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-rw-r--r--src/Contraction/example/CMakeLists.txt17
-rw-r--r--src/Contraction/example/Garland_heckbert.cpp179
-rw-r--r--src/Contraction/example/Garland_heckbert/Error_quadric.h169
-rw-r--r--src/Contraction/example/Rips_contraction.cpp86
4 files changed, 451 insertions, 0 deletions
diff --git a/src/Contraction/example/CMakeLists.txt b/src/Contraction/example/CMakeLists.txt
new file mode 100644
index 00000000..f0dc885d
--- /dev/null
+++ b/src/Contraction/example/CMakeLists.txt
@@ -0,0 +1,17 @@
+project(Contraction_examples)
+
+if (NOT CGAL_VERSION VERSION_LESS 4.11.0)
+ 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")
+
+endif (NOT CGAL_VERSION VERSION_LESS 4.11.0)
diff --git a/src/Contraction/example/Garland_heckbert.cpp b/src/Contraction/example/Garland_heckbert.cpp
new file mode 100644
index 00000000..9c0b5205
--- /dev/null
+++ b/src/Contraction/example/Garland_heckbert.cpp
@@ -0,0 +1,179 @@
+/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+ * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+ * Author(s): David Salinas
+ *
+ * Copyright (C) 2014 Inria
+ *
+ * Modification(s):
+ * - YYYY/MM Author: Description of the modification
+ */
+
+
+#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/src/Contraction/example/Garland_heckbert/Error_quadric.h b/src/Contraction/example/Garland_heckbert/Error_quadric.h
new file mode 100644
index 00000000..49250d7a
--- /dev/null
+++ b/src/Contraction/example/Garland_heckbert/Error_quadric.h
@@ -0,0 +1,169 @@
+/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+ * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+ * Author(s): David Salinas
+ *
+ * Copyright (C) 2014 Inria
+ *
+ * Modification(s):
+ * - YYYY/MM Author: Description of the modification
+ */
+
+#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/src/Contraction/example/Rips_contraction.cpp b/src/Contraction/example/Rips_contraction.cpp
new file mode 100644
index 00000000..b5ce06c1
--- /dev/null
+++ b/src/Contraction/example/Rips_contraction.cpp
@@ -0,0 +1,86 @@
+/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+ * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+ * Author(s): David Salinas
+ *
+ * Copyright (C) 2014 Inria
+ *
+ * Modification(s):
+ * - YYYY/MM Author: Description of the modification
+ */
+#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;
+}
+
+
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