Merge last trunk modificat

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@3212 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: ea6296547b67ad82f5983d4309493e9131da7dd0

12 files changed, 635 insertions, 314 deletions

diff --git a/src/common/doc/examples.h b/src/common/doc/examples.h
new file mode 100644
index 00000000..40f202c7
--- /dev/null
+++ b/src/common/doc/examples.h
@@ -0,0 +1,99 @@
+// List of GUDHI examples - Doxygen needs at least a file tag to analyse comments
+// In user_version, `find . -name "*.cpp"` in example and utilities folders
+/*! @file Examples
+ * @example Alpha_complex/Alpha_complex_from_off.cpp
+ * @example Alpha_complex/Alpha_complex_from_points.cpp
+ * @example Bottleneck_distance/bottleneck_basic_example.cpp
+ * @example Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp
+ * @example Witness_complex/example_nearest_landmark_table.cpp
+ * @example Witness_complex/example_witness_complex_off.cpp
+ * @example Witness_complex/example_witness_complex_sphere.cpp
+ * @example Witness_complex/example_strong_witness_complex_off.cpp
+ * @example Simplex_tree/mini_simplex_tree.cpp
+ * @example Simplex_tree/graph_expansion_with_blocker.cpp
+ * @example Simplex_tree/simple_simplex_tree.cpp
+ * @example Simplex_tree/simplex_tree_from_cliques_of_graph.cpp
+ * @example Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp
+ * @example Simplex_tree/cech_complex_cgal_mini_sphere_3d.cpp
+ * @example Persistent_cohomology/plain_homology.cpp
+ * @example Persistent_cohomology/persistence_from_file.cpp
+ * @example Persistent_cohomology/rips_persistence_step_by_step.cpp
+ * @example Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp
+ * @example Persistent_cohomology/custom_persistence_sort.cpp
+ * @example Persistent_cohomology/persistence_from_simple_simplex_tree.cpp
+ * @example Persistent_cohomology/rips_multifield_persistence.cpp
+ * @example Skeleton_blocker/Skeleton_blocker_from_simplices.cpp
+ * @example Skeleton_blocker/Skeleton_blocker_iteration.cpp
+ * @example Skeleton_blocker/Skeleton_blocker_link.cpp
+ * @example Contraction/Garland_heckbert.cpp
+ * @example Contraction/Rips_contraction.cpp
+ * @example Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp
+ * @example common/example_CGAL_3D_points_off_reader.cpp
+ * @example common/example_vector_double_points_off_reader.cpp
+ * @example common/example_CGAL_points_off_reader.cpp
+ * @example Rips_complex/example_one_skeleton_rips_from_distance_matrix.cpp
+ * @example Rips_complex/example_one_skeleton_rips_from_points.cpp
+ * @example Rips_complex/example_rips_complex_from_csv_distance_matrix_file.cpp
+ * @example Rips_complex/example_rips_complex_from_off_file.cpp
+ * @example Persistence_representations/persistence_intervals.cpp
+ * @example Persistence_representations/persistence_vectors.cpp
+ * @example Persistence_representations/persistence_heat_maps.cpp
+ * @example Persistence_representations/persistence_landscape_on_grid.cpp
+ * @example Persistence_representations/persistence_landscape.cpp
+ * @example Tangential_complex/example_basic.cpp
+ * @example Tangential_complex/example_with_perturb.cpp
+ * @example Subsampling/example_custom_kernel.cpp
+ * @example Subsampling/example_choose_n_farthest_points.cpp
+ * @example Subsampling/example_sparsify_point_set.cpp
+ * @example Subsampling/example_pick_n_random_points.cpp
+ * @example Nerve_GIC/CoordGIC.cpp
+ * @example Nerve_GIC/Nerve.cpp
+ * @example Nerve_GIC/FuncGIC.cpp
+ * @example Nerve_GIC/VoronoiGIC.cpp
+ * @example Spatial_searching/example_spatial_searching.cpp
+ * @example Alpha_complex/alpha_complex_3d_persistence.cpp
+ * @example Alpha_complex/alpha_complex_persistence.cpp
+ * @example Alpha_complex/weighted_periodic_alpha_complex_3d_persistence.cpp
+ * @example Alpha_complex/weighted_alpha_complex_3d_persistence.cpp
+ * @example Alpha_complex/periodic_alpha_complex_3d_persistence.cpp
+ * @example Alpha_complex/exact_alpha_complex_3d_persistence.cpp
+ * @example Bottleneck_distance/bottleneck_distance.cpp
+ * @example Witness_complex/weak_witness_persistence.cpp
+ * @example Witness_complex/strong_witness_persistence.cpp
+ * @example Bitmap_cubical_complex/cubical_complex_persistence.cpp
+ * @example Bitmap_cubical_complex/periodic_cubical_complex_persistence.cpp
+ * @example common/off_file_from_shape_generator.cpp
+ * @example Rips_complex/rips_distance_matrix_persistence.cpp
+ * @example Rips_complex/rips_persistence.cpp
+ * @example Persistence_representations/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp
+ * @example Persistence_representations/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp
+ * @example Persistence_representations/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp
+ * @example Persistence_representations/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp
+ * @example Persistence_representations/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp
+ * @example Persistence_representations/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp
+ * @example Persistence_representations/persistence_intervals/compute_number_of_dominant_intervals.cpp
+ * @example Persistence_representations/persistence_intervals/plot_persistence_Betti_numbers.cpp
+ * @example Persistence_representations/persistence_intervals/plot_persistence_intervals.cpp
+ * @example Persistence_representations/persistence_intervals/plot_histogram_of_intervals_lengths.cpp
+ * @example Persistence_representations/persistence_intervals/compute_bottleneck_distance.cpp
+ * @example Persistence_representations/persistence_heat_maps/create_pssk.cpp
+ * @example Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp
+ * @example Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp
+ * @example Persistence_representations/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp
+ * @example Persistence_representations/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp
+ * @example Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp
+ * @example Persistence_representations/persistence_heat_maps/average_persistence_heat_maps.cpp
+ * @example Persistence_representations/persistence_heat_maps/plot_persistence_heat_map.cpp
+ * @example Persistence_representations/persistence_heat_maps/create_persistence_heat_maps.cpp
+ * @example Persistence_representations/persistence_vectors/plot_persistence_vectors.cpp
+ * @example Persistence_representations/persistence_vectors/compute_distance_of_persistence_vectors.cpp
+ * @example Persistence_representations/persistence_vectors/average_persistence_vectors.cpp
+ * @example Persistence_representations/persistence_vectors/create_persistence_vectors.cpp
+ * @example Persistence_representations/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp
+ * @example Persistence_representations/persistence_landscapes/average_landscapes.cpp
+ * @example Persistence_representations/persistence_landscapes/compute_scalar_product_of_landscapes.cpp
+ * @example Persistence_representations/persistence_landscapes/create_landscapes.cpp
+ * @example Persistence_representations/persistence_landscapes/compute_distance_of_landscapes.cpp
+ * @example Persistence_representations/persistence_landscapes/plot_landscapes.cpp
+ */
+ 
diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h
index d715aa4d..c60ed15a 100644
--- a/src/common/doc/file_formats.h
+++ b/src/common/doc/file_formats.h
@@ -53,6 +53,72 @@ namespace Gudhi {
  Such files can be generated with `Gudhi::persistent_cohomology::Persistent_cohomology::output_diagram()` and read with
  `Gudhi::read_persistence_intervals_and_dimension()`, `Gudhi::read_persistence_intervals_grouped_by_dimension()` or
  `Gudhi::read_persistence_intervals_in_dimension()`.
+ 
+
+ \section FileFormatsIsoCuboid Iso-cuboid
+
+ Such a file describes an iso-oriented cuboid with diagonal opposite vertices (min_x, min_y, min_z,...) and (max_x, max_y, max_z, ...). The format is:<br>
+ \verbatim
+   min_x min_y [min_z ...]
+   max_x max_y [max_z ...]
+ \endverbatim
+
+ Here is a simple sample file in the 3D case:
+ \verbatim
+   -1. -1. -1.
+   1. 1. 1.
+ \endverbatim
+
+
+ \section FileFormatsPerseus Perseus
+
+ This file format is the format used by the Perseus software
+ (http://www.sas.upenn.edu/~vnanda/perseus/) by Vidit Nanda.
+ The first line contains a number d begin the dimension of the
+ bitmap (2 in the example below). Next d lines are the numbers of top dimensional cubes in each dimensions (3 and 3
+ in the example below). Next, in lexicographical order, the filtration of top dimensional cubes is given (1 4 6 8
+ 20 4 7 6 5 in the example below).
+ 
+ \image html "exampleBitmap.png" "Example of a input data."
+ 
+ The input file for the following complex is:
+ \verbatim
+ 2
+ 3
+ 3
+ 1
+ 4
+ 6
+ 8
+ 20
+ 4
+ 7
+ 6
+ 5
+ \endverbatim
+
+ To indicate periodic boundary conditions in a
+ given direction, then number of top dimensional cells in this direction have to be multiplied by -1. For instance:
+
+ \verbatim
+ 2
+ -3
+ 3
+ 1
+ 4
+ 6
+ 8
+ 20
+ 4
+ 7
+ 6
+ 5
+ \endverbatim
+
+ Indicate that we have imposed periodic boundary conditions in the direction x, but not in the direction y.
+
+ Other sample files can be found in the `data/bitmap` folder.
+
 */
 }  // namespace Gudhi
 
diff --git a/src/common/doc/footer.html b/src/common/doc/footer.html
index 7b4cdc5c..a557922b 100644
--- a/src/common/doc/footer.html
+++ b/src/common/doc/footer.html
@@ -6,24 +6,18 @@
 <!--BEGIN PROJECT_NAME--> $projectname
 <!--BEGIN PROJECT_NUMBER-->&#160;Version $projectnumber<!--END PROJECT_NUMBER-->
 <!--BEGIN PROJECT_BRIEF-->&#160;-&#160;$projectbrief<!--END PROJECT_BRIEF-->
+<!--BEGIN PROJECT_BRIEF-->&#160;-&#160;Copyright : GPL v3<!--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
+        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-->
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 </html>
diff --git a/src/common/doc/header.html b/src/common/doc/header.html
index 53b5c0a2..d69b28fa 100644
--- a/src/common/doc/header.html
+++ b/src/common/doc/header.html
@@ -56,6 +56,8 @@ $extrastylesheet
                   <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="https://gforge.inria.fr/frs/download.php/file/37365/2018-02-01-16-59-31_GUDHI_2.1.0_OSX_UTILS.tar.gz" target="_blank">Utils for Mac OSx</a></li>
+                      <li><a href="https://gforge.inria.fr/frs/download.php/file/37366/2018-01-31-09-25-53_GUDHI_2.1.0_WIN64_UTILS.zip" target="_blank">Utils for Win x64</a></li>
                   </ul>
               </li>
               <li class="divider"></li>
@@ -66,6 +68,8 @@ $extrastylesheet
                       <li><a href="http://gudhi.gforge.inria.fr/doc/latest/installation.html">C++ installation manual</a></li>
                       <li><a href="http://gudhi.gforge.inria.fr/python/latest/">Python documentation</a></li>
                       <li><a href="http://gudhi.gforge.inria.fr/python/latest/installation.html">Python installation manual</a></li>
+                      <li><a href="http://gudhi.gforge.inria.fr/utils/">Utilities</a></li>
+                      <li><a href="http://bertrand.michel.perso.math.cnrs.fr/Enseignements/TDA-Gudhi-Python.html" target="_blank">Tutorial</a></li>
                   </ul>
               </li>
               <li class="divider"></li>
diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h
new file mode 100644
index 00000000..25675cc5
--- /dev/null
+++ b/src/common/doc/installation.h
@@ -0,0 +1,263 @@
+/*! \page installation GUDHI installation
+ *  \tableofcontents
+ * As GUDHI is a header only library, there is no need to install the library.
