diff options
Diffstat (limited to 'src/common/doc')
-rw-r--r-- | src/common/doc/examples.h | 5 | ||||
-rw-r--r-- | src/common/doc/file_formats.h | 6 | ||||
-rw-r--r-- | src/common/doc/installation.h | 34 | ||||
-rw-r--r-- | src/common/doc/main_page.h | 24 |
4 files changed, 40 insertions, 29 deletions
diff --git a/src/common/doc/examples.h b/src/common/doc/examples.h index 40f202c7..c19b3444 100644 --- a/src/common/doc/examples.h +++ b/src/common/doc/examples.h @@ -53,10 +53,7 @@ * @example Spatial_searching/example_spatial_searching.cpp * @example Alpha_complex/alpha_complex_3d_persistence.cpp * @example Alpha_complex/alpha_complex_persistence.cpp - * @example Alpha_complex/weighted_periodic_alpha_complex_3d_persistence.cpp - * @example Alpha_complex/weighted_alpha_complex_3d_persistence.cpp - * @example Alpha_complex/periodic_alpha_complex_3d_persistence.cpp - * @example Alpha_complex/exact_alpha_complex_3d_persistence.cpp + * @example Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp * @example Bottleneck_distance/bottleneck_distance.cpp * @example Witness_complex/weak_witness_persistence.cpp * @example Witness_complex/strong_witness_persistence.cpp diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h index 523153b8..23214e25 100644 --- a/src/common/doc/file_formats.h +++ b/src/common/doc/file_formats.h @@ -72,7 +72,7 @@ namespace Gudhi { \section FileFormatsPerseus Perseus - This file format is the format used by the Perseus software + This file format is a format inspired from the Perseus software (http://www.sas.upenn.edu/~vnanda/perseus/) by Vidit Nanda. The first line contains a number d begin the dimension of the bitmap (2 in the example below). Next d lines are the numbers of top dimensional cubes in each dimensions (3 and 3 @@ -118,6 +118,10 @@ namespace Gudhi { Indicate that we have imposed periodic boundary conditions in the direction x, but not in the direction y. Other sample files can be found in the `data/bitmap` folder. + + \note Unlike in Perseus format the filtration on the maximal cubes can be any double precision number. + Consequently one cannot mark the cubes that are not present with `-1`'s. To do that please set their filtration value + to \f$+\infty\f$ (aka. `inf` in the file). */ } // namespace Gudhi diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index c27e4f56..8fb8b330 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -5,7 +5,7 @@ * Examples of GUDHI headers inclusion can be found in \ref utilities. * * \section compiling Compiling - * The library uses c++11 and requires <a target="_blank" href="http://www.boost.org/">Boost</a> ≥ 1.48.0 + * The library uses c++11 and requires <a target="_blank" href="http://www.boost.org/">Boost</a> ≥ 1.56.0 * and <a target="_blank" href="https://www.cmake.org/">CMake</a> ≥ 3.1. * It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015. * @@ -18,7 +18,7 @@ cmake .. make \endverbatim * By default, examples are disabled. You can activate their compilation with * <a href="https://cmake.org/cmake/help/v3.0/manual/ccmake.1.html">ccmake</a> (on Linux and Mac OSX), - * <a href="https://cmake.org/cmake/help/v3.0/manual/cmake-gui.1.html">cmake-gui</a> (on Windows) or y mofifying the + * <a href="https://cmake.org/cmake/help/v3.0/manual/cmake-gui.1.html">cmake-gui</a> (on Windows) or by modifying the * cmake command as follows : \verbatim cmake -DWITH_GUDHI_EXAMPLE=ON .. make \endverbatim @@ -72,12 +72,6 @@ make doxygen * * The following examples/utilities require the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms * Library</a> (CGAL \cite cgal:eb-15b) and will not be built if CGAL is not installed: - * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/alpha_complex_3d_persistence.cpp</a> - * \li <a href="_alpha_complex_2exact_alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/exact_alpha_complex_3d_persistence.cpp</a> - * \li <a href="_alpha_complex_2weighted_alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/weighted_alpha_complex_3d_persistence.cpp</a> * \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> * @@ -100,8 +94,6 @@ make doxygen * Alpha_complex/Alpha_complex_from_points.cpp</a> * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html"> * Alpha_complex/alpha_complex_persistence.cpp</a> - * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/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> * @@ -135,6 +127,12 @@ make doxygen * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html"> * Tangential_complex/example_with_perturb.cpp</a> * + * The following example requires CGAL version ≥ 4.11.0: + * \li <a href="_alpha_complex_2_weighted_alpha_complex_3d_from_points_8cpp-example.html"> + * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp</a> + * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/alpha_complex_3d_persistence.