From 57eb57ed2092beaceb978e31aebb500450b9599b Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 2 Feb 2016 09:07:16 +0000 Subject: rename alpha_shapes_persistence test with alpha_complex_3d_persistence git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@991 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 455ee94450098bbcc000fb2ab2c4d39a326dea2c --- src/Persistent_cohomology/example/CMakeLists.txt | 39 ++- .../example/alpha_complex_3d_persistence.cpp | 294 +++++++++++++++++++++ .../example/alpha_shapes_persistence.cpp | 294 --------------------- 3 files changed, 313 insertions(+), 314 deletions(-) create mode 100644 src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp delete mode 100644 src/Persistent_cohomology/example/alpha_shapes_persistence.cpp (limited to 'src/Persistent_cohomology') diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index 5fec8ad4..779a9e89 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -40,30 +40,29 @@ if(GMPXX_FOUND AND GMP_FOUND) target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) if(CGAL_FOUND) - add_executable(alpha_shapes_persistence alpha_shapes_persistence.cpp) - target_link_libraries(alpha_shapes_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY}) - add_test(alpha_shapes_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 2 0.5) - #add_test(alpha_shapes_persistence_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100) + include( ${CGAL_USE_FILE} ) + # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten. + # cf. http://doc.cgal.org/latest/Manual/installation.html#title40 + # A workaround is to add "-std=c++11" again. + # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html + # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html + # but it implies to use cmake version 3.1 at least. + if(NOT MSVC) + include(CheckCXXCompilerFlag) + CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11) + if(COMPILER_SUPPORTS_CXX11) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") + endif() + endif() + # - End of workaround + + add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp) + target_link_libraries(alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY}) + add_test(alpha_complex_3d_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_3d_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 2 0.5) if (NOT CGAL_VERSION VERSION_LESS 4.7.0) message(STATUS "CGAL version: ${CGAL_VERSION}.") - include( ${CGAL_USE_FILE} ) - # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten. - # cf. http://doc.cgal.org/latest/Manual/installation.html#title40 - # A workaround is to add "-std=c++11" again. - # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html - # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html - # but it implies to use cmake version 3.1 at least. - if(NOT MSVC) - include(CheckCXXCompilerFlag) - CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11) - if(COMPILER_SUPPORTS_CXX11) - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") - endif() - endif() - # - End of workaround - find_package(Eigen3 3.1.0) if (EIGEN3_FOUND) message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp new file mode 100644 index 00000000..ac208957 --- /dev/null +++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp @@ -0,0 +1,294 @@ +/* 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 Saclay (France) + * + * 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 + +using namespace Gudhi; +using namespace Gudhi::persistent_cohomology; + +// Alpha_shape_3 templates type definitions +typedef CGAL::Exact_predicates_inexact_constructions_kernel Kernel; +typedef CGAL::Alpha_shape_vertex_base_3 Vb; +typedef CGAL::Alpha_shape_cell_base_3 Fb; +typedef CGAL::Triangulation_data_structure_3 Tds; +typedef CGAL::Delaunay_triangulation_3 Triangulation_3; +typedef CGAL::Alpha_shape_3 Alpha_shape_3; + +// From file type definition +typedef Kernel::Point_3 Point_3; + +// filtration with alpha values needed type definition +typedef Alpha_shape_3::FT Alpha_value_type; +typedef CGAL::Object Object; +typedef CGAL::Dispatch_output_iterator< +CGAL::cpp11::tuple, +CGAL::cpp11::tuple >, + std::back_insert_iterator< std::vector > > > Dispatch; +typedef Alpha_shape_3::Cell_handle Cell_handle; +typedef Alpha_shape_3::Facet Facet; +typedef Alpha_shape_3::Edge Edge_3; +typedef std::list Vertex_list; + +// gudhi type definition +typedef Simplex_tree ST; +typedef ST::Vertex_handle Simplex_tree_vertex; +typedef std::map Alpha_shape_simplex_tree_map; +typedef std::pair Alpha_shape_simplex_tree_pair; +typedef std::vector< Simplex_tree_vertex > Simplex_tree_vector_vertex; + +Vertex_list from(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; +} + +Vertex_list from(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; +} + +Vertex_list from(const Edge_3& edg) { + Vertex_list the_list; + for (auto i = 0; i < 4; i++) { + if ((edg.second == i) || (edg.third == i)) { +#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; +} + +Vertex_list from(const Alpha_shape_3::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; +} + +void usage(char * const progName) { + std::cerr << "Usage: " << progName << + " path_to_file_graph 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 != 4) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; + usage(argv[0]); + } + + int coeff_field_characteristic = 0; + int returnedScanValue = sscanf(argv[2], "%d", &coeff_field_characteristic); + if ((returnedScanValue == EOF) || (coeff_field_characteristic <= 0)) { + std::cerr << "Error: " << argv[2] << " is not correct\n"; + usage(argv[0]); + } + + Filtration_value min_persistence = 0.0; + returnedScanValue = sscanf(argv[3], "%lf", &min_persistence); + if ((returnedScanValue == EOF) || (min_persistence < -1.0)) { + std::cerr << "Error: " << argv[3] << " is not correct\n"; + usage(argv[0]); + } + + // Read points from file + std::string filegraph = argv[1]; + std::list lp; + std::ifstream is(filegraph.c_str()); + int n; + is >> n; +#ifdef DEBUG_TRACES + std::cout << "Reading " << n << " points " << std::endl; +#endif // DEBUG_TRACES + Point_3 p; + for (; n > 0; n--) { + is >> p; + lp.push_back(p); + } + + // 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(); + 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); + 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); + 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); + count_edges++; + if (dim_max < 1) { + // Edge_3 is of dim 1 + dim_max = 1; + } + } else if (const Alpha_shape_3::Vertex_handle * vertex = + CGAL::object_cast(&object_iterator)) { + count_vertices++; + vertex_list = from(*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< ST, Field_Zp > pcoh(simplex_tree); + // initializes the coefficient field for homology + pcoh.init_coefficients(coeff_field_characteristic); + + pcoh.compute_persistent_cohomology(min_persistence); + + pcoh.output_diagram(); + + return 0; +} diff --git a/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp b/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp deleted file mode 100644 index ac208957..00000000 --- a/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp +++ /dev/null @@ -1,294 +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 Saclay (France) - * - * 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 - -using namespace Gudhi; -using namespace Gudhi::persistent_cohomology; - -// Alpha_shape_3 templates type definitions -typedef CGAL::Exact_predicates_inexact_constructions_kernel Kernel; -typedef CGAL::Alpha_shape_vertex_base_3 Vb; -typedef CGAL::Alpha_shape_cell_base_3 Fb; -typedef CGAL::Triangulation_data_structure_3 Tds; -typedef CGAL::Delaunay_triangulation_3 Triangulation_3; -typedef CGAL::Alpha_shape_3 Alpha_shape_3; - -// From file type definition -typedef Kernel::Point_3 Point_3; - -// filtration with alpha values needed type definition -typedef Alpha_shape_3::FT Alpha_value_type; -typedef CGAL::Object Object; -typedef CGAL::Dispatch_output_iterator< -CGAL::cpp11::tuple, -CGAL::cpp11::tuple >, - std::back_insert_iterator< std::vector > > > Dispatch; -typedef Alpha_shape_3::Cell_handle Cell_handle; -typedef Alpha_shape_3::Facet Facet; -typedef Alpha_shape_3::Edge Edge_3; -typedef std::list Vertex_list; - -// gudhi type definition -typedef Simplex_tree ST; -typedef ST::Vertex_handle Simplex_tree_vertex; -typedef std::map Alpha_shape_simplex_tree_map; -typedef std::pair Alpha_shape_simplex_tree_pair; -typedef std::vector< Simplex_tree_vertex > Simplex_tree_vector_vertex; - -Vertex_list from(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; -} - -Vertex_list from(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; -} - -Vertex_list from(const Edge_3& edg) { - Vertex_list the_list; - for (auto i = 0; i < 4; i++) { - if ((edg.second == i) || (edg.third == i)) { -#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; -} - -Vertex_list from(const Alpha_shape_3::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; -} - -void usage(char * const progName) { - std::cerr << "Usage: " << progName << - " path_to_file_graph 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 != 4) { - std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; - usage(argv[0]); - } - - int coeff_field_characteristic = 0; - int returnedScanValue = sscanf(argv[2], "%d", &coeff_field_characteristic); - if ((returnedScanValue == EOF) || (coeff_field_characteristic <= 0)) { - std::cerr << "Error: " << argv[2] << " is not correct\n"; - usage(argv[0]); - } - - Filtration_value min_persistence = 0.0; - returnedScanValue = sscanf(argv[3], "%lf", &min_persistence); - if ((returnedScanValue == EOF) || (min_persistence < -1.0)) { - std::cerr << "Error: " << argv[3] << " is not correct\n"; - usage(argv[0]); - } - - // Read points from file - std::string filegraph = argv[1]; - std::list lp; - std::ifstream is(filegraph.c_str()); - int n; - is >> n; -#ifdef DEBUG_TRACES - std::cout << "Reading " << n << " points " << std::endl; -#endif // DEBUG_TRACES - Point_3 p; - for (; n > 0; n--) { - is >> p; - lp.push_back(p); - } - - // 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(); - 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); - 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); - 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); - count_edges++; - if (dim_max < 1) { - // Edge_3 is of dim 1 - dim_max = 1; - } - } else if (const Alpha_shape_3::Vertex_handle * vertex = - CGAL::object_cast(&object_iterator)) { - count_vertices++; - vertex_list = from(*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< ST, Field_Zp > pcoh(simplex_tree); - // 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