diff options
author | salinasd <salinasd@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2015-02-10 17:03:43 +0000 |
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committer | salinasd <salinasd@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2015-02-10 17:03:43 +0000 |
commit | def05e2da637a43c02e439af8faaf789214395cd (patch) | |
tree | b2839ae762693a2a09c4876c976772332fc1342a /src/Contraction | |
parent | e50f918673baf48d35c2e2ffa7bfc0e23206612f (diff) |
skbl correction bug constructor + contraction add garland heckbert example
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@466 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 1789e903625df3c4e7c689fa4888bebd86e616eb
Diffstat (limited to 'src/Contraction')
-rw-r--r-- | src/Contraction/example/CMakeLists.txt | 3 | ||||
-rw-r--r-- | src/Contraction/example/Garland_heckbert.cpp | 115 | ||||
-rwxr-xr-x | src/Contraction/example/Garland_heckbert/Error_quadric.h | 164 | ||||
-rw-r--r-- | src/Contraction/example/Garland_heckbert/Garland_heckbert_policies.h | 115 | ||||
-rw-r--r-- | src/Contraction/example/Garland_heckbert/Point.h | 176 | ||||
-rw-r--r-- | src/Contraction/include/gudhi/Skeleton_blocker_contractor.h | 2 |
6 files changed, 573 insertions, 2 deletions
diff --git a/src/Contraction/example/CMakeLists.txt b/src/Contraction/example/CMakeLists.txt index ba411bd4..6d65de73 100644 --- a/src/Contraction/example/CMakeLists.txt +++ b/src/Contraction/example/CMakeLists.txt @@ -1,7 +1,10 @@ cmake_minimum_required(VERSION 2.6) project(GUDHIskbl) + add_executable(RipsContraction Rips_contraction.cpp) +add_executable(GarlandHeckbert Garland_heckbert.cpp) + target_link_libraries(RipsContraction ${Boost_TIMER_LIBRARY} ${Boost_SYSTEM_LIBRARY}) add_test(RipsContraction.sphere.0.2 ${CMAKE_CURRENT_BINARY_DIR}/RipsContraction ${CMAKE_SOURCE_DIR}/data/points/sphere3D_2646.off 0.2) diff --git a/src/Contraction/example/Garland_heckbert.cpp b/src/Contraction/example/Garland_heckbert.cpp new file mode 100644 index 00000000..912199a4 --- /dev/null +++ b/src/Contraction/example/Garland_heckbert.cpp @@ -0,0 +1,115 @@ +/* + * Garland_heckbert.h + * Created on: Feb 10, 2015 + * 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-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/>. + * + */ + + +#ifndef GARLAND_HECKBERT_H_ +#define GARLAND_HECKBERT_H_ + + +#include <iostream> +#include "Garland_heckbert/Point.h" +#include "Garland_heckbert/Error_quadric.h" +#include "Garland_heckbert/Garland_heckbert_policies.h" + +#include "gudhi/Edge_contraction.h" +#include "gudhi/Skeleton_blocker.h" +#include "gudhi/Off_reader.h" + +using namespace std; +using namespace Gudhi; +using namespace skbl; +using namespace contraction; + + +struct Geometry_trait{ + typedef Point_d Point; +}; + +struct Garland_heckbert_traits : public Skeleton_blocker_simple_geometric_traits<Geometry_trait> { + +public: + // the vertex stored in the complex contains a quadric + struct Garland_heckbert_vertex : public Simple_geometric_vertex{ + Error_quadric<Geometry_trait::Point> quadric; + }; + typedef Garland_heckbert_vertex Graph_vertex; + +}; + +typedef Skeleton_blocker_geometric_complex< Garland_heckbert_traits > Complex; +typedef Edge_profile<Complex> Profile; +typedef Skeleton_blocker_contractor<Complex> Complex_contractor; + + + + +int main(int argc, char *argv[]){ + if (argc!=3){ + std::cerr << "Usage "<<argv[0]<<" ../../../data/meshes/test.off N to load the file ../../data/test.off and contract N edges.