diff options
author | Vincent Rouvreau <vincent.rouvreau@inria.fr> | 2021-11-02 10:53:05 +0100 |
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committer | Vincent Rouvreau <vincent.rouvreau@inria.fr> | 2021-11-02 10:53:05 +0100 |
commit | 003abb66b7c657356328bc24306e2c5aef02b1d4 (patch) | |
tree | 0530c8987c824da79ecddd22485f143831a4c71f /src/common | |
parent | b1f604312adb6a9240f8e8b7effcd4bd7251e82b (diff) | |
parent | 8adb46d8a54f1a0dd71ea686473cc4ca9f5d2f67 (diff) |
Merge master and fix conflicts
Diffstat (limited to 'src/common')
-rw-r--r-- | src/common/doc/examples.h | 173 | ||||
-rw-r--r-- | src/common/doc/header.html | 1 | ||||
-rw-r--r-- | src/common/doc/installation.h | 48 | ||||
-rw-r--r-- | src/common/test/test_distance_matrix_reader.cpp | 2 |
4 files changed, 131 insertions, 93 deletions
diff --git a/src/common/doc/examples.h b/src/common/doc/examples.h index b2183990..879fb96a 100644 --- a/src/common/doc/examples.h +++ b/src/common/doc/examples.h @@ -1,99 +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_from_off.cpp - * @example Alpha_complex_from_points.cpp - * @example bottleneck_basic_example.cpp - * @example alpha_rips_persistence_bottleneck_distance.cpp - * @example example_nearest_landmark_table.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_witness_complex_sphere.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 - * @example cech_complex_cgal_mini_sphere_3d.cpp - * @example plain_homology.cpp - * @example persistence_from_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 custom_persistence_sort.cpp - * @example persistence_from_simple_simplex_tree.cpp + * @example plain_homology.cpp * @example rips_multifield_persistence.cpp - * @example Skeleton_blocker_from_simplices.cpp - * @example Skeleton_blocker_iteration.cpp - * @example Skeleton_blocker_link.cpp - * @example Garland_heckbert.cpp - * @example Rips_contraction.cpp - * @example Random_bitmap_cubical_complex.cpp - * @example example_CGAL_3D_points_off_reader.cpp - * @example example_vector_double_points_off_reader.cpp - * @example example_CGAL_points_off_reader.cpp - * @example example_one_skeleton_rips_from_distance_matrix.cpp - * @example example_one_skeleton_rips_from_points.cpp - * @example example_rips_complex_from_csv_distance_matrix_file.cpp - * @example example_rips_complex_from_off_file.cpp - * @example persistence_intervals.cpp - * @example persistence_vectors.cpp - * @example persistence_heat_maps.cpp - * @example persistence_landscape_on_grid.cpp - * @example persistence_landscape.cpp - * @example example_basic.cpp - * @example example_with_perturb.cpp - * @example example_custom_distance.cpp - * @example example_choose_n_farthest_points.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 - * @example CoordGIC.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 - * @example VoronoiGIC.cpp - * @example example_spatial_searching.cpp - * @example alpha_complex_3d_persistence.cpp - * @example alpha_complex_persistence.cpp - * @example Weighted_alpha_complex_3d_from_points.cpp - * @example bottleneck_distance.cpp - * @example weak_witness_persistence.cpp - * @example strong_witness_persistence.cpp - * @example cubical_complex_persistence.cpp - * @example periodic_cubical_complex_persistence.cpp - * @example off_file_from_shape_generator.cpp - * @example rips_distance_matrix_persistence.cpp - * @example rips_persistence.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/plot_landscapes_on_grid.cpp - * @example persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp * @example persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp - * @example persistence_landscapes_on_grid/average_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/compute_number_of_dominant_intervals.cpp * @example persistence_intervals/plot_persistence_Betti_numbers.cpp - * @example persistence_intervals/plot_persistence_intervals.cpp - * @example persistence_intervals/plot_histogram_of_intervals_lengths.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_distance_of_persistence_heat_maps.cpp * @example persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp - * @example persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp - * @example persistence_heat_maps/average_persistence_heat_maps.cpp * @example persistence_heat_maps/plot_persistence_heat_map.cpp * @example persistence_heat_maps/create_persistence_heat_maps.cpp - * @example persistence_vectors/plot_persistence_vectors.cpp - * @example persistence_vectors/compute_distance_of_persistence_vectors.cpp - * @example persistence_vectors/average_persistence_vectors.cpp - * @example persistence_vectors/create_persistence_vectors.cpp - * @example persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp - * @example persistence_landscapes/average_landscapes.cpp - * @example persistence_landscapes/compute_scalar_product_of_landscapes.cpp - * @example persistence_landscapes/create_landscapes.