From def05e2da637a43c02e439af8faaf789214395cd Mon Sep 17 00:00:00 2001 From: salinasd Date: Tue, 10 Feb 2015 17:03:43 +0000 Subject: 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 --- src/Contraction/example/CMakeLists.txt | 3 + src/Contraction/example/Garland_heckbert.cpp | 115 ++++++++++++++ .../example/Garland_heckbert/Error_quadric.h | 164 +++++++++++++++++++ .../Garland_heckbert/Garland_heckbert_policies.h | 115 ++++++++++++++ src/Contraction/example/Garland_heckbert/Point.h | 176 +++++++++++++++++++++ 5 files changed, 573 insertions(+) create mode 100644 src/Contraction/example/Garland_heckbert.cpp create mode 100755 src/Contraction/example/Garland_heckbert/Error_quadric.h create mode 100644 src/Contraction/example/Garland_heckbert/Garland_heckbert_policies.h create mode 100644 src/Contraction/example/Garland_heckbert/Point.h (limited to 'src/Contraction/example') 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 . + * + */ + + +#ifndef GARLAND_HECKBERT_H_ +#define GARLAND_HECKBERT_H_ + + +#include +#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 { + +public: + // the vertex stored in the complex contains a quadric + struct Garland_heckbert_vertex : public Simple_geometric_vertex{ + Error_quadric quadric; + }; + typedef Garland_heckbert_vertex Graph_vertex; + +}; + +typedef Skeleton_blocker_geometric_complex< Garland_heckbert_traits > Complex; +typedef Edge_profile Profile; +typedef Skeleton_blocker_contractor Complex_contractor; + + + + +int main(int argc, char *argv[]){ + if (argc!=3){ + std::cerr << "Usage "< off_reader(argv[1],complex); + if(!off_reader.is_valid()){ + std::cerr << "Unable to read file:"<(complex), + new GH_placement(complex), + contraction::make_link_valid_contraction(), + new GH_visitor(complex) + ); + + std::cout<<"Contract "< 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 +#include +#include + + +template 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 min_cost(double scale=1) const{ + // const double min_determinant = 1e-4 * scale*scale; + const double min_determinant = 1e-5; + boost::optional 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[ "<. + * + */ + + +#ifndef GARLAND_HECKBERT_POLICIES_H_ +#define GARLAND_HECKBERT_POLICIES_H_ + +#include "gudhi/Edge_contraction.h" +#include "Error_quadric.h" + +template +class GH_visitor: public Gudhi::contraction::Contraction_visitor { + 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(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 +class GH_placement : public Gudhi::contraction::Placement_policy{ + typedef typename EdgeProfile::Complex Complex; + Complex& complex_; +public: + typedef typename EdgeProfile::Point Point; + typedef typename Gudhi::contraction::Placement_policy::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 min_quadric_pt(sum_quad.min_cost()); + if (min_quadric_pt) + return Placement_type(*min_quadric_pt); + else + return profile.p0(); + } +}; + +template +class GH_cost : public Gudhi::contraction::Cost_policy{ + typedef typename EdgeProfile::Complex Complex; + Complex& complex_; +public: + + typedef typename Gudhi::contraction::Cost_policy::Cost_type Cost_type; + typedef typename Complex::Point Point; + + GH_cost(Complex& complex):complex_(complex){} + + Cost_type operator()( EdgeProfile const& profile, boost::optional 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 . + * + */ + + +#ifndef BASIC_GEOMETRY_H_ +#define BASIC_GEOMETRY_H_ + +#include +#include +#include +#include + +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 + 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::const_iterator begin() const{ + return coords_.begin(); + } + + std::vector::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 coords_; +}; + + + + + +#endif /* BASIC_GEOMETRY_H_ */ -- cgit v1.2.3