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CoordGIC.cpp
/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
* See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
* Author(s): Mathieu Carrière
*
* Copyright (C) 2017 Inria
*
* Modification(s):
* - YYYY/MM Author: Description of the modification
*/
#include <gudhi/GIC.h>
#include <string>
#include <vector>
void usage(int nbArgs, char *const progName) {
std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n";
std::cerr << "Usage: " << progName << " filename.off coordinate [-v] \n";
std::cerr << " i.e.: " << progName << " ../../data/points/human.off 2 -v \n";
exit(-1); // ----- >>
}
int main(int argc, char **argv) {
if ((argc != 3) && (argc != 4)) usage(argc, argv[0]);
using Point = std::vector<float>;
std::string off_file_name(argv[1]);
int coord = atoi(argv[2]);
bool verb = 0;
if (argc == 4) verb = 1;
// -----------------------------------------
// Init of a functional GIC from an OFF file
// -----------------------------------------
Gudhi::cover_complex::Cover_complex<Point> GIC;
GIC.set_verbose(verb);
bool check = GIC.read_point_cloud(off_file_name);
if (!check) {
std::clog << "Incorrect OFF file." << std::endl;
} else {
GIC.set_type("GIC");
GIC.set_color_from_coordinate(coord);
GIC.set_function_from_coordinate(coord);
GIC.set_graph_from_automatic_rips(Gudhi::Euclidean_distance());
GIC.set_automatic_resolution();
GIC.set_gain();
GIC.set_cover_from_function();
GIC.find_simplices();
GIC.compute_distribution(10);
GIC.compute_p_value();
GIC.plot_DOT();
Gudhi::Simplex_tree<> stree;
GIC.create_complex(stree);
// --------------------------------------------
// Display information about the functional GIC
// --------------------------------------------
if (verb) {
std::clog << "Coordinate GIC is of dimension " << stree.dimension() << " - " << stree.num_simplices()
<< " simplices - " << stree.num_vertices() << " vertices." << std::endl;
std::clog << "Iterator on coordinate GIC simplices" << std::endl;
for (auto f_simplex : stree.filtration_simplex_range()) {
for (auto vertex : stree.simplex_vertex_range(f_simplex)) {
std::clog << vertex << " ";
}
std::clog << std::endl;
}
}
}
return 0;
}
Gudhi::Euclidean_distance
Compute the Euclidean distance between two Points given by a range of coordinates....
Definition distance_functions.h:32
Gudhi::Simplex_tree
Simplex Tree data structure for representing simplicial complexes.
Definition Simplex_tree.h:98
Gudhi::Simplex_tree::simplex_vertex_range
Simplex_vertex_range simplex_vertex_range(Simplex_handle sh) const
Returns a range over the vertices of a simplex.
Definition Simplex_tree.h:369
Gudhi::Simplex_tree::filtration_simplex_range
Filtration_simplex_range const & filtration_simplex_range(Indexing_tag=Indexing_tag()) const
Returns a range over the simplices of the simplicial complex, in the order of the filtration.
Definition Simplex_tree.h:358
Gudhi::Simplex_tree::num_vertices
size_t num_vertices() const
Returns the number of vertices in the complex.
Definition Simplex_tree.h:778
Gudhi::Simplex_tree::num_simplices
size_t num_simplices() const
Returns the number of simplices in the simplex_tree.
Definition Simplex_tree.h:791
Gudhi::cover_complex::Cover_complex
Cover complex data structure.
Definition GIC.h:99
Gudhi::cover_complex::Cover_complex::set_automatic_resolution
double set_automatic_resolution()
Computes the optimal length of intervals (i.e. the smallest interval length avoiding discretization a...
Definition GIC.h:542
Gudhi::cover_complex::Cover_complex::create_complex
void create_complex(SimplicialComplex &complex)
Creates the simplicial complex.
Definition GIC.h:1325
Gudhi::cover_complex::Cover_complex::set_type
void set_type(const std::string &t)
Specifies whether the type of the output simplicial complex.
Definition GIC.h:188
Gudhi::cover_complex::Cover_complex::find_simplices
void find_simplices()
Computes the simplices of the simplicial complex.
Definition GIC.h:1339
Gudhi::cover_complex::Cover_complex::set_cover_from_function
void set_cover_from_function()
Creates a cover C from the preimages of the function f.
Definition GIC.h:601
Gudhi::cover_complex::Cover_complex::plot_DOT
void plot_DOT()
Creates a .dot file called SC.dot for neato (part of the graphviz package) once the simplicial comple...
Definition GIC.h:1034
Gudhi::cover_complex::Cover_complex::set_graph_from_automatic_rips
double set_graph_from_automatic_rips(Distance distance, int N=100)
Creates a graph G from a Rips complex whose threshold value is automatically tuned with subsampling—s...
Definition GIC.h:431
Gudhi::cover_complex::Cover_complex::set_gain
void set_gain(double g=0.3)
Sets a gain from a value stored in memory (default value 0.3).
Definition GIC.h:595
Gudhi::cover_complex::Cover_complex::set_function_from_coordinate
void set_function_from_coordinate(int k)
Creates the function f from the k-th coordinate of the point cloud P.
Definition GIC.h:504
Gudhi::cover_complex::Cover_complex::set_color_from_coordinate
void set_color_from_coordinate(int k=0)
Computes the function used to color the nodes of the simplicial complex from the k-th coordinate.
Definition GIC.h:1005
Gudhi::cover_complex::Cover_complex::compute_distribution
void compute_distribution(unsigned int N=100)
Computes bootstrapped distances distribution.
Definition GIC.h:1228
Gudhi::cover_complex::Cover_complex::compute_p_value
double compute_p_value()
Computes the p-value, i.e. the opposite of the confidence level of the largest bottleneck distance pr...
Definition GIC.h:1306
Gudhi::cover_complex::Cover_complex::read_point_cloud
bool read_point_cloud(const std::string &off_file_name)
Reads and stores the input point cloud from .(n)OFF file.
Definition GIC.h:244
Gudhi::cover_complex::Cover_complex::set_verbose
void set_verbose(bool verb=false)
Specifies whether the program should display information or not.
Definition GIC.h:196