               </li>
- *               <li style="list-style-type: none;">\f$\textbf{else}\f$
- *                 <ul>
- *                   <li style="list-style-type: none;">\f$\textbf{if } \tau is not Gabriel for \sigma \textbf{ then} \f$
- *                     <ul>
- *                       <li style="list-style-type: none;">\f$ filtration( \tau ) = filtration( \sigma ) \f$
- *                       </li>
- *                     </ul>
- *                   </li>
- *                   <li style="list-style-type: none;">\f$\textbf{end if}\f$
- *                   </li>
- *                 </ul>
- *               </li>
- *               <li style="list-style-type: none;">\f$\textbf{end if}\f$
- *               </li>
- *             </ul>
- *           </li>
- *           <li style="list-style-type: none;">\f$\textbf{end for}\f$
- *           </li>
- *         </ul>
- *       </li>
- *       <li style="list-style-type: none;">\f$\textbf{end for}\f$
- *       </li>
- *     </ul>
- *   </li>
- *   <li style="list-style-type: none;">\f$\textbf{end for}\f$
- *   </li>
- *   <li style="list-style-type: none;">\f$make\_filtration\_non\_decreasing()\f$
- *   </li>
- *   <li style="list-style-type: none;">\f$prune\_above\_filtration()\f$
- *   </li>
- * </ul>
- *
+ * <br>
+ * \f$
+ * \textbf{for } \text{i : dimension } \rightarrow 0 \textbf{ do}\\
+ * \quad \textbf{for all } \sigma \text{ of dimension i}\\
+ * \quad\quad \textbf{if } \text{filtration(} \sigma ) \text{ is NaN} \textbf{ then}\\
+ * \quad\quad\quad \text{filtration(} \sigma ) = \alpha^2( \sigma )\\
+ * \quad\quad \textbf{end if}\\
+ * \quad\quad \textbf{for all } \tau \text{ face of } \sigma \textbf{ do}\quad\quad
+ * \textit{// propagate alpha filtration value}\\
+ * \quad\quad\quad \textbf{if } \text{filtration(} \tau ) \text{ is not NaN} \textbf{ then}\\
+ * \quad\quad\quad\quad \text{filtration(} \tau \text{) = min( filtration(} \tau \text{), filtration(} \sigma
+ * \text{) )}\\
+ * \quad\quad\quad \textbf{else}\\
+ * \quad\quad\quad\quad \textbf{if } \textbf{if } \tau \text{ is not Gabriel for } \sigma \textbf{ then}\\
+ * \quad\quad\quad\quad\quad \text{filtration(} \tau \text{) = filtration(} \sigma \text{)}\\
+ * \quad\quad\quad\quad \textbf{end if}\\
+ * \quad\quad\quad \textbf{end if}\\
+ * \quad\quad \textbf{end for}\\
+ * \quad \textbf{end for}\\
+ * \textbf{end for}\\
+ * \text{make_filtration_non_decreasing()}\\
+ * \text{prune_above_filtration()}\\
+ * \f$
  *
  * \subsubsection dimension2 Dimension 2
  * 
diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt
index 5bf553e9..2fc62452 100644
--- a/src/Alpha_complex/example/CMakeLists.txt
+++ b/src/Alpha_complex/example/CMakeLists.txt
@@ -1,4 +1,3 @@
-cmake_minimum_required(VERSION 2.6)
 project(Alpha_complex_examples)
 
 # need CGAL 4.7
diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h
index 63c6675c..4c07eddb 100644
--- a/src/Alpha_complex/include/gudhi/Alpha_complex.h
+++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2015  INRIA
+ *    Copyright (C) 2015 Inria
  *
  *    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
@@ -34,6 +34,7 @@
 #include <CGAL/Epick_d.h>
 #include <CGAL/Spatial_sort_traits_adapter_d.h>
 #include <CGAL/property_map.h>  // for CGAL::Identity_property_map
+#include <CGAL/NT_converter.h>
 
 #include <iostream>
 #include <vector>
@@ -323,8 +324,9 @@ class Alpha_complex {
             if (f_simplex_dim > 0) {
               // squared_radius function initialization
               Squared_Radius squared_radius = kernel_.compute_squared_radius_d_object();
+              CGAL::NT_converter<typename Geom_traits::FT, Filtration_value> cv;
 
-              alpha_complex_filtration = squared_radius(pointVector.begin(), pointVector.end());
+              alpha_complex_filtration = cv(squared_radius(pointVector.begin(), pointVector.end()));
             }
             complex.assign_filtration(f_simplex, alpha_complex_filtration);
 #ifdef DEBUG_TRACES
diff --git a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
index c3ad1a9c..622fcae8 100644
--- a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
+++ b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2015  INRIA
+ *    Copyright (C) 2015 Inria
  *
  *    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
diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt
index 9e0b3b3c..9255d3db 100644
--- a/src/Alpha_complex/test/CMakeLists.txt
+++ b/src/Alpha_complex/test/CMakeLists.txt
@@ -1,4 +1,3 @@
-cmake_minimum_required(VERSION 2.6)
 project(Alpha_complex_tests)
 
