From a99cac04ca5b61d1f9a1c5246829d017a6cf278d Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 15 Jun 2018 08:13:42 +0000 Subject: Weighted, normal and exact version of Alpha_shapes_3 git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@3618 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: f1b2014fe34b3e7814d9c3d02881c63e10f047b2 --- src/Alpha_complex/example/CMakeLists.txt | 2 ++ src/Alpha_complex/example/traits_test.cpp | 35 +++++++++++++++++++++++++++++++ 2 files changed, 37 insertions(+) create mode 100644 src/Alpha_complex/example/traits_test.cpp (limited to 'src/Alpha_complex/example') diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt index 2fc62452..c93832d2 100644 --- a/src/Alpha_complex/example/CMakeLists.txt +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -32,4 +32,6 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) install(TARGETS Alpha_complex_example_from_points DESTINATION bin) install(TARGETS Alpha_complex_example_from_off DESTINATION bin) + add_executable ( traits_test traits_test.cpp ) + endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) diff --git a/src/Alpha_complex/example/traits_test.cpp b/src/Alpha_complex/example/traits_test.cpp new file mode 100644 index 00000000..63b9740c --- /dev/null +++ b/src/Alpha_complex/example/traits_test.cpp @@ -0,0 +1,35 @@ +#include + +#include +#include +#include +#include // for numeric limits + +void usage(int nbArgs, char * const progName) { + std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; + std::cerr << "Usage: " << progName << " [alpha_square_max_value]\n"; + std::cerr << " i.e.: " << progName << " 60.0\n"; + exit(-1); // ----- >> +} + +int main(int argc, char **argv) { + //if ((argc != 1) && (argc != 2)) usage(argc, (argv[0] - 1)); + + using Alpha_shapes_3d = Gudhi::alpha_complex::Alpha_shapes_3d; + std::vector points; + points.push_back(Alpha_shapes_3d::Point_3(1., 2., 3.)); + points.push_back(Alpha_shapes_3d::Point_3(6., 5., 4.)); + + Gudhi::alpha_complex::Alpha_complex_3d alpha_complex(points); + + using Weighted_alpha_shapes_3d = Gudhi::alpha_complex::Weighted_alpha_shapes_3d; + std::vector w_points; + w_points.push_back(Alpha_shapes_3d::Point_3(1., 2., 3.)); + w_points.push_back(Alpha_shapes_3d::Point_3(6., 5., 4.)); + + std::vector weights = {1., 2.}; + + Gudhi::alpha_complex::Alpha_complex_3d weighted_alpha_complex(points, weights); + + return 0; +} -- cgit v1.2.3 From 5a2b1b9c0c79ef2b0595cf1f9428596261824b45 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 18 Jun 2018 21:50:42 +0000 Subject: Add periodic 3d Alpha shapes git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@3622 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a97b603cf83c5f9a80404dd5786896e51015ee08 --- src/Alpha_complex/example/traits_test.cpp | 9 ++++ src/Alpha_complex/include/gudhi/Alpha_complex_3d.h | 56 ++++++++++++++++++++-- .../include/gudhi/Alpha_complex_3d_options.h | 32 +++++++++++-- 3 files changed, 89 insertions(+), 8 deletions(-) (limited to 'src/Alpha_complex/example') diff --git a/src/Alpha_complex/example/traits_test.cpp b/src/Alpha_complex/example/traits_test.cpp index 63b9740c..4402ecf3 100644 --- a/src/Alpha_complex/example/traits_test.cpp +++ b/src/Alpha_complex/example/traits_test.cpp @@ -31,5 +31,14 @@ int main(int argc, char **argv) { Gudhi::alpha_complex::Alpha_complex_3d weighted_alpha_complex(points, weights); + using Periodic_alpha_shapes_3d = Gudhi::alpha_complex::Periodic_alpha_shapes_3d; + std::vector p_points; + p_points.push_back(Alpha_shapes_3d::Point_3(1., 2., 3.)); + p_points.push_back(Alpha_shapes_3d::Point_3(6., 5., 4.)); + + Gudhi::alpha_complex::Alpha_complex_3d periodic_alpha_complex(points, + 0., 0., 0., + 1., 1., 1.); + return 0; } diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index b04aa6d7..21707e5e 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -43,10 +43,9 @@ private: // filtration with alpha values needed type definition using Alpha_value_type = typename Alpha_shape_3::FT; using Object = CGAL::Object; - using Dispatch = - CGAL::Dispatch_output_iterator, - CGAL::cpp11::tuple >, - std::back_insert_iterator > > >; + using Dispatch = CGAL::Dispatch_output_iterator, + CGAL::cpp11::tuple >, + std::back_insert_iterator > > >; using Cell_handle = typename Alpha_shape_3::Cell_handle; using Facet = typename Alpha_shape_3::Facet; using Edge_3 = typename Alpha_shape_3::Edge; @@ -118,6 +117,55 @@ public: #endif // DEBUG_TRACES } + /** \brief Alpha_complex constructor from a list of points. +* +* Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. +* +* @param[in] points Range of points to triangulate. Points must be in Kernel::Point_d +* +* The type InputPointRange must be a range for which std::begin and +* std::end return input iterators on a Kernel::Point_d. +*/ + template + Alpha_complex_3d(const InputPointRange& points, + Alpha_value_type x_min, Alpha_value_type y_min, Alpha_value_type z_min, + Alpha_value_type x_max, Alpha_value_type y_max, Alpha_value_type z_max) { + static_assert(!AlphaComplex3dOptions::weighted, + "This constructor is not available for weighted versions of Alpha_complex_3d"); + static_assert(AlphaComplex3dOptions::periodic, + "This constructor is not available for non-periodic versions of Alpha_complex_3d"); + // Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it. + GUDHI_CHECK((x_max - x_min != y_max - y_min) || (x_max - x_min != z_max - z_min) || (z_max - z_min != y_max - y_min), + std::invalid_argument("The size of the cuboid in every directions is not the same.")); + + using Periodic_delaunay_triangulation_3 = typename AlphaComplex3dOptions::Periodic_delaunay_triangulation_3; + using Iso_cuboid_3 = typename AlphaComplex3dOptions::Iso_cuboid_3; + // Define the periodic cube + Periodic_delaunay_triangulation_3 pdt(Iso_cuboid_3(x_min, y_min, z_min, x_max, y_max, z_max)); + // Heuristic for inserting large point sets (if pts is reasonably large) + pdt.insert(std::begin(points), std::end(points), true); + // As pdt won't be modified anymore switch to 1-sheeted cover if possible + GUDHI_CHECK(pdt.is_triangulation_in_1_sheet(), + std::invalid_argument("Uable to construct a triangulation within a single periodic domain.")); + + // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. This is the default mode + // Maybe need to set it to GENERAL mode + Alpha_shape_3 as(pdt, 0, Alpha_shape_3::GENERAL); + + // filtration with alpha values from alpha shape + std::vector the_objects; + std::vector the_alpha_values; + + Dispatch disp = CGAL::dispatch_output(std::back_inserter(the_objects), + std::back_inserter(the_alpha_values)); + + as.filtration_with_alpha_values(disp); +#ifdef DEBUG_TRACES + std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; +#endif // DEBUG_TRACES + + } + private: std::vector the_objects; std::vector the_alpha_values; diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h index 3b753ee2..e05e5a7f 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h @@ -26,6 +26,8 @@ #include #include +#include +#include #include #include #include @@ -49,7 +51,6 @@ public: using Alpha_shape_3 = CGAL::Alpha_shape_3; using Point_3 = Kernel::Point_3; - static const bool exact = false; static const bool weighted = false; static const bool periodic = false; @@ -69,7 +70,6 @@ public: using Alpha_shape_3 = CGAL::Alpha_shape_3; using Point_3 = Kernel::Point_3; - static const bool exact = true; static const bool weighted = false; static const bool periodic = false; }; @@ -90,13 +90,37 @@ public: using Point_3 = Triangulation_3::Bare_point; using Weighted_point_3 = Triangulation_3::Weighted_point; - static const bool exact = false; static const bool weighted = true; static const bool periodic = false; }; +class Periodic_alpha_shapes_3d { +private: + using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; + using Periodic_kernel = CGAL::Periodic_3_Delaunay_triangulation_traits_3; +// Vertex type + using DsVb = CGAL::Periodic_3_triangulation_ds_vertex_base_3<>; + using Vb = CGAL::Triangulation_vertex_base_3; + using AsVb = CGAL::Alpha_shape_vertex_base_3; +// Cell type + using DsCb = CGAL::Periodic_3_triangulation_ds_cell_base_3<>; + using Cb = CGAL::Triangulation_cell_base_3; + using AsCb = CGAL::Alpha_shape_cell_base_3; + using Tds = CGAL::Triangulation_data_structure_3; + +public: + using Periodic_delaunay_triangulation_3 = CGAL::Periodic_3_Delaunay_triangulation_3; + using Alpha_shape_3 = CGAL::Alpha_shape_3; + using Point_3 = Periodic_kernel::Point_3; + using Alpha_value_type = Alpha_shape_3::FT; + using Iso_cuboid_3 = Periodic_kernel::Iso_cuboid_3; + + static const bool weighted = false; + static const bool periodic = true; +}; + } // namespace alpha_complex } // namespace Gudhi -#endif // ALPHA_COMPLEX_3D_H_ +#endif // ALPHA_COMPLEX_3D_OPTIONS_H_ -- cgit v1.2.3 From 82f15e71f43a5547627699b625830126dad1c4ab Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 19 Jun 2018 21:26:17 +0000 Subject: First create_complex version weighted periodic option git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@3624 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 7d22e307b12aac1390593541f77cabcccffbc6ad --- src/Alpha_complex/example/traits_test.cpp | 20 +- src/Alpha_complex/include/gudhi/Alpha_complex_3d.h | 243 ++++++++++++++++++++- .../include/gudhi/Alpha_complex_3d_options.h | 26 +++ 3 files changed, 283 insertions(+), 6 deletions(-) (limited to 'src/Alpha_complex/example') diff --git a/src/Alpha_complex/example/traits_test.cpp b/src/Alpha_complex/example/traits_test.cpp index 4402ecf3..99f1543c 100644 --- a/src/Alpha_complex/example/traits_test.cpp +++ b/src/Alpha_complex/example/traits_test.cpp @@ -24,21 +24,31 @@ int main(int argc, char **argv) { using Weighted_alpha_shapes_3d = Gudhi::alpha_complex::Weighted_alpha_shapes_3d; std::vector w_points; - w_points.push_back(Alpha_shapes_3d::Point_3(1., 2., 3.)); - w_points.push_back(Alpha_shapes_3d::Point_3(6., 5., 4.)); + w_points.push_back(Weighted_alpha_shapes_3d::Point_3(1., 2., 3.)); + w_points.push_back(Weighted_alpha_shapes_3d::Point_3(6., 5., 4.)); - std::vector weights = {1., 2.}; + std::vector weights = {0.01, 0.005}; Gudhi::alpha_complex::Alpha_complex_3d weighted_alpha_complex(points, weights); using Periodic_alpha_shapes_3d = Gudhi::alpha_complex::Periodic_alpha_shapes_3d; std::vector p_points; - p_points.push_back(Alpha_shapes_3d::Point_3(1., 2., 3.)); - p_points.push_back(Alpha_shapes_3d::Point_3(6., 5., 4.)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(1., 2., 3.)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(6., 5., 4.)); Gudhi::alpha_complex::Alpha_complex_3d periodic_alpha_complex(points, 0., 0., 0., 1., 1., 1.); + using Weighted_periodic_alpha_shapes_3d = Gudhi::alpha_complex::Weighted_periodic_alpha_shapes_3d; + std::vector wp_points; + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.1, 0.2, 0.3)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.5, 0.4)); + + Gudhi::alpha_complex::Alpha_complex_3d + weighted_periodic_alpha_complex(points, weights, + 0., 0., 0., + 1., 1., 1.); + return 0; } diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index 21707e5e..79f8593d 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -23,6 +23,12 @@ #ifndef ALPHA_COMPLEX_3D_H_ #define ALPHA_COMPLEX_3D_H_ +#include +#include + +#if BOOST_VERSION >= 105400 +#include +#endif #include #include @@ -49,7 +55,13 @@ private: using Cell_handle = typename Alpha_shape_3::Cell_handle; using Facet = typename Alpha_shape_3::Facet; using Edge_3 = typename Alpha_shape_3::Edge; - using Vertex_handle = typename Alpha_shape_3::Vertex_handle; + using Alpha_vertex_handle = typename Alpha_shape_3::Vertex_handle; + +#if BOOST_VERSION >= 105400 + using Vertex_list = boost::container::static_vector; +#else + using Vertex_list = std::vector; +#endif public: /** \brief Alpha_complex constructor from a list of points. @@ -166,6 +178,235 @@ public: } + /** \brief Alpha_complex constructor from a list of points. +* +* Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. +* +* @param[in] points Range of points to triangulate. Points must be in Kernel::Point_d +* +* The type InputPointRange must be a range for which std::begin and +* std::end return input iterators on a Kernel::Point_d. +*/ + template + Alpha_complex_3d(const InputPointRange& points, WeightRange weights, + Alpha_value_type x_min, Alpha_value_type y_min, Alpha_value_type z_min, + Alpha_value_type x_max, Alpha_value_type y_max, Alpha_value_type z_max) { + static_assert(AlphaComplex3dOptions::weighted, + "This constructor is not available for non-weighted versions of Alpha_complex_3d"); + static_assert(AlphaComplex3dOptions::periodic, + "This constructor is not available for non-periodic versions of Alpha_complex_3d"); + GUDHI_CHECK((weights.size() == points.size()), + std::invalid_argument("Alpha_complex_3d constructor with weights requires points number to be equal with points number")); + // Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it. + GUDHI_CHECK((x_max - x_min != y_max - y_min) || (x_max - x_min != z_max - z_min) || (z_max - z_min != y_max - y_min), + std::invalid_argument("The size of the cuboid in every directions is not the same.")); + + double maximal_possible_weight = 0.015625 * (x_max - x_min) * (x_max - x_min); + + using Weighted_point_3 = typename AlphaComplex3dOptions::Weighted_point_3; + std::vector weighted_points_3; + + std::size_t index = 0; + weighted_points_3.reserve(points.size()); + while ((index < weights.size()) && (index < points.size())) { + GUDHI_CHECK((weights[index] >= maximal_possible_weight) || (weights[index] < 0), + std::invalid_argument("Invalid weight at line" + std::to_string(index + 1) + + ". Must be positive and less than maximal possible weight = 1/64*cuboid length " + "squared, which is not an acceptable input.")); + weighted_points_3.push_back(Weighted_point_3(points[index], weights[index])); + index++; + } + + using Periodic_delaunay_triangulation_3 = typename AlphaComplex3dOptions::Periodic_delaunay_triangulation_3; + using Iso_cuboid_3 = typename AlphaComplex3dOptions::Iso_cuboid_3; + // Define the periodic cube + Periodic_delaunay_triangulation_3 pdt(Iso_cuboid_3(x_min, y_min, z_min, x_max, y_max, z_max)); + // Heuristic for inserting large point sets (if pts is reasonably large) + pdt.insert(std::begin(weighted_points_3), std::end(weighted_points_3), true); + // As pdt won't be modified anymore switch to 1-sheeted cover if possible + GUDHI_CHECK(pdt.is_triangulation_in_1_sheet(), + std::invalid_argument("Uable to construct a triangulation within a single periodic domain.")); + + // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. This is the default mode + // Maybe need to set it to GENERAL mode + Alpha_shape_3 as(pdt, 0, Alpha_shape_3::GENERAL); + + // filtration with alpha values from alpha shape + std::vector the_objects; + std::vector the_alpha_values; + + Dispatch disp = CGAL::dispatch_output(std::back_inserter(the_objects), + std::back_inserter(the_alpha_values)); + + as.filtration_with_alpha_values(disp); +#ifdef DEBUG_TRACES + std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; +#endif // DEBUG_TRACES + } + + template + void create_complex(SimplicialComplexForAlpha3d& complex) { + using Filtration_value = typename SimplicialComplexForAlpha3d::Filtration_value; + create_complex(complex, std::numeric_limits::infinity()); + } + + /** \brief Inserts all Delaunay triangulation into the simplicial complex. + * It also computes the filtration values accordingly to the \ref createcomplexalgorithm + * + * \tparam SimplicialComplexForAlpha must meet `SimplicialComplexForAlpha` concept. + * + * @param[in] complex SimplicialComplexForAlpha to be created. + * @param[in] max_alpha_square maximum for alpha square value. Default value is +\f$\infty\f$. + * + * @return true if creation succeeds, false otherwise. + * + * @pre Delaunay triangulation must be already constructed with dimension strictly greater than 0. + * @pre The simplicial complex must be empty (no vertices) + * + * Initialization can be launched once. + */ + template + void create_complex(SimplicialComplexForAlpha3d& complex, + typename SimplicialComplexForAlpha3d::Filtration_value max_alpha_square) { + using Filtration_value = typename SimplicialComplexForAlpha3d::Filtration_value; + using Vertex_handle = typename SimplicialComplexForAlpha3d::Vertex_handle; +#ifdef DEBUG_TRACES + Alpha_shape_3::size_type count_vertices = 0; + Alpha_shape_3::size_type count_edges = 0; + Alpha_shape_3::size_type count_facets = 0; + Alpha_shape_3::size_type count_cells = 0; +#endif // DEBUG_TRACES + + // Loop on objects vector + Vertex_list vertex_list; + SimplicialComplexForAlpha3d simplex_tree; + std::map map_cgal_simplex_tree; + typename std::vector::iterator the_alpha_value_iterator = the_alpha_values.begin(); + for (auto object_iterator : the_objects) { + // Retrieve Alpha shape vertex list from object + if (const Cell_handle *cell = CGAL::object_cast(&object_iterator)) { + vertex_list = from_cell(*cell); +#ifdef DEBUG_TRACES + count_cells++; +#endif // DEBUG_TRACES + } else if (const Facet *facet = CGAL::object_cast(&object_iterator)) { + vertex_list = from_facet(*facet); +#ifdef DEBUG_TRACES + count_facets++; +#endif // DEBUG_TRACES + } else if (const Edge_3 *edge = CGAL::object_cast(&object_iterator)) { + vertex_list = from_edge(*edge); +#ifdef DEBUG_TRACES + count_edges++; +#endif // DEBUG_TRACES + } else if (const Vertex_handle *vertex = CGAL::object_cast(&object_iterator)) { + vertex_list = from_vertex(*vertex); +#ifdef DEBUG_TRACES + count_vertices++; +#endif // DEBUG_TRACES + } + // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex + std::vector the_simplex; + for (auto the_alpha_shape_vertex : vertex_list) { + typename std::map::iterator the_map_iterator = + map_cgal_simplex_tree.find(the_alpha_shape_vertex); + if (the_map_iterator == map_cgal_simplex_tree.end()) { + // alpha shape not found + Vertex_handle vertex = map_cgal_simplex_tree.size(); +#ifdef DEBUG_TRACES + std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl; +#endif // DEBUG_TRACES + the_simplex.push_back(vertex); + map_cgal_simplex_tree.emplace(the_alpha_shape_vertex, vertex); + } else { + // alpha shape found + Vertex_handle vertex = the_map_iterator->second; +#ifdef DEBUG_TRACES + std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl; +#endif // DEBUG_TRACES + the_simplex.push_back(vertex); + } + } + // Construction of the simplex_tree + Filtration_value filtr = /*std::sqrt*/ (*the_alpha_value_iterator); +#ifdef DEBUG_TRACES + std::cout << "filtration = " << filtr << std::endl; +#endif // DEBUG_TRACES + simplex_tree.insert_simplex(the_simplex, filtr); + GUDHI_CHECK(the_alpha_value_iterator != the_alpha_values.end(), "CGAL provided more simplices than values"); + ++the_alpha_value_iterator; + } + +#ifdef DEBUG_TRACES + std::cout << "vertices \t\t" << count_vertices << std::endl; + std::cout << "edges \t\t" << count_edges << std::endl; + std::cout << "facets \t\t" << count_facets << std::endl; + std::cout << "cells \t\t" << count_cells << std::endl; + + std::cout << "Information of the Simplex Tree: " << std::endl; + std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; + std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; + std::cout << " Dimension = " << simplex_tree.dimension() << " "; +#endif // DEBUG_TRACES + +#ifdef DEBUG_TRACES + std::cout << "Iterator on vertices: " << std::endl; + for (auto vertex : simplex_tree.complex_vertex_range()) { + std::cout << vertex << " "; + } +#endif // DEBUG_TRACES + + } + +private: + template + Vertex_list from_cell(const Cell_handle& ch) { + Vertex_list the_list; + for (auto i = 0; i < 4; i++) { +#ifdef DEBUG_TRACES + std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl; +#endif // DEBUG_TRACES + the_list.push_back(ch->vertex(i)); + } + return the_list; + } + + template + Vertex_list from_facet(const Facet& fct) { + Vertex_list the_list; + for (auto i = 0; i < 4; i++) { + if (fct.second != i) { +#ifdef DEBUG_TRACES + std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl; +#endif // DEBUG_TRACES + the_list.push_back(fct.first->vertex(i)); + } + } + return the_list; + } + + template + Vertex_list from_edge(const Edge_3& edg) { + Vertex_list the_list; + for (auto i : {edg.second, edg.third}) { +#ifdef DEBUG_TRACES + std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl; +#endif // DEBUG_TRACES + the_list.push_back(edg.first->vertex(i)); + } + return the_list; + } + + template + Vertex_list from_vertex(const Vertex_handle& vh) { + Vertex_list the_list; +#ifdef DEBUG_TRACES + std::cout << "from vertex=" << vh->point() << std::endl; +#endif // DEBUG_TRACES + the_list.push_back(vh); + return the_list; + } + private: std::vector the_objects; std::vector the_alpha_values; diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h index e05e5a7f..9433afdc 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h @@ -28,6 +28,8 @@ #include #include #include +#include +#include #include #include #include @@ -119,6 +121,30 @@ public: static const bool periodic = true; }; +class Weighted_periodic_alpha_shapes_3d { +private: + using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; + using Periodic_kernel = CGAL::Periodic_3_regular_triangulation_traits_3; + using DsVb = CGAL::Periodic_3_triangulation_ds_vertex_base_3<>; + using Vb = CGAL::Regular_triangulation_vertex_base_3; + using AsVb = CGAL::Alpha_shape_vertex_base_3; + using DsCb = CGAL::Periodic_3_triangulation_ds_cell_base_3<>; + using Cb = CGAL::Regular_triangulation_cell_base_3; + using AsCb = CGAL::Alpha_shape_cell_base_3; + using Tds = CGAL::Triangulation_data_structure_3; + +public: + using Periodic_delaunay_triangulation_3 = CGAL::Periodic_3_regular_triangulation_3; + using Alpha_shape_3 = CGAL::Alpha_shape_3; + using Point_3 = Periodic_delaunay_triangulation_3::Bare_point; + using Weighted_point_3 = Periodic_delaunay_triangulation_3::Weighted_point; + using Alpha_value_type = Alpha_shape_3::FT; + using Iso_cuboid_3 = Periodic_kernel::Iso_cuboid_3; + + static const bool weighted = true; + static const bool periodic = true; +}; + } // namespace alpha_complex } // namespace Gudhi -- cgit v1.2.3 From 138ee2657f03206209ff5c7d6c4392168beef819 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 22 Jun 2018 08:30:53 +0000 Subject: Use unique_ptr to store cgal alpha_shapes_3. Required for not objects_ to be freed. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@3626 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 6dc9bbe25757a1a7bef2178ef63876c20d3a38b1 --- src/Alpha_complex/example/traits_test.cpp | 160 ++++++++++- src/Alpha_complex/include/gudhi/Alpha_complex_3d.h | 294 ++++++++++----------- .../include/gudhi/Alpha_complex_3d_options.h | 22 +- src/Alpha_complex/utilities/CMakeLists.txt | 5 + .../utilities/alpha_complex_3d_persistence.cpp | 163 +----------- 5 files changed, 317 insertions(+), 327 deletions(-) (limited to 'src/Alpha_complex/example') diff --git a/src/Alpha_complex/example/traits_test.cpp b/src/Alpha_complex/example/traits_test.cpp index 99f1543c..3be62ad3 100644 --- a/src/Alpha_complex/example/traits_test.cpp +++ b/src/Alpha_complex/example/traits_test.cpp @@ -1,4 +1,5 @@ #include +#include #include #include @@ -15,31 +16,174 @@ void usage(int nbArgs, char * const progName) { int main(int argc, char **argv) { //if ((argc != 1) && (argc != 2)) usage(argc, (argv[0] - 1)); + std::cout << "Alpha complex 3d" << std::endl; using Alpha_shapes_3d = Gudhi::alpha_complex::Alpha_shapes_3d; std::vector points; - points.push_back(Alpha_shapes_3d::Point_3(1., 2., 3.)); - points.push_back(Alpha_shapes_3d::Point_3(6., 5., 4.)); + points.push_back(Alpha_shapes_3d::Point_3(0.0, 0.0, 0.0)); + points.push_back(Alpha_shapes_3d::Point_3(0.0, 0.0, 0.2)); + points.push_back(Alpha_shapes_3d::Point_3(0.2, 0.0, 0.2)); + points.push_back(Alpha_shapes_3d::Point_3(0.6, 0.6, 0.0)); + points.push_back(Alpha_shapes_3d::Point_3(0.8, 0.8, 0.2)); + points.push_back(Alpha_shapes_3d::Point_3(0.2, 0.8, 0.6)); Gudhi::alpha_complex::Alpha_complex_3d alpha_complex(points); + Gudhi::Simplex_tree<> stree; + alpha_complex.create_complex(stree); + + std::cout << "Weighted alpha complex 3d" << std::endl; using Weighted_alpha_shapes_3d = Gudhi::alpha_complex::Weighted_alpha_shapes_3d; std::vector w_points; - w_points.push_back(Weighted_alpha_shapes_3d::Point_3(1., 2., 3.)); - w_points.push_back(Weighted_alpha_shapes_3d::Point_3(6., 5., 4.)); + w_points.push_back(Weighted_alpha_shapes_3d::Point_3(0.0, 0.0, 0.0)); + w_points.push_back(Weighted_alpha_shapes_3d::Point_3(0.0, 0.0, 0.2)); + w_points.push_back(Weighted_alpha_shapes_3d::Point_3(0.2, 0.0, 0.2)); + w_points.push_back(Weighted_alpha_shapes_3d::Point_3(0.6, 0.6, 0.0)); + w_points.push_back(Weighted_alpha_shapes_3d::Point_3(0.8, 0.8, 0.2)); + w_points.push_back(Weighted_alpha_shapes_3d::Point_3(0.2, 0.8, 0.6)); + + std::vector weights = {0.01, 0.005, 0.006, 0.01, 0.009, 0.001}; - std::vector weights = {0.01, 0.005}; + Gudhi::alpha_complex::Alpha_complex_3d weighted_alpha_complex(w_points, weights); - Gudhi::alpha_complex::Alpha_complex_3d weighted_alpha_complex(points, weights); + Gudhi::Simplex_tree<> w_stree; + weighted_alpha_complex.create_complex(w_stree); + std::cout << "Periodic alpha complex 3d" << std::endl; using Periodic_alpha_shapes_3d = Gudhi::alpha_complex::Periodic_alpha_shapes_3d; std::vector p_points; - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(1., 2., 3.)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(6., 5., 4.)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.1, 0.0)); // + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.6)); + //p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.8)); Gudhi::alpha_complex::Alpha_complex_3d periodic_alpha_complex(points, 0., 0., 0., 1., 1., 1.); + std::cout << "Weighted periodic alpha complex 3d" << std::endl; using Weighted_periodic_alpha_shapes_3d = Gudhi::alpha_complex::Weighted_periodic_alpha_shapes_3d; std::vector wp_points; wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.1, 0.2, 0.3)); diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index 79f8593d..c8bc9c8e 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -37,6 +37,12 @@ #include #include +#include +#include +#include +#include +#include +#include // for std::unique_ptr namespace Gudhi { @@ -44,25 +50,26 @@ namespace alpha_complex { template class Alpha_complex_3d { -private: using Alpha_shape_3 = typename AlphaComplex3dOptions::Alpha_shape_3; - // filtration with alpha values needed type definition using Alpha_value_type = typename Alpha_shape_3::FT; - using Object = CGAL::Object; - using Dispatch = CGAL::Dispatch_output_iterator, - CGAL::cpp11::tuple >, - std::back_insert_iterator > > >; + using Dispatch = + CGAL::Dispatch_output_iterator, + CGAL::cpp11::tuple >, + std::back_insert_iterator > > >; + using Cell_handle = typename Alpha_shape_3::Cell_handle; using Facet = typename Alpha_shape_3::Facet; - using Edge_3 = typename Alpha_shape_3::Edge; + using Edge = typename Alpha_shape_3::Edge; using Alpha_vertex_handle = typename Alpha_shape_3::Vertex_handle; - #if BOOST_VERSION >= 105400 using Vertex_list = boost::container::static_vector; #else using Vertex_list = std::vector; #endif +public: + using Point_3 = typename AlphaComplex3dOptions::Point_3; + public: /** \brief Alpha_complex constructor from a list of points. * @@ -75,17 +82,19 @@ public: */ template Alpha_complex_3d(const InputPointRange& points) { - static_assert(!AlphaComplex3dOptions::weighted, "This constructor is not available for weighted versions of Alpha_complex_3d"); - static_assert(!AlphaComplex3dOptions::periodic, "This constructor is not available for periodic versions of Alpha_complex_3d"); - std::cout << points[0] << std::endl; - Alpha_shape_3 alpha_shape_3(std::begin(points), std::end(points), 0, Alpha_shape_3::GENERAL); + static_assert(!AlphaComplex3dOptions::weighted, + "This constructor is not available for weighted versions of Alpha_complex_3d"); + static_assert(!AlphaComplex3dOptions::periodic, + "This constructor is not available for periodic versions of Alpha_complex_3d"); - Dispatch disp = CGAL::dispatch_output(std::back_inserter(the_objects), - std::back_inserter(the_alpha_values)); + alpha_shape_3_ptr_ = std::unique_ptr(new Alpha_shape_3(points.begin(), points.end(), 0, + Alpha_shape_3::GENERAL)); + Dispatch dispatcher = CGAL::dispatch_output(std::back_inserter(objects_), + std::back_inserter(alpha_values_)); - alpha_shape_3.filtration_with_alpha_values(disp); + alpha_shape_3_ptr_->filtration_with_alpha_values(dispatcher); #ifdef DEBUG_TRACES - std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; + std::cout << "filtration_with_alpha_values returns : " << objects_.size() << " objects" << std::endl; #endif // DEBUG_TRACES } @@ -106,7 +115,7 @@ public: static_assert(!AlphaComplex3dOptions::periodic, "This constructor is not available for periodic versions of Alpha_complex_3d"); GUDHI_CHECK((weights.size() == points.size()), - std::invalid_argument("Alpha_complex_3d constructor with weights requires points number to be equal with points number")); + std::invalid_argument("Points number in range different from weights range number")); using Weighted_point_3 = typename AlphaComplex3dOptions::Weighted_point_3; std::vector weighted_points_3; @@ -118,14 +127,17 @@ public: index++; } - Alpha_shape_3 alpha_shape_3(std::begin(weighted_points_3), std::end(weighted_points_3), 0, Alpha_shape_3::GENERAL); + alpha_shape_3_ptr_ = std::unique_ptr(new Alpha_shape_3(std::begin(weighted_points_3), + std::end(weighted_points_3), + 0, + Alpha_shape_3::GENERAL)); - Dispatch disp = CGAL::dispatch_output(std::back_inserter(the_objects), - std::back_inserter(the_alpha_values)); + Dispatch dispatcher = CGAL::dispatch_output(std::back_inserter(objects_), + std::back_inserter(alpha_values_)); - alpha_shape_3.filtration_with_alpha_values(disp); + alpha_shape_3_ptr_->filtration_with_alpha_values(dispatcher); #ifdef DEBUG_TRACES - std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; + std::cout << "filtration_with_alpha_values returns : " << objects_.size() << " objects" << std::endl; #endif // DEBUG_TRACES } @@ -140,14 +152,16 @@ public: */ template Alpha_complex_3d(const InputPointRange& points, - Alpha_value_type x_min, Alpha_value_type y_min, Alpha_value_type z_min, - Alpha_value_type x_max, Alpha_value_type y_max, Alpha_value_type z_max) { + double x_min, double y_min, double z_min, + double x_max, double y_max, double z_max) { static_assert(!AlphaComplex3dOptions::weighted, "This constructor is not available for weighted versions of Alpha_complex_3d"); static_assert(AlphaComplex3dOptions::periodic, "This constructor is not available for non-periodic versions of Alpha_complex_3d"); // Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it. - GUDHI_CHECK((x_max - x_min != y_max - y_min) || (x_max - x_min != z_max - z_min) || (z_max - z_min != y_max - y_min), + GUDHI_CHECK((x_max - x_min == y_max - y_min) || + (x_max - x_min == z_max - z_min) || + (z_max - z_min == y_max - y_min), std::invalid_argument("The size of the cuboid in every directions is not the same.")); using Periodic_delaunay_triangulation_3 = typename AlphaComplex3dOptions::Periodic_delaunay_triangulation_3; @@ -157,23 +171,27 @@ public: // Heuristic for inserting large point sets (if pts is reasonably large) pdt.insert(std::begin(points), std::end(points), true); // As pdt won't be modified anymore switch to 1-sheeted cover if possible - GUDHI_CHECK(pdt.is_triangulation_in_1_sheet(), - std::invalid_argument("Uable to construct a triangulation within a single periodic domain.")); + // GUDHI_CHECK(pdt.is_triangulation_in_1_sheet(), + // std::invalid_argument("Uable to construct a triangulation within a single periodic domain.")); + if (pdt.is_triangulation_in_1_sheet()) { + pdt.convert_to_1_sheeted_covering(); + } else { + std::cerr << "ERROR: we were not able to construct a triangulation within a single periodic domain." << std::endl; + exit(-1); + } + std::cout << "Periodic Delaunay computed." << std::endl; // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. This is the default mode // Maybe need to set it to GENERAL mode - Alpha_shape_3 as(pdt, 0, Alpha_shape_3::GENERAL); - - // filtration with alpha values from alpha shape - std::vector the_objects; - std::vector the_alpha_values; + alpha_shape_3_ptr_ = std::unique_ptr(new Alpha_shape_3(pdt, 0, + Alpha_shape_3::GENERAL)); - Dispatch disp = CGAL::dispatch_output(std::back_inserter(the_objects), - std::back_inserter(the_alpha_values)); + Dispatch dispatcher = CGAL::dispatch_output(std::back_inserter(objects_), + std::back_inserter(alpha_values_)); - as.filtration_with_alpha_values(disp); + alpha_shape_3_ptr_->filtration_with_alpha_values(dispatcher); #ifdef DEBUG_TRACES - std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; + std::cout << "filtration_with_alpha_values returns : " << objects_.size() << " objects" << std::endl; #endif // DEBUG_TRACES } @@ -196,12 +214,17 @@ public: static_assert(AlphaComplex3dOptions::periodic, "This constructor is not available for non-periodic versions of Alpha_complex_3d"); GUDHI_CHECK((weights.size() == points.size()), - std::invalid_argument("Alpha_complex_3d constructor with weights requires points number to be equal with points number")); + std::invalid_argument("Points number in range different from weights range number")); // Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it. - GUDHI_CHECK((x_max - x_min != y_max - y_min) || (x_max - x_min != z_max - z_min) || (z_max - z_min != y_max - y_min), + GUDHI_CHECK((x_max - x_min == y_max - y_min) || + (x_max - x_min == z_max - z_min) || + (z_max - z_min == y_max - y_min), std::invalid_argument("The size of the cuboid in every directions is not the same.")); +#ifdef GUDHI_DEBUG + // Defined in GUDHI_DEBUG to avoid unused variable warning double maximal_possible_weight = 0.015625 * (x_max - x_min) * (x_max - x_min); +#endif using Weighted_point_3 = typename AlphaComplex3dOptions::Weighted_point_3; std::vector weighted_points_3; @@ -225,25 +248,25 @@ public: pdt.insert(std::begin(weighted_points_3), std::end(weighted_points_3), true); // As pdt won't be modified anymore switch to 1-sheeted cover if possible GUDHI_CHECK(pdt.is_triangulation_in_1_sheet(), - std::invalid_argument("Uable to construct a triangulation within a single periodic domain.")); + std::invalid_argument("Unable to construct a triangulation within a single periodic domain.")); + + pdt.convert_to_1_sheeted_covering(); // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. This is the default mode // Maybe need to set it to GENERAL mode - Alpha_shape_3 as(pdt, 0, Alpha_shape_3::GENERAL); + alpha_shape_3_ptr_ = std::unique_ptr(new Alpha_shape_3(pdt, 0, + Alpha_shape_3::GENERAL)); - // filtration with alpha values from alpha shape - std::vector the_objects; - std::vector the_alpha_values; + Dispatch dispatcher = CGAL::dispatch_output(std::back_inserter(objects_), + std::back_inserter(alpha_values_)); - Dispatch disp = CGAL::dispatch_output(std::back_inserter(the_objects), - std::back_inserter(the_alpha_values)); - - as.filtration_with_alpha_values(disp); + alpha_shape_3_ptr_->filtration_with_alpha_values(dispatcher); #ifdef DEBUG_TRACES - std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; + std::cout << "filtration_with_alpha_values returns : " << objects_.size() << " objects" << std::endl; #endif // DEBUG_TRACES } + template void create_complex(SimplicialComplexForAlpha3d& complex) { using Filtration_value = typename SimplicialComplexForAlpha3d::Filtration_value; @@ -251,68 +274,86 @@ public: } /** \brief Inserts all Delaunay triangulation into the simplicial complex. - * It also computes the filtration values accordingly to the \ref createcomplexalgorithm - * - * \tparam SimplicialComplexForAlpha must meet `SimplicialComplexForAlpha` concept. - * - * @param[in] complex SimplicialComplexForAlpha to be created. - * @param[in] max_alpha_square maximum for alpha square value. Default value is +\f$\infty\f$. - * - * @return true if creation succeeds, false otherwise. - * - * @pre Delaunay triangulation must be already constructed with dimension strictly greater than 0. - * @pre The simplicial complex must be empty (no vertices) - * - * Initialization can be launched once. - */ + * It also computes the filtration values accordingly to the \ref createcomplexalgorithm + * + * \tparam SimplicialComplexForAlpha3d must meet `SimplicialComplexForAlpha3d` concept. + * + * @param[in] complex SimplicialComplexForAlpha3d to be created. + * @param[in] max_alpha_square maximum for alpha square value. Default value is +\f$\infty\f$. + * + * @return true if creation succeeds, false otherwise. + * + * @pre The simplicial complex must be empty (no vertices) + * + * Initialization can be launched once. + */ template - void create_complex(SimplicialComplexForAlpha3d& complex, + bool create_complex(SimplicialComplexForAlpha3d& complex, typename SimplicialComplexForAlpha3d::Filtration_value max_alpha_square) { + if (complex.num_vertices() > 0) { + std::cerr << "Alpha_complex_3d create_complex - complex is not empty\n"; + return false; // ----- >> + } + using Filtration_value = typename SimplicialComplexForAlpha3d::Filtration_value; - using Vertex_handle = typename SimplicialComplexForAlpha3d::Vertex_handle; + using Complex_vertex_handle = typename SimplicialComplexForAlpha3d::Vertex_handle; + using Alpha_shape_simplex_tree_map = std::map; + using Simplex_tree_vector_vertex = std::vector; + #ifdef DEBUG_TRACES - Alpha_shape_3::size_type count_vertices = 0; - Alpha_shape_3::size_type count_edges = 0; - Alpha_shape_3::size_type count_facets = 0; - Alpha_shape_3::size_type count_cells = 0; + std::size_t count_vertices = 0; + std::size_t count_edges = 0; + std::size_t count_facets = 0; + std::size_t count_cells = 0; #endif // DEBUG_TRACES - // Loop on objects vector - Vertex_list vertex_list; - SimplicialComplexForAlpha3d simplex_tree; - std::map map_cgal_simplex_tree; - typename std::vector::iterator the_alpha_value_iterator = the_alpha_values.begin(); - for (auto object_iterator : the_objects) { + Alpha_shape_simplex_tree_map map_cgal_simplex_tree; + auto the_alpha_value_iterator = alpha_values_.begin(); + for (auto object_iterator : objects_) { + Vertex_list vertex_list; + // Retrieve Alpha shape vertex list from object if (const Cell_handle *cell = CGAL::object_cast(&object_iterator)) { - vertex_list = from_cell(*cell); + for (auto i = 0; i < 4; i++) { #ifdef DEBUG_TRACES - count_cells++; + std::cout << "from cell[" << i << "]=" << (*cell)->vertex(i)->point() << std::endl; #endif // DEBUG_TRACES + vertex_list.push_back((*cell)->vertex(i)); + } + count_cells++; } else if (const Facet *facet = CGAL::object_cast(&object_iterator)) { - vertex_list = from_facet(*facet); + for (auto i = 0; i < 4; i++) { + if ((*facet).second != i) { #ifdef DEBUG_TRACES - count_facets++; + std::cout << "from facet=[" << i << "]" << (*facet).first->vertex(i)->point() << std::endl; #endif // DEBUG_TRACES - } else if (const Edge_3 *edge = CGAL::object_cast(&object_iterator)) { - vertex_list = from_edge(*edge); + vertex_list.push_back((*facet).first->vertex(i)); + } + } + count_facets++; + } else if (const Edge *edge = CGAL::object_cast(&object_iterator)) { + for (auto i : {(*edge).second, (*edge).third}) { #ifdef DEBUG_TRACES - count_edges++; + std::cout << "from edge[" << i << "]=" << (*edge).first->vertex(i)->point() << std::endl; #endif // DEBUG_TRACES - } else if (const Vertex_handle *vertex = CGAL::object_cast(&object_iterator)) { - vertex_list = from_vertex(*vertex); -#ifdef DEBUG_TRACES + vertex_list.push_back((*edge).first->vertex(i)); + } + count_edges++; + } else if (const Alpha_vertex_handle *vertex = CGAL::object_cast(&object_iterator)) { count_vertices++; +#ifdef DEBUG_TRACES + std::cout << "from vertex=" << (*vertex)->point() << std::endl; #endif // DEBUG_TRACES + vertex_list.push_back((*vertex)); } // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex - std::vector the_simplex; + Simplex_tree_vector_vertex the_simplex; for (auto the_alpha_shape_vertex : vertex_list) { - typename std::map::iterator the_map_iterator = - map_cgal_simplex_tree.find(the_alpha_shape_vertex); + auto the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex); if (the_map_iterator == map_cgal_simplex_tree.end()) { // alpha shape not found - Vertex_handle vertex = map_cgal_simplex_tree.size(); + Complex_vertex_handle vertex = map_cgal_simplex_tree.size(); #ifdef DEBUG_TRACES std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl; #endif // DEBUG_TRACES @@ -320,7 +361,7 @@ public: map_cgal_simplex_tree.emplace(the_alpha_shape_vertex, vertex); } else { // alpha shape found - Vertex_handle vertex = the_map_iterator->second; + Complex_vertex_handle vertex = the_map_iterator->second; #ifdef DEBUG_TRACES std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl; #endif // DEBUG_TRACES @@ -332,84 +373,25 @@ public: #ifdef DEBUG_TRACES std::cout << "filtration = " << filtr << std::endl; #endif // DEBUG_TRACES - simplex_tree.insert_simplex(the_simplex, filtr); - GUDHI_CHECK(the_alpha_value_iterator != the_alpha_values.end(), "CGAL provided more simplices than values"); + complex.insert_simplex(the_simplex, filtr); + GUDHI_CHECK(the_alpha_value_iterator != alpha_values_.end(), "CGAL provided more simplices than values"); ++the_alpha_value_iterator; } #ifdef DEBUG_TRACES - std::cout << "vertices \t\t" << count_vertices << std::endl; + std::cout << "vertices \t" << count_vertices << std::endl; std::cout << "edges \t\t" << count_edges << std::endl; std::cout << "facets \t\t" << count_facets << std::endl; std::cout << "cells \t\t" << count_cells << std::endl; - - std::cout << "Information of the Simplex Tree: " << std::endl; - std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; - std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; - std::cout << " Dimension = " << simplex_tree.dimension() << " "; -#endif // DEBUG_TRACES - -#ifdef DEBUG_TRACES - std::cout << "Iterator on vertices: " << std::endl; - for (auto vertex : simplex_tree.complex_vertex_range()) { - std::cout << vertex << " "; - } -#endif // DEBUG_TRACES - - } - -private: - template - Vertex_list from_cell(const Cell_handle& ch) { - Vertex_list the_list; - for (auto i = 0; i < 4; i++) { -#ifdef DEBUG_TRACES - std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(ch->vertex(i)); - } - return the_list; - } - - template - Vertex_list from_facet(const Facet& fct) { - Vertex_list the_list; - for (auto i = 0; i < 4; i++) { - if (fct.second != i) { -#ifdef DEBUG_TRACES - std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(fct.first->vertex(i)); - } - } - return the_list; - } - - template - Vertex_list from_edge(const Edge_3& edg) { - Vertex_list the_list; - for (auto i : {edg.second, edg.third}) { -#ifdef DEBUG_TRACES - std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(edg.first->vertex(i)); - } - return the_list; - } - - template - Vertex_list from_vertex(const Vertex_handle& vh) { - Vertex_list the_list; -#ifdef DEBUG_TRACES - std::cout << "from vertex=" << vh->point() << std::endl; #endif // DEBUG_TRACES - the_list.push_back(vh); - return the_list; + return true; } private: - std::vector the_objects; - std::vector the_alpha_values; + // Needs to store alpha_shape_3_ptr_ as objects_ and alpha_shape_3_ptr_ are freed with alpha_shape_3_ptr_ + std::unique_ptr alpha_shape_3_ptr_; + std::vector objects_; + std::vector alpha_values_; }; diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h index 9433afdc..3b1981ca 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h @@ -42,7 +42,6 @@ namespace alpha_complex { class Alpha_shapes_3d { private: - // Alpha_shape_3 templates type definitions using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; using Vb = CGAL::Alpha_shape_vertex_base_3; using Fb = CGAL::Alpha_shape_cell_base_3; @@ -55,7 +54,6 @@ public: static const bool weighted = false; static const bool periodic = false; - }; class Exact_alpha_shapes_3d { @@ -98,24 +96,24 @@ public: class Periodic_alpha_shapes_3d { private: - using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; - using Periodic_kernel = CGAL::Periodic_3_Delaunay_triangulation_traits_3; + // Traits + using K = CGAL::Exact_predicates_inexact_constructions_kernel; + using PK = CGAL::Periodic_3_Delaunay_triangulation_traits_3; // Vertex type using DsVb = CGAL::Periodic_3_triangulation_ds_vertex_base_3<>; - using Vb = CGAL::Triangulation_vertex_base_3; - using AsVb = CGAL::Alpha_shape_vertex_base_3; + using Vb = CGAL::Triangulation_vertex_base_3; + using AsVb = CGAL::Alpha_shape_vertex_base_3; // Cell type using DsCb = CGAL::Periodic_3_triangulation_ds_cell_base_3<>; - using Cb = CGAL::Triangulation_cell_base_3; - using AsCb = CGAL::Alpha_shape_cell_base_3; + using Cb = CGAL::Triangulation_cell_base_3; + using AsCb = CGAL::Alpha_shape_cell_base_3; using Tds = CGAL::Triangulation_data_structure_3; public: - using Periodic_delaunay_triangulation_3 = CGAL::Periodic_3_Delaunay_triangulation_3; + using Periodic_delaunay_triangulation_3 = CGAL::Periodic_3_Delaunay_triangulation_3; using Alpha_shape_3 = CGAL::Alpha_shape_3; - using Point_3 = Periodic_kernel::Point_3; - using Alpha_value_type = Alpha_shape_3::FT; - using Iso_cuboid_3 = Periodic_kernel::Iso_cuboid_3; + using Point_3 = PK::Point_3; + using Iso_cuboid_3 = PK::Iso_cuboid_3; static const bool weighted = false; static const bool periodic = true; diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt index 7ace6064..c4d986c4 100644 --- a/src/Alpha_complex/utilities/CMakeLists.txt +++ b/src/Alpha_complex/utilities/CMakeLists.txt @@ -8,10 +8,15 @@ if(CGAL_FOUND) add_executable(weighted_alpha_complex_3d_persistence weighted_alpha_complex_3d_persistence.cpp) target_link_libraries(weighted_alpha_complex_3d_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + add_executable(old_alpha_complex_3d_persistence old_alpha_complex_3d_persistence.cpp) + target_link_libraries(old_alpha_complex_3d_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + if (TBB_FOUND) target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES}) target_link_libraries(exact_alpha_complex_3d_persistence ${TBB_LIBRARIES}) target_link_libraries(weighted_alpha_complex_3d_persistence ${TBB_LIBRARIES}) + + target_link_libraries(old_alpha_complex_3d_persistence ${TBB_LIBRARIES}) endif(TBB_FOUND) add_test(NAME Alpha_complex_utilities_alpha_complex_3d_persistence COMMAND $ diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp index 8cda0b70..669b6e08 100644 --- a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp @@ -20,73 +20,24 @@ * along with this program. If not, see . */ -#include #include -#include - -#if BOOST_VERSION >= 105400 -#include -#endif +#include +#include #include #include #include -#include -#include -#include -#include -#include -#include - -#include -#include +#include #include -#include -#include -#include -#include -#include - -#include "alpha_complex_3d_helper.h" - -// Alpha_shape_3 templates type definitions -using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; -using Vb = CGAL::Alpha_shape_vertex_base_3; -using Fb = CGAL::Alpha_shape_cell_base_3; -using Tds = CGAL::Triangulation_data_structure_3; -using Triangulation_3 = CGAL::Delaunay_triangulation_3; -using Alpha_shape_3 = CGAL::Alpha_shape_3; - -// From file type definition -using Point_3 = Kernel::Point_3; - -// filtration