diff options
Diffstat (limited to 'src/Simplex_tree/example')
-rw-r--r-- | src/Simplex_tree/example/CMakeLists.txt | 15 | ||||
-rw-r--r-- | src/Simplex_tree/example/mini_simplex_tree.cpp | 69 | ||||
-rw-r--r-- | src/Simplex_tree/example/simple_simplex_tree.cpp | 108 | ||||
-rw-r--r-- | src/Simplex_tree/example/simplex_tree_from_alpha_shapes_3.cpp | 440 | ||||
-rw-r--r-- | src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp | 114 | ||||
-rw-r--r-- | src/Simplex_tree/example/simplex_tree_from_file.cpp | 104 |
6 files changed, 436 insertions, 414 deletions
diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt index 1a3cdfbf..c70cfe35 100644 --- a/src/Simplex_tree/example/CMakeLists.txt +++ b/src/Simplex_tree/example/CMakeLists.txt @@ -1,21 +1,24 @@ cmake_minimum_required(VERSION 2.6) project(GUDHISimplexTreeFromFile) -add_executable ( simplex_tree_from_file simplex_tree_from_file.cpp ) -add_test(simplex_tree_from_file_2 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_file ${CMAKE_SOURCE_DIR}/data/points/Klein_bottle_complex.txt 2) -add_test(simplex_tree_from_file_3 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_file ${CMAKE_SOURCE_DIR}/data/points/Klein_bottle_complex.txt 3) +add_executable ( simplex_tree_from_cliques_of_graph simplex_tree_from_cliques_of_graph.cpp ) +add_test(simplex_tree_from_cliques_of_graph_2 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_cliques_of_graph ${CMAKE_SOURCE_DIR}/data/points/Klein_bottle_complex.txt 2) +add_test(simplex_tree_from_cliques_of_graph_3 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_cliques_of_graph ${CMAKE_SOURCE_DIR}/data/points/Klein_bottle_complex.txt 3) add_executable ( simple_simplex_tree simple_simplex_tree.cpp ) add_test(simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/simple_simplex_tree) - + +add_executable ( mini_simplex_tree mini_simplex_tree.cpp ) +add_test(mini_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/mini_simplex_tree) + # An example with Simplex-tree using CGAL alpha_shapes_3 if(GMP_FOUND AND CGAL_FOUND) message("CGAL_lib = ${CGAL_LIBRARIES_DIR}") - message("GMP_LIBRARIES = ${GMP_LIBRARIES}") + message("GMP_LIBRARIES = ${GMP_LIBRARIES}") INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR}) INCLUDE_DIRECTORIES(${CGAL_INCLUDE_DIRS}) add_executable ( simplex_tree_from_alpha_shapes_3 simplex_tree_from_alpha_shapes_3.cpp ) target_link_libraries(simplex_tree_from_alpha_shapes_3 ${GMP_LIBRARIES} ${CGAL_LIBRARY}) add_test(simplex_tree_from_alpha_shapes_3 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_alpha_shapes_3 ${CMAKE_SOURCE_DIR}/data/points/bunny_5000) -endif() +endif() diff --git a/src/Simplex_tree/example/mini_simplex_tree.cpp b/src/Simplex_tree/example/mini_simplex_tree.cpp new file mode 100644 index 00000000..7e48aaaf --- /dev/null +++ b/src/Simplex_tree/example/mini_simplex_tree.cpp @@ -0,0 +1,69 @@ +/* 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): Marc Glisse + * + * Copyright (C) 2015 INRIA Saclay - Ile-de-France (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 <http://www.gnu.org/licenses/>. + */ + +#include <gudhi/Simplex_tree.h> +#include <iostream> +#include <initializer_list> + +using namespace Gudhi; + +struct MyOptions : Simplex_tree_options_full_featured { + // Not doing persistence, so we don't need those + static const bool store_key = false; + static const bool store_filtration = false; + // I have few vertices + typedef short Vertex_handle; +}; +typedef Simplex_tree<MyOptions> ST; + +// Dictionary should be private, but for now this is the easiest way. +static_assert(sizeof(ST::Dictionary::value_type) < sizeof(Simplex_tree<>::Dictionary::value_type), + "Not storing the filtration and key should save some space"); + +int main() { + ST st; + + /* Complex to build. */ + /* 1 */ + /* o */ + /* /X\ */ + /* o---o---o */ + /* 2 0 3 */ + + auto triangle012 = {0, 1, 2}; + auto edge03 = {0, 3}; + st.insert_simplex_and_subfaces(triangle012); + st.insert_simplex_and_subfaces(edge03); + // FIXME: Remove this line + st.set_dimension(2); + + auto edge02 = {0, 2}; + ST::Simplex_handle e = st.find(edge02); + // We