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 From 15d87e9270fa40273c6cfcd707ac0dde01f0373e Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 14 Sep 2016 10:04:40 +0000 Subject: Fix Bottleneck_distance module to compile with official CGAL releases git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1495 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 91047e5d99edbb66fe8ad06d1b930a0c83b47cf2 --- src/Bottleneck_distance/example/CMakeLists.txt | 6 +- src/Bottleneck_distance/include/CGAL/Kd_tree.h | 517 ----------------- .../include/CGAL/Miscellaneous.h | 51 -- .../include/gudhi/CGAL/Kd_tree.h | 516 +++++++++++++++++ .../include/gudhi/CGAL/Kd_tree_node.h | 569 +++++++++++++++++++ .../include/gudhi/CGAL/Miscellaneous.h | 51 ++ .../CGAL/Orthogonal_incremental_neighbor_search.h | 622 +++++++++++++++++++++ .../include/gudhi/Planar_neighbors_finder.h | 12 +- src/Bottleneck_distance/test/CMakeLists.txt | 6 +- 9 files changed, 1774 insertions(+), 576 deletions(-) delete mode 100644 src/Bottleneck_distance/include/CGAL/Kd_tree.h delete mode 100644 src/Bottleneck_distance/include/CGAL/Miscellaneous.h create mode 100644 src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree.h create mode 100644 src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree_node.h create mode 100644 src/Bottleneck_distance/include/gudhi/CGAL/Miscellaneous.h create mode 100644 src/Bottleneck_distance/include/gudhi/CGAL/Orthogonal_incremental_neighbor_search.h (limited to 'src') diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt index adf298aa..6f3204f6 100644 --- a/src/Bottleneck_distance/example/CMakeLists.txt +++ b/src/Bottleneck_distance/example/CMakeLists.txt @@ -1,10 +1,10 @@ cmake_minimum_required(VERSION 2.6) project(Bottleneck_distance_examples) -# need CGAL 4.6 -# cmake -DCGAL_DIR=~/workspace/CGAL-4.6-beta1 ../../.. +# requires CGAL 4.8 +# cmake -DCGAL_DIR=~/workspace/CGAL-4.8 ../../.. if(CGAL_FOUND) - if (NOT CGAL_VERSION VERSION_LESS 4.6.0) + if (NOT CGAL_VERSION VERSION_LESS 4.8.0) if (EIGEN3_FOUND) add_executable (bottleneck_example bottleneck_example.cpp) endif() diff --git a/src/Bottleneck_distance/include/CGAL/Kd_tree.h b/src/Bottleneck_distance/include/CGAL/Kd_tree.h deleted file mode 100644 index 4f874a8b..00000000 --- a/src/Bottleneck_distance/include/CGAL/Kd_tree.h +++ /dev/null @@ -1,517 +0,0 @@ -// 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 diff --git a/src/Bottleneck_distance/include/CGAL/Miscellaneous.h b/src/Bottleneck_distance/include/CGAL/Miscellaneous.h deleted file mode 100644 index 21be0bc7..00000000 --- a/src/Bottleneck_distance/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::Bottleneck_distance::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/CGAL/Kd_tree.h b/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree.h new file mode 100644 index 00000000..5b63b290 --- /dev/null +++ b/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree.h @@ -0,0 +1,516 @@ +// 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 "CGAL/Kd_tree_node.h" + +#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 diff --git a/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree_node.h b/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree_node.h new file mode 100644 index 00000000..acefe926 --- /dev/null +++ b/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree_node.h @@ -0,0 +1,569 @@ +// Copyright (c) 2002,2011 Utrecht University (The Netherlands). +// 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. +// +// $URL$ +// $Id$ +// +// +// Authors : Hans Tangelder () + +#ifndef CGAL_KD_TREE_NODE_H +#define CGAL_KD_TREE_NODE_H + +#include +#include +#include + +namespace CGAL { + + template + class Kd_tree; + + template < class TreeTraits, class Splitter, class UseExtendedNode > + class Kd_tree_node { + + friend class Kd_tree; + + typedef typename Kd_tree::Node_handle Node_handle; + typedef typename Kd_tree::Node_const_handle Node_const_handle; + typedef typename Kd_tree::Internal_node_handle Internal_node_handle; + typedef typename Kd_tree::Internal_node_const_handle Internal_node_const_handle; + typedef typename Kd_tree::Leaf_node_handle Leaf_node_handle; + typedef typename Kd_tree::Leaf_node_const_handle Leaf_node_const_handle; + typedef typename TreeTraits::Point_d Point_d; + + typedef typename TreeTraits::FT FT; + typedef typename Kd_tree::Separator Separator; + typedef typename Kd_tree::Point_d_iterator Point_d_iterator; + typedef typename Kd_tree::iterator iterator; + typedef typename Kd_tree::D D; + + bool leaf; + + public : + Kd_tree_node(bool leaf_) + :leaf(leaf_){} + + bool is_leaf() const{ + return leaf; + } + + std::size_t + num_items() const + { + if (is_leaf()){ + Leaf_node_const_handle node = + static_cast(this); + return node->size(); + } + else { + Internal_node_const_handle node = + static_cast(this); + return node->lower()->num_items() + node->upper()->num_items(); + } + } + + std::size_t + num_nodes() const + { + if (is_leaf()) return 1; + else { + Internal_node_const_handle node = + static_cast(this); + return node->lower()->num_nodes() + node->upper()->num_nodes(); + } + } + + int + depth(const int current_max_depth) const + { + if (is_leaf()){ + return current_max_depth; + } + else { + Internal_node_const_handle node = + static_cast(this); + return + (std::max)( node->lower()->depth(current_max_depth + 1), + node->upper()->depth(current_max_depth + 1)); + } + } + + int + depth() const + { + return depth(1); + } + + template + OutputIterator + tree_items(OutputIterator it) const { + if (is_leaf()) { + Leaf_node_const_handle node = + static_cast(this); + if (node->size()>0) + for (iterator i=node->begin(); i != node->end(); i++) + {*it=*i; ++it;} + } + else { + Internal_node_const_handle node = + static_cast(this); + it=node->lower()->tree_items(it); + it=node->upper()->tree_items(it); + } + return it; + } + + + boost::optional + any_tree_item() const { + boost::optional result = boost::none; + if (is_leaf()) { + Leaf_node_const_handle node = + static_cast(this); + if (node->size()>0){ + return boost::make_optional(*(node->begin())); + } + } + else { + Internal_node_const_handle node = + static_cast(this); + result = node->lower()->any_tree_item(); + if(! result){ + result = node->upper()->any_tree_item(); + } + } + return result; + } + + + void + indent(int d) const + { + for(int i = 0; i < d; i++){ + std::cout << " "; + } + } + + + void + print(int d = 0) const + { + if (is_leaf()) { + Leaf_node_const_handle node = + static_cast(this); + indent(d); + std::cout << "leaf" << std::endl; + if (node->size()>0) + for (iterator i=node->begin(); i != node->end(); i++) + {indent(d);std::cout << *i << std::endl;} + } + else { + Internal_node_const_handle node = + static_cast(this); + indent(d); + std::cout << "lower tree" << std::endl; + node->lower()->print(d+1); + indent(d); + std::cout << "separator: dim = " << node->cutting_dimension() << " val = " << node->cutting_value() << std::endl; + indent(d); + std::cout << "upper tree" << std::endl; + node->upper()->print(d+1); + } + } + + + template + OutputIterator + search(OutputIterator it, const FuzzyQueryItem& q, + Kd_tree_rectangle& b) const + { + if (is_leaf()) { + Leaf_node_const_handle node = + static_cast(this); + if (node->size()>0) + for (iterator i=node->begin(); i != node->end(); i++) + if (q.contains(*i)) + {*it++=*i;} + } + else { + Internal_node_const_handle node = + static_cast(this); + // after splitting b denotes the lower part of b + Kd_tree_rectangle b_upper(b); + b.split(b_upper, node->cutting_dimension(), + node->cutting_value()); + + if (q.outer_range_contains(b)) + it=node->lower()->tree_items(it); + else + if (q.inner_range_intersects(b)) + it=node->lower()->search(it,q,b); + if (q.outer_range_contains(b_upper)) + it=node->upper()->tree_items(it); + else + if (q.inner_range_intersects(b_upper)) + it=node->upper()->search(it,q,b_upper); + }; + return it; + } + + + template + boost::optional + search_any_point(const FuzzyQueryItem& q, + Kd_tree_rectangle& b) const + { + boost::optional result = boost::none; + if (is_leaf()) { + Leaf_node_const_handle node = + static_cast(this); + if (node->size()>0) + for (iterator i=node->begin(); i != node->end(); i++) + if (q.contains(*i)) + { result = *i; break; } + } + else { + Internal_node_const_handle node = + static_cast(this); + // after splitting b denotes the lower part of b + Kd_tree_rectangle b_upper(b); + b.split(b_upper, node->cutting_dimension(), + node->cutting_value()); + + if (q.outer_range_contains(b)){ + result = node->lower()->any_tree_item(); + }else{ + if (q.inner_range_intersects(b)){ + result = node->lower()->search_any_point(q,b); + } + } + if(result){ + return result; + } + if (q.outer_range_contains(b_upper)){ + result = node->upper()->any_tree_item(); + }else{ + if (q.inner_range_intersects(b_upper)) + result = node->upper()->search_any_point(q,b_upper); + } + } + return result; + } + + }; + + + template < class TreeTraits, class Splitter, class UseExtendedNode > + class Kd_tree_leaf_node : public Kd_tree_node< TreeTraits, Splitter, UseExtendedNode >{ + + friend class Kd_tree; + + typedef typename Kd_tree::iterator iterator; + typedef Kd_tree_node< TreeTraits, Splitter, UseExtendedNode> Base; + typedef typename TreeTraits::Point_d Point_d; + + private: + + // private variables for leaf nodes + boost::int32_t n; // denotes number of items in a leaf node + iterator data; // iterator to data in leaf node + + + public: + + // default constructor + Kd_tree_leaf_node() + {} + + Kd_tree_leaf_node(bool leaf_ ) + : Base(leaf_) + {} + + Kd_tree_leaf_node(bool leaf_,unsigned int n_ ) + : Base(leaf_), n(n_) + {} + + // members for all nodes + + // members for leaf nodes only + inline + unsigned int + size() const + { + return n; + } + + inline + iterator + begin() const + { + return data; + } + + inline + iterator + end() const + { + return data + n; + } + + inline + void + drop_last_point() + { + --n; + } + + }; //leaf node + + + + template < class TreeTraits, class Splitter, class UseExtendedNode> + class Kd_tree_internal_node : public Kd_tree_node< TreeTraits, Splitter, UseExtendedNode >{ + + friend class Kd_tree; + + typedef Kd_tree_node< TreeTraits, Splitter, UseExtendedNode> Base; + typedef typename Kd_tree::Node_handle Node_handle; + typedef typename Kd_tree::Node_const_handle Node_const_handle; + + typedef typename TreeTraits::FT FT; + typedef typename Kd_tree::Separator Separator; + + private: + + // private variables for internal nodes + boost::int32_t cut_dim; + FT cut_val; + Node_handle lower_ch, upper_ch; + + + // private variables for extended internal nodes + FT low_val; + FT high_val; + + public: + + // default constructor + Kd_tree_internal_node() + {} + + Kd_tree_internal_node(bool leaf_) + : Base(leaf_) + {} + + + // members for internal node and extended internal node + + inline + Node_const_handle + lower() const + { + return lower_ch; + } + + inline + Node_const_handle + upper() const + { + return upper_ch; + } + + inline + Node_handle + lower() + { + return lower_ch; + } + + inline + Node_handle + upper() + { + return upper_ch; + } + + inline + void + set_lower(Node_handle nh) + { + lower_ch = nh; + } + + inline + void + set_upper(Node_handle nh) + { + upper_ch = nh; + } + + // inline Separator& separator() {return sep; } + // use instead + inline + void set_separator(Separator& sep){ + cut_dim = sep.cutting_dimension(); + cut_val = sep.cutting_value(); + } + + inline + FT + cutting_value() const + { + return cut_val; + } + + inline + int + cutting_dimension() const + { + return cut_dim; + } + + // members for extended internal node only + inline + FT + low_value() const + { + return low_val; + } + + inline + FT + high_value() const + { + return high_val; + } + + + /*Separator& + separator() + { + return Separator(cutting_dimension,cutting_value); + }*/ + + + };//internal node + + template < class TreeTraits, class Splitter> + class Kd_tree_internal_node : public Kd_tree_node< TreeTraits, Splitter, Tag_false >{ + + friend class Kd_tree; + + typedef Kd_tree_node< TreeTraits, Splitter, Tag_false> Base; + typedef typename Kd_tree::Node_handle Node_handle; + typedef typename Kd_tree::Node_const_handle Node_const_handle; + + typedef typename TreeTraits::FT FT; + typedef typename Kd_tree::Separator Separator; + + private: + + // private variables for internal nodes + boost::uint8_t cut_dim; + FT cut_val; + + Node_handle lower_ch, upper_ch; + + public: + + // default constructor + Kd_tree_internal_node() + {} + + Kd_tree_internal_node(bool leaf_) + : Base(leaf_) + {} + + + // members for internal node and extended internal node + + inline + Node_const_handle + lower() const + { + return lower_ch; + } + + inline + Node_const_handle + upper() const + { + return upper_ch; + } + + inline + Node_handle + lower() + { + return lower_ch; + } + + inline + Node_handle + upper() + { + return upper_ch; + } + + inline + void + set_lower(Node_handle nh) + { + lower_ch = nh; + } + + inline + void + set_upper(Node_handle nh) + { + upper_ch = nh; + } + + // inline Separator& separator() {return sep; } + // use instead + + inline + void set_separator(Separator& sep){ + cut_dim = sep.cutting_dimension(); + cut_val = sep.cutting_value(); + } + + inline + FT + cutting_value() const + { + return cut_val; + } + + inline + int + cutting_dimension() const + { + return cut_dim; + } + + /* Separator& + separator() + { + return Separator(cutting_dimension,cutting_value); + }*/ + + + };//internal node + + + +} // namespace CGAL +#endif // CGAL_KDTREE_NODE_H diff --git a/src/Bottleneck_distance/include/gudhi/CGAL/Miscellaneous.h b/src/Bottleneck_distance/include/gudhi/CGAL/Miscellaneous.h new file mode 100644 index 00000000..21be0bc7 --- /dev/null +++ b/src/Bottleneck_distance/include/gudhi/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::Bottleneck_distance::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/CGAL/Orthogonal_incremental_neighbor_search.h b/src/Bottleneck_distance/include/gudhi/CGAL/Orthogonal_incremental_neighbor_search.h new file mode 100644 index 00000000..0e911f41 --- /dev/null +++ b/src/Bottleneck_distance/include/gudhi/CGAL/Orthogonal_incremental_neighbor_search.h @@ -0,0 +1,622 @@ +// Copyright (c) 2002,2011 Utrecht University (The Netherlands). +// 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 () + +#ifndef CGAL_ORTHOGONAL_INCREMENTAL_NEIGHBOR_SEARCH +#define CGAL_ORTHOGONAL_INCREMENTAL_NEIGHBOR_SEARCH + +#include "CGAL/Kd_tree.h" + +#include +#include +#include +#include +#include +#include + +namespace CGAL { + + template ::type, + class Splitter_ = Sliding_midpoint, + class Tree_= Kd_tree > + class Orthogonal_incremental_neighbor_search { + + public: + typedef Splitter_ Splitter; + typedef Tree_ Tree; + typedef Distance_ Distance; + typedef typename SearchTraits::Point_d Point_d; + typedef typename Distance::Query_item Query_item; + typedef typename SearchTraits::FT FT; + typedef typename Tree::Point_d_iterator Point_d_iterator; + typedef typename Tree::Node_const_handle Node_const_handle; + + typedef std::pair Point_with_transformed_distance; + typedef CGAL::cpp11::tuple > Node_with_distance; + typedef std::vector Node_with_distance_vector; + typedef std::vector Point_with_transformed_distance_vector; + + template + struct Object_wrapper + { + T object; + Object_wrapper(const T& t):object(t){} + const T& operator* () const { return object; } + const T* operator-> () const { return &object; } + }; + + class Iterator_implementation { + SearchTraits traits; + public: + + int number_of_neighbours_computed; + int number_of_internal_nodes_visited; + int number_of_leaf_nodes_visited; + int number_of_items_visited; + + private: + + typedef std::vector Distance_vector; + + Distance_vector dists; + + Distance Orthogonal_distance_instance; + + FT multiplication_factor; + + Query_item query_point; + + FT distance_to_root; + + bool search_nearest_neighbour; + + FT rd; + + + class Priority_higher { + public: + + bool search_nearest; + + Priority_higher(bool search_the_nearest_neighbour) + : search_nearest(search_the_nearest_neighbour) + {} + + //highest priority is smallest distance + bool + operator() (Node_with_distance* n1, Node_with_distance* n2) const + { + return (search_nearest) ? (CGAL::cpp11::get<1>(*n1) > CGAL::cpp11::get<1>(*n2)) : (CGAL::cpp11::get<1>(*n2) > CGAL::cpp11::get<1>(*n1)); + } + }; + + class Distance_smaller { + + public: + + bool search_nearest; + + Distance_smaller(bool