diff options
author | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2015-10-08 15:24:27 +0000 |
---|---|---|
committer | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2015-10-08 15:24:27 +0000 |
commit | 58e633f51ffa06aa219231cd1c08eab59457a12f (patch) | |
tree | 83fd798e34b61df36c991de7eccf860ed9194564 /src | |
parent | 6dd03d72142c98c4348e1b95d538de3b184bbc59 (diff) |
Fix cpplint on examples.
Bug fix on persistence_from_simple_simplex_tree.
Add persistence examples tests.
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@843 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 9b7b73abb4a5d6bb110376deb689247bfdae035c
Diffstat (limited to 'src')
15 files changed, 1008 insertions, 1023 deletions
diff --git a/src/Contraction/example/Garland_heckbert.cpp b/src/Contraction/example/Garland_heckbert.cpp index a41f65aa..70f29b6a 100644 --- a/src/Contraction/example/Garland_heckbert.cpp +++ b/src/Contraction/example/Garland_heckbert.cpp @@ -1,7 +1,4 @@ -/* - * Garland_heckbert.h - * Created on: Feb 10, 2015 - * This file is part of the Gudhi Library. The Gudhi library +/* This file is part of the Gudhi Library. The Gudhi library * (Geometric Understanding in Higher Dimensions) is a generic C++ * library for computational topology. * @@ -28,12 +25,13 @@ #ifndef GARLAND_HECKBERT_H_ #define GARLAND_HECKBERT_H_ +#include <gudhi/Point.h> +#include <gudhi/Edge_contraction.h> +#include <gudhi/Skeleton_blocker.h> +#include <gudhi/Off_reader.h> + #include <boost/timer/timer.hpp> #include <iostream> -#include "gudhi/Point.h" -#include "gudhi/Edge_contraction.h" -#include "gudhi/Skeleton_blocker.h" -#include "gudhi/Off_reader.h" #include "Garland_heckbert/Error_quadric.h" @@ -51,7 +49,6 @@ struct Geometry_trait { */ struct Garland_heckbert_traits : public Skeleton_blocker_simple_geometric_traits<Geometry_trait> { public: - struct Garland_heckbert_vertex : public Simple_geometric_vertex { Error_quadric<Geometry_trait::Point> quadric; }; @@ -68,6 +65,7 @@ typedef Skeleton_blocker_contractor<Complex> Complex_contractor; */ class GH_placement : public Gudhi::contraction::Placement_policy<EdgeProfile> { Complex& complex_; + public: typedef Gudhi::contraction::Placement_policy<EdgeProfile>::Placement_type Placement_type; @@ -91,8 +89,8 @@ class GH_placement : public Gudhi::contraction::Placement_policy<EdgeProfile> { */ class GH_cost : public Gudhi::contraction::Cost_policy<EdgeProfile> { Complex& complex_; - public: + public: typedef Gudhi::contraction::Cost_policy<EdgeProfile>::Cost_type Cost_type; GH_cost(Complex& complex) : complex_(complex) { } @@ -115,13 +113,13 @@ class GH_cost : public Gudhi::contraction::Cost_policy<EdgeProfile> { */ class GH_visitor : public Gudhi::contraction::Contraction_visitor<EdgeProfile> { Complex& complex_; - public: + public: GH_visitor(Complex& complex) : complex_(complex) { } - //Compute quadrics for every vertex v - //The quadric of v consists in the sum of quadric - //of every triangles passing through v weighted by its area + // Compute quadrics for every vertex v + // The quadric of v consists in the sum of quadric + // of every triangles passing through v weighted by its area void on_started(Complex & complex) override { for (auto v : complex.vertex_range()) { @@ -147,7 +145,8 @@ class GH_visitor : public Gudhi::contraction::Contraction_visitor<EdgeProfile> { int main(int argc, char *argv[]) { if (argc != 4) { - std::cerr << "Usage " << argv[0] << " input.off output.off N to load the file input.off, contract N edges and save the result to output.off.\n"; + std::cerr << "Usage " << argv[0] << " input.off output.off N to load the file input.off, contract N edges and save " + << "the result to output.off.\n"; return EXIT_FAILURE; } @@ -172,8 +171,7 @@ int main(int argc, char *argv[]) { new GH_cost(complex), new GH_placement(complex), contraction::make_link_valid_contraction<EdgeProfile>(), - new GH_visitor(complex) - ); + new GH_visitor(complex)); std::cout << "Contract " << num_contractions << " edges" << std::endl; contractor.contract_edges(num_contractions); @@ -183,7 +181,7 @@ int main(int argc, char *argv[]) { complex.num_edges() << " edges and" << complex.num_triangles() << " triangles." << std::endl; - //write simplified complex + // write simplified complex Skeleton_blocker_off_writer<Complex> off_writer(argv[2], complex); return EXIT_SUCCESS; @@ -191,4 +189,4 @@ int main(int argc, char *argv[]) { -#endif /* GARLAND_HECKBERT_H_ */ +#endif // GARLAND_HECKBERT_H_ diff --git a/src/Contraction/example/Garland_heckbert/Error_quadric.h b/src/Contraction/example/Garland_heckbert/Error_quadric.h index 72134c9d..a033aa00 100644 --- a/src/Contraction/example/Garland_heckbert/Error_quadric.h +++ b/src/Contraction/example/Garland_heckbert/Error_quadric.h @@ -1,164 +1,182 @@ -/*
- * Error_quadric.h
+/* This file is part of the Gudhi Library. The Gudhi library
+ * (Geometric Understanding in Higher Dimensions) is a generic C++
+ * library for computational topology.
*
- * Created on: 24 janv. 2014
- * Author: dsalinas
+ * Author(s): David Salinas
+ *
+ * Copyright (C) 2014 INRIA Sophia Antipolis-M�diterran�e (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 ERROR_QUADRIC_H_
#define ERROR_QUADRIC_H_
-#include <vector>
-#include <utility>
#include <boost/optional/optional.hpp>
+#include <vector>
+#include <utility>
-template <typename Point> class Error_quadric{
-private :
- double coeff[10];
-
-public :
- Error_quadric(){
- clear();
- }
-
- /**
- * Quadric corresponding to the L2 distance to the plane.
- *
- * According to the notation of Garland Heckbert, they
- * denote a quadric symetric matrix as :
- * Q = [ q11 q12 q13 q14]
- * [ q12 q22 q23 q24]
- * [ q13 q23 q33 q34]
- * [ q14 q24 q34 q44]
- *
- * which is represented by a vector with 10 elts that
- * are denoted ci for clarity with :
- * Q = [ c0 c1 c2 c3 ]
- * [ c1 c4 c5 c6 ]
- * [ c2 c5 c7 c8 ]
- * [ c3 c6 c8 c9 ]
- *
- * The constructor return the quadrics that represents
- * the squared distance to the plane defined by triangle p0,p1,p2
- * times the area of triangle p0,p1,p2.
- */
- Error_quadric(const Point & p0,const Point & p1,const Point & p2){
-
- Point normal(unit_normal(p0,p1,p2));
- double a=normal[0];
- double b=normal[1];
- double c=normal[2];
- double d= -a*p0[0]-b*p0[1]-c*p0[2];
- coeff[0] = a*a ;
- coeff[1] = a*b ;
- coeff[2] = a*c ;
- coeff[3] = a*d ;
- coeff[4] = b*b ;
- coeff[5] = b*c ;
- coeff[6] = b*d ;
- coeff[7] = c*c ;
- coeff[8] = c*d ;
- coeff[9] = d*d ;
-
- double area_p0p1p2 = std::sqrt(squared_area(p0,p1,p2));
- for(auto& x : coeff)
- x*= area_p0p1p2;
- }
-
-
- inline double squared_area(const Point& p0,const Point& p1,const Point& p2) {
- //if (x1,x2,x3) = p1-p0 and (y1,y2,y3) = p2-p0
- //then the squared area is = (u^2+v^2+w^2)/4
- //with: u = x2 * y3 - x3 * y2;
- // v = x3 * y1 - x1 * y3;
- // w = x1 * y2 - x2 * y1;
- Point p0p1(p1-p0);
- Point p0p2(p2-p0);
- double A = p0p1[1] * p0p2[2] - p0p1[2] * p0p2[1];
- double B = p0p1[2] * p0p2[0] - p0p1[0] * p0p2[2];
- double C = p0p1[0] * p0p2[1] - p0p1[1] * p0p2[0];
- return 1./4. * (A*A+B*B+C*C);
- }
-
-
- void clear(){
- for(auto& x:coeff)
- x=0;
- }
-
- Error_quadric& operator+=(const Error_quadric& other){
- if(this!=&other)
- for(int i = 0 ; i < 10; ++i)
- coeff[i] += other.coeff[i];
- return *this;
- }
-
- /**
- * @return The quadric quost defined by the scalar product v^T Q v where Q is the quadratic form of Garland/Heckbert
- */
- inline double cost(const Point& point) const{
- double cost =
- coeff[0]*point.x()*point.x()+coeff[4]*point.y()*point.y()+coeff[7]*point.z()*point.z()
- +2*(coeff[1]*point.x()*point.y()+coeff[5]*point.y()*point.z()+coeff[2]*point.z()*point.x())
- +2*(coeff[3]*point.x()+coeff[6]*point.y()+coeff[8]*point.z())
- +coeff[9];
- if(cost<0) return 0;
- else {
- return cost;
- }
- }
-
- inline double grad_determinant() const{
- return
- coeff[0] * coeff[4] * coeff[7]
- - coeff[0] * coeff[5] * coeff[5]
- - coeff[1] * coeff[1] * coeff[7]
- +2*coeff[1] * coeff[5] * coeff[2]
- - coeff[4] * coeff[2] * coeff[2];
- }
-
- /**
- * Return the point such that it minimizes the gradient of the quadric.
- * Det must be passed with the determinant value of the gradient (should be non zero).
- */
- inline Point solve_linear_gradient(double det) const{
- return Point({
- (-coeff[1]*coeff[5]*coeff[8]+coeff[1]*coeff[7]*coeff[6]+coeff[2]*coeff[8]*coeff[4]-coeff[2]*coeff[5]*coeff[6]-coeff[3]*coeff[4]*coeff[7]+coeff[3]*coeff[5]*coeff[5])/ det,
- (coeff[0]*coeff[5]*coeff[8]-coeff[0]*coeff[7]*coeff[6]-coeff[5]*coeff[2]*coeff[3]-coeff[1]*coeff[2]*coeff[8]+coeff[6]*coeff[2]*coeff[2]+coeff[1]*coeff[3]*coeff[7])/det,
- (-coeff[8]*coeff[0]*coeff[4]+coeff[8]*coeff[1]*coeff[1]+coeff[2]*coeff[3]*coeff[4]+coeff[5]*coeff[0]*coeff[6]-coeff[5]*coeff[1]*coeff[3]-coeff[1]*coeff[2]*coeff[6])/det
- });
- }
-
-
- /**
- * returns the point that minimizes the quadric.
- * It inverses the quadric if its determinant is higher that a given threshold .
- * If the determinant is lower than this value the returned value is uninitialized.
- */
- boost::optional<Point> min_cost(double scale=1) const{
- // const double min_determinant = 1e-4 * scale*scale;
- const double min_determinant = 1e-5;
- boost::optional<Point> pt_res;
- double det = grad_determinant();
- if (std::abs(det)>min_determinant)
- pt_res = solve_linear_gradient(det);
- return pt_res;
- }
-
- friend std::ostream& operator<< (std::ostream& stream, const Error_quadric& quadric) {
- stream << "\n[ "<<quadric.coeff[0]<<","<<quadric.coeff[1]<<","<<quadric.coeff[2]<<","<<quadric.coeff[3]<<";\n";
- stream << " "<<quadric.coeff[1]<<","<<quadric.coeff[4]<<","<<quadric.coeff[5]<<","<<quadric.coeff[6]<<";\n";
- stream << " "<<quadric.coeff[2]<<","<<quadric.coeff[5]<<","<<quadric.coeff[7]<<","<<quadric.coeff[8]<<";\n";
- stream << " "<<quadric.coeff[3]<<","<<quadric.coeff[6]<<","<<quadric.coeff[8]<<","<<quadric.coeff[9]<<"]";
- return stream;
- }
-
-
+template <typename Point> class Error_quadric {
+ private:
+ double coeff[10];
+
+ public:
+ Error_quadric() {
+ clear();
+ }
+
+ /**
+ * Quadric corresponding to the L2 distance to the plane.
+ *
+ * According to the notation of Garland Heckbert, they
+ * denote a quadric symetric matrix as :
+ * Q = [ q11 q12 q13 q14]
+ * [ q12 q22 q23 q24]
+ * [ q13 q23 q33 q34]
+ * [ q14 q24 q34 q44]
+ *
+ * which is represented by a vector with 10 elts that
+ * are denoted ci for clarity with :
+ * Q = [ c0 c1 c2 c3 ]
+ * [ c1 c4 c5 c6 ]
+ * [ c2 c5 c7 c8 ]
+ * [ c3 c6 c8 c9 ]
+ *
+ * The constructor return the quadrics that represents
+ * the squared distance to the plane defined by triangle p0,p1,p2
+ * times the area of triangle p0,p1,p2.
+ */
+ Error_quadric(const Point & p0, const Point & p1, const Point & p2) {
+ Point normal(unit_normal(p0, p1, p2));
+ double a = normal[0];
+ double b = normal[1];
+ double c = normal[2];
+ double d = -a * p0[0] - b * p0[1] - c * p0[2];
+ coeff[0] = a*a;
+ coeff[1] = a*b;
+ coeff[2] = a*c;
+ coeff[3] = a*d;
+ coeff[4] = b*b;
+ coeff[5] = b*c;
+ coeff[6] = b*d;
+ coeff[7] = c*c;
+ coeff[8] = c*d;
+ coeff[9] = d*d;
+
+ double area_p0p1p2 = std::sqrt(squared_area(p0, p1, p2));
+ for (auto& x : coeff)
+ x *= area_p0p1p2;
+ }
+
+ inline double squared_area(const Point& p0, const Point& p1, const Point& p2) {
+ // if (x1,x2,x3) = p1-p0 and (y1,y2,y3) = p2-p0
+ // then the squared area is = (u^2+v^2+w^2)/4
+ // with: u = x2 * y3 - x3 * y2;
+ // v = x3 * y1 - x1 * y3;
+ // w = x1 * y2 - x2 * y1;
+ Point p0p1(p1 - p0);
+ Point p0p2(p2 - p0);
+ double A = p0p1[1] * p0p2[2] - p0p1[2] * p0p2[1];
+ double B = p0p1[2] * p0p2[0] - p0p1[0] * p0p2[2];
+ double C = p0p1[0] * p0p2[1] - p0p1[1] * p0p2[0];
+ return 1. / 4. * (A * A + B * B + C * C);
+ }
+
+ void clear() {
+ for (auto& x : coeff)
+ x = 0;
+ }
+
+ Error_quadric& operator+=(const Error_quadric& other) {
+ if (this != &other) {
+ for (int i = 0; i < 10; ++i)
+ coeff[i] += other.coeff[i];
+ }
+ return *this;
+ }
+
+ /**
+ * @return The quadric quost defined by the scalar product v^T Q v where Q is the quadratic form of Garland/Heckbert
+ */
+ inline double cost(const Point& point) const {
+ double cost =
+ coeff[0] * point.x() * point.x() + coeff[4] * point.y() * point.y() + coeff[7] * point.z() * point.z()
+ + 2 * (coeff[1] * point.x() * point.y() + coeff[5] * point.y() * point.z() + coeff[2] * point.z() * point.x())
+ + 2 * (coeff[3] * point.x() + coeff[6] * point.y() + coeff[8] * point.z())
+ + coeff[9];
+ if (cost < 0) {
+ return 0;
+ } else {
+ return cost;
+ }
+ }
+
+ inline double grad_determinant() const {
+ return
+ coeff[0] * coeff[4] * coeff[7]
+ - coeff[0] * coeff[5] * coeff[5]
+ - coeff[1] * coeff[1] * coeff[7]
+ + 2 * coeff[1] * coeff[5] * coeff[2]
+ - coeff[4] * coeff[2] * coeff[2];
+ }
+
+ /**
+ * Return the point such that it minimizes the gradient of the quadric.
+ * Det must be passed with the determinant value of the gradient (should be non zero).
+ */
+ inline Point solve_linear_gradient(double det) const {
+ return Point({
+ (-coeff[1] * coeff[5] * coeff[8] + coeff[1] * coeff[7] * coeff[6] + coeff[2] * coeff[8] * coeff[4] -
+ coeff[2] * coeff[5] * coeff[6] - coeff[3] * coeff[4] * coeff[7] + coeff[3] * coeff[5] * coeff[5])
+ / det,
+ (coeff[0] * coeff[5] * coeff[8] - coeff[0] * coeff[7] * coeff[6] - coeff[5] * coeff[2] * coeff[3] -
+ coeff[1] * coeff[2] * coeff[8] + coeff[6] * coeff[2] * coeff[2] + coeff[1] * coeff[3] * coeff[7])
+ / det,
+ (-coeff[8] * coeff[0] * coeff[4] + coeff[8] * coeff[1] * coeff[1] + coeff[2] * coeff[3] * coeff[4] +
+ coeff[5] * coeff[0] * coeff[6] - coeff[5] * coeff[1] * coeff[3] - coeff[1] * coeff[2] * coeff[6])
+ / det
+ });
+ }
+
+ /**
+ * returns the point that minimizes the quadric.
+ * It inverses the quadric if its determinant is higher that a given threshold .
+ * If the determinant is lower than this value the returned value is uninitialized.
+ */
+ boost::optional<Point> min_cost(double scale = 1) const {
+ // const double min_determinant = 1e-4 * scale*scale;
+ const double min_determinant = 1e-5;
+ boost::optional<Point> pt_res;
+ double det = grad_determinant();
+ if (std::abs(det) > min_determinant)
+ pt_res = solve_linear_gradient(det);
+ return pt_res;
+ }
+
+ friend std::ostream& operator<<(std::ostream& stream, const Error_quadric& quadric) {
+ stream << "\n[ " << quadric.coeff[0] << "," << quadric.coeff[1] << "," << quadric.coeff[2] << "," <<
+ quadric.coeff[3] << ";\n";
+ stream << " " << quadric.coeff[1] << "," << quadric.coeff[4] << "," << quadric.coeff[5] << "," <<
+ quadric.coeff[6] << ";\n";
+ stream << " " << quadric.coeff[2] << "," << quadric.coeff[5] << "," << quadric.coeff[7] << "," <<
+ quadric.coeff[8] << ";\n";
+ stream << " " << quadric.coeff[3] << "," << quadric.coeff[6] << "," << quadric.coeff[8] << "," <<
+ quadric.coeff[9] << "]";
+ return stream;
+ }
};
-
-
-
-#endif /* ERROR_QUADRIC_H_ */
-
+#endif // ERROR_QUADRIC_H_
diff --git a/src/Contraction/example/Rips_contraction.cpp b/src/Contraction/example/Rips_contraction.cpp index bd0a8b8c..d21246ed 100644 --- a/src/Contraction/example/Rips_contraction.cpp +++ b/src/Contraction/example/Rips_contraction.cpp @@ -19,24 +19,23 @@ * 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/Edge_contraction.h> +#include <gudhi/Skeleton_blocker.h> +#include <gudhi/Off_reader.h> +#include <gudhi/Point.h> + #include <boost/timer/timer.hpp> #include <iostream> -#include "gudhi/Edge_contraction.h" -#include "gudhi/Skeleton_blocker.h" -#include "gudhi/Off_reader.h" -#include "gudhi/Point.h" using namespace std; using namespace Gudhi; using namespace skbl; using namespace contraction; - -struct Geometry_trait{ - typedef Point_d Point; +struct Geometry_trait { + typedef Point_d Point; }; - typedef Geometry_trait::Point Point; typedef Skeleton_blocker_simple_geometric_traits<Geometry_trait> Complex_geometric_traits; typedef Skeleton_blocker_geometric_complex< Complex_geometric_traits > Complex; @@ -44,62 +43,62 @@ typedef Edge_profile<Complex> Profile; typedef Skeleton_blocker_contractor<Complex> Complex_contractor; template<typename ComplexType> -void build_rips(ComplexType& complex, double offset){ - if (offset<=0) return; - auto vertices = complex.vertex_range(); - for (auto p = vertices.begin(); p != vertices.end(); ++p) - for (auto q = p; ++q != vertices.end(); /**/){ - if ( squared_dist(complex.point(*p), complex.point(*q)) < 4 * offset * offset) - complex.add_edge(*p,*q); - } +void build_rips(ComplexType& complex, double offset) { + if (offset <= 0) return; + auto vertices = complex.vertex_range(); + for (auto p = vertices.begin(); p != vertices.end(); ++p) + for (auto q = p; ++q != vertices.end(); /**/) { + if (squared_dist(complex.point(*p), complex.point(*q)) < 4 * offset * offset) + complex.add_edge(*p, *q); + } } -int main (int argc, char *argv[]) -{ - if (argc!=3){ - std::cerr << "Usage "<<argv[0]<<" ../../../data/meshes/SO3_10000.off 0.3 to load the file ../../data/SO3_10000.off and contract the Rips complex built with paremeter 0.3.\n"; - return -1; - } +int main(int argc, char *argv[]) { + if (argc != 3) { + std::cerr << "Usage " << argv[0] << " ../../../data/meshes/SO3_10000.off 0.3 to load the file " << + "../../data/SO3_10000.off and contract the Rips complex built with paremeter 0.3.\n"; + return -1; + } - Complex complex; + Complex complex; - // load only the points - Skeleton_blocker_off_reader<Complex> off_reader(argv[1],complex,true); - if(!off_reader.is_valid()){ - std::cerr << "Unable to read file:"<<argv[1]<<std::endl; - return EXIT_FAILURE; - } + // load only the points + Skeleton_blocker_off_reader<Complex> off_reader(argv[1], complex, true); + if (!off_reader.is_valid()) { + std::cerr << "Unable to read file:" << argv[1] << std::endl; + return EXIT_FAILURE; + } - std::cout << "Build the Rips complex with "<<complex.num_vertices()<<" vertices"<<std::endl; + std::cout << "Build the Rips complex with " << complex.num_vertices() << " vertices" << std::endl; - build_rips(complex,atof(argv[2])); + build_rips(complex, atof(argv[2])); - boost::timer::auto_cpu_timer t; + boost::timer::auto_cpu_timer t; - std::cout << "Initial complex has "<< - complex.num_vertices()<<" vertices and "<< - complex.num_edges()<<" edges"<<std::endl; + std::cout << "Initial complex has " << + complex.num_vertices() << " vertices and " << + complex.num_edges() << " edges" << std::endl; - Complex_contractor contractor(complex, - new Edge_length_cost<Profile>, - contraction::make_first_vertex_placement<Profile>(), - contraction::make_link_valid_contraction<Profile>(), - contraction::make_remove_popable_blockers_visitor<Profile>()); - contractor.contract_edges(); + Complex_contractor contractor(complex, + new Edge_length_cost<Profile>, + contraction::make_first_vertex_placement<Profile>(), + contraction::make_link_valid_contraction<Profile>(), + contraction::make_remove_popable_blockers_visitor<Profile>()); + contractor.contract_edges(); - std::cout << "Counting final number of simplices \n"; - unsigned num_simplices = std::distance(complex.simplex_range().begin(),complex.simplex_range().end()); + std::cout << "Counting final number of simplices \n"; + unsigned num_simplices = std::distance(complex.simplex_range().begin(), complex.simplex_range().end()); - std::cout << "Final complex has "<< - complex.num_vertices()<<" vertices, "<< - complex.num_edges()<<" edges, "<< - complex.num_blockers()<<" blockers and "<< - num_simplices<<" simplices"<<std::endl; + std::cout << "Final complex has " << + complex.num_vertices() << " vertices, " << + complex.num_edges() << " edges, " << + complex.num_blockers() << " blockers and " << + num_simplices << " simplices" << std::endl; - std::cout << "Time to simplify and enumerate simplices:\n"; + std::cout << "Time to simplify and enumerate simplices:\n"; - return EXIT_SUCCESS; + return EXIT_SUCCESS; } diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index 3276989d..435d2f58 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -5,6 +5,7 @@ project(GUDHIExPersCohom) if (NOT MSVC) add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp) target_link_libraries(persistence_from_simple_simplex_tree ${Boost_SYSTEM_LIBRARY}) + add_test(persistence_from_simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_simple_simplex_tree 1 0) add_executable(rips_persistence rips_persistence.cpp) target_link_libraries(rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) diff --git a/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp b/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp index 1e907040..6d5eebcf 100644 --- a/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp +++ b/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp @@ -1,24 +1,29 @@ - /* 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/>. - */ +/* 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/graph_simplicial_complex.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/Persistent_cohomology.h> +#include <boost/variant.hpp> #include <CGAL/Exact_predicates_inexact_constructions_kernel.h> #include <CGAL/Delaunay_triangulation_3.h> @@ -27,36 +32,37 @@ #include <fstream> #include <cmath> - -#include "gudhi/graph_simplicial_complex.h" -#include "gudhi/Simplex_tree.h" -#include "gudhi/Persistent_cohomology.h" -#include <boost/variant.hpp> +#include <string> +#include <tuple> +#include <map> +#include <utility> +#include <list> +#include <vector> using namespace Gudhi; using namespace Gudhi::persistent_cohomology; // Alpha_shape_3 templates type definitions typedef CGAL::Exact_predicates_inexact_constructions_kernel Kernel; -typedef CGAL::Alpha_shape_vertex_base_3<Kernel> Vb; -typedef CGAL::Alpha_shape_cell_base_3<Kernel> 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> Alpha_shape_3; +typedef CGAL::Alpha_shape_vertex_base_3<Kernel> Vb; +typedef CGAL::Alpha_shape_cell_base_3<Kernel> 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> Alpha_shape_3; // From file type definition -typedef Kernel::Point_3 Point_3; +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::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; +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 std::list<Alpha_shape_3::Vertex_handle> Vertex_list; // gudhi type definition @@ -65,70 +71,60 @@ typedef std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex > Alpha_shape 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; -//#define DEBUG_TRACES - -Vertex_list from (const Cell_handle& ch) -{ +Vertex_list from(const Cell_handle& ch) { Vertex_list the_list; - for (auto i = 0; i < 4; i++) - { + for (auto i = 0; i < 4; i++) { #ifdef DEBUG_TRACES std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES +#endif // DEBUG_TRACES the_list.push_back(ch->vertex(i)); } return the_list; } -Vertex_list from (const Facet& fct) -{ + +Vertex_list from(const Facet& fct) { Vertex_list the_list; - for (auto i = 0; i < 4; i++) - { - if (fct.second != i) - { + 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 +#endif // DEBUG_TRACES the_list.push_back(fct.first->vertex(i)); } } return the_list; } -Vertex_list from (const Edge_3& edg) -{ + +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)) - { + 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 +#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 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 +#endif // DEBUG_TRACES the_list.push_back(vh); return the_list; } -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); // ----- >> +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[]) -{ - - int coeff_field_characteristic=0; +int main(int argc, char * const argv[]) { + int coeff_field_characteristic = 0; int returnedScanValue = sscanf(argv[2], "%d", &coeff_field_characteristic); if ((returnedScanValue == EOF) || (coeff_field_characteristic <= 0)) { std::cerr << "Error: " << argv[2] << " is not correct\n"; @@ -149,102 +145,96 @@ int main (int argc, char * const argv[]) } // Read points from file - std::string filegraph = argv[1]; + std::string filegraph = argv[1]; std::list<Point_3> lp; std::ifstream is(filegraph.c_str()); int n; is >> n; #ifdef DEBUG_TRACES std::cout << "Reading " << n << " points " << std::endl; -#endif // DEBUG_TRACES +#endif // DEBUG_TRACES Point_3 p; - for( ; n>0 ; n--) { + for (; n > 0; n--) { is >> p; lp.push_back(p); } // 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); + 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 +#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)); + 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 +#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; + 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; Simplex_tree<> 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) - { + 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)) - { + if (const Cell_handle * cell = CGAL::object_cast<Cell_handle>(&object_iterator)) { vertex_list = from(*cell); count_cells++; if (dim_max < 3) { - dim_max=3; // Cell is of dim 3 + // Cell is of dim 3 + dim_max = 3; } - } - else if (const Facet* facet = CGAL::object_cast<Facet>(&object_iterator)) - { + } else if (const Facet * facet = CGAL::object_cast<Facet>(&object_iterator)) { vertex_list = from(*facet); count_facets++; if (dim_max < 2) { - dim_max=2; // Facet is of dim 2 + // Facet is of dim 2 + dim_max = 2; } - } - else if (const Edge_3* edge = CGAL::object_cast<Edge_3>(&object_iterator)) - { + } else if (const Edge_3 * edge = CGAL::object_cast<Edge_3>(&object_iterator)) { vertex_list = from(*edge); count_edges++; if (dim_max < 1) { - dim_max=1; // Edge_3 is of dim 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)) - { + } 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); } // 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) - { + 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()) - { + 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 +#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 - { + 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 +#endif // DEBUG_TRACES the_simplex_tree.push_back(vertex); } } @@ -252,7 +242,7 @@ int main (int argc, char * const argv[]) Filtration_value filtr = std::sqrt(*the_alpha_value_iterator); #ifdef DEBUG_TRACES std::cout << "filtration = " << filtr << std::endl; -#endif // DEBUG_TRACES +#endif // DEBUG_TRACES if (filtr > filtration_max) { filtration_max = filtr; } @@ -267,9 +257,9 @@ int main (int argc, char * const argv[]) #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 << "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; @@ -277,23 +267,25 @@ int main (int argc, char * const argv[]) 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 +#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 + 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 - Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh( simplex_tree ); - pcoh.init_coefficients( coeff_field_characteristic ); //initializes the coefficient field for homology + Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh(simplex_tree); + // 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(); diff --git a/src/Persistent_cohomology/example/performance_rips_persistence.cpp b/src/Persistent_cohomology/example/performance_rips_persistence.cpp index 077c2b07..0e912d57 100644 --- a/src/Persistent_cohomology/example/performance_rips_persistence.cpp +++ b/src/Persistent_cohomology/example/performance_rips_persistence.cpp @@ -1,49 +1,51 @@ - /* 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): Clément Maria - * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (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/reader_utils.h" -#include "gudhi/graph_simplicial_complex.h" -#include "gudhi/distance_functions.h" -#include "gudhi/Simplex_tree.h" -#include "gudhi/Persistent_cohomology.h" -#include "gudhi/Persistent_cohomology/Multi_field.h" -#include "gudhi/Hasse_complex.h" +/* 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): Clément Maria + * + * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (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/reader_utils.h> +#include <gudhi/graph_simplicial_complex.h> +#include <gudhi/distance_functions.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/Persistent_cohomology.h> +#include <gudhi/Persistent_cohomology/Multi_field.h> +#include <gudhi/Hasse_complex.h> #include <chrono> +#include <string> +#include <vector> using namespace Gudhi; using namespace Gudhi::persistent_cohomology; /* Compute the persistent homology of the complex cpx with coefficients in Z/pZ. */ template< typename FilteredComplex> -void timing_persistence( FilteredComplex & cpx - , int p ); +void timing_persistence(FilteredComplex & cpx + , int p); /* Compute multi-field persistent homology of the complex cpx with coefficients in * Z/rZ for all prime number r in [p;q].*/ template< typename FilteredComplex> -void timing_persistence( FilteredComplex & cpx - , int p - , int q ); +void timing_persistence(FilteredComplex & cpx + , int p + , int q); /* Timings for the computation of persistent homology with different * representations of a Rips complex and different coefficient fields. The @@ -59,111 +61,111 @@ void timing_persistence( FilteredComplex & cpx * We present also timings for the computation of multi-field persistent * homology in all fields Z/rZ for r prime between 2 and 1223. */ -int main (int argc, char * argv[]) -{ +int main(int argc, char * argv[]) { std::chrono::time_point<std::chrono::system_clock> start, end; int enlapsed_sec; - std::string filepoints = "../examples/Kl.txt"; - Filtration_value threshold = 0.3; - int dim_max = 3; - int p = 2; - int q = 1223; + std::string filepoints = "../examples/Kl.txt"; + Filtration_value threshold = 0.3; + int dim_max = 3; + int p = 2; + int q = 1223; -// Extract the points from the file filepoints + // Extract the points from the file filepoints typedef std::vector<double> Point_t; std::vector< Point_t > points; - read_points( filepoints, points ); + read_points(filepoints, points); -// Compute the proximity graph of the points + // Compute the proximity graph of the points start = std::chrono::system_clock::now(); - Graph_t prox_graph = compute_proximity_graph( points, threshold - , euclidean_distance<Point_t> ); + Graph_t prox_graph = compute_proximity_graph(points, threshold + , euclidean_distance<Point_t>); end = std::chrono::system_clock::now(); - enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end-start).count(); + enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count(); std::cout << "Compute Rips graph in " << enlapsed_sec << " sec.\n"; -// Construct the Rips complex in a Simplex Tree - Simplex_tree<> st; + // Construct the Rips complex in a Simplex Tree + Simplex_tree<> st; start = std::chrono::system_clock::now(); - st.insert_graph(prox_graph); // insert the proximity graph in the simplex tree - st.expansion( dim_max ); // expand the graph until dimension dim_max + // insert the proximity graph in the simplex tree + st.insert_graph(prox_graph); + // expand the graph until dimension dim_max + st.expansion(dim_max); end = std::chrono::system_clock::now(); - enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end-start).count(); + enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count(); std::cout << "Compute Rips complex in " << enlapsed_sec << " sec.\n"; std::cout << " - dimension = " << st.dimension() << std::endl; std::cout << " - number of simplices = " << st.num_simplices() << std::endl; -// Sort the simplices in the order of the filtration + // Sort the simplices in the order of the filtration start = std::chrono::system_clock::now(); st.initialize_filtration(); end = std::chrono::system_clock::now(); - enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end-start).count(); + enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count(); std::cout << "Order the simplices of the filtration in " << enlapsed_sec << " sec.\n"; -// Convert the simplex tree into a hasse diagram + // Convert the simplex tree into a hasse diagram start = std::chrono::system_clock::now(); Hasse_complex<> hcpx(st); end = std::chrono::system_clock::now(); - enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end-start).count(); + enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count(); std::cout << "Convert the simplex tree into a Hasse diagram in " << enlapsed_sec << " sec.\n"; std::cout << "Timings when using a simplex tree: \n"; - timing_persistence(st,p); - timing_persistence(st,q); - timing_persistence(st,p,q); + timing_persistence(st, p); + timing_persistence(st, q); + timing_persistence(st, p, q); std::cout << "Timings when using a Hasse complex: \n"; - timing_persistence(hcpx,p); - timing_persistence(hcpx,q); - timing_persistence(hcpx,p,q); + timing_persistence(hcpx, p); + timing_persistence(hcpx, q); + timing_persistence(hcpx, p, q); return 0; } - template< typename FilteredComplex> void -timing_persistence( FilteredComplex & cpx - , int p ) -{ +timing_persistence(FilteredComplex & cpx + , int p) { std::chrono::time_point<std::chrono::system_clock> start, end; int enlapsed_sec; - Persistent_cohomology< FilteredComplex, Field_Zp > pcoh (cpx); - pcoh.init_coefficients( p ); //initilizes the coefficient field for homology - + Persistent_cohomology< FilteredComplex, Field_Zp > pcoh(cpx); + // initializes the coefficient field for homology + pcoh.init_coefficients(p); + start = std::chrono::system_clock::now(); - - pcoh.compute_persistent_cohomology( INFINITY ); - + + pcoh.compute_persistent_cohomology(INFINITY); + end = std::chrono::system_clock::now(); - enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end-start).count(); - std::cout << " Compute persistent homology in Z/"<<p<<"Z in " << enlapsed_sec << " sec.\n"; + enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count(); + std::cout << " Compute persistent homology in Z/" << p << "Z in " << enlapsed_sec << " sec.\n"; } template< typename FilteredComplex> void -timing_persistence( FilteredComplex & cpx - , int p - , int q ) -{ +timing_persistence(FilteredComplex & cpx + , int p + , int q) { std::chrono::time_point<std::chrono::system_clock> start, end; int enlapsed_sec; - Persistent_cohomology< FilteredComplex, Multi_field > pcoh (cpx); - pcoh.init_coefficients( p, q ); //initilizes the coefficient field for homology + Persistent_cohomology< FilteredComplex, Multi_field > pcoh(cpx); + // initializes the coefficient field for homology + pcoh.init_coefficients(p, q); // compute persistent homology, disgarding persistent features of life shorter than min_persistence start = std::chrono::system_clock::now(); - pcoh.compute_persistent_cohomology( INFINITY ); + pcoh.compute_persistent_cohomology(INFINITY); end = std::chrono::system_clock::now(); - enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end-start).count(); + enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count(); std::cout << " Compute multi-field persistent homology in all coefficient fields Z/pZ " - << "with p in ["<<p<<";"<<q<<"] in " << enlapsed_sec << " sec.\n"; + << "with p in [" << p << ";" << q << "] in " << enlapsed_sec << " sec.\n"; } diff --git a/src/Persistent_cohomology/example/persistence_from_file.cpp b/src/Persistent_cohomology/example/persistence_from_file.cpp index e886aea7..8eb8d0f3 100644 --- a/src/Persistent_cohomology/example/persistence_from_file.cpp +++ b/src/Persistent_cohomology/example/persistence_from_file.cpp @@ -1,141 +1,144 @@ - /* 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/reader_utils.h" -#include "gudhi/graph_simplicial_complex.h" -#include "gudhi/distance_functions.h" -#include "gudhi/Simplex_tree.h" -#include "gudhi/Persistent_cohomology.h" +/* 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/reader_utils.h> +#include <gudhi/graph_simplicial_complex.h> +#include <gudhi/distance_functions.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/Persistent_cohomology.h> #include <boost/program_options.hpp> +#include <string> + using namespace Gudhi; using namespace Gudhi::persistent_cohomology; -typedef int Vertex_handle; -typedef double Filtration_value; - -void program_options( int argc, char * argv[] - , std::string & simplex_tree_file - , std::string & output_file - , int & p - , Filtration_value & min_persistence ); - -int main (int argc, char * argv[]) -{ - std::string simplex_tree_file; - std::string output_file ; - int p ; - Filtration_value min_persistence; - - program_options(argc,argv,simplex_tree_file,output_file,p,min_persistence); - - std::cout << "Simplex_tree from file=" << simplex_tree_file.c_str() << " - output_file=" << output_file.c_str() << std::endl; - std::cout << " - p=" << p << " - min_persistence=" << min_persistence << std::endl; - - // Construct the Rips complex in a Simplex Tree - Simplex_tree<> simplex_tree; - - std::ifstream simplex_tree_stream(simplex_tree_file); - simplex_tree_stream >> simplex_tree; - - std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices" << std::endl; - std::cout << " - dimension " << simplex_tree.dimension() << " - filtration " << simplex_tree.filtration() << std::endl; - - /* - std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl; - for( auto f_simplex : simplex_tree.filtration_simplex_range() ) - { std::cout << " " << "[" << simplex_tree.filtration(f_simplex) << "] "; - for( auto vertex : simplex_tree.simplex_vertex_range(f_simplex) ) - { std::cout << vertex << " "; } - std::cout << std::endl; - }*/ - - // Sort the simplices in the order of the filtration - simplex_tree.initialize_filtration(); - - // Compute the persistence diagram of the complex - Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh( simplex_tree ); - pcoh.init_coefficients( p ); //initilizes the coefficient field for homology - - pcoh.compute_persistent_cohomology( min_persistence ); - - // Output the diagram in output_file - if(output_file.empty()) { pcoh.output_diagram(); } - else { - std::ofstream out(output_file); - pcoh.output_diagram(out); - out.close(); } +typedef int Vertex_handle; +typedef double Filtration_value; + +void program_options(int argc, char * argv[] + , std::string & simplex_tree_file + , std::string & output_file + , int & p + , Filtration_value & min_persistence); + +int main(int argc, char * argv[]) { + std::string simplex_tree_file; + std::string output_file; + int p; + Filtration_value min_persistence; + + program_options(argc, argv, simplex_tree_file, output_file, p, min_persistence); + + std::cout << "Simplex_tree from file=" << simplex_tree_file.c_str() << " - output_file=" << output_file.c_str() + << std::endl; + std::cout << " - p=" << p << " - min_persistence=" << min_persistence << std::endl; + + // Construct the Rips complex in a Simplex Tree + Simplex_tree<> simplex_tree; + + std::ifstream simplex_tree_stream(simplex_tree_file); + simplex_tree_stream >> simplex_tree; + + std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices" << std::endl; + std::cout << " - dimension " << simplex_tree.dimension() << " - filtration " << simplex_tree.filtration() + << std::endl; + + /* + std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl; + for( auto f_simplex : simplex_tree.filtration_simplex_range() ) + { std::cout << " " << "[" << simplex_tree.filtration(f_simplex) << "] "; + for( auto vertex : simplex_tree.simplex_vertex_range(f_simplex) ) + { std::cout << vertex << " "; } + std::cout << std::endl; + }*/ + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + // Compute the persistence diagram of the complex + Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh(simplex_tree); + // initializes the coefficient field for homology + pcoh.init_coefficients(p); + + pcoh.compute_persistent_cohomology(min_persistence); + + // Output the diagram in output_file + if (output_file.empty()) { + pcoh.output_diagram(); + } else { + std::ofstream out(output_file); + pcoh.output_diagram(out); + out.close(); + } - return 0; + return 0; } - - -void program_options( int argc, char * argv[] - , std::string & simplex_tree_file - , std::string & output_file - , int & p - , Filtration_value & min_persistence ) -{ +void program_options(int argc, char * argv[] + , std::string & simplex_tree_file + , std::string & output_file + , int & p + , Filtration_value & min_persistence) { namespace po = boost::program_options; - po::options_description hidden("Hidden options"); + po::options_description hidden("Hidden options"); hidden.add_options() - ("input-file", po::value<std::string>(&simplex_tree_file), - "Name of file containing a simplex set. Format is one simplex per line (cf. reader_utils.h - read_simplex): Dim1 X11 X12 ... X1d Fil1 "); - + ("input-file", po::value<std::string>(&simplex_tree_file), + "Name of file containing a simplex set. Format is one simplex per line (cf. reader_utils.h - read_simplex): Dim1 X11 X12 ... X1d Fil1 "); + po::options_description visible("Allowed options", 100); visible.add_options() - ("help,h", "produce help message") - ("output-file,o", po::value<std::string>(&output_file)->default_value(std::string()), - "Name of file in which the persistence diagram is written. Default print in std::cout") - ("field-charac,p", po::value<int>(&p)->default_value(11), - "Characteristic p of the coefficient field Z/pZ for computing homology.") - ("min-persistence,m", po::value<Filtration_value>(&min_persistence), - "Minimal lifetime of homology feature to be recorded. Default is 0"); + ("help,h", "produce help message") + ("output-file,o", po::value<std::string>(&output_file)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout") + ("field-charac,p", po::value<int>(&p)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.") + ("min-persistence,m", po::value<Filtration_value>(&min_persistence), + "Minimal lifetime of homology feature to be recorded. Default is 0"); po::positional_options_description pos; pos.add("input-file", 1); - - po::options_description all; all.add(visible).add(hidden); + + po::options_description all; + all.add(visible).add(hidden); po::variables_map vm; po::store(po::command_line_parser(argc, argv). - options(all).positional(pos).run(), vm); + options(all).positional(pos).run(), vm); po::notify(vm); - if (vm.count("help") || !vm.count("input-file")) - { - std::cout << std::endl; - std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; - std::cout << "of a Rips complex defined on a set of input points.\n \n"; - std::cout << "The output diagram contains one bar per line, written with the convention: \n"; - std::cout << " p dim b d \n"; - std::cout << "where dim is the dimension of the homological feature,\n"; - std::cout << "b and d are respectively the birth and death of the feature and \n"; - std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; - - std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; - std::cout << visible << std::endl; - std::abort(); + if (vm.count("help") || !vm.count("input-file")) { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of a Rips complex defined on a set of input points.\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); } } diff --git a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp index ba82e4e6..ba772f04 100644 --- a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp +++ b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp @@ -20,11 +20,14 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ +#include <gudhi/graph_simplicial_complex.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/Persistent_cohomology.h> + #include <iostream> #include <ctime> -#include "gudhi/graph_simplicial_complex.h" -#include "gudhi/Simplex_tree.h" -#include "gudhi/Persistent_cohomology.h" +#include <utility> +#include <vector> using namespace Gudhi; using namespace Gudhi::persistent_cohomology; @@ -34,15 +37,19 @@ typedef std::pair<typeVectorVertex, Filtration_value> typeSimplex; typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool; typedef Simplex_tree<> typeST; -void usage(char * const progName) -{ +void usage(char * const progName) { std::cerr << "Usage: " << progName << " coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; - exit(-1); // ----- >> + exit(-1); } -int main (int argc, char * const argv[]) -{ - int coeff_field_characteristic=0; +int main(int argc, char * const argv[]) { + // program args management + if (argc != 3) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; + usage(argv[0]); + } + + int coeff_field_characteristic = 0; int returnedScanValue = sscanf(argv[1], "%d", &coeff_field_characteristic); if ((returnedScanValue == EOF) || (coeff_field_characteristic <= 0)) { std::cerr << "Error: " << argv[1] << " is not correct\n"; @@ -56,101 +63,65 @@ int main (int argc, char * const argv[]) usage(argv[0]); } - // program args management - if (argc != 3) { - std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; - usage(argv[0]); - } - // TEST OF INSERTION std::cout << "********************************************************************" << std::endl; std::cout << "TEST OF INSERTION" << std::endl; typeST st; // ++ FIRST - std::cout << " - INSERT (2,1,0)" << std::endl; - typeVectorVertex SimplexVector1; - SimplexVector1.push_back(2); - SimplexVector1.push_back(1); - SimplexVector1.push_back(0); - st.insert_simplex_and_subfaces ( SimplexVector1, 0.3); + std::cout << " - INSERT (0,1,2)" << std::endl; + typeVectorVertex SimplexVector = {0, 1, 2}; + st.insert_simplex_and_subfaces(SimplexVector, 0.3); // ++ SECOND std::cout << " - INSERT 3" << std::endl; - typeVectorVertex SimplexVector2; - SimplexVector2.push_back(3); - st.insert_simplex_and_subfaces ( SimplexVector2, 0.1); + SimplexVector = {3}; + st.insert_simplex_and_subfaces(SimplexVector, 0.1); // ++ THIRD std::cout << " - INSERT (0,3)" << std::endl; - typeVectorVertex SimplexVector3; - SimplexVector3.push_back(3); - SimplexVector3.push_back(0); - st.insert_simplex_and_subfaces ( SimplexVector3, 0.2); + SimplexVector = {0, 3}; + st.insert_simplex_and_subfaces(SimplexVector, 0.2); // ++ FOURTH - std::cout << " - INSERT (1,0) (already inserted)" << std::endl; - typeVectorVertex SimplexVector4; - SimplexVector4.push_back(1); - SimplexVector4.push_back(0); - st.insert_simplex_and_subfaces ( SimplexVector4, 0.2); + std::cout << " - INSERT (0,1) (already inserted)" << std::endl; + SimplexVector = {0, 1}; + st.insert_simplex_and_subfaces(SimplexVector, 0.2); // ++ FIFTH std::cout << " - INSERT (3,4,5)" << std::endl; - typeVectorVertex SimplexVector5; - SimplexVector5.push_back(3); - SimplexVector5.push_back(4); - SimplexVector5.push_back(5); - st.insert_simplex_and_subfaces ( SimplexVector5, 0.3); + SimplexVector = {3, 4, 5}; + st.insert_simplex_and_subfaces(SimplexVector, 0.3); // ++ SIXTH std::cout << " - INSERT (0,1,6,7)" << std::endl; - typeVectorVertex SimplexVector6; - SimplexVector6.push_back(0); - SimplexVector6.push_back(1); - SimplexVector6.push_back(6); - SimplexVector6.push_back(7); - st.insert_simplex_and_subfaces ( SimplexVector6, 0.4); + SimplexVector = {0, 1, 6, 7}; + st.insert_simplex_and_subfaces(SimplexVector, 0.4); // ++ SEVENTH std::cout << " - INSERT (4,5,8,9)" << std::endl; - typeVectorVertex SimplexVector7; - SimplexVector7.push_back(4); - SimplexVector7.push_back(5); - SimplexVector7.push_back(8); - SimplexVector7.push_back(9); - st.insert_simplex_and_subfaces ( SimplexVector7, 0.4); + SimplexVector = {4, 5, 8, 9}; + st.insert_simplex_and_subfaces(SimplexVector, 0.4); // ++ EIGHTH std::cout << " - INSERT (9,10,11)" << std::endl; - typeVectorVertex SimplexVector8; - SimplexVector8.push_back(9); - SimplexVector8.push_back(10); - SimplexVector8.push_back(11); - st.insert_simplex_and_subfaces ( SimplexVector8, 0.3); - + SimplexVector = {9, 10, 11}; + st.insert_simplex_and_subfaces(SimplexVector, 0.3); + // ++ NINETH std::cout << " - INSERT (2,10,12)" << std::endl; - typeVectorVertex SimplexVector9; - SimplexVector9.push_back(2); - SimplexVector9.push_back(10); - SimplexVector9.push_back(12); - st.insert_simplex_and_subfaces ( SimplexVector9, 0.3); - + SimplexVector = {2, 10, 12}; + st.insert_simplex_and_subfaces(SimplexVector, 0.3); + // ++ TENTH std::cout << " - INSERT (11,6)" << std::endl; - typeVectorVertex SimplexVector10; - SimplexVector10.push_back(11); - SimplexVector10.push_back(6); - st.insert_simplex_and_subfaces ( SimplexVector10, 0.2); + SimplexVector = {6, 11}; + st.insert_simplex_and_subfaces(SimplexVector, 0.2); // ++ ELEVENTH std::cout << " - INSERT (13,14,15)" << std::endl; - typeVectorVertex SimplexVector11; - SimplexVector11.push_back(13); - SimplexVector11.push_back(14); - SimplexVector11.push_back(15); - st.insert_simplex_and_subfaces ( SimplexVector11, 0.25); + SimplexVector = {13, 14, 15}; + st.insert_simplex_and_subfaces(SimplexVector, 0.25); /* Inserted simplex: */ /* 1 6 */ @@ -175,33 +146,31 @@ int main (int argc, char * const argv[]) st.set_dimension(2); st.set_filtration(0.4); - std::cout << "The complex contains " << st.num_simplices() << " simplices - " << st.num_vertices() << " vertices " << std::endl; + std::cout << "The complex contains " << st.num_simplices() << " simplices - " << st.num_vertices() << " vertices " + << std::endl; std::cout << " - dimension " << st.dimension() << " - filtration " << st.filtration() << std::endl; - std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl; + std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" + << std::endl; std::cout << "**************************************************************" << std::endl; std::cout << "strict graph G { " << std::endl; - for( auto f_simplex : st.filtration_simplex_range() ) - { + for (auto f_simplex : st.filtration_simplex_range()) { std::cout << " " << "[" << st.filtration(f_simplex) << "] "; - for( auto vertex : st.simplex_vertex_range(f_simplex) ) - { - std::cout << (int)vertex << " -- "; + for (auto vertex : st.simplex_vertex_range(f_simplex)) { + std::cout << static_cast<int>(vertex) << " -- "; } std::cout << ";" << std::endl; } std::cout << "}" << std::endl; - //std::cout << "**************************************************************" << std::endl; - //st.print_hasse(std::cout); std::cout << "**************************************************************" << std::endl; - // Compute the persistence diagram of the complex persistent_cohomology::Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh(st); - pcoh.init_coefficients( coeff_field_characteristic ); //initiliazes the coefficient field for homology + // initializes the coefficient field for homology + pcoh.init_coefficients(coeff_field_characteristic); - pcoh.compute_persistent_cohomology( min_persistence ); + pcoh.compute_persistent_cohomology(min_persistence); // Output the diagram in filediag pcoh.output_diagram(); diff --git a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp index 297a8f98..5277bf7a 100644 --- a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp +++ b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp @@ -1,153 +1,157 @@ - /* 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): Clément Maria - * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (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/reader_utils.h" -#include "gudhi/graph_simplicial_complex.h" -#include "gudhi/distance_functions.h" -#include "gudhi/Simplex_tree.h" -#include "gudhi/Persistent_cohomology.h" -#include "gudhi/Persistent_cohomology/Multi_field.h" +/* 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): Clément Maria + * + * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (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/reader_utils.h> +#include <gudhi/graph_simplicial_complex.h> +#include <gudhi/distance_functions.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/Persistent_cohomology.h> +#include <gudhi/Persistent_cohomology/Multi_field.h> #include <boost/program_options.hpp> +#include <string> +#include <vector> + using namespace Gudhi; using namespace Gudhi::persistent_cohomology; -typedef int Vertex_handle; +typedef int Vertex_handle; typedef double Filtration_value; -void program_options( int argc, char * argv[] - , std::string & filepoints - , std::string & filediag - , Filtration_value & threshold - , int & dim_max - , int & min_p - , int & max_p - , Filtration_value & min_persistence ); - -int main (int argc, char * argv[]) -{ - std::string filepoints; - std::string filediag; +void program_options(int argc, char * argv[] + , std::string & filepoints + , std::string & filediag + , Filtration_value & threshold + , int & dim_max + , int & min_p + , int & max_p + , Filtration_value & min_persistence); + +int main(int argc, char * argv[]) { + std::string filepoints; + std::string filediag; Filtration_value threshold; - int dim_max; - int min_p; - int max_p; + int dim_max; + int min_p; + int max_p; Filtration_value min_persistence; - program_options(argc,argv,filepoints,filediag,threshold,dim_max,min_p,max_p,min_persistence); + program_options(argc, argv, filepoints, filediag, threshold, dim_max, min_p, max_p, min_persistence); -// Extract the points from the file filepoints + // Extract the points from the file filepoints typedef std::vector<double> Point_t; std::vector< Point_t > points; - read_points( filepoints, points ); + read_points(filepoints, points); -// Compute the proximity graph of the points - Graph_t prox_graph = compute_proximity_graph( points, threshold - , euclidean_distance<Point_t> ); + // Compute the proximity graph of the points + Graph_t prox_graph = compute_proximity_graph(points, threshold + , euclidean_distance<Point_t>); -// Construct the Rips complex in a Simplex Tree - Simplex_tree<> st; - st.insert_graph(prox_graph); // insert the proximity graph in the simplex tree - st.expansion( dim_max ); // expand the graph until dimension dim_max + // Construct the Rips complex in a Simplex Tree + Simplex_tree<> st; + // insert the proximity graph in the simplex tree + st.insert_graph(prox_graph); + // expand the graph until dimension dim_max + st.expansion(dim_max); -// Sort the simplices in the order of the filtration + // Sort the simplices in the order of the filtration st.initialize_filtration(); -// Compute the persistence diagram of the complex - Persistent_cohomology< Simplex_tree<>, Multi_field > pcoh( st ); - pcoh.init_coefficients( min_p, max_p ); //initilizes the coefficient field for homology + // Compute the persistence diagram of the complex + Persistent_cohomology< Simplex_tree<>, Multi_field > pcoh(st); + // initializes the coefficient field for homology + pcoh.init_coefficients(min_p, max_p); // compute persistent homology, disgarding persistent features of life shorter than min_persistence - pcoh.compute_persistent_cohomology( min_persistence ); - -// Output the diagram in filediag - if(filediag.empty()) { pcoh.output_diagram(); } - else { - std::ofstream out(filediag); - pcoh.output_diagram(out); - out.close(); } + pcoh.compute_persistent_cohomology(min_persistence); + + // Output the diagram in filediag + if (filediag.empty()) { + pcoh.output_diagram(); + } else { + std::ofstream out(filediag); + pcoh.output_diagram(out); + out.close(); + } return 0; } - - -void program_options( int argc, char * argv[] - , std::string & filepoints - , std::string & filediag - , Filtration_value & threshold - , int & dim_max - , int & min_p - , int & max_p - , Filtration_value & min_persistence ) -{ +void program_options(int argc, char * argv[] + , std::string & filepoints + , std::string & filediag + , Filtration_value & threshold + , int & dim_max + , int & min_p + , int & max_p + , Filtration_value & min_persistence) { namespace po = boost::program_options; - po::options_description hidden("Hidden options"); + po::options_description hidden("Hidden options"); hidden.add_options() - ("input-file", po::value<std::string>(&filepoints), - "Name of file containing a point set. Format is one point per line: X1 ... Xd \n"); - + ("input-file", po::value<std::string>(&filepoints), + "Name of file containing a point set. Format is one point per line: X1 ... Xd \n"); + po::options_description visible("Allowed options"); visible.add_options() - ("help,h", "produce help message") - ("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::cout") - ("max-edge-length,r", po::value<Filtration_value>(&threshold)->default_value(0), - "Maximal length of an edge for the Rips complex construction.") - ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1), - "Maximal dimension of the Rips complex we want to compute.") - ("min-field-charac,p", po::value<int>(&min_p)->default_value(2), - "Minimal characteristic p of the coefficient field Z/pZ.") - ("max-field-charac,q", po::value<int>(&max_p)->default_value(1223), - "Minimial characteristic q of the coefficient field Z/pZ.") - ("min-persistence,m", po::value<Filtration_value>(&min_persistence), - "Minimal lifetime of homology feature to be recorded. Default is 0"); + ("help,h", "produce help message") + ("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::cout") + ("max-edge-length,r", po::value<Filtration_value>(&threshold)->default_value(0), + "Maximal length of an edge for the Rips complex construction.") + ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1), + "Maximal dimension of the Rips complex we want to compute.") + ("min-field-charac,p", po::value<int>(&min_p)->default_value(2), + "Minimal characteristic p of the coefficient field Z/pZ.") + ("max-field-charac,q", po::value<int>(&max_p)->default_value(1223), + "Minimial characteristic q of the coefficient field Z/pZ.") + ("min-persistence,m", po::value<Filtration_value>(&min_persistence), + "Minimal lifetime of homology feature to be recorded. Default is 0"); po::positional_options_description pos; pos.add("input-file", 1); - - po::options_description all; all.add(visible).add(hidden); + + po::options_description all; + all.add(visible).add(hidden); po::variables_map vm; po::store(po::command_line_parser(argc, argv). - options(all).positional(pos).run(), vm); + options(all).positional(pos).run(), vm); po::notify(vm); - if (vm.count("help") || !vm.count("input-file")) - { - std::cout << std::endl; - std::cout << "Compute the persistent homology with various coefficient fields \n"; - std::cout << "of a Rips complex defined on a set of input points. The coefficient \n"; - std::cout << "fields are all the Z/rZ for a prime number r contained in the \n"; - std::cout << "specified range [p,q]\n \n"; - std::cout << "The output diagram contains one bar per line, written with the convention: \n"; - std::cout << " p1*...*pr dim b d \n"; - std::cout << "where dim is the dimension of the homological feature,\n"; - std::cout << "b and d are respectively the birth and death of the feature and \n"; - std::cout << "p1*...*pr is the product of prime numbers pi such that the homology \n"; - std::cout << "feature exists in homology with Z/piZ coefficients."