diff options
author | albert-github <albert.tests@gmail.com> | 2022-05-23 13:25:06 +0200 |
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committer | albert-github <albert.tests@gmail.com> | 2022-05-23 13:25:06 +0200 |
commit | 298ae783896d7a9fee43b58a3a01041c9106962c (patch) | |
tree | 9b40b9f896984166b80b3d8682513f19e0bf859f /src | |
parent | f043cf8aaf676cc88e84082de49f70dd3492ecb0 (diff) |
Documentation: handling references to examples in a more transparent way
Adding the other examples also with `gudhi_example_link`.
Diffstat (limited to 'src')
-rw-r--r-- | src/Cech_complex/doc/Intro_cech_complex.h | 5 | ||||
-rw-r--r-- | src/Persistent_cohomology/doc/Intro_persistent_cohomology.h | 21 | ||||
-rw-r--r-- | src/Rips_complex/doc/Intro_rips_complex.h | 5 | ||||
-rw-r--r-- | src/Simplex_tree/doc/Intro_simplex_tree.h | 12 | ||||
-rw-r--r-- | src/common/doc/installation.h | 3 |
5 files changed, 16 insertions, 30 deletions
diff --git a/src/Cech_complex/doc/Intro_cech_complex.h b/src/Cech_complex/doc/Intro_cech_complex.h index 698f9749..095fd320 100644 --- a/src/Cech_complex/doc/Intro_cech_complex.h +++ b/src/Cech_complex/doc/Intro_cech_complex.h @@ -70,9 +70,8 @@ namespace cech_complex { * This radius computation is the reason why the Cech_complex is taking much more time to be computed than the * \ref rips_complex but it offers more topological guarantees. * - * If the Cech_complex interfaces are not detailed enough for your need, please refer to - * <a href="cech_complex_step_by_step_8cpp-example.html"> - * cech_complex_step_by_step.cpp</a> example, where the graph construction over the Simplex_tree is more detailed. + * If the Cech_complex interfaces are not detailed enough for your need, please refer to the example + * \gudhi_example_link{Cech_complex,cech_complex_step_by_step.cpp}, where the graph construction over the Simplex_tree is more detailed. * * \subsection cechpointscloudexample Example from a point cloud * diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h index a3613d0d..94579564 100644 --- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h +++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h @@ -131,8 +131,7 @@ namespace persistent_cohomology { We provide several example files: run these examples with -h for details on their use, and read the README file. -\li <a href="rips_persistence_8cpp-example.html"> -Rips_complex/rips_persistence.cpp</a> computes the Rips complex of a point cloud and outputs its persistence +\li \gudhi_example_link{Rips_complex,rips_persistence.cpp} computes the Rips complex of a point cloud and outputs its persistence diagram. \code $> ./rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3 \endcode \code The complex contains 177838 simplices @@ -144,12 +143,10 @@ diagram. More details on the <a href="../../ripscomplex/">Rips complex utilities</a> dedicated page. -\li <a href="rips_multifield_persistence_8cpp-example.html"> -Persistent_cohomology/rips_multifield_persistence.cpp</a> computes the Rips complex of a point cloud and outputs its +\li \gudhi_example_link{Persistent_cohomology,rips_multifield_persistence.cpp} computes the Rips complex of a point cloud and outputs its persistence diagram with a family of field coefficients. -\li <a href="rips_distance_matrix_persistence_8cpp-example.html"> -Rips_complex/rips_distance_matrix_persistence.cpp</a> computes the Rips complex of a distance matrix and +\li \gudhi_example_link{Rips_complex,rips_distance_matrix_persistence.cpp} computes the Rips complex of a distance matrix and outputs its persistence diagram. The file should contain square or lower triangular distance matrix with semicolons as separators. @@ -158,8 +155,7 @@ Please refer to data/distance_matrix/lower_triangular_distance_matrix.csv for an More details on the <a href="../../ripscomplex/">Rips complex utilities</a> dedicated page. -\li <a href="rips_correlation_matrix_persistence_8cpp-example.html"> -Rips_complex/rips_correlation_matrix_persistence.cpp</a> +\li \gudhi_example_link{Rips_complex,rips_correlation_matrix_persistence.cpp} computes the Rips complex of a correlation matrix and outputs its persistence diagram. Note that no check is performed if the matrix given as the input is a correlation matrix. @@ -169,8 +165,7 @@ Please refer to data/correlation_matrix/lower_triangular_correlation_matrix.csv More details on the <a href="../../ripscomplex/">Rips complex utilities</a> dedicated page. -\li <a href="alpha_complex_3d_persistence_8cpp-example.html"> -Alpha_complex/alpha_complex_3d_persistence.cpp</a> computes the persistent homology with +\li \gudhi_example_link{Alpha_complex,alpha_complex_3d_persistence.cpp} computes the persistent homology with \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file. \code $> ./alpha_complex_3d_persistence ../../data/points/tore3D_300.off -p 2 -m 0.45 \endcode \code Simplex_tree dim: 3 @@ -235,8 +230,7 @@ Note that the lengths of the sides of the periodic cuboid have to be the same.