with alpha values needed type definition -using Alpha_value_type = Alpha_shape_3::FT; -using Object = CGAL::Object; -using Dispatch = - CGAL::Dispatch_output_iterator, - CGAL::cpp11::tuple >, - std::back_insert_iterator > > >; -using Cell_handle = Alpha_shape_3::Cell_handle; -using Facet = Alpha_shape_3::Facet; -using Edge_3 = Alpha_shape_3::Edge; -using Vertex_handle = Alpha_shape_3::Vertex_handle; - -#if BOOST_VERSION >= 105400 -using Vertex_list = boost::container::static_vector; -#else -using Vertex_list = std::vector; -#endif +#include // for numeric_limits // gudhi type definition -using ST = Gudhi::Simplex_tree; -using Filtration_value = ST::Filtration_value; -using Simplex_tree_vertex = ST::Vertex_handle; -using Alpha_shape_simplex_tree_map = std::map; -using Simplex_tree_vector_vertex = std::vector; +using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Simplex_tree = Gudhi::Simplex_tree; +using Filtration_value = Simplex_tree::Filtration_value; using Persistent_cohomology = - Gudhi::persistent_cohomology::Persistent_cohomology; + Gudhi::persistent_cohomology::Persistent_cohomology; void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag, int &coeff_field_characteristic, Filtration_value &min_persistence); @@ -100,108 +51,18 @@ int main(int argc, char **argv) { program_options(argc, argv, off_file_points, output_file_diag, coeff_field_characteristic, min_persistence); // Read the OFF file (input file name given as parameter) and triangulate points - Gudhi::Points_3D_off_reader off_reader(off_file_points); + Gudhi::Points_3D_off_reader off_reader(off_file_points); // Check the read operation was correct if (!off_reader.is_valid()) { std::cerr << "Unable to read file " << off_file_points << std::endl; exit(-1); } - // Retrieve the points - std::vector lp = off_reader.get_point_cloud(); - - // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. - Alpha_shape_3 as(lp.begin(), lp.end(), 0, Alpha_shape_3::GENERAL); -#ifdef DEBUG_TRACES - std::cout << "Alpha shape computed in GENERAL mode" << std::endl; -#endif // DEBUG_TRACES - - // filtration with alpha values from alpha shape - std::vector the_objects; - std::vector the_alpha_values; - - Dispatch disp = CGAL::dispatch_output(std::back_inserter(the_objects), - std::back_inserter(the_alpha_values)); - - as.filtration_with_alpha_values(disp); -#ifdef DEBUG_TRACES - std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; -#endif // DEBUG_TRACES - - Alpha_shape_3::size_type count_vertices = 0; - Alpha_shape_3::size_type count_edges = 0; - Alpha_shape_3::size_type count_facets = 0; - Alpha_shape_3::size_type count_cells = 0; - - // Loop on objects vector - Vertex_list vertex_list; - ST simplex_tree; - Alpha_shape_simplex_tree_map map_cgal_simplex_tree; - std::vector::iterator the_alpha_value_iterator = the_alpha_values.begin(); - for (auto object_iterator : the_objects) { - // Retrieve Alpha shape vertex list from object - if (const Cell_handle *cell = CGAL::object_cast(&object_iterator)) { - vertex_list = from_cell(*cell); - count_cells++; - } else if (const Facet *facet = CGAL::object_cast(&object_iterator)) { - vertex_list = from_facet(*facet); - count_facets++; - } else if (const Edge_3 *edge = CGAL::object_cast(&object_iterator)) { - vertex_list = from_edge(*edge); - count_edges++; - } else if (const Vertex_handle *vertex = CGAL::object_cast(&object_iterator)) { - count_vertices++; - vertex_list = from_vertex(*vertex); - } - // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex - Simplex_tree_vector_vertex the_simplex; - for (auto the_alpha_shape_vertex : vertex_list) { - Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex); - if (the_map_iterator == map_cgal_simplex_tree.end()) { - // alpha shape not found - Simplex_tree_vertex vertex = map_cgal_simplex_tree.size(); -#ifdef DEBUG_TRACES - std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl; -#endif // DEBUG_TRACES - the_simplex.push_back(vertex); - map_cgal_simplex_tree.emplace(the_alpha_shape_vertex, vertex); - } else { - // alpha shape found - Simplex_tree_vertex vertex = the_map_iterator->second; -#ifdef DEBUG_TRACES - std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl; -#endif // DEBUG_TRACES - the_simplex.push_back(vertex); - } - } - // Construction of the simplex_tree - Filtration_value filtr = /*std::sqrt*/ (*the_alpha_value_iterator); -#ifdef DEBUG_TRACES - std::cout << "filtration = " << filtr << std::endl; -#endif // DEBUG_TRACES - simplex_tree.insert_simplex(the_simplex, filtr); - GUDHI_CHECK(the_alpha_value_iterator != the_alpha_values.end(), "CGAL provided more simplices than values"); - ++the_alpha_value_iterator; - } - -#ifdef DEBUG_TRACES - std::cout << "vertices \t\t" << count_vertices << std::endl; - std::cout << "edges \t\t" << count_edges << std::endl; - std::cout << "facets \t\t" << count_facets << std::endl; - std::cout << "cells \t\t" << count_cells << std::endl; + Alpha_complex_3d alpha_complex(off_reader.get_point_cloud()); - std::cout << "Information of the Simplex Tree: " << std::endl; - std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; - std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; - std::cout << " Dimension = " << simplex_tree.dimension() << " "; -#endif // DEBUG_TRACES + Simplex_tree simplex_tree; -#ifdef DEBUG_TRACES - std::cout << "Iterator on vertices: " << std::endl; - for (auto vertex : simplex_tree.complex_vertex_range()) { - std::cout << vertex << " "; - } -#endif // DEBUG_TRACES + alpha_complex.create_complex(simplex_tree); // Sort the simplices in the order of the filtration simplex_tree.initialize_filtration(); -- cgit v1.2.3 From c5ccdfae66f8e3a33bec20a310df134d3e1ab4bf Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 22 Jun 2018 15:50:51 +0000 Subject: Compiles run and tests for Alpha_3d, exact, weighted, periodic and weighted periodic git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@3627 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: e24d7de108d3e77eaf6319a8165a7c65bec57884 --- src/Alpha_complex/example/traits_test.cpp | 170 ++++++++++++++++++++- src/Alpha_complex/include/gudhi/Alpha_complex_3d.h | 43 +++--- .../include/gudhi/Alpha_complex_3d_options.h | 30 +++- .../periodic_alpha_complex_3d_persistence.cpp | 2 +- 4 files changed, 219 insertions(+), 26 deletions(-) (limited to 'src/Alpha_complex/example') diff --git a/src/Alpha_complex/example/traits_test.cpp b/src/Alpha_complex/example/traits_test.cpp index 3be62ad3..1dd062de 100644 --- a/src/Alpha_complex/example/traits_test.cpp +++ b/src/Alpha_complex/example/traits_test.cpp @@ -5,6 +5,7 @@ #include #include #include // for numeric limits +#include void usage(int nbArgs, char * const progName) { std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; @@ -31,6 +32,21 @@ int main(int argc, char **argv) { Gudhi::Simplex_tree<> stree; alpha_complex.create_complex(stree); + std::cout << "Exact alpha complex 3d" << std::endl; + using Exact_alpha_shapes_3d = Gudhi::alpha_complex::Exact_alpha_shapes_3d; + std::vector e_points; + e_points.push_back(Exact_alpha_shapes_3d::Point_3(0.0, 0.0, 0.0)); + e_points.push_back(Exact_alpha_shapes_3d::Point_3(0.0, 0.0, 0.2)); + e_points.push_back(Exact_alpha_shapes_3d::Point_3(0.2, 0.0, 0.2)); + e_points.push_back(Exact_alpha_shapes_3d::Point_3(0.6, 0.6, 0.0)); + e_points.push_back(Exact_alpha_shapes_3d::Point_3(0.8, 0.8, 0.2)); + e_points.push_back(Exact_alpha_shapes_3d::Point_3(0.2, 0.8, 0.6)); + + Gudhi::alpha_complex::Alpha_complex_3d exact_alpha_complex(e_points); + + Gudhi::Simplex_tree exact_stree; + exact_alpha_complex.create_complex(exact_stree); + std::cout << "Weighted alpha complex 3d" << std::endl; using Weighted_alpha_shapes_3d = Gudhi::alpha_complex::Weighted_alpha_shapes_3d; std::vector w_points; @@ -51,6 +67,7 @@ int main(int argc, char **argv) { std::cout << "Periodic alpha complex 3d" << std::endl; using Periodic_alpha_shapes_3d = Gudhi::alpha_complex::Periodic_alpha_shapes_3d; std::vector p_points; + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.0)); p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.2)); p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.4)); @@ -131,8 +148,7 @@ int main(int argc, char **argv) { p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.4)); p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.6)); p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.8)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.0)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.1, 0.0)); // + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.1, 0.0)); p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.0)); p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.2)); p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.4)); @@ -177,22 +193,162 @@ int main(int argc, char **argv) { p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.2)); p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.4)); p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.6)); - //p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.8)); - Gudhi::alpha_complex::Alpha_complex_3d periodic_alpha_complex(points, + Gudhi::alpha_complex::Alpha_complex_3d periodic_alpha_complex(p_points, 0., 0., 0., 1., 1., 1.); + Gudhi::Simplex_tree<> p_stree; + periodic_alpha_complex.create_complex(p_stree); + std::cout << "Weighted periodic alpha complex 3d" << std::endl; using Weighted_periodic_alpha_shapes_3d = Gudhi::alpha_complex::Weighted_periodic_alpha_shapes_3d; std::vector wp_points; - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.1, 0.2, 0.3)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.5, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.1, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.6)); + + std::vector p_weights; + + std::random_device rd; + std::mt19937 mt(rd()); + // Weights must be in range [0, <1/64] + std::uniform_real_distribution dist(0.0, 0.0156245); + + for (std::size_t i = 0; i < wp_points.size(); ++i) { + double value = dist(mt); + std::cout << value << std::endl; + p_weights.push_back(value); + } Gudhi::alpha_complex::Alpha_complex_3d - weighted_periodic_alpha_complex(points, weights, + weighted_periodic_alpha_complex(wp_points, p_weights, 0., 0., 0., 1., 1., 1.); + Gudhi::Simplex_tree<> wp_stree; + weighted_periodic_alpha_complex.create_complex(wp_stree); return 0; } diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index c8bc9c8e..ff6eb3e6 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -36,6 +36,7 @@ #include #include #include +#include #include #include @@ -44,6 +45,12 @@ #include #include // for std::unique_ptr +#if CGAL_VERSION_NR < 1041101000 + // Make compilation fail - required for external projects - https://gitlab.inria.fr/GUDHI/gudhi-devel/issues/10 + static_assert(false, + "Alpha_complex_3d is only available for CGAL >= 4.11"); +#endif + namespace Gudhi { namespace alpha_complex { @@ -87,7 +94,7 @@ public: static_assert(!AlphaComplex3dOptions::periodic, "This constructor is not available for periodic versions of Alpha_complex_3d"); - alpha_shape_3_ptr_ = std::unique_ptr(new Alpha_shape_3(points.begin(), points.end(), 0, + alpha_shape_3_ptr_ = std::unique_ptr(new Alpha_shape_3(std::begin(points), std::end(points), 0, Alpha_shape_3::GENERAL)); Dispatch dispatcher = CGAL::dispatch_output(std::back_inserter(objects_), std::back_inserter(alpha_values_)); @@ -149,11 +156,13 @@ public: * * The type InputPointRange must be a range for which std::begin and * std::end return input iterators on a Kernel::Point_d. +* +* @exception std::invalid_argument In case the number of simplices is more than Simplex_key type numeric limit. */ template Alpha_complex_3d(const InputPointRange& points, - double x_min, double y_min, double z_min, - double x_max, double y_max, double z_max) { + Alpha_value_type x_min, Alpha_value_type y_min, Alpha_value_type z_min, + Alpha_value_type x_max, Alpha_value_type y_max, Alpha_value_type z_max) { static_assert(!AlphaComplex3dOptions::weighted, "This constructor is not available for weighted versions of Alpha_complex_3d"); static_assert(AlphaComplex3dOptions::periodic, @@ -171,15 +180,10 @@ public: // Heuristic for inserting large point sets (if pts is reasonably large) pdt.insert(std::begin(points), std::end(points), true); // As pdt won't be modified anymore switch to 1-sheeted cover if possible - // GUDHI_CHECK(pdt.is_triangulation_in_1_sheet(), - // std::invalid_argument("Uable to construct a triangulation within a single periodic domain.")); - if (pdt.is_triangulation_in_1_sheet()) { - pdt.convert_to_1_sheeted_covering(); - } else { - std::cerr << "ERROR: we were not able to construct a triangulation within a single periodic domain." << std::endl; - exit(-1); + if (!pdt.is_triangulation_in_1_sheet()) { + throw std::invalid_argument("Unable to construct a triangulation within a single periodic domain."); } - std::cout << "Periodic Delaunay computed." << std::endl; + pdt.convert_to_1_sheeted_covering(); // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. This is the default mode // Maybe need to set it to GENERAL mode @@ -232,7 +236,7 @@ public: std::size_t index = 0; weighted_points_3.reserve(points.size()); while ((index < weights.size()) && (index < points.size())) { - GUDHI_CHECK((weights[index] >= maximal_possible_weight) || (weights[index] < 0), + GUDHI_CHECK((weights[index] < maximal_possible_weight) || (weights[index] >= 0), std::invalid_argument("Invalid weight at line" + std::to_string(index + 1) + ". Must be positive and less than maximal possible weight = 1/64*cuboid length " "squared, which is not an acceptable input.")); @@ -247,9 +251,9 @@ public: // Heuristic for inserting large point sets (if pts is reasonably large) pdt.insert(std::begin(weighted_points_3), std::end(weighted_points_3), true); // As pdt won't be modified anymore switch to 1-sheeted cover if possible - GUDHI_CHECK(pdt.is_triangulation_in_1_sheet(), - std::invalid_argument("Unable to construct a triangulation within a single periodic domain.")); - + if (!pdt.is_triangulation_in_1_sheet()) { + throw std::invalid_argument("Unable to construct a triangulation within a single periodic domain."); + } pdt.convert_to_1_sheeted_covering(); // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. This is the default mode @@ -369,11 +373,16 @@ public: } } // Construction of the simplex_tree - Filtration_value filtr = /*std::sqrt*/ (*the_alpha_value_iterator); + //Alpha_value_type filtr; + Filtration_value filtr = + AlphaComplex3dOptions::template value_from_iterator::iterator> + (the_alpha_value_iterator); + //Filtration_value filtr = CGAL::to_double(the_alpha_value_iterator->exact()); #ifdef DEBUG_TRACES std::cout << "filtration = " << filtr << std::endl; #endif // DEBUG_TRACES - complex.insert_simplex(the_simplex, filtr); + //complex.insert_simplex(the_simplex, static_cast(filtr)); GUDHI_CHECK(the_alpha_value_iterator != alpha_values_.end(), "CGAL provided more simplices than values"); ++the_alpha_value_iterator; } diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h index 3b1981ca..32911a84 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h @@ -54,6 +54,11 @@ public: static const bool weighted = false; static const bool periodic = false; + + template + static Filtration_value value_from_iterator(const Alpha_value_iterator avi){ + return /*std::sqrt*/ *avi; + } }; class Exact_alpha_shapes_3d { @@ -72,6 +77,12 @@ public: static const bool weighted = false; static const bool periodic = false; + static const bool exact = true; + + template + static Filtration_value value_from_iterator(const Alpha_value_iterator avi){ + return /*std::sqrt*/ CGAL::to_double(avi->exact()); + } }; class Weighted_alpha_shapes_3d { @@ -92,6 +103,12 @@ public: static const bool weighted = true; static const bool periodic = false; + static const bool exact = false; + + template + static Filtration_value value_from_iterator(const Alpha_value_iterator avi){ + return /*std::sqrt*/ *avi; + } }; class Periodic_alpha_shapes_3d { @@ -117,6 +134,12 @@ public: static const bool weighted = false; static const bool periodic = true; + static const bool exact = false; + + template + static Filtration_value value_from_iterator(const Alpha_value_iterator avi){ + return /*std::sqrt*/ *avi; + } }; class Weighted_periodic_alpha_shapes_3d { @@ -136,11 +159,16 @@ public: using Alpha_shape_3 = CGAL::Alpha_shape_3; using Point_3 = Periodic_delaunay_triangulation_3::Bare_point; using Weighted_point_3 = Periodic_delaunay_triangulation_3::Weighted_point; - using Alpha_value_type = Alpha_shape_3::FT; using Iso_cuboid_3 = Periodic_kernel::Iso_cuboid_3; static const bool weighted = true; static const bool periodic = true; + static const bool exact = false; + + template + static Filtration_value value_from_iterator(const Alpha_value_iterator avi){ + return /*std::sqrt*/ *avi; + } }; } // namespace alpha_complex diff --git a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp index 11010701..42f3ddcb 100644 --- a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp @@ -101,7 +101,7 @@ int main(int argc, char **argv) { // Read the OFF file (input file name given as parameter) and triangulate points Gudhi::Points_3D_off_reader off_reader(off_file_points); // Check the read operation was correct - if (!off_reader.is_valid()) { + if (off_reader.is_valid()) { std::cerr << "Unable to read OFF file " << off_file_points << std::endl; exit(-1); } -- cgit v1.2.3 From 5ae0226e2871ba8cfcf28830a6cc753578be9fe4 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 27 Jun 2018 11:11:13 +0000 Subject: Fix examples and utilities git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@3645 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 67ac8f8151a85988303c48c9453ee42fecb7a97a --- src/Alpha_complex/example/CMakeLists.txt | 64 ++--- src/Alpha_complex/include/gudhi/Alpha_complex_3d.h | 4 +- .../include/gudhi/Alpha_complex_3d_options.h | 10 +- src/Alpha_complex/utilities/CMakeLists.txt | 75 +++--- .../utilities/alpha_complex_3d_helper.h | 74 ------ .../utilities/alpha_complex_3d_persistence.cpp | 132 ++++++++-- .../exact_alpha_complex_3d_persistence.cpp | 265 ------------------- .../periodic_alpha_complex_3d_persistence.cpp | 160 ------------ .../weighted_alpha_complex_3d_persistence.cpp | 154 ----------- ...ghted_periodic_alpha_complex_3d_persistence.cpp | 288 --------------------- 10 files changed, 189 insertions(+), 1037 deletions(-) delete mode 100644 src/Alpha_complex/utilities/alpha_complex_3d_helper.h delete mode 100644 src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp delete mode 100644 src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp delete mode 100644 src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp delete mode 100644 src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp (limited to 'src/Alpha_complex/example') diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt index c93832d2..5a66067c 100644 --- a/src/Alpha_complex/example/CMakeLists.txt +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -1,37 +1,43 @@ project(Alpha_complex_examples) -# need CGAL 4.7 -# cmake -DCGAL_DIR=~/workspace/CGAL-4.7 .. -if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) - add_executable ( Alpha_complex_example_from_points Alpha_complex_from_points.cpp ) - target_link_libraries(Alpha_complex_example_from_points ${CGAL_LIBRARY}) - add_executable ( Alpha_complex_example_from_off Alpha_complex_from_off.cpp ) - target_link_libraries(Alpha_complex_example_from_off ${CGAL_LIBRARY}) - if (TBB_FOUND) - target_link_libraries(Alpha_complex_example_from_points ${TBB_LIBRARIES}) - target_link_libraries(Alpha_complex_example_from_off ${TBB_LIBRARIES}) - endif() +if(CGAL_FOUND) + add_executable(alpha_complex_3d_step_by_step alpha_complex_3d_step_by_step.cpp) + target_link_libraries(alpha_complex_3d_step_by_step ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) - add_test(NAME Alpha_complex_example_from_points COMMAND $) + if (TBB_FOUND) + target_link_libraries(alpha_complex_3d_step_by_step ${TBB_LIBRARIES}) + endif(TBB_FOUND) - add_test(NAME Alpha_complex_example_from_off_60 COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" "60.0" "${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt") - add_test(NAME Alpha_complex_example_from_off_32 COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" "32.0" "${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt") - if (DIFF_PATH) - # Do not forget to copy test results files in current binary dir - file(COPY "alphaoffreader_for_doc_32.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - file(COPY "alphaoffreader_for_doc_60.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + add_test(NAME Alpha_complex_example_alpha_complex_3d_step_by_step COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off") - add_test(Alpha_complex_example_from_off_60_diff_files ${DIFF_PATH} - ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_60.txt) - add_test(Alpha_complex_example_from_off_32_diff_files ${DIFF_PATH} - ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt) - endif() + # need CGAL 4.7 + # cmake -DCGAL_DIR=~/workspace/CGAL-4.7 .. + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) + add_executable ( Alpha_complex_example_from_points Alpha_complex_from_points.cpp ) + target_link_libraries(Alpha_complex_example_from_points ${CGAL_LIBRARY}) + add_executable ( Alpha_complex_example_from_off Alpha_complex_from_off.cpp ) + target_link_libraries(Alpha_complex_example_from_off ${CGAL_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(Alpha_complex_example_from_points ${TBB_LIBRARIES}) + target_link_libraries(Alpha_complex_example_from_off ${TBB_LIBRARIES}) + endif() - install(TARGETS Alpha_complex_example_from_points DESTINATION bin) - install(TARGETS Alpha_complex_example_from_off DESTINATION bin) + add_test(NAME Alpha_complex_example_from_points COMMAND $) - add_executable ( traits_test traits_test.cpp ) + add_test(NAME Alpha_complex_example_from_off_60 COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" "60.0" "${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt") + add_test(NAME Alpha_complex_example_from_off_32 COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" "32.0" "${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt") + if (DIFF_PATH) + # Do not forget to copy test results files in current binary dir + file(COPY "alphaoffreader_for_doc_32.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + file(COPY "alphaoffreader_for_doc_60.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) -endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) + add_test(Alpha_complex_example_from_off_60_diff_files ${DIFF_PATH} + ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_60.txt) + add_test(Alpha_complex_example_from_off_32_diff_files ${DIFF_PATH} + ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt) + endif() + endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) +endif() \ No newline at end of file diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index 58364802..50e344e8 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -273,9 +273,9 @@ public: template - void create_complex(SimplicialComplexForAlpha3d& complex) { + bool create_complex(SimplicialComplexForAlpha3d& complex) { using Filtration_value = typename SimplicialComplexForAlpha3d::Filtration_value; - create_complex(complex, std::numeric_limits::infinity()); + return create_complex(complex, std::numeric_limits::infinity()); } /** \brief Inserts all Delaunay triangulation into the simplicial complex. diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h index 32911a84..e1b246c5 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h @@ -56,7 +56,7 @@ public: static const bool periodic = false; template - static Filtration_value value_from_iterator(const Alpha_value_iterator avi){ + static Filtration_value value_from_iterator(const Alpha_value_iterator avi) { return /*std::sqrt*/ *avi; } }; @@ -80,7 +80,7 @@ public: static const bool exact = true; template - static Filtration_value value_from_iterator(const Alpha_value_iterator avi){ + static Filtration_value value_from_iterator(const Alpha_value_iterator avi) { return /*std::sqrt*/ CGAL::to_double(avi->exact()); } }; @@ -106,7 +106,7 @@ public: static const bool exact = false; template - static Filtration_value value_from_iterator(const Alpha_value_iterator avi){ + static Filtration_value value_from_iterator(const Alpha_value_iterator avi) { return /*std::sqrt*/ *avi; } }; @@ -137,7 +137,7 @@ public: static const bool exact = false; template - static Filtration_value value_from_iterator(const Alpha_value_iterator avi){ + static Filtration_value value_from_iterator(const Alpha_value_iterator avi) { return /*std::sqrt*/ *avi; } }; @@ -166,7 +166,7 @@ public: static const bool exact = false; template - static Filtration_value value_from_iterator(const Alpha_value_iterator avi){ + static Filtration_value value_from_iterator(const Alpha_value_iterator avi) { return /*std::sqrt*/ *avi; } }; diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt index c4d986c4..b43fb6e2 100644 --- a/src/Alpha_complex/utilities/CMakeLists.txt +++ b/src/Alpha_complex/utilities/CMakeLists.txt @@ -1,68 +1,57 @@ project(Alpha_complex_utilities) if(CGAL_FOUND) - add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp) - target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) - add_executable(exact_alpha_complex_3d_persistence exact_alpha_complex_3d_persistence.cpp) - target_link_libraries(exact_alpha_complex_3d_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) - add_executable(weighted_alpha_complex_3d_persistence weighted_alpha_complex_3d_persistence.cpp) - target_link_libraries(weighted_alpha_complex_3d_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) - - add_executable(old_alpha_complex_3d_persistence old_alpha_complex_3d_persistence.cpp) - target_link_libraries(old_alpha_complex_3d_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) - - if (TBB_FOUND) - target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES}) - target_link_libraries(exact_alpha_complex_3d_persistence ${TBB_LIBRARIES}) - target_link_libraries(weighted_alpha_complex_3d_persistence ${TBB_LIBRARIES}) - - target_link_libraries(old_alpha_complex_3d_persistence ${TBB_LIBRARIES}) - endif(TBB_FOUND) - - add_test(NAME Alpha_complex_utilities_alpha_complex_3d_persistence COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45") - add_test(NAME Alpha_complex_utilities_exact_alpha_complex_3d COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45") - add_test(NAME Alpha_complex_utilities_weighted_alpha_complex_3d COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.weights" "-p" "2" "-m" "0.45") - - install(TARGETS alpha_complex_3d_persistence DESTINATION bin) - install(TARGETS exact_alpha_complex_3d_persistence DESTINATION bin) - install(TARGETS weighted_alpha_complex_3d_persistence DESTINATION bin) - if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) add_executable (alpha_complex_persistence alpha_complex_persistence.cpp) target_link_libraries(alpha_complex_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) - add_executable(periodic_alpha_complex_3d_persistence periodic_alpha_complex_3d_persistence.cpp) - target_link_libraries(periodic_alpha_complex_3d_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) - if (TBB_FOUND) target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES}) - target_link_libraries(periodic_alpha_complex_3d_persistence ${TBB_LIBRARIES}) endif(TBB_FOUND) add_test(NAME Alpha_complex_utilities_alpha_complex_persistence COMMAND $ "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45") - add_test(NAME Alpha_complex_utilities_periodic_alpha_complex_3d_persistence COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" "-p" "2" "-m" "0") install(TARGETS alpha_complex_persistence DESTINATION bin) - install(TARGETS periodic_alpha_complex_3d_persistence DESTINATION bin) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) if (NOT CGAL_VERSION VERSION_LESS 4.11.0) - add_executable(weighted_periodic_alpha_complex_3d_persistence weighted_periodic_alpha_complex_3d_persistence.cpp) - target_link_libraries(weighted_periodic_alpha_complex_3d_persistence ${CGAL_LIBRARY}) + add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp) + target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) if (TBB_FOUND) - target_link_libraries(weighted_periodic_alpha_complex_3d_persistence ${TBB_LIBRARIES}) + target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES}) endif(TBB_FOUND) - add_test(NAME Alpha_complex_utilities_weigted_periodic_alpha_complex_3d COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.weights" - "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" "3" "1.0") + add_test(NAME Alpha_complex_utilities_alpha_complex_3d COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" + "-p" "2" "-m" "0.45" "-o" "alpha.pers") + + add_test(NAME Alpha_complex_utilities_exact_alpha_complex_3d COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" + "-p" "2" "-m" "0.45" "-o" "exact.pers" "-e") + + if (DIFF_PATH) + add_test(Alpha_complex_utilities_diff_alpha_complex_3d ${DIFF_PATH} + "exact.pers" "alpha.pers") + endif() + + add_test(NAME Alpha_complex_utilities_periodic_alpha_complex_3d_persistence COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" + "-c" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" + "-p" "2" "-m" "0") + + add_test(NAME Alpha_complex_utilities_weighted_alpha_complex_3d COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" + "-w" "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.weights" + "-p" "2" "-m" "0") + + add_test(NAME Alpha_complex_utilities_weighted_periodic_alpha_complex_3d COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" + "-w" "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.weights" + "-c" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" + "-p" "2" "-m" "0") - install(TARGETS weighted_periodic_alpha_complex_3d_persistence DESTINATION bin) + install(TARGETS alpha_complex_3d_persistence DESTINATION bin) endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_helper.h b/src/Alpha_complex/utilities/alpha_complex_3d_helper.h deleted file mode 100644 index a72fd96d..00000000 --- a/src/Alpha_complex/utilities/alpha_complex_3d_helper.h +++ /dev/null @@ -1,74 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Vincent Rouvreau - * - * Copyright (C) 2014 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -#ifndef ALPHA_COMPLEX_3D_HELPER_H_ -#define ALPHA_COMPLEX_3D_HELPER_H_ - -template -Vertex_list from_cell(const Cell_handle& ch) { - Vertex_list the_list; - for (auto i = 0; i < 4; i++) { -#ifdef DEBUG_TRACES - std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(ch->vertex(i)); - } - return the_list; -} - -template -Vertex_list from_facet(const Facet& fct) { - Vertex_list the_list; - for (auto i = 0; i < 4; i++) { - if (fct.second != i) { -#ifdef DEBUG_TRACES - std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(fct.first->vertex(i)); - } - } - return the_list; -} - -template -Vertex_list from_edge(const Edge_3& edg) { - Vertex_list the_list; - for (auto i : {edg.second, edg.third}) { -#ifdef DEBUG_TRACES - std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(edg.first->vertex(i)); - } - return the_list; -} - -template -Vertex_list from_vertex(const Vertex_handle& vh) { - Vertex_list the_list; -#ifdef DEBUG_TRACES - std::cout << "from vertex=" << vh->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(vh); - return the_list; -} - -#endif // ALPHA_COMPLEX_3D_HELPER_H_ diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp index 669b6e08..00ede9ce 100644 --- a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp @@ -21,6 +21,7 @@ */ #include +#include #include #include @@ -28,41 +29,130 @@ #include #include -#include +#include #include -#include // for numeric_limits +#include // gudhi type definition +using Weighted_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Weighted_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Exact_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; using Simplex_tree = Gudhi::Simplex_tree; using Filtration_value = Simplex_tree::Filtration_value; using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; -void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag, - int &coeff_field_characteristic, Filtration_value &min_persistence); +void program_options(int argc, char *argv[], std::string &off_file_points, bool& exact, std::string &weight_file, + std::string &cuboid_file, std::string &output_file_diag, int &coeff_field_characteristic, + Filtration_value &min_persistence); + +template +bool create_complex(AlphaComplex3d& alpha_complex, Simplex_tree& simplex_tree) { + return alpha_complex.create_complex(simplex_tree); +} + +bool read_weight_file(const std::string& weight_file, std::vector& weights) { + // Read weights information from file + std::ifstream weights_ifstr(weight_file); + if (weights_ifstr.good()) { + double weight = 0.0; + // Attempt read the weight in a double format, return false if it fails + while (weights_ifstr >> weight) { + weights.push_back(weight); + } + } else { + return false; + } + return true; +} + +bool read_cuboid_file(const std::string& cuboid_file, double& x_min, double& y_min, double& z_min, + double& x_max, double& y_max, double& z_max) { + // Read weights information from file + std::ifstream iso_cuboid_str(cuboid_file); + if (iso_cuboid_str.is_open()) { + if (!(iso_cuboid_str >> x_min >> y_min >> z_min >> x_max >> y_max >> z_max)) { + return false; + } + } else { + return false; + } + return true; +} int main(int argc, char **argv) { std::string off_file_points; + std::string weight_file; + std::string cuboid_file; std::string output_file_diag; - int coeff_field_characteristic; - Filtration_value min_persistence; + int coeff_field_characteristic = 0; + Filtration_value min_persistence = 0.; + bool exact_version = false; + bool weighted_version = false; + bool periodic_version = false; - program_options(argc, argv, off_file_points, output_file_diag, coeff_field_characteristic, min_persistence); + program_options(argc, argv, off_file_points, exact_version, weight_file, cuboid_file, output_file_diag, + coeff_field_characteristic, min_persistence); // Read the OFF file (input file name given as parameter) and triangulate points Gudhi::Points_3D_off_reader off_reader(off_file_points); // Check the read operation was correct if (!off_reader.is_valid()) { - std::cerr << "Unable to read file " << off_file_points << std::endl; + std::cerr << "Unable to read OFF file " << off_file_points << std::endl; exit(-1); } - Alpha_complex_3d alpha_complex(off_reader.get_point_cloud()); + std::vector weights; + if (weight_file != std::string()) { + if (!read_weight_file(weight_file, weights)) { + std::cerr << "Unable to read weights file " << weight_file << std::endl; + exit(-1); + } + weighted_version = true; + } + + double x_min=0., y_min=0., z_min=0., x_max=0., y_max=0., z_max=0.; + std::ifstream iso_cuboid_str(argv[3]); + if (cuboid_file != std::string()) { + if (!read_cuboid_file(cuboid_file, x_min, y_min, z_min, x_max, y_max, z_max)) { + std::cerr << "Unable to read cuboid file " << cuboid_file << std::endl; + exit(-1); + } + periodic_version = true; + } Simplex_tree simplex_tree; - alpha_complex.create_complex(simplex_tree); + if (exact_version) { + if ((weighted_version) || (periodic_version)) { + std::cerr << "Unable to compute exact version of a weighted and/or periodic alpha shape" << std::endl; + exit(-1); + } else { + Exact_alpha_complex_3d alpha_complex(off_reader.get_point_cloud()); + create_complex(alpha_complex, simplex_tree); + } + } else { + if (weighted_version) { + if (periodic_version) { + Weighted_periodic_alpha_complex_3d alpha_complex(off_reader.get_point_cloud(), weights, + x_min, y_min, z_min, x_max, y_max, z_max); + create_complex(alpha_complex, simplex_tree); + } else { + Weighted_alpha_complex_3d alpha_complex(off_reader.get_point_cloud(), weights); + create_complex(alpha_complex, simplex_tree); + } + } else { + if (periodic_version) { + Periodic_alpha_complex_3d alpha_complex(off_reader.get_point_cloud(), x_min, y_min, z_min, x_max, y_max, z_max); + create_complex(alpha_complex, simplex_tree); + } else { + Alpha_complex_3d alpha_complex(off_reader.get_point_cloud()); + create_complex(alpha_complex, simplex_tree); + } + } + } // Sort the simplices in the order of the filtration simplex_tree.initialize_filtration(); @@ -88,8 +178,9 @@ int main(int argc, char **argv) { return 0; } -void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag, - int &coeff_field_characteristic, Filtration_value &min_persistence) { +void program_options(int argc, char *argv[], std::string &off_file_points, bool& exact, std::string &weight_file, + std::string &cuboid_file, std::string &output_file_diag, int &coeff_field_characteristic, + Filtration_value &min_persistence) { namespace po = boost::program_options; po::options_description hidden("Hidden options"); hidden.add_options()("input-file", po::value(&off_file_points), @@ -97,6 +188,12 @@ void program_options(int argc, char *argv[], std::string &off_file_points, std:: po::options_description visible("Allowed options", 100); visible.add_options()("help,h", "produce help message")( + "exact,e", po::bool_switch(&exact), + "To activate exact version of Alpha complex 3d (default is false, not available for weighted and/or periodic)")( + "weight-file,w", po::value(&weight_file)->default_value(std::string()), + "Name of file containing a point weights. Format is one weight per line:\n W1\n ...\n Wn ")( + "cuboid-file,c", po::value(&cuboid_file), + "Name of file describing the periodic domain. Format is:\n min_hx min_hy min_hz\n max_hx max_hy max_hz")( "output-file,o", po::value(&output_file_diag)->default_value(std::string()), "Name of file in which the persistence diagram is written. Default print in std::cout")( "field-charac,p", po::value(&coeff_field_characteristic)->default_value(11), @@ -115,18 +212,19 @@ void program_options(int argc, char *argv[], std::string &off_file_points, std:: po::store(po::command_line_parser(argc, argv).options(all).positional(pos).run(), vm); po::notify(vm); - if (vm.count("help") || !vm.count("input-file")) { + if (vm.count("help") || !vm.count("input-file") || !vm.count("weight-file")) { std::cout << std::endl; std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; - std::cout << "of a 3D Alpha complex defined on a set of input points.\n \n"; + std::cout << "of a 3D Alpha complex defined on a set of input points.\n"; + std::cout << "3D Alpha complex can be exact or weighted and/or periodic\n\n"; std::cout << "The output diagram contains one bar per line, written with the convention: \n"; std::cout << " p dim b d \n"; std::cout << "where dim is the dimension of the homological feature,\n"; std::cout << "b and d are respectively the birth and death of the feature and \n"; - std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients.\n\n"; - std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << "Usage: " << argv[0] << " [options] input-file weight-file\n\n"; std::cout << visible << std::endl; - std::abort(); + exit(-1); } } diff --git a/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp deleted file mode 100644 index cbe003ff..00000000 --- a/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp +++ /dev/null @@ -1,265 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Vincent Rouvreau - * - * Copyright (C) 2014 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -#include -#include - -#include -#include -#include - -#include -#include -#include -#include -#include -#include - -#include -#include -#include -#include -#include -#include -#include -#include - -#include "alpha_complex_3d_helper.h" - -// Alpha_shape_3 templates type definitions -using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; -using Exact_tag = CGAL::Tag_true; -using Vb = CGAL::Alpha_shape_vertex_base_3; -using Fb = CGAL::Alpha_shape_cell_base_3; -using Tds = CGAL::Triangulation_data_structure_3; -using Triangulation_3 = CGAL::Delaunay_triangulation_3; -using Alpha_shape_3 = CGAL::Alpha_shape_3; - -// From file type definition -using Point_3 = Kernel::Point_3; - -// filtration with alpha values needed type definition -using Alpha_value_type = Alpha_shape_3::FT; -using Object = CGAL::Object; -using Dispatch = - CGAL::Dispatch_output_iterator, - CGAL::cpp11::tuple >, - std::back_insert_iterator > > >; -using Cell_handle = Alpha_shape_3::Cell_handle; -using Facet = Alpha_shape_3::Facet; -using Edge_3 = Alpha_shape_3::Edge; -using Vertex_handle = Alpha_shape_3::Vertex_handle; -using Vertex_list = std::vector; - -// gudhi type definition -using ST = Gudhi::Simplex_tree; -using Filtration_value = ST::Filtration_value; -using Simplex_tree_vertex = ST::Vertex_handle; -using Alpha_shape_simplex_tree_map = std::map; -using Simplex_tree_vector_vertex = std::vector; -using Persistent_cohomology = - Gudhi::persistent_cohomology::Persistent_cohomology; - -void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag, - int &coeff_field_characteristic, Filtration_value &min_persistence); - -int main(int argc, char **argv) { - std::string off_file_points; - std::string output_file_diag; - int coeff_field_characteristic; - Filtration_value min_persistence; - - program_options(argc, argv, off_file_points, output_file_diag, coeff_field_characteristic, min_persistence); - - // Read the OFF file (input file name given as parameter) and triangulate points - Gudhi::Points_3D_off_reader off_reader(off_file_points); - // Check the read operation was correct - if (!off_reader.is_valid()) { - std::cerr << "Unable to read file " << off_file_points << std::endl; - exit(-1); - } - - // Retrieve the points - std::vector lp = off_reader.get_point_cloud(); - - // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. - Alpha_shape_3 as(lp.begin(), lp.end(), 0, Alpha_shape_3::GENERAL); -#ifdef DEBUG_TRACES - std::cout << "Alpha shape computed in GENERAL mode" << std::endl; -#endif // DEBUG_TRACES - - // filtration with alpha values from alpha shape - std::vector the_objects; - std::vector the_alpha_values; - - Dispatch disp = CGAL::dispatch_output(std::back_inserter(the_objects), - std::back_inserter(the_alpha_values)); - - as.filtration_with_alpha_values(disp); -#ifdef DEBUG_TRACES - std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; -#endif // DEBUG_TRACES - - Alpha_shape_3::size_type count_vertices = 0; - Alpha_shape_3::size_type count_edges = 0; - Alpha_shape_3::size_type count_facets = 0; - Alpha_shape_3::size_type count_cells = 0; - - // Loop on objects vector - Vertex_list vertex_list; - ST simplex_tree; - Alpha_shape_simplex_tree_map map_cgal_simplex_tree; - std::vector::iterator the_alpha_value_iterator = the_alpha_values.begin(); - for (auto object_iterator : the_objects) { - // Retrieve Alpha shape vertex list from object - if (const Cell_handle *cell = CGAL::object_cast(&object_iterator)) { - vertex_list = from_cell(*cell); - count_cells++; - } else if (const Facet *facet = CGAL::object_cast(&object_iterator)) { - vertex_list = from_facet(*facet); - count_facets++; - } else if (const Edge_3 *edge = CGAL::object_cast(&object_iterator)) { - vertex_list = from_edge(*edge); - count_edges++; - } else if (const Vertex_handle *vertex = CGAL::object_cast(&object_iterator)) { - count_vertices++; - vertex_list = from_vertex(*vertex); - } - // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex - Simplex_tree_vector_vertex the_simplex; - for (auto the_alpha_shape_vertex : vertex_list) { - Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex); - if (the_map_iterator == map_cgal_simplex_tree.end()) { - // alpha shape not found - Simplex_tree_vertex vertex = map_cgal_simplex_tree.size(); -#ifdef DEBUG_TRACES - std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl; -#endif // DEBUG_TRACES - the_simplex.push_back(vertex); - map_cgal_simplex_tree.emplace(the_alpha_shape_vertex, vertex); - } else { - // alpha shape found - Simplex_tree_vertex vertex = the_map_iterator->second; -#ifdef DEBUG_TRACES - std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl; -#endif // DEBUG_TRACES - the_simplex.push_back(vertex); - } - } - // Construction of the simplex_tree - // you can also use the_alpha_value_iterator->exact() - Filtration_value filtr = /*std::sqrt*/ CGAL::to_double(the_alpha_value_iterator->exact()); -#ifdef DEBUG_TRACES - std::cout << "filtration = " << filtr << std::endl; -#endif // DEBUG_TRACES - simplex_tree.insert_simplex(the_simplex, filtr); - if (the_alpha_value_iterator != the_alpha_values.end()) - ++the_alpha_value_iterator; - else - std::cout << "This shall not happen" << std::endl; - } - -#ifdef DEBUG_TRACES - std::cout << "vertices \t\t" << count_vertices << std::endl; - std::cout << "edges \t\t" << count_edges << std::endl; - std::cout << "facets \t\t" << count_facets << std::endl; - std::cout << "cells \t\t" << count_cells << std::endl; - - std::cout << "Information of the Simplex Tree: " << std::endl; - std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; - std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; - std::cout << " Dimension = " << simplex_tree.dimension() << " "; -#endif // DEBUG_TRACES - -#ifdef DEBUG_TRACES - std::cout << "Iterator on vertices: " << std::endl; - for (auto vertex : simplex_tree.complex_vertex_range()) { - std::cout << vertex << " "; - } -#endif // DEBUG_TRACES - - // Sort the simplices in the order of the filtration - simplex_tree.initialize_filtration(); - - std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl; - // Compute the persistence diagram of the complex - Persistent_cohomology pcoh(simplex_tree, true); - // initializes the coefficient field for homology - pcoh.init_coefficients(coeff_field_characteristic); - - pcoh.compute_persistent_cohomology(min_persistence); - - // Output the diagram in filediag - if (output_file_diag.empty()) { - pcoh.output_diagram(); - } else { - std::cout << "Result in file: " << output_file_diag << std::endl; - std::ofstream out(output_file_diag); - pcoh.output_diagram(out); - out.close(); - } - - return 0; -} - -void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag, - int &coeff_field_characteristic, Filtration_value &min_persistence) { - namespace po = boost::program_options; - po::options_description hidden("Hidden options"); - hidden.add_options()("input-file", po::value(&off_file_points), - "Name of file containing a point set. Format is one point per line: X1 ... Xd "); - - po::options_description visible("Allowed options", 100); - visible.add_options()("help,h", "produce help message")( - "output-file,o", po::value(&output_file_diag)->default_value(std::string()), - "Name of file in which the persistence diagram is written. Default print in std::cout")( - "field-charac,p", po::value(&coeff_field_characteristic)->default_value(11), - "Characteristic p of the coefficient field Z/pZ for computing homology.")( - "min-persistence,m", po::value(&min_persistence), - "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length " - "intervals"); - - po::positional_options_description pos; - pos.add("input-file", 1); - - po::options_description all; - all.add(visible).add(hidden); - - po::variables_map vm; - po::store(po::command_line_parser(argc, argv).options(all).positional(pos).run(), vm); - po::notify(vm); - - if (vm.count("help") || !vm.count("input-file")) { - std::cout << std::endl; - std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; - std::cout << "of a 3D Alpha complex defined on a set of input points.