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-rw-r--r--src/common/doc/examples.h224
-rw-r--r--src/common/doc/header.html1
-rw-r--r--src/common/doc/installation.h177
-rw-r--r--src/common/doc/main_page.md28
4 files changed, 253 insertions, 177 deletions
diff --git a/src/common/doc/examples.h b/src/common/doc/examples.h
index 474f8699..879fb96a 100644
--- a/src/common/doc/examples.h
+++ b/src/common/doc/examples.h
@@ -1,96 +1,134 @@
-// 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
+// List of GUDHI examples and utils - Doxygen needs at least a file tag to analyse comments
+// Generated from scripts/cpp_examples_for_doxygen.py
/*! @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_distance.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_alpha_complex_3d_from_points.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
+ * \section Witness_complex_example_section Witness_complex
+ * @example strong_witness_persistence.cpp
+ * @example weak_witness_persistence.cpp
+ * @example example_witness_complex_off.cpp
+ * @example example_strong_witness_complex_off.cpp
+ * @example example_nearest_landmark_table.cpp
+ * @example example_witness_complex_sphere.cpp
+ * \section Contraction_example_section Contraction
+ * @example Rips_contraction.cpp
+ * @example Garland_heckbert.cpp
+ * \section Simplex_tree_example_section Simplex_tree
+ * @example mini_simplex_tree.cpp
+ * @example cech_complex_cgal_mini_sphere_3d.cpp
+ * @example graph_expansion_with_blocker.cpp
+ * @example simple_simplex_tree.cpp
+ * @example simplex_tree_from_cliques_of_graph.cpp
+ * @example example_alpha_shapes_3_simplex_tree_from_off_file.cpp
+ * \section Persistent_cohomology_example_section Persistent_cohomology
+ * @example custom_persistence_sort.cpp
+ * @example rips_persistence_step_by_step.cpp
+ * @example persistence_from_file.cpp
+ * @example rips_persistence_via_boundary_matrix.cpp
+ * @example plain_homology.cpp
+ * @example rips_multifield_persistence.cpp
+ * @example persistence_from_simple_simplex_tree.cpp
+ * \section Subsampling_example_section Subsampling
+ * @example example_sparsify_point_set.cpp
+ * @example example_choose_n_farthest_points.cpp
+ * @example example_custom_distance.cpp
+ * @example example_pick_n_random_points.cpp
+ * \section Toplex_map_example_section Toplex_map
+ * @example simple_toplex_map.cpp
+ * \section Collapse_example_section Collapse
+ * @example distance_matrix_edge_collapse_rips_persistence.cpp
+ * @example point_cloud_edge_collapse_rips_persistence.cpp
+ * @example edge_collapse_conserve_persistence.cpp
+ * @example edge_collapse_basic_example.cpp
+ * \section Cech_complex_example_section Cech_complex
+ * @example cech_persistence.cpp
+ * @example cech_complex_step_by_step.cpp
+ * @example cech_complex_example_from_points.cpp
+ * \section Bitmap_cubical_complex_example_section Bitmap_cubical_complex
+ * @example periodic_cubical_complex_persistence.cpp
+ * @example cubical_complex_persistence.cpp
+ * @example Random_bitmap_cubical_complex.cpp
+ * \section Coxeter_triangulation_example_section Coxeter_triangulation
+ * @example cell_complex_from_basic_circle_manifold.cpp
+ * @example manifold_tracing_flat_torus_with_boundary.cpp
+ * @example manifold_tracing_custom_function.cpp
+ * \section Nerve_GIC_example_section Nerve_GIC
+ * @example VoronoiGIC.cpp
+ * @example Nerve.cpp
+ * @example CoordGIC.cpp
+ * @example FuncGIC.cpp
+ * \section Tangential_complex_example_section Tangential_complex
+ * @example example_basic.cpp
+ * @example example_with_perturb.cpp
+ * \section Persistence_representations_example_section Persistence_representations
+ * @example persistence_vectors/create_persistence_vectors.cpp
+ * @example persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp
+ * @example persistence_vectors/plot_persistence_vectors.cpp
+ * @example persistence_vectors/average_persistence_vectors.cpp
+ * @example persistence_vectors/compute_distance_of_persistence_vectors.cpp
+ * @example persistence_landscapes_on_grid/average_landscapes_on_grid.cpp
+ * @example persistence_landscapes_on_grid/create_landscapes_on_grid.cpp
+ * @example persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp
+ * @example persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp
+ * @example persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp
+ * @example persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp
+ * @example persistence_intervals/plot_persistence_Betti_numbers.cpp
+ * @example persistence_intervals/compute_bottleneck_distance.cpp
+ * @example persistence_intervals/compute_number_of_dominant_intervals.cpp
+ * @example persistence_intervals/plot_histogram_of_intervals_lengths.cpp
+ * @example persistence_intervals/plot_persistence_intervals.cpp
+ * @example persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp
+ * @example persistence_heat_maps/create_pssk.cpp
+ * @example persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp
+ * @example persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp
+ * @example persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp
+ * @example persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp
+ * @example persistence_heat_maps/plot_persistence_heat_map.cpp
+ * @example persistence_heat_maps/create_persistence_heat_maps.cpp
+ * @example persistence_heat_maps/average_persistence_heat_maps.cpp
+ * @example persistence_landscapes/compute_distance_of_landscapes.cpp
+ * @example persistence_landscapes/compute_scalar_product_of_landscapes.cpp
+ * @example persistence_landscapes/average_landscapes.cpp
+ * @example persistence_landscapes/plot_landscapes.cpp
+ * @example persistence_landscapes/create_landscapes.cpp
+ * @example persistence_landscape_on_grid.cpp
+ * @example persistence_intervals.cpp
+ * @example persistence_landscape.cpp
+ * @example persistence_vectors.cpp
+ * @example sliced_wasserstein.cpp
+ * @example persistence_heat_maps.cpp
+ * \section Spatial_searching_example_section Spatial_searching
+ * @example example_spatial_searching.cpp
+ * \section Bottleneck_distance_example_section Bottleneck_distance
+ * @example bottleneck_distance.cpp
+ * @example bottleneck_basic_example.cpp
+ * @example alpha_rips_persistence_bottleneck_distance.cpp
+ * \section common_example_section common
+ * @example off_file_from_shape_generator.cpp
+ * @example example_vector_double_points_off_reader.cpp
+ * @example example_CGAL_points_off_reader.cpp
+ * @example example_CGAL_3D_points_off_reader.cpp
+ * \section Alpha_complex_example_section Alpha_complex
+ * @example alpha_complex_3d_persistence.cpp
+ * @example alpha_complex_persistence.cpp
+ * @example Fast_alpha_complex_from_off.cpp
+ * @example Alpha_complex_3d_from_points.cpp
+ * @example Alpha_complex_from_off.cpp
+ * @example Weighted_alpha_complex_3d_from_points.cpp
+ * @example Weighted_alpha_complex_from_points.cpp
+ * @example Alpha_complex_from_points.cpp
+ * \section Skeleton_blocker_example_section Skeleton_blocker
+ * @example Skeleton_blocker_from_simplices.cpp
+ * @example Skeleton_blocker_link.cpp
+ * @example Skeleton_blocker_iteration.cpp
+ * \section Rips_complex_example_section Rips_complex
+ * @example rips_persistence.cpp
+ * @example rips_correlation_matrix_persistence.cpp
+ * @example sparse_rips_persistence.cpp
+ * @example rips_distance_matrix_persistence.cpp
+ * @example example_sparse_rips.cpp
+ * @example example_rips_complex_from_csv_distance_matrix_file.cpp
+ * @example example_one_skeleton_rips_from_correlation_matrix.cpp
+ * @example example_one_skeleton_rips_from_distance_matrix.cpp
+ * @example example_one_skeleton_rips_from_points.cpp
+ * @example example_rips_complex_from_off_file.cpp
*/
diff --git a/src/common/doc/header.html b/src/common/doc/header.html
index 9da20bbc..7c20478b 100644
--- a/src/common/doc/header.html
+++ b/src/common/doc/header.html
@@ -49,6 +49,7 @@ $extrastylesheet
<li><a href="/relatedprojects/">Related projects</a></li>
<li><a href="/theyaretalkingaboutus/">They are talking about us</a></li>
<li><a href="/inaction/">GUDHI in action</a></li>
+ <li><a href="/etymology/">Etymology</a></li>
</ul>
</li>
<li class="divider"></li>
diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h
index c2e63a24..ef668dfb 100644
--- a/src/common/doc/installation.h
+++ b/src/common/doc/installation.h
@@ -30,6 +30,10 @@ make \endverbatim
* This action may require to be in the sudoer or administrator of the machine in function of the operating system and
* of <a href="https://cmake.org/cmake/help/latest/variable/CMAKE_INSTALL_PREFIX.html">CMAKE_INSTALL_PREFIX</a>.
*
+ * \note Python module will be compiled by the `make` command, but `make install` will not install it. Please refer to
+ * the <a href="https://gudhi.inria.fr/python/latest/installation.html#gudhi-python-module-installation">Python
+ * module installation documentation</a>.
+ *
* \subsection testsuites Test suites
* To test your build, run the following command in a terminal:
* \verbatim make test \endverbatim
@@ -40,11 +44,8 @@ make \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
+ * \verbatim make doxygen \endverbatim
+ * Documentation will be generated in a folder named <code>html</code>.
*
* \subsection helloworld Hello world !
* The <a target="_blank" href="https://github.com/GUDHI/hello-gudhi-world">Hello world for GUDHI</a>
@@ -57,7 +58,7 @@ make doxygen
*
* 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">
+ * \li <a href="rips_multifield_persistence_8cpp-example.html">
* Persistent_cohomology/rips_multifield_persistence.cpp</a>
*
* Having GMP version 4.2 or higher installed is recommended.
@@ -75,56 +76,58 @@ make doxygen
*
* The following examples/utilities require the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms
* Library</a> (CGAL \cite cgal:eb-19b) and will not be built if CGAL version 4.11.0 or higher is not installed:
- * \li <a href="_simplex_tree_2example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html">
+ * \li <a href="example_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="_witness_complex_2strong_witness_persistence_8cpp-example.html">
+ * \li <a href="strong_witness_persistence_8cpp-example.html">
* Witness_complex/strong_witness_persistence.cpp</a>
- * \li <a href="_witness_complex_2weak_witness_persistence_8cpp-example.html">
+ * \li <a href="weak_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">
+ * \li <a href="example_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">
+ * \li <a href="example_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">
+ * \li <a href="example_witness_complex_sphere_8cpp-example.html">
* Witness_complex/example_witness_complex_sphere.cpp</a>
- * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html">
+ * \li <a href="_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">
+ * \li <a href="_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">
+ * \li <a href="alpha_complex_persistence_8cpp-example.html">
* Alpha_complex/alpha_complex_persistence.cpp</a>
- * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">
+ * \li <a href="custom_persistence_sort_8cpp-example.html">
* Persistent_cohomology/custom_persistence_sort.cpp</a>
- * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html">
+ * \li <a href="alpha_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">
+ * \li <a href="bottleneck_basic_example_8cpp-example.html">
* Bottleneck_distance/bottleneck_basic_example.cpp</a>
- * \li <a href="_bottleneck_distance_2bottleneck_read_file_8cpp-example.html">
+ * \li <a href="bottleneck_distance_8cpp-example.html">
* Bottleneck_distance/bottleneck_distance.cpp</a>
- * \li <a href="_nerve__g_i_c_2_coord_g_i_c_8cpp-example.html">
+ * \li <a href="_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">
+ * \li <a href="_func_g_i_c_8cpp-example.html">
* Nerve_GIC/FuncGIC.cpp</a>
- * \li <a href="_nerve__g_i_c_2_nerve_8cpp-example.html">
+ * \li <a href="_nerve_8cpp-example.html">
* Nerve_GIC/Nerve.cpp</a>
- * \li <a href="_nerve__g_i_c_2_voronoi_g_i_c_8cpp-example.html">
+ * \li <a href="_voronoi_g_i_c_8cpp-example.html">
* Nerve_GIC/VoronoiGIC.cpp</a>
- * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html">
+ * \li <a href="example_spatial_searching_8cpp-example.html">
* Spatial_searching/example_spatial_searching.cpp</a>
- * \li <a href="_subsampling_2example_choose_n_farthest_points_8cpp-example.html">
+ * \li <a href="example_choose_n_farthest_points_8cpp-example.html">
* Subsampling/example_choose_n_farthest_points.cpp</a>
- * \li <a href="_subsampling_2example_pick_n_random_points_8cpp-example.html">
+ * \li <a href="example_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">
+ * \li <a href="example_sparsify_point_set_8cpp-example.html">
* Subsampling/example_sparsify_point_set.cpp</a>
- * \li <a href="_tangential_complex_2example_basic_8cpp-example.html">
+ * \li <a href="example_basic_8cpp-example.html">
* Tangential_complex/example_basic.cpp</a>
- * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html">
+ * \li <a href="example_with_perturb_8cpp-example.html">
* Tangential_complex/example_with_perturb.cpp</a>
- * \li <a href="_alpha_complex_2_weighted_alpha_complex_3d_from_points_8cpp-example.html">
+ * \li <a href="_weighted_alpha_complex_3d_from_points_8cpp-example.html">
* Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp</a>
- * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html">
+ * \li <a href="alpha_complex_3d_persistence_8cpp-example.html">
* Alpha_complex/alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_coxeter_triangulation_2manifold_tracing_flat_torus_with_boundary_8cpp-example.html">
+ * Coxeter_triangulation/manifold_tracing_flat_torus_with_boundary.cpp</a>
*
* \subsection eigen Eigen
* Some GUDHI modules (cf. \ref main_page "modules list"), and few examples require
@@ -133,42 +136,48 @@ make doxygen
*
* The following examples/utilities require the <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen</a> and will not be
* built if Eigen is not installed:
- * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html">
+ * \li <a href="_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">
+ * \li <a href="_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">
+ * \li <a href="alpha_complex_persistence_8cpp-example.html">
* Alpha_complex/alpha_complex_persistence.cpp</a>
- * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html">
+ * \li <a href="alpha_complex_3d_persistence_8cpp-example.html">
* Alpha_complex/alpha_complex_3d_persistence.cpp</a>
- * \li <a href="_alpha_complex_2_weighted_alpha_complex_3d_from_points_8cpp-example.html">
+ * \li <a href="_weighted_alpha_complex_3d_from_points_8cpp-example.html">
* Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp</a>
- * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html">
+ * \li <a href="alpha_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">
+ * \li <a href="custom_persistence_sort_8cpp-example.html">
* Persistent_cohomology/custom_persistence_sort.cpp</a>
- * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html">
+ * \li <a href="example_spatial_searching_8cpp-example.html">
* Spatial_searching/example_spatial_searching.cpp</a>
- * \li <a href="_subsampling_2example_choose_n_farthest_points_8cpp-example.html">
+ * \li <a href="example_choose_n_farthest_points_8cpp-example.html">
* Subsampling/example_choose_n_farthest_points.cpp</a>
- * \li <a href="_subsampling_2example_pick_n_random_points_8cpp-example.html">
+ * \li <a href="example_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">
+ * \li <a href="example_sparsify_point_set_8cpp-example.html">
* Subsampling/example_sparsify_point_set.cpp</a>
- * \li <a href="_tangential_complex_2example_basic_8cpp-example.html">
+ * \li <a href="example_basic_8cpp-example.html">
* Tangential_complex/example_basic.cpp</a>
- * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html">
+ * \li <a href="example_with_perturb_8cpp-example.html">
* Tangential_complex/example_with_perturb.cpp</a>
- * \li <a href="_witness_complex_2strong_witness_persistence_8cpp-example.html">
+ * \li <a href="strong_witness_persistence_8cpp-example.html">
* Witness_complex/strong_witness_persistence.cpp</a>
- * \li <a href="_witness_complex_2weak_witness_persistence_8cpp-example.html">
+ * \li <a href="weak_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">
+ * \li <a href="example_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">
+ * \li <a href="example_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">
+ * \li <a href="example_witness_complex_sphere_8cpp-example.html">
* Witness_complex/example_witness_complex_sphere.cpp</a>
+ * \li <a href="_coxeter_triangulation_2cell_complex_from_basic_circle_manifold_8cpp-example.html">
+ * Coxeter_triangulation/cell_complex_from_basic_circle_manifold.cpp</a>
+ * \li <a href="_coxeter_triangulation_2manifold_tracing_custom_function_8cpp-example.html">
+ * Coxeter_triangulation/manifold_tracing_custom_function.cpp</a>
+ * \li <a href="_coxeter_triangulation_2manifold_tracing_flat_torus_with_boundary_8cpp-example.html">
+ * Coxeter_triangulation/manifold_tracing_flat_torus_with_boundary.cpp</a>
*
* \subsection tbb Threading Building Blocks
* <a target="_blank" href="https://www.threadingbuildingblocks.org/">Intel&reg; TBB</a> lets you easily write parallel
@@ -178,74 +187,76 @@ make doxygen
* 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">
+ * \li <a href="_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">
+ * \li <a href="_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">
+ * \li <a href="alpha_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">
+ * \li <a href="alpha_complex_persistence_8cpp-example.html">
* Alpha_complex/alpha_complex_persistence.cpp</a>
- * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_8cpp-example.html">
+ * \li <a href="cubical_complex_persistence_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">