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 cell_complex_from_basic_circle_manifold.cpp - * @example manifold_tracing_custom_function.cpp - * @example manifold_tracing_flat_torus_with_boundary.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 91d30081..ef668dfb 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -88,9 +88,9 @@ make \endverbatim * Witness_complex/example_witness_complex_off.cpp</a> * \li <a href="example_witness_complex_sphere_8cpp-example.html"> * Witness_complex/example_witness_complex_sphere.cpp</a> - * \li <a href="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_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_persistence_8cpp-example.html"> * Alpha_complex/alpha_complex_persistence.cpp</a> @@ -100,15 +100,15 @@ make \endverbatim * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a> * \li <a href="bottleneck_basic_example_8cpp-example.html"> * Bottleneck_distance/bottleneck_basic_example.cpp</a> - * \li <a href="bottleneck_read_file_8cpp-example.html"> + * \li <a href="bottleneck_distance_8cpp-example.html"> * Bottleneck_distance/bottleneck_distance.cpp</a> - * \li <a href="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="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_8cpp-example.html"> + * \li <a href="_nerve_8cpp-example.html"> * Nerve_GIC/Nerve.cpp</a> - * \li <a href="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="example_spatial_searching_8cpp-example.html"> * Spatial_searching/example_spatial_searching.cpp</a> @@ -122,7 +122,7 @@ make \endverbatim * Tangential_complex/example_basic.cpp</a> * \li <a href="example_with_perturb_8cpp-example.html"> * Tangential_complex/example_with_perturb.cpp</a> - * \li <a href="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_3d_persistence_8cpp-example.html"> * Alpha_complex/alpha_complex_3d_persistence.cpp</a> @@ -136,15 +136,15 @@ make \endverbatim * * 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_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_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_persistence_8cpp-example.html"> * Alpha_complex/alpha_complex_persistence.cpp</a> * \li <a href="alpha_complex_3d_persistence_8cpp-example.html"> * Alpha_complex/alpha_complex_3d_persistence.cpp</a> - * \li <a href="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_rips_persistence_bottleneck_distance_8cpp-example.html"> * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a> @@ -187,27 +187,27 @@ make \endverbatim * Having Intel® TBB installed is recommended to parallelize and accelerate some GUDHI computations. * * The following examples/utilities are using Intel® TBB if installed: - * \li <a href="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_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_3d_persistence_8cpp-example.html"> * Alpha_complex/alpha_complex_3d_persistence.cpp</a> * \li <a href="alpha_complex_persistence_8cpp-example.html"> * Alpha_complex/alpha_complex_persistence.cpp</a> - * \li <a href="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_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="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="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="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_8cpp-example.html"> + * \li <a href="_nerve_8cpp-example.html"> * Nerve_GIC/Nerve.cpp</a> - * \li <a href="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="simple_simplex_tree_8cpp-example.html"> * Simplex_tree/simple_simplex_tree.cpp</a> @@ -251,10 +251,12 @@ make \endverbatim * 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/test/test_distance_matrix_reader.cpp b/src/common/test/test_distance_matrix_reader.cpp index 73be8104..92e899b8 100644 --- a/src/common/test/test_distance_matrix_reader.cpp +++ b/src/common/test/test_distance_matrix_reader.cpp @@ -57,7 +57,7 @@ BOOST_AUTO_TEST_CASE( full_square_distance_matrix ) { Distance_matrix from_full_square; // Read full_square_distance_matrix.csv file where the separator is the default one ';' - from_full_square = Gudhi::read_lower_triangular_matrix_from_csv_file<double>("full_square_distance_matrix.csv"); + from_full_square = Gudhi::read_lower_triangular_matrix_from_csv_file<double>("full_square_distance_matrix.csv", ';'); for (auto& i : from_full_square) { for (auto j : i) { std::clog << j << " "; |