\n \n"; - std::cout << "The output diagram contains one bar per line, written with the convention: \n"; - std::cout << " p dim b d \n"; - std::cout << "where dim is the dimension of the homological feature,\n"; - std::cout << "b and d are respectively the birth and death of the feature and \n"; - std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; - - std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; - std::cout << visible << std::endl; - std::abort(); - } -} diff --git a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp deleted file mode 100644 index 6a3728fb..00000000 --- a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp +++ /dev/null @@ -1,160 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Vincent Rouvreau - * Pawel Dlotko - 2017 - Swansea University, UK - * - * Copyright (C) 2014 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -#include -#include - -#include -#include -#include -#include -#include - -#include -#include -#include -#include -#include -#include -#include -#include - -// gudhi type definition -using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Simplex_tree = Gudhi::Simplex_tree; -using Filtration_value = Simplex_tree::Filtration_value; -using Persistent_cohomology = - Gudhi::persistent_cohomology::Persistent_cohomology; - -void program_options(int argc, char *argv[], std::string &off_file_points, std::string &cuboid_file, - std::string &output_file_diag, int &coeff_field_characteristic, Filtration_value &min_persistence); - -int main(int argc, char **argv) { - std::string off_file_points; - std::string cuboid_file; - std::string output_file_diag; - int coeff_field_characteristic; - Filtration_value min_persistence; - - program_options(argc, argv, off_file_points, cuboid_file, output_file_diag, coeff_field_characteristic, - min_persistence); - - // Read the OFF file (input file name given as parameter) and triangulate points - Gudhi::Points_3D_off_reader off_reader(off_file_points); - // Check the read operation was correct - if (!off_reader.is_valid()) { - std::cerr << "Unable to read file " << off_file_points << std::endl; - exit(-1); - } - - // Read iso_cuboid_3 information from file - std::ifstream iso_cuboid_str(cuboid_file); - double x_min, y_min, z_min, x_max, y_max, z_max; - if (iso_cuboid_str.good()) { - iso_cuboid_str >> x_min >> y_min >> z_min >> x_max >> y_max >> z_max; - } else { - std::cerr << "Unable to read file " << cuboid_file << std::endl; - exit(-1); - } - // Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it. - if ((x_max - x_min != y_max - y_min) || (x_max - x_min != z_max - z_min) || (z_max - z_min != y_max - y_min)) { - std::cerr << "The size of the cuboid in every directions is not the same." << std::endl; - exit(-1); - } - - Alpha_complex_3d alpha_complex(off_reader.get_point_cloud(), x_min, y_min, z_min, x_max, y_max, z_max); - - Simplex_tree simplex_tree; - - alpha_complex.create_complex(simplex_tree); - - // Sort the simplices in the order of the filtration - simplex_tree.initialize_filtration(); - - std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl; - // Compute the persistence diagram of the complex - Persistent_cohomology pcoh(simplex_tree, true); - // initializes the coefficient field for homology - pcoh.init_coefficients(coeff_field_characteristic); - - pcoh.compute_persistent_cohomology(min_persistence); - - // Output the diagram in filediag - if (output_file_diag.empty()) { - pcoh.output_diagram(); - } else { - std::cout << "Result in file: " << output_file_diag << std::endl; - std::ofstream out(output_file_diag); - pcoh.output_diagram(out); - out.close(); - } - - return 0; -} - -void program_options(int argc, char *argv[], std::string &off_file_points, std::string &cuboid_file, - std::string &output_file_diag, int &coeff_field_characteristic, - Filtration_value &min_persistence) { - namespace po = boost::program_options; - po::options_description hidden("Hidden options"); - hidden.add_options()("input-file", po::value(&off_file_points), - "Name of file containing a point set. Format is one point per line: X1 ... Xd ")( - "cuboid-file", po::value(&cuboid_file), - "Name of file describing the periodic domain. Format is: min_hx min_hy min_hz\nmax_hx max_hy max_hz"); - - po::options_description visible("Allowed options", 100); - visible.add_options()("help,h", "produce help message")( - "output-file,o", po::value(&output_file_diag)->default_value(std::string()), - "Name of file in which the persistence diagram is written. Default print in std::cout")( - "field-charac,p", po::value(&coeff_field_characteristic)->default_value(11), - "Characteristic p of the coefficient field Z/pZ for computing homology.")( - "min-persistence,m", po::value(&min_persistence), - "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length " - "intervals"); - - po::positional_options_description pos; - pos.add("input-file", 1); - pos.add("cuboid-file", 2); - - po::options_description all; - all.add(visible).add(hidden); - - po::variables_map vm; - po::store(po::command_line_parser(argc, argv).options(all).positional(pos).run(), vm); - po::notify(vm); - - if (vm.count("help") || !vm.count("input-file") || !vm.count("cuboid-file")) { - std::cout << std::endl; - std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; - std::cout << "of a periodic 3D Alpha complex defined on a set of input points.\n \n"; - std::cout << "The output diagram contains one bar per line, written with the convention: \n"; - std::cout << " p dim b d \n"; - std::cout << "where dim is the dimension of the homological feature,\n"; - std::cout << "b and d are respectively the birth and death of the feature and \n"; - std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; - - std::cout << "Usage: " << argv[0] << " [options] input-file cuboid-file" << std::endl << std::endl; - std::cout << visible << std::endl; - std::abort(); - } -} diff --git a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp deleted file mode 100644 index 25512f98..00000000 --- a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp +++ /dev/null @@ -1,154 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Vincent Rouvreau - * - * Copyright (C) 2014 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -#include -#include - -#include -#include -#include -#include -#include - -#include -#include -#include - -// gudhi type definition -using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Simplex_tree = Gudhi::Simplex_tree; -using Filtration_value = Simplex_tree::Filtration_value; -using Persistent_cohomology = - Gudhi::persistent_cohomology::Persistent_cohomology; - -void program_options(int argc, char *argv[], std::string &off_file_points, std::string &weight_file, - std::string &output_file_diag, int &coeff_field_characteristic, Filtration_value &min_persistence); - -int main(int argc, char **argv) { - std::string off_file_points; - std::string weight_file; - std::string output_file_diag; - int coeff_field_characteristic; - Filtration_value min_persistence; - - program_options(argc, argv, off_file_points, weight_file, output_file_diag, coeff_field_characteristic, - min_persistence); - - // Read the OFF file (input file name given as parameter) and triangulate points - Gudhi::Points_3D_off_reader off_reader(off_file_points); - // Check the read operation was correct - if (!off_reader.is_valid()) { - std::cerr << "Unable to read OFF file " << off_file_points << std::endl; - exit(-1); - } - - // Read weights information from file - std::ifstream weights_ifstr(weight_file); - std::vector weights; - if (weights_ifstr.good()) { - double weight = 0.0; - // Attempt read the weight in a double format, return false if it fails - while (weights_ifstr >> weight) { - weights.push_back(weight); - } - } else { - std::cerr << "Unable to read weights file " << weight_file << std::endl; - exit(-1); - } - - Alpha_complex_3d alpha_complex(off_reader.get_point_cloud(), weights); - - Simplex_tree simplex_tree; - - alpha_complex.create_complex(simplex_tree); - - - // Sort the simplices in the order of the filtration - simplex_tree.initialize_filtration(); - - std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl; - // Compute the persistence diagram of the complex - Persistent_cohomology pcoh(simplex_tree, true); - // initializes the coefficient field for homology - pcoh.init_coefficients(coeff_field_characteristic); - - pcoh.compute_persistent_cohomology(min_persistence); - - // Output the diagram in filediag - if (output_file_diag.empty()) { - pcoh.output_diagram(); - } else { - std::cout << "Result in file: " << output_file_diag << std::endl; - std::ofstream out(output_file_diag); - pcoh.output_diagram(out); - out.close(); - } - - return 0; -} - -void program_options(int argc, char *argv[], std::string &off_file_points, std::string &weight_file, - std::string &output_file_diag, int &coeff_field_characteristic, - Filtration_value &min_persistence) { - namespace po = boost::program_options; - po::options_description hidden("Hidden options"); - hidden.add_options()("input-file", po::value(&off_file_points), - "Name of file containing a point set. Format is one point per line: X1 ... Xd ")( - "weight-file", po::value(&weight_file), - "Name of file containing a point weights. Format is one weigt per line: W1\n...\nWn "); - - po::options_description visible("Allowed options", 100); - visible.add_options()("help,h", "produce help message")( - "output-file,o", po::value(&output_file_diag)->default_value(std::string()), - "Name of file in which the persistence diagram is written. Default print in std::cout")( - "field-charac,p", po::value(&coeff_field_characteristic)->default_value(11), - "Characteristic p of the coefficient field Z/pZ for computing homology.")( - "min-persistence,m", po::value(&min_persistence), - "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length " - "intervals"); - - po::positional_options_description pos; - pos.add("input-file", 1); - pos.add("weight-file", 2); - - po::options_description all; - all.add(visible).add(hidden); - - po::variables_map vm; - po::store(po::command_line_parser(argc, argv).options(all).positional(pos).run(), vm); - po::notify(vm); - - if (vm.count("help") || !vm.count("input-file") || !vm.count("weight-file")) { - std::cout << std::endl; - std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; - std::cout << "of a weighted 3D Alpha complex defined on a set of input points.\n \n"; - std::cout << "The output diagram contains one bar per line, written with the convention: \n"; - std::cout << " p dim b d \n"; - std::cout << "where dim is the dimension of the homological feature,\n"; - std::cout << "b and d are respectively the birth and death of the feature and \n"; - std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; - - std::cout << "Usage: " << argv[0] << " [options] input-file weight-file" << std::endl << std::endl; - std::cout << visible << std::endl; - std::abort(); - } -} diff --git a/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp deleted file mode 100644 index d030c88c..00000000 --- a/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp +++ /dev/null @@ -1,288 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Vincent Rouvreau - * Pawel Dlotko - 2017 - Swansea University, UK - * - * Copyright (C) 2014 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -#include - -#include -#include -#include - -#include -#include -#include -#include -#include -#include -#include - -#include -#include -#include -#include -#include -#include -#include -#include - -#include "alpha_complex_3d_helper.h" - -// Traits -using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; -using PK = CGAL::Periodic_3_regular_triangulation_traits_3; - -// Vertex type -using DsVb = CGAL::Periodic_3_triangulation_ds_vertex_base_3<>; -using Vb = CGAL::Regular_triangulation_vertex_base_3; -using AsVb = CGAL::Alpha_shape_vertex_base_3; -// Cell type -using DsCb = CGAL::Periodic_3_triangulation_ds_cell_base_3<>; -using Cb = CGAL::Regular_triangulation_cell_base_3; -using AsCb = CGAL::Alpha_shape_cell_base_3; -using Tds = CGAL::Triangulation_data_structure_3; -using P3RT3 = CGAL::Periodic_3_regular_triangulation_3; -using Alpha_shape_3 = CGAL::Alpha_shape_3; - -using Point_3 = P3RT3::Bare_point; -using Weighted_point_3 = P3RT3::Weighted_point; - -// filtration with alpha values needed type definition -using Alpha_value_type = Alpha_shape_3::FT; -using Object = CGAL::Object; -using Dispatch = - CGAL::Dispatch_output_iterator, - CGAL::cpp11::tuple >, - std::back_insert_iterator > > >; -using Cell_handle = Alpha_shape_3::Cell_handle; -using Facet = Alpha_shape_3::Facet; -using Edge_3 = Alpha_shape_3::Edge; -using Vertex_handle = Alpha_shape_3::Vertex_handle; -using Vertex_list = std::vector; - -// gudhi type definition -using ST = Gudhi::Simplex_tree; -using Filtration_value = ST::Filtration_value; -using Simplex_tree_vertex = ST::Vertex_handle; -using Alpha_shape_simplex_tree_map = std::map; -using Simplex_tree_vector_vertex = std::vector; -using Persistent_cohomology = - Gudhi::persistent_cohomology::Persistent_cohomology; - -void usage(const std::string& progName) { - std::cerr << "Usage: " << progName << " path_to_the_OFF_file path_to_weight_file path_to_the_cuboid_file " - "coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; - exit(-1); -} - -int main(int argc, char* const argv[]) { - // program args management - if (argc != 6) { - std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; - usage(argv[0]); - } - - int coeff_field_characteristic = atoi(argv[4]); - Filtration_value min_persistence = strtof(argv[5], nullptr); - - // Read points from file - std::string offInputFile(argv[1]); - // Read the OFF file (input file name given as parameter) and triangulate points - Gudhi::Points_3D_off_reader off_reader(offInputFile); - // Check the read operation was correct - if (!off_reader.is_valid()) { - std::cerr << "Unable to read file " << offInputFile << std::endl; - usage(argv[0]); - } - - // Retrieve the points - std::vector lp = off_reader.get_point_cloud(); - - // Read iso_cuboid_3 information from file - std::ifstream iso_cuboid_str(argv[3]); - double x_min, y_min, z_min, x_max, y_max, z_max; - if (iso_cuboid_str.is_open()) { - if (!(iso_cuboid_str >> x_min >> y_min >> z_min >> x_max >> y_max >> z_max)) { - std::cerr << argv[3] << " - Bad file format." << std::endl; - usage(argv[0]); - } - - } else { - std::cerr << "Unable to read file " << argv[3] << std::endl; - usage(argv[0]); - } - // Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it. - if ((x_max - x_min != y_max - y_min) || (x_max - x_min != z_max - z_min) || (z_max - z_min != y_max - y_min)) { - std::cerr << "The size of the cuboid in every directions is not the same." << std::endl; - exit(-1); - } - - double maximal_possible_weight = 0.015625 * (x_max - x_min) * (x_max - x_min); - - // Read weights information from file - std::ifstream weights_ifstr(argv[2]); - std::vector wp; - if (weights_ifstr.is_open()) { - double weight = 0.0; - std::size_t index = 0; - wp.reserve(lp.size()); - // Attempt read the weight in a double format, return false if it fails - while ((weights_ifstr >> weight) && (index < lp.size())) { - if ((weight >= maximal_possible_weight) || (weight < 0)) { - std::cerr << "At line " << (index + 1) << ", the weight (" << weight - << ") is negative or more than or equal to maximal possible weight (" << maximal_possible_weight - << ") = 1/64*cuboid length squared, which is not an acceptable input." << std::endl; - exit(-1); - } - - wp.push_back(Weighted_point_3(lp[index], weight)); - index++; - } - if (index != lp.size()) { - std::cerr << "Bad number of weights in file " << argv[2] << std::endl; - usage(argv[0]); - } - } else { - std::cerr << "Unable to read file " << argv[2] << std::endl; - usage(argv[0]); - } - - // Define the periodic cube - P3RT3 prt(PK::Iso_cuboid_3(x_min, y_min, z_min, x_max, y_max, z_max)); - // Heuristic for inserting large point sets (if pts is reasonably large) - prt.insert(wp.begin(), wp.end(), true); - // As prt won't be modified anymore switch to 1-sheeted cover if possible - if (prt.is_triangulation_in_1_sheet()) { - prt.convert_to_1_sheeted_covering(); - } else { - std::cerr << "ERROR: we were not able to construct a triangulation within a single periodic domain." << std::endl; - exit(-1); - } - std::cout << "Weighted Periodic Delaunay computed." << std::endl; - - // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. This is the default mode - // Maybe need to set it to GENERAL mode - Alpha_shape_3 as(prt, 0, Alpha_shape_3::GENERAL); - - // filtration with alpha values from alpha shape - std::vector the_objects; - std::vector the_alpha_values; - - Dispatch disp = CGAL::dispatch_output(std::back_inserter(the_objects), - std::back_inserter(the_alpha_values)); - - as.filtration_with_alpha_values(disp); -#ifdef DEBUG_TRACES - std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; -#endif // DEBUG_TRACES - - Alpha_shape_3::size_type count_vertices = 0; - Alpha_shape_3::size_type count_edges = 0; - Alpha_shape_3::size_type count_facets = 0; - Alpha_shape_3::size_type count_cells = 0; - - // Loop on objects vector - Vertex_list vertex_list; - ST simplex_tree; - Alpha_shape_simplex_tree_map map_cgal_simplex_tree; - std::vector::iterator the_alpha_value_iterator = the_alpha_values.begin(); - for (auto object_iterator : the_objects) { - // Retrieve Alpha shape vertex list from object - if (const Cell_handle* cell = CGAL::object_cast(&object_iterator)) { - vertex_list = from_cell(*cell); - count_cells++; - } else if (const Facet* facet = CGAL::object_cast(&object_iterator)) { - vertex_list = from_facet(*facet); - count_facets++; - } else if (const Edge_3* edge = CGAL::object_cast(&object_iterator)) { - vertex_list = from_edge(*edge); - count_edges++; - } else if (const Vertex_handle* vertex = CGAL::object_cast(&object_iterator)) { - count_vertices++; - vertex_list = from_vertex(*vertex); - } - // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex - Simplex_tree_vector_vertex the_simplex; - for (auto the_alpha_shape_vertex : vertex_list) { - Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex); - if (the_map_iterator == map_cgal_simplex_tree.end()) { - // alpha shape not found - Simplex_tree_vertex vertex = map_cgal_simplex_tree.size(); -#ifdef DEBUG_TRACES - std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl; -#endif // DEBUG_TRACES - the_simplex.push_back(vertex); - map_cgal_simplex_tree.emplace(the_alpha_shape_vertex, vertex); - } else { - // alpha shape found - Simplex_tree_vertex vertex = the_map_iterator->second; -#ifdef DEBUG_TRACES - std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl; -#endif // DEBUG_TRACES - the_simplex.push_back(vertex); - } - } - // Construction of the simplex_tree - Filtration_value filtr = /*std::sqrt*/ (*the_alpha_value_iterator); -#ifdef DEBUG_TRACES - std::cout << "filtration = " << filtr << std::endl; -#endif // DEBUG_TRACES - simplex_tree.insert_simplex(the_simplex, filtr); - if (the_alpha_value_iterator != the_alpha_values.end()) - ++the_alpha_value_iterator; - else - std::cout << "This shall not happen" << std::endl; - } - -#ifdef DEBUG_TRACES - std::cout << "vertices \t\t" << count_vertices << std::endl; - std::cout << "edges \t\t" << count_edges << std::endl; - std::cout << "facets \t\t" << count_facets << std::endl; - std::cout << "cells \t\t" << count_cells << std::endl; - - std::cout << "Information of the Simplex Tree: " << std::endl; - std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; - std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; - std::cout << " Dimension = " << simplex_tree.dimension() << " "; -#endif // DEBUG_TRACES - -#ifdef DEBUG_TRACES - std::cout << "Iterator on vertices: " << std::endl; - for (auto vertex : simplex_tree.complex_vertex_range()) { - std::cout << vertex << " "; - } -#endif // DEBUG_TRACES - - // Sort the simplices in the order of the filtration - simplex_tree.initialize_filtration(); - - std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl; - // Compute the persistence diagram of the complex - Persistent_cohomology pcoh(simplex_tree, true); - // initializes the coefficient field for homology - pcoh.init_coefficients(coeff_field_characteristic); - - pcoh.compute_persistent_cohomology(min_persistence); - - pcoh.output_diagram(); - - return 0; -} -- cgit v1.2.3 From 9b8bb34ff06b08119b8fa1e78c260886287c5a92 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 3 Jul 2018 16:08:32 +0000 Subject: Documentation for Alpha complex 3d git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@3664 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: c6d824cdab7ac5ea79ce458dac666d35a9a21ab7 --- src/Alpha_complex/example/CMakeLists.txt | 10 - .../example/alpha_complex_3d_step_by_step.cpp | 309 +++++++++++++++++++++ src/Alpha_complex/include/gudhi/Alpha_complex_3d.h | 120 ++++++-- src/Alpha_complex/utilities/CMakeLists.txt | 2 +- src/Alpha_complex/utilities/alphacomplex.md | 101 ++++--- src/common/doc/examples.h | 4 - src/common/doc/installation.h | 20 +- src/common/doc/main_page.h | 2 +- 8 files changed, 454 insertions(+), 114 deletions(-) create mode 100644 src/Alpha_complex/example/alpha_complex_3d_step_by_step.cpp (limited to 'src/Alpha_complex/example') diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt index 5a66067c..af4bfd74 100644 --- a/src/Alpha_complex/example/CMakeLists.txt +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -1,16 +1,6 @@ project(Alpha_complex_examples) if(CGAL_FOUND) - add_executable(alpha_complex_3d_step_by_step alpha_complex_3d_step_by_step.cpp) - target_link_libraries(alpha_complex_3d_step_by_step ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) - - if (TBB_FOUND) - target_link_libraries(alpha_complex_3d_step_by_step ${TBB_LIBRARIES}) - endif(TBB_FOUND) - - add_test(NAME Alpha_complex_example_alpha_complex_3d_step_by_step COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off") - # need CGAL 4.7 # cmake -DCGAL_DIR=~/workspace/CGAL-4.7 .. if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) diff --git a/src/Alpha_complex/example/alpha_complex_3d_step_by_step.cpp b/src/Alpha_complex/example/alpha_complex_3d_step_by_step.cpp new file mode 100644 index 00000000..d76402e5 --- /dev/null +++ b/src/Alpha_complex/example/alpha_complex_3d_step_by_step.cpp @@ -0,0 +1,309 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Vincent Rouvreau + * + * Copyright (C) 2014 Inria + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include +#include +#include + +#if BOOST_VERSION >= 105400 +#include +#endif + +#include +#include + +#include +#include +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include +#include + +template +Vertex_list from_cell(const Cell_handle& ch) { + Vertex_list the_list; + for (auto i = 0; i < 4; i++) { +#ifdef DEBUG_TRACES + std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl; +#endif // DEBUG_TRACES + the_list.push_back(ch->vertex(i)); + } + return the_list; +} + +template +Vertex_list from_facet(const Facet& fct) { + Vertex_list the_list; + for (auto i = 0; i < 4; i++) { + if (fct.second != i) { +#ifdef DEBUG_TRACES + std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl; +#endif // DEBUG_TRACES + the_list.push_back(fct.first->vertex(i)); + } + } + return the_list; +} + +template +Vertex_list from_edge(const Edge_3& edg) { + Vertex_list the_list; + for (auto i : {edg.second, edg.third}) { +#ifdef DEBUG_TRACES + std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl; +#endif // DEBUG_TRACES + the_list.push_back(edg.first->vertex(i)); + } + return the_list; +} + +template +Vertex_list from_vertex(const Vertex_handle& vh) { + Vertex_list the_list; +#ifdef DEBUG_TRACES + std::cout << "from vertex=" << vh->point() << std::endl; +#endif // DEBUG_TRACES + the_list.push_back(vh); + return the_list; +} + +// Alpha_shape_3 templates type definitions +using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; +using Vb = CGAL::Alpha_shape_vertex_base_3; +using Fb = CGAL::Alpha_shape_cell_base_3; +using Tds = CGAL::Triangulation_data_structure_3; +using Triangulation_3 = CGAL::Delaunay_triangulation_3; +using Alpha_shape_3 = CGAL::Alpha_shape_3; + +// From file type definition +using Point_3 = Kernel::Point_3; + +// filtration with alpha values needed type definition +using Alpha_value_type = Alpha_shape_3::FT; +using Object = CGAL::Object; +using Dispatch = + CGAL::Dispatch_output_iterator, + CGAL::cpp11::tuple >, + std::back_insert_iterator > > >; +using Cell_handle = Alpha_shape_3::Cell_handle; +using Facet = Alpha_shape_3::Facet; +using Edge_3 = Alpha_shape_3::Edge; +using Vertex_handle = Alpha_shape_3::Vertex_handle; + +#if BOOST_VERSION >= 105400 +using Vertex_list = boost::container::static_vector; +#else +using Vertex_list = std::vector; +#endif + +// gudhi type definition +using ST = Gudhi::Simplex_tree; +using Filtration_value = ST::Filtration_value; +using Simplex_tree_vertex = ST::Vertex_handle; +using Alpha_shape_simplex_tree_map = std::map; +using Simplex_tree_vector_vertex = std::vector; + +void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag); + +int main(int argc, char **argv) { + std::string off_file_points; + std::string output_file_diag; + + program_options(argc, argv, off_file_points, output_file_diag); + + // Read the OFF file (input file name given as parameter) and triangulate points + Gudhi::Points_3D_off_reader off_reader(off_file_points); + // Check the read operation was correct + if (!off_reader.is_valid()) { + std::cerr << "Unable to read file " << off_file_points << std::endl; + exit(-1); + } + + // Retrieve the points + std::vector lp = off_reader.get_point_cloud(); + + // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. + Alpha_shape_3 as(lp.begin(), lp.end(), 0, Alpha_shape_3::GENERAL); +#ifdef DEBUG_TRACES + std::cout << "Alpha shape computed in GENERAL mode" << std::endl; +#endif // DEBUG_TRACES + + // filtration with alpha values from alpha shape + std::vector the_objects; + std::vector the_alpha_values; + + Dispatch disp = CGAL::dispatch_output(std::back_inserter(the_objects), + std::back_inserter(the_alpha_values)); + + as.filtration_with_alpha_values(disp); +#ifdef DEBUG_TRACES + std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; +#endif // DEBUG_TRACES + + Alpha_shape_3::size_type count_vertices = 0; + Alpha_shape_3::size_type count_edges = 0; + Alpha_shape_3::size_type count_facets = 0; + Alpha_shape_3::size_type count_cells = 0; + + // Loop on objects vector + Vertex_list vertex_list; + ST simplex_tree; + Alpha_shape_simplex_tree_map map_cgal_simplex_tree; + std::vector::iterator the_alpha_value_iterator = the_alpha_values.begin(); + for (auto object_iterator : the_objects) { + // Retrieve Alpha shape vertex list from object + if (const Cell_handle *cell = CGAL::object_cast(&object_iterator)) { + vertex_list = from_cell(*cell); + count_cells++; + } else if (const Facet *facet = CGAL::object_cast(&object_iterator)) { + vertex_list = from_facet(*facet); + count_facets++; + } else if (const Edge_3 *edge = CGAL::object_cast(&object_iterator)) { + vertex_list = from_edge(*edge); + count_edges++; + } else if (const Vertex_handle *vertex = CGAL::object_cast(&object_iterator)) { + count_vertices++; + vertex_list = from_vertex(*vertex); + } + // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex + Simplex_tree_vector_vertex the_simplex; + for (auto the_alpha_shape_vertex : vertex_list) { + Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex); + if (the_map_iterator == map_cgal_simplex_tree.end()) { + // alpha shape not found + Simplex_tree_vertex vertex = map_cgal_simplex_tree.size(); +#ifdef DEBUG_TRACES + std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl; +#endif // DEBUG_TRACES + the_simplex.push_back(vertex); + map_cgal_simplex_tree.emplace(the_alpha_shape_vertex, vertex); + } else { + // alpha shape found + Simplex_tree_vertex vertex = the_map_iterator->second; +#ifdef DEBUG_TRACES + std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl; +#endif // DEBUG_TRACES + the_simplex.push_back(vertex); + } + } + // Construction of the simplex_tree + Filtration_value filtr = /*std::sqrt*/ (*the_alpha_value_iterator); +#ifdef DEBUG_TRACES + std::cout << "filtration = " << filtr << std::endl; +#endif // DEBUG_TRACES + simplex_tree.insert_simplex(the_simplex, filtr); + GUDHI_CHECK(the_alpha_value_iterator != the_alpha_values.end(), "CGAL provided more simplices than values"); + ++the_alpha_value_iterator; + } + +#ifdef DEBUG_TRACES + std::cout << "vertices \t\t" << count_vertices << std::endl; + std::cout << "edges \t\t" << count_edges << std::endl; + std::cout << "facets \t\t" << count_facets << std::endl; + std::cout << "cells \t\t" << count_cells << std::endl; + + std::cout << "Information of the Simplex Tree: " << std::endl; + std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; + std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; + std::cout << " Dimension = " << simplex_tree.dimension() << " "; +#endif // DEBUG_TRACES + +#ifdef DEBUG_TRACES + std::cout << "Iterator on vertices: " << std::endl; + for (auto vertex : simplex_tree.complex_vertex_range()) { + std::cout << vertex << " "; + } +#endif // DEBUG_TRACES + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + std::streambuf* streambufffer; + std::ofstream ouput_file_stream; + if (output_file_diag != std::string()) { + ouput_file_stream.open(output_file_diag); + streambufffer = ouput_file_stream.rdbuf(); + } else { + streambufffer = std::cout.rdbuf(); + } + + std::ostream output_stream(streambufffer); + + // ---------------------------------------------------------------------------- + // Display information about the alpha complex + // ---------------------------------------------------------------------------- + output_stream << "Alpha complex is of dimension " << simplex_tree.dimension() << + " - " << simplex_tree.num_simplices() << " simplices - " << + simplex_tree.num_vertices() << " vertices." << std::endl; + + output_stream << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << + std::endl; + for (auto f_simplex : simplex_tree.filtration_simplex_range()) { + output_stream << " ( "; + for (auto vertex : simplex_tree.simplex_vertex_range(f_simplex)) { + output_stream << vertex << " "; + } + output_stream << ") -> " << "[" << simplex_tree.filtration(f_simplex) << "] "; + output_stream << std::endl; + } + + return 0; +} + +void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag) { + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options()("input-file", po::value(&off_file_points), + "Name of file containing a point set. Format is one point per line: X1 ... Xd "); + + po::options_description visible("Allowed options", 100); + visible.add_options()("help,h", "produce help message")( + "output-file,o", po::value(&output_file_diag)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout"); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; + all.add(visible).add(hidden); + + po::variables_map vm; + po::store(po::command_line_parser(argc, argv).options(all).positional(pos).run(), vm); + po::notify(vm); + + if (vm.count("help") || !vm.count("input-file")) { + std::cout << std::endl; + std::cout << "Compute and displays the 3D Alpha complex defined on a set of input points.\n \n"; + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + exit(-1); + } +} diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index 50e344e8..1d171f7d 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -55,6 +55,22 @@ namespace Gudhi { namespace alpha_complex { +/** + * \class Alpha_complex_3d Alpha_complex_3d.h gudhi/Alpha_complex_3d.h + * \brief Alpha complex data structure for 3d specific case. + * + * \ingroup alpha_complex + * + * \details + * The data structure is constructing a CGAL Delaunay triangulation (for more informations on CGAL Delaunay + * triangulation, please refer to the corresponding chapter in page http://doc.cgal.org/latest/Triangulation/) from a + * range of points or from an OFF file (cf. Points_off_reader). + * + * Please refer to \ref alpha_complex for examples. + * + * \remark When Alpha_complex is constructed with an infinite value of alpha, the complex is a Delaunay complex. + * + */ template class Alpha_complex_3d { using Alpha_shape_3 = typename AlphaComplex3dOptions::Alpha_shape_3; @@ -106,15 +122,24 @@ public: } - /** \brief Alpha_complex constructor from a list of points. -* -* Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. -* -* @param[in] points Range of points to triangulate. Points must be in Kernel::Point_d -* -* The type InputPointRange must be a range for which std::begin and -* std::end return input iterators on a Kernel::Point_d. -*/ + /** \brief Alpha_complex constructor from a list of points and associated weights. + * + * Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. + * Weights values are explained on CGAL Alpha + * shape and + * Regular + * triangulation documentation. + * + * @exception std::invalid_argument In debug mode, if points and weights do not have the same size. + * + * @param[in] points Range of points to triangulate. Points must be in AlphaComplex3dOptions::Point_3 + * @param[in] weights Range of weights on points. Points must be in AlphaComplex3dOptions::Point_3 + * + * The type InputPointRange must be a range for which std::begin and + * std::end return input iterators on a AlphaComplex3dOptions::Point_3. + * The type WeightRange must be a range for which std::begin and + * std::end return an input iterator on a AlphaComplex3dOptions::Alpha_shape_3::FT. + */ template Alpha_complex_3d(const InputPointRange& points, WeightRange weights) { static_assert(AlphaComplex3dOptions::weighted, @@ -148,17 +173,29 @@ public: #endif // DEBUG_TRACES } - /** \brief Alpha_complex constructor from a list of points. -* -* Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. -* -* @param[in] points Range of points to triangulate. Points must be in Kernel::Point_d -* -* The type InputPointRange must be a range for which std::begin and -* std::end return input iterators on a Kernel::Point_d. -* -* @exception std::invalid_argument In case the number of simplices is more than Simplex_key type numeric limit. -*/ + /** \brief Alpha_complex constructor from a list of points and an iso-cuboid coordinates. + * + * Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. + * + * Refer to the CGAL’s 3D Periodic + * Triangulations User Manual for more details. + * The periodicity is defined by an iso-oriented cuboid with diagonal opposite vertices (x_min, y_min, z_min) and + * (x_max, y_max, z_max). + * + * @exception std::invalid_argument In debug mode, if the size of the cuboid in every directions is not the same. + * + * @param[in] points Range of points to triangulate. Points must be in AlphaComplex3dOptions::Point_3 + * @param[in] x_min Iso-oriented cuboid x_min. + * @param[in] y_min Iso-oriented cuboid y_min. + * @param[in] z_min Iso-oriented cuboid z_min. + * @param[in] x_max Iso-oriented cuboid x_max. + * @param[in] y_max Iso-oriented cuboid y_max. + * @param[in] z_max Iso-oriented cuboid z_max. + * + * The type InputPointRange must be a range for which std::begin and + * std::end return input iterators on a AlphaComplex3dOptions::Point_3. + * The type of x_min, y_min, z_min, x_max, y_max and z_max is AlphaComplex3dOptions::Alpha_shape_3::FT. + */ template Alpha_complex_3d(const InputPointRange& points, Alpha_value_type x_min, Alpha_value_type y_min, Alpha_value_type z_min, @@ -200,15 +237,40 @@ public: } - /** \brief Alpha_complex constructor from a list of points. -* -* Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. -* -* @param[in] points Range of points to triangulate. Points must be in Kernel::Point_d -* -* The type InputPointRange must be a range for which std::begin and -* std::end return input iterators on a Kernel::Point_d. -*/ + /** \brief Alpha_complex constructor from a list of points, associated weights and an iso-cuboid coordinates. + * + * Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. + * + * Weights values are explained on CGAL Alpha + * shape and + * Regular + * triangulation documentation. + * + * Refer to the CGAL’s 3D Periodic + * Triangulations User Manual for more details. + * The periodicity is defined by an iso-oriented cuboid with diagonal opposite vertices (x_min, y_min, z_min) and + * (x_max, y_max, z_max). + * + * @exception std::invalid_argument In debug mode, if points and weights do not have the same size. + * @exception std::invalid_argument In debug mode, if the size of the cuboid in every directions is not the same. + * @exception std::invalid_argument In debug mode, if a weight is negative, zero, or greater than 1/64*cuboid length + * squared. + * + * @param[in] points Range of points to triangulate. Points must be in AlphaComplex3dOptions::Point_3 + * @param[in] weights Range of weights on points. Points must be in AlphaComplex3dOptions::Point_3 + * @param[in] x_min Iso-oriented cuboid x_min. + * @param[in] y_min Iso-oriented cuboid y_min. + * @param[in] z_min Iso-oriented cuboid z_min. + * @param[in] x_max Iso-oriented cuboid x_max. + * @param[in] y_max Iso-oriented cuboid y_max. + * @param[in] z_max Iso-oriented cuboid z_max. + * + * The type InputPointRange must be a range for which std::begin and + * std::end return input iterators on a AlphaComplex3dOptions::Point_3. + * The type WeightRange must be a range for which std::begin and + * std::end return an input iterator on a AlphaComplex3dOptions::Alpha_shape_3::FT. + * The type of x_min, y_min, z_min, x_max, y_max and z_max is AlphaComplex3dOptions::Alpha_shape_3::FT. + */ template Alpha_complex_3d(const InputPointRange& points, WeightRange weights, Alpha_value_type x_min, Alpha_value_type y_min, Alpha_value_type z_min, diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt index b43fb6e2..86e761ef 100644 --- a/src/Alpha_complex/utilities/CMakeLists.txt +++ b/src/Alpha_complex/utilities/CMakeLists.txt @@ -15,7 +15,7 @@ if(CGAL_FOUND) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) - if (NOT CGAL_VERSION VERSION_LESS 4.11.0) + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp) target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) if (TBB_FOUND) diff --git a/src/Alpha_complex/utilities/alphacomplex.md b/src/Alpha_complex/utilities/alphacomplex.md index 0fe98837..7ae5f913 100644 --- a/src/Alpha_complex/utilities/alphacomplex.md +++ b/src/Alpha_complex/utilities/alphacomplex.md @@ -12,15 +12,18 @@ Leave the lines above as it is required by the web site generator 'Jekyll' ## alpha_complex_persistence ## -This program computes the persistent homology with coefficient field Z/pZ of the dD alpha complex built from a dD point cloud. +This program computes the persistent homology with coefficient field Z/pZ of +the dD alpha complex built from a dD point cloud. The output diagram contains one bar per line, written with the convention: ``` p dim birth death ``` -where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature, -and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p` must be a prime number). +where `dim` is the dimension of the homological feature, `birth` and `death` +are respectively the birth and death of the feature, and `p` is the +characteristic of the field *Z/pZ* used for homology coefficients (`p` must be +a prime number). **Usage** @@ -29,15 +32,20 @@ and `p` is the characteristic of the field *Z/pZ* used for homology coefficients ``` where -`` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html). +`` is the path to the input point cloud in +[nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html). **Allowed options** * `-h [ --help ]` Produce help message -* `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output. -* `-r [ --max-alpha-square-value ]` (default = inf) Maximal alpha square value for the Alpha complex construction. -* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology. -* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. +* `-o [ --output-file ]` Name of file in which the persistence diagram is +written. Default print in standard output. +* `-r [ --max-alpha-square-value ]` (default = inf) Maximal alpha square value +for the Alpha complex construction. +* `-p [ --field-charac ]` (default = 11) Characteristic p of the +coefficient field Z/pZ for computing homology. +* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature +to be recorded. Enter a negative value to see zero length intervals. **Example** @@ -51,13 +59,26 @@ N.B.: ## alpha_complex_3d_persistence ## -This program computes the persistent homology with coefficient field Z/pZ of the 3D alpha complex built from a 3D point cloud. The output diagram contains one bar per line, written with the convention: +This program computes the persistent homology with coefficient field Z/pZ of +the 3D alpha complex built from a 3D point cloud. +One can use exact computation. It is slower, but it is necessary when points +are on a grid for instance. +Alpha complex 3d can be weighted and/or periodic (refer to the +[CGAL's 3D Periodic Triangulations User Manual]( +https://doc.cgal.org/latest/Periodic_3_triangulation_3/index.html) +for more details). + +The output diagram contains +one bar per line, written with the convention: ``` p dim birth death ``` -where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p` must be a prime number). +where `dim` is the dimension of the homological feature, `birth` and `death` +are respectively the birth and death of the feature, and `p` is the +characteristic of the field *Z/pZ* used for homology coefficients (`p` must be +a prime number). **Usage** @@ -65,14 +86,25 @@ where `dim` is the dimension of the homological feature, `birth` and `death` are alpha_complex_3d_persistence [options] ``` -where `` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html). +where `` is the path to the input point cloud in +[nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html). **Allowed options** * `-h [ --help ]` Produce help message -* `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output. -* `-p [ --field-charac ]` (default=11) Characteristic p of the coefficient field Z/pZ for computing homology. -* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. +* `-o [ --output-file ]` Name of file in which the persistence diagram is +written. Default print in standard output. +* `-p [ --field-charac ]` (default=11) Characteristic p of the coefficient +field Z/pZ for computing homology. +* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature +to be recorded. Enter a negative value to see zero length intervals. +* `-c [ --cuboid-file ]` is the path to the file describing the periodic domain. +It must be in the format described +[here](/doc/latest/fileformats.html#FileFormatsIsoCuboid). +* `-w [ --weight-file ]` is the path to the file containing the weights of the +points (one value per line). +* `-e [ --exact ]` for the exact computation version (not compatible with +weight and periodic version). **Example** @@ -84,49 +116,16 @@ N.B.: * `alpha_complex_3d_persistence` only accepts OFF files in dimension 3. * Filtration values are alpha square values. - - -## exact_alpha_complex_3d_persistence ## - -Same as `alpha_complex_3d_persistence`, but using exact computation. -It is slower, but it is necessary when points are on a grid for instance. +* Weights values are explained on CGAL +[Alpha shape](https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title0) +and +[Regular triangulation](https://doc.cgal.org/latest/Triangulation_3/index.html#Triangulation3secclassRegulartriangulation) documentation. -## weighted_alpha_complex_3d_persistence ## -Same as `alpha_complex_3d_persistence`, but using weighted points. -**Usage** - -``` - weighted_alpha_complex_3d_persistence [options] -``` - -where - -* `` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html). -* `` is the path to the file containing the weights of the points (one value per line). -**Allowed options** - -* `-h [ --help ]` Produce help message -* `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output. -* `-p [ --field-charac ]` (default=11) Characteristic p of the coefficient field Z/pZ for computing homology. -* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. - -**Example** - -``` - weighted_alpha_complex_3d_persistence ../../data/points/tore3D_300.off ../../data/points/tore3D_300.weights -p 2 -m 0.45 -``` - - -N.B.: - -* Weights values are explained on CGAL [Alpha shape](https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title0) -and [Regular triangulation](https://doc.cgal.org/latest/Triangulation_3/index.html#Triangulation3secclassRegulartriangulation) documentation. -* Filtration values are alpha square values. ## periodic_alpha_complex_3d_persistence ## diff --git a/src/common/doc/examples.h b/src/common/doc/examples.h index 40f202c7..7c2a8f69 100644 --- a/src/common/doc/examples.h +++ b/src/common/doc/examples.h @@ -53,10 +53,6 @@ * @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 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/installation.h b/src/common/doc/installation.h index 12407c18..8f91e9c1 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -58,10 +58,6 @@ make doxygen * Library (CGAL \cite cgal:eb-15b) and will not be built if CGAL is not installed: * \li * Alpha_complex/alpha_complex_3d_persistence.cpp - * \li - * Alpha_complex/exact_alpha_complex_3d_persistence.cpp - * \li - * Alpha_complex/weighted_alpha_complex_3d_persistence.cpp * \li * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp * @@ -84,8 +80,6 @@ make doxygen * Alpha_complex/Alpha_complex_from_points.cpp * \li * Alpha_complex/alpha_complex_persistence.cpp - * \li - * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp * \li * Persistent_cohomology/custom_persistence_sort.cpp * @@ -132,8 +126,8 @@ make doxygen * Alpha_complex/Alpha_complex_from_points.cpp * \li * Alpha_complex/alpha_complex_persistence.cpp - * \li - * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp + * \li + * Alpha_complex/alpha_complex_3d_persistence.cpp * \li * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp * \li @@ -179,12 +173,6 @@ make doxygen * Alpha_complex/alpha_complex_3d_persistence.cpp * \li * Alpha_complex/alpha_complex_persistence.cpp - * \li - * Alpha_complex/exact_alpha_complex_3d_persistence.cpp - * \li - * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp - * \li - * Alpha_complex/weighted_alpha_complex_3d_persistence.cpp * \li * Bitmap_cubical_complex/cubical_complex_persistence.cpp * \li @@ -223,10 +211,6 @@ make doxygen * Persistent_cohomology/rips_multifield_persistence.cpp * \li * Persistent_cohomology/rips_persistence_step_by_step.cpp - * \li - * Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp - * \li - * Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp * \li * Persistent_cohomology/custom_persistence_sort.cpp * \li diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index db1e80ce..35b84d2e 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -29,7 +29,7 @@ Author: Vincent Rouvreau
Introduced in: GUDHI 1.3.0
Copyright: GPL v3
- Requires: \ref cgal ≥ 4.7.0 and \ref eigen3 + Requires: \ref cgal ≥ 4.11.0 and \ref eigen3 Alpha_complex is a simplicial complex constructed from the finite cells of a Delaunay Triangulation.