<< std::endl << std::endl; - - std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; - std::cout << visible << std::endl; - std::abort(); + if (vm.count("help") || !vm.count("input-file")) { + std::cout << std::endl; + std::cout << "Compute the persistent homology with various coefficient fields \n"; + std::cout << "of a Rips complex defined on a set of input points. The coefficient \n"; + std::cout << "fields are all the Z/rZ for a prime number r contained in the \n"; + std::cout << "specified range [p,q]\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p1*...*pr dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p1*...*pr is the product of prime numbers pi such that the homology \n"; + std::cout << "feature exists in homology with Z/piZ coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); } } diff --git a/src/Persistent_cohomology/example/rips_persistence.cpp b/src/Persistent_cohomology/example/rips_persistence.cpp index 4253def9..9b1ef42f 100644 --- a/src/Persistent_cohomology/example/rips_persistence.cpp +++ b/src/Persistent_cohomology/example/rips_persistence.cpp @@ -1,147 +1,151 @@ - /* 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): Clément Maria - * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (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/reader_utils.h" -#include "gudhi/graph_simplicial_complex.h" -#include "gudhi/distance_functions.h" -#include "gudhi/Simplex_tree.h" -#include "gudhi/Persistent_cohomology.h" +/* 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): Clément Maria + * + * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (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/reader_utils.h> +#include <gudhi/graph_simplicial_complex.h> +#include <gudhi/distance_functions.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/Persistent_cohomology.h> #include <boost/program_options.hpp> +#include <string> +#include <vector> + using namespace Gudhi; using namespace Gudhi::persistent_cohomology; -typedef int Vertex_handle; -typedef double Filtration_value; - -void program_options( int argc, char * argv[] - , std::string & filepoints - , std::string & filediag - , Filtration_value & threshold - , int & dim_max - , int & p - , Filtration_value & min_persistence ); - -int main (int argc, char * argv[]) -{ - std::string filepoints; - std::string filediag ; - Filtration_value threshold ; - int dim_max ; - int p ; +typedef int Vertex_handle; +typedef double Filtration_value; + +void program_options(int argc, char * argv[] + , std::string & filepoints + , std::string & filediag + , Filtration_value & threshold + , int & dim_max + , int & p + , Filtration_value & min_persistence); + +int main(int argc, char * argv[]) { + std::string filepoints; + std::string filediag; + Filtration_value threshold; + int dim_max; + int p; Filtration_value min_persistence; - program_options(argc,argv,filepoints,filediag,threshold,dim_max,p,min_persistence); + program_options(argc, argv, filepoints, filediag, threshold, dim_max, p, min_persistence); -// Extract the points from the file filepoints + // Extract the points from the file filepoints typedef std::vector<double> Point_t; std::vector< Point_t > points; - read_points( filepoints, points ); + read_points(filepoints, points); -// Compute the proximity graph of the points - Graph_t prox_graph = compute_proximity_graph( points, threshold - , euclidean_distance<Point_t> ); + // Compute the proximity graph of the points + Graph_t prox_graph = compute_proximity_graph(points, threshold + , euclidean_distance<Point_t>); -// Construct the Rips complex in a Simplex Tree - Simplex_tree<> st; - st.insert_graph(prox_graph); // insert the proximity graph in the simplex tree - st.expansion( dim_max ); // expand the graph until dimension dim_max + // Construct the Rips complex in a Simplex Tree + Simplex_tree<> st; + // insert the proximity graph in the simplex tree + st.insert_graph(prox_graph); + // expand the graph until dimension dim_max + st.expansion(dim_max); std::cout << "The complex contains " << st.num_simplices() << " simplices \n"; std::cout << " and has dimension " << st.dimension() << " \n"; -// Sort the simplices in the order of the filtration + // Sort the simplices in the order of the filtration st.initialize_filtration(); -// Compute the persistence diagram of the complex + // Compute the persistence diagram of the complex persistent_cohomology::Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh(st); - pcoh.init_coefficients( p ); //initilizes the coefficient field for homology - - pcoh.compute_persistent_cohomology( min_persistence ); - -// Output the diagram in filediag - if(filediag.empty()) { pcoh.output_diagram(); } - else { - std::ofstream out(filediag); - pcoh.output_diagram(out); - out.close(); } + // initializes the coefficient field for homology + pcoh.init_coefficients(p); + + pcoh.compute_persistent_cohomology(min_persistence); + + // Output the diagram in filediag + if (filediag.empty()) { + pcoh.output_diagram(); + } else { + std::ofstream out(filediag); + pcoh.output_diagram(out); + out.close(); + } return 0; } - - -void program_options( int argc, char * argv[] - , std::string & filepoints - , std::string & filediag - , Filtration_value & threshold - , int & dim_max - , int & p - , Filtration_value & min_persistence ) -{ +void program_options(int argc, char * argv[] + , std::string & filepoints + , std::string & filediag + , Filtration_value & threshold + , int & dim_max + , int & p + , Filtration_value & min_persistence) { namespace po = boost::program_options; - po::options_description hidden("Hidden options"); + po::options_description hidden("Hidden options"); hidden.add_options() - ("input-file", po::value<std::string>(&filepoints), - "Name of file containing a point set. Format is one point per line: X1 ... Xd "); - + ("input-file", po::value<std::string>(&filepoints), + "Name of file containing a point set. Format is one point per line: X1 ... Xd "); + po::options_description visible("Allowed options", 100); visible.add_options() - ("help,h", "produce help message") - ("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::cout") - ("max-edge-length,r", po::value<Filtration_value>(&threshold)->default_value(0), - "Maximal length of an edge for the Rips complex construction.") - ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1), - "Maximal dimension of the Rips complex we want to compute.") - ("field-charac,p", po::value<int>(&p)->default_value(11), - "Characteristic p of the coefficient field Z/pZ for computing homology.") - ("min-persistence,m", po::value<Filtration_value>(&min_persistence), - "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals"); + ("help,h", "produce help message") + ("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::cout") + ("max-edge-length,r", po::value<Filtration_value>(&threshold)->default_value(0), + "Maximal length of an edge for the Rips complex construction.") + ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1), + "Maximal dimension of the Rips complex we want to compute.") + ("field-charac,p", po::value<int>(&p)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.") + ("min-persistence,m", po::value<Filtration_value>(&min_persistence), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals"); po::positional_options_description pos; pos.add("input-file", 1); - - po::options_description all; all.add(visible).add(hidden); + + po::options_description all; + all.add(visible).add(hidden); po::variables_map vm; po::store(po::command_line_parser(argc, argv). - options(all).positional(pos).run(), vm); + options(all).positional(pos).run(), vm); po::notify(vm); - if (vm.count("help") || !vm.count("input-file")) - { - std::cout << std::endl; - std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; - std::cout << "of a Rips complex defined on a set of input points.\n \n"; - std::cout << "The output diagram contains one bar per line, written with the convention: \n"; - std::cout << " p dim b d \n"; - std::cout << "where dim is the dimension of the homological feature,\n"; - std::cout << "b and d are respectively the birth and death of the feature and \n"; - std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; - - std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; - std::cout << visible << std::endl; - std::abort(); + if (vm.count("help") || !vm.count("input-file")) { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of a Rips complex defined on a set of input points.\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); } } diff --git a/src/Skeleton_blocker/example/CMakeLists.txt b/src/Skeleton_blocker/example/CMakeLists.txt index d1228526..de0c7bba 100644 --- a/src/Skeleton_blocker/example/CMakeLists.txt +++ b/src/Skeleton_blocker/example/CMakeLists.txt @@ -1,10 +1,12 @@ cmake_minimum_required(VERSION 2.6) project(GUDHIskbl) - add_executable(SkeletonBlockerFromSimplices Skeleton_blocker_from_simplices.cpp) add_executable(SkeletonBlockerIteration Skeleton_blocker_iteration.cpp) add_executable(SkeletonBlockerLink Skeleton_blocker_link.cpp) +target_link_libraries(SkeletonBlockerIteration ${Boost_TIMER_LIBRARY} ${Boost_SYSTEM_LIBRARY}) -target_link_libraries(SkeletonBlockerIteration ${Boost_TIMER_LIBRARY} ${Boost_SYSTEM_LIBRARY}) +add_test(SkeletonBlockerFromSimplices ${CMAKE_CURRENT_BINARY_DIR}/SkeletonBlockerFromSimplices) +add_test(SkeletonBlockerIteration ${CMAKE_CURRENT_BINARY_DIR}/SkeletonBlockerIteration) +add_test(SkeletonBlockerLink ${CMAKE_CURRENT_BINARY_DIR}/SkeletonBlockerLink) diff --git a/src/Skeleton_blocker/example/Skeleton_blocker_from_simplices.cpp b/src/Skeleton_blocker/example/Skeleton_blocker_from_simplices.cpp index 9f9b3d52..2738c01c 100644 --- a/src/Skeleton_blocker/example/Skeleton_blocker_from_simplices.cpp +++ b/src/Skeleton_blocker/example/Skeleton_blocker_from_simplices.cpp @@ -1,34 +1,33 @@ - /* 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): David Salinas - * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (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/>. - */ - +/* 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): David Salinas + * + * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (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/Skeleton_blocker.h> #include <stdio.h> #include <stdlib.h> #include <string> #include <fstream> #include <sstream> - - -#include "gudhi/Skeleton_blocker.h" +#include <vector> using namespace std; using namespace Gudhi; @@ -39,45 +38,44 @@ typedef Complex::Vertex_handle Vertex_handle; typedef Complex::Simplex_handle Simplex_handle; typedef Complex::Simplex_handle Simplex; -int main (int argc, char *argv[]){ - std::vector<Simplex_handle> simplices; +int main(int argc, char *argv[]) { + std::vector<Simplex_handle> simplices; - //add 4 triangles of a tetrahedron 0123 - simplices.push_back(Simplex_handle(Vertex_handle(0),Vertex_handle(1),Vertex_handle(2))); - simplices.push_back(Simplex_handle(Vertex_handle(1),Vertex_handle(2),Vertex_handle(3))); - simplices.push_back(Simplex_handle(Vertex_handle(3),Vertex_handle(0),Vertex_handle(2))); - simplices.push_back(Simplex_handle(Vertex_handle(3),Vertex_handle(0),Vertex_handle(1))); + // add 