From eaae83fc6b471bb05891addd35863fe00c351565 Mon Sep 17 00:00:00 2001 From: fgodi Date: Sun, 29 Mar 2015 22:37:12 +0000 Subject: Copyrigth Sophia + tests git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@512 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 353baa0c191df44a3bc420efd4424de2f5c6859e --- src/Bottleneck/example/random_diagrams.cpp | 2 +- src/Bottleneck/include/gudhi/Graph_matching.h | 53 ++++----- .../include/gudhi/Layered_neighbors_finder.h | 2 +- src/Bottleneck/include/gudhi/Neighbors_finder.h | 2 +- .../include/gudhi/Persistence_diagrams_graph.h | 113 +++++++++---------- .../include/gudhi/Planar_neighbors_finder.h | 3 +- src/Bottleneck/test/bottleneck_unit_test.cpp | 122 ++++++++++++++++++--- 7 files changed, 192 insertions(+), 105 deletions(-) (limited to 'src') diff --git a/src/Bottleneck/example/random_diagrams.cpp b/src/Bottleneck/example/random_diagrams.cpp index 71f152a6..a9d0968d 100644 --- a/src/Bottleneck/example/random_diagrams.cpp +++ b/src/Bottleneck/example/random_diagrams.cpp @@ -4,7 +4,7 @@ * * Author(s): Francois Godi * - * Copyright (C) 2015 INRIA Saclay (France) + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 diff --git a/src/Bottleneck/include/gudhi/Graph_matching.h b/src/Bottleneck/include/gudhi/Graph_matching.h index ea47e1d5..4cd3180e 100644 --- a/src/Bottleneck/include/gudhi/Graph_matching.h +++ b/src/Bottleneck/include/gudhi/Graph_matching.h @@ -4,7 +4,7 @@ * * Author(s): Francois Godi * - * Copyright (C) 2015 INRIA Saclay (France) + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 @@ -34,11 +34,11 @@ namespace Gudhi { namespace bottleneck { template -double bottleneck_distance(Persistence_diagram1& diag1, Persistence_diagram2& diag2, double e = 0.); +double bottleneck_distance(const Persistence_diagram1& diag1, const Persistence_diagram2& diag2, double e = 0.); class Graph_matching { public: - Graph_matching(const Persistence_diagrams_graph& g); + explicit Graph_matching(const Persistence_diagrams_graph& g); Graph_matching& operator=(const Graph_matching& m); bool perfect() const; bool multi_augment(); @@ -52,7 +52,7 @@ class Graph_matching { Layered_neighbors_finder* layering() const; bool augment(Layered_neighbors_finder* layered_nf, int u_start_index, int max_depth); - void update(std::deque& path); + void update(std::deque* path); }; Graph_matching::Graph_matching(const Persistence_diagrams_graph& g) @@ -128,36 +128,37 @@ Layered_neighbors_finder* Graph_matching::layering() const { } bool Graph_matching::augment(Layered_neighbors_finder *layered_nf, int u_start_index, int max_depth) { - std::deque path; - path.emplace_back(u_start_index); + std::deque* path = new std::deque(); + path->emplace_back(u_start_index); // start is a point from U do { - if (static_cast(path.size()) > max_depth) { - path.pop_back(); - path.pop_back(); + if (static_cast(path->size()) > max_depth) { + path->pop_back(); + path->pop_back(); } - if (path.empty()) + if (path->empty()) return false; - int w = path.back(); - path.emplace_back(layered_nf->pull_near(w, path.size() / 2)); - while (path.back() == null_point_index()) { - path.pop_back(); - path.pop_back(); - if (path.empty()) + int w = path->back(); + path->emplace_back(layered_nf->pull_near(w, path->size() / 2)); + while (path->back() == null_point_index()) { + path->pop_back(); + path->pop_back(); + if (path->empty()) return false; - path.pop_back(); - path.emplace_back(layered_nf->pull_near(path.back(), path.size() / 2)); + path->pop_back(); + path->emplace_back(layered_nf->pull_near(path->back(), path->size() / 2)); } - path.emplace_back(v_to_u.at(path.back())); - } while (path.back() != null_point_index()); - path.pop_back(); + path->emplace_back(v_to_u.at(path->back())); + } while (path->back() != null_point_index()); + path->pop_back(); update(path); + delete path; return true; } -void Graph_matching::update(std::deque& path) { - unmatched_in_u.remove(path.front()); - for (auto it = path.cbegin(); it != path.cend(); ++it) { +void Graph_matching::update(std::deque *path) { + unmatched_in_u.remove(path->front()); + for (auto it = path->cbegin(); it != path->cend(); ++it) { int tmp = *it; ++it; v_to_u[*it] = tmp; @@ -165,14 +166,14 @@ void Graph_matching::update(std::deque& path) { } template -double bottleneck_distance(Persistence_diagram1& diag1, Persistence_diagram2& diag2, double e) { +double bottleneck_distance(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e) { Persistence_diagrams_graph g(diag1, diag2, e); std::vector* sd = g.sorted_distances(); int idmin = 0; int idmax = sd->size() - 1; double alpha = pow(sd->size(), 0.25); Graph_matching m(g); - Graph_matching biggest_unperfect = m; + Graph_matching biggest_unperfect(g); while (idmin != idmax) { int pas = static_cast((idmax - idmin) / alpha); m.set_r(sd->at(idmin + pas)); diff --git a/src/Bottleneck/include/gudhi/Layered_neighbors_finder.h b/src/Bottleneck/include/gudhi/Layered_neighbors_finder.h index de36e00b..80e5b5ed 100644 --- a/src/Bottleneck/include/gudhi/Layered_neighbors_finder.h +++ b/src/Bottleneck/include/gudhi/Layered_neighbors_finder.h @@ -4,7 +4,7 @@ * * Author(s): Francois Godi * - * Copyright (C) 2015 INRIA Saclay (France) + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 diff --git a/src/Bottleneck/include/gudhi/Neighbors_finder.h b/src/Bottleneck/include/gudhi/Neighbors_finder.h index 98256571..6a05e1a0 100644 --- a/src/Bottleneck/include/gudhi/Neighbors_finder.h +++ b/src/Bottleneck/include/gudhi/Neighbors_finder.h @@ -4,7 +4,7 @@ * * Author(s): Francois Godi * - * Copyright (C) 2015 INRIA Saclay (France) + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 diff --git a/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h b/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h index 7e278209..8e9eaaf6 100644 --- a/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h +++ b/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h @@ -4,7 +4,7 @@ * * Author(s): Francois Godi * - * Copyright (C) 2015 INRIA Saclay (France) + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 @@ -44,100 +44,101 @@ int null_point_index(); class Persistence_diagrams_graph { public: - // Persistence_diagram1 and 2 are the types of any externals representations of persistence diagrams. - // They have to have an iterator over points, which have to have fields first (for birth) and second (for death). - template - Persistence_diagrams_graph(Persistence_diagram1& diag1, Persistence_diagram2& diag2, double e = 0.); - Persistence_diagrams_graph(); - bool on_the_u_diagonal(int u_point_index) const; - bool on_the_v_diagonal(int v_point_index) const; - int corresponding_point_in_u(int v_point_index) const; - int corresponding_point_in_v(int u_point_index) const; - double distance(int u_point_index, int v_point_index) const; - int size() const; - std::vector* sorted_distances(); + // Persistence_diagram1 and 2 are the types of any externals representations of persistence diagrams. + // They have to have an iterator over points, which have to have fields first (for birth) and second (for death). + template + Persistence_diagrams_graph(const Persistence_diagram1& diag1, const Persistence_diagram2& diag2, double e); + Persistence_diagrams_graph(); + bool on_the_u_diagonal(int u_point_index) const; + bool on_the_v_diagonal(int v_point_index) const; + int corresponding_point_in_u(int v_point_index) const; + int corresponding_point_in_v(int u_point_index) const; + double distance(int u_point_index, int v_point_index) const; + int size() const; + std::vector* sorted_distances(); private: - std::vector u; - std::vector v; - Diagram_point get_u_point(int u_point_index) const; - Diagram_point get_v_point(int v_point_index) const; + std::vector u; + std::vector v; + Diagram_point get_u_point(int u_point_index) const; + Diagram_point get_v_point(int v_point_index) const; }; inline int null_point_index() { - return -1; + return -1; } template -Persistence_diagrams_graph::Persistence_diagrams_graph(Persistence_diagram1& diag1, Persistence_diagram2& diag2, double e) +Persistence_diagrams_graph::Persistence_diagrams_graph(const Persistence_diagram1 &diag1, + const Persistence_diagram2 &diag2, double e) : u(), v() { - for (auto it = diag1.cbegin(); it != diag1.cend(); ++it) - if (it->second - it->first > e) - u.emplace_back(*it); - for (auto it = diag2.cbegin(); it != diag2.cend(); ++it) - if (it->second - it->first > e) - v.emplace_back(*it); - if (u.size() < v.size()) - swap(u, v); + for (auto it = diag1.cbegin(); it != diag1.cend(); ++it) + if (it->second - it->first > e) + u.emplace_back(*it); + for (auto it = diag2.cbegin(); it != diag2.cend(); ++it) + if (it->second - it->first > e) + v.emplace_back(*it); + if (u.size() < v.size()) + swap(u, v); } Persistence_diagrams_graph::Persistence_diagrams_graph::Persistence_diagrams_graph() : u(), v() { } inline bool Persistence_diagrams_graph::on_the_u_diagonal(int u_point_index) const { - return u_point_index >= static_cast (u.size()); + return u_point_index >= static_cast (u.size()); } inline bool Persistence_diagrams_graph::on_the_v_diagonal(int v_point_index) const { - return v_point_index >= static_cast (v.size()); + return v_point_index >= static_cast (v.size()); } inline int Persistence_diagrams_graph::corresponding_point_in_u(int v_point_index) const { - return on_the_v_diagonal(v_point_index) ? - v_point_index - static_cast (v.size()) : v_point_index + static_cast (u.size()); + return on_the_v_diagonal(v_point_index) ? + v_point_index - static_cast (v.size()) : v_point_index + static_cast (u.size()); } inline int Persistence_diagrams_graph::corresponding_point_in_v(int u_point_index) const { - return on_the_u_diagonal(u_point_index) ? - u_point_index - static_cast (u.size()) : u_point_index + static_cast (v.size()); + return on_the_u_diagonal(u_point_index) ? + u_point_index - static_cast (u.size()) : u_point_index + static_cast (v.size()); } inline double Persistence_diagrams_graph::distance(int u_point_index, int v_point_index) const { - // could be optimized for the case where one point is the projection of the other - if (on_the_u_diagonal(u_point_index) && on_the_v_diagonal(v_point_index)) - return 0; - Diagram_point p_u = get_u_point(u_point_index); - Diagram_point p_v = get_v_point(v_point_index); - return std::max(std::fabs(p_u.first - p_v.first), std::fabs(p_u.second - p_v.second)); + // could be optimized for the case where one point is the projection of the other + if (on_the_u_diagonal(u_point_index) && on_the_v_diagonal(v_point_index)) + return 0; + Diagram_point p_u = get_u_point(u_point_index); + Diagram_point p_v = get_v_point(v_point_index); + return std::max(std::fabs(p_u.first - p_v.first), std::fabs(p_u.second - p_v.second)); } inline int Persistence_diagrams_graph::size() const { - return static_cast (u.size() + v.size()); + return static_cast (u.size() + v.size()); } inline std::vector* Persistence_diagrams_graph::sorted_distances() { - // could be optimized - std::set sorted_distances; - for (int u_point_index = 0; u_point_index < size(); ++u_point_index) - for (int v_point_index = 0; v_point_index < size(); ++v_point_index) - sorted_distances.emplace(distance(u_point_index, v_point_index)); - return new std::vector(sorted_distances.cbegin(), sorted_distances.cend()); + // could be optimized + std::set sorted_distances; + for (int u_point_index = 0; u_point_index < size(); ++u_point_index) + for (int v_point_index = 0; v_point_index < size(); ++v_point_index) + sorted_distances.emplace(distance(u_point_index, v_point_index)); + return new std::vector(sorted_distances.cbegin(), sorted_distances.cend()); } inline Diagram_point Persistence_diagrams_graph::get_u_point(int u_point_index) const { - if (!on_the_u_diagonal(u_point_index)) - return u.at(u_point_index); - Diagram_point projector = v.at(corresponding_point_in_v(u_point_index)); - double x = (projector.first + projector.second) / 2; - return Diagram_point(x, x); + if (!on_the_u_diagonal(u_point_index)) + return u.at(u_point_index); + Diagram_point projector = v.at(corresponding_point_in_v(u_point_index)); + double x = (projector.first + projector.second) / 2; + return Diagram_point(x, x); } inline Diagram_point Persistence_diagrams_graph::get_v_point(int v_point_index) const { - if (!on_the_v_diagonal(v_point_index)) - return v.at(v_point_index); - Diagram_point projector = u.at(corresponding_point_in_u(v_point_index)); - double x = (projector.first + projector.second) / 2; - return Diagram_point(x, x); + if (!on_the_v_diagonal(v_point_index)) + return v.at(v_point_index); + Diagram_point projector = u.at(corresponding_point_in_u(v_point_index)); + double x = (projector.first + projector.second) / 2; + return Diagram_point(x, x); } } // namespace bottleneck diff --git a/src/Bottleneck/include/gudhi/Planar_neighbors_finder.h b/src/Bottleneck/include/gudhi/Planar_neighbors_finder.h index 4af672e4..3d04aa97 100644 --- a/src/Bottleneck/include/gudhi/Planar_neighbors_finder.h +++ b/src/Bottleneck/include/gudhi/Planar_neighbors_finder.h @@ -4,7 +4,7 @@ * * Author(s): Francois Godi * - * Copyright (C) 2015 INRIA Saclay (France) + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 @@ -24,7 +24,6 @@ #define SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_ #include -#include #include #include "Persistence_diagrams_graph.h" diff --git a/src/Bottleneck/test/bottleneck_unit_test.cpp b/src/Bottleneck/test/bottleneck_unit_test.cpp index 068b8690..ea7f51f2 100644 --- a/src/Bottleneck/test/bottleneck_unit_test.cpp +++ b/src/Bottleneck/test/bottleneck_unit_test.cpp @@ -1,26 +1,112 @@ #define BOOST_TEST_MODULE bottleneck test #include - +#include #include "gudhi/Graph_matching.h" -#include using namespace Gudhi::bottleneck; -BOOST_AUTO_TEST_CASE(random_diagrams) { - int n = 100; - // Random construction - std::vector< std::pair > v1, v2; - for (int i = 0; i < n; i++) { - int a = rand() % n; - v1.emplace_back(a, a + rand() % (n - a)); - int b = rand() % n; - v2.emplace_back(b, b + rand() % (n - b)); - } - // v1 and v2 are persistence diagrams containing each 100 randoms points. - double b = bottleneck_distance(v1, v2, 0); - // - std::cout << b << std::endl; - const double EXPECTED_DISTANCE = 98.5; - BOOST_CHECK(b == EXPECTED_DISTANCE); +Persistence_diagrams_graph* random_graph_generator(){ + int n1 = 100; + int n2 = 120; + double upper_bound = 80; + // Random construction + std::uniform_real_distribution unif(0.,upper_bound); + std::default_random_engine re; + std::vector< std::pair > v1, v2; + for (int i = 0; i < n1; i++) { + double a = unif(re); + double b = unif(re); + v1.emplace_back(std::min(a,b), std::max(a,b)); + } + for (int i = 0; i < n2; i++) { + double a = unif(re); + double b = unif(re); + v2.emplace_back(std::min(a,b), std::max(a,b)); + } + return new Persistence_diagrams_graph(v1, v2, 0.); +} + +BOOST_AUTO_TEST_CASE(global){ + int n = 100; + // Random construction + std::vector< std::pair > v1, v2; + for (int i = 0; i < n; i++) { + int a = rand() % n; + v1.emplace_back(a, a + rand() % (n - a)); + int b = rand() % n; + v2.emplace_back(b, b + rand() % (n - b)); + } + // + BOOST_CHECK(bottleneck_distance(v1, v2, 1.) == 98); } + + +BOOST_AUTO_TEST_CASE(persistence_diagrams_graph) { + Persistence_diagrams_graph* g = random_graph_generator(); + std::vector* d = g->sorted_distances(); + // + BOOST_CHECK(!g->on_the_u_diagonal(99)); + BOOST_CHECK(!g->on_the_u_diagonal(100)); + BOOST_CHECK(!g->on_the_u_diagonal(119)); + BOOST_CHECK(g->on_the_u_diagonal(120)); + BOOST_CHECK(!g->on_the_v_diagonal(99)); + BOOST_CHECK(g->on_the_v_diagonal(100)); + BOOST_CHECK(g->on_the_v_diagonal(119)); + BOOST_CHECK(g->on_the_v_diagonal(120)); + // + BOOST_CHECK(g->corresponding_point_in_u(0)==120); + BOOST_CHECK(g->corresponding_point_in_u(100)==0); + BOOST_CHECK(g->corresponding_point_in_v(0)==100); + BOOST_CHECK(g->corresponding_point_in_v(120)==0); + // + BOOST_CHECK(g->size()==220); + // + BOOST_CHECK((int) d->size() <= 220*220 - 100*120 + 1); // could be more strict + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(0,0))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(0,99))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(0,100))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(0,119))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(0,120))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(0,219))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(100,0))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(100,99))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(100,100))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(100,119))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(100,120))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(100,219))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(219,0))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(219,99))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(219,100))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(219,119))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(219,120))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(219,219))==1); + // + delete g; + delete d; +} + +BOOST_AUTO_TEST_CASE(planar_nf) { + Persistence_diagrams_graph* g = random_graph_generator(); + Planar_neighbors_finder pnf = Planar_neighbors_finder(*g,1.); + for(int v_point_index=0; v_point_index<100; v_point_index+=2) + pnf.add(v_point_index); + pnf.remove(0); + pnf.remove(1); + // + BOOST_CHECK(!pnf.contains(0)); + BOOST_CHECK(!pnf.contains(1)); + BOOST_CHECK(pnf.contains(2)); + BOOST_CHECK(!pnf.contains(3)); + // + int v_point_index_1 = pnf.pull_near(120/2); + BOOST_CHECK((v_point_index_1 == -1) || (g->distance(120/2,v_point_index_1)<1.)); + BOOST_CHECK(!pnf.contains(v_point_index_1)); + int v_point_index_2 = pnf.pull_near(120/2); + BOOST_CHECK((v_point_index_2 == -1) || (g->distance(120/2,v_point_index_2)<1.)); + BOOST_CHECK(!pnf.contains(v_point_index_2)); + BOOST_CHECK((v_point_index_2 != -1) || (v_point_index_1 == -1)); + pnf.add(v_point_index_1); + BOOST_CHECK(pnf.contains(v_point_index_1)); +} + -- cgit v1.2.3 From ef48b9447c7270ba63d45a76e4d2e6ecb1a7d199 Mon Sep 17 00:00:00 2001 From: fgodi Date: Thu, 25 Jun 2015 10:19:49 +0000 Subject: tests unitaires terminés MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@647 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: aca61ea029d72ddfbf8eca3e4db00da3e7b268c3 --- src/Bottleneck/example/CMakeLists.txt | 23 +- src/Bottleneck/include/gudhi/Graph_matching.h | 284 +++++++++++---------- .../include/gudhi/Layered_neighbors_finder.h | 8 +- src/Bottleneck/include/gudhi/Neighbors_finder.h | 93 ++++--- .../include/gudhi/Persistence_diagrams_graph.h | 27 +- .../include/gudhi/Planar_neighbors_finder.h | 16 +- src/Bottleneck/test/CMakeLists.txt | 6 + src/Bottleneck/test/bottleneck_unit_test.cpp | 187 +++++++++----- 8 files changed, 385 insertions(+), 259 deletions(-) (limited to 'src') diff --git a/src/Bottleneck/example/CMakeLists.txt b/src/Bottleneck/example/CMakeLists.txt index 2ff009c4..8bf61c50 100644 --- a/src/Bottleneck/example/CMakeLists.txt +++ b/src/Bottleneck/example/CMakeLists.txt @@ -1,5 +1,24 @@ cmake_minimum_required(VERSION 2.6) project(GUDHIBottleneckExample) -add_executable ( RandomDiagrams random_diagrams.cpp ) -add_test(RandomDiagrams ${CMAKE_CURRENT_BINARY_DIR}/RandomDiagrams) +if (GCOVR_PATH) + # for gcovr to make coverage reports - Corbera Jenkins plugin + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage") + set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage") +endif() +if (GPROF_PATH) + # for gprof to make coverage reports - Jenkins + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg") + set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg") +endif() + message("CMAKE_CXX_FLAGS = ${CMAKE_CXX_FLAGS}") + message("CMAKE_CXX_FLAGS_DEBUG = ${CMAKE_CXX_FLAGS_DEBUG}") + message("CMAKE_CXX_FLAGS_RELEASE = ${CMAKE_CXX_FLAGS_RELEASE}") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O2 -std=c++11 -Wall -Wpedantic -Wsign-compare") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -ggdb -O0") + set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE}") + +add_executable ( BottleneckExample example.cpp ) + diff --git a/src/Bottleneck/include/gudhi/Graph_matching.h b/src/Bottleneck/include/gudhi/Graph_matching.h index 4cd3180e..9f36e936 100644 --- a/src/Bottleneck/include/gudhi/Graph_matching.h +++ b/src/Bottleneck/include/gudhi/Graph_matching.h @@ -22,12 +22,12 @@ #ifndef SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ #define SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ - +//#define DEBUG #include #include #include -#include "gudhi/Layered_neighbors_finder.h" +#include "Layered_neighbors_finder.h" namespace Gudhi { @@ -37,158 +37,182 @@ template double bottleneck_distance(const Persistence_diagram1& diag1, const Persistence_diagram2& diag2, double e = 0.); class Graph_matching { - public: - explicit Graph_matching(const Persistence_diagrams_graph& g); - Graph_matching& operator=(const Graph_matching& m); - bool perfect() const; - bool multi_augment(); - void set_r(double r); - - private: - const Persistence_diagrams_graph& g; - double r; - std::vector v_to_u; - std::list unmatched_in_u; - - Layered_neighbors_finder* layering() const; - bool augment(Layered_neighbors_finder* layered_nf, int u_start_index, int max_depth); - void update(std::deque* path); +public: + explicit Graph_matching(const Persistence_diagrams_graph& g); + Graph_matching& operator=(const Graph_matching& m); + bool perfect() const; + bool multi_augment(); + void set_r(double r); + +private: + const Persistence_diagrams_graph& g; + double r; + std::vector v_to_u; + std::list unmatched_in_u; + + std::unique_ptr layering() const; + bool augment(Layered_neighbors_finder & layered_nf, int u_start_index, int max_depth); + void update(std::deque & path); }; Graph_matching::Graph_matching(const Persistence_diagrams_graph& g) - : g(g), r(0), v_to_u(g.size()), unmatched_in_u() { - for (int u_point_index = 0; u_point_index < g.size(); ++u_point_index) - unmatched_in_u.emplace_back(u_point_index); + : g(g), r(0), v_to_u(g.size(), null_point_index()), unmatched_in_u() { + for (int u_point_index = 0; u_point_index < g.size(); ++u_point_index) + unmatched_in_u.emplace_back(u_point_index); } Graph_matching& Graph_matching::operator=(const Graph_matching& m) { - r = m.r; - v_to_u = m.v_to_u; - unmatched_in_u = m.unmatched_in_u; - return *this; + r = m.r; + v_to_u = m.v_to_u; + unmatched_in_u = m.unmatched_in_u; + return *this; } -inline bool Graph_matching::perfect() const { - return unmatched_in_u.empty(); +/* inline */ bool Graph_matching::perfect() const { +#ifdef DEBUG + std::cout << " perfect? unmatched_in_u.size = " << unmatched_in_u.size() << std::endl << std::flush; +#endif + return unmatched_in_u.empty(); } -inline bool Graph_matching::multi_augment() { - if (perfect()) - return false; - Layered_neighbors_finder* layered_nf = layering(); - double rn = sqrt(g.size()); - int nblmax = layered_nf->vlayers_number()*2 + 1; - // verification of a necessary criterion - if ((unmatched_in_u.size() > rn && nblmax > rn) || nblmax == 0) - return false; - bool successful = false; - std::list* tries = new std::list(unmatched_in_u); - for (auto it = tries->cbegin(); it != tries->cend(); it++) - successful = successful || augment(layered_nf, *it, nblmax); - delete tries; - delete layered_nf; - return successful; +/* inline */ bool Graph_matching::multi_augment() { + if (perfect()) + return false; +#ifdef DEBUG + std::cout << " multi augment" << std::endl << std::flush; +#endif + Layered_neighbors_finder layered_nf = *layering(); + double rn = sqrt(g.size()); + int max_depth = layered_nf.vlayers_number()*2 - 1; +#ifdef DEBUG + std::cout<< " nb_max_layer = " << max_depth << std::endl << std::flush; +#endif + // verification of a necessary criterion + if (max_depth <0 || (unmatched_in_u.size() > rn && max_depth >= rn)) + return false; + bool successful = false; + std::list tries(unmatched_in_u); + for (auto it = tries.cbegin(); it != tries.cend(); it++){ + const bool tmp = augment(layered_nf, *it, max_depth); //force augment evaluation even if successful is already true + successful = successful || tmp; + } + return successful; } -inline void Graph_matching::set_r(double r) { - this->r = r; +/* inline */ void Graph_matching::set_r(double r) { + this->r = r; } -Layered_neighbors_finder* Graph_matching::layering() const { - bool end = false; - int layer = 0; - std::list u_vertices(unmatched_in_u); - std::list v_vertices; - Neighbors_finder nf(g, r); - Layered_neighbors_finder* layered_nf = new Layered_neighbors_finder(g, r); - for (int v_point_index = 0; v_point_index < g.size(); ++v_point_index) - nf.add(v_point_index); - while (!u_vertices.empty()) { - for (auto it = u_vertices.cbegin(); it != u_vertices.cend(); ++it) { - std::list* u_succ = nf.pull_all_near(*it); - for (auto it = u_succ->cbegin(); it != u_succ->cend(); ++it) { - layered_nf->add(*it, layer); - v_vertices.emplace_back(*it); - } - delete u_succ; - } - u_vertices.clear(); - for (auto it = v_vertices.cbegin(); it != v_vertices.cend(); it++) { - if (v_to_u.at(*it) == null_point_index()) - end = true; - else - u_vertices.emplace_back(v_to_u.at(*it)); - } - if (end) - return layered_nf; - v_vertices.clear(); - layer++; - } - return layered_nf; +bool Graph_matching::augment(Layered_neighbors_finder & layered_nf, int u_start_index, int max_depth) { +#ifdef DEBUG + std::cout << " augment" << std::endl << std::flush; +#endif +#ifdef DEBUG + std::cout << " u_start_index = " << u_start_index << std::endl << std::flush; +#endif + std::deque path; + path.emplace_back(u_start_index); + // u_start is a point from U + do { +#ifdef DEBUG + std::cout << " do" << std::endl << std::flush; + std::cout << " path.size = " << static_cast(path.size()) << std::endl << std::flush; +#endif + if (static_cast(path.size()) > max_depth) { + path.pop_back(); + path.pop_back(); + } + if (path.empty()) + return false; + path.emplace_back(layered_nf.pull_near(path.back(), static_cast(path.size())/2)); + while (path.back() == null_point_index()) { + path.pop_back(); + path.pop_back(); + if (path.empty()) + return false; + path.pop_back(); + path.emplace_back(layered_nf.pull_near(path.back(), path.size() / 2)); + } + path.emplace_back(v_to_u.at(path.back())); +#ifdef DEBUG + std::cout << " v_to_u = " << path.back() << std::endl << std::flush; +#endif + } while (path.back() != null_point_index()); + path.pop_back(); + update(path); + return true; } -bool Graph_matching::augment(Layered_neighbors_finder *layered_nf, int u_start_index, int max_depth) { - std::deque* path = new std::deque(); - path->emplace_back(u_start_index); - // start is a point from U - do { - if (static_cast(path->size()) > max_depth) { - path->pop_back(); - path->pop_back(); - } - if (path->empty()) - return false; - int w = path->back(); - path->emplace_back(layered_nf->pull_near(w, path->size() / 2)); - while (path->back() == null_point_index()) { - path->pop_back(); - path->pop_back(); - if (path->empty()) - return false; - path->pop_back(); - path->emplace_back(layered_nf->pull_near(path->back(), path->size() / 2)); +std::unique_ptr Graph_matching::layering() const { +#ifdef DEBUG + std::cout << " layering" << std::endl << std::flush; +#endif + bool end = false; + int layer = 0; + std::list u_vertices(unmatched_in_u); + std::list v_vertices; + Neighbors_finder nf(g, r); + for (int v_point_index = 0; v_point_index < g.size(); ++v_point_index) + nf.add(v_point_index); + std::unique_ptr layered_nf(new Layered_neighbors_finder(g, r)); + while (!u_vertices.empty()) { + for (auto it = u_vertices.cbegin(); it != u_vertices.cend(); ++it) { + std::unique_ptr< std::list > u_succ = std::move(nf.pull_all_near(*it)); + for (auto it = u_succ->cbegin(); it != u_succ->cend(); ++it) { + layered_nf->add(*it, layer); + v_vertices.emplace_back(*it); + } + } + u_vertices.clear(); + for (auto it = v_vertices.cbegin(); it != v_vertices.cend(); it++) { + if (v_to_u.at(*it) == null_point_index()) + end = true; + else + u_vertices.emplace_back(v_to_u.at(*it)); + } + if (end) + return layered_nf; + v_vertices.clear(); + layer++; } - path->emplace_back(v_to_u.at(path->back())); - } while (path->back() != null_point_index()); - path->pop_back(); - update(path); - delete path; - return true; + return layered_nf; } -void Graph_matching::update(std::deque *path) { - unmatched_in_u.remove(path->front()); - for (auto it = path->cbegin(); it != path->cend(); ++it) { - int tmp = *it; - ++it; - v_to_u[*it] = tmp; - } +void Graph_matching::update(std::deque& path) { +#ifdef DEBUG + std::cout << " update" << std::endl << std::flush; +#endif + unmatched_in_u.remove(path.front()); + for (auto it = path.cbegin(); it != path.cend(); ++it) { + int tmp = *it; + ++it; + v_to_u[*it] = tmp; + } } template double bottleneck_distance(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e) { - Persistence_diagrams_graph g(diag1, diag2, e); - std::vector* sd = g.sorted_distances(); - int idmin = 0; - int idmax = sd->size() - 1; - double alpha = pow(sd->size(), 0.25); - Graph_matching m(g); - Graph_matching biggest_unperfect(g); - while (idmin != idmax) { - int pas = static_cast((idmax - idmin) / alpha); - m.set_r(sd->at(idmin + pas)); - while (m.multi_augment()) {} - if (m.perfect()) { - idmax = idmin + pas; - m = biggest_unperfect; - } else { - biggest_unperfect = m; - idmin = idmin + pas + 1; + Persistence_diagrams_graph g(diag1, diag2, e); + std::unique_ptr< std::vector > sd = std::move(g.sorted_distances()); + int idmin = 0; + int idmax = sd->size() - 1; + double alpha = pow(sd->size(), 0.25); + Graph_matching m(g); + Graph_matching biggest_unperfect(g); + while (idmin != idmax) { + int pas = static_cast((idmax - idmin) / alpha); + m.set_r(sd->at(idmin + pas)); + while (m.multi_augment()); + if (m.perfect()) { + idmax = idmin + pas; + m = biggest_unperfect; + } else { + biggest_unperfect = m; + idmin = idmin + pas + 1; + } } - } - double b = sd->at(idmin); - delete sd; - return b; + double b = sd->at(idmin); + return b; } } // namespace bottleneck diff --git a/src/Bottleneck/include/gudhi/Layered_neighbors_finder.h b/src/Bottleneck/include/gudhi/Layered_neighbors_finder.h index 80e5b5ed..1cf83393 100644 --- a/src/Bottleneck/include/gudhi/Layered_neighbors_finder.h +++ b/src/Bottleneck/include/gudhi/Layered_neighbors_finder.h @@ -51,20 +51,20 @@ class Layered_neighbors_finder { Layered_neighbors_finder::Layered_neighbors_finder(const Persistence_diagrams_graph& g, double r) : g(g), r(r), neighbors_finder() { } -inline void Layered_neighbors_finder::add(int v_point_index, int vlayer) { +/* inline */ void Layered_neighbors_finder::add(int v_point_index, int vlayer) { for (int l = neighbors_finder.size(); l <= vlayer; l++) neighbors_finder.emplace_back(Neighbors_finder(g, r)); neighbors_finder.at(vlayer).add(v_point_index); } -inline int Layered_neighbors_finder::pull_near(int u_point_index, int vlayer) { +/* inline */ int Layered_neighbors_finder::pull_near(int u_point_index, int vlayer) { if (static_cast (neighbors_finder.size()) <= vlayer) return null_point_index(); return neighbors_finder.at(vlayer).pull_near(u_point_index); } -inline int Layered_neighbors_finder::vlayers_number() const { - return neighbors_finder.size(); +/* inline */ int Layered_neighbors_finder::vlayers_number() const { + return static_cast(neighbors_finder.size()); } } // namespace bottleneck diff --git a/src/Bottleneck/include/gudhi/Neighbors_finder.h b/src/Bottleneck/include/gudhi/Neighbors_finder.h index 6a05e1a0..0fad9889 100644 --- a/src/Bottleneck/include/gudhi/Neighbors_finder.h +++ b/src/Bottleneck/include/gudhi/Neighbors_finder.h @@ -26,7 +26,7 @@ #include #include -#include "gudhi/Planar_neighbors_finder.h" +#include "Planar_neighbors_finder.h" namespace Gudhi { @@ -37,56 +37,65 @@ namespace bottleneck { // V's points have to be added manually using their index. A neighbor returned is automatically removed. class Neighbors_finder { - public: - Neighbors_finder(const Persistence_diagrams_graph& g, double r); - void add(int v_point_index); - int pull_near(int u_point_index); - std::list* pull_all_near(int u_point_index); - - private: - const Persistence_diagrams_graph& g; - const double r; - Planar_neighbors_finder planar_neighbors_f; - std::unordered_set projections_f; +public: + Neighbors_finder(const Persistence_diagrams_graph& g, double r); + void add(int v_point_index); + int pull_near(int u_point_index); + std::unique_ptr< std::list > pull_all_near(int u_point_index); + +private: + const Persistence_diagrams_graph& g; + const double r; + Planar_neighbors_finder planar_neighbors_f; + std::unordered_set projections_f; + void remove(int v_point_index); + bool contains(int v_point_index); }; Neighbors_finder::Neighbors_finder(const Persistence_diagrams_graph& g, double r) : g(g), r(r), planar_neighbors_f(g, r), projections_f() { } -inline void Neighbors_finder::add(int v_point_index) { - if (g.on_the_v_diagonal(v_point_index)) - projections_f.emplace(v_point_index); - else - planar_neighbors_f.add(v_point_index); +/* inline */ void Neighbors_finder::add(int v_point_index) { + if (g.on_the_v_diagonal(v_point_index)) + projections_f.emplace(v_point_index); + else + planar_neighbors_f.add(v_point_index); } -inline int Neighbors_finder::pull_near(int u_point_index) { - int v_challenger = g.corresponding_point_in_v(u_point_index); - if (planar_neighbors_f.contains(v_challenger) && g.distance(u_point_index, v_challenger) < r) { - planar_neighbors_f.remove(v_challenger); - return v_challenger; - } - if (g.on_the_u_diagonal(u_point_index)) { - auto it = projections_f.cbegin(); - if (it != projections_f.cend()) { - int tmp = *it; - projections_f.erase(it); - return tmp; - } - } else { - return planar_neighbors_f.pull_near(u_point_index); - } - return null_point_index(); +/* inline */ void Neighbors_finder::remove(int v_point_index) { + if(v_point_index == null_point_index()) + return; + if (g.on_the_v_diagonal(v_point_index)) + projections_f.erase(v_point_index); + else + planar_neighbors_f.remove(v_point_index); +} + +/* inline */ bool Neighbors_finder::contains(int v_point_index) { + return planar_neighbors_f.contains(v_point_index) || (projections_f.count(v_point_index)>0); } -inline std::list* Neighbors_finder::pull_all_near(int u_point_index) { - std::list* all_pull = planar_neighbors_f.pull_all_near(u_point_index); - int last_pull = pull_near(u_point_index); - while (last_pull != null_point_index()) { - all_pull->emplace_back(last_pull); - last_pull = pull_near(u_point_index); - } - return all_pull; +/* inline */ int Neighbors_finder::pull_near(int u_point_index) { + int tmp; + int c = g.corresponding_point_in_v(u_point_index); + if (g.on_the_u_diagonal(u_point_index) && projections_f.cbegin()!=projections_f.cend()) + tmp = *projections_f.cbegin(); + else if (contains(c) && (g.distance(u_point_index, c) <= r)) + tmp = c; + else + tmp = planar_neighbors_f.pull_near(u_point_index); + remove(tmp); + return tmp; +} + +std::unique_ptr< std::list > Neighbors_finder::pull_all_near(int u_point_index) { + std::unique_ptr< std::list > all_pull = std::move(planar_neighbors_f.pull_all_near(u_point_index)); + int last_pull = pull_near(u_point_index); + while (last_pull != null_point_index()) { + all_pull->emplace_back(last_pull); + last_pull = pull_near(u_point_index); + } + return all_pull; } } // namespace bottleneck diff --git a/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h b/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h index 105f9059..644c1cd8 100644 --- a/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h +++ b/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h @@ -55,7 +55,7 @@ class Persistence_diagrams_graph { int corresponding_point_in_v(int u_point_index) const; double distance(int u_point_index, int v_point_index) const; int size() const; - std::vector* sorted_distances(); + std::unique_ptr< std::vector > sorted_distances(); private: std::vector u; @@ -64,7 +64,7 @@ class Persistence_diagrams_graph { Diagram_point get_v_point(int v_point_index) const; }; -inline int null_point_index() { +/* inline */ int null_point_index() { return -1; } @@ -85,47 +85,48 @@ Persistence_diagrams_graph::Persistence_diagrams_graph(const Persistence_diagram Persistence_diagrams_graph::Persistence_diagrams_graph() : u(), v() { } -inline bool Persistence_diagrams_graph::on_the_u_diagonal(int u_point_index) const { +/* inline */ bool Persistence_diagrams_graph::on_the_u_diagonal(int u_point_index) const { return u_point_index >= static_cast (u.size()); } -inline bool Persistence_diagrams_graph::on_the_v_diagonal(int v_point_index) const { +/* inline */ bool Persistence_diagrams_graph::on_the_v_diagonal(int v_point_index) const { return v_point_index >= static_cast (v.size()); } -inline int Persistence_diagrams_graph::corresponding_point_in_u(int v_point_index) const { +/* inline */ int Persistence_diagrams_graph::corresponding_point_in_u(int v_point_index) const { return on_the_v_diagonal(v_point_index) ? v_point_index - static_cast (v.size()) : v_point_index + static_cast (u.size()); } -inline int Persistence_diagrams_graph::corresponding_point_in_v(int u_point_index) const { +/* inline */ int Persistence_diagrams_graph::corresponding_point_in_v(int u_point_index) const { return on_the_u_diagonal(u_point_index) ? u_point_index - static_cast (u.size()) : u_point_index + static_cast (v.size()); } -inline double Persistence_diagrams_graph::distance(int u_point_index, int v_point_index) const { +/* inline */ double Persistence_diagrams_graph::distance(int u_point_index, int v_point_index) const { // could be optimized for the case where one point is the projection of the other if (on_the_u_diagonal(u_point_index) && on_the_v_diagonal(v_point_index)) return 0; Diagram_point p_u = get_u_point(u_point_index); Diagram_point p_v = get_v_point(v_point_index); - return (std::max)(std::fabs(p_u.first - p_v.first), std::fabs(p_u.second - p_v.second)); + return std::max(std::fabs(p_u.first - p_v.first), std::fabs(p_u.second - p_v.second)); } -inline int Persistence_diagrams_graph::size() const { +/* inline */ int Persistence_diagrams_graph::size() const { return static_cast (u.size() + v.size()); } -inline std::vector* Persistence_diagrams_graph::sorted_distances() { +/* inline */ std::unique_ptr< std::vector > Persistence_diagrams_graph::sorted_distances() { // could be optimized std::set sorted_distances; for (int u_point_index = 0; u_point_index < size(); ++u_point_index) for (int v_point_index = 0; v_point_index < size(); ++v_point_index) sorted_distances.emplace(distance(u_point_index, v_point_index)); - return new std::vector(sorted_distances.cbegin(), sorted_distances.cend()); + std::unique_ptr< std::vector > sd_up(new std::vector(sorted_distances.cbegin(), sorted_distances.cend())); + return sd_up; } -inline Diagram_point Persistence_diagrams_graph::get_u_point(int u_point_index) const { +/* inline */ Diagram_point Persistence_diagrams_graph::get_u_point(int u_point_index) const { if (!on_the_u_diagonal(u_point_index)) return u.at(u_point_index); Diagram_point projector = v.at(corresponding_point_in_v(u_point_index)); @@ -133,7 +134,7 @@ inline Diagram_point Persistence_diagrams_graph::get_u_point(int u_point_index) return Diagram_point(x, x); } -inline Diagram_point Persistence_diagrams_graph::get_v_point(int v_point_index) const { +/* inline */ Diagram_point Persistence_diagrams_graph::get_v_point(int v_point_index) const { if (!on_the_v_diagonal(v_point_index)) return v.at(v_point_index); Diagram_point projector = u.at(corresponding_point_in_u(v_point_index)); diff --git a/src/Bottleneck/include/gudhi/Planar_neighbors_finder.h b/src/Bottleneck/include/gudhi/Planar_neighbors_finder.h index 3d04aa97..e558239d 100644 --- a/src/Bottleneck/include/gudhi/Planar_neighbors_finder.h +++ b/src/Bottleneck/include/gudhi/Planar_neighbors_finder.h @@ -45,7 +45,7 @@ class Abstract_planar_neighbors_finder { virtual void remove(int v_point_index) = 0; virtual bool contains(int v_point_index) const = 0; virtual int pull_near(int u_point_index) = 0; - virtual std::list* pull_all_near(int u_point_index); + virtual std::unique_ptr< std::list > pull_all_near(int u_point_index); protected: const Persistence_diagrams_graph& g; @@ -74,10 +74,10 @@ typedef Naive_pnf Planar_neighbors_finder; Abstract_planar_neighbors_finder::Abstract_planar_neighbors_finder(const Persistence_diagrams_graph& g, double r) : g(g), r(r) { } -inline Abstract_planar_neighbors_finder::~Abstract_planar_neighbors_finder() { } +/* inline */ Abstract_planar_neighbors_finder::~Abstract_planar_neighbors_finder() { } -inline std::list* Abstract_planar_neighbors_finder::pull_all_near(int u_point_index) { - std::list* all_pull = new std::list(); +/* inline */ std::unique_ptr< std::list > Abstract_planar_neighbors_finder::pull_all_near(int u_point_index) { + std::unique_ptr< std::list > all_pull(new std::list); int last_pull = pull_near(u_point_index); while (last_pull != null_point_index()) { all_pull->emplace_back(last_pull); @@ -89,19 +89,19 @@ inline std::list* Abstract_planar_neighbors_finder::pull_all_near(int u_poi Naive_pnf::Naive_pnf(const Persistence_diagrams_graph& g, double r) : Abstract_planar_neighbors_finder(g, r), candidates() { } -inline void Naive_pnf::add(int v_point_index) { +/* inline */ void Naive_pnf::add(int v_point_index) { candidates.emplace(v_point_index); } -inline void Naive_pnf::remove(int v_point_index) { +/* inline */ void Naive_pnf::remove(int v_point_index) { candidates.erase(v_point_index); } -inline bool Naive_pnf::contains(int v_point_index) const { +/* inline */ bool Naive_pnf::contains(int v_point_index) const { return (candidates.count(v_point_index) > 0); } -inline int Naive_pnf::pull_near(int u_point_index) { +/* inline */ int Naive_pnf::pull_near(int u_point_index) { for (auto it = candidates.begin(); it != candidates.end(); ++it) if (g.distance(u_point_index, *it) <= r) { int tmp = *it; diff --git a/src/Bottleneck/test/CMakeLists.txt b/src/Bottleneck/test/CMakeLists.txt index 3dfd80cd..8e4371b8 100644 --- a/src/Bottleneck/test/CMakeLists.txt +++ b/src/Bottleneck/test/CMakeLists.txt @@ -13,6 +13,12 @@ if (GPROF_PATH) set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg") set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg") endif() + message("CMAKE_CXX_FLAGS = ${CMAKE_CXX_FLAGS}") + message("CMAKE_CXX_FLAGS_DEBUG = ${CMAKE_CXX_FLAGS_DEBUG}") + message("CMAKE_CXX_FLAGS_RELEASE = ${CMAKE_CXX_FLAGS_RELEASE}") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O2 -std=c++11 -Wall -Wpedantic -Wsign-compare") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -ggdb -O0") + set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE}") add_executable ( BottleneckUT bottleneck_unit_test.cpp ) target_link_libraries(BottleneckUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) diff --git a/src/Bottleneck/test/bottleneck_unit_test.cpp b/src/Bottleneck/test/bottleneck_unit_test.cpp index ea7f51f2..77f45867 100644 --- a/src/Bottleneck/test/bottleneck_unit_test.cpp +++ b/src/Bottleneck/test/bottleneck_unit_test.cpp @@ -2,14 +2,15 @@ #include #include -#include "gudhi/Graph_matching.h" +#include "../include/gudhi/Graph_matching.h" using namespace Gudhi::bottleneck; -Persistence_diagrams_graph* random_graph_generator(){ - int n1 = 100; - int n2 = 120; - double upper_bound = 80; +int n1 = 81; // a natural number >0 +int n2 = 180; // a natural number >0 +double upper_bound = 400.5; // any real >0 + +std::unique_ptr random_graph_generator(){ // Random construction std::uniform_real_distribution unif(0.,upper_bound); std::default_random_engine re; @@ -24,73 +25,83 @@ Persistence_diagrams_graph* random_graph_generator(){ double b = unif(re); v2.emplace_back(std::min(a,b), std::max(a,b)); } - return new Persistence_diagrams_graph(v1, v2, 0.); + return std::unique_ptr(new Persistence_diagrams_graph(v1, v2, 0.)); } + BOOST_AUTO_TEST_CASE(global){ - int n = 100; - // Random construction + std::uniform_real_distribution unif1(0.,upper_bound); + std::uniform_real_distribution unif2(upper_bound/1000.,upper_bound/100.); + std::default_random_engine re; std::vector< std::pair > v1, v2; - for (int i = 0; i < n; i++) { - int a = rand() % n; - v1.emplace_back(a, a + rand() % (n - a)); - int b = rand() % n; - v2.emplace_back(b, b + rand() % (n - b)); + for (int i = 0; i < n1; i++) { + double a = unif1(re); + double b = unif1(re); + double x = unif2(re); + double y = unif2(re); + v1.emplace_back(std::min(a,b), std::max(a,b)); + v2.emplace_back(std::min(a,b)+std::min(x,y), std::max(a,b)+std::max(x,y)); + if(i%5==0) + v1.emplace_back(std::min(a,b),std::min(a,b)+x); + if(i%3==0) + v2.emplace_back(std::max(a,b),std::max(a,b)+y); } - // - BOOST_CHECK(bottleneck_distance(v1, v2, 1.) == 98); + BOOST_CHECK(bottleneck_distance(v1, v2) <= upper_bound/100.); } BOOST_AUTO_TEST_CASE(persistence_diagrams_graph) { - Persistence_diagrams_graph* g = random_graph_generator(); - std::vector* d = g->sorted_distances(); + std::unique_ptr g = std::move(random_graph_generator()); + std::unique_ptr< std::vector > d = std::move(g->sorted_distances()); // - BOOST_CHECK(!g->on_the_u_diagonal(99)); - BOOST_CHECK(!g->on_the_u_diagonal(100)); - BOOST_CHECK(!g->on_the_u_diagonal(119)); - BOOST_CHECK(g->on_the_u_diagonal(120)); - BOOST_CHECK(!g->on_the_v_diagonal(99)); - BOOST_CHECK(g->on_the_v_diagonal(100)); - BOOST_CHECK(g->on_the_v_diagonal(119)); - BOOST_CHECK(g->on_the_v_diagonal(120)); + BOOST_CHECK(!g->on_the_u_diagonal(n1-1)); + BOOST_CHECK(!g->on_the_u_diagonal(n1)); + BOOST_CHECK(!g->on_the_u_diagonal(n2-1)); + BOOST_CHECK(g->on_the_u_diagonal(n2)); + BOOST_CHECK(!g->on_the_v_diagonal(n1-1)); + BOOST_CHECK(g->on_the_v_diagonal(n1)); + BOOST_CHECK(g->on_the_v_diagonal(n2-1)); + BOOST_CHECK(g->on_the_v_diagonal(n2)); // - BOOST_CHECK(g->corresponding_point_in_u(0)==120); - BOOST_CHECK(g->corresponding_point_in_u(100)==0); - BOOST_CHECK(g->corresponding_point_in_v(0)==100); - BOOST_CHECK(g->corresponding_point_in_v(120)==0); + BOOST_CHECK(g->corresponding_point_in_u(0)==n2); + BOOST_CHECK(g->corresponding_point_in_u(n1)==0); + BOOST_CHECK(g->corresponding_point_in_v(0)==n1); + BOOST_CHECK(g->corresponding_point_in_v(n2)==0); // - BOOST_CHECK(g->size()==220); + BOOST_CHECK(g->size()==(n1+n2)); // - BOOST_CHECK((int) d->size() <= 220*220 - 100*120 + 1); // could be more strict + BOOST_CHECK((int) d->size() <= (n1+n2)*(n1+n2) - n1*n2 + 1); BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(0,0))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(0,99))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(0,100))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(0,119))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(0,120))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(0,219))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(100,0))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(100,99))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(100,100))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(100,119))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(100,120))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(100,219))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(219,0))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(219,99))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(219,100))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(219,119))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(219,120))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(219,219))==1); - // - delete g; - delete d; + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(0,n1-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(0,n1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(0,n2-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(0,n2))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(0,(n1+n2)-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(n1,0))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(n1,n1-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(n1,n1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(n1,n2-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(n1,n2))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(n1,(n1+n2)-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance((n1+n2)-1,0))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance((n1+n2)-1,n1-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance((n1+n2)-1,n1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance((n1+n2)-1,n2-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance((n1+n2)-1,n2))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), g->distance((n1+n2)-1,(n1+n2)-1))==1); } -BOOST_AUTO_TEST_CASE(planar_nf) { - Persistence_diagrams_graph* g = random_graph_generator(); +BOOST_AUTO_TEST_CASE(planar_neighbors_finder) { + std::unique_ptr g = std::move(random_graph_generator()); Planar_neighbors_finder pnf = Planar_neighbors_finder(*g,1.); - for(int v_point_index=0; v_point_index<100; v_point_index+=2) + for(int v_point_index=0; v_point_indexdistance(120/2,v_point_index_1)<1.)); + int v_point_index_1 = pnf.pull_near(n2/2); + BOOST_CHECK((v_point_index_1 == -1) || (g->distance(n2/2,v_point_index_1)<=1.)); BOOST_CHECK(!pnf.contains(v_point_index_1)); - int v_point_index_2 = pnf.pull_near(120/2); - BOOST_CHECK((v_point_index_2 == -1) || (g->distance(120/2,v_point_index_2)<1.)); - BOOST_CHECK(!pnf.contains(v_point_index_2)); - BOOST_CHECK((v_point_index_2 != -1) || (v_point_index_1 == -1)); + std::list l = *pnf.pull_all_near(n2/2); + bool v = true; + for(auto it = l.cbegin(); it != l.cend(); ++it) + v = v && (g->distance(n2/2,*it)>1.); + BOOST_CHECK(v); + int v_point_index_2 = pnf.pull_near(n2/2); + BOOST_CHECK(v_point_index_2 == -1); pnf.add(v_point_index_1); BOOST_CHECK(pnf.contains(v_point_index_1)); } + +BOOST_AUTO_TEST_CASE(neighbors_finder) { + std::unique_ptr g = std::move(random_graph_generator()); + Neighbors_finder nf = Neighbors_finder(*g,1.); + for(int v_point_index=1; v_point_index<((n2+n1)*9/10); v_point_index+=2) + nf.add(v_point_index); + // + int v_point_index_1 = nf.pull_near(n2/2); + BOOST_CHECK((v_point_index_1 == -1) || (g->distance(n2/2,v_point_index_1)<=1.)); + std::list l = *nf.pull_all_near(n2/2); + bool v = true; + for(auto it = l.cbegin(); it != l.cend(); ++it) + v = v && (g->distance(n2/2,*it)>1.); + BOOST_CHECK(v); + int v_point_index_2 = nf.pull_near(n2/2); + BOOST_CHECK(v_point_index_2 == -1); +} + +BOOST_AUTO_TEST_CASE(layered_neighbors_finder) { + std::unique_ptr g = std::move(random_graph_generator()); + Layered_neighbors_finder lnf = Layered_neighbors_finder(*g,1.); + for(int v_point_index=1; v_point_index<((n2+n1)*9/10); v_point_index+=2) + lnf.add(v_point_index, v_point_index % 7); + // + int v_point_index_1 = lnf.pull_near(n2/2,6); + BOOST_CHECK((v_point_index_1 == -1) || (g->distance(n2/2,v_point_index_1)<=1.)); + int v_point_index_2 = lnf.pull_near(n2/2,6); + BOOST_CHECK(v_point_index_2 == -1); + v_point_index_1 = lnf.pull_near(n2/2,0); + BOOST_CHECK((v_point_index_1 == -1) || (g->distance(n2/2,v_point_index_1)<=1.)); + v_point_index_2 = lnf.pull_near(n2/2,0); + BOOST_CHECK(v_point_index_2 == -1); +} + + +BOOST_AUTO_TEST_CASE(graph_matching) { + std::unique_ptr g = std::move(random_graph_generator()); + Graph_matching m1(*g); + m1.set_r(0.); + int e = 0; + while (m1.multi_augment()) + ++e; + BOOST_CHECK(e <= 2*sqrt(2*(n1+n2))); + Graph_matching m2 = m1; + BOOST_CHECK(!m2.multi_augment()); + m2.set_r(upper_bound); + e = 0; + while (m2.multi_augment()) + ++e; + BOOST_CHECK(e <= 2*sqrt(2*(n1+n2))); + BOOST_CHECK(m2.perfect()); + BOOST_CHECK(!m1.perfect()); +} -- cgit v1.2.3 From 6b78cf351666cc34ac81f9bd67df50f231c5f5fd Mon Sep 17 00:00:00 2001 From: fgodi Date: Thu, 25 Jun 2015 10:23:07 +0000 Subject: example git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@648 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 6ce05db956878f422d0f8b37e352c32074696fc1 --- src/Bottleneck/example/CMakeLists.txt | 24 ------------------- src/Bottleneck/example/example.cpp | 44 +++++++++++++++++++++++++++++++++++ 2 files changed, 44 insertions(+), 24 deletions(-) delete mode 100644 src/Bottleneck/example/CMakeLists.txt create mode 100644 src/Bottleneck/example/example.cpp (limited to 'src') diff --git a/src/Bottleneck/example/CMakeLists.txt b/src/Bottleneck/example/CMakeLists.txt deleted file mode 100644 index 8bf61c50..00000000 --- a/src/Bottleneck/example/CMakeLists.txt +++ /dev/null @@ -1,24 +0,0 @@ -cmake_minimum_required(VERSION 2.6) -project(GUDHIBottleneckExample) - -if (GCOVR_PATH) - # for gcovr to make coverage reports - Corbera Jenkins plugin - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage") - set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage") - set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage") -endif() -if (GPROF_PATH) - # for gprof to make coverage reports - Jenkins - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") - set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg") - set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg") -endif() - message("CMAKE_CXX_FLAGS = ${CMAKE_CXX_FLAGS}") - message("CMAKE_CXX_FLAGS_DEBUG = ${CMAKE_CXX_FLAGS_DEBUG}") - message("CMAKE_CXX_FLAGS_RELEASE = ${CMAKE_CXX_FLAGS_RELEASE}") - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O2 -std=c++11 -Wall -Wpedantic -Wsign-compare") - set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -ggdb -O0") - set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE}") - -add_executable ( BottleneckExample example.cpp ) - diff --git a/src/Bottleneck/example/example.cpp b/src/Bottleneck/example/example.cpp new file mode 100644 index 00000000..683f7723 --- /dev/null +++ b/src/Bottleneck/example/example.cpp @@ -0,0 +1,44 @@ +/* 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): Francois Godi + * + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 . + */ + +#include "../include/gudhi/Graph_matching.h" +#include + +using namespace Gudhi::bottleneck; + +int main() { + + std::vector< std::pair > v1, v2; + + v1.emplace_back(2.7,3.7); + v1.emplace_back(9.6,14); + v1.emplace_back(34.2,34.974); + + v2.emplace_back(2.8,4.45); + v2.emplace_back(9.5,14.1); + + + double b = bottleneck_distance(v1, v2); + + std::cout << "Bottleneck distance = " << b << std::endl; + +} -- cgit v1.2.3 From 38af16a7b5b958b9f27f36a8b94bd8d0327117e8 Mon Sep 17 00:00:00 2001 From: fgodi Date: Thu, 25 Jun 2015 10:23:49 +0000 Subject: example git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@649 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 6bde13921757cba057eb37c314719d51de262649 --- src/Bottleneck/example/random_diagrams.cpp | 40 ------------------------------ 1 file changed, 40 deletions(-) delete mode 100644 src/Bottleneck/example/random_diagrams.cpp (limited to 'src') diff --git a/src/Bottleneck/example/random_diagrams.cpp b/src/Bottleneck/example/random_diagrams.cpp deleted file mode 100644 index a9d0968d..00000000 --- a/src/Bottleneck/example/random_diagrams.cpp +++ /dev/null @@ -1,40 +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): Francois Godi - * - * Copyright (C) 2015 INRIA Sophia-Antipolis (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 . - */ - -#include "gudhi/Graph_matching.h" -#include - -using namespace Gudhi::bottleneck; - -int main() { - int n = 100; - std::vector< std::pair > v1, v2; - for (int i = 0; i < n; i++) { - int a = rand() % n; - v1.emplace_back(a, a + rand() % (n - a)); - int b = rand() % n; - v2.emplace_back(b, b + rand() % (n - b)); - } - // v1 and v2 are persistence diagrams containing each 100 randoms points. - double b = bottleneck_distance(v1, v2, 0); - std::cout << b << std::endl; -} -- cgit v1.2.3 From 4ffac47ea18e63f40e6175055166d6bf3d08cff9 Mon Sep 17 00:00:00 2001 From: fgodi Date: Mon, 29 Jun 2015 10:01:45 +0000 Subject: persistence_diagrams_graph static + others things git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@659 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 2562cbd49534373dae6d6d23ec52ba5984080729 --- src/Bottleneck/include/gudhi/Graph_matching.h | 126 +++++++++---------- .../include/gudhi/Layered_neighbors_finder.h | 56 +++++---- src/Bottleneck/include/gudhi/Neighbors_finder.h | 45 ++++--- .../include/gudhi/Persistence_diagrams_graph.h | 132 ++++++++++++-------- .../include/gudhi/Planar_neighbors_finder.h | 130 +++++++++++--------- src/Bottleneck/test/bottleneck_unit_test.cpp | 134 ++++++++++----------- 6 files changed, 332 insertions(+), 291 deletions(-) (limited to 'src') diff --git a/src/Bottleneck/include/gudhi/Graph_matching.h b/src/Bottleneck/include/gudhi/Graph_matching.h index 9f36e936..17412e6c 100644 --- a/src/Bottleneck/include/gudhi/Graph_matching.h +++ b/src/Bottleneck/include/gudhi/Graph_matching.h @@ -22,7 +22,7 @@ #ifndef SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ #define SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ -//#define DEBUG + #include #include #include @@ -33,31 +33,50 @@ namespace Gudhi { namespace bottleneck { +/** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams. + * + * + * + * \ingroup bottleneck_distance + */ template double bottleneck_distance(const Persistence_diagram1& diag1, const Persistence_diagram2& diag2, double e = 0.); +/** \internal \brief Structure representing a graph matching. The graph is a Persistence_diagrams_graph. + * + * \ingroup bottleneck_distance + */ class Graph_matching { public: - explicit Graph_matching(const Persistence_diagrams_graph& g); + /** \internal \brief Constructor constructing an empty matching. */ + explicit Graph_matching(); + /** \internal \brief Copy operator. */ Graph_matching& operator=(const Graph_matching& m); + /** \internal \brief Is the matching perfect ? */ bool perfect() const; + /** \internal \brief Augments the matching with a maximal set of edge-disjoint shortest augmenting paths. */ bool multi_augment(); + /** \internal \brief Sets the maximum length of the edges allowed to be added in the matching, 0 initially. */ void set_r(double r); private: - const Persistence_diagrams_graph& g; double r; + /** \internal \brief Given a point from V, provides its matched point in U, null_point_index() if there isn't. */ std::vector v_to_u; + /** \internal \brief All the unmatched points in U. */ std::list unmatched_in_u; + /** \internal \brief Provides a Layered_neighbors_finder dividing the graph in layers. Basically a BFS. */ std::unique_ptr layering() const; + /** \internal \brief Augments the matching with a simple path no longer than max_depth. Basically a DFS. */ bool augment(Layered_neighbors_finder & layered_nf, int u_start_index, int max_depth); + /** \internal \brief Update the matching with the simple augmenting path given as parameter. */ void update(std::deque & path); }; -Graph_matching::Graph_matching(const Persistence_diagrams_graph& g) - : g(g), r(0), v_to_u(g.size(), null_point_index()), unmatched_in_u() { - for (int u_point_index = 0; u_point_index < g.size(); ++u_point_index) +Graph_matching::Graph_matching() + : r(0.), v_to_u(G::size(), null_point_index()), unmatched_in_u() { + for (int u_point_index = 0; u_point_index < G::size(); ++u_point_index) unmatched_in_u.emplace_back(u_point_index); } @@ -68,56 +87,36 @@ Graph_matching& Graph_matching::operator=(const Graph_matching& m) { return *this; } -/* inline */ bool Graph_matching::perfect() const { -#ifdef DEBUG - std::cout << " perfect? unmatched_in_u.size = " << unmatched_in_u.size() << std::endl << std::flush; -#endif +inline bool Graph_matching::perfect() const { return unmatched_in_u.empty(); } -/* inline */ bool Graph_matching::multi_augment() { +inline bool Graph_matching::multi_augment() { if (perfect()) return false; -#ifdef DEBUG - std::cout << " multi augment" << std::endl << std::flush; -#endif Layered_neighbors_finder layered_nf = *layering(); - double rn = sqrt(g.size()); int max_depth = layered_nf.vlayers_number()*2 - 1; -#ifdef DEBUG - std::cout<< " nb_max_layer = " << max_depth << std::endl << std::flush; -#endif - // verification of a necessary criterion + double rn = sqrt(G::size()); + // verification of a necessary criterion in order to shortcut if possible if (max_depth <0 || (unmatched_in_u.size() > rn && max_depth >= rn)) return false; bool successful = false; std::list tries(unmatched_in_u); - for (auto it = tries.cbegin(); it != tries.cend(); it++){ - const bool tmp = augment(layered_nf, *it, max_depth); //force augment evaluation even if successful is already true - successful = successful || tmp; - } + for (auto it = tries.cbegin(); it != tries.cend(); it++) + // 'augment' has side-effects which have to be always executed, don't change order + successful = augment(layered_nf, *it, max_depth) || successful; return successful; } -/* inline */ void Graph_matching::set_r(double r) { +inline void Graph_matching::set_r(double r) { this->r = r; } -bool Graph_matching::augment(Layered_neighbors_finder & layered_nf, int u_start_index, int max_depth) { -#ifdef DEBUG - std::cout << " augment" << std::endl << std::flush; -#endif -#ifdef DEBUG - std::cout << " u_start_index = " << u_start_index << std::endl << std::flush; -#endif +inline bool Graph_matching::augment(Layered_neighbors_finder & layered_nf, int u_start_index, int max_depth) { + //V vertices have at most one successor, thus when we backtrack from U we can directly pop_back 2 vertices. std::deque path; path.emplace_back(u_start_index); - // u_start is a point from U do { -#ifdef DEBUG - std::cout << " do" << std::endl << std::flush; - std::cout << " path.size = " << static_cast(path.size()) << std::endl << std::flush; -#endif if (static_cast(path.size()) > max_depth) { path.pop_back(); path.pop_back(); @@ -134,28 +133,22 @@ bool Graph_matching::augment(Layered_neighbors_finder & layered_nf, int u_start_ path.emplace_back(layered_nf.pull_near(path.back(), path.size() / 2)); } path.emplace_back(v_to_u.at(path.back())); -#ifdef DEBUG - std::cout << " v_to_u = " << path.back() << std::endl << std::flush; -#endif } while (path.back() != null_point_index()); + //if v_to_u.at(path.back()) has no successor, path.back() is an exposed vertex path.pop_back(); update(path); return true; } -std::unique_ptr Graph_matching::layering() const { -#ifdef DEBUG - std::cout << " layering" << std::endl << std::flush; -#endif - bool end = false; - int layer = 0; +inline std::unique_ptr Graph_matching::layering() const { std::list u_vertices(unmatched_in_u); std::list v_vertices; - Neighbors_finder nf(g, r); - for (int v_point_index = 0; v_point_index < g.size(); ++v_point_index) + Neighbors_finder nf(r); + for (int v_point_index = 0; v_point_index < G::size(); ++v_point_index) nf.add(v_point_index); - std::unique_ptr layered_nf(new Layered_neighbors_finder(g, r)); - while (!u_vertices.empty()) { + std::unique_ptr layered_nf(new Layered_neighbors_finder(r)); + for(int layer = 0; !u_vertices.empty(); layer++) { + // one layer is one step in the BFS for (auto it = u_vertices.cbegin(); it != u_vertices.cend(); ++it) { std::unique_ptr< std::list > u_succ = std::move(nf.pull_all_near(*it)); for (auto it = u_succ->cbegin(); it != u_succ->cend(); ++it) { @@ -163,27 +156,27 @@ std::unique_ptr Graph_matching::layering() const { v_vertices.emplace_back(*it); } } + // When the above for finishes, we have progress of one half-step (from U to V) in the BFS u_vertices.clear(); - for (auto it = v_vertices.cbegin(); it != v_vertices.cend(); it++) { + bool end = false; + for (auto it = v_vertices.cbegin(); it != v_vertices.cend(); it++) if (v_to_u.at(*it) == null_point_index()) + // we stop when a nearest exposed V vertex (from U exposed vertices) has been found end = true; else u_vertices.emplace_back(v_to_u.at(*it)); - } + // When the above for finishes, we have progress of one half-step (from V to U) in the BFS if (end) return layered_nf; v_vertices.clear(); - layer++; } return layered_nf; } -void Graph_matching::update(std::deque& path) { -#ifdef DEBUG - std::cout << " update" << std::endl << std::flush; -#endif +inline void Graph_matching::update(std::deque& path) { unmatched_in_u.remove(path.front()); for (auto it = path.cbegin(); it != path.cend(); ++it) { + // Be careful, the iterator is incremented twice each time int tmp = *it; ++it; v_to_u[*it] = tmp; @@ -192,27 +185,28 @@ void Graph_matching::update(std::deque& path) { template double bottleneck_distance(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e) { - Persistence_diagrams_graph g(diag1, diag2, e); - std::unique_ptr< std::vector > sd = std::move(g.sorted_distances()); + G::initialize(diag1, diag2, e); + std::unique_ptr< std::vector > sd = std::move(G::sorted_distances()); int idmin = 0; int idmax = sd->size() - 1; + // alpha can be modified, this will change the complexity double alpha = pow(sd->size(), 0.25); - Graph_matching m(g); - Graph_matching biggest_unperfect(g); + Graph_matching m; + Graph_matching biggest_unperfect; while (idmin != idmax) { - int pas = static_cast((idmax - idmin) / alpha); - m.set_r(sd->at(idmin + pas)); + int step = static_cast((idmax - idmin) / alpha); + m.set_r(sd->at(idmin + step)); while (m.multi_augment()); + // The above while compute a maximum matching (according to the r setted before) if (m.perfect()) { - idmax = idmin + pas; + idmax = idmin + step; m = biggest_unperfect; } else { biggest_unperfect = m; - idmin = idmin + pas + 1; + idmin = idmin + step + 1; } } - double b = sd->at(idmin); - return b; + return sd->at(idmin); } } // namespace bottleneck diff --git a/src/Bottleneck/include/gudhi/Layered_neighbors_finder.h b/src/Bottleneck/include/gudhi/Layered_neighbors_finder.h index 1cf83393..e6b7f30d 100644 --- a/src/Bottleneck/include/gudhi/Layered_neighbors_finder.h +++ b/src/Bottleneck/include/gudhi/Layered_neighbors_finder.h @@ -27,44 +27,50 @@ #include "Neighbors_finder.h" -// Layered_neighbors_finder is a data structure used to find if a query point from U has neighbors in V in a given -// vlayer of the vlayered persistence diagrams graph. V's points have to be added manually using their index. -// A neighbor returned is automatically removed. - namespace Gudhi { namespace bottleneck { +/** \internal \brief data structure used to find any point (including projections) in V near to a query point from U + * (which can be a projection) in a layered graph layer given as parmeter. + * + * V points have to be added manually using their index and before the first pull. A neighbor pulled is automatically removed. + * + * \ingroup bottleneck_distance + */ class Layered_neighbors_finder { - public: - Layered_neighbors_finder(const Persistence_diagrams_graph& g, double r); - void add(int v_point_index, int vlayer); - int pull_near(int u_point_index, int vlayer); - int vlayers_number() const; +public: + /** \internal \brief Constructor taking the near distance definition as parameter. */ + Layered_neighbors_finder(double r); + /** \internal \brief A point added will be possibly pulled. */ + void add(int v_point_index, int vlayer); + /** \internal \brief Returns and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ + int pull_near(int u_point_index, int vlayer); + /** \internal \brief Returns the number of layers. */ + int vlayers_number() const; - private: - const Persistence_diagrams_graph& g; - const double r; - std::vector neighbors_finder; +private: + const double r; + std::vector neighbors_finder; }; -Layered_neighbors_finder::Layered_neighbors_finder(const Persistence_diagrams_graph& g, double r) : - g(g), r(r), neighbors_finder() { } +Layered_neighbors_finder::Layered_neighbors_finder(double r) : + r(r), neighbors_finder() { } -/* inline */ void Layered_neighbors_finder::add(int v_point_index, int vlayer) { - for (int l = neighbors_finder.size(); l <= vlayer; l++) - neighbors_finder.emplace_back(Neighbors_finder(g, r)); - neighbors_finder.at(vlayer).add(v_point_index); +inline void Layered_neighbors_finder::add(int v_point_index, int vlayer) { + for (int l = neighbors_finder.size(); l <= vlayer; l++) + neighbors_finder.emplace_back(Neighbors_finder(r)); + neighbors_finder.at(vlayer).add(v_point_index); } -/* inline */ int Layered_neighbors_finder::pull_near(int u_point_index, int vlayer) { - if (static_cast (neighbors_finder.size()) <= vlayer) - return null_point_index(); - return neighbors_finder.at(vlayer).pull_near(u_point_index); +inline int Layered_neighbors_finder::pull_near(int u_point_index, int vlayer) { + if (static_cast (neighbors_finder.size()) <= vlayer) + return null_point_index(); + return neighbors_finder.at(vlayer).pull_near(u_point_index); } -/* inline */ int Layered_neighbors_finder::vlayers_number() const { - return static_cast(neighbors_finder.size()); +inline int Layered_neighbors_finder::vlayers_number() const { + return static_cast(neighbors_finder.size()); } } // namespace bottleneck diff --git a/src/Bottleneck/include/gudhi/Neighbors_finder.h b/src/Bottleneck/include/gudhi/Neighbors_finder.h index 0fad9889..ac3f8600 100644 --- a/src/Bottleneck/include/gudhi/Neighbors_finder.h +++ b/src/Bottleneck/include/gudhi/Neighbors_finder.h @@ -32,19 +32,25 @@ namespace Gudhi { namespace bottleneck { -// Neighbors_finder is a data structure used to find if a query point from U has neighbors in V -// in the persistence diagrams graph. -// V's points have to be added manually using their index. A neighbor returned is automatically removed. - +/** \internal \brief data structure used to find any point (including projections) in V near to a query point from U + * (which can be a projection). + * + * V points have to be added manually using their index and before the first pull. A neighbor pulled is automatically removed. + * + * \ingroup bottleneck_distance + */ class Neighbors_finder { public: - Neighbors_finder(const Persistence_diagrams_graph& g, double r); + /** \internal \brief Constructor taking the near distance definition as parameter. */ + Neighbors_finder(double r); + /** \internal \brief A point added will be possibly pulled. */ void add(int v_point_index); + /** \internal \brief Returns and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ int pull_near(int u_point_index); + /** \internal \brief Returns and remove all the V points near to the U point given as parameter. */ std::unique_ptr< std::list > pull_all_near(int u_point_index); private: - const Persistence_diagrams_graph& g; const double r; Planar_neighbors_finder planar_neighbors_f; std::unordered_set projections_f; @@ -52,43 +58,46 @@ private: bool contains(int v_point_index); }; -Neighbors_finder::Neighbors_finder(const Persistence_diagrams_graph& g, double r) : - g(g), r(r), planar_neighbors_f(g, r), projections_f() { } +Neighbors_finder::Neighbors_finder(double r) : + r(r), planar_neighbors_f(r), projections_f() { } -/* inline */ void Neighbors_finder::add(int v_point_index) { - if (g.on_the_v_diagonal(v_point_index)) +inline void Neighbors_finder::add(int v_point_index) { + if (G::on_the_v_diagonal(v_point_index)) projections_f.emplace(v_point_index); else planar_neighbors_f.add(v_point_index); } -/* inline */ void Neighbors_finder::remove(int v_point_index) { +inline void Neighbors_finder::remove(int v_point_index) { if(v_point_index == null_point_index()) return; - if (g.on_the_v_diagonal(v_point_index)) + if (G::on_the_v_diagonal(v_point_index)) projections_f.erase(v_point_index); else planar_neighbors_f.remove(v_point_index); } -/* inline */ bool Neighbors_finder::contains(int v_point_index) { +inline bool Neighbors_finder::contains(int v_point_index) { return planar_neighbors_f.contains(v_point_index) || (projections_f.count(v_point_index)>0); } -/* inline */ int Neighbors_finder::pull_near(int u_point_index) { +inline int Neighbors_finder::pull_near(int u_point_index) { int tmp; - int c = g.corresponding_point_in_v(u_point_index); - if (g.on_the_u_diagonal(u_point_index) && projections_f.cbegin()!