From 5db457afb8e3214bdd83bef51198b65e53267a8c Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Wed, 23 Sep 2020 10:12:22 +0200 Subject: Add coxeter on main page --- src/common/doc/main_page.md | 28 +++++++++++++++++++++++++++- 1 file changed, 27 insertions(+), 1 deletion(-) (limited to 'src/common/doc') diff --git a/src/common/doc/main_page.md b/src/common/doc/main_page.md index e19af537..c58b6994 100644 --- a/src/common/doc/main_page.md +++ b/src/common/doc/main_page.md @@ -135,7 +135,7 @@ -## Filtrations and reconstructions {#FiltrationsReconstructions} +## Filtrations ### Alpha complex @@ -298,6 +298,32 @@
+## Manifold reconstructions +### Coxeter triangulation + + + + + + + + + + +
+ \image html "manifold_tracing_on_custom_function_example.png" + + 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. + + Author: Siargey Kachanovich
+ Introduced in: GUDHI 3.4.0
+ Copyright: MIT [(LGPL v3)](../../licensing/)
+ Requires: \ref cgal ≥ 4.11.0 +
+ User manual: \ref coxeter_triangulation +
+ ### Tangential complex -- cgit v1.2.3 From 29fa56b6768d7314fcddf39d7681aa6a82417b4e Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Wed, 21 Apr 2021 10:08:19 +0200 Subject: cell complex is only for coxeter. eigen is required for coxeter, not cgal --- src/Coxeter_triangulation/doc/intro_coxeter_triangulation.h | 5 +++++ src/Coxeter_triangulation/include/gudhi/Cell_complex.h | 10 +++------- src/common/doc/main_page.md | 2 +- 3 files changed, 9 insertions(+), 8 deletions(-) (limited to 'src/common/doc') diff --git a/src/Coxeter_triangulation/doc/intro_coxeter_triangulation.h b/src/Coxeter_triangulation/doc/intro_coxeter_triangulation.h index 3316bd81..99239e3a 100644 --- a/src/Coxeter_triangulation/doc/intro_coxeter_triangulation.h +++ b/src/Coxeter_triangulation/doc/intro_coxeter_triangulation.h @@ -166,6 +166,8 @@ The base function classes above can be composed or modified into new functions u The type of \f$T\f$ is required to be a model of the concept \ref Gudhi::coxeter_triangulation::TriangulationForManifoldTracing "TriangulationForManifoldTracing". +It is also possible to implement your own function as detailed in this \ref exampleswithcustomfunction. + \section cellcomplex Cell complex construction The output of the manifold tracing algorithm can be transformed into the Hasse diagram of a cell complex that @@ -194,6 +196,9 @@ triangulation. \li The method \ref Gudhi::coxeter_triangulation::Cell_complex::cell_point_map() "cell_point_map()" returns a map from the vertex cells in the cell complex to their Cartesian coordinates. +The use and interfaces of this \ref Gudhi::coxeter_triangulation::Cell_complex "Cell_complex" is limited to the +Coxeter_triangulation implementation. + \section example Examples \subsection examplewithoutboundaries Basic example without boundaries diff --git a/src/Coxeter_triangulation/include/gudhi/Cell_complex.h b/src/Coxeter_triangulation/include/gudhi/Cell_complex.h index b386e369..219f525b 100644 --- a/src/Coxeter_triangulation/include/gudhi/Cell_complex.h +++ b/src/Coxeter_triangulation/include/gudhi/Cell_complex.h @@ -25,18 +25,14 @@ namespace Gudhi { namespace coxeter_triangulation { -/** - * \ingroup coxeter_triangulation - */ - /** \class Cell_complex * \brief A class that constructs the cell complex from the output provided by the class - * Gudhi::Manifold_tracing. + * \ref Gudhi::coxeter_triangulation::Manifold_tracing. + * + * The use and interfaces of this cell complex is limited to the \ref coxeter_triangulation implementation. * * \tparam Out_simplex_map_ The type of a map from a simplex type that is a * model of SimplexInCoxeterTriangulation to Eigen::VectorXd. - * - * \ingroup coxeter_triangulation */ template class Cell_complex { diff --git a/src/common/doc/main_page.md b/src/common/doc/main_page.md index c58b6994..17354179 100644 --- a/src/common/doc/main_page.md +++ b/src/common/doc/main_page.md @@ -314,7 +314,7 @@ Author: Siargey Kachanovich
Introduced in: GUDHI 3.4.0
Copyright: MIT [(LGPL v3)](../../licensing/)