-- cgit v1.2.3 From c89ae478ea5d6685c862533fac1aea973e9cda02 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 31 Jul 2018 14:33:49 +0000 Subject: Add unitary tests and documentation Fix debug exception mechanism git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@3712 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 43f66f3843981ab9cd74c117c2b1c6bb9b94810b --- src/Alpha_complex/doc/Intro_alpha_complex.h | 23 + src/Alpha_complex/example/CMakeLists.txt | 10 + .../Weighted_alpha_complex_3d_from_points.cpp | 71 +++ src/Alpha_complex/example/traits_test.cpp | 354 ----------- .../example/weightedalpha3dfrompoints_for_doc.txt | 31 + src/Alpha_complex/include/gudhi/Alpha_complex_3d.h | 10 +- .../test/Alpha_complex_3d_unit_test.cpp | 663 +++++++++++++++++++++ src/Alpha_complex/test/CMakeLists.txt | 7 + .../utilities/alpha_complex_3d_persistence.cpp | 29 +- src/Alpha_complex/utilities/alphacomplex.md | 44 +- 10 files changed, 829 insertions(+), 413 deletions(-) create mode 100644 src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp delete mode 100644 src/Alpha_complex/example/traits_test.cpp create mode 100644 src/Alpha_complex/example/weightedalpha3dfrompoints_for_doc.txt create mode 100644 src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp (limited to 'src/Alpha_complex/example') diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h index 7a375c9f..82aee275 100644 --- a/src/Alpha_complex/doc/Intro_alpha_complex.h +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -165,6 +165,29 @@ namespace alpha_complex { * * \include Alpha_complex/alphaoffreader_for_doc_32.txt * + * + * \section weighted3dexample 3d specific example + * + * A specific module for Alpha complex is available in 3d (cf. Alpha_complex_3d) and allows to construct default, exact, + * weighted, periodic or weighted and periodic versions of alpha complexes + * + * This example builds the CGAL 3d weighted alpha shapes from a small molecule, and initializes the alpha complex with + * it. This example is taken from CGAL 3d + * weighted alpha shapes. + * + * Then, it is asked to display information about the alpha complex. + * + * \include Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp + * + * When launching: + * + * \code $> ./Alpha_complex_example_weighted_3d_from_points + * \endcode + * + * the program output is: + * + * \include Alpha_complex/weightedalpha3dfrompoints_for_doc.txt + * */ /** @} */ // end defgroup alpha_complex diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt index af4bfd74..4a1cd26d 100644 --- a/src/Alpha_complex/example/CMakeLists.txt +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -30,4 +30,14 @@ if(CGAL_FOUND) ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt) endif() endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) + add_executable ( Alpha_complex_example_weighted_3d_from_points Weighted_alpha_complex_3d_from_points.cpp ) + target_link_libraries(Alpha_complex_example_weighted_3d_from_points ${CGAL_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(Alpha_complex_example_weighted_3d_from_points ${TBB_LIBRARIES}) + endif() + add_test(NAME Alpha_complex_example_weighted_3d_from_points + COMMAND $) + + endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) endif() \ No newline at end of file diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp new file mode 100644 index 00000000..abb73427 --- /dev/null +++ b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp @@ -0,0 +1,71 @@ +#include +#include +// to construct a simplex_tree from alpha complex +#include + +#include +#include +#include +#include // for numeric limits + +using Weighted_alpha_shapes_3d = Gudhi::alpha_complex::Weighted_alpha_shapes_3d; +using Weighted_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Point = Gudhi::alpha_complex::Weighted_alpha_shapes_3d::Point_3 ; +using Vector_of_points = std::vector; +using Vector_of_weights = std::vector; + +void usage(int nbArgs, char * const progName) { + std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; + std::cerr << "Usage: " << progName << " \n"; + exit(-1); // ----- >> +} + +int main(int argc, char **argv) { + if (argc != 1) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; + std::cerr << "Usage: " << (argv[0] - 1) << " \n"; + exit(-1); // ----- >> + } + + // ---------------------------------------------------------------------------- + // Init of a list of points and weights from a small molecule + // ---------------------------------------------------------------------------- + Vector_of_points points; + Vector_of_weights weights; + points.push_back(Point(1, -1, -1)); + weights.push_back(4.); + points.push_back(Point(-1, 1, -1)); + weights.push_back(4.); + points.push_back(Point(-1, -1, 1)); + weights.push_back(4.); + points.push_back(Point(1, 1, 1)); + weights.push_back(4.); + points.push_back(Point(2, 2, 2)); + weights.push_back(1.); + + // ---------------------------------------------------------------------------- + // Init of an alpha complex from the list of points + // ---------------------------------------------------------------------------- + Weighted_alpha_complex_3d alpha_complex_from_points(points, weights); + + Gudhi::Simplex_tree<> simplex; + if (alpha_complex_from_points.create_complex(simplex)) { + // ---------------------------------------------------------------------------- + // Display information about the alpha complex + // ---------------------------------------------------------------------------- + std::cout << "Alpha complex is of dimension " << simplex.dimension() << + " - " << simplex.num_simplices() << " simplices - " << + simplex.num_vertices() << " vertices." << std::endl; + + std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; + for (auto f_simplex : simplex.filtration_simplex_range()) { + std::cout << " ( "; + for (auto vertex : simplex.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << ") -> " << "[" << simplex.filtration(f_simplex) << "] "; + std::cout << std::endl; + } + } + return 0; +} diff --git a/src/Alpha_complex/example/traits_test.cpp b/src/Alpha_complex/example/traits_test.cpp deleted file mode 100644 index 1dd062de..00000000 --- a/src/Alpha_complex/example/traits_test.cpp +++ /dev/null @@ -1,354 +0,0 @@ -#include -#include - -#include -#include -#include -#include // for numeric limits -#include - -void usage(int nbArgs, char * const progName) { - std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; - std::cerr << "Usage: " << progName << " [alpha_square_max_value]\n"; - std::cerr << " i.e.: " << progName << " 60.0\n"; - exit(-1); // ----- >> -} - -int main(int argc, char **argv) { - //if ((argc != 1) && (argc != 2)) usage(argc, (argv[0] - 1)); - - std::cout << "Alpha complex 3d" << std::endl; - using Alpha_shapes_3d = Gudhi::alpha_complex::Alpha_shapes_3d; - std::vector points; - points.push_back(Alpha_shapes_3d::Point_3(0.0, 0.0, 0.0)); - points.push_back(Alpha_shapes_3d::Point_3(0.0, 0.0, 0.2)); - points.push_back(Alpha_shapes_3d::Point_3(0.2, 0.0, 0.2)); - points.push_back(Alpha_shapes_3d::Point_3(0.6, 0.6, 0.0)); - points.push_back(Alpha_shapes_3d::Point_3(0.8, 0.8, 0.2)); - points.push_back(Alpha_shapes_3d::Point_3(0.2, 0.8, 0.6)); - - Gudhi::alpha_complex::Alpha_complex_3d alpha_complex(points); - - Gudhi::Simplex_tree<> stree; - alpha_complex.create_complex(stree); - - std::cout << "Exact alpha complex 3d" << std::endl; - using Exact_alpha_shapes_3d = Gudhi::alpha_complex::Exact_alpha_shapes_3d; - std::vector e_points; - e_points.push_back(Exact_alpha_shapes_3d::Point_3(0.0, 0.0, 0.0)); - e_points.push_back(Exact_alpha_shapes_3d::Point_3(0.0, 0.0, 0.2)); - e_points.push_back(Exact_alpha_shapes_3d::Point_3(0.2, 0.0, 0.2)); - e_points.push_back(Exact_alpha_shapes_3d::Point_3(0.6, 0.6, 0.0)); - e_points.push_back(Exact_alpha_shapes_3d::Point_3(0.8, 0.8, 0.2)); - e_points.push_back(Exact_alpha_shapes_3d::Point_3(0.2, 0.8, 0.6)); - - Gudhi::alpha_complex::Alpha_complex_3d exact_alpha_complex(e_points); - - Gudhi::Simplex_tree exact_stree; - exact_alpha_complex.create_complex(exact_stree); - - std::cout << "Weighted alpha complex 3d" << std::endl; - using Weighted_alpha_shapes_3d = Gudhi::alpha_complex::Weighted_alpha_shapes_3d; - std::vector w_points; - w_points.push_back(Weighted_alpha_shapes_3d::Point_3(0.0, 0.0, 0.0)); - w_points.push_back(Weighted_alpha_shapes_3d::Point_3(0.0, 0.0, 0.2)); - w_points.push_back(Weighted_alpha_shapes_3d::Point_3(0.2, 0.0, 0.2)); - w_points.push_back(Weighted_alpha_shapes_3d::Point_3(0.6, 0.6, 0.0)); - w_points.push_back(Weighted_alpha_shapes_3d::Point_3(0.8, 0.8, 0.2)); - w_points.push_back(Weighted_alpha_shapes_3d::Point_3(0.2, 0.8, 0.6)); - - std::vector weights = {0.01, 0.005, 0.006, 0.01, 0.009, 0.001}; - - Gudhi::alpha_complex::Alpha_complex_3d weighted_alpha_complex(w_points, weights); - - Gudhi::Simplex_tree<> w_stree; - weighted_alpha_complex.create_complex(w_stree); - - std::cout << "Periodic alpha complex 3d" << std::endl; - using Periodic_alpha_shapes_3d = Gudhi::alpha_complex::Periodic_alpha_shapes_3d; - std::vector p_points; - - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.0)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.2)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.4)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.6)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.8)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.0)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.2)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.4)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.6)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.8)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.0)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.2)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.4)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.6)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.8)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.0)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.2)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.4)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.6)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.8)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.0)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.2)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.4)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.6)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.8)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.0)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.2)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.4)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.6)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.8)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.0)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.2)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.4)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.6)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.8)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.0)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.2)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.4)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.6)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.8)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.0)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.2)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.4)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.6)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.8)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.0)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.2)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.4)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.6)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.8)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.0)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.2)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.4)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.6)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.8)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.0)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.2)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.4)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.6)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.8)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.0)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.2)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.4)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.6)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.8)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.0)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.2)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.4)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.6)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.8)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.0)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.2)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.4)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.6)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.8)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.0)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.2)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.4)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.6)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.8)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.1, 0.0)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.0)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.2)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.4)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.6)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.8)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.0)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.2)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.4)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.6)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.8)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.0)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.2)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.4)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.6)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.8)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.0)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.2)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.4)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.6)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.8)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.0)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.2)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.4)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.6)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.8)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.0)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.2)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.4)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.6)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.8)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.0)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.2)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.4)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.6)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.8)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.0)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.2)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.4)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.6)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.8)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.0)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.2)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.4)); - p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.6)); - - Gudhi::alpha_complex::Alpha_complex_3d periodic_alpha_complex(p_points, - 0., 0., 0., - 1., 1., 1.); - - Gudhi::Simplex_tree<> p_stree; - periodic_alpha_complex.create_complex(p_stree); - - std::cout << "Weighted periodic alpha complex 3d" << std::endl; - using Weighted_periodic_alpha_shapes_3d = Gudhi::alpha_complex::Weighted_periodic_alpha_shapes_3d; - std::vector wp_points; - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.0)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.2)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.4)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.6)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.8)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.0)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.2)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.4)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.6)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.8)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.0)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.2)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.4)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.6)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.8)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.0)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.2)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.4)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.6)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.8)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.0)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.2)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.4)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.6)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.8)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.0)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.2)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.4)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.6)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.8)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.0)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.2)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.4)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.6)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.8)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.0)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.2)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.4)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.6)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.8)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.0)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.2)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.4)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.6)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.8)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.0)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.2)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.4)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.6)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.8)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.0)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.2)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.4)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.6)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.8)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.0)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.2)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.4)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.6)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.8)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.0)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.2)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.4)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.6)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.8)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.0)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.2)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.4)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.6)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.8)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.0)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.2)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.4)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.6)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.8)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.0)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.2)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.4)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.6)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.8)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.1, 0.0)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.0)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.2)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.4)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.6)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.8)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.0)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.2)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.4)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.6)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.8)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.0)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.2)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.4)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.6)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.8)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.0)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.2)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.4)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.6)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.8)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.0)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.2)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.4)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.6)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.8)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.0)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.2)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.4)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.6)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.8)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.0)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.2)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.4)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.6)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.8)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.0)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.2)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.4)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.6)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.8)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.0)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.2)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.4)); - wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.6)); - - std::vector p_weights; - - std::random_device rd; - std::mt19937 mt(rd()); - // Weights must be in range [0, <1/64] - std::uniform_real_distribution dist(0.0, 0.0156245); - - for (std::size_t i = 0; i < wp_points.size(); ++i) { - double value = dist(mt); - std::cout << value << std::endl; - p_weights.push_back(value); - } - - Gudhi::alpha_complex::Alpha_complex_3d - weighted_periodic_alpha_complex(wp_points, p_weights, - 0., 0., 0., - 1., 1., 1.); - Gudhi::Simplex_tree<> wp_stree; - weighted_periodic_alpha_complex.create_complex(wp_stree); - - return 0; -} diff --git a/src/Alpha_complex/example/weightedalpha3dfrompoints_for_doc.txt b/src/Alpha_complex/example/weightedalpha3dfrompoints_for_doc.txt new file mode 100644 index 00000000..7a09998d --- /dev/null +++ b/src/Alpha_complex/example/weightedalpha3dfrompoints_for_doc.txt @@ -0,0 +1,31 @@ +Alpha complex is of dimension 3 - 29 simplices - 5 vertices. +Iterator on alpha complex simplices in the filtration order, with [filtration value]: + ( 0 ) -> [-4] + ( 1 ) -> [-4] + ( 2 ) -> [-4] + ( 3 ) -> [-4] + ( 1 0 ) -> [-2] + ( 2 0 ) -> [-2] + ( 2 1 ) -> [-2] + ( 3 0 ) -> [-2] + ( 3 1 ) -> [-2] + ( 3 2 ) -> [-2] + ( 2 1 0 ) -> [-1.33333] + ( 3 1 0 ) -> [-1.33333] + ( 3 2 0 ) -> [-1.33333] + ( 3 2 1 ) -> [-1.33333] + ( 3 2 1 0 ) -> [-1] + ( 4 ) -> [-1] + ( 4 2 ) -> [-1] + ( 4 0 ) -> [23] + ( 4 1 ) -> [23] + ( 4 2 0 ) -> [23] + ( 4 2 1 ) -> [23] + ( 4 3 ) -> [23] + ( 4 3 2 ) -> [23] + ( 4 1 0 ) -> [95] + ( 4 2 1 0 ) -> [95] + ( 4 3 0 ) -> [95] + ( 4 3 1 ) -> [95] + ( 4 3 2 0 ) -> [95] + ( 4 3 2 1 ) -> [95] diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index f37c0816..15acd7bd 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -216,8 +216,8 @@ public: static_assert(AlphaComplex3dOptions::periodic, "This constructor is not available for non-periodic versions of Alpha_complex_3d"); // Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it. - GUDHI_CHECK((x_max - x_min == y_max - y_min) || - (x_max - x_min == z_max - z_min) || + GUDHI_CHECK((x_max - x_min == y_max - y_min) && + (x_max - x_min == z_max - z_min) && (z_max - z_min == y_max - y_min), std::invalid_argument("The size of the cuboid in every directions is not the same.")); @@ -295,8 +295,8 @@ public: GUDHI_CHECK((weights.size() == points.size()), std::invalid_argument("Points number in range different from weights range number")); // Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it. - GUDHI_CHECK((x_max - x_min == y_max - y_min) || - (x_max - x_min == z_max - z_min) || + GUDHI_CHECK((x_max - x_min == y_max - y_min) && + (x_max - x_min == z_max - z_min) && (z_max - z_min == y_max - y_min), std::invalid_argument("The size of the cuboid in every directions is not the same.")); @@ -312,7 +312,7 @@ public: #endif while ((index < weights.size()) && (index < points.size())) { - GUDHI_CHECK((weights[index] < maximal_possible_weight) || (weights[index] >= 0), + GUDHI_CHECK((weights[index] < maximal_possible_weight) && (weights[index] >= 0), std::invalid_argument("Invalid weight at line" + std::to_string(index + 1) + ". Must be positive and less than maximal possible weight = 1/64*cuboid length " "squared, which is not an acceptable input.")); diff --git a/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp new file mode 100644 index 00000000..7873deca --- /dev/null +++ b/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp @@ -0,0 +1,663 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Vincent Rouvreau + * + * Copyright (C) 2015 Inria + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE "alpha_complex_3d" +#include +#include + +#include // float comparison +#include +#include +#include +#include + +#include +#include +// to construct a simplex_tree from Delaunay_triangulation +#include +#include +#include +#include + +using Alpha_shapes_3d = Gudhi::alpha_complex::Alpha_shapes_3d; +using Exact_alpha_shapes_3d = Gudhi::alpha_complex::Exact_alpha_shapes_3d; +using Weighted_alpha_shapes_3d = Gudhi::alpha_complex::Weighted_alpha_shapes_3d; +using Periodic_alpha_shapes_3d = Gudhi::alpha_complex::Periodic_alpha_shapes_3d; +using Weighted_periodic_alpha_shapes_3d = Gudhi::alpha_complex::Weighted_periodic_alpha_shapes_3d; + +BOOST_AUTO_TEST_CASE(Alpha_complex_3d_from_points) { + // ----------------- + // Non exact version + // ----------------- + std::cout << "Alpha complex 3d" << std::endl; + std::vector points; + points.push_back(Alpha_shapes_3d::Point_3(0.0, 0.0, 0.0)); + points.push_back(Alpha_shapes_3d::Point_3(0.0, 0.0, 0.2)); + points.push_back(Alpha_shapes_3d::Point_3(0.2, 0.0, 0.2)); + points.push_back(Alpha_shapes_3d::Point_3(0.6, 0.6, 0.0)); + points.push_back(Alpha_shapes_3d::Point_3(0.8, 0.8, 0.2)); + points.push_back(Alpha_shapes_3d::Point_3(0.2, 0.8, 0.6)); + + Gudhi::alpha_complex::Alpha_complex_3d alpha_complex(points); + + Gudhi::Simplex_tree<> stree; + alpha_complex.create_complex(stree); + + // ----------------- + // Exact version + // ----------------- + std::cout << "Exact alpha complex 3d" << std::endl; + using Exact_alpha_shapes_3d = Gudhi::alpha_complex::Exact_alpha_shapes_3d; + + Gudhi::alpha_complex::Alpha_complex_3d exact_alpha_complex(points); + + Gudhi::Simplex_tree<> exact_stree; + exact_alpha_complex.create_complex(exact_stree); + + // --------------------- + // Compare both versions + // --------------------- + std::cout << "Exact Alpha complex 3d is of dimension " << exact_stree.dimension() + << " - Non exact is " << stree.dimension() << std::endl; + BOOST_CHECK(exact_stree.dimension() == stree.dimension()); + std::cout << "Exact Alpha complex 3d num_simplices " << exact_stree.num_simplices() + << " - Non exact is " << stree.num_simplices() << std::endl; + BOOST_CHECK(exact_stree.num_simplices() == stree.num_simplices()); + std::cout << "Exact Alpha complex 3d num_vertices " << exact_stree.num_vertices() + << " - Non exact is " << stree.num_vertices() << std::endl; + BOOST_CHECK(exact_stree.num_vertices() == stree.num_vertices()); + + auto sh = stree.filtration_simplex_range().begin(); + auto sh_exact = exact_stree.filtration_simplex_range().begin(); + while(sh != stree.filtration_simplex_range().end() && sh_exact != exact_stree.filtration_simplex_range().end()) { + std::vector simplex; + std::vector exact_simplex; + std::cout << "Non-exact ( "; + for (auto vertex : stree.simplex_vertex_range(*sh)) { + simplex.push_back(vertex); + std::cout << vertex << " "; + } + std::cout << ") -> " << "[" << stree.filtration(*sh) << "] "; + std::cout << std::endl; + std::cout << "Exact ( "; + for (auto vertex : exact_stree.simplex_vertex_range(*sh_exact)) { + exact_simplex.push_back(vertex); + std::cout << vertex << " "; + } + std::cout << ") -> " << "[" << exact_stree.filtration(*sh_exact) << "] "; + std::cout << std::endl; + BOOST_CHECK(exact_simplex == simplex); + + // Exact and non-exact version is not exactly the same due to float comparison + GUDHI_TEST_FLOAT_EQUALITY_CHECK(exact_stree.filtration(*sh_exact), stree.filtration(*sh)); + ++sh; + ++sh_exact; + } +} + +#ifdef GUDHI_DEBUG +BOOST_AUTO_TEST_CASE(Alpha_complex_weighted_throw) { + std::vector w_points; + w_points.push_back(Weighted_alpha_shapes_3d::Point_3(0.0, 0.0, 0.0)); + w_points.push_back(Weighted_alpha_shapes_3d::Point_3(0.0, 0.0, 0.2)); + w_points.push_back(Weighted_alpha_shapes_3d::Point_3(0.2, 0.0, 0.2)); + // w_points.push_back(Weighted_alpha_shapes_3d::Point_3(0.6, 0.6, 0.0)); + // w_points.push_back(Weighted_alpha_shapes_3d::Point_3(0.8, 0.8, 0.2)); + // w_points.push_back(Weighted_alpha_shapes_3d::Point_3(0.2, 0.8, 0.6)); + + // weights size is different from w_points size to make weighted Alpha_complex_3d throw in debug mode + std::vector weights = {0.01, 0.005, 0.006, 0.01, 0.009, 0.001}; + + std::cout << "Check exception throw in debug mode" << std::endl; + BOOST_CHECK_THROW (Gudhi::alpha_complex::Alpha_complex_3d wac(w_points, weights), + std::invalid_argument); +} +#endif + +BOOST_AUTO_TEST_CASE(Alpha_complex_weighted) { + std::cout << "Weighted alpha complex 3d" << std::endl; + using Weighted_alpha_shapes_3d = Gudhi::alpha_complex::Weighted_alpha_shapes_3d; + std::vector w_points; + w_points.push_back(Weighted_alpha_shapes_3d::Point_3(0.0, 0.0, 0.0)); + w_points.push_back(Weighted_alpha_shapes_3d::Point_3(0.0, 0.0, 0.2)); + w_points.push_back(Weighted_alpha_shapes_3d::Point_3(0.2, 0.0, 0.2)); + w_points.push_back(Weighted_alpha_shapes_3d::Point_3(0.6, 0.6, 0.0)); + w_points.push_back(Weighted_alpha_shapes_3d::Point_3(0.8, 0.8, 0.2)); + w_points.push_back(Weighted_alpha_shapes_3d::Point_3(0.2, 0.8, 0.6)); + + // weights size is different from w_points size to make weighted Alpha_complex_3d throw in debug mode + std::vector weights = {0.01, 0.005, 0.006, 0.01, 0.009, 0.001}; + + Gudhi::alpha_complex::Alpha_complex_3d weighted_alpha_complex(w_points, weights); + Gudhi::Simplex_tree<> w_stree; + weighted_alpha_complex.create_complex(w_stree); + + std::cout << "Weighted Alpha complex 3d is of dimension " << w_stree.dimension() << std::endl; + BOOST_CHECK(w_stree.dimension() == 3); + std::cout << " num_simplices " << w_stree.num_simplices() << std::endl; + BOOST_CHECK(w_stree.num_simplices() == 35); + std::cout << " num_vertices " << w_stree.num_vertices() << std::endl; + BOOST_CHECK(w_stree.num_vertices() == 6); +} + +#ifdef GUDHI_DEBUG +BOOST_AUTO_TEST_CASE(Alpha_complex_periodic_throw) { + std::cout << "Periodic alpha complex 3d exception throw" << std::endl; + std::vector p_points; + + // Not important, this is not what we want to check + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.0)); + + std::cout << "Check exception throw in debug mode" << std::endl; + using Periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + // Check it throws an exception when the cuboid is not iso + BOOST_CHECK_THROW (Periodic_alpha_complex_3d periodic_alpha_complex(p_points, 0., 0., 0., 0.9, 1., 1.), + std::invalid_argument); + BOOST_CHECK_THROW (Periodic_alpha_complex_3d periodic_alpha_complex(p_points, 0., 0., 0., 1., 0.9, 1.), + std::invalid_argument); + BOOST_CHECK_THROW (Periodic_alpha_complex_3d periodic_alpha_complex(p_points, 0., 0., 0., 1., 1., 0.9), + std::invalid_argument); + +} +#endif + +BOOST_AUTO_TEST_CASE(Alpha_complex_periodic) { + std::cout << "Periodic alpha complex 3d" << std::endl; + std::vector p_points; + + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.1, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.6)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.8)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.0)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.2)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.4)); + p_points.push_back(Periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.6)); + + Gudhi::alpha_complex::Alpha_complex_3d periodic_alpha_complex(p_points, + 0., 0., 0., + 1., 1., 1.); + + Gudhi::Simplex_tree<> p_stree; + periodic_alpha_complex.create_complex(p_stree); + + std::cout << "Periodic Alpha complex 3d is of dimension " << p_stree.dimension() << std::endl; + BOOST_CHECK(p_stree.dimension() == 3); + std::cout << " num_simplices " << p_stree.num_simplices() << std::endl; + BOOST_CHECK(p_stree.num_simplices() == 3266); + std::cout << " num_vertices " << p_stree.num_vertices() << std::endl; + BOOST_CHECK(p_stree.num_vertices() == 125); + +} + +#ifdef GUDHI_DEBUG +BOOST_AUTO_TEST_CASE(Alpha_complex_weighted_periodic_throw) { + std::cout << "Weighted periodic alpha complex 3d exception throw" << std::endl; + + std::vector wp_points; + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.1, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.6)); + + std::vector p_weights; + + std::random_device rd; + std::mt19937 mt(rd()); + // Weights must be in range [0, <1/64] + std::uniform_real_distribution dist(0.0, 0.0156245); + + for (std::size_t i = 0; i < wp_points.size(); ++i) { + double value = dist(mt); + p_weights.push_back(value); + } + + std::cout << "Cuboid is not iso exception" << std::endl; + using Weighted_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + // Check it throws an exception when the cuboid is not iso + BOOST_CHECK_THROW (Weighted_periodic_alpha_complex_3d periodic_alpha_complex(wp_points, p_weights, 0., 0., 0., 0.9, 1., 1.), + std::invalid_argument); + BOOST_CHECK_THROW (Weighted_periodic_alpha_complex_3d periodic_alpha_complex(wp_points, p_weights, 0., 0., 0., 1., 0.9, 1.), + std::invalid_argument); + BOOST_CHECK_THROW (Weighted_periodic_alpha_complex_3d periodic_alpha_complex(wp_points, p_weights, 0., 0., 0., 1., 1., 0.9), + std::invalid_argument); + + std::cout << "0 <= point.weight() < 1/64 * domain_size * domain_size exception" << std::endl; + // Weights must be in range [0, <1/64] + p_weights[25] = 1.0; + BOOST_CHECK_THROW (Weighted_periodic_alpha_complex_3d periodic_alpha_complex(wp_points, p_weights, 0., 0., 0., 1., 1., 1.), + std::invalid_argument); + // Weights must be in range [0, <1/64] + p_weights[25] = 0.012; + p_weights[14] = -0.012; + BOOST_CHECK_THROW (Weighted_periodic_alpha_complex_3d periodic_alpha_complex(wp_points, p_weights, 0., 0., 0., 1., 1., 1.), + std::invalid_argument); + p_weights[14] = 0.005; + + std::cout << "wp_points and p_weights size exception" << std::endl; + // Weights and points must have the same size + // + 1 + p_weights.push_back(0.007); + BOOST_CHECK_THROW (Weighted_periodic_alpha_complex_3d periodic_alpha_complex(wp_points, p_weights, 0., 0., 0., 1., 1., 1.), + std::invalid_argument); + // - 1 + p_weights.pop_back(); + p_weights.pop_back(); + BOOST_CHECK_THROW (Weighted_periodic_alpha_complex_3d periodic_alpha_complex(wp_points, p_weights, 0., 0., 0., 1., 1., 1.), + std::invalid_argument); +} +#endif + +BOOST_AUTO_TEST_CASE(Alpha_complex_weighted_periodic) { + std::cout << "Weighted periodic alpha complex 3d" << std::endl; + + std::vector wp_points; + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.0, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.2, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.4, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.6, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.0, 0.8, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.0, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.2, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.4, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.6, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.2, 0.8, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.0, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.2, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.4, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.6, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.4, 0.8, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.0, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.1, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.2, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.4, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.6, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.6, 0.8, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.0, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.2, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.4, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.6)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.6, 0.8)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.0)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.2)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.4)); + wp_points.push_back(Weighted_periodic_alpha_shapes_3d::Point_3(0.8, 0.8, 0.6)); + + std::vector p_weights; + + std::random_device rd; + std::mt19937 mt(rd()); + // Weights must be in range [0, <1/64] + std::uniform_real_distribution dist(0.01, 0.0156245); + + for (std::size_t i = 0; i < wp_points.size(); ++i) { + double value = dist(mt); + p_weights.push_back(value); + } + + using Weighted_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + Weighted_periodic_alpha_complex_3d weighted_periodic_alpha_complex(wp_points, p_weights, 0., 0., 0., 1., 1., 1.); + + Gudhi::Simplex_tree<> wp_stree; + weighted_periodic_alpha_complex.create_complex(wp_stree); + + std::cout << "Weighted periodic Alpha complex 3d is of dimension " << wp_stree.dimension() << std::endl; + BOOST_CHECK(wp_stree.dimension() == 3); + std::cout << " num_simplices " << wp_stree.num_simplices() << std::endl; + BOOST_CHECK(wp_stree.num_simplices() >= 3100); + std::cout << " num_vertices " << wp_stree.num_vertices() << std::endl; + BOOST_CHECK(wp_stree.num_vertices() == 125); +} diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt index 9255d3db..7b6de748 100644 --- a/src/Alpha_complex/test/CMakeLists.txt +++ b/src/Alpha_complex/test/CMakeLists.txt @@ -9,10 +9,17 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) target_link_libraries(Alpha_complex_test_unit ${TBB_LIBRARIES}) endif() + add_executable ( Alpha_complex_3d_test_unit Alpha_complex_3d_unit_test.cpp ) + target_link_libraries(Alpha_complex_3d_test_unit ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(Alpha_complex_3d_test_unit ${TBB_LIBRARIES}) + endif() + # Do not forget to copy test files in current binary dir file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) gudhi_add_coverage_test(Alpha_complex_test_unit) + gudhi_add_coverage_test(Alpha_complex_3d_test_unit) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp index 00ede9ce..536de444 100644 --- a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp @@ -45,12 +45,13 @@ using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; void program_options(int argc, char *argv[], std::string &off_file_points, bool& exact, std::string &weight_file, - std::string &cuboid_file, std::string &output_file_diag, int &coeff_field_characteristic, - Filtration_value &min_persistence); + std::string &cuboid_file, std::string &output_file_diag, Filtration_value &alpha_square_max_value, + int &coeff_field_characteristic, Filtration_value &min_persistence); template -bool create_complex(AlphaComplex3d& alpha_complex, Simplex_tree& simplex_tree) { - return alpha_complex.create_complex(simplex_tree); +bool create_complex(AlphaComplex3d& alpha_complex, Simplex_tree& simplex_tree, + Filtration_value alpha_square_max_value) { + return alpha_complex.create_complex(simplex_tree, alpha_square_max_value); } bool read_weight_file(const std::string& weight_file, std::vector& weights) { @@ -87,6 +88,7 @@ int main(int argc, char **argv) { std::string weight_file; std::string cuboid_file; std::string output_file_diag; + Filtration_value alpha_square_max_value = 0.; int coeff_field_characteristic = 0; Filtration_value min_persistence = 0.; bool exact_version = false; @@ -94,7 +96,7 @@ int main(int argc, char **argv) { bool periodic_version = false; program_options(argc, argv, off_file_points, exact_version, weight_file, cuboid_file, output_file_diag, - coeff_field_characteristic, min_persistence); + alpha_square_max_value, coeff_field_characteristic, min_persistence); // Read the OFF file (input file name given as parameter) and triangulate points Gudhi::Points_3D_off_reader off_reader(off_file_points); @@ -131,25 +133,25 @@ int main(int argc, char **argv) { exit(-1); } else { Exact_alpha_complex_3d alpha_complex(off_reader.get_point_cloud()); - create_complex(alpha_complex, simplex_tree); + create_complex(alpha_complex, simplex_tree, alpha_square_max_value); } } else { if (weighted_version) { if (periodic_version) { Weighted_periodic_alpha_complex_3d alpha_complex(off_reader.get_point_cloud(), weights, x_min, y_min, z_min, x_max, y_max, z_max); - create_complex(alpha_complex, simplex_tree); + create_complex(alpha_complex, simplex_tree, alpha_square_max_value); } else { Weighted_alpha_complex_3d alpha_complex(off_reader.get_point_cloud(), weights); - create_complex(alpha_complex, simplex_tree); + create_complex(alpha_complex, simplex_tree, alpha_square_max_value); } } else { if (periodic_version) { Periodic_alpha_complex_3d alpha_complex(off_reader.get_point_cloud(), x_min, y_min, z_min, x_max, y_max, z_max); - create_complex(alpha_complex, simplex_tree); + create_complex(alpha_complex, simplex_tree, alpha_square_max_value); } else { Alpha_complex_3d alpha_complex(off_reader.get_point_cloud()); - create_complex(alpha_complex, simplex_tree); + create_complex(alpha_complex, simplex_tree, alpha_square_max_value); } } } @@ -179,8 +181,8 @@ int main(int argc, char **argv) { } void program_options(int argc, char *argv[], std::string &off_file_points, bool& exact, std::string &weight_file, - std::string &cuboid_file, std::string &output_file_diag, int &coeff_field_characteristic, - Filtration_value &min_persistence) { + std::string &cuboid_file, std::string &output_file_diag, Filtration_value &alpha_square_max_value, + int &coeff_field_characteristic, Filtration_value &min_persistence) { namespace po = boost::program_options; po::options_description hidden("Hidden options"); hidden.add_options()("input-file", po::value(&off_file_points), @@ -196,6 +198,9 @@ void program_options(int argc, char *argv[], std::string &off_file_points, bool& "Name of file describing the periodic domain. Format is:\n min_hx min_hy min_hz\n max_hx max_hy max_hz")( "output-file,o", po::value(&output_file_diag)->default_value(std::string()), "Name of file in which the persistence diagram is written. Default print in std::cout")( + "max-alpha-square-value,r", po::value(&alpha_square_max_value) + ->default_value(std::numeric_limits::infinity()), + "Maximal alpha square value for the Alpha complex construction.")( "field-charac,p", po::value(&coeff_field_characteristic)->default_value(11), "Characteristic p of the coefficient field Z/pZ for computing homology.")( "min-persistence,m", po::value(&min_persistence), diff --git a/src/Alpha_complex/utilities/alphacomplex.md b/src/Alpha_complex/utilities/alphacomplex.md index 7ae5f913..7fc6cc0c 100644 --- a/src/Alpha_complex/utilities/alphacomplex.md +++ b/src/Alpha_complex/utilities/alphacomplex.md @@ -94,6 +94,8 @@ where `` is the path to the input point cloud in * `-h [ --help ]` Produce help message * `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output. +* `-r [ --max-alpha-square-value ]` (default = inf) Maximal alpha square value +for the Alpha complex construction. * `-p [ --field-charac ]` (default=11) Characteristic p of the coefficient field Z/pZ for computing homology. * `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature @@ -120,45 +122,3 @@ N.B.: [Alpha shape](https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title0) and [Regular triangulation](https://doc.cgal.org/latest/Triangulation_3/index.html#Triangulation3secclassRegulartriangulation) documentation. - - - - - - - - -## periodic_alpha_complex_3d_persistence ## -Same as `alpha_complex_3d_persistence`, but using periodic alpha shape 3d. -Refer to the [CGAL's 3D Periodic Triangulations User Manual](https://doc.cgal.org/latest/Periodic_3_triangulation_3/index.html) for more details. - -**Usage** - -``` - periodic_alpha_complex_3d_persistence [options] -``` - -where - -* `` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html). -* `` is the path to the file describing the periodic domain. It must be in the format described -[here](/doc/latest/fileformats.html#FileFormatsIsoCuboid). - -**Allowed options** - -* `-h [ --help ]` Produce help message -* `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output. -* `-p [ --field-charac ]` (default=11) Characteristic p of the coefficient field Z/pZ for computing homology. -* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals - - -**Example** - -``` -periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off ../../data/points/iso_cuboid_3_in_0_1.txt -p 3 -m 1.0 -``` - -N.B.: - -* Cuboid file must be in the format described [here](/doc/latest/fileformats.html#FileFormatsIsoCuboid). -* Filtration values are alpha square values. -- cgit v1.2.3 From a114ccb40558615139eeb23dfc05e3ceeb909d7f Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 31 Jul 2018 15:47:22 +0000 Subject: Fix documentation for CGAL version required by 3d version Remove duplicated example (cf. the one in the Simplex tree) Add the example for documentation git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@3713 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 204f77982c61bc30a6ad3218c82b98f8bb49d711 --- .../example/alpha_complex_3d_step_by_step.cpp | 309 --------------------- src/common/doc/examples.h | 1 + src/common/doc/installation.h | 10 +- 3 files changed, 9 insertions(+), 311 deletions(-) delete mode 100644 src/Alpha_complex/example/alpha_complex_3d_step_by_step.cpp (limited to 'src/Alpha_complex/example') diff --git a/src/Alpha_complex/example/alpha_complex_3d_step_by_step.cpp b/src/Alpha_complex/example/alpha_complex_3d_step_by_step.cpp deleted file mode 100644 index d76402e5..00000000 --- a/src/Alpha_complex/example/alpha_complex_3d_step_by_step.cpp +++ /dev/null @@ -1,309 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Vincent Rouvreau - * - * Copyright (C) 2014 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -#include -#include -#include - -#if BOOST_VERSION >= 105400 -#include -#endif - -#include -#include - -#include -#include -#include -#include -#include -#include - -#include -#include -#include -#include -#include -#include -#include -#include - -template -Vertex_list from_cell(const Cell_handle& ch) { - Vertex_list the_list; - for (auto i = 0; i < 4; i++) { -#ifdef DEBUG_TRACES - std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(ch->vertex(i)); - } - return the_list; -} - -template -Vertex_list from_facet(const Facet& fct) { - Vertex_list the_list; - for (auto i = 0; i < 4; i++) { - if (fct.second != i) { -#ifdef DEBUG_TRACES - std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(fct.first->vertex(i)); - } - } - return the_list; -} - -template -Vertex_list from_edge(const Edge_3& edg) { - Vertex_list the_list; - for (auto i : {edg.second, edg.third}) { -#ifdef DEBUG_TRACES - std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(edg.first->vertex(i)); - } - return the_list; -} - -template -Vertex_list from_vertex(const Vertex_handle& vh) { - Vertex_list the_list; -#ifdef DEBUG_TRACES - std::cout << "from vertex=" << vh->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(vh); - return the_list; -} - -// Alpha_shape_3 templates type definitions -using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; -using Vb = CGAL::Alpha_shape_vertex_base_3; -using Fb = CGAL::Alpha_shape_cell_base_3; -using Tds = CGAL::Triangulation_data_structure_3; -using Triangulation_3 = CGAL::Delaunay_triangulation_3; -using Alpha_shape_3 = CGAL::Alpha_shape_3; - -// From file type definition -using Point_3 = Kernel::Point_3; - -// filtration with alpha values needed type definition -using Alpha_value_type = Alpha_shape_3::FT; -using Object = CGAL::Object; -using Dispatch = - CGAL::Dispatch_output_iterator, - CGAL::cpp11::tuple >, - std::back_insert_iterator > > >; -using Cell_handle = Alpha_shape_3::Cell_handle; -using Facet = Alpha_shape_3::Facet; -using Edge_3 = Alpha_shape_3::Edge; -using Vertex_handle = Alpha_shape_3::Vertex_handle; - -#if BOOST_VERSION >= 105400 -using Vertex_list = boost::container::static_vector; -#else -using Vertex_list = std::vector; -#endif - -// gudhi type definition -using ST = Gudhi::Simplex_tree; -using Filtration_value = ST::Filtration_value; -using Simplex_tree_vertex = ST::Vertex_handle; -using Alpha_shape_simplex_tree_map = std::map; -using Simplex_tree_vector_vertex = std::vector; - -void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag); - -int main(int argc, char **argv) { - std::string off_file_points; - std::string output_file_diag; - - program_options(argc, argv, off_file_points, output_file_diag); - - // Read the OFF file (input file name given as parameter) and triangulate points - Gudhi::Points_3D_off_reader off_reader(off_file_points); - // Check the read operation was correct - if (!off_reader.is_valid()) { - std::cerr << "Unable to read file " << off_file_points << std::endl; - exit(-1); - } - - // Retrieve the points - std::vector lp = off_reader.get_point_cloud(); - - // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. - Alpha_shape_3 as(lp.begin(), lp.end(), 0, Alpha_shape_3::GENERAL); -#ifdef DEBUG_TRACES - std::cout << "Alpha shape computed in GENERAL mode" << std::endl; -#endif // DEBUG_TRACES - - // filtration with alpha values from alpha shape - std::vector the_objects; - std::vector the_alpha_values; - - Dispatch disp = CGAL::dispatch_output(std::back_inserter(the_objects), - std::back_inserter(the_alpha_values)); - - as.filtration_with_alpha_values(disp); -#ifdef DEBUG_TRACES - std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; -#endif // DEBUG_TRACES - - Alpha_shape_3::size_type count_vertices = 0; - Alpha_shape_3::size_type count_edges = 0; - Alpha_shape_3::size_type count_facets = 0; - Alpha_shape_3::size_type count_cells = 0; - - // Loop on objects vector - Vertex_list vertex_list; - ST simplex_tree; - Alpha_shape_simplex_tree_map map_cgal_simplex_tree; - std::vector::iterator the_alpha_value_iterator = the_alpha_values.begin(); - for (auto object_iterator : the_objects) { - // Retrieve Alpha shape vertex list from object - if (const Cell_handle *cell = CGAL::object_cast(&object_iterator)) { - vertex_list = from_cell(*cell); - count_cells++; - } else if (const Facet *facet = CGAL::object_cast(&object_iterator)) { - vertex_list = from_facet(*facet); - count_facets++; - } else if (const Edge_3 *edge = CGAL::object_cast(&object_iterator)) { - vertex_list = from_edge(*edge); - count_edges++; - } else if (const Vertex_handle *vertex = CGAL::object_cast(&object_iterator)) { - count_vertices++; - vertex_list = from_vertex(*vertex); - } - // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex - Simplex_tree_vector_vertex the_simplex; - for (auto the_alpha_shape_vertex : vertex_list) { - Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex); - if (the_map_iterator == map_cgal_simplex_tree.end()) { - // alpha shape not found - Simplex_tree_vertex vertex = map_cgal_simplex_tree.size(); -#ifdef DEBUG_TRACES - std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl; -#endif // DEBUG_TRACES - the_simplex.push_back(vertex); - map_cgal_simplex_tree.emplace(the_alpha_shape_vertex, vertex); - } else { - // alpha shape found - Simplex_tree_vertex vertex = the_map_iterator->second; -#ifdef DEBUG_TRACES - std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl; -#endif // DEBUG_TRACES - the_simplex.push_back(vertex); - } - } - // Construction of the simplex_tree - Filtration_value filtr = /*std::sqrt*/ (*the_alpha_value_iterator); -#ifdef DEBUG_TRACES - std::cout << "filtration = " << filtr << std::endl; -#endif // DEBUG_TRACES - simplex_tree.insert_simplex(the_simplex, filtr); - GUDHI_CHECK(the_alpha_value_iterator != the_alpha_values.end(), "CGAL provided more simplices than values"); - ++the_alpha_value_iterator; - } - -#ifdef DEBUG_TRACES - std::cout << "vertices \t\t" << count_vertices << std::endl; - std::cout << "edges \t\t" << count_edges << std::endl; - std::cout << "facets \t\t" << count_facets << std::endl; - std::cout << "cells \t\t" << count_cells << std::endl; - - std::cout << "Information of the Simplex Tree: " << std::endl; - std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; - std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; - std::cout << " Dimension = " << simplex_tree.dimension() << " "; -#endif // DEBUG_TRACES - -#ifdef DEBUG_TRACES - std::cout << "Iterator on vertices: " << std::endl; - for (auto vertex : simplex_tree.complex_vertex_range()) { - std::cout << vertex << " "; - } -#endif // DEBUG_TRACES - - // Sort the simplices in the order of the filtration - simplex_tree.initialize_filtration(); - - std::streambuf* streambufffer; - std::ofstream ouput_file_stream; - if (output_file_diag != std::string()) { - ouput_file_stream.open(output_file_diag); - streambufffer = ouput_file_stream.rdbuf(); - } else { - streambufffer = std::cout.rdbuf(); - } - - std::ostream output_stream(streambufffer); - - // ---------------------------------------------------------------------------- - // Display information about the alpha complex - // ---------------------------------------------------------------------------- - output_stream << "Alpha complex is of dimension " << simplex_tree.dimension() << - " - " << simplex_tree.num_simplices() << " simplices - " << - simplex_tree.num_vertices() << " vertices." << std::endl; - - output_stream << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << - std::endl; - for (auto f_simplex : simplex_tree.filtration_simplex_range()) { - output_stream << " ( "; - for (auto vertex : simplex_tree.simplex_vertex_range(f_simplex)) { - output_stream << vertex << " "; - } - output_stream << ") -> " << "[" << simplex_tree.filtration(f_simplex) << "] "; - output_stream << std::endl; - } - - return 0; -} - -void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag) { - namespace po = boost::program_options; - po::options_description hidden("Hidden options"); - hidden.add_options()("input-file", po::value(&off_file_points), - "Name of file containing a point set. Format is one point per line: X1 ... Xd "); - - po::options_description visible("Allowed options", 100); - visible.add_options()("help,h", "produce help message")( - "output-file,o", po::value(&output_file_diag)->default_value(std::string()), - "Name of file in which the persistence diagram is written. Default print in std::cout"); - - po::positional_options_description pos; - pos.add("input-file", 1); - - po::options_description all; - all.add(visible).add(hidden); - - po::variables_map vm; - po::store(po::command_line_parser(argc, argv).options(all).positional(pos).run(), vm); - po::notify(vm); - - if (vm.count("help") || !vm.count("input-file")) { - std::cout << std::endl; - std::cout << "Compute and displays the 3D Alpha complex defined on a set of input points.