are not using filtrations so everything has value 0 + assert(st.filtration(e) == 0); + for (ST::Simplex_handle t : st.cofaces_simplex_range(e, 1)) { + // Only coface is 012 + for (ST::Vertex_handle v : st.simplex_vertex_range(t)) // v in { 0, 1, 2 } + std::cout << v; + std::cout << '\n'; + } +} diff --git a/src/Simplex_tree/example/simple_simplex_tree.cpp b/src/Simplex_tree/example/simple_simplex_tree.cpp index 6d20e43e..5146b906 100644 --- a/src/Simplex_tree/example/simple_simplex_tree.cpp +++ b/src/Simplex_tree/example/simple_simplex_tree.cpp @@ -20,10 +20,12 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ +#include <gudhi/graph_simplicial_complex.h> +#include <gudhi/Simplex_tree.h> + #include <iostream> -#include <ctime> -#include "gudhi/graph_simplicial_complex.h" -#include "gudhi/Simplex_tree.h" +#include <utility> // for pair +#include <vector> using namespace Gudhi; @@ -35,15 +37,11 @@ int main(int argc, char * const argv[]) { const Filtration_value SECOND_FILTRATION_VALUE = 0.2; const Filtration_value THIRD_FILTRATION_VALUE = 0.3; const Filtration_value FOURTH_FILTRATION_VALUE = 0.4; - Vertex_handle FIRST_VERTEX_HANDLE = (Vertex_handle) 0; - Vertex_handle SECOND_VERTEX_HANDLE = (Vertex_handle) 1; - Vertex_handle THIRD_VERTEX_HANDLE = (Vertex_handle) 2; - Vertex_handle FOURTH_VERTEX_HANDLE = (Vertex_handle) 3; // TEST OF INSERTION std::cout << "********************************************************************" << std::endl; std::cout << "EXAMPLE OF SIMPLE INSERTION" << std::endl; - //Construct the Simplex Tree + // Construct the Simplex Tree Simplex_tree<> simplexTree; /* Simplex to be inserted: */ @@ -55,190 +53,149 @@ int main(int argc, char * const argv[]) { // ++ FIRST std::cout << " * INSERT 0" << std::endl; - typeVectorVertex firstSimplexVector; - firstSimplexVector.push_back(FIRST_VERTEX_HANDLE); + typeVectorVertex firstSimplexVector = { 0 }; typePairSimplexBool returnValue = simplexTree.insert_simplex(firstSimplexVector, Filtration_value(FIRST_FILTRATION_VALUE)); if (returnValue.second == true) { std::cout << " + 0 INSERTED" << std::endl; - int nb_simplices = simplexTree.num_simplices() + 1; - simplexTree.set_num_simplices(nb_simplices); } else { std::cout << " - 0 NOT INSERTED" << std::endl; } // ++ SECOND std::cout << " * INSERT 1" << std::endl; - typeVectorVertex secondSimplexVector; - secondSimplexVector.push_back(SECOND_VERTEX_HANDLE); + typeVectorVertex secondSimplexVector = { 1 }; returnValue = simplexTree.insert_simplex(secondSimplexVector, Filtration_value(FIRST_FILTRATION_VALUE)); if (returnValue.second == true) { std::cout << " + 1 INSERTED" << std::endl; - int nb_simplices = simplexTree.num_simplices() + 1; - simplexTree.set_num_simplices(nb_simplices); } else { std::cout << " - 1 NOT INSERTED" << std::endl; } // ++ THIRD std::cout << " * INSERT (0,1)" << std::endl; - typeVectorVertex thirdSimplexVector; - thirdSimplexVector.push_back(FIRST_VERTEX_HANDLE); - thirdSimplexVector.push_back(SECOND_VERTEX_HANDLE); + typeVectorVertex thirdSimplexVector = { 0, 1 }; returnValue = simplexTree.insert_simplex(thirdSimplexVector, Filtration_value(SECOND_FILTRATION_VALUE)); if (returnValue.second == true) { std::cout << " + (0,1) INSERTED" << std::endl; - int nb_simplices = simplexTree.num_simplices() + 1; - simplexTree.set_num_simplices(nb_simplices); } else { std::cout << " - (0,1) NOT INSERTED" << std::endl; } // ++ FOURTH std::cout << " * INSERT 2" << std::endl; - typeVectorVertex fourthSimplexVector; - fourthSimplexVector.push_back(THIRD_VERTEX_HANDLE); + typeVectorVertex fourthSimplexVector = { 2 }; returnValue = simplexTree.insert_simplex(fourthSimplexVector, Filtration_value(FIRST_FILTRATION_VALUE)); if (returnValue.second == true) { std::cout << " + 2 INSERTED" << std::endl; - int nb_simplices = simplexTree.num_simplices() + 1; - simplexTree.set_num_simplices(nb_simplices); } else { std::cout << " - 2 NOT INSERTED" << std::endl; } // ++ FIFTH std::cout << " * INSERT (2,0)" << std::endl; - typeVectorVertex fifthSimplexVector; - fifthSimplexVector.push_back(THIRD_VERTEX_HANDLE); - fifthSimplexVector.push_back(FIRST_VERTEX_HANDLE); + typeVectorVertex