search_the_nearest_neighbour) + : search_nearest(search_the_nearest_neighbour) + {} + + //highest priority is smallest distance + bool operator() (Point_with_transformed_distance* p1, Point_with_transformed_distance* p2) const + { + return (search_nearest) ? (p1->second > p2->second) : (p2->second > p1->second); + } + }; + + + std::priority_queue PriorityQueue; + + public: + std::priority_queue Item_PriorityQueue; + + + public: + + int reference_count; + + + + // constructor + Iterator_implementation(const Tree& tree,const Query_item& q, const Distance& tr, + FT Eps=FT(0.0), bool search_nearest=true) + : traits(tree.traits()),number_of_neighbours_computed(0), number_of_internal_nodes_visited(0), + number_of_leaf_nodes_visited(0), number_of_items_visited(0), + Orthogonal_distance_instance(tr), multiplication_factor(Orthogonal_distance_instance.transformed_distance(FT(1.0)+Eps)), + query_point(q), search_nearest_neighbour(search_nearest), + PriorityQueue(Priority_higher(search_nearest)), Item_PriorityQueue(Distance_smaller(search_nearest)), + reference_count(1) + + + { + if (tree.empty()) return; + + typename SearchTraits::Construct_cartesian_const_iterator_d ccci=traits.construct_cartesian_const_iterator_d_object(); + int dim = static_cast(std::distance(ccci(q), ccci(q,0))); + + dists.resize(dim); + for(int i=0 ; i(*The_Root); + Compute_the_next_nearest_neighbour(); + } + else{ + distance_to_root= + Orthogonal_distance_instance.max_distance_to_rectangle(q, + tree.bounding_box()); + Node_with_distance *The_Root = new Node_with_distance(tree.root(), + distance_to_root, dists); + PriorityQueue.push(The_Root); + + // rd is the distance of the top of the priority queue to q + rd=CGAL::cpp11::get<1>(*The_Root); + Compute_the_next_furthest_neighbour(); + } + + + } + + // * operator + const Point_with_transformed_distance& + operator* () const + { + return *(Item_PriorityQueue.top()); + } + + // prefix operator + Iterator_implementation& + operator++() + { + Delete_the_current_item_top(); + if(search_nearest_neighbour) + Compute_the_next_nearest_neighbour(); + else + Compute_the_next_furthest_neighbour(); + return *this; + } + + // postfix operator + Object_wrapper + operator++(int) + { + Object_wrapper result( *(Item_PriorityQueue.top()) ); + ++*this; + return result; + } + + // Print statistics of the general priority search process. + std::ostream& + statistics (std::ostream& s) const { + s << "Orthogonal priority search statistics:" + << std::endl; + s << "Number of internal nodes visited:" + << number_of_internal_nodes_visited << std::endl; + s << "Number of leaf nodes visited:" + << number_of_leaf_nodes_visited << std::endl; + s << "Number of items visited:" + << number_of_items_visited << std::endl; + s << "Number of neighbours computed:" + << number_of_neighbours_computed << std::endl; + return s; + } + + + //destructor + ~Iterator_implementation() + { + while (!PriorityQueue.empty()) { + Node_with_distance* The_top=PriorityQueue.top(); + PriorityQueue.pop(); + delete The_top; + } + while (!Item_PriorityQueue.empty()) { + Point_with_transformed_distance* The_top=Item_PriorityQueue.top(); + Item_PriorityQueue.pop(); + delete The_top; + } + } + + private: + + void + Delete_the_current_item_top() + { + Point_with_transformed_distance* The_item_top=Item_PriorityQueue.top(); + Item_PriorityQueue.pop(); + delete The_item_top; + } + + void + Compute_the_next_nearest_neighbour() + { + // compute the next item + bool next_neighbour_found=false; + if (!(Item_PriorityQueue.empty())) { + next_neighbour_found= + (multiplication_factor*rd > Item_PriorityQueue.top()->second); + } + typename SearchTraits::Construct_cartesian_const_iterator_d construct_it=traits.construct_cartesian_const_iterator_d_object(); + typename SearchTraits::Cartesian_const_iterator_d query_point_it = construct_it(query_point); + // otherwise browse the tree further + while ((!next_neighbour_found) && (!PriorityQueue.empty())) { + Node_with_distance* The_node_top=PriorityQueue.top(); + Node_const_handle N= CGAL::cpp11::get<0>(*The_node_top); + dists = CGAL::cpp11::get<2>(*The_node_top); + PriorityQueue.pop(); + delete The_node_top; + FT copy_rd=rd; + while (!(N->is_leaf())) { // compute new distance + typename Tree::Internal_node_const_handle node = + static_cast(N); + number_of_internal_nodes_visited++; + int new_cut_dim=node->cutting_dimension(); + FT new_rd,dst = dists[new_cut_dim]; + FT val = *(query_point_it + new_cut_dim); + FT diff1 = val - node->high_value(); + FT diff2 = val - node->low_value(); + if (diff1 + diff2 < FT(0.0)) { + new_rd= + Orthogonal_distance_instance.new_distance(copy_rd,dst,diff1,new_cut_dim); + + CGAL_assertion(new_rd >= copy_rd); + dists[new_cut_dim] = diff1; + Node_with_distance *Upper_Child = + new Node_with_distance(node->upper(), new_rd, dists); + PriorityQueue.push(Upper_Child); + dists[new_cut_dim] = dst; + N=node->lower(); + + } + else { // compute new distance + new_rd=Orthogonal_distance_instance.new_distance(copy_rd,dst,diff2,new_cut_dim); + CGAL_assertion(new_rd >= copy_rd); + dists[new_cut_dim] = diff2; + Node_with_distance *Lower_Child = + new Node_with_distance(node->lower(), new_rd, dists); + PriorityQueue.push(Lower_Child); + dists[new_cut_dim] = dst; + N=node->upper(); + } + } + // n is a leaf + typename Tree::Leaf_node_const_handle node = + static_cast(N); + number_of_leaf_nodes_visited++; + if (node->size() > 0) { + for (typename Tree::iterator it=node->begin(); it != node->end(); it++) { + number_of_items_visited++; + FT distance_to_query_point= + Orthogonal_distance_instance.transformed_distance(query_point,*it); + Point_with_transformed_distance *NN_Candidate= + new Point_with_transformed_distance(*it,distance_to_query_point); + Item_PriorityQueue.push(NN_Candidate); + } + // old top of PriorityQueue has been processed, + // hence update rd + + if (!(PriorityQueue.empty())) { + rd = CGAL::cpp11::get<1>(*PriorityQueue.top()); + next_neighbour_found = + (multiplication_factor*rd > + Item_PriorityQueue.top()->second); + } + else // priority queue empty => last neighbour found + { + next_neighbour_found=true; + } + + number_of_neighbours_computed++; + } + } // next_neighbour_found or priority queue is empty + // in the latter case also the item priority quee is empty + } + + + void + Compute_the_next_furthest_neighbour() + { + // compute the next item + bool next_neighbour_found=false; + if (!(Item_PriorityQueue.empty())) { + next_neighbour_found= + (rd < multiplication_factor*Item_PriorityQueue.top()->second); + } + typename SearchTraits::Construct_cartesian_const_iterator_d construct_it=traits.construct_cartesian_const_iterator_d_object(); + typename SearchTraits::Cartesian_const_iterator_d query_point_it = construct_it(query_point); + // otherwise browse the tree further + while ((!next_neighbour_found) && (!PriorityQueue.empty())) { + Node_with_distance* The_node_top=PriorityQueue.top(); + Node_const_handle N= CGAL::cpp11::get<0>(*The_node_top); + dists = CGAL::cpp11::get<2>(*The_node_top); + PriorityQueue.pop(); + delete The_node_top; + FT copy_rd=rd; + while (!(N->is_leaf())) { // compute new distance + typename Tree::Internal_node_const_handle node = + static_cast(N); + number_of_internal_nodes_visited++; + int new_cut_dim=node->cutting_dimension(); + FT new_rd,dst = dists[new_cut_dim]; + FT val = *(query_point_it + new_cut_dim); + FT diff1 = val - node->high_value(); + FT diff2 = val - node->low_value(); + if (diff1 + diff2 < FT(0.0)) { + new_rd= + Orthogonal_distance_instance.new_distance(copy_rd,dst,diff1,new_cut_dim); + + CGAL_assertion(new_rd >= copy_rd); + Node_with_distance *Lower_Child = + new Node_with_distance(node->lower(), copy_rd, dists); + PriorityQueue.push(Lower_Child); + N=node->upper(); + dists[new_cut_dim] = diff1; + copy_rd=new_rd; + + } + else { // compute new distance + new_rd=Orthogonal_distance_instance.new_distance(copy_rd,dst,diff2,new_cut_dim); + CGAL_assertion(new_rd >= copy_rd); + Node_with_distance *Upper_Child = + new Node_with_distance(node->upper(), copy_rd, dists); + PriorityQueue.push(Upper_Child); + N=node->lower(); + dists[new_cut_dim] = diff2; + copy_rd=new_rd; + } + } + // n is a leaf + typename Tree::Leaf_node_const_handle node = + static_cast(N); + number_of_leaf_nodes_visited++; + if (node->size() > 0) { + for (typename Tree::iterator it=node->begin(); it != node->end(); it++) { + number_of_items_visited++; + FT distance_to_query_point= + Orthogonal_distance_instance.transformed_distance(query_point,*it); + Point_with_transformed_distance *NN_Candidate= + new Point_with_transformed_distance(*it,distance_to_query_point); + Item_PriorityQueue.push(NN_Candidate); + } + // old top of PriorityQueue has been processed, + // hence update rd + + if (!(PriorityQueue.empty())) { + rd = CGAL::cpp11::get<1>(*PriorityQueue.top()); + next_neighbour_found = + (multiplication_factor*rd < + Item_PriorityQueue.top()->second); + } + else // priority queue empty => last neighbour found + { + next_neighbour_found=true; + } + + number_of_neighbours_computed++; + } + } // next_neighbour_found or priority queue is empty + // in the latter case also the item priority quee is empty + } + }; // class Iterator_implementaion + + + + + + + + + + public: + class iterator; + typedef iterator const_iterator; + + // constructor + Orthogonal_incremental_neighbor_search(const Tree& tree, + const Query_item& q, FT Eps = FT(0.0), + bool search_nearest=true, const Distance& tr=Distance()) + : m_tree(tree),m_query(q),m_dist(tr),m_Eps(Eps),m_search_nearest(search_nearest) + {} + + iterator + begin() const + { + return iterator(m_tree,m_query,m_dist,m_Eps,m_search_nearest); + } + + iterator + end() const + { + return iterator(); + } + + std::ostream& + statistics(std::ostream& s) + { + begin()->statistics(s); + return s; + } + + + + + class iterator { + + public: + + typedef std::input_iterator_tag iterator_category; + typedef Point_with_transformed_distance value_type; + typedef Point_with_transformed_distance* pointer; + typedef const Point_with_transformed_distance& reference; + typedef std::size_t size_type; + typedef std::ptrdiff_t difference_type; + typedef int distance_type; + + //class Iterator_implementation; + Iterator_implementation *Ptr_implementation; + + + public: + + // default constructor + iterator() + : Ptr_implementation(0) + {} + + int + the_number_of_items_visited() + { + return Ptr_implementation->number_of_items_visited; + } + + // constructor + iterator(const Tree& tree,const Query_item& q, const Distance& tr=Distance(), FT eps=FT(0.0), + bool search_nearest=true) + : Ptr_implementation(new Iterator_implementation(tree, q, tr, eps, search_nearest)) + {} + + // copy constructor + iterator(const iterator& Iter) + { + Ptr_implementation = Iter.Ptr_implementation; + if (Ptr_implementation != 0) Ptr_implementation->reference_count++; + } + + iterator& operator=(const iterator& Iter) + { + if (Ptr_implementation != Iter.Ptr_implementation){ + if (Ptr_implementation != 0 && --(Ptr_implementation->reference_count)==0) { + delete Ptr_implementation; + } + Ptr_implementation = Iter.Ptr_implementation; + if (Ptr_implementation != 0) Ptr_implementation->reference_count++; + } + return *this; + } + + + const Point_with_transformed_distance& + operator* () const + { + return *(*Ptr_implementation); + } + + // -> operator + const Point_with_transformed_distance* + operator-> () const + { + return &*(*Ptr_implementation); + } + + // prefix operator + iterator& + operator++() + { + ++(*Ptr_implementation); + return *this; + } + + // postfix operator + Object_wrapper + operator++(int) + { + return (*Ptr_implementation)++; + } + + + bool + operator==(const iterator& It) const + { + if ( + ((Ptr_implementation == 0) || + Ptr_implementation->Item_PriorityQueue.empty()) && + ((It.Ptr_implementation == 0) || + It.Ptr_implementation->Item_PriorityQueue.empty()) + ) + return true; + // else + return (Ptr_implementation == It.Ptr_implementation); + } + + bool + operator!=(const iterator& It) const + { + return !(*this == It); + } + + std::ostream& + statistics (std::ostream& s) + { + Ptr_implementation->statistics(s); + return s; + } + + ~iterator() + { + if (Ptr_implementation != 0) { + Ptr_implementation->reference_count--; + if (Ptr_implementation->reference_count==0) { + delete Ptr_implementation; + Ptr_implementation = 0; + } + } + } + + + }; // class iterator + + //data members + const Tree& m_tree; + Query_item m_query; + Distance m_dist; + FT m_Eps; + bool m_search_nearest; + }; // class + + template + void swap (typename Orthogonal_incremental_neighbor_search::iterator& x, + typename Orthogonal_incremental_neighbor_search::iterator& y) + { + typename Orthogonal_incremental_neighbor_search::iterator::Iterator_implementation + *tmp = x.Ptr_implementation; + x.Ptr_implementation = y.Ptr_implementation; + y.Ptr_implementation = tmp; + } + +} // namespace CGAL + +#endif // CGAL_ORTHOGONAL_INCREMENTAL_NEIGHBOR_SEARCH_H diff --git a/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h index 9356e879..30f7dc3c 100644 --- a/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h +++ b/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h @@ -25,8 +25,16 @@ #include #include -#include "../CGAL/Kd_tree.h" -#include "../CGAL/Miscellaneous.h" + +// Inclusion order is important for CGAL patch +#include "CGAL/Kd_tree_node.h" +#include "CGAL/Kd_tree.h" +#include "CGAL/Orthogonal_incremental_neighbor_search.h" +#include "CGAL/Miscellaneous.h" + +#include +#include + #include diff --git a/src/Bottleneck_distance/test/CMakeLists.txt b/src/Bottleneck_distance/test/CMakeLists.txt index ba0f5fee..13213075 100644 --- a/src/Bottleneck_distance/test/CMakeLists.txt +++ b/src/Bottleneck_distance/test/CMakeLists.txt @@ -11,10 +11,10 @@ if (GPROF_PATH) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") endif() -# need CGAL 4.7 -# cmake -DCGAL_DIR=~/workspace/CGAL-4.7-Ic-41 ../../.. +# requires CGAL 4.8 +# cmake -DCGAL_DIR=~/workspace/CGAL-4.8 ../../.. if(CGAL_FOUND) - if (NOT CGAL_VERSION VERSION_LESS 4.7.0) + if (NOT CGAL_VERSION VERSION_LESS 4.8.0) if (EIGEN3_FOUND) add_executable ( bottleneckUT bottleneck_unit_test.cpp ) add_executable ( bottleneck_chrono bottleneck_chrono.cpp ) -- cgit v1.2.3 From 9ffc108705ace9910cabc79225d984fe1d15b794 Mon Sep 17 00:00:00 2001 From: fgodi Date: Mon, 26 Sep 2016 12:55:44 +0000 Subject: tentative ajout documentation bottleneck git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1567 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 5177eb3197263cfe272f981439317cdb4e8909c3 --- .../concept/Persistence_diagram.h | 8 +++++ .../doc/Intro_bottleneck_distance.h | 40 ++++++++++++++++++++++ .../include/gudhi/Graph_matching.h | 3 +- 3 files changed, 49 insertions(+), 2 deletions(-) create mode 100644 src/Bottleneck_distance/doc/Intro_bottleneck_distance.h (limited to 'src') diff --git a/src/Bottleneck_distance/concept/Persistence_diagram.h b/src/Bottleneck_distance/concept/Persistence_diagram.h index 27a258d8..bd90cc11 100644 --- a/src/Bottleneck_distance/concept/Persistence_diagram.h +++ b/src/Bottleneck_distance/concept/Persistence_diagram.h @@ -2,11 +2,19 @@ namespace Gudhi { namespace Bottleneck_distance { namespace Concept { +/** \brief Concept of persistence diagram point. The double first is the birth of the component and the double second is the death of the component. + * + * \ingroup bottleneck_distance + */ struct Diagram_point{ double first; double second; }; +/** \brief Concept of persistence diagram. + * + * \ingroup bottleneck_distance + */ struct Persistence_Diagram { const_iterator cbegin() const; diff --git a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h new file mode 100644 index 00000000..2cf10975 --- /dev/null +++ b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h @@ -0,0 +1,40 @@ +/* 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): François 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 DOC_BOTTLENECK_DISTANCE_H_ +#define DOC_BOTTLENECK_DISTANCE_H_ + +// needs namespace for Doxygen to link on classes +namespace Gudhi { +// needs namespace for Doxygen to link on classes +namespace Bottleneck_distance { + +/** \defgroup bottleneck_distance Bottleneck distance + * + * \author François Godi + * + */ + +} // namespace Bottleneck_distance + +} // namespace Gudhi + diff --git a/src/Bottleneck_distance/include/gudhi/Graph_matching.h b/src/Bottleneck_distance/include/gudhi/Graph_matching.h index 69470067..7a8c8ee0 100644 --- a/src/Bottleneck_distance/include/gudhi/Graph_matching.h +++ b/src/Bottleneck_distance/include/gudhi/Graph_matching.h @@ -31,8 +31,7 @@ namespace Gudhi { namespace Bottleneck_distance { -/** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams. - * +/** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams. You get an additive e-approximation. * * * \ingroup bottleneck_distance -- cgit v1.2.3 From 7a701f8a2326268b2aadb369fbc0848b227078a1 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 27 Sep 2016 08:53:57 +0000 Subject: Fix naming conventions and cpplint Add Bottleneck_distance to GUDHI_MODULES in GUDHI_user_version_target.txt git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1569 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: b96a2be25477ddf227e43d9941989f93a0f626bb --- .../concept/Persistence_diagram.h | 37 +++++++++++++++++++--- .../doc/Intro_bottleneck_distance.h | 9 ++++-- .../example/bottleneck_example.cpp | 13 ++++---- .../include/gudhi/CGAL/Miscellaneous.h | 2 +- .../include/gudhi/Graph_matching.h | 10 +++--- .../include/gudhi/Internal_point.h | 10 +++--- .../include/gudhi/Neighbors_finder.h | 10 +++--- .../include/gudhi/Persistence_diagrams_graph.h | 10 +++--- .../include/gudhi/Planar_neighbors_finder.h | 10 +++--- src/Bottleneck_distance/test/bottleneck_chrono.cpp | 2 +- .../test/bottleneck_unit_test.cpp | 2 +- src/cmake/modules/GUDHI_user_version_target.txt | 2 +- 12 files changed, 74 insertions(+), 43 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/concept/Persistence_diagram.h b/src/Bottleneck_distance/concept/Persistence_diagram.h index bd90cc11..4c69343c 100644 --- a/src/Bottleneck_distance/concept/Persistence_diagram.h +++ b/src/Bottleneck_distance/concept/Persistence_diagram.h @@ -1,6 +1,31 @@ +/* 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): François Godi + * + * Copyright (C) 2016 INRIA + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#ifndef CONCEPT_BOTTLENECK_DISTANCE_PERSISTENCE_DIAGRAM_H_ +#define CONCEPT_BOTTLENECK_DISTANCE_PERSISTENCE_DIAGRAM_H_ + namespace Gudhi { -namespace Bottleneck_distance { -namespace Concept { + +namespace bottleneck_distance { /** \brief Concept of persistence diagram point. The double first is the birth of the component and the double second is the death of the component. * @@ -21,6 +46,8 @@ struct Persistence_Diagram const_iterator cend() const; }; -} //namespace Concept -} //namespace Bottleneck_distance -} //namespace Gudhi +} // namespace bottleneck_distance + +} // namespace Gudhi + +#endif // CONCEPT_BOTTLENECK_DISTANCE_PERSISTENCE_DIAGRAM_H_ diff --git a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h index 2cf10975..9a792048 100644 --- a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h +++ b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h @@ -26,15 +26,20 @@ // needs namespace for Doxygen to link on classes namespace Gudhi { // needs namespace for Doxygen to link on classes -namespace Bottleneck_distance { +namespace bottleneck_distance { /** \defgroup bottleneck_distance Bottleneck distance * * \author François Godi + * @{ * + * \section bottleneckdefinition Definition + * + * Bottleneck distance is blablabla... */ +/** @} */ // end defgroup bottleneck_distance -} // namespace Bottleneck_distance +} // namespace bottleneck_distance } // namespace Gudhi diff --git a/src/Bottleneck_distance/example/bottleneck_example.cpp b/src/Bottleneck_distance/example/bottleneck_example.cpp index 472c5c84..0bec9746 100644 --- a/src/Bottleneck_distance/example/bottleneck_example.cpp +++ b/src/Bottleneck_distance/example/bottleneck_example.cpp @@ -28,12 +28,9 @@ #include #include -using namespace std; - -//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; + std::ifstream in; in.open( filename ); std::vector< std::pair > result; if ( !in.is_open() ) @@ -58,13 +55,15 @@ std::vector< std::pair > read_diagram_from_file( const char* fil } in.close(); return result; -}//read_diagram_from_file +} //read_diagram_from_file 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::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] ); @@ -73,6 +72,6 @@ int main( int argc , char** argv ) { tolerance = atof( argv[3] ); } - double b = Gudhi::Bottleneck_distance::compute(diag1, diag2, tolerance); + double b = Gudhi::bottleneck_distance::compute(diag1, diag2, tolerance); std::cout << "The distance between the diagrams is : " << b << ". The tolerace is : " << tolerance << std::endl; } diff --git a/src/Bottleneck_distance/include/gudhi/CGAL/Miscellaneous.h b/src/Bottleneck_distance/include/gudhi/CGAL/Miscellaneous.h index 21be0bc7..91632149 100644 --- a/src/Bottleneck_distance/include/gudhi/CGAL/Miscellaneous.h +++ b/src/Bottleneck_distance/include/gudhi/CGAL/Miscellaneous.h @@ -27,7 +27,7 @@ namespace CGAL { -typedef Gudhi::Bottleneck_distance::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 7a8c8ee0..5f579a0c 100644 --- a/src/Bottleneck_distance/include/gudhi/Graph_matching.h +++ b/src/Bottleneck_distance/include/gudhi/Graph_matching.h @@ -20,8 +20,8 @@ * along with this program. If not, see . */ -#ifndef SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ -#define SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ +#ifndef GRAPH_MATCHING_H_ +#define GRAPH_MATCHING_H_ #include @@ -29,7 +29,7 @@ namespace Gudhi { -namespace Bottleneck_distance { +namespace bottleneck_distance { /** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams. You get an additive e-approximation. * @@ -238,11 +238,11 @@ double compute(const Persistence_diagram1 &diag1, const Persistence_diagram2 &di -} // namespace Bottleneck_distance +} // namespace bottleneck_distance } // namespace Gudhi -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ +#endif // GRAPH_MATCHING_H_ /* Dichotomic version template diff --git a/src/Bottleneck_distance/include/gudhi/Internal_point.h b/src/Bottleneck_distance/include/gudhi/Internal_point.h index 2080900d..f05d5fc9 100644 --- a/src/Bottleneck_distance/include/gudhi/Internal_point.h +++ b/src/Bottleneck_distance/include/gudhi/Internal_point.h @@ -20,12 +20,12 @@ * along with this program. If not, see . */ -#ifndef SRC_BOTTLENECK_INCLUDE_GUDHI_INTERNAL_POINT_H_ -#define SRC_BOTTLENECK_INCLUDE_GUDHI_INTERNAL_POINT_H_ +#ifndef INTERNAL_POINT_H_ +#define INTERNAL_POINT_H_ namespace Gudhi { -namespace Bottleneck_distance { +namespace bottleneck_distance { /** \internal \brief Returns the used index for encoding none of the points */ int null_point_index(); @@ -67,8 +67,8 @@ inline int null_point_index() { return -1; } -} // namespace Bottleneck_distance +} // namespace bottleneck_distance } // namespace Gudhi -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_INTERNAL_POINT_H_ +#endif // INTERNAL_POINT_H_ diff --git a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h index 7ad79126..1bd5879c 100644 --- a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h +++ b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h @@ -20,15 +20,15 @@ * along with this program. If not, see . */ -#ifndef SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_ -#define SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_ +#ifndef NEIGHBORS_FINDER_H_ +#define NEIGHBORS_FINDER_H_ #include #include namespace Gudhi { -namespace Bottleneck_distance { +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). @@ -147,8 +147,8 @@ inline int Layered_neighbors_finder::vlayers_number() const { return static_cast(neighbors_finder.size()); } -} // namespace Bottleneck_distance +} // namespace bottleneck_distance } // namespace Gudhi -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_ +#endif // 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 index e31b2dae..1f6d6683 100644 --- a/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h +++ b/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h @@ -20,8 +20,8 @@ * 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_ +#ifndef PERSISTENCE_DIAGRAMS_GRAPH_H_ +#define PERSISTENCE_DIAGRAMS_GRAPH_H_ #include #include @@ -34,7 +34,7 @@ namespace Gudhi { -namespace Bottleneck_distance { +namespace bottleneck_distance { /** \internal \brief Structure representing an euclidean bipartite graph containing @@ -162,8 +162,8 @@ inline double G::diameter() { return max; } -} // namespace Bottleneck_distance +} // namespace bottleneck_distance } // namespace Gudhi -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_ +#endif // 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 index 30f7dc3c..bf70ed0b 100644 --- a/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h +++ b/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h @@ -20,8 +20,8 @@ * 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_ +#ifndef PLANAR_NEIGHBORS_FINDER_H_ +#define PLANAR_NEIGHBORS_FINDER_H_ #include #include @@ -40,7 +40,7 @@ namespace Gudhi { -namespace Bottleneck_distance { +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. * @@ -217,8 +217,8 @@ inline std::shared_ptr< std::list > Cgal_pnf::pull_all_near(int u_point_ind } -} // namespace Bottleneck_distance +} // namespace bottleneck_distance } // namespace Gudhi -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_ +#endif // PLANAR_NEIGHBORS_FINDER_H_ diff --git a/src/Bottleneck_distance/test/bottleneck_chrono.cpp b/src/Bottleneck_distance/test/bottleneck_chrono.cpp index 8b49b6be..8b143b18 100644 --- a/src/Bottleneck_distance/test/bottleneck_chrono.cpp +++ b/src/Bottleneck_distance/test/bottleneck_chrono.cpp @@ -24,7 +24,7 @@ #include #include -using namespace Gudhi::Bottleneck_distance; +using namespace Gudhi::bottleneck_distance; double upper_bound = 400.; // any real >0 diff --git a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp index d5b71156..d2331c5d 100644 --- a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp +++ b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp @@ -27,7 +27,7 @@ #include #include -using namespace Gudhi::Bottleneck_distance; +using namespace Gudhi::bottleneck_distance; int n1 = 81; // a natural number >0 int n2 = 180; // a natural number >0 diff --git a/src/cmake/modules/GUDHI_user_version_target.txt b/src/cmake/modules/GUDHI_user_version_target.txt index 805f0a83..de16ef4c 100644 --- a/src/cmake/modules/GUDHI_user_version_target.txt +++ b/src/cmake/modules/GUDHI_user_version_target.txt @@ -48,7 +48,7 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11) add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_SOURCE_DIR}/src/GudhUI ${GUDHI_USER_VERSION_DIR}/GudhUI) - set(GUDHI_MODULES "common;Alpha_complex;Bitmap_cubical_complex;Contraction;Hasse_complex;Persistent_cohomology;Simplex_tree;Skeleton_blocker;Witness_complex") + set(GUDHI_MODULES "common;Alpha_complex;Bitmap_cubical_complex;Bottleneck_distance;Contraction;Hasse_complex;Persistent_cohomology;Simplex_tree;Skeleton_blocker;Witness_complex") foreach(GUDHI_MODULE ${GUDHI_MODULES}) # doc files -- cgit v1.2.3 From d83e3f03bafd28664bd91e59a58a1fac8081fe76 Mon Sep 17 00:00:00 2001 From: fgodi Date: Tue, 27 Sep 2016 09:12:30 +0000 Subject: more details on bottleneck distance git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1570 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: b784a4721fca70c5a556ef0251241ad153a2b301 --- src/Bottleneck_distance/doc/Intro_bottleneck_distance.h | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) (limited to 'src') diff --git a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h index 9a792048..8e99ad73 100644 --- a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h +++ b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h @@ -35,7 +35,11 @@ namespace bottleneck_distance { * * \section bottleneckdefinition Definition * - * Bottleneck distance is blablabla... + * Bottleneck distance mesures the similarity between two persistence diagrams. + * It's the shortest distance b for which there exists a perfect matching between + * the points of the two diagrams (+ all the diagonal points) such that + * any couple of matched points are at distance at most b. + * */ /** @} */ // end defgroup bottleneck_distance -- cgit v1.2.3 From 4b781e56b1bbe308fe1559bf1615720942c951b4 Mon Sep 17 00:00:00 2001 From: fgodi Date: Tue, 27 Sep 2016 09:23:58 +0000 Subject: ajout image botlleneck distance git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1571 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: dc043ad1f4dc213dd893277eb4f5b43c79acbae0 --- .../doc/Intro_bottleneck_distance.h | 2 + src/Bottleneck_distance/doc/perturb_pd.png | 192 +++++++++++++++++++++ 2 files changed, 194 insertions(+) create mode 100644 src/Bottleneck_distance/doc/perturb_pd.png (limited to 'src') diff --git a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h index 8e99ad73..795bcbea 100644 --- a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h +++ b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h @@ -40,6 +40,8 @@ namespace bottleneck_distance { * the points of the two diagrams (+ all the diagonal points) such that * any couple of matched points are at distance at most b. * + * \image html perturb_pd.png La bottleneck distance est la longueur de la plus longue arête. + * */ /** @} */ // end defgroup bottleneck_distance diff --git a/src/Bottleneck_distance/doc/perturb_pd.png b/src/Bottleneck_distance/doc/perturb_pd.png new file mode 100644 index 00000000..0121170c --- /dev/null +++ b/src/Bottleneck_distance/doc/perturb_pd.png @@ -0,0 +1,192 @@ + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + -- cgit v1.2.3 From 854e61dc5f31ab4528c104119007276a81916293 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 28 Sep 2016 05:57:24 +0000 Subject: Fix bottleneck doxygen issues git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1574 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: d85f8399427bb2518650adaf5f9e849b53e13048 --- biblio/how_to_cite_gudhi.bib | 9 ++++ .../doc/Intro_bottleneck_distance.h | 6 +-- src/Doxyfile | 3 +- src/common/doc/main_page.h | 50 +++++++++++++++++----- 4 files changed, 53 insertions(+), 15 deletions(-) (limited to 'src') diff --git a/biblio/how_to_cite_gudhi.bib b/biblio/how_to_cite_gudhi.bib index 3c0d0b20..cba59f54 100644 --- a/biblio/how_to_cite_gudhi.bib +++ b/biblio/how_to_cite_gudhi.bib @@ -68,3 +68,12 @@ , url = "http://gudhi.gforge.inria.fr/doc/latest/group__witness__complex.html" , year = 2015 } + +@incollection{gudhi:Bottleneck distance +, author = "Fran{{\c{c}}ois Godi" +, title = "Bottleneck distance" +, publisher = "{GUDHI Editorial Board}" +, booktitle = "{GUDHI} User and Reference Manual" +, url = "http://gudhi.gforge.inria.fr/doc/latest/group__bottleneck__distance.html" +, year = 2016 +} diff --git a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h index 795bcbea..00e614f6 100644 --- a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h +++ b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h @@ -30,17 +30,17 @@ namespace bottleneck_distance { /** \defgroup bottleneck_distance Bottleneck distance * - * \author François Godi + * \author François Godi * @{ * * \section bottleneckdefinition Definition * - * Bottleneck distance mesures the similarity between two persistence diagrams. + * Bottleneck distance measures the similarity between two persistence diagrams. * It's the shortest distance b for which there exists a perfect matching between * the points of the two diagrams (+ all the diagonal points) such that * any couple of matched points are at distance at most b. * - * \image html perturb_pd.png La bottleneck distance est la longueur de la plus longue arête. + * \image html perturb_pd.png Bottleneck distance is the length of the longest edge. * */ /** @} */ // end defgroup bottleneck_distance diff --git a/src/Doxyfile b/src/Doxyfile index dd9a33fb..db77d69d 100644 --- a/src/Doxyfile +++ b/src/Doxyfile @@ -845,7 +845,8 @@ IMAGE_PATH = doc/Skeleton_blocker/ \ doc/Simplex_tree/ \ doc/Persistent_cohomology/ \ doc/Witness_complex/ \ - doc/Bitmap_cubical_complex/ + doc/Bitmap_cubical_complex/ \ + doc/Bottleneck_distance/ # The INPUT_FILTER tag can be used to specify a program that doxygen should # invoke to filter for each input file. Doxygen will invoke the filter program diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index 21cf6925..76401724 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -28,6 +28,7 @@ Author: Vincent Rouvreau
Introduced in: GUDHI 1.3.0
Copyright: GPL v3
+ Requires: \ref cgal ≥ 4.7.0 and \ref eigen3 Alpha_complex is a simplicial complex constructed from the finite cells of a Delaunay Triangulation.
