summaryrefslogtreecommitdiff
path: root/example/Contraction
diff options
context:
space:
mode:
Diffstat (limited to 'example/Contraction')
-rw-r--r--example/Contraction/CMakeLists.txt17
-rw-r--r--example/Contraction/Garland_heckbert.cpp192
-rw-r--r--example/Contraction/Garland_heckbert/Error_quadric.h182
-rw-r--r--example/Contraction/Rips_contraction.cpp98
4 files changed, 0 insertions, 489 deletions
diff --git a/example/Contraction/CMakeLists.txt b/example/Contraction/CMakeLists.txt
deleted file mode 100644
index 582b7ab8..00000000
--- a/example/Contraction/CMakeLists.txt
+++ /dev/null
@@ -1,17 +0,0 @@
-project(Contraction_examples)
-
-add_executable(RipsContraction Rips_contraction.cpp)
-
-add_executable(GarlandHeckbert Garland_heckbert.cpp)
-target_link_libraries(GarlandHeckbert ${Boost_TIMER_LIBRARY})
-
-add_test(NAME Contraction_example_tore3D_0.2 COMMAND $<TARGET_FILE:RipsContraction>
- "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "0.2")
-# TODO(DS) : These tests are too long under Windows
-#add_test(NAME Contraction_example_sphere_0.2 COMMAND $<TARGET_FILE:RipsContraction>
-# "${CMAKE_SOURCE_DIR}/data/points/sphere3D_2646.off" "0.2")
-#add_test(NAME Contraction_example_SO3_0.3 COMMAND $<TARGET_FILE:RipsContraction>
-# "${CMAKE_SOURCE_DIR}/data/points/SO3_10000.off" "0.3")
-
-install(TARGETS RipsContraction DESTINATION bin)
-install(TARGETS GarlandHeckbert DESTINATION bin)
diff --git a/example/Contraction/Garland_heckbert.cpp b/example/Contraction/Garland_heckbert.cpp
deleted file mode 100644
index 08dd932e..00000000
--- a/example/Contraction/Garland_heckbert.cpp
+++ /dev/null
@@ -1,192 +0,0 @@
-/* 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
- *
- * 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 <gudhi/Point.h>
-#include <gudhi/Edge_contraction.h>
-#include <gudhi/Skeleton_blocker.h>
-#include <gudhi/Off_reader.h>
-
-#include <iostream>
-
-#include "Garland_heckbert/Error_quadric.h"
-
-struct Geometry_trait {
- typedef Point_d Point;
-};
-
-/**
- * The vertex stored in the complex contains a quadric.
- */
-struct Garland_heckbert_traits
- : public Gudhi::skeleton_blocker::Skeleton_blocker_simple_geometric_traits<Geometry_trait> {
- public:
- struct Garland_heckbert_vertex : public Simple_geometric_vertex {
- Error_quadric<Geometry_trait::Point> quadric;
- };
- typedef Garland_heckbert_vertex Graph_vertex;
-};
-
-using Complex = Gudhi::skeleton_blocker::Skeleton_blocker_geometric_complex< Garland_heckbert_traits >;
-using EdgeProfile = Gudhi::contraction::Edge_profile<Complex>;
-using Complex_contractor = Gudhi::contraction::Skeleton_blocker_contractor<Complex>;
-
-/**
- * How the new vertex is placed after an edge collapse : here it is placed at
- * the point minimizing the cost of the quadric.
- */
-class GH_placement : public Gudhi::contraction::Placement_policy<EdgeProfile> {
- Complex& complex_;
-
- public:
- typedef Gudhi::contraction::Placement_policy<EdgeProfile>::Placement_type Placement_type;
-
- GH_placement(Complex& complex) : complex_(complex) { (void)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();
- }
-};
-
-/**
- * How much cost an edge collapse : here the costs is given by a quadric
- * which expresses a squared distances with triangles planes.
- */
-class GH_cost : public Gudhi::contraction::Cost_policy<EdgeProfile> {
- Complex& complex_;
-
- public:
- typedef Gudhi::contraction::Cost_policy<EdgeProfile>::Cost_type Cost_type;
-
- GH_cost(Complex& complex) : complex_(complex) { (void)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;
- }
-};
-
-/**
- * Visitor that is called at several moment.
- * Here we initializes the quadrics of every vertex at the on_started call back
- * and we update them when contracting an edge (the quadric become the sum of both quadrics).
