diff options
3 files changed, 325 insertions, 51 deletions
diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_helper.h b/src/Persistent_cohomology/example/alpha_complex_3d_helper.h new file mode 100644 index 00000000..ceefd2ba --- /dev/null +++ b/src/Persistent_cohomology/example/alpha_complex_3d_helper.h @@ -0,0 +1,76 @@ +/* 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/>. + */ + +#ifndef EXAMPLE_PERSISTENT_COHOMOLOGY_ALPHA_COMPLEX_3D_HELPER_H_ +#define EXAMPLE_PERSISTENT_COHOMOLOGY_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 = 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; +} + +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 // EXAMPLE_PERSISTENT_COHOMOLOGY_ALPHA_COMPLEX_3D_HELPER_H_ diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp index 48fbb91a..b5084e5b 100644 --- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp @@ -30,6 +30,8 @@ #include <CGAL/Alpha_shape_3.h> #include <CGAL/iterator.h> +#include "alpha_complex_3d_helper.h" + #include <fstream> #include <cmath> #include <string> @@ -70,53 +72,7 @@ typedef std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex> Alpha_shape typedef std::vector< Simplex_tree_vertex > Simplex_tree_vector_vertex; typedef Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp > PCOH; -Vertex_list from(const Cell_handle& ch) { - Vertex_list the_list; - for (auto i = 0; i < 4; i++) { -#ifdef DEBUG_TRACES - std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(ch->vertex(i)); - } - return the_list; -} - -Vertex_list from(const Facet& fct) { - Vertex_list the_list; - for (auto i = 0; i < 4; i++) { - if (fct.second != i) { -#ifdef DEBUG_TRACES - std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(fct.first->vertex(i)); - } - } - return the_list; -} - -Vertex_list from(const Edge_3& edg) { - Vertex_list the_list; - for (auto i = 0; i < 4; i++) { - if ((edg.second == i) || (edg.third == i)) { -#ifdef DEBUG_TRACES - std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(edg.first->vertex(i)); - } - } - return the_list; -} - -Vertex_list from(const Alpha_shape_3::Vertex_handle& vh) { - Vertex_list the_list; -#ifdef DEBUG_TRACES - std::cout << "from vertex=" << vh->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(vh); - return the_list; -} - -void usage(char * const progName) { +void usage(const std::string& progName) { std::cerr << "Usage: " << progName << " path_to_file_graph coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; exit(-1); @@ -184,21 +140,21 @@ int main(int argc, char * const argv[]) { 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 = from_cell<Vertex_list, Cell_handle>(*cell); count_cells++; if (dim_max < 3) { // Cell is of dim 3 dim_max = 3; } } else if (const Facet * facet = CGAL::object_cast<Facet>(&object_iterator)) { - vertex_list = from(*facet); + vertex_list = from_facet<Vertex_list, Facet>(*facet); count_facets++; if (dim_max < 2) { // Facet is of dim 2 dim_max = 2; } } else if (const Edge_3 * edge = CGAL::object_cast<Edge_3>(&object_iterator)) { - vertex_list = from(*edge); + vertex_list = from_edge<Vertex_list, Edge_3>(*edge); count_edges++; if (dim_max < 1) { // Edge_3 is of dim 1 @@ -207,7 +163,7 @@ int main(int argc, char * const argv[]) { } 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); + vertex_list = from_vertex<Vertex_list, Alpha_shape_3::Vertex_handle>(*vertex); } // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex Simplex_tree_vector_vertex the_simplex_tree; diff --git a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp new file mode 100644 index 00000000..fc6ee8dd --- /dev/null +++ b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp @@ -0,0 +1,242 @@ +/* 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/Simplex_tree.h> +#include <gudhi/Persistent_cohomology.h> +#include <gudhi/Points_3D_off_io.h> +#include <boost/variant.hpp> + +#include <CGAL/Exact_predicates_inexact_constructions_kernel.h> +#include <CGAL/Delaunay_triangulation_3.h> +#include <CGAL/Alpha_shape_3.h> +#include <CGAL/iterator.h> + +#include "alpha_complex_3d_helper.h" + +#include <fstream> +#include <cmath> +#include <string> +#include <tuple> +#include <map> +#include <utility> +#include <list> +#include <vector> + +// Alpha_shape_3 templates type definitions +typedef CGAL::Exact_predicates_inexact_constructions_kernel Kernel; +typedef CGAL::Tag_true Exact_tag; +typedef CGAL::Alpha_shape_vertex_base_3<Kernel, CGAL::Default, Exact_tag> Vb; +typedef CGAL::Alpha_shape_cell_base_3<Kernel, CGAL::Default, Exact_tag> 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, Exact_tag> Alpha_shape_3; + +// From file type definition +typedef Kernel::Point_3 Point_3; + +// filtration with alpha values needed type definition +typedef Alpha_shape_3::FT Alpha_value_type; +typedef CGAL::Object Object; +typedef