+ * 
+ * Examples of GUDHI headers inclusion can be found in \ref demos.
+ * 
+ * \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 2015.
+ * 
+ * \subsection demos Demos and examples
+ * 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:
+ * \verbatim  make test \endverbatim
+ * 
+ * \subsection documentationgeneration Documentation
+ * To generate the documentation, <a target="_blank" href="http://www.doxygen.org/">Doxygen</a> is required.
+ * Run the following command in a terminal:
+\verbatim
+make doxygen
+# Documentation will be generated in the folder YYYY-MM-DD-hh-mm-ss_GUDHI_X.Y.Z/doc/html/
+# You can customize the directory name by calling `cmake -DUSER_VERSION_DIR=/my/custom/folder`
+\endverbatim
+ *
+ * \section optionallibrary Optional third-party library
+ * \subsection gmp GMP
+ * The multi-field persistent homology algorithm requires GMP which is a free library for arbitrary-precision
+ * arithmetic, operating on signed integers, rational numbers, and floating point numbers.
+ * 
+ * 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 <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html">
+ * Persistent_cohomology/rips_multifield_persistence.cpp</a>
+ *
+ * Having GMP version 4.2 or higher installed is recommended.
+ * 
+ * \subsection cgal CGAL
+ * The \ref alpha_complex data structure, \ref bottleneck_distance, and few examples requires CGAL, which is a C++
+ * library which provides easy access to efficient and reliable geometric algorithms.
+ *
+ * \note There is no need to install CGAL, you can just <CODE>cmake . && make</CODE> CGAL (or even
+ * <CODE>cmake -DCGAL_HEADER_ONLY=ON .</CODE> for CGAL version &ge; 4.8.0), thereafter you will be able to compile
+ * GUDHI by calling <CODE>cmake -DCGAL_DIR=/your/path/to/CGAL-X.Y .. && make</CODE>
+ * 
+ * Having CGAL version 4.4.0 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/utilities 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="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html">
+ * Alpha_complex/alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_alpha_complex_2exact_alpha_complex_3d_persistence_8cpp-example.html">
+ * Alpha_complex/exact_alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_alpha_complex_2weighted_alpha_complex_3d_persistence_8cpp-example.html">
+ * Alpha_complex/weighted_alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_simplex_tree_2example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html">
+ * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a>
+ * 
+ * The following examples/utilities require CGAL version &ge; 4.6.0:
+ * \li <a href="_witness_complex_2strong_witness_persistence_8cpp-example.html">
+ * Witness_complex/strong_witness_persistence.cpp</a>
+ * \li <a href="_witness_complex_2weak_witness_persistence_8cpp-example.html">
+ * Witness_complex/weak_witness_persistence.cpp</a>
+ * \li <a href="_witness_complex_2example_strong_witness_complex_off_8cpp-example.html">
+ * Witness_complex/example_strong_witness_complex_off.cpp</a>
+ * \li <a href="_witness_complex_2example_witness_complex_off_8cpp-example.html">
+ * Witness_complex/example_witness_complex_off.cpp</a>
+ * \li <a href="_witness_complex_2example_witness_complex_sphere_8cpp-example.html">
+ * Witness_complex/example_witness_complex_sphere.cpp</a>
+ *
+ * The following example requires CGAL version &ge; 4.7.0:
+ * \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="_alpha_complex_2alpha_complex_persistence_8cpp-example.html">
+ * Alpha_complex/alpha_complex_persistence.cpp</a>
+ * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
+ * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">
+ * Persistent_cohomology/custom_persistence_sort.cpp</a>
+ * 
+ * The following example requires CGAL version &ge; 4.8.1:
+ * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html">
+ * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a>
+ * \li <a href="_bottleneck_distance_2bottleneck_basic_example_8cpp-example.html">
+ * Bottleneck_distance/bottleneck_basic_example.cpp</a>
+ * \li <a href="_bottleneck_distance_2bottleneck_read_file_8cpp-example.html">
+ * Bottleneck_distance/bottleneck_distance.cpp</a>
+ * \li <a href="_nerve__g_i_c_2_coord_g_i_c_8cpp-example.html">
+ * Nerve_GIC/CoordGIC.cpp</a>
+ * \li <a href="_nerve__g_i_c_2_func_g_i_c_8cpp-example.html">
+ * Nerve_GIC/FuncGIC.cpp</a>
+ * \li <a href="_nerve__g_i_c_2_nerve_8cpp-example.html">
+ * Nerve_GIC/Nerve.cpp</a>
+ * \li <a href="_nerve__g_i_c_2_voronoi_g_i_c_8cpp-example.html">
+ * Nerve_GIC/VoronoiGIC.cpp</a>
+ * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html">
+ * Spatial_searching/example_spatial_searching.cpp</a>
+ * \li <a href="_subsampling_2example_choose_n_farthest_points_8cpp-example.html">
+ * Subsampling/example_choose_n_farthest_points.cpp</a>
+ * \li <a href="_subsampling_2example_custom_kernel_8cpp-example.html">
+ * Subsampling/example_custom_kernel.cpp</a>
+ * \li <a href="_subsampling_2example_pick_n_random_points_8cpp-example.html">
+ * Subsampling/example_pick_n_random_points.cpp</a>
+ * \li <a href="_subsampling_2example_sparsify_point_set_8cpp-example.html">
+ * Subsampling/example_sparsify_point_set.cpp</a>
+ * \li <a href="_tangential_complex_2example_basic_8cpp-example.html">
+ * Tangential_complex/example_basic.cpp</a>
+ * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html">
+ * Tangential_complex/example_with_perturb.cpp</a>
+ *
+ * \subsection eigen3 Eigen3
+ * The \ref alpha_complex data structure and few examples requires
+ * <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 examples/utilities require 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>
+ * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
+ * Alpha_complex/Alpha_complex_from_points.cpp</a>
+ * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html">
+ * Alpha_complex/alpha_complex_persistence.cpp</a>
+ * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
+ * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html">
+ * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a>
+ * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">
+ * Persistent_cohomology/custom_persistence_sort.cpp</a>
+ * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html">
+ * Spatial_searching/example_spatial_searching.cpp</a>
+ * \li <a href="_subsampling_2example_choose_n_farthest_points_8cpp-example.html">
+ * Subsampling/example_choose_n_farthest_points.cpp</a>
+ * \li <a href="_subsampling_2example_custom_kernel_8cpp-example.html">
+ * Subsampling/example_custom_kernel.cpp</a>
+ * \li <a href="_subsampling_2example_pick_n_random_points_8cpp-example.html">
+ * Subsampling/example_pick_n_random_points.cpp</a>
+ * \li <a href="_subsampling_2example_sparsify_point_set_8cpp-example.html">
+ * Subsampling/example_sparsify_point_set.cpp</a>
+ * \li <a href="_tangential_complex_2example_basic_8cpp-example.html">
+ * Tangential_complex/example_basic.cpp</a>
+ * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html">
+ * Tangential_complex/example_with_perturb.cpp</a>
+ * \li <a href="_witness_complex_2strong_witness_persistence_8cpp-example.html">
+ * Witness_complex/strong_witness_persistence.cpp</a>
+ * \li <a href="_witness_complex_2weak_witness_persistence_8cpp-example.html">
+ * Witness_complex/weak_witness_persistence.cpp</a>
+ * \li <a href="_witness_complex_2example_strong_witness_complex_off_8cpp-example.html">
+ * Witness_complex/example_strong_witness_complex_off.cpp</a>
+ * \li <a href="_witness_complex_2example_witness_complex_off_8cpp-example.html">
+ * Witness_complex/example_witness_complex_off.cpp</a>
+ * \li <a href="_witness_complex_2example_witness_complex_sphere_8cpp-example.html">
+ * Witness_complex/example_witness_complex_sphere.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/utilities 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="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html">
+ * Alpha_complex/alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html">
+ * Alpha_complex/alpha_complex_persistence.cpp</a>
+ * \li <a href="_alpha_complex_2exact_alpha_complex_3d_persistence_8cpp-example.html">
+ * Alpha_complex/exact_alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
+ * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_alpha_complex_2weighted_alpha_complex_3d_persistence_8cpp-example.html">
+ * Alpha_complex/weighted_alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_8cpp-example.html">
+ * Bitmap_cubical_complex/cubical_complex_persistence.cpp</a>
+ * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_periodic_boundary_conditions_8cpp-example.html">
+ * Bitmap_cubical_complex/periodic_cubical_complex_persistence.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="_nerve__g_i_c_2_coord_g_i_c_8cpp-example.html">
+ * Nerve_GIC/CoordGIC.cpp</a>
+ * \li <a href="_nerve__g_i_c_2_func_g_i_c_8cpp-example.html">
+ * Nerve_GIC/FuncGIC.cpp</a>
+ * \li <a href="_nerve__g_i_c_2_nerve_8cpp-example.html">
+ * Nerve_GIC/Nerve.cpp</a>
+ * \li <a href="_nerve__g_i_c_2_voronoi_g_i_c_8cpp-example.html">
+ * Nerve_GIC/VoronoiGIC.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_2example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html">
+ * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.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="_simplex_tree_2graph_expansion_with_blocker_8cpp-example.html">
+ * Simplex_tree/graph_expansion_with_blocker.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="_persistent_cohomology_2rips_persistence_via_boundary_matrix_8cpp-example.html">
+ * Persistent_cohomology/rips_persistence_via_boundary_matrix.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_step_by_step_8cpp-example.html">
+ * Persistent_cohomology/rips_persistence_step_by_step.cpp</a>
+ * \li <a href="_persistent_cohomology_2exact_alpha_complex_3d_persistence_8cpp-example.html">
+ * Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2weighted_alpha_complex_3d_persistence_8cpp-example.html">
+ * Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">
+ * Persistent_cohomology/custom_persistence_sort.cpp</a>
+ * \li <a href="_rips_complex_2example_one_skeleton_rips_from_points_8cpp-example.html">
+ * Rips_complex/example_one_skeleton_rips_from_points.cpp</a>
+ * \li <a href="_rips_complex_2example_rips_complex_from_off_file_8cpp-example.html">
+ * Rips_complex/example_rips_complex_from_off_file.cpp</a>
+ * \li <a href="_rips_complex_2rips_distance_matrix_persistence_8cpp-example.html">
+ * Rips_complex/rips_distance_matrix_persistence.cpp</a>
+ * \li <a href="_rips_complex_2rips_persistence_8cpp-example.html">
+ * Rips_complex/rips_persistence.cpp</a>
+ * \li <a href="_witness_complex_2strong_witness_persistence_8cpp-example.html">
+ * Witness_complex/strong_witness_persistence.cpp</a>
+ * \li <a href="_witness_complex_2weak_witness_persistence_8cpp-example.html">
+ * Witness_complex/weak_witness_persistence.cpp</a>
+ * \li <a href="_witness_complex_2example_nearest_landmark_table_8cpp-example.html">
+ * Witness_complex/example_nearest_landmark_table.cpp</a>
+ *
+ * \section Contributions Bug reports and contributions
+ * Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to:
+ * \verbatim  Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
+ * 
+ * GUDHI is open to external contributions. If you want to join our development team, please contact us.