@@ -111,6 +112,26 @@ \section Toolbox Toolbox + \subsection BottleneckDistanceToolbox Bottleneck distance + \image html "perturb_pd.png" "Bottleneck distance is the length of the longest edge" + + + + + +
+ Author: François Godi
+ Introduced in: GUDHI 1.4.0
+ Copyright: GPL v3
+ Requires: \ref cgal ≥ 4.8.0 and \ref eigen3 + 		+ Bottleneck distance measures the similarity between two persistence diagrams. + It's the shortest distance b for which there exists a perfect matching between + the points of the two diagrams (+ all the diagonal points) such that + any couple of matched points are at distance at most b. +
+ User manual: \ref bottleneck_distance +
\subsection ContractionToolbox Contraction \image html "sphere_contraction_representation.png" "Sphere contraction example" @@ -177,7 +198,7 @@ make \endverbatim * \verbatim make test \endverbatim * * \section optionallibrary Optional third-party library - * \subsection gmp GMP: + * \subsection gmp GMP * The multi-field persistent homology algorithm requires GMP which is a free library for arbitrary-precision * arithmetic, operating on signed integers, rational numbers, and floating point numbers. * @@ -190,11 +211,11 @@ make \endverbatim * * Having GMP version 4.2 or higher installed is recommended. * - * \subsection cgal CGAL: - * The \ref alpha_complex data structure and few examples requires CGAL, which is a C++ library which provides easy - * access to efficient and reliable geometric algorithms. + * \subsection cgal CGAL + * The \ref alpha_complex data structure, \ref bottleneck_distance, and few examples requires CGAL, which is a C++ + * library which provides easy access to efficient and reliable geometric algorithms. * - * Having CGAL version 4.4 or higher installed is recommended. The procedure to install this library according to + * Having CGAL version 4.4.0 or higher installed is recommended. The procedure to install this library according to * your operating system is detailed here http://doc.cgal.org/latest/Manual/installation.html * * The following examples require the Computational Geometry Algorithms @@ -204,11 +225,11 @@ make \endverbatim * \li * Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp * - * The following example requires CGAL version ≥ 4.6: + * The following example requires CGAL version ≥ 4.6.0: * \li * Witness_complex/witness_complex_sphere.cpp * - * The following example requires CGAL version ≥ 4.7: + * The following example requires CGAL version ≥ 4.7.0: * \li * Alpha_complex/Alpha_complex_from_off.cpp * \li @@ -220,7 +241,11 @@ make \endverbatim * \li * Persistent_cohomology/custom_persistence_sort.cpp * - * \subsection eigen3 Eigen3: + * The following example requires CGAL version ≥ 4.8.0: + * \li + * + * Bottleneck_distance/bottleneck_example.cpp + * \subsection eigen3 Eigen3 * The \ref alpha_complex data structure and few examples requires * Eigen3 is a C++ template library for linear algebra: * matrices, vectors, numerical solvers, and related algorithms. @@ -228,9 +253,11 @@ make \endverbatim * The following example requires the Eigen3 and will not be * built if Eigen3 is not installed: * \li - * Alpha_complex/Alpha_complex_from_off.cpp (requires also Eigen3) + * Alpha_complex/Alpha_complex_from_off.cpp * \li - * Alpha_complex/Alpha_complex_from_points.cpp (requires also Eigen3) + * Alpha_complex/Alpha_complex_from_points.cpp + * \li + * Bottleneck_distance/bottleneck_example.cpp * \li * Persistent_cohomology/alpha_complex_persistence.cpp * \li @@ -238,7 +265,7 @@ make \endverbatim * \li * Persistent_cohomology/custom_persistence_sort.cpp * - * \subsection tbb Threading Building Blocks: + * \subsection tbb Threading Building Blocks * Intel® TBB lets you easily write parallel * C++ programs that take full advantage of multicore performance, that are portable and composable, and that have * future-proof scalability. @@ -312,6 +339,7 @@ make \endverbatim /*! @file Examples * @example Alpha_complex/Alpha_complex_from_off.cpp * @example Alpha_complex/Alpha_complex_from_points.cpp + * @example Bottleneck_distance/bottleneck_example.cpp * @example Bitmap_cubical_complex/Bitmap_cubical_complex.cpp * @example Bitmap_cubical_complex/Bitmap_cubical_complex_periodic_boundary_conditions.cpp * @example Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp -- cgit v1.2.3 From 0fbb1aa5a076e8b3afaa467f5cf17e04afa89b93 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 28 Sep 2016 06:10:41 +0000 Subject: Move Miscellaneous from CGAL to gudhi git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1575 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a67dfe43c5915965468481ad4a8560b3a81d02a5 --- .../include/gudhi/CGAL/Miscellaneous.h | 51 ---------------------- .../include/gudhi/Miscellaneous.h | 51 ++++++++++++++++++++++ .../include/gudhi/Planar_neighbors_finder.h | 2 +- 3 files changed, 52 insertions(+), 52 deletions(-) delete mode 100644 src/Bottleneck_distance/include/gudhi/CGAL/Miscellaneous.h create mode 100644 src/Bottleneck_distance/include/gudhi/Miscellaneous.h (limited to 'src') diff --git a/src/Bottleneck_distance/include/gudhi/CGAL/Miscellaneous.h b/src/Bottleneck_distance/include/gudhi/CGAL/Miscellaneous.h deleted file mode 100644 index 91632149..00000000 --- a/src/Bottleneck_distance/include/gudhi/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::bottleneck_distance::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/Miscellaneous.h b/src/Bottleneck_distance/include/gudhi/Miscellaneous.h new file mode 100644 index 00000000..91632149 --- /dev/null +++ b/src/Bottleneck_distance/include/gudhi/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::bottleneck_distance::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/Planar_neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h index bf70ed0b..3a748169 100644 --- a/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h +++ b/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h @@ -30,12 +30,12 @@ #include "CGAL/Kd_tree_node.h" #include "CGAL/Kd_tree.h" #include "CGAL/Orthogonal_incremental_neighbor_search.h" -#include "CGAL/Miscellaneous.h" #include #include #include +#include namespace Gudhi { -- cgit v1.2.3 From 097af7c3003e559e1e4abceafaef869b22ac4862 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 28 Sep 2016 08:57:03 +0000 Subject: Image was corrupted git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1576 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 84d138d307b8ba54d49e04d8f05f70c846dcfdb4 --- src/Bottleneck_distance/doc/perturb_pd.png | Bin 13423 -> 20864 bytes 1 file changed, 0 insertions(+), 0 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/doc/perturb_pd.png b/src/Bottleneck_distance/doc/perturb_pd.png index 0121170c..be638de0 100644 Binary files a/src/Bottleneck_distance/doc/perturb_pd.png and b/src/Bottleneck_distance/doc/perturb_pd.png differ -- cgit v1.2.3 From a984232cd500db3a8b38de19ef079a2cf58df071 Mon Sep 17 00:00:00 2001 From: fgodi Date: Tue, 22 Nov 2016 16:55:56 +0000 Subject: include random git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1770 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 85a4424852b370b5bbf4edb95463575c921aeea3 --- src/Bottleneck_distance/test/bottleneck_chrono.cpp | 1 + 1 file changed, 1 insertion(+) (limited to 'src') diff --git a/src/Bottleneck_distance/test/bottleneck_chrono.cpp b/src/Bottleneck_distance/test/bottleneck_chrono.cpp index 8b143b18..6eed38c5 100644 --- a/src/Bottleneck_distance/test/bottleneck_chrono.cpp +++ b/src/Bottleneck_distance/test/bottleneck_chrono.cpp @@ -23,6 +23,7 @@ #include #include #include +#include using namespace Gudhi::bottleneck_distance; -- cgit v1.2.3 From e2e5701fd5e778863f5891b84531ccf1493e68c0 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 23 Nov 2016 07:56:58 +0000 Subject: Fix bottleneckUT SegFault on Mac git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1772 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: da2f18461e957b0d3f4d8e0f08ce1d46a3322888 --- src/Bottleneck_distance/test/bottleneck_unit_test.cpp | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp index d2331c5d..1d753dd8 100644 --- a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp +++ b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp @@ -21,9 +21,10 @@ */ -#define BOOST_TEST_MODULE bottleneck test +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE "bottleneck distance" +#include -#include #include #include -- cgit v1.2.3 From 6dd7403da12dff125e1dedacbc2ed0ec67e643ba Mon Sep 17 00:00:00 2001 From: fgodi Date: Wed, 23 Nov 2016 14:55:25 +0000 Subject: Bottleneck.h git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1774 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 3b2f26c67ceb8a61f3efe3952f0618fff98465e4 --- .../doc/Intro_bottleneck_distance.h | 4 +- .../example/bottleneck_example.cpp | 2 +- src/Bottleneck_distance/include/gudhi/Bottleneck.h | 125 +++++++++++++++++++++ .../include/gudhi/CGAL/Kd_tree.h | 2 +- .../include/gudhi/Graph_matching.h | 88 --------------- src/Bottleneck_distance/test/bottleneck_chrono.cpp | 2 +- .../test/bottleneck_unit_test.cpp | 2 +- 7 files changed, 131 insertions(+), 94 deletions(-) create mode 100644 src/Bottleneck_distance/include/gudhi/Bottleneck.h (limited to 'src') diff --git a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h index 00e614f6..ccb558c5 100644 --- a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h +++ b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h @@ -37,10 +37,10 @@ namespace bottleneck_distance { * * Bottleneck distance measures the similarity between two persistence diagrams. * It's the shortest distance b for which there exists a perfect matching between - * the points of the two diagrams (+ all the diagonal points) such that + * the points of the two diagrams (and also all the points of the diagonal) such that * any couple of matched points are at distance at most b. * - * \image html perturb_pd.png Bottleneck distance is the length of the longest edge. + * \image html perturb_pd.png Bottleneck distance is the length of the longest edge on this picture. * */ /** @} */ // end defgroup bottleneck_distance diff --git a/src/Bottleneck_distance/example/bottleneck_example.cpp b/src/Bottleneck_distance/example/bottleneck_example.cpp index 0bec9746..fd0f8ed5 100644 --- a/src/Bottleneck_distance/example/bottleneck_example.cpp +++ b/src/Bottleneck_distance/example/bottleneck_example.cpp @@ -22,7 +22,7 @@ #define CGAL_HAS_THREADS -#include +#include #include #include #include diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h new file mode 100644 index 00000000..6b6b1552 --- /dev/null +++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h @@ -0,0 +1,125 @@ +/* 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 BOTTLENECK_H_ +#define BOTTLENECK_H_ + +#include + +namespace Gudhi { + +namespace bottleneck_distance { + +/** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams. You get an additive e-approximation. + * + * + * \ingroup 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); + +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); + 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 // BOTTLENECK_H_ + +/* Dichotomic version +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; +} */ + diff --git a/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree.h b/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree.h index 5b63b290..7b1676cf 100644 --- a/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree.h +++ b/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree.h @@ -21,7 +21,7 @@ #ifndef CGAL_KD_TREE_H #define CGAL_KD_TREE_H -#include "CGAL/Kd_tree_node.h" +#include "Kd_tree_node.h" #include #include diff --git a/src/Bottleneck_distance/include/gudhi/Graph_matching.h b/src/Bottleneck_distance/include/gudhi/Graph_matching.h index 5f579a0c..a8d68a9d 100644 --- a/src/Bottleneck_distance/include/gudhi/Graph_matching.h +++ b/src/Bottleneck_distance/include/gudhi/Graph_matching.h @@ -31,17 +31,6 @@ namespace Gudhi { namespace bottleneck_distance { -/** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams. You get an additive e-approximation. - * - * - * \ingroup 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 @@ -182,86 +171,9 @@ inline void Graph_matching::update(std::deque& path) { } } -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); - 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 // GRAPH_MATCHING_H_ - -/* Dichotomic version -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; -} */ - diff --git a/src/Bottleneck_distance/test/bottleneck_chrono.cpp b/src/Bottleneck_distance/test/bottleneck_chrono.cpp index 6eed38c5..4c4f4ee6 100644 --- a/src/Bottleneck_distance/test/bottleneck_chrono.cpp +++ b/src/Bottleneck_distance/test/bottleneck_chrono.cpp @@ -20,7 +20,7 @@ * along with this program. If not, see . */ -#include +#include #include #include #include diff --git a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp index 1d753dd8..a3d50ef8 100644 --- a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp +++ b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp @@ -26,7 +26,7 @@ #include #include -#include +#include using namespace Gudhi::bottleneck_distance; -- cgit v1.2.3 From 4f3df33523249ebd0dbb5e5a5412b5c4bd9df5a8 Mon Sep 17 00:00:00 2001 From: fgodi Date: Wed, 23 Nov 2016 15:16:58 +0000 Subject: Construct_coord_iterator git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1775 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: fd492a001d49e2a11dbd9ac04d3174acff888d5f --- src/Bottleneck_distance/include/gudhi/Internal_point.h | 16 ---------------- .../include/gudhi/Planar_neighbors_finder.h | 2 +- 2 files changed, 1 insertion(+), 17 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/include/gudhi/Internal_point.h b/src/Bottleneck_distance/include/gudhi/Internal_point.h index f05d5fc9..90b5dd14 100644 --- a/src/Bottleneck_distance/include/gudhi/Internal_point.h +++ b/src/Bottleneck_distance/include/gudhi/Internal_point.h @@ -45,22 +45,6 @@ struct Internal_point { 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() { diff --git a/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h index 3a748169..8bd21267 100644 --- a/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h +++ b/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h @@ -35,7 +35,7 @@ #include #include -#include +#include namespace Gudhi { -- cgit v1.2.3 From ff8be430ea38a96332b6c8d63881c441bd5dec74 Mon Sep 17 00:00:00 2001 From: fgodi Date: Wed, 23 Nov 2016 15:17:40 +0000 Subject: miscelianous git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1776 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: fdb8adfaa111e3d5897fa19427ee2171ee8b1e83 --- .../include/gudhi/Construct_coord_iterator.h | 42 ++++++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 src/Bottleneck_distance/include/gudhi/Construct_coord_iterator.h (limited to 'src') diff --git a/src/Bottleneck_distance/include/gudhi/Construct_coord_iterator.h b/src/Bottleneck_distance/include/gudhi/Construct_coord_iterator.h new file mode 100644 index 00000000..278b7955 --- /dev/null +++ b/src/Bottleneck_distance/include/gudhi/Construct_coord_iterator.h @@ -0,0 +1,42 @@ +/* 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::bottleneck_distance::Internal_point Internal_point; + +struct Construct_coord_iterator { + typedef