fifthSimplexVector = { 2, 0 }; returnValue = simplexTree.insert_simplex(fifthSimplexVector, Filtration_value(SECOND_FILTRATION_VALUE)); if (returnValue.second == true) { std::cout << " + (2,0) INSERTED" << std::endl; - int nb_simplices = simplexTree.num_simplices() + 1; - simplexTree.set_num_simplices(nb_simplices); } else { std::cout << " - (2,0) NOT INSERTED" << std::endl; } // ++ SIXTH std::cout << " * INSERT (2,1)" << std::endl; - typeVectorVertex sixthSimplexVector; - sixthSimplexVector.push_back(THIRD_VERTEX_HANDLE); - sixthSimplexVector.push_back(SECOND_VERTEX_HANDLE); + typeVectorVertex sixthSimplexVector = { 2, 1 }; returnValue = simplexTree.insert_simplex(sixthSimplexVector, Filtration_value(SECOND_FILTRATION_VALUE)); if (returnValue.second == true) { std::cout << " + (2,1) INSERTED" << std::endl; - int nb_simplices = simplexTree.num_simplices() + 1; - simplexTree.set_num_simplices(nb_simplices); } else { std::cout << " - (2,1) NOT INSERTED" << std::endl; } // ++ SEVENTH std::cout << " * INSERT (2,1,0)" << std::endl; - typeVectorVertex seventhSimplexVector; - seventhSimplexVector.push_back(THIRD_VERTEX_HANDLE); - seventhSimplexVector.push_back(SECOND_VERTEX_HANDLE); - seventhSimplexVector.push_back(FIRST_VERTEX_HANDLE); + typeVectorVertex seventhSimplexVector = { 2, 1, 0 }; returnValue = simplexTree.insert_simplex(seventhSimplexVector, Filtration_value(THIRD_FILTRATION_VALUE)); if (returnValue.second == true) { std::cout << " + (2,1,0) INSERTED" << std::endl; - int nb_simplices = simplexTree.num_simplices() + 1; - simplexTree.set_num_simplices(nb_simplices); } else { std::cout << " - (2,1,0) NOT INSERTED" << std::endl; } // ++ EIGHTH std::cout << " * INSERT 3" << std::endl; - typeVectorVertex eighthSimplexVector; - eighthSimplexVector.push_back(FOURTH_VERTEX_HANDLE); + typeVectorVertex eighthSimplexVector = { 3 }; returnValue = simplexTree.insert_simplex(eighthSimplexVector, Filtration_value(FIRST_FILTRATION_VALUE)); if (returnValue.second == true) { std::cout << " + 3 INSERTED" << std::endl; - int nb_simplices = simplexTree.num_simplices() + 1; - simplexTree.set_num_simplices(nb_simplices); } else { std::cout << " - 3 NOT INSERTED" << std::endl; } // ++ NINETH std::cout << " * INSERT (3,0)" << std::endl; - typeVectorVertex ninethSimplexVector; - ninethSimplexVector.push_back(FOURTH_VERTEX_HANDLE); - ninethSimplexVector.push_back(FIRST_VERTEX_HANDLE); + typeVectorVertex ninethSimplexVector = { 3, 0 }; returnValue = simplexTree.insert_simplex(ninethSimplexVector, Filtration_value(SECOND_FILTRATION_VALUE)); if (returnValue.second == true) { std::cout << " + (3,0) INSERTED" << std::endl; - int nb_simplices = simplexTree.num_simplices() + 1; - simplexTree.set_num_simplices(nb_simplices); } else { std::cout << " - (3,0) NOT INSERTED" << std::endl; } // ++ TENTH std::cout << " * INSERT 0 (already inserted)" << std::endl; - typeVectorVertex tenthSimplexVector; - tenthSimplexVector.push_back(FIRST_VERTEX_HANDLE); - returnValue = - simplexTree.insert_simplex(tenthSimplexVector, Filtration_value(FOURTH_FILTRATION_VALUE)); // With a different filtration value + typeVectorVertex tenthSimplexVector = { 0 }; + // With a different filtration value + returnValue = simplexTree.insert_simplex(tenthSimplexVector, Filtration_value(FOURTH_FILTRATION_VALUE)); if (returnValue.second == true) { std::cout << " + 0 INSERTED" << std::endl; - int nb_simplices = simplexTree.num_simplices() + 1; - simplexTree.set_num_simplices(nb_simplices); } else { std::cout << " - 0 NOT INSERTED" << std::endl; } // ++ ELEVENTH std::cout << " * INSERT (2,1,0) (already inserted)" << std::endl; - typeVectorVertex eleventhSimplexVector; - eleventhSimplexVector.push_back(THIRD_VERTEX_HANDLE); - eleventhSimplexVector.push_back(SECOND_VERTEX_HANDLE); - eleventhSimplexVector.push_back(FIRST_VERTEX_HANDLE); + typeVectorVertex eleventhSimplexVector = { 2, 1, 0 }; returnValue = simplexTree.insert_simplex(eleventhSimplexVector, Filtration_value(FOURTH_FILTRATION_VALUE)); if (returnValue.second == true) { std::cout << " + (2,1,0) INSERTED" << std::endl; - int