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-rw-r--r--src/Cech_complex/utilities/cech_persistence.cpp69
1 files changed, 50 insertions, 19 deletions
diff --git a/src/Cech_complex/utilities/cech_persistence.cpp b/src/Cech_complex/utilities/cech_persistence.cpp
index 75d10c0f..e6419f3d 100644
--- a/src/Cech_complex/utilities/cech_persistence.cpp
+++ b/src/Cech_complex/utilities/cech_persistence.cpp
@@ -16,6 +16,7 @@
#include <boost/program_options.hpp>
#include <CGAL/Epeck_d.h> // For EXACT or SAFE version
+#include <CGAL/Epick_d.h> // For FAST version
#include <string>
#include <vector>
@@ -25,41 +26,66 @@
using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
using Filtration_value = Simplex_tree::Filtration_value;
-using Kernel = CGAL::Epeck_d<CGAL::Dynamic_dimension_tag>;
-using Point = typename Kernel::Point_d;
-using Points_off_reader = Gudhi::Points_off_reader<Point>;
-using Cech_complex = Gudhi::cech_complex::Cech_complex<Kernel, Simplex_tree>;
using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp>;
-void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag,
- Filtration_value& max_radius, int& dim_max, int& p, Filtration_value& min_persistence);
+void program_options(int argc, char* argv[], std::string& off_file_points, bool& exact, bool& fast,
+ std::string& filediag, Filtration_value& max_radius, int& dim_max, int& p,
+ Filtration_value& min_persistence);
+
+template<class Kernel>
+Simplex_tree create_simplex_tree(const std::string &off_file_points, bool exact_version,
+ Filtration_value max_radius, int dim_max) {
+ using Point = typename Kernel::Point_d;
+ using Points_off_reader = Gudhi::Points_off_reader<Point>;
+ using Cech_complex = Gudhi::cech_complex::Cech_complex<Kernel, Simplex_tree>;
+
+ Simplex_tree stree;
+
+ Points_off_reader off_reader(off_file_points);
+ Cech_complex cech_complex_from_file(off_reader.get_point_cloud(), max_radius, exact_version);
+ cech_complex_from_file.create_complex(stree, dim_max);
+
+ return stree;
+}
int main(int argc, char* argv[]) {
std::string off_file_points;
std::string filediag;
+ bool exact_version = false;
+ bool fast_version = false;
Filtration_value max_radius;
int dim_max;
int p;
Filtration_value min_persistence;
- program_options(argc, argv, off_file_points, filediag, max_radius, dim_max, p, min_persistence);
+ program_options(argc, argv, off_file_points, exact_version, fast_version, filediag, max_radius, dim_max, p,
+ min_persistence);
- Points_off_reader off_reader(off_file_points);
- Cech_complex cech_complex_from_file(off_reader.get_point_cloud(), max_radius);
+ if ((exact_version) && (fast_version)) {
+ std::cerr << "You cannot set the exact and the fast version." << std::endl;
+ exit(-1);
+ }
- // Construct the Cech complex in a Simplex Tree
- Simplex_tree simplex_tree;
+ Simplex_tree stree;
+ if (fast_version) {
+ // WARNING : CGAL::Epick_d is fast but not safe (unlike CGAL::Epeck_d)
+ // (i.e. when the points are on a grid)
+ using Fast_kernel = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>;
+ stree = create_simplex_tree<Fast_kernel>(off_file_points, exact_version, max_radius, dim_max);
+ } else {
+ using Kernel = CGAL::Epeck_d<CGAL::Dynamic_dimension_tag>;
+ stree = create_simplex_tree<Kernel>(off_file_points, exact_version, max_radius, dim_max);
+ }
- cech_complex_from_file.create_complex(simplex_tree, dim_max);
- std::clog << "The complex contains " << simplex_tree.num_simplices() << " simplices \n";
- std::clog << " and has dimension " << simplex_tree.dimension() << " \n";
+ std::clog << "The complex contains " << stree.num_simplices() << " simplices \n";
+ std::clog << " and has dimension " << stree.dimension() << " \n";
// Sort the simplices in the order of the filtration
- simplex_tree.initialize_filtration();
+ stree.initialize_filtration();
// Compute the persistence diagram of the complex
- Persistent_cohomology pcoh(simplex_tree);
+ Persistent_cohomology pcoh(stree);
// initializes the coefficient field for homology
pcoh.init_coefficients(p);
@@ -77,8 +103,9 @@ int main(int argc, char* argv[]) {
return 0;
}
-void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag,
- Filtration_value& max_radius, int& dim_max, int& p, Filtration_value& min_persistence) {
+void program_options(int argc, char* argv[], std::string& off_file_points, bool& exact, bool& fast,
+ std::string& filediag, Filtration_value& max_radius, int& dim_max, int& p,
+ 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),
@@ -86,8 +113,12 @@ 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 Cech complex (default is false, not available if fast is set)")(
+ "fast,f", po::bool_switch(&fast),
+ "To activate fast version of Cech complex (default is false, not available if exact is set)")(
"output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
- "Name of file in which the persistence diagram is written. Default print in std::clog")(
+ "Name of file in which the persistence diagram is written. Default print in standard output")(
"max-radius,r",
po::value<Filtration_value>(&max_radius)->default_value(std::numeric_limits<Filtration_value>::infinity()),
"Maximal length of an edge for the Cech complex construction.")(