=projections_f.cend()) + int c = G::corresponding_point_in_v(u_point_index); + if (G::on_the_u_diagonal(u_point_index) && !projections_f.empty()) + //All projections are at distance 0 tmp = *projections_f.cbegin(); - else if (contains(c) && (g.distance(u_point_index, c) <= r)) + else if (contains(c) && (G::distance(u_point_index, c) <= r)) + //Is the query point near to its projection ? tmp = c; else + //Is the query point near to a V point in the plane ? tmp = planar_neighbors_f.pull_near(u_point_index); remove(tmp); return tmp; } -std::unique_ptr< std::list > Neighbors_finder::pull_all_near(int u_point_index) { +inline std::unique_ptr< std::list > Neighbors_finder::pull_all_near(int u_point_index) { std::unique_ptr< std::list > all_pull = std::move(planar_neighbors_f.pull_all_near(u_point_index)); int last_pull = pull_near(u_point_index); while (last_pull != null_point_index()) { diff --git a/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h b/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h index 644c1cd8..66e43145 100644 --- a/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h +++ b/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h @@ -26,52 +26,70 @@ #include #include #include -#include // for pair<> -#include // for max +#include +#include namespace Gudhi { namespace bottleneck { -// Diagram_point is the type of the persistence diagram's points -typedef std::pair Diagram_point; - -// Return the used index for encoding none of the points +/** \internal \brief Returns the used index for encoding none of the points */ int null_point_index(); -// Persistence_diagrams_graph is the interface beetwen any external representation of the two persistence diagrams and -// the bottleneck distance computation. An interface is necessary to ensure basic functions complexity. - +/** \internal \brief Structure representing an euclidean bipartite graph containing + * the points from the two persistence diagrams (including the projections). + * + * \ingroup bottleneck_distance + */ class Persistence_diagrams_graph { - public: - // Persistence_diagram1 and 2 are the types of any externals representations of persistence diagrams. - // They have to have an iterator over points, which have to have fields first (for birth) and second (for death). +public: + /** \internal \brief Initializer taking 2 Point (concept) ranges as parameters. */ template - Persistence_diagrams_graph(const Persistence_diagram1& diag1, const Persistence_diagram2& diag2, double e); - Persistence_diagrams_graph(); - bool on_the_u_diagonal(int u_point_index) const; - bool on_the_v_diagonal(int v_point_index) const; - int corresponding_point_in_u(int v_point_index) const; - int corresponding_point_in_v(int u_point_index) const; - double distance(int u_point_index, int v_point_index) const; - int size() const; - std::unique_ptr< std::vector > sorted_distances(); - - private: - std::vector u; - std::vector v; - Diagram_point get_u_point(int u_point_index) const; - Diagram_point get_v_point(int v_point_index) const; + static void initialize(const Persistence_diagram1& diag1, const Persistence_diagram2& diag2, double e); + /** \internal \brief Is the given point from U the projection of a point in V ? */ + static bool on_the_u_diagonal(int u_point_index); + /** \internal \brief Is the given point from V the projection of a point in U ? */ + static bool on_the_v_diagonal(int v_point_index); + /** \internal \brief Given a point from V, returns the corresponding (projection or projector) point in U. */ + static int corresponding_point_in_u(int v_point_index); + /** \internal \brief Given a point from U, returns the corresponding (projection or projector) point in V. */ + static int corresponding_point_in_v(int u_point_index); + /** \internal \brief Given a point from U and a point from V, returns the distance between those points. */ + static double distance(int u_point_index, int v_point_index); + /** \internal \brief Returns size = |U| = |V|. */ + static int size(); + /** \internal \brief Returns the O(n^2) sorted distances between the points. */ + static std::unique_ptr< std::vector > sorted_distances(); + /** \internal \brief Compare points regarding x coordinate. Use v_point_index for V points and u_point_index + G::size() for U points. */ + struct Compare_x{bool operator() (const int point_index_1, const int point_index_2) const;}; + /** \internal \brief Compare points regarding y coordinate. Use v_point_index for V points and u_point_index + G::size() for U points. */ + struct Compare_y{bool operator() (const int point_index_1, const int point_index_2) const;}; + +private: + /** \internal \typedef \brief Internal_point is the internal points representation, indexes used outside. */ + typedef std::pair Internal_point; + static std::vector u; + static std::vector v; + static Internal_point get_u_point(int u_point_index); + static Internal_point get_v_point(int v_point_index); }; -/* inline */ int null_point_index() { +/** \internal \typedef \brief Alias used outside. */ +typedef Persistence_diagrams_graph G; + +// static initialization, seems to work but strange +std::vector Persistence_diagrams_graph::u = [] {return std::vector();}(); +std::vector Persistence_diagrams_graph::v = [] {return std::vector();}(); + +inline int null_point_index() { return -1; } template -Persistence_diagrams_graph::Persistence_diagrams_graph(const Persistence_diagram1 &diag1, - const Persistence_diagram2 &diag2, double e) - : u(), v() { +void Persistence_diagrams_graph::initialize(const Persistence_diagram1 &diag1, + const Persistence_diagram2 &diag2, double e){ + u.clear(); + v.clear(); for (auto it = diag1.cbegin(); it != diag1.cend(); ++it) if (it->second - it->first > e) u.emplace_back(*it); @@ -82,41 +100,37 @@ Persistence_diagrams_graph::Persistence_diagrams_graph(const Persistence_diagram swap(u, v); } -Persistence_diagrams_graph::Persistence_diagrams_graph() - : u(), v() { } - -/* inline */ bool Persistence_diagrams_graph::on_the_u_diagonal(int u_point_index) const { +inline bool Persistence_diagrams_graph::on_the_u_diagonal(int u_point_index) { return u_point_index >= static_cast (u.size()); } -/* inline */ bool Persistence_diagrams_graph::on_the_v_diagonal(int v_point_index) const { +inline bool Persistence_diagrams_graph::on_the_v_diagonal(int v_point_index) { return v_point_index >= static_cast (v.size()); } -/* inline */ int Persistence_diagrams_graph::corresponding_point_in_u(int v_point_index) const { +inline int Persistence_diagrams_graph::corresponding_point_in_u(int v_point_index) { return on_the_v_diagonal(v_point_index) ? v_point_index - static_cast (v.size()) : v_point_index + static_cast (u.size()); } -/* inline */ int Persistence_diagrams_graph::corresponding_point_in_v(int u_point_index) const { +inline int Persistence_diagrams_graph::corresponding_point_in_v(int u_point_index) { return on_the_u_diagonal(u_point_index) ? u_point_index - static_cast (u.size()) : u_point_index + static_cast (v.size()); } -/* inline */ double Persistence_diagrams_graph::distance(int u_point_index, int v_point_index) const { - // could be optimized for the case where one point is the projection of the other - if (on_the_u_diagonal(u_point_index) && on_the_v_diagonal(v_point_index)) - return 0; - Diagram_point p_u = get_u_point(u_point_index); - Diagram_point p_v = get_v_point(v_point_index); - return std::max(std::fabs(p_u.first - p_v.first), std::fabs(p_u.second - p_v.second)); +inline double Persistence_diagrams_graph::distance(int u_point_index, int v_point_index) { + if (on_the_u_diagonal(u_point_index) && on_the_v_diagonal(v_point_index)) + return 0; + Internal_point p_u = get_u_point(u_point_index); + Internal_point p_v = get_v_point(v_point_index); + return std::max(std::fabs(p_u.first - p_v.first), std::fabs(p_u.second - p_v.second)); } -/* inline */ int Persistence_diagrams_graph::size() const { +inline int Persistence_diagrams_graph::size() { return static_cast (u.size() + v.size()); } -/* inline */ std::unique_ptr< std::vector > Persistence_diagrams_graph::sorted_distances() { +inline std::unique_ptr< std::vector > Persistence_diagrams_graph::sorted_distances() { // could be optimized std::set sorted_distances; for (int u_point_index = 0; u_point_index < size(); ++u_point_index) @@ -126,20 +140,32 @@ Persistence_diagrams_graph::Persistence_diagrams_graph() return sd_up; } -/* inline */ Diagram_point Persistence_diagrams_graph::get_u_point(int u_point_index) const { +inline Persistence_diagrams_graph::Internal_point Persistence_diagrams_graph::get_u_point(int u_point_index) { if (!on_the_u_diagonal(u_point_index)) return u.at(u_point_index); - Diagram_point projector = v.at(corresponding_point_in_v(u_point_index)); + Internal_point projector = v.at(corresponding_point_in_v(u_point_index)); double x = (projector.first + projector.second) / 2; - return Diagram_point(x, x); + return Internal_point(x, x); } -/* inline */ Diagram_point Persistence_diagrams_graph::get_v_point(int v_point_index) const { +inline Persistence_diagrams_graph::Internal_point Persistence_diagrams_graph::get_v_point(int v_point_index) { if (!on_the_v_diagonal(v_point_index)) return v.at(v_point_index); - Diagram_point projector = u.at(corresponding_point_in_u(v_point_index)); + Internal_point projector = u.at(corresponding_point_in_u(v_point_index)); double x = (projector.first + projector.second) / 2; - return Diagram_point(x, x); + return Internal_point(x, x); +} + +inline bool Persistence_diagrams_graph::Compare_x::operator() (const int point_index_1, const int point_index_2) const{ + G::Internal_point p1 = point_index_1 < G::size() ? G::get_v_point(point_index_1) : G::get_u_point(point_index_1 - G::size()); + G::Internal_point p2 = point_index_2 < G::size() ? G::get_v_point(point_index_2) : G::get_u_point(point_index_2 - G::size()); + return p1.first < p2.first; +} + +inline bool Persistence_diagrams_graph::Compare_y::operator() (const int point_index_1, const int point_index_2) const{ + G::Internal_point p1 = point_index_1 < G::size() ? G::get_v_point(point_index_1) : G::get_u_point(point_index_1 - G::size()); + G::Internal_point p2 = point_index_2 < G::size() ? G::get_v_point(point_index_2) : G::get_u_point(point_index_2 - G::size()); + return p1.second < p2.second; } } // namespace bottleneck diff --git a/src/Bottleneck/include/gudhi/Planar_neighbors_finder.h b/src/Bottleneck/include/gudhi/Planar_neighbors_finder.h index e558239d..4d820c7f 100644 --- a/src/Bottleneck/include/gudhi/Planar_neighbors_finder.h +++ b/src/Bottleneck/include/gudhi/Planar_neighbors_finder.h @@ -27,88 +27,102 @@ #include #include "Persistence_diagrams_graph.h" +#include "Grid_cell.h" namespace Gudhi { namespace bottleneck { -// Planar_neighbors_finder is a data structure used to find if a query point from U has planar neighbors in V with the -// planar distance. -// V's points have to be added manually using their index. A neighbor returned is automatically removed but we can also -// remove points manually using their index. - +/** \internal \brief Structure used to find any point in V near (according to the planar distance) to a query point from U. + * + * V points have to be added manually using their index and before the first remove/pull. A neighbor pulled is automatically removed. but we can also + * remove points manually using their index. + * + * \ingroup bottleneck_distance + */ class Abstract_planar_neighbors_finder { - public: - Abstract_planar_neighbors_finder(const Persistence_diagrams_graph& g, double r); - virtual ~Abstract_planar_neighbors_finder() = 0; - virtual void add(int v_point_index) = 0; - virtual void remove(int v_point_index) = 0; - virtual bool contains(int v_point_index) const = 0; - virtual int pull_near(int u_point_index) = 0; - virtual std::unique_ptr< std::list > pull_all_near(int u_point_index); - - protected: - const Persistence_diagrams_graph& g; - const double r; +public: + /** \internal \brief Constructor TODO. */ + Abstract_planar_neighbors_finder(double r); + virtual ~Abstract_planar_neighbors_finder() = 0; + /** \internal \brief A point added will be possibly pulled. */ + virtual void add(int v_point_index) = 0; + /** \internal \brief A point manually removed will no longer be possibly pulled. */ + virtual void remove(int v_point_index) = 0; + /** \internal \brief Can the point given as parameter be returned ? */ + virtual bool contains(int v_point_index) const = 0; + /** \internal \brief Provide and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ + virtual int pull_near(int u_point_index) = 0; + /** \internal \brief Provide and remove all the V points near to the U point given as parameter. */ + virtual std::unique_ptr< std::list > pull_all_near(int u_point_index); + +protected: + const double r; }; - -// Naive_pnf is a nave implementation of Abstract_planar_neighbors_finder - +/** \internal \brief Naive_pnf is an naïve Abstract_planar_neighbors_finder implementation + * + * \ingroup bottleneck_distance + */ class Naive_pnf : public Abstract_planar_neighbors_finder { - public: - Naive_pnf(const Persistence_diagrams_graph& g, double r); - void add(int v_point_index); - void remove(int v_point_index); - bool contains(int v_point_index) const; - int pull_near(int u_point_index); - - private: - std::set candidates; +public: + /** \internal \brief Constructor taking the near distance definition as parameter. */ + Naive_pnf(double r); + /** \internal \brief A point added will be possibly pulled. */ + void add(int v_point_index); + /** \internal \brief A point manually removed will no longer be possibly pulled. */ + void remove(int v_point_index); + /** \internal \brief Can the point given as parameter be returned ? */ + bool contains(int v_point_index) const; + /** \internal \brief Provide and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ + int pull_near(int u_point_index); + +private: + std::set candidates; }; - -// Planar_neighbors_finder is the used Abstract_planar_neighbors_finder's implementation +/** \internal \typedef \brief Planar_neighbors_finder is the used Abstract_planar_neighbors_finder's implementation. */ typedef Naive_pnf Planar_neighbors_finder; -Abstract_planar_neighbors_finder::Abstract_planar_neighbors_finder(const Persistence_diagrams_graph& g, double r) : - g(g), r(r) { } -/* inline */ Abstract_planar_neighbors_finder::~Abstract_planar_neighbors_finder() { } +Abstract_planar_neighbors_finder::Abstract_planar_neighbors_finder(double r) : + r(r) { } -/* inline */ std::unique_ptr< std::list > Abstract_planar_neighbors_finder::pull_all_near(int u_point_index) { - std::unique_ptr< std::list > all_pull(new std::list); - int last_pull = pull_near(u_point_index); - while (last_pull != null_point_index()) { - all_pull->emplace_back(last_pull); - last_pull = pull_near(u_point_index); - } - return all_pull; +inline Abstract_planar_neighbors_finder::~Abstract_planar_neighbors_finder() {} + +inline std::unique_ptr< std::list > Abstract_planar_neighbors_finder::pull_all_near(int u_point_index) { + std::unique_ptr< std::list > all_pull(new std::list); + int last_pull = pull_near(u_point_index); + while (last_pull != null_point_index()) { + all_pull->emplace_back(last_pull); + last_pull = pull_near(u_point_index); + } + return all_pull; } -Naive_pnf::Naive_pnf(const Persistence_diagrams_graph& g, double r) : - Abstract_planar_neighbors_finder(g, r), candidates() { } +Naive_pnf::Naive_pnf(double r) : + Abstract_planar_neighbors_finder(r), candidates() { } -/* inline */ void Naive_pnf::add(int v_point_index) { - candidates.emplace(v_point_index); +inline void Naive_pnf::add(int v_point_index) { + candidates.emplace(v_point_index); } -/* inline */ void Naive_pnf::remove(int v_point_index) { - candidates.erase(v_point_index); +inline void Naive_pnf::remove(int v_point_index) { + candidates.erase(v_point_index); } -/* inline */ bool Naive_pnf::contains(int v_point_index) const { - return (candidates.count(v_point_index) > 0); +inline bool Naive_pnf::contains(int v_point_index) const { + return (candidates.count(v_point_index) > 0); } -/* inline */ int Naive_pnf::pull_near(int u_point_index) { - for (auto it = candidates.begin(); it != candidates.end(); ++it) - if (g.distance(u_point_index, *it) <= r) { - int tmp = *it; - candidates.erase(it); - return tmp; - } - return null_point_index(); +inline int Naive_pnf::pull_near(int u_point_index) { + for (auto it = candidates.begin(); it != candidates.end(); ++it) + if (G::distance(u_point_index, *it) <= r) { + int tmp = *it; + candidates.erase(it); + return tmp; + } + return null_point_index(); } } // namespace bottleneck diff --git a/src/Bottleneck/test/bottleneck_unit_test.cpp b/src/Bottleneck/test/bottleneck_unit_test.cpp index 77f45867..926c8430 100644 --- a/src/Bottleneck/test/bottleneck_unit_test.cpp +++ b/src/Bottleneck/test/bottleneck_unit_test.cpp @@ -10,25 +10,6 @@ int n1 = 81; // a natural number >0 int n2 = 180; // a natural number >0 double upper_bound = 400.5; // any real >0 -std::unique_ptr random_graph_generator(){ - // Random construction - std::uniform_real_distribution unif(0.,upper_bound); - std::default_random_engine re; - std::vector< std::pair > v1, v2; - for (int i = 0; i < n1; i++) { - double a = unif(re); - double b = unif(re); - v1.emplace_back(std::min(a,b), std::max(a,b)); - } - for (int i = 0; i < n2; i++) { - double a = unif(re); - double b = unif(re); - v2.emplace_back(std::min(a,b), std::max(a,b)); - } - return std::unique_ptr(new Persistence_diagrams_graph(v1, v2, 0.)); -} - - BOOST_AUTO_TEST_CASE(global){ std::uniform_real_distribution unif1(0.,upper_bound); std::uniform_real_distribution unif2(upper_bound/1000.,upper_bound/100.); @@ -49,51 +30,64 @@ BOOST_AUTO_TEST_CASE(global){ BOOST_CHECK(bottleneck_distance(v1, v2) <= upper_bound/100.); } - -BOOST_AUTO_TEST_CASE(persistence_diagrams_graph) { - std::unique_ptr g = std::move(random_graph_generator()); - std::unique_ptr< std::vector > d = std::move(g->sorted_distances()); +BOOST_AUTO_TEST_CASE(persistence_diagrams_graph){ + // Random construction + std::uniform_real_distribution unif(0.,upper_bound); + std::default_random_engine re; + std::vector< std::pair > v1, v2; + for (int i = 0; i < n1; i++) { + double a = unif(re); + double b = unif(re); + v1.emplace_back(std::min(a,b), std::max(a,b)); + } + for (int i = 0; i < n2; i++) { + double a = unif(re); + double b = unif(re); + v2.emplace_back(std::min(a,b), std::max(a,b)); + } + G::initialize(v1, v2, 0.); + std::unique_ptr< std::vector > d = std::move(G::sorted_distances()); // - BOOST_CHECK(!g->on_the_u_diagonal(n1-1)); - BOOST_CHECK(!g->on_the_u_diagonal(n1)); - BOOST_CHECK(!g->on_the_u_diagonal(n2-1)); - BOOST_CHECK(g->on_the_u_diagonal(n2)); - BOOST_CHECK(!g->on_the_v_diagonal(n1-1)); - BOOST_CHECK(g->on_the_v_diagonal(n1)); - BOOST_CHECK(g->on_the_v_diagonal(n2-1)); - BOOST_CHECK(g->on_the_v_diagonal(n2)); + BOOST_CHECK(!G::on_the_u_diagonal(n1-1)); + BOOST_CHECK(!G::on_the_u_diagonal(n1)); + BOOST_CHECK(!G::on_the_u_diagonal(n2-1)); + BOOST_CHECK(G::on_the_u_diagonal(n2)); + BOOST_CHECK(!G::on_the_v_diagonal(n1-1)); + BOOST_CHECK(G::on_the_v_diagonal(n1)); + BOOST_CHECK(G::on_the_v_diagonal(n2-1)); + BOOST_CHECK(G::on_the_v_diagonal(n2)); // - BOOST_CHECK(g->corresponding_point_in_u(0)==n2); - BOOST_CHECK(g->corresponding_point_in_u(n1)==0); - BOOST_CHECK(g->corresponding_point_in_v(0)==n1); - BOOST_CHECK(g->corresponding_point_in_v(n2)==0); + BOOST_CHECK(G::corresponding_point_in_u(0)==n2); + BOOST_CHECK(G::corresponding_point_in_u(n1)==0); + BOOST_CHECK(G::corresponding_point_in_v(0)==n1); + BOOST_CHECK(G::corresponding_point_in_v(n2)==0); // - BOOST_CHECK(g->size()==(n1+n2)); + BOOST_CHECK(G::size()==(n1+n2)); // BOOST_CHECK((int) d->size() <= (n1+n2)*(n1+n2) - n1*n2 + 1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(0,0))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(0,n1-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(0,n1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(0,n2-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(0,n2))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(0,(n1+n2)-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(n1,0))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(n1,n1-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(n1,n1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(n1,n2-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(n1,n2))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance(n1,(n1+n2)-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance((n1+n2)-1,0))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance((n1+n2)-1,n1-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance((n1+n2)-1,n1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance((n1+n2)-1,n2-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance((n1+n2)-1,n2))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), g->distance((n1+n2)-1,(n1+n2)-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,0))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n1-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n2-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n2))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,(n1+n2)-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,0))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n1-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n2-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n2))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,(n1+n2)-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,0))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n1-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n2-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n2))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,(n1+n2)-1))==1); } + BOOST_AUTO_TEST_CASE(planar_neighbors_finder) { - std::unique_ptr g = std::move(random_graph_generator()); - Planar_neighbors_finder pnf = Planar_neighbors_finder(*g,1.); + Planar_neighbors_finder pnf = Planar_neighbors_finder(1.); for(int v_point_index=0; v_point_indexdistance(n2/2,v_point_index_1)<=1.)); + BOOST_CHECK((v_point_index_1 == -1) || (G::distance(n2/2,v_point_index_1)<=1.)); BOOST_CHECK(!pnf.contains(v_point_index_1)); std::list l = *pnf.pull_all_near(n2/2); bool v = true; for(auto it = l.cbegin(); it != l.cend(); ++it) - v = v && (g->distance(n2/2,*it)>1.); + v = v && (G::distance(n2/2,*it)>1.); BOOST_CHECK(v); int v_point_index_2 = pnf.pull_near(n2/2); BOOST_CHECK(v_point_index_2 == -1); - pnf.add(v_point_index_1); - BOOST_CHECK(pnf.contains(v_point_index_1)); } BOOST_AUTO_TEST_CASE(neighbors_finder) { - std::unique_ptr g = std::move(random_graph_generator()); - Neighbors_finder nf = Neighbors_finder(*g,1.); + Neighbors_finder nf = Neighbors_finder(1.); for(int v_point_index=1; v_point_index<((n2+n1)*9/10); v_point_index+=2) nf.add(v_point_index); // int v_point_index_1 = nf.pull_near(n2/2); - BOOST_CHECK((v_point_index_1 == -1) || (g->distance(n2/2,v_point_index_1)<=1.)); + BOOST_CHECK((v_point_index_1 == -1) || (G::distance(n2/2,v_point_index_1)<=1.)); std::list l = *nf.pull_all_near(n2/2); bool v = true; for(auto it = l.cbegin(); it != l.cend(); ++it) - v = v && (g->distance(n2/2,*it)>1.); + v = v && (G::distance(n2/2,*it)>1.); BOOST_CHECK(v); int v_point_index_2 = nf.pull_near(n2/2); BOOST_CHECK(v_point_index_2 == -1); } BOOST_AUTO_TEST_CASE(layered_neighbors_finder) { - std::unique_ptr g = std::move(random_graph_generator()); - Layered_neighbors_finder lnf = Layered_neighbors_finder(*g,1.); + Layered_neighbors_finder lnf = Layered_neighbors_finder(1.); for(int v_point_index=1; v_point_index<((n2+n1)*9/10); v_point_index+=2) lnf.add(v_point_index, v_point_index % 7); // int v_point_index_1 = lnf.pull_near(n2/2,6); - BOOST_CHECK((v_point_index_1 == -1) || (g->distance(n2/2,v_point_index_1)<=1.)); + BOOST_CHECK((v_point_index_1 == -1) || (G::distance(n2/2,v_point_index_1)<=1.)); int v_point_index_2 = lnf.pull_near(n2/2,6); BOOST_CHECK(v_point_index_2 == -1); v_point_index_1 = lnf.pull_near(n2/2,0); - BOOST_CHECK((v_point_index_1 == -1) || (g->distance(n2/2,v_point_index_1)<=1.)); + BOOST_CHECK((v_point_index_1 == -1) || (G::distance(n2/2,v_point_index_1)<=1.)); v_point_index_2 = lnf.pull_near(n2/2,0); BOOST_CHECK(v_point_index_2 == -1); } - BOOST_AUTO_TEST_CASE(graph_matching) { - std::unique_ptr g = std::move(random_graph_generator()); - Graph_matching m1(*g); + Graph_matching m1; m1.set_r(0.); int e = 0; while (m1.multi_augment()) @@ -177,3 +165,7 @@ BOOST_AUTO_TEST_CASE(graph_matching) { BOOST_CHECK(m2.perfect()); BOOST_CHECK(!m1.perfect()); } + +BOOST_AUTO_TEST_CASE(grid_cell) { + +} -- cgit v1.2.3 From 6bc84d6e645cc4aada745fe779e985a2f62718e7 Mon Sep 17 00:00:00 2001 From: fgodi Date: Mon, 29 Jun 2015 18:16:07 +0000 Subject: Ajout de Grid_cell.h git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@660 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: e1b4ccdcb482c992c444adc91d67531bfa3e90dc --- src/Bottleneck/include/gudhi/Graph_matching.h | 4 +- src/Bottleneck/include/gudhi/Grid_cell.h | 188 +++++++++++++++++++++ .../include/gudhi/Layered_neighbors_finder.h | 2 +- src/Bottleneck/include/gudhi/Neighbors_finder.h | 2 +- .../include/gudhi/Persistence_diagrams_graph.h | 59 ++++--- .../include/gudhi/Planar_neighbors_finder.h | 4 +- 6 files changed, 231 insertions(+), 28 deletions(-) create mode 100644 src/Bottleneck/include/gudhi/Grid_cell.h (limited to 'src') diff --git a/src/Bottleneck/include/gudhi/Graph_matching.h b/src/Bottleneck/include/gudhi/Graph_matching.h index 17412e6c..2bcc6a61 100644 --- a/src/Bottleneck/include/gudhi/Graph_matching.h +++ b/src/Bottleneck/include/gudhi/Graph_matching.h @@ -74,13 +74,13 @@ private: void update(std::deque & path); }; -Graph_matching::Graph_matching() +inline Graph_matching::Graph_matching() : r(0.), v_to_u(G::size(), null_point_index()), unmatched_in_u() { for (int u_point_index = 0; u_point_index < G::size(); ++u_point_index) unmatched_in_u.emplace_back(u_point_index); } -Graph_matching& Graph_matching::operator=(const Graph_matching& m) { +inline Graph_matching& Graph_matching::operator=(const Graph_matching& m) { r = m.r; v_to_u = m.v_to_u; unmatched_in_u = m.unmatched_in_u; diff --git a/src/Bottleneck/include/gudhi/Grid_cell.h b/src/Bottleneck/include/gudhi/Grid_cell.h new file mode 100644 index 00000000..eee938cb --- /dev/null +++ b/src/Bottleneck/include/gudhi/Grid_cell.h @@ -0,0 +1,188 @@ +/* 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): Francois Godi + * + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_GRID_CELL_H_ +#define SRC_BOTTLENECK_INCLUDE_GUDHI_GRID_CELL_H_ + +#include +#include +#include + +#include "Persistence_diagrams_graph.h" + +namespace Gudhi { + +namespace bottleneck { + +/** \internal \brief TODO + * + * \ingroup bottleneck_distance + */ +class Grid_cell { +public: + Grid_cell(double r); + void add(int v_point_index); + void remove(int v_point_index); + bool contains(int v_point_index) const; + int pull_center(); + int pull_xi(int u_point_index); + int pull_xd(int u_point_index); + int pull_yi(int u_point_index); + int pull_yd(int u_point_index); + int pull_xi_yi(int u_point_index); + int pull_xi_yd(int u_point_index); + int pull_xd_yi(int u_point_index); + int pull_xd_yd(int u_point_index); + +private: + double r; + std::set xi_order; + std::set yi_order; + struct Hidden_points_tree{int point; std::list hidden;}; + typedef std::map, G::Compare_x> Corner_tree; + Corner_tree xi_yi_order; + Corner_tree xi_yd_order; + Corner_tree xd_yi_order; + Corner_tree xd_yd_order; + void remove_aux(Corner_tree t, int v_point_index); + void build_xi_yi(); + void build_xi_yd(); + void build_xd_yi(); + void build_xd_yd(); +}; + + +inline Grid_cell::Grid_cell(double r) + : r(r), xi_order(G::Compare_x(r)), yi_order(G::Compare_y(r)), xi_yi_order(G::Compare_x(r)), + xi_yd_order(G::Compare_x(r)), xd_yi_order(G::Compare_x(r)), xd_yd_order(G::Compare_x(r)) {} + +inline void Grid_cell::add(int v_point_index){ + xi_order.emplace(v_point_index); +} + +inline bool Grid_cell::contains(int v_point_index) const{ + return (xi_order.count(v_point_index) > 0); +} + +inline void Grid_cell::remove_aux(Corner_tree t, int v_point_index){ + if(t.empty()) + return; + std::list hidden_points = t.at(v_point_index); + t.erase(v_point_index); + for(auto it = hidden_points.begin(); it != hidden_points.end(); ++it) + t.emplace(it->point,it->hidden); + +} + +inline void Grid_cell::remove(int v_point_index){ + xi_order.erase(v_point_index); + yi_order.erase(v_point_index); + remove_aux(xi_yi_order,v_point_index); + remove_aux(xi_yd_order,v_point_index); + remove_aux(xd_yi_order,v_point_index); + remove_aux(xd_yd_order,v_point_index); +} + +//factorization needed \/ \/ \/ + +inline int Grid_cell::pull_center(){ + if(xi_order.empty()) + return null_point_index(); + int v_point_index = *xi_order.begin(); + remove(v_point_index); + return v_point_index; +} + +inline int Grid_cell::pull_xi(int u_point_index){ + if(xi_order.empty()) + return null_point_index(); + int v_point_index = *xi_order.begin(); //! + if(G::distance(u_point_index,v_point_index)<=r){ + remove(v_point_index); + return v_point_index; + } + return null_point_index(); +} + +inline int Grid_cell::pull_xd(int u_point_index){ + if(xi_order.empty()) + return null_point_index(); + int v_point_index = *xi_order.rbegin(); //! + if(G::distance(u_point_index,v_point_index)<=r){ + remove(v_point_index); + return v_point_index; + } + return null_point_index(); +} + +inline int Grid_cell::pull_yi(int u_point_index){ + if(xi_order.empty()) + return null_point_index(); + if(yi_order.empty()) + for(auto it = xi_order.begin(); it!= xi_order.end(); ++it) + yi_order.emplace(*it); + int v_point_index = *yi_order.begin(); //! + if(G::distance(u_point_index,v_point_index)<=r){ + remove(v_point_index); + return v_point_index; + } + return null_point_index(); +} + +inline int Grid_cell::pull_yd(int u_point_index){ + if(xi_order.empty()) + return null_point_index(); + if(yi_order.empty()) + for(auto it = xi_order.begin(); it!= xi_order.end(); ++it) + yi_order.emplace(*it); + int v_point_index = *yi_order.rbegin(); //! + if(G::distance(u_point_index,v_point_index)<=r){ + remove(v_point_index); + return v_point_index; + } + return null_point_index(); +} + +inline int Grid_cell::pull_xi_yi(int u_point_index){ + if(xi_order.empty()) + return null_point_index(); + if(xi_yi_order.empty()) + build_xi_yi(); + auto it = xi_yi_order.upper_bound(u_point_index+G::size()); + if(it==xi_yi_order.cbegin()) //! + return null_point_index(); + it--; //! + int v_point_index = it->first; + for(auto it2=it->second.begin();it2!=it->second.end();it2++) + xi_yi_order.emplace(it2->point,it2->hidden); + if(G::distance(u_point_index,v_point_index)<=r){ + remove(v_point_index); + return v_point_index; + } + return null_point_index(); +} + +} // namespace bottleneck + +} // namespace Gudhi + +#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_GRID_CELL_H_ diff --git a/src/Bottleneck/include/gudhi/Layered_neighbors_finder.h b/src/Bottleneck/include/gudhi/Layered_neighbors_finder.h index e6b7f30d..58805b86 100644 --- a/src/Bottleneck/include/gudhi/Layered_neighbors_finder.h +++ b/src/Bottleneck/include/gudhi/Layered_neighbors_finder.h @@ -54,7 +54,7 @@ private: std::vector neighbors_finder; }; -Layered_neighbors_finder::Layered_neighbors_finder(double r) : +inline Layered_neighbors_finder::Layered_neighbors_finder(double r) : r(r), neighbors_finder() { } inline void Layered_neighbors_finder::add(int v_point_index, int vlayer) { diff --git a/src/Bottleneck/include/gudhi/Neighbors_finder.h b/src/Bottleneck/include/gudhi/Neighbors_finder.h index ac3f8600..be81877a 100644 --- a/src/Bottleneck/include/gudhi/Neighbors_finder.h +++ b/src/Bottleneck/include/gudhi/Neighbors_finder.h @@ -58,7 +58,7 @@ private: bool contains(int v_point_index); }; -Neighbors_finder::Neighbors_finder(double r) : +inline Neighbors_finder::Neighbors_finder(double r) : r(r), planar_neighbors_f(r), projections_f() { } inline void Neighbors_finder::add(int v_point_index) { diff --git a/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h b/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h index 66e43145..aed328e2 100644 --- a/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h +++ b/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h @@ -28,6 +28,7 @@ #include #include #include +#include namespace Gudhi { @@ -60,10 +61,10 @@ public: static int size(); /** \internal \brief Returns the O(n^2) sorted distances between the points. */ static std::unique_ptr< std::vector > sorted_distances(); - /** \internal \brief Compare points regarding x coordinate. Use v_point_index for V points and u_point_index + G::size() for U points. */ - struct Compare_x{bool operator() (const int point_index_1, const int point_index_2) const;}; - /** \internal \brief Compare points regarding y coordinate. Use v_point_index for V points and u_point_index + G::size() for U points. */ - struct Compare_y{bool operator() (const int point_index_1, const int point_index_2) const;}; + /** \internal \brief Compare points regarding x%r coordinate. Use v_point_index for V points and u_point_index + G::size() for U points. */ + struct Compare_x{double r; Compare_x(double r); bool operator()(const int point_index_1, const int point_index_2) const;}; + /** \internal \brief Compare points regarding y%r coordinate. Use v_point_index for V points and u_point_index + G::size() for U points. */ + struct Compare_y{double r; Compare_y(double r);bool operator()(const int point_index_1, const int point_index_2) const;}; private: /** \internal \typedef \brief Internal_point is the internal points representation, indexes used outside. */ @@ -74,20 +75,20 @@ private: static Internal_point get_v_point(int v_point_index); }; -/** \internal \typedef \brief Alias used outside. */ +/** \internal \typedef \brief Shorter alias */ typedef Persistence_diagrams_graph G; // static initialization, seems to work but strange -std::vector Persistence_diagrams_graph::u = [] {return std::vector();}(); -std::vector Persistence_diagrams_graph::v = [] {return std::vector();}(); +std::vector G::u = [] {return std::vector();}(); +std::vector G::v = [] {return std::vector();}(); inline int null_point_index() { return -1; } template -void Persistence_diagrams_graph::initialize(const Persistence_diagram1 &diag1, - const Persistence_diagram2 &diag2, double e){ +inline void G::initialize(const Persistence_diagram1 &diag1, + const Persistence_diagram2 &diag2, double e){ u.clear(); v.clear(); for (auto it = diag1.cbegin(); it != diag1.cend(); ++it) @@ -100,25 +101,25 @@ void Persistence_diagrams_graph::initialize(const Persistence_diagram1 &diag1, swap(u, v); } -inline bool Persistence_diagrams_graph::on_the_u_diagonal(int u_point_index) { +inline bool G::on_the_u_diagonal(int u_point_index) { return u_point_index >= static_cast (u.size()); } -inline bool Persistence_diagrams_graph::on_the_v_diagonal(int v_point_index) { +inline bool G::on_the_v_diagonal(int v_point_index) { return v_point_index >= static_cast (v.size()); } -inline int Persistence_diagrams_graph::corresponding_point_in_u(int v_point_index) { +inline int G::corresponding_point_in_u(int v_point_index) { return on_the_v_diagonal(v_point_index) ? v_point_index - static_cast (v.size()) : v_point_index + static_cast (u.size()); } -inline int Persistence_diagrams_graph::corresponding_point_in_v(int u_point_index) { +inline int G::corresponding_point_in_v(int u_point_index) { return on_the_u_diagonal(u_point_index) ? u_point_index - static_cast (u.size()) : u_point_index + static_cast (v.size()); } -inline double Persistence_diagrams_graph::distance(int u_point_index, int v_point_index) { +inline double G::distance(int u_point_index, int v_point_index) { if (on_the_u_diagonal(u_point_index) && on_the_v_diagonal(v_point_index)) return 0; Internal_point p_u = get_u_point(u_point_index); @@ -126,11 +127,11 @@ inline double Persistence_diagrams_graph::distance(int u_point_index, int v_poin return std::max(std::fabs(p_u.first - p_v.first), std::fabs(p_u.second - p_v.second)); } -inline int Persistence_diagrams_graph::size() { +inline int G::size() { return static_cast (u.size() + v.size()); } -inline std::unique_ptr< std::vector > Persistence_diagrams_graph::sorted_distances() { +inline std::unique_ptr< std::vector > G::sorted_distances() { // could be optimized std::set sorted_distances; for (int u_point_index = 0; u_point_index < size(); ++u_point_index) @@ -140,7 +141,7 @@ inline std::unique_ptr< std::vector > Persistence_diagrams_graph::sorted return sd_up; } -inline Persistence_diagrams_graph::Internal_point Persistence_diagrams_graph::get_u_point(int u_point_index) { +inline G::Internal_point G::get_u_point(int u_point_index) { if (!on_the_u_diagonal(u_point_index)) return u.at(u_point_index); Internal_point projector = v.at(corresponding_point_in_v(u_point_index)); @@ -148,7 +149,7 @@ inline Persistence_diagrams_graph::Internal_point Persistence_diagrams_graph::ge return Internal_point(x, x); } -inline Persistence_diagrams_graph::Internal_point Persistence_diagrams_graph::get_v_point(int v_point_index) { +inline G::Internal_point G::get_v_point(int v_point_index) { if (!on_the_v_diagonal(v_point_index)) return v.at(v_point_index); Internal_point projector = u.at(corresponding_point_in_u(v_point_index)); @@ -156,16 +157,30 @@ inline Persistence_diagrams_graph::Internal_point Persistence_diagrams_graph::ge return Internal_point(x, x); } -inline bool Persistence_diagrams_graph::Compare_x::operator() (const int point_index_1, const int point_index_2) const{ +G::Compare_x::Compare_x(double r) + : r(r){ } + +G::Compare_y::Compare_y(double r) + : r(r){ } + +inline bool G::Compare_x::operator()(const int point_index_1, const int point_index_2) const{ G::Internal_point p1 = point_index_1 < G::size() ? G::get_v_point(point_index_1) : G::get_u_point(point_index_1 - G::size()); G::Internal_point p2 = point_index_2 < G::size() ? G::get_v_point(point_index_2) : G::get_u_point(point_index_2 - G::size()); - return p1.first < p2.first; + double x1 = fmod(p1.first,r); + double x2 = fmod(p2.first,r); + if(x1 == x2) + return point_index_1 > point_index_2; + return x1 < x2; } -inline bool Persistence_diagrams_graph::Compare_y::operator() (const int point_index_1, const int point_index_2) const{ +inline bool G::Compare_y::operator()(const int point_index_1, const int point_index_2) const{ G::Internal_point p1 = point_index_1 < G::size() ? G::get_v_point(point_index_1) : G::get_u_point(point_index_1 - G::size()); G::Internal_point p2 = point_index_2 < G::size() ? G::get_v_point(point_index_2) : G::get_u_point(point_index_2 - G::size()); - return p1.second < p2.second; + double y1 = fmod(p1.second,r); + double y2 = fmod(p2.second,r); + if(y1 == y2) + return point_index_1 > point_index_2; + return y1 < y2; } } // namespace bottleneck diff --git a/src/Bottleneck/include/gudhi/Planar_neighbors_finder.h b/src/Bottleneck/include/gudhi/Planar_neighbors_finder.h index 4d820c7f..e403735c 100644 --- a/src/Bottleneck/include/gudhi/Planar_neighbors_finder.h +++ b/src/Bottleneck/include/gudhi/Planar_neighbors_finder.h @@ -85,7 +85,7 @@ private: typedef Naive_pnf Planar_neighbors_finder; -Abstract_planar_neighbors_finder::Abstract_planar_neighbors_finder(double r) : +inline Abstract_planar_neighbors_finder::Abstract_planar_neighbors_finder(double r) : r(r) { } inline Abstract_planar_neighbors_finder::~Abstract_planar_neighbors_finder() {} @@ -100,7 +100,7 @@ inline std::unique_ptr< std::list > Abstract_planar_neighbors_finder::pull_ return all_pull; } -Naive_pnf::Naive_pnf(double r) : +inline Naive_pnf::Naive_pnf(double r) : Abstract_planar_neighbors_finder(r), candidates() { } inline void Naive_pnf::add(int v_point_index) { -- cgit v1.2.3 From c0543ba5794592af4b0ea01d35710d44e206a8a3 Mon Sep 17 00:00:00 2001 From: fgodi Date: Tue, 30 Jun 2015 05:54:52 +0000 Subject: renommage git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@661 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 3316ed6b6f7d865605786547b62ee1e5d9118d19 --- .../concept/Persistence_diagram.h | 7 + src/Bipartite_graph_matching/example/example.cpp | 44 +++++ .../include/gudhi/Graph_matching.h | 216 +++++++++++++++++++++ .../include/gudhi/Grid_cell.h | 188 ++++++++++++++++++ .../include/gudhi/Layered_neighbors_finder.h | 80 ++++++++ .../include/gudhi/Neighbors_finder.h | 114 +++++++++++ .../include/gudhi/Persistence_diagrams_graph.h | 190 ++++++++++++++++++ .../include/gudhi/Planar_neighbors_finder.h | 132 +++++++++++++ src/Bipartite_graph_matching/test/CMakeLists.txt | 31 +++ src/Bipartite_graph_matching/test/README | 12 ++ .../test/bottleneck_unit_test.cpp | 171 ++++++++++++++++ src/Bottleneck/concept/Persistence_diagram.h | 7 - src/Bottleneck/example/example.cpp | 44 ----- src/Bottleneck/include/gudhi/Graph_matching.h | 216 --------------------- src/Bottleneck/include/gudhi/Grid_cell.h | 188 ------------------ .../include/gudhi/Layered_neighbors_finder.h | 80 -------- src/Bottleneck/include/gudhi/Neighbors_finder.h | 114 ----------- .../include/gudhi/Persistence_diagrams_graph.h | 190 ------------------ .../include/gudhi/Planar_neighbors_finder.h | 132 ------------- src/Bottleneck/test/CMakeLists.txt | 31 --- src/Bottleneck/test/README | 12 -- src/Bottleneck/test/bottleneck_unit_test.cpp | 171 ---------------- 22 files changed, 1185 insertions(+), 1185 deletions(-) create mode 100644 src/Bipartite_graph_matching/concept/Persistence_diagram.h create mode 100644 src/Bipartite_graph_matching/example/example.cpp create mode 100644 src/Bipartite_graph_matching/include/gudhi/Graph_matching.h create mode 100644 src/Bipartite_graph_matching/include/gudhi/Grid_cell.h create mode 100644 src/Bipartite_graph_matching/include/gudhi/Layered_neighbors_finder.h create mode 100644 src/Bipartite_graph_matching/include/gudhi/Neighbors_finder.h create mode 100644 src/Bipartite_graph_matching/include/gudhi/Persistence_diagrams_graph.h create mode 100644 src/Bipartite_graph_matching/include/gudhi/Planar_neighbors_finder.h create mode 100644 src/Bipartite_graph_matching/test/CMakeLists.txt create mode 100644 src/Bipartite_graph_matching/test/README create mode 100644 src/Bipartite_graph_matching/test/bottleneck_unit_test.cpp delete mode 100644 src/Bottleneck/concept/Persistence_diagram.h delete mode 100644 src/Bottleneck/example/example.cpp delete mode 100644 src/Bottleneck/include/gudhi/Graph_matching.h delete mode 100644 src/Bottleneck/include/gudhi/Grid_cell.h delete mode 100644 src/Bottleneck/include/gudhi/Layered_neighbors_finder.h delete mode 100644 src/Bottleneck/include/gudhi/Neighbors_finder.h delete mode 100644 src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h delete mode 100644 src/Bottleneck/include/gudhi/Planar_neighbors_finder.h delete mode 100644 src/Bottleneck/test/CMakeLists.txt delete mode 100644 src/Bottleneck/test/README delete mode 100644 src/Bottleneck/test/bottleneck_unit_test.cpp (limited to 'src') diff --git a/src/Bipartite_graph_matching/concept/Persistence_diagram.h b/src/Bipartite_graph_matching/concept/Persistence_diagram.h new file mode 100644 index 00000000..eaaf8bc5 --- /dev/null +++ b/src/Bipartite_graph_matching/concept/Persistence_diagram.h @@ -0,0 +1,7 @@ +typedef typename std::pair Diagram_point; + +struct Persistence_Diagram +{ + const_iterator cbegin() const; + const_iterator cend() const; +}; diff --git a/src/Bipartite_graph_matching/example/example.cpp b/src/Bipartite_graph_matching/example/example.cpp new file mode 100644 index 00000000..683f7723 --- /dev/null +++ b/src/Bipartite_graph_matching/example/example.cpp @@ -0,0 +1,44 @@ +/* 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): Francois Godi + * + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 . + */ + +#include "../include/gudhi/Graph_matching.h" +#include + +using namespace Gudhi::bottleneck; + +int main() { + + std::vector< std::pair > v1, v2; + + v1.emplace_back(2.7,3.7); + v1.emplace_back(9.6,14); + v1.emplace_back(34.2,34.974); + + v2.emplace_back(2.8,4.45); + v2.emplace_back(9.5,14.1); + + + double b = bottleneck_distance(v1, v2); + + std::cout << "Bottleneck distance = " << b << std::endl; + +} diff --git a/src/Bipartite_graph_matching/include/gudhi/Graph_matching.h b/src/Bipartite_graph_matching/include/gudhi/Graph_matching.h new file mode 100644 index 00000000..2bcc6a61 --- /dev/null +++ b/src/Bipartite_graph_matching/include/gudhi/Graph_matching.h @@ -0,0 +1,216 @@ +/* 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): Francois Godi + * + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ +#define SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ + +#include +#include +#include + +#include "Layered_neighbors_finder.h" + +namespace Gudhi { + +namespace bottleneck { + +/** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams. + * + * + * + * \ingroup bottleneck_distance + */ +template +double bottleneck_distance(const Persistence_diagram1& diag1, const Persistence_diagram2& diag2, double e = 0.); + +/** \internal \brief Structure representing a graph matching. The graph is a Persistence_diagrams_graph. + * + * \ingroup bottleneck_distance + */ +class Graph_matching { +public: + /** \internal \brief Constructor constructing an empty matching. */ + explicit Graph_matching(); + /** \internal \brief Copy operator. */ + Graph_matching& operator=(const Graph_matching& m); + /** \internal \brief Is the matching perfect ? */ + bool perfect() const; + /** \internal \brief Augments the matching with a maximal set of edge-disjoint shortest augmenting paths. */ + bool multi_augment(); + /** \internal \brief Sets the maximum length of the edges allowed to be added in the matching, 0 initially. */ + void set_r(double r); + +private: + double r; + /** \internal \brief Given a point from V, provides its matched point in U, null_point_index() if there isn't. */ + std::vector v_to_u; + /** \internal \brief All the unmatched points in U. */ + std::list unmatched_in_u; + + /** \internal \brief Provides a Layered_neighbors_finder dividing the graph in layers. Basically a BFS. */ + std::unique_ptr layering() const; + /** \internal \brief Augments the matching with a simple path no longer than max_depth. Basically a DFS. */ + bool augment(Layered_neighbors_finder & layered_nf, int u_start_index, int max_depth); + /** \internal \brief Update the matching with the simple augmenting path given as parameter. */ + void update(std::deque & path); +}; + +inline Graph_matching::Graph_matching() + : r(0.), v_to_u(G::size(), null_point_index()), unmatched_in_u() { + for (int u_point_index = 0; u_point_index < G::size(); ++u_point_index) + unmatched_in_u.emplace_back(u_point_index); +} + +inline Graph_matching& Graph_matching::operator=(const Graph_matching& m) { + r = m.r; + v_to_u = m.v_to_u; + unmatched_in_u = m.unmatched_in_u; + return *this; +} + +inline bool Graph_matching::perfect() const { + return unmatched_in_u.empty(); +} + +inline bool Graph_matching::multi_augment() { + if (perfect()) + return false; + Layered_neighbors_finder layered_nf = *layering(); + int max_depth = layered_nf.vlayers_number()*2 - 1; + double rn = sqrt(G::size()); + // verification of a necessary criterion in order to shortcut if possible + if (max_depth <0 || (unmatched_in_u.size() > rn && max_depth >= rn)) + return false; + bool successful = false; + std::list tries(unmatched_in_u); + for (auto it = tries.cbegin(); it != tries.cend(); it++) + // 'augment' has side-effects which have to be always executed, don't change order + successful = augment(layered_nf, *it, max_depth) || successful; + return successful; +} + +inline void Graph_matching::set_r(double r) { + this->r = r; +} + +inline bool Graph_matching::augment(Layered_neighbors_finder & layered_nf, int u_start_index, int max_depth) { + //V vertices have at most one successor, thus when we backtrack from U we can directly pop_back 2 vertices. + std::deque path; + path.emplace_back(u_start_index); + do { + if (static_cast(path.size()) > max_depth) { + path.pop_back(); + path.pop_back(); + } + if (path.empty()) + return false; + path.emplace_back(layered_nf.pull_near(path.back(), static_cast(path.size())/2)); + while (path.back() == null_point_index()) { + path.pop_back(); + path.pop_back(); + if (path.empty()) + return false; + path.pop_back(); + path.emplace_back(layered_nf.pull_near(path.back(), path.size() / 2)); + } + path.emplace_back(v_to_u.at(path.back())); + } while (path.back() != null_point_index()); + //if v_to_u.at(path.back()) has no successor, path.back() is an exposed vertex + path.pop_back(); + update(path); + return true; +} + +inline std::unique_ptr Graph_matching::layering() const { + std::list u_vertices(unmatched_in_u); + std::list v_vertices; + Neighbors_finder nf(r); + for (int v_point_index = 0; v_point_index < G::size(); ++v_point_index) + nf.add(v_point_index); + std::unique_ptr layered_nf(new Layered_neighbors_finder(r)); + for(int layer = 0; !u_vertices.empty(); layer++) { + // one layer is one step in the BFS + for (auto it = u_vertices.cbegin(); it != u_vertices.cend(); ++it) { + std::unique_ptr< std::list > u_succ = std::move(nf.pull_all_near(*it)); + for (auto it = u_succ->cbegin(); it != u_succ->cend(); ++it) { + layered_nf->add(*it, layer); + v_vertices.emplace_back(*it); + } + } + // When the above for finishes, we have progress of one half-step (from U to V) in the BFS + u_vertices.clear(); + bool end = false; + for (auto it = v_vertices.cbegin(); it != v_vertices.cend(); it++) + if (v_to_u.at(*it) == null_point_index()) + // we stop when a nearest exposed V vertex (from U exposed vertices) has been found + end = true; + else + u_vertices.emplace_back(v_to_u.at(*it)); + // When the above for finishes, we have progress of one half-step (from V to U) in the BFS + if (end) + return layered_nf; + v_vertices.clear(); + } + return layered_nf; +} + +inline void Graph_matching::update(std::deque& path) { + unmatched_in_u.remove(path.front()); + for (auto it = path.cbegin(); it != path.cend(); ++it) { + // Be careful, the iterator is incremented twice each time + int tmp = *it; + ++it; + v_to_u[*it] = tmp; + } +} + +template +double bottleneck_distance(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e) { + G::initialize(diag1, diag2, e); + std::unique_ptr< std::vector > sd = std::move(G::sorted_distances()); + int idmin = 0; + int idmax = sd->size() - 1; + // alpha can be modified, this will change the complexity + double alpha = pow(sd->size(), 0.25); + Graph_matching m; + Graph_matching biggest_unperfect; + while (idmin != idmax) { + int step = static_cast((idmax - idmin) / alpha); + m.set_r(sd->at(idmin + step)); + while (m.multi_augment()); + // The above while compute a maximum matching (according to the r setted before) + if (m.perfect()) { + idmax = idmin + step; + m = biggest_unperfect; + } else { + biggest_unperfect = m; + idmin = idmin + step + 1; + } + } + return sd->at(idmin); +} + +} // namespace bottleneck + +} // namespace Gudhi + +#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ diff --git a/src/Bipartite_graph_matching/include/gudhi/Grid_cell.h b/src/Bipartite_graph_matching/include/gudhi/Grid_cell.h new file mode 100644 index 00000000..eee938cb --- /dev/null +++ b/src/Bipartite_graph_matching/include/gudhi/Grid_cell.h @@ -0,0 +1,188 @@ +/* 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): Francois Godi + * + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_GRID_CELL_H_ +#define SRC_BOTTLENECK_INCLUDE_GUDHI_GRID_CELL_H_ + +#include +#include +#include + +#include "Persistence_diagrams_graph.h" + +namespace Gudhi { + +namespace bottleneck { + +/** \internal \brief TODO + * + * \ingroup bottleneck_distance + */ +class Grid_cell { +public: + Grid_cell(double r); + void add(int v_point_index); + void remove(int v_point_index); + bool contains(int v_point_index) const; + int pull_center(); + int pull_xi(int u_point_index); + int pull_xd(int u_point_index); + int pull_yi(int u_point_index); + int pull_yd(int u_point_index); + int pull_xi_yi(int u_point_index); + int pull_xi_yd(int u_point_index); + int pull_xd_yi(int u_point_index); + int pull_xd_yd(int u_point_index); + +private: + double r; + std::set xi_order; + std::set yi_order; + struct Hidden_points_tree{int point; std::list hidden;}; + typedef std::map, G::Compare_x> Corner_tree; + Corner_tree xi_yi_order; + Corner_tree xi_yd_order; + Corner_tree xd_yi_order; + Corner_tree xd_yd_order; + void remove_aux(Corner_tree t, int v_point_index); + void build_xi_yi(); + void build_xi_yd(); + void build_xd_yi(); + void build_xd_yd(); +}; + + +inline Grid_cell::Grid_cell(double r) + : r(r), xi_order(G::Compare_x(r)), yi_order(G::Compare_y(r)), xi_yi_order(G::Compare_x(r)), + xi_yd_order(G::Compare_x(r)), xd_yi_order(G::Compare_x(r)), xd_yd_order(G::Compare_x(r)) {} + +inline void Grid_cell::add(int v_point_index){ + xi_order.emplace(v_point_index); +} + +inline bool Grid_cell::contains(int v_point_index) const{ + return (xi_order.count(v_point_index) > 0); +} + +inline void Grid_cell::remove_aux(Corner_tree t, int v_point_index){ + if(t.empty()) + return; + std::list hidden_points = t.at(v_point_index); + t.erase(v_point_index); + for(auto it = hidden_points.begin(); it != hidden_points.end(); ++it) + t.emplace(it->point,it->hidden); + +} + +inline void Grid_cell::remove(int v_point_index){ + xi_order.erase(v_point_index); + yi_order.erase(v_point_index); + remove_aux(xi_yi_order,v_point_index); + remove_aux(xi_yd_order,v_point_index); + remove_aux(xd_yi_order,v_point_index); + remove_aux(xd_yd_order,v_point_index); +} + +//factorization needed \/ \/ \/ + +inline int Grid_cell::pull_center(){ + if(xi_order.empty()) + return null_point_index(); + int v_point_index = *xi_order.begin(); + remove(v_point_index); + return v_point_index; +} + +inline int Grid_cell::pull_xi(int u_point_index){ + if(xi_order.empty()) + return null_point_index(); + int v_point_index = *xi_order.begin(); //! + if(G::distance(u_point_index,v_point_index)<=r){ + remove(v_point_index); + return v_point_index; + } + return null_point_index(); +} + +inline int Grid_cell::pull_xd(int u_point_index){ + if(xi_order.empty()) + return null_point_index(); + int v_point_index = *xi_order.rbegin(); //! + if(G::distance(u_point_index,v_point_index)<=r){ + remove(v_point_index); + return v_point_index; + } + return null_point_index(); +} + +inline int Grid_cell::pull_yi(int u_point_index){ + if(xi_order.empty()) + return null_point_index(); + if(yi_order.empty()) + for(auto it = xi_order.begin(); it!