\n \n"; - std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; - std::cout << visible << std::endl; - exit(-1); - } -} diff --git a/src/common/doc/examples.h b/src/common/doc/examples.h index 7c2a8f69..c19b3444 100644 --- a/src/common/doc/examples.h +++ b/src/common/doc/examples.h @@ -53,6 +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_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/installation.h b/src/common/doc/installation.h index 8f91e9c1..d36a216f 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -56,8 +56,6 @@ make doxygen * * The following examples/utilities require the Computational Geometry Algorithms * Library (CGAL \cite cgal:eb-15b) and will not be built if CGAL is not installed: - * \li - * Alpha_complex/alpha_complex_3d_persistence.cpp * \li * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp * @@ -113,6 +111,12 @@ make doxygen * \li * Tangential_complex/example_with_perturb.cpp * + * The following example requires CGAL version ≥ 4.11.0: + * \li + * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp + * \li + * Alpha_complex/alpha_complex_3d_persistence.cpp + * * \subsection eigen3 Eigen3 * The \ref alpha_complex data structure and few examples requires * Eigen3 is a C++ template library for linear algebra: @@ -128,6 +132,8 @@ make doxygen * Alpha_complex/alpha_complex_persistence.cpp * \li * Alpha_complex/alpha_complex_3d_persistence.cpp + * \li + * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp * \li * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp * \li -- cgit v1.2.3 From ef84bab542eb07d83515293652841969dd462b1c Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 28 Aug 2018 21:11:26 +0000 Subject: Make fast/safe/exact, weighted/non-weighted, periodic/non-periodic more orthogonal choices Only examples work for the moment. Periodic to be tested. Add Alpha_complex_3d_from_points.cpp example. Maybe to be removed. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@3840 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: f5621df603bdb149c52400a6095271ea0f54b84c --- .../example/Alpha_complex_3d_from_points.cpp | 56 +++++++++++ src/Alpha_complex/example/CMakeLists.txt | 8 ++ .../Weighted_alpha_complex_3d_from_points.cpp | 13 +-- src/Alpha_complex/include/gudhi/Alpha_complex_3d.h | 102 ++++++++++++++++----- 4 files changed, 147 insertions(+), 32 deletions(-) create mode 100644 src/Alpha_complex/example/Alpha_complex_3d_from_points.cpp (limited to 'src/Alpha_complex/example') diff --git a/src/Alpha_complex/example/Alpha_complex_3d_from_points.cpp b/src/Alpha_complex/example/Alpha_complex_3d_from_points.cpp new file mode 100644 index 00000000..e96385c0 --- /dev/null +++ b/src/Alpha_complex/example/Alpha_complex_3d_from_points.cpp @@ -0,0 +1,56 @@ +#include +// to construct a simplex_tree from alpha complex +#include + +#include +#include +#include +#include // for numeric limits + +using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Point = Alpha_complex_3d::Point_3 ; +using Vector_of_points = std::vector; + +int main(int argc, char **argv) { + if (argc != 1) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; + std::cerr << "Usage: " << (argv[0] - 1) << " \n"; + exit(-1); // ----- >> + } + + // ---------------------------------------------------------------------------- + // Init of a list of points from a small molecule + // ---------------------------------------------------------------------------- + Vector_of_points points; + points.push_back(Point(1, -1, -1)); + points.push_back(Point(-1, 1, -1)); + points.push_back(Point(-1, -1, 1)); + points.push_back(Point(1, 1, 1)); + points.push_back(Point(2, 2, 2)); + + // ---------------------------------------------------------------------------- + // Init of an alpha complex from the list of points + // ---------------------------------------------------------------------------- + Alpha_complex_3d alpha_complex_from_points(points); + + Gudhi::Simplex_tree<> simplex; + if (alpha_complex_from_points.create_complex(simplex)) { + // ---------------------------------------------------------------------------- + // Display information about the alpha complex + // ---------------------------------------------------------------------------- + std::cout << "Alpha complex is of dimension " << simplex.dimension() << + " - " << simplex.num_simplices() << " simplices - " << + simplex.num_vertices() << " vertices." << std::endl; + + std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; + for (auto f_simplex : simplex.filtration_simplex_range()) { + std::cout << " ( "; + for (auto vertex : simplex.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << ") -> " << "[" << simplex.filtration(f_simplex) << "] "; + std::cout << std::endl; + } + } + return 0; +} diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt index 4a1cd26d..1f127972 100644 --- a/src/Alpha_complex/example/CMakeLists.txt +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -39,5 +39,13 @@ if(CGAL_FOUND) add_test(NAME Alpha_complex_example_weighted_3d_from_points COMMAND $) + add_executable ( Alpha_complex_example_3d_from_points Alpha_complex_3d_from_points.cpp ) + target_link_libraries(Alpha_complex_example_3d_from_points ${CGAL_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(Alpha_complex_example_3d_from_points ${TBB_LIBRARIES}) + endif() + add_test(NAME Alpha_complex_example_3d_from_points + COMMAND $) + endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) endif() \ No newline at end of file diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp index abb73427..1b60ccd8 100644 --- a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp +++ b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp @@ -8,17 +8,10 @@ #include #include // for numeric limits -using Weighted_alpha_shapes_3d = Gudhi::alpha_complex::Weighted_alpha_shapes_3d; -using Weighted_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Point = Gudhi::alpha_complex::Weighted_alpha_shapes_3d::Point_3 ; +using Weighted_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Point = Weighted_alpha_complex_3d::Point_3 ; using Vector_of_points = std::vector; -using Vector_of_weights = std::vector; - -void usage(int nbArgs, char * const progName) { - std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; - std::cerr << "Usage: " << progName << " \n"; - exit(-1); // ----- >> -} +using Vector_of_weights = std::vector; int main(int argc, char **argv) { if (argc != 1) { diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index 15acd7bd..ed58c1c0 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -44,6 +44,8 @@ #include #include #include // for std::unique_ptr +#include // for std::conditional and std::enable_if + #if CGAL_VERSION_NR < 1041101000 // Make compilation fail - required for external projects - https://gitlab.inria.fr/GUDHI/gudhi-devel/issues/10 @@ -55,6 +57,13 @@ namespace Gudhi { namespace alpha_complex { +enum class complexity: char +{ + fast='f', + safe='s', + exact='e', +}; + /** * \class Alpha_complex_3d * \brief Alpha complex data structure for 3d specific case. @@ -75,9 +84,51 @@ namespace alpha_complex { * Delaunay complex. * */ -template +template class Alpha_complex_3d { - using Alpha_shape_3 = typename AlphaComplex3dOptions::Alpha_shape_3; + using Predicates = typename std::conditional<((!Weighted && !Periodic) || (Complexity == complexity::fast)), + CGAL::Exact_predicates_inexact_constructions_kernel, + CGAL::Exact_predicates_exact_constructions_kernel>::type; + + using Kernel = typename std::conditional, + Predicates>::type; + + using Exact_tag = typename std::conditional<(Complexity == complexity::fast), + CGAL::Tag_false, + CGAL::Tag_true>::type; + + using TdsVb = typename std::conditional, + CGAL::Triangulation_ds_vertex_base_3<>>::type; + + using Tvb = typename std::conditional, + CGAL::Triangulation_vertex_base_3>::type; + + using Vb = CGAL::Alpha_shape_vertex_base_3; + + using Tcb = typename std::conditional, + CGAL::Triangulation_cell_base_3>::type; + + using Cb = CGAL::Alpha_shape_cell_base_3; + using Tds = CGAL::Triangulation_data_structure_3; + + using Pre_triangulation_3 = typename std::conditional, + CGAL::Delaunay_triangulation_3>::type; + + using Triangulation_3 = typename std::conditional<(Weighted && Periodic), + CGAL::Periodic_3_regular_triangulation_3, + Pre_triangulation_3>::type; + +public: + using Alpha_shape_3 = CGAL::Alpha_shape_3; + + using Point_3 = typename Kernel::Point_3; + +private: using Alpha_value_type = typename Alpha_shape_3::FT; using Dispatch = CGAL::Dispatch_output_iterator, @@ -94,9 +145,6 @@ class Alpha_complex_3d { using Vertex_list = std::vector; #endif -public: - using Point_3 = typename AlphaComplex3dOptions::Point_3; - public: /** \brief Alpha_complex constructor from a list of points. * @@ -112,9 +160,9 @@ public: */ template Alpha_complex_3d(const InputPointRange& points) { - static_assert(!AlphaComplex3dOptions::weighted, + static_assert(!Weighted, "This constructor is not available for weighted versions of Alpha_complex_3d"); - static_assert(!AlphaComplex3dOptions::periodic, + static_assert(!Periodic, "This constructor is not available for periodic versions of Alpha_complex_3d"); alpha_shape_3_ptr_ = std::unique_ptr(new Alpha_shape_3(std::begin(points), std::end(points), 0, @@ -151,14 +199,14 @@ public: */ template Alpha_complex_3d(const InputPointRange& points, WeightRange weights) { - static_assert(AlphaComplex3dOptions::weighted, + static_assert(Weighted, "This constructor is not available for non-weighted versions of Alpha_complex_3d"); - static_assert(!AlphaComplex3dOptions::periodic, + static_assert(!Periodic, "This constructor is not available for periodic versions of Alpha_complex_3d"); GUDHI_CHECK((weights.size() == points.size()), std::invalid_argument("Points number in range different from weights range number")); - using Weighted_point_3 = typename AlphaComplex3dOptions::Weighted_point_3; + using Weighted_point_3 = typename Triangulation_3::Weighted_point; std::vector weighted_points_3; std::size_t index = 0; @@ -207,13 +255,13 @@ public: * std::end return input iterators on a AlphaComplex3dOptions::Point_3. * The type of x_min, y_min, z_min, x_max, y_max and z_max is AlphaComplex3dOptions::Alpha_shape_3::FT. */ - template + /*template Alpha_complex_3d(const InputPointRange& points, Alpha_value_type x_min, Alpha_value_type y_min, Alpha_value_type z_min, Alpha_value_type x_max, Alpha_value_type y_max, Alpha_value_type z_max) { - static_assert(!AlphaComplex3dOptions::weighted, + static_assert(!Weighted, "This constructor is not available for weighted versions of Alpha_complex_3d"); - static_assert(AlphaComplex3dOptions::periodic, + static_assert(Periodic, "This constructor is not available for non-periodic versions of Alpha_complex_3d"); // Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it. GUDHI_CHECK((x_max - x_min == y_max - y_min) && @@ -246,7 +294,7 @@ public: std::cout << "filtration_with_alpha_values returns : " << objects_.size() << " objects" << std::endl; #endif // DEBUG_TRACES - } + }*/ /** \brief Alpha_complex constructor from a list of points, associated weights and an iso-cuboid coordinates. * @@ -284,13 +332,13 @@ public: * std::end return an input iterator on a AlphaComplex3dOptions::Alpha_shape_3::FT. * The type of x_min, y_min, z_min, x_max, y_max and z_max is AlphaComplex3dOptions::Alpha_shape_3::FT. */ - template + /*template Alpha_complex_3d(const InputPointRange& points, WeightRange weights, Alpha_value_type x_min, Alpha_value_type y_min, Alpha_value_type z_min, Alpha_value_type x_max, Alpha_value_type y_max, Alpha_value_type z_max) { - static_assert(AlphaComplex3dOptions::weighted, + static_assert(Weighted, "This constructor is not available for non-weighted versions of Alpha_complex_3d"); - static_assert(AlphaComplex3dOptions::periodic, + static_assert(Periodic, "This constructor is not available for non-periodic versions of Alpha_complex_3d"); GUDHI_CHECK((weights.size() == points.size()), std::invalid_argument("Points number in range different from weights range number")); @@ -344,6 +392,19 @@ public: #ifdef DEBUG_TRACES std::cout << "filtration_with_alpha_values returns : " << objects_.size() << " objects" << std::endl; #endif // DEBUG_TRACES + }*/ + template + typename std::enable_if::value, Filtration_value>::type + value_from_iterator(Alpha_value_iterator the_alpha_value_iterator) + { + return *(the_alpha_value_iterator); + } + + template + typename std::enable_if::value, Filtration_value>::type + value_from_iterator(Alpha_value_iterator the_alpha_value_iterator) + { + return CGAL::to_double(the_alpha_value_iterator->exact()); } @@ -455,11 +516,8 @@ public: } } // Construction of the simplex_tree - //Alpha_value_type filtr; - Filtration_value filtr = - AlphaComplex3dOptions::template value_from_iterator::iterator> - (the_alpha_value_iterator); + Filtration_value filtr = value_from_iterator(the_alpha_value_iterator); + #ifdef DEBUG_TRACES std::cout << "filtration = " << filtr << std::endl; #endif // DEBUG_TRACES -- cgit v1.2.3 From 35fee4017481fd3f62fceb76a1b2bc8cd0f15b95 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 7 Sep 2018 14:17:13 +0000 Subject: Code review : rearrange documentation and examples according to making choices more orthogonal Rename Alpha_complex_3d_options.h Alpha_complex_options.h as it can be used by Alpha complex dD git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@3875 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 6c5b105248e4766a44438a187bb130a3722b310f --- .../Weighted_alpha_complex_3d_from_points.cpp | 26 +- src/Alpha_complex/include/gudhi/Alpha_complex_3d.h | 112 ++--- .../include/gudhi/Alpha_complex_3d_options.h | 179 ------- .../include/gudhi/Alpha_complex_options.h | 64 +++ .../test/Alpha_complex_3d_unit_test.cpp | 535 ++++++++------------- .../utilities/alpha_complex_3d_persistence.cpp | 120 +++-- 6 files changed, 415 insertions(+), 621 deletions(-) delete mode 100644 src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h create mode 100644 src/Alpha_complex/include/gudhi/Alpha_complex_options.h (limited to 'src/Alpha_complex/example') diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp index 1b60ccd8..61ceab6d 100644 --- a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp +++ b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp @@ -1,5 +1,4 @@ #include -#include // to construct a simplex_tree from alpha complex #include @@ -9,8 +8,9 @@ #include // for numeric limits using Weighted_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Point = Weighted_alpha_complex_3d::Point_3 ; -using Vector_of_points = std::vector; +using Point = Weighted_alpha_complex_3d::Point_3; +using Weighted_point = Weighted_alpha_complex_3d::Triangulation_3::Weighted_point; +using Vector_of_weighted_points = std::vector; using Vector_of_weights = std::vector; int main(int argc, char **argv) { @@ -23,23 +23,17 @@ int main(int argc, char **argv) { // ---------------------------------------------------------------------------- // Init of a list of points and weights from a small molecule // ---------------------------------------------------------------------------- - Vector_of_points points; - Vector_of_weights weights; - points.push_back(Point(1, -1, -1)); - weights.push_back(4.); - points.push_back(Point(-1, 1, -1)); - weights.push_back(4.); - points.push_back(Point(-1, -1, 1)); - weights.push_back(4.); - points.push_back(Point(1, 1, 1)); - weights.push_back(4.); - points.push_back(Point(2, 2, 2)); - weights.push_back(1.); + Vector_of_weighted_points weighted_points; + weighted_points.push_back(Weighted_point(Point(1, -1, -1), 4.)); + weighted_points.push_back(Weighted_point(Point(-1, 1, -1), 4.)); + weighted_points.push_back(Weighted_point(Point(-1, -1, 1), 4.)); + weighted_points.push_back(Weighted_point(Point(1, 1, 1), 4.)); + weighted_points.push_back(Weighted_point(Point(2, 2, 2), 1.)); // ---------------------------------------------------------------------------- // Init of an alpha complex from the list of points // ---------------------------------------------------------------------------- - Weighted_alpha_complex_3d alpha_complex_from_points(points, weights); + Weighted_alpha_complex_3d alpha_complex_from_points(weighted_points); Gudhi::Simplex_tree<> simplex; if (alpha_complex_from_points.create_complex(simplex)) { diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index bbe13be2..bf1aaa99 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -31,7 +31,7 @@ #endif #include -#include +#include #include #include @@ -57,13 +57,6 @@ namespace Gudhi { namespace alpha_complex { -enum class complexity: char -{ - fast='f', - safe='s', - exact='e', -}; - /** * \class Alpha_complex_3d * \brief Alpha complex data structure for 3d specific case. @@ -73,15 +66,30 @@ enum class complexity: char * \details * The data structure is constructing a CGAL 3D Alpha * Shapes from a range of points (can be read from an OFF file, cf. Points_off_reader). + * Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. + * + * \tparam Complexity shall be `Gudhi::alpha_complex::complexity`. Default value is + * `Gudhi::alpha_complex::complexity::fast`. + * + * \tparam Weighted Boolean used to set/unset the weighted version of Alpha_complex_3d. Default value is false. + * + * \tparam Periodic Boolean used to set/unset the periodic version of Alpha_complex_3d. Default value is false. * - * \tparam AlphaComplex3dOptions can be `Gudhi::alpha_complex::Alpha_shapes_3d`, - * `Gudhi::alpha_complex::Exact_alpha_shapes_3d`, `Gudhi::alpha_complex::Weighted_alpha_shapes_3d`, - * `Gudhi::alpha_complex::Periodic_alpha_shapes_3d` or `Gudhi::alpha_complex::Weighted_periodic_alpha_shapes_3d`. + * For the weighted version, weights values are explained on CGAL + * Alpha shapes 3d and + * Regular + * triangulation documentation. + * + * For the periodic version, refer to the + * CGAL’s 3D Periodic Triangulations User + * Manual for more details. + * The periodicity is defined by an iso-oriented cuboid with diagonal opposite vertices (x_min, y_min, z_min) and + * (x_max, y_max, z_max). * * Please refer to \ref alpha_complex for examples. * * \remark When Alpha_complex_3d is constructed with an infinite value of alpha (default value), the complex is a - * Delaunay complex. + * 3d Delaunay complex. * */ template @@ -157,9 +165,9 @@ class Alpha_complex_3d { using Triangulation_3 = CGAL::Periodic_3_regular_triangulation_3; }; +public: using Triangulation_3 = typename Triangulation::Triangulation_3; -public: using Alpha_shape_3 = CGAL::Alpha_shape_3; using Point_3 = typename Kernel::Point_3; @@ -184,20 +192,16 @@ private: public: /** \brief Alpha_complex constructor from a list of points. * - * Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. + * @param[in] points Range of points to triangulate. Points must be in `Alpha_complex_3d::Point_3` or + * `Alpha_complex_3d::Triangulation_3::Weighted_point`. * - * @param[in] points Range of points to triangulate. Points must be in AlphaComplex3dOptions::Point_3 + * @pre Available if Alpha_complex_3d is not Periodic. * - * @pre Available if AlphaComplex3dOptions is `Gudhi::alpha_complex::Alpha_shapes_3d` or - * `Gudhi::alpha_complex::Exact_alpha_shapes_3d`. - * - * The type InputPointRange must be a range for which std::begin and - * std::end return input iterators on a AlphaComplex3dOptions::Point_3. + * The type InputPointRange must be a range for which std::begin and std::end return input iterators on a + * `Alpha_complex_3d::Point_3` or a `Alpha_complex_3d::Triangulation_3::Weighted_point`. */ template Alpha_complex_3d(const InputPointRange& points) { - static_assert(!Weighted, - "This constructor is not available for weighted versions of Alpha_complex_3d"); static_assert(!Periodic, "This constructor is not available for periodic versions of Alpha_complex_3d"); @@ -215,23 +219,17 @@ public: /** \brief Alpha_complex constructor from a list of points and associated weights. * - * Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. - * Weights values are explained on CGAL Alpha - * shape and - * Regular - * triangulation documentation. - * * @exception std::invalid_argument In debug mode, if points and weights do not have the same size. * - * @param[in] points Range of points to triangulate. Points must be in AlphaComplex3dOptions::Point_3 - * @param[in] weights Range of weights on points. Points must be in AlphaComplex3dOptions::Point_3 + * @param[in] points Range of points to triangulate. Points must be in `Alpha_complex_3d::Point_3` + * @param[in] weights Range of weights on points. Weights shall be in `Alpha_complex_3d::Alpha_shape_3::FT` * - * @pre Available if AlphaComplex3dOptions is `Weighted_alpha_shapes_3d`. + * @pre Available if Alpha_complex_3d is Weighted and not Periodic. * * The type InputPointRange must be a range for which std::begin and - * std::end return input iterators on a AlphaComplex3dOptions::Point_3. + * std::end return input iterators on a `Alpha_complex_3d::Point_3`. * The type WeightRange must be a range for which std::begin and - * std::end return an input iterator on a AlphaComplex3dOptions::Alpha_shape_3::FT. + * std::end return an input iterator on a `Alpha_complex_3d::Alpha_shape_3::FT`. */ template Alpha_complex_3d(const InputPointRange& points, WeightRange weights) { @@ -268,16 +266,10 @@ public: /** \brief Alpha_complex constructor from a list of points and an iso-cuboid coordinates. * - * Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. - * - * Refer to the CGAL’s 3D Periodic - * Triangulations User Manual for more details. - * The periodicity is defined by an iso-oriented cuboid with diagonal opposite vertices (x_min, y_min, z_min) and - * (x_max, y_max, z_max). - * * @exception std::invalid_argument In debug mode, if the size of the cuboid in every directions is not the same. * - * @param[in] points Range of points to triangulate. Points must be in AlphaComplex3dOptions::Point_3 + * @param[in] points Range of points to triangulate. Points must be in `Alpha_complex_3d::Point_3` or + * `Alpha_complex_3d::Triangulation_3::Weighted_point`. * @param[in] x_min Iso-oriented cuboid x_min. * @param[in] y_min Iso-oriented cuboid y_min. * @param[in] z_min Iso-oriented cuboid z_min. @@ -285,18 +277,18 @@ public: * @param[in] y_max Iso-oriented cuboid y_max. * @param[in] z_max Iso-oriented cuboid z_max. * - * @pre Available if AlphaComplex3dOptions is `Periodic_alpha_shapes_3d`. + * @pre Available if Alpha_complex_3d is Periodic. * - * The type InputPointRange must be a range for which std::begin and - * std::end return input iterators on a AlphaComplex3dOptions::Point_3. - * The type of x_min, y_min, z_min, x_max, y_max and z_max is AlphaComplex3dOptions::Alpha_shape_3::FT. + * The type InputPointRange must be a range for which std::begin and std::end return input iterators on a + * `Alpha_complex_3d::Point_3` or a `Alpha_complex_3d::Triangulation_3::Weighted_point`. + * + * @note In weighted version, please check weights are greater than zero, and lower than 1/64*cuboid length + * squared. */ template Alpha_complex_3d(const InputPointRange& points, Alpha_value_type x_min, Alpha_value_type y_min, Alpha_value_type z_min, Alpha_value_type x_max, Alpha_value_type y_max, Alpha_value_type z_max) { - static_assert(!Weighted, - "This constructor is not available for weighted versions of Alpha_complex_3d"); static_assert(Periodic, "This constructor is not available for non-periodic versions of Alpha_complex_3d"); // Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it. @@ -332,25 +324,13 @@ public: /** \brief Alpha_complex constructor from a list of points, associated weights and an iso-cuboid coordinates. * - * Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. - * - * Weights values are explained on CGAL Alpha - * shape and - * Regular - * triangulation documentation. - * - * Refer to the CGAL’s 3D Periodic - * Triangulations User Manual for more details. - * The periodicity is defined by an iso-oriented cuboid with diagonal opposite vertices (x_min, y_min, z_min) and - * (x_max, y_max, z_max). - * * @exception std::invalid_argument In debug mode, if points and weights do not have the same size. * @exception std::invalid_argument In debug mode, if the size of the cuboid in every directions is not the same. * @exception std::invalid_argument In debug mode, if a weight is negative, zero, or greater than 1/64*cuboid length * squared. * - * @param[in] points Range of points to triangulate. Points must be in AlphaComplex3dOptions::Point_3 - * @param[in] weights Range of weights on points. Points must be in AlphaComplex3dOptions::Point_3 + * @param[in] points Range of points to triangulate. Points must be in `Alpha_complex_3d::Point_3` + * @param[in] weights Range of weights on points. Weights shall be in `Alpha_complex_3d::Alpha_shape_3::FT` * @param[in] x_min Iso-oriented cuboid x_min. * @param[in] y_min Iso-oriented cuboid y_min. * @param[in] z_min Iso-oriented cuboid z_min. @@ -358,13 +338,13 @@ public: * @param[in] y_max Iso-oriented cuboid y_max. * @param[in] z_max Iso-oriented cuboid z_max. * - * @pre Available if AlphaComplex3dOptions is `Weighted_periodic_alpha_shapes_3d`. + * @pre Available if Alpha_complex_3d is Weighted and Periodic. * * The type InputPointRange must be a range for which std::begin and - * std::end return input iterators on a AlphaComplex3dOptions::Point_3. + * std::end return input iterators on a `Alpha_complex_3d::Point_3`. * The type WeightRange must be a range for which std::begin and - * std::end return an input iterator on a AlphaComplex3dOptions::Alpha_shape_3::FT. - * The type of x_min, y_min, z_min, x_max, y_max and z_max is AlphaComplex3dOptions::Alpha_shape_3::FT. + * std::end return an input iterator on a `Alpha_complex_3d::Alpha_shape_3::FT`. + * The type of x_min, y_min, z_min, x_max, y_max and z_max is `Alpha_complex_3d::Alpha_shape_3::FT`. */ template Alpha_complex_3d(const InputPointRange& points, WeightRange weights, @@ -395,7 +375,7 @@ public: while ((index < weights.size()) && (index < points.size())) { GUDHI_CHECK((weights[index] < maximal_possible_weight) && (weights[index] >= 0), - std::invalid_argument("Invalid weight at line" + std::to_string(index + 1) + + std::invalid_argument("Invalid weight at index " + std::to_string(index + 1) + ". Must be positive and less than maximal possible weight = 1/64*cuboid length " "squared, which is not an acceptable input.")); weighted_points_3.push_back(Weighted_point_3(points[index], weights[index])); diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h deleted file mode 100644 index 567b19cb..00000000 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d_options.h +++ /dev/null @@ -1,179 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Vincent Rouvreau - * - * Copyright (C) 2018 Inria - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -#ifndef ALPHA_COMPLEX_3D_OPTIONS_H_ -#define ALPHA_COMPLEX_3D_OPTIONS_H_ - - -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include - - -namespace Gudhi { - -namespace alpha_complex { - -class Alpha_shapes_3d { -private: - using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; - using Vb = CGAL::Alpha_shape_vertex_base_3; - using Fb = CGAL::Alpha_shape_cell_base_3; - using Tds = CGAL::Triangulation_data_structure_3; - using Triangulation_3 = CGAL::Delaunay_triangulation_3; - -public: - using Alpha_shape_3 = CGAL::Alpha_shape_3; - using Point_3 = Kernel::Point_3; - - static const bool weighted = false; - static const bool periodic = false; - - // Default value_from_iterator as Alpha_shape_3 is not exact - template - static Filtration_value value_from_iterator(const Alpha_value_iterator avi) { - return /*std::sqrt*/ *avi; - } -}; - -class Exact_alpha_shapes_3d { -private: - // Alpha_shape_3 templates type definitions - using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; - using Exact_tag = CGAL::Tag_true; - using Vb = CGAL::Alpha_shape_vertex_base_3; - using Fb = CGAL::Alpha_shape_cell_base_3; - using Tds = CGAL::Triangulation_data_structure_3; - using Triangulation_3 = CGAL::Delaunay_triangulation_3; - -public: - using Alpha_shape_3 = CGAL::Alpha_shape_3; - using Point_3 = Kernel::Point_3; - - static const bool weighted = false; - static const bool periodic = false; - - // value_from_iterator needs to compute filtration value as Alpha_shape_3 is exact - template - static Filtration_value value_from_iterator(const Alpha_value_iterator avi) { - return /*std::sqrt*/ CGAL::to_double(avi->exact()); - } -}; - -class Weighted_alpha_shapes_3d { -private: - using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; - using Rvb = CGAL::Regular_triangulation_vertex_base_3; - using Vb = CGAL::Alpha_shape_vertex_base_3; - using Rcb = CGAL::Regular_triangulation_cell_base_3; - using Cb = CGAL::Alpha_shape_cell_base_3; - using Tds = CGAL::Triangulation_data_structure_3; - using Triangulation_3 = CGAL::Regular_triangulation_3; - - -public: - using Alpha_shape_3 = CGAL::Alpha_shape_3; - using Point_3 = Triangulation_3::Bare_point; - using Weighted_point_3 = Triangulation_3::Weighted_point; - - static const bool weighted = true; - static const bool periodic = false; - - // Default value_from_iterator as Alpha_shape_3 is not exact - template - static Filtration_value value_from_iterator(const Alpha_value_iterator avi) { - return /*std::sqrt*/ *avi; - } -}; - -class Periodic_alpha_shapes_3d { -private: - // Traits - using K = CGAL::Exact_predicates_inexact_constructions_kernel; - using PK = CGAL::Periodic_3_Delaunay_triangulation_traits_3; -// Vertex type - using DsVb = CGAL::Periodic_3_triangulation_ds_vertex_base_3<>; - using Vb = CGAL::Triangulation_vertex_base_3; - using AsVb = CGAL::Alpha_shape_vertex_base_3; -// Cell type - using DsCb = CGAL::Periodic_3_triangulation_ds_cell_base_3<>; - using Cb = CGAL::Triangulation_cell_base_3; - using AsCb = CGAL::Alpha_shape_cell_base_3; - using Tds = CGAL::Triangulation_data_structure_3; - -public: - using Periodic_delaunay_triangulation_3 = CGAL::Periodic_3_Delaunay_triangulation_3; - using Alpha_shape_3 = CGAL::Alpha_shape_3; - using Point_3 = PK::Point_3; - using Iso_cuboid_3 = PK::Iso_cuboid_3; - - static const bool weighted = false; - static const bool periodic = true; - - // Default value_from_iterator as Alpha_shape_3 is not exact - template - static Filtration_value value_from_iterator(const Alpha_value_iterator avi) { - return /*std::sqrt*/ *avi; - } -}; - -class Weighted_periodic_alpha_shapes_3d { -private: - using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; - using Periodic_kernel = CGAL::Periodic_3_regular_triangulation_traits_3; - using DsVb = CGAL::Periodic_3_triangulation_ds_vertex_base_3<>; - using Vb = CGAL::Regular_triangulation_vertex_base_3; - using AsVb = CGAL::Alpha_shape_vertex_base_3; - using DsCb = CGAL::Periodic_3_triangulation_ds_cell_base_3<>; - using Cb = CGAL::Regular_triangulation_cell_base_3; - using AsCb = CGAL::Alpha_shape_cell_base_3; - using Tds = CGAL::Triangulation_data_structure_3; - -public: - using Periodic_delaunay_triangulation_3 = CGAL::Periodic_3_regular_triangulation_3; - using Alpha_shape_3 = CGAL::Alpha_shape_3; - using Point_3 = Periodic_delaunay_triangulation_3::Bare_point; - using Weighted_point_3 = Periodic_delaunay_triangulation_3::Weighted_point; - using Iso_cuboid_3 = Periodic_kernel::Iso_cuboid_3; - - static const bool weighted = true; - static const bool periodic = true; - - // Default value_from_iterator as Alpha_shape_3 is not exact - template - static Filtration_value value_from_iterator(const Alpha_value_iterator avi) { - return /*std::sqrt*/ *avi; - } -}; - -} // namespace alpha_complex - -} // namespace Gudhi - -#endif // ALPHA_COMPLEX_3D_OPTIONS_H_ diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_options.h b/src/Alpha_complex/include/gudhi/Alpha_complex_options.h new file mode 100644 index 00000000..32980fa7 --- /dev/null +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_options.h @@ -0,0 +1,64 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Vincent Rouvreau + * + * Copyright (C) 2018 Inria + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#ifndef ALPHA_COMPLEX_OPTIONS_H_ +#define ALPHA_COMPLEX_OPTIONS_H_ + + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + + +namespace Gudhi { + +namespace alpha_complex { + + +/** + * \class complexity + * \brief Alpha complex complexity template parameter possible values. + * + * \ingroup alpha_complex + */ +enum class complexity: char +{ + /** \brief Fast version.*/ + fast='f', + /** \brief Safe version.*/ + safe='s', + /** \brief Exact version.*/ + exact='e', +}; + +} // namespace alpha_complex + +} // namespace Gudhi + +#endif // ALPHA_COMPLEX_OPTIONS_H_ diff --git a/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp index 7cc21475..2bd925d3 100644 --- a/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp +++ b/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp @@ -30,9 +30,9 @@ #include #include #include +#include // for std::size_t #include -#include #include #include #include @@ -111,9 +111,9 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_3d_from_points) { } } -#ifdef GUDHI_DEBUG typedef boost::mpl::list weighted_variants_type_list; +#ifdef GUDHI_DEBUG BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_weighted_throw, Weighted_alpha_complex_3d, weighted_variants_type_list) { using Point_3 = typename Weighted_alpha_complex_3d::Point_3; std::vector w_points; @@ -132,61 +132,55 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_weighted_throw, Weighted_alpha_compl } #endif -BOOST_AUTO_TEST_CASE(Alpha_complex_weighted) { - // --------------------- - // Fast weighted version - // --------------------- - std::cout << "Fast weighted alpha complex 3d" << std::endl; - std::vector w_points; - w_points.push_back(Fast_weighted_alpha_complex_3d::Point_3(0.0, 0.0, 0.0)); - w_points.push_back(Fast_weighted_alpha_complex_3d::Point_3(0.0, 0.0, 0.2)); - w_points.push_back(Fast_weighted_alpha_complex_3d::Point_3(0.2, 0.0, 0.2)); - w_points.push_back(Fast_weighted_alpha_complex_3d::Point_3(0.6, 0.6, 0.0)); - w_points.push_back(Fast_weighted_alpha_complex_3d::Point_3(0.8, 0.8, 0.2)); - w_points.push_back(Fast_weighted_alpha_complex_3d::Point_3(0.2, 0.8, 0.6)); +BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_weighted, Weighted_alpha_complex_3d, weighted_variants_type_list) { + std::cout << "Weighted alpha complex 3d from points and weights" << std::endl; + using Point_3 = typename Weighted_alpha_complex_3d::Point_3; + std::vector w_points; + w_points.push_back(Point_3(0.0, 0.0, 0.0)); + w_points.push_back(Point_3(0.0, 0.0, 0.2)); + w_points.push_back(Point_3(0.2, 0.0, 0.2)); + w_points.push_back(Point_3(0.6, 0.6, 0.0)); + w_points.push_back(Point_3(0.8, 0.8, 0.2)); + w_points.push_back(Point_3(0.2, 0.8, 0.6)); // weights size is different from w_points size to make weighted Alpha_complex_3d throw in debug mode std::vector weights = {0.01, 0.005, 0.006, 0.01, 0.009, 0.001}; - Fast_weighted_alpha_complex_3d weighted_alpha_complex(w_points, weights); + Weighted_alpha_complex_3d alpha_complex_p_a_w(w_points, weights); Gudhi::Simplex_tree<> stree; - weighted_alpha_complex.create_complex(stree); + alpha_complex_p_a_w.create_complex(stree); - // ---------------------- - // Exact weighted version - // ---------------------- - std::cout << "Exact weighted alpha complex 3d" << std::endl; + std::cout << "Weighted alpha complex 3d from weighted points" << std::endl; + using Weighted_point_3 = typename Weighted_alpha_complex_3d::Triangulation_3::Weighted_point; - std::vector e_w_points; - e_w_points.push_back(Exact_weighted_alpha_complex_3d::Point_3(0.0, 0.0, 0.0)); - e_w_points.push_back(Exact_weighted_alpha_complex_3d::Point_3(0.0, 0.0, 0.2)); - e_w_points.push_back(Exact_weighted_alpha_complex_3d::Point_3(0.2, 0.0, 0.2)); - e_w_points.push_back(Exact_weighted_alpha_complex_3d::Point_3(0.6, 0.6, 0.0)); - e_w_points.push_back(Exact_weighted_alpha_complex_3d::Point_3(0.8, 0.8, 0.2)); - e_w_points.push_back(Exact_weighted_alpha_complex_3d::Point_3(0.2, 0.8, 0.6)); - Exact_weighted_alpha_complex_3d exact_alpha_complex(e_w_points, weights); + std::vector weighted_points; - Gudhi::Simplex_tree<> exact_stree; - exact_alpha_complex.create_complex(exact_stree); + for (std::size_t i=0; i < w_points.size(); i++) { + weighted_points.push_back(Weighted_point_3(w_points[i], weights[i])); + } + Weighted_alpha_complex_3d alpha_complex_w_p(weighted_points); + + Gudhi::Simplex_tree<> stree_bis; + alpha_complex_w_p.create_complex(stree_bis); // --------------------- // Compare both versions // --------------------- - std::cout << "Exact weighted alpha complex 3d is of dimension " << exact_stree.dimension() - << " - Non exact is " << stree.dimension() << std::endl; - BOOST_CHECK(exact_stree.dimension() == stree.dimension()); - std::cout << "Exact weighted alpha complex 3d num_simplices " << exact_stree.num_simplices() - << " - Non exact is " << stree.num_simplices() << std::endl; - BOOST_CHECK(exact_stree.num_simplices() == stree.num_simplices()); - std::cout << "Exact weighted alpha complex 3d num_vertices " << exact_stree.num_vertices() - << " - Non exact is " << stree.num_vertices() << std::endl; - BOOST_CHECK(exact_stree.num_vertices() == stree.num_vertices()); + std::cout << "Weighted alpha complex 3d is of dimension " << stree_bis.dimension() + << " - versus " << stree.dimension() << std::endl; + BOOST_CHECK(stree_bis.dimension() == stree.dimension()); + std::cout << "Weighted alpha complex 3d num_simplices " << stree_bis.num_simplices() + << " - versus " << stree.num_simplices() << std::endl; + BOOST_CHECK(stree_bis.num_simplices() == stree.num_simplices()); + std::cout << "Weighted alpha complex 3d num_vertices " << stree_bis.num_vertices() + << " - versus " << stree.num_vertices() << std::endl; + BOOST_CHECK(stree_bis.num_vertices() == stree.num_vertices()); auto sh = stree.filtration_simplex_range().begin(); while(sh != stree.filtration_simplex_range().end()) { std::vector simplex; std::vector exact_simplex; - std::cout << "Non-exact ( "; + std::cout << " ( "; for (auto vertex : stree.simplex_vertex_range(*sh)) { simplex.push_back(vertex); std::cout << vertex << " "; @@ -195,11 +189,11 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_weighted) { std::cout << std::endl; // Find it in the exact structure - auto sh_exact = exact_stree.find(simplex); - BOOST_CHECK(sh_exact != exact_stree.null_simplex()); + auto sh_exact = stree_bis.find(simplex); + BOOST_CHECK(sh_exact != stree_bis.null_simplex()); // Exact and non-exact version is not exactly the same due to float comparison - GUDHI_TEST_FLOAT_EQUALITY_CHECK(exact_stree.filtration(sh_exact), stree.filtration(*sh)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(stree_bis.filtration(sh_exact), stree.filtration(*sh)); ++sh; } @@ -207,7 +201,7 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_weighted) { } #ifdef GUDHI_DEBUG -typedef boost::mpl::list periodic_variants_type_list; +typedef boost::mpl::list periodic_variants_type_list; BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_periodic_throw, Periodic_alpha_complex_3d, periodic_variants_type_list) { std::cout << "Periodic alpha complex 3d exception throw" << std::endl; @@ -541,10 +535,11 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_periodic) { } -#ifdef GUDHI_DEBUG -typedef boost::mpl::list wp_variants_type_list; +typedef boost::mpl::list wp_variants_type_list; -BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_weighted_periodic_throw, Weighted_periodic_alpha_complex_3d, wp_variants_type_list) { +#ifdef GUDHI_DEBUG +BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_weighted_periodic_throw, Weighted_periodic_alpha_complex_3d, + wp_variants_type_list) { std::cout << "Weighted periodic alpha complex 3d exception throw" << std::endl; using Point_3 = typename Weighted_periodic_alpha_complex_3d::Point_3; @@ -722,311 +717,186 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_weighted_periodic_throw, Weighted_pe } #endif -BOOST_AUTO_TEST_CASE(Alpha_complex_weighted_periodic) { - // ------------------------------ - // Fast weighted periodic version - // ------------------------------ - std::cout << "Fast weighted periodic alpha complex 3d" << std::endl; - - std::vector wp_points; - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.0, 0.2)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.0, 0.4)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.0, 0.6)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.0, 0.8)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.2, 0.0)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.2, 0.2)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.2, 0.4)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.2, 0.6)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.2, 0.8)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.4, 0.0)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.4, 0.2)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.4, 0.4)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.4, 0.6)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.4, 0.8)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.6, 0.0)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.6, 0.2)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.6, 0.4)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.6, 0.6)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.6, 0.8)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.8, 0.0)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.8, 0.2)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.8, 0.4)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.8, 0.6)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.8, 0.8)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.0, 0.0)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.0, 0.2)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.0, 0.4)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.0, 0.6)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.0, 0.8)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.2, 0.0)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.2, 0.2)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.2, 0.4)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.2, 0.6)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.2, 0.8)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.4, 0.0)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.4, 0.2)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.4, 0.4)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.4, 0.6)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.4, 0.8)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.6, 0.0)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.6, 0.2)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.6, 0.4)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.6, 0.6)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.6, 0.8)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.0, 0.0)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.8, 0.0)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.8, 0.2)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.8, 0.4)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.8, 0.6)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.8, 0.8)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.0, 0.0)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.0, 0.2)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.0, 0.4)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.0, 0.6)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.0, 0.8)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.2, 0.0)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.2, 0.2)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.2, 0.4)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.2, 0.6)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.2, 0.8)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.4, 0.0)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.4, 0.2)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.4, 0.4)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.4, 0.6)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.4, 0.8)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.6, 0.0)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.6, 0.2)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.6, 0.4)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.6, 0.6)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.6, 0.8)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.8, 0.0)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.8, 0.2)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.8, 0.4)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.8, 0.6)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.8, 0.8)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.0, 0.0)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.0, 0.2)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.0, 0.4)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.0, 0.6)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.0, 0.8)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.1, 0.0)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.2, 0.0)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.2, 0.2)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.2, 0.4)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.2, 0.6)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.2, 0.8)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.4, 0.0)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.4, 0.2)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.4, 0.4)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.4, 0.6)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.4, 0.8)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.6, 0.0)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.6, 0.2)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.6, 0.4)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.6, 0.6)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.6, 0.8)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.8, 0.0)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.8, 0.2)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.8, 0.4)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.8, 0.6)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.8, 0.8)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.0, 0.0)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.0, 0.2)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.0, 0.4)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.0, 0.6)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.0, 0.8)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.2, 0.0)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.2, 0.2)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.2, 0.4)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.2, 0.6)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.2, 0.8)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.4, 0.0)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.4, 0.2)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.4, 0.4)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.4, 0.6)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.4, 0.8)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.6, 0.0)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.6, 0.2)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.6, 0.4)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.6, 0.6)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.6, 0.8)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.8, 0.0)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.8, 0.2)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.8, 0.4)); - wp_points.push_back(Fast_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.8, 0.6)); - - std::vector p_weights; +BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_weighted_periodic, Weighted_periodic_alpha_complex_3d, + wp_variants_type_list) { + std::cout << "Weighted Periodic alpha complex 3d from points and weights" << std::endl; + using Point_3 = typename Weighted_periodic_alpha_complex_3d::Point_3; + std::vector points; + + points.push_back(Point_3(0.0, 0.0, 0.2)); + points.push_back(Point_3(0.0, 0.0, 0.4)); + points.push_back(Point_3(0.0, 0.0, 0.6)); + points.push_back(Point_3(0.0, 0.0, 0.8)); + points.push_back(Point_3(0.0, 0.2, 0.0)); + points.push_back(Point_3(0.0, 0.2, 0.2)); + points.push_back(Point_3(0.0, 0.2, 0.4)); + points.push_back(Point_3(0.0, 0.2, 0.6)); + points.push_back(Point_3(0.0, 0.2, 0.8)); + points.push_back(Point_3(0.0, 0.4, 0.0)); + points.push_back(Point_3(0.0, 0.4, 0.2)); + points.push_back(Point_3(0.0, 0.4, 0.4)); + points.push_back(Point_3(0.0, 0.4, 0.6)); + points.push_back(Point_3(0.0, 0.4, 0.8)); + points.push_back(Point_3(0.0, 0.6, 0.0)); + points.push_back(Point_3(0.0, 0.6, 0.2)); + points.push_back(Point_3(0.0, 0.6, 0.4)); + points.push_back(Point_3(0.0, 0.6, 0.6)); + points.push_back(Point_3(0.0, 0.6, 0.8)); + points.push_back(Point_3(0.0, 0.8, 0.0)); + points.push_back(Point_3(0.0, 0.8, 0.2)); + points.push_back(Point_3(0.0, 0.8, 0.4)); + points.push_back(Point_3(0.0, 0.8, 0.6)); + points.push_back(Point_3(0.0, 0.8, 0.8)); + points.push_back(Point_3(0.2, 0.0, 0.0)); + points.push_back(Point_3(0.2, 0.0, 0.2)); + points.push_back(Point_3(0.2, 0.0, 0.4)); + points.push_back(Point_3(0.2, 0.0, 0.6)); + points.push_back(Point_3(0.2, 0.0, 0.8)); + points.push_back(Point_3(0.2, 0.2, 0.0)); + points.push_back(Point_3(0.2, 0.2, 0.2)); + points.push_back(Point_3(0.2, 0.2, 0.4)); + points.push_back(Point_3(0.2, 0.2, 0.6)); + points.push_back(Point_3(0.2, 0.2, 0.8)); + points.push_back(Point_3(0.2, 0.4, 0.0)); + points.push_back(Point_3(0.2, 0.4, 0.2)); + points.push_back(Point_3(0.2, 0.4, 0.4)); + points.push_back(Point_3(0.2, 0.4, 0.6)); + points.push_back(Point_3(0.2, 0.4, 0.8)); + points.push_back(Point_3(0.2, 0.6, 0.0)); + points.push_back(Point_3(0.2, 0.6, 0.2)); + points.push_back(Point_3(0.2, 0.6, 0.4)); + points.push_back(Point_3(0.2, 0.6, 0.6)); + points.push_back(Point_3(0.2, 0.6, 0.8)); + points.push_back(Point_3(0.0, 0.0, 0.0)); + points.push_back(Point_3(0.2, 0.8, 0.0)); + points.push_back(Point_3(0.2, 0.8, 0.2)); + points.push_back(Point_3(0.2, 0.8, 0.4)); + points.push_back(Point_3(0.2, 0.8, 0.6)); + points.push_back(Point_3(0.2, 0.8, 0.8)); + points.push_back(Point_3(0.4, 0.0, 0.0)); + points.push_back(Point_3(0.4, 0.0, 0.2)); + points.push_back(Point_3(0.4, 0.0, 0.4)); + points.push_back(Point_3(0.4, 0.0, 0.6)); + points.push_back(Point_3(0.4, 0.0, 0.8)); + points.push_back(Point_3(0.4, 0.2, 0.0)); + points.push_back(Point_3(0.4, 0.2, 0.2)); + points.push_back(Point_3(0.4, 0.2, 0.4)); + points.push_back(Point_3(0.4, 0.2, 0.6)); + points.push_back(Point_3(0.4, 0.2, 0.8)); + points.push_back(Point_3(0.4, 0.4, 