diff options
author | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2018-06-27 11:11:13 +0000 |
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committer | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2018-06-27 11:11:13 +0000 |
commit | 5ae0226e2871ba8cfcf28830a6cc753578be9fe4 (patch) | |
tree | 123db784ca212f58acb356f3affdbee29e06bfb8 /src/Alpha_complex/utilities | |
parent | 704bd19db466ae028917453e5c4e040e15b52b26 (diff) |
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
Diffstat (limited to 'src/Alpha_complex/utilities')
7 files changed, 147 insertions, 1001 deletions
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 $<TARGET_FILE:alpha_complex_3d_persistence> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45") - add_test(NAME Alpha_complex_utilities_exact_alpha_complex_3d COMMAND $<TARGET_FILE:exact_alpha_complex_3d_persistence> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-p" "2" "-m" "0.45") - add_test(NAME Alpha_complex_utilities_weighted_alpha_complex_3d COMMAND $<TARGET_FILE:weighted_alpha_complex_3d_persistence> - "${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 $<TARGET_FILE:alpha_complex_persistence> "${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 $<TARGET_FILE:periodic_alpha_complex_3d_persistence> - "${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 $<TARGET_FILE:weighted_periodic_alpha_complex_3d_persistence> - "${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 $<TARGET_FILE:alpha_complex_3d_persistence> + "${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 $<TARGET_FILE:alpha_complex_3d_persistence> + "${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 $<TARGET_FILE:alpha_complex_3d_persistence> + "${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 $<TARGET_FILE:alpha_complex_3d_persistence> + "${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 $<TARGET_FILE:alpha_complex_3d_persistence> + "${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 <http://www.gnu.org/licenses/>. - */ - -#ifndef ALPHA_COMPLEX_3D_HELPER_H_ -#define ALPHA_COMPLEX_3D_HELPER_H_ - -template <class Vertex_list, class Cell_handle> -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 <class Vertex_list, class Facet> -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 <class Vertex_list, class Edge_3> -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 <class Vertex_list, class Vertex_handle> -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 <boost/program_options.hpp> +#include <boost/variant.hpp> #include <gudhi/Alpha_complex_3d.h> #include <gudhi/Alpha_complex_3d_options.h> @@ -28,41 +29,130 @@ #include <gudhi/Persistent_cohomology.h> #include <gudhi/Points_3D_off_io.h> -#include <iostream> +#include <fstream> #include <string> -#include <limits> // for numeric_limits +#include <vector> // gudhi type definition +using Weighted_periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::Weighted_periodic_alpha_shapes_3d>; +using Periodic_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::Periodic_alpha_shapes_3d>; +using Weighted_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::Weighted_alpha_shapes_3d>; +using Exact_alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::Exact_alpha_shapes_3d>; using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::Alpha_shapes_3d>; using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; using Filtration_value = Simplex_tree::Filtration_value; using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Gudhi::persistent_cohomology::Field_Zp>; -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<typename AlphaComplex3d> +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<double>& 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<Alpha_complex_3d::Point_3> 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<double> 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<std::string>(&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<std::string>(&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<std::string>(&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<std::string>(&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<int>(&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 <http://www.gnu.org/licenses/>. - */ - -#include <boost/program_options.hpp> -#include <boost/variant.hpp> - -#include <gudhi/Simplex_tree.h> -#include <gudhi/Persistent_cohomology.h> -#include <gudhi/Points_3D_off_io.h> - -#include <CGAL/Exact_predicates_inexact_constructions_kernel.h> -#include <CGAL/Delaunay_triangulation_3.h> -#include <CGAL/Alpha_shape_3.h> -#include <CGAL/Alpha_shape_cell_base_3.h> -#include <CGAL/Alpha_shape_vertex_base_3.h> -#include <CGAL/iterator.h> - -#include <fstream> -#include <cmath> -#include <string> -#include <tuple> -#include <map> -#include <utility> -#include <vector> -#include <cstdlib> - -#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<Kernel, CGAL::Default, Exact_tag>; -using Fb = CGAL::Alpha_shape_cell_base_3<Kernel, CGAL::Default, Exact_tag>; -using Tds = CGAL::Triangulation_data_structure_3<Vb, Fb>; -using Triangulation_3 = CGAL::Delaunay_triangulation_3<Kernel, Tds>; -using Alpha_shape_3 = CGAL::Alpha_shape_3<Triangulation_3, Exact_tag>; - -// 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<Object, Alpha_value_type>, - CGAL::cpp11::tuple<std::back_insert_iterator<std::vector<Object> >, - std::back_insert_iterator<std::vector<Alpha_value_type> > > >; -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<Vertex_handle>; - -// gudhi type definition -using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; -using Filtration_value = ST::Filtration_value; -using Simplex_tree_vertex = ST::Vertex_handle; -using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>; -using Simplex_tree_vector_vertex = std::vector<Simplex_tree_vertex>; -using Persistent_cohomology = - Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>; - -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<Point_3> 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<Point_3> 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<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)); - - 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<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<Vertex_list, Cell_handle>(*cell); - count_cells++; - } else if (const Facet *facet = CGAL::object_cast<Facet>(&object_iterator)) { - vertex_list = from_facet<Vertex_list, Facet>(*facet); - count_facets++; - } else if (const Edge_3 *edge = CGAL::object_cast<Edge_3>(&object_iterator)) { - vertex_list = from_edge<Vertex_list, Edge_3>(*edge); - count_edges++; - } else if (const Vertex_handle *vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) { - count_vertices++; - vertex_list = from_vertex<Vertex_list, Vertex_handle>(*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<std::string>(&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<std::string>(&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<int>(&coeff_field_characteristic)->default_value(11), - "Characteristic p of the coefficient field Z/pZ for computing homology.")