nb_simplices = simplexTree.num_simplices() + 1; - simplexTree.set_num_simplices(nb_simplices); } else { std::cout << " - (2,1,0) NOT INSERTED" << std::endl; } // ++ GENERAL VARIABLE SET - simplexTree.set_filtration(FOURTH_FILTRATION_VALUE); // Max filtration value - simplexTree.set_dimension(2); // Max dimension = 2 -> (2,1,0) + simplexTree.set_filtration(FOURTH_FILTRATION_VALUE); // Max filtration value + simplexTree.set_dimension(2); // Max dimension = 2 -> (2,1,0) - std::cout << "********************************************************************" << std::endl; + std::cout << "********************************************************************\n"; // Display the Simplex_tree - Can not be done in the middle of 2 inserts - std::cout << "* The complex contains " << simplexTree.num_simplices() << " simplices" << std::endl; - std::cout << " - dimension " << simplexTree.dimension() << " - filtration " << simplexTree.filtration() << std::endl; - std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:" << std::endl; + std::cout << "* The complex contains " << simplexTree.num_simplices() << " simplices\n"; + std::cout << " - dimension " << simplexTree.dimension() << " - filtration " << simplexTree.filtration() << "\n"; + std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; for (auto f_simplex : simplexTree.filtration_simplex_range()) { std::cout << " " << "[" << simplexTree.filtration(f_simplex) << "] "; for (auto vertex : simplexTree.simplex_vertex_range(f_simplex)) { - std::cout << (int) vertex << " "; + std::cout << static_cast<int>(vertex) << " "; } std::cout << std::endl; } @@ -262,9 +219,7 @@ int main(int argc, char * const argv[]) { else std::cout << "***- NO IT ISN'T\n"; - Vertex_handle UNKNOWN_VERTEX_HANDLE = (Vertex_handle) 15; - typeVectorVertex unknownSimplexVector; - unknownSimplexVector.push_back(UNKNOWN_VERTEX_HANDLE); + typeVectorVertex unknownSimplexVector = { 15 }; simplexFound = simplexTree.find(unknownSimplexVector); std::cout << "**************IS THE SIMPLEX {15} IN THE SIMPLEX TREE ?\n"; if (simplexFound != simplexTree.null_simplex()) @@ -279,9 +234,7 @@ int main(int argc, char * const argv[]) { else std::cout << "***- NO IT ISN'T\n"; - typeVectorVertex otherSimplexVector; - otherSimplexVector.push_back(UNKNOWN_VERTEX_HANDLE); - otherSimplexVector.push_back(SECOND_VERTEX_HANDLE); + typeVectorVertex otherSimplexVector = { 1, 15 }; simplexFound = simplexTree.find(otherSimplexVector); std::cout << "**************IS THE SIMPLEX {15,1} IN THE SIMPLEX TREE ?\n"; if (simplexFound != simplexTree.null_simplex()) @@ -289,10 +242,7 @@ int main(int argc, char * const argv[]) { else std::cout << "***- NO IT ISN'T\n"; - typeVectorVertex invSimplexVector; - invSimplexVector.push_back(SECOND_VERTEX_HANDLE); - invSimplexVector.push_back(THIRD_VERTEX_HANDLE); - invSimplexVector.push_back(FIRST_VERTEX_HANDLE); + typeVectorVertex invSimplexVector = { 1, 2, 0 }; simplexFound = simplexTree.find(invSimplexVector); std::cout << "**************IS THE SIMPLEX {1,2,0} IN THE SIMPLEX TREE ?\n"; if (simplexFound != simplexTree.null_simplex()) diff --git a/src/Simplex_tree/example/simplex_tree_from_alpha_shapes_3.cpp b/src/Simplex_tree/example/simplex_tree_from_alpha_shapes_3.cpp index 5f797e93..45efe3ed 100644 --- a/src/Simplex_tree/example/simplex_tree_from_alpha_shapes_3.cpp +++ b/src/Simplex_tree/example/simplex_tree_from_alpha_shapes_3.cpp @@ -1,24 +1,28 @@ - /* 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 <http://www.gnu.org/licenses/>. - */ +/* 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 <http://www.gnu.org/licenses/>. + */ + +#include <gudhi/graph_simplicial_complex.h> +#include <gudhi/Simplex_tree.h> +#include <boost/variant.hpp> #include <CGAL/Exact_predicates_inexact_constructions_kernel.h> #include <CGAL/Delaunay_triangulation_3.h> @@ -27,32 +31,34 @@ #include <fstream> #include <cmath> - -#include "gudhi/graph_simplicial_complex.h" -#include "gudhi/Simplex_tree.h" -#include <boost/variant.hpp> +#include <string> +#include <tuple> // for tuple<> +#include <map> +#include <utility> // for pair<> +#include <list> +#include <vector> // Alpha_shape_3 templates type definitions typedef CGAL::Exact_predicates_inexact_constructions_kernel Kernel; -typedef CGAL::Alpha_shape_vertex_base_3<Kernel> Vb; -typedef CGAL::Alpha_shape_cell_base_3<Kernel> Fb; -typedef CGAL::Triangulation_data_structure_3<Vb,Fb> Tds; -typedef CGAL::Delaunay_triangulation_3<Kernel,Tds> Triangulation_3; -typedef CGAL::Alpha_shape_3<Triangulation_3> Alpha_shape_3; +typedef CGAL::Alpha_shape_vertex_base_3<Kernel> Vb; +typedef CGAL::Alpha_shape_cell_base_3<Kernel> Fb; +typedef CGAL::Triangulation_data_structure_3<Vb, Fb> Tds; +typedef CGAL::Delaunay_triangulation_3<Kernel, Tds> Triangulation_3; +typedef CGAL::Alpha_shape_3<Triangulation_3> Alpha_shape_3; // From file type definition -typedef Kernel::Point_3 Point; +typedef Kernel::Point_3 Point; // filtration with alpha values needed type definition typedef Alpha_shape_3::FT Alpha_value_type; -typedef CGAL::Object Object; +typedef CGAL::Object Object; typedef CGAL::Dispatch_output_iterator< - CGAL::cpp11::tuple<Object, Alpha_value_type>, - CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >, std::back_insert_iterator< std::vector<Alpha_value_type> > - > > Dispatch; -typedef Alpha_shape_3::Cell_handle Cell_handle; -typedef Alpha_shape_3::Facet Facet; -typedef Alpha_shape_3::Edge Edge; +CGAL::cpp11::tuple<Object, Alpha_value_type>, +CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >, + std::back_insert_iterator< std::vector<Alpha_value_type> > > > Dispatch; +typedef Alpha_shape_3::Cell_handle Cell_handle; +typedef Alpha_shape_3::Facet Facet; +typedef Alpha_shape_3::Edge Edge; typedef std::list<Alpha_shape_3::Vertex_handle> Vertex_list; // gudhi type definition @@ -61,225 +67,209 @@ typedef std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex > Alpha_shape typedef std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex> Alpha_shape_simplex_tree_pair; typedef std::vector< Simplex_tree_vertex > Simplex_tree_vector_vertex; -//#define DEBUG_TRACES - -Vertex_list from (const Cell_handle& ch) -{ - Vertex_list the_list; - for (auto i = 0; i < 4; i++) - { +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; + 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) - { + +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; + 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& edg) -{ - Vertex_list the_list; - for (auto i = 0; i < 4; i++) - { - if ((edg.second == i) ||(edg.third == i)) - { + +Vertex_list from(const Edge& 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; + 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; + +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; + std::cout << "from vertex=" << vh->point() << std::endl; +#endif // DEBUG_TRACES + the_list.push_back(vh); + return the_list; } +int main(int argc, char * const argv[]) { + // program args management + if (argc != 2) { + std::cerr << "Usage: " << argv[0] + << " path_to_file_graph \n"; + return 0; + } -int main (int argc, char * const argv[]) -{ - // program args management - if (argc != 2) { - std::cerr << "Usage: " << argv[0] - << " path_to_file_graph \n"; - return 0; // ----- >> - } - - // Read points from file - std::string filegraph = argv[1]; - std::list<Point> lp; - std::ifstream is(filegraph.c_str()); - int n; - is >> n; + // Read points from file + std::string filegraph = argv[1]; + std::list<Point> 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 p; - for( ; n>0 ; n--) { - is >> p; - lp.push_back(p); - } + std::cout << "Reading " << n << " points " << std::endl; +#endif // DEBUG_TRACES + Point 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); + // 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 + std::cout << "Alpha shape computed in GENERAL mode" << std::endl; +#endif // DEBUG_TRACES - // filtration with alpha values from alpha shape - std::vector<Object> the_objects; - std::vector<Alpha_value_type> the_alpha_values; + // filtration with alpha values from alpha shape + std::vector<Object> the_objects; + std::vector<Alpha_value_type> the_alpha_values; - Dispatch disp = CGAL::dispatch_output<Object, Alpha_value_type>( std::back_inserter(the_objects), std::back_inserter(the_alpha_values)); + Dispatch disp = CGAL::dispatch_output<Object, Alpha_value_type>(std::back_inserter(the_objects), + std::back_inserter(the_alpha_values)); - as.filtration_with_alpha_values(disp); + 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 + 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; + 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; - Gudhi::Simplex_tree<> simplex_tree; - Alpha_shape_simplex_tree_map map_cgal_simplex_tree; - std::vector<Alpha_value_type>::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<Cell_handle>(&object_iterator)) - { - vertex_list = from(*cell); - count_cells++; - } - else if (const Facet* facet = CGAL::object_cast<Facet>(&object_iterator)) - { - vertex_list = from(*facet); - count_facets++; - } - else if (const Edge* edge = CGAL::object_cast<Edge>(&object_iterator)) - { - vertex_list = from(*edge); - count_edges++; - } - else if (const Alpha_shape_3::Vertex_handle* vertex = CGAL::object_cast<Alpha_shape_3::Vertex_handle>(&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(); + // Loop on objects vector + Vertex_list vertex_list; + Gudhi::Simplex_tree<> simplex_tree; + Alpha_shape_simplex_tree_map map_cgal_simplex_tree; + std::vector<Alpha_value_type>::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<Cell_handle>(&object_iterator)) { + vertex_list = from(*cell); + count_cells++; + } else if (const Facet * facet = CGAL::object_cast<Facet>(&object_iterator)) { + vertex_list = from(*facet); + count_facets++; + } else if (const Edge * edge = CGAL::object_cast<Edge>(&object_iterator)) { + vertex_list = from(*edge); + count_edges++; + } else if (const Alpha_shape_3::Vertex_handle * vertex = + CGAL::object_cast<Alpha_shape_3::Vertex_handle>(&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_simplex " << 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; + std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert_simplex " << vertex << "\n"; +#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 + 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 #ifdef DEBUG_TRACES - std::cout << "filtration = " << *the_alpha_value_iterator << std::endl; -#endif // DEBUG_TRACES - simplex_tree.insert_simplex(the_simplex_tree, std::sqrt(*the_alpha_value_iterator)); - if (the_alpha_value_iterator != the_alpha_values.end()) - ++the_alpha_value_iterator; - else - std::cout << "This shall not happen" << std::endl; - } + std::cout << "filtration = " << *the_alpha_value_iterator << std::endl; +#endif // DEBUG_TRACES + simplex_tree.insert_simplex(the_simplex_tree, std::sqrt(*the_alpha_value_iterator)); + if (the_alpha_value_iterator != the_alpha_values.end()) + ++the_alpha_value_iterator; + else + std::cerr << "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 << "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; -#endif // DEBUG_TRACES + std::cout << "Information of the Simplex Tree:\n"; + std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; + std::cout << " Number of simplices = " << simplex_tree.num_simplices() << 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 + std::cout << "Iterator on vertices: \n"; + for (auto vertex : simplex_tree.complex_vertex_range()) { + std::cout << vertex << " "; + } +#endif // DEBUG_TRACES - std::cout << simplex_tree << std::endl; + std::cout << simplex_tree << std::endl; #ifdef DEBUG_TRACES - std::cout << std::endl << std::endl << "Iterator on simplices: " << std::endl; - for( auto simplex : simplex_tree.complex_simplex_range() ) - { - std::cout << " "; - for( auto vertex : simplex_tree.simplex_vertex_range(simplex) ) { std::cout << vertex << " "; } - std::cout << std::endl; - } -#endif // DEBUG_TRACES + std::cout << std::endl << std::endl << "Iterator on simplices:\n"; + for (auto simplex : simplex_tree.complex_simplex_range()) { + std::cout << " "; + for (auto vertex : simplex_tree.simplex_vertex_range(simplex)) { + std::cout << vertex << " "; + } + std::cout << std::endl; + } +#endif // DEBUG_TRACES #ifdef DEBUG_TRACES - std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl; - for( auto f_simplex : simplex_tree.filtration_simplex_range() ) - { std::cout << " " << "[" << simplex_tree.filtration(f_simplex) << "] "; - for( auto vertex : simplex_tree.simplex_vertex_range(f_simplex) ) - { std::cout << vertex << " "; } - std::cout << std::endl; - } -#endif // DEBUG_TRACES + std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:\n"; + for (auto f_simplex : simplex_tree.filtration_simplex_range()) { + std::cout << " " << "[" << simplex_tree.filtration(f_simplex) << "] "; + for (auto vertex : simplex_tree.