= xi_order.end(); ++it) + yi_order.emplace(*it); + int v_point_index = *yi_order.begin(); //! + if(G::distance(u_point_index,v_point_index)<=r){ + remove(v_point_index); + return v_point_index; + } + return null_point_index(); +} + +inline int Grid_cell::pull_yd(int u_point_index){ + if(xi_order.empty()) + return null_point_index(); + if(yi_order.empty()) + for(auto it = xi_order.begin(); it!= xi_order.end(); ++it) + yi_order.emplace(*it); + int v_point_index = *yi_order.rbegin(); //! + if(G::distance(u_point_index,v_point_index)<=r){ + remove(v_point_index); + return v_point_index; + } + return null_point_index(); +} + +inline int Grid_cell::pull_xi_yi(int u_point_index){ + if(xi_order.empty()) + return null_point_index(); + if(xi_yi_order.empty()) + build_xi_yi(); + auto it = xi_yi_order.upper_bound(u_point_index+G::size()); + if(it==xi_yi_order.cbegin()) //! + return null_point_index(); + it--; //! + int v_point_index = it->first; + for(auto it2=it->second.begin();it2!=it->second.end();it2++) + xi_yi_order.emplace(it2->point,it2->hidden); + if(G::distance(u_point_index,v_point_index)<=r){ + remove(v_point_index); + return v_point_index; + } + return null_point_index(); +} + +} // namespace bottleneck + +} // namespace Gudhi + +#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_GRID_CELL_H_ diff --git a/src/Bipartite_graph_matching/include/gudhi/Layered_neighbors_finder.h b/src/Bipartite_graph_matching/include/gudhi/Layered_neighbors_finder.h new file mode 100644 index 00000000..58805b86 --- /dev/null +++ b/src/Bipartite_graph_matching/include/gudhi/Layered_neighbors_finder.h @@ -0,0 +1,80 @@ +/* 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): Francois Godi + * + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_LAYERED_NEIGHBORS_FINDER_H_ +#define SRC_BOTTLENECK_INCLUDE_GUDHI_LAYERED_NEIGHBORS_FINDER_H_ + +#include + +#include "Neighbors_finder.h" + +namespace Gudhi { + +namespace bottleneck { + +/** \internal \brief data structure used to find any point (including projections) in V near to a query point from U + * (which can be a projection) in a layered graph layer given as parmeter. + * + * V points have to be added manually using their index and before the first pull. A neighbor pulled is automatically removed. + * + * \ingroup bottleneck_distance + */ +class Layered_neighbors_finder { +public: + /** \internal \brief Constructor taking the near distance definition as parameter. */ + Layered_neighbors_finder(double r); + /** \internal \brief A point added will be possibly pulled. */ + void add(int v_point_index, int vlayer); + /** \internal \brief Returns and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ + int pull_near(int u_point_index, int vlayer); + /** \internal \brief Returns the number of layers. */ + int vlayers_number() const; + +private: + const double r; + std::vector neighbors_finder; +}; + +inline Layered_neighbors_finder::Layered_neighbors_finder(double r) : + r(r), neighbors_finder() { } + +inline void Layered_neighbors_finder::add(int v_point_index, int vlayer) { + for (int l = neighbors_finder.size(); l <= vlayer; l++) + neighbors_finder.emplace_back(Neighbors_finder(r)); + neighbors_finder.at(vlayer).add(v_point_index); +} + +inline int Layered_neighbors_finder::pull_near(int u_point_index, int vlayer) { + if (static_cast (neighbors_finder.size()) <= vlayer) + return null_point_index(); + return neighbors_finder.at(vlayer).pull_near(u_point_index); +} + +inline int Layered_neighbors_finder::vlayers_number() const { + return static_cast(neighbors_finder.size()); +} + +} // namespace bottleneck + +} // namespace Gudhi + +#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_LAYERED_NEIGHBORS_FINDER_H_ diff --git a/src/Bipartite_graph_matching/include/gudhi/Neighbors_finder.h b/src/Bipartite_graph_matching/include/gudhi/Neighbors_finder.h new file mode 100644 index 00000000..be81877a --- /dev/null +++ b/src/Bipartite_graph_matching/include/gudhi/Neighbors_finder.h @@ -0,0 +1,114 @@ +/* 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): Francois Godi + * + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_ +#define SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_ + +#include +#include + +#include "Planar_neighbors_finder.h" + +namespace Gudhi { + +namespace bottleneck { + +/** \internal \brief data structure used to find any point (including projections) in V near to a query point from U + * (which can be a projection). + * + * V points have to be added manually using their index and before the first pull. A neighbor pulled is automatically removed. + * + * \ingroup bottleneck_distance + */ +class Neighbors_finder { +public: + /** \internal \brief Constructor taking the near distance definition as parameter. */ + Neighbors_finder(double r); + /** \internal \brief A point added will be possibly pulled. */ + void add(int v_point_index); + /** \internal \brief Returns and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ + int pull_near(int u_point_index); + /** \internal \brief Returns and remove all the V points near to the U point given as parameter. */ + std::unique_ptr< std::list > pull_all_near(int u_point_index); + +private: + const double r; + Planar_neighbors_finder planar_neighbors_f; + std::unordered_set projections_f; + void remove(int v_point_index); + bool contains(int v_point_index); +}; + +inline Neighbors_finder::Neighbors_finder(double r) : + r(r), planar_neighbors_f(r), projections_f() { } + +inline void Neighbors_finder::add(int v_point_index) { + if (G::on_the_v_diagonal(v_point_index)) + projections_f.emplace(v_point_index); + else + planar_neighbors_f.add(v_point_index); +} + +inline void Neighbors_finder::remove(int v_point_index) { + if(v_point_index == null_point_index()) + return; + if (G::on_the_v_diagonal(v_point_index)) + projections_f.erase(v_point_index); + else + planar_neighbors_f.remove(v_point_index); +} + +inline bool Neighbors_finder::contains(int v_point_index) { + return planar_neighbors_f.contains(v_point_index) || (projections_f.count(v_point_index)>0); +} + +inline int Neighbors_finder::pull_near(int u_point_index) { + int tmp; + int c = G::corresponding_point_in_v(u_point_index); + if (G::on_the_u_diagonal(u_point_index) && !projections_f.empty()) + //All projections are at distance 0 + tmp = *projections_f.cbegin(); + else if (contains(c) && (G::distance(u_point_index, c) <= r)) + //Is the query point near to its projection ? + tmp = c; + else + //Is the query point near to a V point in the plane ? + tmp = planar_neighbors_f.pull_near(u_point_index); + remove(tmp); + return tmp; +} + +inline std::unique_ptr< std::list > Neighbors_finder::pull_all_near(int u_point_index) { + std::unique_ptr< std::list > all_pull = std::move(planar_neighbors_f.pull_all_near(u_point_index)); + int last_pull = pull_near(u_point_index); + while (last_pull != null_point_index()) { + all_pull->emplace_back(last_pull); + last_pull = pull_near(u_point_index); + } + return all_pull; +} + +} // namespace bottleneck + +} // namespace Gudhi + +#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_ diff --git a/src/Bipartite_graph_matching/include/gudhi/Persistence_diagrams_graph.h b/src/Bipartite_graph_matching/include/gudhi/Persistence_diagrams_graph.h new file mode 100644 index 00000000..aed328e2 --- /dev/null +++ b/src/Bipartite_graph_matching/include/gudhi/Persistence_diagrams_graph.h @@ -0,0 +1,190 @@ +/* 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): Francois Godi + * + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_ +#define SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_ + +#include +#include +#include +#include +#include +#include + +namespace Gudhi { + +namespace bottleneck { + +/** \internal \brief Returns the used index for encoding none of the points */ +int null_point_index(); + +/** \internal \brief Structure representing an euclidean bipartite graph containing + * the points from the two persistence diagrams (including the projections). + * + * \ingroup bottleneck_distance + */ +class Persistence_diagrams_graph { +public: + /** \internal \brief Initializer taking 2 Point (concept) ranges as parameters. */ + template + static void initialize(const Persistence_diagram1& diag1, const Persistence_diagram2& diag2, double e); + /** \internal \brief Is the given point from U the projection of a point in V ? */ + static bool on_the_u_diagonal(int u_point_index); + /** \internal \brief Is the given point from V the projection of a point in U ? */ + static bool on_the_v_diagonal(int v_point_index); + /** \internal \brief Given a point from V, returns the corresponding (projection or projector) point in U. */ + static int corresponding_point_in_u(int v_point_index); + /** \internal \brief Given a point from U, returns the corresponding (projection or projector) point in V. */ + static int corresponding_point_in_v(int u_point_index); + /** \internal \brief Given a point from U and a point from V, returns the distance between those points. */ + static double distance(int u_point_index, int v_point_index); + /** \internal \brief Returns size = |U| = |V|. */ + static int size(); + /** \internal \brief Returns the O(n^2) sorted distances between the points. */ + static std::unique_ptr< std::vector > sorted_distances(); + /** \internal \brief Compare points regarding x%r coordinate. Use v_point_index for V points and u_point_index + G::size() for U points. */ + struct Compare_x{double r; Compare_x(double r); bool operator()(const int point_index_1, const int point_index_2) const;}; + /** \internal \brief Compare points regarding y%r coordinate. Use v_point_index for V points and u_point_index + G::size() for U points. */ + struct Compare_y{double r; Compare_y(double r);bool operator()(const int point_index_1, const int point_index_2) const;}; + +private: + /** \internal \typedef \brief Internal_point is the internal points representation, indexes used outside. */ + typedef std::pair Internal_point; + static std::vector u; + static std::vector v; + static Internal_point get_u_point(int u_point_index); + static Internal_point get_v_point(int v_point_index); +}; + +/** \internal \typedef \brief Shorter alias */ +typedef Persistence_diagrams_graph G; + +// static initialization, seems to work but strange +std::vector G::u = [] {return std::vector();}(); +std::vector G::v = [] {return std::vector();}(); + +inline int null_point_index() { + return -1; +} + +template +inline void G::initialize(const Persistence_diagram1 &diag1, + const Persistence_diagram2 &diag2, double e){ + u.clear(); + v.clear(); + for (auto it = diag1.cbegin(); it != diag1.cend(); ++it) + if (it->second - it->first > e) + u.emplace_back(*it); + for (auto it = diag2.cbegin(); it != diag2.cend(); ++it) + if (it->second - it->first > e) + v.emplace_back(*it); + if (u.size() < v.size()) + swap(u, v); +} + +inline bool G::on_the_u_diagonal(int u_point_index) { + return u_point_index >= static_cast (u.size()); +} + +inline bool G::on_the_v_diagonal(int v_point_index) { + return v_point_index >= static_cast (v.size()); +} + +inline int G::corresponding_point_in_u(int v_point_index) { + return on_the_v_diagonal(v_point_index) ? + v_point_index - static_cast (v.size()) : v_point_index + static_cast (u.size()); +} + +inline int G::corresponding_point_in_v(int u_point_index) { + return on_the_u_diagonal(u_point_index) ? + u_point_index - static_cast (u.size()) : u_point_index + static_cast (v.size()); +} + +inline double G::distance(int u_point_index, int v_point_index) { + if (on_the_u_diagonal(u_point_index) && on_the_v_diagonal(v_point_index)) + return 0; + Internal_point p_u = get_u_point(u_point_index); + Internal_point p_v = get_v_point(v_point_index); + return std::max(std::fabs(p_u.first - p_v.first), std::fabs(p_u.second - p_v.second)); +} + +inline int G::size() { + return static_cast (u.size() + v.size()); +} + +inline std::unique_ptr< std::vector > G::sorted_distances() { + // could be optimized + std::set sorted_distances; + for (int u_point_index = 0; u_point_index < size(); ++u_point_index) + for (int v_point_index = 0; v_point_index < size(); ++v_point_index) + sorted_distances.emplace(distance(u_point_index, v_point_index)); + std::unique_ptr< std::vector > sd_up(new std::vector(sorted_distances.cbegin(), sorted_distances.cend())); + return sd_up; +} + +inline G::Internal_point G::get_u_point(int u_point_index) { + if (!on_the_u_diagonal(u_point_index)) + return u.at(u_point_index); + Internal_point projector = v.at(corresponding_point_in_v(u_point_index)); + double x = (projector.first + projector.second) / 2; + return Internal_point(x, x); +} + +inline G::Internal_point G::get_v_point(int v_point_index) { + if (!on_the_v_diagonal(v_point_index)) + return v.at(v_point_index); + Internal_point projector = u.at(corresponding_point_in_u(v_point_index)); + double x = (projector.first + projector.second) / 2; + return Internal_point(x, x); +} + +G::Compare_x::Compare_x(double r) + : r(r){ } + +G::Compare_y::Compare_y(double r) + : r(r){ } + +inline bool G::Compare_x::operator()(const int point_index_1, const int point_index_2) const{ + G::Internal_point p1 = point_index_1 < G::size() ? G::get_v_point(point_index_1) : G::get_u_point(point_index_1 - G::size()); + G::Internal_point p2 = point_index_2 < G::size() ? G::get_v_point(point_index_2) : G::get_u_point(point_index_2 - G::size()); + double x1 = fmod(p1.first,r); + double x2 = fmod(p2.first,r); + if(x1 == x2) + return point_index_1 > point_index_2; + return x1 < x2; +} + +inline bool G::Compare_y::operator()(const int point_index_1, const int point_index_2) const{ + G::Internal_point p1 = point_index_1 < G::size() ? G::get_v_point(point_index_1) : G::get_u_point(point_index_1 - G::size()); + G::Internal_point p2 = point_index_2 < G::size() ? G::get_v_point(point_index_2) : G::get_u_point(point_index_2 - G::size()); + double y1 = fmod(p1.second,r); + double y2 = fmod(p2.second,r); + if(y1 == y2) + return point_index_1 > point_index_2; + return y1 < y2; +} + +} // namespace bottleneck + +} // namespace Gudhi + +#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_ diff --git a/src/Bipartite_graph_matching/include/gudhi/Planar_neighbors_finder.h b/src/Bipartite_graph_matching/include/gudhi/Planar_neighbors_finder.h new file mode 100644 index 00000000..e403735c --- /dev/null +++ b/src/Bipartite_graph_matching/include/gudhi/Planar_neighbors_finder.h @@ -0,0 +1,132 @@ +/* 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): Francois Godi + * + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_ +#define SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_ + +#include +#include + +#include "Persistence_diagrams_graph.h" +#include "Grid_cell.h" + +namespace Gudhi { + +namespace bottleneck { + +/** \internal \brief Structure used to find any point in V near (according to the planar distance) to a query point from U. + * + * V points have to be added manually using their index and before the first remove/pull. A neighbor pulled is automatically removed. but we can also + * remove points manually using their index. + * + * \ingroup bottleneck_distance + */ +class Abstract_planar_neighbors_finder { +public: + /** \internal \brief Constructor TODO. */ + Abstract_planar_neighbors_finder(double r); + virtual ~Abstract_planar_neighbors_finder() = 0; + /** \internal \brief A point added will be possibly pulled. */ + virtual void add(int v_point_index) = 0; + /** \internal \brief A point manually removed will no longer be possibly pulled. */ + virtual void remove(int v_point_index) = 0; + /** \internal \brief Can the point given as parameter be returned ? */ + virtual bool contains(int v_point_index) const = 0; + /** \internal \brief Provide and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ + virtual int pull_near(int u_point_index) = 0; + /** \internal \brief Provide and remove all the V points near to the U point given as parameter. */ + virtual std::unique_ptr< std::list > pull_all_near(int u_point_index); + +protected: + const double r; +}; + +/** \internal \brief Naive_pnf is an naïve Abstract_planar_neighbors_finder implementation + * + * \ingroup bottleneck_distance + */ +class Naive_pnf : public Abstract_planar_neighbors_finder { +public: + /** \internal \brief Constructor taking the near distance definition as parameter. */ + Naive_pnf(double r); + /** \internal \brief A point added will be possibly pulled. */ + void add(int v_point_index); + /** \internal \brief A point manually removed will no longer be possibly pulled. */ + void remove(int v_point_index); + /** \internal \brief Can the point given as parameter be returned ? */ + bool contains(int v_point_index) const; + /** \internal \brief Provide and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ + int pull_near(int u_point_index); + +private: + std::set candidates; +}; + +/** \internal \typedef \brief Planar_neighbors_finder is the used Abstract_planar_neighbors_finder's implementation. */ +typedef Naive_pnf Planar_neighbors_finder; + + +inline Abstract_planar_neighbors_finder::Abstract_planar_neighbors_finder(double r) : + r(r) { } + +inline Abstract_planar_neighbors_finder::~Abstract_planar_neighbors_finder() {} + +inline std::unique_ptr< std::list > Abstract_planar_neighbors_finder::pull_all_near(int u_point_index) { + std::unique_ptr< std::list > all_pull(new std::list); + int last_pull = pull_near(u_point_index); + while (last_pull != null_point_index()) { + all_pull->emplace_back(last_pull); + last_pull = pull_near(u_point_index); + } + return all_pull; +} + +inline Naive_pnf::Naive_pnf(double r) : + Abstract_planar_neighbors_finder(r), candidates() { } + +inline void Naive_pnf::add(int v_point_index) { + candidates.emplace(v_point_index); +} + +inline void Naive_pnf::remove(int v_point_index) { + candidates.erase(v_point_index); +} + +inline bool Naive_pnf::contains(int v_point_index) const { + return (candidates.count(v_point_index) > 0); +} + +inline int Naive_pnf::pull_near(int u_point_index) { + for (auto it = candidates.begin(); it != candidates.end(); ++it) + if (G::distance(u_point_index, *it) <= r) { + int tmp = *it; + candidates.erase(it); + return tmp; + } + return null_point_index(); +} + +} // namespace bottleneck + +} // namespace Gudhi + +#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_ diff --git a/src/Bipartite_graph_matching/test/CMakeLists.txt b/src/Bipartite_graph_matching/test/CMakeLists.txt new file mode 100644 index 00000000..8e4371b8 --- /dev/null +++ b/src/Bipartite_graph_matching/test/CMakeLists.txt @@ -0,0 +1,31 @@ +cmake_minimum_required(VERSION 2.6) +project(GUDHIBottleneckUT) + +if (GCOVR_PATH) + # for gcovr to make coverage reports - Corbera Jenkins plugin + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage") + set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage") +endif() +if (GPROF_PATH) + # for gprof to make coverage reports - Jenkins + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg") + set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg") +endif() + message("CMAKE_CXX_FLAGS = ${CMAKE_CXX_FLAGS}") + message("CMAKE_CXX_FLAGS_DEBUG = ${CMAKE_CXX_FLAGS_DEBUG}") + message("CMAKE_CXX_FLAGS_RELEASE = ${CMAKE_CXX_FLAGS_RELEASE}") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O2 -std=c++11 -Wall -Wpedantic -Wsign-compare") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -ggdb -O0") + set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE}") + +add_executable ( BottleneckUT bottleneck_unit_test.cpp ) +target_link_libraries(BottleneckUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) + +# Unitary tests +add_test(NAME BottleneckUT + COMMAND ${CMAKE_CURRENT_BINARY_DIR}/BottleneckUT + # XML format for Jenkins xUnit plugin + --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/BottleneckUT.xml --log_level=test_suite --report_level=no) + diff --git a/src/Bipartite_graph_matching/test/README b/src/Bipartite_graph_matching/test/README new file mode 100644 index 00000000..0e7b8673 --- /dev/null +++ b/src/Bipartite_graph_matching/test/README @@ -0,0 +1,12 @@ +To compile: +*********** + +cmake . +make + +To launch with details: +*********************** + +./BottleneckUnitTest --report_level=detailed --log_level=all + + ==> echo $? returns 0 in case of success (non-zero otherwise) diff --git a/src/Bipartite_graph_matching/test/bottleneck_unit_test.cpp b/src/Bipartite_graph_matching/test/bottleneck_unit_test.cpp new file mode 100644 index 00000000..926c8430 --- /dev/null +++ b/src/Bipartite_graph_matching/test/bottleneck_unit_test.cpp @@ -0,0 +1,171 @@ +#define BOOST_TEST_MODULE bottleneck test + +#include +#include +#include "../include/gudhi/Graph_matching.h" + +using namespace Gudhi::bottleneck; + +int n1 = 81; // a natural number >0 +int n2 = 180; // a natural number >0 +double upper_bound = 400.5; // any real >0 + +BOOST_AUTO_TEST_CASE(global){ + std::uniform_real_distribution unif1(0.,upper_bound); + std::uniform_real_distribution unif2(upper_bound/1000.,upper_bound/100.); + std::default_random_engine re; + std::vector< std::pair > v1, v2; + for (int i = 0; i < n1; i++) { + double a = unif1(re); + double b = unif1(re); + double x = unif2(re); + double y = unif2(re); + v1.emplace_back(std::min(a,b), std::max(a,b)); + v2.emplace_back(std::min(a,b)+std::min(x,y), std::max(a,b)+std::max(x,y)); + if(i%5==0) + v1.emplace_back(std::min(a,b),std::min(a,b)+x); + if(i%3==0) + v2.emplace_back(std::max(a,b),std::max(a,b)+y); + } + BOOST_CHECK(bottleneck_distance(v1, v2) <= upper_bound/100.); +} + +BOOST_AUTO_TEST_CASE(persistence_diagrams_graph){ + // Random construction + std::uniform_real_distribution unif(0.,upper_bound); + std::default_random_engine re; + std::vector< std::pair > v1, v2; + for (int i = 0; i < n1; i++) { + double a = unif(re); + double b = unif(re); + v1.emplace_back(std::min(a,b), std::max(a,b)); + } + for (int i = 0; i < n2; i++) { + double a = unif(re); + double b = unif(re); + v2.emplace_back(std::min(a,b), std::max(a,b)); + } + G::initialize(v1, v2, 0.); + std::unique_ptr< std::vector > d = std::move(G::sorted_distances()); + // + BOOST_CHECK(!G::on_the_u_diagonal(n1-1)); + BOOST_CHECK(!G::on_the_u_diagonal(n1)); + BOOST_CHECK(!G::on_the_u_diagonal(n2-1)); + BOOST_CHECK(G::on_the_u_diagonal(n2)); + BOOST_CHECK(!G::on_the_v_diagonal(n1-1)); + BOOST_CHECK(G::on_the_v_diagonal(n1)); + BOOST_CHECK(G::on_the_v_diagonal(n2-1)); + BOOST_CHECK(G::on_the_v_diagonal(n2)); + // + BOOST_CHECK(G::corresponding_point_in_u(0)==n2); + BOOST_CHECK(G::corresponding_point_in_u(n1)==0); + BOOST_CHECK(G::corresponding_point_in_v(0)==n1); + BOOST_CHECK(G::corresponding_point_in_v(n2)==0); + // + BOOST_CHECK(G::size()==(n1+n2)); + // + BOOST_CHECK((int) d->size() <= (n1+n2)*(n1+n2) - n1*n2 + 1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,0))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n1-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n2-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n2))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,(n1+n2)-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,0))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n1-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n2-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n2))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,(n1+n2)-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,0))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n1-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n2-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n2))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,(n1+n2)-1))==1); +} + + +BOOST_AUTO_TEST_CASE(planar_neighbors_finder) { + Planar_neighbors_finder pnf = Planar_neighbors_finder(1.); + for(int v_point_index=0; v_point_index l = *pnf.pull_all_near(n2/2); + bool v = true; + for(auto it = l.cbegin(); it != l.cend(); ++it) + v = v && (G::distance(n2/2,*it)>1.); + BOOST_CHECK(v); + int v_point_index_2 = pnf.pull_near(n2/2); + BOOST_CHECK(v_point_index_2 == -1); +} + + +BOOST_AUTO_TEST_CASE(neighbors_finder) { + Neighbors_finder nf = Neighbors_finder(1.); + for(int v_point_index=1; v_point_index<((n2+n1)*9/10); v_point_index+=2) + nf.add(v_point_index); + // + int v_point_index_1 = nf.pull_near(n2/2); + BOOST_CHECK((v_point_index_1 == -1) || (G::distance(n2/2,v_point_index_1)<=1.)); + std::list l = *nf.pull_all_near(n2/2); + bool v = true; + for(auto it = l.cbegin(); it != l.cend(); ++it) + v = v && (G::distance(n2/2,*it)>1.); + BOOST_CHECK(v); + int v_point_index_2 = nf.pull_near(n2/2); + BOOST_CHECK(v_point_index_2 == -1); +} + +BOOST_AUTO_TEST_CASE(layered_neighbors_finder) { + Layered_neighbors_finder lnf = Layered_neighbors_finder(1.); + for(int v_point_index=1; v_point_index<((n2+n1)*9/10); v_point_index+=2) + lnf.add(v_point_index, v_point_index % 7); + // + int v_point_index_1 = lnf.pull_near(n2/2,6); + BOOST_CHECK((v_point_index_1 == -1) || (G::distance(n2/2,v_point_index_1)<=1.)); + int v_point_index_2 = lnf.pull_near(n2/2,6); + BOOST_CHECK(v_point_index_2 == -1); + v_point_index_1 = lnf.pull_near(n2/2,0); + BOOST_CHECK((v_point_index_1 == -1) || (G::distance(n2/2,v_point_index_1)<=1.)); + v_point_index_2 = lnf.pull_near(n2/2,0); + BOOST_CHECK(v_point_index_2 == -1); +} + +BOOST_AUTO_TEST_CASE(graph_matching) { + Graph_matching m1; + m1.set_r(0.); + int e = 0; + while (m1.multi_augment()) + ++e; + BOOST_CHECK(e <= 2*sqrt(2*(n1+n2))); + Graph_matching m2 = m1; + BOOST_CHECK(!m2.multi_augment()); + m2.set_r(upper_bound); + e = 0; + while (m2.multi_augment()) + ++e; + BOOST_CHECK(e <= 2*sqrt(2*(n1+n2))); + BOOST_CHECK(m2.perfect()); + BOOST_CHECK(!m1.perfect()); +} + +BOOST_AUTO_TEST_CASE(grid_cell) { + +} diff --git a/src/Bottleneck/concept/Persistence_diagram.h b/src/Bottleneck/concept/Persistence_diagram.h deleted file mode 100644 index eaaf8bc5..00000000 --- a/src/Bottleneck/concept/Persistence_diagram.h +++ /dev/null @@ -1,7 +0,0 @@ -typedef typename std::pair Diagram_point; - -struct Persistence_Diagram -{ - const_iterator cbegin() const; - const_iterator cend() const; -}; diff --git a/src/Bottleneck/example/example.cpp b/src/Bottleneck/example/example.cpp deleted file mode 100644 index 683f7723..00000000 --- a/src/Bottleneck/example/example.cpp +++ /dev/null @@ -1,44 +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): Francois Godi - * - * Copyright (C) 2015 INRIA Sophia-Antipolis (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 . - */ - -#include "../include/gudhi/Graph_matching.h" -#include - -using namespace Gudhi::bottleneck; - -int main() { - - std::vector< std::pair > v1, v2; - - v1.emplace_back(2.7,3.7); - v1.emplace_back(9.6,14); - v1.emplace_back(34.2,34.974); - - v2.emplace_back(2.8,4.45); - v2.emplace_back(9.5,14.1); - - - double b = bottleneck_distance(v1, v2); - - std::cout << "Bottleneck distance = " << b << std::endl; - -} diff --git a/src/Bottleneck/include/gudhi/Graph_matching.h b/src/Bottleneck/include/gudhi/Graph_matching.h deleted file mode 100644 index 2bcc6a61..00000000 --- a/src/Bottleneck/include/gudhi/Graph_matching.h +++ /dev/null @@ -1,216 +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): Francois Godi - * - * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ -#define SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ - -#include -#include -#include - -#include "Layered_neighbors_finder.h" - -namespace Gudhi { - -namespace bottleneck { - -/** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams. - * - * - * - * \ingroup bottleneck_distance - */ -template -double bottleneck_distance(const Persistence_diagram1& diag1, const Persistence_diagram2& diag2, double e = 0.); - -/** \internal \brief Structure representing a graph matching. The graph is a Persistence_diagrams_graph. - * - * \ingroup bottleneck_distance - */ -class Graph_matching { -public: - /** \internal \brief Constructor constructing an empty matching. */ - explicit Graph_matching(); - /** \internal \brief Copy operator. */ - Graph_matching& operator=(const Graph_matching& m); - /** \internal \brief Is the matching perfect ? */ - bool perfect() const; - /** \internal \brief Augments the matching with a maximal set of edge-disjoint shortest augmenting paths. */ - bool multi_augment(); - /** \internal \brief Sets the maximum length of the edges allowed to be added in the matching, 0 initially. */ - void set_r(double r); - -private: - double r; - /** \internal \brief Given a point from V, provides its matched point in U, null_point_index() if there isn't. */ - std::vector v_to_u; - /** \internal \brief All the unmatched points in U. */ - std::list unmatched_in_u; - - /** \internal \brief Provides a Layered_neighbors_finder dividing the graph in layers. Basically a BFS. */ - std::unique_ptr layering() const; - /** \internal \brief Augments the matching with a simple path no longer than max_depth. Basically a DFS. */ - bool augment(Layered_neighbors_finder & layered_nf, int u_start_index, int max_depth); - /** \internal \brief Update the matching with the simple augmenting path given as parameter. */ - void update(std::deque & path); -}; - -inline Graph_matching::Graph_matching() - : r(0.), v_to_u(G::size(), null_point_index()), unmatched_in_u() { - for (int u_point_index = 0; u_point_index < G::size(); ++u_point_index) - unmatched_in_u.emplace_back(u_point_index); -} - -inline Graph_matching& Graph_matching::operator=(const Graph_matching& m) { - r = m.r; - v_to_u = m.v_to_u; - unmatched_in_u = m.unmatched_in_u; - return *this; -} - -inline bool Graph_matching::perfect() const { - return unmatched_in_u.empty(); -} - -inline bool Graph_matching::multi_augment() { - if (perfect()) - return false; - Layered_neighbors_finder layered_nf = *layering(); - int max_depth = layered_nf.vlayers_number()*2 - 1; - double rn = sqrt(G::size()); - // verification of a necessary criterion in order to shortcut if possible - if (max_depth <0 || (unmatched_in_u.size() > rn && max_depth >= rn)) - return false; - bool successful = false; - std::list tries(unmatched_in_u); - for (auto it = tries.cbegin(); it != tries.cend(); it++) - // 'augment' has side-effects which have to be always executed, don't change order - successful = augment(layered_nf, *it, max_depth) || successful; - return successful; -} - -inline void Graph_matching::set_r(double r) { - this->r = r; -} - -inline bool Graph_matching::augment(Layered_neighbors_finder & layered_nf, int u_start_index, int max_depth) { - //V vertices have at most one successor, thus when we backtrack from U we can directly pop_back 2 vertices. - std::deque path; - path.emplace_back(u_start_index); - do { - if (static_cast(path.size()) > max_depth) { - path.pop_back(); - path.pop_back(); - } - if (path.empty()) - return false; - path.emplace_back(layered_nf.pull_near(path.back(), static_cast(path.size())/2)); - while (path.back() == null_point_index()) { - path.pop_back(); - path.pop_back(); - if (path.empty()) - return false; - path.pop_back(); - path.emplace_back(layered_nf.pull_near(path.back(), path.size() / 2)); - } - path.emplace_back(v_to_u.at(path.back())); - } while (path.back() != null_point_index()); - //if v_to_u.at(path.back()) has no successor, path.back() is an exposed vertex - path.pop_back(); - update(path); - return true; -} - -inline std::unique_ptr Graph_matching::layering() const { - std::list u_vertices(unmatched_in_u); - std::list v_vertices; - Neighbors_finder nf(r); - for (int v_point_index = 0; v_point_index < G::size(); ++v_point_index) - nf.add(v_point_index); - std::unique_ptr layered_nf(new Layered_neighbors_finder(r)); - for(int layer = 0; !u_vertices.empty(); layer++) { - // one layer is one step in the BFS - for (auto it = u_vertices.cbegin(); it != u_vertices.cend(); ++it) { - std::unique_ptr< std::list > u_succ = std::move(nf.pull_all_near(*it)); - for (auto it = u_succ->cbegin(); it != u_succ->cend(); ++it) { - layered_nf->add(*it, layer); - v_vertices.emplace_back(*it); - } - } - // When the above for finishes, we have progress of one half-step (from U to V) in the BFS - u_vertices.clear(); - bool end = false; - for (auto it = v_vertices.cbegin(); it != v_vertices.cend(); it++) - if (v_to_u.at(*it) == null_point_index()) - // we stop when a nearest exposed V vertex (from U exposed vertices) has been found - end = true; - else - u_vertices.emplace_back(v_to_u.at(*it)); - // When the above for finishes, we have progress of one half-step (from V to U) in the BFS - if (end) - return layered_nf; - v_vertices.clear(); - } - return layered_nf; -} - -inline void Graph_matching::update(std::deque& path) { - unmatched_in_u.remove(path.front()); - for (auto it = path.cbegin(); it != path.cend(); ++it) { - // Be careful, the iterator is incremented twice each time - int tmp = *it; - ++it; - v_to_u[*it] = tmp; - } -} - -template -double bottleneck_distance(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e) { - G::initialize(diag1, diag2, e); - std::unique_ptr< std::vector > sd = std::move(G::sorted_distances()); - int idmin = 0; - int idmax = sd->size() - 1; - // alpha can be modified, this will change the complexity - double alpha = pow(sd->size(), 0.25); - Graph_matching m; - Graph_matching biggest_unperfect; - while (idmin != idmax) { - int step = static_cast((idmax - idmin) / alpha); - m.set_r(sd->at(idmin + step)); - while (m.multi_augment()); - // The above while compute a maximum matching (according to the r setted before) - if (m.perfect()) { - idmax = idmin + step; - m = biggest_unperfect; - } else { - biggest_unperfect = m; - idmin = idmin + step + 1; - } - } - return sd->at(idmin); -} - -} // namespace bottleneck - -} // namespace Gudhi - -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ diff --git a/src/Bottleneck/include/gudhi/Grid_cell.h b/src/Bottleneck/include/gudhi/Grid_cell.h deleted file mode 100644 index eee938cb..00000000 --- a/src/Bottleneck/include/gudhi/Grid_cell.h +++ /dev/null @@ -1,188 +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): Francois Godi - * - * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_GRID_CELL_H_ -#define SRC_BOTTLENECK_INCLUDE_GUDHI_GRID_CELL_H_ - -#include -#include -#include - -#include "Persistence_diagrams_graph.h" - -namespace Gudhi { - -namespace bottleneck { - -/** \internal \brief TODO - * - * \ingroup bottleneck_distance - */ -class Grid_cell { -public: - Grid_cell(double r); - void add(int v_point_index); - void remove(int v_point_index); - bool contains(int v_point_index) const; - int pull_center(); - int pull_xi(int u_point_index); - int pull_xd(int u_point_index); - int pull_yi(int u_point_index); - int pull_yd(int u_point_index); - int pull_xi_yi(int u_point_index); - int pull_xi_yd(int u_point_index); - int pull_xd_yi(int u_point_index); - int pull_xd_yd(int u_point_index); - -private: - double r; - std::set xi_order; - std::set yi_order; - struct Hidden_points_tree{int point; std::list hidden;}; - typedef std::map, G::Compare_x> Corner_tree; - Corner_tree xi_yi_order; - Corner_tree xi_yd_order; - Corner_tree xd_yi_order; - Corner_tree xd_yd_order; - void remove_aux(Corner_tree t, int v_point_index); - void build_xi_yi(); - void build_xi_yd(); - void build_xd_yi(); - void build_xd_yd(); -}; - - -inline Grid_cell::Grid_cell(double r) - : r(r), xi_order(G::Compare_x(r)), yi_order(G::Compare_y(r)), xi_yi_order(G::Compare_x(r)), - xi_yd_order(G::Compare_x(r)), xd_yi_order(G::Compare_x(r)), xd_yd_order(G::Compare_x(r)) {} - -inline void Grid_cell::add(int v_point_index){ - xi_order.emplace(v_point_index); -} - -inline bool Grid_cell::contains(int v_point_index) const{ - return (xi_order.count(v_point_index) > 0); -} - -inline void Grid_cell::remove_aux(Corner_tree t, int v_point_index){ - if(t.empty()) - return; - std::list hidden_points = t.at(v_point_index); - t.erase(v_point_index); - for(auto it = hidden_points.begin(); it != hidden_points.end(); ++it) - t.emplace(it->point,it->hidden); - -} - -inline void Grid_cell::remove(int v_point_index){ - xi_order.erase(v_point_index); - yi_order.erase(v_point_index); - remove_aux(xi_yi_order,v_point_index); - remove_aux(xi_yd_order,v_point_index); - remove_aux(xd_yi_order,v_point_index); - remove_aux(xd_yd_order,v_point_index); -} - -//factorization needed \/ \/ \/ - -inline int Grid_cell::pull_center(){ - if(xi_order.empty()) - return null_point_index(); - int v_point_index = *xi_order.begin(); - remove(v_point_index); - return v_point_index; -} - -inline int Grid_cell::pull_xi(int u_point_index){ - if(xi_order.empty()) - return null_point_index(); - int v_point_index = *xi_order.begin(); //! - if(G::distance(u_point_index,v_point_index)<=r){ - remove(v_point_index); - return v_point_index; - } - return null_point_index(); -} - -inline int Grid_cell::pull_xd(int u_point_index){ - if(xi_order.empty()) - return null_point_index(); - int v_point_index = *xi_order.rbegin(); //! - if(G::distance(u_point_index,v_point_index)<=r){ - remove(v_point_index); - return v_point_index; - } - return null_point_index(); -} - -inline int Grid_cell::pull_yi(int u_point_index){ - if(xi_order.empty()) - return null_point_index(); - if(yi_order.empty()) - for(auto it = xi_order.begin(); it!= xi_order.end(); ++it) - yi_order.emplace(*it); - int v_point_index = *yi_order.begin(); //! - if(G::distance(u_point_index,v_point_index)<=r){ - remove(v_point_index); - return v_point_index; - } - return null_point_index(); -} - -inline int Grid_cell::pull_yd(int u_point_index){ - if(xi_order.empty()) - return null_point_index(); - if(yi_order.empty()) - for(auto it = xi_order.begin(); it!= xi_order.end(); ++it) - yi_order.emplace(*it); - int v_point_index = *yi_order.rbegin(); //! - if(G::distance(u_point_index,v_point_index)<=r){ - remove(v_point_index); - return v_point_index; - } - return null_point_index(); -} - -inline int Grid_cell::pull_xi_yi(int u_point_index){ - if(xi_order.empty()) - return null_point_index(); - if(xi_yi_order.empty()) - build_xi_yi(); - auto it = xi_yi_order.upper_bound(u_point_index+G::size()); - if(it==xi_yi_order.cbegin()) //! - return null_point_index(); - it--; //! - int v_point_index = it->first; - for(auto it2=it->second.begin();it2!=it->second.end();it2++) - xi_yi_order.emplace(it2->point,it2->hidden); - if(G::distance(u_point_index,v_point_index)<=r){ - remove(v_point_index); - return v_point_index; - } - return null_point_index(); -} - -} // namespace bottleneck - -} // namespace Gudhi - -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_GRID_CELL_H_ diff --git a/src/Bottleneck/include/gudhi/Layered_neighbors_finder.h b/src/Bottleneck/include/gudhi/Layered_neighbors_finder.h deleted file mode 100644 index 58805b86..00000000 --- a/src/Bottleneck/include/gudhi/Layered_neighbors_finder.h +++ /dev/null @@ -1,80 +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): Francois Godi - * - * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_LAYERED_NEIGHBORS_FINDER_H_ -#define SRC_BOTTLENECK_INCLUDE_GUDHI_LAYERED_NEIGHBORS_FINDER_H_ - -#include - -#include "Neighbors_finder.h" - -namespace Gudhi { - -namespace bottleneck { - -/** \internal \brief data structure used to find any point (including projections) in V near to a query point from U - * (which can be a projection) in a layered graph layer given as parmeter. - * - * V points have to be added manually using their index and before the first pull. A neighbor pulled is automatically removed. - * - * \ingroup bottleneck_distance - */ -class Layered_neighbors_finder { -public: - /** \internal \brief Constructor taking the near distance definition as parameter. */ - Layered_neighbors_finder(double r); - /** \internal \brief A point added will be possibly pulled. */ - void add(int v_point_index, int vlayer); - /** \internal \brief Returns and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ - int pull_near(int u_point_index, int vlayer); - /** \internal \brief Returns the number of layers. */ - int vlayers_number() const; - -private: - const double r; - std::vector neighbors_finder; -}; - -inline Layered_neighbors_finder::Layered_neighbors_finder(double r) : - r(r), neighbors_finder() { } - -inline void Layered_neighbors_finder::add(int v_point_index, int vlayer) { - for (int l = neighbors_finder.size(); l <= vlayer; l++) - neighbors_finder.emplace_back(Neighbors_finder(r)); - neighbors_finder.at(vlayer).add(v_point_index); -} - -inline int Layered_neighbors_finder::pull_near(int u_point_index, int vlayer) { - if (static_cast (neighbors_finder.size()) <= vlayer) - return null_point_index(); - return neighbors_finder.at(vlayer).pull_near(u_point_index); -} - -inline int Layered_neighbors_finder::vlayers_number() const { - return static_cast(neighbors_finder.size()); -} - -} // namespace bottleneck - -} // namespace Gudhi - -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_LAYERED_NEIGHBORS_FINDER_H_ diff --git a/src/Bottleneck/include/gudhi/Neighbors_finder.h b/src/Bottleneck/include/gudhi/Neighbors_finder.h deleted file mode 100644 index be81877a..00000000 --- a/src/Bottleneck/include/gudhi/Neighbors_finder.h +++ /dev/null @@ -1,114 +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): Francois Godi - * - * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_ -#define SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_ - -#include -#include - -#include "Planar_neighbors_finder.h" - -namespace Gudhi { - -namespace bottleneck { - -/** \internal \brief data structure used to find any point (including projections) in V near to a query point from U - * (which can be a projection). - * - * V points have to be added manually using their index and before the first pull. A neighbor pulled is automatically removed. - * - * \ingroup bottleneck_distance - */ -class Neighbors_finder { -public: - /** \internal \brief Constructor taking the near distance definition as parameter. */ - Neighbors_finder(double r); - /** \internal \brief A point added will be possibly pulled. */ - void add(int v_point_index); - /** \internal \brief Returns and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ - int pull_near(int u_point_index); - /** \internal \brief Returns and remove all the V points near to the U point given as parameter. */ - std::unique_ptr< std::list > pull_all_near(int u_point_index); - -private: - const double r; - Planar_neighbors_finder planar_neighbors_f; - std::unordered_set projections_f; - void remove(int v_point_index); - bool contains(int v_point_index); -}; - -inline Neighbors_finder::Neighbors_finder(double r) : - r(r), planar_neighbors_f(r), projections_f() { } - -inline void Neighbors_finder::add(int v_point_index) { - if (G::on_the_v_diagonal(v_point_index)) - projections_f.emplace(v_point_index); - else - planar_neighbors_f.add(v_point_index); -} - -inline void Neighbors_finder::remove(int v_point_index) { - if(v_point_index == null_point_index()) - return; - if (G::on_the_v_diagonal(v_point_index)) - projections_f.erase(v_point_index); - else - planar_neighbors_f.remove(v_point_index); -} - -inline bool Neighbors_finder::contains(int v_point_index) { - return planar_neighbors_f.contains(v_point_index) || (projections_f.count(v_point_index)>0); -} - -inline int Neighbors_finder::pull_near(int u_point_index) { - int tmp; - int c = G::corresponding_point_in_v(u_point_index); - if (G::on_the_u_diagonal(u_point_index) && !projections_f.empty()) - //All projections are at distance 0 - tmp = *projections_f.cbegin(); - else if (contains(c) && (G::distance(u_point_index, c) <= r)) - //Is the query point near to its projection ? - tmp = c; - else - //Is the query point near to a V point in the plane ? - tmp = planar_neighbors_f.pull_near(u_point_index); - remove(tmp); - return tmp; -} - -inline std::unique_ptr< std::list > Neighbors_finder::pull_all_near(int u_point_index) { - std::unique_ptr< std::list > all_pull = std::move(planar_neighbors_f.pull_all_near(u_point_index)); - int last_pull = pull_near(u_point_index); - while (last_pull != null_point_index()) { - all_pull->emplace_back(last_pull); - last_pull = pull_near(u_point_index); - } - return all_pull; -} - -} // namespace bottleneck - -} // namespace Gudhi - -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_ diff --git a/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h b/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h deleted file mode 100644 index aed328e2..00000000 --- a/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h +++ /dev/null @@ -1,190 +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): Francois Godi - * - * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_ -#define SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_ - -#include -#include -#include -#include -#include -#include - -namespace Gudhi { - -namespace bottleneck { - -/** \internal \brief Returns the used index for encoding none of the points */ -int null_point_index(); - -/** \internal \brief Structure representing an euclidean bipartite graph containing - * the points from the two persistence diagrams (including the projections). - * - * \ingroup bottleneck_distance - */ -class Persistence_diagrams_graph { -public: - /** \internal \brief Initializer taking 2 Point (concept) ranges as parameters. */ - template - static void initialize(const Persistence_diagram1& diag1, const Persistence_diagram2& diag2, double e); - /** \internal \brief Is the given point from U the projection of a point in V ? */ - static bool on_the_u_diagonal(int u_point_index); - /** \internal \brief Is the given point from V the projection of a point in U ? */ - static bool on_the_v_diagonal(int v_point_index); - /** \internal \brief Given a point from V, returns the corresponding (projection or projector) point in U. */ - static int corresponding_point_in_u(int v_point_index); - /** \internal \brief Given a point from U, returns the corresponding (projection or projector) point in V. */ - static int corresponding_point_in_v(int u_point_index); - /** \internal \brief Given a point from U and a point from V, returns the distance between those points. */ - static double distance(int u_point_index, int v_point_index); - /** \internal \brief Returns size = |U| = |V|. */ - static int size(); - /** \internal \brief Returns the O(n^2) sorted distances between the points. */ - static std::unique_ptr< std::vector > sorted_distances(); - /** \internal \brief Compare points regarding x%r coordinate. Use v_point_index for V points and u_point_index + G::size() for U points. */ - struct Compare_x{double r; Compare_x(double r); bool operator()(const int point_index_1, const int point_index_2) const;}; - /** \internal \brief Compare points regarding y%r coordinate. Use v_point_index for V points and u_point_index + G::size() for U points. */ - struct Compare_y{double r; Compare_y(double r);bool operator()(const int point_index_1, const int point_index_2) const;}; - -private: - /** \internal \typedef \brief Internal_point is the internal points representation, indexes used outside. */ - typedef std::pair Internal_point; - static std::vector u; - static std::vector v; - static Internal_point get_u_point(int u_point_index); - static Internal_point get_v_point(int v_point_index); -}; - -/** \internal \typedef \brief Shorter alias */ -typedef Persistence_diagrams_graph G; - -// static initialization, seems to work but strange -std::vector G::u = [] {return std::vector();}(); -std::vector G::v = [] {return std::vector();}(); - -inline int null_point_index() { - return -1; -} - -template -inline void G::initialize(const Persistence_diagram1 &diag1, - const Persistence_diagram2 &diag2, double e){ - u.clear(); - v.clear(); - for (auto it = diag1.cbegin(); it != diag1.cend(); ++it) - if (it->second - it->first > e) - u.emplace_back(*it); - for (auto it = diag2.cbegin(); it != diag2.cend(); ++it) - if (it->second - it->first > e) - v.emplace_back(*it); - if (u.size() < v.size()) - swap(u, v); -} - -inline bool G::on_the_u_diagonal(int u_point_index) { - return u_point_index >= static_cast (u.size()); -} - -inline bool G::on_the_v_diagonal(int v_point_index) { - return v_point_index >= static_cast (v.size()); -} - -inline int G::corresponding_point_in_u(int v_point_index) { - return on_the_v_diagonal(v_point_index) ? - v_point_index - static_cast (v.size()) : v_point_index + static_cast (u.size()); -} - -inline int G::corresponding_point_in_v(int u_point_index) { - return on_the_u_diagonal(u_point_index) ? - u_point_index - static_cast (u.size()) : u_point_index + static_cast (v.size()); -} - -inline double G::distance(int u_point_index, int v_point_index) { - if (on_the_u_diagonal(u_point_index) && on_the_v_diagonal(v_point_index)) - return 0; - Internal_point p_u = get_u_point(u_point_index); - Internal_point p_v = get_v_point(v_point_index); - return std::max(std::fabs(p_u.first - p_v.first), std::fabs(p_u.second - p_v.second)); -} - -inline int G::size() { - return static_cast (u.size() + v.size()); -} - -inline std::unique_ptr< std::vector > G::sorted_distances() { - // could be optimized - std::set sorted_distances; - for (int u_point_index = 0; u_point_index < size(); ++u_point_index) - for (int v_point_index = 0; v_point_index < size(); ++v_point_index) - sorted_distances.emplace(distance(u_point_index, v_point_index)); - std::unique_ptr< std::vector > sd_up(new std::vector(sorted_distances.cbegin(), sorted_distances.cend())); - return sd_up; -} - -inline G::Internal_point G::get_u_point(int u_point_index) { - if (!on_the_u_diagonal(u_point_index)) - return u.at(u_point_index); - Internal_point projector = v.at(corresponding_point_in_v(u_point_index)); - double x = (projector.first + projector.second) / 2; - return Internal_point(x, x); -} - -inline G::Internal_point G::get_v_point(int v_point_index) { - if (!on_the_v_diagonal(v_point_index)) - return v.at(v_point_index); - Internal_point projector = u.at(corresponding_point_in_u(v_point_index)); - double x = (projector.first + projector.second) / 2; - return Internal_point(x, x); -} - -G::Compare_x::Compare_x(double r) - : r(r){ } - -G::Compare_y::Compare_y(double r) - : r(r){ } - -inline bool G::Compare_x::operator()(const int point_index_1, const int point_index_2) const{ - G::Internal_point p1 = point_index_1 < G::size() ? G::get_v_point(point_index_1) : G::get_u_point(point_index_1 - G::size()); - G::Internal_point p2 = point_index_2 < G::size() ? G::get_v_point(point_index_2) : G::get_u_point(point_index_2 - G::size()); - double x1 = fmod(p1.first,r); - double x2 = fmod(p2.first,r); - if(x1 == x2) - return point_index_1 > point_index_2; - return x1 < x2; -} - -inline bool G::Compare_y::operator()(const int point_index_1, const int point_index_2) const{ - G::Internal_point p1 = point_index_1 < G::size() ? G::get_v_point(point_index_1) : G::get_u_point(point_index_1 - G::size()); - G::Internal_point p2 = point_index_2 < G::size() ? G::get_v_point(point_index_2) : G::get_u_point(point_index_2 - G::size()); - double y1 = fmod(p1.second,r); - double y2 = fmod(p2.second,r); - if(y1 == y2) - return point_index_1 > point_index_2; - return y1 < y2; -} - -} // namespace bottleneck - -} // namespace Gudhi - -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_ diff --git a/src/Bottleneck/include/gudhi/Planar_neighbors_finder.h b/src/Bottleneck/include/gudhi/Planar_neighbors_finder.h deleted file mode 100644 index e403735c..00000000 --- a/src/Bottleneck/include/gudhi/Planar_neighbors_finder.h +++ /dev/null @@ -1,132 +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): Francois Godi - * - * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_ -#define SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_ - -#include -#include - -#include "Persistence_diagrams_graph.h" -#include "Grid_cell.h" - -namespace Gudhi { - -namespace bottleneck { - -/** \internal \brief Structure used to find any point in V near (according to the planar distance) to a query point from U. - * - * V points have to be added manually using their index and before the first remove/pull. A neighbor pulled is automatically removed. but we can also - * remove points manually using their index. - * - * \ingroup bottleneck_distance - */ -class Abstract_planar_neighbors_finder { -public: - /** \internal \brief Constructor TODO. */ - Abstract_planar_neighbors_finder(double r); - virtual ~Abstract_planar_neighbors_finder() = 0; - /** \internal \brief A point added will be possibly pulled. */ - virtual void add(int v_point_index) = 0; - /** \internal \brief A point manually removed will no longer be possibly pulled. */ - virtual void remove(int v_point_index) = 0; - /** \internal \brief Can the point given as parameter be returned ? */ - virtual bool contains(int v_point_index) const = 0; - /** \internal \brief Provide and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ - virtual int pull_near(int u_point_index) = 0; - /** \internal \brief Provide and remove all the V points near to the U point given as parameter. */ - virtual std::unique_ptr< std::list > pull_all_near(int u_point_index); - -protected: - const double r; -}; - -/** \internal \brief Naive_pnf is an naïve Abstract_planar_neighbors_finder implementation - * - * \ingroup bottleneck_distance - */ -class Naive_pnf : public Abstract_planar_neighbors_finder { -public: - /** \internal \brief Constructor taking the near distance definition as parameter. */ - Naive_pnf(double r); - /** \internal \brief A point added will be possibly pulled. */ - void add(int v_point_index); - /** \internal \brief A point manually removed will no longer be possibly pulled. */ - void remove(int v_point_index); - /** \internal \brief Can the point given as parameter be returned ? */ - bool contains(int v_point_index) const; - /** \internal \brief Provide and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ - int pull_near(int u_point_index); - -private: - std::set candidates; -}; - -/** \internal \typedef \brief Planar_neighbors_finder is the used Abstract_planar_neighbors_finder's implementation. */ -typedef Naive_pnf Planar_neighbors_finder; - - -inline Abstract_planar_neighbors_finder::Abstract_planar_neighbors_finder(double r) : - r(r) { } - -inline Abstract_planar_neighbors_finder::~Abstract_planar_neighbors_finder() {} - -inline std::unique_ptr< std::list > Abstract_planar_neighbors_finder::pull_all_near(int u_point_index) { - std::unique_ptr< std::list > all_pull(new std::list); - int last_pull = pull_near(u_point_index); - while (last_pull != null_point_index()) { - all_pull->emplace_back(last_pull); - last_pull = pull_near(u_point_index); - } - return all_pull; -} - -inline Naive_pnf::Naive_pnf(double r) : - Abstract_planar_neighbors_finder(r), candidates() { } - -inline void Naive_pnf::add(int v_point_index) { - candidates.emplace(v_point_index); -} - -inline void Naive_pnf::remove(int v_point_index) { - candidates.erase(v_point_index); -} - -inline bool Naive_pnf::contains(int v_point_index) const { - return (candidates.count(v_point_index) > 0); -} - -inline int Naive_pnf::pull_near(int u_point_index) { - for (auto it = candidates.begin(); it != candidates.end(); ++it) - if (G::distance(u_point_index, *it) <= r) { - int tmp = *it; - candidates.erase(it); - return tmp; - } - return null_point_index(); -} - -} // namespace bottleneck - -} // namespace Gudhi - -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_ diff --git a/src/Bottleneck/test/CMakeLists.txt b/src/Bottleneck/test/CMakeLists.txt deleted file mode 100644 index 8e4371b8..00000000 --- a/src/Bottleneck/test/CMakeLists.txt +++ /dev/null @@ -1,31 +0,0 @@ -cmake_minimum_required(VERSION 2.6) -project(GUDHIBottleneckUT) - -if (GCOVR_PATH) - # for gcovr to make coverage reports - Corbera Jenkins plugin - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage") - set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage") - set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage") -endif() -if (GPROF_PATH) - # for gprof to make coverage reports - Jenkins - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") - set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg") - set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg") -endif() - message("CMAKE_CXX_FLAGS = ${CMAKE_CXX_FLAGS}") - message("CMAKE_CXX_FLAGS_DEBUG = ${CMAKE_CXX_FLAGS_DEBUG}") - message("CMAKE_CXX_FLAGS_RELEASE = ${CMAKE_CXX_FLAGS_RELEASE}") - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O2 -std=c++11 -Wall -Wpedantic -Wsign-compare") - set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -ggdb -O0") - set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE}") - -add_executable ( BottleneckUT bottleneck_unit_test.cpp ) -target_link_libraries(BottleneckUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) - -# Unitary tests -add_test(NAME BottleneckUT - COMMAND ${CMAKE_CURRENT_BINARY_DIR}/BottleneckUT - # XML format for Jenkins xUnit plugin - --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/BottleneckUT.xml --log_level=test_suite --report_level=no) - diff --git a/src/Bottleneck/test/README b/src/Bottleneck/test/README deleted file mode 100644 index 0e7b8673..00000000 --- a/src/Bottleneck/test/README +++ /dev/null @@ -1,12 +0,0 @@ -To compile: -*********** - -cmake . -make - -To launch with details: -*********************** - -./BottleneckUnitTest --report_level=detailed --log_level=all - - ==> echo $? returns 0 in case of success (non-zero otherwise) diff --git a/src/Bottleneck/test/bottleneck_unit_test.cpp b/src/Bottleneck/test/bottleneck_unit_test.cpp deleted file mode 100644 index 926c8430..00000000 --- a/src/Bottleneck/test/bottleneck_unit_test.cpp +++ /dev/null @@ -1,171 +0,0 @@ -#define BOOST_TEST_MODULE bottleneck test - -#include -#include -#include "../include/gudhi/Graph_matching.h" - -using namespace Gudhi::bottleneck; - -int n1 = 81; // a natural number >0 -int n2 = 180; // a natural number >0 -double upper_bound = 400.5; // any real >0 - -BOOST_AUTO_TEST_CASE(global){ - std::uniform_real_distribution unif1(0.,upper_bound); - std::uniform_real_distribution unif2(upper_bound/1000.,upper_bound/100.); - std::default_random_engine re; - std::vector< std::pair > v1, v2; - for (int i = 0; i < n1; i++) { - double a = unif1(re); - double b = unif1(re); - double x = unif2(re); - double y = unif2(re); - v1.emplace_back(std::min(a,b), std::max(a,b)); - v2.emplace_back(std::min(a,b)+std::min(x,y), std::max(a,b)+std::max(x,y)); - if(i%5==0) - v1.emplace_back(std::min(a,b),std::min(a,b)+x); - if(i%3==0) - v2.emplace_back(std::max(a,b),std::max(a,b)+y); - } - BOOST_CHECK(bottleneck_distance(v1, v2) <= upper_bound/100.); -} - -BOOST_AUTO_TEST_CASE(persistence_diagrams_graph){ - // Random construction - std::uniform_real_distribution unif(0.,upper_bound); - std::default_random_engine re; - std::vector< std::pair > v1, v2; - for (int i = 0; i < n1; i++) { - double a = unif(re); - double b = unif(re); - v1.emplace_back(std::min(a,b), std::max(a,b)); - } - for (int i = 0; i < n2; i++) { - double a = unif(re); - double b = unif(re); - v2.emplace_back(std::min(a,b), std::max(a,b)); - } - G::initialize(v1, v2, 0.); - std::unique_ptr< std::vector > d = std::move(G::sorted_distances()); - // - BOOST_CHECK(!G::on_the_u_diagonal(n1-1)); - BOOST_CHECK(!G::on_the_u_diagonal(n1)); - BOOST_CHECK(!G::on_the_u_diagonal(n2-1)); - BOOST_CHECK(G::on_the_u_diagonal(n2)); - BOOST_CHECK(!G::on_the_v_diagonal(n1-1)); - BOOST_CHECK(G::on_the_v_diagonal(n1)); - BOOST_CHECK(G::on_the_v_diagonal(n2-1)); - BOOST_CHECK(G::on_the_v_diagonal(n2)); - // - BOOST_CHECK(G::corresponding_point_in_u(0)==n2); - BOOST_CHECK(G::corresponding_point_in_u(n1)==0); - BOOST_CHECK(G::corresponding_point_in_v(0)==n1); - BOOST_CHECK(G::corresponding_point_in_v(n2)==0); - // - BOOST_CHECK(G::size()==(n1+n2)); - // - BOOST_CHECK((int) d->size() <= (n1+n2)*(n1+n2) - n1*n2 + 1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,0))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n1-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n2-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n2))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,(n1+n2)-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,0))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n1-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n2-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n2))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,(n1+n2)-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,0))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n1-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n2-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n2))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,(n1+n2)-1))==1); -} - - -BOOST_AUTO_TEST_CASE(planar_neighbors_finder) { - Planar_neighbors_finder pnf = Planar_neighbors_finder(1.); - for(int v_point_index=0; v_point_index l = *pnf.pull_all_near(n2/2); - bool v = true; - for(auto it = l.cbegin(); it != l.cend(); ++it) - v = v && (G::distance(n2/2,*it)>1.); - BOOST_CHECK(v); - int v_point_index_2 = pnf.pull_near(n2/2); - BOOST_CHECK(v_point_index_2 == -1); -} - - -BOOST_AUTO_TEST_CASE(neighbors_finder) { - Neighbors_finder nf = Neighbors_finder(1.); - for(int v_point_index=1; v_point_index<((n2+n1)*9/10); v_point_index+=2) - nf.add(v_point_index); - // - int v_point_index_1 = nf.pull_near(n2/2); - BOOST_CHECK((v_point_index_1 == -1) || (G::distance(n2/2,v_point_index_1)<=1.)); - std::list l = *nf.pull_all_near(n2/2); - bool v = true; - for(auto it = l.cbegin(); it != l.cend(); ++it) - v = v && (G::distance(n2/2,*it)>1.); - BOOST_CHECK(v); - int v_point_index_2 = nf.pull_near(n2/2); - BOOST_CHECK(v_point_index_2 == -1); -} - -BOOST_AUTO_TEST_CASE(layered_neighbors_finder) { - Layered_neighbors_finder lnf = Layered_neighbors_finder(1.); - for(int v_point_index=1; v_point_index<((n2+n1)*9/10); v_point_index+=2) - lnf.add(v_point_index, v_point_index % 7); - // - int v_point_index_1 = lnf.pull_near(n2/2,6); - BOOST_CHECK((v_point_index_1 == -1) || (G::distance(n2/2,v_point_index_1)<=1.)); - int v_point_index_2 = lnf.pull_near(n2/2,6); - BOOST_CHECK(v_point_index_2 == -1); - v_point_index_1 = lnf.pull_near(n2/2,0); - BOOST_CHECK((v_point_index_1 == -1) || (G::distance(n2/2,v_point_index_1)<=1.)); - v_point_index_2 = lnf.pull_near(n2/2,0); - BOOST_CHECK(v_point_index_2 == -1); -} - -BOOST_AUTO_TEST_CASE(graph_matching) { - Graph_matching m1; - m1.set_r(0.); - int e = 0; - while (m1.multi_augment()) - ++e; - BOOST_CHECK(e <= 2*sqrt(2*(n1+n2))); - Graph_matching m2 = m1; - BOOST_CHECK(!m2.multi_augment()); - m2.set_r(upper_bound); - e = 0; - while (m2.multi_augment()) - ++e; - BOOST_CHECK(e <= 2*sqrt(2*(n1+n2))); - BOOST_CHECK(m2.perfect()); - BOOST_CHECK(!m1.perfect()); -} - -BOOST_AUTO_TEST_CASE(grid_cell) { - -} -- cgit v1.2.3 From 936b0edbee931d8145729e08bbde2b053c82e637 Mon Sep 17 00:00:00 2001 From: fgodi Date: Tue, 30 Jun 2015 05:59:11 +0000 Subject: non du namespace git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@662 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 889d4646f58d2eec59f790bc2a101d1e0e7a87b7 --- src/Bipartite_graph_matching/include/gudhi/Graph_matching.h | 4 ++-- src/Bipartite_graph_matching/include/gudhi/Grid_cell.h | 4 ++-- src/Bipartite_graph_matching/include/gudhi/Layered_neighbors_finder.h | 4 ++-- src/Bipartite_graph_matching/include/gudhi/Neighbors_finder.h | 4 ++-- .../include/gudhi/Persistence_diagrams_graph.h | 4 ++-- src/Bipartite_graph_matching/include/gudhi/Planar_neighbors_finder.h | 4 ++-- 6 files changed, 12 insertions(+), 12 deletions(-) (limited to 'src') diff --git a/src/Bipartite_graph_matching/include/gudhi/Graph_matching.h b/src/Bipartite_graph_matching/include/gudhi/Graph_matching.h index 2bcc6a61..46a5f375 100644 --- a/src/Bipartite_graph_matching/include/gudhi/Graph_matching.h +++ b/src/Bipartite_graph_matching/include/gudhi/Graph_matching.h @@ -31,7 +31,7 @@ namespace Gudhi { -namespace bottleneck { +namespace bipartite_graph_matching { /** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams. * @@ -209,7 +209,7 @@ double bottleneck_distance(const Persistence_diagram1 &diag1, const Persistence_ return sd->at(idmin); } -} // namespace bottleneck +} // namespace bipartite_graph_matching } // namespace Gudhi diff --git a/src/Bipartite_graph_matching/include/gudhi/Grid_cell.h b/src/Bipartite_graph_matching/include/gudhi/Grid_cell.h index eee938cb..e9cf08b9 100644 --- a/src/Bipartite_graph_matching/include/gudhi/Grid_cell.h +++ b/src/Bipartite_graph_matching/include/gudhi/Grid_cell.h @@ -31,7 +31,7 @@ namespace Gudhi { -namespace bottleneck { +namespace bipartite_graph_matching { /** \internal \brief TODO * @@ -181,7 +181,7 @@ inline int Grid_cell::pull_xi_yi(int u_point_index){ return null_point_index(); } -} // namespace bottleneck +} // namespace bipartite_graph_matching } // namespace Gudhi diff --git a/src/Bipartite_graph_matching/include/gudhi/Layered_neighbors_finder.h b/src/Bipartite_graph_matching/include/gudhi/Layered_neighbors_finder.h index 58805b86..8303627a 100644 --- a/src/Bipartite_graph_matching/include/gudhi/Layered_neighbors_finder.h +++ b/src/Bipartite_graph_matching/include/gudhi/Layered_neighbors_finder.h @@ -29,7 +29,7 @@ namespace Gudhi { -namespace bottleneck { +namespace bipartite_graph_matching { /** \internal \brief data structure used to find any point (including projections) in V near to a query point from U * (which can be a projection) in a layered graph layer given as parmeter. @@ -73,7 +73,7 @@ inline int Layered_neighbors_finder::vlayers_number() const { return static_cast(neighbors_finder.size()); } -} // namespace bottleneck +} // namespace bipartite_graph_matching } // namespace Gudhi diff --git a/src/Bipartite_graph_matching/include/gudhi/Neighbors_finder.h b/src/Bipartite_graph_matching/include/gudhi/Neighbors_finder.h index be81877a..879ba300 100644 --- a/src/Bipartite_graph_matching/include/gudhi/Neighbors_finder.h +++ b/src/Bipartite_graph_matching/include/gudhi/Neighbors_finder.h @@ -30,7 +30,7 @@ namespace Gudhi { -namespace bottleneck { +namespace bipartite_graph_matching { /** \internal \brief data structure used to find any point (including projections) in V near to a query point from U * (which can be a projection). @@ -107,7 +107,7 @@ inline std::unique_ptr< std::list > Neighbors_finder::pull_all_near(int u_p return all_pull; } -} // namespace bottleneck +} // namespace bipartite_graph_matching } // namespace Gudhi diff --git a/src/Bipartite_graph_matching/include/gudhi/Persistence_diagrams_graph.h b/src/Bipartite_graph_matching/include/gudhi/Persistence_diagrams_graph.h index aed328e2..1b23a1b2 100644 --- a/src/Bipartite_graph_matching/include/gudhi/Persistence_diagrams_graph.h +++ b/src/Bipartite_graph_matching/include/gudhi/Persistence_diagrams_graph.h @@ -32,7 +32,7 @@ namespace Gudhi { -namespace bottleneck { +namespace bipartite_graph_matching { /** \internal \brief Returns the used index for encoding none of the points */ int null_point_index(); @@ -183,7 +183,7 @@ inline bool G::Compare_y::operator()(const int point_index_1, const int point_in return y1 < y2; } -} // namespace bottleneck +} // namespace bipartite_graph_matching } // namespace Gudhi diff --git a/src/Bipartite_graph_matching/include/gudhi/Planar_neighbors_finder.h b/src/Bipartite_graph_matching/include/gudhi/Planar_neighbors_finder.h index e403735c..60a1dd96 100644 --- a/src/Bipartite_graph_matching/include/gudhi/Planar_neighbors_finder.h +++ b/src/Bipartite_graph_matching/include/gudhi/Planar_neighbors_finder.h @@ -31,7 +31,7 @@ namespace Gudhi { -namespace bottleneck { +namespace bipartite_graph_matching { /** \internal \brief Structure used to find any point in V near (according to the planar distance) to a query point from U. * @@ -125,7 +125,7 @@ inline int Naive_pnf::pull_near(int u_point_index) { return null_point_index(); } -} // namespace bottleneck +} // namespace bipartite_graph_matching } // namespace Gudhi -- cgit v1.2.3 From 4dfa2f897553c172fa142ceb72bca8667a247996 Mon Sep 17 00:00:00 2001 From: fgodi Date: Tue, 30 Jun 2015 06:35:42 +0000 Subject: test2 git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@663 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 7bff8467274d6c4177d8c6e9dc58f5276ca2a550 --- .../include/gudhi/Grid_cell.h | 22 ++++++++++++++++++++-- 1 file changed, 20 insertions(+), 2 deletions(-) (limited to 'src') diff --git a/src/Bipartite_graph_matching/include/gudhi/Grid_cell.h b/src/Bipartite_graph_matching/include/gudhi/Grid_cell.h index e9cf08b9..6a970b16 100644 --- a/src/Bipartite_graph_matching/include/gudhi/Grid_cell.h +++ b/src/Bipartite_graph_matching/include/gudhi/Grid_cell.h @@ -63,7 +63,10 @@ private: Corner_tree xi_yd_order; Corner_tree xd_yi_order; Corner_tree xd_yd_order; - void remove_aux(Corner_tree t, int v_point_index); + void remove_aux(Corner_tree t, int v_point_index, bool reverse); + template + int pull_contiguous_aux(); + int pull_corner_aux(); void build_xi_yi(); void build_xi_yd(); void build_xd_yi(); @@ -83,7 +86,7 @@ inline bool Grid_cell::contains(int v_point_index) const{ return (xi_order.count(v_point_index) > 0); } -inline void Grid_cell::remove_aux(Corner_tree t, int v_point_index){ +inline void Grid_cell::remove_aux(Corner_tree t, int v_point_index, bool reverse){ if(t.empty()) return; std::list hidden_points = t.at(v_point_index); @@ -102,6 +105,21 @@ inline void Grid_cell::remove(int v_point_index){ remove_aux(xd_yd_order,v_point_index); } +template +inline int Grid_cell::pull_contiguous_aux(Contiguous_tree t, bool reverse){ + if(xi_order.empty()) + return null_point_index(); + if(t.empty()) + for(auto it = xi_order.begin(); it!