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt
index a2dfac20..7ace6064 100644
--- a/src/Alpha_complex/utilities/CMakeLists.txt
+++ b/src/Alpha_complex/utilities/CMakeLists.txt
@@ -1,4 +1,3 @@
-cmake_minimum_required(VERSION 2.6)
 project(Alpha_complex_utilities)
 
 if(CGAL_FOUND)
diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_helper.h b/src/Alpha_complex/utilities/alpha_complex_3d_helper.h
index a59f0654..a72fd96d 100644
--- a/src/Alpha_complex/utilities/alpha_complex_3d_helper.h
+++ b/src/Alpha_complex/utilities/alpha_complex_3d_helper.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2014  INRIA Saclay (France)
+ *    Copyright (C) 2014 Inria
  *
  *    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
diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
index 8ef5ffb2..8cda0b70 100644
--- a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2014  INRIA
+ *    Copyright (C) 2014 Inria
  *
  *    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
@@ -35,6 +35,8 @@
 #include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
 #include <CGAL/Delaunay_triangulation_3.h>
 #include <CGAL/Alpha_shape_3.h>
+#include <CGAL/Alpha_shape_cell_base_3.h>
+#include <CGAL/Alpha_shape_vertex_base_3.h>
 #include <CGAL/iterator.h>
 
 #include <fstream>
diff --git a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp
index 2105220a..42390b0e 100644
--- a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp
+++ b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp
@@ -1,3 +1,25 @@
+/*    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) 2016 Inria
+ *
+ *    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 <boost/program_options.hpp>
 
 #include <CGAL/Epick_d.h>
diff --git a/src/Alpha_complex/utilities/alphacomplex.md b/src/Alpha_complex/utilities/alphacomplex.md
index ede749a9..0fe98837 100644
--- a/src/Alpha_complex/utilities/alphacomplex.md
+++ b/src/Alpha_complex/utilities/alphacomplex.md
@@ -10,9 +10,6 @@ Leave the lines above as it is required by the web site generator 'Jekyll'
 {:/comment}

 

 

-# Alpha complex #

-

-

 ## alpha_complex_persistence ##

 

 This program computes the persistent homology with coefficient field Z/pZ of the dD alpha complex built from a dD point cloud.

diff --git a/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp
index cceac46e..cbe003ff 100644
--- a/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2014  INRIA
+ *    Copyright (C) 2014 Inria
  *
  *    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
@@ -30,6 +30,8 @@
 #include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
 #include <CGAL/Delaunay_triangulation_3.h>
 #include <CGAL/Alpha_shape_3.h>
+#include <CGAL/Alpha_shape_cell_base_3.h>
+#include <CGAL/Alpha_shape_vertex_base_3.h>
 #include <CGAL/iterator.h>
 
 #include <fstream>
diff --git a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp
index 188cf604..11010701 100644
--- a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp
@@ -5,7 +5,7 @@
  *    Author(s):       Vincent Rouvreau
  *                     Pawel Dlotko - 2017 - Swansea University, UK
  *
- *    Copyright (C) 2014  INRIA
+ *    Copyright (C) 2014 Inria
  *
  *    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
@@ -32,6 +32,8 @@
 #include <CGAL/Periodic_3_Delaunay_triangulation_traits_3.h>
 #include <CGAL/Periodic_3_Delaunay_triangulation_3.h>
 #include <CGAL/Alpha_shape_3.h>
+#include <CGAL/Alpha_shape_cell_base_3.h>
+#include <CGAL/Alpha_shape_vertex_base_3.h>
 #include <CGAL/iterator.h>
 
 #include <fstream>
diff --git a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp
index 93be8a05..cdeeabfc 100644
--- a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       Vincent Rouvreau
  *
- *    Copyright (C) 2014  INRIA
+ *    Copyright (C) 2014 Inria
  *
  *    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
@@ -31,6 +31,8 @@
 #include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
 #include <CGAL/Regular_triangulation_3.h>
 #include <CGAL/Alpha_shape_3.h>
+#include <CGAL/Alpha_shape_cell_base_3.h>
+#include <CGAL/Alpha_shape_vertex_base_3.h>
 #include <CGAL/iterator.h>
 
 // For CGAL < 4.11
diff --git a/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp
index 5321bb0a..d030c88c 100644
--- a/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp
@@ -5,7 +5,7 @@
  *    Author(s):       Vincent Rouvreau
  *                     Pawel Dlotko - 2017 - Swansea University, UK
  *
- *    Copyright (C) 2014  INRIA
+ *    Copyright (C) 2014 Inria
  *
  *    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
@@ -31,6 +31,8 @@
 #include <CGAL/Periodic_3_regular_triangulation_traits_3.h>
 #include <CGAL/Periodic_3_regular_triangulation_3.h>
 #include <CGAL/Alpha_shape_3.h>
+#include <CGAL/Alpha_shape_cell_base_3.h>
+#include <CGAL/Alpha_shape_vertex_base_3.h>
 #include <CGAL/iterator.h>
 
 #include <fstream>