+ * 
+*/
+
+/*! \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.
+ * Feel free to contact us in case you have any question or remark on this topic.
+ * 
+ * We provide \ref GudhiBibtex entries for the modules of the User and Reference Manual, as well as for publications
+ * directly related to the GUDHI library.
+ * \section GudhiBibtex GUDHI bibtex
+ * \verbinclude  biblio/how_to_cite_gudhi.bib
+*/
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index 701ea8ff..b3e9ea03 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -93,6 +93,25 @@
     </td>
  </tr>
 </table>
+ \subsection CoverComplexDataStructure Cover Complexes
+ \image html "gicvisu.jpg" "Graph Induced Complex of a point cloud."
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> Mathieu Carri&egrave;re<br>
+      <b>Introduced in:</b> GUDHI 2.1.0<br>
+      <b>Copyright:</b> GPL v3<br>
+      <b>Requires:</b> \ref cgal &ge; 4.8.1
+    </td>
+    <td width="75%">
+    Nerves and Graph Induced Complexes are cover complexes, i.e. simplicial complexes that provably contain
+    topological information about the input data. They can be computed with a cover of the
+    data, that comes i.e. from the preimage of a family of intervals covering the image
+    of a scalar-valued function defined on the data. <br>
+    <b>User manual:</b> \ref cover_complex - <b>Reference manual:</b> Gudhi::cover_complex::Cover_complex
+    </td>
+ </tr>
+</table>
  \subsection SkeletonBlockerDataStructure Skeleton blocker
  \image html "ds_representation.png" "Skeleton blocker representation"
 <table border="0">
@@ -152,6 +171,7 @@
 </table>
  
  \section Toolbox Toolbox
+ 
  \subsection BottleneckDistanceToolbox Bottleneck distance
  \image html "perturb_pd.png" "Bottleneck distance is the length of the longest edge"
 <table border="0">
@@ -211,283 +231,23 @@
     <b>User manual:</b> \ref persistent_cohomology - <b>Reference manual:</b> Gudhi::persistent_cohomology::Persistent_cohomology
     </td>
  </tr>
+</table> 
+ \subsection PersistenceRepresentationsToolbox Persistence representations
+ \image html "average_landscape.png" "Persistence representations"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> Pawel Dlotko<br>
+      <b>Introduced in:</b> GUDHI 2.1.0<br>
+      <b>Copyright:</b> GPL v3<br>      
+    </td>
+    <td width="75%">
+    It contains implementation of various representations of persistence diagrams; diagrams themselves, persistence
+    landscapes (rigorous and grid version), persistence heath maps, vectors and others. It implements basic
+    functionalities which are neccessary to use persistence in statistics and machine learning.<br>
+    <b>User manual:</b> \ref Persistence_representations
+    </td>
+ </tr>
 </table>
+ 
 */
-
-/*! \page installation GUDHI installation
- *  \tableofcontents
- * As GUDHI is a header only library, there is no need to install the library.
- * 
- * Examples of GUDHI headers inclusion can be found in \ref demos.
- * 
- * \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 2015.
- * 
- * \subsection demos Demos and examples
- * 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:
- * \verbatim  make test \endverbatim
- * 
- * \subsection documentationgeneration Documentation
- * To generate the documentation, <a target="_blank" href="http://www.doxygen.org/">Doxygen</a> is required.
- * Run the following command in a terminal:
-\verbatim
-make doxygen
-# Documentation will be generated in the folder YYYY-MM-DD-hh-mm-ss_GUDHI_X.Y.Z/doc/html/
-# You can customize the directory name by calling `cmake -DUSER_VERSION_DIR=/my/custom/folder`
-\endverbatim
- *
- * \section optionallibrary Optional third-party library
- * \subsection gmp GMP
- * The multi-field persistent homology algorithm requires GMP which is a free library for arbitrary-precision
- * arithmetic, operating on signed integers, rational numbers, and floating point numbers.
- * 
- * 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 <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html">
- * Persistent_cohomology/rips_multifield_persistence.cpp</a>
- *
- * Having GMP version 4.2 or higher installed is recommended.
- * 
- * \subsection cgal CGAL
- * The \ref alpha_complex data structure, \ref bottleneck_distance, and few examples requires CGAL, which is a C++
- * library which provides easy access to efficient and reliable geometric algorithms.