= xi_order.end(); ++it) + t.emplace(*it); + int v_point_index = reverse ? *(t.rbegin()) : *(t.begin()); + if(G::distance(u_point_index,v_point_index)<=r){ + remove(v_point_index); + return v_point_index; + } + return null_point_index(); +} + //factorization needed \/ \/ \/ inline int Grid_cell::pull_center(){ -- cgit v1.2.3 From a79d06bc9ffb42e0281b5d25cb55170b564f5574 Mon Sep 17 00:00:00 2001 From: fgodi Date: Tue, 30 Jun 2015 15:15:36 +0000 Subject: two classes merged git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@667 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: f344cff04db17902f1a74d857037d0f9aeb05686 --- .../include/gudhi/Graph_matching.h | 2 +- .../include/gudhi/Grid_cell.h | 128 +++++++++++---------- .../include/gudhi/Layered_neighbors_finder.h | 80 ------------- .../include/gudhi/Neighbors_finder.h | 42 +++++++ 4 files changed, 110 insertions(+), 142 deletions(-) delete mode 100644 src/Bipartite_graph_matching/include/gudhi/Layered_neighbors_finder.h (limited to 'src') diff --git a/src/Bipartite_graph_matching/include/gudhi/Graph_matching.h b/src/Bipartite_graph_matching/include/gudhi/Graph_matching.h index 46a5f375..9cd8d75a 100644 --- a/src/Bipartite_graph_matching/include/gudhi/Graph_matching.h +++ b/src/Bipartite_graph_matching/include/gudhi/Graph_matching.h @@ -27,7 +27,7 @@ #include #include -#include "Layered_neighbors_finder.h" +#include "Neighbors_finder.h" namespace Gudhi { diff --git a/src/Bipartite_graph_matching/include/gudhi/Grid_cell.h b/src/Bipartite_graph_matching/include/gudhi/Grid_cell.h index 6a970b16..8745e6eb 100644 --- a/src/Bipartite_graph_matching/include/gudhi/Grid_cell.h +++ b/src/Bipartite_graph_matching/include/gudhi/Grid_cell.h @@ -63,14 +63,10 @@ private: Corner_tree xi_yd_order; Corner_tree xd_yi_order; Corner_tree xd_yd_order; - void remove_aux(Corner_tree t, int v_point_index, bool reverse); - template - int pull_contiguous_aux(); - int pull_corner_aux(); - void build_xi_yi(); - void build_xi_yd(); - void build_xd_yi(); - void build_xd_yd(); + void remove_aux(Corner_tree t, int v_point_index); + template + int pull_contiguous_aux(Contiguous_tree t, bool reverse, int u_point_index); + //int pull_corner_aux(Corner_tree t, bool reverse, int u_point_index); }; @@ -86,7 +82,7 @@ inline bool Grid_cell::contains(int v_point_index) const{ return (xi_order.count(v_point_index) > 0); } -inline void Grid_cell::remove_aux(Corner_tree t, int v_point_index, bool reverse){ +inline void Grid_cell::remove_aux(Corner_tree t, int v_point_index){ if(t.empty()) return; std::list hidden_points = t.at(v_point_index); @@ -105,8 +101,8 @@ inline void Grid_cell::remove(int v_point_index){ remove_aux(xd_yd_order,v_point_index); } -template -inline int Grid_cell::pull_contiguous_aux(Contiguous_tree t, bool reverse){ +template +inline int Grid_cell::pull_contiguous_aux(Contiguous_tree t, bool reverse, int u_point_index){ if(xi_order.empty()) return null_point_index(); if(t.empty()) @@ -120,85 +116,95 @@ inline int Grid_cell::pull_contiguous_aux(Contiguous_tree t, bool reverse){ return null_point_index(); } -//factorization needed \/ \/ \/ - inline int Grid_cell::pull_center(){ if(xi_order.empty()) return null_point_index(); - int v_point_index = *xi_order.begin(); + int v_point_index = *(xi_order.begin()); remove(v_point_index); return v_point_index; } inline int Grid_cell::pull_xi(int u_point_index){ - if(xi_order.empty()) - return null_point_index(); - int v_point_index = *xi_order.begin(); //! - if(G::distance(u_point_index,v_point_index)<=r){ - remove(v_point_index); - return v_point_index; - } - return null_point_index(); + return pull_contiguous_aux(xi_order, false, u_point_index); } inline int Grid_cell::pull_xd(int u_point_index){ - if(xi_order.empty()) - return null_point_index(); - int v_point_index = *xi_order.rbegin(); //! - if(G::distance(u_point_index,v_point_index)<=r){ - remove(v_point_index); - return v_point_index; - } - return null_point_index(); + return pull_contiguous_aux(xi_order, true, u_point_index); } inline int Grid_cell::pull_yi(int u_point_index){ - if(xi_order.empty()) - return null_point_index(); - if(yi_order.empty()) - for(auto it = xi_order.begin(); it!= xi_order.end(); ++it) - yi_order.emplace(*it); - int v_point_index = *yi_order.begin(); //! - if(G::distance(u_point_index,v_point_index)<=r){ - remove(v_point_index); - return v_point_index; - } - return null_point_index(); + return pull_contiguous_aux(yi_order, false, u_point_index); } inline int Grid_cell::pull_yd(int u_point_index){ - if(xi_order.empty()) - return null_point_index(); - if(yi_order.empty()) - for(auto it = xi_order.begin(); it!= xi_order.end(); ++it) - yi_order.emplace(*it); - int v_point_index = *yi_order.rbegin(); //! - if(G::distance(u_point_index,v_point_index)<=r){ - remove(v_point_index); - return v_point_index; - } - return null_point_index(); + return pull_contiguous_aux(yi_order, true, u_point_index); } - -inline int Grid_cell::pull_xi_yi(int u_point_index){ - if(xi_order.empty()) +/* +inline int Grid_cell::pull_corner_aux(Corner_tree t, bool reverse, int u_point_index){ + if(xi_order.empty()) return null_point_index(); - if(xi_yi_order.empty()) - build_xi_yi(); - auto it = xi_yi_order.upper_bound(u_point_index+G::size()); - if(it==xi_yi_order.cbegin()) //! + if(t.empty()) + build_corner(t); + auto it = t.upper_bound(u_point_index+G::size()); + if(it == (reverse ? t.end() : t.begin())) return null_point_index(); - it--; //! + if(!reverse) + it--; int v_point_index = it->first; for(auto it2=it->second.begin();it2!=it->second.end();it2++) - xi_yi_order.emplace(it2->point,it2->hidden); + t.emplace(it2->point,it2->hidden); if(G::distance(u_point_index,v_point_index)<=r){ remove(v_point_index); return v_point_index; } return null_point_index(); +}*/ + +inline int Grid_cell::pull_xi_yi(int u_point_index){ + for(auto it = xi_order.begin(); it!=xi_order.end(); ++it) + if(G::distance(u_point_index,*it)<=r){ + int tmp = *it; + remove(tmp); + return tmp; + } + return(null_point_index()); + //return pull_corner_aux(xi_yi_order, false, u_point_index); +} + +inline int Grid_cell::pull_xi_yd(int u_point_index){ + for(auto it = xi_order.begin(); it!=xi_order.end(); ++it) + if(G::distance(u_point_index,*it)<=r){ + int tmp = *it; + remove(tmp); + return tmp; + } + return(null_point_index()); + //return pull_corner_aux(xi_yd_order, false, u_point_index); } +inline int Grid_cell::pull_xd_yi(int u_point_index){ + for(auto it = xi_order.rbegin(); it!=xi_order.rend(); ++it) + if(G::distance(u_point_index,*it)<=r){ + int tmp = *it; + remove(tmp); + return tmp; + } + return(null_point_index()); + //return pull_corner_aux(xd_yi_order, true, u_point_index); +} + +inline int Grid_cell::pull_xd_yd(int u_point_index){ + for(auto it = xi_order.begin(); it!=xi_order.end(); ++it) + if(G::distance(u_point_index,*it)<=r){ + int tmp = *it; + remove(tmp); + return tmp; + } + return(null_point_index()); + //return pull_corner_aux(xd_yd_order, true, u_point_index); +} + + } // namespace bipartite_graph_matching } // namespace Gudhi diff --git a/src/Bipartite_graph_matching/include/gudhi/Layered_neighbors_finder.h b/src/Bipartite_graph_matching/include/gudhi/Layered_neighbors_finder.h deleted file mode 100644 index 8303627a..00000000 --- a/src/Bipartite_graph_matching/include/gudhi/Layered_neighbors_finder.h +++ /dev/null @@ -1,80 +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): Francois Godi - * - * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_LAYERED_NEIGHBORS_FINDER_H_ -#define SRC_BOTTLENECK_INCLUDE_GUDHI_LAYERED_NEIGHBORS_FINDER_H_ - -#include - -#include "Neighbors_finder.h" - -namespace Gudhi { - -namespace bipartite_graph_matching { - -/** \internal \brief data structure used to find any point (including projections) in V near to a query point from U - * (which can be a projection) in a layered graph layer given as parmeter. - * - * V points have to be added manually using their index and before the first pull. A neighbor pulled is automatically removed. - * - * \ingroup bottleneck_distance - */ -class Layered_neighbors_finder { -public: - /** \internal \brief Constructor taking the near distance definition as parameter. */ - Layered_neighbors_finder(double r); - /** \internal \brief A point added will be possibly pulled. */ - void add(int v_point_index, int vlayer); - /** \internal \brief Returns and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ - int pull_near(int u_point_index, int vlayer); - /** \internal \brief Returns the number of layers. */ - int vlayers_number() const; - -private: - const double r; - std::vector neighbors_finder; -}; - -inline Layered_neighbors_finder::Layered_neighbors_finder(double r) : - r(r), neighbors_finder() { } - -inline void Layered_neighbors_finder::add(int v_point_index, int vlayer) { - for (int l = neighbors_finder.size(); l <= vlayer; l++) - neighbors_finder.emplace_back(Neighbors_finder(r)); - neighbors_finder.at(vlayer).add(v_point_index); -} - -inline int Layered_neighbors_finder::pull_near(int u_point_index, int vlayer) { - if (static_cast (neighbors_finder.size()) <= vlayer) - return null_point_index(); - return neighbors_finder.at(vlayer).pull_near(u_point_index); -} - -inline int Layered_neighbors_finder::vlayers_number() const { - return static_cast(neighbors_finder.size()); -} - -} // namespace bipartite_graph_matching - -} // namespace Gudhi - -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_LAYERED_NEIGHBORS_FINDER_H_ diff --git a/src/Bipartite_graph_matching/include/gudhi/Neighbors_finder.h b/src/Bipartite_graph_matching/include/gudhi/Neighbors_finder.h index 879ba300..cae47793 100644 --- a/src/Bipartite_graph_matching/include/gudhi/Neighbors_finder.h +++ b/src/Bipartite_graph_matching/include/gudhi/Neighbors_finder.h @@ -58,6 +58,29 @@ private: bool contains(int v_point_index); }; +/** \internal \brief data structure used to find any point (including projections) in V near to a query point from U + * (which can be a projection) in a layered graph layer given as parmeter. + * + * V points have to be added manually using their index and before the first pull. A neighbor pulled is automatically removed. + * + * \ingroup bottleneck_distance + */ +class Layered_neighbors_finder { +public: + /** \internal \brief Constructor taking the near distance definition as parameter. */ + Layered_neighbors_finder(double r); + /** \internal \brief A point added will be possibly pulled. */ + void add(int v_point_index, int vlayer); + /** \internal \brief Returns and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ + int pull_near(int u_point_index, int vlayer); + /** \internal \brief Returns the number of layers. */ + int vlayers_number() const; + +private: + const double r; + std::vector neighbors_finder; +}; + inline Neighbors_finder::Neighbors_finder(double r) : r(r), planar_neighbors_f(r), projections_f() { } @@ -107,6 +130,25 @@ inline std::unique_ptr< std::list > Neighbors_finder::pull_all_near(int u_p return all_pull; } +inline Layered_neighbors_finder::Layered_neighbors_finder(double r) : + r(r), neighbors_finder() { } + +inline void Layered_neighbors_finder::add(int v_point_index, int vlayer) { + for (int l = neighbors_finder.size(); l <= vlayer; l++) + neighbors_finder.emplace_back(Neighbors_finder(r)); + neighbors_finder.at(vlayer).add(v_point_index); +} + +inline int Layered_neighbors_finder::pull_near(int u_point_index, int vlayer) { + if (static_cast (neighbors_finder.size()) <= vlayer) + return null_point_index(); + return neighbors_finder.at(vlayer).pull_near(u_point_index); +} + +inline int Layered_neighbors_finder::vlayers_number() const { + return static_cast(neighbors_finder.size()); +} + } // namespace bipartite_graph_matching } // namespace Gudhi -- cgit v1.2.3 From 835b8ac56556a71e39738775d2d2572cba03a5e4 Mon Sep 17 00:00:00 2001 From: fgodi Date: Tue, 30 Jun 2015 16:34:18 +0000 Subject: before rm Grid_Cell git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@668 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: bfa8c56429a2d4a9f38822ac9cfbe4c4b360cede --- .../include/gudhi/Graph_matching.h | 2 - .../include/gudhi/Grid_cell.h | 10 ++--- .../include/gudhi/Neighbors_finder.h | 1 - .../include/gudhi/Persistence_diagrams_graph.h | 32 +-------------- .../include/gudhi/Planar_neighbors_finder.h | 45 ++++++++++++++++------ 5 files changed, 39 insertions(+), 51 deletions(-) (limited to 'src') diff --git a/src/Bipartite_graph_matching/include/gudhi/Graph_matching.h b/src/Bipartite_graph_matching/include/gudhi/Graph_matching.h index 9cd8d75a..5133646d 100644 --- a/src/Bipartite_graph_matching/include/gudhi/Graph_matching.h +++ b/src/Bipartite_graph_matching/include/gudhi/Graph_matching.h @@ -24,8 +24,6 @@ #define SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ #include -#include -#include #include "Neighbors_finder.h" diff --git a/src/Bipartite_graph_matching/include/gudhi/Grid_cell.h b/src/Bipartite_graph_matching/include/gudhi/Grid_cell.h index 8745e6eb..f0b09b52 100644 --- a/src/Bipartite_graph_matching/include/gudhi/Grid_cell.h +++ b/src/Bipartite_graph_matching/include/gudhi/Grid_cell.h @@ -33,10 +33,7 @@ namespace Gudhi { namespace bipartite_graph_matching { -/** \internal \brief TODO - * - * \ingroup bottleneck_distance - */ + class Grid_cell { public: Grid_cell(double r); @@ -139,7 +136,7 @@ inline int Grid_cell::pull_yi(int u_point_index){ inline int Grid_cell::pull_yd(int u_point_index){ return pull_contiguous_aux(yi_order, true, u_point_index); } -/* + inline int Grid_cell::pull_corner_aux(Corner_tree t, bool reverse, int u_point_index){ if(xi_order.empty()) return null_point_index(); @@ -158,7 +155,7 @@ inline int Grid_cell::pull_corner_aux(Corner_tree t, bool reverse, int u_point_i return v_point_index; } return null_point_index(); -}*/ +} inline int Grid_cell::pull_xi_yi(int u_point_index){ for(auto it = xi_order.begin(); it!=xi_order.end(); ++it) @@ -210,3 +207,4 @@ inline int Grid_cell::pull_xd_yd(int u_point_index){ } // namespace Gudhi #endif // SRC_BOTTLENECK_INCLUDE_GUDHI_GRID_CELL_H_ + diff --git a/src/Bipartite_graph_matching/include/gudhi/Neighbors_finder.h b/src/Bipartite_graph_matching/include/gudhi/Neighbors_finder.h index cae47793..78b9debc 100644 --- a/src/Bipartite_graph_matching/include/gudhi/Neighbors_finder.h +++ b/src/Bipartite_graph_matching/include/gudhi/Neighbors_finder.h @@ -24,7 +24,6 @@ #define SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_ #include -#include #include "Planar_neighbors_finder.h" diff --git a/src/Bipartite_graph_matching/include/gudhi/Persistence_diagrams_graph.h b/src/Bipartite_graph_matching/include/gudhi/Persistence_diagrams_graph.h index 1b23a1b2..a1fe9285 100644 --- a/src/Bipartite_graph_matching/include/gudhi/Persistence_diagrams_graph.h +++ b/src/Bipartite_graph_matching/include/gudhi/Persistence_diagrams_graph.h @@ -61,10 +61,6 @@ public: static int size(); /** \internal \brief Returns the O(n^2) sorted distances between the points. */ static std::unique_ptr< std::vector > sorted_distances(); - /** \internal \brief Compare points regarding x%r coordinate. Use v_point_index for V points and u_point_index + G::size() for U points. */ - struct Compare_x{double r; Compare_x(double r); bool operator()(const int point_index_1, const int point_index_2) const;}; - /** \internal \brief Compare points regarding y%r coordinate. Use v_point_index for V points and u_point_index + G::size() for U points. */ - struct Compare_y{double r; Compare_y(double r);bool operator()(const int point_index_1, const int point_index_2) const;}; private: /** \internal \typedef \brief Internal_point is the internal points representation, indexes used outside. */ @@ -73,6 +69,8 @@ private: static std::vector v; static Internal_point get_u_point(int u_point_index); static Internal_point get_v_point(int v_point_index); + + friend class Naive_pnf; }; /** \internal \typedef \brief Shorter alias */ @@ -157,32 +155,6 @@ inline G::Internal_point G::get_v_point(int v_point_index) { return Internal_point(x, x); } -G::Compare_x::Compare_x(double r) - : r(r){ } - -G::Compare_y::Compare_y(double r) - : r(r){ } - -inline bool G::Compare_x::operator()(const int point_index_1, const int point_index_2) const{ - G::Internal_point p1 = point_index_1 < G::size() ? G::get_v_point(point_index_1) : G::get_u_point(point_index_1 - G::size()); - G::Internal_point p2 = point_index_2 < G::size() ? G::get_v_point(point_index_2) : G::get_u_point(point_index_2 - G::size()); - double x1 = fmod(p1.first,r); - double x2 = fmod(p2.first,r); - if(x1 == x2) - return point_index_1 > point_index_2; - return x1 < x2; -} - -inline bool G::Compare_y::operator()(const int point_index_1, const int point_index_2) const{ - G::Internal_point p1 = point_index_1 < G::size() ? G::get_v_point(point_index_1) : G::get_u_point(point_index_1 - G::size()); - G::Internal_point p2 = point_index_2 < G::size() ? G::get_v_point(point_index_2) : G::get_u_point(point_index_2 - G::size()); - double y1 = fmod(p1.second,r); - double y2 = fmod(p2.second,r); - if(y1 == y2) - return point_index_1 > point_index_2; - return y1 < y2; -} - } // namespace bipartite_graph_matching } // namespace Gudhi diff --git a/src/Bipartite_graph_matching/include/gudhi/Planar_neighbors_finder.h b/src/Bipartite_graph_matching/include/gudhi/Planar_neighbors_finder.h index 60a1dd96..50829be6 100644 --- a/src/Bipartite_graph_matching/include/gudhi/Planar_neighbors_finder.h +++ b/src/Bipartite_graph_matching/include/gudhi/Planar_neighbors_finder.h @@ -24,7 +24,7 @@ #define SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_ #include -#include +#include #include "Persistence_diagrams_graph.h" #include "Grid_cell.h" @@ -78,7 +78,8 @@ public: int pull_near(int u_point_index); private: - std::set candidates; + std::pair get_v_key(int v_point_index) const; + std::multimap,int> grid; }; /** \internal \typedef \brief Planar_neighbors_finder is the used Abstract_planar_neighbors_finder's implementation. */ @@ -101,27 +102,47 @@ inline std::unique_ptr< std::list > Abstract_planar_neighbors_finder::pull_ } inline Naive_pnf::Naive_pnf(double r) : - Abstract_planar_neighbors_finder(r), candidates() { } + Abstract_planar_neighbors_finder(r), grid() { } + + +inline std::pair Naive_pnf::get_v_key(int v_point_index) const{ + G::Internal_point v_point = G::get_v_point(v_point_index); + return std::make_pair(static_cast(v_point.first/r), static_cast(v_point.second/r)); +} inline void Naive_pnf::add(int v_point_index) { - candidates.emplace(v_point_index); + grid.emplace(get_v_key(v_point_index),v_point_index); } inline void Naive_pnf::remove(int v_point_index) { - candidates.erase(v_point_index); + for(auto it = grid.find(get_v_key(v_point_index)); it!=grid.end(); it++) + if(it->second==v_point_index){ + grid.erase(it); + return; + } } inline bool Naive_pnf::contains(int v_point_index) const { - return (candidates.count(v_point_index) > 0); + if(v_point_index == null_point_index()) + return false; + for(auto it = grid.find(get_v_key(v_point_index)); it!=grid.end(); it++) + if(it->second==v_point_index) + return true; + return false; } inline int Naive_pnf::pull_near(int u_point_index) { - for (auto it = candidates.begin(); it != candidates.end(); ++it) - if (G::distance(u_point_index, *it) <= r) { - int tmp = *it; - candidates.erase(it); - return tmp; - } + G::Internal_point u_point = G::get_u_point(u_point_index); + int i0 = static_cast(u_point.first/r); + int j0 = static_cast(u_point.second/r); + for(int i = i0 -1; i<= i0 + 1; i++) + for(int j = j0 -1; j<= j0 + 1; j++) + for(auto it = grid.find(std::make_pair(i,j)); it!=grid.end(); it++) + if (G::distance(u_point_index, it->second) <= r) { + int tmp = it->second; + grid.erase(it); + return tmp; + } return null_point_index(); } -- cgit v1.2.3 From de45f2d9bb77f0256c1ae36b3c1f99afebd3ec2d Mon Sep 17 00:00:00 2001 From: fgodi Date: Tue, 30 Jun 2015 16:35:20 +0000 Subject: rm Grid_Cell (this sub-algorithm doesn't work) :( git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@669 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: ae3e4c7bf16676fd2335c2813dbc1d1e939eecd8 --- .../include/gudhi/Grid_cell.h | 210 --------------------- 1 file changed, 210 deletions(-) delete mode 100644 src/Bipartite_graph_matching/include/gudhi/Grid_cell.h (limited to 'src') diff --git a/src/Bipartite_graph_matching/include/gudhi/Grid_cell.h b/src/Bipartite_graph_matching/include/gudhi/Grid_cell.h deleted file mode 100644 index f0b09b52..00000000 --- a/src/Bipartite_graph_matching/include/gudhi/Grid_cell.h +++ /dev/null @@ -1,210 +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): Francois Godi - * - * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_GRID_CELL_H_ -#define SRC_BOTTLENECK_INCLUDE_GUDHI_GRID_CELL_H_ - -#include -#include -#include - -#include "Persistence_diagrams_graph.h" - -namespace Gudhi { - -namespace bipartite_graph_matching { - - -class Grid_cell { -public: - Grid_cell(double r); - void add(int v_point_index); - void remove(int v_point_index); - bool contains(int v_point_index) const; - int pull_center(); - int pull_xi(int u_point_index); - int pull_xd(int u_point_index); - int pull_yi(int u_point_index); - int pull_yd(int u_point_index); - int pull_xi_yi(int u_point_index); - int pull_xi_yd(int u_point_index); - int pull_xd_yi(int u_point_index); - int pull_xd_yd(int u_point_index); - -private: - double r; - std::set xi_order; - std::set yi_order; - struct Hidden_points_tree{int point; std::list hidden;}; - typedef std::map, G::Compare_x> Corner_tree; - Corner_tree xi_yi_order; - Corner_tree xi_yd_order; - Corner_tree xd_yi_order; - Corner_tree xd_yd_order; - void remove_aux(Corner_tree t, int v_point_index); - template - int pull_contiguous_aux(Contiguous_tree t, bool reverse, int u_point_index); - //int pull_corner_aux(Corner_tree t, bool reverse, int u_point_index); -}; - - -inline Grid_cell::Grid_cell(double r) - : r(r), xi_order(G::Compare_x(r)), yi_order(G::Compare_y(r)), xi_yi_order(G::Compare_x(r)), - xi_yd_order(G::Compare_x(r)), xd_yi_order(G::Compare_x(r)), xd_yd_order(G::Compare_x(r)) {} - -inline void Grid_cell::add(int v_point_index){ - xi_order.emplace(v_point_index); -} - -inline bool Grid_cell::contains(int v_point_index) const{ - return (xi_order.count(v_point_index) > 0); -} - -inline void Grid_cell::remove_aux(Corner_tree t, int v_point_index){ - if(t.empty()) - return; - std::list hidden_points = t.at(v_point_index); - t.erase(v_point_index); - for(auto it = hidden_points.begin(); it != hidden_points.end(); ++it) - t.emplace(it->point,it->hidden); - -} - -inline void Grid_cell::remove(int v_point_index){ - xi_order.erase(v_point_index); - yi_order.erase(v_point_index); - remove_aux(xi_yi_order,v_point_index); - remove_aux(xi_yd_order,v_point_index); - remove_aux(xd_yi_order,v_point_index); - remove_aux(xd_yd_order,v_point_index); -} - -template -inline int Grid_cell::pull_contiguous_aux(Contiguous_tree t, bool reverse, int u_point_index){ - if(xi_order.empty()) - return null_point_index(); - if(t.empty()) - for(auto it = xi_order.begin(); it!= xi_order.end(); ++it) - t.emplace(*it); - int v_point_index = reverse ? *(t.rbegin()) : *(t.begin()); - if(G::distance(u_point_index,v_point_index)<=r){ - remove(v_point_index); - return v_point_index; - } - return null_point_index(); -} - -inline int Grid_cell::pull_center(){ - if(xi_order.empty()) - return null_point_index(); - int v_point_index = *(xi_order.begin()); - remove(v_point_index); - return v_point_index; -} - -inline int Grid_cell::pull_xi(int u_point_index){ - return pull_contiguous_aux(xi_order, false, u_point_index); -} - -inline int Grid_cell::pull_xd(int u_point_index){ - return pull_contiguous_aux(xi_order, true, u_point_index); -} - -inline int Grid_cell::pull_yi(int u_point_index){ - return pull_contiguous_aux(yi_order, false, u_point_index); -} - -inline int Grid_cell::pull_yd(int u_point_index){ - return pull_contiguous_aux(yi_order, true, u_point_index); -} - -inline int Grid_cell::pull_corner_aux(Corner_tree t, bool reverse, int u_point_index){ - if(xi_order.empty()) - return null_point_index(); - if(t.empty()) - build_corner(t); - auto it = t.upper_bound(u_point_index+G::size()); - if(it == (reverse ? t.end() : t.begin())) - return null_point_index(); - if(!reverse) - it--; - int v_point_index = it->first; - for(auto it2=it->second.begin();it2!=it->second.end();it2++) - t.emplace(it2->point,it2->hidden); - if(G::distance(u_point_index,v_point_index)<=r){ - remove(v_point_index); - return v_point_index; - } - return null_point_index(); -} - -inline int Grid_cell::pull_xi_yi(int u_point_index){ - for(auto it = xi_order.begin(); it!=xi_order.end(); ++it) - if(G::distance(u_point_index,*it)<=r){ - int tmp = *it; - remove(tmp); - return tmp; - } - return(null_point_index()); - //return pull_corner_aux(xi_yi_order, false, u_point_index); -} - -inline int Grid_cell::pull_xi_yd(int u_point_index){ - for(auto it = xi_order.begin(); it!=xi_order.end(); ++it) - if(G::distance(u_point_index,*it)<=r){ - int tmp = *it; - remove(tmp); - return tmp; - } - return(null_point_index()); - //return pull_corner_aux(xi_yd_order, false, u_point_index); -} - -inline int Grid_cell::pull_xd_yi(int u_point_index){ - for(auto it = xi_order.rbegin(); it!=xi_order.rend(); ++it) - if(G::distance(u_point_index,*it)<=r){ - int tmp = *it; - remove(tmp); - return tmp; - } - return(null_point_index()); - //return pull_corner_aux(xd_yi_order, true, u_point_index); -} - -inline int Grid_cell::pull_xd_yd(int u_point_index){ - for(auto it = xi_order.begin(); it!=xi_order.end(); ++it) - if(G::distance(u_point_index,*it)<=r){ - int tmp = *it; - remove(tmp); - return tmp; - } - return(null_point_index()); - //return pull_corner_aux(xd_yd_order, true, u_point_index); -} - - -} // namespace bipartite_graph_matching - -} // namespace Gudhi - -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_GRID_CELL_H_ - -- cgit v1.2.3 From 438f5078b455f4b8dfbe0b5ed217685f6c50260c Mon Sep 17 00:00:00 2001 From: fgodi Date: Tue, 30 Jun 2015 17:21:39 +0000 Subject: base ok git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@671 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 4bbba1a0309a98403ebc22cbdf68865c5c8f5d79 --- .../test/bottleneck_unit_test.cpp | 42 ++++++++++++++++++++-- 1 file changed, 39 insertions(+), 3 deletions(-) (limited to 'src') diff --git a/src/Bipartite_graph_matching/test/bottleneck_unit_test.cpp b/src/Bipartite_graph_matching/test/bottleneck_unit_test.cpp index 926c8430..dc33f76b 100644 --- a/src/Bipartite_graph_matching/test/bottleneck_unit_test.cpp +++ b/src/Bipartite_graph_matching/test/bottleneck_unit_test.cpp @@ -4,7 +4,10 @@ #include #include "../include/gudhi/Graph_matching.h" -using namespace Gudhi::bottleneck; +#include +#include + +using namespace Gudhi::bipartite_graph_matching; int n1 = 81; // a natural number >0 int n2 = 180; // a natural number >0 @@ -27,7 +30,8 @@ BOOST_AUTO_TEST_CASE(global){ if(i%3==0) v2.emplace_back(std::max(a,b),std::max(a,b)+y); } - BOOST_CHECK(bottleneck_distance(v1, v2) <= upper_bound/100.); + //99.5 and not 100 to avoid float errors. + BOOST_CHECK(bottleneck_distance(v1, v2) <= upper_bound/99.5); } BOOST_AUTO_TEST_CASE(persistence_diagrams_graph){ @@ -166,6 +170,38 @@ BOOST_AUTO_TEST_CASE(graph_matching) { BOOST_CHECK(!m1.perfect()); } -BOOST_AUTO_TEST_CASE(grid_cell) { +/* +BOOST_AUTO_TEST_CASE(chrono) { + std::ofstream objetfichier; + objetfichier.open("results.csv", std::ios::out); + + for(int n =50; n<=1000; n+=100){ + std::uniform_real_distribution unif1(0.,upper_bound); + std::uniform_real_distribution unif2(upper_bound/1000.,upper_bound/100.); + std::default_random_engine re; + std::vector< std::pair > v1, v2; + for (int i = 0; i < n; i++) { + double a = unif1(re); + double b = unif1(re); + double x = unif2(re); + double y = unif2(re); + v1.emplace_back(std::min(a,b), std::max(a,b)); + v2.emplace_back(std::min(a,b)+std::min(x,y), std::max(a,b)+std::max(x,y)); + if(i%5==0) + v1.emplace_back(std::min(a,b),std::min(a,b)+x); + if(i%3==0) + v2.emplace_back(std::max(a,b),std::max(a,b)+y); + } + + std::chrono::steady_clock::time_point start = std::chrono::steady_clock::now(); + double b = bottleneck_distance(v1,v2); + std::chrono::steady_clock::time_point end = std::chrono::steady_clock::now(); + typedef std::chrono::duration millisecs_t; + millisecs_t duration(std::chrono::duration_cast(end-start)); + objetfichier << n << ";" << duration.count() << ";" << b << std::endl; + } + objetfichier.close(); } +*/ + -- cgit v1.2.3 From 42a123c74255be2e2471eb35fd9226ceea5a011c Mon Sep 17 00:00:00 2001 From: fgodi Date: Fri, 3 Jul 2015 18:03:02 +0000 Subject: envelope tree git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@675 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 7a66384ac0aaa5678d87d2a0b1eb59a45cbaf8ee --- src/Bipartite_graph_matching/example/example.cpp | 2 +- .../include/gudhi/Graph_matching.h | 3 +-- .../include/gudhi/Persistence_diagrams_graph.h | 1 + .../include/gudhi/Planar_neighbors_finder.h | 26 ++++++++++++++++++---- 4 files changed, 25 insertions(+), 7 deletions(-) (limited to 'src') diff --git a/src/Bipartite_graph_matching/example/example.cpp b/src/Bipartite_graph_matching/example/example.cpp index 683f7723..d190ab48 100644 --- a/src/Bipartite_graph_matching/example/example.cpp +++ b/src/Bipartite_graph_matching/example/example.cpp @@ -23,7 +23,7 @@ #include "../include/gudhi/Graph_matching.h" #include -using namespace Gudhi::bottleneck; +using namespace Gudhi::bipartite_graph_matching; int main() { diff --git a/src/Bipartite_graph_matching/include/gudhi/Graph_matching.h b/src/Bipartite_graph_matching/include/gudhi/Graph_matching.h index 5133646d..a2754333 100644 --- a/src/Bipartite_graph_matching/include/gudhi/Graph_matching.h +++ b/src/Bipartite_graph_matching/include/gudhi/Graph_matching.h @@ -176,8 +176,7 @@ inline void Graph_matching::update(std::deque& path) { for (auto it = path.cbegin(); it != path.cend(); ++it) { // Be careful, the iterator is incremented twice each time int tmp = *it; - ++it; - v_to_u[*it] = tmp; + v_to_u[*(++it)] = tmp; } } diff --git a/src/Bipartite_graph_matching/include/gudhi/Persistence_diagrams_graph.h b/src/Bipartite_graph_matching/include/gudhi/Persistence_diagrams_graph.h index a1fe9285..1f8e83e7 100644 --- a/src/Bipartite_graph_matching/include/gudhi/Persistence_diagrams_graph.h +++ b/src/Bipartite_graph_matching/include/gudhi/Persistence_diagrams_graph.h @@ -71,6 +71,7 @@ private: static Internal_point get_v_point(int v_point_index); friend class Naive_pnf; + friend class Upper_envelope_tree; }; /** \internal \typedef \brief Shorter alias */ diff --git a/src/Bipartite_graph_matching/include/gudhi/Planar_neighbors_finder.h b/src/Bipartite_graph_matching/include/gudhi/Planar_neighbors_finder.h index 50829be6..32155b91 100644 --- a/src/Bipartite_graph_matching/include/gudhi/Planar_neighbors_finder.h +++ b/src/Bipartite_graph_matching/include/gudhi/Planar_neighbors_finder.h @@ -27,7 +27,7 @@ #include #include "Persistence_diagrams_graph.h" -#include "Grid_cell.h" +#include "Envelope_tree.h" namespace Gudhi { @@ -76,6 +76,8 @@ public: bool contains(int v_point_index) const; /** \internal \brief Provide and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ int pull_near(int u_point_index); + /** \internal \brief Provide and remove all the V points near to the U point given as parameter. */ + virtual std::unique_ptr< std::list > pull_all_near(int u_point_index); private: std::pair get_v_key(int v_point_index) const; @@ -135,9 +137,9 @@ inline int Naive_pnf::pull_near(int u_point_index) { G::Internal_point u_point = G::get_u_point(u_point_index); int i0 = static_cast(u_point.first/r); int j0 = static_cast(u_point.second/r); - for(int i = i0 -1; i<= i0 + 1; i++) - for(int j = j0 -1; j<= j0 + 1; j++) - for(auto it = grid.find(std::make_pair(i,j)); it!=grid.end(); it++) + for(int i = 1; i<= 3; i++) + for(int j = 1; j<= 3; j++) + for(auto it = grid.find(std::make_pair(i0 +(i%3)-1, j0+(j%3)-1)); it!=grid.end(); it++) if (G::distance(u_point_index, it->second) <= r) { int tmp = it->second; grid.erase(it); @@ -146,6 +148,22 @@ inline int Naive_pnf::pull_near(int u_point_index) { return null_point_index(); } +inline std::unique_ptr< std::list > Naive_pnf::pull_all_near(int u_point_index) { + std::unique_ptr< std::list > all_pull(new std::list); + G::Internal_point u_point = G::get_u_point(u_point_index); + int i0 = static_cast(u_point.first/r); + int j0 = static_cast(u_point.second/r); + for(int i = 1; i<= 3; i++) + for(int j = 1; j<= 3; j++) + for(auto it = grid.find(std::make_pair(i0 +(i%3)-1, j0+(j%3)-1)); it!=grid.end(); it++) + if (G::distance(u_point_index, it->second) <= r) { + int tmp = it->second; + grid.erase(it); + all_pull->emplace_back(tmp); + } + return all_pull; +} + } // namespace bipartite_graph_matching } // namespace Gudhi -- cgit v1.2.3 From fa1ff1284f51341d452b6adc3a667d13a5d35747 Mon Sep 17 00:00:00 2001 From: fgodi Date: Mon, 4 Apr 2016 13:14:31 +0000 Subject: cmake lists git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@1092 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 77b2a427cb3ff80b9a0c5d1c71f9f1de11547530 --- CMakeLists.txt | 19 +- build/CMakeCache.txt | 453 ++ build/CMakeFiles/3.0.2/CMakeCCompiler.cmake | 58 + build/CMakeFiles/3.0.2/CMakeCXXCompiler.cmake | 59 + 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create mode 100644 src/Bipartite_graphs_matching/test/README create mode 100644 src/Bipartite_graphs_matching/test/bottleneck_unit_test.cpp (limited to 'src') diff --git a/CMakeLists.txt b/CMakeLists.txt index f30c1785..6ed0aedd 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -42,7 +42,6 @@ if (GPROF_PATH) message("gprof found in ${GPROF_PATH}") endif() - if(NOT Boost_FOUND) message(FATAL_ERROR "NOTICE: This demo requires Boost and will not be compiled.") else() @@ -75,12 +74,24 @@ else() add_subdirectory(src/Hasse_complex/example) add_subdirectory(src/Alpha_shapes/example) add_subdirectory(src/Alpha_shapes/test) - add_subdirectory(src/Bottleneck/example) - add_subdirectory(src/Bottleneck/test) + add_subdirectory(src/Bipartite_graphs_matching/example) + add_subdirectory(src/Bipartite_graphs_matching/test) # data points generator add_subdirectory(data/points/generator) -endif() +endif() +include( ${CGAL_USE_FILE} ) +# In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten. +# cf. http://doc.cgal.org/latest/Manual/installation.html#title40 +# A workaround is to add "-std=c++11" again. +if(NOT MSVC) +include(CheckCXXCompilerFlag) +CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11) +if(COMPILER_SUPPORTS_CXX11) +set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") +endif() +endif() +# - End of workaround diff --git a/build/CMakeCache.txt b/build/CMakeCache.txt new file mode 100644 index 00000000..5e7a923a --- /dev/null +++ b/build/CMakeCache.txt @@ -0,0 +1,453 @@ +# This is the CMakeCache file. +# For build in directory: /home/frg/Bureau/mWorkingDirectory/build +# It was generated by CMake: /usr/bin/cmake +# You can edit this file to change values found and used by cmake. +# If you do not want to change any of the values, simply exit the editor. +# If you do want to change a value, simply edit, save, and exit the editor. +# The syntax for the file is as follows: +# KEY:TYPE=VALUE +# KEY is the name of a variable in the cache. +# TYPE is a hint to GUIs for the type of VALUE, DO NOT EDIT TYPE!. +# VALUE is the current value for the KEY. + +######################## +# EXTERNAL cache entries +######################## + +//The threading library used by boost-thread +BOOST_THREAD_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libpthread.so + +//Activate the debug messages of the script FindBoost +Boost_DEBUG:BOOL=OFF + +//The directory containing a CMake configuration file for Boost. +Boost_DIR:PATH=Boost_DIR-NOTFOUND + +//Path to a file. +Boost_INCLUDE_DIR:PATH=/usr/include + +//Boost library directory +Boost_LIBRARY_DIR:PATH=/usr/lib/x86_64-linux-gnu + +//Link with static Boost libraries +CGAL_Boost_USE_STATIC_LIBS:BOOL=OFF + +//The directory containing a CMake configuration file for CGAL. +CGAL_DIR:PATH=/usr/local/lib/CGAL + +//Set this to TRUE if you want to define or modify any of CMAKE_*_FLAGS. +// When this is FALSE, all the CMAKE_*_FLAGS flags are overriden +// with the values used when building the CGAL libs. 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define COMPILER_ID "TinyCC" + +#elif defined(__SCO_VERSION__) +# define COMPILER_ID "SCO" + +#elif defined(__GNUC__) +# define COMPILER_ID "GNU" +# define COMPILER_VERSION_MAJOR DEC(__GNUC__) +# define COMPILER_VERSION_MINOR DEC(__GNUC_MINOR__) +# if defined(__GNUC_PATCHLEVEL__) +# define COMPILER_VERSION_PATCH DEC(__GNUC_PATCHLEVEL__) +# endif + +#elif defined(_MSC_VER) +# define COMPILER_ID "MSVC" + /* _MSC_VER = VVRR */ +# define COMPILER_VERSION_MAJOR DEC(_MSC_VER / 100) +# define COMPILER_VERSION_MINOR DEC(_MSC_VER % 100) +# if defined(_MSC_FULL_VER) +# if _MSC_VER >= 1400 + /* _MSC_FULL_VER = VVRRPPPPP */ +# define COMPILER_VERSION_PATCH DEC(_MSC_FULL_VER % 100000) +# else + /* _MSC_FULL_VER = VVRRPPPP */ +# define COMPILER_VERSION_PATCH DEC(_MSC_FULL_VER % 10000) +# endif +# endif +# if defined(_MSC_BUILD) +# define COMPILER_VERSION_TWEAK DEC(_MSC_BUILD) +# endif + +/* Analog VisualDSP++ >= 4.5.6 */ +#elif defined(__VISUALDSPVERSION__) +# define COMPILER_ID "ADSP" + /* __VISUALDSPVERSION__ = 0xVVRRPP00 */ +# define COMPILER_VERSION_MAJOR HEX(__VISUALDSPVERSION__>>24) +# define COMPILER_VERSION_MINOR HEX(__VISUALDSPVERSION__>>16 & 0xFF) +# define COMPILER_VERSION_PATCH HEX(__VISUALDSPVERSION__>>8 & 0xFF) + +/* Analog VisualDSP++ < 4.5.6 */ +#elif defined(__ADSPBLACKFIN__) || defined(__ADSPTS__) || defined(__ADSP21000__) +# define COMPILER_ID "ADSP" + +/* IAR Systems compiler for embedded systems. + http://www.iar.com */ +#elif defined(__IAR_SYSTEMS_ICC__ ) || defined(__IAR_SYSTEMS_ICC) +# define COMPILER_ID "IAR" + +/* sdcc, the small devices C compiler for embedded systems, + http://sdcc.sourceforge.net */ +#elif defined(SDCC) +# define COMPILER_ID "SDCC" + /* SDCC = VRP */ +# define COMPILER_VERSION_MAJOR DEC(SDCC/100) +# define COMPILER_VERSION_MINOR DEC(SDCC/10 % 10) +# define COMPILER_VERSION_PATCH DEC(SDCC % 10) + +#elif defined(_SGI_COMPILER_VERSION) || defined(_COMPILER_VERSION) +# define COMPILER_ID "MIPSpro" +# if defined(_SGI_COMPILER_VERSION) + /* _SGI_COMPILER_VERSION = VRP */ +# define COMPILER_VERSION_MAJOR DEC(_SGI_COMPILER_VERSION/100) +# define COMPILER_VERSION_MINOR DEC(_SGI_COMPILER_VERSION/10 % 10) +# define COMPILER_VERSION_PATCH DEC(_SGI_COMPILER_VERSION % 10) +# else + /* _COMPILER_VERSION = VRP */ +# define COMPILER_VERSION_MAJOR DEC(_COMPILER_VERSION/100) +# define COMPILER_VERSION_MINOR DEC(_COMPILER_VERSION/10 % 10) +# define COMPILER_VERSION_PATCH DEC(_COMPILER_VERSION % 10) +# endif + +/* This compiler is either not known or is too old to define an + identification macro. Try to identify the platform and guess that + it is the native compiler. */ +#elif defined(__sgi) +# define COMPILER_ID "MIPSpro" + +#elif defined(__hpux) || defined(__hpua) +# define COMPILER_ID "HP" + +#else /* unknown compiler */ +# define COMPILER_ID "" + +#endif + +/* Construct the string literal in pieces to prevent the source from + getting matched. Store it in a pointer rather than an array + because some compilers will just produce instructions to fill the + array rather than assigning a pointer to a static array. */ +char const* info_compiler = "INFO" ":" "compiler[" COMPILER_ID "]"; +#ifdef SIMULATE_ID +char const* info_simulate = "INFO" ":" "simulate[" SIMULATE_ID "]"; +#endif + +#ifdef __QNXNTO__ +char const* qnxnto = "INFO" ":" "qnxnto"; +#endif + +/* Identify known platforms by name. */ +#if defined(__linux) || defined(__linux__) || defined(linux) +# define PLATFORM_ID "Linux" + +#elif defined(__CYGWIN__) +# define PLATFORM_ID "Cygwin" + +#elif defined(__MINGW32__) +# define PLATFORM_ID "MinGW" + +#elif defined(__APPLE__) +# define PLATFORM_ID "Darwin" + +#elif defined(_WIN32) || defined(__WIN32__) || defined(WIN32) +# define PLATFORM_ID "Windows" + +#elif defined(__FreeBSD__) || defined(__FreeBSD) +# define PLATFORM_ID "FreeBSD" + +#elif defined(__NetBSD__) || defined(__NetBSD) +# define PLATFORM_ID "NetBSD" + +#elif defined(__OpenBSD__) || defined(__OPENBSD) +# define PLATFORM_ID "OpenBSD" + +#elif defined(__sun) || defined(sun) +# define PLATFORM_ID "SunOS" + +#elif defined(_AIX) || defined(__AIX) || defined(__AIX__) || defined(__aix) || defined(__aix__) +# define PLATFORM_ID "AIX" + +#elif defined(__sgi) || defined(__sgi__) || defined(_SGI) +# define PLATFORM_ID "IRIX" + +#elif defined(__hpux) || defined(__hpux__) +# define PLATFORM_ID "HP-UX" + +#elif defined(__HAIKU__) +# define PLATFORM_ID "Haiku" + +#elif defined(__BeOS) || defined(__BEOS__) || defined(_BEOS) +# define PLATFORM_ID "BeOS" + +#elif defined(__QNX__) || defined(__QNXNTO__) +# define PLATFORM_ID "QNX" + +#elif defined(__tru64) || defined(_tru64) || defined(__TRU64__) +# define PLATFORM_ID "Tru64" + +#elif defined(__riscos) || defined(__riscos__) +# define PLATFORM_ID "RISCos" + +#elif defined(__sinix) || defined(__sinix__) || defined(__SINIX__) +# define PLATFORM_ID "SINIX" + +#elif defined(__UNIX_SV__) +# define PLATFORM_ID "UNIX_SV" + +#elif defined(__bsdos__) +# define PLATFORM_ID "BSDOS" + +#elif defined(_MPRAS) || defined(MPRAS) +# define PLATFORM_ID "MP-RAS" + +#elif defined(__osf) || defined(__osf__) +# define PLATFORM_ID "OSF1" + +#elif defined(_SCO_SV) || defined(SCO_SV) || defined(sco_sv) +# define PLATFORM_ID "SCO_SV" + +#elif defined(__ultrix) || defined(__ultrix__) || defined(_ULTRIX) +# define PLATFORM_ID "ULTRIX" + +#elif defined(__XENIX__) || defined(_XENIX) || defined(XENIX) +# define PLATFORM_ID "Xenix" + +#else /* unknown platform */ +# define PLATFORM_ID "" + +#endif + +/* For windows compilers MSVC and Intel we can determine + the architecture of the compiler being used. This is because + the compilers do not have flags that can change the architecture, + but rather depend on which compiler is being used +*/ +#if defined(_WIN32) && defined(_MSC_VER) +# if defined(_M_IA64) +# define ARCHITECTURE_ID "IA64" + +# elif defined(_M_X64) || defined(_M_AMD64) +# define ARCHITECTURE_ID "x64" + +# elif defined(_M_IX86) +# define ARCHITECTURE_ID "X86" + +# elif defined(_M_ARM) +# define ARCHITECTURE_ID "ARM" + +# elif defined(_M_MIPS) +# define ARCHITECTURE_ID "MIPS" + +# elif defined(_M_SH) +# define ARCHITECTURE_ID "SHx" + +# else /* unknown architecture */ +# define ARCHITECTURE_ID "" +# endif + +#else +# define ARCHITECTURE_ID "" +#endif + +/* Convert integer to decimal digit literals. */ +#define DEC(n) \ + ('0' + (((n) / 10000000)%10)), \ + ('0' + (((n) / 1000000)%10)), \ + ('0' + (((n) / 100000)%10)), \ + ('0' + (((n) / 10000)%10)), \ + ('0' + (((n) / 1000)%10)), \ + ('0' + (((n) / 100)%10)), \ + ('0' + (((n) / 10)%10)), \ + ('0' + ((n) % 10)) + +/* Convert integer to hex digit literals. */ +#define HEX(n) \ + ('0' + ((n)>>28 & 0xF)), \ + ('0' + ((n)>>24 & 0xF)), \ + ('0' + ((n)>>20 & 0xF)), \ + ('0' + ((n)>>16 & 0xF)), \ + ('0' + ((n)>>12 & 0xF)), \ + ('0' + ((n)>>8 & 0xF)), \ + ('0' + ((n)>>4 & 0xF)), \ + ('0' + ((n) & 0xF)) + +/* Construct a string literal encoding the version number components. */ +#ifdef COMPILER_VERSION_MAJOR +char const info_version[] = { + 'I', 'N', 'F', 'O', ':', + 'c','o','m','p','i','l','e','r','_','v','e','r','s','i','o','n','[', + COMPILER_VERSION_MAJOR, +# ifdef COMPILER_VERSION_MINOR + '.', COMPILER_VERSION_MINOR, +# ifdef COMPILER_VERSION_PATCH + '.', COMPILER_VERSION_PATCH, +# ifdef COMPILER_VERSION_TWEAK + '.', COMPILER_VERSION_TWEAK, +# endif +# endif +# endif + ']','\0'}; +#endif + +/* Construct a string literal encoding the version number components. */ +#ifdef SIMULATE_VERSION_MAJOR +char const info_simulate_version[] = { + 'I', 'N', 'F', 'O', ':', + 's','i','m','u','l','a','t','e','_','v','e','r','s','i','o','n','[', + SIMULATE_VERSION_MAJOR, +# ifdef SIMULATE_VERSION_MINOR + '.', SIMULATE_VERSION_MINOR, +# ifdef SIMULATE_VERSION_PATCH + '.', SIMULATE_VERSION_PATCH, +# ifdef SIMULATE_VERSION_TWEAK + '.', SIMULATE_VERSION_TWEAK, +# endif +# endif +# endif + ']','\0'}; +#endif + +/* Construct the string literal in pieces to prevent the source from + getting matched. Store it in a pointer rather than an array + because some compilers will just produce instructions to fill the + array rather than assigning a pointer to a static array. */ +char const* info_platform = "INFO" ":" "platform[" PLATFORM_ID "]"; +char const* info_arch = "INFO" ":" "arch[" ARCHITECTURE_ID "]"; + + + + +/*--------------------------------------------------------------------------*/ + +#ifdef ID_VOID_MAIN +void main() {} +#else +int main(int argc, char* argv[]) +{ + int require = 0; + require += info_compiler[argc]; + require += info_platform[argc]; + require += info_arch[argc]; +#ifdef COMPILER_VERSION_MAJOR + require += info_version[argc]; +#endif +#ifdef SIMULATE_ID + require += info_simulate[argc]; +#endif +#ifdef SIMULATE_VERSION_MAJOR + require += info_simulate_version[argc]; +#endif + (void)argv; + return require; +} +#endif diff --git a/build/CMakeFiles/3.0.2/CompilerIdC/a.out b/build/CMakeFiles/3.0.2/CompilerIdC/a.out new file mode 100755 index 00000000..50a51b30 Binary files /dev/null and b/build/CMakeFiles/3.0.2/CompilerIdC/a.out differ diff --git a/build/CMakeFiles/3.0.2/CompilerIdCXX/CMakeCXXCompilerId.cpp b/build/CMakeFiles/3.0.2/CompilerIdCXX/CMakeCXXCompilerId.cpp new file mode 100644 index 00000000..a315c6a6 --- /dev/null +++ b/build/CMakeFiles/3.0.2/CompilerIdCXX/CMakeCXXCompilerId.cpp @@ -0,0 +1,430 @@ +/* This source file must have a .cpp extension so that all C++ compilers + recognize the extension without flags. Borland does not know .cxx for + example. */ +#ifndef __cplusplus +# error "A C compiler has been selected for C++." +#endif + +/* Version number components: V=Version, R=Revision, P=Patch + Version date components: YYYY=Year, MM=Month, DD=Day */ + +#if defined(__COMO__) +# define COMPILER_ID "Comeau" + /* __COMO_VERSION__ = VRR */ +# define COMPILER_VERSION_MAJOR DEC(__COMO_VERSION__ / 100) +# define COMPILER_VERSION_MINOR DEC(__COMO_VERSION__ % 100) + +#elif defined(__INTEL_COMPILER) || defined(__ICC) +# define COMPILER_ID "Intel" + /* __INTEL_COMPILER = VRP */ +# define COMPILER_VERSION_MAJOR DEC(__INTEL_COMPILER/100) +# define COMPILER_VERSION_MINOR DEC(__INTEL_COMPILER/10 % 10) +# if defined(__INTEL_COMPILER_UPDATE) +# define COMPILER_VERSION_PATCH DEC(__INTEL_COMPILER_UPDATE) +# else +# define COMPILER_VERSION_PATCH DEC(__INTEL_COMPILER % 10) +# endif +# if defined(__INTEL_COMPILER_BUILD_DATE) + /* __INTEL_COMPILER_BUILD_DATE = YYYYMMDD */ +# define COMPILER_VERSION_TWEAK DEC(__INTEL_COMPILER_BUILD_DATE) +# endif +# if defined(_MSC_VER) +# define SIMULATE_ID "MSVC" + /* _MSC_VER = VVRR */ +# define SIMULATE_VERSION_MAJOR DEC(_MSC_VER / 100) +# define SIMULATE_VERSION_MINOR DEC(_MSC_VER % 100) +# endif + +#elif defined(__PATHCC__) +# define COMPILER_ID "PathScale" +# define COMPILER_VERSION_MAJOR DEC(__PATHCC__) +# define COMPILER_VERSION_MINOR DEC(__PATHCC_MINOR__) +# if defined(__PATHCC_PATCHLEVEL__) +# define COMPILER_VERSION_PATCH DEC(__PATHCC_PATCHLEVEL__) +# endif + +#elif defined(__clang__) +# if defined(__apple_build_version__) +# define COMPILER_ID "AppleClang" +# define COMPILER_VERSION_TWEAK DEC(__apple_build_version__) +# else +# define COMPILER_ID "Clang" +# endif +# define COMPILER_VERSION_MAJOR DEC(__clang_major__) +# define COMPILER_VERSION_MINOR DEC(__clang_minor__) +# define COMPILER_VERSION_PATCH DEC(__clang_patchlevel__) +# if defined(_MSC_VER) +# define SIMULATE_ID "MSVC" + /* _MSC_VER = VVRR */ +# define SIMULATE_VERSION_MAJOR DEC(_MSC_VER / 100) +# define SIMULATE_VERSION_MINOR DEC(_MSC_VER % 100) +# endif + +#elif defined(__BORLANDC__) && defined(__CODEGEARC_VERSION__) +# define COMPILER_ID "Embarcadero" +# define COMPILER_VERSION_MAJOR HEX(__CODEGEARC_VERSION__>>24 & 0x00FF) +# define COMPILER_VERSION_MINOR HEX(__CODEGEARC_VERSION__>>16 & 0x00FF) +# define COMPILER_VERSION_PATCH HEX(__CODEGEARC_VERSION__ & 0xFFFF) + +#elif defined(__BORLANDC__) +# define COMPILER_ID "Borland" + /* __BORLANDC__ = 0xVRR */ +# define COMPILER_VERSION_MAJOR HEX(__BORLANDC__>>8) +# define COMPILER_VERSION_MINOR HEX(__BORLANDC__ & 0xFF) + +#elif defined(__WATCOMC__) +# define COMPILER_ID "Watcom" + /* __WATCOMC__ = VVRR */ +# define COMPILER_VERSION_MAJOR DEC(__WATCOMC__ / 100) +# define COMPILER_VERSION_MINOR DEC(__WATCOMC__ % 100) + +#elif defined(__SUNPRO_CC) +# define COMPILER_ID "SunPro" +# if __SUNPRO_CC >= 0x5100 + /* __SUNPRO_CC = 0xVRRP */ +# define COMPILER_VERSION_MAJOR HEX(__SUNPRO_CC>>12) +# define COMPILER_VERSION_MINOR HEX(__SUNPRO_CC>>4 & 0xFF) +# define COMPILER_VERSION_PATCH HEX(__SUNPRO_CC & 0xF) +# else + /* __SUNPRO_CC = 0xVRP */ +# define COMPILER_VERSION_MAJOR HEX(__SUNPRO_CC>>8) +# define COMPILER_VERSION_MINOR HEX(__SUNPRO_CC>>4 & 0xF) +# define COMPILER_VERSION_PATCH HEX(__SUNPRO_CC & 0xF) +# endif + +#elif defined(__HP_aCC) +# define COMPILER_ID "HP" + /* __HP_aCC = VVRRPP */ +# define COMPILER_VERSION_MAJOR DEC(__HP_aCC/10000) +# define COMPILER_VERSION_MINOR DEC(__HP_aCC/100 % 100) +# define COMPILER_VERSION_PATCH DEC(__HP_aCC % 100) + +#elif defined(__DECCXX) +# define COMPILER_ID "Compaq" + /* __DECCXX_VER = VVRRTPPPP */ +# define COMPILER_VERSION_MAJOR DEC(__DECCXX_VER/10000000) +# define COMPILER_VERSION_MINOR DEC(__DECCXX_VER/100000 % 100) +# define COMPILER_VERSION_PATCH DEC(__DECCXX_VER % 10000) + +#elif defined(__IBMCPP__) +# if defined(__COMPILER_VER__) +# define COMPILER_ID "zOS" +# else +# if __IBMCPP__ >= 800 +# define COMPILER_ID "XL" +# else +# define COMPILER_ID "VisualAge" +# endif + /* __IBMCPP__ = VRP */ +# define COMPILER_VERSION_MAJOR DEC(__IBMCPP__/100) +# define COMPILER_VERSION_MINOR DEC(__IBMCPP__/10 % 10) +# define COMPILER_VERSION_PATCH DEC(__IBMCPP__ % 10) +# endif + +#elif defined(__PGI) +# define COMPILER_ID "PGI" +# define COMPILER_VERSION_MAJOR DEC(__PGIC__) +# define COMPILER_VERSION_MINOR DEC(__PGIC_MINOR__) +# if defined(__PGIC_PATCHLEVEL__) +# define COMPILER_VERSION_PATCH DEC(__PGIC_PATCHLEVEL__) +# endif + +#elif defined(_CRAYC) +# define COMPILER_ID "Cray" +# define COMPILER_VERSION_MAJOR DEC(_RELEASE) +# define COMPILER_VERSION_MINOR DEC(_RELEASE_MINOR) + +#elif defined(__TI_COMPILER_VERSION__) +# define COMPILER_ID "TI" + /* __TI_COMPILER_VERSION__ = VVVRRRPPP */ +# define COMPILER_VERSION_MAJOR DEC(__TI_COMPILER_VERSION__/1000000) +# define COMPILER_VERSION_MINOR DEC(__TI_COMPILER_VERSION__/1000 % 1000) +# define COMPILER_VERSION_PATCH DEC(__TI_COMPILER_VERSION__ % 1000) + +#elif defined(__SCO_VERSION__) +# define COMPILER_ID "SCO" + +#elif defined(__GNUC__) +# define COMPILER_ID "GNU" +# define COMPILER_VERSION_MAJOR DEC(__GNUC__) +# define COMPILER_VERSION_MINOR DEC(__GNUC_MINOR__) +# if defined(__GNUC_PATCHLEVEL__) +# define COMPILER_VERSION_PATCH DEC(__GNUC_PATCHLEVEL__) +# endif + +#elif defined(_MSC_VER) +# define COMPILER_ID "MSVC" + /* _MSC_VER = VVRR */ +# define COMPILER_VERSION_MAJOR DEC(_MSC_VER / 100) +# define COMPILER_VERSION_MINOR DEC(_MSC_VER % 100) +# if defined(_MSC_FULL_VER) +# if _MSC_VER >= 1400 + /* _MSC_FULL_VER = VVRRPPPPP */ +# define COMPILER_VERSION_PATCH DEC(_MSC_FULL_VER % 100000) +# else + /* _MSC_FULL_VER = VVRRPPPP */ +# define COMPILER_VERSION_PATCH DEC(_MSC_FULL_VER % 10000) +# endif +# endif +# if defined(_MSC_BUILD) +# define COMPILER_VERSION_TWEAK DEC(_MSC_BUILD) +# endif + +/* Analog VisualDSP++ >= 4.5.6 */ +#elif defined(__VISUALDSPVERSION__) +# define COMPILER_ID "ADSP" + /* __VISUALDSPVERSION__ = 0xVVRRPP00 */ +# define COMPILER_VERSION_MAJOR HEX(__VISUALDSPVERSION__>>24) +# define COMPILER_VERSION_MINOR HEX(__VISUALDSPVERSION__>>16 & 0xFF) +# define COMPILER_VERSION_PATCH HEX(__VISUALDSPVERSION__>>8 & 0xFF) + +/* Analog VisualDSP++ < 4.5.6 */ +#elif defined(__ADSPBLACKFIN__) || defined(__ADSPTS__) || defined(__ADSP21000__) +# define COMPILER_ID "ADSP" + +/* IAR Systems compiler for embedded systems. + http://www.iar.com */ +#elif defined(__IAR_SYSTEMS_ICC__ ) || defined(__IAR_SYSTEMS_ICC) +# define COMPILER_ID "IAR" + +#elif defined(_SGI_COMPILER_VERSION) || defined(_COMPILER_VERSION) +# define COMPILER_ID "MIPSpro" +# if defined(_SGI_COMPILER_VERSION) + /* _SGI_COMPILER_VERSION = VRP */ +# define COMPILER_VERSION_MAJOR DEC(_SGI_COMPILER_VERSION/100) +# define COMPILER_VERSION_MINOR DEC(_SGI_COMPILER_VERSION/10 % 10) +# define COMPILER_VERSION_PATCH DEC(_SGI_COMPILER_VERSION % 10) +# else + /* _COMPILER_VERSION = VRP */ +# define COMPILER_VERSION_MAJOR DEC(_COMPILER_VERSION/100) +# define COMPILER_VERSION_MINOR DEC(_COMPILER_VERSION/10 % 10) +# define COMPILER_VERSION_PATCH DEC(_COMPILER_VERSION % 10) +# endif + +/* This compiler is either not known or is too old to define an + identification macro. Try to identify the platform and guess that + it is the native compiler. */ +#elif defined(__sgi) +# define COMPILER_ID "MIPSpro" + +#elif defined(__hpux) || defined(__hpua) +# define COMPILER_ID "HP" + +#else /* unknown compiler */ +# define COMPILER_ID "" + +#endif + +/* Construct the string literal in pieces to prevent the source from + getting matched. Store it in a pointer rather than an array + because some compilers will just produce instructions to fill the + array rather than assigning a pointer to a static array. */ +char const* info_compiler = "INFO" ":" "compiler[" COMPILER_ID "]"; +#ifdef SIMULATE_ID +char const* info_simulate = "INFO" ":" "simulate[" SIMULATE_ID "]"; +#endif + +#ifdef __QNXNTO__ +char const* qnxnto = "INFO" ":" "qnxnto"; +#endif + +/* Identify known platforms by name. */ +#if defined(__linux) || defined(__linux__) || defined(linux) +# define PLATFORM_ID "Linux" + +#elif defined(__CYGWIN__) +# define PLATFORM_ID "Cygwin" + +#elif defined(__MINGW32__) +# define PLATFORM_ID "MinGW" + +#elif defined(__APPLE__) +# define PLATFORM_ID "Darwin" + +#elif defined(_WIN32) || defined(__WIN32__) || defined(WIN32) +# define PLATFORM_ID "Windows" + +#elif defined(__FreeBSD__) || defined(__FreeBSD) +# define PLATFORM_ID "FreeBSD" + +#elif defined(__NetBSD__) || defined(__NetBSD) +# define PLATFORM_ID "NetBSD" + +#elif defined(__OpenBSD__) || defined(__OPENBSD) +# define PLATFORM_ID "OpenBSD" + +#elif defined(__sun) || defined(sun) +# define PLATFORM_ID "SunOS" + +#elif defined(_AIX) || defined(__AIX) || defined(__AIX__) || defined(__aix) || defined(__aix__) +# define PLATFORM_ID "AIX" + +#elif defined(__sgi) || defined(__sgi__) || defined(_SGI) +# define PLATFORM_ID "IRIX" + +#elif defined(__hpux) || defined(__hpux__) +# define PLATFORM_ID "HP-UX" + +#elif defined(__HAIKU__) +# define PLATFORM_ID "Haiku" + +#elif defined(__BeOS) || defined(__BEOS__) || defined(_BEOS) +# define PLATFORM_ID "BeOS" + +#elif defined(__QNX__) || defined(__QNXNTO__) +# define PLATFORM_ID "QNX" + +#elif defined(__tru64) || defined(_tru64) || defined(__TRU64__) +# define PLATFORM_ID "Tru64" + +#elif defined(__riscos) || defined(__riscos__) +# define PLATFORM_ID "RISCos" + +#elif defined(__sinix) || defined(__sinix__) || defined(__SINIX__) +# define PLATFORM_ID "SINIX" + +#elif defined(__UNIX_SV__) +# define PLATFORM_ID "UNIX_SV" + +#elif defined(__bsdos__) +# define PLATFORM_ID "BSDOS" + +#elif defined(_MPRAS) || defined(MPRAS) +# define PLATFORM_ID "MP-RAS" + +#elif defined(__osf) || defined(__osf__) +# define PLATFORM_ID "OSF1" + +#elif defined(_SCO_SV) || defined(SCO_SV) || defined(sco_sv) +# define PLATFORM_ID "SCO_SV" + +#elif defined(__ultrix) || defined(__ultrix__) || defined(_ULTRIX) +# define PLATFORM_ID "ULTRIX" + +#elif defined(__XENIX__) || defined(_XENIX) || defined(XENIX) +# define PLATFORM_ID "Xenix" + +#else /* unknown platform */ +# define PLATFORM_ID "" + +#endif + +/* For windows compilers MSVC and Intel we can determine + the architecture of the compiler being used. This is because + the compilers do not have flags that can change the architecture, + but rather depend on which compiler is being used +*/ +#if defined(_WIN32) && defined(_MSC_VER) +# if defined(_M_IA64) +# define ARCHITECTURE_ID "IA64" + +# elif defined(_M_X64) || defined(_M_AMD64) +# define ARCHITECTURE_ID "x64" + +# elif defined(_M_IX86) +# define ARCHITECTURE_ID "X86" + +# elif defined(_M_ARM) +# define ARCHITECTURE_ID "ARM" + +# elif defined(_M_MIPS) +# define ARCHITECTURE_ID "MIPS" + +# elif defined(_M_SH) +# define ARCHITECTURE_ID "SHx" + +# else /* unknown architecture */ +# define ARCHITECTURE_ID "" +# endif + +#else +# define ARCHITECTURE_ID "" +#endif + +/* Convert integer to decimal digit literals. */ +#define DEC(n) \ + ('0' + (((n) / 10000000)%10)), \ + ('0' + (((n) / 1000000)%10)), \ + ('0' + (((n) / 100000)%10)), \ + ('0' + (((n) / 10000)%10)), \ + ('0' + (((n) / 1000)%10)), \ + ('0' + (((n) / 100)%10)), \ + ('0' + (((n) / 10)%10)), \ + ('0' + ((n) % 10)) + +/* Convert integer to hex digit literals. */ +#define HEX(n) \ + ('0' + ((n)>>28 & 0xF)), \ + ('0' + ((n)>>24 & 0xF)), \ + ('0' + ((n)>>20 & 0xF)), \ + ('0' + ((n)>>16 & 0xF)), \ + ('0' + ((n)>>12 & 0xF)), \ + ('0' + ((n)>>8 & 0xF)), \ + ('0' + ((n)>>4 & 0xF)), \ + ('0' + ((n) & 0xF)) + +/* Construct a string literal encoding the version number components. */ +#ifdef COMPILER_VERSION_MAJOR +char const info_version[] = { + 'I', 'N', 'F', 'O', ':', + 'c','o','m','p','i','l','e','r','_','v','e','r','s','i','o','n','[', + COMPILER_VERSION_MAJOR, +# ifdef COMPILER_VERSION_MINOR + '.', COMPILER_VERSION_MINOR, +# ifdef COMPILER_VERSION_PATCH + '.', COMPILER_VERSION_PATCH, +# ifdef COMPILER_VERSION_TWEAK + '.', COMPILER_VERSION_TWEAK, +# endif +# endif +# endif + ']','\0'}; +#endif + +/* Construct a string literal encoding the version number components. */ +#ifdef SIMULATE_VERSION_MAJOR +char const info_simulate_version[] = { + 'I', 'N', 'F', 'O', ':', + 's','i','m','u','l','a','t','e','_','v','e','r','s','i','o','n','[', + SIMULATE_VERSION_MAJOR, +# ifdef SIMULATE_VERSION_MINOR + '.', SIMULATE_VERSION_MINOR, +# ifdef SIMULATE_VERSION_PATCH + '.', SIMULATE_VERSION_PATCH, +# ifdef SIMULATE_VERSION_TWEAK + '.', SIMULATE_VERSION_TWEAK, +# endif +# endif +# endif + ']','\0'}; +#endif + +/* Construct the string literal in pieces to prevent the source from + getting matched. 