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Diffstat (limited to 'src/common/doc/main_page.h')
| -rw-r--r-- | src/common/doc/main_page.h | 90 |
1 files changed, 74 insertions, 16 deletions
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index 1a2cb6ba..ca5a919c 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -28,6 +28,7 @@ <b>Author:</b> Vincent Rouvreau<br> <b>Introduced in:</b> GUDHI 1.3.0<br> <b>Copyright:</b> GPL v3<br> + <b>Requires:</b> \ref cgal ≥ 4.7.0 and \ref eigen3 </td> <td width="75%"> Alpha_complex is a simplicial complex constructed from the finite cells of a Delaunay Triangulation.<br> @@ -55,6 +56,24 @@ <b>User manual:</b> \ref cubical_complex - <b>Reference manual:</b> Gudhi::cubical_complex::Bitmap_cubical_complex </td> </tr> + \subsection RipsComplexDataStructure Rips complex + \image html "rips_complex_representation.png" "Rips complex representation" +<table border="0"> + <tr> + <td width="25%"> + <b>Author:</b> Clément Maria, Pawel Dlotko, Vincent Rouvreau<br> + <b>Introduced in:</b> GUDHI 1.4.0<br> + <b>Copyright:</b> GPL v3<br> + </td> + <td width="75%"> + Rips_complex is a simplicial complex constructed from a one skeleton graph.<br> + The filtration value of each edge is computed from a user-given distance function and is inserted until a + user-given threshold value.<br> + This complex can be built from a point cloud and a distance function, or from a distance matrix.<br> + <b>User manual:</b> \ref rips_complex - <b>Reference manual:</b> Gudhi::rips_complex::Rips_complex + </td> + </tr> +</table> </table> \subsection SimplexTreeDataStructure Simplex tree \image html "Simplex_tree_representation.png" "Simplex tree representation" @@ -130,6 +149,26 @@ </table> \section Toolbox Toolbox + \subsection BottleneckDistanceToolbox Bottleneck distance + \image html "perturb_pd.png" "Bottleneck distance is the length of the longest edge" +<table border="0"> + <tr> + <td width="25%"> + <b>Author:</b> François Godi<br> + <b>Introduced in:</b> GUDHI 1.4.0<br> + <b>Copyright:</b> GPL v3<br> + <b>Requires:</b> \ref cgal ≥ 4.8.0 and \ref eigen3 + </td> + <td width="75%"> + Bottleneck distance measures the similarity between two persistence diagrams. + It's the shortest distance b for which there exists a perfect matching between + the points of the two diagrams (+ all the diagonal points) such that + any couple of matched points are at distance at most b. + <br> + <b>User manual:</b> \ref bottleneck_distance + </td> + </tr> +</table> \subsection ContractionToolbox Contraction \image html "sphere_contraction_representation.png" "Sphere contraction example" <table border="0"> @@ -196,24 +235,22 @@ make \endverbatim * \verbatim make test \endverbatim * * \section optionallibrary Optional third-party library - * \subsection gmp GMP: + * \subsection gmp GMP * The multi-field persistent homology algorithm requires GMP which is a free library for arbitrary-precision * arithmetic, operating on signed integers, rational numbers, and floating point numbers. * * The following example requires the <a target="_blank" href="http://gmplib.org/">GNU Multiple Precision Arithmetic * Library</a> (GMP) and will not be built if GMP is not installed: - * \li <a href="_persistent_cohomology_2performance_rips_persistence_8cpp-example.html"> - * Persistent_cohomology/performance_rips_persistence.cpp</a> * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html"> * Persistent_cohomology/rips_multifield_persistence.cpp</a> * * Having GMP version 4.2 or higher installed is recommended. * - * \subsection cgal CGAL: - * The \ref alpha_complex data structure and few examples requires CGAL, which is a C++ library which provides easy - * access to efficient and reliable geometric algorithms. + * \subsection cgal CGAL + * The \ref alpha_complex data structure, \ref bottleneck_distance, and few examples requires CGAL, which is a C++ + * library which provides easy access to efficient and reliable geometric algorithms. * - * Having CGAL version 4.4 or higher installed is recommended. The procedure to install this library according to + * Having CGAL version 4.4.0 or higher installed is recommended. The procedure to install this library according to * your operating system is detailed here http://doc.cgal.org/latest/Manual/installation.html * * The following examples require the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms @@ -223,11 +260,11 @@ make \endverbatim * \li <a href="_simplex_tree_2example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html"> * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a> * - * The following example requires CGAL version ≥ 4.6: + * The following example requires CGAL version ≥ 4.6.0: * \li <a href="_witness_complex_2witness_complex_sphere_8cpp-example.html"> * Witness_complex/witness_complex_sphere.cpp</a> * - * The following example requires CGAL version ≥ 4.7: + * The following example requires CGAL version ≥ 4.7.0: * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html"> * Alpha_complex/Alpha_complex_from_off.cpp</a> * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html"> @@ -239,7 +276,13 @@ make \endverbatim * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> * Persistent_cohomology/custom_persistence_sort.cpp</a> * - * \subsection eigen3 Eigen3: + * The following example requires CGAL version ≥ 4.8.0: + * \li <a href="_bottleneck_distance_2_bottleneck_basic_example_8cpp-example.html"> + * Bottleneck_distance/bottleneck_basic_example.cpp</a> + * \li <a href="_bottleneck_distance_2_bottleneck_read_file_example_8cpp-example.html"> + * Bottleneck_distance/bottleneck_read_file_example.cpp</a> + * + * \subsection eigen3 Eigen3 * The \ref alpha_complex data structure and few examples requires * <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen3</a> is a C++ template library for linear algebra: * matrices, vectors, numerical solvers, and related algorithms. @@ -247,9 +290,13 @@ make \endverbatim * The following example requires the <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen3</a> and will not be * built if Eigen3 is not installed: * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html"> - * Alpha_complex/Alpha_complex_from_off.cpp</a> (requires also Eigen3) + * Alpha_complex/Alpha_complex_from_off.cpp</a> * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html"> - * Alpha_complex/Alpha_complex_from_points.cpp</a> (requires also Eigen3) + * Alpha_complex/Alpha_complex_from_points.cpp</a> + * \li <a href="_bottleneck_distance_2_bottleneck_basic_example_8cpp-example.html"> + * Bottleneck_distance/bottleneck_basic_example.cpp</a> + * \li <a href="_bottleneck_distance_2_bottleneck_read_file_example_8cpp-example.html"> + * Bottleneck_distance/bottleneck_read_file_example.cpp</a> * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html"> * Persistent_cohomology/alpha_complex_persistence.cpp</a> * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> @@ -257,7 +304,7 @@ make \endverbatim * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> * Persistent_cohomology/custom_persistence_sort.cpp</a> * - * \subsection tbb Threading Building Blocks: + * \subsection tbb Threading Building Blocks * <a target="_blank" href="https://www.threadingbuildingblocks.org/">Intel® TBB</a> lets you easily write parallel * C++ programs that take full advantage of multicore performance, that are portable and composable, and that have * future-proof scalability. @@ -291,22 +338,28 @@ make \endverbatim * Persistent_cohomology/alpha_complex_persistence.cpp</a> * \li <a href="_persistent_cohomology_2rips_persistence_via_boundary_matrix_8cpp-example.html"> * Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp</a> - * \li <a href="_persistent_cohomology_2performance_rips_persistence_8cpp-example.html"> - * Persistent_cohomology/performance_rips_persistence.cpp</a> * \li <a href="_persistent_cohomology_2persistence_from_file_8cpp-example.html"> * Persistent_cohomology/persistence_from_file.cpp</a> * \li <a href="_persistent_cohomology_2persistence_from_simple_simplex_tree_8cpp-example.html"> * Persistent_cohomology/persistence_from_simple_simplex_tree.cpp</a> * \li <a href="_persistent_cohomology_2plain_homology_8cpp-example.html"> * Persistent_cohomology/plain_homology.cpp</a> + * \li <a href="_persistent_cohomology_2rips_distance_matrix_persistence_8cpp-example.html"> + * Persistent_cohomology/rips_distance_matrix_persistence.cpp</a> * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html"> * Persistent_cohomology/rips_multifield_persistence.cpp</a> * \li <a href="_persistent_cohomology_2rips_persistence_8cpp-example.html"> * Persistent_cohomology/rips_persistence.cpp</a> + * \li <a href="_persistent_cohomology_2rips_persistence_step_by_step_8cpp-example.html"> + * Persistent_cohomology/rips_persistence_step_by_step.cpp</a> * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a> * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> * Persistent_cohomology/custom_persistence_sort.cpp</a> + * \li <a href="_rips_complex_2example_one_skeleton_rips_from_points_8cpp-example.html"> + * Rips_complex/example_one_skeleton_rips_from_points.cpp</a> + * \li <a href="_rips_complex_2example_rips_complex_from_off_file_8cpp-example.html"> + * Rips_complex/example_rips_complex_from_off_file.cpp</a> * * \section Contributions Bug reports and contributions * Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to: @@ -331,6 +384,8 @@ make \endverbatim /*! @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/bottleneck_read_file_example.cpp * @example Bitmap_cubical_complex/Bitmap_cubical_complex.cpp * @example Bitmap_cubical_complex/Bitmap_cubical_complex_periodic_boundary_conditions.cpp * @example Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp @@ -341,14 +396,17 @@ make \endverbatim * @example Persistent_cohomology/alpha_complex_3d_persistence.cpp * @example Persistent_cohomology/alpha_complex_persistence.cpp * @example Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp - * @example Persistent_cohomology/performance_rips_persistence.cpp * @example Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp * @example Persistent_cohomology/persistence_from_file.cpp * @example Persistent_cohomology/persistence_from_simple_simplex_tree.cpp * @example Persistent_cohomology/plain_homology.cpp * @example Persistent_cohomology/rips_multifield_persistence.cpp + * @example Persistent_cohomology/rips_distance_matrix_persistence.cpp * @example Persistent_cohomology/rips_persistence.cpp * @example Persistent_cohomology/custom_persistence_sort.cpp + * @example Persistent_cohomology/rips_persistence_step_by_step.cpp + * @example Rips_complex/example_one_skeleton_rips_from_points.cpp + * @example Rips_complex/example_rips_complex_from_off_file.cpp * @example Simplex_tree/mini_simplex_tree.cpp * @example Simplex_tree/simple_simplex_tree.cpp * @example Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp |