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/* 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) 2015 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 SRC_ALPHA_SHAPES_INCLUDE_GUDHI_ALPHA_SHAPES_H_
#define SRC_ALPHA_SHAPES_INCLUDE_GUDHI_ALPHA_SHAPES_H_
// to construct a Delaunay_triangulation from a OFF file
#include <gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h>
// to construct a simplex_tree from Delaunay_triangulation
#include <gudhi/graph_simplicial_complex.h>
#include <gudhi/Simplex_tree.h>
#include <stdio.h>
#include <stdlib.h>
#include <CGAL/Delaunay_triangulation.h>
#include <CGAL/Epick_d.h>
#include <CGAL/algorithm.h>
#include <CGAL/assertions.h>
#include <iostream>
#include <iterator>
#include <vector>
#include <string>
namespace Gudhi {
namespace alphashapes {
#define Kinit(f) =k.f()
/** \defgroup alpha_shapes Alpha shapes in dimension N
*
<DT>Implementations:</DT>
Alpha shapes in dimension N are a subset of Delaunay Triangulation in dimension N.
* \author Vincent Rouvreau
* \version 1.0
* \date 2015
* \copyright GNU General Public License v3.
* @{
*/
/**
* \brief Alpha shapes data structure.
*
* \details Every simplex \f$[v_0, \cdots ,v_d]\f$ admits a canonical orientation
* induced by the order relation on vertices \f$ v_0 < \cdots < v_d \f$.
*
* Details may be found in \cite boissonnatmariasimplextreealgorithmica.
*
* \implements FilteredComplex
*
*/
class Alpha_shapes {
private:
// From Simplex_tree
/** \brief Type required to insert into a simplex_tree (with or without subfaces).*/
typedef std::vector<Vertex_handle> typeVectorVertex;
// From CGAL
/** \brief Kernel for the Delaunay_triangulation.
* Dimension can be set dynamically.
*/
typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel;
/** \brief Delaunay_triangulation type required to create an alpha-shape.
*/
typedef CGAL::Delaunay_triangulation<Kernel> Delaunay_triangulation;
typedef typename Kernel::Compute_squared_radius_d Squared_Radius;
typedef typename Kernel::Side_of_bounded_sphere_d Is_Gabriel;
/** \brief Type required to insert into a simplex_tree (with or without subfaces).*/
typedef std::vector<Kernel::Point_d> typeVectorPoint;
private:
/** \brief Upper bound on the simplex tree of the simplicial complex.*/
Gudhi::Simplex_tree<> _st;
public:
Alpha_shapes(std::string off_file_name) {
// Construct a default Delaunay_triangulation (dim=0) - dim will be set in visitor reader init function
Delaunay_triangulation dt(3);
Gudhi::alphashapes::Delaunay_triangulation_off_reader<Delaunay_triangulation> off_reader(off_file_name, dt);
if (!off_reader.is_valid()) {
std::cerr << "Unable to read file " << off_file_name << std::endl;
exit(-1); // ----- >>
}
#ifdef DEBUG_TRACES
std::cout << "number of vertices=" << dt.number_of_vertices() << std::endl;
std::cout << "number of full cells=" << dt.number_of_full_cells() << std::endl;
std::cout << "number of finite full cells=" << dt.number_of_finite_full_cells() << std::endl;
#endif // DEBUG_TRACES
init<Delaunay_triangulation>(dt);
}
template<typename T>
Alpha_shapes(T triangulation) {
init<T>(triangulation);
}
~Alpha_shapes() { }
private:
template<typename T>
void init(T triangulation) {
_st.set_dimension(triangulation.maximal_dimension());
Filtration_value filtration_max = 0.0;
Kernel k;
Squared_Radius squared_radius Kinit(compute_squared_radius_d_object);
Is_Gabriel is_gabriel Kinit(side_of_bounded_sphere_d_object);
// triangulation full cells list
for (auto cit = triangulation.full_cells_begin(); cit != triangulation.full_cells_end(); ++cit) {
typeVectorVertex vertexVector;
typeVectorPoint pointVector;
for (auto vit = cit->vertices_begin(); vit != cit->vertices_end(); ++vit) {
if (!triangulation.is_infinite(*vit)) {
// Vector of vertex construction for simplex_tree structure
// Vertex handle is distance - 1
Vertex_handle vertexHdl = std::distance(triangulation.vertices_begin(), *vit) - 1;
// infinite cell is -1 for infinite
vertexVector.push_back(vertexHdl);
// Vector of points for alpha_shapes filtration value computation
pointVector.push_back((*vit)->point());
#ifdef DEBUG_TRACES
std::cout << "Point ";
for (auto Coord = (*vit)->point().cartesian_begin(); Coord != (*vit)->point().cartesian_end(); ++Coord) {
std::cout << *Coord << " | ";
}
std::cout << std::endl;
#endif // DEBUG_TRACES
}
}
Filtration_value alpha_shapes_filtration = 0.0;
if (!triangulation.is_infinite(cit)) {
alpha_shapes_filtration = squared_radius(pointVector.begin(), pointVector.end());
#ifdef DEBUG_TRACES
std::cout << "Alpha_shape filtration value = " << alpha_shapes_filtration << std::endl;
#endif // DEBUG_TRACES
} else {
Filtration_value tmp_filtration = 0.0;
bool is_gab = true;
for (auto vit = triangulation.finite_vertices_begin(); vit != triangulation.finite_vertices_end(); ++vit) {
if (CGAL::ON_UNBOUNDED_SIDE != is_gabriel(pointVector.begin(), pointVector.end(), vit->point())) {
is_gab = false;
// TODO(VR) : Compute minimum
}
}
if (true == is_gab) {
alpha_shapes_filtration = squared_radius(pointVector.begin(), pointVector.end());
#ifdef DEBUG_TRACES
std::cout << "Alpha_shape filtration value = " << alpha_shapes_filtration << std::endl;
#endif // DEBUG_TRACES
}
}
// Insert each point in the simplex tree
_st.insert_simplex_and_subfaces(vertexVector, alpha_shapes_filtration);
#ifdef DEBUG_TRACES
std::cout << "C" << std::distance(triangulation.full_cells_begin(), cit) << ":";
for (auto value : vertexVector) {
std::cout << value << ' ';
}
std::cout << std::endl;
#endif // DEBUG_TRACES
}
_st.set_filtration(filtration_max);
}
public:
/** \brief Returns the number of vertices in the complex. */
size_t num_vertices() {
return _st.num_vertices();
}
/** \brief Returns the number of simplices in the complex.
*
* Does not count the empty simplex. */
const unsigned int& num_simplices() const {
return _st.num_simplices();
}
/** \brief Returns an upper bound on the dimension of the simplicial complex. */
int dimension() {
return _st.dimension();
}
/** \brief Returns an upper bound of the filtration values of the simplices. */
Filtration_value filtration() {
return _st.filtration();
}
friend std::ostream& operator<<(std::ostream& os, const Alpha_shapes& alpha_shape) {
// TODO: Program terminated with signal SIGABRT, Aborted - Maybe because of copy constructor
Gudhi::Simplex_tree<> st = alpha_shape._st;
os << st << std::endl;
return os;
}
};
} // namespace alphashapes
} // namespace Gudhi
#endif // SRC_ALPHA_SHAPES_INCLUDE_GUDHI_ALPHA_SHAPES_H_
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