- Requires: \ref cgal ≥ 4.11.0 + Requires: \ref eigen ≥ 3.1.0 -- cgit v1.2.3 From 1d7011f32573bb617894a3f263e2537c1f3a8649 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 22 Apr 2021 09:28:45 +0200 Subject: Add examples in doc and removes TBB link as not required by coxeter --- src/Coxeter_triangulation/example/CMakeLists.txt | 9 --------- src/Coxeter_triangulation/test/CMakeLists.txt | 3 --- src/common/doc/examples.h | 3 +++ src/common/doc/installation.h | 8 ++++++++ 4 files changed, 11 insertions(+), 12 deletions(-) (limited to 'src/common/doc') diff --git a/src/Coxeter_triangulation/example/CMakeLists.txt b/src/Coxeter_triangulation/example/CMakeLists.txt index 840e24e4..7f81c599 100644 --- a/src/Coxeter_triangulation/example/CMakeLists.txt +++ b/src/Coxeter_triangulation/example/CMakeLists.txt @@ -5,24 +5,15 @@ if (NOT EIGEN3_VERSION VERSION_LESS 3.1.0) if (NOT CGAL_VERSION VERSION_LESS 4.11.0) add_executable ( Coxeter_triangulation_manifold_tracing_flat_torus_with_boundary_example manifold_tracing_flat_torus_with_boundary.cpp ) target_link_libraries(Coxeter_triangulation_manifold_tracing_flat_torus_with_boundary_example ${CGAL_LIBRARY}) - if (TBB_FOUND) - target_link_libraries(Coxeter_triangulation_manifold_tracing_flat_torus_with_boundary_example ${TBB_LIBRARIES}) - endif() add_test(NAME Coxeter_triangulation_manifold_tracing_flat_torus_with_boundary_example COMMAND $) endif() add_executable ( Coxeter_triangulation_manifold_tracing_custom_function_example manifold_tracing_custom_function.cpp ) - if (TBB_FOUND) - target_link_libraries(Coxeter_triangulation_manifold_tracing_custom_function_example ${TBB_LIBRARIES}) - endif() add_test(NAME Coxeter_triangulation_manifold_tracing_custom_function_example COMMAND $) add_executable ( Coxeter_triangulation_cell_complex_from_basic_circle_manifold_example cell_complex_from_basic_circle_manifold.cpp ) - if (TBB_FOUND) - target_link_libraries(Coxeter_triangulation_cell_complex_from_basic_circle_manifold_example ${TBB_LIBRARIES}) - endif() add_test(NAME Coxeter_triangulation_cell_complex_from_basic_circle_manifold_example COMMAND $) endif() \ No newline at end of file diff --git a/src/Coxeter_triangulation/test/CMakeLists.txt b/src/Coxeter_triangulation/test/CMakeLists.txt index 3da2410f..74ded91e 100644 --- a/src/Coxeter_triangulation/test/CMakeLists.txt +++ b/src/Coxeter_triangulation/test/CMakeLists.txt @@ -26,8 +26,5 @@ if (NOT EIGEN3_VERSION VERSION_LESS 3.1.0) gudhi_add_boost_test(Coxeter_triangulation_manifold_tracing_test) add_executable ( Coxeter_triangulation_cell_complex_test cell_complex_test.cpp ) - if (TBB_FOUND) - target_link_libraries(Coxeter_triangulation_cell_complex_test ${TBB_LIBRARIES}) - endif() gudhi_add_boost_test(Coxeter_triangulation_cell_complex_test) endif() \ No newline at end of file diff --git a/src/common/doc/examples.h b/src/common/doc/examples.h index 474f8699..a8548f6a 100644 --- a/src/common/doc/examples.h +++ b/src/common/doc/examples.h @@ -92,5 +92,8 @@ * @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 + * @example Coxeter_triangulation/cell_complex_from_basic_circle_manifold.cpp + * @example Coxeter_triangulation/manifold_tracing_custom_function.cpp + * @example Coxeter_triangulation/manifold_tracing_flat_torus_with_boundary.cpp */ diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index c2e63a24..c0e36a59 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -125,6 +125,8 @@ make doxygen * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp * \li * Alpha_complex/alpha_complex_3d_persistence.cpp + * \li + * Coxeter_triangulation/manifold_tracing_flat_torus_with_boundary.cpp * * \subsection eigen Eigen * Some GUDHI modules (cf. \ref main_page "modules list"), and few examples require @@ -169,6 +171,12 @@ make doxygen * Witness_complex/example_witness_complex_off.cpp * \li * Witness_complex/example_witness_complex_sphere.cpp + * \li + * Coxeter_triangulation/cell_complex_from_basic_circle_manifold.cpp + * \li + * Coxeter_triangulation/manifold_tracing_custom_function.cpp + * \li + * Coxeter_triangulation/manifold_tracing_flat_torus_with_boundary.cpp * * \subsection tbb Threading Building Blocks * Intel® TBB lets you easily write parallel -- cgit v1.2.3 From c0cca8dbd60e3da5147517f6f8f37d9bdeefe511 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Fri, 