- */
-class GH_visitor : public Gudhi::contraction::Contraction_visitor<EdgeProfile> {
- Complex& complex_;
-
- public:
- GH_visitor(Complex& complex) : complex_(complex) { (void)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
-
- void on_started(Complex & complex) override {
- 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;
- }
-};
-
-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";
- return EXIT_FAILURE;
- }
-
- Complex complex;
- typedef Complex::Vertex_handle Vertex_handle;
-
- // load the points
- Gudhi::skeleton_blocker::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;
- }
-
- if (!complex.empty() && !(complex.point(Vertex_handle(0)).dimension() == 3)) {
- std::cerr << "Only points of dimension 3 are supported." << std::endl;
- return EXIT_FAILURE;
- }
-
- std::cout << "Load complex with " << complex.num_vertices() << " vertices" << std::endl;
-
- int num_contractions = atoi(argv[3]);
-
- // constructs the contractor object with Garland Heckbert policies.
- Complex_contractor contractor(complex,
- new GH_cost(complex),
- new GH_placement(complex),
- Gudhi::contraction::make_link_valid_contraction<EdgeProfile>(),
- new GH_visitor(complex));
-
- std::cout << "Contract " << num_contractions << " edges" << std::endl;
- contractor.contract_edges(num_contractions);
-
- std::cout << "Final complex has " <<
- complex.num_vertices() << " vertices, " <<
- complex.num_edges() << " edges and " <<
- complex.num_triangles() << " triangles." << std::endl;
-
- // write simplified complex
- Gudhi::skeleton_blocker::Skeleton_blocker_off_writer<Complex> off_writer(argv[2], complex);
-
- return EXIT_SUCCESS;
-}
-
-#endif // GARLAND_HECKBERT_H_
-
-
-
-
diff --git a/example/Contraction/Garland_heckbert/Error_quadric.h b/example/Contraction/Garland_heckbert/Error_quadric.h
deleted file mode 100644
index 8bd9b545..00000000
--- a/example/Contraction/Garland_heckbert/Error_quadric.h
+++ /dev/null
@@ -1,182 +0,0 @@
-/* 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
- *
- * 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_ERROR_QUADRIC_H_
-#define GARLAND_HECKBERT_ERROR_QUADRIC_H_
-
-#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;
- }
-};
-
-#endif // GARLAND_HECKBERT_ERROR_QUADRIC_H_
diff --git a/example/Contraction/Rips_contraction.cpp b/example/Contraction/Rips_contraction.cpp
deleted file mode 100644
index 7f9b150a..00000000
--- a/example/Contraction/Rips_contraction.cpp
+++ /dev/null
@@ -1,98 +0,0 @@
-/* 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
- *
- * 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/Edge_contraction.h>
-#include <gudhi/Skeleton_blocker.h>
-#include <gudhi/Off_reader.h>
-#include <gudhi/Point.h>
-#include <gudhi/Clock.h>
-
-#include <iostream>
-
-struct Geometry_trait {
- typedef Point_d Point;
-};
-
-using Complex_geometric_traits = Gudhi::skeleton_blocker::Skeleton_blocker_simple_geometric_traits<Geometry_trait>;
-using Complex = Gudhi::skeleton_blocker::Skeleton_blocker_geometric_complex< Complex_geometric_traits >;
-using Profile = Gudhi::contraction::Edge_profile<Complex>;
-using Complex_contractor = Gudhi::contraction::Skeleton_blocker_contractor<Complex>;
-
-
-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_without_blockers(*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;
- }
-
- Complex complex;
-
- // load only the points
- Gudhi::skeleton_blocker::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;
-
- build_rips(complex, atof(argv[2]));
-
- Gudhi::Clock contraction_chrono("Time to simplify and enumerate simplices");
-
- std::cout << "Initial complex has " <<
- complex.num_vertices() << " vertices and " <<
- complex.num_edges() << " edges" << std::endl;
-
- Complex_contractor contractor(complex,
- new Gudhi::contraction::Edge_length_cost<Profile>,
- Gudhi::contraction::make_first_vertex_placement<Profile>(),
- Gudhi::contraction::make_link_valid_contraction<Profile>(),
- Gudhi::contraction::make_remove_popable_blockers_visitor<Profile>());
- contractor.contract_edges();
-
- std::cout << "Counting final number of simplices \n";
- unsigned num_simplices = std::distance(complex.complex_simplex_range().begin(), complex.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 << contraction_chrono;
-
- return EXIT_SUCCESS;
-}
-
-
generated by cgit v1.2.3 (git 2.39.1) at 2024-05-15 14:49:22 +0000