- *
- * \note There is no need to install CGAL, you can just <CODE>cmake . && make</CODE> CGAL (or even
- * <CODE>cmake -DCGAL_HEADER_ONLY=ON .</CODE> for CGAL version &ge; 4.8.0), thereafter you will be able to compile
- * GUDHI by calling <CODE>cmake -DCGAL_DIR=/your/path/to/CGAL-X.Y .. && make</CODE>
- * 
- * Having CGAL version 4.4.0 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_2exact_alpha_complex_3d_persistence_8cpp-example.html">
- * Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp</a>
- * \li <a href="_persistent_cohomology_2weighted_alpha_complex_3d_persistence_8cpp-example.html">
- * Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp</a>
- * \li <a href="_simplex_tree_2example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html">
- * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a>
- * 
- * The following example requires CGAL version &ge; 4.6.0:
- * \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; 4.7.0:
- * \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="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
- * Persistent_cohomology/alpha_complex_persistence.cpp</a>
- * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
- * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a>
- * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">
- * Persistent_cohomology/custom_persistence_sort.cpp</a>
- * 
- * The following example requires CGAL version &ge; 4.8.1:
- * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html">
- * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a>
- * \li <a href="_bottleneck_distance_2bottleneck_basic_example_8cpp-example.html">
- * Bottleneck_distance/bottleneck_basic_example.cpp</a>
- * \li <a href="_bottleneck_distance_2bottleneck_read_file_example_8cpp-example.html">
- * Bottleneck_distance/bottleneck_read_file_example.cpp</a>
- * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html">
- * Spatial_searching/example_spatial_searching.cpp</a>
- * \li <a href="_subsampling_2example_choose_n_farthest_points_8cpp-example.html">
- * Subsampling/example_choose_n_farthest_points.cpp</a>
- * \li <a href="_subsampling_2example_custom_kernel_8cpp-example.html">
- * Subsampling/example_custom_kernel.cpp</a>
- * \li <a href="_subsampling_2example_pick_n_random_points_8cpp-example.html">
- * Subsampling/example_pick_n_random_points.cpp</a>
- * \li <a href="_subsampling_2example_sparsify_point_set_8cpp-example.html">
- * Subsampling/example_sparsify_point_set.cpp</a>
- * \li <a href="_tangential_complex_2example_basic_8cpp-example.html">
- * Tangential_complex/example_basic.cpp</a>
- * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html">
- * Tangential_complex/example_with_perturb.cpp</a>
- *
- * \subsection eigen3 Eigen3
- * The \ref alpha_complex data structure and few examples requires
- * <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>
- * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
- * Alpha_complex/Alpha_complex_from_points.cpp</a>
- * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html">
- * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a>
- * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
- * Persistent_cohomology/alpha_complex_persistence.cpp</a>
- * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
- * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a>
- * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">
- * Persistent_cohomology/custom_persistence_sort.cpp</a>
- * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html">
- * Spatial_searching/example_spatial_searching.cpp</a>
- * \li <a href="_subsampling_2example_choose_n_farthest_points_8cpp-example.html">
- * Subsampling/example_choose_n_farthest_points.cpp</a>
- * \li <a href="_subsampling_2example_custom_kernel_8cpp-example.html">
- * Subsampling/example_custom_kernel.cpp</a>
- * \li <a href="_subsampling_2example_pick_n_random_points_8cpp-example.html">
- * Subsampling/example_pick_n_random_points.cpp</a>
- * \li <a href="_subsampling_2example_sparsify_point_set_8cpp-example.html">
- * Subsampling/example_sparsify_point_set.cpp</a>
- * \li <a href="_tangential_complex_2example_basic_8cpp-example.html">
- * Tangential_complex/example_basic.cpp</a>
- * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html">
- * Tangential_complex/example_with_perturb.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_2example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html">
- * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.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="_simplex_tree_2graph_expansion_with_blocker_8cpp-example.html">
- * Simplex_tree/graph_expansion_with_blocker.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="_persistent_cohomology_2rips_persistence_via_boundary_matrix_8cpp-example.html">
- * Persistent_cohomology/rips_persistence_via_boundary_matrix.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_distance_matrix_persistence_8cpp-example.html">
- * Persistent_cohomology/rips_distance_matrix_persistence.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>
- * \li <a href="_persistent_cohomology_2rips_persistence_step_by_step_8cpp-example.html">
- * Persistent_cohomology/rips_persistence_step_by_step.cpp</a>
- * \li <a href="_persistent_cohomology_2exact_alpha_complex_3d_persistence_8cpp-example.html">
- * Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp</a>
- * \li <a href="_persistent_cohomology_2weighted_alpha_complex_3d_persistence_8cpp-example.html">
- * Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp</a>
- * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
- * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a>
- * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">
- * Persistent_cohomology/custom_persistence_sort.cpp</a>
- * \li <a href="_rips_complex_2example_one_skeleton_rips_from_points_8cpp-example.html">
- * Rips_complex/example_one_skeleton_rips_from_points.cpp</a>
- * \li <a href="_rips_complex_2example_rips_complex_from_off_file_8cpp-example.html">
- * Rips_complex/example_rips_complex_from_off_file.cpp</a>
- * 
- * \section Contributions Bug reports and contributions
- * Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to:
- * \verbatim  Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
- * 
- * GUDHI is open to external contributions. If you want to join our development team, please contact us.
- * 
-*/
-
-/*! \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.
- * Feel free to contact us in case you have any question or remark on this topic.
- * 
- * We provide \ref GudhiBibtex entries for the modules of the User and Reference Manual, as well as for publications
- * directly related to the GUDHI library.