0.0)); + points.push_back(Point_3(0.4, 0.4, 0.2)); + points.push_back(Point_3(0.4, 0.4, 0.4)); + points.push_back(Point_3(0.4, 0.4, 0.6)); + points.push_back(Point_3(0.4, 0.4, 0.8)); + points.push_back(Point_3(0.4, 0.6, 0.0)); + points.push_back(Point_3(0.4, 0.6, 0.2)); + points.push_back(Point_3(0.4, 0.6, 0.4)); + points.push_back(Point_3(0.4, 0.6, 0.6)); + points.push_back(Point_3(0.4, 0.6, 0.8)); + points.push_back(Point_3(0.4, 0.8, 0.0)); + points.push_back(Point_3(0.4, 0.8, 0.2)); + points.push_back(Point_3(0.4, 0.8, 0.4)); + points.push_back(Point_3(0.4, 0.8, 0.6)); + points.push_back(Point_3(0.4, 0.8, 0.8)); + points.push_back(Point_3(0.6, 0.0, 0.0)); + points.push_back(Point_3(0.6, 0.0, 0.2)); + points.push_back(Point_3(0.6, 0.0, 0.4)); + points.push_back(Point_3(0.6, 0.0, 0.6)); + points.push_back(Point_3(0.6, 0.0, 0.8)); + points.push_back(Point_3(0.6, 0.1, 0.0)); + points.push_back(Point_3(0.6, 0.2, 0.0)); + points.push_back(Point_3(0.6, 0.2, 0.2)); + points.push_back(Point_3(0.6, 0.2, 0.4)); + points.push_back(Point_3(0.6, 0.2, 0.6)); + points.push_back(Point_3(0.6, 0.2, 0.8)); + points.push_back(Point_3(0.6, 0.4, 0.0)); + points.push_back(Point_3(0.6, 0.4, 0.2)); + points.push_back(Point_3(0.6, 0.4, 0.4)); + points.push_back(Point_3(0.6, 0.4, 0.6)); + points.push_back(Point_3(0.6, 0.4, 0.8)); + points.push_back(Point_3(0.6, 0.6, 0.0)); + points.push_back(Point_3(0.6, 0.6, 0.2)); + points.push_back(Point_3(0.6, 0.6, 0.4)); + points.push_back(Point_3(0.6, 0.6, 0.6)); + points.push_back(Point_3(0.6, 0.6, 0.8)); + points.push_back(Point_3(0.6, 0.8, 0.0)); + points.push_back(Point_3(0.6, 0.8, 0.2)); + points.push_back(Point_3(0.6, 0.8, 0.4)); + points.push_back(Point_3(0.6, 0.8, 0.6)); + points.push_back(Point_3(0.6, 0.8, 0.8)); + points.push_back(Point_3(0.8, 0.0, 0.0)); + points.push_back(Point_3(0.8, 0.0, 0.2)); + points.push_back(Point_3(0.8, 0.0, 0.4)); + points.push_back(Point_3(0.8, 0.0, 0.6)); + points.push_back(Point_3(0.8, 0.0, 0.8)); + points.push_back(Point_3(0.8, 0.2, 0.0)); + points.push_back(Point_3(0.8, 0.2, 0.2)); + points.push_back(Point_3(0.8, 0.2, 0.4)); + points.push_back(Point_3(0.8, 0.2, 0.6)); + points.push_back(Point_3(0.8, 0.2, 0.8)); + points.push_back(Point_3(0.8, 0.4, 0.0)); + points.push_back(Point_3(0.8, 0.4, 0.2)); + points.push_back(Point_3(0.8, 0.4, 0.4)); + points.push_back(Point_3(0.8, 0.4, 0.6)); + points.push_back(Point_3(0.8, 0.4, 0.8)); + points.push_back(Point_3(0.8, 0.6, 0.0)); + points.push_back(Point_3(0.8, 0.6, 0.2)); + points.push_back(Point_3(0.8, 0.6, 0.4)); + points.push_back(Point_3(0.8, 0.6, 0.6)); + points.push_back(Point_3(0.8, 0.6, 0.8)); + points.push_back(Point_3(0.8, 0.8, 0.0)); + points.push_back(Point_3(0.8, 0.8, 0.2)); + points.push_back(Point_3(0.8, 0.8, 0.4)); + points.push_back(Point_3(0.8, 0.8, 0.6)); + + std::vector weights; std::random_device rd; std::mt19937 mt(rd()); // Weights must be in range [0, <1/64] std::uniform_real_distribution dist(0.01, 0.0156245); - for (std::size_t i = 0; i < wp_points.size(); ++i) { + for (std::size_t i = 0; i < points.size(); ++i) { double value = dist(mt); - p_weights.push_back(value); + weights.push_back(value); } - Fast_weighted_periodic_alpha_complex_3d weighted_periodic_alpha_complex(wp_points, p_weights, 0., 0., 0., 1., 1., 1.); + Weighted_periodic_alpha_complex_3d weighted_periodic_alpha_complex(points, weights, 0., 0., 0., 1., 1., 1.); Gudhi::Simplex_tree<> stree; weighted_periodic_alpha_complex.create_complex(stree); - // ------------------------------- - // Exact weighted periodic version - // ------------------------------- - std::cout << "Exact weighted periodic alpha complex 3d" << std::endl; - - std::vector e_wp_points; - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.0, 0.4)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.0, 0.6)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.0, 0.8)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.2, 0.0)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.2, 0.2)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.2, 0.4)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.2, 0.6)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.2, 0.8)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.4, 0.0)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.4, 0.2)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.4, 0.4)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.4, 0.6)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.4, 0.8)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.6, 0.0)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.6, 0.2)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.6, 0.4)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.0, 0.2)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.6, 0.6)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.6, 0.8)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.8, 0.0)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.8, 0.2)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.8, 0.4)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.8, 0.6)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.8, 0.8)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.0, 0.0)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.0, 0.2)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.0, 0.4)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.0, 0.6)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.0, 0.8)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.2, 0.0)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.2, 0.2)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.2, 0.4)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.2, 0.6)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.2, 0.8)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.4, 0.0)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.4, 0.2)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.4, 0.4)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.4, 0.6)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.4, 0.8)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.6, 0.0)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.6, 0.2)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.6, 0.4)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.6, 0.6)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.6, 0.8)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.0, 0.0, 0.0)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.8, 0.0)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.8, 0.2)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.8, 0.4)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.8, 0.6)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.2, 0.8, 0.8)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.0, 0.0)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.0, 0.2)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.0, 0.4)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.0, 0.6)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.0, 0.8)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.2, 0.0)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.2, 0.2)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.2, 0.4)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.2, 0.6)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.2, 0.8)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.4, 0.0)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.4, 0.2)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.4, 0.4)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.4, 0.6)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.4, 0.8)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.6, 0.0)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.6, 0.2)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.6, 0.4)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.6, 0.6)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.6, 0.8)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.8, 0.0)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.8, 0.2)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.8, 0.4)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.8, 0.6)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.4, 0.8, 0.8)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.0, 0.0)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.0, 0.2)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.0, 0.4)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.0, 0.6)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.0, 0.8)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.1, 0.0)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.2, 0.0)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.2, 0.2)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.2, 0.4)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.2, 0.6)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.2, 0.8)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.4, 0.0)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.4, 0.2)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.4, 0.4)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.4, 0.6)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.4, 0.8)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.6, 0.0)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.6, 0.2)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.6, 0.4)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.6, 0.6)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.6, 0.8)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.8, 0.0)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.8, 0.2)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.8, 0.4)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.8, 0.6)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.6, 0.8, 0.8)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.0, 0.0)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.0, 0.2)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.0, 0.4)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.0, 0.6)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.0, 0.8)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.2, 0.0)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.2, 0.2)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.2, 0.4)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.2, 0.6)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.2, 0.8)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.4, 0.0)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.4, 0.2)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.4, 0.4)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.4, 0.6)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.4, 0.8)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.6, 0.0)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.6, 0.2)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.6, 0.4)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.6, 0.6)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.6, 0.8)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.8, 0.0)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.8, 0.2)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.8, 0.4)); - e_wp_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(0.8, 0.8, 0.6)); - - Exact_weighted_periodic_alpha_complex_3d e_weighted_periodic_alpha_complex(e_wp_points, p_weights, 0., 0., 0., 1., 1., 1.); + std::cout << "Weighted periodic alpha complex 3d from weighted points" << std::endl; + using Weighted_point_3 = typename Weighted_periodic_alpha_complex_3d::Triangulation_3::Weighted_point; - Gudhi::Simplex_tree<> exact_stree; - e_weighted_periodic_alpha_complex.create_complex(exact_stree); + std::vector weighted_points; + + for (std::size_t i=0; i < points.size(); i++) { + weighted_points.push_back(Weighted_point_3(points[i], weights[i])); + } + Weighted_periodic_alpha_complex_3d alpha_complex_w_p(weighted_points, 0., 0., 0., 1., 1., 1.); + + Gudhi::Simplex_tree<> stree_bis; + alpha_complex_w_p.create_complex(stree_bis); // --------------------- // Compare both versions // --------------------- - std::cout << "Exact periodic alpha complex 3d is of dimension " << exact_stree.dimension() - << " - Non exact is " << stree.dimension() << std::endl; - BOOST_CHECK(exact_stree.dimension() == stree.dimension()); - std::cout << "Exact periodic alpha complex 3d num_simplices " << exact_stree.num_simplices() - << " - Non exact is " << stree.num_simplices() << std::endl; - // TODO(VR): BOOST_CHECK(exact_stree.num_simplices() == stree.num_simplices()); - std::cout << "Exact periodic alpha complex 3d num_vertices " << exact_stree.num_vertices() - << " - Non exact is " << stree.num_vertices() << std::endl; - BOOST_CHECK(exact_stree.num_vertices() == stree.num_vertices()); + std::cout << "Weighted periodic alpha complex 3d is of dimension " << stree_bis.dimension() + << " - versus " << stree.dimension() << std::endl; + BOOST_CHECK(stree_bis.dimension() == stree.dimension()); + std::cout << "Weighted periodic alpha complex 3d num_simplices " << stree_bis.num_simplices() + << " - versus " << stree.num_simplices() << std::endl; + BOOST_CHECK(stree_bis.num_simplices() == stree.num_simplices()); + std::cout << "Weighted periodic alpha complex 3d num_vertices " << stree_bis.num_vertices() + << " - versus " << stree.num_vertices() << std::endl; + BOOST_CHECK(stree_bis.num_vertices() == stree.num_vertices()); auto sh = stree.filtration_simplex_range().begin(); while(sh != stree.filtration_simplex_range().end()) { std::vector simplex; std::vector exact_simplex; - std::cout << "Non-exact ( "; + std::cout << " ( "; for (auto vertex : stree.simplex_vertex_range(*sh)) { simplex.push_back(vertex); std::cout << vertex << " "; @@ -1035,11 +905,12 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_weighted_periodic) { std::cout << std::endl; // Find it in the exact structure - auto sh_exact = exact_stree.find(simplex); - // TODO(VR): BOOST_CHECK(sh_exact != exact_stree.null_simplex()); + auto sh_exact = stree_bis.find(simplex); + BOOST_CHECK(sh_exact != stree_bis.null_simplex()); // Exact and non-exact version is not exactly the same due to float comparison - // TODO(VR): GUDHI_TEST_FLOAT_EQUALITY_CHECK(exact_stree.filtration(sh_exact), stree.filtration(*sh)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(stree_bis.filtration(sh_exact), stree.filtration(*sh)); + ++sh; } diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp index 536de444..1a152541 100644 --- a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp @@ -24,7 +24,6 @@ #include #include -#include #include #include #include @@ -34,16 +33,24 @@ #include // gudhi type definition -using Weighted_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Weighted_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Exact_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; using Simplex_tree = Gudhi::Simplex_tree; using Filtration_value = Simplex_tree::Filtration_value; using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; +using Fast_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Safe_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Exact_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Fast_weighted_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Safe_weighted_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Exact_weighted_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Fast_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Safe_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Exact_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Fast_weighted_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Safe_weighted_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Exact_weighted_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + void program_options(int argc, char *argv[], std::string &off_file_points, bool& exact, std::string &weight_file, std::string &cuboid_file, std::string &output_file_diag, Filtration_value &alpha_square_max_value, int &coeff_field_characteristic, Filtration_value &min_persistence); @@ -98,6 +105,72 @@ int main(int argc, char **argv) { program_options(argc, argv, off_file_points, exact_version, weight_file, cuboid_file, output_file_diag, alpha_square_max_value, coeff_field_characteristic, min_persistence); + Gudhi::alpha_complex::complexity complexity = Gudhi::alpha_complex::complexity::fast; + if (exact_version) { + complexity = Gudhi::alpha_complex::complexity::exact; + } + + switch(complexity) { + case Gudhi::alpha_complex::complexity::fast: + if (weighted_version) { + if (periodic_version) { + using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + } else { + using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + } + } else { + if (periodic_version) { + using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + } else { + using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + } + } + break; + case Gudhi::alpha_complex::complexity::exact: + if (weighted_version) { + if (periodic_version) { + using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + } else { + using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + } + } else { + if (periodic_version) { + using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + } else { + using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + } + } + break; + case Gudhi::alpha_complex::complexity::safe: + if (weighted_version) { + if (periodic_version) { + using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + } else { + using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + } + } else { + if (periodic_version) { + using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + } else { + using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + } + } + break; + } + + /*const Gudhi::alpha_complex::complexity complexity_(complexity); // Read the OFF file (input file name given as parameter) and triangulate points Gudhi::Points_3D_off_reader off_reader(off_file_points); // Check the read operation was correct @@ -127,35 +200,26 @@ int main(int argc, char **argv) { Simplex_tree simplex_tree; - if (exact_version) { - if ((weighted_version) || (periodic_version)) { - std::cerr << "Unable to compute exact version of a weighted and/or periodic alpha shape" << std::endl; - exit(-1); + if (weighted_version) { + if (periodic_version) { + Alpha_complex_3d alpha_complex(off_reader.get_point_cloud(), weights, + x_min, y_min, z_min, x_max, y_max, z_max); + create_complex(alpha_complex, simplex_tree, alpha_square_max_value); } else { - Exact_alpha_complex_3d alpha_complex(off_reader.get_point_cloud()); + Alpha_complex_3d alpha_complex(off_reader.get_point_cloud(), weights); create_complex(alpha_complex, simplex_tree, alpha_square_max_value); } } else { - if (weighted_version) { - if (periodic_version) { - Weighted_periodic_alpha_complex_3d alpha_complex(off_reader.get_point_cloud(), weights, - x_min, y_min, z_min, x_max, y_max, z_max); - create_complex(alpha_complex, simplex_tree, alpha_square_max_value); - } else { - Weighted_alpha_complex_3d alpha_complex(off_reader.get_point_cloud(), weights); - create_complex(alpha_complex, simplex_tree, alpha_square_max_value); - } + if (periodic_version) { + Alpha_complex_3d alpha_complex(off_reader.get_point_cloud(), x_min, y_min, z_min, x_max, y_max, z_max); + create_complex(alpha_complex, simplex_tree, alpha_square_max_value); } else { - if (periodic_version) { - Periodic_alpha_complex_3d alpha_complex(off_reader.get_point_cloud(), x_min, y_min, z_min, x_max, y_max, z_max); - create_complex(alpha_complex, simplex_tree, alpha_square_max_value); - } else { - Alpha_complex_3d alpha_complex(off_reader.get_point_cloud()); - create_complex(alpha_complex, simplex_tree, alpha_square_max_value); - } + Alpha_complex_3d alpha_complex(off_reader.get_point_cloud()); + create_complex(alpha_complex, simplex_tree, alpha_square_max_value); } } + // Sort the simplices in the order of the filtration simplex_tree.initialize_filtration(); @@ -175,7 +239,7 @@ int main(int argc, char **argv) { std::ofstream out(output_file_diag); pcoh.output_diagram(out); out.close(); - } + }*/ return 0; } -- cgit v1.2.3 From 5624cfc39b51dd7f201b11c45b5ca5f218591c04 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 25 Sep 2018 15:26:41 +0000 Subject: Constants shall be upper case git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@3906 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: fcafbe39665a69c6645f8b9d73fc67b98709540e --- .../benchmark/Alpha_complex_3d_benchmark.cpp | 24 ++++++------ .../example/Alpha_complex_3d_from_points.cpp | 2 +- .../Weighted_alpha_complex_3d_from_points.cpp | 2 +- src/Alpha_complex/include/gudhi/Alpha_complex_3d.h | 34 +++++++++++++---- .../include/gudhi/Alpha_complex_options.h | 10 ++--- .../test/Alpha_complex_3d_unit_test.cpp | 24 ++++++------ .../utilities/alpha_complex_3d_persistence.cpp | 44 +++++++++++----------- 7 files changed, 77 insertions(+), 63 deletions(-) (limited to 'src/Alpha_complex/example') diff --git a/src/Alpha_complex/benchmark/Alpha_complex_3d_benchmark.cpp b/src/Alpha_complex/benchmark/Alpha_complex_3d_benchmark.cpp index ad785f4e..3e556cdf 100644 --- a/src/Alpha_complex/benchmark/Alpha_complex_3d_benchmark.cpp +++ b/src/Alpha_complex/benchmark/Alpha_complex_3d_benchmark.cpp @@ -233,33 +233,33 @@ int main(int argc, char **argv) { benchmark_points_on_torus_dD >>("Exact static dimension version"); benchmark_points_on_torus_dD>("Exact dynamic dimension version"); - benchmark_points_on_torus_3D>("Fast version"); - benchmark_points_on_torus_3D>("Safe version"); - benchmark_points_on_torus_3D>("Exact version"); - benchmark_weighted_points_on_torus_3D>("Fast version"); - benchmark_weighted_points_on_torus_3D>("Safe version"); - benchmark_weighted_points_on_torus_3D>("Exact version"); - benchmark_periodic_points>("Fast version"); - benchmark_periodic_points>("Safe version"); - benchmark_periodic_points>("Exact version"); - benchmark_weighted_periodic_points>("Fast version"); - benchmark_weighted_periodic_points>("Safe version"); - benchmark_weighted_periodic_points>("Exact version"); return 0; diff --git a/src/Alpha_complex/example/Alpha_complex_3d_from_points.cpp b/src/Alpha_complex/example/Alpha_complex_3d_from_points.cpp index e96385c0..5d6e65cb 100644 --- a/src/Alpha_complex/example/Alpha_complex_3d_from_points.cpp +++ b/src/Alpha_complex/example/Alpha_complex_3d_from_points.cpp @@ -7,7 +7,7 @@ #include #include // for numeric limits -using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; using Point = Alpha_complex_3d::Point_3 ; using Vector_of_points = std::vector; diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp index 61ceab6d..52c39bf3 100644 --- a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp +++ b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp @@ -7,7 +7,7 @@ #include #include // for numeric limits -using Weighted_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Weighted_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; using Point = Weighted_alpha_complex_3d::Point_3; using Weighted_point = Weighted_alpha_complex_3d::Triangulation_3::Weighted_point; using Vector_of_weighted_points = std::vector; diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index 42f49e15..1ba52ad0 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -69,6 +69,11 @@ namespace Gudhi { namespace alpha_complex { +// Value_from_iterator returns the filtration value from an iterator on alpha shapes values +// +// FAST SAFE EXACT +// *iterator CGAL::to_double(*iterator) CGAL::to_double(iterator->exact()) + template struct Value_from_iterator { @@ -81,23 +86,23 @@ struct Value_from_iterator }; template <> -struct Value_from_iterator +struct Value_from_iterator { template static double perform(Iterator it) { - // In safe mode, we are with Epeck or Epick with exact value set to CGAL::Tag_true. + // In SAFE mode, we are with Epeck or Epick with EXACT value set to CGAL::Tag_true. return CGAL::to_double(*it); } }; template <> -struct Value_from_iterator +struct Value_from_iterator { template static double perform(Iterator it) { - // In exact mode, we are with Epeck or Epick with exact value set to CGAL::Tag_true. + // In EXACT mode, we are with Epeck or Epick with EXACT value set to CGAL::Tag_true. return CGAL::to_double(it->exact()); } }; @@ -115,7 +120,7 @@ struct Value_from_iterator * Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. * * \tparam Complexity shall be `Gudhi::alpha_complex::complexity`. Default value is - * `Gudhi::alpha_complex::complexity::fast`. + * `Gudhi::alpha_complex::complexity::FAST`. * * \tparam Weighted Boolean used to set/unset the weighted version of Alpha_complex_3d. Default value is false. * @@ -138,9 +143,22 @@ struct Value_from_iterator * 3d Delaunay complex. * */ -template +template class Alpha_complex_3d { - using Predicates = typename std::conditional<((!Weighted && !Periodic) || (Complexity == complexity::fast)), + // Epick = Exact_predicates_inexact_constructions_kernel + // Epeck = Exact_predicates_exact_constructions_kernel + // ExactAlphaComparisonTag = exact version of CGAL Alpha_shape_3 and of its objects (Alpha_shape_vertex_base_3 and + // Alpha_shape_cell_base_3). Not available if weighted or periodic. + // Can be CGAL::Tag_false or CGAL::Tag_true + // cf. https://doc.cgal.org/latest/Alpha_shapes_3/classCGAL_1_1Alpha__shape__3.html + // + // + // FAST SAFE EXACT + // not weighted and Epick + CGAL::Tag_false Epick + CGAL::Tag_true Epick + CGAL::Tag_true + // not periodic + // + // otherwise Epick + CGAL::Tag_false Epeck Epeck + using Predicates = typename std::conditional<((!Weighted && !Periodic) || (Complexity == complexity::FAST)), CGAL::Exact_predicates_inexact_constructions_kernel, CGAL::Exact_predicates_exact_constructions_kernel>::type; @@ -166,7 +184,7 @@ class Alpha_complex_3d { using Kernel = typename Kernel_3::Kernel; - using Exact_tag = typename std::conditional<(Complexity == complexity::fast), + using Exact_tag = typename std::conditional<(Complexity == complexity::FAST), CGAL::Tag_false, CGAL::Tag_true>::type; diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_options.h b/src/Alpha_complex/include/gudhi/Alpha_complex_options.h index cd9fe799..29eb514a 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_options.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_options.h @@ -29,19 +29,15 @@ namespace Gudhi { namespace alpha_complex { /** - * \class complexity * \brief Alpha complex complexity template parameter possible values. * * \ingroup alpha_complex */ enum class complexity: char { - /** \brief Fast version.*/ - fast='f', - /** \brief Safe version.*/ - safe='s', - /** \brief Exact version.*/ - exact='e', + FAST='f', ///< Fast version. + SAFE='s', ///< Safe version. + EXACT='e', ///< Exact version. }; } // namespace alpha_complex diff --git a/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp index d09e8c10..a32e88a6 100644 --- a/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp +++ b/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp @@ -42,21 +42,21 @@ #include #include -using Fast_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Safe_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Exact_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Fast_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Safe_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Exact_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Fast_weighted_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Safe_weighted_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Exact_weighted_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Fast_weighted_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Safe_weighted_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Exact_weighted_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Fast_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Safe_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Exact_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Fast_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Safe_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Exact_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Fast_weighted_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Safe_weighted_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Exact_weighted_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Fast_weighted_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Safe_weighted_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Exact_weighted_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; BOOST_AUTO_TEST_CASE(Alpha_complex_3d_from_points) { // ----------------- diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp index fb1418bb..c2b49fed 100644 --- a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp @@ -38,7 +38,7 @@ using Filtration_value = Simplex_tree::Filtration_value; using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; -void program_options(int argc, char *argv[], std::string &off_file_points, bool& exact, std::string &weight_file, +void program_options(int argc, char *argv[], std::string &off_file_points, bool& EXACT, std::string &weight_file, std::string &cuboid_file, std::string &output_file_diag, Filtration_value &alpha_square_max_value, int &coeff_field_characteristic, Filtration_value &min_persistence); @@ -117,24 +117,24 @@ int main(int argc, char **argv) { periodic_version = true; } - Gudhi::alpha_complex::complexity complexity = Gudhi::alpha_complex::complexity::fast; + Gudhi::alpha_complex::complexity complexity = Gudhi::alpha_complex::complexity::FAST; if (exact_version) { - complexity = Gudhi::alpha_complex::complexity::exact; + complexity = Gudhi::alpha_complex::complexity::EXACT; } Simplex_tree simplex_tree; switch(complexity) { - case Gudhi::alpha_complex::complexity::fast: + case Gudhi::alpha_complex::complexity::FAST: if (weighted_version) { if (periodic_version) { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; auto points = read_off(off_file_points); Alpha_complex_3d alpha_complex(points, weights, x_min, y_min, z_min, x_max, y_max, z_max); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); } else { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; auto points = read_off(off_file_points); Alpha_complex_3d alpha_complex(points, weights); @@ -142,13 +142,13 @@ int main(int argc, char **argv) { } } else { if (periodic_version) { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; auto points = read_off(off_file_points); Alpha_complex_3d alpha_complex(points, x_min, y_min, z_min, x_max, y_max, z_max); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); } else { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; auto points = read_off(off_file_points); Alpha_complex_3d alpha_complex(points); @@ -156,16 +156,16 @@ int main(int argc, char **argv) { } } break; - case Gudhi::alpha_complex::complexity::exact: + case Gudhi::alpha_complex::complexity::EXACT: if (weighted_version) { if (periodic_version) { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; auto points = read_off(off_file_points); Alpha_complex_3d alpha_complex(points, weights, x_min, y_min, z_min, x_max, y_max, z_max); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); } else { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; auto points = read_off(off_file_points); Alpha_complex_3d alpha_complex(points, weights); @@ -173,13 +173,13 @@ int main(int argc, char **argv) { } } else { if (periodic_version) { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; auto points = read_off(off_file_points); Alpha_complex_3d alpha_complex(points, x_min, y_min, z_min, x_max, y_max, z_max); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); } else { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; auto points = read_off(off_file_points); Alpha_complex_3d alpha_complex(points); @@ -187,16 +187,16 @@ int main(int argc, char **argv) { } } break; - case Gudhi::alpha_complex::complexity::safe: + case Gudhi::alpha_complex::complexity::SAFE: if (weighted_version) { if (periodic_version) { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; auto points = read_off(off_file_points); Alpha_complex_3d alpha_complex(points, weights, x_min, y_min, z_min, x_max, y_max, z_max); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); } else { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; auto points = read_off(off_file_points); Alpha_complex_3d alpha_complex(points, weights); @@ -204,13 +204,13 @@ int main(int argc, char **argv) { } } else { if (periodic_version) { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; auto points = read_off(off_file_points); Alpha_complex_3d alpha_complex(points, x_min, y_min, z_min, x_max, y_max, z_max); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); } else { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; auto points = read_off(off_file_points); Alpha_complex_3d alpha_complex(points); @@ -248,7 +248,7 @@ int main(int argc, char **argv) { return 0; } -void program_options(int argc, char *argv[], std::string &off_file_points, bool& exact, std::string &weight_file, +void program_options(int argc, char *argv[], std::string &off_file_points, bool& EXACT, std::string &weight_file, std::string &cuboid_file, std::string &output_file_diag, Filtration_value &alpha_square_max_value, int &coeff_field_characteristic, Filtration_value &min_persistence) { namespace po = boost::program_options; @@ -258,8 +258,8 @@ void program_options(int argc, char *argv[], std::string &off_file_points, bool& po::options_description visible("Allowed options", 100); visible.add_options()("help,h", "produce help message")( - "exact,e", po::bool_switch(&exact), - "To activate exact version of Alpha complex 3d (default is false, not available for weighted and/or periodic)")( + "EXACT,e", po::bool_switch(&EXACT), + "To activate EXACT version of Alpha complex 3d (default is false, not available for weighted and/or periodic)")( "weight-file,w", po::value(&weight_file)->default_value(std::string()), "Name of file containing a point weights. Format is one weight per line:\n W1\n ...\n Wn ")( "cuboid-file,c", po::value(&cuboid_file), @@ -289,7 +289,7 @@ void program_options(int argc, char *argv[], std::string &off_file_points, bool& std::cout << std::endl; std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; std::cout << "of a 3D Alpha complex defined on a set of input points.\n"; - std::cout << "3D Alpha complex can be exact or weighted and/or periodic\n\n"; + std::cout << "3D Alpha complex can be EXACT or weighted and/or periodic\n\n"; std::cout << "The output diagram contains one bar per line, written with the convention: \n"; std::cout << " p dim b d \n"; std::cout << "where dim is the dimension of the homological feature,\n"; -- cgit v1.2.3 From 7865ef2cc4abd972b2ba1eb50790912820fa2ee2 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 25 Sep 2018 16:05:33 +0000 Subject: clang-format all files Add safe version alpha complex 3d persistence utility git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@3907 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 54b2d0de9231511864df9fa637b60b7ccf34f50f --- .../benchmark/Alpha_complex_3d_benchmark.cpp | 208 ++++++------ .../concept/SimplicialComplexForAlpha3d.h | 7 +- src/Alpha_complex/doc/Intro_alpha_complex.h | 76 ++--- .../example/Alpha_complex_3d_from_points.cpp | 10 +- .../Weighted_alpha_complex_3d_from_points.cpp | 15 +- src/Alpha_complex/include/gudhi/Alpha_complex_3d.h | 365 ++++++++++----------- .../include/gudhi/Alpha_complex_options.h | 10 +- .../test/Alpha_complex_3d_unit_test.cpp | 234 ++++++------- src/Alpha_complex/utilities/CMakeLists.txt | 6 + .../utilities/alpha_complex_3d_persistence.cpp | 97 +++--- 10 files changed, 520 insertions(+), 508 deletions(-) (limited to 'src/Alpha_complex/example') diff --git a/src/Alpha_complex/benchmark/Alpha_complex_3d_benchmark.cpp b/src/Alpha_complex/benchmark/Alpha_complex_3d_benchmark.cpp index 3e556cdf..1a33f2b4 100644 --- a/src/Alpha_complex/benchmark/Alpha_complex_3d_benchmark.cpp +++ b/src/Alpha_complex/benchmark/Alpha_complex_3d_benchmark.cpp @@ -18,92 +18,100 @@ std::ofstream results_csv("results.csv"); template -void benchmark_points_on_torus_dD(const std::string& msg ) { +void benchmark_points_on_torus_dD(const std::string& msg) { std::cout << "+ " << msg << std::endl; results_csv << "\"" << msg << "\";" << std::endl; - results_csv << "\"nb_points\";" << "\"nb_simplices\";" << "\"alpha_creation_time(sec.)\";" << - "\"simplex_creation_time(sec.)\";" << std::endl; + results_csv << "\"nb_points\";" + << "\"nb_simplices\";" + << "\"alpha_creation_time(sec.)\";" + << "\"simplex_creation_time(sec.)\";" << std::endl; - using K = CGAL::Epick_d< CGAL::Dimension_tag<3> >; - for (int nb_points = 1000; nb_points <= 125000 ; nb_points *= 5) { + using K = CGAL::Epick_d>; + for (int nb_points = 1000; nb_points <= 125000; nb_points *= 5) { std::cout << " Alpha complex dD on torus with " << nb_points << " points." << std::endl; std::vector points_on_torus = Gudhi::generate_points_on_torus_3D(nb_points, 1.0, 0.5); std::vector points; - for(auto p:points_on_torus) { - points.push_back(typename Kernel::Point_d(p.begin(),p.end())); + for (auto p : points_on_torus) { + points.push_back(typename Kernel::Point_d(p.begin(), p.end())); } Gudhi::Clock ac_create_clock(" benchmark_points_on_torus_dD - Alpha complex 3d creation"); ac_create_clock.begin(); Gudhi::alpha_complex::Alpha_complex alpha_complex_from_points(points); - ac_create_clock.end(); std::cout << ac_create_clock; + ac_create_clock.end(); + std::cout << ac_create_clock; Gudhi::Simplex_tree<> simplex; Gudhi::Clock st_create_clock(" benchmark_points_on_torus_dD - simplex tree creation"); st_create_clock.begin(); alpha_complex_from_points.create_complex(simplex); - st_create_clock.end(); std::cout << st_create_clock; + st_create_clock.end(); + std::cout << st_create_clock; - results_csv << nb_points << ";" << simplex.num_simplices() << ";" << ac_create_clock.num_seconds() << ";" << - st_create_clock.num_seconds() << ";" << std::endl; + results_csv << nb_points << ";" << simplex.num_simplices() << ";" << ac_create_clock.num_seconds() << ";" + << st_create_clock.num_seconds() << ";" << std::endl; std::cout << " benchmark_points_on_torus_dD - nb simplices = " << simplex.num_simplices() << std::endl; } - } template -void benchmark_points_on_torus_3D(const std::string& msg ) { - using K = CGAL::Epick_d< CGAL::Dimension_tag<3> >; +void benchmark_points_on_torus_3D(const std::string& msg) { + using K = CGAL::Epick_d>; std::cout << "+ " << msg << std::endl; results_csv << "\"" << msg << "\";" << std::endl; - results_csv << "\"nb_points\";" << "\"nb_simplices\";" << "\"alpha_creation_time(sec.)\";" << - "\"simplex_creation_time(sec.)\";" << std::endl; + results_csv << "\"nb_points\";" + << "\"nb_simplices\";" + << "\"alpha_creation_time(sec.)\";" + << "\"simplex_creation_time(sec.)\";" << std::endl; - for (int nb_points = 1000; nb_points <= 125000 ; nb_points *= 5) { + for (int nb_points = 1000; nb_points <= 125000; nb_points *= 5) { std::cout << " Alpha complex 3d on torus with " << nb_points << " points." << std::endl; std::vector points_on_torus = Gudhi::generate_points_on_torus_3D(nb_points, 1.0, 0.5); std::vector points; - for(auto p:points_on_torus) { - points.push_back(typename Alpha_complex_3d::Point_3(p[0],p[1],p[2])); + for (auto p : points_on_torus) { + points.push_back(typename Alpha_complex_3d::Point_3(p[0], p[1], p[2])); } Gudhi::Clock ac_create_clock(" benchmark_points_on_torus_3D - Alpha complex 3d creation"); ac_create_clock.begin(); Alpha_complex_3d alpha_complex_from_points(points); - ac_create_clock.end(); std::cout << ac_create_clock; + ac_create_clock.end(); + std::cout << ac_create_clock; Gudhi::Simplex_tree<> simplex; Gudhi::Clock st_create_clock(" benchmark_points_on_torus_3D - simplex tree creation"); st_create_clock.begin(); alpha_complex_from_points.create_complex(simplex); - st_create_clock.end(); std::cout << st_create_clock; + st_create_clock.end(); + std::cout << st_create_clock; - results_csv << nb_points << ";" << simplex.num_simplices() << ";" << ac_create_clock.num_seconds() << ";" << - st_create_clock.num_seconds() << ";" << std::endl; + results_csv << nb_points << ";" << simplex.num_simplices() << ";" << ac_create_clock.num_seconds() << ";" + << st_create_clock.num_seconds() << ";" << std::endl; std::cout << " benchmark_points_on_torus_3D - nb simplices = " << simplex.num_simplices() << std::endl; } - } template -void benchmark_weighted_points_on_torus_3D(const std::string& msg ) { - using K = CGAL::Epick_d< CGAL::Dimension_tag<3> >; +void benchmark_weighted_points_on_torus_3D(const std::string& msg) { + using K = CGAL::Epick_d>; std::cout << "+ " << msg << std::endl; results_csv << "\"" << msg << "\";" << std::endl; - results_csv << "\"nb_points\";" << "\"nb_simplices\";" << "\"alpha_creation_time(sec.)\";" << - "\"simplex_creation_time(sec.)\";" << std::endl; + results_csv << "\"nb_points\";" + << "\"nb_simplices\";" + << "\"alpha_creation_time(sec.)\";" + << "\"simplex_creation_time(sec.)\";" << std::endl; CGAL::Random random(8); - for (int nb_points = 1000; nb_points <= 125000 ; nb_points *= 5) { + for (int nb_points = 1000; nb_points <= 125000; nb_points *= 5) { std::cout << " Alpha complex 3d on torus with " << nb_points << " points." << std::endl; std::vector points_on_torus = Gudhi::generate_points_on_torus_3D(nb_points, 1.0, 0.5); @@ -112,50 +120,52 @@ void benchmark_weighted_points_on_torus_3D(const std::string& msg ) { std::vector points; - for(auto p:points_on_torus) { - points.push_back(Weighted_point(Point(p[0],p[1],p[2]), 0.9 + random.get_double(0., 0.01))); + for (auto p : points_on_torus) { + points.push_back(Weighted_point(Point(p[0], p[1], p[2]), 0.9 + random.get_double(0., 0.01))); } Gudhi::Clock ac_create_clock(" benchmark_weighted_points_on_torus_3D - Alpha complex 3d creation"); ac_create_clock.begin(); Weighted_alpha_complex_3d alpha_complex_from_points(points); - ac_create_clock.end(); std::cout << ac_create_clock; + ac_create_clock.end(); + std::cout << ac_create_clock; Gudhi::Simplex_tree<> simplex; Gudhi::Clock st_create_clock(" benchmark_weighted_points_on_torus_3D - simplex tree creation"); st_create_clock.begin(); alpha_complex_from_points.create_complex(simplex); - st_create_clock.end(); std::cout << st_create_clock; + st_create_clock.end(); + std::cout << st_create_clock; - results_csv << nb_points << ";" << simplex.num_simplices() << ";" << ac_create_clock.num_seconds() << ";" << - st_create_clock.num_seconds() << ";" << std::endl; + results_csv << nb_points << ";" << simplex.num_simplices() << ";" << ac_create_clock.num_seconds() << ";" + << st_create_clock.num_seconds() << ";" << std::endl; std::cout << " benchmark_weighted_points_on_torus_3D - nb simplices = " << simplex.num_simplices() << std::endl; } - } template -void benchmark_periodic_points(const std::string& msg ) { +void benchmark_periodic_points(const std::string& msg) { std::cout << "+ " << msg << std::endl; results_csv << "\"" << msg << "\";" << std::endl; - results_csv << "\"nb_points\";" << "\"nb_simplices\";" << "\"alpha_creation_time(sec.)\";" << - "\"simplex_creation_time(sec.)\";" << std::endl; + results_csv << "\"nb_points\";" + << "\"nb_simplices\";" + << "\"alpha_creation_time(sec.)\";" + << "\"simplex_creation_time(sec.)\";" << std::endl; CGAL::Random random(8); - for (double nb_points = 10.; nb_points <= 40. ; nb_points += 10.) { - std::cout << " Periodic alpha complex 3d with " << nb_points*nb_points*nb_points << " points." << std::endl; + for (double nb_points = 10.; nb_points <= 40.; nb_points += 10.) { + std::cout << " Periodic alpha complex 3d with " << nb_points * nb_points * nb_points << " points." << std::endl; using Point = typename Periodic_alpha_complex_3d::Point_3; std::vector points; for (double i = 0; i < nb_points; i++) { for (double j = 0; j < nb_points; j++) { for (double k = 0; k < nb_points; k++) { - points.push_back(Point(i + random.get_double(0., 0.1), - j + random.get_double(0., 0.1), - k + random.get_double(0., 0.1))); + points.push_back( + Point(i + random.get_double(0., 0.1), j + random.get_double(0., 0.1), k + random.get_double(0., 0.1))); } } } @@ -163,34 +173,38 @@ void benchmark_periodic_points(const std::string& msg ) { Gudhi::Clock ac_create_clock(" benchmark_periodic_points - Alpha complex 3d creation"); ac_create_clock.begin(); Periodic_alpha_complex_3d alpha_complex_from_points(points, 0., 0., 0., nb_points, nb_points, nb_points); - ac_create_clock.end(); std::cout << ac_create_clock; + ac_create_clock.end(); + std::cout << ac_create_clock; Gudhi::Simplex_tree<> simplex; Gudhi::Clock st_create_clock(" benchmark_periodic_points - simplex tree creation"); st_create_clock.begin(); alpha_complex_from_points.create_complex(simplex); - st_create_clock.end(); std::cout << st_create_clock; + st_create_clock.end(); + std::cout << st_create_clock; - results_csv << nb_points*nb_points*nb_points << ";" << simplex.num_simplices() << ";" << - ac_create_clock.num_seconds() << ";" << st_create_clock.num_seconds() << ";" << std::endl; + results_csv << nb_points * nb_points * nb_points << ";" << simplex.num_simplices() << ";" + << ac_create_clock.num_seconds() << ";" << st_create_clock.num_seconds() << ";" << std::endl; std::cout << " benchmark_periodic_points - nb simplices = " << simplex.num_simplices() << std::endl; } - } template -void benchmark_weighted_periodic_points(const std::string& msg ) { +void benchmark_weighted_periodic_points(const std::string& msg) { std::cout << "+ " << msg << std::endl; results_csv << "\"" << msg << "\";" << std::endl; - results_csv << "\"nb_points\";" << "\"nb_simplices\";" << "\"alpha_creation_time(sec.)\";" << - "\"simplex_creation_time(sec.)\";" << std::endl; + results_csv << "\"nb_points\";" + << "\"nb_simplices\";" + << "\"alpha_creation_time(sec.)\";" + << "\"simplex_creation_time(sec.)\";" << std::endl; CGAL::Random random(8); - for (double nb_points = 10.; nb_points <= 40. ; nb_points += 10.) { - std::cout << " Weighted periodic alpha complex 3d with " << nb_points*nb_points*nb_points << " points." << std::endl; + for (double nb_points = 10.; nb_points <= 40.; nb_points += 10.) { + std::cout << " Weighted periodic alpha complex 3d with " << nb_points * nb_points * nb_points << " points." + << std::endl; using Point = typename Weighted_periodic_alpha_complex_3d::Point_3; using Weighted_point = typename Weighted_periodic_alpha_complex_3d::Triangulation_3::Weighted_point; @@ -199,10 +213,9 @@ void benchmark_weighted_periodic_points(const std::string& msg ) { for (double i = 0; i < nb_points; i++) { for (double j = 0; j < nb_points; j++) { for (double k = 0; k < nb_points; k++) { - points.push_back(Weighted_point(Point(i + random.get_double(0., 0.1), - j + random.get_double(0., 0.1), - k + random.get_double(0., 0.1)), - random.get_double(0., (nb_points*nb_points)/64.))); + points.push_back(Weighted_point( + Point(i + random.get_double(0., 0.1), j + random.get_double(0., 0.1), k + random.get_double(0., 0.1)), + random.get_double(0., (nb_points * nb_points) / 64.))); } } } @@ -210,57 +223,56 @@ void benchmark_weighted_periodic_points(const std::string& msg ) { Gudhi::Clock ac_create_clock(" benchmark_weighted_periodic_points - Alpha complex 3d creation"); ac_create_clock.begin(); Weighted_periodic_alpha_complex_3d alpha_complex_from_points(points, 0., 0., 0., nb_points, nb_points, nb_points); - ac_create_clock.end(); std::cout << ac_create_clock; + ac_create_clock.end(); + std::cout << ac_create_clock; Gudhi::Simplex_tree<> simplex; Gudhi::Clock st_create_clock(" benchmark_weighted_periodic_points - simplex tree creation"); st_create_clock.begin(); alpha_complex_from_points.create_complex(simplex); - st_create_clock.end(); std::cout << st_create_clock; + st_create_clock.end(); + std::cout << st_create_clock; - results_csv << nb_points*nb_points*nb_points << ";" << simplex.num_simplices() << ";" << - ac_create_clock.num_seconds() << ";" << st_create_clock.num_seconds() << ";" << std::endl; + results_csv << nb_points * nb_points * nb_points << ";" << simplex.num_simplices() << ";" + << ac_create_clock.num_seconds() << ";" << st_create_clock.num_seconds() << ";" << std::endl; std::cout << " benchmark_weighted_periodic_points - nb simplices = " << simplex.num_simplices() << std::endl; } - } -int main(int argc, char **argv) { - - benchmark_points_on_torus_dD >>("Fast static dimension version"); - benchmark_points_on_torus_dD>("Fast dynamic dimension version"); - benchmark_points_on_torus_dD >>("Exact static dimension version"); - benchmark_points_on_torus_dD>("Exact dynamic dimension version"); - - benchmark_points_on_torus_3D>("Fast version"); - benchmark_points_on_torus_3D>("Safe version"); - benchmark_points_on_torus_3D>("Exact version"); - - - benchmark_weighted_points_on_torus_3D>("Fast version"); - benchmark_weighted_points_on_torus_3D>("Safe version"); - benchmark_weighted_points_on_torus_3D>("Exact version"); - - benchmark_periodic_points>("Fast version"); - benchmark_periodic_points>("Safe version"); - benchmark_periodic_points>("Exact version"); - - benchmark_weighted_periodic_points>("Fast version"); - benchmark_weighted_periodic_points>("Safe version"); - benchmark_weighted_periodic_points>("Exact version"); +int main(int argc, char** argv) { + benchmark_points_on_torus_dD>>("Fast static dimension version"); + benchmark_points_on_torus_dD>("Fast dynamic dimension version"); + benchmark_points_on_torus_dD>>("Exact static dimension version"); + benchmark_points_on_torus_dD>("Exact dynamic dimension version"); + + benchmark_points_on_torus_3D< + Gudhi::alpha_complex::Alpha_complex_3d>("Fast version"); + benchmark_points_on_torus_3D< + Gudhi::alpha_complex::Alpha_complex_3d>("Safe version"); + benchmark_points_on_torus_3D< + Gudhi::alpha_complex::Alpha_complex_3d>("Exact version"); + + benchmark_weighted_points_on_torus_3D< + Gudhi::alpha_complex::Alpha_complex_3d>("Fast version"); + benchmark_weighted_points_on_torus_3D< + Gudhi::alpha_complex::Alpha_complex_3d>("Safe version"); + benchmark_weighted_points_on_torus_3D< + Gudhi::alpha_complex::Alpha_complex_3d>("Exact version"); + + benchmark_periodic_points< + Gudhi::alpha_complex::Alpha_complex_3d>("Fast version"); + benchmark_periodic_points< + Gudhi::alpha_complex::Alpha_complex_3d>("Safe version"); + benchmark_periodic_points< + Gudhi::alpha_complex::Alpha_complex_3d>("Exact version"); + + benchmark_weighted_periodic_points< + Gudhi::alpha_complex::Alpha_complex_3d>("Fast version"); + benchmark_weighted_periodic_points< + Gudhi::alpha_complex::Alpha_complex_3d>("Safe version"); + benchmark_weighted_periodic_points< + Gudhi::alpha_complex::Alpha_complex_3d>("Exact version"); return 0; } diff --git a/src/Alpha_complex/concept/SimplicialComplexForAlpha3d.h b/src/Alpha_complex/concept/SimplicialComplexForAlpha3d.h index f6085a26..7acdf105 100644 --- a/src/Alpha_complex/concept/SimplicialComplexForAlpha3d.h +++ b/src/Alpha_complex/concept/SimplicialComplexForAlpha3d.h @@ -1,5 +1,5 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ * library for computational topology. * * Author(s): Vincent Rouvreau @@ -41,14 +41,13 @@ struct SimplicialComplexForAlpha3d { /** \brief Inserts a simplex from a given simplex (represented by a vector of Vertex_handle) in the * simplicial complex with the given 'filtration' value. */ - void insert_simplex(std::vector const & vertex_range, Filtration_value filtration); + void insert_simplex(std::vector const& vertex_range, Filtration_value filtration); /** Browses the simplicial complex to make the filtration non-decreasing. */ void make_filtration_non_decreasing(); /** Prune the simplicial complex above 'filtration' value given as parameter. */ void prune_above_filtration(Filtration_value filtration); - }; } // namespace alpha_complex diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h index 82aee275..648fb6d6 100644 --- a/src/Alpha_complex/doc/Intro_alpha_complex.h +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -29,34 +29,34 @@ namespace Gudhi { namespace alpha_complex { /** \defgroup alpha_complex Alpha complex - * + * * \author Vincent Rouvreau * * @{ - * + * * \section definition Definition - * + * * Alpha_complex is a simplicial complex * constructed from the finite cells of a Delaunay Triangulation. - * + * * The filtration value of each simplex is computed as the square of the circumradius of the simplex if the * circumsphere is empty (the simplex is then said to be Gabriel), and as the minimum of the filtration * 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. - * + * * \image html "alpha_complex_representation.png" "Alpha-complex representation" - * + * * Alpha_complex is constructing a Delaunay Triangulation * \cite cgal:hdj-t-15b from CGAL (the Computational Geometry * Algorithms Library \cite cgal:eb-15b) and is able to create a `SimplicialComplexForAlpha`. - * + * * The complex is a template class requiring an Epick_d dD Geometry Kernel * \cite cgal:s-gkd-15b from CGAL as template parameter. - * + * * \remark * - When the simplicial complex is constructed with an infinite value of alpha, the complex is a Delaunay * complex. @@ -65,30 +65,30 @@ namespace alpha_complex { * \ref cech_complex can still make sense in higher dimension precisely because you can bound the radii. * * \section pointsexample Example from points - * + * * This example builds the Delaunay triangulation from the given points in a 2D static kernel, and creates a * `Simplex_tree` with it. - * + * * Then, it is asked to display information about the simplicial complex. - * + * * \include Alpha_complex/Alpha_complex_from_points.cpp - * + * * When launching: - * + * * \code $> ./Alpha_complex_example_from_points * \endcode * * the program output is: - * + * * \include Alpha_complex/alphaoffreader_for_doc_60.txt - * + * * \section createcomplexalgorithm Create complex algorithm - * + * * \subsection datastructure Data structure - * + * * In order to create the simplicial complex, first, it is built from the cells of the