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << std::endl; + } +#endif // DEBUG_TRACES #ifdef DEBUG_TRACES - std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, and their boundary simplices:" << std::endl; - for( auto f_simplex : simplex_tree.filtration_simplex_range() ) - { - std::cout << " " << "[" << simplex_tree.filtration(f_simplex) << "] "; - for( auto vertex : simplex_tree.simplex_vertex_range(f_simplex) ) - { std::cout << vertex << " "; } - std::cout << std::endl; + std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, and their boundary simplices:\n"; + for (auto f_simplex : simplex_tree.filtration_simplex_range()) { + std::cout << " " << "[" << simplex_tree.filtration(f_simplex) << "] "; + for (auto vertex : simplex_tree.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << std::endl; - for( auto b_simplex : simplex_tree.boundary_simplex_range(f_simplex) ) - { - std::cout << " " << "[" << simplex_tree.filtration(b_simplex) << "] "; - for( auto vertex : simplex_tree.simplex_vertex_range(b_simplex) ) - { std::cout << vertex << " "; } - std::cout << std::endl; - } - } -#endif // DEBUG_TRACES + for (auto b_simplex : simplex_tree.boundary_simplex_range(f_simplex)) { + std::cout << " " << "[" << simplex_tree.filtration(b_simplex) << "] "; + for (auto vertex : simplex_tree.simplex_vertex_range(b_simplex)) { + std::cout << vertex << " "; + } + std::cout << std::endl; + } + } +#endif // DEBUG_TRACES - return 0; + return 0; } diff --git a/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp b/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp new file mode 100644 index 00000000..58085014 --- /dev/null +++ b/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp @@ -0,0 +1,114 @@ +/* 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): Clément Maria + * + * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (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 <http://www.gnu.org/licenses/>. + */ + +#include <gudhi/reader_utils.h> +#include <gudhi/Simplex_tree.h> + +#include <iostream> +#include <ctime> +#include <string> + +using namespace Gudhi; + +int main(int argc, char * const argv[]) { + if (argc != 3) { + std::cerr << "Usage: " << argv[0] + << " path_to_file_graph max_dim \n"; + return 0; + } + std::string filegraph = argv[1]; + int max_dim = atoi(argv[2]); + + clock_t start, end; + // Construct the Simplex Tree + Simplex_tree<> st; + + start = clock(); + auto g = read_graph(filegraph); + // insert the graph in the simplex tree as 1-skeleton + st.insert_graph(g); + end = clock(); + std::cout << "Insert the 1-skeleton in the simplex tree in " + << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n"; + + start = clock(); + // expand the 1-skeleton until dimension max_dim + st.expansion(max_dim); + end = clock(); + std::cout << "max_dim = " << max_dim << "\n"; + std::cout << "Expand the simplex tree in " + << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n"; + + std::cout << "Information of the Simplex Tree: " << std::endl; + std::cout << " Number of vertices = " << st.num_vertices() << " "; + std::cout << " Number of simplices = " << st.num_simplices() << std::endl; + std::cout << std::endl << std::endl; + + std::cout << "Iterator on vertices: "; + for (auto vertex : st.complex_vertex_range()) { + std::cout << vertex << " "; + } + + std::cout << std::endl; + + std::cout << std::endl << std::endl; + + std::cout << "Iterator on simplices: " << std::endl; + for (auto simplex : st.complex_simplex_range()) { + std::cout << " "; + for (auto vertex : st.simplex_vertex_range(simplex)) { + std::cout << vertex << " "; + } + std::cout << std::endl; + } + + std::cout << std::endl << std::endl; + + std::cout << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl; + for (auto f_simplex : st.filtration_simplex_range()) { + std::cout << " " << "[" << st.filtration(f_simplex) << "] "; + for (auto vertex : st.