From fb7c3e76da15aca382ed7a6795d1a6fb3c1716c2 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 10 Oct 2017 12:52:35 +0000 Subject: Fix CGAL 4.11 bug and remove old_interface file. Better done with #if git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/weighted_alpha_complex_fix@2774 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 9a905b04cfa2718f9d5abc80e14ab1ee26d16279 --- src/Persistent_cohomology/example/CMakeLists.txt | 8 +- .../weighted_alpha_complex_3d_persistence.cpp | 25 +- ...a_complex_3d_persistence_old_cgal_interface.cpp | 262 --------------------- 3 files changed, 25 insertions(+), 270 deletions(-) delete mode 100644 src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence_old_cgal_interface.cpp (limited to 'src/Persistent_cohomology') diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index be23de35..e82ef04c 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -127,15 +127,9 @@ if(CGAL_FOUND) install(TARGETS weighted_periodic_alpha_complex_3d_persistence DESTINATION bin) - # On CGAL 4.11, the weighted alpha shape 3 interface was changed - the new interface - add_executable(weighted_alpha_complex_3d_persistence weighted_alpha_complex_3d_persistence.cpp) - else(NOT CGAL_VERSION VERSION_LESS 4.11.0) - # On CGAL 4.11, the weighted alpha shape 3 interface was changed - the old interface - add_executable(weighted_alpha_complex_3d_persistence weighted_alpha_complex_3d_persistence_old_cgal_interface.cpp) endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) - # cf. if (NOT CGAL_VERSION VERSION_LESS 4.11.0) and else(NOT CGAL_VERSION VERSION_LESS 4.11.0) - # same target name on purpose + add_executable(weighted_alpha_complex_3d_persistence weighted_alpha_complex_3d_persistence.cpp) target_link_libraries(weighted_alpha_complex_3d_persistence ${CGAL_LIBRARY}) if (TBB_FOUND) target_link_libraries(weighted_alpha_complex_3d_persistence ${TBB_LIBRARIES}) diff --git a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp index 92fed4c1..85b0ab34 100644 --- a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp @@ -26,11 +26,17 @@ #include #include +#include #include #include #include #include +// For CGAL < 4.11 +#if CGAL_VERSION_NR < 1041100000 +#include +#endif // CGAL_VERSION_NR < 1041100000 + #include #include #include @@ -44,17 +50,34 @@ #include "alpha_complex_3d_helper.h" using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; + +// For CGAL < 4.11 +#if CGAL_VERSION_NR < 1041100000 +using Gt = CGAL::Regular_triangulation_euclidean_traits_3; +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::Regular_triangulation_3; + +// From file type definition +using Point_3 = Gt::Bare_point; +using Weighted_point_3 = Gt::Weighted_point; + +// For CGAL >= 4.11 +#else // CGAL_VERSION_NR < 1041100000 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; -using Alpha_shape_3 = CGAL::Alpha_shape_3; // From file type definition using Point_3 = Triangulation_3::Bare_point; using Weighted_point_3 = Triangulation_3::Weighted_point; +#endif // CGAL_VERSION_NR < 1041100000 + +using Alpha_shape_3 = CGAL::Alpha_shape_3; // filtration with alpha values needed type definition using Alpha_value_type = Alpha_shape_3::FT; diff --git a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence_old_cgal_interface.cpp b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence_old_cgal_interface.cpp deleted file mode 100644 index e2c48755..00000000 --- a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence_old_cgal_interface.cpp +++ /dev/null @@ -1,262 +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 "alpha_complex_3d_helper.h" - -// Traits -using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; -using Gt = CGAL::Regular_triangulation_euclidean_traits_3; -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::Regular_triangulation_3; -using Alpha_shape_3 = CGAL::Alpha_shape_3; - -// From file type definition -using Point_3 = Gt::Bare_point; -using Weighted_point_3 = Gt::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::list; - -// 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 Alpha_shape_simplex_tree_pair = std::pair; -using Simplex_tree_vector_vertex = std::vector; -using Persistent_cohomology = - Gudhi::persistent_cohomology::Persistent_cohomology; - -void usage(char* const progName) { - std::cerr << "Usage: " << progName << " path_to_file_graph path_to_weight_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 != 5) { - std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; - usage(argv[0]); - } - - int coeff_field_characteristic = atoi(argv[3]); - Filtration_value min_persistence = strtof(argv[4], 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 triangulation - std::vector lp = off_reader.get_point_cloud(); - - // Read weights information from file - std::ifstream weights_ifstr(argv[2]); - std::vector wp; - if (weights_ifstr.good()) { - 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())) { - 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]); - } - - // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. - Alpha_shape_3 as(wp.begin(), wp.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(); - int dim_max = 0; - Filtration_value filtration_max = 0.0; - 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++; - if (dim_max < 3) { - // Cell is of dim 3 - dim_max = 3; - } - } else if (const Facet* facet = CGAL::object_cast(&object_iterator)) { - vertex_list = from_facet(*facet); - count_facets++; - if (dim_max < 2) { - // Facet is of dim 2 - dim_max = 2; - } - } else if (const Edge_3* edge = CGAL::object_cast(&object_iterator)) { - vertex_list = from_edge(*edge); - count_edges++; - if (dim_max < 1) { - // Edge_3 is of dim 1 - dim_max = 1; - } - } 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_tree; - 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_tree.push_back(vertex); - map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(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_tree.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 - if (filtr > filtration_max) { - filtration_max = filtr; - } - simplex_tree.insert_simplex(the_simplex_tree, filtr); - if (the_alpha_value_iterator != the_alpha_values.end()) - ++the_alpha_value_iterator; - else - std::cout << "This shall not happen" << std::endl; - } - simplex_tree.set_filtration(filtration_max); - simplex_tree.set_dimension(dim_max); - -#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() << " "; - std::cout << " filtration = " << simplex_tree.filtration() << std::endl << std::endl; -#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