+ * \li <a href="periodic_cubical_complex_persistence_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">
+ * \li <a href="_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">
+ * \li <a href="_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">
+ * \li <a href="_func_g_i_c_8cpp-example.html">
* Nerve_GIC/FuncGIC.cpp</a>
- * \li <a href="_nerve__g_i_c_2_nerve_8cpp-example.html">
+ * \li <a href="_nerve_8cpp-example.html">
* Nerve_GIC/Nerve.cpp</a>
- * \li <a href="_nerve__g_i_c_2_voronoi_g_i_c_8cpp-example.html">
+ * \li <a href="_voronoi_g_i_c_8cpp-example.html">
* Nerve_GIC/VoronoiGIC.cpp</a>
- * \li <a href="_simplex_tree_2simple_simplex_tree_8cpp-example.html">
+ * \li <a href="simple_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">
+ * \li <a href="example_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">
+ * \li <a href="simplex_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">
+ * \li <a href="graph_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">
+ * \li <a href="alpha_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">
+ * \li <a href="alpha_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">
+ * \li <a href="rips_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">
+ * \li <a href="persistence_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">
+ * \li <a href="persistence_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">
+ * \li <a href="plain_homology_8cpp-example.html">
* Persistent_cohomology/plain_homology.cpp</a>
- * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html">
+ * \li <a href="rips_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">
+ * \li <a href="rips_persistence_step_by_step_8cpp-example.html">
* Persistent_cohomology/rips_persistence_step_by_step.cpp</a>
- * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">
+ * \li <a href="custom_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">
+ * \li <a href="example_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">
+ * \li <a href="example_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">
+ * \li <a href="rips_distance_matrix_persistence_8cpp-example.html">
* Rips_complex/rips_distance_matrix_persistence.cpp</a>
- * \li <a href="_rips_complex_2rips_persistence_8cpp-example.html">
+ * \li <a href="rips_persistence_8cpp-example.html">
* Rips_complex/rips_persistence.cpp</a>
- * \li <a href="_witness_complex_2strong_witness_persistence_8cpp-example.html">
+ * \li <a href="strong_witness_persistence_8cpp-example.html">
* Witness_complex/strong_witness_persistence.cpp</a>
- * \li <a href="_witness_complex_2weak_witness_persistence_8cpp-example.html">
+ * \li <a href="weak_witness_persistence_8cpp-example.html">
* Witness_complex/weak_witness_persistence.cpp</a>
- * \li <a href="_witness_complex_2example_nearest_landmark_table_8cpp-example.html">
+ * \li <a href="example_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
+ * Please help us improving the quality of the GUDHI library.
+ * You may <a href="https://github.com/GUDHI/gudhi-devel/issues">report bugs</a> or
+ * <a href="https://gudhi.inria.fr/contact/">contact us</a> for any suggestions.
*
- * GUDHI is open to external contributions. If you want to join our development team, please contact us.
+ * GUDHI is open to external contributions. If you want to join our development team, please take some time to read our
+ * <a href="https://github.com/GUDHI/gudhi-devel/blob/master/.github/CONTRIBUTING.md">contributing guide</a>.
*
*/
diff --git a/src/common/doc/main_page.md b/src/common/doc/main_page.md
index e19af537..17354179 100644
--- a/src/common/doc/main_page.md
+++ b/src/common/doc/main_page.md
@@ -135,7 +135,7 @@
</tr>
</table>
-## Filtrations and reconstructions {#FiltrationsReconstructions}
+## Filtrations
### Alpha complex
<table>
@@ -298,6 +298,32 @@
</tr>
</table>
+## Manifold reconstructions
+### Coxeter triangulation
+
+<table>
+ <tr>
+ <td width="35%" rowspan=2>
+ \image html "manifold_tracing_on_custom_function_example.png"
+ </td>
+ <td width="50%">
+ Coxeter triangulation module is designed to provide tools for constructing a piecewise-linear approximation of an
+ \f$m\f$-dimensional smooth manifold embedded in \f$ \mathbb{R}^d \f$ using an ambient triangulation.
+ </td>
+ <td width="15%">
+ <b>Author:</b> Siargey Kachanovich<br>
+ <b>Introduced in:</b> GUDHI 3.4.0<br>
+ <b>Copyright:</b> MIT [(LGPL v3)](../../licensing/)<br>
+ <b>Requires:</b> \ref eigen &ge; 3.1.0
+ </td>
+ </tr>
+ <tr>
+ <td colspan=2 height="25">
+ <b>User manual:</b> \ref coxeter_triangulation
+ </td>
+ </tr>
+</table>
+
### Tangential complex
<table>
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