Delaunay Triangulation. * The filtration values are set to NaN, which stands for unknown value. - * + * * In example, : * \image html "alpha_complex_doc.png" "Simplicial complex structure construction example" * @@ -118,53 +118,53 @@ namespace alpha_complex { * \f$ * * \subsubsection dimension2 Dimension 2 - * + * * From the example above, it means the algorithm looks into each triangle ([0,1,2], [0,2,4], [1,2,3], ...), * computes the filtration value of the triangle, and then propagates the filtration value as described * here : * \image html "alpha_complex_doc_420.png" "Filtration value propagation example" - * + * * \subsubsection dimension1 Dimension 1 - * + * * Then, the algorithm looks into each edge ([0,1], [0,2], [1,2], ...), * computes the filtration value of the edge (in this case, propagation will have no effect). - * + * * \subsubsection dimension0 Dimension 0 - * + * * Finally, the algorithm looks into each vertex ([0], [1], [2], [3], [4], [5] and [6]) and * sets the filtration value (0 in case of a vertex - propagation will have no effect). - * + * * \subsubsection nondecreasing Non decreasing filtration values - * + * * As the squared radii computed by CGAL are an approximation, it might happen that these alpha squared values do not * quite define a proper filtration (i.e. non-decreasing with respect to inclusion). * We fix that up by calling `SimplicialComplexForAlpha::make_filtration_non_decreasing()`. - * + * * \subsubsection pruneabove Prune above given filtration value - * + * * The simplex tree is pruned from the given maximum alpha squared value (cf. * `SimplicialComplexForAlpha::prune_above_filtration()`). * In the following example, the value is given by the user as argument of the program. - * - * + * + * * \section offexample Example from OFF file - * + * * This example builds the Delaunay triangulation in a dynamic kernel, and initializes the alpha complex with it. - * - * + * + * * Then, it is asked to display information about the alpha complex. - * + * * \include Alpha_complex/Alpha_complex_from_off.cpp - * + * * When launching: - * + * * \code $> ./Alpha_complex_example_from_off ../../data/points/alphacomplexdoc.off 32.0 * \endcode * * the program output is: - * + * * \include Alpha_complex/alphaoffreader_for_doc_32.txt - * + * * * \section weighted3dexample 3d specific example * diff --git a/src/Alpha_complex/example/Alpha_complex_3d_from_points.cpp b/src/Alpha_complex/example/Alpha_complex_3d_from_points.cpp index 5d6e65cb..3acebd2e 100644 --- a/src/Alpha_complex/example/Alpha_complex_3d_from_points.cpp +++ b/src/Alpha_complex/example/Alpha_complex_3d_from_points.cpp @@ -8,7 +8,7 @@ #include // for numeric limits using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Point = Alpha_complex_3d::Point_3 ; +using Point = Alpha_complex_3d::Point_3; using Vector_of_points = std::vector; int main(int argc, char **argv) { @@ -38,9 +38,8 @@ int main(int argc, char **argv) { // ---------------------------------------------------------------------------- // Display information about the alpha complex // ---------------------------------------------------------------------------- - std::cout << "Alpha complex is of dimension " << simplex.dimension() << - " - " << simplex.num_simplices() << " simplices - " << - simplex.num_vertices() << " vertices." << std::endl; + std::cout << "Alpha complex is of dimension " << simplex.dimension() << " - " << simplex.num_simplices() + << " simplices - " << simplex.num_vertices() << " vertices." << std::endl; std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; for (auto f_simplex : simplex.filtration_simplex_range()) { @@ -48,7 +47,8 @@ int main(int argc, char **argv) { for (auto vertex : simplex.simplex_vertex_range(f_simplex)) { std::cout << vertex << " "; } - std::cout << ") -> " << "[" << simplex.filtration(f_simplex) << "] "; + std::cout << ") -> " + << "[" << simplex.filtration(f_simplex) << "] "; std::cout << std::endl; } } diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp index 52c39bf3..68f72f0a 100644 --- a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp +++ b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp @@ -7,7 +7,8 @@ #include #include // for numeric limits -using Weighted_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Weighted_alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; using Point = Weighted_alpha_complex_3d::Point_3; using Weighted_point = Weighted_alpha_complex_3d::Triangulation_3::Weighted_point; using Vector_of_weighted_points = std::vector; @@ -27,8 +28,8 @@ int main(int argc, char **argv) { weighted_points.push_back(Weighted_point(Point(1, -1, -1), 4.)); weighted_points.push_back(Weighted_point(Point(-1, 1, -1), 4.)); weighted_points.push_back(Weighted_point(Point(-1, -1, 1), 4.)); - weighted_points.push_back(Weighted_point(Point(1, 1, 1), 4.)); - weighted_points.push_back(Weighted_point(Point(2, 2, 2), 1.)); + weighted_points.push_back(Weighted_point(Point(1, 1, 1), 4.)); + weighted_points.push_back(Weighted_point(Point(2, 2, 2), 1.)); // ---------------------------------------------------------------------------- // Init of an alpha complex from the list of points @@ -40,9 +41,8 @@ int main(int argc, char **argv) { // ---------------------------------------------------------------------------- // Display information about the alpha complex // ---------------------------------------------------------------------------- - std::cout << "Alpha complex is of dimension " << simplex.dimension() << - " - " << simplex.num_simplices() << " simplices - " << - simplex.num_vertices() << " vertices." << std::endl; + std::cout << "Alpha complex is of dimension " << simplex.dimension() << " - " << simplex.num_simplices() + << " simplices - " << simplex.num_vertices() << " vertices." << std::endl; std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; for (auto f_simplex : simplex.filtration_simplex_range()) { @@ -50,7 +50,8 @@ int main(int argc, char **argv) { for (auto vertex : simplex.simplex_vertex_range(f_simplex)) { std::cout << vertex << " "; } - std::cout << ") -> " << "[" << simplex.filtration(f_simplex) << "] "; + std::cout << ") -> " + << "[" << simplex.filtration(f_simplex) << "] "; std::cout << std::endl; } } diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index 1ba52ad0..0333abbd 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -55,14 +55,12 @@ #include #include #include -#include // for std::unique_ptr +#include // for std::unique_ptr #include // for std::conditional and std::enable_if - #if CGAL_VERSION_NR < 1041101000 - // Make compilation fail - required for external projects - https://gitlab.inria.fr/GUDHI/gudhi-devel/issues/10 - static_assert(false, - "Alpha_complex_3d is only available for CGAL >= 4.11"); +// Make compilation fail - required for external projects - https://gitlab.inria.fr/GUDHI/gudhi-devel/issues/10 +static_assert(false, "Alpha_complex_3d is only available for CGAL >= 4.11"); #endif namespace Gudhi { @@ -75,39 +73,32 @@ namespace alpha_complex { // *iterator CGAL::to_double(*iterator) CGAL::to_double(iterator->exact()) template -struct Value_from_iterator -{ - template - static double perform(Iterator it) - { +struct Value_from_iterator { + template + static double perform(Iterator it) { // Default behaviour is to return the value pointed by the given iterator return *it; } }; template <> -struct Value_from_iterator -{ - template - static double perform(Iterator it) - { +struct Value_from_iterator { + template + static double perform(Iterator it) { // In SAFE mode, we are with Epeck or Epick with EXACT value set to CGAL::Tag_true. return CGAL::to_double(*it); } }; template <> -struct Value_from_iterator -{ - template - static double perform(Iterator it) - { +struct Value_from_iterator { + template + static double perform(Iterator it) { // In EXACT mode, we are with Epeck or Epick with EXACT value set to CGAL::Tag_true. return CGAL::to_double(it->exact()); } }; - /** * \class Alpha_complex_3d * \brief Alpha complex data structure for 3d specific case. @@ -143,7 +134,7 @@ struct Value_from_iterator * 3d Delaunay complex. * */ -template +template class Alpha_complex_3d { // Epick = Exact_predicates_inexact_constructions_kernel // Epeck = Exact_predicates_exact_constructions_kernel @@ -159,89 +150,85 @@ class Alpha_complex_3d { // // otherwise Epick + CGAL::Tag_false Epeck Epeck using Predicates = typename std::conditional<((!Weighted && !Periodic) || (Complexity == complexity::FAST)), - CGAL::Exact_predicates_inexact_constructions_kernel, - CGAL::Exact_predicates_exact_constructions_kernel>::type; + CGAL::Exact_predicates_inexact_constructions_kernel, + CGAL::Exact_predicates_exact_constructions_kernel>::type; // The other way to do a conditional type. Here there are 3 possibilities - template struct Kernel_3 {}; + template + struct Kernel_3 {}; - template < typename Predicates > + template struct Kernel_3 { using Kernel = Predicates; }; - template < typename Predicates > + template struct Kernel_3 { using Kernel = Predicates; }; - template < typename Predicates > + template struct Kernel_3 { using Kernel = CGAL::Periodic_3_Delaunay_triangulation_traits_3; }; - template < typename Predicates > + template struct Kernel_3 { using Kernel = CGAL::Periodic_3_regular_triangulation_traits_3; }; using Kernel = typename Kernel_3::Kernel; - using Exact_tag = typename std::conditional<(Complexity == complexity::FAST), - CGAL::Tag_false, - CGAL::Tag_true>::type; + using Exact_tag = typename std::conditional<(Complexity == complexity::FAST), CGAL::Tag_false, CGAL::Tag_true>::type; - using TdsVb = typename std::conditional, - CGAL::Triangulation_ds_vertex_base_3<>>::type; + using TdsVb = typename std::conditional, + CGAL::Triangulation_ds_vertex_base_3<>>::type; - using Tvb = typename std::conditional, - CGAL::Triangulation_vertex_base_3>::type; + using Tvb = typename std::conditional, + CGAL::Triangulation_vertex_base_3>::type; using Vb = CGAL::Alpha_shape_vertex_base_3; - using TdsCb = typename std::conditional, - CGAL::Triangulation_ds_cell_base_3<>>::type; + using TdsCb = typename std::conditional, + CGAL::Triangulation_ds_cell_base_3<>>::type; - using Tcb = typename std::conditional, - CGAL::Triangulation_cell_base_3>::type; + using Tcb = typename std::conditional, + CGAL::Triangulation_cell_base_3>::type; using Cb = CGAL::Alpha_shape_cell_base_3; using Tds = CGAL::Triangulation_data_structure_3; // The other way to do a conditional type. Here there 4 possibilities, cannot use std::conditional - template struct Triangulation {}; + template + struct Triangulation {}; - template < typename Kernel, typename Tds > + template struct Triangulation { using Triangulation_3 = CGAL::Delaunay_triangulation_3; }; - template < typename Kernel, typename Tds > + template struct Triangulation { using Triangulation_3 = CGAL::Regular_triangulation_3; }; - template < typename Kernel, typename Tds > + template struct Triangulation { using Triangulation_3 = CGAL::Periodic_3_Delaunay_triangulation_3; }; - template < typename Kernel, typename Tds > + template struct Triangulation { using Triangulation_3 = CGAL::Periodic_3_regular_triangulation_3; }; -public: + public: using Triangulation_3 = typename Triangulation::Triangulation_3; using Alpha_shape_3 = CGAL::Alpha_shape_3; using Point_3 = typename Kernel::Point_3; -private: + private: using Alpha_value_type = typename Alpha_shape_3::FT; using Dispatch = - CGAL::Dispatch_output_iterator, - CGAL::cpp11::tuple >, - std::back_insert_iterator > > >; + CGAL::Dispatch_output_iterator, + CGAL::cpp11::tuple>, + std::back_insert_iterator>>>; using Cell_handle = typename Alpha_shape_3::Cell_handle; using Facet = typename Alpha_shape_3::Facet; @@ -253,46 +240,43 @@ private: using Vertex_list = std::vector; #endif -public: + public: /** \brief Alpha_complex constructor from a list of points. - * - * @param[in] points Range of points to triangulate. Points must be in `Alpha_complex_3d::Point_3` or - * `Alpha_complex_3d::Triangulation_3::Weighted_point`. - * - * @pre Available if Alpha_complex_3d is not Periodic. - * - * The type InputPointRange must be a range for which std::begin and std::end return input iterators on a - * `Alpha_complex_3d::Point_3` or a `Alpha_complex_3d::Triangulation_3::Weighted_point`. - */ - template + * + * @param[in] points Range of points to triangulate. Points must be in `Alpha_complex_3d::Point_3` or + * `Alpha_complex_3d::Triangulation_3::Weighted_point`. + * + * @pre Available if Alpha_complex_3d is not Periodic. + * + * The type InputPointRange must be a range for which std::begin and std::end return input iterators on a + * `Alpha_complex_3d::Point_3` or a `Alpha_complex_3d::Triangulation_3::Weighted_point`. + */ + template Alpha_complex_3d(const InputPointRange& points) { - static_assert(!Periodic, - "This constructor is not available for periodic versions of Alpha_complex_3d"); + static_assert(!Periodic, "This constructor is not available for periodic versions of Alpha_complex_3d"); - alpha_shape_3_ptr_ = std::unique_ptr(new Alpha_shape_3(std::begin(points), std::end(points), 0, - Alpha_shape_3::GENERAL)); + alpha_shape_3_ptr_ = std::unique_ptr( + new Alpha_shape_3(std::begin(points), std::end(points), 0, Alpha_shape_3::GENERAL)); } /** \brief Alpha_complex constructor from a list of points and associated weights. - * - * @exception std::invalid_argument In debug mode, if points and weights do not have the same size. - * - * @param[in] points Range of points to triangulate. Points must be in `Alpha_complex_3d::Point_3` - * @param[in] weights Range of weights on points. Weights shall be in `Alpha_complex_3d::Alpha_shape_3::FT` - * - * @pre Available if Alpha_complex_3d is Weighted and not Periodic. - * - * The type InputPointRange must be a range for which std::begin and - * std::end return input iterators on a `Alpha_complex_3d::Point_3`. - * The type WeightRange must be a range for which std::begin and - * std::end return an input iterator on a `Alpha_complex_3d::Alpha_shape_3::FT`. - */ - template + * + * @exception std::invalid_argument In debug mode, if points and weights do not have the same size. + * + * @param[in] points Range of points to triangulate. Points must be in `Alpha_complex_3d::Point_3` + * @param[in] weights Range of weights on points. Weights shall be in `Alpha_complex_3d::Alpha_shape_3::FT` + * + * @pre Available if Alpha_complex_3d is Weighted and not Periodic. + * + * The type InputPointRange must be a range for which std::begin and + * std::end return input iterators on a `Alpha_complex_3d::Point_3`. + * The type WeightRange must be a range for which std::begin and + * std::end return an input iterator on a `Alpha_complex_3d::Alpha_shape_3::FT`. + */ + template Alpha_complex_3d(const InputPointRange& points, WeightRange weights) { - static_assert(Weighted, - "This constructor is not available for non-weighted versions of Alpha_complex_3d"); - static_assert(!Periodic, - "This constructor is not available for periodic versions of Alpha_complex_3d"); + static_assert(Weighted, "This constructor is not available for non-weighted versions of Alpha_complex_3d"); + static_assert(!Periodic, "This constructor is not available for periodic versions of Alpha_complex_3d"); GUDHI_CHECK((weights.size() == points.size()), std::invalid_argument("Points number in range different from weights range number")); @@ -306,44 +290,39 @@ public: index++; } - alpha_shape_3_ptr_ = std::unique_ptr(new Alpha_shape_3(std::begin(weighted_points_3), - std::end(weighted_points_3), - 0, - Alpha_shape_3::GENERAL)); + alpha_shape_3_ptr_ = std::unique_ptr( + new Alpha_shape_3(std::begin(weighted_points_3), std::end(weighted_points_3), 0, Alpha_shape_3::GENERAL)); } /** \brief Alpha_complex constructor from a list of points and an iso-cuboid coordinates. - * - * @exception std::invalid_argument In debug mode, if the size of the cuboid in every directions is not the same. - * - * @param[in] points Range of points to triangulate. Points must be in `Alpha_complex_3d::Point_3` or - * `Alpha_complex_3d::Triangulation_3::Weighted_point`. - * @param[in] x_min Iso-oriented cuboid x_min. - * @param[in] y_min Iso-oriented cuboid y_min. - * @param[in] z_min Iso-oriented cuboid z_min. - * @param[in] x_max Iso-oriented cuboid x_max. - * @param[in] y_max Iso-oriented cuboid y_max. - * @param[in] z_max Iso-oriented cuboid z_max. - * - * @pre Available if Alpha_complex_3d is Periodic. - * - * The type InputPointRange must be a range for which std::begin and std::end return input iterators on a - * `Alpha_complex_3d::Point_3` or a `Alpha_complex_3d::Triangulation_3::Weighted_point`. - * - * @note In weighted version, please check weights are greater than zero, and lower than 1/64*cuboid length - * squared. - */ - template - Alpha_complex_3d(const InputPointRange& points, - Alpha_value_type x_min, Alpha_value_type y_min, Alpha_value_type z_min, - Alpha_value_type x_max, Alpha_value_type y_max, Alpha_value_type z_max) { - static_assert(Periodic, - "This constructor is not available for non-periodic versions of Alpha_complex_3d"); + * + * @exception std::invalid_argument In debug mode, if the size of the cuboid in every directions is not the same. + * + * @param[in] points Range of points to triangulate. Points must be in `Alpha_complex_3d::Point_3` or + * `Alpha_complex_3d::Triangulation_3::Weighted_point`. + * @param[in] x_min Iso-oriented cuboid x_min. + * @param[in] y_min Iso-oriented cuboid y_min. + * @param[in] z_min Iso-oriented cuboid z_min. + * @param[in] x_max Iso-oriented cuboid x_max. + * @param[in] y_max Iso-oriented cuboid y_max. + * @param[in] z_max Iso-oriented cuboid z_max. + * + * @pre Available if Alpha_complex_3d is Periodic. + * + * The type InputPointRange must be a range for which std::begin and std::end return input iterators on a + * `Alpha_complex_3d::Point_3` or a `Alpha_complex_3d::Triangulation_3::Weighted_point`. + * + * @note In weighted version, please check weights are greater than zero, and lower than 1/64*cuboid length + * squared. + */ + template + Alpha_complex_3d(const InputPointRange& points, Alpha_value_type x_min, Alpha_value_type y_min, + Alpha_value_type z_min, Alpha_value_type x_max, Alpha_value_type y_max, Alpha_value_type z_max) { + static_assert(Periodic, "This constructor is not available for non-periodic versions of Alpha_complex_3d"); // Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it. - GUDHI_CHECK((x_max - x_min == y_max - y_min) && - (x_max - x_min == z_max - z_min) && - (z_max - z_min == y_max - y_min), - std::invalid_argument("The size of the cuboid in every directions is not the same.")); + GUDHI_CHECK( + (x_max - x_min == y_max - y_min) && (x_max - x_min == z_max - z_min) && (z_max - z_min == y_max - y_min), + std::invalid_argument("The size of the cuboid in every directions is not the same.")); // Define the periodic cube Triangulation_3 pdt(typename Kernel::Iso_cuboid_3(x_min, y_min, z_min, x_max, y_max, z_max)); @@ -357,49 +336,44 @@ public: // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. This is the default mode // Maybe need to set it to GENERAL mode - alpha_shape_3_ptr_ = std::unique_ptr(new Alpha_shape_3(pdt, 0, - Alpha_shape_3::GENERAL)); + alpha_shape_3_ptr_ = std::unique_ptr(new Alpha_shape_3(pdt, 0, Alpha_shape_3::GENERAL)); } /** \brief Alpha_complex constructor from a list of points, associated weights and an iso-cuboid coordinates. - * - * @exception std::invalid_argument In debug mode, if points and weights do not have the same size. - * @exception std::invalid_argument In debug mode, if the size of the cuboid in every directions is not the same. - * @exception std::invalid_argument In debug mode, if a weight is negative, zero, or greater than 1/64*cuboid length - * squared. - * - * @param[in] points Range of points to triangulate. Points must be in `Alpha_complex_3d::Point_3` - * @param[in] weights Range of weights on points. Weights shall be in `Alpha_complex_3d::Alpha_shape_3::FT` - * @param[in] x_min Iso-oriented cuboid x_min. - * @param[in] y_min Iso-oriented cuboid y_min. - * @param[in] z_min Iso-oriented cuboid z_min. - * @param[in] x_max Iso-oriented cuboid x_max. - * @param[in] y_max Iso-oriented cuboid y_max. - * @param[in] z_max Iso-oriented cuboid z_max. - * - * @pre Available if Alpha_complex_3d is Weighted and Periodic. - * - * The type InputPointRange must be a range for which std::begin and - * std::end return input iterators on a `Alpha_complex_3d::Point_3`. - * The type WeightRange must be a range for which std::begin and - * std::end return an input iterator on a `Alpha_complex_3d::Alpha_shape_3::FT`. - * The type of x_min, y_min, z_min, x_max, y_max and z_max is `Alpha_complex_3d::Alpha_shape_3::FT`. - */ - template - Alpha_complex_3d(const InputPointRange& points, WeightRange weights, - Alpha_value_type x_min, Alpha_value_type y_min, Alpha_value_type z_min, - Alpha_value_type x_max, Alpha_value_type y_max, Alpha_value_type z_max) { - static_assert(Weighted, - "This constructor is not available for non-weighted versions of Alpha_complex_3d"); - static_assert(Periodic, - "This constructor is not available for non-periodic versions of Alpha_complex_3d"); + * + * @exception std::invalid_argument In debug mode, if points and weights do not have the same size. + * @exception std::invalid_argument In debug mode, if the size of the cuboid in every directions is not the same. + * @exception std::invalid_argument In debug mode, if a weight is negative, zero, or greater than 1/64*cuboid length + * squared. + * + * @param[in] points Range of points to triangulate. Points must be in `Alpha_complex_3d::Point_3` + * @param[in] weights Range of weights on points. Weights shall be in `Alpha_complex_3d::Alpha_shape_3::FT` + * @param[in] x_min Iso-oriented cuboid x_min. + * @param[in] y_min Iso-oriented cuboid y_min. + * @param[in] z_min Iso-oriented cuboid z_min. + * @param[in] x_max Iso-oriented cuboid x_max. + * @param[in] y_max Iso-oriented cuboid y_max. + * @param[in] z_max Iso-oriented cuboid z_max. + * + * @pre Available if Alpha_complex_3d is Weighted and Periodic. + * + * The type InputPointRange must be a range for which std::begin and + * std::end return input iterators on a `Alpha_complex_3d::Point_3`. + * The type WeightRange must be a range for which std::begin and + * std::end return an input iterator on a `Alpha_complex_3d::Alpha_shape_3::FT`. + * The type of x_min, y_min, z_min, x_max, y_max and z_max is `Alpha_complex_3d::Alpha_shape_3::FT`. + */ + template + Alpha_complex_3d(const InputPointRange& points, WeightRange weights, Alpha_value_type x_min, Alpha_value_type y_min, + Alpha_value_type z_min, Alpha_value_type x_max, Alpha_value_type y_max, Alpha_value_type z_max) { + static_assert(Weighted, "This constructor is not available for non-weighted versions of Alpha_complex_3d"); + static_assert(Periodic, "This constructor is not available for non-periodic versions of Alpha_complex_3d"); GUDHI_CHECK((weights.size() == points.size()), std::invalid_argument("Points number in range different from weights range number")); // Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it. - GUDHI_CHECK((x_max - x_min == y_max - y_min) && - (x_max - x_min == z_max - z_min) && - (z_max - z_min == y_max - y_min), - std::invalid_argument("The size of the cuboid in every directions is not the same.")); + GUDHI_CHECK( + (x_max - x_min == y_max - y_min) && (x_max - x_min == z_max - z_min) && (z_max - z_min == y_max - y_min), + std::invalid_argument("The size of the cuboid in every directions is not the same.")); using Weighted_point_3 = typename Triangulation_3::Weighted_point; std::vector weighted_points_3; @@ -433,38 +407,36 @@ public: // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. This is the default mode // Maybe need to set it to GENERAL mode - alpha_shape_3_ptr_ = std::unique_ptr(new Alpha_shape_3(pdt, 0, - Alpha_shape_3::GENERAL)); + alpha_shape_3_ptr_ = std::unique_ptr(new Alpha_shape_3(pdt, 0, Alpha_shape_3::GENERAL)); } /** \brief Inserts all Delaunay triangulation into the simplicial complex. - * It also computes the filtration values accordingly to the \ref createcomplexalgorithm - * - * \tparam SimplicialComplexForAlpha3d must meet `SimplicialComplexForAlpha3d` concept. - * - * @param[in] complex SimplicialComplexForAlpha3d to be created. - * @param[in] max_alpha_square maximum for alpha square value. Default value is +\f$\infty\f$. - * - * @return true if creation succeeds, false otherwise. - * - * @pre The simplicial complex must be empty (no vertices) - * - * Initialization can be launched once. - * - */ - template - bool create_complex(SimplicialComplexForAlpha3d& complex, Filtration_value max_alpha_square = - std::numeric_limits::infinity()) { + * It also computes the filtration values accordingly to the \ref createcomplexalgorithm + * + * \tparam SimplicialComplexForAlpha3d must meet `SimplicialComplexForAlpha3d` concept. + * + * @param[in] complex SimplicialComplexForAlpha3d to be created. + * @param[in] max_alpha_square maximum for alpha square value. Default value is +\f$\infty\f$. + * + * @return true if creation succeeds, false otherwise. + * + * @pre The simplicial complex must be empty (no vertices) + * + * Initialization can be launched once. + * + */ + template + bool create_complex(SimplicialComplexForAlpha3d& complex, + Filtration_value max_alpha_square = std::numeric_limits::infinity()) { if (complex.num_vertices() > 0) { std::cerr << "Alpha_complex_3d create_complex - complex is not empty\n"; return false; // ----- >> } - //using Filtration_value = typename SimplicialComplexForAlpha3d::Filtration_value; + // using Filtration_value = typename SimplicialComplexForAlpha3d::Filtration_value; using Complex_vertex_handle = typename SimplicialComplexForAlpha3d::Vertex_handle; - using Alpha_shape_simplex_tree_map = std::unordered_map; + using Alpha_shape_simplex_tree_map = std::unordered_map; using Simplex_tree_vector_vertex = std::vector; #ifdef DEBUG_TRACES @@ -483,7 +455,7 @@ public: #ifdef DEBUG_TRACES std::cout << "filtration_with_alpha_values returns : " << objects.size() << " objects" << std::endl; #endif // DEBUG_TRACES - + Alpha_shape_simplex_tree_map map_cgal_simplex_tree; using Alpha_value_iterator = typename std::vector::const_iterator; Alpha_value_iterator alpha_value_iterator = alpha_values.begin(); @@ -491,7 +463,7 @@ public: Vertex_list vertex_list; // Retrieve Alpha shape vertex list from object - if (const Cell_handle *cell = CGAL::object_cast(&object_iterator)) { + if (const Cell_handle* cell = CGAL::object_cast(&object_iterator)) { for (auto i = 0; i < 4; i++) { #ifdef DEBUG_TRACES std::cout << "from cell[" << i << "]=" << (*cell)->vertex(i)->point() << std::endl; @@ -501,29 +473,29 @@ public: #ifdef DEBUG_TRACES count_cells++; #endif // DEBUG_TRACES - } else if (const Facet *facet = CGAL::object_cast(&object_iterator)) { - for (auto i = 0; i < 4; i++) { - if ((*facet).second != i) { + } else if (const Facet* facet = CGAL::object_cast(&object_iterator)) { + for (auto i = 0; i < 4; i++) { + if ((*facet).second != i) { #ifdef DEBUG_TRACES - std::cout << "from facet=[" << i << "]" << (*facet).first->vertex(i)->point() << std::endl; + std::cout << "from facet=[" << i << "]" << (*facet).first->vertex(i)->point() << std::endl; #endif // DEBUG_TRACES - vertex_list.push_back((*facet).first->vertex(i)); - } + vertex_list.push_back((*facet).first->vertex(i)); } + } #ifdef DEBUG_TRACES count_facets++; #endif // DEBUG_TRACES - } else if (const Edge *edge = CGAL::object_cast(&object_iterator)) { - for (auto i : {(*edge).second, (*edge).third}) { + } else if (const Edge* edge = CGAL::object_cast(&object_iterator)) { + for (auto i : {(*edge).second, (*edge).third}) { #ifdef DEBUG_TRACES - std::cout << "from edge[" << i << "]=" << (*edge).first->vertex(i)->point() << std::endl; + std::cout << "from edge[" << i << "]=" << (*edge).first->vertex(i)->point() << std::endl; #endif // DEBUG_TRACES - vertex_list.push_back((*edge).first->vertex(i)); - } + vertex_list.push_back((*edge).first->vertex(i)); + } #ifdef DEBUG_TRACES count_edges++; #endif // DEBUG_TRACES - } else if (const Alpha_vertex_handle *vertex = CGAL::object_cast(&object_iterator)) { + } else if (const Alpha_vertex_handle* vertex = CGAL::object_cast(&object_iterator)) { #ifdef DEBUG_TRACES count_vertices++; std::cout << "from vertex=" << (*vertex)->point() << std::endl; @@ -577,10 +549,9 @@ public: return true; } -private: + private: // use of a unique_ptr on cgal Alpha_shape_3, as copy and default constructor is not available - no need to be freed std::unique_ptr alpha_shape_3_ptr_; - }; } // namespace alpha_complex diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_options.h b/src/Alpha_complex/include/gudhi/Alpha_complex_options.h index 29eb514a..7a555fa1 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_options.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_options.h @@ -23,7 +23,6 @@ #ifndef ALPHA_COMPLEX_OPTIONS_H_ #define ALPHA_COMPLEX_OPTIONS_H_ - namespace Gudhi { namespace alpha_complex { @@ -33,11 +32,10 @@ namespace alpha_complex { * * \ingroup alpha_complex */ -enum class complexity: char -{ - FAST='f', ///< Fast version. - SAFE='s', ///< Safe version. - EXACT='e', ///< Exact version. +enum class complexity : char { + FAST = 'f', ///< Fast version. + SAFE = 's', ///< Safe version. + EXACT = 'e', ///< Exact version. }; } // namespace alpha_complex diff --git a/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp index a32e88a6..9e071195 100644 --- a/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp +++ b/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp @@ -42,21 +42,33 @@ #include #include -using Fast_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Safe_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Exact_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; - -using Fast_weighted_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Safe_weighted_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Exact_weighted_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; - -using Fast_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Safe_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Exact_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; - -using Fast_weighted_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Safe_weighted_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; -using Exact_weighted_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Fast_alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; +using Safe_alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; +using Exact_alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; + +using Fast_weighted_alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; +using Safe_weighted_alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; +using Exact_weighted_alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; + +using Fast_periodic_alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; +using Safe_periodic_alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; +using Exact_periodic_alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; + +using Fast_weighted_periodic_alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; +using Safe_weighted_periodic_alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; +using Exact_weighted_periodic_alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; BOOST_AUTO_TEST_CASE(Alpha_complex_3d_from_points) { // ----------------- @@ -89,18 +101,18 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_3d_from_points) { // --------------------- // Compare both versions // --------------------- - std::cout << "Exact Alpha complex 3d is of dimension " << exact_stree.dimension() - << " - Non exact is " << stree.dimension() << std::endl; + std::cout << "Exact Alpha complex 3d is of dimension " << exact_stree.dimension() << " - Non exact is " + << stree.dimension() << std::endl; BOOST_CHECK(exact_stree.dimension() == stree.dimension()); - std::cout << "Exact Alpha complex 3d num_simplices " << exact_stree.num_simplices() - << " - Non exact is " << stree.num_simplices() << std::endl; + std::cout << "Exact Alpha complex 3d num_simplices " << exact_stree.num_simplices() << " - Non exact is " + << stree.num_simplices() << std::endl; BOOST_CHECK(exact_stree.num_simplices() == stree.num_simplices()); - std::cout << "Exact Alpha complex 3d num_vertices " << exact_stree.num_vertices() - << " - Non exact is " << stree.num_vertices() << std::endl; + std::cout << "Exact Alpha complex 3d num_vertices " << exact_stree.num_vertices() << " - Non exact is " + << stree.num_vertices() << std::endl; BOOST_CHECK(exact_stree.num_vertices() == stree.num_vertices()); auto sh = stree.filtration_simplex_range().begin(); - while(sh != stree.filtration_simplex_range().end()) { + while (sh != stree.filtration_simplex_range().end()) { std::vector simplex; std::vector exact_simplex; std::cout << "Non-exact ( "; @@ -108,7 +120,8 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_3d_from_points) { simplex.push_back(vertex); std::cout << vertex << " "; } - std::cout << ") -> " << "[" << stree.filtration(*sh) << "] "; + std::cout << ") -> " + << "[" << stree.filtration(*sh) << "] "; std::cout << std::endl; // Find it in the exact structure @@ -133,18 +146,18 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_3d_from_points) { // --------------------- // Compare both versions // --------------------- - std::cout << "Exact Alpha complex 3d is of dimension " << safe_stree.dimension() - << " - Non exact is " << stree.dimension() << std::endl; + std::cout << "Exact Alpha complex 3d is of dimension " << safe_stree.dimension() << " - Non exact is " + << stree.dimension() << std::endl; BOOST_CHECK(safe_stree.dimension() == stree.dimension()); - std::cout << "Exact Alpha complex 3d num_simplices " << safe_stree.num_simplices() - << " - Non exact is " << stree.num_simplices() << std::endl; + std::cout << "Exact Alpha complex 3d num_simplices " << safe_stree.num_simplices() << " - Non exact is " + << stree.num_simplices() << std::endl; BOOST_CHECK(safe_stree.num_simplices() == stree.num_simplices()); - std::cout << "Exact Alpha complex 3d num_vertices " << safe_stree.num_vertices() - << " - Non exact is " << stree.num_vertices() << std::endl; + std::cout << "Exact Alpha complex 3d num_vertices " << safe_stree.num_vertices() << " - Non exact is " + << stree.num_vertices() << std::endl; BOOST_CHECK(safe_stree.num_vertices() == stree.num_vertices()); auto safe_sh = stree.filtration_simplex_range().begin(); - while(safe_sh != stree.filtration_simplex_range().end()) { + while (safe_sh != stree.filtration_simplex_range().end()) { std::vector simplex; std::vector exact_simplex; #ifdef DEBUG_TRACES @@ -157,7 +170,8 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_3d_from_points) { #endif } #ifdef DEBUG_TRACES - std::cout << ") -> " << "[" << stree.filtration(*safe_sh) << "] "; + std::cout << ") -> " + << "[" << stree.filtration(*safe_sh) << "] "; std::cout << std::endl; #endif @@ -172,9 +186,9 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_3d_from_points) { } } -typedef boost::mpl::list weighted_variants_type_list; +typedef boost::mpl::list + weighted_variants_type_list; #ifdef GUDHI_DEBUG BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_weighted_throw, Weighted_alpha_complex_3d, weighted_variants_type_list) { @@ -191,7 +205,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_weighted_throw, Weighted_alpha_compl std::vector weights = {0.01, 0.005, 0.006, 0.01, 0.009, 0.001}; std::cout << "Check exception throw in debug mode" << std::endl; - BOOST_CHECK_THROW (Weighted_alpha_complex_3d wac(w_points, weights), std::invalid_argument); + BOOST_CHECK_THROW(Weighted_alpha_complex_3d wac(w_points, weights), std::invalid_argument); } #endif @@ -218,7 +232,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_weighted, Weighted_alpha_complex_3d, std::vector weighted_points; - for (std::size_t i=0; i < w_points.size(); i++) { + for (std::size_t i = 0; i < w_points.size(); i++) { weighted_points.push_back(Weighted_point_3(w_points[i], weights[i])); } Weighted_alpha_complex_3d alpha_complex_w_p(weighted_points); @@ -229,18 +243,18 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_weighted, Weighted_alpha_complex_3d, // --------------------- // Compare both versions // --------------------- - std::cout << "Weighted alpha complex 3d is of dimension " << stree_bis.dimension() - << " - versus " << stree.dimension() << std::endl; + std::cout << "Weighted alpha complex 3d is of dimension " << stree_bis.dimension() << " - versus " + << stree.dimension() << std::endl; BOOST_CHECK(stree_bis.dimension() == stree.dimension()); - std::cout << "Weighted alpha complex 3d num_simplices " << stree_bis.num_simplices() - << " - versus " << stree.num_simplices() << std::endl; + std::cout << "Weighted alpha complex 3d num_simplices " << stree_bis.num_simplices() << " - versus " + << stree.num_simplices() << std::endl; BOOST_CHECK(stree_bis.num_simplices() == stree.num_simplices()); - std::cout << "Weighted alpha complex 3d num_vertices " << stree_bis.num_vertices() - << " - versus " << stree.num_vertices() << std::endl; + std::cout << "Weighted alpha complex 3d num_vertices " << stree_bis.num_vertices() << " - versus " + << stree.num_vertices() << std::endl; BOOST_CHECK(stree_bis.num_vertices() == stree.num_vertices()); auto sh = stree.filtration_simplex_range().begin(); - while(sh != stree.filtration_simplex_range().end()) { + while (sh != stree.filtration_simplex_range().end()) { std::vector simplex; std::vector exact_simplex; #ifdef DEBUG_TRACES @@ -253,7 +267,8 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_weighted, Weighted_alpha_complex_3d, #endif } #ifdef DEBUG_TRACES - std::cout << ") -> " << "[" << stree.filtration(*sh) << "] "; + std::cout << ") -> " + << "[" << stree.filtration(*sh) << "] "; std::cout << std::endl; #endif @@ -266,13 +281,12 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_weighted, Weighted_alpha_complex_3d, ++sh; } - } #ifdef GUDHI_DEBUG -typedef boost::mpl::list periodic_variants_type_list; +typedef boost::mpl::list + periodic_variants_type_list; BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_periodic_throw, Periodic_alpha_complex_3d, periodic_variants_type_list) { std::cout << "Periodic alpha complex 3d exception throw" << std::endl; @@ -284,18 +298,18 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_periodic_throw, Periodic_alpha_compl std::cout << "Check exception throw in debug mode" << std::endl; // Check it throws an exception when the cuboid is not iso - BOOST_CHECK_THROW (Periodic_alpha_complex_3d periodic_alpha_complex(p_points, 0., 0., 0., 0.9, 1., 1.), - std::invalid_argument); - BOOST_CHECK_THROW (Periodic_alpha_complex_3d periodic_alpha_complex(p_points, 0., 0., 0., 1., 0.9, 1.), - std::invalid_argument); - BOOST_CHECK_THROW (Periodic_alpha_complex_3d periodic_alpha_complex(p_points, 0., 0., 0., 1., 1., 0.9), - std::invalid_argument); - BOOST_CHECK_THROW (Periodic_alpha_complex_3d periodic_alpha_complex(p_points, 0., 0., 0., 1.1, 1., 1.), - std::invalid_argument); - BOOST_CHECK_THROW (Periodic_alpha_complex_3d periodic_alpha_complex(p_points, 0., 0., 0., 1., 1.1, 1.), - std::invalid_argument); - BOOST_CHECK_THROW (Periodic_alpha_complex_3d periodic_alpha_complex(p_points, 0., 0., 0., 1., 1., 1.1), - std::invalid_argument); + BOOST_CHECK_THROW(Periodic_alpha_complex_3d periodic_alpha_complex(p_points, 0., 0., 0., 0.9, 1., 1.), + std::invalid_argument); + BOOST_CHECK_THROW(Periodic_alpha_complex_3d periodic_alpha_complex(p_points, 0., 0., 0., 1., 0.9, 1.), + std::invalid_argument); + BOOST_CHECK_THROW(Periodic_alpha_complex_3d periodic_alpha_complex(p_points, 0., 0., 0., 1., 1., 0.9), + std::invalid_argument); + BOOST_CHECK_THROW(Periodic_alpha_complex_3d periodic_alpha_complex(p_points, 0., 0., 0., 1.1, 1., 1.), + std::invalid_argument); + BOOST_CHECK_THROW(Periodic_alpha_complex_3d periodic_alpha_complex(p_points, 0., 0., 0., 1., 1.1, 1.), + std::invalid_argument); + BOOST_CHECK_THROW(Periodic_alpha_complex_3d periodic_alpha_complex(p_points, 0., 0., 0., 1., 1., 1.1), + std::invalid_argument); } #endif @@ -310,7 +324,7 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_periodic) { CGAL::Random_points_in_cube_3 in_cube(1, random); std::vector p_points; - for (int i=0 ; i < 50 ; i++) { + for (int i = 0; i < 50; i++) { Fast_periodic_alpha_complex_3d::Point_3 p = *in_cube++; p_points.push_back(p); } @@ -327,7 +341,7 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_periodic) { std::vector e_p_points; - for (auto p: p_points) { + for (auto p : p_points) { e_p_points.push_back(Exact_periodic_alpha_complex_3d::Point_3(p[0], p[1], p[2])); } @@ -339,27 +353,25 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_periodic) { // --------------------- // Compare both versions // --------------------- - std::cout << "Exact periodic alpha complex 3d is of dimension " << exact_stree.dimension() - << " - Non exact is " << stree.dimension() << std::endl; + std::cout << "Exact periodic alpha complex 3d is of dimension " << exact_stree.dimension() << " - Non exact is " + << stree.dimension() << std::endl; BOOST_CHECK(exact_stree.dimension() == stree.dimension()); - std::cout << "Exact periodic alpha complex 3d num_simplices " << exact_stree.num_simplices() - << " - Non exact is " << stree.num_simplices() << std::endl; + std::cout << "Exact periodic alpha complex 3d num_simplices " << exact_stree.num_simplices() << " - Non exact is " + << stree.num_simplices() << std::endl; BOOST_CHECK(exact_stree.num_simplices() == stree.num_simplices()); - std::cout << "Exact periodic alpha complex 3d num_vertices " << exact_stree.num_vertices() - << " - Non exact is " << stree.num_vertices() << std::endl; + std::cout << "Exact periodic alpha complex 3d num_vertices " << exact_stree.num_vertices() << " - Non exact is " + << stree.num_vertices() << std::endl; BOOST_CHECK(exact_stree.num_vertices() == stree.num_vertices()); - // We cannot compare as objects from dispatcher on the alpha shape is not deterministic. // cf. https://github.com/CGAL/cgal/issues/3346 auto sh = stree.filtration_simplex_range().begin(); auto sh_exact = exact_stree.filtration_simplex_range().begin(); - while(sh != stree.filtration_simplex_range().end() || sh_exact != exact_stree.filtration_simplex_range().end()) { + while (sh != stree.filtration_simplex_range().end() || sh_exact != exact_stree.filtration_simplex_range().end()) { GUDHI_TEST_FLOAT_EQUALITY_CHECK(stree.filtration(*sh), exact_stree.filtration(*sh_exact), 1e-14); - std::vector vh(stree.simplex_vertex_range(*sh).begin(), - stree.simplex_vertex_range(*sh).end()); + std::vector vh(stree.simplex_vertex_range(*sh).begin(), stree.simplex_vertex_range(*sh).end()); std::vector exact_vh(exact_stree.simplex_vertex_range(*sh_exact).begin(), exact_stree.simplex_vertex_range(*sh_exact).end()); @@ -371,7 +383,6 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_periodic) { BOOST_CHECK(sh == stree.filtration_simplex_range().end()); BOOST_CHECK(sh_exact == exact_stree.filtration_simplex_range().end()); - // ---------------------- // Safe periodic version // ---------------------- @@ -379,7 +390,7 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_periodic) { std::vector s_p_points; - for (auto p: p_points) { + for (auto p : p_points) { s_p_points.push_back(Safe_periodic_alpha_complex_3d::Point_3(p[0], p[1], p[2])); } @@ -396,11 +407,10 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_periodic) { sh = stree.filtration_simplex_range().begin(); auto sh_safe = safe_stree.filtration_simplex_range().begin(); - while(sh != stree.filtration_simplex_range().end() || sh_safe != safe_stree.filtration_simplex_range().end()) { + while (sh != stree.filtration_simplex_range().end() || sh_safe != safe_stree.filtration_simplex_range().end()) { GUDHI_TEST_FLOAT_EQUALITY_CHECK(stree.filtration(*sh), safe_stree.filtration(*sh_safe), 1e-14); - std::vector vh(stree.simplex_vertex_range(*sh).begin(), - stree.simplex_vertex_range(*sh).end()); + std::vector vh(stree.simplex_vertex_range(*sh).begin(), stree.simplex_vertex_range(*sh).end()); std::vector safe_vh(safe_stree.simplex_vertex_range(*sh_safe).begin(), safe_stree.simplex_vertex_range(*sh_safe).end()); @@ -411,11 +421,11 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_periodic) { BOOST_CHECK(sh == stree.filtration_simplex_range().end()); BOOST_CHECK(sh_safe == safe_stree.filtration_simplex_range().end()); - } typedef boost::mpl::list wp_variants_type_list; + Safe_weighted_periodic_alpha_complex_3d> + wp_variants_type_list; #ifdef GUDHI_DEBUG BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_weighted_periodic_throw, Weighted_periodic_alpha_complex_3d, @@ -427,7 +437,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_weighted_periodic_throw, Weighted_pe CGAL::Random_points_in_cube_3 in_cube(1, random); std::vector wp_points; - for (int i=0 ; i < 50 ; i++) { + for (int i = 0; i < 50; i++) { Weighted_periodic_alpha_complex_3d::Point_3 p = *in_cube++; wp_points.push_back(p); } @@ -439,44 +449,50 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_weighted_periodic_throw, Weighted_pe std::cout << "Cuboid is not iso exception" << std::endl; // Check it throws an exception when the cuboid is not iso - BOOST_CHECK_THROW (Weighted_periodic_alpha_complex_3d wp_alpha_complex(wp_points, p_weights, -1., -1., -1., 0.9, 1., 1.), - std::invalid_argument); - BOOST_CHECK_THROW (Weighted_periodic_alpha_complex_3d wp_alpha_complex(wp_points, p_weights, -1., -1., -1., 1., 0.9, 1.), - std::invalid_argument); - BOOST_CHECK_THROW (Weighted_periodic_alpha_complex_3d wp_alpha_complex(wp_points, p_weights, -1., -1., -1., 1., 1., 0.9), - std::invalid_argument); - BOOST_CHECK_THROW (Weighted_periodic_alpha_complex_3d wp_alpha_complex(wp_points, p_weights, -1., -1., -1., 1.1, 1., 1.), - std::invalid_argument); - BOOST_CHECK_THROW (Weighted_periodic_alpha_complex_3d wp_alpha_complex(wp_points, p_weights, -1., -1., -1., 1., 1.1, 1.), - std::invalid_argument); - BOOST_CHECK_THROW (Weighted_periodic_alpha_complex_3d wp_alpha_complex(wp_points, p_weights, -1., -1., -1., 1., 1., 1.1), - std::invalid_argument); + BOOST_CHECK_THROW( + Weighted_periodic_alpha_complex_3d wp_alpha_complex(wp_points, p_weights, -1., -1., -1., 0.9, 1., 1.), + std::invalid_argument); + BOOST_CHECK_THROW( + Weighted_periodic_alpha_complex_3d wp_alpha_complex(wp_points, p_weights, -1., -1., -1., 1., 0.9, 1.), + std::invalid_argument); + BOOST_CHECK_THROW( + Weighted_periodic_alpha_complex_3d wp_alpha_complex(wp_points, p_weights, -1., -1., -1., 1., 1., 0.9), + std::invalid_argument); + BOOST_CHECK_THROW( + Weighted_periodic_alpha_complex_3d wp_alpha_complex(wp_points, p_weights, -1., -1., -1., 1.1, 1., 1.), + std::invalid_argument); + BOOST_CHECK_THROW( + Weighted_periodic_alpha_complex_3d wp_alpha_complex(wp_points, p_weights, -1., -1., -1., 1., 1.1, 1.), + std::invalid_argument); + BOOST_CHECK_THROW( + Weighted_periodic_alpha_complex_3d wp_alpha_complex(wp_points, p_weights, -1., -1., -1., 1., 1., 1.1), + std::invalid_argument); std::cout << "0 <= point.weight() < 1/64 * domain_size * domain_size exception" << std::endl; // Weights must be in range ]0, 1/64 = 0.015625[ double temp = p_weights[25]; p_weights[25] = 1.0; - BOOST_CHECK_THROW (Weighted_periodic_alpha_complex_3d wp_alpha_complex(wp_points, p_weights, 0., 0., 0., 1., 1., 1.), - std::invalid_argument); + BOOST_CHECK_THROW(Weighted_periodic_alpha_complex_3d wp_alpha_complex(wp_points, p_weights, 0., 0., 0., 1., 1., 1.), + std::invalid_argument); // Weights must be in range ]0, 1/64 = 0.015625[ p_weights[25] = temp; temp = p_weights[14]; p_weights[14] = -1e-10; - BOOST_CHECK_THROW (Weighted_periodic_alpha_complex_3d wp_alpha_complex(wp_points, p_weights, 0., 0., 0., 1., 1., 1.), - std::invalid_argument); + BOOST_CHECK_THROW(Weighted_periodic_alpha_complex_3d wp_alpha_complex(wp_points, p_weights, 0., 0., 0., 1., 1., 1.), + std::invalid_argument); p_weights[14] = temp; std::cout << "wp_points and p_weights size exception" << std::endl; // Weights and points must have the same size // + 1 p_weights.push_back(1e-10); - BOOST_CHECK_THROW (Weighted_periodic_alpha_complex_3d wp_alpha_complex(wp_points, p_weights, 0., 0., 0., 1., 1., 1.), - std::invalid_argument); + BOOST_CHECK_THROW(Weighted_periodic_alpha_complex_3d wp_alpha_complex(wp_points, p_weights, 0., 0., 0., 1., 1., 1.), + std::invalid_argument); // - 1 p_weights.pop_back(); p_weights.pop_back(); - BOOST_CHECK_THROW (Weighted_periodic_alpha_complex_3d wp_alpha_complex(wp_points, p_weights, 0., 0., 0., 1., 1., 1.), - std::invalid_argument); + BOOST_CHECK_THROW(Weighted_periodic_alpha_complex_3d wp_alpha_complex(wp_points, p_weights, 0., 0., 0., 1., 1., 1.), + std::invalid_argument); } #endif @@ -491,7 +507,7 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_weighted_periodic) { CGAL::Random_points_in_cube_3 in_cube(1, random); std::vector p_points; - for (int i=0 ; i < 50 ; i++) { + for (int i = 0; i < 50; i++) { Fast_weighted_periodic_alpha_complex_3d::Point_3 p = *in_cube++; p_points.push_back(p); } @@ -513,7 +529,7 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_weighted_periodic) { std::vector e_p_points; - for (auto p: p_points) { + for (auto p : p_points) { e_p_points.push_back(Exact_weighted_periodic_alpha_complex_3d::Point_3(p[0], p[1], p[2])); } @@ -535,17 +551,15 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_weighted_periodic) { << " - Non exact is " << stree.num_vertices() << std::endl; BOOST_CHECK(exact_stree.num_vertices() == stree.num_vertices()); - // We cannot compare as objects from dispatcher on the alpha shape is not deterministic. // cf. https://github.com/CGAL/cgal/issues/3346 auto sh = stree.filtration_simplex_range().begin(); auto sh_exact = exact_stree.filtration_simplex_range().begin(); - while(sh != stree.filtration_simplex_range().end() || sh_exact != exact_stree.filtration_simplex_range().end()) { + while (sh != stree.filtration_simplex_range().end() || sh_exact != exact_stree.filtration_simplex_range().end()) { GUDHI_TEST_FLOAT_EQUALITY_CHECK(stree.filtration(*sh), exact_stree.filtration(*sh_exact), 1e-14); - std::vector vh(stree.simplex_vertex_range(*sh).begin(), - stree.simplex_vertex_range(*sh).end()); + std::vector vh(stree.simplex_vertex_range(*sh).begin(), stree.simplex_vertex_range(*sh).end()); std::vector exact_vh(exact_stree.simplex_vertex_range(*sh_exact).begin(), exact_stree.simplex_vertex_range(*sh_exact).end()); @@ -557,7 +571,6 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_weighted_periodic) { BOOST_CHECK(sh == stree.filtration_simplex_range().end()); BOOST_CHECK(sh_exact == exact_stree.filtration_simplex_range().end()); - // ---------------------- // Safe weighted periodic version // ---------------------- @@ -565,7 +578,7 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_weighted_periodic) { std::vector s_p_points; - for (auto p: p_points) { + for (auto p : p_points) { s_p_points.push_back(Safe_weighted_periodic_alpha_complex_3d::Point_3(p[0], p[1], p[2])); } @@ -582,11 +595,10 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_weighted_periodic) { sh = stree.filtration_simplex_range().begin(); auto sh_safe = safe_stree.filtration_simplex_range().begin(); - while(sh != stree.filtration_simplex_range().end() || sh_safe != safe_stree.filtration_simplex_range().end()) { + while (sh != stree.filtration_simplex_range().end() || sh_safe != safe_stree.filtration_simplex_range().end()) { GUDHI_TEST_FLOAT_EQUALITY_CHECK(stree.filtration(*sh), safe_stree.filtration(*sh_safe), 1e-14); - std::vector vh(stree.simplex_vertex_range(*sh).begin(), - stree.simplex_vertex_range(*sh).end()); + std::vector vh(stree.simplex_vertex_range(*sh).begin(), stree.simplex_vertex_range(*sh).end()); std::vector safe_vh(safe_stree.simplex_vertex_range(*sh_safe).begin(), safe_stree.simplex_vertex_range(*sh_safe).end()); diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt index 80444de8..65ca1624 100644 --- a/src/Alpha_complex/utilities/CMakeLists.txt +++ b/src/Alpha_complex/utilities/CMakeLists.txt @@ -30,9 +30,15 @@ if(CGAL_FOUND) "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45" "-o" "exact.pers" "-e") + add_test(NAME Alpha_complex_utilities_safe_alpha_complex_3d COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" + "-p" "2" "-m" "0.45" "-o" "safe.pers" "-s") + if (DIFF_PATH) add_test(Alpha_complex_utilities_diff_alpha_complex_3d ${DIFF_PATH} "exact.pers" "alpha.pers") + add_test(Alpha_complex_utilities_diff_alpha_complex_3d ${DIFF_PATH} + "safe.pers" "alpha.pers") endif() add_test(NAME Alpha_complex_utilities_periodic_alpha_complex_3d_persistence COMMAND $ diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp index c2b49fed..d14ba375 100644 --- a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp @@ -38,11 +38,12 @@ using Filtration_value = Simplex_tree::Filtration_value; using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; -void program_options(int argc, char *argv[], std::string &off_file_points, bool& EXACT, std::string &weight_file, - std::string &cuboid_file, std::string &output_file_diag, Filtration_value &alpha_square_max_value, - int &coeff_field_characteristic, Filtration_value &min_persistence); +void program_options(int argc, char *argv[], std::string &off_file_points, bool &exact, bool &safe, + std::string &weight_file, std::string &cuboid_file, std::string &output_file_diag, + Filtration_value &alpha_square_max_value, int &coeff_field_characteristic, + Filtration_value &min_persistence); -bool read_weight_file(const std::string& weight_file, std::vector& weights) { +bool read_weight_file(const std::string &weight_file, std::vector &weights) { // Read weights information from file std::ifstream weights_ifstr(weight_file); if (weights_ifstr.good()) { @@ -57,8 +58,8 @@ bool read_weight_file(const std::string& weight_file, std::vector& weigh return true; } -bool read_cuboid_file(const std::string& cuboid_file, double& x_min, double& y_min, double& z_min, - double& x_max, double& y_max, double& z_max) { +bool read_cuboid_file(const std::string &cuboid_file, double &x_min, double &y_min, double &z_min, double &x_max, + double &y_max, double &z_max) { // Read weights information from file std::ifstream iso_cuboid_str(cuboid_file); if (iso_cuboid_str.is_open()) { @@ -71,8 +72,8 @@ bool read_cuboid_file(const std::string& cuboid_file, double& x_min, double& y_m return true; } -template -std::vector read_off(const std::string& off_file_points) { +template +std::vector read_off(const std::string &off_file_points) { // Read the OFF file (input file name given as parameter) and triangulate points Gudhi::Points_3D_off_reader off_reader(off_file_points); // Check the read operation was correct @@ -92,10 +93,11 @@ int main(int argc, char **argv) { int coeff_field_characteristic = 0; Filtration_value min_persistence = 0.; bool exact_version = false; + bool safe_version = false; bool weighted_version = false; bool periodic_version = false; - program_options(argc, argv, off_file_points, exact_version, weight_file, cuboid_file, output_file_diag, + program_options(argc, argv, off_file_points, exact_version, safe_version, weight_file, cuboid_file, output_file_diag, alpha_square_max_value, coeff_field_characteristic, min_persistence); std::vector weights; @@ -107,7 +109,7 @@ int main(int argc, char **argv) { weighted_version = true; } - double x_min=0., y_min=0., z_min=0., x_max=0., y_max=0., z_max=0.; + double x_min = 0., y_min = 0., z_min = 0., x_max = 0., y_max = 0., z_max = 0.; std::ifstream iso_cuboid_str(argv[3]); if (cuboid_file != std::string()) { if (!read_cuboid_file(cuboid_file, x_min, y_min, z_min, x_max, y_max, z_max)) { @@ -119,37 +121,44 @@ int main(int argc, char **argv) { Gudhi::alpha_complex::complexity complexity = Gudhi::alpha_complex::complexity::FAST; if (exact_version) { + if (safe_version) { + std::cerr << "You cannot set the exact and the safe version." << std::endl; + exit(-1); + } complexity = Gudhi::alpha_complex::complexity::EXACT; } + if (safe_version) { + complexity = Gudhi::alpha_complex::complexity::SAFE; + } Simplex_tree simplex_tree; - switch(complexity) { + switch (complexity) { case Gudhi::alpha_complex::complexity::FAST: if (weighted_version) { if (periodic_version) { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; auto points = read_off(off_file_points); Alpha_complex_3d alpha_complex(points, weights, x_min, y_min, z_min, x_max, y_max, z_max); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); } else { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; auto points = read_off(off_file_points); Alpha_complex_3d alpha_complex(points, weights); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); } } else { if (periodic_version) { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; auto points = read_off(off_file_points); Alpha_complex_3d alpha_complex(points, x_min, y_min, z_min, x_max, y_max, z_max); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); } else { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; auto points = read_off(off_file_points); Alpha_complex_3d alpha_complex(points); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); @@ -159,28 +168,28 @@ int main(int argc, char **argv) { case Gudhi::alpha_complex::complexity::EXACT: if (weighted_version) { if (periodic_version) { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; auto points = read_off(off_file_points); Alpha_complex_3d alpha_complex(points, weights, x_min, y_min, z_min, x_max, y_max, z_max); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); } else { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; auto points = read_off(off_file_points); Alpha_complex_3d alpha_complex(points, weights); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); } } else { if (periodic_version) { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; auto points = read_off(off_file_points); Alpha_complex_3d alpha_complex(points, x_min, y_min, z_min, x_max, y_max, z_max); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); } else { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; auto points = read_off(off_file_points); Alpha_complex_3d alpha_complex(points); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); @@ -190,28 +199,28 @@ int main(int argc, char **argv) { case Gudhi::alpha_complex::complexity::SAFE: if (weighted_version) { if (periodic_version) { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; auto points = read_off(off_file_points); Alpha_complex_3d alpha_complex(points, weights, x_min, y_min, z_min, x_max, y_max, z_max); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); } else { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; auto points = read_off(off_file_points); Alpha_complex_3d alpha_complex(points, weights); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); } } else { if (periodic_version) { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; auto points = read_off(off_file_points); Alpha_complex_3d alpha_complex(points, x_min, y_min, z_min, x_max, y_max, z_max); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); } else { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; auto points = read_off(off_file_points); Alpha_complex_3d alpha_complex(points); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); @@ -248,9 +257,10 @@ int main(int argc, char **argv) { return 0; } -void program_options(int argc, char *argv[], std::string &off_file_points, bool& EXACT, std::string &weight_file, - std::string &cuboid_file, std::string &output_file_diag, Filtration_value &alpha_square_max_value, - int &coeff_field_characteristic, Filtration_value &min_persistence) { +void program_options(int argc, char *argv[], std::string &off_file_points, bool &exact, bool &safe, + std::string &weight_file, std::string &cuboid_file, std::string &output_file_diag, + Filtration_value &alpha_square_max_value, int &coeff_field_characteristic, + Filtration_value &min_persistence) { namespace po = boost::program_options; po::options_description hidden("Hidden options"); hidden.add_options()("input-file", po::value(&off_file_points), @@ -258,15 +268,18 @@ void program_options(int argc, char *argv[], std::string &off_file_points, bool& po::options_description visible("Allowed options", 100); visible.add_options()("help,h", "produce help message")( - "EXACT,e", po::bool_switch(&EXACT), - "To activate EXACT version of Alpha complex 3d (default is false, not available for weighted and/or periodic)")( + "exact,e", po::bool_switch(&exact), + "To activate exact version of Alpha complex 3d (default is false, not available if safe is set)")( + "safe,s", po::bool_switch(&safe), + "To activate safe version of Alpha complex 3d (default is false, not available if exact is set)")( "weight-file,w", po::value(&weight_file)->default_value(std::string()), "Name of file containing a point weights. Format is one weight per line:\n W1\n ...