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-rw-r--r--src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp263
1 files changed, 130 insertions, 133 deletions
diff --git a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
index 9e806c7a..92fed4c1 100644
--- a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
@@ -27,7 +27,6 @@
#include <gudhi/Points_3D_off_io.h>
#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
-#include <CGAL/Regular_triangulation_euclidean_traits_3.h>
#include <CGAL/Regular_triangulation_3.h>
#include <CGAL/Alpha_shape_3.h>
#include <CGAL/iterator.h>
@@ -44,26 +43,26 @@
#include "alpha_complex_3d_helper.h"
-// Traits
using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel;
-using Gt = CGAL::Regular_triangulation_euclidean_traits_3<Kernel>;
-using Vb = CGAL::Alpha_shape_vertex_base_3<Gt>;
-using Fb = CGAL::Alpha_shape_cell_base_3<Gt>;
-using Tds = CGAL::Triangulation_data_structure_3<Vb, Fb>;
-using Triangulation_3 = CGAL::Regular_triangulation_3<Gt, Tds>;
+using Rvb = CGAL::Regular_triangulation_vertex_base_3<Kernel>;
+using Vb = CGAL::Alpha_shape_vertex_base_3<Kernel,Rvb>;
+using Rcb = CGAL::Regular_triangulation_cell_base_3<Kernel>;
+using Cb = CGAL::Alpha_shape_cell_base_3<Kernel,Rcb>;
+using Tds = CGAL::Triangulation_data_structure_3<Vb,Cb>;
+using Triangulation_3 = CGAL::Regular_triangulation_3<Kernel,Tds>;
using Alpha_shape_3 = CGAL::Alpha_shape_3<Triangulation_3>;
// From file type definition
-using Point_3 = Gt::Bare_point;
-using Weighted_point_3 = Gt::Weighted_point;
+using Point_3 = Triangulation_3::Bare_point;
+using Weighted_point_3 = Triangulation_3::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 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;
@@ -74,19 +73,19 @@ using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>;
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 Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
using Alpha_shape_simplex_tree_pair = std::pair<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 >;
+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(char * const progName) {
- std::cerr << "Usage: " << progName <<
- " path_to_file_graph path_to_weight_file coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n";
+void usage(char* const progName) {
+ std::cerr << "Usage: " << progName << " path_to_file_graph path_to_weight_file coeff_field_characteristic[integer > "
+ "0] min_persistence[float >= -1.0]\n";
exit(-1);
}
-int main(int argc, char * const argv[]) {
+int main(int argc, char* const argv[]) {
// program args management
if (argc != 5) {
std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
@@ -136,129 +135,127 @@ int main(int argc, char * const argv[]) {
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);
- #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;
+ 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
- // 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 Alpha_shape_3::Vertex_handle * vertex =
- CGAL::object_cast<Alpha_shape_3::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*/(*the_alpha_value_iterator);
- #ifdef DEBUG_TRACES
- std::cout << "filtration = " << filtr << std::endl;
- #endif // DEBUG_TRACES
- if (filtr > filtration_max) {
- filtration_max = filtr;
- }
- simplex_tree.insert_simplex(the_simplex_tree, filtr);
- if (the_alpha_value_iterator != the_alpha_values.end())
- ++the_alpha_value_iterator;
- else
- std::cout << "This shall not happen" << std::endl;
- }
- simplex_tree.set_filtration(filtration_max);
- simplex_tree.set_dimension(dim_max);
+ 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;
- #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;
+ // 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*/ (*the_alpha_value_iterator);
+#ifdef DEBUG_TRACES
+ std::cout << "filtration = " << filtr << std::endl;
+#endif // DEBUG_TRACES
+ if (filtr > filtration_max) {
+ filtration_max = filtr;
+ }
+ simplex_tree.insert_simplex(the_simplex_tree, filtr);
+ if (the_alpha_value_iterator != the_alpha_values.end())
+ ++the_alpha_value_iterator;
+ else
+ std::cout << "This shall not happen" << std::endl;
+ }
+ simplex_tree.set_filtration(filtration_max);
+ simplex_tree.set_dimension(dim_max);
+#ifdef DEBUG_TRACES
+ std::cout << "vertices \t\t" << count_vertices << std::endl;
+ std::cout << "edges \t\t" << count_edges << std::endl;
+ std::cout << "facets \t\t" << count_facets << std::endl;
+ std::cout << "cells \t\t" << count_cells << std::endl;
- std::cout << "Information of the Simplex Tree: " << std::endl;
- std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " ";
- std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl;
- std::cout << " Dimension = " << simplex_tree.dimension() << " ";
- std::cout << " filtration = " << simplex_tree.filtration() << std::endl << std::endl;
- #endif // DEBUG_TRACES
+ 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
+#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();
+ // 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);
+ 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.compute_persistent_cohomology(min_persistence);
- pcoh.output_diagram();
+ pcoh.output_diagram();
return 0;
}
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