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TestSkeletonBlockerComplex.s" +.PHONY : help + + + +#============================================================================= +# Special targets to cleanup operation of make. + +# Special rule to run CMake to check the build system integrity. +# No rule that depends on this can have commands that come from listfiles +# because they might be regenerated. +cmake_check_build_system: + cd /home/frg/Bureau/mWorkingDirectory/build && $(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 0 +.PHONY : cmake_check_build_system + diff --git a/build/src/Skeleton_blocker/test/cmake_install.cmake b/build/src/Skeleton_blocker/test/cmake_install.cmake new file mode 100644 index 00000000..119780a6 --- /dev/null +++ b/build/src/Skeleton_blocker/test/cmake_install.cmake @@ -0,0 +1,34 @@ +# Install script for directory: /home/frg/Bureau/mWorkingDirectory/src/Skeleton_blocker/test + +# Set the install prefix +if(NOT DEFINED CMAKE_INSTALL_PREFIX) + set(CMAKE_INSTALL_PREFIX "/usr/local") +endif() +string(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}") + +# Set the install configuration name. +if(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME) + if(BUILD_TYPE) + string(REGEX REPLACE "^[^A-Za-z0-9_]+" "" + CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}") + else() + set(CMAKE_INSTALL_CONFIG_NAME "Release") + endif() + message(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"") +endif() + +# Set the component getting installed. +if(NOT CMAKE_INSTALL_COMPONENT) + if(COMPONENT) + message(STATUS "Install component: \"${COMPONENT}\"") + set(CMAKE_INSTALL_COMPONENT "${COMPONENT}") + else() + set(CMAKE_INSTALL_COMPONENT) + endif() +endif() + +# Install shared libraries without execute permission? +if(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE) + set(CMAKE_INSTALL_SO_NO_EXE "1") +endif() + diff --git a/src/Bipartite_graphs_matching/concept/Persistence_diagram.h b/src/Bipartite_graphs_matching/concept/Persistence_diagram.h new file mode 100644 index 00000000..eaaf8bc5 --- /dev/null +++ b/src/Bipartite_graphs_matching/concept/Persistence_diagram.h @@ -0,0 +1,7 @@ +typedef typename std::pair Diagram_point; + +struct Persistence_Diagram +{ + const_iterator cbegin() const; + const_iterator cend() const; +}; diff --git a/src/Bipartite_graphs_matching/example/CMakeLists.txt b/src/Bipartite_graphs_matching/example/CMakeLists.txt new file mode 100644 index 00000000..aaf32abd --- /dev/null +++ b/src/Bipartite_graphs_matching/example/CMakeLists.txt @@ -0,0 +1,27 @@ +cmake_minimum_required(VERSION 2.6) +project(GUDHIBottleneckExample) + +# need CGAL 4.6 +# cmake -DCGAL_DIR=~/workspace/CGAL-4.6-beta1 ../../.. +if(CGAL_FOUND) + if (NOT CGAL_VERSION VERSION_LESS 4.6.0) + message(STATUS "CGAL version: ${CGAL_VERSION}.") + + include( ${CGAL_USE_FILE} ) + + find_package(Eigen3 3.1.0) + if (EIGEN3_FOUND) + message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") + include( ${EIGEN3_USE_FILE} ) + include_directories (BEFORE "../../include") + + add_executable (basic_example basic.cpp) + #add_test(dtoffrw_tore3D ${CMAKE_CURRENT_BINARY_DIR}/dtoffrw ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off 3) + + else() + message(WARNING "Eigen3 not found. Version 3.1.0 is required.") + endif() + else() + message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.") + endif () +endif() diff --git a/src/Bipartite_graphs_matching/example/basic.cpp b/src/Bipartite_graphs_matching/example/basic.cpp new file mode 100644 index 00000000..d190ab48 --- /dev/null +++ b/src/Bipartite_graphs_matching/example/basic.cpp @@ -0,0 +1,44 @@ +/* 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): Francois Godi + * + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 . + */ + +#include "../include/gudhi/Graph_matching.h" +#include + +using namespace Gudhi::bipartite_graph_matching; + +int main() { + + std::vector< std::pair > v1, v2; + + v1.emplace_back(2.7,3.7); + v1.emplace_back(9.6,14); + v1.emplace_back(34.2,34.974); + + v2.emplace_back(2.8,4.45); + v2.emplace_back(9.5,14.1); + + + double b = bottleneck_distance(v1, v2); + + std::cout << "Bottleneck distance = " << b << std::endl; + +} diff --git a/src/Bipartite_graphs_matching/include/gudhi/Graph_matching.h b/src/Bipartite_graphs_matching/include/gudhi/Graph_matching.h new file mode 100644 index 00000000..a2754333 --- /dev/null +++ b/src/Bipartite_graphs_matching/include/gudhi/Graph_matching.h @@ -0,0 +1,213 @@ +/* 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): Francois Godi + * + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ +#define SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ + +#include + +#include "Neighbors_finder.h" + +namespace Gudhi { + +namespace bipartite_graph_matching { + +/** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams. + * + * + * + * \ingroup bottleneck_distance + */ +template +double bottleneck_distance(const Persistence_diagram1& diag1, const Persistence_diagram2& diag2, double e = 0.); + +/** \internal \brief Structure representing a graph matching. The graph is a Persistence_diagrams_graph. + * + * \ingroup bottleneck_distance + */ +class Graph_matching { +public: + /** \internal \brief Constructor constructing an empty matching. */ + explicit Graph_matching(); + /** \internal \brief Copy operator. */ + Graph_matching& operator=(const Graph_matching& m); + /** \internal \brief Is the matching perfect ? */ + bool perfect() const; + /** \internal \brief Augments the matching with a maximal set of edge-disjoint shortest augmenting paths. */ + bool multi_augment(); + /** \internal \brief Sets the maximum length of the edges allowed to be added in the matching, 0 initially. */ + void set_r(double r); + +private: + double r; + /** \internal \brief Given a point from V, provides its matched point in U, null_point_index() if there isn't. */ + std::vector v_to_u; + /** \internal \brief All the unmatched points in U. */ + std::list unmatched_in_u; + + /** \internal \brief Provides a Layered_neighbors_finder dividing the graph in layers. Basically a BFS. */ + std::unique_ptr layering() const; + /** \internal \brief Augments the matching with a simple path no longer than max_depth. Basically a DFS. */ + bool augment(Layered_neighbors_finder & layered_nf, int u_start_index, int max_depth); + /** \internal \brief Update the matching with the simple augmenting path given as parameter. */ + void update(std::deque & path); +}; + +inline Graph_matching::Graph_matching() + : r(0.), v_to_u(G::size(), null_point_index()), unmatched_in_u() { + for (int u_point_index = 0; u_point_index < G::size(); ++u_point_index) + unmatched_in_u.emplace_back(u_point_index); +} + +inline Graph_matching& Graph_matching::operator=(const Graph_matching& m) { + r = m.r; + v_to_u = m.v_to_u; + unmatched_in_u = m.unmatched_in_u; + return *this; +} + +inline bool Graph_matching::perfect() const { + return unmatched_in_u.empty(); +} + +inline bool Graph_matching::multi_augment() { + if (perfect()) + return false; + Layered_neighbors_finder layered_nf = *layering(); + int max_depth = layered_nf.vlayers_number()*2 - 1; + double rn = sqrt(G::size()); + // verification of a necessary criterion in order to shortcut if possible + if (max_depth <0 || (unmatched_in_u.size() > rn && max_depth >= rn)) + return false; + bool successful = false; + std::list tries(unmatched_in_u); + for (auto it = tries.cbegin(); it != tries.cend(); it++) + // 'augment' has side-effects which have to be always executed, don't change order + successful = augment(layered_nf, *it, max_depth) || successful; + return successful; +} + +inline void Graph_matching::set_r(double r) { + this->r = r; +} + +inline bool Graph_matching::augment(Layered_neighbors_finder & layered_nf, int u_start_index, int max_depth) { + //V vertices have at most one successor, thus when we backtrack from U we can directly pop_back 2 vertices. + std::deque path; + path.emplace_back(u_start_index); + do { + if (static_cast(path.size()) > max_depth) { + path.pop_back(); + path.pop_back(); + } + if (path.empty()) + return false; + path.emplace_back(layered_nf.pull_near(path.back(), static_cast(path.size())/2)); + while (path.back() == null_point_index()) { + path.pop_back(); + path.pop_back(); + if (path.empty()) + return false; + path.pop_back(); + path.emplace_back(layered_nf.pull_near(path.back(), path.size() / 2)); + } + path.emplace_back(v_to_u.at(path.back())); + } while (path.back() != null_point_index()); + //if v_to_u.at(path.back()) has no successor, path.back() is an exposed vertex + path.pop_back(); + update(path); + return true; +} + +inline std::unique_ptr Graph_matching::layering() const { + std::list u_vertices(unmatched_in_u); + std::list v_vertices; + Neighbors_finder nf(r); + for (int v_point_index = 0; v_point_index < G::size(); ++v_point_index) + nf.add(v_point_index); + std::unique_ptr layered_nf(new Layered_neighbors_finder(r)); + for(int layer = 0; !u_vertices.empty(); layer++) { + // one layer is one step in the BFS + for (auto it = u_vertices.cbegin(); it != u_vertices.cend(); ++it) { + std::unique_ptr< std::list > u_succ = std::move(nf.pull_all_near(*it)); + for (auto it = u_succ->cbegin(); it != u_succ->cend(); ++it) { + layered_nf->add(*it, layer); + v_vertices.emplace_back(*it); + } + } + // When the above for finishes, we have progress of one half-step (from U to V) in the BFS + u_vertices.clear(); + bool end = false; + for (auto it = v_vertices.cbegin(); it != v_vertices.cend(); it++) + if (v_to_u.at(*it) == null_point_index()) + // we stop when a nearest exposed V vertex (from U exposed vertices) has been found + end = true; + else + u_vertices.emplace_back(v_to_u.at(*it)); + // When the above for finishes, we have progress of one half-step (from V to U) in the BFS + if (end) + return layered_nf; + v_vertices.clear(); + } + return layered_nf; +} + +inline void Graph_matching::update(std::deque& path) { + unmatched_in_u.remove(path.front()); + for (auto it = path.cbegin(); it != path.cend(); ++it) { + // Be careful, the iterator is incremented twice each time + int tmp = *it; + v_to_u[*(++it)] = tmp; + } +} + +template +double bottleneck_distance(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e) { + G::initialize(diag1, diag2, e); + std::unique_ptr< std::vector > sd = std::move(G::sorted_distances()); + int idmin = 0; + int idmax = sd->size() - 1; + // alpha can be modified, this will change the complexity + double alpha = pow(sd->size(), 0.25); + Graph_matching m; + Graph_matching biggest_unperfect; + while (idmin != idmax) { + int step = static_cast((idmax - idmin) / alpha); + m.set_r(sd->at(idmin + step)); + while (m.multi_augment()); + // The above while compute a maximum matching (according to the r setted before) + if (m.perfect()) { + idmax = idmin + step; + m = biggest_unperfect; + } else { + biggest_unperfect = m; + idmin = idmin + step + 1; + } + } + return sd->at(idmin); +} + +} // namespace bipartite_graph_matching + +} // namespace Gudhi + +#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ diff --git a/src/Bipartite_graphs_matching/include/gudhi/Neighbors_finder.h b/src/Bipartite_graphs_matching/include/gudhi/Neighbors_finder.h new file mode 100644 index 00000000..78b9debc --- /dev/null +++ b/src/Bipartite_graphs_matching/include/gudhi/Neighbors_finder.h @@ -0,0 +1,155 @@ +/* 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): Francois Godi + * + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_ +#define SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_ + +#include + +#include "Planar_neighbors_finder.h" + +namespace Gudhi { + +namespace bipartite_graph_matching { + +/** \internal \brief data structure used to find any point (including projections) in V near to a query point from U + * (which can be a projection). + * + * V points have to be added manually using their index and before the first pull. A neighbor pulled is automatically removed. + * + * \ingroup bottleneck_distance + */ +class Neighbors_finder { +public: + /** \internal \brief Constructor taking the near distance definition as parameter. */ + Neighbors_finder(double r); + /** \internal \brief A point added will be possibly pulled. */ + void add(int v_point_index); + /** \internal \brief Returns and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ + int pull_near(int u_point_index); + /** \internal \brief Returns and remove all the V points near to the U point given as parameter. */ + std::unique_ptr< std::list > pull_all_near(int u_point_index); + +private: + const double r; + Planar_neighbors_finder planar_neighbors_f; + std::unordered_set projections_f; + void remove(int v_point_index); + bool contains(int v_point_index); +}; + +/** \internal \brief data structure used to find any point (including projections) in V near to a query point from U + * (which can be a projection) in a layered graph layer given as parmeter. + * + * V points have to be added manually using their index and before the first pull. A neighbor pulled is automatically removed. + * + * \ingroup bottleneck_distance + */ +class Layered_neighbors_finder { +public: + /** \internal \brief Constructor taking the near distance definition as parameter. */ + Layered_neighbors_finder(double r); + /** \internal \brief A point added will be possibly pulled. */ + void add(int v_point_index, int vlayer); + /** \internal \brief Returns and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ + int pull_near(int u_point_index, int vlayer); + /** \internal \brief Returns the number of layers. */ + int vlayers_number() const; + +private: + const double r; + std::vector neighbors_finder; +}; + +inline Neighbors_finder::Neighbors_finder(double r) : + r(r), planar_neighbors_f(r), projections_f() { } + +inline void Neighbors_finder::add(int v_point_index) { + if (G::on_the_v_diagonal(v_point_index)) + projections_f.emplace(v_point_index); + else + planar_neighbors_f.add(v_point_index); +} + +inline void Neighbors_finder::remove(int v_point_index) { + if(v_point_index == null_point_index()) + return; + if (G::on_the_v_diagonal(v_point_index)) + projections_f.erase(v_point_index); + else + planar_neighbors_f.remove(v_point_index); +} + +inline bool Neighbors_finder::contains(int v_point_index) { + return planar_neighbors_f.contains(v_point_index) || (projections_f.count(v_point_index)>0); +} + +inline int Neighbors_finder::pull_near(int u_point_index) { + int tmp; + int c = G::corresponding_point_in_v(u_point_index); + if (G::on_the_u_diagonal(u_point_index) && !projections_f.empty()) + //All projections are at distance 0 + tmp = *projections_f.cbegin(); + else if (contains(c) && (G::distance(u_point_index, c) <= r)) + //Is the query point near to its projection ? + tmp = c; + else + //Is the query point near to a V point in the plane ? + tmp = planar_neighbors_f.pull_near(u_point_index); + remove(tmp); + return tmp; +} + +inline std::unique_ptr< std::list > Neighbors_finder::pull_all_near(int u_point_index) { + std::unique_ptr< std::list > all_pull = std::move(planar_neighbors_f.pull_all_near(u_point_index)); + int last_pull = pull_near(u_point_index); + while (last_pull != null_point_index()) { + all_pull->emplace_back(last_pull); + last_pull = pull_near(u_point_index); + } + return all_pull; +} + +inline Layered_neighbors_finder::Layered_neighbors_finder(double r) : + r(r), neighbors_finder() { } + +inline void Layered_neighbors_finder::add(int v_point_index, int vlayer) { + for (int l = neighbors_finder.size(); l <= vlayer; l++) + neighbors_finder.emplace_back(Neighbors_finder(r)); + neighbors_finder.at(vlayer).add(v_point_index); +} + +inline int Layered_neighbors_finder::pull_near(int u_point_index, int vlayer) { + if (static_cast (neighbors_finder.size()) <= vlayer) + return null_point_index(); + return neighbors_finder.at(vlayer).pull_near(u_point_index); +} + +inline int Layered_neighbors_finder::vlayers_number() const { + return static_cast(neighbors_finder.size()); +} + +} // namespace bipartite_graph_matching + +} // namespace Gudhi + +#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_ diff --git a/src/Bipartite_graphs_matching/include/gudhi/Persistence_diagrams_graph.h b/src/Bipartite_graphs_matching/include/gudhi/Persistence_diagrams_graph.h new file mode 100644 index 00000000..6420b772 --- /dev/null +++ b/src/Bipartite_graphs_matching/include/gudhi/Persistence_diagrams_graph.h @@ -0,0 +1,164 @@ +/* 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): Francois Godi + * + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_ +#define SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_ + +#include +#include +#include +#include +#include +#include +#include + +namespace Gudhi { + +namespace bipartite_graph_matching { + +/** \internal \brief Returns the used index for encoding none of the points */ +int null_point_index(); + +/** \internal \brief Structure representing an euclidean bipartite graph containing + * the points from the two persistence diagrams (including the projections). + * + * \ingroup bottleneck_distance + */ +class Persistence_diagrams_graph { +public: + /** \internal \brief Initializer taking 2 Point (concept) ranges as parameters. */ + template + static void initialize(const Persistence_diagram1& diag1, const Persistence_diagram2& diag2, double e); + /** \internal \brief Is the given point from U the projection of a point in V ? */ + static bool on_the_u_diagonal(int u_point_index); + /** \internal \brief Is the given point from V the projection of a point in U ? */ + static bool on_the_v_diagonal(int v_point_index); + /** \internal \brief Given a point from V, returns the corresponding (projection or projector) point in U. */ + static int corresponding_point_in_u(int v_point_index); + /** \internal \brief Given a point from U, returns the corresponding (projection or projector) point in V. */ + static int corresponding_point_in_v(int u_point_index); + /** \internal \brief Given a point from U and a point from V, returns the distance between those points. */ + static double distance(int u_point_index, int v_point_index); + /** \internal \brief Returns size = |U| = |V|. */ + static int size(); + /** \internal \brief Returns the O(n^2) sorted distances between the points. */ + static std::unique_ptr< std::vector > sorted_distances(); + +private: + /** \internal \typedef \brief Internal_point is the internal points representation, indexes used outside. */ + typedef std::pair Internal_point; + static std::vector u; + static std::vector v; + static Internal_point get_u_point(int u_point_index); + static Internal_point get_v_point(int v_point_index); + + friend class Naive_pnf; + friend class Upper_envelope_tree; +}; + +/** \internal \typedef \brief Shorter alias */ +typedef Persistence_diagrams_graph G; + +// static initialization, seems to work but strange +std::vector G::u = [] {return std::vector();}(); +std::vector G::v = [] {return std::vector();}(); + +inline int null_point_index() { + return -1; +} + +template +inline void G::initialize(const Persistence_diagram1 &diag1, + const Persistence_diagram2 &diag2, double e){ + u.clear(); + v.clear(); + for (auto it = diag1.cbegin(); it != diag1.cend(); ++it) + if (it->second - it->first > e) + u.emplace_back(*it); + for (auto it = diag2.cbegin(); it != diag2.cend(); ++it) + if (it->second - it->first > e) + v.emplace_back(*it); + if (u.size() < v.size()) + swap(u, v); +} + +inline bool G::on_the_u_diagonal(int u_point_index) { + return u_point_index >= static_cast (u.size()); +} + +inline bool G::on_the_v_diagonal(int v_point_index) { + return v_point_index >= static_cast (v.size()); +} + +inline int G::corresponding_point_in_u(int v_point_index) { + return on_the_v_diagonal(v_point_index) ? + v_point_index - static_cast (v.size()) : v_point_index + static_cast (u.size()); +} + +inline int G::corresponding_point_in_v(int u_point_index) { + return on_the_u_diagonal(u_point_index) ? + u_point_index - static_cast (u.size()) : u_point_index + static_cast (v.size()); +} + +inline double G::distance(int u_point_index, int v_point_index) { + if (on_the_u_diagonal(u_point_index) && on_the_v_diagonal(v_point_index)) + return 0; + Internal_point p_u = get_u_point(u_point_index); + Internal_point p_v = get_v_point(v_point_index); + return std::max(std::fabs(p_u.first - p_v.first), std::fabs(p_u.second - p_v.second)); +} + +inline int G::size() { + return static_cast (u.size() + v.size()); +} + +inline std::unique_ptr< std::vector > G::sorted_distances() { + // could be optimized + std::set sorted_distances; + for (int u_point_index = 0; u_point_index < size(); ++u_point_index) + for (int v_point_index = 0; v_point_index < size(); ++v_point_index) + sorted_distances.emplace(distance(u_point_index, v_point_index)); + std::unique_ptr< std::vector > sd_up(new std::vector(sorted_distances.cbegin(), sorted_distances.cend())); + return sd_up; +} + +inline G::Internal_point G::get_u_point(int u_point_index) { + if (!on_the_u_diagonal(u_point_index)) + return u.at(u_point_index); + Internal_point projector = v.at(corresponding_point_in_v(u_point_index)); + double x = (projector.first + projector.second) / 2; + return Internal_point(x, x); +} + +inline G::Internal_point G::get_v_point(int v_point_index) { + if (!on_the_v_diagonal(v_point_index)) + return v.at(v_point_index); + Internal_point projector = u.at(corresponding_point_in_u(v_point_index)); + double x = (projector.first + projector.second) / 2; + return Internal_point(x, x); +} + +} // namespace bipartite_graph_matching + +} // namespace Gudhi + +#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_ diff --git a/src/Bipartite_graphs_matching/include/gudhi/Planar_neighbors_finder.h b/src/Bipartite_graphs_matching/include/gudhi/Planar_neighbors_finder.h new file mode 100644 index 00000000..3564dcf9 --- /dev/null +++ b/src/Bipartite_graphs_matching/include/gudhi/Planar_neighbors_finder.h @@ -0,0 +1,170 @@ +/* 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): Francois Godi + * + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_ +#define SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_ + +#include +#include + +#include "Persistence_diagrams_graph.h" + +namespace Gudhi { + +namespace bipartite_graph_matching { + +/** \internal \brief Structure used to find any point in V near (according to the planar distance) to a query point from U. + * + * V points have to be added manually using their index and before the first remove/pull. A neighbor pulled is automatically removed. but we can also + * remove points manually using their index. + * + * \ingroup bottleneck_distance + */ +class Abstract_planar_neighbors_finder { +public: + /** \internal \brief Constructor TODO. */ + Abstract_planar_neighbors_finder(double r); + virtual ~Abstract_planar_neighbors_finder() = 0; + /** \internal \brief A point added will be possibly pulled. */ + virtual void add(int v_point_index) = 0; + /** \internal \brief A point manually removed will no longer be possibly pulled. */ + virtual void remove(int v_point_index) = 0; + /** \internal \brief Can the point given as parameter be returned ? */ + virtual bool contains(int v_point_index) const = 0; + /** \internal \brief Provide and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ + virtual int pull_near(int u_point_index) = 0; + /** \internal \brief Provide and remove all the V points near to the U point given as parameter. */ + virtual std::unique_ptr< std::list > pull_all_near(int u_point_index); + +protected: + const double r; +}; + +/** \internal \brief Naive_pnf is an naïve Abstract_planar_neighbors_finder implementation + * + * \ingroup bottleneck_distance + */ +class Naive_pnf : public Abstract_planar_neighbors_finder { +public: + /** \internal \brief Constructor taking the near distance definition as parameter. */ + Naive_pnf(double r); + /** \internal \brief A point added will be possibly pulled. */ + void add(int v_point_index); + /** \internal \brief A point manually removed will no longer be possibly pulled. */ + void remove(int v_point_index); + /** \internal \brief Can the point given as parameter be returned ? */ + bool contains(int v_point_index) const; + /** \internal \brief Provide and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ + int pull_near(int u_point_index); + /** \internal \brief Provide and remove all the V points near to the U point given as parameter. */ + virtual std::unique_ptr< std::list > pull_all_near(int u_point_index); + +private: + std::pair get_v_key(int v_point_index) const; + std::multimap,int> grid; +}; + +/** \internal \typedef \brief Planar_neighbors_finder is the used Abstract_planar_neighbors_finder's implementation. */ +typedef Naive_pnf Planar_neighbors_finder; + + +inline Abstract_planar_neighbors_finder::Abstract_planar_neighbors_finder(double r) : + r(r) { } + +inline Abstract_planar_neighbors_finder::~Abstract_planar_neighbors_finder() {} + +inline std::unique_ptr< std::list > Abstract_planar_neighbors_finder::pull_all_near(int u_point_index) { + std::unique_ptr< std::list > all_pull(new std::list); + int last_pull = pull_near(u_point_index); + while (last_pull != null_point_index()) { + all_pull->emplace_back(last_pull); + last_pull = pull_near(u_point_index); + } + return all_pull; +} + +inline Naive_pnf::Naive_pnf(double r) : + Abstract_planar_neighbors_finder(r), grid() { } + + +inline std::pair Naive_pnf::get_v_key(int v_point_index) const{ + G::Internal_point v_point = G::get_v_point(v_point_index); + return std::make_pair(static_cast(v_point.first/r), static_cast(v_point.second/r)); +} + +inline void Naive_pnf::add(int v_point_index) { + grid.emplace(get_v_key(v_point_index),v_point_index); +} + +inline void Naive_pnf::remove(int v_point_index) { + for(auto it = grid.find(get_v_key(v_point_index)); it!=grid.end(); it++) + if(it->second==v_point_index){ + grid.erase(it); + return; + } +} + +inline bool Naive_pnf::contains(int v_point_index) const { + if(v_point_index == null_point_index()) + return false; + for(auto it = grid.find(get_v_key(v_point_index)); it!=grid.end(); it++) + if(it->second==v_point_index) + return true; + return false; +} + +inline int Naive_pnf::pull_near(int u_point_index) { + G::Internal_point u_point = G::get_u_point(u_point_index); + int i0 = static_cast(u_point.first/r); + int j0 = static_cast(u_point.second/r); + for(int i = 1; i<= 3; i++) + for(int j = 1; j<= 3; j++) + for(auto it = grid.find(std::make_pair(i0 +(i%3)-1, j0+(j%3)-1)); it!=grid.end(); it++) + if (G::distance(u_point_index, it->second) <= r) { + int tmp = it->second; + grid.erase(it); + return tmp; + } + return null_point_index(); +} + +inline std::unique_ptr< std::list > Naive_pnf::pull_all_near(int u_point_index) { + std::unique_ptr< std::list > all_pull(new std::list); + G::Internal_point u_point = G::get_u_point(u_point_index); + int i0 = static_cast(u_point.first/r); + int j0 = static_cast(u_point.second/r); + for(int i = 1; i<= 3; i++) + for(int j = 1; j<= 3; j++) + for(auto it = grid.find(std::make_pair(i0 +(i%3)-1, j0+(j%3)-1)); it!=grid.end(); it++) + if (G::distance(u_point_index, it->second) <= r) { + int tmp = it->second; + grid.erase(it); + all_pull->emplace_back(tmp); + } + return all_pull; +} + +} // namespace bipartite_graph_matching + +} // namespace Gudhi + +#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_ diff --git a/src/Bipartite_graphs_matching/test/CMakeLists.txt b/src/Bipartite_graphs_matching/test/CMakeLists.txt new file mode 100644 index 00000000..abf18b1b --- /dev/null +++ b/src/Bipartite_graphs_matching/test/CMakeLists.txt @@ -0,0 +1,54 @@ +cmake_minimum_required(VERSION 2.6) +project(GUDHIBottleneckUT) + + + + +if(CGAL_FOUND) + if (NOT CGAL_VERSION VERSION_LESS 4.6.0) + message(STATUS "CGAL version: ${CGAL_VERSION}.") + + include( ${CGAL_USE_FILE} ) + + find_package(Eigen3 3.1.0) + if (EIGEN3_FOUND) + message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") + include( ${EIGEN3_USE_FILE} ) + include_directories (BEFORE "../../include") + + if (GCOVR_PATH) + # for gcovr to make coverage reports - Corbera Jenkins plugin + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage") + set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage") +endif() +if (GPROF_PATH) + # for gprof to make coverage reports - Jenkins + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg") + set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg") +endif() + message("CMAKE_CXX_FLAGS = ${CMAKE_CXX_FLAGS}") + message("CMAKE_CXX_FLAGS_DEBUG = ${CMAKE_CXX_FLAGS_DEBUG}") + message("CMAKE_CXX_FLAGS_RELEASE = ${CMAKE_CXX_FLAGS_RELEASE}") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O2 -std=c++11 -Wall -Wpedantic -Wsign-compare") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -ggdb -O0") + set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE}") + +add_executable ( BottleneckUT bottleneck_unit_test.cpp ) +target_link_libraries(BottleneckUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) + +# Unitary tests +add_test(NAME BottleneckUT + COMMAND ${CMAKE_CURRENT_BINARY_DIR}/BottleneckUT + # XML format for Jenkins xUnit plugin + --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/BottleneckUT.xml --log_level=test_suite --report_level=no) + + + else() + message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.") + endif() + else() + message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile bipartite graphs matching feature. Version 4.6.0 is required.") + endif () +endif() diff --git a/src/Bipartite_graphs_matching/test/README b/src/Bipartite_graphs_matching/test/README new file mode 100644 index 00000000..0e7b8673 --- /dev/null +++ b/src/Bipartite_graphs_matching/test/README @@ -0,0 +1,12 @@ +To compile: +*********** + +cmake . +make + +To launch with details: +*********************** + +./BottleneckUnitTest --report_level=detailed --log_level=all + + ==> echo $? returns 0 in case of success (non-zero otherwise) diff --git a/src/Bipartite_graphs_matching/test/bottleneck_unit_test.cpp b/src/Bipartite_graphs_matching/test/bottleneck_unit_test.cpp new file mode 100644 index 00000000..dc33f76b --- /dev/null +++ b/src/Bipartite_graphs_matching/test/bottleneck_unit_test.cpp @@ -0,0 +1,207 @@ +#define BOOST_TEST_MODULE bottleneck test + +#include +#include +#include "../include/gudhi/Graph_matching.h" + +#include +#include + +using namespace Gudhi::bipartite_graph_matching; + +int n1 = 81; // a natural number >0 +int n2 = 180; // a natural number >0 +double upper_bound = 400.5; // any real >0 + +BOOST_AUTO_TEST_CASE(global){ + std::uniform_real_distribution unif1(0.,upper_bound); + std::uniform_real_distribution unif2(upper_bound/1000.,upper_bound/100.); + std::default_random_engine re; + std::vector< std::pair > v1, v2; + for (int i = 0; i < n1; i++) { + double a = unif1(re); + double b = unif1(re); + double x = unif2(re); + double y = unif2(re); + v1.emplace_back(std::min(a,b), std::max(a,b)); + v2.emplace_back(std::min(a,b)+std::min(x,y), std::max(a,b)+std::max(x,y)); + if(i%5==0) + v1.emplace_back(std::min(a,b),std::min(a,b)+x); + if(i%3==0) + v2.emplace_back(std::max(a,b),std::max(a,b)+y); + } + //99.5 and not 100 to avoid float errors. + BOOST_CHECK(bottleneck_distance(v1, v2) <= upper_bound/99.5); +} + +BOOST_AUTO_TEST_CASE(persistence_diagrams_graph){ + // Random construction + std::uniform_real_distribution unif(0.,upper_bound); + std::default_random_engine re; + std::vector< std::pair > v1, v2; + for (int i = 0; i < n1; i++) { + double a = unif(re); + double b = unif(re); + v1.emplace_back(std::min(a,b), std::max(a,b)); + } + for (int i = 0; i < n2; i++) { + double a = unif(re); + double b = unif(re); + v2.emplace_back(std::min(a,b), std::max(a,b)); + } + G::initialize(v1, v2, 0.); + std::unique_ptr< std::vector > d = std::move(G::sorted_distances()); + // + BOOST_CHECK(!G::on_the_u_diagonal(n1-1)); + BOOST_CHECK(!G::on_the_u_diagonal(n1)); + BOOST_CHECK(!G::on_the_u_diagonal(n2-1)); + BOOST_CHECK(G::on_the_u_diagonal(n2)); + BOOST_CHECK(!G::on_the_v_diagonal(n1-1)); + BOOST_CHECK(G::on_the_v_diagonal(n1)); + BOOST_CHECK(G::on_the_v_diagonal(n2-1)); + BOOST_CHECK(G::on_the_v_diagonal(n2)); + // + BOOST_CHECK(G::corresponding_point_in_u(0)==n2); + BOOST_CHECK(G::corresponding_point_in_u(n1)==0); + BOOST_CHECK(G::corresponding_point_in_v(0)==n1); + BOOST_CHECK(G::corresponding_point_in_v(n2)==0); + // + BOOST_CHECK(G::size()==(n1+n2)); + // + BOOST_CHECK((int) d->size() <= (n1+n2)*(n1+n2) - n1*n2 + 1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,0))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n1-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n2-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n2))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,(n1+n2)-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,0))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n1-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n2-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n2))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,(n1+n2)-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,0))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n1-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n2-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n2))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,(n1+n2)-1))==1); +} + + +BOOST_AUTO_TEST_CASE(planar_neighbors_finder) { + Planar_neighbors_finder pnf = Planar_neighbors_finder(1.); + for(int v_point_index=0; v_point_index l = *pnf.pull_all_near(n2/2); + bool v = true; + for(auto it = l.cbegin(); it != l.cend(); ++it) + v = v && (G::distance(n2/2,*it)>1.); + BOOST_CHECK(v); + int v_point_index_2 = pnf.pull_near(n2/2); + BOOST_CHECK(v_point_index_2 == -1); +} + + +BOOST_AUTO_TEST_CASE(neighbors_finder) { + Neighbors_finder nf = Neighbors_finder(1.); + for(int v_point_index=1; v_point_index<((n2+n1)*9/10); v_point_index+=2) + nf.add(v_point_index); + // + int v_point_index_1 = nf.pull_near(n2/2); + BOOST_CHECK((v_point_index_1 == -1) || (G::distance(n2/2,v_point_index_1)<=1.)); + std::list l = *nf.pull_all_near(n2/2); + bool v = true; + for(auto it = l.cbegin(); it != l.cend(); ++it) + v = v && (G::distance(n2/2,*it)>1.); + BOOST_CHECK(v); + int v_point_index_2 = nf.pull_near(n2/2); + BOOST_CHECK(v_point_index_2 == -1); +} + +BOOST_AUTO_TEST_CASE(layered_neighbors_finder) { + Layered_neighbors_finder lnf = Layered_neighbors_finder(1.); + for(int v_point_index=1; v_point_index<((n2+n1)*9/10); v_point_index+=2) + lnf.add(v_point_index, v_point_index % 7); + // + int v_point_index_1 = lnf.pull_near(n2/2,6); + BOOST_CHECK((v_point_index_1 == -1) || (G::distance(n2/2,v_point_index_1)<=1.)); + int v_point_index_2 = lnf.pull_near(n2/2,6); + BOOST_CHECK(v_point_index_2 == -1); + v_point_index_1 = lnf.pull_near(n2/2,0); + BOOST_CHECK((v_point_index_1 == -1) || (G::distance(n2/2,v_point_index_1)<=1.)); + v_point_index_2 = lnf.pull_near(n2/2,0); + BOOST_CHECK(v_point_index_2 == -1); +} + +BOOST_AUTO_TEST_CASE(graph_matching) { + Graph_matching m1; + m1.set_r(0.); + int e = 0; + while (m1.multi_augment()) + ++e; + BOOST_CHECK(e <= 2*sqrt(2*(n1+n2))); + Graph_matching m2 = m1; + BOOST_CHECK(!m2.multi_augment()); + m2.set_r(upper_bound); + e = 0; + while (m2.multi_augment()) + ++e; + BOOST_CHECK(e <= 2*sqrt(2*(n1+n2))); + BOOST_CHECK(m2.perfect()); + BOOST_CHECK(!m1.perfect()); +} + +/* +BOOST_AUTO_TEST_CASE(chrono) { + std::ofstream objetfichier; + objetfichier.open("results.csv", std::ios::out); + + for(int n =50; n<=1000; n+=100){ + std::uniform_real_distribution unif1(0.,upper_bound); + std::uniform_real_distribution unif2(upper_bound/1000.,upper_bound/100.); + std::default_random_engine re; + std::vector< std::pair > v1, v2; + for (int i = 0; i < n; i++) { + double a = unif1(re); + double b = unif1(re); + double x = unif2(re); + double y = unif2(re); + v1.emplace_back(std::min(a,b), std::max(a,b)); + v2.emplace_back(std::min(a,b)+std::min(x,y), std::max(a,b)+std::max(x,y)); + if(i%5==0) + v1.emplace_back(std::min(a,b),std::min(a,b)+x); + if(i%3==0) + v2.emplace_back(std::max(a,b),std::max(a,b)+y); + } + + std::chrono::steady_clock::time_point start = std::chrono::steady_clock::now(); + double b = bottleneck_distance(v1,v2); + std::chrono::steady_clock::time_point end = std::chrono::steady_clock::now(); + + typedef std::chrono::duration millisecs_t; + millisecs_t duration(std::chrono::duration_cast(end-start)); + objetfichier << n << ";" << duration.count() << ";" << b << std::endl; + } + objetfichier.close(); +} +*/ + diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index ceb993fa..1436d65a 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -40,4 +40,20 @@ else() add_subdirectory(example/Alpha_shapes) add_subdirectory(example/Bottleneck) -endif() +endif() + + include( ${CGAL_USE_FILE} ) + # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten. + # cf. http://doc.cgal.org/latest/Manual/installation.html#title40 + # A workaround is to add "-std=c++11" again. + # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html + # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html + # but it implies to use cmake version 3.1 at least. + if(NOT MSVC) + include(CheckCXXCompilerFlag) + CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11) + if(COMPILER_SUPPORTS_CXX11) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") + endif() + endif() + # - End of workaround -- cgit v1.2.3 From 02be2aeb7f0a2197d943736aeb9796dc2f5a6f4d Mon Sep 17 00:00:00 2001 From: fgodi Date: Mon, 4 Apr 2016 13:17:50 +0000 Subject: test git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@1094 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 2709dd2557768dcc175a1a626db9308dd9ddec96 --- .../concept/Persistence_diagram.h | 7 - src/Bipartite_graph_matching/example/example.cpp | 44 ----- .../include/gudhi/Graph_matching.h | 213 --------------------- .../include/gudhi/Neighbors_finder.h | 155 --------------- .../include/gudhi/Persistence_diagrams_graph.h | 163 ---------------- .../include/gudhi/Planar_neighbors_finder.h | 171 ----------------- src/Bipartite_graph_matching/test/CMakeLists.txt | 31 --- src/Bipartite_graph_matching/test/README | 12 -- .../test/bottleneck_unit_test.cpp | 207 -------------------- 9 files changed, 1003 deletions(-) delete mode 100644 src/Bipartite_graph_matching/concept/Persistence_diagram.h delete mode 100644 src/Bipartite_graph_matching/example/example.cpp delete mode 100644 src/Bipartite_graph_matching/include/gudhi/Graph_matching.h delete mode 100644 src/Bipartite_graph_matching/include/gudhi/Neighbors_finder.h delete mode 100644 src/Bipartite_graph_matching/include/gudhi/Persistence_diagrams_graph.h delete mode 100644 src/Bipartite_graph_matching/include/gudhi/Planar_neighbors_finder.h delete mode 100644 src/Bipartite_graph_matching/test/CMakeLists.txt delete mode 100644 src/Bipartite_graph_matching/test/README delete mode 100644 src/Bipartite_graph_matching/test/bottleneck_unit_test.cpp (limited to 'src') diff --git a/src/Bipartite_graph_matching/concept/Persistence_diagram.h b/src/Bipartite_graph_matching/concept/Persistence_diagram.h deleted file mode 100644 index eaaf8bc5..00000000 --- a/src/Bipartite_graph_matching/concept/Persistence_diagram.h +++ /dev/null @@ -1,7 +0,0 @@ -typedef typename std::pair Diagram_point; - -struct Persistence_Diagram -{ - const_iterator cbegin() const; - const_iterator cend() const; -}; diff --git a/src/Bipartite_graph_matching/example/example.cpp b/src/Bipartite_graph_matching/example/example.cpp deleted file mode 100644 index d190ab48..00000000 --- a/src/Bipartite_graph_matching/example/example.cpp +++ /dev/null @@ -1,44 +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): Francois Godi - * - * Copyright (C) 2015 INRIA Sophia-Antipolis (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 . - */ - -#include "../include/gudhi/Graph_matching.h" -#include - -using namespace Gudhi::bipartite_graph_matching; - -int main() { - - std::vector< std::pair > v1, v2; - - v1.emplace_back(2.7,3.7); - v1.emplace_back(9.6,14); - v1.emplace_back(34.2,34.974); - - v2.emplace_back(2.8,4.45); - v2.emplace_back(9.5,14.1); - - - double b = bottleneck_distance(v1, v2); - - std::cout << "Bottleneck distance = " << b << std::endl; - -} diff --git a/src/Bipartite_graph_matching/include/gudhi/Graph_matching.h b/src/Bipartite_graph_matching/include/gudhi/Graph_matching.h deleted file mode 100644 index a2754333..00000000 --- a/src/Bipartite_graph_matching/include/gudhi/Graph_matching.h +++ /dev/null @@ -1,213 +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): Francois Godi - * - * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ -#define SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ - -#include - -#include "Neighbors_finder.h" - -namespace Gudhi { - -namespace bipartite_graph_matching { - -/** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams. - * - * - * - * \ingroup bottleneck_distance - */ -template -double bottleneck_distance(const Persistence_diagram1& diag1, const Persistence_diagram2& diag2, double e = 0.); - -/** \internal \brief Structure representing a graph matching. The graph is a Persistence_diagrams_graph. - * - * \ingroup bottleneck_distance - */ -class Graph_matching { -public: - /** \internal \brief Constructor constructing an empty matching. */ - explicit Graph_matching(); - /** \internal \brief Copy operator. */ - Graph_matching& operator=(const Graph_matching& m); - /** \internal \brief Is the matching perfect ? */ - bool perfect() const; - /** \internal \brief Augments the matching with a maximal set of edge-disjoint shortest augmenting paths. */ - bool multi_augment(); - /** \internal \brief Sets the maximum length of the edges allowed to be added in the matching, 0 initially. */ - void set_r(double r); - -private: - double r; - /** \internal \brief Given a point from V, provides its matched point in U, null_point_index() if there isn't. */ - std::vector v_to_u; - /** \internal \brief All the unmatched points in U. */ - std::list unmatched_in_u; - - /** \internal \brief Provides a Layered_neighbors_finder dividing the graph in layers. Basically a BFS. */ - std::unique_ptr layering() const; - /** \internal \brief Augments the matching with a simple path no longer than max_depth. Basically a DFS. */ - bool augment(Layered_neighbors_finder & layered_nf, int u_start_index, int max_depth); - /** \internal \brief Update the matching with the simple augmenting path given as parameter. */ - void update(std::deque & path); -}; - -inline Graph_matching::Graph_matching() - : r(0.), v_to_u(G::size(), null_point_index()), unmatched_in_u() { - for (int u_point_index = 0; u_point_index < G::size(); ++u_point_index) - unmatched_in_u.emplace_back(u_point_index); -} - -inline Graph_matching& Graph_matching::operator=(const Graph_matching& m) { - r = m.r; - v_to_u = m.v_to_u; - unmatched_in_u = m.unmatched_in_u; - return *this; -} - -inline bool Graph_matching::perfect() const { - return unmatched_in_u.empty(); -} - -inline bool Graph_matching::multi_augment() { - if (perfect()) - return false; - Layered_neighbors_finder layered_nf = *layering(); - int max_depth = layered_nf.vlayers_number()*2 - 1; - double rn = sqrt(G::size()); - // verification of a necessary criterion in order to shortcut if possible - if (max_depth <0 || (unmatched_in_u.size() > rn && max_depth >= rn)) - return false; - bool successful = false; - std::list tries(unmatched_in_u); - for (auto it = tries.cbegin(); it != tries.cend(); it++) - // 'augment' has side-effects which have to be always executed, don't change order - successful = augment(layered_nf, *it, max_depth) || successful; - return successful; -} - -inline void Graph_matching::set_r(double r) { - this->r = r; -} - -inline bool Graph_matching::augment(Layered_neighbors_finder & layered_nf, int u_start_index, int max_depth) { - //V vertices have at most one successor, thus when we backtrack from U we can directly pop_back 2 vertices. - std::deque path; - path.emplace_back(u_start_index); - do { - if (static_cast(path.size()) > max_depth) { - path.pop_back(); - path.pop_back(); - } - if (path.empty()) - return false; - path.emplace_back(layered_nf.pull_near(path.back(), static_cast(path.size())/2)); - while (path.back() == null_point_index()) { - path.pop_back(); - path.pop_back(); - if (path.empty()) - return false; - path.pop_back(); - path.emplace_back(layered_nf.pull_near(path.back(), path.size() / 2)); - } - path.emplace_back(v_to_u.at(path.back())); - } while (path.back() != null_point_index()); - //if v_to_u.at(path.back()) has no successor, path.back() is an exposed vertex - path.pop_back(); - update(path); - return true; -} - -inline std::unique_ptr Graph_matching::layering() const { - std::list u_vertices(unmatched_in_u); - std::list v_vertices; - Neighbors_finder nf(r); - for (int v_point_index = 0; v_point_index < G::size(); ++v_point_index) - nf.add(v_point_index); - std::unique_ptr layered_nf(new Layered_neighbors_finder(r)); - for(int layer = 0; !u_vertices.empty(); layer++) { - // one layer is one step in the BFS - for (auto it = u_vertices.cbegin(); it != u_vertices.cend(); ++it) { - std::unique_ptr< std::list > u_succ = std::move(nf.pull_all_near(*it)); - for (auto it = u_succ->cbegin(); it != u_succ->cend(); ++it) { - layered_nf->add(*it, layer); - v_vertices.emplace_back(*it); - } - } - // When the above for finishes, we have progress of one half-step (from U to V) in the BFS - u_vertices.clear(); - bool end = false; - for (auto it = v_vertices.cbegin(); it != v_vertices.cend(); it++) - if (v_to_u.at(*it) == null_point_index()) - // we stop when a nearest exposed V vertex (from U exposed vertices) has been found - end = true; - else - u_vertices.emplace_back(v_to_u.at(*it)); - // When the above for finishes, we have progress of one half-step (from V to U) in the BFS - if (end) - return layered_nf; - v_vertices.clear(); - } - return layered_nf; -} - -inline void Graph_matching::update(std::deque& path) { - unmatched_in_u.remove(path.front()); - for (auto it = path.cbegin(); it != path.cend(); ++it) { - // Be careful, the iterator is incremented twice each time - int tmp = *it; - v_to_u[*(++it)] = tmp; - } -} - -template -double bottleneck_distance(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e) { - G::initialize(diag1, diag2, e); - std::unique_ptr< std::vector > sd = std::move(G::sorted_distances()); - int idmin = 0; - int idmax = sd->size() - 1; - // alpha can be modified, this will change the complexity - double alpha = pow(sd->size(), 0.25); - Graph_matching m; - Graph_matching biggest_unperfect; - while (idmin != idmax) { - int step = static_cast((idmax - idmin) / alpha); - m.set_r(sd->at(idmin + step)); - while (m.multi_augment()); - // The above while compute a maximum matching (according to the r setted before) - if (m.perfect()) { - idmax = idmin + step; - m = biggest_unperfect; - } else { - biggest_unperfect = m; - idmin = idmin + step + 1; - } - } - return sd->at(idmin); -} - -} // namespace bipartite_graph_matching - -} // namespace Gudhi - -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ diff --git a/src/Bipartite_graph_matching/include/gudhi/Neighbors_finder.h b/src/Bipartite_graph_matching/include/gudhi/Neighbors_finder.h deleted file mode 100644 index 78b9debc..00000000 --- a/src/Bipartite_graph_matching/include/gudhi/Neighbors_finder.h +++ /dev/null @@ -1,155 +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): Francois Godi - * - * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_ -#define SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_ - -#include - -#include "Planar_neighbors_finder.h" - -namespace Gudhi { - -namespace bipartite_graph_matching { - -/** \internal \brief data structure used to find any point (including projections) in V near to a query point from U - * (which can be a projection). - * - * V points have to be added manually using their index and before the first pull. A neighbor pulled is automatically removed. - * - * \ingroup bottleneck_distance - */ -class Neighbors_finder { -public: - /** \internal \brief Constructor taking the near distance definition as parameter. */ - Neighbors_finder(double r); - /** \internal \brief A point added will be possibly pulled. */ - void add(int v_point_index); - /** \internal \brief Returns and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ - int pull_near(int u_point_index); - /** \internal \brief Returns and remove all the V points near to the U point given as parameter. */ - std::unique_ptr< std::list > pull_all_near(int u_point_index); - -private: - const double r; - Planar_neighbors_finder planar_neighbors_f; - std::unordered_set projections_f; - void remove(int v_point_index); - bool contains(int v_point_index); -}; - -/** \internal \brief data structure used to find any point (including projections) in V near to a query point from U - * (which can be a projection) in a layered graph layer given as parmeter. - * - * V points have to be added manually using their index and before the first pull. A neighbor pulled is automatically removed. - * - * \ingroup bottleneck_distance - */ -class Layered_neighbors_finder { -public: - /** \internal \brief Constructor taking the near distance definition as parameter. */ - Layered_neighbors_finder(double r); - /** \internal \brief A point added will be possibly pulled. */ - void add(int v_point_index, int vlayer); - /** \internal \brief Returns and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ - int pull_near(int u_point_index, int vlayer); - /** \internal \brief Returns the number of layers. */ - int vlayers_number() const; - -private: - const double r; - std::vector neighbors_finder; -}; - -inline Neighbors_finder::Neighbors_finder(double r) : - r(r), planar_neighbors_f(r), projections_f() { } - -inline void Neighbors_finder::add(int v_point_index) { - if (G::on_the_v_diagonal(v_point_index)) - projections_f.emplace(v_point_index); - else - planar_neighbors_f.add(v_point_index); -} - -inline void Neighbors_finder::remove(int v_point_index) { - if(v_point_index == null_point_index()) - return; - if (G::on_the_v_diagonal(v_point_index)) - projections_f.erase(v_point_index); - else - planar_neighbors_f.remove(v_point_index); -} - -inline bool Neighbors_finder::contains(int v_point_index) { - return planar_neighbors_f.contains(v_point_index) || (projections_f.count(v_point_index)>0); -} - -inline int Neighbors_finder::pull_near(int u_point_index) { - int tmp; - int c = G::corresponding_point_in_v(u_point_index); - if (G::on_the_u_diagonal(u_point_index) && !projections_f.empty()) - //All projections are at distance 0 - tmp = *projections_f.cbegin(); - else if (contains(c) && (G::distance(u_point_index, c) <= r)) - //Is the query point near to its projection ? - tmp = c; - else - //Is the query point near to a V point in the plane ? - tmp = planar_neighbors_f.pull_near(u_point_index); - remove(tmp); - return tmp; -} - -inline std::unique_ptr< std::list > Neighbors_finder::pull_all_near(int u_point_index) { - std::unique_ptr< std::list > all_pull = std::move(planar_neighbors_f.pull_all_near(u_point_index)); - int last_pull = pull_near(u_point_index); - while (last_pull != null_point_index()) { - all_pull->emplace_back(last_pull); - last_pull = pull_near(u_point_index); - } - return all_pull; -} - -inline Layered_neighbors_finder::Layered_neighbors_finder(double r) : - r(r), neighbors_finder() { } - -inline void Layered_neighbors_finder::add(int v_point_index, int vlayer) { - for (int l = neighbors_finder.size(); l <= vlayer; l++) - neighbors_finder.emplace_back(Neighbors_finder(r)); - neighbors_finder.at(vlayer).add(v_point_index); -} - -inline int Layered_neighbors_finder::pull_near(int u_point_index, int vlayer) { - if (static_cast (neighbors_finder.size()) <= vlayer) - return null_point_index(); - return neighbors_finder.at(vlayer).pull_near(u_point_index); -} - -inline int Layered_neighbors_finder::vlayers_number() const { - return static_cast(neighbors_finder.size()); -} - -} // namespace bipartite_graph_matching - -} // namespace Gudhi - -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_ diff --git a/src/Bipartite_graph_matching/include/gudhi/Persistence_diagrams_graph.h b/src/Bipartite_graph_matching/include/gudhi/Persistence_diagrams_graph.h deleted file mode 100644 index 1f8e83e7..00000000 --- a/src/Bipartite_graph_matching/include/gudhi/Persistence_diagrams_graph.h +++ /dev/null @@ -1,163 +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): Francois Godi - * - * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_ -#define SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_ - -#include -#include -#include -#include -#include -#include - -namespace Gudhi { - -namespace bipartite_graph_matching { - -/** \internal \brief Returns the used index for encoding none of the points */ -int null_point_index(); - -/** \internal \brief Structure representing an euclidean bipartite graph containing - * the points from the two persistence diagrams (including the projections). - * - * \ingroup bottleneck_distance - */ -class Persistence_diagrams_graph { -public: - /** \internal \brief Initializer taking 2 Point (concept) ranges as parameters. */ - template - static void initialize(const Persistence_diagram1& diag1, const Persistence_diagram2& diag2, double e); - /** \internal \brief Is the given point from U the projection of a point in V ? */ - static bool on_the_u_diagonal(int u_point_index); - /** \internal \brief Is the given point from V the projection of a point in U ? */ - static bool on_the_v_diagonal(int v_point_index); - /** \internal \brief Given a point from V, returns the corresponding (projection or projector) point in U. */ - static int corresponding_point_in_u(int v_point_index); - /** \internal \brief Given a point from U, returns the corresponding (projection or projector) point in V. */ - static int corresponding_point_in_v(int u_point_index); - /** \internal \brief Given a point from U and a point from V, returns the distance between those points. */ - static double distance(int u_point_index, int v_point_index); - /** \internal \brief Returns size = |U| = |V|. */ - static int size(); - /** \internal \brief Returns the O(n^2) sorted distances between the points. */ - static std::unique_ptr< std::vector > sorted_distances(); - -private: - /** \internal \typedef \brief Internal_point is the internal points representation, indexes used outside. */ - typedef std::pair Internal_point; - static std::vector u; - static std::vector v; - static Internal_point get_u_point(int u_point_index); - static Internal_point get_v_point(int v_point_index); - - friend class Naive_pnf; - friend class Upper_envelope_tree; -}; - -/** \internal \typedef \brief Shorter alias */ -typedef Persistence_diagrams_graph G; - -// static initialization, seems to work but strange -std::vector G::u = [] {return std::vector();}(); -std::vector G::v = [] {return std::vector();}(); - -inline int null_point_index() { - return -1; -} - -template -inline void G::initialize(const Persistence_diagram1 &diag1, - const Persistence_diagram2 &diag2, double e){ - u.clear(); - v.clear(); - for (auto it = diag1.cbegin(); it != diag1.cend(); ++it) - if (it->second - it->first > e) - u.emplace_back(*it); - for (auto it = diag2.cbegin(); it != diag2.cend(); ++it) - if (it->second - it->first > e) - v.emplace_back(*it); - if (u.size() < v.size()) - swap(u, v); -} - -inline bool G::on_the_u_diagonal(int u_point_index) { - return u_point_index >= static_cast (u.size()); -} - -inline bool G::on_the_v_diagonal(int v_point_index) { - return v_point_index >= static_cast (v.size()); -} - -inline int G::corresponding_point_in_u(int v_point_index) { - return on_the_v_diagonal(v_point_index) ? - v_point_index - static_cast (v.size()) : v_point_index + static_cast (u.size()); -} - -inline int G::corresponding_point_in_v(int u_point_index) { - return on_the_u_diagonal(u_point_index) ? - u_point_index - static_cast (u.size()) : u_point_index + static_cast (v.size()); -} - -inline double G::distance(int u_point_index, int v_point_index) { - if (on_the_u_diagonal(u_point_index) && on_the_v_diagonal(v_point_index)) - return 0; - Internal_point p_u = get_u_point(u_point_index); - Internal_point p_v = get_v_point(v_point_index); - return std::max(std::fabs(p_u.first - p_v.first), std::fabs(p_u.second - p_v.second)); -} - -inline int G::size() { - return static_cast (u.size() + v.size()); -} - -inline std::unique_ptr< std::vector > G::sorted_distances() { - // could be optimized - std::set sorted_distances; - for (int u_point_index = 0; u_point_index < size(); ++u_point_index) - for (int v_point_index = 0; v_point_index < size(); ++v_point_index) - sorted_distances.emplace(distance(u_point_index, v_point_index)); - std::unique_ptr< std::vector > sd_up(new std::vector(sorted_distances.cbegin(), sorted_distances.cend())); - return sd_up; -} - -inline G::Internal_point G::get_u_point(int u_point_index) { - if (!on_the_u_diagonal(u_point_index)) - return u.at(u_point_index); - Internal_point projector = v.at(corresponding_point_in_v(u_point_index)); - double x = (projector.first + projector.second) / 2; - return Internal_point(x, x); -} - -inline G::Internal_point G::get_v_point(int v_point_index) { - if (!on_the_v_diagonal(v_point_index)) - return v.at(v_point_index); - Internal_point projector = u.at(corresponding_point_in_u(v_point_index)); - double x = (projector.first + projector.second) / 2; - return Internal_point(x, x); -} - -} // namespace bipartite_graph_matching - -} // namespace Gudhi - -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_ diff --git a/src/Bipartite_graph_matching/include/gudhi/Planar_neighbors_finder.h b/src/Bipartite_graph_matching/include/gudhi/Planar_neighbors_finder.h deleted file mode 100644 index 32155b91..00000000 --- a/src/Bipartite_graph_matching/include/gudhi/Planar_neighbors_finder.h +++ /dev/null @@ -1,171 +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): Francois Godi - * - * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_ -#define SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_ - -#include -#include - -#include "Persistence_diagrams_graph.h" -#include "Envelope_tree.h" - -namespace Gudhi { - -namespace bipartite_graph_matching { - -/** \internal \brief Structure used to find any point in V near (according to the planar distance) to a query point from U. - * - * V points have to be added manually using their index and before the first remove/pull. A neighbor pulled is automatically removed. but we can also - * remove points manually using their index. - * - * \ingroup bottleneck_distance - */ -class Abstract_planar_neighbors_finder { -public: - /** \internal \brief Constructor TODO. */ - Abstract_planar_neighbors_finder(double r); - virtual ~Abstract_planar_neighbors_finder() = 0; - /** \internal \brief A point added will be possibly pulled. */ - virtual void add(int v_point_index) = 0; - /** \internal \brief A point manually removed will no longer be possibly pulled. */ - virtual void remove(int v_point_index) = 0; - /** \internal \brief Can the point given as parameter be returned ? */ - virtual bool contains(int v_point_index) const = 0; - /** \internal \brief Provide and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ - virtual int pull_near(int u_point_index) = 0; - /** \internal \brief Provide and remove all the V points near to the U point given as parameter. */ - virtual std::unique_ptr< std::list > pull_all_near(int u_point_index); - -protected: - const double r; -}; - -/** \internal \brief Naive_pnf is an naïve Abstract_planar_neighbors_finder implementation - * - * \ingroup bottleneck_distance - */ -class Naive_pnf : public Abstract_planar_neighbors_finder { -public: - /** \internal \brief Constructor taking the near distance definition as parameter. */ - Naive_pnf(double r); - /** \internal \brief A point added will be possibly pulled. */ - void add(int v_point_index); - /** \internal \brief A point manually removed will no longer be possibly pulled. */ - void remove(int v_point_index); - /** \internal \brief Can the point given as parameter be returned ? */ - bool contains(int v_point_index) const; - /** \internal \brief Provide and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ - int pull_near(int u_point_index); - /** \internal \brief Provide and remove all the V points near to the U point given as parameter. */ - virtual std::unique_ptr< std::list > pull_all_near(int u_point_index); - -private: - std::pair get_v_key(int v_point_index) const; - std::multimap,int> grid; -}; - -/** \internal \typedef \brief Planar_neighbors_finder is the used Abstract_planar_neighbors_finder's implementation. */ -typedef Naive_pnf Planar_neighbors_finder; - - -inline Abstract_planar_neighbors_finder::Abstract_planar_neighbors_finder(double r) : - r(r) { } - -inline Abstract_planar_neighbors_finder::~Abstract_planar_neighbors_finder() {} - -inline std::unique_ptr< std::list > Abstract_planar_neighbors_finder::pull_all_near(int u_point_index) { - std::unique_ptr< std::list > all_pull(new std::list); - int last_pull = pull_near(u_point_index); - while (last_pull != null_point_index()) { - all_pull->emplace_back(last_pull); - last_pull = pull_near(u_point_index); - } - return all_pull; -} - -inline Naive_pnf::Naive_pnf(double r) : - Abstract_planar_neighbors_finder(r), grid() { } - - -inline std::pair Naive_pnf::get_v_key(int v_point_index) const{ - G::Internal_point v_point = G::get_v_point(v_point_index); - return std::make_pair(static_cast(v_point.first/r), static_cast(v_point.second/r)); -} - -inline void Naive_pnf::add(int v_point_index) { - grid.emplace(get_v_key(v_point_index),v_point_index); -} - -inline void Naive_pnf::remove(int v_point_index) { - for(auto it = grid.find(get_v_key(v_point_index)); it!