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << std::endl; + } + + std::cout << std::endl << std::endl; + + std::cout << "Iterator on Simplices in the filtration, and their boundary simplices:" << std::endl; + for (auto f_simplex : st.filtration_simplex_range()) { + std::cout << " " << "[" << st.filtration(f_simplex) << "] "; + for (auto vertex : st.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << std::endl; + + for (auto b_simplex : st.boundary_simplex_range(f_simplex)) { + std::cout << " " << "[" << st.filtration(b_simplex) << "] "; + for (auto vertex : st.simplex_vertex_range(b_simplex)) { + std::cout << vertex << " "; + } + std::cout << std::endl; + } + } + return 0; +} diff --git a/src/Simplex_tree/example/simplex_tree_from_file.cpp b/src/Simplex_tree/example/simplex_tree_from_file.cpp deleted file mode 100644 index 20e8f067..00000000 --- a/src/Simplex_tree/example/simplex_tree_from_file.cpp +++ /dev/null @@ -1,104 +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): Clément Maria - * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (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 <http://www.gnu.org/licenses/>. - */ - -#include <iostream> -#include <ctime> -#include "gudhi/reader_utils.h" -#include "gudhi/Simplex_tree.h" - -using namespace Gudhi; - -int main (int argc, char * const argv[]) -{ - if (argc != 3) { - std::cerr << "Usage: " << argv[0] - << " path_to_file_graph max_dim \n"; - return 0; - } - std::string filegraph = argv[1]; - int max_dim = atoi(argv[2]); - - clock_t start, end; - //Construct the Simplex Tree - Simplex_tree<> st; - - start = clock(); - auto g = read_graph(filegraph); - st.insert_graph (g); //insert the graph in the simplex tree as 1-skeleton - end = clock(); - std::cout << "Insert the 1-skeleton in the simplex tree in " - << (double)(end-start)/CLOCKS_PER_SEC << " s. \n"; - - start = clock(); - st.expansion ( max_dim ); //expand the 1-skeleton until dimension max_dim - end = clock(); - std::cout << "max_dim = " << max_dim << "\n"; - std::cout << "Expand the simplex tree in " - << (double)(end-start)/CLOCKS_PER_SEC << " s. \n"; - - std::cout << "Information of the Simplex Tree: " << std::endl; - std::cout << " Number of vertices = " << st.num_vertices() << " "; - std::cout << " Number of simplices = " << st.num_simplices() << std::endl; - std::cout << std::endl << std::endl; - - std::cout << "Iterator on vertices: "; - for( auto vertex : st.complex_vertex_range() ) { std::cout << vertex << " "; } - - std::cout << std::endl; - - std::cout << std::endl << std::endl; - - std::cout << "Iterator on simplices: " << std::endl; - for( auto simplex : st.complex_simplex_range() ) - { - std::cout << " "; - for( auto vertex : st.simplex_vertex_range(simplex) ) { std::cout << vertex << " "; } - std::cout << std::endl; - } - - std::cout << std::endl << std::endl; - - std::cout << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl; - for( auto f_simplex : st.filtration_simplex_range() ) - { std::cout << " " << "[" << st.filtration(f_simplex) << "] "; - for( auto vertex : st.simplex_vertex_range(f_simplex) ) - { std::cout << vertex << " "; } std::cout << std::endl; - } - - std::cout << std::endl << std::endl; - - std::cout << "Iterator on Simplices in the filtration, and their boundary simplices:" << std::endl; - for( auto f_simplex : st.filtration_simplex_range() ) - { - std::cout << " " << "[" << st.filtration(f_simplex) << "] "; - for( auto vertex : st.simplex_vertex_range(f_simplex) ) - { std::cout << vertex << " "; } std::cout << std::endl; - - for( auto b_simplex : st.boundary_simplex_range(f_simplex) ) - { - std::cout << " " << "[" << st.filtration(b_simplex) << "] "; - for( auto vertex : st.simplex_vertex_range(b_simplex) ) - { std::cout << vertex << " "; } std::cout << std::endl; - } - } - return 0; -} |