GUDHI 2.1.0 as released by upstream in a tarball.upstream/2.1.0

6 files changed, 472 insertions, 279 deletions

diff --git a/doc/common/examples.h b/doc/common/examples.h
new file mode 100644
index 00000000..40f202c7
--- /dev/null
+++ b/doc/common/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/doc/common/file_formats.h b/doc/common/file_formats.h
index d715aa4d..c60ed15a 100644
--- a/doc/common/file_formats.h
+++ b/doc/common/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/doc/common/footer.html b/doc/common/footer.html
index 7b4cdc5c..a557922b 100644
--- a/doc/common/footer.html
+++ b/doc/common/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>
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diff --git a/doc/common/header.html b/doc/common/header.html
index 53b5c0a2..9c514381 100644
--- a/doc/common/header.html
+++ b/doc/common/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/37113/GUDHI_2.0.0_OSX_UTILS.beta.tar.gz" target="_blank">Utils for Mac OSx</a></li>
+                      <li><a href="https://gforge.inria.fr/frs/download.php/file/37112/GUDHI_2.0.0_WIN64_UTILS.beta.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/doc/common/installation.h b/doc/common/installation.h
new file mode 100644
index 00000000..25675cc5
--- /dev/null
+++ b/doc/common/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/doc/common/main_page.h b/doc/common/main_page.h
index 1a7994a5..b3e9ea03 100644
--- a/doc/common/main_page.h
+++ b/doc/common/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">
@@ -211,276 +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="_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_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_points.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 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
- */
-