=grid.end(); it++) - if(it->second==v_point_index){ - grid.erase(it); - return; - } -} - -inline bool Naive_pnf::contains(int v_point_index) const { - if(v_point_index == null_point_index()) - return false; - for(auto it = grid.find(get_v_key(v_point_index)); it!=grid.end(); it++) - if(it->second==v_point_index) - return true; - return false; -} - -inline int Naive_pnf::pull_near(int u_point_index) { - G::Internal_point u_point = G::get_u_point(u_point_index); - int i0 = static_cast(u_point.first/r); - int j0 = static_cast(u_point.second/r); - for(int i = 1; i<= 3; i++) - for(int j = 1; j<= 3; j++) - for(auto it = grid.find(std::make_pair(i0 +(i%3)-1, j0+(j%3)-1)); it!=grid.end(); it++) - if (G::distance(u_point_index, it->second) <= r) { - int tmp = it->second; - grid.erase(it); - return tmp; - } - return null_point_index(); -} - -inline std::unique_ptr< std::list > Naive_pnf::pull_all_near(int u_point_index) { - std::unique_ptr< std::list > all_pull(new std::list); - G::Internal_point u_point = G::get_u_point(u_point_index); - int i0 = static_cast(u_point.first/r); - int j0 = static_cast(u_point.second/r); - for(int i = 1; i<= 3; i++) - for(int j = 1; j<= 3; j++) - for(auto it = grid.find(std::make_pair(i0 +(i%3)-1, j0+(j%3)-1)); it!=grid.end(); it++) - if (G::distance(u_point_index, it->second) <= r) { - int tmp = it->second; - grid.erase(it); - all_pull->emplace_back(tmp); - } - return all_pull; -} - -} // namespace bipartite_graph_matching - -} // namespace Gudhi - -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_ diff --git a/src/Bipartite_graph_matching/test/CMakeLists.txt b/src/Bipartite_graph_matching/test/CMakeLists.txt deleted file mode 100644 index 8e4371b8..00000000 --- a/src/Bipartite_graph_matching/test/CMakeLists.txt +++ /dev/null @@ -1,31 +0,0 @@ -cmake_minimum_required(VERSION 2.6) -project(GUDHIBottleneckUT) - -if (GCOVR_PATH) - # for gcovr to make coverage reports - Corbera Jenkins plugin - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage") - set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage") - set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage") -endif() -if (GPROF_PATH) - # for gprof to make coverage reports - Jenkins - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") - set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg") - set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg") -endif() - message("CMAKE_CXX_FLAGS = ${CMAKE_CXX_FLAGS}") - message("CMAKE_CXX_FLAGS_DEBUG = ${CMAKE_CXX_FLAGS_DEBUG}") - message("CMAKE_CXX_FLAGS_RELEASE = ${CMAKE_CXX_FLAGS_RELEASE}") - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O2 -std=c++11 -Wall -Wpedantic -Wsign-compare") - set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -ggdb -O0") - set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE}") - -add_executable ( BottleneckUT bottleneck_unit_test.cpp ) -target_link_libraries(BottleneckUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) - -# Unitary tests -add_test(NAME BottleneckUT - COMMAND ${CMAKE_CURRENT_BINARY_DIR}/BottleneckUT - # XML format for Jenkins xUnit plugin - --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/BottleneckUT.xml --log_level=test_suite --report_level=no) - diff --git a/src/Bipartite_graph_matching/test/README b/src/Bipartite_graph_matching/test/README deleted file mode 100644 index 0e7b8673..00000000 --- a/src/Bipartite_graph_matching/test/README +++ /dev/null @@ -1,12 +0,0 @@ -To compile: -*********** - -cmake . -make - -To launch with details: -*********************** - -./BottleneckUnitTest --report_level=detailed --log_level=all - - ==> echo $? returns 0 in case of success (non-zero otherwise) diff --git a/src/Bipartite_graph_matching/test/bottleneck_unit_test.cpp b/src/Bipartite_graph_matching/test/bottleneck_unit_test.cpp deleted file mode 100644 index dc33f76b..00000000 --- a/src/Bipartite_graph_matching/test/bottleneck_unit_test.cpp +++ /dev/null @@ -1,207 +0,0 @@ -#define BOOST_TEST_MODULE bottleneck test - -#include -#include -#include "../include/gudhi/Graph_matching.h" - -#include -#include - -using namespace Gudhi::bipartite_graph_matching; - -int n1 = 81; // a natural number >0 -int n2 = 180; // a natural number >0 -double upper_bound = 400.5; // any real >0 - -BOOST_AUTO_TEST_CASE(global){ - std::uniform_real_distribution unif1(0.,upper_bound); - std::uniform_real_distribution unif2(upper_bound/1000.,upper_bound/100.); - std::default_random_engine re; - std::vector< std::pair > v1, v2; - for (int i = 0; i < n1; i++) { - double a = unif1(re); - double b = unif1(re); - double x = unif2(re); - double y = unif2(re); - v1.emplace_back(std::min(a,b), std::max(a,b)); - v2.emplace_back(std::min(a,b)+std::min(x,y), std::max(a,b)+std::max(x,y)); - if(i%5==0) - v1.emplace_back(std::min(a,b),std::min(a,b)+x); - if(i%3==0) - v2.emplace_back(std::max(a,b),std::max(a,b)+y); - } - //99.5 and not 100 to avoid float errors. - BOOST_CHECK(bottleneck_distance(v1, v2) <= upper_bound/99.5); -} - -BOOST_AUTO_TEST_CASE(persistence_diagrams_graph){ - // Random construction - std::uniform_real_distribution unif(0.,upper_bound); - std::default_random_engine re; - std::vector< std::pair > v1, v2; - for (int i = 0; i < n1; i++) { - double a = unif(re); - double b = unif(re); - v1.emplace_back(std::min(a,b), std::max(a,b)); - } - for (int i = 0; i < n2; i++) { - double a = unif(re); - double b = unif(re); - v2.emplace_back(std::min(a,b), std::max(a,b)); - } - G::initialize(v1, v2, 0.); - std::unique_ptr< std::vector > d = std::move(G::sorted_distances()); - // - BOOST_CHECK(!G::on_the_u_diagonal(n1-1)); - BOOST_CHECK(!G::on_the_u_diagonal(n1)); - BOOST_CHECK(!G::on_the_u_diagonal(n2-1)); - BOOST_CHECK(G::on_the_u_diagonal(n2)); - BOOST_CHECK(!G::on_the_v_diagonal(n1-1)); - BOOST_CHECK(G::on_the_v_diagonal(n1)); - BOOST_CHECK(G::on_the_v_diagonal(n2-1)); - BOOST_CHECK(G::on_the_v_diagonal(n2)); - // - BOOST_CHECK(G::corresponding_point_in_u(0)==n2); - BOOST_CHECK(G::corresponding_point_in_u(n1)==0); - BOOST_CHECK(G::corresponding_point_in_v(0)==n1); - BOOST_CHECK(G::corresponding_point_in_v(n2)==0); - // - BOOST_CHECK(G::size()==(n1+n2)); - // - BOOST_CHECK((int) d->size() <= (n1+n2)*(n1+n2) - n1*n2 + 1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,0))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n1-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n2-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n2))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,(n1+n2)-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,0))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n1-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n2-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n2))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,(n1+n2)-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,0))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n1-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n2-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n2))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,(n1+n2)-1))==1); -} - - -BOOST_AUTO_TEST_CASE(planar_neighbors_finder) { - Planar_neighbors_finder pnf = Planar_neighbors_finder(1.); - for(int v_point_index=0; v_point_index l = *pnf.pull_all_near(n2/2); - bool v = true; - for(auto it = l.cbegin(); it != l.cend(); ++it) - v = v && (G::distance(n2/2,*it)>1.); - BOOST_CHECK(v); - int v_point_index_2 = pnf.pull_near(n2/2); - BOOST_CHECK(v_point_index_2 == -1); -} - - -BOOST_AUTO_TEST_CASE(neighbors_finder) { - Neighbors_finder nf = Neighbors_finder(1.); - for(int v_point_index=1; v_point_index<((n2+n1)*9/10); v_point_index+=2) - nf.add(v_point_index); - // - int v_point_index_1 = nf.pull_near(n2/2); - BOOST_CHECK((v_point_index_1 == -1) || (G::distance(n2/2,v_point_index_1)<=1.)); - std::list l = *nf.pull_all_near(n2/2); - bool v = true; - for(auto it = l.cbegin(); it != l.cend(); ++it) - v = v && (G::distance(n2/2,*it)>1.); - BOOST_CHECK(v); - int v_point_index_2 = nf.pull_near(n2/2); - BOOST_CHECK(v_point_index_2 == -1); -} - -BOOST_AUTO_TEST_CASE(layered_neighbors_finder) { - Layered_neighbors_finder lnf = Layered_neighbors_finder(1.); - for(int v_point_index=1; v_point_index<((n2+n1)*9/10); v_point_index+=2) - lnf.add(v_point_index, v_point_index % 7); - // - int v_point_index_1 = lnf.pull_near(n2/2,6); - BOOST_CHECK((v_point_index_1 == -1) || (G::distance(n2/2,v_point_index_1)<=1.)); - int v_point_index_2 = lnf.pull_near(n2/2,6); - BOOST_CHECK(v_point_index_2 == -1); - v_point_index_1 = lnf.pull_near(n2/2,0); - BOOST_CHECK((v_point_index_1 == -1) || (G::distance(n2/2,v_point_index_1)<=1.)); - v_point_index_2 = lnf.pull_near(n2/2,0); - BOOST_CHECK(v_point_index_2 == -1); -} - -BOOST_AUTO_TEST_CASE(graph_matching) { - Graph_matching m1; - m1.set_r(0.); - int e = 0; - while (m1.multi_augment()) - ++e; - BOOST_CHECK(e <= 2*sqrt(2*(n1+n2))); - Graph_matching m2 = m1; - BOOST_CHECK(!m2.multi_augment()); - m2.set_r(upper_bound); - e = 0; - while (m2.multi_augment()) - ++e; - BOOST_CHECK(e <= 2*sqrt(2*(n1+n2))); - BOOST_CHECK(m2.perfect()); - BOOST_CHECK(!m1.perfect()); -} - -/* -BOOST_AUTO_TEST_CASE(chrono) { - std::ofstream objetfichier; - objetfichier.open("results.csv", std::ios::out); - - for(int n =50; n<=1000; n+=100){ - std::uniform_real_distribution unif1(0.,upper_bound); - std::uniform_real_distribution unif2(upper_bound/1000.,upper_bound/100.); - std::default_random_engine re; - std::vector< std::pair > v1, v2; - for (int i = 0; i < n; i++) { - double a = unif1(re); - double b = unif1(re); - double x = unif2(re); - double y = unif2(re); - v1.emplace_back(std::min(a,b), std::max(a,b)); - v2.emplace_back(std::min(a,b)+std::min(x,y), std::max(a,b)+std::max(x,y)); - if(i%5==0) - v1.emplace_back(std::min(a,b),std::min(a,b)+x); - if(i%3==0) - v2.emplace_back(std::max(a,b),std::max(a,b)+y); - } - - std::chrono::steady_clock::time_point start = std::chrono::steady_clock::now(); - double b = bottleneck_distance(v1,v2); - std::chrono::steady_clock::time_point end = std::chrono::steady_clock::now(); - - typedef std::chrono::duration millisecs_t; - millisecs_t duration(std::chrono::duration_cast(end-start)); - objetfichier << n << ";" << duration.count() << ";" << b << std::endl; - } - objetfichier.close(); -} -*/ - -- cgit v1.2.3 From 84973edfb1110b39d01e0089c6361c10e20a0cf7 Mon Sep 17 00:00:00 2001 From: fgodi Date: Mon, 4 Apr 2016 15:03:20 +0000 Subject: workaround git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@1096 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: bf66a203ab0cd9f8fcf437cbb20db0646639b7c0 --- src/Alpha_shapes/example/CMakeLists.txt | 9 +++++++++ src/Alpha_shapes/test/CMakeLists.txt | 9 +++++++++ src/Bipartite_graphs_matching/example/CMakeLists.txt | 9 +++++++++ src/Bipartite_graphs_matching/test/CMakeLists.txt | 9 +++++++++ 4 files changed, 36 insertions(+) (limited to 'src') diff --git a/src/Alpha_shapes/example/CMakeLists.txt b/src/Alpha_shapes/example/CMakeLists.txt index fb94ca05..8692c7a7 100644 --- a/src/Alpha_shapes/example/CMakeLists.txt +++ b/src/Alpha_shapes/example/CMakeLists.txt @@ -8,6 +8,15 @@ if(CGAL_FOUND) message(STATUS "CGAL version: ${CGAL_VERSION}.") include( ${CGAL_USE_FILE} ) + + if(NOT MSVC) + include(CheckCXXCompilerFlag) + CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11) + if(COMPILER_SUPPORTS_CXX11) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") + endif() + endif() + # - End of workaround find_package(Eigen3 3.1.0) if (EIGEN3_FOUND) diff --git a/src/Alpha_shapes/test/CMakeLists.txt b/src/Alpha_shapes/test/CMakeLists.txt index 7d61a3dd..e2dd786c 100644 --- a/src/Alpha_shapes/test/CMakeLists.txt +++ b/src/Alpha_shapes/test/CMakeLists.txt @@ -8,6 +8,15 @@ if(CGAL_FOUND) message(STATUS "CGAL version: ${CGAL_VERSION}.") include( ${CGAL_USE_FILE} ) + + if(NOT MSVC) + include(CheckCXXCompilerFlag) + CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11) + if(COMPILER_SUPPORTS_CXX11) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") + endif() + endif() + # - End of workaround find_package(Eigen3 3.1.0) if (EIGEN3_FOUND) diff --git a/src/Bipartite_graphs_matching/example/CMakeLists.txt b/src/Bipartite_graphs_matching/example/CMakeLists.txt index aaf32abd..4e8766cc 100644 --- a/src/Bipartite_graphs_matching/example/CMakeLists.txt +++ b/src/Bipartite_graphs_matching/example/CMakeLists.txt @@ -8,6 +8,15 @@ if(CGAL_FOUND) message(STATUS "CGAL version: ${CGAL_VERSION}.") include( ${CGAL_USE_FILE} ) + + if(NOT MSVC) + include(CheckCXXCompilerFlag) + CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11) + if(COMPILER_SUPPORTS_CXX11) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") + endif() + endif() + # - End of workaround find_package(Eigen3 3.1.0) if (EIGEN3_FOUND) diff --git a/src/Bipartite_graphs_matching/test/CMakeLists.txt b/src/Bipartite_graphs_matching/test/CMakeLists.txt index abf18b1b..ab0461cc 100644 --- a/src/Bipartite_graphs_matching/test/CMakeLists.txt +++ b/src/Bipartite_graphs_matching/test/CMakeLists.txt @@ -9,6 +9,15 @@ if(CGAL_FOUND) message(STATUS "CGAL version: ${CGAL_VERSION}.") include( ${CGAL_USE_FILE} ) + + if(NOT MSVC) + include(CheckCXXCompilerFlag) + CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11) + if(COMPILER_SUPPORTS_CXX11) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") + endif() + endif() + # - End of workaround find_package(Eigen3 3.1.0) if (EIGEN3_FOUND) -- cgit v1.2.3 From 651ab90b9f8209a97761103581dc4c00121a16ef Mon Sep 17 00:00:00 2001 From: fgodi Date: Mon, 23 May 2016 16:34:18 +0000 Subject: save git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@1185 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 4be2335267f7ad5253cde7f0573199013034c00e --- .../include/gudhi/Graph_matching.h | 18 +-- .../include/gudhi/Internal_point.h | 134 ++++++++++++++++++ .../include/gudhi/Neighbors_finder.h | 14 +- .../include/gudhi/Persistence_diagrams_graph.h | 41 +++--- .../include/gudhi/Planar_neighbors_finder.h | 152 ++++++++++++++------- 5 files changed, 268 insertions(+), 91 deletions(-) create mode 100644 src/Bipartite_graphs_matching/include/gudhi/Internal_point.h (limited to 'src') diff --git a/src/Bipartite_graphs_matching/include/gudhi/Graph_matching.h b/src/Bipartite_graphs_matching/include/gudhi/Graph_matching.h index a2754333..228de584 100644 --- a/src/Bipartite_graphs_matching/include/gudhi/Graph_matching.h +++ b/src/Bipartite_graphs_matching/include/gudhi/Graph_matching.h @@ -65,7 +65,7 @@ private: std::list unmatched_in_u; /** \internal \brief Provides a Layered_neighbors_finder dividing the graph in layers. Basically a BFS. */ - std::unique_ptr layering() const; + std::shared_ptr layering() const; /** \internal \brief Augments the matching with a simple path no longer than max_depth. Basically a DFS. */ bool augment(Layered_neighbors_finder & layered_nf, int u_start_index, int max_depth); /** \internal \brief Update the matching with the simple augmenting path given as parameter. */ @@ -138,20 +138,20 @@ inline bool Graph_matching::augment(Layered_neighbors_finder & layered_nf, int u return true; } -inline std::unique_ptr Graph_matching::layering() const { +inline std::shared_ptr Graph_matching::layering() const { std::list u_vertices(unmatched_in_u); std::list v_vertices; Neighbors_finder nf(r); for (int v_point_index = 0; v_point_index < G::size(); ++v_point_index) nf.add(v_point_index); - std::unique_ptr layered_nf(new Layered_neighbors_finder(r)); + std::shared_ptr layered_nf(new Layered_neighbors_finder(r)); for(int layer = 0; !u_vertices.empty(); layer++) { // one layer is one step in the BFS - for (auto it = u_vertices.cbegin(); it != u_vertices.cend(); ++it) { - std::unique_ptr< std::list > u_succ = std::move(nf.pull_all_near(*it)); - for (auto it = u_succ->cbegin(); it != u_succ->cend(); ++it) { - layered_nf->add(*it, layer); - v_vertices.emplace_back(*it); + for (auto it1 = u_vertices.cbegin(); it1 != u_vertices.cend(); ++it1) { + std::shared_ptr> u_succ(nf.pull_all_near(*it1)); + for (auto it2 = u_succ->begin(); it2 != u_succ->end(); ++it2) { + layered_nf->add(*it2, layer); + v_vertices.emplace_back(*it2); } } // When the above for finishes, we have progress of one half-step (from U to V) in the BFS @@ -183,7 +183,7 @@ inline void Graph_matching::update(std::deque& path) { template double bottleneck_distance(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e) { G::initialize(diag1, diag2, e); - std::unique_ptr< std::vector > sd = std::move(G::sorted_distances()); + std::shared_ptr< std::vector > sd(G::sorted_distances()); int idmin = 0; int idmax = sd->size() - 1; // alpha can be modified, this will change the complexity diff --git a/src/Bipartite_graphs_matching/include/gudhi/Internal_point.h b/src/Bipartite_graphs_matching/include/gudhi/Internal_point.h new file mode 100644 index 00000000..633a3767 --- /dev/null +++ b/src/Bipartite_graphs_matching/include/gudhi/Internal_point.h @@ -0,0 +1,134 @@ +/* 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): Francois Godi + * + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_INTERNAL_POINT_H_ +#define SRC_BOTTLENECK_INCLUDE_GUDHI_INTERNAL_POINT_H_ + +//namespace Gudhi { + +//namespace bipartite_graph_matching { + +/** \internal \brief Returns the used index for encoding none of the points */ +int null_point_index(); + +/** \internal \typedef \brief Internal_point is the internal points representation, indexes used outside. */ +struct Internal_point { + double vec[2]; + int point_index; + Internal_point() { vec[0]= vec[1] = 0.; point_index = null_point_index(); } + Internal_point(double x, double y) { vec[0]=x; vec[1]=y; point_index = null_point_index(); } + double x() const { return vec[ 0 ]; } + double y() const { return vec[ 1 ]; } + double& x() { return vec[ 0 ]; } + double& y() { return vec[ 1 ]; } + bool operator==(const Internal_point& p) const + { + return (x() == p.x()) && (y() == p.y()); + } + bool operator!=(const Internal_point& p) const { return ! (*this == p); } +}; + +namespace CGAL { +template <> +struct Kernel_traits { + struct Kernel { + typedef double FT; + typedef double RT; + }; +}; +} + +struct Construct_coord_iterator { + typedef const double* result_type; + const double* operator()(const Internal_point& p) const + { return static_cast(p.vec); } + const double* operator()(const Internal_point& p, int) const + { return static_cast(p.vec+2); } +}; +/* +struct Distance { + typedef Internal_point Query_item; + typedef Internal_point Point_d; + typedef double FT; + typedef CGAL::Dimension_tag<2> D; + + FT transformed_distance(const Query_item& q, const Point_d& p) const { + FT d0= std::abs(q.x()-p.x()); + FT d1= std::abs(q.y()-p.y()); + return std::max(d0,d1); + } + FT min_distance_to_rectangle(const Query_item& q, + const CGAL::Kd_tree_rectangle& b) const { + FT d0(0.), d1(0.); + if (q.x() < b.min_coord(0)) + d0 += (b.min_coord(0)-q.x()); + if (q.x() > b.max_coord(0)) + d0 += (q.x()-b.max_coord(0)); + if (q.y() < b.min_coord(1)) + d1 += (b.min_coord(1)-q.y()); + if (q.y() > b.max_coord(1)) + d1 += (q.y()-b.max_coord(1)); + return std::max(d0,d1); + } + FT min_distance_to_rectangle(const Query_item& q, const CGAL::Kd_tree_rectangle& b,std::vector& dists){ + dists[0] = dists[1] = 0.; + if (q.x() < b.min_coord(0)) + dists[0] = (b.min_coord(0)- q.x()); + if (q.x() > b.max_coord(0)) + dists[0] = (q.x()-b.max_coord(0)); + if (q.y() < b.min_coord(1)) + dists[1] = (b.min_coord(1)-q.y()); + if (q.y() > b.max_coord(1)) + dists[1] = (q.y()-b.max_coord(1)); + return std::max(dists[0],dists[1]); + } + FT max_distance_to_rectangle(const Query_item& q, const CGAL::Kd_tree_rectangle& b) const { + FT d0 = (q.x() >= (b.min_coord(0)+b.max_coord(0))/2.) ? + (q.x()-b.min_coord(0)) : (b.max_coord(0)-q.x()); + FT d1 = (q.y() >= (b.min_coord(1)+b.max_coord(1))/2.) ? + (q.y()-b.min_coord(1)) : (b.max_coord(1)-q.y()); + return std::max(d0, d1); + } + FT max_distance_to_rectangle(const Query_item& q, const CGAL::Kd_tree_rectangle& b,std::vector& dists){ + dists[0] = (q.x() >= (b.min_coord(0)+b.max_coord(0))/2.0) ? + (q.x()-b.min_coord(0)) : (b.max_coord(0)-q.x()); + dists[1] = (q.y() >= (b.min_coord(1)+b.max_coord(1))/2.0) ? + (q.y()-b.min_coord(1)) : (b.max_coord(1)-q.y()); + return std::max(dists[0], dists[1]); + } + FT new_distance(FT& dist, FT old_off, FT new_off, + int) const { + return dist + new_off - old_off; //works ? + } + FT transformed_distance(FT d) const { return d; } + FT inverse_of_transformed_distance(FT d) { return d; } +}; // end of struct Distance +*/ +inline int null_point_index() { + return -1; +} + +//} // namespace bipartite_graph_matching + +//} // namespace Gudhi + +#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_ diff --git a/src/Bipartite_graphs_matching/include/gudhi/Neighbors_finder.h b/src/Bipartite_graphs_matching/include/gudhi/Neighbors_finder.h index 78b9debc..2ef7f768 100644 --- a/src/Bipartite_graphs_matching/include/gudhi/Neighbors_finder.h +++ b/src/Bipartite_graphs_matching/include/gudhi/Neighbors_finder.h @@ -47,7 +47,7 @@ public: /** \internal \brief Returns and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ int pull_near(int u_point_index); /** \internal \brief Returns and remove all the V points near to the U point given as parameter. */ - std::unique_ptr< std::list > pull_all_near(int u_point_index); + std::shared_ptr< std::list > pull_all_near(int u_point_index); private: const double r; @@ -77,7 +77,7 @@ public: private: const double r; - std::vector neighbors_finder; + std::vector> neighbors_finder; }; inline Neighbors_finder::Neighbors_finder(double r) : @@ -119,8 +119,8 @@ inline int Neighbors_finder::pull_near(int u_point_index) { return tmp; } -inline std::unique_ptr< std::list > Neighbors_finder::pull_all_near(int u_point_index) { - std::unique_ptr< std::list > all_pull = std::move(planar_neighbors_f.pull_all_near(u_point_index)); +inline std::shared_ptr< std::list > Neighbors_finder::pull_all_near(int u_point_index) { + std::shared_ptr< std::list > all_pull(planar_neighbors_f.pull_all_near(u_point_index)); int last_pull = pull_near(u_point_index); while (last_pull != null_point_index()) { all_pull->emplace_back(last_pull); @@ -134,14 +134,14 @@ inline Layered_neighbors_finder::Layered_neighbors_finder(double r) : inline void Layered_neighbors_finder::add(int v_point_index, int vlayer) { for (int l = neighbors_finder.size(); l <= vlayer; l++) - neighbors_finder.emplace_back(Neighbors_finder(r)); - neighbors_finder.at(vlayer).add(v_point_index); + neighbors_finder.emplace_back(std::shared_ptr(new Neighbors_finder(r))); + neighbors_finder.at(vlayer)->add(v_point_index); } inline int Layered_neighbors_finder::pull_near(int u_point_index, int vlayer) { if (static_cast (neighbors_finder.size()) <= vlayer) return null_point_index(); - return neighbors_finder.at(vlayer).pull_near(u_point_index); + return neighbors_finder.at(vlayer)->pull_near(u_point_index); } inline int Layered_neighbors_finder::vlayers_number() const { diff --git a/src/Bipartite_graphs_matching/include/gudhi/Persistence_diagrams_graph.h b/src/Bipartite_graphs_matching/include/gudhi/Persistence_diagrams_graph.h index 6420b772..2ba960a7 100644 --- a/src/Bipartite_graphs_matching/include/gudhi/Persistence_diagrams_graph.h +++ b/src/Bipartite_graphs_matching/include/gudhi/Persistence_diagrams_graph.h @@ -30,13 +30,12 @@ #include #include #include +#include "Internal_point.h" namespace Gudhi { namespace bipartite_graph_matching { -/** \internal \brief Returns the used index for encoding none of the points */ -int null_point_index(); /** \internal \brief Structure representing an euclidean bipartite graph containing * the points from the two persistence diagrams (including the projections). @@ -61,30 +60,24 @@ public: /** \internal \brief Returns size = |U| = |V|. */ static int size(); /** \internal \brief Returns the O(n^2) sorted distances between the points. */ - static std::unique_ptr< std::vector > sorted_distances(); + static std::shared_ptr< std::vector > sorted_distances(); private: - /** \internal \typedef \brief Internal_point is the internal points representation, indexes used outside. */ - typedef std::pair Internal_point; static std::vector u; static std::vector v; static Internal_point get_u_point(int u_point_index); static Internal_point get_v_point(int v_point_index); friend class Naive_pnf; - friend class Upper_envelope_tree; + friend class Cgal_pnf; }; /** \internal \typedef \brief Shorter alias */ typedef Persistence_diagrams_graph G; -// static initialization, seems to work but strange -std::vector G::u = [] {return std::vector();}(); -std::vector G::v = [] {return std::vector();}(); - -inline int null_point_index() { - return -1; -} +// static initialization +std::vector G::u = [] {return std::vector();}(); +std::vector G::v = [] {return std::vector();}(); template inline void G::initialize(const Persistence_diagram1 &diag1, @@ -92,10 +85,10 @@ inline void G::initialize(const Persistence_diagram1 &diag1, u.clear(); v.clear(); for (auto it = diag1.cbegin(); it != diag1.cend(); ++it) - if (it->second - it->first > e) + if (it->y() - it->x() > e) u.emplace_back(*it); for (auto it = diag2.cbegin(); it != diag2.cend(); ++it) - if (it->second - it->first > e) + if (it->y() - it->x() > e) v.emplace_back(*it); if (u.size() < v.size()) swap(u, v); @@ -124,37 +117,37 @@ inline double G::distance(int u_point_index, int v_point_index) { return 0; Internal_point p_u = get_u_point(u_point_index); Internal_point p_v = get_v_point(v_point_index); - return std::max(std::fabs(p_u.first - p_v.first), std::fabs(p_u.second - p_v.second)); + return std::max(std::fabs(p_u.x() - p_v.x()), std::fabs(p_u.y() - p_v.y())); } inline int G::size() { return static_cast (u.size() + v.size()); } -inline std::unique_ptr< std::vector > G::sorted_distances() { +inline std::shared_ptr< std::vector > G::sorted_distances() { // could be optimized std::set sorted_distances; for (int u_point_index = 0; u_point_index < size(); ++u_point_index) for (int v_point_index = 0; v_point_index < size(); ++v_point_index) sorted_distances.emplace(distance(u_point_index, v_point_index)); - std::unique_ptr< std::vector > sd_up(new std::vector(sorted_distances.cbegin(), sorted_distances.cend())); + std::shared_ptr< std::vector > sd_up(new std::vector(sorted_distances.cbegin(), sorted_distances.cend())); return sd_up; } -inline G::Internal_point G::get_u_point(int u_point_index) { +inline Internal_point G::get_u_point(int u_point_index) { if (!on_the_u_diagonal(u_point_index)) return u.at(u_point_index); Internal_point projector = v.at(corresponding_point_in_v(u_point_index)); - double x = (projector.first + projector.second) / 2; - return Internal_point(x, x); + double m = (projector.x() + projector.y()) / 2; + return Internal_point(m, m); } -inline G::Internal_point G::get_v_point(int v_point_index) { +inline Internal_point G::get_v_point(int v_point_index) { if (!on_the_v_diagonal(v_point_index)) return v.at(v_point_index); Internal_point projector = u.at(corresponding_point_in_u(v_point_index)); - double x = (projector.first + projector.second) / 2; - return Internal_point(x, x); + double m = (projector.x() + projector.y()) / 2; + return Internal_point(m, m); } } // namespace bipartite_graph_matching diff --git a/src/Bipartite_graphs_matching/include/gudhi/Planar_neighbors_finder.h b/src/Bipartite_graphs_matching/include/gudhi/Planar_neighbors_finder.h index 3564dcf9..47c1a8fc 100644 --- a/src/Bipartite_graphs_matching/include/gudhi/Planar_neighbors_finder.h +++ b/src/Bipartite_graphs_matching/include/gudhi/Planar_neighbors_finder.h @@ -25,9 +25,12 @@ #include #include - +#include +#include +#include #include "Persistence_diagrams_graph.h" + namespace Gudhi { namespace bipartite_graph_matching { @@ -39,34 +42,39 @@ namespace bipartite_graph_matching { * * \ingroup bottleneck_distance */ -class Abstract_planar_neighbors_finder { +class Naive_pnf { public: - /** \internal \brief Constructor TODO. */ - Abstract_planar_neighbors_finder(double r); - virtual ~Abstract_planar_neighbors_finder() = 0; + /** \internal \brief Constructor taking the near distance definition as parameter. */ + Naive_pnf(double r_); /** \internal \brief A point added will be possibly pulled. */ - virtual void add(int v_point_index) = 0; + void add(int v_point_index); /** \internal \brief A point manually removed will no longer be possibly pulled. */ - virtual void remove(int v_point_index) = 0; + void remove(int v_point_index); /** \internal \brief Can the point given as parameter be returned ? */ - virtual bool contains(int v_point_index) const = 0; + bool contains(int v_point_index) const; /** \internal \brief Provide and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ - virtual int pull_near(int u_point_index) = 0; + int pull_near(int u_point_index); /** \internal \brief Provide and remove all the V points near to the U point given as parameter. */ - virtual std::unique_ptr< std::list > pull_all_near(int u_point_index); + virtual std::shared_ptr< std::list > pull_all_near(int u_point_index); -protected: - const double r; +private: + double r; + std::pair get_v_key(int v_point_index) const; + std::multimap,int> grid; }; -/** \internal \brief Naive_pnf is an naïve Abstract_planar_neighbors_finder implementation - * - * \ingroup bottleneck_distance - */ -class Naive_pnf : public Abstract_planar_neighbors_finder { +class Cgal_pnf { + + typedef CGAL::Dimension_tag<2> D; + typedef CGAL::Search_traits Cgal_traits; + typedef CGAL::Weighted_Minkowski_distance Distance; + typedef CGAL::Orthogonal_incremental_neighbor_search K_neighbor_search; + typedef K_neighbor_search::Tree Kd_tree; + + public: /** \internal \brief Constructor taking the near distance definition as parameter. */ - Naive_pnf(double r); + Cgal_pnf(double r_); /** \internal \brief A point added will be possibly pulled. */ void add(int v_point_index); /** \internal \brief A point manually removed will no longer be possibly pulled. */ @@ -76,39 +84,24 @@ public: /** \internal \brief Provide and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ int pull_near(int u_point_index); /** \internal \brief Provide and remove all the V points near to the U point given as parameter. */ - virtual std::unique_ptr< std::list > pull_all_near(int u_point_index); + virtual std::shared_ptr< std::list > pull_all_near(int u_point_index); private: - std::pair get_v_key(int v_point_index) const; - std::multimap,int> grid; + double r; + std::set contents; + Kd_tree kd_t; }; -/** \internal \typedef \brief Planar_neighbors_finder is the used Abstract_planar_neighbors_finder's implementation. */ -typedef Naive_pnf Planar_neighbors_finder; - - -inline Abstract_planar_neighbors_finder::Abstract_planar_neighbors_finder(double r) : - r(r) { } - -inline Abstract_planar_neighbors_finder::~Abstract_planar_neighbors_finder() {} - -inline std::unique_ptr< std::list > Abstract_planar_neighbors_finder::pull_all_near(int u_point_index) { - std::unique_ptr< std::list > all_pull(new std::list); - int last_pull = pull_near(u_point_index); - while (last_pull != null_point_index()) { - all_pull->emplace_back(last_pull); - last_pull = pull_near(u_point_index); - } - return all_pull; -} +/** \internal \typedef \brief Planar_neighbors_finder is the used implementation. */ +typedef Cgal_pnf Planar_neighbors_finder; -inline Naive_pnf::Naive_pnf(double r) : - Abstract_planar_neighbors_finder(r), grid() { } +inline Naive_pnf::Naive_pnf(double r_) : + r(r_), grid() { } inline std::pair Naive_pnf::get_v_key(int v_point_index) const{ - G::Internal_point v_point = G::get_v_point(v_point_index); - return std::make_pair(static_cast(v_point.first/r), static_cast(v_point.second/r)); + Internal_point v_point = G::get_v_point(v_point_index); + return std::make_pair(static_cast(v_point.x()/r), static_cast(v_point.y()/r)); } inline void Naive_pnf::add(int v_point_index) { @@ -133,9 +126,9 @@ inline bool Naive_pnf::contains(int v_point_index) const { } inline int Naive_pnf::pull_near(int u_point_index) { - G::Internal_point u_point = G::get_u_point(u_point_index); - int i0 = static_cast(u_point.first/r); - int j0 = static_cast(u_point.second/r); + Internal_point u_point = G::get_u_point(u_point_index); + int i0 = static_cast(u_point.x()/r); + int j0 = static_cast(u_point.y()/r); for(int i = 1; i<= 3; i++) for(int j = 1; j<= 3; j++) for(auto it = grid.find(std::make_pair(i0 +(i%3)-1, j0+(j%3)-1)); it!=grid.end(); it++) @@ -147,11 +140,11 @@ inline int Naive_pnf::pull_near(int u_point_index) { return null_point_index(); } -inline std::unique_ptr< std::list > Naive_pnf::pull_all_near(int u_point_index) { - std::unique_ptr< std::list > all_pull(new std::list); - G::Internal_point u_point = G::get_u_point(u_point_index); - int i0 = static_cast(u_point.first/r); - int j0 = static_cast(u_point.second/r); +inline std::shared_ptr< std::list > Naive_pnf::pull_all_near(int u_point_index) { + std::shared_ptr< std::list > all_pull(new std::list); + Internal_point u_point = G::get_u_point(u_point_index); + int i0 = static_cast(u_point.x()/r); + int j0 = static_cast(u_point.y()/r); for(int i = 1; i<= 3; i++) for(int j = 1; j<= 3; j++) for(auto it = grid.find(std::make_pair(i0 +(i%3)-1, j0+(j%3)-1)); it!=grid.end(); it++) @@ -163,6 +156,63 @@ inline std::unique_ptr< std::list > Naive_pnf::pull_all_near(int u_point_in return all_pull; } + +/** \internal \brief Constructor taking the near distance definition as parameter. */ +inline Cgal_pnf::Cgal_pnf(double r_) + : r(r_), contents(), kd_t() {} + + +/** \internal \brief A point added will be possibly pulled. */ +inline void Cgal_pnf::add(int v_point_index){ + Internal_point v_point = G::get_v_point(v_point_index); + v_point.point_index = v_point_index; + kd_t.insert(v_point); + contents.insert(v_point_index); +} + +/** \internal \brief A point manually removed will no longer be possibly pulled. */ +inline void Cgal_pnf::remove(int v_point_index){ + contents.erase(v_point_index); +} + +/** \internal \brief Can the point given as parameter be returned ? */ +inline bool Cgal_pnf::contains(int v_point_index) const{ + return contents.count(v_point_index)>0; +} + +/** \internal \brief Provide and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ +inline int Cgal_pnf::pull_near(int u_point_index){ + Internal_point u_point = G::get_u_point(u_point_index); + K_neighbor_search search(kd_t, u_point, 0., true, Distance(0.)); + for (auto it = search.begin(); it != search.end(); it++) + if(contents.count(it->first.point_index)==0) + kd_t.remove(it->first); + else if(G::distance(u_point_index, it->first.point_index) > r){ + for(auto itc=contents.cbegin(); itc != contents.cend(); itc++) + if(G::distance(u_point_index, *itc) <= r) + std::cout << G::distance(u_point_index, *itc) << " ! > " << r << std::endl; + return null_point_index(); + } + else + { + kd_t.remove(it->first); + contents.erase(it->first.point_index); + return it->first.point_index; + } + return null_point_index(); +} + +inline std::shared_ptr< std::list > Cgal_pnf::pull_all_near(int u_point_index) { + std::shared_ptr< std::list > all_pull(new std::list); + int last_pull = pull_near(u_point_index); + while (last_pull != null_point_index()) { + all_pull->emplace_back(last_pull); + last_pull = pull_near(u_point_index); + } + return all_pull; +} + + } // namespace bipartite_graph_matching } // namespace Gudhi -- cgit v1.2.3 From 6a9c5196e3115f323677172fa0f03ef545604509 Mon Sep 17 00:00:00 2001 From: fgodi Date: Mon, 23 May 2016 16:35:04 +0000 Subject: save git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@1186 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 9fa716e4f240d0f829527666f19330c7c63f6c30 --- .../test/bottleneck_unit_test.cpp | 27 +++++++++------------- 1 file changed, 11 insertions(+), 16 deletions(-) (limited to 'src') diff --git a/src/Bipartite_graphs_matching/test/bottleneck_unit_test.cpp b/src/Bipartite_graphs_matching/test/bottleneck_unit_test.cpp index dc33f76b..2e79ccdc 100644 --- a/src/Bipartite_graphs_matching/test/bottleneck_unit_test.cpp +++ b/src/Bipartite_graphs_matching/test/bottleneck_unit_test.cpp @@ -11,13 +11,13 @@ using namespace Gudhi::bipartite_graph_matching; int n1 = 81; // a natural number >0 int n2 = 180; // a natural number >0 -double upper_bound = 400.5; // any real >0 +double upper_bound = 406.43; // any real >0 BOOST_AUTO_TEST_CASE(global){ std::uniform_real_distribution unif1(0.,upper_bound); std::uniform_real_distribution unif2(upper_bound/1000.,upper_bound/100.); std::default_random_engine re; - std::vector< std::pair > v1, v2; + std::vector< Internal_point > v1, v2; for (int i = 0; i < n1; i++) { double a = unif1(re); double b = unif1(re); @@ -30,15 +30,14 @@ BOOST_AUTO_TEST_CASE(global){ if(i%3==0) v2.emplace_back(std::max(a,b),std::max(a,b)+y); } - //99.5 and not 100 to avoid float errors. - BOOST_CHECK(bottleneck_distance(v1, v2) <= upper_bound/99.5); + BOOST_CHECK(bottleneck_distance(v1, v2) <= upper_bound/100.); } BOOST_AUTO_TEST_CASE(persistence_diagrams_graph){ // Random construction std::uniform_real_distribution unif(0.,upper_bound); std::default_random_engine re; - std::vector< std::pair > v1, v2; + std::vector< Internal_point > v1, v2; for (int i = 0; i < n1; i++) { double a = unif(re); double b = unif(re); @@ -50,7 +49,7 @@ BOOST_AUTO_TEST_CASE(persistence_diagrams_graph){ v2.emplace_back(std::min(a,b), std::max(a,b)); } G::initialize(v1, v2, 0.); - std::unique_ptr< std::vector > d = std::move(G::sorted_distances()); + std::shared_ptr< std::vector > d(G::sorted_distances()); // BOOST_CHECK(!G::on_the_u_diagonal(n1-1)); BOOST_CHECK(!G::on_the_u_diagonal(n1)); @@ -91,7 +90,7 @@ BOOST_AUTO_TEST_CASE(persistence_diagrams_graph){ BOOST_AUTO_TEST_CASE(planar_neighbors_finder) { - Planar_neighbors_finder pnf = Planar_neighbors_finder(1.); + Planar_neighbors_finder pnf(1.); for(int v_point_index=0; v_point_index l = *pnf.pull_all_near(n2/2); bool v = true; @@ -120,9 +119,8 @@ BOOST_AUTO_TEST_CASE(planar_neighbors_finder) { BOOST_CHECK(v_point_index_2 == -1); } - BOOST_AUTO_TEST_CASE(neighbors_finder) { - Neighbors_finder nf = Neighbors_finder(1.); + Neighbors_finder nf(1.); for(int v_point_index=1; v_point_index<((n2+n1)*9/10); v_point_index+=2) nf.add(v_point_index); // @@ -138,7 +136,7 @@ BOOST_AUTO_TEST_CASE(neighbors_finder) { } BOOST_AUTO_TEST_CASE(layered_neighbors_finder) { - Layered_neighbors_finder lnf = Layered_neighbors_finder(1.); + Layered_neighbors_finder lnf(1.); for(int v_point_index=1; v_point_index<((n2+n1)*9/10); v_point_index+=2) lnf.add(v_point_index, v_point_index % 7); // @@ -169,7 +167,6 @@ BOOST_AUTO_TEST_CASE(graph_matching) { BOOST_CHECK(m2.perfect()); BOOST_CHECK(!m1.perfect()); } - /* BOOST_AUTO_TEST_CASE(chrono) { std::ofstream objetfichier; @@ -179,7 +176,7 @@ BOOST_AUTO_TEST_CASE(chrono) { std::uniform_real_distribution unif1(0.,upper_bound); std::uniform_real_distribution unif2(upper_bound/1000.,upper_bound/100.); std::default_random_engine re; - std::vector< std::pair > v1, v2; + std::vector< Internal_point > v1, v2; for (int i = 0; i < n; i++) { double a = unif1(re); double b = unif1(re); @@ -202,6 +199,4 @@ BOOST_AUTO_TEST_CASE(chrono) { objetfichier << n << ";" << duration.count() << ";" << b << std::endl; } objetfichier.close(); -} -*/ - +}*/ -- cgit v1.2.3 From 12a58fd627a6ad59d663ae746b881ef794e951c8 Mon Sep 17 00:00:00 2001 From: fgodi Date: Mon, 23 May 2016 16:35:30 +0000 Subject: save git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@1187 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 5f7f7b5f900f8123daeaeff90beb1fbd676334ac --- src/Bipartite_graphs_matching/example/basic.cpp | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) (limited to 'src') diff --git a/src/Bipartite_graphs_matching/example/basic.cpp b/src/Bipartite_graphs_matching/example/basic.cpp index d190ab48..26f9519e 100644 --- a/src/Bipartite_graphs_matching/example/basic.cpp +++ b/src/Bipartite_graphs_matching/example/basic.cpp @@ -26,15 +26,14 @@ using namespace Gudhi::bipartite_graph_matching; int main() { + std::vector< Internal_point > v1, v2; - std::vector< std::pair > v1, v2; + v1.push_back(Internal_point(2.7,3.7)); + v1.push_back(Internal_point(9.6,14)); + v1.push_back(Internal_point(34.2,34.974)); - v1.emplace_back(2.7,3.7); - v1.emplace_back(9.6,14); - v1.emplace_back(34.2,34.974); - - v2.emplace_back(2.8,4.45); - v2.emplace_back(9.5,14.1); + v2.push_back(Internal_point(2.8,4.45)); + v2.push_back(Internal_point(9.5,14.1)); double b = bottleneck_distance(v1, v2); -- cgit v1.2.3 From fe56bdfec68dc9994c4c72ac3e70a6c1c1f42891 Mon Sep 17 00:00:00 2001 From: fgodi Date: Tue, 24 May 2016 16:45:19 +0000 Subject: save 24/05/2016 git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@1191 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 046c7bccbd04ebc20ce3970a60b880a696a31266 --- src/Bipartite_graphs_matching/example/basic.cpp | 12 +-- .../include/gudhi/Internal_point.h | 92 ++-------------------- .../include/gudhi/Neighbors_finder.h | 1 - .../include/gudhi/Persistence_diagrams_graph.h | 12 +-- .../include/gudhi/Planar_neighbors_finder.h | 39 ++++----- .../test/bottleneck_unit_test.cpp | 46 +++++------ 6 files changed, 59 insertions(+), 143 deletions(-) (limited to 'src') diff --git a/src/Bipartite_graphs_matching/example/basic.cpp b/src/Bipartite_graphs_matching/example/basic.cpp index 26f9519e..772bcd4a 100644 --- a/src/Bipartite_graphs_matching/example/basic.cpp +++ b/src/Bipartite_graphs_matching/example/basic.cpp @@ -26,14 +26,14 @@ using namespace Gudhi::bipartite_graph_matching; int main() { - std::vector< Internal_point > v1, v2; + std::vector< std::pair > v1, v2; - v1.push_back(Internal_point(2.7,3.7)); - v1.push_back(Internal_point(9.6,14)); - v1.push_back(Internal_point(34.2,34.974)); + v1.push_back(std::pair(2.7,3.7)); + v1.push_back(std::pair(9.6,14)); + v1.push_back(std::pair(34.2,34.974)); - v2.push_back(Internal_point(2.8,4.45)); - v2.push_back(Internal_point(9.5,14.1)); + v2.push_back(std::pair(2.8,4.45)); + v2.push_back(std::pair(9.5,14.1)); double b = bottleneck_distance(v1, v2); diff --git a/src/Bipartite_graphs_matching/include/gudhi/Internal_point.h b/src/Bipartite_graphs_matching/include/gudhi/Internal_point.h index 633a3767..5d96ab93 100644 --- a/src/Bipartite_graphs_matching/include/gudhi/Internal_point.h +++ b/src/Bipartite_graphs_matching/include/gudhi/Internal_point.h @@ -23,9 +23,9 @@ #ifndef SRC_BOTTLENECK_INCLUDE_GUDHI_INTERNAL_POINT_H_ #define SRC_BOTTLENECK_INCLUDE_GUDHI_INTERNAL_POINT_H_ -//namespace Gudhi { +namespace Gudhi { -//namespace bipartite_graph_matching { +namespace bipartite_graph_matching { /** \internal \brief Returns the used index for encoding none of the points */ int null_point_index(); @@ -34,101 +34,25 @@ int null_point_index(); struct Internal_point { double vec[2]; int point_index; - Internal_point() { vec[0]= vec[1] = 0.; point_index = null_point_index(); } - Internal_point(double x, double y) { vec[0]=x; vec[1]=y; point_index = null_point_index(); } + Internal_point() {} + Internal_point(double x, double y, int p_i = null_point_index()) { vec[0]=x; vec[1]=y; point_index = p_i; } double x() const { return vec[ 0 ]; } double y() const { return vec[ 1 ]; } double& x() { return vec[ 0 ]; } double& y() { return vec[ 1 ]; } bool operator==(const Internal_point& p) const { - return (x() == p.x()) && (y() == p.y()); + return (x() == p.x()) && (y() == p.y()) && (point_index==p.point_index); } bool operator!=(const Internal_point& p) const { return ! (*this == p); } }; -namespace CGAL { -template <> -struct Kernel_traits { - struct Kernel { - typedef double FT; - typedef double RT; - }; -}; -} - -struct Construct_coord_iterator { - typedef const double* result_type; - const double* operator()(const Internal_point& p) const - { return static_cast(p.vec); } - const double* operator()(const Internal_point& p, int) const - { return static_cast(p.vec+2); } -}; -/* -struct Distance { - typedef Internal_point Query_item; - typedef Internal_point Point_d; - typedef double FT; - typedef CGAL::Dimension_tag<2> D; - - FT transformed_distance(const Query_item& q, const Point_d& p) const { - FT d0= std::abs(q.x()-p.x()); - FT d1= std::abs(q.y()-p.y()); - return std::max(d0,d1); - } - FT min_distance_to_rectangle(const Query_item& q, - const CGAL::Kd_tree_rectangle& b) const { - FT d0(0.), d1(0.); - if (q.x() < b.min_coord(0)) - d0 += (b.min_coord(0)-q.x()); - if (q.x() > b.max_coord(0)) - d0 += (q.x()-b.max_coord(0)); - if (q.y() < b.min_coord(1)) - d1 += (b.min_coord(1)-q.y()); - if (q.y() > b.max_coord(1)) - d1 += (q.y()-b.max_coord(1)); - return std::max(d0,d1); - } - FT min_distance_to_rectangle(const Query_item& q, const CGAL::Kd_tree_rectangle& b,std::vector& dists){ - dists[0] = dists[1] = 0.; - if (q.x() < b.min_coord(0)) - dists[0] = (b.min_coord(0)- q.x()); - if (q.x() > b.max_coord(0)) - dists[0] = (q.x()-b.max_coord(0)); - if (q.y() < b.min_coord(1)) - dists[1] = (b.min_coord(1)-q.y()); - if (q.y() > b.max_coord(1)) - dists[1] = (q.y()-b.max_coord(1)); - return std::max(dists[0],dists[1]); - } - FT max_distance_to_rectangle(const Query_item& q, const CGAL::Kd_tree_rectangle& b) const { - FT d0 = (q.x() >= (b.min_coord(0)+b.max_coord(0))/2.) ? - (q.x()-b.min_coord(0)) : (b.max_coord(0)-q.x()); - FT d1 = (q.y() >= (b.min_coord(1)+b.max_coord(1))/2.) ? - (q.y()-b.min_coord(1)) : (b.max_coord(1)-q.y()); - return std::max(d0, d1); - } - FT max_distance_to_rectangle(const Query_item& q, const CGAL::Kd_tree_rectangle& b,std::vector& dists){ - dists[0] = (q.x() >= (b.min_coord(0)+b.max_coord(0))/2.0) ? - (q.x()-b.min_coord(0)) : (b.max_coord(0)-q.x()); - dists[1] = (q.y() >= (b.min_coord(1)+b.max_coord(1))/2.0) ? - (q.y()-b.min_coord(1)) : (b.max_coord(1)-q.y()); - return std::max(dists[0], dists[1]); - } - FT new_distance(FT& dist, FT old_off, FT new_off, - int) const { - return dist + new_off - old_off; //works ? - } - FT transformed_distance(FT d) const { return d; } - FT inverse_of_transformed_distance(FT d) { return d; } -}; // end of struct Distance -*/ inline int null_point_index() { return -1; } -//} // namespace bipartite_graph_matching +} // namespace bipartite_graph_matching -//} // namespace Gudhi +} // namespace Gudhi -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_ +#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_INTERNAL_POINT_H_ diff --git a/src/Bipartite_graphs_matching/include/gudhi/Neighbors_finder.h b/src/Bipartite_graphs_matching/include/gudhi/Neighbors_finder.h index 2ef7f768..bb6f5ea0 100644 --- a/src/Bipartite_graphs_matching/include/gudhi/Neighbors_finder.h +++ b/src/Bipartite_graphs_matching/include/gudhi/Neighbors_finder.h @@ -24,7 +24,6 @@ #define SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_ #include - #include "Planar_neighbors_finder.h" namespace Gudhi { diff --git a/src/Bipartite_graphs_matching/include/gudhi/Persistence_diagrams_graph.h b/src/Bipartite_graphs_matching/include/gudhi/Persistence_diagrams_graph.h index 2ba960a7..a460d814 100644 --- a/src/Bipartite_graphs_matching/include/gudhi/Persistence_diagrams_graph.h +++ b/src/Bipartite_graphs_matching/include/gudhi/Persistence_diagrams_graph.h @@ -85,11 +85,11 @@ inline void G::initialize(const Persistence_diagram1 &diag1, u.clear(); v.clear(); for (auto it = diag1.cbegin(); it != diag1.cend(); ++it) - if (it->y() - it->x() > e) - u.emplace_back(*it); + if (it->second - it->first > e) + u.push_back(Internal_point(it->first, it->second, u.size())); for (auto it = diag2.cbegin(); it != diag2.cend(); ++it) - if (it->y() - it->x() > e) - v.emplace_back(*it); + if (it->second - it->first > e) + v.push_back(Internal_point(it->first, it->second, v.size())); if (u.size() < v.size()) swap(u, v); } @@ -139,7 +139,7 @@ inline Internal_point G::get_u_point(int u_point_index) { return u.at(u_point_index); Internal_point projector = v.at(corresponding_point_in_v(u_point_index)); double m = (projector.x() + projector.y()) / 2; - return Internal_point(m, m); + return Internal_point(m,m,u_point_index); } inline Internal_point G::get_v_point(int v_point_index) { @@ -147,7 +147,7 @@ inline Internal_point G::get_v_point(int v_point_index) { return v.at(v_point_index); Internal_point projector = u.at(corresponding_point_in_u(v_point_index)); double m = (projector.x() + projector.y()) / 2; - return Internal_point(m, m); + return Internal_point(m,m,v_point_index); } } // namespace bipartite_graph_matching diff --git a/src/Bipartite_graphs_matching/include/gudhi/Planar_neighbors_finder.h b/src/Bipartite_graphs_matching/include/gudhi/Planar_neighbors_finder.h index 47c1a8fc..abb14e29 100644 --- a/src/Bipartite_graphs_matching/include/gudhi/Planar_neighbors_finder.h +++ b/src/Bipartite_graphs_matching/include/gudhi/Planar_neighbors_finder.h @@ -28,6 +28,7 @@ #include #include #include +#include "../CGAL/Miscellaneous.h" #include "Persistence_diagrams_graph.h" @@ -66,9 +67,9 @@ private: class Cgal_pnf { typedef CGAL::Dimension_tag<2> D; - typedef CGAL::Search_traits Cgal_traits; - typedef CGAL::Weighted_Minkowski_distance Distance; - typedef CGAL::Orthogonal_incremental_neighbor_search K_neighbor_search; + typedef CGAL::Search_traits Traits; + typedef CGAL::Weighted_Minkowski_distance Distance; + typedef CGAL::Orthogonal_incremental_neighbor_search K_neighbor_search; typedef K_neighbor_search::Tree Kd_tree; @@ -164,15 +165,14 @@ inline Cgal_pnf::Cgal_pnf(double r_) /** \internal \brief A point added will be possibly pulled. */ inline void Cgal_pnf::add(int v_point_index){ - Internal_point v_point = G::get_v_point(v_point_index); - v_point.point_index = v_point_index; - kd_t.insert(v_point); contents.insert(v_point_index); + kd_t.insert(G::get_v_point(v_point_index)); } /** \internal \brief A point manually removed will no longer be possibly pulled. */ inline void Cgal_pnf::remove(int v_point_index){ contents.erase(v_point_index); + kd_t.remove(G::get_v_point(v_point_index)); } /** \internal \brief Can the point given as parameter be returned ? */ @@ -183,23 +183,16 @@ inline bool Cgal_pnf::contains(int v_point_index) const{ /** \internal \brief Provide and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ inline int Cgal_pnf::pull_near(int u_point_index){ Internal_point u_point = G::get_u_point(u_point_index); - K_neighbor_search search(kd_t, u_point, 0., true, Distance(0.)); - for (auto it = search.begin(); it != search.end(); it++) - if(contents.count(it->first.point_index)==0) - kd_t.remove(it->first); - else if(G::distance(u_point_index, it->first.point_index) > r){ - for(auto itc=contents.cbegin(); itc != contents.cend(); itc++) - if(G::distance(u_point_index, *itc) <= r) - std::cout << G::distance(u_point_index, *itc) << " ! > " << r << std::endl; - return null_point_index(); - } - else - { - kd_t.remove(it->first); - contents.erase(it->first.point_index); - return it->first.point_index; - } - return null_point_index(); + std::vector w = {1., 1.}; + K_neighbor_search search(kd_t, u_point, 0., true, Distance(0, 2, w)); + auto it = search.begin(); + if(it==search.end() || G::distance(u_point_index, it->first.point_index) > r){ + for(auto itc=contents.cbegin(); itc != contents.cend(); itc++) + if(G::distance(u_point_index, *itc) <= r) + std::cout << G::distance(u_point_index, *itc) << " ! > " << r << std::endl; + return null_point_index(); + } + return it->first.point_index; } inline std::shared_ptr< std::list > Cgal_pnf::pull_all_near(int u_point_index) { diff --git a/src/Bipartite_graphs_matching/test/bottleneck_unit_test.cpp b/src/Bipartite_graphs_matching/test/bottleneck_unit_test.cpp index 2e79ccdc..d53a5a3c 100644 --- a/src/Bipartite_graphs_matching/test/bottleneck_unit_test.cpp +++ b/src/Bipartite_graphs_matching/test/bottleneck_unit_test.cpp @@ -13,31 +13,11 @@ int n1 = 81; // a natural number >0 int n2 = 180; // a natural number >0 double upper_bound = 406.43; // any real >0 -BOOST_AUTO_TEST_CASE(global){ - std::uniform_real_distribution unif1(0.,upper_bound); - std::uniform_real_distribution unif2(upper_bound/1000.,upper_bound/100.); - std::default_random_engine re; - std::vector< Internal_point > v1, v2; - for (int i = 0; i < n1; i++) { - double a = unif1(re); - double b = unif1(re); - double x = unif2(re); - double y = unif2(re); - v1.emplace_back(std::min(a,b), std::max(a,b)); - v2.emplace_back(std::min(a,b)+std::min(x,y), std::max(a,b)+std::max(x,y)); - if(i%5==0) - v1.emplace_back(std::min(a,b),std::min(a,b)+x); - if(i%3==0) - v2.emplace_back(std::max(a,b),std::max(a,b)+y); - } - BOOST_CHECK(bottleneck_distance(v1, v2) <= upper_bound/100.); -} - BOOST_AUTO_TEST_CASE(persistence_diagrams_graph){ // Random construction std::uniform_real_distribution unif(0.,upper_bound); std::default_random_engine re; - std::vector< Internal_point > v1, v2; + std::vector< std::pair > v1, v2; for (int i = 0; i < n1; i++) { double a = unif(re); double b = unif(re); @@ -88,7 +68,6 @@ BOOST_AUTO_TEST_CASE(persistence_diagrams_graph){ BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,(n1+n2)-1))==1); } - BOOST_AUTO_TEST_CASE(planar_neighbors_finder) { Planar_neighbors_finder pnf(1.); for(int v_point_index=0; v_point_index unif1(0.,upper_bound); + std::uniform_real_distribution unif2(upper_bound/1000.,upper_bound/100.); + std::default_random_engine re; + std::vector< std::pair > v1, v2; + for (int i = 0; i < n1; i++) { + double a = unif1(re); + double b = unif1(re); + double x = unif2(re); + double y = unif2(re); + v1.emplace_back(std::min(a,b), std::max(a,b)); + v2.emplace_back(std::min(a,b)+std::min(x,y), std::max(a,b)+std::max(x,y)); + if(i%5==0) + v1.emplace_back(std::min(a,b),std::min(a,b)+x); + if(i%3==0) + v2.emplace_back(std::max(a,b),std::max(a,b)+y); + } + BOOST_CHECK(bottleneck_distance(v1, v2) <= upper_bound/100.); +} + /* BOOST_AUTO_TEST_CASE(chrono) { std::ofstream objetfichier; @@ -176,7 +176,7 @@ BOOST_AUTO_TEST_CASE(chrono) { std::uniform_real_distribution unif1(0.,upper_bound); std::uniform_real_distribution unif2(upper_bound/1000.,upper_bound/100.); std::default_random_engine re; - std::vector< Internal_point > v1, v2; + std::vector< std::pair > v1, v2; for (int i = 0; i < n; i++) { double a = unif1(re); double b = unif1(re); -- cgit v1.2.3 From 9db309ff6abbcd2ba3ebbc74fa387b55d9660789 Mon Sep 17 00:00:00 2001 From: fgodi Date: Wed, 25 May 2016 14:02:14 +0000 Subject: save git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@1199 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 00868265725afaf47ed8292c0d6f7cff235a016f --- CMakeLists.txt | 2 +- src/Bipartite_graphs_matching/example/basic.cpp | 42 +++++++++++++++++++++- .../include/gudhi/Planar_neighbors_finder.h | 11 +++--- .../test/bottleneck_unit_test.cpp | 37 ------------------- 4 files changed, 46 insertions(+), 46 deletions(-) (limited to 'src') diff --git a/CMakeLists.txt b/CMakeLists.txt index 54165c59..0f031a49 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -14,7 +14,7 @@ if(MSVC) # Turn off some VC++ warnings SET (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018") else() - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O2 -std=c++11 -Wall -Wpedantic -Wsign-compare") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O0 -g -std=c++11 -Wall -Wpedantic -Wsign-compare") set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -ggdb -O0") set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE}") endif() diff --git a/src/Bipartite_graphs_matching/example/basic.cpp b/src/Bipartite_graphs_matching/example/basic.cpp index 772bcd4a..797968cc 100644 --- a/src/Bipartite_graphs_matching/example/basic.cpp +++ b/src/Bipartite_graphs_matching/example/basic.cpp @@ -23,8 +23,48 @@ #include "../include/gudhi/Graph_matching.h" #include +#include +#include + using namespace Gudhi::bipartite_graph_matching; + +double upper_bound = 400.; // any real >0 + +int main(){ + std::ofstream objetfichier; + objetfichier.open("results.csv", std::ios::out); + + for(int n =50; n<=1000; n+=100){ + std::uniform_real_distribution unif1(0.,upper_bound); + std::uniform_real_distribution unif2(upper_bound/1000.,upper_bound/100.); + std::default_random_engine re; + std::vector< std::pair > v1, v2; + for (int i = 0; i < n; i++) { + double a = unif1(re); + double b = unif1(re); + double x = unif2(re); + double y = unif2(re); + v1.emplace_back(std::min(a,b), std::max(a,b)); + v2.emplace_back(std::min(a,b)+std::min(x,y), std::max(a,b)+std::max(x,y)); + if(i%5==0) + v1.emplace_back(std::min(a,b),std::min(a,b)+x); + if(i%3==0) + v2.emplace_back(std::max(a,b),std::max(a,b)+y); + } + + std::chrono::steady_clock::time_point start = std::chrono::steady_clock::now(); + double b = bottleneck_distance(v1,v2); + std::chrono::steady_clock::time_point end = std::chrono::steady_clock::now(); + + typedef std::chrono::duration millisecs_t; + millisecs_t duration(std::chrono::duration_cast(end-start)); + objetfichier << n << ";" << duration.count() << ";" << b << std::endl; + } + objetfichier.close(); +} + +/* int main() { std::vector< std::pair > v1, v2; @@ -40,4 +80,4 @@ int main() { std::cout << "Bottleneck distance = " << b << std::endl; -} +}*/ diff --git a/src/Bipartite_graphs_matching/include/gudhi/Planar_neighbors_finder.h b/src/Bipartite_graphs_matching/include/gudhi/Planar_neighbors_finder.h index abb14e29..8231409c 100644 --- a/src/Bipartite_graphs_matching/include/gudhi/Planar_neighbors_finder.h +++ b/src/Bipartite_graphs_matching/include/gudhi/Planar_neighbors_finder.h @@ -82,7 +82,7 @@ public: void remove(int v_point_index); /** \internal \brief Can the point given as parameter be returned ? */ bool contains(int v_point_index) const; - /** \internal \brief Provide and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ + /** \internal \brief Provide a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ int pull_near(int u_point_index); /** \internal \brief Provide and remove all the V points near to the U point given as parameter. */ virtual std::shared_ptr< std::list > pull_all_near(int u_point_index); @@ -110,6 +110,7 @@ inline void Naive_pnf::add(int v_point_index) { } inline void Naive_pnf::remove(int v_point_index) { + if(!contains(v_point_index)) for(auto it = grid.find(get_v_key(v_point_index)); it!=grid.end(); it++) if(it->second==v_point_index){ grid.erase(it); @@ -135,7 +136,6 @@ inline int Naive_pnf::pull_near(int u_point_index) { for(auto it = grid.find(std::make_pair(i0 +(i%3)-1, j0+(j%3)-1)); it!=grid.end(); it++) if (G::distance(u_point_index, it->second) <= r) { int tmp = it->second; - grid.erase(it); return tmp; } return null_point_index(); @@ -186,12 +186,8 @@ inline int Cgal_pnf::pull_near(int u_point_index){ std::vector w = {1., 1.}; K_neighbor_search search(kd_t, u_point, 0., true, Distance(0, 2, w)); auto it = search.begin(); - if(it==search.end() || G::distance(u_point_index, it->first.point_index) > r){ - for(auto itc=contents.cbegin(); itc != contents.cend(); itc++) - if(G::distance(u_point_index, *itc) <= r) - std::cout << G::distance(u_point_index, *itc) << " ! > " << r << std::endl; + if(it==search.end() || G::distance(u_point_index, it->first.point_index) > r) return null_point_index(); - } return it->first.point_index; } @@ -200,6 +196,7 @@ inline std::shared_ptr< std::list > Cgal_pnf::pull_all_near(int u_point_ind int last_pull = pull_near(u_point_index); while (last_pull != null_point_index()) { all_pull->emplace_back(last_pull); + remove(last_pull); last_pull = pull_near(u_point_index); } return all_pull; diff --git a/src/Bipartite_graphs_matching/test/bottleneck_unit_test.cpp b/src/Bipartite_graphs_matching/test/bottleneck_unit_test.cpp index d53a5a3c..7c1d5614 100644 --- a/src/Bipartite_graphs_matching/test/bottleneck_unit_test.cpp +++ b/src/Bipartite_graphs_matching/test/bottleneck_unit_test.cpp @@ -4,9 +4,6 @@ #include #include "../include/gudhi/Graph_matching.h" -#include -#include - using namespace Gudhi::bipartite_graph_matching; int n1 = 81; // a natural number >0 @@ -166,37 +163,3 @@ BOOST_AUTO_TEST_CASE(global){ } BOOST_CHECK(bottleneck_distance(v1, v2) <= upper_bound/100.); } - -/* -BOOST_AUTO_TEST_CASE(chrono) { - std::ofstream objetfichier; - objetfichier.open("results.csv", std::ios::out); - - for(int n =50; n<=1000; n+=100){ - std::uniform_real_distribution unif1(0.,upper_bound); - std::uniform_real_distribution unif2(upper_bound/1000.,upper_bound/100.); - std::default_random_engine re; - std::vector< std::pair > v1, v2; - for (int i = 0; i < n; i++) { - double a = unif1(re); - double b = unif1(re); - double x = unif2(re); - double y = unif2(re); - v1.emplace_back(std::min(a,b), std::max(a,b)); - v2.emplace_back(std::min(a,b)+std::min(x,y), std::max(a,b)+std::max(x,y)); - if(i%5==0) - v1.emplace_back(std::min(a,b),std::min(a,b)+x); - if(i%3==0) - v2.emplace_back(std::max(a,b),std::max(a,b)+y); - } - - std::chrono::steady_clock::time_point start = std::chrono::steady_clock::now(); - double b = bottleneck_distance(v1,v2); - std::chrono::steady_clock::time_point end = std::chrono::steady_clock::now(); - - typedef std::chrono::duration millisecs_t; - millisecs_t duration(std::chrono::duration_cast(end-start)); - objetfichier << n << ";" << duration.count() << ";" << b << std::endl; - } - objetfichier.close(); -}*/ -- cgit v1.2.3 From 40a293e774742d308ce02416326e67d5375cc371 Mon Sep 17 00:00:00 2001 From: cjamin Date: Wed, 25 May 2016 15:31:07 +0000 Subject: Missing include_directories git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@1203 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: f75268759affc6ce3e7c5a2929ba00971a1c48a1 --- CMakeLists.txt | 1 + src/Bipartite_graphs_matching/example/basic.cpp | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) (limited to 'src') diff --git a/CMakeLists.txt b/CMakeLists.txt index 0f031a49..066a49cf 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -57,6 +57,7 @@ else() include_directories(src/common/include/) include_directories(src/Alpha_shapes/include/) + include_directories(src/Bipartite_graphs_matching/include/) include_directories(src/Bottleneck/include/) include_directories(src/Contraction/include/) include_directories(src/Hasse_complex/include/) diff --git a/src/Bipartite_graphs_matching/example/basic.cpp b/src/Bipartite_graphs_matching/example/basic.cpp index 797968cc..f8585fe6 100644 --- a/src/Bipartite_graphs_matching/example/basic.cpp +++ b/src/Bipartite_graphs_matching/example/basic.cpp @@ -20,7 +20,7 @@ * along with this program. If not, see . */ -#include "../include/gudhi/Graph_matching.h" +#include #include #include -- cgit v1.2.3 From 0b53f46b7ced798e7c1dcfeb3475672e0c2d2850 Mon Sep 17 00:00:00 2001 From: fgodi Date: Thu, 26 May 2016 08:07:10 +0000 Subject: include <..