diff options
Diffstat (limited to 'src/Alpha_complex/include/gudhi/Alpha_complex.h')
| -rw-r--r-- | src/Alpha_complex/include/gudhi/Alpha_complex.h | 57 |
1 files changed, 44 insertions, 13 deletions
diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index 8919cdb9..6b4d8463 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -20,11 +20,12 @@ #include <math.h> // isnan, fmax #include <CGAL/Delaunay_triangulation.h> -#include <CGAL/Epick_d.h> +#include <CGAL/Epeck_d.h> // For EXACT or SAFE version +#include <CGAL/Epick_d.h> // For FAST version #include <CGAL/Spatial_sort_traits_adapter_d.h> #include <CGAL/property_map.h> // for CGAL::Identity_property_map -#include <CGAL/NT_converter.h> #include <CGAL/version.h> // for CGAL_VERSION_NR +#include <CGAL/NT_converter.h> #include <Eigen/src/Core/util/Macros.h> // for EIGEN_VERSION_AT_LEAST @@ -39,17 +40,20 @@ // Make compilation fail - required for external projects - https://github.com/GUDHI/gudhi-devel/issues/10 #if CGAL_VERSION_NR < 1041101000 -# error Alpha_complex_3d is only available for CGAL >= 4.11 +# error Alpha_complex is only available for CGAL >= 4.11 #endif #if !EIGEN_VERSION_AT_LEAST(3,1,0) -# error Alpha_complex_3d is only available for Eigen3 >= 3.1.0 installed with CGAL +# error Alpha_complex is only available for Eigen3 >= 3.1.0 installed with CGAL #endif namespace Gudhi { namespace alpha_complex { +template<typename D> struct Is_Epeck_D { static const bool value = false; }; +template<typename D> struct Is_Epeck_D<CGAL::Epeck_d<D>> { static const bool value = true; }; + /** * \class Alpha_complex Alpha_complex.h gudhi/Alpha_complex.h * \brief Alpha complex data structure. @@ -63,17 +67,31 @@ namespace alpha_complex { * * Please refer to \ref alpha_complex for examples. * - * The complex is a template class requiring an Epick_d <a target="_blank" + * The complex is a template class requiring an <a target="_blank" + * href="https://doc.cgal.org/latest/Kernel_d/structCGAL_1_1Epeck__d.html">CGAL::Epeck_d</a>, + * or an <a target="_blank" + * href="https://doc.cgal.org/latest/Kernel_d/structCGAL_1_1Epick__d.html">CGAL::Epick_d</a> <a target="_blank" * href="http://doc.cgal.org/latest/Kernel_d/index.html#Chapter_dD_Geometry_Kernel">dD Geometry Kernel</a> - * \cite cgal:s-gkd-15b from CGAL as template, default value is <a target="_blank" - * href="http://doc.cgal.org/latest/Kernel_d/classCGAL_1_1Epick__d.html">CGAL::Epick_d</a> + * \cite cgal:s-gkd-19b from CGAL as template, default value is <a target="_blank" + * href="https://doc.cgal.org/latest/Kernel_d/structCGAL_1_1Epeck__d.html">CGAL::Epeck_d</a> * < <a target="_blank" href="http://doc.cgal.org/latest/Kernel_23/classCGAL_1_1Dynamic__dimension__tag.html"> * CGAL::Dynamic_dimension_tag </a> > * - * \remark When Alpha_complex is constructed with an infinite value of alpha, the complex is a Delaunay complex. - * + * \remark + * - When Alpha_complex is constructed with an infinite value of alpha, the complex is a Delaunay complex. + * - Using the default `CGAL::Epeck_d` makes the construction safe. If you pass exact=true to create_complex, the + * filtration values are the exact ones converted to the filtration value type of the simplicial complex. This can be + * very slow. If you pass exact=false (the default), the filtration values are only guaranteed to have a small + * multiplicative error compared to the exact value, see <code><a class="el" target="_blank" + * href="https://doc.cgal.org/latest/Number_types/classCGAL_1_1Lazy__exact__nt.html"> + * CGAL::Lazy_exact_nt<NT>::set_relative_precision_of_to_double</a></code> for details. A drawback, when computing + * persistence, is that an empty exact interval [10^12,10^12] may become a non-empty approximate interval + * [10^12,10^12+10^6]. Using `CGAL::Epick_d` makes the computations slightly faster, and the combinatorics are still + * exact, but the computation of filtration values can exceptionally be arbitrarily bad. In all cases, we still + * guarantee that the output is a valid filtration (faces have a filtration value no larger than their cofaces). + * - For performances reasons, it is advised to use `Alpha_complex` with \ref cgal ≥ 5.0.0. */ -template<class Kernel = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>> +template<class Kernel = CGAL::Epeck_d<CGAL::Dynamic_dimension_tag>> class Alpha_complex { public: // Add an int in TDS to save point index in the structure @@ -184,6 +202,12 @@ class Alpha_complex { private: template<typename InputPointRange > void init_from_range(const InputPointRange& points) { + #if CGAL_VERSION_NR < 1050000000 + if (Is_Epeck_D<Kernel>::value) + std::cerr << "It is strongly advised to use a CGAL version >= 5.0 with Epeck_d Kernel for performance reasons." + << std::endl; + #endif + auto first = std::begin(points); auto last = std::end(points); @@ -237,6 +261,8 @@ class Alpha_complex { * @param[in] complex SimplicialComplexForAlpha to be created. * @param[in] max_alpha_square maximum for alpha square value. Default value is +\f$\infty\f$, and there is very * little point using anything else since it does not save time. + * @param[in] exact Exact filtration values computation. Not exact if `Kernel` is not <a target="_blank" + * href="https://doc.cgal.org/latest/Kernel_d/structCGAL_1_1Epeck__d.html">CGAL::Epeck_d</a>. * * @return true if creation succeeds, false otherwise. * @@ -248,7 +274,8 @@ class Alpha_complex { template <typename SimplicialComplexForAlpha, typename Filtration_value = typename SimplicialComplexForAlpha::Filtration_value> bool create_complex(SimplicialComplexForAlpha& complex, - Filtration_value max_alpha_square = std::numeric_limits<Filtration_value>::infinity()) { + Filtration_value max_alpha_square = std::numeric_limits<Filtration_value>::infinity(), + bool exact = false) { // From SimplicialComplexForAlpha type required to insert into a simplicial complex (with or without subfaces). typedef typename SimplicialComplexForAlpha::Vertex_handle Vertex_handle; typedef typename SimplicialComplexForAlpha::Simplex_handle Simplex_handle; @@ -324,9 +351,13 @@ class Alpha_complex { if (f_simplex_dim > 0) { // squared_radius function initialization Squared_Radius squared_radius = kernel_.compute_squared_radius_d_object(); - CGAL::NT_converter<typename Geom_traits::FT, Filtration_value> cv; - alpha_complex_filtration = cv(squared_radius(pointVector.begin(), pointVector.end())); + CGAL::NT_converter<typename Geom_traits::FT, Filtration_value> cv; + auto sqrad = squared_radius(pointVector.begin(), pointVector.end()); +#if CGAL_VERSION_NR >= 1050000000 + if(exact) CGAL::exact(sqrad); +#endif + alpha_complex_filtration = cv(sqrad); } complex.assign_filtration(f_simplex, alpha_complex_filtration); #ifdef DEBUG_TRACES |