25 Jun 2021 16:26:55 +0200 Subject: update headers, conf.py for the new theme and bottleneck image to be smaller --- src/Bottleneck_distance/doc/perturb_pd.png | Bin 20864 -> 15532 bytes src/common/doc/header.html | 1 + src/python/doc/_templates/layout.html | 1 + src/python/doc/conf.py | 3 --- 4 files changed, 2 insertions(+), 3 deletions(-) (limited to 'src/common/doc') diff --git a/src/Bottleneck_distance/doc/perturb_pd.png b/src/Bottleneck_distance/doc/perturb_pd.png index be638de0..eabf3c8c 100644 Binary files a/src/Bottleneck_distance/doc/perturb_pd.png and b/src/Bottleneck_distance/doc/perturb_pd.png differ 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
  • Related projects
  • They are talking about us
  • GUDHI in action
    • +
  • Etymology
  • diff --git a/src/python/doc/_templates/layout.html b/src/python/doc/_templates/layout.html index cd40a51b..e074b6c7 100644 --- a/src/python/doc/_templates/layout.html +++ b/src/python/doc/_templates/layout.html @@ -194,6 +194,7 @@
  • Related projects
  • They are talking about us
  • GUDHI in action
    • +
  • Etymology
  • diff --git a/src/python/doc/conf.py b/src/python/doc/conf.py index 46debd87..e69e2751 100755 --- a/src/python/doc/conf.py +++ b/src/python/doc/conf.py @@ -126,9 +126,6 @@ html_theme = 'python_docs_theme' # further. For a list of options available for each theme, see the # documentation. html_theme_options = { - "sidebarbgcolor": "#A1ADCD", - "sidebartextcolor": "black", - "sidebarlinkcolor": "#334D5C", "body_max_width": "100%", } -- cgit v1.2.3 From a91e3bc16d511ef66bb296da6a990a0723100657 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 5 Aug 2021 18:00:40 +0200 Subject: mailing lists migration and rephrase contributions in installation guides --- .github/for_maintainers/new_gudhi_version_creation.md | 4 ++-- src/common/doc/installation.h | 8 +++++--- src/python/doc/installation.rst | 9 +++++---- src/python/setup.py.in | 2 +- 4 files changed, 13 insertions(+), 10 deletions(-) (limited to 'src/common/doc') diff --git a/.github/for_maintainers/new_gudhi_version_creation.md b/.github/for_maintainers/new_gudhi_version_creation.md index d6c4cdd3..3e5295c5 100644 --- a/.github/for_maintainers/new_gudhi_version_creation.md +++ b/.github/for_maintainers/new_gudhi_version_creation.md @@ -128,5 +128,5 @@ docker image on docker hub. ## Mail sending Send version mail to the following lists : -* gudhi-devel@lists.gforge.inria.fr -* gudhi-users@lists.gforge.inria.fr (not for release candidate) +* gudhi-devel@inria.fr +* gudhi-users@inria.fr (not for release candidate) diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index 610aa17e..5d40a48e 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -243,10 +243,12 @@ make \endverbatim * Witness_complex/example_nearest_landmark_table.cpp * * \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 report bugs or + * contact us 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 + * contributing guide. * */ diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst index 9c16b04e..56f27b21 100644 --- a/src/python/doc/installation.rst +++ b/src/python/doc/installation.rst @@ -396,8 +396,9 @@ TensorFlow Bug reports and contributions ***************************** -Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to: +Please help us improving the quality of the GUDHI library. +You may `report bugs `_ or +`contact us `_ for any suggestions. - Contact: gudhi-users@lists.gforge.inria.fr - -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 +`contributing guide `_. diff --git a/src/python/setup.py.in b/src/python/setup.py.in index 759ec8d8..c400b601 100644 --- a/src/python/setup.py.in +++ b/src/python/setup.py.in @@ -71,7 +71,7 @@ setup( name = 'gudhi', packages=find_packages(), # find_namespace_packages(include=["gudhi*"]) author='GUDHI Editorial Board', - author_email='gudhi-contact@lists.gforge.inria.fr', + author_email='gudhi-contact@inria.fr', version='@GUDHI_VERSION@', url='https://gudhi.inria.fr/', project_urls={ -- cgit v1.2.3 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 (limited to 'src/common/doc') 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