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: @@ -148,8 +146,10 @@ make doxygen * Alpha_complex/Alpha_complex_from_points.cpp</a> * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html"> * Alpha_complex/alpha_complex_persistence.cpp</a> - * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/alpha_complex_3d_persistence.cpp</a> + * \li <a href="_alpha_complex_2_weighted_alpha_complex_3d_from_points_8cpp-example.html"> + * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp</a> * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html"> * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a> * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> @@ -195,12 +195,6 @@ make doxygen * Alpha_complex/alpha_complex_3d_persistence.cpp</a> * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html"> * Alpha_complex/alpha_complex_persistence.cpp</a> - * \li <a href="_alpha_complex_2exact_alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/exact_alpha_complex_3d_persistence.cpp</a> - * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a> - * \li <a href="_alpha_complex_2weighted_alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/weighted_alpha_complex_3d_persistence.cpp</a> * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_8cpp-example.html"> * Bitmap_cubical_complex/cubical_complex_persistence.cpp</a> * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_periodic_boundary_conditions_8cpp-example.html"> @@ -239,10 +233,6 @@ make doxygen * Persistent_cohomology/rips_multifield_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_2exact_alpha_complex_3d_persistence_8cpp-example.html"> - * Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2weighted_alpha_complex_3d_persistence_8cpp-example.html"> - * Persistent_cohomology/weighted_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"> diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index db1e80ce..afe9b68c 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -29,7 +29,9 @@ <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 + <b>Requires:</b> \ref eigen3 and<br> + \ref cgal ≥ 4.7.0 for Alpha_complex<br> + \ref cgal ≥ 4.11.0 for Alpha_complex_3d </td> <td width="75%"> Alpha_complex is a simplicial complex constructed from the finite cells of a Delaunay Triangulation.<br> @@ -38,7 +40,8 @@ values of the codimension 1 cofaces that make it not Gabriel otherwise. All simplices that have a filtration value strictly greater than a given alpha squared value are not inserted into the complex.<br> - <b>User manual:</b> \ref alpha_complex - <b>Reference manual:</b> Gudhi::alpha_complex::Alpha_complex + <b>User manual:</b> \ref alpha_complex - <b>Reference manual:</b> Gudhi::alpha_complex::Alpha_complex and + Gudhi::alpha_complex::Alpha_complex_3d </td> </tr> </table> @@ -168,6 +171,23 @@ </td> </tr> </table> + \subsection ToplexMapDataStructure Toplex Map + \image html "map.png" "Toplex map representation" +<table border="0"> + <tr> + <td width="25%"> + <b>Author:</b> François Godi<br> + <b>Introduced in:</b> GUDHI 2.1.0<br> + <b>Copyright:</b> GPL v3<br> + </td> + <td width="75%"> + The Toplex map data structure is composed firstly of a raw storage of toplices (the maximal simplices) + and secondly of a map which associate any vertex to a set of pointers toward all toplices + containing this vertex. + <b>User manual:</b> \ref toplex_map - <b>Reference manual:</b> Gudhi::Toplex_map + </td> + </tr> + \subsection WitnessComplexDataStructure Witness complex \image html "Witness_complex_representation.png" "Witness complex representation" <table border="0"> |