- * \section GudhiBibtex GUDHI bibtex
- * \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 Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp
- * @example Bottleneck_distance/bottleneck_basic_example.cpp
- * @example Bottleneck_distance/bottleneck_read_file_example.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/example_CGAL_3D_points_off_reader.cpp
- * @example common/example_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/rips_persistence_via_boundary_matrix.cpp
- * @example Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp
- * @example Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp
- * @example Persistent_cohomology/periodic_alpha_complex_3d_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_correlation_matrix_persistence.cpp
- * @example Persistent_cohomology/rips_distance_matrix_persistence.cpp
- * @example Persistent_cohomology/rips_persistence.cpp
- * @example Persistent_cohomology/custom_persistence_sort.cpp
- * @example Persistent_cohomology/rips_persistence_step_by_step.cpp
- * @example Rips_complex/example_one_skeleton_rips_from_correlation_matrix.cpp
- * @example Rips_complex/example_one_skeleton_rips_from_distance_matrix.cpp
- * @example Rips_complex/example_one_skeleton_rips_from_points.cpp
- * @example Rips_complex/example_rips_complex_from_csv_distance_matrix_file.cpp
- * @example Rips_complex/example_rips_complex_from_off_file.cpp
- * @example Simplex_tree/mini_simplex_tree.cpp
- * @example Simplex_tree/simple_simplex_tree.cpp
- * @example Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp
- * @example Simplex_tree/simplex_tree_from_cliques_of_graph.cpp
- * @example Simplex_tree/graph_expansion_with_blocker.cpp
- * @example Skeleton_blocker/Skeleton_blocker_from_simplices.cpp
- * @example Skeleton_blocker/Skeleton_blocker_iteration.cpp
- * @example Skeleton_blocker/Skeleton_blocker_link.cpp
- * @example Spatial_searching/example_spatial_searching.cpp
- * @example Subsampling/example_choose_n_farthest_points.cpp
- * @example Subsampling/example_custom_kernel.cpp
- * @example Subsampling/example_pick_n_random_points.cpp
- * @example Subsampling/example_sparsify_point_set.cpp
- * @example Tangential_complex/example_basic.cpp
- * @example Tangential_complex/example_with_perturb.cpp
- * @example Witness_complex/example_nearest_landmark_table.cpp
- * @example Witness_complex/example_strong_witness_complex_off.cpp
- * @example Witness_complex/example_strong_witness_persistence.cpp
- * @example Witness_complex/example_witness_complex_off.cpp
- * @example Witness_complex/example_witness_complex_persistence.cpp
- * @example Witness_complex/example_witness_complex_sphere.cpp
- */
-
diff --git a/src/common/include/gudhi/Debug_utils.h b/src/common/include/gudhi/Debug_utils.h
index 8ed3b7b3..90d3cf47 100644
--- a/src/common/include/gudhi/Debug_utils.h
+++ b/src/common/include/gudhi/Debug_utils.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (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
@@ -32,7 +32,7 @@
 // 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
+  #define GUDHI_CHECK(expression, excpt) ((expression) ? (void) 0 : (throw excpt))
   #define GUDHI_CHECK_code(CODE) CODE
 #else
   #define GUDHI_CHECK(expression, excpt) (void) 0
diff --git a/src/common/include/gudhi/Unitary_tests_utils.h b/src/common/include/gudhi/Unitary_tests_utils.h
new file mode 100644
index 00000000..8394a062
--- /dev/null
+++ b/src/common/include/gudhi/Unitary_tests_utils.h
@@ -0,0 +1,40 @@
+/*    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) 2017  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/>.
+ */
+#ifndef UNITARY_TESTS_UTILS_H_
+#define UNITARY_TESTS_UTILS_H_
+
+#include <boost/test/unit_test.hpp>
+
+#include <iostream>
+#include <limits>  // for std::numeric_limits<>
+
+template<typename FloatingType >
+void GUDHI_TEST_FLOAT_EQUALITY_CHECK(FloatingType a, FloatingType b,
+                                     FloatingType epsilon = std::numeric_limits<FloatingType>::epsilon()) {
+#ifdef DEBUG_TRACES
+  std::cout << "GUDHI_TEST_FLOAT_EQUALITY_CHECK - " << a << " versus " << b
+            << " | diff = " << std::fabs(a - b) << " - epsilon = " << epsilon << std::endl;
+#endif
+  BOOST_CHECK(std::fabs(a - b) < epsilon);
+}
+
+#endif  // UNITARY_TESTS_UTILS_H_
diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h
index f6e2ab5a..3a5d1fd5 100644
--- a/src/common/include/gudhi/distance_functions.h
+++ b/src/common/include/gudhi/distance_functions.h
@@ -23,9 +23,14 @@
 #ifndef DISTANCE_FUNCTIONS_H_
 #define DISTANCE_FUNCTIONS_H_
 
+#include <gudhi/Debug_utils.h>
+
+#include <boost/range/metafunctions.hpp>
+
 #include <cmath>  // for std::sqrt
 #include <type_traits>  // for std::decay
 #include <iterator>  // for std::begin, std::end
+#include <utility>
 
 namespace Gudhi {
 
@@ -37,16 +42,29 @@ namespace Gudhi {
  * have the same dimension. */
 class Euclidean_distance {
  public:
+  // boost::range_value is not SFINAE-friendly so we cannot use it in the return type
   template< typename Point >
-  auto operator()(const Point& p1, const Point& p2) const -> typename std::decay<decltype(*std::begin(p1))>::type {
-    auto it1 = p1.begin();
-    auto it2 = p2.begin();
-    typename Point::value_type dist = 0.;
-    for (; it1 != p1.end(); ++it1, ++it2) {
-      typename Point::value_type tmp = (*it1) - (*it2);
+  typename std::iterator_traits<typename boost::range_iterator<Point>::type>::value_type
+  operator()(const Point& p1, const Point& p2) const {
+    auto it1 = std::begin(p1);
+    auto it2 = std::begin(p2);
+    typedef typename boost::range_value<Point>::type NT;
+    NT dist = 0;
+    for (; it1 != std::end(p1); ++it1, ++it2) {
+      GUDHI_CHECK(it2 != std::end(p2), "inconsistent point dimensions");
+      NT tmp = *it1 - *it2;
       dist += tmp*tmp;
     }
-    return std::sqrt(dist);
+    GUDHI_CHECK(it2 == std::end(p2), "inconsistent point dimensions");
+    using std::sqrt;
+    return sqrt(dist);
+  }
+  template< typename T >
+  T operator() (const std::pair< T, T >& f, const std::pair< T, T >& s) const {
+    T dx = f.first - s.first;
+    T dy = f.second - s.second;
+    using std::sqrt;
+    return sqrt(dx*dx + dy*dy);
   }
 };
 
diff --git a/src/common/include/gudhi/graph_simplicial_complex.h b/src/common/include/gudhi/graph_simplicial_complex.h
index 5fe7c826..d84421b2 100644
--- a/src/common/include/gudhi/graph_simplicial_complex.h
+++ b/src/common/include/gudhi/graph_simplicial_complex.h
@@ -28,6 +28,9 @@
 #include <utility>  // for pair<>
 #include <vector>
 #include <map>
+#include <tuple>  // for std::tie
+
+namespace Gudhi {
 
 /* Edge tag for Boost PropertyGraph. */
 struct edge_filtration_t {
@@ -39,4 +42,64 @@ struct vertex_filtration_t {
   typedef boost::vertex_property_tag kind;
 };
 
+template <typename SimplicialComplexForProximityGraph>
+using Proximity_graph = typename boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS
+, boost::property < vertex_filtration_t, typename SimplicialComplexForProximityGraph::Filtration_value >
+, boost::property < edge_filtration_t, typename SimplicialComplexForProximityGraph::Filtration_value >>;
+
+/** \brief Computes the proximity graph of the points.