\n"; + return -1; + } + + Complex complex; + + // load the points + Skeleton_blocker_off_reader<Complex> off_reader(argv[1],complex); + if(!off_reader.is_valid()){ + std::cerr << "Unable to read file:"<<argv[1]<<std::endl; + return EXIT_FAILURE; + } + + int num_contractions = atoi(argv[2]); + + std::cout << "Initial complex has "<< + complex.num_vertices()<<" vertices, "<< + complex.num_blockers()<<" blockers, "<< + complex.num_edges()<<" edges and" << + complex.num_triangles()<<" triangles."; + + Complex_contractor contractor(complex, + new GH_cost<Profile>(complex), + new GH_placement<Profile>(complex), + contraction::make_link_valid_contraction<Profile>(), + new GH_visitor<Profile>(complex) + ); + + std::cout<<"Contract "<<num_contractions<<" edges\n"; + contractor.contract_edges(num_contractions); + + std::cout << "Final complex has "<< + complex.num_vertices()<<" vertices, "<< + complex.num_edges()<<" edges and" << + complex.num_triangles()<<" triangles."; + + Skeleton_blocker_off_writer<Complex> off_writer("reduced.off",complex); + + + return EXIT_SUCCESS; +} + + + +#endif /* GARLAND_HECKBERT_H_ */ diff --git a/src/Contraction/example/Garland_heckbert/Error_quadric.h b/src/Contraction/example/Garland_heckbert/Error_quadric.h new file mode 100755 index 00000000..7a30c35a --- /dev/null +++ b/src/Contraction/example/Garland_heckbert/Error_quadric.h @@ -0,0 +1,164 @@ +/*
+ * Error_quadric.h
+ *
+ * Created on: 24 janv. 2014
+ * Author: dsalinas
+ */
+
+#ifndef ERROR_QUADRIC_H_
+#define ERROR_QUADRIC_H_
+
+#include <vector>
+#include <utility>
+#include <boost/optional/optional.hpp>
+
+
+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 = grad_determinant()) 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_ */
+
diff --git a/src/Contraction/example/Garland_heckbert/Garland_heckbert_policies.h b/src/Contraction/example/Garland_heckbert/Garland_heckbert_policies.h new file mode 100644 index 00000000..c792b5b3 --- /dev/null +++ b/src/Contraction/example/Garland_heckbert/Garland_heckbert_policies.h @@ -0,0 +1,115 @@ +/* + * Garland_heckbert_policies.h + * Created on: Feb 10, 2015 + * 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-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/>. + * + */ + + +#ifndef GARLAND_HECKBERT_POLICIES_H_ +#define GARLAND_HECKBERT_POLICIES_H_ + +#include "gudhi/Edge_contraction.h" +#include "Error_quadric.h" + +template<typename EdgeProfile> +class GH_visitor: public Gudhi::contraction::Contraction_visitor<EdgeProfile> { + typedef typename EdgeProfile::Complex Complex; + typedef typename Complex::Point Point; + Complex& complex_; +public: + GH_visitor(Complex& complex):complex_(complex){} + + + void on_started(Complex & complex) override{ + //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 + for(auto v : complex.vertex_range()){ + auto & quadric_v(complex[v].quadric); + for(auto t : complex.triangle_range(v)){ + auto t_it = t.begin(); + const auto& p0(complex.point(*t_it++)); + const auto& p1(complex.point(*t_it++)); + const auto& p2(complex.point(*t_it++)); + quadric_v+=Error_quadric<Point>(p0,p1,p2); + } + } + } + + /** + * @brief Called when an edge is about to be contracted and replaced by a vertex whose position is *placement. + */ + void on_contracting(EdgeProfile const &profile, boost::optional< Point > placement) + override{ + profile.v0().quadric += profile.v1().quadric; + } +}; + + +template<typename EdgeProfile> +class GH_placement : public Gudhi::contraction::Placement_policy<EdgeProfile>{ + typedef typename EdgeProfile::Complex Complex; + Complex& complex_; +public: + typedef typename EdgeProfile::Point Point; + typedef typename Gudhi::contraction::Placement_policy<EdgeProfile>::Placement_type Placement_type; + + GH_placement(Complex& complex):complex_(complex){} + + Placement_type operator()(const EdgeProfile& profile) const override{ + auto sum_quad(profile.v0().quadric); + sum_quad += profile.v1().quadric; + + boost::optional<Point> min_quadric_pt(sum_quad.min_cost()); + if (min_quadric_pt) + return Placement_type(*min_quadric_pt); + else + return profile.p0(); + } +}; + +template<typename EdgeProfile> +class GH_cost : public Gudhi::contraction::Cost_policy<EdgeProfile>{ + typedef typename EdgeProfile::Complex Complex; + Complex& complex_; +public: + + typedef typename Gudhi::contraction::Cost_policy<EdgeProfile>::Cost_type Cost_type; + typedef typename Complex::Point Point; + + GH_cost(Complex& complex):complex_(complex){} + + Cost_type operator()( EdgeProfile const& profile, boost::optional<Point> const& new_point ) const override { + Cost_type res; + if (new_point){ + auto sum_quad(profile.v0().quadric); + sum_quad += profile.v1().quadric; + res = sum_quad.cost(*new_point); + } + return res; + } +}; + + + +#endif /* GARLAND_HECKBERT_POLICIES_H_ */ diff --git a/src/Contraction/example/Garland_heckbert/Point.h b/src/Contraction/example/Garland_heckbert/Point.h new file mode 100644 index 00000000..eb250347 --- /dev/null +++ b/src/Contraction/example/Garland_heckbert/Point.h @@ -0,0 +1,176 @@ +/* + * Basic_geometry.h + * Created on: Feb 10, 2015 + * 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-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/>. + * + */ + + +#ifndef BASIC_GEOMETRY_H_ +#define BASIC_GEOMETRY_H_ + +#include <cmath> +#include <vector> +#include <cassert> +#include <cstddef> + +class Point_d{ +public: + Point_d():coords_(3,0){} + Point_d(size_t dim):coords_(dim,0){} + Point_d(const Point_d& other):coords_(other.coords_){} + Point_d(double x,double y,double z):coords_({x,y,z}){} + + template<typename CoordsIt> + Point_d(CoordsIt begin,CoordsIt end):coords_(begin,end){} + + size_t dimension() const{ + return coords_.size(); + } + + double x() const{ + return coords_[0]; + } + + double y() const{ + return coords_[1]; + } + + double z() const{ + return coords_[2]; + } + + double& x(){ + return coords_[0]; + } + + double& y(){ + return coords_[1]; + } + + double& z(){ + return coords_[2]; + } + + std::vector<double>::const_iterator begin() const{ + return coords_.begin(); + } + + std::vector<double>::const_iterator end() const{ + return coords_.end(); + } + + double& operator[](unsigned i){ + return coords_[i]; + } + const double& operator[](unsigned i) const{ + return coords_[i]; + } + + double squared_norm() const{ + double res = 0; + for(auto x : coords_) + res+= x*x; + return res; + } + + double squared_dist(const Point_d& other) const{ + assert(dimension()==other.dimension()); + double res = 0; + for(unsigned i = 0; i < coords_.size(); ++i) + res+= coords_[i]*coords_[i] + other[i]*other[i]; + return res; + } + + /** + * dot product + */ + double operator*(const Point_d& other) const{ + assert(dimension()==other.dimension()); + double res = 0; + for(unsigned i = 0; i < coords_.size(); ++i) + res+= coords_[i]*other[i]; + return res; + } + + /** + * only if points have dimension 3 + */ + Point_d cross_product(const Point_d& other){ + assert(dimension()==3 && other.dimension()==3); + Point_d res(3); + res[0] = (*this)[1] * other[2] - (*this)[2] * other[1]; + res[1] = (*this)[2] * other[0] - (*this)[0] * other[2]; + res[2] = (*this)[0] * other[1] - (*this)[1] * other[0]; + return res; + } + + Point_d operator+(const Point_d& other) const{ + assert(dimension()==other.dimension()); + Point_d res(dimension()); + for(unsigned i = 0; i < coords_.size(); ++i) + res[i] = (*this)[i] + other[i]; + return res; + } + + Point_d operator*(double lambda) const{ + Point_d res(dimension()); + for(unsigned i = 0; i < coords_.size(); ++i) + res[i] = (*this)[i] * lambda; + return res; + } + + Point_d operator/(double lambda) const{ + Point_d res(dimension()); + for(unsigned i = 0; i < coords_.size(); ++i) + res[i] = (*this)[i] / lambda; + return res; + } + + Point_d operator-(const Point_d& other) const{ + assert(dimension()==other.dimension()); + Point_d res(dimension()); + for(unsigned i = 0; i < coords_.size(); ++i) + res[i] = (*this)[i] - other[i]; + return res; + } + + friend Point_d unit_normal(const Point_d& p1,const Point_d& p2,const Point_d& p3){ + assert(p1.dimension()==3); + assert(p2.dimension()==3); + assert(p3.dimension()==3); + Point_d p1p2 = p2 - p1; + Point_d p1p3 = p3 - p1; + Point_d res(p1p2.cross_product(p1p3)); + return res / std::sqrt(res.squared_norm()); + } + + +private: + std::vector<double> coords_; +}; + + + + + +#endif /* BASIC_GEOMETRY_H_ */ diff --git a/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h b/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h index c7941bfd..ba2138a1 100644 --- a/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h +++ b/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h @@ -391,9 +391,7 @@ public: } } else - { DBG("uncomputable cost"); - } } if(contraction_visitor_) contraction_visitor_->on_stop_condition_reached(); } |