> git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@1206 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 4f3e5c3b334b854cb81a8945f27874babd874e98 --- src/Bipartite_graphs_matching/example/basic.cpp | 7 +-- .../include/CGAL/Miscellaneous.h | 51 ++++++++++++++++++++++ .../include/gudhi/Graph_matching.h | 2 +- .../include/gudhi/Neighbors_finder.h | 2 +- .../include/gudhi/Persistence_diagrams_graph.h | 2 +- .../include/gudhi/Planar_neighbors_finder.h | 4 +- .../test/bottleneck_unit_test.cpp | 2 +- 7 files changed, 61 insertions(+), 9 deletions(-) create mode 100644 src/Bipartite_graphs_matching/include/CGAL/Miscellaneous.h (limited to 'src') diff --git a/src/Bipartite_graphs_matching/example/basic.cpp b/src/Bipartite_graphs_matching/example/basic.cpp index f8585fe6..ad299225 100644 --- a/src/Bipartite_graphs_matching/example/basic.cpp +++ b/src/Bipartite_graphs_matching/example/basic.cpp @@ -28,7 +28,7 @@ using namespace Gudhi::bipartite_graph_matching; - +/* double upper_bound = 400.; // any real >0 int main(){ @@ -63,8 +63,9 @@ int main(){ } objetfichier.close(); } +*/ + -/* int main() { std::vector< std::pair > v1, v2; @@ -80,4 +81,4 @@ int main() { std::cout << "Bottleneck distance = " << b << std::endl; -}*/ +} diff --git a/src/Bipartite_graphs_matching/include/CGAL/Miscellaneous.h b/src/Bipartite_graphs_matching/include/CGAL/Miscellaneous.h new file mode 100644 index 00000000..4de787fb --- /dev/null +++ b/src/Bipartite_graphs_matching/include/CGAL/Miscellaneous.h @@ -0,0 +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): Francois Godi + * + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_CGAL_MISCELLANEOUS_H_ +#define SRC_BOTTLENECK_INCLUDE_CGAL_MISCELLANEOUS_H_ + +#include + +namespace CGAL { + +typedef Gudhi::bipartite_graph_matching::Internal_point Internal_point; + +template <> +struct Kernel_traits { + struct Kernel { + typedef double FT; + typedef double RT; + }; +}; + + +struct Construct_coord_iterator { + typedef const double* result_type; + const double* operator()(const Internal_point& p) const + { return static_cast(p.vec); } + const double* operator()(const Internal_point& p, int) const + { return static_cast(p.vec+2); } +}; + +} //namespace CGAL + +#endif // SRC_BOTTLENECK_INCLUDE_CGAL_MISCELLANEOUS_H_ diff --git a/src/Bipartite_graphs_matching/include/gudhi/Graph_matching.h b/src/Bipartite_graphs_matching/include/gudhi/Graph_matching.h index 228de584..fa05aa7c 100644 --- a/src/Bipartite_graphs_matching/include/gudhi/Graph_matching.h +++ b/src/Bipartite_graphs_matching/include/gudhi/Graph_matching.h @@ -25,7 +25,7 @@ #include -#include "Neighbors_finder.h" +#include namespace Gudhi { diff --git a/src/Bipartite_graphs_matching/include/gudhi/Neighbors_finder.h b/src/Bipartite_graphs_matching/include/gudhi/Neighbors_finder.h index bb6f5ea0..7fa9453d 100644 --- a/src/Bipartite_graphs_matching/include/gudhi/Neighbors_finder.h +++ b/src/Bipartite_graphs_matching/include/gudhi/Neighbors_finder.h @@ -24,7 +24,7 @@ #define SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_ #include -#include "Planar_neighbors_finder.h" +#include namespace Gudhi { diff --git a/src/Bipartite_graphs_matching/include/gudhi/Persistence_diagrams_graph.h b/src/Bipartite_graphs_matching/include/gudhi/Persistence_diagrams_graph.h index a460d814..139caa8c 100644 --- a/src/Bipartite_graphs_matching/include/gudhi/Persistence_diagrams_graph.h +++ b/src/Bipartite_graphs_matching/include/gudhi/Persistence_diagrams_graph.h @@ -30,7 +30,7 @@ #include #include #include -#include "Internal_point.h" +#include namespace Gudhi { diff --git a/src/Bipartite_graphs_matching/include/gudhi/Planar_neighbors_finder.h b/src/Bipartite_graphs_matching/include/gudhi/Planar_neighbors_finder.h index 8231409c..ec5c6f91 100644 --- a/src/Bipartite_graphs_matching/include/gudhi/Planar_neighbors_finder.h +++ b/src/Bipartite_graphs_matching/include/gudhi/Planar_neighbors_finder.h @@ -28,8 +28,8 @@ #include #include #include -#include "../CGAL/Miscellaneous.h" -#include "Persistence_diagrams_graph.h" +#include +#include namespace Gudhi { diff --git a/src/Bipartite_graphs_matching/test/bottleneck_unit_test.cpp b/src/Bipartite_graphs_matching/test/bottleneck_unit_test.cpp index 7c1d5614..ffe05614 100644 --- a/src/Bipartite_graphs_matching/test/bottleneck_unit_test.cpp +++ b/src/Bipartite_graphs_matching/test/bottleneck_unit_test.cpp @@ -2,7 +2,7 @@ #include #include -#include "../include/gudhi/Graph_matching.h" +#include using namespace Gudhi::bipartite_graph_matching; -- cgit v1.2.3 From e0033c746444d46d0dfbd703e11e4a3a444059ae Mon Sep 17 00:00:00 2001 From: fgodi Date: Thu, 26 May 2016 08:49:36 +0000 Subject: détails MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@1208 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 360093cd6a67d08b98682362ec80271fb82dc2b2 --- .../include/gudhi/Internal_point.h | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) (limited to 'src') diff --git a/src/Bipartite_graphs_matching/include/gudhi/Internal_point.h b/src/Bipartite_graphs_matching/include/gudhi/Internal_point.h index 5d96ab93..6c9389b7 100644 --- a/src/Bipartite_graphs_matching/include/gudhi/Internal_point.h +++ b/src/Bipartite_graphs_matching/include/gudhi/Internal_point.h @@ -45,6 +45,22 @@ struct Internal_point { return (x() == p.x()) && (y() == p.y()) && (point_index==p.point_index); } bool operator!=(const Internal_point& p) const { return ! (*this == p); } +/* +Useless + friend void swap(Internal_point& a, Internal_point& b) + { + using std::swap; + double x_tmp = a.vec[0]; + double y_tmp = a.vec[1]; + int pi_tmp = a.point_index; + a.vec[0] = b.vec[0]; + a.vec[1] = b.vec[1]; + a.point_index = b.point_index; + b.vec[0] = x_tmp; + b.vec[1] = y_tmp; + b.point_index = pi_tmp; + } +*/ }; inline int null_point_index() { -- cgit v1.2.3 From 8c2cc1f42a779a5774b8330d5630b91c5258fac4 Mon Sep 17 00:00:00 2001 From: fgodi Date: Thu, 26 May 2016 08:50:03 +0000 Subject: détails MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@1209 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 68dcb3d217126ee638284d9b3951d1fa20be5904 --- src/Bipartite_graphs_matching/example/basic.cpp | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'src') diff --git a/src/Bipartite_graphs_matching/example/basic.cpp b/src/Bipartite_graphs_matching/example/basic.cpp index ad299225..09530f9a 100644 --- a/src/Bipartite_graphs_matching/example/basic.cpp +++ b/src/Bipartite_graphs_matching/example/basic.cpp @@ -28,7 +28,7 @@ using namespace Gudhi::bipartite_graph_matching; -/* + double upper_bound = 400.; // any real >0 int main(){ @@ -63,9 +63,9 @@ int main(){ } objetfichier.close(); } -*/ +/* int main() { std::vector< std::pair > v1, v2; @@ -81,4 +81,4 @@ int main() { std::cout << "Bottleneck distance = " << b << std::endl; -} +}*/ -- cgit v1.2.3 From 8f455abec0d349949960eaefdd0aedd8dff8e7ca Mon Sep 17 00:00:00 2001 From: fgodi Date: Tue, 31 May 2016 14:15:46 +0000 Subject: works git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@1227 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 6b7d024adef25ef52ac48a2a0ead692be798a708 --- src/Bipartite_graphs_matching/example/basic.cpp | 1 + .../include/gudhi/Internal_point.h | 2 +- .../include/gudhi/Neighbors_finder.h | 2 +- .../include/gudhi/Planar_neighbors_finder.h | 30 ++++++++++++++-------- 4 files changed, 22 insertions(+), 13 deletions(-) (limited to 'src') diff --git a/src/Bipartite_graphs_matching/example/basic.cpp b/src/Bipartite_graphs_matching/example/basic.cpp index 09530f9a..f1c9d36e 100644 --- a/src/Bipartite_graphs_matching/example/basic.cpp +++ b/src/Bipartite_graphs_matching/example/basic.cpp @@ -36,6 +36,7 @@ int main(){ objetfichier.open("results.csv", std::ios::out); for(int n =50; n<=1000; n+=100){ +std::cout << n << "\n"; std::uniform_real_distribution unif1(0.,upper_bound); std::uniform_real_distribution unif2(upper_bound/1000.,upper_bound/100.); std::default_random_engine re; diff --git a/src/Bipartite_graphs_matching/include/gudhi/Internal_point.h b/src/Bipartite_graphs_matching/include/gudhi/Internal_point.h index 6c9389b7..3dc37962 100644 --- a/src/Bipartite_graphs_matching/include/gudhi/Internal_point.h +++ b/src/Bipartite_graphs_matching/include/gudhi/Internal_point.h @@ -42,7 +42,7 @@ struct Internal_point { double& y() { return vec[ 1 ]; } bool operator==(const Internal_point& p) const { - return (x() == p.x()) && (y() == p.y()) && (point_index==p.point_index); + return point_index==p.point_index; } bool operator!=(const Internal_point& p) const { return ! (*this == p); } /* diff --git a/src/Bipartite_graphs_matching/include/gudhi/Neighbors_finder.h b/src/Bipartite_graphs_matching/include/gudhi/Neighbors_finder.h index 7fa9453d..f346c62f 100644 --- a/src/Bipartite_graphs_matching/include/gudhi/Neighbors_finder.h +++ b/src/Bipartite_graphs_matching/include/gudhi/Neighbors_finder.h @@ -106,7 +106,7 @@ inline int Neighbors_finder::pull_near(int u_point_index) { int tmp; int c = G::corresponding_point_in_v(u_point_index); if (G::on_the_u_diagonal(u_point_index) && !projections_f.empty()) - //All projections are at distance 0 + //Any pair of projection is at distance 0 tmp = *projections_f.cbegin(); else if (contains(c) && (G::distance(u_point_index, c) <= r)) //Is the query point near to its projection ? diff --git a/src/Bipartite_graphs_matching/include/gudhi/Planar_neighbors_finder.h b/src/Bipartite_graphs_matching/include/gudhi/Planar_neighbors_finder.h index ec5c6f91..3d6d0084 100644 --- a/src/Bipartite_graphs_matching/include/gudhi/Planar_neighbors_finder.h +++ b/src/Bipartite_graphs_matching/include/gudhi/Planar_neighbors_finder.h @@ -94,7 +94,7 @@ private: }; /** \internal \typedef \brief Planar_neighbors_finder is the used implementation. */ -typedef Cgal_pnf Planar_neighbors_finder; +typedef Naive_pnf Planar_neighbors_finder; inline Naive_pnf::Naive_pnf(double r_) : r(r_), grid() { } @@ -110,12 +110,12 @@ inline void Naive_pnf::add(int v_point_index) { } inline void Naive_pnf::remove(int v_point_index) { - if(!contains(v_point_index)) - for(auto it = grid.find(get_v_key(v_point_index)); it!=grid.end(); it++) - if(it->second==v_point_index){ - grid.erase(it); - return; - } + if(v_point_index != null_point_index()) + for(auto it = grid.find(get_v_key(v_point_index)); it!=grid.end(); it++) + if(it->second==v_point_index){ + grid.erase(it); + return; + } } inline bool Naive_pnf::contains(int v_point_index) const { @@ -136,6 +136,7 @@ inline int Naive_pnf::pull_near(int u_point_index) { for(auto it = grid.find(std::make_pair(i0 +(i%3)-1, j0+(j%3)-1)); it!=grid.end(); it++) if (G::distance(u_point_index, it->second) <= r) { int tmp = it->second; + grid.erase(it); return tmp; } return null_point_index(); @@ -165,18 +166,24 @@ inline Cgal_pnf::Cgal_pnf(double r_) /** \internal \brief A point added will be possibly pulled. */ inline void Cgal_pnf::add(int v_point_index){ + if(v_point_index == null_point_index()) + return; contents.insert(v_point_index); kd_t.insert(G::get_v_point(v_point_index)); } /** \internal \brief A point manually removed will no longer be possibly pulled. */ inline void Cgal_pnf::remove(int v_point_index){ - contents.erase(v_point_index); - kd_t.remove(G::get_v_point(v_point_index)); + if(contains(v_point_index)){ + contents.erase(v_point_index); + kd_t.remove(G::get_v_point(v_point_index)); + } } /** \internal \brief Can the point given as parameter be returned ? */ inline bool Cgal_pnf::contains(int v_point_index) const{ + if(v_point_index == null_point_index()) + return false; return contents.count(v_point_index)>0; } @@ -188,7 +195,9 @@ inline int Cgal_pnf::pull_near(int u_point_index){ auto it = search.begin(); if(it==search.end() || G::distance(u_point_index, it->first.point_index) > r) return null_point_index(); - return it->first.point_index; + int tmp = it->first.point_index; + remove(tmp); + return tmp; } inline std::shared_ptr< std::list > Cgal_pnf::pull_all_near(int u_point_index) { @@ -196,7 +205,6 @@ inline std::shared_ptr< std::list > Cgal_pnf::pull_all_near(int u_point_ind int last_pull = pull_near(u_point_index); while (last_pull != null_point_index()) { all_pull->emplace_back(last_pull); - remove(last_pull); last_pull = pull_near(u_point_index); } return all_pull; -- cgit v1.2.3 From 3b5b94c90c81ae4938a89b2b4df8b1173f100ee3 Mon Sep 17 00:00:00 2001 From: fgodi Date: Thu, 2 Jun 2016 17:09:48 +0000 Subject: renaming git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@1240 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 53bcbf20e176a21dc41ef3c4d4295b1e9aa959b0 --- src/Bottleneck_distance/concept/Diagram_point.h | 6 + .../concept/Persistence_diagram.h | 7 + src/Bottleneck_distance/example/CMakeLists.txt | 36 ++++ .../example/bottleneck_example.cpp | 43 ++++ .../include/CGAL/Miscellaneous.h | 51 +++++ .../include/gudhi/Graph_matching.h | 233 +++++++++++++++++++++ .../include/gudhi/Internal_point.h | 74 +++++++ .../include/gudhi/Neighbors_finder.h | 154 ++++++++++++++ .../include/gudhi/Persistence_diagrams_graph.h | 168 +++++++++++++++ .../include/gudhi/Planar_neighbors_finder.h | 218 +++++++++++++++++++ src/Bottleneck_distance/test/CMakeLists.txt | 63 ++++++ src/Bottleneck_distance/test/README | 12 ++ src/Bottleneck_distance/test/bottleneck_chrono.cpp | 61 ++++++ .../test/bottleneck_unit_test.cpp | 188 +++++++++++++++++ 14 files changed, 1314 insertions(+) create mode 100644 src/Bottleneck_distance/concept/Diagram_point.h create mode 100644 src/Bottleneck_distance/concept/Persistence_diagram.h create mode 100644 src/Bottleneck_distance/example/CMakeLists.txt create mode 100644 src/Bottleneck_distance/example/bottleneck_example.cpp create mode 100644 src/Bottleneck_distance/include/CGAL/Miscellaneous.h create mode 100644 src/Bottleneck_distance/include/gudhi/Graph_matching.h create mode 100644 src/Bottleneck_distance/include/gudhi/Internal_point.h create mode 100644 src/Bottleneck_distance/include/gudhi/Neighbors_finder.h create mode 100644 src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h create mode 100644 src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h create mode 100644 src/Bottleneck_distance/test/CMakeLists.txt create mode 100644 src/Bottleneck_distance/test/README create mode 100644 src/Bottleneck_distance/test/bottleneck_chrono.cpp create mode 100644 src/Bottleneck_distance/test/bottleneck_unit_test.cpp (limited to 'src') diff --git a/src/Bottleneck_distance/concept/Diagram_point.h b/src/Bottleneck_distance/concept/Diagram_point.h new file mode 100644 index 00000000..ce9c6d5b --- /dev/null +++ b/src/Bottleneck_distance/concept/Diagram_point.h @@ -0,0 +1,6 @@ + + +struct Diagram_point{ + double first; + double second; +}; diff --git a/src/Bottleneck_distance/concept/Persistence_diagram.h b/src/Bottleneck_distance/concept/Persistence_diagram.h new file mode 100644 index 00000000..4951af32 --- /dev/null +++ b/src/Bottleneck_distance/concept/Persistence_diagram.h @@ -0,0 +1,7 @@ + + +struct Persistence_Diagram +{ + const_iterator cbegin() const; + const_iterator cend() const; +}; diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt new file mode 100644 index 00000000..4e8766cc --- /dev/null +++ b/src/Bottleneck_distance/example/CMakeLists.txt @@ -0,0 +1,36 @@ +cmake_minimum_required(VERSION 2.6) +project(GUDHIBottleneckExample) + +# need CGAL 4.6 +# cmake -DCGAL_DIR=~/workspace/CGAL-4.6-beta1 ../../.. +if(CGAL_FOUND) + if (NOT CGAL_VERSION VERSION_LESS 4.6.0) + message(STATUS "CGAL version: ${CGAL_VERSION}.") + + include( ${CGAL_USE_FILE} ) + + if(NOT MSVC) + include(CheckCXXCompilerFlag) + CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11) + if(COMPILER_SUPPORTS_CXX11) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") + endif() + endif() + # - End of workaround + + find_package(Eigen3 3.1.0) + if (EIGEN3_FOUND) + message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") + include( ${EIGEN3_USE_FILE} ) + include_directories (BEFORE "../../include") + + add_executable (basic_example basic.cpp) + #add_test(dtoffrw_tore3D ${CMAKE_CURRENT_BINARY_DIR}/dtoffrw ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off 3) + + else() + message(WARNING "Eigen3 not found. Version 3.1.0 is required.") + endif() + else() + message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.") + endif () +endif() diff --git a/src/Bottleneck_distance/example/bottleneck_example.cpp b/src/Bottleneck_distance/example/bottleneck_example.cpp new file mode 100644 index 00000000..bbd83547 --- /dev/null +++ b/src/Bottleneck_distance/example/bottleneck_example.cpp @@ -0,0 +1,43 @@ +/* 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): Francois Godi + * + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 . + */ + +#include +#include + +using namespace Gudhi::Bottleneck_distance; + +int main() { + std::vector< std::pair > v1, v2; + + v1.push_back(std::pair(2.7,3.7)); + v1.push_back(std::pair(9.6,14)); + v1.push_back(std::pair(34.2,34.974)); + + v2.push_back(std::pair(2.8,4.45)); + v2.push_back(std::pair(9.5,14.1)); + + + double b = bottleneck_distance(v1, v2); + + std::cout << "Bottleneck distance = " << b << std::endl; + +} diff --git a/src/Bottleneck_distance/include/CGAL/Miscellaneous.h b/src/Bottleneck_distance/include/CGAL/Miscellaneous.h new file mode 100644 index 00000000..4de787fb --- /dev/null +++ b/src/Bottleneck_distance/include/CGAL/Miscellaneous.h @@ -0,0 +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): Francois Godi + * + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_CGAL_MISCELLANEOUS_H_ +#define SRC_BOTTLENECK_INCLUDE_CGAL_MISCELLANEOUS_H_ + +#include + +namespace CGAL { + +typedef Gudhi::bipartite_graph_matching::Internal_point Internal_point; + +template <> +struct Kernel_traits { + struct Kernel { + typedef double FT; + typedef double RT; + }; +}; + + +struct Construct_coord_iterator { + typedef const double* result_type; + const double* operator()(const Internal_point& p) const + { return static_cast(p.vec); } + const double* operator()(const Internal_point& p, int) const + { return static_cast(p.vec+2); } +}; + +} //namespace CGAL + +#endif // SRC_BOTTLENECK_INCLUDE_CGAL_MISCELLANEOUS_H_ diff --git a/src/Bottleneck_distance/include/gudhi/Graph_matching.h b/src/Bottleneck_distance/include/gudhi/Graph_matching.h new file mode 100644 index 00000000..d8860841 --- /dev/null +++ b/src/Bottleneck_distance/include/gudhi/Graph_matching.h @@ -0,0 +1,233 @@ +/* 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): Francois Godi + * + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ +#define SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ + +#include + +#include + +namespace Gudhi { + +namespace Bottleneck_distance { + +/** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams. + * + * + * + * \ingroup bottleneck_distance + */ +template +double compute(const Persistence_diagram1& diag1, const Persistence_diagram2& diag2, double e = 0.); + +/** \internal \brief Structure representing a graph matching. The graph is a Persistence_diagrams_graph. + * + * \ingroup bottleneck_distance + */ +class Graph_matching { +public: + /** \internal \brief Constructor constructing an empty matching. */ + explicit Graph_matching(); + /** \internal \brief Copy operator. */ + Graph_matching& operator=(const Graph_matching& m); + /** \internal \brief Is the matching perfect ? */ + bool perfect() const; + /** \internal \brief Augments the matching with a maximal set of edge-disjoint shortest augmenting paths. */ + bool multi_augment(); + /** \internal \brief Sets the maximum length of the edges allowed to be added in the matching, 0 initially. */ + void set_r(double r); + +private: + double r; + /** \internal \brief Given a point from V, provides its matched point in U, null_point_index() if there isn't. */ + std::vector v_to_u; + /** \internal \brief All the unmatched points in U. */ + std::list unmatched_in_u; + + /** \internal \brief Provides a Layered_neighbors_finder dividing the graph in layers. Basically a BFS. */ + std::shared_ptr layering() const; + /** \internal \brief Augments the matching with a simple path no longer than max_depth. Basically a DFS. */ + bool augment(Layered_neighbors_finder & layered_nf, int u_start_index, int max_depth); + /** \internal \brief Update the matching with the simple augmenting path given as parameter. */ + void update(std::deque & path); +}; + +inline Graph_matching::Graph_matching() + : r(0.), v_to_u(G::size(), null_point_index()), unmatched_in_u() { + for (int u_point_index = 0; u_point_index < G::size(); ++u_point_index) + unmatched_in_u.emplace_back(u_point_index); +} + +inline Graph_matching& Graph_matching::operator=(const Graph_matching& m) { + r = m.r; + v_to_u = m.v_to_u; + unmatched_in_u = m.unmatched_in_u; + return *this; +} + +inline bool Graph_matching::perfect() const { + return unmatched_in_u.empty(); +} + +inline bool Graph_matching::multi_augment() { + if (perfect()) + return false; + Layered_neighbors_finder layered_nf = *layering(); + int max_depth = layered_nf.vlayers_number()*2 - 1; + double rn = sqrt(G::size()); + // verification of a necessary criterion in order to shortcut if possible + if (max_depth <0 || (unmatched_in_u.size() > rn && max_depth >= rn)) + return false; + bool successful = false; + std::list tries(unmatched_in_u); + for (auto it = tries.cbegin(); it != tries.cend(); it++) + // 'augment' has side-effects which have to be always executed, don't change order + successful = augment(layered_nf, *it, max_depth) || successful; + return successful; +} + +inline void Graph_matching::set_r(double r) { + this->r = r; +} + +inline bool Graph_matching::augment(Layered_neighbors_finder & layered_nf, int u_start_index, int max_depth) { + //V vertices have at most one successor, thus when we backtrack from U we can directly pop_back 2 vertices. + std::deque path; + path.emplace_back(u_start_index); + do { + if (static_cast(path.size()) > max_depth) { + path.pop_back(); + path.pop_back(); + } + if (path.empty()) + return false; + path.emplace_back(layered_nf.pull_near(path.back(), static_cast(path.size())/2)); + while (path.back() == null_point_index()) { + path.pop_back(); + path.pop_back(); + if (path.empty()) + return false; + path.pop_back(); + path.emplace_back(layered_nf.pull_near(path.back(), path.size() / 2)); + } + path.emplace_back(v_to_u.at(path.back())); + } while (path.back() != null_point_index()); + //if v_to_u.at(path.back()) has no successor, path.back() is an exposed vertex + path.pop_back(); + update(path); + return true; +} + +inline std::shared_ptr Graph_matching::layering() const { + std::list u_vertices(unmatched_in_u); + std::list v_vertices; + Neighbors_finder nf(r); + for (int v_point_index = 0; v_point_index < G::size(); ++v_point_index) + nf.add(v_point_index); + std::shared_ptr layered_nf(new Layered_neighbors_finder(r)); + for(int layer = 0; !u_vertices.empty(); layer++) { + // one layer is one step in the BFS + for (auto it1 = u_vertices.cbegin(); it1 != u_vertices.cend(); ++it1) { + std::shared_ptr> u_succ(nf.pull_all_near(*it1)); + for (auto it2 = u_succ->begin(); it2 != u_succ->end(); ++it2) { + layered_nf->add(*it2, layer); + v_vertices.emplace_back(*it2); + } + } + // When the above for finishes, we have progress of one half-step (from U to V) in the BFS + u_vertices.clear(); + bool end = false; + for (auto it = v_vertices.cbegin(); it != v_vertices.cend(); it++) + if (v_to_u.at(*it) == null_point_index()) + // we stop when a nearest exposed V vertex (from U exposed vertices) has been found + end = true; + else + u_vertices.emplace_back(v_to_u.at(*it)); + // When the above for finishes, we have progress of one half-step (from V to U) in the BFS + if (end) + return layered_nf; + v_vertices.clear(); + } + return layered_nf; +} + +inline void Graph_matching::update(std::deque& path) { + unmatched_in_u.remove(path.front()); + for (auto it = path.cbegin(); it != path.cend(); ++it) { + // Be careful, the iterator is incremented twice each time + int tmp = *it; + v_to_u[*(++it)] = tmp; + } +} + +template +double compute_exactly(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2) { + G::initialize(diag1, diag2, 0.); + std::shared_ptr< std::vector > sd(G::sorted_distances()); + int idmin = 0; + int idmax = sd->size() - 1; + // alpha can be modified, this will change the complexity + double alpha = pow(sd->size(), 0.25); + Graph_matching m; + Graph_matching biggest_unperfect; + while (idmin != idmax) { + int step = static_cast((idmax - idmin) / alpha); + m.set_r(sd->at(idmin + step)); + while (m.multi_augment()); + //The above while compute a maximum matching (according to the r setted before) + if (m.perfect()) { + idmax = idmin + step; + m = biggest_unperfect; + } else { + biggest_unperfect = m; + idmin = idmin + step + 1; + } + } + return sd->at(idmin); +} + +template +double compute(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e) { + if(e< std::numeric_limits::min()) + return compute_exactly(diag1, diag2); + G::initialize(diag1, diag2, e); + double d = 0.; + double f = G::diameter(); + while (f-d > e){ + Graph_matching m; + m.set_r((d+f)/2.); + while (m.multi_augment()); + //The above while compute a maximum matching (according to the r setted before) + if (m.perfect()) + f = (d+f)/2.; + else + d= (d+f)/2.; + } + return d; +} + +} // namespace Bottleneck_distance + +} // namespace Gudhi + +#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ diff --git a/src/Bottleneck_distance/include/gudhi/Internal_point.h b/src/Bottleneck_distance/include/gudhi/Internal_point.h new file mode 100644 index 00000000..2080900d --- /dev/null +++ b/src/Bottleneck_distance/include/gudhi/Internal_point.h @@ -0,0 +1,74 @@ +/* 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): Francois Godi + * + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_INTERNAL_POINT_H_ +#define SRC_BOTTLENECK_INCLUDE_GUDHI_INTERNAL_POINT_H_ + +namespace Gudhi { + +namespace Bottleneck_distance { + +/** \internal \brief Returns the used index for encoding none of the points */ +int null_point_index(); + +/** \internal \typedef \brief Internal_point is the internal points representation, indexes used outside. */ +struct Internal_point { + double vec[2]; + int point_index; + Internal_point() {} + Internal_point(double x, double y, int p_i = null_point_index()) { vec[0]=x; vec[1]=y; point_index = p_i; } + double x() const { return vec[ 0 ]; } + double y() const { return vec[ 1 ]; } + double& x() { return vec[ 0 ]; } + double& y() { return vec[ 1 ]; } + bool operator==(const Internal_point& p) const + { + return point_index==p.point_index; + } + bool operator!=(const Internal_point& p) const { return ! (*this == p); } +/* +Useless + friend void swap(Internal_point& a, Internal_point& b) + { + using std::swap; + double x_tmp = a.vec[0]; + double y_tmp = a.vec[1]; + int pi_tmp = a.point_index; + a.vec[0] = b.vec[0]; + a.vec[1] = b.vec[1]; + a.point_index = b.point_index; + b.vec[0] = x_tmp; + b.vec[1] = y_tmp; + b.point_index = pi_tmp; + } +*/ +}; + +inline int null_point_index() { + return -1; +} + +} // namespace Bottleneck_distance + +} // namespace Gudhi + +#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_INTERNAL_POINT_H_ diff --git a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h new file mode 100644 index 00000000..7ad79126 --- /dev/null +++ b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h @@ -0,0 +1,154 @@ +/* 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): Francois Godi + * + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_ +#define SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_ + +#include +#include + +namespace Gudhi { + +namespace Bottleneck_distance { + +/** \internal \brief data structure used to find any point (including projections) in V near to a query point from U + * (which can be a projection). + * + * V points have to be added manually using their index and before the first pull. A neighbor pulled is automatically removed. + * + * \ingroup bottleneck_distance + */ +class Neighbors_finder { +public: + /** \internal \brief Constructor taking the near distance definition as parameter. */ + Neighbors_finder(double r); + /** \internal \brief A point added will be possibly pulled. */ + void add(int v_point_index); + /** \internal \brief Returns and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ + int pull_near(int u_point_index); + /** \internal \brief Returns and remove all the V points near to the U point given as parameter. */ + std::shared_ptr< std::list > pull_all_near(int u_point_index); + +private: + const double r; + Planar_neighbors_finder planar_neighbors_f; + std::unordered_set projections_f; + void remove(int v_point_index); + bool contains(int v_point_index); +}; + +/** \internal \brief data structure used to find any point (including projections) in V near to a query point from U + * (which can be a projection) in a layered graph layer given as parmeter. + * + * V points have to be added manually using their index and before the first pull. A neighbor pulled is automatically removed. + * + * \ingroup bottleneck_distance + */ +class Layered_neighbors_finder { +public: + /** \internal \brief Constructor taking the near distance definition as parameter. */ + Layered_neighbors_finder(double r); + /** \internal \brief A point added will be possibly pulled. */ + void add(int v_point_index, int vlayer); + /** \internal \brief Returns and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ + int pull_near(int u_point_index, int vlayer); + /** \internal \brief Returns the number of layers. */ + int vlayers_number() const; + +private: + const double r; + std::vector> neighbors_finder; +}; + +inline Neighbors_finder::Neighbors_finder(double r) : + r(r), planar_neighbors_f(r), projections_f() { } + +inline void Neighbors_finder::add(int v_point_index) { + if (G::on_the_v_diagonal(v_point_index)) + projections_f.emplace(v_point_index); + else + planar_neighbors_f.add(v_point_index); +} + +inline void Neighbors_finder::remove(int v_point_index) { + if(v_point_index == null_point_index()) + return; + if (G::on_the_v_diagonal(v_point_index)) + projections_f.erase(v_point_index); + else + planar_neighbors_f.remove(v_point_index); +} + +inline bool Neighbors_finder::contains(int v_point_index) { + return planar_neighbors_f.contains(v_point_index) || (projections_f.count(v_point_index)>0); +} + +inline int Neighbors_finder::pull_near(int u_point_index) { + int tmp; + int c = G::corresponding_point_in_v(u_point_index); + if (G::on_the_u_diagonal(u_point_index) && !projections_f.empty()) + //Any pair of projection is at distance 0 + tmp = *projections_f.cbegin(); + else if (contains(c) && (G::distance(u_point_index, c) <= r)) + //Is the query point near to its projection ? + tmp = c; + else + //Is the query point near to a V point in the plane ? + tmp = planar_neighbors_f.pull_near(u_point_index); + remove(tmp); + return tmp; +} + +inline std::shared_ptr< std::list > Neighbors_finder::pull_all_near(int u_point_index) { + std::shared_ptr< std::list > all_pull(planar_neighbors_f.pull_all_near(u_point_index)); + int last_pull = pull_near(u_point_index); + while (last_pull != null_point_index()) { + all_pull->emplace_back(last_pull); + last_pull = pull_near(u_point_index); + } + return all_pull; +} + +inline Layered_neighbors_finder::Layered_neighbors_finder(double r) : + r(r), neighbors_finder() { } + +inline void Layered_neighbors_finder::add(int v_point_index, int vlayer) { + for (int l = neighbors_finder.size(); l <= vlayer; l++) + neighbors_finder.emplace_back(std::shared_ptr(new Neighbors_finder(r))); + neighbors_finder.at(vlayer)->add(v_point_index); +} + +inline int Layered_neighbors_finder::pull_near(int u_point_index, int vlayer) { + if (static_cast (neighbors_finder.size()) <= vlayer) + return null_point_index(); + return neighbors_finder.at(vlayer)->pull_near(u_point_index); +} + +inline int Layered_neighbors_finder::vlayers_number() const { + return static_cast(neighbors_finder.size()); +} + +} // namespace Bottleneck_distance + +} // namespace Gudhi + +#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_ diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h new file mode 100644 index 00000000..e8a46f1c --- /dev/null +++ b/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h @@ -0,0 +1,168 @@ +/* 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): Francois Godi + * + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_ +#define SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_ + +#include +#include +#include +#include +#include +#include +#include +#include + +namespace Gudhi { + +namespace Bottleneck_distance { + + +/** \internal \brief Structure representing an euclidean bipartite graph containing + * the points from the two persistence diagrams (including the projections). + * + * \ingroup bottleneck_distance + */ +class Persistence_diagrams_graph { +public: + /** \internal \brief Initializer taking 2 Point (concept) ranges as parameters. */ + template + static void initialize(const Persistence_diagram1& diag1, const Persistence_diagram2& diag2, double e); + /** \internal \brief Is the given point from U the projection of a point in V ? */ + static bool on_the_u_diagonal(int u_point_index); + /** \internal \brief Is the given point from V the projection of a point in U ? */ + static bool on_the_v_diagonal(int v_point_index); + /** \internal \brief Given a point from V, returns the corresponding (projection or projector) point in U. */ + static int corresponding_point_in_u(int v_point_index); + /** \internal \brief Given a point from U, returns the corresponding (projection or projector) point in V. */ + static int corresponding_point_in_v(int u_point_index); + /** \internal \brief Given a point from U and a point from V, returns the distance between those points. */ + static double distance(int u_point_index, int v_point_index); + /** \internal \brief Returns size = |U| = |V|. */ + static int size(); + /** \internal \brief Returns the O(n^2) sorted distances between the points. */ + static std::shared_ptr< std::vector > sorted_distances(); + /** \internal \brief Returns an upper bound of the diameter of the convex hull */ + static double diameter(); + +private: + static std::vector u; + static std::vector v; + static Internal_point get_u_point(int u_point_index); + static Internal_point get_v_point(int v_point_index); + + friend class Naive_pnf; + friend class Cgal_pnf; +}; + +/** \internal \typedef \brief Shorter alias */ +typedef Persistence_diagrams_graph G; + +// static initialization +std::vector G::u = [] {return std::vector();}(); +std::vector G::v = [] {return std::vector();}(); + +template +inline void G::initialize(const Persistence_diagram1 &diag1, + const Persistence_diagram2 &diag2, double e){ + u.clear(); + v.clear(); + for (auto it = diag1.cbegin(); it != diag1.cend(); ++it) + if (it->second - it->first > e) + u.push_back(Internal_point(it->first, it->second, u.size())); + for (auto it = diag2.cbegin(); it != diag2.cend(); ++it) + if (it->second - it->first > e) + v.push_back(Internal_point(it->first, it->second, v.size())); + if (u.size() < v.size()) + swap(u, v); +} + +inline bool G::on_the_u_diagonal(int u_point_index) { + return u_point_index >= static_cast (u.size()); +} + +inline bool G::on_the_v_diagonal(int v_point_index) { + return v_point_index >= static_cast (v.size()); +} + +inline int G::corresponding_point_in_u(int v_point_index) { + return on_the_v_diagonal(v_point_index) ? + v_point_index - static_cast (v.size()) : v_point_index + static_cast (u.size()); +} + +inline int G::corresponding_point_in_v(int u_point_index) { + return on_the_u_diagonal(u_point_index) ? + u_point_index - static_cast (u.size()) : u_point_index + static_cast (v.size()); +} + +inline double G::distance(int u_point_index, int v_point_index) { + if (on_the_u_diagonal(u_point_index) && on_the_v_diagonal(v_point_index)) + return 0; + Internal_point p_u = get_u_point(u_point_index); + Internal_point p_v = get_v_point(v_point_index); + return std::max(std::fabs(p_u.x() - p_v.x()), std::fabs(p_u.y() - p_v.y())); +} + +inline int G::size() { + return static_cast (u.size() + v.size()); +} + +inline std::shared_ptr< std::vector > G::sorted_distances() { + // could be optimized + std::set sorted_distances; + for (int u_point_index = 0; u_point_index < size(); ++u_point_index) + for (int v_point_index = 0; v_point_index < size(); ++v_point_index) + sorted_distances.emplace(distance(u_point_index, v_point_index)); + std::shared_ptr< std::vector > sd_up(new std::vector(sorted_distances.cbegin(), sorted_distances.cend())); + return sd_up; +} + +inline Internal_point G::get_u_point(int u_point_index) { + if (!on_the_u_diagonal(u_point_index)) + return u.at(u_point_index); + Internal_point projector = v.at(corresponding_point_in_v(u_point_index)); + double m = (projector.x() + projector.y()) / 2; + return Internal_point(m,m,u_point_index); +} + +inline Internal_point G::get_v_point(int v_point_index) { + if (!on_the_v_diagonal(v_point_index)) + return v.at(v_point_index); + Internal_point projector = u.at(corresponding_point_in_u(v_point_index)); + double m = (projector.x() + projector.y()) / 2; + return Internal_point(m,m,v_point_index); +} + +inline double G::diameter() { + double max = 0.; + for(it = u.cbegin(); it != u.cend(); it++) + max = std::max(max,it->y()); + for(it = v.cbegin(); it != v.cend(); it++) + max = std::max(max,it->y()); + return max; +} + +} // namespace Bottleneck_distance + +} // namespace Gudhi + +#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_ diff --git a/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h new file mode 100644 index 00000000..c0b6383f --- /dev/null +++ b/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h @@ -0,0 +1,218 @@ +/* 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): Francois Godi + * + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_ +#define SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_ + +#include +#include +#include +#include +#include +#include +#include + + +namespace Gudhi { + +namespace Bottleneck_distance { + +/** \internal \brief Structure used to find any point in V near (according to the planar distance) to a query point from U. + * + * V points have to be added manually using their index and before the first remove/pull. A neighbor pulled is automatically removed. but we can also + * remove points manually using their index. + * + * \ingroup bottleneck_distance + */ +class Naive_pnf { +public: + /** \internal \brief Constructor taking the near distance definition as parameter. */ + Naive_pnf(double r_); + /** \internal \brief A point added will be possibly pulled. */ + void add(int v_point_index); + /** \internal \brief A point manually removed will no longer be possibly pulled. */ + void remove(int v_point_index); + /** \internal \brief Can the point given as parameter be returned ? */ + bool contains(int v_point_index) const; + /** \internal \brief Provide and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ + int pull_near(int u_point_index); + /** \internal \brief Provide and remove all the V points near to the U point given as parameter. */ + virtual std::shared_ptr< std::list > pull_all_near(int u_point_index); + +private: + double r; + std::pair get_v_key(int v_point_index) const; + std::multimap,int> grid; +}; + +class Cgal_pnf { + + typedef CGAL::Dimension_tag<2> D; + typedef CGAL::Search_traits Traits; + typedef CGAL::Weighted_Minkowski_distance Distance; + typedef CGAL::Orthogonal_incremental_neighbor_search K_neighbor_search; + typedef K_neighbor_search::Tree Kd_tree; + + +public: + /** \internal \brief Constructor taking the near distance definition as parameter. */ + Cgal_pnf(double r_); + /** \internal \brief A point added will be possibly pulled. */ + void add(int v_point_index); + /** \internal \brief A point manually removed will no longer be possibly pulled. */ + void remove(int v_point_index); + /** \internal \brief Can the point given as parameter be returned ? */ + bool contains(int v_point_index) const; + /** \internal \brief Provide a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ + int pull_near(int u_point_index); + /** \internal \brief Provide and remove all the V points near to the U point given as parameter. */ + virtual std::shared_ptr< std::list > pull_all_near(int u_point_index); + +private: + double r; + std::set contents; + Kd_tree kd_t; +}; + +/** \internal \typedef \brief Planar_neighbors_finder is the used implementation. */ +typedef Naive_pnf Planar_neighbors_finder; + +inline Naive_pnf::Naive_pnf(double r_) : + r(r_), grid() { } + + +inline std::pair Naive_pnf::get_v_key(int v_point_index) const{ + Internal_point v_point = G::get_v_point(v_point_index); + return std::make_pair(static_cast(v_point.x()/r), static_cast(v_point.y()/r)); +} + +inline void Naive_pnf::add(int v_point_index) { + grid.emplace(get_v_key(v_point_index),v_point_index); +} + +inline void Naive_pnf::remove(int v_point_index) { + if(v_point_index != null_point_index()) + for(auto it = grid.find(get_v_key(v_point_index)); it!=grid.end(); it++) + if(it->second==v_point_index){ + grid.erase(it); + return; + } +} + +inline bool Naive_pnf::contains(int v_point_index) const { + if(v_point_index == null_point_index()) + return false; + for(auto it = grid.find(get_v_key(v_point_index)); it!=grid.end(); it++) + if(it->second==v_point_index) + return true; + return false; +} + +inline int Naive_pnf::pull_near(int u_point_index) { + Internal_point u_point = G::get_u_point(u_point_index); + int i0 = static_cast(u_point.x()/r); + int j0 = static_cast(u_point.y()/r); + for(int i = 1; i<= 3; i++) + for(int j = 1; j<= 3; j++) + for(auto it = grid.find(std::make_pair(i0 +(i%3)-1, j0+(j%3)-1)); it!=grid.end(); it++) + if (G::distance(u_point_index, it->second) <= r) { + int tmp = it->second; + grid.erase(it); + return tmp; + } + return null_point_index(); +} + +inline std::shared_ptr< std::list > Naive_pnf::pull_all_near(int u_point_index) { + std::shared_ptr< std::list > all_pull(new std::list); + Internal_point u_point = G::get_u_point(u_point_index); + int i0 = static_cast(u_point.x()/r); + int j0 = static_cast(u_point.y()/r); + for(int i = 1; i<= 3; i++) + for(int j = 1; j<= 3; j++) + for(auto it = grid.find(std::make_pair(i0 +(i%3)-1, j0+(j%3)-1)); it!=grid.end();) + if (G::distance(u_point_index, it->second) <= r) { + all_pull->emplace_back(it->second); + it = grid.erase(it); + } + else it++; + return all_pull; +} + + +/** \internal \brief Constructor taking the near distance definition as parameter. */ +inline Cgal_pnf::Cgal_pnf(double r_) + : r(r_), contents(), kd_t() {} + + +/** \internal \brief A point added will be possibly pulled. */ +inline void Cgal_pnf::add(int v_point_index){ + if(v_point_index == null_point_index()) + return; + contents.insert(v_point_index); + kd_t.insert(G::get_v_point(v_point_index)); +} + +/** \internal \brief A point manually removed will no longer be possibly pulled. */ +inline void Cgal_pnf::remove(int v_point_index){ + if(contains(v_point_index)){ + contents.erase(v_point_index); + kd_t.remove(G::get_v_point(v_point_index)); + } +} + +/** \internal \brief Can the point given as parameter be returned ? */ +inline bool Cgal_pnf::contains(int v_point_index) const{ + if(v_point_index == null_point_index()) + return false; + return contents.count(v_point_index)>0; +} + +/** \internal \brief Provide and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ +inline int Cgal_pnf::pull_near(int u_point_index){ + Internal_point u_point = G::get_u_point(u_point_index); + std::vector w = {1., 1.}; + K_neighbor_search search(kd_t, u_point, 0., true, Distance(0, 2, w)); + auto it = search.begin(); + if(it==search.end() || G::distance(u_point_index, it->first.point_index) > r) + return null_point_index(); + int tmp = it->first.point_index; + remove(tmp); + return tmp; +} + +inline std::shared_ptr< std::list > Cgal_pnf::pull_all_near(int u_point_index) { + std::shared_ptr< std::list > all_pull(new std::list); + int last_pull = pull_near(u_point_index); + while (last_pull != null_point_index()) { + all_pull->emplace_back(last_pull); + last_pull = pull_near(u_point_index); + } + return all_pull; +} + + +} // namespace Bottleneck_distance + +} // namespace Gudhi + +#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_ diff --git a/src/Bottleneck_distance/test/CMakeLists.txt b/src/Bottleneck_distance/test/CMakeLists.txt new file mode 100644 index 00000000..ab0461cc --- /dev/null +++ b/src/Bottleneck_distance/test/CMakeLists.txt @@ -0,0 +1,63 @@ +cmake_minimum_required(VERSION 2.6) +project(GUDHIBottleneckUT) + + + + +if(CGAL_FOUND) + if (NOT CGAL_VERSION VERSION_LESS 4.6.0) + message(STATUS "CGAL version: ${CGAL_VERSION}.") + + include( ${CGAL_USE_FILE} ) + + if(NOT MSVC) + include(CheckCXXCompilerFlag) + CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11) + if(COMPILER_SUPPORTS_CXX11) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") + endif() + endif() + # - End of workaround + + find_package(Eigen3 3.1.0) + if (EIGEN3_FOUND) + message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") + include( ${EIGEN3_USE_FILE} ) + include_directories (BEFORE "../../include") + + if (GCOVR_PATH) + # for gcovr to make coverage reports - Corbera Jenkins plugin + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage") + set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage") +endif() +if (GPROF_PATH) + # for gprof to make coverage reports - Jenkins + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg") + set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg") +endif() + message("CMAKE_CXX_FLAGS = ${CMAKE_CXX_FLAGS}") + message("CMAKE_CXX_FLAGS_DEBUG = ${CMAKE_CXX_FLAGS_DEBUG}") + message("CMAKE_CXX_FLAGS_RELEASE = ${CMAKE_CXX_FLAGS_RELEASE}") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O2 -std=c++11 -Wall -Wpedantic -Wsign-compare") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -ggdb -O0") + set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE}") + +add_executable ( BottleneckUT bottleneck_unit_test.cpp ) +target_link_libraries(BottleneckUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) + +# Unitary tests +add_test(NAME BottleneckUT + COMMAND ${CMAKE_CURRENT_BINARY_DIR}/BottleneckUT + # XML format for Jenkins xUnit plugin + --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/BottleneckUT.xml --log_level=test_suite --report_level=no) + + + else() + message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.") + endif() + else() + message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile bipartite graphs matching feature. Version 4.6.0 is required.") + endif () +endif() diff --git a/src/Bottleneck_distance/test/README b/src/Bottleneck_distance/test/README new file mode 100644 index 00000000..0e7b8673 --- /dev/null +++ b/src/Bottleneck_distance/test/README @@ -0,0 +1,12 @@ +To compile: +*********** + +cmake . +make + +To launch with details: +*********************** + +./BottleneckUnitTest --report_level=detailed --log_level=all + + ==> echo $? returns 0 in case of success (non-zero otherwise) diff --git a/src/Bottleneck_distance/test/bottleneck_chrono.cpp b/src/Bottleneck_distance/test/bottleneck_chrono.cpp new file mode 100644 index 00000000..8f187a91 --- /dev/null +++ b/src/Bottleneck_distance/test/bottleneck_chrono.cpp @@ -0,0 +1,61 @@ +/* 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): Francois Godi + * + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 . + */ + +#include +#include +#include + +using namespace Gudhi::Bottleneck_distance; + + +double upper_bound = 400.; // any real >0 + +int main(){ + std::ofstream objetfichier; + objetfichier.open("results.csv", std::ios::out); + + for(int n=0; n<=2500; n+=250){ + std::uniform_real_distribution unif1(0.,upper_bound); + std::uniform_real_distribution unif2(upper_bound/1000.,upper_bound/100.); + std::default_random_engine re; + std::vector< std::pair > v1, v2; + for (int i = 0; i < n; i++) { + double a = unif1(re); + double b = unif1(re); + double x = unif2(re); + double y = unif2(re); + v1.emplace_back(std::min(a,b), std::max(a,b)); + v2.emplace_back(std::min(a,b)+std::min(x,y), std::max(a,b)+std::max(x,y)); + if(i%5==0) + v1.emplace_back(std::min(a,b),std::min(a,b)+x); + if(i%3==0) + v2.emplace_back(std::max(a,b),std::max(a,b)+y); + } + std::chrono::steady_clock::time_point start = std::chrono::steady_clock::now(); + double b = bottleneck_approx(v1,v2, 0.); + std::chrono::steady_clock::time_point end = std::chrono::steady_clock::now(); + typedef std::chrono::duration millisecs_t; + millisecs_t duration(std::chrono::duration_cast(end-start)); + objetfichier << n << ";" << duration.count() << ";" << b << std::endl; + } + objetfichier.close(); +} diff --git a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp new file mode 100644 index 00000000..33ac3f1b --- /dev/null +++ b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp @@ -0,0 +1,188 @@ +/* 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): Francois Godi + * + * Copyright (C) 2015 INRIA Sophia-Antipolis (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 . + */ + + +#define BOOST_TEST_MODULE bottleneck test + +#include +#include +#include + +using namespace Gudhi::Bottleneck_distance; + +int n1 = 81; // a natural number >0 +int n2 = 180; // a natural number >0 +double upper_bound = 406.43; // any real >0 + +BOOST_AUTO_TEST_CASE(persistence_diagrams_graph){ + // Random construction + std::uniform_real_distribution unif(0.,upper_bound); + std::default_random_engine re; + std::vector< std::pair > v1, v2; + for (int i = 0; i < n1; i++) { + double a = unif(re); + double b = unif(re); + v1.emplace_back(std::min(a,b), std::max(a,b)); + } + for (int i = 0; i < n2; i++) { + double a = unif(re); + double b = unif(re); + v2.emplace_back(std::min(a,b), std::max(a,b)); + } + G::initialize(v1, v2, 0.); + std::shared_ptr< std::vector > d(G::sorted_distances()); + // + BOOST_CHECK(!G::on_the_u_diagonal(n1-1)); + BOOST_CHECK(!G::on_the_u_diagonal(n1)); + BOOST_CHECK(!G::on_the_u_diagonal(n2-1)); + BOOST_CHECK(G::on_the_u_diagonal(n2)); + BOOST_CHECK(!G::on_the_v_diagonal(n1-1)); + BOOST_CHECK(G::on_the_v_diagonal(n1)); + BOOST_CHECK(G::on_the_v_diagonal(n2-1)); + BOOST_CHECK(G::on_the_v_diagonal(n2)); + // + BOOST_CHECK(G::corresponding_point_in_u(0)==n2); + BOOST_CHECK(G::corresponding_point_in_u(n1)==0); + BOOST_CHECK(G::corresponding_point_in_v(0)==n1); + BOOST_CHECK(G::corresponding_point_in_v(n2)==0); + // + BOOST_CHECK(G::size()==(n1+n2)); + // + BOOST_CHECK((int) d->size() <= (n1+n2)*(n1+n2) - n1*n2 + 1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,0))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n1-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n2-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n2))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,(n1+n2)-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,0))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n1-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n2-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n2))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,(n1+n2)-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,0))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n1-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n2-1))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n2))==1); + BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,(n1+n2)-1))==1); +} + +BOOST_AUTO_TEST_CASE(planar_neighbors_finder) { + Planar_neighbors_finder pnf(1.); + for(int v_point_index=0; v_point_index l = *pnf.pull_all_near(n2/2); + bool v = true; + for(auto it = l.cbegin(); it != l.cend(); ++it) + v = v && (G::distance(n2/2,*it)>1.); + BOOST_CHECK(v); + int v_point_index_2 = pnf.pull_near(n2/2); + BOOST_CHECK(v_point_index_2 == -1); +} + +BOOST_AUTO_TEST_CASE(neighbors_finder) { + Neighbors_finder nf(1.); + for(int v_point_index=1; v_point_index<((n2+n1)*9/10); v_point_index+=2) + nf.add(v_point_index); + // + int v_point_index_1 = nf.pull_near(n2/2); + BOOST_CHECK((v_point_index_1 == -1) || (G::distance(n2/2,v_point_index_1)<=1.)); + std::list l = *nf.pull_all_near(n2/2); + bool v = true; + for(auto it = l.cbegin(); it != l.cend(); ++it) + v = v && (G::distance(n2/2,*it)>1.); + BOOST_CHECK(v); + int v_point_index_2 = nf.pull_near(n2/2); + BOOST_CHECK(v_point_index_2 == -1); +} + +BOOST_AUTO_TEST_CASE(layered_neighbors_finder) { + Layered_neighbors_finder lnf(1.); + for(int v_point_index=1; v_point_index<((n2+n1)*9/10); v_point_index+=2) + lnf.add(v_point_index, v_point_index % 7); + // + int v_point_index_1 = lnf.pull_near(n2/2,6); + BOOST_CHECK((v_point_index_1 == -1) || (G::distance(n2/2,v_point_index_1)<=1.)); + int v_point_index_2 = lnf.pull_near(n2/2,6); + BOOST_CHECK(v_point_index_2 == -1); + v_point_index_1 = lnf.pull_near(n2/2,0); + BOOST_CHECK((v_point_index_1 == -1) || (G::distance(n2/2,v_point_index_1)<=1.)); + v_point_index_2 = lnf.pull_near(n2/2,0); + BOOST_CHECK(v_point_index_2 == -1); +} + +BOOST_AUTO_TEST_CASE(graph_matching) { + Graph_matching m1; + m1.set_r(0.); + int e = 0; + while (m1.multi_augment()) + ++e; + BOOST_CHECK(e <= 2*sqrt(2*(n1+n2))); + Graph_matching m2 = m1; + BOOST_CHECK(!m2.multi_augment()); + m2.set_r(upper_bound); + e = 0; + while (m2.multi_augment()) + ++e; + BOOST_CHECK(e <= 2*sqrt(2*(n1+n2))); + BOOST_CHECK(m2.perfect()); + BOOST_CHECK(!m1.perfect()); +} + +BOOST_AUTO_TEST_CASE(global){ + std::uniform_real_distribution unif1(0.,upper_bound); + std::uniform_real_distribution unif2(upper_bound/1000.,upper_bound/100.); + std::default_random_engine re; + std::vector< std::pair > v1, v2; + for (int i = 0; i < n1; i++) { + double a = unif1(re); + double b = unif1(re); + double x = unif2(re); + double y = unif2(re); + v1.emplace_back(std::min(a,b), std::max(a,b)); + v2.emplace_back(std::min(a,b)+std::min(x,y), std::max(a,b)+std::max(x,y)); + if(i%5==0) + v1.emplace_back(std::min(a,b),std::min(a,b)+x); + if(i%3==0) + v2.emplace_back(std::max(a,b),std::max(a,b)+y); + } + BOOST_CHECK(bottleneck_distance(v1, v2) <= upper_bound/100.); +} -- cgit v1.2.3 From 8068835924d52b8bbc1943f117dcda36c49d32f6 Mon Sep 17 00:00:00 2001 From: fgodi Date: Thu, 2 Jun 2016 17:11:11 +0000 Subject: old name removed git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@1241 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 66627d6e4e4d292717d8991351a7d31062b734a8 --- .../concept/Persistence_diagram.h | 7 - .../example/CMakeLists.txt | 36 ---- src/Bipartite_graphs_matching/example/basic.cpp | 85 -------- .../include/CGAL/Miscellaneous.h | 51 ----- .../include/gudhi/Graph_matching.h | 213 -------------------- .../include/gudhi/Internal_point.h | 74 ------- .../include/gudhi/Neighbors_finder.h | 154 --------------- .../include/gudhi/Persistence_diagrams_graph.h | 157 --------------- .../include/gudhi/Planar_neighbors_finder.h | 218 --------------------- src/Bipartite_graphs_matching/test/CMakeLists.txt | 63 ------ src/Bipartite_graphs_matching/test/README | 12 -- .../test/bottleneck_unit_test.cpp | 165 ---------------- 12 files changed, 1235 deletions(-) delete mode 100644 src/Bipartite_graphs_matching/concept/Persistence_diagram.h delete mode 100644 src/Bipartite_graphs_matching/example/CMakeLists.txt delete mode 100644 src/Bipartite_graphs_matching/example/basic.cpp delete mode 100644 src/Bipartite_graphs_matching/include/CGAL/Miscellaneous.h delete mode 100644 src/Bipartite_graphs_matching/include/gudhi/Graph_matching.h delete mode 100644 src/Bipartite_graphs_matching/include/gudhi/Internal_point.h delete mode 100644 src/Bipartite_graphs_matching/include/gudhi/Neighbors_finder.h delete mode 100644 src/Bipartite_graphs_matching/include/gudhi/Persistence_diagrams_graph.h delete mode 100644 src/Bipartite_graphs_matching/include/gudhi/Planar_neighbors_finder.h delete mode 100644 src/Bipartite_graphs_matching/test/CMakeLists.txt delete mode 100644 src/Bipartite_graphs_matching/test/README delete mode 100644 src/Bipartite_graphs_matching/test/bottleneck_unit_test.cpp (limited to 'src') diff --git a/src/Bipartite_graphs_matching/concept/Persistence_diagram.h b/src/Bipartite_graphs_matching/concept/Persistence_diagram.h deleted file mode 100644 index eaaf8bc5..00000000 --- a/src/Bipartite_graphs_matching/concept/Persistence_diagram.h +++ /dev/null @@ -1,7 +0,0 @@ -typedef typename std::pair Diagram_point; - -struct Persistence_Diagram -{ - const_iterator cbegin() const; - const_iterator cend() const; -}; diff --git a/src/Bipartite_graphs_matching/example/CMakeLists.txt b/src/Bipartite_graphs_matching/example/CMakeLists.txt deleted file mode 100644 index 4e8766cc..00000000 --- a/src/Bipartite_graphs_matching/example/CMakeLists.txt +++ /dev/null @@ -1,36 +0,0 @@ -cmake_minimum_required(VERSION 2.6) -project(GUDHIBottleneckExample) - -# need CGAL 4.6 -# cmake -DCGAL_DIR=~/workspace/CGAL-4.6-beta1 ../../.. -if(CGAL_FOUND) - if (NOT CGAL_VERSION VERSION_LESS 4.6.0) - message(STATUS "CGAL version: ${CGAL_VERSION}.") - - include( ${CGAL_USE_FILE} ) - - if(NOT MSVC) - include(CheckCXXCompilerFlag) - CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11) - if(COMPILER_SUPPORTS_CXX11) - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") - endif() - endif() - # - End of workaround - - find_package(Eigen3 3.1.0) - if (EIGEN3_FOUND) - message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") - include( ${EIGEN3_USE_FILE} ) - include_directories (BEFORE "../../include") - - add_executable (basic_example basic.cpp) - #add_test(dtoffrw_tore3D ${CMAKE_CURRENT_BINARY_DIR}/dtoffrw ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off 3) - - else() - message(WARNING "Eigen3 not found. Version 3.1.0 is required.") - endif() - else() - message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.") - endif () -endif() diff --git a/src/Bipartite_graphs_matching/example/basic.cpp b/src/Bipartite_graphs_matching/example/basic.cpp deleted file mode 100644 index f1c9d36e..00000000 --- a/src/Bipartite_graphs_matching/example/basic.cpp +++ /dev/null @@ -1,85 +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): Francois Godi - * - * Copyright (C) 2015 INRIA Sophia-Antipolis (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 . - */ - -#include -#include - -#include -#include - -using namespace Gudhi::bipartite_graph_matching; - - -double upper_bound = 400.; // any real >0 - -int main(){ - std::ofstream objetfichier; - objetfichier.open("results.csv", std::ios::out); - - for(int n =50; n<=1000; n+=100){ -std::cout << n << "\n"; - std::uniform_real_distribution unif1(0.,upper_bound); - std::uniform_real_distribution unif2(upper_bound/1000.,upper_bound/100.); - std::default_random_engine re; - std::vector< std::pair > v1, v2; - for (int i = 0; i < n; i++) { - double a = unif1(re); - double b = unif1(re); - double x = unif2(re); - double y = unif2(re); - v1.emplace_back(std::min(a,b), std::max(a,b)); - v2.emplace_back(std::min(a,b)+std::min(x,y), std::max(a,b)+std::max(x,y)); - if(i%5==0) - v1.emplace_back(std::min(a,b),std::min(a,b)+x); - if(i%3==0) - v2.emplace_back(std::max(a,b),std::max(a,b)+y); - } - - std::chrono::steady_clock::time_point start = std::chrono::steady_clock::now(); - double b = bottleneck_distance(v1,v2); - std::chrono::steady_clock::time_point end = std::chrono::steady_clock::now(); - - typedef std::chrono::duration millisecs_t; - millisecs_t duration(std::chrono::duration_cast(end-start)); - objetfichier << n << ";" << duration.count() << ";" << b << std::endl; - } - objetfichier.close(); -} - - -/* -int main() { - std::vector< std::pair > v1, v2; - - v1.push_back(std::pair(2.7,3.7)); - v1.push_back(std::pair(9.6,14)); - v1.push_back(std::pair(34.2,34.974)); - - v2.push_back(std::pair(2.8,4.45)); - v2.push_back(std::pair(9.5,14.1)); - - - double b = bottleneck_distance(v1, v2); - - std::cout << "Bottleneck distance = " << b << std::endl; - -}*/ diff --git a/src/Bipartite_graphs_matching/include/CGAL/Miscellaneous.h b/src/Bipartite_graphs_matching/include/CGAL/Miscellaneous.h deleted file mode 100644 index 4de787fb..00000000 --- a/src/Bipartite_graphs_matching/include/CGAL/Miscellaneous.h +++ /dev/null @@ -1,51 +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): Francois Godi - * - * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_CGAL_MISCELLANEOUS_H_ -#define SRC_BOTTLENECK_INCLUDE_CGAL_MISCELLANEOUS_H_ - -#include - -namespace CGAL { - -typedef Gudhi::bipartite_graph_matching::Internal_point Internal_point; - -template <> -struct Kernel_traits { - struct Kernel { - typedef double FT; - typedef double RT; - }; -}; - - -struct Construct_coord_iterator { - typedef const double* result_type; - const double* operator()(const Internal_point& p) const - { return static_cast(p.vec); } - const double* operator()(const Internal_point& p, int) const - { return static_cast(p.vec+2); } -}; - -} //namespace CGAL - -#endif // SRC_BOTTLENECK_INCLUDE_CGAL_MISCELLANEOUS_H_ diff --git a/src/Bipartite_graphs_matching/include/gudhi/Graph_matching.h b/src/Bipartite_graphs_matching/include/gudhi/Graph_matching.h deleted file mode 100644 index fa05aa7c..00000000 --- a/src/Bipartite_graphs_matching/include/gudhi/Graph_matching.h +++ /dev/null @@ -1,213 +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): Francois Godi - * - * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ -#define SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ - -#include - -#include - -namespace Gudhi { - -namespace bipartite_graph_matching { - -/** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams. - * - * - * - * \ingroup bottleneck_distance - */ -template -double bottleneck_distance(const Persistence_diagram1& diag1, const Persistence_diagram2& diag2, double e = 0.); - -/** \internal \brief Structure representing a graph matching. The graph is a Persistence_diagrams_graph. - * - * \ingroup bottleneck_distance - */ -class Graph_matching { -public: - /** \internal \brief Constructor constructing an empty matching. */ - explicit Graph_matching(); - /** \internal \brief Copy operator. */ - Graph_matching& operator=(const Graph_matching& m); - /** \internal \brief Is the matching perfect ? */ - bool perfect() const; - /** \internal \brief Augments the matching with a maximal set of edge-disjoint shortest augmenting paths. */ - bool multi_augment(); - /** \internal \brief Sets the maximum length of the edges allowed to be added in the matching, 0 initially. */ - void set_r(double r); - -private: - double r; - /** \internal \brief Given a point from V, provides its matched point in U, null_point_index() if there isn't. */ - std::vector v_to_u; - /** \internal \brief All the unmatched points in U. */ - std::list unmatched_in_u; - - /** \internal \brief Provides a Layered_neighbors_finder dividing the graph in layers. Basically a BFS. */ - std::shared_ptr layering() const; - /** \internal \brief Augments the matching with a simple path no longer than max_depth. Basically a DFS. */ - bool augment(Layered_neighbors_finder & layered_nf, int u_start_index, int max_depth); - /** \internal \brief Update the matching with the simple augmenting path given as parameter. */ - void update(std::deque & path); -}; - -inline Graph_matching::Graph_matching() - : r(0.), v_to_u(G::size(), null_point_index()), unmatched_in_u() { - for (int u_point_index = 0; u_point_index < G::size(); ++u_point_index) - unmatched_in_u.emplace_back(u_point_index); -} - -inline Graph_matching& Graph_matching::operator=(const Graph_matching& m) { - r = m.r; - v_to_u = m.v_to_u; - unmatched_in_u = m.unmatched_in_u; - return *this; -} - -inline bool Graph_matching::perfect() const { - return unmatched_in_u.empty(); -} - -inline bool Graph_matching::multi_augment() { - if (perfect()) - return false; - Layered_neighbors_finder layered_nf = *layering(); - int max_depth = layered_nf.vlayers_number()*2 - 1; - double rn = sqrt(G::size()); - // verification of a necessary criterion in order to shortcut if possible - if (max_depth <0 || (unmatched_in_u.size() > rn && max_depth >= rn)) - return false; - bool successful = false; - std::list tries(unmatched_in_u); - for (auto it = tries.cbegin(); it != tries.cend(); it++) - // 'augment' has side-effects which have to be always executed, don't change order - successful = augment(layered_nf, *it, max_depth) || successful; - return successful; -} - -inline void Graph_matching::set_r(double r) { - this->r = r; -} - -inline bool Graph_matching::augment(Layered_neighbors_finder & layered_nf, int u_start_index, int max_depth) { - //V vertices have at most one successor, thus when we backtrack from U we can directly pop_back 2 vertices. - std::deque path; - path.emplace_back(u_start_index); - do { - if (static_cast(path.size()) > max_depth) { - path.pop_back(); - path.pop_back(); - } - if (path.empty()) - return false; - path.emplace_back(layered_nf.pull_near(path.back(), static_cast(path.size())/2)); - while (path.back() == null_point_index()) { - path.pop_back(); - path.pop_back(); - if (path.empty()) - return false; - path.pop_back(); - path.emplace_back(layered_nf.pull_near(path.back(), path.size() / 2)); - } - path.emplace_back(v_to_u.at(path.back())); - } while (path.back() != null_point_index()); - //if v_to_u.at(path.back()) has no successor, path.back() is an exposed vertex - path.pop_back(); - update(path); - return true; -} - -inline std::shared_ptr Graph_matching::layering() const { - std::list u_vertices(unmatched_in_u); - std::list v_vertices; - Neighbors_finder nf(r); - for (int v_point_index = 0; v_point_index < G::size(); ++v_point_index) - nf.add(v_point_index); - std::shared_ptr layered_nf(new Layered_neighbors_finder(r)); - for(int layer = 0; !u_vertices.empty(); layer++) { - // one layer is one step in the BFS - for (auto it1 = u_vertices.cbegin(); it1 != u_vertices.cend(); ++it1) { - std::shared_ptr> u_succ(nf.pull_all_near(*it1)); - for (auto it2 = u_succ->begin(); it2 != u_succ->end(); ++it2) { - layered_nf->add(*it2, layer); - v_vertices.emplace_back(*it2); - } - } - // When the above for finishes, we have progress of one half-step (from U to V) in the BFS - u_vertices.clear(); - bool end = false; - for (auto it = v_vertices.cbegin(); it != v_vertices.cend(); it++) - if (v_to_u.at(*it) == null_point_index()) - // we stop when a nearest exposed V vertex (from U exposed vertices) has been found - end = true; - else - u_vertices.emplace_back(v_to_u.at(*it)); - // When the above for finishes, we have progress of one half-step (from V to U) in the BFS - if (end) - return layered_nf; - v_vertices.clear(); - } - return layered_nf; -} - -inline void Graph_matching::update(std::deque& path) { - unmatched_in_u.remove(path.front()); - for (auto it = path.cbegin(); it != path.cend(); ++it) { - // Be careful, the iterator is incremented twice each time - int tmp = *it; - v_to_u[*(++it)] = tmp; - } -} - -template -double bottleneck_distance(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e) { - G::initialize(diag1, diag2, e); - std::shared_ptr< std::vector > sd(G::sorted_distances()); - int idmin = 0; - int idmax = sd->size() - 1; - // alpha can be modified, this will change the complexity - double alpha = pow(sd->size(), 0.25); - Graph_matching m; - Graph_matching biggest_unperfect; - while (idmin != idmax) { - int step = static_cast((idmax - idmin) / alpha); - m.set_r(sd->at(idmin + step)); - while (m.multi_augment()); - // The above while compute a maximum matching (according to the r setted before) - if (m.perfect()) { - idmax = idmin + step; - m = biggest_unperfect; - } else { - biggest_unperfect = m; - idmin = idmin + step + 1; - } - } - return sd->at(idmin); -} - -} // namespace bipartite_graph_matching - -} // namespace Gudhi - -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ diff --git a/src/Bipartite_graphs_matching/include/gudhi/Internal_point.h b/src/Bipartite_graphs_matching/include/gudhi/Internal_point.h deleted file mode 100644 index 3dc37962..00000000 --- a/src/Bipartite_graphs_matching/include/gudhi/Internal_point.h +++ /dev/null @@ -1,74 +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): Francois Godi - * - * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_INTERNAL_POINT_H_ -#define SRC_BOTTLENECK_INCLUDE_GUDHI_INTERNAL_POINT_H_ - -namespace Gudhi { - -namespace bipartite_graph_matching { - -/** \internal \brief Returns the used index for encoding none of the points */ -int null_point_index(); - -/** \internal \typedef \brief Internal_point is the internal points representation, indexes used outside. */ -struct Internal_point { - double vec[2]; - int point_index; - Internal_point() {} - Internal_point(double x, double y, int p_i = null_point_index()) { vec[0]=x; vec[1]=y; point_index = p_i; } - double x() const { return vec[ 0 ]; } - double y() const { return vec[ 1 ]; } - double& x() { return vec[ 0 ]; } - double& y() { return vec[ 1 ]; } - bool operator==(const Internal_point& p) const - { - return point_index==p.point_index; - } - bool operator!