From 4db14bad8006638fc8249cb867a1720f581e044d Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 31 Aug 2021 18:18:51 +0200 Subject: Fix broken links. Add a tool to generate cpp example page --- biblio/bibliography.bib | 1 - scripts/cpp_examples_for_doxygen.py | 16 ++ .../utilities/bottleneckdistance.md | 4 +- src/common/doc/examples.h | 164 ++++++++++++--------- src/common/doc/installation.h | 40 ++--- src/python/doc/installation.rst | 2 +- 6 files changed, 137 insertions(+), 90 deletions(-) create mode 100644 scripts/cpp_examples_for_doxygen.py diff --git a/biblio/bibliography.bib b/biblio/bibliography.bib index 16fa29d0..eed871be 100644 --- a/biblio/bibliography.bib +++ b/biblio/bibliography.bib @@ -15,7 +15,6 @@ title = {{Statistical analysis and parameter selection for Mapper}}, volume = {19}, year = {2018}, url = {http://jmlr.org/papers/v19/17-291.html}, -doi = {10.5555/3291125.3291137} } @inproceedings{Dey13, diff --git a/scripts/cpp_examples_for_doxygen.py b/scripts/cpp_examples_for_doxygen.py new file mode 100644 index 00000000..5c091c4f --- /dev/null +++ b/scripts/cpp_examples_for_doxygen.py @@ -0,0 +1,16 @@ +import os +import glob + +for gd_mod in glob.glob("src/*/"): + mod_files = [] + for paths in [gd_mod + 'utilities', gd_mod + 'example']: + if os.path.isdir(paths): + for root, dirs, files in os.walk(paths): + for file in files: + if file.endswith(".cpp"): + mod_files.append(str(os.path.join(root, file)).split(paths)[1][1:]) + if len(mod_files) > 0: + mod = str(gd_mod).split('/')[1] + print(' * \section ' + mod + '_example_section ' + mod) + for file in mod_files: + print(' * @example ' + file) diff --git a/src/Bottleneck_distance/utilities/bottleneckdistance.md b/src/Bottleneck_distance/utilities/bottleneckdistance.md index a81426cf..2f5dedc9 100644 --- a/src/Bottleneck_distance/utilities/bottleneckdistance.md +++ b/src/Bottleneck_distance/utilities/bottleneckdistance.md @@ -10,14 +10,14 @@ Leave the lines above as it is required by the web site generator 'Jekyll' {:/comment} -## bottleneck_read_file_example ## +## bottleneck_distance ## This program computes the Bottleneck distance between two persistence diagram files. **Usage** ``` - bottleneck_read_file_example [] + bottleneck_distance [] ``` where diff --git a/src/common/doc/examples.h b/src/common/doc/examples.h index b557727b..a2de4335 100644 --- a/src/common/doc/examples.h +++ b/src/common/doc/examples.h @@ -1,98 +1,130 @@ -// 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 - * \section Alpha_complex_examples Alpha complex - * @example Alpha_complex_from_off.cpp + * \section Skeleton_blocker_example_section Skeleton_blocker + * @example Skeleton_blocker_iteration.cpp + * @example Skeleton_blocker_from_simplices.cpp + * @example Skeleton_blocker_link.cpp + * \section Alpha_complex_example_section Alpha_complex + * @example alpha_complex_persistence.cpp + * @example alpha_complex_3d_persistence.cpp * @example Alpha_complex_from_points.cpp - * \section bottleneck_examples bottleneck - * @example bottleneck_basic_example.cpp - * @example alpha_rips_persistence_bottleneck_distance.cpp - * @example example_nearest_landmark_table.cpp - * @example example_witness_complex_off.cpp - * @example example_witness_complex_sphere.cpp - * @example example_strong_witness_complex_off.cpp + * @example Alpha_complex_3d_from_points.cpp + * @example Weighted_alpha_complex_3d_from_points.cpp + * @example Fast_alpha_complex_from_off.cpp + * @example Alpha_complex_from_off.cpp + * @example Weighted_alpha_complex_from_points.cpp + * \section Simplex_tree_example_section Simplex_tree + * @example cech_complex_cgal_mini_sphere_3d.cpp * @example mini_simplex_tree.cpp + * @example example_alpha_shapes_3_simplex_tree_from_off_file.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 - * @example rips_persistence_step_by_step.cpp + * \section Collapse_example_section Collapse + * @example point_cloud_edge_collapse_rips_persistence.cpp + * @example distance_matrix_edge_collapse_rips_persistence.cpp + * @example edge_collapse_basic_example.cpp + * @example edge_collapse_conserve_persistence.cpp + * \section Persistent_cohomology_example_section Persistent_cohomology * @example rips_persistence_via_boundary_matrix.cpp + * @example rips_persistence_step_by_step.cpp + * @example plain_homology.cpp * @example custom_persistence_sort.cpp * @example persistence_from_simple_simplex_tree.cpp + * @example persistence_from_file.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 example_sparsify_point_set.cpp - * @example example_pick_n_random_points.cpp - * @example CoordGIC.cpp + * \section Nerve_GIC_example_section Nerve_GIC + * @example VoronoiGIC.cpp * @example Nerve.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 CoordGIC.cpp + * \section Rips_complex_example_section Rips_complex * @example rips_persistence.cpp + * @example sparse_rips_persistence.cpp + * @example rips_correlation_matrix_persistence.cpp + * @example rips_distance_matrix_persistence.cpp + * @example example_one_skeleton_rips_from_correlation_matrix.cpp + * @example example_rips_complex_from_csv_distance_matrix_file.cpp + * @example example_sparse_rips.cpp + * @example example_one_skeleton_rips_from_distance_matrix.cpp + * @example example_rips_complex_from_off_file.cpp + * @example example_one_skeleton_rips_from_points.cpp + * \section Persistence_representations_example_section Persistence_representations + * @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/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_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_heat_maps/create_pssk.cpp - * @example persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp + * @example persistence_intervals/plot_persistence_Betti_numbers.cpp + * @example persistence_intervals/compute_number_of_dominant_intervals.cpp + * @example persistence_heat_maps/average_persistence_heat_maps.