( - "min-persistence,m", po::value<Filtration_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 <http://www.gnu.org/licenses/>. - */ - -#include <boost/program_options.hpp> -#include <boost/variant.hpp> - -#include <gudhi/Alpha_complex_3d.h> -#include <gudhi/Alpha_complex_3d_options.h> -#include <gudhi/Simplex_tree.h> -#include <gudhi/Persistent_cohomology.h> -#include <gudhi/Points_3D_off_io.h> - -#include <fstream> -#include <cmath> -#include <string> -#include <tuple> -#include <map> -#include <utility> -#include <vector> -#include <cstdlib> - -// gudhi type definition -using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::Periodic_alpha_shapes_3d>; -using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; -using Filtration_value = Simplex_tree::Filtration_value; -using Persistent_cohomology = - Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Gudhi::persistent_cohomology::Field_Zp>; - -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<Alpha_complex_3d::Point_3> 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<std::string>(&off_file_points), - "Name of file containing a point set. Format is one point per line: X1 ... Xd ")( - "cuboid-file", po::value<std::string>(&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<std::string>(&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<int>(&coeff_field_characteristic)->default_value(11), - "Characteristic p of the coefficient field Z/pZ for computing homology.")( - "min-persistence,m", po::value<Filtration_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 <http://www.gnu.org/licenses/>. - */ - -#include <boost/program_options.hpp> -#include <boost/variant.hpp> - -#include <gudhi/Alpha_complex_3d.h> -#include <gudhi/Alpha_complex_3d_options.h> -#include <gudhi/Simplex_tree.h> -#include <gudhi/Persistent_cohomology.h> -#include <gudhi/Points_3D_off_io.h> - -#include <fstream> -#include <string> -#include <vector> - -// gudhi type definition -using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::Weighted_alpha_shapes_3d>; -using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; -using Filtration_value = Simplex_tree::Filtration_value; -using Persistent_cohomology = - Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Gudhi::persistent_cohomology::Field_Zp>; - -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<Alpha_complex_3d::Point_3> 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<double> 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<std::string>(&off_file_points), - "Name of file containing a point set. Format is one point per line: X1 ... Xd ")( - "weight-file", po::value<std::string>(&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<std::string>(&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<int>(&coeff_field_characteristic)->default_value(11), - "Characteristic p of the coefficient field Z/pZ for computing homology.")( - "min-persistence,m", po::value<Filtration_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 <http://www.gnu.org/licenses/>. - */ - -#include <boost/variant.hpp> - -#include <gudhi/Simplex_tree.h> -#include <gudhi/Persistent_cohomology.h> -#include <gudhi/Points_3D_off_io.h> - -#include <CGAL/Exact_predicates_inexact_constructions_kernel.h> -#include <CGAL/Periodic_3_regular_triangulation_traits_3.h> -#include <CGAL/Periodic_3_regular_triangulation_3.h> -#include <CGAL/Alpha_shape_3.h> -#include <CGAL/Alpha_shape_cell_base_3.h> -#include <CGAL/Alpha_shape_vertex_base_3.h> -#include <CGAL/iterator.h> - -#include <fstream> -#include <cmath> -#include <string> -#include <tuple> -#include <map> -#include <utility> -#include <vector> -#include <cstdlib> - -#include "alpha_complex_3d_helper.h" - -// Traits -using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; -using PK = CGAL::Periodic_3_regular_triangulation_traits_3<Kernel>; - -// Vertex type -using DsVb = CGAL::Periodic_3_triangulation_ds_vertex_base_3<>; -using Vb = CGAL::Regular_triangulation_vertex_base_3<PK, DsVb>; -using AsVb = CGAL::Alpha_shape_vertex_base_3<PK, Vb>; -// Cell type -using DsCb = CGAL::Periodic_3_triangulation_ds_cell_base_3<>; -using Cb = CGAL::Regular_triangulation_cell_base_3<PK, DsCb>; -using AsCb = CGAL::Alpha_shape_cell_base_3<PK, Cb>; -using Tds = CGAL::Triangulation_data_structure_3<AsVb, AsCb>; -using P3RT3 = CGAL::Periodic_3_regular_triangulation_3<PK, Tds>; -using Alpha_shape_3 = CGAL::Alpha_shape_3<P3RT3>; - -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<Object, Alpha_value_type>, - CGAL::cpp11::tuple<std::back_insert_iterator<std::vector<Object> >, - std::back_insert_iterator<std::vector<Alpha_value_type> > > >; -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<Alpha_shape_3::Vertex_handle>; - -// gudhi type definition -using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; -using Filtration_value = ST::Filtration_value; -using Simplex_tree_vertex = ST::Vertex_handle; -using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>; -using Simplex_tree_vector_vertex = std::vector<Simplex_tree_vertex>; -using Persistent_cohomology = - Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>; - -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<Point_3> 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<Point_3> 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<Weighted_point_3> 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<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)); - - 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<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<Vertex_list, Cell_handle>(*cell); - count_cells++; - } else if (const Facet* facet = CGAL::object_cast<Facet>(&object_iterator)) { - vertex_list = from_facet<Vertex_list, Facet>(*facet); - count_facets++; - } else if (const Edge_3* edge = CGAL::object_cast<Edge_3>(&object_iterator)) { - vertex_list = from_edge<Vertex_list, Edge_3>(*edge); - count_edges++; - } else if (const Vertex_handle* vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) { - count_vertices++; - vertex_list = from_vertex<Vertex_list, Vertex_handle>(*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; -} |