const double* result_type; + const double* operator()(const Internal_point& p) const + { return p.vec; } + const double* operator()(const Internal_point& p, int) const + { return p.vec+2; } +}; + +} //namespace CGAL + +#endif // SRC_BOTTLENECK_INCLUDE_CGAL_MISCELLANEOUS_H_ -- cgit v1.2.3 From 053521743afdd831c110d9a5a5a2e165158c2cb9 Mon Sep 17 00:00:00 2001 From: fgodi Date: Wed, 23 Nov 2016 15:18:12 +0000 Subject: miscelianous git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1777 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 51bee7554819c6840ed6ba2264ecbb8d1f66f333 --- .../include/gudhi/Miscellaneous.h | 51 ---------------------- 1 file changed, 51 deletions(-) delete mode 100644 src/Bottleneck_distance/include/gudhi/Miscellaneous.h (limited to 'src') diff --git a/src/Bottleneck_distance/include/gudhi/Miscellaneous.h b/src/Bottleneck_distance/include/gudhi/Miscellaneous.h deleted file mode 100644 index 91632149..00000000 --- a/src/Bottleneck_distance/include/gudhi/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::bottleneck_distance::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_ -- cgit v1.2.3 From d93bbddf7692569c69e3f477914b6def597942fa Mon Sep 17 00:00:00 2001 From: fgodi Date: Wed, 23 Nov 2016 16:02:25 +0000 Subject: functions no longer return smart pointers git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1778 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 2fabef4be518b9e25963dbc8e6fe09aeb3f28f8e --- .../test/bottleneck_unit_test.cpp | 44 +++++++++++----------- 1 file changed, 22 insertions(+), 22 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp index a3d50ef8..b757ce54 100644 --- a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp +++ b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp @@ -50,7 +50,7 @@ BOOST_AUTO_TEST_CASE(persistence_diagrams_graph){ v2.emplace_back(std::min(a,b), std::max(a,b)); } G::initialize(v1, v2, 0.); - std::shared_ptr< std::vector > d(G::sorted_distances()); + std::vector d(G::sorted_distances()); // BOOST_CHECK(!G::on_the_u_diagonal(n1-1)); BOOST_CHECK(!G::on_the_u_diagonal(n1)); @@ -68,25 +68,25 @@ BOOST_AUTO_TEST_CASE(persistence_diagrams_graph){ // 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((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) { @@ -110,7 +110,7 @@ BOOST_AUTO_TEST_CASE(planar_neighbors_finder) { 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)); - std::list l = *pnf.pull_all_near(n2/2); + std::vector 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.); @@ -126,7 +126,7 @@ BOOST_AUTO_TEST_CASE(neighbors_finder) { // 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); + std::vector 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.); -- cgit v1.2.3 From 33ce062bf29b9bb7db9e83cde39cab6411d613dc Mon Sep 17 00:00:00 2001 From: fgodi Date: Wed, 23 Nov 2016 16:02:39 +0000 Subject: functions no longer return smart pointers git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1779 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: bc5e1b480774441c9af5e0ed902c455c6453c480 --- src/Bottleneck_distance/include/gudhi/Bottleneck.h | 10 +++++----- .../include/gudhi/CGAL/Kd_tree.h | 1 - .../include/gudhi/CGAL/Kd_tree_node.h | 3 ++- .../include/gudhi/Graph_matching.h | 22 ++++++++++------------ .../include/gudhi/Neighbors_finder.h | 8 ++++---- .../include/gudhi/Persistence_diagrams_graph.h | 12 +++--------- .../include/gudhi/Planar_neighbors_finder.h | 19 ++++++++----------- 7 files changed, 32 insertions(+), 43 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h index 6b6b1552..1ae7788c 100644 --- a/src/Bottleneck_distance/include/gudhi/Bottleneck.h +++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h @@ -43,16 +43,16 @@ double compute_exactly(const Persistence_diagram1& diag1, const Persistence_diag 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()); + std::vector sd(G::sorted_distances()); int idmin = 0; - int idmax = sd->size() - 1; + int idmax = sd.size() - 1; // alpha can be modified, this will change the complexity - double alpha = pow(sd->size(), 0.25); + 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)); + 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()) { @@ -63,7 +63,7 @@ double compute_exactly(const Persistence_diagram1 &diag1, const Persistence_diag idmin = idmin + step + 1; } } - return sd->at(idmin); + return sd.at(idmin); } template diff --git a/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree.h b/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree.h index 7b1676cf..9db9b8b6 100644 --- a/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree.h +++ b/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree.h @@ -28,7 +28,6 @@ #include #include -#include #include #include diff --git a/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree_node.h b/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree_node.h index acefe926..d6d01439 100644 --- a/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree_node.h +++ b/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree_node.h @@ -21,7 +21,8 @@ #ifndef CGAL_KD_TREE_NODE_H #define CGAL_KD_TREE_NODE_H -#include +#include "Splitters.h" + #include #include diff --git a/src/Bottleneck_distance/include/gudhi/Graph_matching.h b/src/Bottleneck_distance/include/gudhi/Graph_matching.h index a8d68a9d..c50c3a9e 100644 --- a/src/Bottleneck_distance/include/gudhi/Graph_matching.h +++ b/src/Bottleneck_distance/include/gudhi/Graph_matching.h @@ -23,8 +23,6 @@ #ifndef GRAPH_MATCHING_H_ #define GRAPH_MATCHING_H_ -#include - #include namespace Gudhi { @@ -56,11 +54,11 @@ private: 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; + Layered_neighbors_finder 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); + void update(std::vector & path); }; inline Graph_matching::Graph_matching() @@ -83,7 +81,7 @@ inline bool Graph_matching::perfect() const { inline bool Graph_matching::multi_augment() { if (perfect()) return false; - Layered_neighbors_finder layered_nf = *layering(); + 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 @@ -103,7 +101,7 @@ inline void Graph_matching::set_r(double 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; + std::vector path; path.emplace_back(u_start_index); do { if (static_cast(path.size()) > max_depth) { @@ -129,19 +127,19 @@ inline bool Graph_matching::augment(Layered_neighbors_finder & layered_nf, int u return true; } -inline std::shared_ptr Graph_matching::layering() const { +inline Layered_neighbors_finder 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)); + Layered_neighbors_finder layered_nf(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); + std::vector 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); } } @@ -162,7 +160,7 @@ inline std::shared_ptr Graph_matching::layering() cons return layered_nf; } -inline void Graph_matching::update(std::deque& path) { +inline void Graph_matching::update(std::vector& 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 diff --git a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h index 1bd5879c..e8560559 100644 --- a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h +++ b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h @@ -46,7 +46,7 @@ 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::shared_ptr< std::list > pull_all_near(int u_point_index); + std::vector pull_all_near(int u_point_index); private: const double r; @@ -118,11 +118,11 @@ inline int Neighbors_finder::pull_near(int u_point_index) { 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)); +inline std::vector Neighbors_finder::pull_all_near(int u_point_index) { + std::vector 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); + all_pull.emplace_back(last_pull); last_pull = pull_near(u_point_index); } return all_pull; diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h index 1f6d6683..7af149e4 100644 --- a/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h +++ b/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h @@ -25,11 +25,6 @@ #include #include -#include -#include -#include -#include -#include #include namespace Gudhi { @@ -60,7 +55,7 @@ public: /** \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(); + static std::vector sorted_distances(); /** \internal \brief Returns an upper bound of the diameter of the convex hull */ static double diameter(); @@ -126,15 +121,14 @@ inline int G::size() { return static_cast (u.size() + v.size()); } -inline std::shared_ptr< std::vector > G::sorted_distances() { +inline 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)); - std::shared_ptr< std::vector > sd_up(new std::vector(sorted_distances.cbegin(), sorted_distances.cend())); - return sd_up; + return std::vector(sorted_distances.begin(),sorted_distances.end()); } inline Internal_point G::get_u_point(int u_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 8bd21267..f574231e 100644 --- a/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h +++ b/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h @@ -23,9 +23,6 @@ #ifndef PLANAR_NEIGHBORS_FINDER_H_ #define PLANAR_NEIGHBORS_FINDER_H_ -#include -#include - // Inclusion order is important for CGAL patch #include "CGAL/Kd_tree_node.h" #include "CGAL/Kd_tree.h" @@ -62,7 +59,7 @@ 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::shared_ptr< std::list > pull_all_near(int u_point_index); + std::vector pull_all_near(int u_point_index); private: double r; @@ -91,7 +88,7 @@ public: /** \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); + virtual std::vector pull_all_near(int u_point_index); private: double r; @@ -148,8 +145,8 @@ inline int Naive_pnf::pull_near(int u_point_index) { 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); +inline std::vector Naive_pnf::pull_all_near(int u_point_index) { + std::vector all_pull; 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); @@ -157,7 +154,7 @@ inline std::shared_ptr< std::list > Naive_pnf::pull_all_near(int u_point_in 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); + all_pull.emplace_back(it->second); it = grid.erase(it); } else it++; @@ -206,11 +203,11 @@ inline int Cgal_pnf::pull_near(int u_point_index){ 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); +inline std::vector Cgal_pnf::pull_all_near(int u_point_index) { + std::vector all_pull; int last_pull = pull_near(u_point_index); while (last_pull != null_point_index()) { - all_pull->emplace_back(last_pull); + all_pull.emplace_back(last_pull); last_pull = pull_near(u_point_index); } return all_pull; -- cgit v1.2.3 From 5bd04a9433462965aecf000e5044e70405e968ff Mon Sep 17 00:00:00 2001 From: fgodi Date: Wed, 23 Nov 2016 16:57:49 +0000 Subject: fix git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1780 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 9001cd1b33dfea3b34e5d12ef8e20b5624a50ba9 --- .../concept/Persistence_diagram.h | 11 +++++------ .../example/bottleneck_example.cpp | 2 +- src/Bottleneck_distance/include/gudhi/Bottleneck.h | 20 +++++++------------- .../include/gudhi/Persistence_diagrams_graph.h | 4 ++-- .../test/bottleneck_unit_test.cpp | 1 + 5 files changed, 16 insertions(+), 22 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/concept/Persistence_diagram.h b/src/Bottleneck_distance/concept/Persistence_diagram.h index 4c69343c..1ab768ba 100644 --- a/src/Bottleneck_distance/concept/Persistence_diagram.h +++ b/src/Bottleneck_distance/concept/Persistence_diagram.h @@ -27,23 +27,22 @@ namespace Gudhi { namespace bottleneck_distance { -/** \brief Concept of persistence diagram point. The double first is the birth of the component and the double second is the death of the component. +/** \brief Concept of persistence diagram point. get<0>() must return the birth of the component and get<1>() its death. * * \ingroup bottleneck_distance */ struct Diagram_point{ - double first; - double second; + double get(); }; -/** \brief Concept of persistence diagram. +/** \brief Concept of persistence diagram. It's a range of Diagram_point. * * \ingroup bottleneck_distance */ struct Persistence_Diagram { - const_iterator cbegin() const; - const_iterator cend() const; + const_iterator begin(); + const_iterator end(); }; } // namespace bottleneck_distance diff --git a/src/Bottleneck_distance/example/bottleneck_example.cpp b/src/Bottleneck_distance/example/bottleneck_example.cpp index fd0f8ed5..b1b98a82 100644 --- a/src/Bottleneck_distance/example/bottleneck_example.cpp +++ b/src/Bottleneck_distance/example/bottleneck_example.cpp @@ -73,5 +73,5 @@ int main( int argc , char** argv ) 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; + std::cout << "The distance between the diagrams is : " << b << ". The tolerance is : " << tolerance << std::endl; } diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h index 1ae7788c..71845e25 100644 --- a/src/Bottleneck_distance/include/gudhi/Bottleneck.h +++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h @@ -29,17 +29,6 @@ namespace Gudhi { namespace bottleneck_distance { -/** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams. You get an additive e-approximation. - * - * - * \ingroup 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); - template double compute_exactly(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2) { G::initialize(diag1, diag2, 0.); @@ -66,9 +55,14 @@ double compute_exactly(const Persistence_diagram1 &diag1, const Persistence_diag return sd.at(idmin); } +/** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams. + * If the last parameter e is not 0 (default value if not explicited), you get an additive e-approximation. + * + * \ingroup bottleneck_distance + */ template -double compute(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e) { - if(e< std::numeric_limits::min()) +double compute(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e=0.) { + if(e == 0.) return compute_exactly(diag1, diag2); G::initialize(diag1, diag2, e); int in = G::diameter()/e; diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h index 7af149e4..7d37b9e0 100644 --- a/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h +++ b/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h @@ -83,10 +83,10 @@ inline void G::initialize(const Persistence_diagram1 &diag1, 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())); + u.push_back(Internal_point(std::get<0>(*it), std::get<1>(*it), 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())); + v.push_back(Internal_point(std::get<0>(*it), std::get<1>(*it), v.size())); if (u.size() < v.size()) swap(u, v); } diff --git a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp index b757ce54..e2cd3c05 100644 --- a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp +++ b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp @@ -186,4 +186,5 @@ BOOST_AUTO_TEST_CASE(global){ v2.emplace_back(std::max(a,b),std::max(a,b)+y); } BOOST_CHECK(compute(v1, v2) <= upper_bound/100.); + BOOST_CHECK(compute(v1, v2, upper_bound/1000.) <= upper_bound/100. + upper_bound/1000.); } -- cgit v1.2.3 From e15d7f55c337596e988cd84425bbfc4815913074 Mon Sep 17 00:00:00 2001 From: fgodi Date: Fri, 25 Nov 2016 13:17:50 +0000 Subject: copyrigths git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1783 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: c045f59d4f2810aa2193add84ac97a2632888dc4 --- src/Bottleneck_distance/include/gudhi/Bottleneck.h | 6 +- .../include/gudhi/Construct_coord_iterator.h | 4 +- .../include/gudhi/Graph_matching.h | 4 +- .../include/gudhi/Internal_point.h | 4 +- .../include/gudhi/Neighbors_finder.h | 4 +- .../include/gudhi/Persistence_diagrams_graph.h | 7 +- .../include/gudhi/Planar_neighbors_finder.h | 89 +++------------------- 7 files changed, 26 insertions(+), 92 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h index 71845e25..bb0a13d2 100644 --- a/src/Bottleneck_distance/include/gudhi/Bottleneck.h +++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h @@ -2,9 +2,9 @@ * (Geometric Understanding in Higher Dimensions) is a generic C++ * library for computational topology. * - * Author(s): Francois Godi + * Author: Francois Godi * - * Copyright (C) 2015 INRIA Sophia-Antipolis (France) + * Copyright (C) 2015 INRIA (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 @@ -65,7 +65,7 @@ double compute(const Persistence_diagram1 &diag1, const Persistence_diagram2 &di if(e == 0.) return compute_exactly(diag1, diag2); G::initialize(diag1, diag2, e); - int in = G::diameter()/e; + int in = G::diameter()/e + 1; int idmin = 0; int idmax = in; // alpha can be modified, this will change the complexity diff --git a/src/Bottleneck_distance/include/gudhi/Construct_coord_iterator.h b/src/Bottleneck_distance/include/gudhi/Construct_coord_iterator.h index 278b7955..0959dd03 100644 --- a/src/Bottleneck_distance/include/gudhi/Construct_coord_iterator.h +++ b/src/Bottleneck_distance/include/gudhi/Construct_coord_iterator.h @@ -2,9 +2,9 @@ * (Geometric Understanding in Higher Dimensions) is a generic C++ * library for computational topology. * - * Author(s): Francois Godi + * Author: Francois Godi * - * Copyright (C) 2015 INRIA Sophia-Antipolis (France) + * Copyright (C) 2015 INRIA (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_distance/include/gudhi/Graph_matching.h b/src/Bottleneck_distance/include/gudhi/Graph_matching.h index c50c3a9e..fa20b2a2 100644 --- a/src/Bottleneck_distance/include/gudhi/Graph_matching.h +++ b/src/Bottleneck_distance/include/gudhi/Graph_matching.h @@ -2,9 +2,9 @@ * (Geometric Understanding in Higher Dimensions) is a generic C++ * library for computational topology. * - * Author(s): Francois Godi + * Author: Francois Godi * - * Copyright (C) 2015 INRIA Sophia-Antipolis (France) + * Copyright (C) 2015 INRIA (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_distance/include/gudhi/Internal_point.h b/src/Bottleneck_distance/include/gudhi/Internal_point.h index 90b5dd14..78aad470 100644 --- a/src/Bottleneck_distance/include/gudhi/Internal_point.h +++ b/src/Bottleneck_distance/include/gudhi/Internal_point.h @@ -2,9 +2,9 @@ * (Geometric Understanding in Higher Dimensions) is a generic C++ * library for computational topology. * - * Author(s): Francois Godi + * Author: Francois Godi * - * Copyright (C) 2015 INRIA Sophia-Antipolis (France) + * Copyright (C) 2015 INRIA (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_distance/include/gudhi/Neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h index e8560559..20b47d0b 100644 --- a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h +++ b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h @@ -2,9 +2,9 @@ * (Geometric Understanding in Higher Dimensions) is a generic C++ * library for computational topology. * - * Author(s): Francois Godi + * Author: Francois Godi * - * Copyright (C) 2015 INRIA Sophia-Antipolis (France) + * Copyright (C) 2015 INRIA (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_distance/include/gudhi/Persistence_diagrams_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h index 7d37b9e0..8242ce2b 100644 --- a/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h +++ b/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h @@ -2,9 +2,9 @@ * (Geometric Understanding in Higher Dimensions) is a generic C++ * library for computational topology. * - * Author(s): Francois Godi + * Author: Francois Godi * - * Copyright (C) 2015 INRIA Sophia-Antipolis (France) + * Copyright (C) 2015 INRIA (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 @@ -65,8 +65,7 @@ private: 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; + friend class Planar_neighbors_finder; }; /** \internal \typedef \brief Shorter alias */ diff --git a/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h index f574231e..c1f4d908 100644 --- a/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h +++ b/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h @@ -2,9 +2,9 @@ * (Geometric Understanding in Higher Dimensions) is a generic C++ * library for computational topology. * - * Author(s): Francois Godi + * Author: Francois Godi * - * Copyright (C) 2015 INRIA Sophia-Antipolis (France) + * Copyright (C) 2015 INRIA (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 @@ -67,7 +67,7 @@ private: std::multimap,int> grid; }; -class Cgal_pnf { +class Planar_neighbors_finder { typedef CGAL::Dimension_tag<2> D; typedef CGAL::Search_traits Traits; @@ -78,7 +78,7 @@ class Cgal_pnf { public: /** \internal \brief Constructor taking the near distance definition as parameter. */ - Cgal_pnf(double r_); + Planar_neighbors_finder(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. */ @@ -96,79 +96,14 @@ private: Kd_tree kd_t; }; -/** \internal \typedef \brief Planar_neighbors_finder is the used implementation. */ -typedef Cgal_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::vector Naive_pnf::pull_all_near(int u_point_index) { - std::vector all_pull; - 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_) +inline Planar_neighbors_finder::Planar_neighbors_finder(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){ +inline void Planar_neighbors_finder::add(int v_point_index){ if(v_point_index == null_point_index()) return; contents.insert(v_point_index); @@ -176,22 +111,20 @@ inline void Cgal_pnf::add(int 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)){ +inline void Planar_neighbors_finder::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 ? */ -inline bool Cgal_pnf::contains(int v_point_index) const{ +inline bool Planar_neighbors_finder::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){ +inline int Planar_neighbors_finder::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)); @@ -199,11 +132,13 @@ inline int Cgal_pnf::pull_near(int u_point_index){ if(it==search.end() || G::distance(u_point_index, it->first.point_index) > r) return null_point_index(); int tmp = it->first.point_index; + if(!contains(tmp)) + std::cout << "!! A kd_tree returns a point (Point_index:" << tmp << ") previously removed !!" << std::endl; remove(tmp); return tmp; } -inline std::vector Cgal_pnf::pull_all_near(int u_point_index) { +inline std::vector Planar_neighbors_finder::pull_all_near(int u_point_index) { std::vector all_pull; int last_pull = pull_near(u_point_index); while (last_pull != null_point_index()) { -- cgit v1.2.3 From 135c83e90e3c0421f6ca08622552edf5e18023d6 Mon Sep 17 00:00:00 2001 From: fgodi Date: Fri, 25 Nov 2016 13:22:08 +0000 Subject: copyrigths git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1784 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 0f17a81c0c8ef507d49f0b8a78afc195a957e7f1 --- .../concept/Persistence_diagram.h | 4 +- .../doc/Intro_bottleneck_distance.h | 4 +- .../example/bottleneck_example.cpp | 4 +- src/Bottleneck_distance/test/bottleneck_chrono.cpp | 49 +++++++++++----------- .../test/bottleneck_unit_test.cpp | 4 +- 5 files changed, 32 insertions(+), 33 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/concept/Persistence_diagram.h b/src/Bottleneck_distance/concept/Persistence_diagram.h index 1ab768ba..fe13e859 100644 --- a/src/Bottleneck_distance/concept/Persistence_diagram.h +++ b/src/Bottleneck_distance/concept/Persistence_diagram.h @@ -2,9 +2,9 @@ * (Geometric Understanding in Higher Dimensions) is a generic C++ * library for computational topology. * - * Author(s): François Godi + * Author: François Godi * - * Copyright (C) 2016 INRIA + * Copyright (C) 2015 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by diff --git a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h index ccb558c5..1f443f7f 100644 --- a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h +++ b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h @@ -2,9 +2,9 @@ * (Geometric Understanding in Higher Dimensions) is a generic C++ * library for computational topology. * - * Author(s): François Godi + * Author: François Godi * - * Copyright (C) 2015 INRIA Sophia-Antipolis (France) + * Copyright (C) 2015 INRIA (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_distance/example/bottleneck_example.cpp b/src/Bottleneck_distance/example/bottleneck_example.cpp index b1b98a82..28e458a5 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, small modifications by Pawel Dlotko + * Authors: Francois Godi, small modifications by Pawel Dlotko * - * Copyright (C) 2015 INRIA Saclay (France) + * Copyright (C) 2015 INRIA (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_distance/test/bottleneck_chrono.cpp b/src/Bottleneck_distance/test/bottleneck_chrono.cpp index 4c4f4ee6..a7440ecd 100644 --- a/src/Bottleneck_distance/test/bottleneck_chrono.cpp +++ b/src/Bottleneck_distance/test/bottleneck_chrono.cpp @@ -2,9 +2,9 @@ * (Geometric Understanding in Higher Dimensions) is a generic C++ * library for computational topology. * - * Author(s): Francois Godi + * Author: Francois Godi * - * Copyright (C) 2015 INRIA Sophia-Antipolis (France) + * Copyright (C) 2015 INRIA (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 @@ -34,29 +34,28 @@ int main(){ std::ofstream objetfichier; objetfichier.open("results.csv", std::ios::out); - 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; - 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 = 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)); - objetfichier << n << ";" << duration.count() << ";" << b << std::endl; + int n = 1200; + 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 = 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)); + 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 index e2cd3c05..31ba18ad 100644 --- a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp +++ b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp @@ -2,9 +2,9 @@ * (Geometric Understanding in Higher Dimensions) is a generic C++ * library for computational topology. * - * Author(s): Francois Godi + * Author: Francois Godi * - * Copyright (C) 2015 INRIA Sophia-Antipolis (France) + * Copyright (C) 2015 INRIA (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 -- cgit v1.2.3 From e9a84b460949d382b018ce3cc26c5743d09dffa5 Mon Sep 17 00:00:00 2001 From: fgodi Date: Fri, 25 Nov 2016 13:57:43 +0000 Subject: dernière version du kd_tree 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/bottleneck_integration@1785 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a9c6dd3085c1a6a1f48fe624394f662b7f579781 --- .../include/gudhi/CGAL/Kd_tree.h | 826 +++++++++++---------- .../include/gudhi/CGAL/Kd_tree_node.h | 400 +++++----- 2 files changed, 655 insertions(+), 571 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree.h b/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree.h index 9db9b8b6..16043b76 100644 --- a/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree.h +++ b/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree.h @@ -47,465 +47,533 @@ template , cl 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; + 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; + SearchTraits traits_; + Splitter split; - // wokaround for https://svn.boost.org/trac/boost/ticket/9332 + // 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; + std::deque internal_nodes; + std::deque leaf_nodes; #else - boost::container::deque internal_nodes; - boost::container::deque leaf_nodes; + boost::container::deque internal_nodes; + boost::container::deque leaf_nodes; #endif - Node_handle tree_root; + Node_handle tree_root; - Kd_tree_rectangle* bbox; - std::vector pts; + 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; + // 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_; + #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_) - {}; + // 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. + // 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; + // 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(); + leaf_nodes.push_back(node); + Leaf_node_handle nh = &leaf_nodes.back(); - return nh; - } + return nh; + } - // The internal node + // 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_true&) + { + return create_internal_node_use_extension(c); + } - Node_handle - create_internal_node(Point_container& c, const Tag_false&) - { - return create_internal_node(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(); + // 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); + 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); + int cd = nh->cutting_dimension(); + if(!c_low.empty()){ + nh->lower_low_val = c_low.tight_bounding_box().min_coord(cd); + nh->lower_high_val = c_low.tight_bounding_box().max_coord(cd); + } + else{ + nh->lower_low_val = nh->cutting_value(); + nh->lower_high_val = nh->cutting_value(); + } + if(!c.empty()){ + nh->upper_low_val = c.tight_bounding_box().min_coord(cd); + nh->upper_high_val = c.tight_bounding_box().max_coord(cd); + } + else{ + nh->upper_low_val = nh->cutting_value(); + nh->upper_high_val = nh->cutting_value(); + } - CGAL_assertion(nh->cutting_value() >= nh->low_val); - CGAL_assertion(nh->cutting_value() <= nh->high_val); + CGAL_assertion(nh->cutting_value() >= nh->lower_low_val); + CGAL_assertion(nh->cutting_value() <= nh->upper_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); - } + 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; - } + 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; + // 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); + 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); - } + 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; - } + 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); + 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() + { + // This function is not ready to be called when a tree already exists, one + // must call invalidate_built() first. + CGAL_assertion(!is_built()); + CGAL_assertion(!removed_); + 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]); } - - bool empty() const { - return pts.empty(); + 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()); } - 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; + //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]; } - -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 + 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; } -public: + pts.swap(ptstmp); - bool is_built() const - { - return built_; - } + data.clear(); - void invalidate_built() - { - if(is_built()){ - internal_nodes.clear(); - leaf_nodes.clear(); - data.clear(); - delete bbox; - built_ = false; - } - } + built_ = true; + } - void clear() - { - invalidate_built(); - pts.clear(); - removed_ = false; - } +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: - 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); + bool is_built() const + { + return built_; + } + + void invalidate_built() + { + if(removed_){ + // Walk the tree to collect the remaining points. + // Writing directly to pts would likely work, but better be safe. + std::vector