<b 3 2 36.8838 inf 3 3 58.6783 inf \endcode -\li <a href="alpha_complex_persistence_8cpp-example.html"> -Alpha_complex/alpha_complex_persistence.cpp</a> computes the persistent homology with +\li \gudhi_example_link{Alpha_complex,alpha_complex_persistence.cpp} computes the persistent homology with \f$\mathbb{Z}/p\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file. \code $> ./alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off \endcode \code Alpha complex is of dimension 3 - 9273 simplices - 300 vertices. @@ -248,8 +242,7 @@ Simplex_tree dim: 3 More details on the <a href="../../alphacomplex/">Alpha complex utilities</a> dedicated page. -\li <a href="plain_homology_8cpp-example.html"> -Persistent_cohomology/plain_homology.cpp</a> computes the plain homology of a simple simplicial complex without +\li \gudhi_example_link{Persistent_cohomology,plain_homology.cpp} computes the plain homology of a simple simplicial complex without filtration values. */ diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h index 3888ec8f..cd77b327 100644 --- a/src/Rips_complex/doc/Intro_rips_complex.h +++ b/src/Rips_complex/doc/Intro_rips_complex.h @@ -63,9 +63,8 @@ namespace rips_complex { * value set with \f$max(filtration(4,5), filtration(4,6), filtration(5,6))\f$. * And so on for simplex (0,1,2,3). * - * If the Rips_complex interfaces are not detailed enough for your need, please refer to - * <a href="rips_persistence_step_by_step_8cpp-example.html"> - * rips_persistence_step_by_step.cpp</a> example, where the constructions of the graph and + * If the Rips_complex interfaces are not detailed enough for your need, please refer to the example + * \gudhi_example_link{Persistent_cohomology,rips_persistence_step_by_step.cpp} , where the constructions of the graph and * the Simplex_tree are more detailed. * * \section sparserips Sparse Rips complex diff --git a/src/Simplex_tree/doc/Intro_simplex_tree.h b/src/Simplex_tree/doc/Intro_simplex_tree.h index ef8dec91..2d3ecdec 100644 --- a/src/Simplex_tree/doc/Intro_simplex_tree.h +++ b/src/Simplex_tree/doc/Intro_simplex_tree.h @@ -39,11 +39,9 @@ namespace Gudhi { * \subsubsection filteredcomplexessimplextreeexamples Examples * * Here is a list of simplex tree examples : - * \li <a href="simple_simplex_tree_8cpp-example.html"> - * Simplex_tree/simple_simplex_tree.cpp</a> - Simple simplex tree construction and basic function use. + * \li \gudhi_example_link{Simplex_tree,simple_simplex_tree.cpp} - Simple simplex tree construction and basic function use. * - * \li <a href="simplex_tree_from_cliques_of_graph_8cpp-example.html"> - * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp</a> - Simplex tree construction from cliques of graph read in + * \li \gudhi_example_link{Simplex_tree,simplex_tree_from_cliques_of_graph.cpp} - Simplex tree construction from cliques of graph read in * a file. * * Simplex tree construction with \f$\mathbb{Z}/3\mathbb{Z}\f$ coefficients on weighted graph Klein bottle file: @@ -54,12 +52,10 @@ Expand the simplex tree in 3.8e-05 s. Information of the Simplex Tree: Number of vertices = 10 Number of simplices = 98 \endcode * - * \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> - Simplex tree is computed and displayed + * \li \gudhi_example_link{Simplex_tree,example_alpha_shapes_3_simplex_tree_from_off_file.cpp} - Simplex tree is computed and displayed * from a 3D alpha complex (Requires CGAL, GMP and GMPXX to be installed). * - * \li <a href="graph_expansion_with_blocker_8cpp-example.html"> - * Simplex_tree/graph_expansion_with_blocker.cpp</a> - Simple simplex tree construction from a one-skeleton graph with + * \li \gudhi_example_link{Simplex_tree,graph_expansion_with_blocker.cpp} - Simple simplex tree construction from a one-skeleton graph with * a simple blocker expansion method. * * \subsection filteredcomplexeshassecomplex Hasse complex diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index fb5ee665..e786f53a 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -58,8 +58,7 @@ make \endverbatim * * 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="rips_multifield_persistence_8cpp-example.html"> - * Persistent_cohomology/rips_multifield_persistence.cpp</a> + * \li \gudhi_example_link{Persistent_cohomology,rips_multifield_persistence.cpp} * * Having GMP version 4.2 or higher installed is recommended. * |