=(const Internal_point& p) const { return ! (*this == p); } -/* -Useless - friend void swap(Internal_point& a, Internal_point& b) - { - using std::swap; - double x_tmp = a.vec[0]; - double y_tmp = a.vec[1]; - int pi_tmp = a.point_index; - a.vec[0] = b.vec[0]; - a.vec[1] = b.vec[1]; - a.point_index = b.point_index; - b.vec[0] = x_tmp; - b.vec[1] = y_tmp; - b.point_index = pi_tmp; - } -*/ -}; - -inline int null_point_index() { - return -1; -} - -} // namespace bipartite_graph_matching - -} // namespace Gudhi - -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_INTERNAL_POINT_H_ diff --git a/src/Bipartite_graphs_matching/include/gudhi/Neighbors_finder.h b/src/Bipartite_graphs_matching/include/gudhi/Neighbors_finder.h deleted file mode 100644 index f346c62f..00000000 --- a/src/Bipartite_graphs_matching/include/gudhi/Neighbors_finder.h +++ /dev/null @@ -1,154 +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): Francois Godi - * - * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_ -#define SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_ - -#include -#include - -namespace Gudhi { - -namespace bipartite_graph_matching { - -/** \internal \brief data structure used to find any point (including projections) in V near to a query point from U - * (which can be a projection). - * - * V points have to be added manually using their index and before the first pull. A neighbor pulled is automatically removed. - * - * \ingroup bottleneck_distance - */ -class Neighbors_finder { -public: - /** \internal \brief Constructor taking the near distance definition as parameter. */ - Neighbors_finder(double r); - /** \internal \brief A point added will be possibly pulled. */ - void add(int v_point_index); - /** \internal \brief Returns and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ - int pull_near(int u_point_index); - /** \internal \brief Returns and remove all the V points near to the U point given as parameter. */ - std::shared_ptr< std::list > pull_all_near(int u_point_index); - -private: - const double r; - Planar_neighbors_finder planar_neighbors_f; - std::unordered_set projections_f; - void remove(int v_point_index); - bool contains(int v_point_index); -}; - -/** \internal \brief data structure used to find any point (including projections) in V near to a query point from U - * (which can be a projection) in a layered graph layer given as parmeter. - * - * V points have to be added manually using their index and before the first pull. A neighbor pulled is automatically removed. - * - * \ingroup bottleneck_distance - */ -class Layered_neighbors_finder { -public: - /** \internal \brief Constructor taking the near distance definition as parameter. */ - Layered_neighbors_finder(double r); - /** \internal \brief A point added will be possibly pulled. */ - void add(int v_point_index, int vlayer); - /** \internal \brief Returns and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ - int pull_near(int u_point_index, int vlayer); - /** \internal \brief Returns the number of layers. */ - int vlayers_number() const; - -private: - const double r; - std::vector> neighbors_finder; -}; - -inline Neighbors_finder::Neighbors_finder(double r) : - r(r), planar_neighbors_f(r), projections_f() { } - -inline void Neighbors_finder::add(int v_point_index) { - if (G::on_the_v_diagonal(v_point_index)) - projections_f.emplace(v_point_index); - else - planar_neighbors_f.add(v_point_index); -} - -inline void Neighbors_finder::remove(int v_point_index) { - if(v_point_index == null_point_index()) - return; - if (G::on_the_v_diagonal(v_point_index)) - projections_f.erase(v_point_index); - else - planar_neighbors_f.remove(v_point_index); -} - -inline bool Neighbors_finder::contains(int v_point_index) { - return planar_neighbors_f.contains(v_point_index) || (projections_f.count(v_point_index)>0); -} - -inline int Neighbors_finder::pull_near(int u_point_index) { - int tmp; - int c = G::corresponding_point_in_v(u_point_index); - if (G::on_the_u_diagonal(u_point_index) && !projections_f.empty()) - //Any pair of projection is at distance 0 - tmp = *projections_f.cbegin(); - else if (contains(c) && (G::distance(u_point_index, c) <= r)) - //Is the query point near to its projection ? - tmp = c; - else - //Is the query point near to a V point in the plane ? - tmp = planar_neighbors_f.pull_near(u_point_index); - remove(tmp); - return tmp; -} - -inline std::shared_ptr< std::list > Neighbors_finder::pull_all_near(int u_point_index) { - std::shared_ptr< std::list > all_pull(planar_neighbors_f.pull_all_near(u_point_index)); - int last_pull = pull_near(u_point_index); - while (last_pull != null_point_index()) { - all_pull->emplace_back(last_pull); - last_pull = pull_near(u_point_index); - } - return all_pull; -} - -inline Layered_neighbors_finder::Layered_neighbors_finder(double r) : - r(r), neighbors_finder() { } - -inline void Layered_neighbors_finder::add(int v_point_index, int vlayer) { - for (int l = neighbors_finder.size(); l <= vlayer; l++) - neighbors_finder.emplace_back(std::shared_ptr(new Neighbors_finder(r))); - neighbors_finder.at(vlayer)->add(v_point_index); -} - -inline int Layered_neighbors_finder::pull_near(int u_point_index, int vlayer) { - if (static_cast (neighbors_finder.size()) <= vlayer) - return null_point_index(); - return neighbors_finder.at(vlayer)->pull_near(u_point_index); -} - -inline int Layered_neighbors_finder::vlayers_number() const { - return static_cast(neighbors_finder.size()); -} - -} // namespace bipartite_graph_matching - -} // namespace Gudhi - -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_ diff --git a/src/Bipartite_graphs_matching/include/gudhi/Persistence_diagrams_graph.h b/src/Bipartite_graphs_matching/include/gudhi/Persistence_diagrams_graph.h deleted file mode 100644 index 139caa8c..00000000 --- a/src/Bipartite_graphs_matching/include/gudhi/Persistence_diagrams_graph.h +++ /dev/null @@ -1,157 +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): Francois Godi - * - * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_ -#define SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_ - -#include -#include -#include -#include -#include -#include -#include -#include - -namespace Gudhi { - -namespace bipartite_graph_matching { - - -/** \internal \brief Structure representing an euclidean bipartite graph containing - * the points from the two persistence diagrams (including the projections). - * - * \ingroup bottleneck_distance - */ -class Persistence_diagrams_graph { -public: - /** \internal \brief Initializer taking 2 Point (concept) ranges as parameters. */ - template - static void initialize(const Persistence_diagram1& diag1, const Persistence_diagram2& diag2, double e); - /** \internal \brief Is the given point from U the projection of a point in V ? */ - static bool on_the_u_diagonal(int u_point_index); - /** \internal \brief Is the given point from V the projection of a point in U ? */ - static bool on_the_v_diagonal(int v_point_index); - /** \internal \brief Given a point from V, returns the corresponding (projection or projector) point in U. */ - static int corresponding_point_in_u(int v_point_index); - /** \internal \brief Given a point from U, returns the corresponding (projection or projector) point in V. */ - static int corresponding_point_in_v(int u_point_index); - /** \internal \brief Given a point from U and a point from V, returns the distance between those points. */ - static double distance(int u_point_index, int v_point_index); - /** \internal \brief Returns size = |U| = |V|. */ - static int size(); - /** \internal \brief Returns the O(n^2) sorted distances between the points. */ - static std::shared_ptr< std::vector > sorted_distances(); - -private: - static std::vector u; - static std::vector v; - static Internal_point get_u_point(int u_point_index); - static Internal_point get_v_point(int v_point_index); - - friend class Naive_pnf; - friend class Cgal_pnf; -}; - -/** \internal \typedef \brief Shorter alias */ -typedef Persistence_diagrams_graph G; - -// static initialization -std::vector G::u = [] {return std::vector();}(); -std::vector G::v = [] {return std::vector();}(); - -template -inline void G::initialize(const Persistence_diagram1 &diag1, - const Persistence_diagram2 &diag2, double e){ - u.clear(); - v.clear(); - for (auto it = diag1.cbegin(); it != diag1.cend(); ++it) - if (it->second - it->first > e) - u.push_back(Internal_point(it->first, it->second, u.size())); - for (auto it = diag2.cbegin(); it != diag2.cend(); ++it) - if (it->second - it->first > e) - v.push_back(Internal_point(it->first, it->second, v.size())); - if (u.size() < v.size()) - swap(u, v); -} - -inline bool G::on_the_u_diagonal(int u_point_index) { - return u_point_index >= static_cast (u.size()); -} - -inline bool G::on_the_v_diagonal(int v_point_index) { - return v_point_index >= static_cast (v.size()); -} - -inline int G::corresponding_point_in_u(int v_point_index) { - return on_the_v_diagonal(v_point_index) ? - v_point_index - static_cast (v.size()) : v_point_index + static_cast (u.size()); -} - -inline int G::corresponding_point_in_v(int u_point_index) { - return on_the_u_diagonal(u_point_index) ? - u_point_index - static_cast (u.size()) : u_point_index + static_cast (v.size()); -} - -inline double G::distance(int u_point_index, int v_point_index) { - if (on_the_u_diagonal(u_point_index) && on_the_v_diagonal(v_point_index)) - return 0; - Internal_point p_u = get_u_point(u_point_index); - Internal_point p_v = get_v_point(v_point_index); - return std::max(std::fabs(p_u.x() - p_v.x()), std::fabs(p_u.y() - p_v.y())); -} - -inline int G::size() { - return static_cast (u.size() + v.size()); -} - -inline std::shared_ptr< std::vector > G::sorted_distances() { - // could be optimized - std::set sorted_distances; - for (int u_point_index = 0; u_point_index < size(); ++u_point_index) - for (int v_point_index = 0; v_point_index < size(); ++v_point_index) - sorted_distances.emplace(distance(u_point_index, v_point_index)); - std::shared_ptr< std::vector > sd_up(new std::vector(sorted_distances.cbegin(), sorted_distances.cend())); - return sd_up; -} - -inline Internal_point G::get_u_point(int u_point_index) { - if (!on_the_u_diagonal(u_point_index)) - return u.at(u_point_index); - Internal_point projector = v.at(corresponding_point_in_v(u_point_index)); - double m = (projector.x() + projector.y()) / 2; - return Internal_point(m,m,u_point_index); -} - -inline Internal_point G::get_v_point(int v_point_index) { - if (!on_the_v_diagonal(v_point_index)) - return v.at(v_point_index); - Internal_point projector = u.at(corresponding_point_in_u(v_point_index)); - double m = (projector.x() + projector.y()) / 2; - return Internal_point(m,m,v_point_index); -} - -} // namespace bipartite_graph_matching - -} // namespace Gudhi - -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_ diff --git a/src/Bipartite_graphs_matching/include/gudhi/Planar_neighbors_finder.h b/src/Bipartite_graphs_matching/include/gudhi/Planar_neighbors_finder.h deleted file mode 100644 index 3d6d0084..00000000 --- a/src/Bipartite_graphs_matching/include/gudhi/Planar_neighbors_finder.h +++ /dev/null @@ -1,218 +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): Francois Godi - * - * Copyright (C) 2015 INRIA Sophia-Antipolis (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 SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_ -#define SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_ - -#include -#include -#include -#include -#include -#include -#include - - -namespace Gudhi { - -namespace bipartite_graph_matching { - -/** \internal \brief Structure used to find any point in V near (according to the planar distance) to a query point from U. - * - * V points have to be added manually using their index and before the first remove/pull. A neighbor pulled is automatically removed. but we can also - * remove points manually using their index. - * - * \ingroup bottleneck_distance - */ -class Naive_pnf { -public: - /** \internal \brief Constructor taking the near distance definition as parameter. */ - Naive_pnf(double r_); - /** \internal \brief A point added will be possibly pulled. */ - void add(int v_point_index); - /** \internal \brief A point manually removed will no longer be possibly pulled. */ - void remove(int v_point_index); - /** \internal \brief Can the point given as parameter be returned ? */ - bool contains(int v_point_index) const; - /** \internal \brief Provide and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ - int pull_near(int u_point_index); - /** \internal \brief Provide and remove all the V points near to the U point given as parameter. */ - virtual std::shared_ptr< std::list > pull_all_near(int u_point_index); - -private: - double r; - std::pair get_v_key(int v_point_index) const; - std::multimap,int> grid; -}; - -class Cgal_pnf { - - typedef CGAL::Dimension_tag<2> D; - typedef CGAL::Search_traits Traits; - typedef CGAL::Weighted_Minkowski_distance Distance; - typedef CGAL::Orthogonal_incremental_neighbor_search K_neighbor_search; - typedef K_neighbor_search::Tree Kd_tree; - - -public: - /** \internal \brief Constructor taking the near distance definition as parameter. */ - Cgal_pnf(double r_); - /** \internal \brief A point added will be possibly pulled. */ - void add(int v_point_index); - /** \internal \brief A point manually removed will no longer be possibly pulled. */ - void remove(int v_point_index); - /** \internal \brief Can the point given as parameter be returned ? */ - bool contains(int v_point_index) const; - /** \internal \brief Provide a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ - int pull_near(int u_point_index); - /** \internal \brief Provide and remove all the V points near to the U point given as parameter. */ - virtual std::shared_ptr< std::list > pull_all_near(int u_point_index); - -private: - double r; - std::set contents; - Kd_tree kd_t; -}; - -/** \internal \typedef \brief Planar_neighbors_finder is the used implementation. */ -typedef Naive_pnf Planar_neighbors_finder; - -inline Naive_pnf::Naive_pnf(double r_) : - r(r_), grid() { } - - -inline std::pair Naive_pnf::get_v_key(int v_point_index) const{ - Internal_point v_point = G::get_v_point(v_point_index); - return std::make_pair(static_cast(v_point.x()/r), static_cast(v_point.y()/r)); -} - -inline void Naive_pnf::add(int v_point_index) { - grid.emplace(get_v_key(v_point_index),v_point_index); -} - -inline void Naive_pnf::remove(int v_point_index) { - if(v_point_index != null_point_index()) - for(auto it = grid.find(get_v_key(v_point_index)); it!=grid.end(); it++) - if(it->second==v_point_index){ - grid.erase(it); - return; - } -} - -inline bool Naive_pnf::contains(int v_point_index) const { - if(v_point_index == null_point_index()) - return false; - for(auto it = grid.find(get_v_key(v_point_index)); it!=grid.end(); it++) - if(it->second==v_point_index) - return true; - return false; -} - -inline int Naive_pnf::pull_near(int u_point_index) { - Internal_point u_point = G::get_u_point(u_point_index); - int i0 = static_cast(u_point.x()/r); - int j0 = static_cast(u_point.y()/r); - for(int i = 1; i<= 3; i++) - for(int j = 1; j<= 3; j++) - for(auto it = grid.find(std::make_pair(i0 +(i%3)-1, j0+(j%3)-1)); it!=grid.end(); it++) - if (G::distance(u_point_index, it->second) <= r) { - int tmp = it->second; - grid.erase(it); - return tmp; - } - return null_point_index(); -} - -inline std::shared_ptr< std::list > Naive_pnf::pull_all_near(int u_point_index) { - std::shared_ptr< std::list > all_pull(new std::list); - Internal_point u_point = G::get_u_point(u_point_index); - int i0 = static_cast(u_point.x()/r); - int j0 = static_cast(u_point.y()/r); - for(int i = 1; i<= 3; i++) - for(int j = 1; j<= 3; j++) - for(auto it = grid.find(std::make_pair(i0 +(i%3)-1, j0+(j%3)-1)); it!=grid.end(); it++) - if (G::distance(u_point_index, it->second) <= r) { - int tmp = it->second; - grid.erase(it); - all_pull->emplace_back(tmp); - } - return all_pull; -} - - -/** \internal \brief Constructor taking the near distance definition as parameter. */ -inline Cgal_pnf::Cgal_pnf(double r_) - : r(r_), contents(), kd_t() {} - - -/** \internal \brief A point added will be possibly pulled. */ -inline void Cgal_pnf::add(int v_point_index){ - if(v_point_index == null_point_index()) - return; - contents.insert(v_point_index); - kd_t.insert(G::get_v_point(v_point_index)); -} - -/** \internal \brief A point manually removed will no longer be possibly pulled. */ -inline void Cgal_pnf::remove(int v_point_index){ - if(contains(v_point_index)){ - contents.erase(v_point_index); - kd_t.remove(G::get_v_point(v_point_index)); - } -} - -/** \internal \brief Can the point given as parameter be returned ? */ -inline bool Cgal_pnf::contains(int v_point_index) const{ - if(v_point_index == null_point_index()) - return false; - return contents.count(v_point_index)>0; -} - -/** \internal \brief Provide and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */ -inline int Cgal_pnf::pull_near(int u_point_index){ - Internal_point u_point = G::get_u_point(u_point_index); - std::vector w = {1., 1.}; - K_neighbor_search search(kd_t, u_point, 0., true, Distance(0, 2, w)); - auto it = search.begin(); - if(it==search.end() || G::distance(u_point_index, it->first.point_index) > r) - return null_point_index(); - int tmp = it->first.point_index; - remove(tmp); - return tmp; -} - -inline std::shared_ptr< std::list > Cgal_pnf::pull_all_near(int u_point_index) { - std::shared_ptr< std::list > all_pull(new std::list); - int last_pull = pull_near(u_point_index); - while (last_pull != null_point_index()) { - all_pull->emplace_back(last_pull); - last_pull = pull_near(u_point_index); - } - return all_pull; -} - - -} // namespace bipartite_graph_matching - -} // namespace Gudhi - -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_ diff --git a/src/Bipartite_graphs_matching/test/CMakeLists.txt b/src/Bipartite_graphs_matching/test/CMakeLists.txt deleted file mode 100644 index ab0461cc..00000000 --- a/src/Bipartite_graphs_matching/test/CMakeLists.txt +++ /dev/null @@ -1,63 +0,0 @@ -cmake_minimum_required(VERSION 2.6) -project(GUDHIBottleneckUT) - - - - -if(CGAL_FOUND) - if (NOT CGAL_VERSION VERSION_LESS 4.6.0) - message(STATUS "CGAL version: ${CGAL_VERSION}.") - - include( ${CGAL_USE_FILE} ) - - if(NOT MSVC) - include(CheckCXXCompilerFlag) - CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11) - if(COMPILER_SUPPORTS_CXX11) - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11") - endif() - endif() - # - End of workaround - - find_package(Eigen3 3.1.0) - if (EIGEN3_FOUND) - message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") - include( ${EIGEN3_USE_FILE} ) - include_directories (BEFORE "../../include") - - if (GCOVR_PATH) - # for gcovr to make coverage reports - Corbera Jenkins plugin - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage") - set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage") - set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage") -endif() -if (GPROF_PATH) - # for gprof to make coverage reports - Jenkins - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") - set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg") - set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg") -endif() - message("CMAKE_CXX_FLAGS = ${CMAKE_CXX_FLAGS}") - message("CMAKE_CXX_FLAGS_DEBUG = ${CMAKE_CXX_FLAGS_DEBUG}") - message("CMAKE_CXX_FLAGS_RELEASE = ${CMAKE_CXX_FLAGS_RELEASE}") - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O2 -std=c++11 -Wall -Wpedantic -Wsign-compare") - set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -ggdb -O0") - set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE}") - -add_executable ( BottleneckUT bottleneck_unit_test.cpp ) -target_link_libraries(BottleneckUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) - -# Unitary tests -add_test(NAME BottleneckUT - COMMAND ${CMAKE_CURRENT_BINARY_DIR}/BottleneckUT - # XML format for Jenkins xUnit plugin - --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/BottleneckUT.xml --log_level=test_suite --report_level=no) - - - else() - message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.") - endif() - else() - message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile bipartite graphs matching feature. Version 4.6.0 is required.") - endif () -endif() diff --git a/src/Bipartite_graphs_matching/test/README b/src/Bipartite_graphs_matching/test/README deleted file mode 100644 index 0e7b8673..00000000 --- a/src/Bipartite_graphs_matching/test/README +++ /dev/null @@ -1,12 +0,0 @@ -To compile: -*********** - -cmake . -make - -To launch with details: -*********************** - -./BottleneckUnitTest --report_level=detailed --log_level=all - - ==> echo $? returns 0 in case of success (non-zero otherwise) diff --git a/src/Bipartite_graphs_matching/test/bottleneck_unit_test.cpp b/src/Bipartite_graphs_matching/test/bottleneck_unit_test.cpp deleted file mode 100644 index ffe05614..00000000 --- a/src/Bipartite_graphs_matching/test/bottleneck_unit_test.cpp +++ /dev/null @@ -1,165 +0,0 @@ -#define BOOST_TEST_MODULE bottleneck test - -#include -#include -#include - -using namespace Gudhi::bipartite_graph_matching; - -int n1 = 81; // a natural number >0 -int n2 = 180; // a natural number >0 -double upper_bound = 406.43; // any real >0 - -BOOST_AUTO_TEST_CASE(persistence_diagrams_graph){ - // Random construction - std::uniform_real_distribution unif(0.,upper_bound); - std::default_random_engine re; - std::vector< std::pair > v1, v2; - for (int i = 0; i < n1; i++) { - double a = unif(re); - double b = unif(re); - v1.emplace_back(std::min(a,b), std::max(a,b)); - } - for (int i = 0; i < n2; i++) { - double a = unif(re); - double b = unif(re); - v2.emplace_back(std::min(a,b), std::max(a,b)); - } - G::initialize(v1, v2, 0.); - std::shared_ptr< std::vector > d(G::sorted_distances()); - // - BOOST_CHECK(!G::on_the_u_diagonal(n1-1)); - BOOST_CHECK(!G::on_the_u_diagonal(n1)); - BOOST_CHECK(!G::on_the_u_diagonal(n2-1)); - BOOST_CHECK(G::on_the_u_diagonal(n2)); - BOOST_CHECK(!G::on_the_v_diagonal(n1-1)); - BOOST_CHECK(G::on_the_v_diagonal(n1)); - BOOST_CHECK(G::on_the_v_diagonal(n2-1)); - BOOST_CHECK(G::on_the_v_diagonal(n2)); - // - BOOST_CHECK(G::corresponding_point_in_u(0)==n2); - BOOST_CHECK(G::corresponding_point_in_u(n1)==0); - BOOST_CHECK(G::corresponding_point_in_v(0)==n1); - BOOST_CHECK(G::corresponding_point_in_v(n2)==0); - // - BOOST_CHECK(G::size()==(n1+n2)); - // - BOOST_CHECK((int) d->size() <= (n1+n2)*(n1+n2) - n1*n2 + 1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,0))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n1-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n2-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,n2))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(0,(n1+n2)-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,0))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n1-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n2-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,n2))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance(n1,(n1+n2)-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,0))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n1-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n2-1))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,n2))==1); - BOOST_CHECK(std::count(d->begin(), d->end(), G::distance((n1+n2)-1,(n1+n2)-1))==1); -} - -BOOST_AUTO_TEST_CASE(planar_neighbors_finder) { - Planar_neighbors_finder pnf(1.); - for(int v_point_index=0; v_point_index l = *pnf.pull_all_near(n2/2); - bool v = true; - for(auto it = l.cbegin(); it != l.cend(); ++it) - v = v && (G::distance(n2/2,*it)>1.); - BOOST_CHECK(v); - int v_point_index_2 = pnf.pull_near(n2/2); - BOOST_CHECK(v_point_index_2 == -1); -} - -BOOST_AUTO_TEST_CASE(neighbors_finder) { - Neighbors_finder nf(1.); - for(int v_point_index=1; v_point_index<((n2+n1)*9/10); v_point_index+=2) - nf.add(v_point_index); - // - int v_point_index_1 = nf.pull_near(n2/2); - BOOST_CHECK((v_point_index_1 == -1) || (G::distance(n2/2,v_point_index_1)<=1.)); - std::list l = *nf.pull_all_near(n2/2); - bool v = true; - for(auto it = l.cbegin(); it != l.cend(); ++it) - v = v && (G::distance(n2/2,*it)>1.); - BOOST_CHECK(v); - int v_point_index_2 = nf.pull_near(n2/2); - BOOST_CHECK(v_point_index_2 == -1); -} - -BOOST_AUTO_TEST_CASE(layered_neighbors_finder) { - Layered_neighbors_finder lnf(1.); - for(int v_point_index=1; v_point_index<((n2+n1)*9/10); v_point_index+=2) - lnf.add(v_point_index, v_point_index % 7); - // - int v_point_index_1 = lnf.pull_near(n2/2,6); - BOOST_CHECK((v_point_index_1 == -1) || (G::distance(n2/2,v_point_index_1)<=1.)); - int v_point_index_2 = lnf.pull_near(n2/2,6); - BOOST_CHECK(v_point_index_2 == -1); - v_point_index_1 = lnf.pull_near(n2/2,0); - BOOST_CHECK((v_point_index_1 == -1) || (G::distance(n2/2,v_point_index_1)<=1.)); - v_point_index_2 = lnf.pull_near(n2/2,0); - BOOST_CHECK(v_point_index_2 == -1); -} - -BOOST_AUTO_TEST_CASE(graph_matching) { - Graph_matching m1; - m1.set_r(0.); - int e = 0; - while (m1.multi_augment()) - ++e; - BOOST_CHECK(e <= 2*sqrt(2*(n1+n2))); - Graph_matching m2 = m1; - BOOST_CHECK(!m2.multi_augment()); - m2.set_r(upper_bound); - e = 0; - while (m2.multi_augment()) - ++e; - BOOST_CHECK(e <= 2*sqrt(2*(n1+n2))); - BOOST_CHECK(m2.perfect()); - BOOST_CHECK(!m1.perfect()); -} - -BOOST_AUTO_TEST_CASE(global){ - std::uniform_real_distribution unif1(0.,upper_bound); - std::uniform_real_distribution unif2(upper_bound/1000.,upper_bound/100.); - std::default_random_engine re; - std::vector< std::pair > v1, v2; - for (int i = 0; i < n1; i++) { - double a = unif1(re); - double b = unif1(re); - double x = unif2(re); - double y = unif2(re); - v1.emplace_back(std::min(a,b), std::max(a,b)); - v2.emplace_back(std::min(a,b)+std::min(x,y), std::max(a,b)+std::max(x,y)); - if(i%5==0) - v1.emplace_back(std::min(a,b),std::min(a,b)+x); - if(i%3==0) - v2.emplace_back(std::max(a,b),std::max(a,b)+y); - } - BOOST_CHECK(bottleneck_distance(v1, v2) <= upper_bound/100.); -} -- cgit v1.2.3 From bd9b3b687b715a968216032f20f08fbaea7f3baa Mon Sep 17 00:00:00 2001 From: fgodi Date: Thu, 2 Jun 2016 17:16:04 +0000 Subject: lists git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@1242 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 134d7d5c1f940ac342eb1721de6ee9cb41f1102b --- CMakeLists.txt | 6 +++--- src/Bottleneck_distance/example/CMakeLists.txt | 2 +- src/Bottleneck_distance/test/CMakeLists.txt | 3 ++- 3 files changed, 6 insertions(+), 5 deletions(-) (limited to 'src') diff --git a/CMakeLists.txt b/CMakeLists.txt index 066a49cf..dccd59d8 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -57,7 +57,7 @@ else() include_directories(src/common/include/) include_directories(src/Alpha_shapes/include/) - include_directories(src/Bipartite_graphs_matching/include/) + include_directories(src/Bottleneck_distance/include/) include_directories(src/Bottleneck/include/) include_directories(src/Contraction/include/) include_directories(src/Hasse_complex/include/) @@ -75,8 +75,8 @@ else() add_subdirectory(src/Hasse_complex/example) add_subdirectory(src/Alpha_shapes/example) add_subdirectory(src/Alpha_shapes/test) - add_subdirectory(src/Bipartite_graphs_matching/example) - add_subdirectory(src/Bipartite_graphs_matching/test) + add_subdirectory(src/Bottleneck_distance/example) + add_subdirectory(src/Bottleneck_distance/test) # data points generator add_subdirectory(data/points/generator) diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt index 4e8766cc..cc1b9091 100644 --- a/src/Bottleneck_distance/example/CMakeLists.txt +++ b/src/Bottleneck_distance/example/CMakeLists.txt @@ -24,7 +24,7 @@ if(CGAL_FOUND) include( ${EIGEN3_USE_FILE} ) include_directories (BEFORE "../../include") - add_executable (basic_example basic.cpp) + add_executable (bottleneck_example bottleneck_example.cpp) #add_test(dtoffrw_tore3D ${CMAKE_CURRENT_BINARY_DIR}/dtoffrw ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off 3) else() diff --git a/src/Bottleneck_distance/test/CMakeLists.txt b/src/Bottleneck_distance/test/CMakeLists.txt index ab0461cc..1338ed6b 100644 --- a/src/Bottleneck_distance/test/CMakeLists.txt +++ b/src/Bottleneck_distance/test/CMakeLists.txt @@ -44,7 +44,8 @@ endif() set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -ggdb -O0") set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE}") -add_executable ( BottleneckUT bottleneck_unit_test.cpp ) +add_executable ( bottleneckUT bottleneck_unit_test.cpp ) +add_executable ( bottleneck_chrono bottleneck_chrono.cpp ) target_link_libraries(BottleneckUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) # Unitary tests -- cgit v1.2.3 From ab8c111e6a9abc4ba718083266c3dbb238ab94e3 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 2 Jun 2016 18:23:10 +0000 Subject: CMake fix after executable renaming git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@1244 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 5238ff5ecdc70b6e97539625b687ac0626c49ef2 --- src/Bottleneck_distance/test/CMakeLists.txt | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/test/CMakeLists.txt b/src/Bottleneck_distance/test/CMakeLists.txt index 1338ed6b..54a2fe95 100644 --- a/src/Bottleneck_distance/test/CMakeLists.txt +++ b/src/Bottleneck_distance/test/CMakeLists.txt @@ -46,13 +46,13 @@ endif() add_executable ( bottleneckUT bottleneck_unit_test.cpp ) add_executable ( bottleneck_chrono bottleneck_chrono.cpp ) -target_link_libraries(BottleneckUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +target_link_libraries(bottleneckUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) # Unitary tests -add_test(NAME BottleneckUT - COMMAND ${CMAKE_CURRENT_BINARY_DIR}/BottleneckUT +add_test(NAME bottleneckUT + COMMAND ${CMAKE_CURRENT_BINARY_DIR}/bottleneckUT # XML format for Jenkins xUnit plugin - --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/BottleneckUT.xml --log_level=test_suite --report_level=no) + --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/bottleneckUT.xml --log_level=test_suite --report_level=no) else() -- cgit v1.2.3 From 714a97d8b9c64a0a5ccc837184def8122ec8b4cd Mon Sep 17 00:00:00 2001 From: fgodi Date: Fri, 3 Jun 2016 09:32:46 +0000 Subject: compile git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@1245 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a26ddc43a1f71052b594d5e0d65d28d952a0917e --- src/Bottleneck_distance/example/bottleneck_example.cpp | 3 +-- src/Bottleneck_distance/include/CGAL/Miscellaneous.h | 2 +- src/Bottleneck_distance/include/gudhi/Graph_matching.h | 3 +++ src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h | 4 ++-- src/Bottleneck_distance/test/bottleneck_chrono.cpp | 2 +- src/Bottleneck_distance/test/bottleneck_unit_test.cpp | 2 +- 6 files changed, 9 insertions(+), 7 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/example/bottleneck_example.cpp b/src/Bottleneck_distance/example/bottleneck_example.cpp index bbd83547..c6a06235 100644 --- a/src/Bottleneck_distance/example/bottleneck_example.cpp +++ b/src/Bottleneck_distance/example/bottleneck_example.cpp @@ -23,7 +23,6 @@ #include #include -using namespace Gudhi::Bottleneck_distance; int main() { std::vector< std::pair > v1, v2; @@ -36,7 +35,7 @@ int main() { v2.push_back(std::pair(9.5,14.1)); - double b = bottleneck_distance(v1, v2); + double b = Gudhi::Bottleneck_distance::compute(v1, v2); std::cout << "Bottleneck distance = " << b << std::endl; diff --git a/src/Bottleneck_distance/include/CGAL/Miscellaneous.h b/src/Bottleneck_distance/include/CGAL/Miscellaneous.h index 4de787fb..21be0bc7 100644 --- a/src/Bottleneck_distance/include/CGAL/Miscellaneous.h +++ b/src/Bottleneck_distance/include/CGAL/Miscellaneous.h @@ -27,7 +27,7 @@ namespace CGAL { -typedef Gudhi::bipartite_graph_matching::Internal_point Internal_point; +typedef Gudhi::Bottleneck_distance::Internal_point Internal_point; template <> struct Kernel_traits { diff --git a/src/Bottleneck_distance/include/gudhi/Graph_matching.h b/src/Bottleneck_distance/include/gudhi/Graph_matching.h index d8860841..f0ce633f 100644 --- a/src/Bottleneck_distance/include/gudhi/Graph_matching.h +++ b/src/Bottleneck_distance/include/gudhi/Graph_matching.h @@ -40,6 +40,9 @@ namespace Bottleneck_distance { template double compute(const Persistence_diagram1& diag1, const Persistence_diagram2& diag2, double e = 0.); +template +double compute_exactly(const Persistence_diagram1& diag1, const Persistence_diagram2& diag2); + /** \internal \brief Structure representing a graph matching. The graph is a Persistence_diagrams_graph. * * \ingroup bottleneck_distance diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h index e8a46f1c..52e7c583 100644 --- a/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h +++ b/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h @@ -154,9 +154,9 @@ inline Internal_point G::get_v_point(int v_point_index) { inline double G::diameter() { double max = 0.; - for(it = u.cbegin(); it != u.cend(); it++) + for(auto it = u.cbegin(); it != u.cend(); it++) max = std::max(max,it->y()); - for(it = v.cbegin(); it != v.cend(); it++) + for(auto it = v.cbegin(); it != v.cend(); it++) max = std::max(max,it->y()); return max; } diff --git a/src/Bottleneck_distance/test/bottleneck_chrono.cpp b/src/Bottleneck_distance/test/bottleneck_chrono.cpp index 8f187a91..cde8afb1 100644 --- a/src/Bottleneck_distance/test/bottleneck_chrono.cpp +++ b/src/Bottleneck_distance/test/bottleneck_chrono.cpp @@ -51,7 +51,7 @@ int main(){ v2.emplace_back(std::max(a,b),std::max(a,b)+y); } std::chrono::steady_clock::time_point start = std::chrono::steady_clock::now(); - double b = bottleneck_approx(v1,v2, 0.); + double b = compute(v1,v2, 0.01); std::chrono::steady_clock::time_point end = std::chrono::steady_clock::now(); typedef std::chrono::duration millisecs_t; millisecs_t duration(std::chrono::duration_cast(end-start)); diff --git a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp index 33ac3f1b..d5b71156 100644 --- a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp +++ b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp @@ -184,5 +184,5 @@ BOOST_AUTO_TEST_CASE(global){ if(i%3==0) v2.emplace_back(std::max(a,b),std::max(a,b)+y); } - BOOST_CHECK(bottleneck_distance(v1, v2) <= upper_bound/100.); + BOOST_CHECK(compute(v1, v2) <= upper_bound/100.); } -- cgit v1.2.3 From d85314eb2cd5b8487ee5cc5c9069e1c8ff311931 Mon Sep 17 00:00:00 2001 From: fgodi Date: Fri, 3 Jun 2016 10:22:53 +0000 Subject: CGAL+ VERSION git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@1246 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: b9bde0a97e56042b84d1850dea34e559dc196b91 --- .../example/bottleneck_example.cpp | 6 +-- .../include/gudhi/Graph_matching.h | 48 ++++++++++++++++++---- .../include/gudhi/Persistence_diagrams_graph.h | 1 + .../include/gudhi/Planar_neighbors_finder.h | 2 +- src/Bottleneck_distance/test/bottleneck_chrono.cpp | 4 +- 5 files changed, 47 insertions(+), 14 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/example/bottleneck_example.cpp b/src/Bottleneck_distance/example/bottleneck_example.cpp index c6a06235..b3d26f3c 100644 --- a/src/Bottleneck_distance/example/bottleneck_example.cpp +++ b/src/Bottleneck_distance/example/bottleneck_example.cpp @@ -34,9 +34,9 @@ int main() { v2.push_back(std::pair(2.8,4.45)); v2.push_back(std::pair(9.5,14.1)); + double b = Gudhi::Bottleneck_distance::compute(v1, v2, 0.0001); + std::cout << "Approx. bottleneck distance = " << b << std::endl; - double b = Gudhi::Bottleneck_distance::compute(v1, v2); - + b = Gudhi::Bottleneck_distance::compute(v1, v2); std::cout << "Bottleneck distance = " << b << std::endl; - } diff --git a/src/Bottleneck_distance/include/gudhi/Graph_matching.h b/src/Bottleneck_distance/include/gudhi/Graph_matching.h index f0ce633f..69470067 100644 --- a/src/Bottleneck_distance/include/gudhi/Graph_matching.h +++ b/src/Bottleneck_distance/include/gudhi/Graph_matching.h @@ -209,6 +209,43 @@ double compute_exactly(const Persistence_diagram1 &diag1, const Persistence_diag return sd->at(idmin); } +template +double compute(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e) { + if(e< std::numeric_limits::min()) + return compute_exactly(diag1, diag2); + G::initialize(diag1, diag2, e); + int in = G::diameter()/e; + int idmin = 0; + int idmax = in; + // alpha can be modified, this will change the complexity + double alpha = pow(in, 0.25); + Graph_matching m; + Graph_matching biggest_unperfect; + while (idmin != idmax) { + int step = static_cast((idmax - idmin) / alpha); + m.set_r(e*(idmin + step)); + while (m.multi_augment()); + //The above while compute a maximum matching (according to the r setted before) + if (m.perfect()) { + idmax = idmin + step; + m = biggest_unperfect; + } else { + biggest_unperfect = m; + idmin = idmin + step + 1; + } + } + return e*(idmin); +} + + + +} // namespace Bottleneck_distance + +} // namespace Gudhi + +#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ + +/* Dichotomic version template double compute(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e) { if(e< std::numeric_limits::min()) @@ -221,16 +258,11 @@ double compute(const Persistence_diagram1 &diag1, const Persistence_diagram2 &di m.set_r((d+f)/2.); while (m.multi_augment()); //The above while compute a maximum matching (according to the r setted before) - if (m.perfect()) + if (m.perfect()) f = (d+f)/2.; - else + else d= (d+f)/2.; } return d; -} +} */ -} // namespace Bottleneck_distance - -} // namespace Gudhi - -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h index 52e7c583..e31b2dae 100644 --- a/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h +++ b/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h @@ -129,6 +129,7 @@ inline int G::size() { inline std::shared_ptr< std::vector > G::sorted_distances() { // could be optimized std::set sorted_distances; + sorted_distances.emplace(0.); for (int u_point_index = 0; u_point_index < size(); ++u_point_index) for (int v_point_index = 0; v_point_index < size(); ++v_point_index) sorted_distances.emplace(distance(u_point_index, v_point_index)); diff --git a/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h index c0b6383f..3f3723c3 100644 --- a/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h +++ b/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h @@ -94,7 +94,7 @@ private: }; /** \internal \typedef \brief Planar_neighbors_finder is the used implementation. */ -typedef Naive_pnf Planar_neighbors_finder; +typedef Cgal_pnf Planar_neighbors_finder; inline Naive_pnf::Naive_pnf(double r_) : r(r_), grid() { } diff --git a/src/Bottleneck_distance/test/bottleneck_chrono.cpp b/src/Bottleneck_distance/test/bottleneck_chrono.cpp index cde8afb1..8b49b6be 100644 --- a/src/Bottleneck_distance/test/bottleneck_chrono.cpp +++ b/src/Bottleneck_distance/test/bottleneck_chrono.cpp @@ -33,7 +33,7 @@ int main(){ std::ofstream objetfichier; objetfichier.open("results.csv", std::ios::out); - for(int n=0; n<=2500; n+=250){ + for(int n=0; n<=4000; n+=400){ std::uniform_real_distribution unif1(0.,upper_bound); std::uniform_real_distribution unif2(upper_bound/1000.,upper_bound/100.); std::default_random_engine re; @@ -51,7 +51,7 @@ int main(){ v2.emplace_back(std::max(a,b),std::max(a,b)+y); } std::chrono::steady_clock::time_point start = std::chrono::steady_clock::now(); - double b = compute(v1,v2, 0.01); + double b = compute(v1,v2, 0.0001); std::chrono::steady_clock::time_point end = std::chrono::steady_clock::now(); typedef std::chrono::duration millisecs_t; millisecs_t duration(std::chrono::duration_cast(end-start)); -- cgit v1.2.3 From 284a45fc6ffcf049e667065acda71c17165b4f5c Mon Sep 17 00:00:00 2001 From: fgodi Date: Fri, 3 Jun 2016 12:28:19 +0000 Subject: concept git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@1247 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 7bfce006ccae0784f3e0f3747f670eddaa9aba48 --- src/Bottleneck_distance/concept/Diagram_point.h | 6 ------ src/Bottleneck_distance/concept/Persistence_diagram.h | 15 +++++++++++++-- 2 files changed, 13 insertions(+), 8 deletions(-) delete mode 100644 src/Bottleneck_distance/concept/Diagram_point.h (limited to 'src') diff --git a/src/Bottleneck_distance/concept/Diagram_point.h b/src/Bottleneck_distance/concept/Diagram_point.h deleted file mode 100644 index ce9c6d5b..00000000 --- a/src/Bottleneck_distance/concept/Diagram_point.h +++ /dev/null @@ -1,6 +0,0 @@ - - -struct Diagram_point{ - double first; - double second; -}; diff --git a/src/Bottleneck_distance/concept/Persistence_diagram.h b/src/Bottleneck_distance/concept/Persistence_diagram.h index 4951af32..27a258d8 100644 --- a/src/Bottleneck_distance/concept/Persistence_diagram.h +++ b/src/Bottleneck_distance/concept/Persistence_diagram.h @@ -1,7 +1,18 @@ +namespace Gudhi { +namespace Bottleneck_distance { +namespace Concept { +struct Diagram_point{ + double first; + double second; +}; struct Persistence_Diagram { - const_iterator cbegin() const; - const_iterator cend() const; + const_iterator cbegin() const; + const_iterator cend() const; }; + +} //namespace Concept +} //namespace Bottleneck_distance +} //namespace Gudhi -- cgit v1.2.3 From e1d3c44120619ace7d64b1bb5151e873867c9639 Mon Sep 17 00:00:00 2001 From: fgodi Date: Mon, 6 Jun 2016 08:27:19 +0000 Subject: kd_tree modified added git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@1249 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: c2c617e0f808bb2c51042174c5d2b4bbdd3998c9 --- src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h index 3f3723c3..37c6a122 100644 --- a/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h +++ b/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h @@ -25,9 +25,7 @@ #include #include -#include -#include -#include +#include "../CGAL/Kd_tree.h" #include #include -- cgit v1.2.3 From 6c611b11c08bc314d8075ae6a038d4af549a7f2e Mon Sep 17 00:00:00 2001 From: fgodi Date: Mon, 6 Jun 2016 08:27:57 +0000 Subject: kd_tree modified added git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@1250 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 07254aea5d1921f8bb43f73ac1fe9d76b63c5c3e --- src/Bottleneck_distance/include/CGAL/Kd_tree.h | 517 +++++++++++++++++++++++++ 1 file changed, 517 insertions(+) create mode 100644 src/Bottleneck_distance/include/CGAL/Kd_tree.h (limited to 'src') diff --git a/src/Bottleneck_distance/include/CGAL/Kd_tree.h b/src/Bottleneck_distance/include/CGAL/Kd_tree.h new file mode 100644 index 00000000..4f874a8b --- /dev/null +++ b/src/Bottleneck_distance/include/CGAL/Kd_tree.h @@ -0,0 +1,517 @@ +// Copyright (c) 2002,2011,2014 Utrecht University (The Netherlands), Max-Planck-Institute Saarbruecken (Germany). +// All rights reserved. +// +// This file is part of CGAL (www.cgal.org). +// 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. +// +// Licensees holding a valid commercial license may use this file in +// accordance with the commercial license agreement provided with the software. +// +// This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE +// WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. +// +// $URL$ +// $Id$ +// +// Author(s) : Hans Tangelder (), +// : Waqar Khan + +#ifndef CGAL_KD_TREE_H +#define CGAL_KD_TREE_H + +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include + + +#include +#include +#include + +#ifdef CGAL_HAS_THREADS +#include +#endif + +namespace CGAL { + +//template , class UseExtendedNode = Tag_true > +template , class UseExtendedNode = Tag_true > +class Kd_tree { + +public: + typedef SearchTraits Traits; + typedef Splitter_ Splitter; + typedef typename SearchTraits::Point_d Point_d; + typedef typename Splitter::Container Point_container; + + typedef typename SearchTraits::FT FT; + typedef Kd_tree_node Node; + typedef Kd_tree_leaf_node Leaf_node; + typedef Kd_tree_internal_node Internal_node; + typedef Kd_tree Tree; + typedef Kd_tree Self; + + typedef Node* Node_handle; + typedef const Node* Node_const_handle; + typedef Leaf_node* Leaf_node_handle; + typedef const Leaf_node* Leaf_node_const_handle; + typedef Internal_node* Internal_node_handle; + typedef const Internal_node* Internal_node_const_handle; + typedef typename std::vector::const_iterator Point_d_iterator; + typedef typename std::vector::const_iterator Point_d_const_iterator; + typedef typename Splitter::Separator Separator; + typedef typename std::vector::const_iterator iterator; + typedef typename std::vector::const_iterator const_iterator; + + typedef typename std::vector::size_type size_type; + + typedef typename internal::Get_dimension_tag::Dimension D; + +private: + SearchTraits traits_; + Splitter split; + + + // wokaround for https://svn.boost.org/trac/boost/ticket/9332 +#if (_MSC_VER == 1800) && (BOOST_VERSION == 105500) + std::deque internal_nodes; + std::deque leaf_nodes; +#else + boost::container::deque internal_nodes; + boost::container::deque leaf_nodes; +#endif + + Node_handle tree_root; + + Kd_tree_rectangle* bbox; + std::vector pts; + + // Instead of storing the points in arrays in the Kd_tree_node + // we put all the data in a vector in the Kd_tree. + // and we only store an iterator range in the Kd_tree_node. + // + std::vector data; + + +#ifdef CGAL_HAS_THREADS + mutable CGAL_MUTEX building_mutex;//mutex used to protect const calls inducing build() +#endif + bool built_; + bool removed_; + + // protected copy constructor + Kd_tree(const Tree& tree) + : traits_(tree.traits_),built_(tree.built_) + {}; + + + // Instead of the recursive construction of the tree in the class Kd_tree_node + // we do this in the tree class. The advantage is that we then can optimize + // the allocation of the nodes. + + // The leaf node + Node_handle + create_leaf_node(Point_container& c) + { + Leaf_node node(true , static_cast(c.size())); + std::ptrdiff_t tmp = c.begin() - data.begin(); + node.data = pts.begin() + tmp; + + leaf_nodes.push_back(node); + Leaf_node_handle nh = &leaf_nodes.back(); + + + return nh; + } + + + // The internal node + + Node_handle + create_internal_node(Point_container& c, const Tag_true&) + { + return create_internal_node_use_extension(c); + } + + Node_handle + create_internal_node(Point_container& c, const Tag_false&) + { + return create_internal_node(c); + } + + + + // TODO: Similiar to the leaf_init function above, a part of the code should be + // moved to a the class Kd_tree_node. + // It is not proper yet, but the goal was to see if there is + // a potential performance gain through the Compact_container + Node_handle + create_internal_node_use_extension(Point_container& c) + { + Internal_node node(false); + internal_nodes.push_back(node); + Internal_node_handle nh = &internal_nodes.back(); + + Separator sep; + Point_container c_low(c.dimension(),traits_); + split(sep, c, c_low); + nh->set_separator(sep); + + int cd = nh->cutting_dimension(); + if(!c_low.empty()) + nh->low_val = c_low.tight_bounding_box().max_coord(cd); + else + nh->low_val = c_low.bounding_box().min_coord(cd); + if(!c.empty()) + nh->high_val = c.tight_bounding_box().min_coord(cd); + else + nh->high_val = c.bounding_box().max_coord(cd); + + CGAL_assertion(nh->cutting_value() >= nh->low_val); + CGAL_assertion(nh->cutting_value() <= nh->high_val); + + if (c_low.size() > split.bucket_size()){ + nh->lower_ch = create_internal_node_use_extension(c_low); + }else{ + nh->lower_ch = create_leaf_node(c_low); + } + if (c.size() > split.bucket_size()){ + nh->upper_ch = create_internal_node_use_extension(c); + }else{ + nh->upper_ch = create_leaf_node(c); + } + + + + + return nh; + } + + + // Note also that I duplicated the code to get rid if the if's for + // the boolean use_extension which was constant over the construction + Node_handle + create_internal_node(Point_container& c) + { + Internal_node node(false); + internal_nodes.push_back(node); + Internal_node_handle nh = &internal_nodes.back(); + Separator sep; + + Point_container c_low(c.dimension(),traits_); + split(sep, c, c_low); + nh->set_separator(sep); + + if (c_low.size() > split.bucket_size()){ + nh->lower_ch = create_internal_node(c_low); + }else{ + nh->lower_ch = create_leaf_node(c_low); + } + if (c.size() > split.bucket_size()){ + nh->upper_ch = create_internal_node(c); + }else{ + nh->upper_ch = create_leaf_node(c); + } + + + + return nh; + } + + + +public: + + Kd_tree(Splitter s = Splitter(),const SearchTraits traits=SearchTraits()) + : traits_(traits),split(s), built_(false), removed_(false) + {} + + template + Kd_tree(InputIterator first, InputIterator beyond, + Splitter s = Splitter(),const SearchTraits traits=SearchTraits()) + : traits_(traits),split(s), built_(false), removed_(false) + { + pts.insert(pts.end(), first, beyond); + } + + bool empty() const { + return pts.empty(); + } + + void + build() + { + const Point_d& p = *pts.begin(); + typename SearchTraits::Construct_cartesian_const_iterator_d ccci=traits_.construct_cartesian_const_iterator_d_object(); + int dim = static_cast(std::distance(ccci(p), ccci(p,0))); + + data.reserve(pts.size()); + for(unsigned int i = 0; i < pts.size(); i++){ + data.push_back(&pts[i]); + } + Point_container c(dim, data.begin(), data.end(),traits_); + bbox = new Kd_tree_rectangle(c.bounding_box()); + if (c.size() <= split.bucket_size()){ + tree_root = create_leaf_node(c); + }else { + tree_root = create_internal_node(c, UseExtendedNode()); + } + + //Reorder vector for spatial locality + std::vector ptstmp; + ptstmp.resize(pts.size()); + for (std::size_t i = 0; i < pts.size(); ++i){ + ptstmp[i] = *data[i]; + } + for(std::size_t i = 0; i < leaf_nodes.size(); ++i){ + std::ptrdiff_t tmp = leaf_nodes[i].begin() - pts.begin(); + leaf_nodes[i].data = ptstmp.begin() + tmp; + } + pts.swap(ptstmp); + + data.clear(); + + built_ = true; + } + +private: + //any call to this function is for the moment not threadsafe + void const_build() const { +#ifdef CGAL_HAS_THREADS + //this ensure that build() will be called once + CGAL_SCOPED_LOCK(building_mutex); + if(!is_built()) +#endif + const_cast(this)->build(); //THIS IS NOT THREADSAFE + } +public: + + bool is_built() const + { + return built_; + } + + void invalidate_built() + { + if(is_built()){ + internal_nodes.clear(); + leaf_nodes.clear(); + data.clear(); + delete bbox; + built_ = false; + } + } + + void clear() + { + invalidate_built(); + pts.clear(); + removed_ = false; + } + + void + insert(const Point_d& p) + { + if (removed_) throw std::logic_error("Once you start removing points, you cannot insert anymore, you need to start again from scratch."); + invalidate_built(); + pts.push_back(p); + } + + template + void + insert(InputIterator first, InputIterator beyond) + { + if (removed_ && first != beyond) throw std::logic_error("Once you start removing points, you cannot insert anymore, you need to start again from scratch."); + invalidate_built(); + pts.insert(pts.end(),first, beyond); + } + + void + remove(const Point_d& p) + { + // This does not actually remove points, and further insertions + // would make the points reappear, so we disallow it. + removed_ = true; + // Locate the point + Internal_node_handle grandparent = 0; + Internal_node_handle parent = 0; + bool islower = false, islower2; + Node_handle node = root(); // Calls build() if needed. + while (!node->is_leaf()) { + grandparent = parent; islower2 = islower; + parent = static_cast(node); + islower = traits().construct_cartesian_const_iterator_d_object()(p)[parent->cutting_dimension()] < parent->cutting_value(); + if (islower) { + node = parent->lower(); + } else { + node = parent->upper(); + } + } + Leaf_node_handle lnode = static_cast(node); + if (lnode->size() > 1) { + iterator pi = std::find(lnode->begin(), lnode->end(), p); + CGAL_assertion (pi != lnode->end()); + iterator lasti = lnode->end() - 1; + if (pi != lasti) { + // Hack to get a non-const iterator + std::iter_swap(pts.begin()+(pi-pts.begin()), pts.begin()+(lasti-pts.begin())); + } + lnode->drop_last_point(); + } else if (grandparent) { + CGAL_assertion (p == *lnode->begin()); + Node_handle brother = islower ? parent->upper() : parent->lower(); + if (islower2) + grandparent->set_lower(brother); + else + grandparent->set_upper(brother); + } else if (parent) { + tree_root = islower ? parent->upper() : parent->lower(); + } else { + clear(); + } + } + + //For efficiency; reserve the size of the points vectors in advance (if the number of points is already known). + void reserve(size_t size) + { + pts.reserve(size); + } + + //Get the capacity of the underlying points vector. + size_t capacity() + { + return pts.capacity(); + } + + + template + OutputIterator + search(OutputIterator it, const FuzzyQueryItem& q) const + { + if(! pts.empty()){ + + if(! is_built()){ + const_build(); + } + Kd_tree_rectangle b(*bbox); + return tree_root->search(it,q,b); + } + return it; + } + + + template + boost::optional + search_any_point(const FuzzyQueryItem& q) const + { + if(! pts.empty()){ + + if(! is_built()){ + const_build(); + } + Kd_tree_rectangle b(*bbox); + return tree_root->search_any_point(q,b); + } + return boost::none; + } + + + ~Kd_tree() { + if(is_built()){ + delete bbox; + } + } + + + const SearchTraits& + traits() const + { + return traits_; + } + + Node_const_handle + root() const + { + if(! is_built()){ + const_build(); + } + return tree_root; + } + + Node_handle + root() + { + if(! is_built()){ + build(); + } + return tree_root; + } + + void + print() const + { + if(! is_built()){ + const_build(); + } + root()->print(); + } + + const Kd_tree_rectangle& + bounding_box() const + { + if(! is_built()){ + const_build(); + } + return *bbox; + } + + const_iterator + begin() const + { + return pts.begin(); + } + + const_iterator + end() const + { + return pts.end(); + } + + size_type + size() const + { + return pts.size(); + } + + // Print statistics of the tree. + std::ostream& + statistics(std::ostream& s) const + { + if(! is_built()){ + const_build(); + } + s << "Tree statistics:" << std::endl; + s << "Number of items stored: " + << root()->num_items() << std::endl; + s << "Number of nodes: " + << root()->num_nodes() << std::endl; + s << " Tree depth: " << root()->depth() << std::endl; + return s; + } + + +}; + +} // namespace CGAL + +#endif // CGAL_KD_TREE_H -- cgit v1.2.3 From aa9705ab541323e1d7aa0129c8faf0416b0489e0 Mon Sep 17 00:00:00 2001 From: fgodi Date: Sat, 23 Jul 2016 11:07:58 +0000 Subject: read files git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@1393 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: d7f1b1166b65f7d7abc007abb47d86f8d4ba4157 --- .../example/bottleneck_example.cpp | 64 +++++++++++++++++----- 1 file changed, 49 insertions(+), 15 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/example/bottleneck_example.cpp b/src/Bottleneck_distance/example/bottleneck_example.cpp index b3d26f3c..b581a3be 100644 --- a/src/Bottleneck_distance/example/bottleneck_example.cpp +++ b/src/Bottleneck_distance/example/bottleneck_example.cpp @@ -2,9 +2,9 @@ * (Geometric Understanding in Higher Dimensions) is a generic C++ * library for computational topology. * - * Author(s): Francois Godi + * Author(s): Francois Godi, small modifications by Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Antipolis (France) + * Copyright (C) 2015 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 @@ -22,21 +22,55 @@ #include #include +#include +#include +#include +using namespace std; -int main() { - std::vector< std::pair > v1, v2; +//PD: I am using this type of procedures a lot in Gudhi stat. We should make one for all at some point. +std::vector< std::pair > read_diagram_from_file( const char* filename ) +{ + ifstream in; + in.open( filename ); + std::vector< std::pair > result; + if ( !in.is_open() ) + { + std::cerr << "File : " << filename << " do not exist. The program will now terminate \n"; + throw "File do not exist \n"; + } - v1.push_back(std::pair(2.7,3.7)); - v1.push_back(std::pair(9.6,14)); - v1.push_back(std::pair(34.2,34.974)); + std::string line; + while (!in.eof()) + { + getline(in,line); + if ( line.length() != 0 ) + { + std::stringstream lineSS; + lineSS << line; + double beginn, endd; + lineSS >> beginn; + lineSS >> endd; + result.push_back( std::make_pair( beginn , endd ) ); + } + } + in.close(); + return result; +}//read_diagram_from_file - v2.push_back(std::pair(2.8,4.45)); - v2.push_back(std::pair(9.5,14.1)); - - double b = Gudhi::Bottleneck_distance::compute(v1, v2, 0.0001); - std::cout << "Approx. bottleneck distance = " << b << std::endl; - - b = Gudhi::Bottleneck_distance::compute(v1, v2); - std::cout << "Bottleneck distance = " << b << std::endl; +int main( int argc , char** argv ) +{ + if ( argc < 3 ) + { + std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck distance (set by default to zero). The program will now terminate \n"; + } + std::vector< std::pair< double , double > > diag1 = read_diagram_from_file( argv[1] ); + std::vector< std::pair< double , double > > diag2 = read_diagram_from_file( argv[2] ); + double tolerance = 0; + if ( argc == 4 ) + { + tolerance = atof( argv[3] ); + } + double b = Gudhi::Bottleneck_distance::compute(diag1, diag2, tolerance); + std::cout << "The distance between the diagrams is : " << b << ". The tolerace is : " << tolerance << std::endl; } -- cgit v1.2.3