ptstmp; + //ptstmp.resize(root()->num_items()); + root()->tree_items(std::back_inserter(ptstmp)); + pts.swap(ptstmp); + removed_=false; + CGAL_assertion(is_built()); // the rest of the cleanup must happen } - - 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); + 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) + { + invalidate_built(); + pts.push_back(p); + } + + template + void + insert(InputIterator first, InputIterator beyond) + { + 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(); - } +private: + struct Equal_by_coordinates { + SearchTraits const* traits; + Point_d const* pp; + bool operator()(Point_d const&q) const { + typename SearchTraits::Construct_cartesian_const_iterator_d ccci=traits->construct_cartesian_const_iterator_d_object(); + return std::equal(ccci(*pp), ccci(*pp,0), ccci(q)); } + }; + Equal_by_coordinates equal_by_coordinates(Point_d const&p){ + Equal_by_coordinates ret = { &traits(), &p }; + return ret; + } - //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); +public: + void + remove(const Point_d& p) + { + remove(p, equal_by_coordinates(p)); + } + + template + void + remove(const Point_d& p, Equal const& equal_to_p) + { +#if 0 + // This code could have quadratic runtime. + if (!is_built()) { + std::vector::iterator pi = std::find(pts.begin(), pts.end(), p); + // Precondition: the point must be there. + CGAL_assertion (pi != pts.end()); + pts.erase(pi); + return; } - - //Get the capacity of the underlying points vector. - size_t capacity() - { - return pts.capacity(); +#endif + // This does not actually remove points, and further insertions + // would make the points reappear, so we disallow it. + removed_ = true; + + CGAL_assertion_code(bool success = ) + remove_(p, 0, false, 0, false, root(), equal); + CGAL_assertion(success); + } +private: + template + bool remove_(const Point_d& p, + Internal_node_handle grandparent, bool islower, + Internal_node_handle parent, bool islower2, + Node_handle node, Equal const& equal_to_p) { + // Recurse to locate the point + if (!node->is_leaf()) { + Internal_node_handle newparent = static_cast(node); + // FIXME: This should be if(xcutting_dimension()] <= newparent->cutting_value()) { + if (remove_(p, parent, islower2, newparent, true, newparent->lower(), equal_to_p)) + return true; + } + //if (traits().construct_cartesian_const_iterator_d_object()(p)[newparent->cutting_dimension()] >= newparent->cutting_value()) + return remove_(p, parent, islower2, newparent, false, newparent->upper(), equal_to_p); + + CGAL_assertion(false); // Point was not found } - - 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; + // Actual removal + Leaf_node_handle lnode = static_cast(node); + if (lnode->size() > 1) { + iterator pi = std::find_if(lnode->begin(), lnode->end(), equal_to_p); + // FIXME: we should ensure this never happens + if (pi == lnode->end()) return false; + 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 (!equal_to_p(*lnode->begin())) { + // FIXME: we should ensure this never happens + return false; + } else if (grandparent) { + 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(); } + return true; + } - - 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; +public: + //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; + } - ~Kd_tree() { - if(is_built()){ - delete bbox; - } - } - + template + boost::optional + search_any_point(const FuzzyQueryItem& q) const + { + if(! pts.empty()){ - const SearchTraits& - traits() const - { - return traits_; + if(! is_built()){ + const_build(); + } + Kd_tree_rectangle b(*bbox); + return tree_root->search_any_point(q,b); } + return boost::none; + } - Node_const_handle - root() const - { - if(! is_built()){ - const_build(); - } - return tree_root; - } - Node_handle - root() - { - if(! is_built()){ - build(); - } - return tree_root; + ~Kd_tree() { + if(is_built()){ + delete bbox; } + } - 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 SearchTraits& + traits() const + { + return traits_; + } - const_iterator - begin() const - { - return pts.begin(); + Node_const_handle + root() const + { + if(! is_built()){ + const_build(); } - - const_iterator - end() const - { - return pts.end(); + return tree_root; + } + + Node_handle + root() + { + if(! is_built()){ + build(); } - - size_type - size() const - { - return pts.size(); + return tree_root; + } + + void + print() const + { + if(! is_built()){ + const_build(); } - - // 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; + 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; + } }; diff --git a/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree_node.h b/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree_node.h index d6d01439..49b0c022 100644 --- a/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree_node.h +++ b/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree_node.h @@ -28,10 +28,10 @@ namespace CGAL { - template + template class Kd_tree; - template < class TreeTraits, class Splitter, class UseExtendedNode > + template < class TreeTraits, class Splitter, class UseExtendedNode > class Kd_tree_node { friend class Kd_tree; @@ -52,7 +52,7 @@ namespace CGAL { bool leaf; - public : + public : Kd_tree_node(bool leaf_) :leaf(leaf_){} @@ -60,18 +60,18 @@ namespace CGAL { return leaf; } - std::size_t + std::size_t num_items() const { if (is_leaf()){ - Leaf_node_const_handle node = + Leaf_node_const_handle node = static_cast(this); return node->size(); } else { - Internal_node_const_handle node = + Internal_node_const_handle node = static_cast(this); - return node->lower()->num_items() + node->upper()->num_items(); + return node->lower()->num_items() + node->upper()->num_items(); } } @@ -80,48 +80,48 @@ namespace CGAL { { if (is_leaf()) return 1; else { - Internal_node_const_handle node = + Internal_node_const_handle node = static_cast(this); - return node->lower()->num_nodes() + node->upper()->num_nodes(); + return node->lower()->num_nodes() + node->upper()->num_nodes(); } } - int + int depth(const int current_max_depth) const { if (is_leaf()){ - return current_max_depth; + return current_max_depth; } else { - Internal_node_const_handle node = + Internal_node_const_handle node = static_cast(this); - return - (std::max)( node->lower()->depth(current_max_depth + 1), - node->upper()->depth(current_max_depth + 1)); + return + (std::max)( node->lower()->depth(current_max_depth + 1), + node->upper()->depth(current_max_depth + 1)); } } - int + int depth() const { - return depth(1); + return depth(1); } template - OutputIterator + OutputIterator tree_items(OutputIterator it) const { if (is_leaf()) { - Leaf_node_const_handle node = + Leaf_node_const_handle node = static_cast(this); - if (node->size()>0) - for (iterator i=node->begin(); i != node->end(); i++) - {*it=*i; ++it;} - } + if (node->size()>0) + for (iterator i=node->begin(); i != node->end(); i++) + {*it=*i; ++it;} + } else { - Internal_node_const_handle node = + Internal_node_const_handle node = static_cast(this); - it=node->lower()->tree_items(it); - it=node->upper()->tree_items(it); + it=node->lower()->tree_items(it); + it=node->upper()->tree_items(it); } return it; } @@ -133,14 +133,14 @@ namespace CGAL { if (is_leaf()) { Leaf_node_const_handle node = static_cast(this); - if (node->size()>0){ + if (node->size()>0){ return boost::make_optional(*(node->begin())); } - } + } else { Internal_node_const_handle node = static_cast(this); - result = node->lower()->any_tree_item(); + result = node->lower()->any_tree_item(); if(! result){ result = node->upper()->any_tree_item(); } @@ -149,75 +149,75 @@ namespace CGAL { } - void + void indent(int d) const { for(int i = 0; i < d; i++){ - std::cout << " "; + std::cout << " "; } } - void - print(int d = 0) const + void + print(int d = 0) const { if (is_leaf()) { - Leaf_node_const_handle node = + Leaf_node_const_handle node = static_cast(this); - indent(d); - std::cout << "leaf" << std::endl; - if (node->size()>0) - for (iterator i=node->begin(); i != node->end(); i++) - {indent(d);std::cout << *i << std::endl;} + indent(d); + std::cout << "leaf" << std::endl; + if (node->size()>0) + for (iterator i=node->begin(); i != node->end(); i++) + {indent(d);std::cout << *i << std::endl;} } else { - Internal_node_const_handle node = + Internal_node_const_handle node = static_cast(this); - indent(d); - std::cout << "lower tree" << std::endl; - node->lower()->print(d+1); - indent(d); - std::cout << "separator: dim = " << node->cutting_dimension() << " val = " << node->cutting_value() << std::endl; - indent(d); - std::cout << "upper tree" << std::endl; - node->upper()->print(d+1); + indent(d); + std::cout << "lower tree" << std::endl; + node->lower()->print(d+1); + indent(d); + std::cout << "separator: dim = " << node->cutting_dimension() << " val = " << node->cutting_value() << std::endl; + indent(d); + std::cout << "upper tree" << std::endl; + node->upper()->print(d+1); } } template - OutputIterator + OutputIterator search(OutputIterator it, const FuzzyQueryItem& q, - Kd_tree_rectangle& b) const + Kd_tree_rectangle& b) const { - if (is_leaf()) { - Leaf_node_const_handle node = + if (is_leaf()) { + Leaf_node_const_handle node = static_cast(this); - if (node->size()>0) - for (iterator i=node->begin(); i != node->end(); i++) - if (q.contains(*i)) - {*it++=*i;} + if (node->size()>0) + for (iterator i=node->begin(); i != node->end(); i++) + if (q.contains(*i)) + {*it++=*i;} } else { - Internal_node_const_handle node = + Internal_node_const_handle node = static_cast(this); - // after splitting b denotes the lower part of b - Kd_tree_rectangle b_upper(b); - b.split(b_upper, node->cutting_dimension(), - node->cutting_value()); - - if (q.outer_range_contains(b)) - it=node->lower()->tree_items(it); - else - if (q.inner_range_intersects(b)) - it=node->lower()->search(it,q,b); - if (q.outer_range_contains(b_upper)) - it=node->upper()->tree_items(it); - else - if (q.inner_range_intersects(b_upper)) - it=node->upper()->search(it,q,b_upper); + // after splitting b denotes the lower part of b + Kd_tree_rectangle b_upper(b); + b.split(b_upper, node->cutting_dimension(), + node->cutting_value()); + + if (q.outer_range_contains(b)) + it=node->lower()->tree_items(it); + else + if (q.inner_range_intersects(b)) + it=node->lower()->search(it,q,b); + if (q.outer_range_contains(b_upper)) + it=node->upper()->tree_items(it); + else + if (q.inner_range_intersects(b_upper)) + it=node->upper()->search(it,q,b_upper); }; - return it; + return it; } @@ -227,99 +227,99 @@ namespace CGAL { Kd_tree_rectangle& b) const { boost::optional result = boost::none; - if (is_leaf()) { - Leaf_node_const_handle node = + if (is_leaf()) { + Leaf_node_const_handle node = static_cast(this); - if (node->size()>0) - for (iterator i=node->begin(); i != node->end(); i++) - if (q.contains(*i)) - { result = *i; break; } + if (node->size()>0) + for (iterator i=node->begin(); i != node->end(); i++) + if (q.contains(*i)) + { result = *i; break; } } else { - Internal_node_const_handle node = + Internal_node_const_handle node = static_cast(this); - // after splitting b denotes the lower part of b - Kd_tree_rectangle b_upper(b); - b.split(b_upper, node->cutting_dimension(), - node->cutting_value()); - - if (q.outer_range_contains(b)){ + // after splitting b denotes the lower part of b + Kd_tree_rectangle b_upper(b); + b.split(b_upper, node->cutting_dimension(), + node->cutting_value()); + + if (q.outer_range_contains(b)){ result = node->lower()->any_tree_item(); - }else{ - if (q.inner_range_intersects(b)){ - result = node->lower()->search_any_point(q,b); + }else{ + if (q.inner_range_intersects(b)){ + result = node->lower()->search_any_point(q,b); } } if(result){ return result; } - if (q.outer_range_contains(b_upper)){ - result = node->upper()->any_tree_item(); - }else{ - if (q.inner_range_intersects(b_upper)) - result = node->upper()->search_any_point(q,b_upper); + if (q.outer_range_contains(b_upper)){ + result = node->upper()->any_tree_item(); + }else{ + if (q.inner_range_intersects(b_upper)) + result = node->upper()->search_any_point(q,b_upper); } } - return result; + return result; } }; - template < class TreeTraits, class Splitter, class UseExtendedNode > + template < class TreeTraits, class Splitter, class UseExtendedNode > class Kd_tree_leaf_node : public Kd_tree_node< TreeTraits, Splitter, UseExtendedNode >{ friend class Kd_tree; - + typedef typename Kd_tree::iterator iterator; typedef Kd_tree_node< TreeTraits, Splitter, UseExtendedNode> Base; typedef typename TreeTraits::Point_d Point_d; private: - + // private variables for leaf nodes boost::int32_t n; // denotes number of items in a leaf node iterator data; // iterator to data in leaf node - + public: - + // default constructor - Kd_tree_leaf_node() + Kd_tree_leaf_node() {} - Kd_tree_leaf_node(bool leaf_ ) + Kd_tree_leaf_node(bool leaf_ ) : Base(leaf_) {} - Kd_tree_leaf_node(bool leaf_,unsigned int n_ ) + Kd_tree_leaf_node(bool leaf_,unsigned int n_ ) : Base(leaf_), n(n_) {} // members for all nodes - + // members for leaf nodes only - inline - unsigned int - size() const - { + inline + unsigned int + size() const + { return n; } - - inline + + inline iterator - begin() const + begin() const { return data; } - inline - iterator - end() const + inline + iterator + end() const { return data + n; } - + inline void drop_last_point() @@ -331,7 +331,7 @@ namespace CGAL { - template < class TreeTraits, class Splitter, class UseExtendedNode> + template < class TreeTraits, class Splitter, class UseExtendedNode> class Kd_tree_internal_node : public Kd_tree_node< TreeTraits, Splitter, UseExtendedNode >{ friend class Kd_tree; @@ -344,7 +344,7 @@ namespace CGAL { typedef typename Kd_tree::Separator Separator; private: - + // private variables for internal nodes boost::int32_t cut_dim; FT cut_val; @@ -352,50 +352,53 @@ namespace CGAL { // private variables for extended internal nodes - FT low_val; - FT high_val; - + FT upper_low_val; + FT upper_high_val; + FT lower_low_val; + FT lower_high_val; + + public: // default constructor - Kd_tree_internal_node() + Kd_tree_internal_node() {} - Kd_tree_internal_node(bool leaf_) + Kd_tree_internal_node(bool leaf_) : Base(leaf_) {} - - + + // members for internal node and extended internal node - inline - Node_const_handle - lower() const + inline + Node_const_handle + lower() const { - return lower_ch; + return lower_ch; } - inline - Node_const_handle - upper() const + inline + Node_const_handle + upper() const { - return upper_ch; + return upper_ch; } - inline - Node_handle + inline + Node_handle lower() { - return lower_ch; + return lower_ch; } - inline - Node_handle + inline + Node_handle upper() { - return upper_ch; + return upper_ch; } - + inline void set_lower(Node_handle nh) @@ -417,47 +420,60 @@ namespace CGAL { cut_dim = sep.cutting_dimension(); cut_val = sep.cutting_value(); } - - inline - FT - cutting_value() const + + inline + FT + cutting_value() const { return cut_val; } - - inline - int - cutting_dimension() const + + inline + int + cutting_dimension() const { return cut_dim; } // members for extended internal node only - inline + inline + FT + upper_low_value() const + { + return upper_low_val; + } + + inline FT - low_value() const - { - return low_val; + upper_high_value() const + { + return upper_high_val; } - - inline + + inline FT - high_value() const + lower_low_value() const { - return