CGAL::Dispatch_output_iterator< +CGAL::cpp11::tuple<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_3; +typedef Alpha_shape_3::Vertex_handle Vertex_handle; +typedef std::list<Vertex_handle> Vertex_list; + +// gudhi type definition +typedef Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence> ST; +typedef ST::Vertex_handle Simplex_tree_vertex; +typedef std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex > Alpha_shape_simplex_tree_map; +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; +typedef Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp > PCOH; + +void usage(char * const progName) { + std::cerr << "Usage: " << progName << + " path_to_file_graph coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; + exit(-1); +} + +int main(int argc, char * const argv[]) { + // program args management + if (argc != 4) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; + usage(argv[0]); + } + + int coeff_field_characteristic = atoi(argv[2]); + + Filtration_value min_persistence = 0.0; + int returnedScanValue = sscanf(argv[3], "%lf", &min_persistence); + if ((returnedScanValue == EOF) || (min_persistence < -1.0)) { + std::cerr << "Error: " << argv[3] << " is not correct\n"; + usage(argv[0]); + } + + // Read points from file + std::string 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 triangulation + 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(); + int dim_max = 0; + Filtration_value filtration_max = 0.0; + for (auto object_iterator : the_objects) { + // Retrieve Alpha shape vertex list from object + if (const Cell_handle * cell = CGAL::object_cast<Cell_handle>(&object_iterator)) { + vertex_list = from_cell<Vertex_list, Cell_handle>(*cell); + count_cells++; + if (dim_max < 3) { + // Cell is of dim 3 + dim_max = 3; + } + } else if (const Facet * facet = CGAL::object_cast<Facet>(&object_iterator)) { + vertex_list = from_facet<Vertex_list, Facet>(*facet); + count_facets++; + if (dim_max < 2) { + // Facet is of dim 2 + dim_max = 2; + } + } else if (const Edge_3 * edge = CGAL::object_cast<Edge_3>(&object_iterator)) { + vertex_list = from_edge<Vertex_list, Edge_3>(*edge); + count_edges++; + if (dim_max < 1) { + // Edge_3 is of dim 1 + dim_max = 1; + } + } else if (const Vertex_handle * vertex = CGAL::object_cast<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_tree; + for (auto the_alpha_shape_vertex : vertex_list) { + Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex); + if (the_map_iterator == map_cgal_simplex_tree.end()) { + // alpha shape not found + Simplex_tree_vertex vertex = map_cgal_simplex_tree.size(); +#ifdef DEBUG_TRACES + std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl; +#endif // DEBUG_TRACES + the_simplex_tree.push_back(vertex); + map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex)); + } else { + // alpha shape found + Simplex_tree_vertex vertex = the_map_iterator->second; +#ifdef DEBUG_TRACES + std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl; +#endif // DEBUG_TRACES + the_simplex_tree.push_back(vertex); + } + } + // Construction of the simplex_tree + Filtration_value filtr = /*std::sqrt*/CGAL::to_double(the_alpha_value_iterator->approx()); +#ifdef DEBUG_TRACES + std::cout << "filtration = " << filtr << std::endl; +#endif // DEBUG_TRACES + if (filtr > filtration_max) { + filtration_max = filtr; + } + simplex_tree.insert_simplex(the_simplex_tree, filtr); + if (the_alpha_value_iterator != the_alpha_values.end()) + ++the_alpha_value_iterator; + else + std::cout << "This shall not happen" << std::endl; + } + simplex_tree.set_filtration(filtration_max); + simplex_tree.set_dimension(dim_max); + +#ifdef DEBUG_TRACES + std::cout << "vertices \t\t" << count_vertices << std::endl; + std::cout << "edges \t\t" << count_edges << std::endl; + std::cout << "facets \t\t" << count_facets << std::endl; + std::cout << "cells \t\t" << count_cells << std::endl; + + + std::cout << "Information of the Simplex Tree: " << std::endl; + std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; + std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; + std::cout << " Dimension = " << simplex_tree.dimension() << " "; + std::cout << " filtration = " << simplex_tree.filtration() << std::endl << std::endl; +#endif // DEBUG_TRACES + +#ifdef DEBUG_TRACES + std::cout << "Iterator on vertices: " << std::endl; + for (auto vertex : simplex_tree.complex_vertex_range()) { + std::cout << vertex << " "; + } +#endif // DEBUG_TRACES + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl; + // Compute the persistence diagram of the complex + PCOH pcoh(simplex_tree); + // initializes the coefficient field for homology + pcoh.init_coefficients(coeff_field_characteristic); + + pcoh.compute_persistent_cohomology(min_persistence); + + pcoh.output_diagram(); + + return 0; +} |