+ *
+ * If points contains n elements, the proximity graph is the graph with n vertices, and an edge [u,v] iff the
+ * distance function between points u and v is smaller than threshold.
+ *
+ * \tparam ForwardPointRange furnishes `.begin()` and `.end()` methods.
+ *
+ * \tparam Distance furnishes `operator()(const Point& p1, const Point& p2)`, where
+ * `Point` is a point from the `ForwardPointRange`, and that returns a `Filtration_value`.
+ */
+template< typename SimplicialComplexForProximityGraph
+          , typename ForwardPointRange
+          , typename Distance >
+Proximity_graph<SimplicialComplexForProximityGraph> compute_proximity_graph(
+    const ForwardPointRange& points,
+    typename SimplicialComplexForProximityGraph::Filtration_value threshold,
+    Distance distance) {
+  using Vertex_handle = typename SimplicialComplexForProximityGraph::Vertex_handle;
+  using Filtration_value = typename SimplicialComplexForProximityGraph::Filtration_value;
+
+  std::vector<std::pair< Vertex_handle, Vertex_handle >> edges;
+  std::vector< Filtration_value > edges_fil;
+  std::map< Vertex_handle, Filtration_value > vertices;
+
+  Vertex_handle idx_u, idx_v;
+  Filtration_value fil;
+  idx_u = 0;
+  for (auto it_u = points.begin(); it_u != points.end(); ++it_u) {
+    idx_v = idx_u + 1;
+    for (auto it_v = it_u + 1; it_v != points.end(); ++it_v, ++idx_v) {
+      fil = distance(*it_u, *it_v);
+      if (fil <= threshold) {
+        edges.emplace_back(idx_u, idx_v);
+        edges_fil.push_back(fil);
+      }
+    }
+    ++idx_u;
+  }
+
+  // Points are labeled from 0 to idx_u-1
+  Proximity_graph<SimplicialComplexForProximityGraph> skel_graph(edges.begin(), edges.end(), edges_fil.begin(), idx_u);
+
+  auto vertex_prop = boost::get(vertex_filtration_t(), skel_graph);
+
+  typename boost::graph_traits<Proximity_graph<SimplicialComplexForProximityGraph>>::vertex_iterator vi, vi_end;
+  for (std::tie(vi, vi_end) = boost::vertices(skel_graph);
+       vi != vi_end; ++vi) {
+    boost::put(vertex_prop, *vi, 0.);
+  }
+
+  return skel_graph;
+}
+
+}  // namespace Gudhi
+
 #endif  // GRAPH_SIMPLICIAL_COMPLEX_H_
diff --git a/src/common/utilities/README b/src/common/utilities/README
deleted file mode 100644
index dc841521..00000000
--- a/src/common/utilities/README
+++ /dev/null
@@ -1,19 +0,0 @@
-======================= off_file_from_shape_generator ==================================
-
-Example of use :
-
-*** on|in sphere|cube|curve|torus|klein generator
-
-./off_file_from_shape_generator on sphere onSphere.off 1000 3 15.2
-
- => generates a onSphere.off file with 1000 points randomized on a sphere of dimension 3 and radius 15.2
-
-./off_file_from_shape_generator in sphere inSphere.off 100 2
-
- => generates a inSphere.off file with 100 points randomized in a sphere of dimension 2 (circle) and radius 1.0 (default)
-
-./off_file_from_shape_generator in cube inCube.off 10000 3 5.8
-
- => generates a inCube.off file with 10000 points randomized in a cube of dimension 3 and side 5.8
-
-!! Warning: hypegenerator on cube is not available !!
diff --git a/src/common/utilities/pointsetgenerator.md b/src/common/utilities/pointsetgenerator.md
new file mode 100644
index 00000000..284715d4
--- /dev/null
+++ b/src/common/utilities/pointsetgenerator.md
@@ -0,0 +1,33 @@
+
+
+# common #
+
+## off_file_from_shape_generator ##
+
+Generates a pointset and save it in an OFF file. Command-line is:
+
+```
+off_file_from_shape_generator on|in sphere|cube|curve|torus|klein <filename> <num_points> <dimension> <parameter1> <parameter2>...
+```
+
+Warning: "on cube" generator is not available!
+
+**Examples**
+
+```
+off_file_from_shape_generator on sphere onSphere.off 1000 3 15.2
+```
+
+* Generates an onSphere.off file with 1000 points randomized on a sphere of dimension 3 and radius 15.2.
+
+```
+off_file_from_shape_generator in sphere inSphere.off 100 2
+```
+
+* Generates an inSphere.off file with 100 points randomized in a sphere of dimension 2 (circle) and radius 1.0 (default).
+
+```
+off_file_from_shape_generator in cube inCube.off 10000 3 5.8
+```
+
+* Generates a inCube.off file with 10000 points randomized in a cube of dimension 3 and side 5.8.