4 triangles of a tetrahedron 0123 + simplices.push_back(Simplex_handle(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2))); + simplices.push_back(Simplex_handle(Vertex_handle(1), Vertex_handle(2), Vertex_handle(3))); + simplices.push_back(Simplex_handle(Vertex_handle(3), Vertex_handle(0), Vertex_handle(2))); + simplices.push_back(Simplex_handle(Vertex_handle(3), Vertex_handle(0), Vertex_handle(1))); - //get complex from top faces - Complex complex(make_complex_from_top_faces<Complex>(simplices.begin(),simplices.end())); + // get complex from top faces + Complex complex(make_complex_from_top_faces<Complex>(simplices.begin(), simplices.end())); - std::cout << "Simplices:"<<std::endl; - for(const Simplex & s : complex.simplex_range()) - std::cout << s << " "; - std::cout << std::endl; + std::cout << "Simplices:" << std::endl; + for (const Simplex & s : complex.simplex_range()) + std::cout << s << " "; + std::cout << std::endl; - //One blocker as simplex 0123 is not in the complex but all its proper faces are. - std::cout << "Blockers: "<<complex.blockers_to_string()<<std::endl; + // One blocker as simplex 0123 is not in the complex but all its proper faces are. + std::cout << "Blockers: " << complex.blockers_to_string() << std::endl; - //now build a complex from its full list of simplices - simplices.clear(); - simplices.push_back(Simplex_handle(Vertex_handle(0))); - simplices.push_back(Simplex_handle(Vertex_handle(1))); - simplices.push_back(Simplex_handle(Vertex_handle(2))); - simplices.push_back(Simplex_handle(Vertex_handle(0),Vertex_handle(1))); - simplices.push_back(Simplex_handle(Vertex_handle(1),Vertex_handle(2))); - simplices.push_back(Simplex_handle(Vertex_handle(2),Vertex_handle(0))); - complex = Complex(simplices.begin(),simplices.end()); + // now build a complex from its full list of simplices + simplices.clear(); + simplices.push_back(Simplex_handle(Vertex_handle(0))); + simplices.push_back(Simplex_handle(Vertex_handle(1))); + simplices.push_back(Simplex_handle(Vertex_handle(2))); + simplices.push_back(Simplex_handle(Vertex_handle(0), Vertex_handle(1))); + simplices.push_back(Simplex_handle(Vertex_handle(1), Vertex_handle(2))); + simplices.push_back(Simplex_handle(Vertex_handle(2), Vertex_handle(0))); + complex = Complex(simplices.begin(), simplices.end()); - std::cout << "Simplices:"<<std::endl; - for(const Simplex & s : complex.simplex_range()) - std::cout << s << " "; - std::cout << std::endl; + std::cout << "Simplices:" << std::endl; + for (const Simplex & s : complex.simplex_range()) + std::cout << s << " "; + std::cout << std::endl; - //One blocker as simplex 012 is not in the complex but all its proper faces are. - std::cout << "Blockers: "<<complex.blockers_to_string()<<std::endl; + // One blocker as simplex 012 is not in the complex but all its proper faces are. + std::cout << "Blockers: " << complex.blockers_to_string() << std::endl; - return EXIT_SUCCESS; + return EXIT_SUCCESS; } - diff --git a/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp b/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp index 126e32ec..69557694 100644 --- a/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp +++ b/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp @@ -1,24 +1,26 @@ - /* 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): David Salinas - * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (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/>. - */ +/* 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): David Salinas + * + * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (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/Skeleton_blocker.h> #include <boost/timer/timer.hpp> @@ -29,8 +31,6 @@ #include <sstream> -#include "gudhi/Skeleton_blocker.h" - using namespace std; using namespace Gudhi; using namespace skbl; @@ -39,54 +39,53 @@ typedef Skeleton_blocker_complex<Skeleton_blocker_simple_traits> Complex; typedef Complex::Vertex_handle Vertex_handle; typedef Complex::Simplex_handle Simplex; - -Complex build_complete_complex(int n){ - // build a full complex with n vertices and 2^n-1 simplices - Complex complex; - for(int i=0;i<n;i++) - complex.add_vertex(); - for(int i=0;i<n;i++) - for(int j=0;j<i;j++) - //note that add_edge, add the edge and all its cofaces - complex.add_edge(Vertex_handle(i),Vertex_handle(j)); - return complex; +Complex build_complete_complex(int n) { + // build a full complex with n vertices and 2^n-1 simplices + Complex complex; + for (int i = 0; i < n; i++) + complex.add_vertex(); + for (int i = 0; i < n; i++) + for (int j = 0; j < i; j++) + // note that add_edge, add the edge and all its cofaces + complex.add_edge(Vertex_handle(i), Vertex_handle(j)); + return complex; } -int main (int argc, char *argv[]){ - boost::timer::auto_cpu_timer t; +int main(int argc, char *argv[]) { + boost::timer::auto_cpu_timer t; - const int n = 15; + const int n = 15; - // build a full complex with n vertices and 2^n-1 simplices - Complex complex(build_complete_complex(n)); + // build a full complex with n vertices and 2^n-1 simplices + Complex complex(build_complete_complex(n)); - // this is just to illustrate iterators, to count number of vertices - // or edges, complex.num_vertices() and complex.num_edges() are - // more appropriated! - unsigned num_vertices = 0; - for(auto v : complex.vertex_range()) { - std::cout << "Vertex " << v <<std::endl; - ++num_vertices; - } + // this is just to illustrate iterators, to count number of vertices + // or edges, complex.num_vertices() and complex.num_edges() are + // more appropriated! + unsigned num_vertices = 0; + for (auto v : complex.vertex_range()) { + std::cout << "Vertex " << v << std::endl; + ++num_vertices; + } - // such loop can also be done directly with distance as iterators are STL compliant - auto edges = complex.edge_range(); - unsigned num_edges = std::distance(edges.begin(), edges.end()); + // such loop can also be done directly with distance as iterators are STL compliant + auto edges = complex.edge_range(); + unsigned num_edges = std::distance(edges.begin(), edges.end()); - unsigned euler = 0; - unsigned num_simplices = 0; - // we use a reference to a simplex instead of a copy - // value here because a simplex is a set of integers - // and copying it cost time - for(const Simplex & s : complex.simplex_range()){ - ++num_simplices; - if(s.dimension()%2 == 0) - euler += 1; - else - euler -= 1; - } - std::cout << "Saw "<<num_vertices<<" vertices, "<<num_edges<<" edges and "<<num_simplices<<" simplices"<<std::endl; - std::cout << "The Euler Characteristic is "<<euler<<std::endl; - return EXIT_SUCCESS; + unsigned euler = 0; + unsigned num_simplices = 0; + // we use a reference to a simplex instead of a copy + // value here because a simplex is a set of integers + // and copying it cost time + for (const Simplex & s : complex.simplex_range()) { + ++num_simplices; + if (s.dimension() % 2 == 0) + euler += 1; + else + euler -= 1; + } + std::cout << "Saw " << num_vertices << " vertices, " << num_edges << " edges and " << num_simplices << " simplices" + << std::endl; + std::cout << "The Euler Characteristic is " << euler << std::endl; + return EXIT_SUCCESS; } - diff --git a/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp b/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp index 0987cc89..002cbc49 100644 --- a/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp +++ b/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp @@ -1,25 +1,26 @@ - /* 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): David Salinas - * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (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/>. - */ +/* 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): David Salinas + * + * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (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/Skeleton_blocker.h> #include <stdio.h> #include <stdlib.h> @@ -27,9 +28,6 @@ #include <fstream> #include <sstream> - -#include "gudhi/Skeleton_blocker.h" - using namespace std; using namespace Gudhi; using namespace skbl; @@ -39,33 +37,31 @@ typedef Complex::Vertex_handle Vertex_handle; typedef Complex::Root_vertex_handle Root_vertex_handle; typedef Complex::Simplex_handle Simplex; +int main(int argc, char *argv[]) { + // build a full complex with 4 vertices and 2^4-1 simplices + // Initial vertices are (0,1,2,3,4) + Simplex tetrahedron(Vertex_handle(0), Vertex_handle(1), Vertex_handle(2), Vertex_handle(3)); + Complex complex; + complex.add_simplex(tetrahedron); -int main (int argc, char *argv[]){ - // build a full complex with 4 vertices and 2^4-1 simplices - // Initial vertices are (0,1,2,3,4) - Simplex tetrahedron(Vertex_handle(0),Vertex_handle(1),Vertex_handle(2),Vertex_handle(3)); - Complex complex; - complex.add_simplex(tetrahedron); + cout << "complex:" << complex.to_string() << endl; - cout<<"complex:"<<complex.to_string()<<endl; + // build the link of vertex 1, eg a triangle {0,2,3} + auto link = complex.link(Vertex_handle(1)); + cout << "link:" << link.to_string() << endl; - //build the link of vertex 1, eg a triangle {0,2,3} - auto link = complex.link(Vertex_handle(1)); - cout<<"link:"<<link.to_string()<<endl; + // Internally link is a subcomplex of 'complex' and its vertices are stored in a vector. + // They can be accessed via Vertex_handle(x) where x is an index of the vector. + // In that example, link has three vertices and thus it contains only + // Vertex_handle(0),Vertex_handle(1) and Vertex_handle(2) are). + for (int i = 0; i < 5; ++i) + cout << "link.contains_vertex(Vertex_handle(" << i << ")):" << link.contains_vertex(Vertex_handle(i)) << endl; + cout << endl; - //Internally link is a subcomplex of 'complex' and its vertices are stored in a vector. - //They can be accessed via Vertex_handle(x) where x is an index of the vector. - //In that example, link has three vertices and thus it contains only - // Vertex_handle(0),Vertex_handle(1) and Vertex_handle(2) are). - for(int i = 0; i<5; ++i) - cout << "link.contains_vertex(Vertex_handle("<<i<<")):"<<link.contains_vertex(Vertex_handle(i))<<endl; - cout<<endl; + // To access to the initial vertices eg (0,1,2,3,4), Root_vertex_handle must be used. + // For instance, to test if the link contains the vertex that was labeled i: + for (int i = 0; i < 5; ++i) + cout << "link.contains_vertex(Root_vertex_handle(" << i << ")):" << link.contains_vertex(Root_vertex_handle(i)) << endl; - //To access to the initial vertices eg (0,1,2,3,4), Root_vertex_handle must be used. - //For instance, to test if the link contains the vertex that was labeled i: - for(int i = 0; i<5; ++i) - cout << "link.contains_vertex(Root_vertex_handle("<<i<<")):"<<link.contains_vertex(Root_vertex_handle(i))<<endl; - - return EXIT_SUCCESS; + return EXIT_SUCCESS; } - diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h index 10d552ec..0d2de767 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h @@ -179,4 +179,4 @@ struct Skeleton_blocker_simple_traits { } // namespace Gudhi -#endif // SRC_SKELETON_BLOCKER_INCLUDE_GUDHI_SKELETON_BLOCKER_SKELETON_BLOCKER_SIMPLE_TRAITS_H_ +#endif // SKELETON_BLOCKER_SKELETON_BLOCKER_SIMPLE_TRAITS_H_ |