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_pssk.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/compute_distance_of_persistence_heat_maps.cpp + * @example persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp * @example persistence_heat_maps/plot_persistence_heat_map.cpp + * @example persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.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/plot_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_vectors/compute_distance_of_persistence_vectors.cpp * @example persistence_landscapes/create_landscapes.cpp + * @example persistence_landscapes/average_landscapes.cpp * @example persistence_landscapes/compute_distance_of_landscapes.cpp * @example persistence_landscapes/plot_landscapes.cpp + * @example persistence_landscapes/compute_scalar_product_of_landscapes.cpp + * @example persistence_heat_maps.cpp + * @example sliced_wasserstein.cpp + * @example persistence_intervals.cpp + * @example persistence_vectors.cpp + * @example persistence_landscape.cpp + * @example persistence_landscape_on_grid.cpp + * \section common_example_section common + * @example off_file_from_shape_generator.cpp + * @example example_CGAL_points_off_reader.cpp + * @example example_vector_double_points_off_reader.cpp + * @example example_CGAL_3D_points_off_reader.cpp + * \section Subsampling_example_section Subsampling + * @example example_pick_n_random_points.cpp + * @example example_choose_n_farthest_points.cpp + * @example example_sparsify_point_set.cpp + * @example example_custom_distance.cpp + * \section Contraction_example_section Contraction + * @example Rips_contraction.cpp + * @example Garland_heckbert.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 Tangential_complex_example_section Tangential_complex + * @example example_basic.cpp + * @example example_with_perturb.cpp + * \section Cech_complex_example_section Cech_complex + * @example cech_persistence.cpp + * @example cech_complex_example_from_points.cpp + * @example cech_complex_step_by_step.cpp + * \section Spatial_searching_example_section Spatial_searching + * @example example_spatial_searching.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 Toplex_map_example_section Toplex_map + * @example simple_toplex_map.cpp + * \section Witness_complex_example_section Witness_complex + * @example weak_witness_persistence.cpp + * @example strong_witness_persistence.cpp + * @example example_witness_complex_sphere.cpp + * @example example_strong_witness_complex_off.cpp + * @example example_nearest_landmark_table.cpp + * @example example_witness_complex_off.cpp */ diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index 5d40a48e..609f2f2f 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 * \li * Witness_complex/example_witness_complex_sphere.cpp - * \li + * \li * Alpha_complex/Alpha_complex_from_off.cpp - * \li + * \li * Alpha_complex/Alpha_complex_from_points.cpp * \li * Alpha_complex/alpha_complex_persistence.cpp @@ -100,15 +100,15 @@ make \endverbatim * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp * \li * Bottleneck_distance/bottleneck_basic_example.cpp - * \li + * \li * Bottleneck_distance/bottleneck_distance.cpp - * \li + * \li * Nerve_GIC/CoordGIC.cpp - * \li + * \li * Nerve_GIC/FuncGIC.cpp - * \li + * \li * Nerve_GIC/Nerve.cpp - * \li + * \li * Nerve_GIC/VoronoiGIC.cpp * \li * Spatial_searching/example_spatial_searching.cpp @@ -122,7 +122,7 @@ make \endverbatim * Tangential_complex/example_basic.cpp * \li * Tangential_complex/example_with_perturb.cpp - * \li + * \li * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp * \li * Alpha_complex/alpha_complex_3d_persistence.cpp @@ -134,15 +134,15 @@ make \endverbatim * * The following examples/utilities require the Eigen and will not be * built if Eigen is not installed: - * \li + * \li * Alpha_complex/Alpha_complex_from_off.cpp - * \li + * \li * Alpha_complex/Alpha_complex_from_points.cpp * \li * Alpha_complex/alpha_complex_persistence.cpp * \li * Alpha_complex/alpha_complex_3d_persistence.cpp - * \li + * \li * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp * \li * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp @@ -179,27 +179,27 @@ 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 + * \li * Alpha_complex/Alpha_complex_from_off.cpp - * \li + * \li * Alpha_complex/Alpha_complex_from_points.cpp * \li * Alpha_complex/alpha_complex_3d_persistence.cpp * \li * Alpha_complex/alpha_complex_persistence.cpp - * \li + * \li * Bitmap_cubical_complex/cubical_complex_persistence.cpp - * \li + * \li * Bitmap_cubical_complex/periodic_cubical_complex_persistence.cpp - * \li + * \li * Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp - * \li + * \li * Nerve_GIC/CoordGIC.cpp - * \li + * \li * Nerve_GIC/FuncGIC.cpp - * \li + * \li * Nerve_GIC/Nerve.cpp - * \li + * \li * Nerve_GIC/VoronoiGIC.cpp * \li * Simplex_tree/simple_simplex_tree.cpp diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst index cb7700ce..35c344e3 100644 --- a/src/python/doc/installation.rst +++ b/src/python/doc/installation.rst @@ -359,7 +359,7 @@ Python Optimal Transport ------------------------ The :doc:`Wasserstein distance ` -module requires `POT `_, a library that provides +module requires `POT `_, a library that provides several solvers for optimization problems related to Optimal Transport. PyTorch -- cgit v1.2.3