\n Wn ")( "cuboid-file,c", po::value(&cuboid_file), "Name of file describing the periodic domain. Format is:\n min_hx min_hy min_hz\n max_hx max_hy max_hz")( "output-file,o", po::value(&output_file_diag)->default_value(std::string()), "Name of file in which the persistence diagram is written. Default print in std::cout")( - "max-alpha-square-value,r", po::value(&alpha_square_max_value) + "max-alpha-square-value,r", + po::value(&alpha_square_max_value) ->default_value(std::numeric_limits::infinity()), "Maximal alpha square value for the Alpha complex construction.")( "field-charac,p", po::value(&coeff_field_characteristic)->default_value(11), @@ -289,7 +302,7 @@ void program_options(int argc, char *argv[], std::string &off_file_points, bool& std::cout << std::endl; std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; std::cout << "of a 3D Alpha complex defined on a set of input points.\n"; - std::cout << "3D Alpha complex can be EXACT or weighted and/or periodic\n\n"; + std::cout << "3D Alpha complex can be exact or safe, weighted and/or periodic\n\n"; std::cout << "The output diagram contains one bar per line, written with the convention: \n"; std::cout << " p dim b d \n"; std::cout << "where dim is the dimension of the homological feature,\n"; -- cgit v1.2.3 From c5ced45c3efd3ccfe2d2b94ee04727ba66c76e6a Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 17 Oct 2018 09:34:55 +0000 Subject: Alpha complex 3d test was not checking CGAL is 4.11 Rewrite CMakeLists.txt to detect CGAL 4.11 for Alpha complex 3d git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@3962 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 7ccddf06201760ef4fddc4432a3b208b8b0213f7 --- src/Alpha_complex/example/CMakeLists.txt | 85 ++++++++++---------- src/Alpha_complex/test/CMakeLists.txt | 18 +++-- src/Alpha_complex/utilities/CMakeLists.txt | 121 ++++++++++++++--------------- 3 files changed, 110 insertions(+), 114 deletions(-) (limited to 'src/Alpha_complex/example') diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt index 1f127972..c62a220c 100644 --- a/src/Alpha_complex/example/CMakeLists.txt +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -1,51 +1,48 @@ project(Alpha_complex_examples) -if(CGAL_FOUND) - # need CGAL 4.7 - # cmake -DCGAL_DIR=~/workspace/CGAL-4.7 .. - if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) - add_executable ( Alpha_complex_example_from_points Alpha_complex_from_points.cpp ) - target_link_libraries(Alpha_complex_example_from_points ${CGAL_LIBRARY}) - add_executable ( Alpha_complex_example_from_off Alpha_complex_from_off.cpp ) - target_link_libraries(Alpha_complex_example_from_off ${CGAL_LIBRARY}) - if (TBB_FOUND) - target_link_libraries(Alpha_complex_example_from_points ${TBB_LIBRARIES}) - target_link_libraries(Alpha_complex_example_from_off ${TBB_LIBRARIES}) - endif() +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) + add_executable ( Alpha_complex_example_from_points Alpha_complex_from_points.cpp ) + target_link_libraries(Alpha_complex_example_from_points ${CGAL_LIBRARY}) + add_executable ( Alpha_complex_example_from_off Alpha_complex_from_off.cpp ) + target_link_libraries(Alpha_complex_example_from_off ${CGAL_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(Alpha_complex_example_from_points ${TBB_LIBRARIES}) + target_link_libraries(Alpha_complex_example_from_off ${TBB_LIBRARIES}) + endif() - add_test(NAME Alpha_complex_example_from_points COMMAND $) + add_test(NAME Alpha_complex_example_from_points COMMAND $) - add_test(NAME Alpha_complex_example_from_off_60 COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" "60.0" "${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt") - add_test(NAME Alpha_complex_example_from_off_32 COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" "32.0" "${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt") - if (DIFF_PATH) - # Do not forget to copy test results files in current binary dir - file(COPY "alphaoffreader_for_doc_32.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - file(COPY "alphaoffreader_for_doc_60.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + add_test(NAME Alpha_complex_example_from_off_60 COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" "60.0" "${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt") + add_test(NAME Alpha_complex_example_from_off_32 COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" "32.0" "${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt") + if (DIFF_PATH) + # Do not forget to copy test results files in current binary dir + file(COPY "alphaoffreader_for_doc_32.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + file(COPY "alphaoffreader_for_doc_60.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - add_test(Alpha_complex_example_from_off_60_diff_files ${DIFF_PATH} - ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_60.txt) - add_test(Alpha_complex_example_from_off_32_diff_files ${DIFF_PATH} - ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt) - endif() - endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) - if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) - add_executable ( Alpha_complex_example_weighted_3d_from_points Weighted_alpha_complex_3d_from_points.cpp ) - target_link_libraries(Alpha_complex_example_weighted_3d_from_points ${CGAL_LIBRARY}) - if (TBB_FOUND) - target_link_libraries(Alpha_complex_example_weighted_3d_from_points ${TBB_LIBRARIES}) - endif() - add_test(NAME Alpha_complex_example_weighted_3d_from_points - COMMAND $) + add_test(Alpha_complex_example_from_off_60_diff_files ${DIFF_PATH} + ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_60.txt) + add_test(Alpha_complex_example_from_off_32_diff_files ${DIFF_PATH} + ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt) + endif() +endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) - add_executable ( Alpha_complex_example_3d_from_points Alpha_complex_3d_from_points.cpp ) - target_link_libraries(Alpha_complex_example_3d_from_points ${CGAL_LIBRARY}) - if (TBB_FOUND) - target_link_libraries(Alpha_complex_example_3d_from_points ${TBB_LIBRARIES}) - endif() - add_test(NAME Alpha_complex_example_3d_from_points - COMMAND $) +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) + add_executable ( Alpha_complex_example_weighted_3d_from_points Weighted_alpha_complex_3d_from_points.cpp ) + target_link_libraries(Alpha_complex_example_weighted_3d_from_points ${CGAL_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(Alpha_complex_example_weighted_3d_from_points ${TBB_LIBRARIES}) + endif() + add_test(NAME Alpha_complex_example_weighted_3d_from_points + COMMAND $) - endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) -endif() \ No newline at end of file + add_executable ( Alpha_complex_example_3d_from_points Alpha_complex_3d_from_points.cpp ) + target_link_libraries(Alpha_complex_example_3d_from_points ${CGAL_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(Alpha_complex_example_3d_from_points ${TBB_LIBRARIES}) + endif() + add_test(NAME Alpha_complex_example_3d_from_points + COMMAND $) + +endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt index 61a9e6b5..380380f4 100644 --- a/src/Alpha_complex/test/CMakeLists.txt +++ b/src/Alpha_complex/test/CMakeLists.txt @@ -1,7 +1,10 @@ project(Alpha_complex_tests) +include(GUDHI_test_coverage) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) - include(GUDHI_test_coverage) + + # Do not forget to copy test files in current binary dir + file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) add_executable ( Alpha_complex_test_unit Alpha_complex_unit_test.cpp ) target_link_libraries(Alpha_complex_test_unit ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) @@ -9,18 +12,17 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) target_link_libraries(Alpha_complex_test_unit ${TBB_LIBRARIES}) endif() + gudhi_add_coverage_test(Alpha_complex_test_unit) + +endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) + +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_executable ( Alpha_complex_3d_test_unit Alpha_complex_3d_unit_test.cpp ) target_link_libraries(Alpha_complex_3d_test_unit ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) if (TBB_FOUND) target_link_libraries(Alpha_complex_3d_test_unit ${TBB_LIBRARIES}) endif() - # Do not forget to copy test files in current binary dir - file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - file(COPY "${CMAKE_SOURCE_DIR}/data/points/grid_5_5_5_in_0_1.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - - gudhi_add_coverage_test(Alpha_complex_test_unit) gudhi_add_coverage_test(Alpha_complex_3d_test_unit) -endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) - +endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt index 65ca1624..b12c9690 100644 --- a/src/Alpha_complex/utilities/CMakeLists.txt +++ b/src/Alpha_complex/utilities/CMakeLists.txt @@ -1,64 +1,61 @@ project(Alpha_complex_utilities) -if(CGAL_FOUND) - if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) - add_executable (alpha_complex_persistence alpha_complex_persistence.cpp) - target_link_libraries(alpha_complex_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) - - if (TBB_FOUND) - target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES}) - endif(TBB_FOUND) - add_test(NAME Alpha_complex_utilities_alpha_complex_persistence COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45") - - install(TARGETS alpha_complex_persistence DESTINATION bin) - - endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) - - if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) - add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp) - target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) - if (TBB_FOUND) - target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES}) - endif(TBB_FOUND) - - add_test(NAME Alpha_complex_utilities_alpha_complex_3d COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" - "-p" "2" "-m" "0.45" "-o" "alpha.pers") - - add_test(NAME Alpha_complex_utilities_exact_alpha_complex_3d COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" - "-p" "2" "-m" "0.45" "-o" "exact.pers" "-e") - - add_test(NAME Alpha_complex_utilities_safe_alpha_complex_3d COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" - "-p" "2" "-m" "0.45" "-o" "safe.pers" "-s") - - if (DIFF_PATH) - add_test(Alpha_complex_utilities_diff_alpha_complex_3d ${DIFF_PATH} - "exact.pers" "alpha.pers") - add_test(Alpha_complex_utilities_diff_alpha_complex_3d ${DIFF_PATH} - "safe.pers" "alpha.pers") - endif() - - add_test(NAME Alpha_complex_utilities_periodic_alpha_complex_3d_persistence COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" - "-c" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" - "-p" "2" "-m" "0") - - add_test(NAME Alpha_complex_utilities_weighted_alpha_complex_3d COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" - "-w" "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.weights" - "-p" "2" "-m" "0") - - add_test(NAME Alpha_complex_utilities_weighted_periodic_alpha_complex_3d COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" - "-w" "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.weights" - "-c" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" - "-p" "2" "-m" "0" "-e") - - install(TARGETS alpha_complex_3d_persistence DESTINATION bin) - - endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) - -endif(CGAL_FOUND) +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) + add_executable (alpha_complex_persistence alpha_complex_persistence.cpp) + target_link_libraries(alpha_complex_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + + if (TBB_FOUND) + target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES}) + endif(TBB_FOUND) + add_test(NAME Alpha_complex_utilities_alpha_complex_persistence COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45") + + install(TARGETS alpha_complex_persistence DESTINATION bin) + +endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) + +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) + add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp) + target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES}) + endif(TBB_FOUND) + + add_test(NAME Alpha_complex_utilities_alpha_complex_3d COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" + "-p" "2" "-m" "0.45" "-o" "alpha.pers") + + add_test(NAME Alpha_complex_utilities_exact_alpha_complex_3d COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" + "-p" "2" "-m" "0.45" "-o" "exact.pers" "-e") + + add_test(NAME Alpha_complex_utilities_safe_alpha_complex_3d COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" + "-p" "2" "-m" "0.45" "-o" "safe.pers" "-s") + + if (DIFF_PATH) + add_test(Alpha_complex_utilities_diff_alpha_complex_3d ${DIFF_PATH} + "exact.pers" "alpha.pers") + add_test(Alpha_complex_utilities_diff_alpha_complex_3d ${DIFF_PATH} + "safe.pers" "alpha.pers") + endif() + + add_test(NAME Alpha_complex_utilities_periodic_alpha_complex_3d_persistence COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" + "-c" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" + "-p" "2" "-m" "0") + + add_test(NAME Alpha_complex_utilities_weighted_alpha_complex_3d COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" + "-w" "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.weights" + "-p" "2" "-m" "0") + + add_test(NAME Alpha_complex_utilities_weighted_periodic_alpha_complex_3d COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" + "-w" "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.weights" + "-c" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" + "-p" "2" "-m" "0" "-e") + + install(TARGETS alpha_complex_3d_persistence DESTINATION bin) + +endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) -- cgit v1.2.3 From 9fc5621abbf55da2883a33e53e7d1a18218dc99a Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 16 Nov 2018 14:23:54 +0000 Subject: Doc review : User version bad description for Alpha complex 3d Add a comment for alpha complex 3d example creation for templates Code review : SAFE is now the default version git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@3990 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a283cc630ac78634d6700aefb981d130c9464024 --- src/Alpha_complex/doc/Intro_alpha_complex.h | 6 ++++-- src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp | 1 + src/Alpha_complex/include/gudhi/Alpha_complex_3d.h | 4 ++-- 3 files changed, 7 insertions(+), 4 deletions(-) (limited to 'src/Alpha_complex/example') diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h index 648fb6d6..fddab003 100644 --- a/src/Alpha_complex/doc/Intro_alpha_complex.h +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -168,8 +168,10 @@ namespace alpha_complex { * * \section weighted3dexample 3d specific example * - * A specific module for Alpha complex is available in 3d (cf. Alpha_complex_3d) and allows to construct default, exact, - * weighted, periodic or weighted and periodic versions of alpha complexes + * A specific module for Alpha complex is available in 3d (cf. Alpha_complex_3d) and allows to construct standard, + * weighted, periodic or weighted and periodic versions of alpha complexes. Alpha values computation can be + * Gudhi::alpha_complex::complexity::FAST, Gudhi::alpha_complex::complexity::SAFE (default value) or + * Gudhi::alpha_complex::complexity::EXACT. * * This example builds the CGAL 3d weighted alpha shapes from a small molecule, and initializes the alpha complex with * it. This example is taken from CGAL 3d diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp index 68f72f0a..3a69623f 100644 --- a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp +++ b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp @@ -7,6 +7,7 @@ #include #include // for numeric limits +// Complexity = EXACT, weighted = true, periodic = false using Weighted_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; using Point = Weighted_alpha_complex_3d::Point_3; diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index 00a47d5c..b441a5b2 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -146,7 +146,7 @@ struct Value_from_iterator { * Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. * * \tparam Complexity shall be `Gudhi::alpha_complex::complexity`. Default value is - * `Gudhi::alpha_complex::complexity::FAST`. + * `Gudhi::alpha_complex::complexity::SAFE`. * * \tparam Weighted Boolean used to set/unset the weighted version of Alpha_complex_3d. Default value is false. * @@ -169,7 +169,7 @@ struct Value_from_iterator { * 3d Delaunay complex. * */ -template +template class Alpha_complex_3d { // Epick = Exact_predicates_inexact_constructions_kernel // Epeck = Exact_predicates_exact_constructions_kernel -- cgit v1.2.3 From 5bf47de6d86a0ea718937ca1dc950bfefad4f211 Mon Sep 17 00:00:00 2001 From: glisse Date: Sat, 17 Nov 2018 16:55:05 +0000 Subject: Simplify example. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/AC-glisse@3999 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: ec94f4c900994fea36d76663a352bf9a5cf232c9 --- .../example/Alpha_complex_from_points.cpp | 20 ++------------------ 1 file changed, 2 insertions(+), 18 deletions(-) (limited to 'src/Alpha_complex/example') diff --git a/src/Alpha_complex/example/Alpha_complex_from_points.cpp b/src/Alpha_complex/example/Alpha_complex_from_points.cpp index c19f7cc8..981aa470 100644 --- a/src/Alpha_complex/example/Alpha_complex_from_points.cpp +++ b/src/Alpha_complex/example/Alpha_complex_from_points.cpp @@ -5,29 +5,13 @@ #include #include -#include #include -#include // for numeric limits using Kernel = CGAL::Epick_d< CGAL::Dimension_tag<2> >; using Point = Kernel::Point_d; using Vector_of_points = std::vector; -void usage(int nbArgs, char * const progName) { - std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; - std::cerr << "Usage: " << progName << " [alpha_square_max_value]\n"; - std::cerr << " i.e.: " << progName << " 60.0\n"; - exit(-1); // ----- >> -} - -int main(int argc, char **argv) { - if ((argc != 1) && (argc != 2)) usage(argc, (argv[0] - 1)); - - // Delaunay complex if alpha_square_max_value is not given by the user. - double alpha_square_max_value {std::numeric_limits::infinity()}; - if (argc == 2) - alpha_square_max_value = atof(argv[1]); - +int main() { // ---------------------------------------------------------------------------- // Init of a list of points // ---------------------------------------------------------------------------- @@ -46,7 +30,7 @@ int main(int argc, char **argv) { Gudhi::alpha_complex::Alpha_complex alpha_complex_from_points(points); Gudhi::Simplex_tree<> simplex; - if (alpha_complex_from_points.create_complex(simplex, alpha_square_max_value)) { + if (alpha_complex_from_points.create_complex(simplex)) { // ---------------------------------------------------------------------------- // Display information about the alpha complex // ---------------------------------------------------------------------------- -- cgit v1.2.3 From eef89bb492169faeb57dfdc65222b6a0483cb7c8 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 21 Nov 2018 08:49:55 +0000 Subject: Code review : Use # error instead of static_assert(false, ...) for CGAL version detection Doc review : Better document CGAL types (FT, Weighted_point_3, Point_3, ...) Weighted alpha complex 3d example simplification git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@4009 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 187d7a08468c96192b3cb82c93a2df5b425290f9 --- .../benchmark/Alpha_complex_3d_benchmark.cpp | 4 +- .../Weighted_alpha_complex_3d_from_points.cpp | 12 +- src/Alpha_complex/include/gudhi/Alpha_complex_3d.h | 129 ++++++++++++++------- .../test/Alpha_complex_3d_unit_test.cpp | 2 +- src/common/doc/main_page.h | 7 +- 5 files changed, 94 insertions(+), 60 deletions(-) (limited to 'src/Alpha_complex/example') diff --git a/src/Alpha_complex/benchmark/Alpha_complex_3d_benchmark.cpp b/src/Alpha_complex/benchmark/Alpha_complex_3d_benchmark.cpp index 96a4baf3..005a712a 100644 --- a/src/Alpha_complex/benchmark/Alpha_complex_3d_benchmark.cpp +++ b/src/Alpha_complex/benchmark/Alpha_complex_3d_benchmark.cpp @@ -116,7 +116,7 @@ void benchmark_weighted_points_on_torus_3D(const std::string& msg) { std::vector points_on_torus = Gudhi::generate_points_on_torus_3D(nb_points, 1.0, 0.5); using Point = typename Weighted_alpha_complex_3d::Point_3; - using Weighted_point = typename Weighted_alpha_complex_3d::Triangulation_3::Weighted_point; + using Weighted_point = typename Weighted_alpha_complex_3d::Weighted_point_3; std::vector points; @@ -207,7 +207,7 @@ void benchmark_weighted_periodic_points(const std::string& msg) { << std::endl; using Point = typename Weighted_periodic_alpha_complex_3d::Point_3; - using Weighted_point = typename Weighted_periodic_alpha_complex_3d::Triangulation_3::Weighted_point; + using Weighted_point = typename Weighted_periodic_alpha_complex_3d::Weighted_point_3; std::vector points; for (double i = 0; i < nb_points; i++) { diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp index 3a69623f..734b4f37 100644 --- a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp +++ b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp @@ -11,21 +11,13 @@ using Weighted_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; using Point = Weighted_alpha_complex_3d::Point_3; -using Weighted_point = Weighted_alpha_complex_3d::Triangulation_3::Weighted_point; -using Vector_of_weighted_points = std::vector; -using Vector_of_weights = std::vector; +using Weighted_point = Weighted_alpha_complex_3d::Weighted_point_3; int main(int argc, char **argv) { - if (argc != 1) { - std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; - std::cerr << "Usage: " << (argv[0] - 1) << " \n"; - exit(-1); // ----- >> - } - // ---------------------------------------------------------------------------- // Init of a list of points and weights from a small molecule // ---------------------------------------------------------------------------- - Vector_of_weighted_points weighted_points; + std::vector weighted_points; weighted_points.push_back(Weighted_point(Point(1, -1, -1), 4.)); weighted_points.push_back(Weighted_point(Point(-1, 1, -1), 4.)); weighted_points.push_back(Weighted_point(Point(-1, -1, 1), 4.)); diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index ca3c5fc3..c33b9cf8 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -58,7 +58,7 @@ #if CGAL_VERSION_NR < 1041101000 // Make compilation fail - required for external projects - https://gitlab.inria.fr/GUDHI/gudhi-devel/issues/10 -static_assert(false, "Alpha_complex_3d is only available for CGAL >= 4.11"); +# error Alpha_complex_3d is only available for CGAL >= 4.11 #endif namespace Gudhi { @@ -153,7 +153,7 @@ template ::Kernel; - using Exact_tag = typename std::conditional<(Complexity == complexity::FAST), CGAL::Tag_false, CGAL::Tag_true>::type; + using Exact_alpha_comparison_tag = typename std::conditional<(Complexity == complexity::FAST), CGAL::Tag_false, CGAL::Tag_true>::type; using TdsVb = typename std::conditional, CGAL::Triangulation_ds_vertex_base_3<>>::type; @@ -196,7 +196,7 @@ class Alpha_complex_3d { using Tvb = typename std::conditional, CGAL::Triangulation_vertex_base_3>::type; - using Vb = CGAL::Alpha_shape_vertex_base_3; + using Vb = CGAL::Alpha_shape_vertex_base_3; using TdsCb = typename std::conditional, CGAL::Triangulation_ds_cell_base_3<>>::type; @@ -204,43 +204,84 @@ class Alpha_complex_3d { using Tcb = typename std::conditional, CGAL::Triangulation_cell_base_3>::type; - using Cb = CGAL::Alpha_shape_cell_base_3; + using Cb = CGAL::Alpha_shape_cell_base_3; using Tds = CGAL::Triangulation_data_structure_3; // The other way to do a conditional type. Here there 4 possibilities, cannot use std::conditional template - struct Triangulation {}; + struct Triangulation_3 {}; template - struct Triangulation { - using Triangulation_3 = CGAL::Delaunay_triangulation_3; + struct Triangulation_3 { + using Dt = CGAL::Delaunay_triangulation_3; + using Weighted_point_3 = void; }; template - struct Triangulation { - using Triangulation_3 = CGAL::Regular_triangulation_3; + struct Triangulation_3 { + using Dt = CGAL::Regular_triangulation_3; + using Weighted_point_3 = typename Dt::Weighted_point; }; template - struct Triangulation { - using Triangulation_3 = CGAL::Periodic_3_Delaunay_triangulation_3; + struct Triangulation_3 { + using Dt = CGAL::Periodic_3_Delaunay_triangulation_3; + using Weighted_point_3 = void; }; template - struct Triangulation { - using Triangulation_3 = CGAL::Periodic_3_regular_triangulation_3; + struct Triangulation_3 { + using Dt = CGAL::Periodic_3_regular_triangulation_3; + using Weighted_point_3 = typename Dt::Weighted_point; }; - public: - using Triangulation_3 = typename Triangulation::Triangulation_3; - - using Alpha_shape_3 = CGAL::Alpha_shape_3; + /** \brief Is either Delaunay_triangulation_3 (Weighted = false and Periodic = false), + * Regular_triangulation_3 (Weighted = true and Periodic = false), + * Periodic_3_Delaunay_triangulation_3 (Weighted = false and Periodic = true) + * or Periodic_3_regular_triangulation_3 (Weighted = true and Periodic = true). + * + * This type is required by `Gudhi::alpha_complex::Alpha_complex_3d::Alpha_shape_3`. + * */ + using Dt = typename Triangulation_3::Dt; +public: + /** \brief The CGAL 3D Alpha + * Shapes type. + * + * The `Gudhi::alpha_complex::Alpha_complex_3d` is a wrapper on top of this class to ease the standard, weighted + * and/or periodic build of the Alpha complex 3d.*/ + using Alpha_shape_3 = CGAL::Alpha_shape_3; + + /** \brief The alpha values type. + * Must be compatible with double. */ + using FT = typename Alpha_shape_3::FT; + + /** \brief Gives public access to the Point_3 type. Here is a Point_3 constructor example: +\code{.cpp} +using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; + +// x0 = 1., y0 = -1.1, z0 = -1.. +Alpha_complex_3d::Point_3 p0(1., -1.1, -1.); +\endcode + * */ using Point_3 = typename Kernel::Point_3; - private: - using Alpha_value_type = typename Alpha_shape_3::FT; + /** \brief Gives public access to the Weighted_point_3 type. A Weighted point can be constructed as follows: +\code{.cpp} +using Weighted_alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d; + +// x0 = 1., y0 = -1.1, z0 = -1., weight = 4. +Weighted_alpha_complex_3d::Weighted_point_3 wp0(Weighted_alpha_complex_3d::Point_3(1., -1.1, -1.), 4.); +\endcode + * + * Note: This type is defined to void if Alpha complex is not weighted. + * + * */ + using Weighted_point_3 = typename Triangulation_3::Weighted_point_3; + +private: using Dispatch = - CGAL::Dispatch_output_iterator, + CGAL::Dispatch_output_iterator, CGAL::cpp11::tuple>, - std::back_insert_iterator>>>; + std::back_insert_iterator>>>; using Cell_handle = typename Alpha_shape_3::Cell_handle; using Facet = typename Alpha_shape_3::Facet; @@ -252,12 +293,12 @@ class Alpha_complex_3d { /** \brief Alpha_complex constructor from a list of points. * * @param[in] points Range of points to triangulate. Points must be in `Alpha_complex_3d::Point_3` or - * `Alpha_complex_3d::Triangulation_3::Weighted_point`. + * `Alpha_complex_3d::Weighted_point_3`. * * @pre Available if Alpha_complex_3d is not Periodic. * * The type InputPointRange must be a range for which std::begin and std::end return input iterators on a - * `Alpha_complex_3d::Point_3` or a `Alpha_complex_3d::Triangulation_3::Weighted_point`. + * `Alpha_complex_3d::Point_3` or a `Alpha_complex_3d::Weighted_point_3`. */ template Alpha_complex_3d(const InputPointRange& points) { @@ -271,15 +312,15 @@ class Alpha_complex_3d { * * @exception std::invalid_argument In debug mode, if points and weights do not have the same size. * - * @param[in] points Range of points to triangulate. Points must be in `Alpha_complex_3d::Point_3` - * @param[in] weights Range of weights on points. Weights shall be in `Alpha_complex_3d::Alpha_shape_3::FT` + * @param[in] points Range of points to triangulate. Points must be in `Alpha_complex_3d::Point_3`. + * @param[in] weights Range of weights on points. Weights shall be in double. * * @pre Available if Alpha_complex_3d is Weighted and not Periodic. * * The type InputPointRange must be a range for which std::begin and * std::end return input iterators on a `Alpha_complex_3d::Point_3`. * The type WeightRange must be a range for which std::begin and - * std::end return an input iterator on a `Alpha_complex_3d::Alpha_shape_3::FT`. + * std::end return an input iterator on a double. */ template Alpha_complex_3d(const InputPointRange& points, WeightRange weights) { @@ -288,7 +329,6 @@ class Alpha_complex_3d { GUDHI_CHECK((weights.size() == points.size()), std::invalid_argument("Points number in range different from weights range number")); - using Weighted_point_3 = typename Triangulation_3::Weighted_point; std::vector weighted_points_3; std::size_t index = 0; @@ -307,7 +347,7 @@ class Alpha_complex_3d { * @exception std::invalid_argument In debug mode, if the size of the cuboid in every directions is not the same. * * @param[in] points Range of points to triangulate. Points must be in `Alpha_complex_3d::Point_3` or - * `Alpha_complex_3d::Triangulation_3::Weighted_point`. + * `Alpha_complex_3d::Weighted_point_3`. * @param[in] x_min Iso-oriented cuboid x_min. * @param[in] y_min Iso-oriented cuboid y_min. * @param[in] z_min Iso-oriented cuboid z_min. @@ -318,14 +358,14 @@ class Alpha_complex_3d { * @pre Available if Alpha_complex_3d is Periodic. * * The type InputPointRange must be a range for which std::begin and std::end return input iterators on a - * `Alpha_complex_3d::Point_3` or a `Alpha_complex_3d::Triangulation_3::Weighted_point`. + * `Alpha_complex_3d::Point_3` or a `Alpha_complex_3d::Weighted_point_3`. * * @note In weighted version, please check weights are greater than zero, and lower than 1/64*cuboid length * squared. */ template - Alpha_complex_3d(const InputPointRange& points, Alpha_value_type x_min, Alpha_value_type y_min, - Alpha_value_type z_min, Alpha_value_type x_max, Alpha_value_type y_max, Alpha_value_type z_max) { + Alpha_complex_3d(const InputPointRange& points, FT x_min, FT y_min, + FT z_min, FT x_max, FT y_max, FT z_max) { static_assert(Periodic, "This constructor is not available for non-periodic versions of Alpha_complex_3d"); // Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it. GUDHI_CHECK( @@ -333,7 +373,7 @@ class Alpha_complex_3d { std::invalid_argument("The size of the cuboid in every directions is not the same.")); // Define the periodic cube - Triangulation_3 pdt(typename Kernel::Iso_cuboid_3(x_min, y_min, z_min, x_max, y_max, z_max)); + Dt pdt(typename Kernel::Iso_cuboid_3(x_min, y_min, z_min, x_max, y_max, z_max)); // Heuristic for inserting large point sets (if pts is reasonably large) pdt.insert(std::begin(points), std::end(points), true); // As pdt won't be modified anymore switch to 1-sheeted cover if possible @@ -354,8 +394,8 @@ class Alpha_complex_3d { * @exception std::invalid_argument In debug mode, if a weight is negative, zero, or greater than 1/64*cuboid length * squared. * - * @param[in] points Range of points to triangulate. Points must be in `Alpha_complex_3d::Point_3` - * @param[in] weights Range of weights on points. Weights shall be in `Alpha_complex_3d::Alpha_shape_3::FT` + * @param[in] points Range of points to triangulate. Points must be in `Alpha_complex_3d::Point_3`. + * @param[in] weights Range of weights on points. Weights shall be in double. * @param[in] x_min Iso-oriented cuboid x_min. * @param[in] y_min Iso-oriented cuboid y_min. * @param[in] z_min Iso-oriented cuboid z_min. @@ -368,12 +408,12 @@ class Alpha_complex_3d { * The type InputPointRange must be a range for which std::begin and * std::end return input iterators on a `Alpha_complex_3d::Point_3`. * The type WeightRange must be a range for which std::begin and - * std::end return an input iterator on a `Alpha_complex_3d::Alpha_shape_3::FT`. - * The type of x_min, y_min, z_min, x_max, y_max and z_max is `Alpha_complex_3d::Alpha_shape_3::FT`. + * std::end return an input iterator on a double. + * The type of x_min, y_min, z_min, x_max, y_max and z_max must be a double. */ template - Alpha_complex_3d(const InputPointRange& points, WeightRange weights, Alpha_value_type x_min, Alpha_value_type y_min, - Alpha_value_type z_min, Alpha_value_type x_max, Alpha_value_type y_max, Alpha_value_type z_max) { + Alpha_complex_3d(const InputPointRange& points, WeightRange weights, FT x_min, FT y_min, + FT z_min, FT x_max, FT y_max, FT z_max) { static_assert(Weighted, "This constructor is not available for non-weighted versions of Alpha_complex_3d"); static_assert(Periodic, "This constructor is not available for non-periodic versions of Alpha_complex_3d"); GUDHI_CHECK((weights.size() == points.size()), @@ -383,7 +423,6 @@ class Alpha_complex_3d { (x_max - x_min == y_max - y_min) && (x_max - x_min == z_max - z_min) && (z_max - z_min == y_max - y_min), std::invalid_argument("The size of the cuboid in every directions is not the same.")); - using Weighted_point_3 = typename Triangulation_3::Weighted_point; std::vector weighted_points_3; std::size_t index = 0; @@ -391,7 +430,7 @@ class Alpha_complex_3d { #ifdef GUDHI_DEBUG // Defined in GUDHI_DEBUG to avoid unused variable warning for GUDHI_CHECK - Alpha_value_type maximal_possible_weight = 0.015625 * (x_max - x_min) * (x_max - x_min); + FT maximal_possible_weight = 0.015625 * (x_max - x_min) * (x_max - x_min); #endif while ((index < weights.size()) && (index < points.size())) { @@ -404,7 +443,7 @@ class Alpha_complex_3d { } // Define the periodic cube - Triangulation_3 pdt(typename Kernel::Iso_cuboid_3(x_min, y_min, z_min, x_max, y_max, z_max)); + Dt pdt(typename Kernel::Iso_cuboid_3(x_min, y_min, z_min, x_max, y_max, z_max)); // Heuristic for inserting large point sets (if pts is reasonably large) pdt.insert(std::begin(weighted_points_3), std::end(weighted_points_3), true); // As pdt won't be modified anymore switch to 1-sheeted cover if possible @@ -453,9 +492,9 @@ class Alpha_complex_3d { std::size_t count_cells = 0; #endif // DEBUG_TRACES std::vector objects; - std::vector alpha_values; + std::vector alpha_values; - Dispatch dispatcher = CGAL::dispatch_output(std::back_inserter(objects), + Dispatch dispatcher = CGAL::dispatch_output(std::back_inserter(objects), std::back_inserter(alpha_values)); alpha_shape_3_ptr_->filtration_with_alpha_values(dispatcher); @@ -464,7 +503,7 @@ class Alpha_complex_3d { #endif // DEBUG_TRACES Alpha_shape_simplex_tree_map map_cgal_simplex_tree; - using Alpha_value_iterator = typename std::vector::const_iterator; + using Alpha_value_iterator = typename std::vector::const_iterator; Alpha_value_iterator alpha_value_iterator = alpha_values.begin(); for (auto object_iterator : objects) { Vertex_list vertex_list; diff --git a/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp index b818fb2e..e4a45791 100644 --- a/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp +++ b/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp @@ -228,7 +228,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_weighted, Weighted_alpha_complex_3d, alpha_complex_p_a_w.create_complex(stree); std::cout << "Weighted alpha complex 3d from weighted points" << std::endl; - using Weighted_point_3 = typename Weighted_alpha_complex_3d::Triangulation_3::Weighted_point; + using Weighted_point_3 = typename Weighted_alpha_complex_3d::Weighted_point_3; std::vector weighted_points; diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index 35b84d2e..b33a95a1 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -29,7 +29,9 @@ Author: Vincent Rouvreau
Introduced in: GUDHI 1.3.0
Copyright: GPL v3
- Requires: \ref cgal ≥ 4.11.0 and \ref eigen3 + Requires: \ref eigen3 and
+ \ref cgal ≥ 4.7.0 for Alpha_complex
+ \ref cgal ≥ 4.11.0 for Alpha_complex_3d Alpha_complex is a simplicial complex constructed from the finite cells of a Delaunay Triangulation.
@@ -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.
- User manual: \ref alpha_complex - Reference manual: Gudhi::alpha_complex::Alpha_complex + User manual: \ref alpha_complex - Reference manual: Gudhi::alpha_complex::Alpha_complex and + Gudhi::alpha_complex::Alpha_complex_3d -- cgit v1.2.3 From 88a83fe20ce9100f2292c3945d26e4696fd2e7d2 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 23 Nov 2018 09:06:04 +0000 Subject: // We could use Epick + CGAL::Tag_true for not weighted nor periodic, but during benchmark, we found a bug // https://github.com/CGAL/cgal/issues/3460 // This is the reason we only use Epick + CGAL::Tag_false, or Epeck // // FAST SAFE EXACT // Epick + CGAL::Tag_false Epeck Epeck git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@4012 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 88e844333b5bae8fcfd1104e493cdada1e4a4a3b --- .../example/Alpha_complex_3d_from_points.cpp | 2 +- .../Weighted_alpha_complex_3d_from_points.cpp | 4 +- src/Alpha_complex/include/gudhi/Alpha_complex_3d.h | 22 ++++---- .../test/Alpha_complex_3d_unit_test.cpp | 61 +++++++++++----------- 4 files changed, 43 insertions(+), 46 deletions(-) (limited to 'src/Alpha_complex/example') diff --git a/src/Alpha_complex/example/Alpha_complex_3d_from_points.cpp b/src/Alpha_complex/example/Alpha_complex_3d_from_points.cpp index 3acebd2e..0e359a27 100644 --- a/src/Alpha_complex/example/Alpha_complex_3d_from_points.cpp +++ b/src/Alpha_complex/example/Alpha_complex_3d_from_points.cpp @@ -7,7 +7,7 @@ #include #include // for numeric limits -using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; using Point = Alpha_complex_3d::Point_3; using Vector_of_points = std::vector; diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp index 734b4f37..ac11b68c 100644 --- a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp +++ b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp @@ -7,9 +7,9 @@ #include #include // for numeric limits -// Complexity = EXACT, weighted = true, periodic = false +// Complexity = FAST, weighted = true, periodic = false using Weighted_alpha_complex_3d = - Gudhi::alpha_complex::Alpha_complex_3d; + Gudhi::alpha_complex::Alpha_complex_3d; using Point = Weighted_alpha_complex_3d::Point_3; using Weighted_point = Weighted_alpha_complex_3d::Weighted_point_3; diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index c33b9cf8..b5d4201d 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -155,16 +155,16 @@ class Alpha_complex_3d { // Epeck = Exact_predicates_exact_constructions_kernel // Exact_alpha_comparison_tag = exact version of CGAL Alpha_shape_3 and of its objects (Alpha_shape_vertex_base_3 and // Alpha_shape_cell_base_3). Not available if weighted or periodic. - // Can be CGAL::Tag_false or CGAL::Tag_true + // Can be CGAL::Tag_false or CGAL::Tag_true. Default is False. // cf. https://doc.cgal.org/latest/Alpha_shapes_3/classCGAL_1_1Alpha__shape__3.html // + // We could use Epick + CGAL::Tag_true for not weighted nor periodic, but during benchmark, we found a bug + // https://github.com/CGAL/cgal/issues/3460 + // This is the reason we only use Epick + CGAL::Tag_false, or Epeck // - // FAST SAFE EXACT - // not weighted and Epick + CGAL::Tag_false Epick + CGAL::Tag_true Epick + CGAL::Tag_true - // not periodic - // - // otherwise Epick + CGAL::Tag_false Epeck Epeck - using Predicates = typename std::conditional<((!Weighted && !Periodic) || (Complexity == complexity::FAST)), + // FAST SAFE EXACT + // Epick + CGAL::Tag_false Epeck Epeck + using Predicates = typename std::conditional<(Complexity == complexity::FAST), CGAL::Exact_predicates_inexact_constructions_kernel, CGAL::Exact_predicates_exact_constructions_kernel>::type; @@ -188,15 +188,13 @@ class Alpha_complex_3d { using Kernel = typename Kernel_3::Kernel; - using Exact_alpha_comparison_tag = typename std::conditional<(Complexity == complexity::FAST), CGAL::Tag_false, CGAL::Tag_true>::type; - using TdsVb = typename std::conditional, CGAL::Triangulation_ds_vertex_base_3<>>::type; using Tvb = typename std::conditional, CGAL::Triangulation_vertex_base_3>::type; - using Vb = CGAL::Alpha_shape_vertex_base_3; + using Vb = CGAL::Alpha_shape_vertex_base_3; using TdsCb = typename std::conditional, CGAL::Triangulation_ds_cell_base_3<>>::type; @@ -204,7 +202,7 @@ class Alpha_complex_3d { using Tcb = typename std::conditional, CGAL::Triangulation_cell_base_3>::type; - using Cb = CGAL::Alpha_shape_cell_base_3; + using Cb = CGAL::Alpha_shape_cell_base_3; using Tds = CGAL::Triangulation_data_structure_3; // The other way to do a conditional type. Here there 4 possibilities, cannot use std::conditional @@ -247,7 +245,7 @@ public: * * The `Gudhi::alpha_complex::Alpha_complex_3d` is a wrapper on top of this class to ease the standard, weighted * and/or periodic build of the Alpha complex 3d.*/ - using Alpha_shape_3 = CGAL::Alpha_shape_3; + using Alpha_shape_3 = CGAL::Alpha_shape_3
; /** \brief The alpha values type. * Must be compatible with double. */ diff --git a/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp index c408dc75..ec905d5b 100644 --- a/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp +++ b/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp @@ -48,20 +48,27 @@ using Safe_alpha_complex_3d = using Exact_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d; +template +std::vector get_points() { + std::vector points; + points.push_back(Point(0.0, 0.0, 0.0)); + points.push_back(Point(0.0, 0.0, 0.2)); + points.push_back(Point(0.2, 0.0, 0.2)); + points.push_back(Point(0.6, 0.6, 0.0)); + points.push_back(Point(0.8, 0.8, 0.2)); + points.push_back(Point(0.2, 0.8, 0.6)); + + return points; +} + + BOOST_AUTO_TEST_CASE(Alpha_complex_3d_from_points) { // ----------------- // Fast version // ----------------- std::cout << "Fast alpha complex 3d" << std::endl; - std::vector points; - points.push_back(Fast_alpha_complex_3d::Point_3(0.0, 0.0, 0.0)); - points.push_back(Fast_alpha_complex_3d::Point_3(0.0, 0.0, 0.2)); - points.push_back(Fast_alpha_complex_3d::Point_3(0.2, 0.0, 0.2)); - points.push_back(Fast_alpha_complex_3d::Point_3(0.6, 0.6, 0.0)); - points.push_back(Fast_alpha_complex_3d::Point_3(0.8, 0.8, 0.2)); - points.push_back(Fast_alpha_complex_3d::Point_3(0.2, 0.8, 0.6)); - Fast_alpha_complex_3d alpha_complex(points); + Fast_alpha_complex_3d alpha_complex(get_points()); Gudhi::Simplex_tree<> stree; alpha_complex.create_complex(stree); @@ -71,7 +78,7 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_3d_from_points) { // ----------------- std::cout << "Exact alpha complex 3d" << std::endl; - Exact_alpha_complex_3d exact_alpha_complex(points); + Exact_alpha_complex_3d exact_alpha_complex(get_points()); Gudhi::Simplex_tree<> exact_stree; exact_alpha_complex.create_complex(exact_stree); @@ -79,13 +86,13 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_3d_from_points) { // --------------------- // Compare both versions // --------------------- - std::cout << "Exact Alpha complex 3d is of dimension " << exact_stree.dimension() << " - Non exact is " + std::cout << "Exact Alpha complex 3d is of dimension " << exact_stree.dimension() << " - Fast is " << stree.dimension() << std::endl; BOOST_CHECK(exact_stree.dimension() == stree.dimension()); - std::cout << "Exact Alpha complex 3d num_simplices " << exact_stree.num_simplices() << " - Non exact is " + std::cout << "Exact Alpha complex 3d num_simplices " << exact_stree.num_simplices() << " - Fast is " << stree.num_simplices() << std::endl; BOOST_CHECK(exact_stree.num_simplices() == stree.num_simplices()); - std::cout << "Exact Alpha complex 3d num_vertices " << exact_stree.num_vertices() << " - Non exact is " + std::cout << "Exact Alpha complex 3d num_vertices " << exact_stree.num_vertices() << " - Fast is " << stree.num_vertices() << std::endl; BOOST_CHECK(exact_stree.num_vertices() == stree.num_vertices()); @@ -93,19 +100,18 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_3d_from_points) { while (sh != stree.filtration_simplex_range().end()) { std::vector simplex; std::vector exact_simplex; - std::cout << "Non-exact ( "; + std::cout << "Fast ( "; for (auto vertex : stree.simplex_vertex_range(*sh)) { simplex.push_back(vertex); std::cout << vertex << " "; } - std::cout << ") -> " - << "[" << stree.filtration(*sh) << "] "; - std::cout << std::endl; + std::cout << ") -> [" << stree.filtration(*sh) << "] "; // Find it in the exact structure auto sh_exact = exact_stree.find(simplex); BOOST_CHECK(sh_exact != exact_stree.null_simplex()); + std::cout << " versus [" << exact_stree.filtration(sh_exact) << "] " << std::endl; // Exact and non-exact version is not exactly the same due to float comparison GUDHI_TEST_FLOAT_EQUALITY_CHECK(exact_stree.filtration(sh_exact), stree.filtration(*sh)); @@ -116,7 +122,7 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_3d_from_points) { // ----------------- std::cout << "Safe alpha complex 3d" << std::endl; - Safe_alpha_complex_3d safe_alpha_complex(points); + Safe_alpha_complex_3d safe_alpha_complex(get_points()); Gudhi::Simplex_tree<> safe_stree; safe_alpha_complex.create_complex(safe_stree); @@ -124,13 +130,13 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_3d_from_points) { // --------------------- // Compare both versions // --------------------- - std::cout << "Exact Alpha complex 3d is of dimension " << safe_stree.dimension() << " - Non exact is " + std::cout << "Safe Alpha complex 3d is of dimension " << safe_stree.dimension() << " - Fast is " << stree.dimension() << std::endl; BOOST_CHECK(safe_stree.dimension() == stree.dimension()); - std::cout << "Exact Alpha complex 3d num_simplices " << safe_stree.num_simplices() << " - Non exact is " + std::cout << "Safe Alpha complex 3d num_simplices " << safe_stree.num_simplices() << " - Fast is " << stree.num_simplices() << std::endl; BOOST_CHECK(safe_stree.num_simplices() == stree.num_simplices()); - std::cout << "Exact Alpha complex 3d num_vertices " << safe_stree.num_vertices() << " - Non exact is " + std::cout << "Safe Alpha complex 3d num_vertices " << safe_stree.num_vertices() << " - Fast is " << stree.num_vertices() << std::endl; BOOST_CHECK(safe_stree.num_vertices() == stree.num_vertices()); @@ -138,27 +144,20 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_3d_from_points) { while (safe_sh != stree.filtration_simplex_range().end()) { std::vector simplex; std::vector exact_simplex; -#ifdef DEBUG_TRACES - std::cout << "Non-exact ( "; -#endif + std::cout << "Fast ( "; for (auto vertex : stree.simplex_vertex_range(*safe_sh)) { simplex.push_back(vertex); -#ifdef DEBUG_TRACES std::cout << vertex << " "; -#endif } -#ifdef DEBUG_TRACES - std::cout << ") -> " - << "[" << stree.filtration(*safe_sh) << "] "; - std::cout << std::endl; -#endif + std::cout << ") -> [" << stree.filtration(*safe_sh) << "] "; // Find it in the exact structure auto sh_exact = safe_stree.find(simplex); BOOST_CHECK(sh_exact != safe_stree.null_simplex()); + std::cout << " versus [" << safe_stree.filtration(sh_exact) << "] " << std::endl; // Exact and non-exact version is not exactly the same due to float comparison - GUDHI_TEST_FLOAT_EQUALITY_CHECK(safe_stree.filtration(sh_exact), stree.filtration(*safe_sh)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(safe_stree.filtration(sh_exact), stree.filtration(*safe_sh), 1e-15); ++safe_sh; } -- cgit v1.2.3