high_val; + return lower_low_val; } - - /*Separator& - separator() + inline + FT + lower_high_value() const + { + return lower_high_val; + } + + /*Separator& + separator() { return Separator(cutting_dimension,cutting_value); }*/ - + };//internal node - template < class TreeTraits, class Splitter> + template < class TreeTraits, class Splitter> class Kd_tree_internal_node : public Kd_tree_node< TreeTraits, Splitter, Tag_false >{ friend class Kd_tree; @@ -470,54 +486,54 @@ namespace CGAL { typedef typename Kd_tree::Separator Separator; private: - + // private variables for internal nodes boost::uint8_t cut_dim; FT cut_val; Node_handle lower_ch, upper_ch; - + public: // default constructor - Kd_tree_internal_node() + Kd_tree_internal_node() {} - Kd_tree_internal_node(bool leaf_) + Kd_tree_internal_node(bool leaf_) : Base(leaf_) {} - - + + // members for internal node and extended internal node - inline - Node_const_handle - lower() const + inline + Node_const_handle + lower() const { - return lower_ch; + return lower_ch; } - inline - Node_const_handle - upper() const + inline + Node_const_handle + upper() const { - return upper_ch; + return upper_ch; } - inline - Node_handle + inline + Node_handle lower() { - return lower_ch; + return lower_ch; } - inline - Node_handle + inline + Node_handle upper() { - return upper_ch; + return upper_ch; } - + inline void set_lower(Node_handle nh) @@ -540,27 +556,27 @@ namespace CGAL { cut_dim = sep.cutting_dimension(); cut_val = sep.cutting_value(); } - - inline - FT - cutting_value() const + + inline + FT + cutting_value() const { return cut_val; } - - inline - int - cutting_dimension() const + + inline + int + cutting_dimension() const { return cut_dim; } - /* Separator& - separator() + /* Separator& + separator() { return Separator(cutting_dimension,cutting_value); }*/ - + };//internal node -- cgit v1.2.3 From 4109c9e203e37bc21b30228f609b0c7e1750a285 Mon Sep 17 00:00:00 2001 From: fgodi Date: Fri, 25 Nov 2016 14:55:17 +0000 Subject: compile git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1786 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 858679e1c90ce83e546dd60da2d82ede7b23272f --- .../include/gudhi/CGAL/Kd_tree.h | 9 +- .../CGAL/Orthogonal_incremental_neighbor_search.h | 497 ++++++++++----------- 2 files changed, 251 insertions(+), 255 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree.h b/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree.h index 16043b76..dbdf5259 100644 --- a/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree.h +++ b/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree.h @@ -389,13 +389,10 @@ public: return; } #endif - // This does not actually remove points, and further insertions - // would make the points reappear, so we disallow it. - removed_ = true; - - CGAL_assertion_code(bool success = ) - remove_(p, 0, false, 0, false, root(), equal); + bool success = remove_(p, 0, false, 0, false, root(), equal_to_p); CGAL_assertion(success); + + removed_ |= success; } private: template diff --git a/src/Bottleneck_distance/include/gudhi/CGAL/Orthogonal_incremental_neighbor_search.h b/src/Bottleneck_distance/include/gudhi/CGAL/Orthogonal_incremental_neighbor_search.h index 0e911f41..dbe707ed 100644 --- a/src/Bottleneck_distance/include/gudhi/CGAL/Orthogonal_incremental_neighbor_search.h +++ b/src/Bottleneck_distance/include/gudhi/CGAL/Orthogonal_incremental_neighbor_search.h @@ -32,7 +32,7 @@ namespace CGAL { - template ::type, class Splitter_ = Sliding_midpoint, class Tree_= Kd_tree > @@ -55,7 +55,7 @@ namespace CGAL { template struct Object_wrapper - { + { T object; Object_wrapper(const T& t):object(t){} const T& operator* () const { return object; } @@ -74,11 +74,11 @@ namespace CGAL { private: typedef std::vector Distance_vector; - + Distance_vector dists; Distance Orthogonal_distance_instance; - + FT multiplication_factor; Query_item query_point; @@ -95,15 +95,15 @@ namespace CGAL { bool search_nearest; - Priority_higher(bool search_the_nearest_neighbour) - : search_nearest(search_the_nearest_neighbour) - {} + Priority_higher(bool search_the_nearest_neighbour) + : search_nearest(search_the_nearest_neighbour) + {} //highest priority is smallest distance - bool - operator() (Node_with_distance* n1, Node_with_distance* n2) const - { - return (search_nearest) ? (CGAL::cpp11::get<1>(*n1) > CGAL::cpp11::get<1>(*n2)) : (CGAL::cpp11::get<1>(*n2) > CGAL::cpp11::get<1>(*n1)); + bool + operator() (Node_with_distance* n1, Node_with_distance* n2) const + { + return (search_nearest) ? (CGAL::cpp11::get<1>(*n1) > CGAL::cpp11::get<1>(*n2)) : (CGAL::cpp11::get<1>(*n2) > CGAL::cpp11::get<1>(*n1)); } }; @@ -113,43 +113,43 @@ namespace CGAL { bool search_nearest; - Distance_smaller(bool search_the_nearest_neighbour) - : search_nearest(search_the_nearest_neighbour) - {} + Distance_smaller(bool search_the_nearest_neighbour) + : search_nearest(search_the_nearest_neighbour) + {} //highest priority is smallest distance bool operator() (Point_with_transformed_distance* p1, Point_with_transformed_distance* p2) const - { - return (search_nearest) ? (p1->second > p2->second) : (p2->second > p1->second); + { + return (search_nearest) ? (p1->second > p2->second) : (p2->second > p1->second); } }; std::priority_queue PriorityQueue; + Priority_higher> PriorityQueue; public: std::priority_queue Item_PriorityQueue; + Distance_smaller> Item_PriorityQueue; public: int reference_count; - + // constructor Iterator_implementation(const Tree& tree,const Query_item& q, const Distance& tr, - FT Eps=FT(0.0), bool search_nearest=true) - : traits(tree.traits()),number_of_neighbours_computed(0), number_of_internal_nodes_visited(0), - number_of_leaf_nodes_visited(0), number_of_items_visited(0), - Orthogonal_distance_instance(tr), multiplication_factor(Orthogonal_distance_instance.transformed_distance(FT(1.0)+Eps)), - query_point(q), search_nearest_neighbour(search_nearest), - PriorityQueue(Priority_higher(search_nearest)), Item_PriorityQueue(Distance_smaller(search_nearest)), - reference_count(1) - - + FT Eps=FT(0.0), bool search_nearest=true) + : traits(tree.traits()),number_of_neighbours_computed(0), number_of_internal_nodes_visited(0), + number_of_leaf_nodes_visited(0), number_of_items_visited(0), + Orthogonal_distance_instance(tr), multiplication_factor(Orthogonal_distance_instance.transformed_distance(FT(1.0)+Eps)), + query_point(q), search_nearest_neighbour(search_nearest), + PriorityQueue(Priority_higher(search_nearest)), Item_PriorityQueue(Distance_smaller(search_nearest)), + reference_count(1) + + { if (tree.empty()) return; @@ -160,12 +160,12 @@ namespace CGAL { for(int i=0 ; i - operator++(int) + operator++(int) { Object_wrapper result( *(Item_PriorityQueue.top()) ); ++*this; @@ -217,252 +217,251 @@ namespace CGAL { } // Print statistics of the general priority search process. - std::ostream& + std::ostream& statistics (std::ostream& s) const { - s << "Orthogonal priority search statistics:" - << std::endl; - s << "Number of internal nodes visited:" - << number_of_internal_nodes_visited << std::endl; - s << "Number of leaf nodes visited:" - << number_of_leaf_nodes_visited << std::endl; - s << "Number of items visited:" - << number_of_items_visited << std::endl; - s << "Number of neighbours computed:" - << number_of_neighbours_computed << std::endl; + s << "Orthogonal priority search statistics:" + << std::endl; + s << "Number of internal nodes visited:" + << number_of_internal_nodes_visited << std::endl; + s << "Number of leaf nodes visited:" + << number_of_leaf_nodes_visited << std::endl; + s << "Number of items visited:" + << number_of_items_visited << std::endl; + s << "Number of neighbours computed:" + << number_of_neighbours_computed << std::endl; return s; } //destructor - ~Iterator_implementation() + ~Iterator_implementation() { - while (!PriorityQueue.empty()) { - Node_with_distance* The_top=PriorityQueue.top(); - PriorityQueue.pop(); - delete The_top; - } - while (!Item_PriorityQueue.empty()) { - Point_with_transformed_distance* The_top=Item_PriorityQueue.top(); - Item_PriorityQueue.pop(); - delete The_top; + while (!PriorityQueue.empty()) { + Node_with_distance* The_top=PriorityQueue.top(); + PriorityQueue.pop(); + delete The_top; + } + while (!Item_PriorityQueue.empty()) { + Point_with_transformed_distance* The_top=Item_PriorityQueue.top(); + Item_PriorityQueue.pop(); + delete The_top; } } private: - void - Delete_the_current_item_top() + void + Delete_the_current_item_top() { Point_with_transformed_distance* The_item_top=Item_PriorityQueue.top(); Item_PriorityQueue.pop(); delete The_item_top; } - void - Compute_the_next_nearest_neighbour() + void + Compute_the_next_nearest_neighbour() { // compute the next item bool next_neighbour_found=false; if (!(Item_PriorityQueue.empty())) { - next_neighbour_found= - (multiplication_factor*rd > Item_PriorityQueue.top()->second); + next_neighbour_found= + (multiplication_factor*rd > Item_PriorityQueue.top()->second); } - typename SearchTraits::Construct_cartesian_const_iterator_d construct_it=traits.construct_cartesian_const_iterator_d_object(); - typename SearchTraits::Cartesian_const_iterator_d query_point_it = construct_it(query_point); + typename SearchTraits::Construct_cartesian_const_iterator_d construct_it=traits.construct_cartesian_const_iterator_d_object(); + typename SearchTraits::Cartesian_const_iterator_d query_point_it = construct_it(query_point); // otherwise browse the tree further while ((!next_neighbour_found) && (!PriorityQueue.empty())) { - Node_with_distance* The_node_top=PriorityQueue.top(); - Node_const_handle N= CGAL::cpp11::get<0>(*The_node_top); + Node_with_distance* The_node_top=PriorityQueue.top(); + Node_const_handle N= CGAL::cpp11::get<0>(*The_node_top); dists = CGAL::cpp11::get<2>(*The_node_top); - PriorityQueue.pop(); - delete The_node_top; - FT copy_rd=rd; - while (!(N->is_leaf())) { // compute new distance + PriorityQueue.pop(); + delete The_node_top; + FT copy_rd=rd; + while (!(N->is_leaf())) { // compute new distance typename Tree::Internal_node_const_handle node = static_cast(N); - number_of_internal_nodes_visited++; - int new_cut_dim=node->cutting_dimension(); - FT new_rd,dst = dists[new_cut_dim]; - FT val = *(query_point_it + new_cut_dim); - FT diff1 = val - node->high_value(); - FT diff2 = val - node->low_value(); - if (diff1 + diff2 < FT(0.0)) { + number_of_internal_nodes_visited++; + int new_cut_dim=node->cutting_dimension(); + FT new_rd,dst = dists[new_cut_dim]; + FT val = *(query_point_it + new_cut_dim); + FT diff1 = val - node->upper_low_value(); + FT diff2 = val - node->lower_high_value(); + if (diff1 + diff2 < FT(0.0)) { new_rd= - Orthogonal_distance_instance.new_distance(copy_rd,dst,diff1,new_cut_dim); - - CGAL_assertion(new_rd >= copy_rd); + Orthogonal_distance_instance.new_distance(copy_rd,dst,diff1,new_cut_dim); + + CGAL_assertion(new_rd >= copy_rd); dists[new_cut_dim] = diff1; Node_with_distance *Upper_Child = - new Node_with_distance(node->upper(), new_rd, dists); - PriorityQueue.push(Upper_Child); + new Node_with_distance(node->upper(), new_rd, dists); + PriorityQueue.push(Upper_Child); dists[new_cut_dim] = dst; - N=node->lower(); + N=node->lower(); - } - else { // compute new distance - new_rd=Orthogonal_distance_instance.new_distance(copy_rd,dst,diff2,new_cut_dim); - CGAL_assertion(new_rd >= copy_rd); + } + else { // compute new distance + new_rd=Orthogonal_distance_instance.new_distance(copy_rd,dst,diff2,new_cut_dim); + CGAL_assertion(new_rd >= copy_rd); dists[new_cut_dim] = diff2; - Node_with_distance *Lower_Child = - new Node_with_distance(node->lower(), new_rd, dists); - PriorityQueue.push(Lower_Child); + Node_with_distance *Lower_Child = + new Node_with_distance(node->lower(), new_rd, dists); + PriorityQueue.push(Lower_Child); dists[new_cut_dim] = dst; - N=node->upper(); - } - } - // n is a leaf + N=node->upper(); + } + } + // n is a leaf typename Tree::Leaf_node_const_handle node = static_cast(N); - number_of_leaf_nodes_visited++; - if (node->size() > 0) { - for (typename Tree::iterator it=node->begin(); it != node->end(); it++) { - number_of_items_visited++; - FT distance_to_query_point= - Orthogonal_distance_instance.transformed_distance(query_point,*it); - Point_with_transformed_distance *NN_Candidate= - new Point_with_transformed_distance(*it,distance_to_query_point); - Item_PriorityQueue.push(NN_Candidate); - } - // old top of PriorityQueue has been processed, - // hence update rd - - if (!(PriorityQueue.empty())) { - rd = CGAL::cpp11::get<1>(*PriorityQueue.top()); - next_neighbour_found = - (multiplication_factor*rd > - Item_PriorityQueue.top()->second); - } - else // priority queue empty => last neighbour found - { - next_neighbour_found=true; - } - - number_of_neighbours_computed++; - } + number_of_leaf_nodes_visited++; + if (node->size() > 0) { + for (typename Tree::iterator it=node->begin(); it != node->end(); it++) { + number_of_items_visited++; + FT distance_to_query_point= + Orthogonal_distance_instance.transformed_distance(query_point,*it); + Point_with_transformed_distance *NN_Candidate= + new Point_with_transformed_distance(*it,distance_to_query_point); + Item_PriorityQueue.push(NN_Candidate); + } + // old top of PriorityQueue has been processed, + // hence update rd + + if (!(PriorityQueue.empty())) { + rd = CGAL::cpp11::get<1>(*PriorityQueue.top()); + next_neighbour_found = + (multiplication_factor*rd > + Item_PriorityQueue.top()->second); + } + else // priority queue empty => last neighbour found + { + next_neighbour_found=true; + } + + number_of_neighbours_computed++; + } } // next_neighbour_found or priority queue is empty // in the latter case also the item priority quee is empty } - void - Compute_the_next_furthest_neighbour() + void + Compute_the_next_furthest_neighbour() { // compute the next item bool next_neighbour_found=false; if (!(Item_PriorityQueue.empty())) { - next_neighbour_found= - (rd < multiplication_factor*Item_PriorityQueue.top()->second); + next_neighbour_found= + (rd < multiplication_factor*Item_PriorityQueue.top()->second); } - typename SearchTraits::Construct_cartesian_const_iterator_d construct_it=traits.construct_cartesian_const_iterator_d_object(); - typename SearchTraits::Cartesian_const_iterator_d query_point_it = construct_it(query_point); + typename SearchTraits::Construct_cartesian_const_iterator_d construct_it=traits.construct_cartesian_const_iterator_d_object(); + typename SearchTraits::Cartesian_const_iterator_d query_point_it = construct_it(query_point); // otherwise browse the tree further while ((!next_neighbour_found) && (!PriorityQueue.empty())) { - Node_with_distance* The_node_top=PriorityQueue.top(); - Node_const_handle N= CGAL::cpp11::get<0>(*The_node_top); + Node_with_distance* The_node_top=PriorityQueue.top(); + Node_const_handle N= CGAL::cpp11::get<0>(*The_node_top); dists = CGAL::cpp11::get<2>(*The_node_top); - PriorityQueue.pop(); - delete The_node_top; - FT copy_rd=rd; - while (!(N->is_leaf())) { // compute new distance + PriorityQueue.pop(); + delete The_node_top; + FT copy_rd=rd; + while (!(N->is_leaf())) { // compute new distance typename Tree::Internal_node_const_handle node = static_cast(N); - number_of_internal_nodes_visited++; - int new_cut_dim=node->cutting_dimension(); - FT new_rd,dst = dists[new_cut_dim]; - FT val = *(query_point_it + new_cut_dim); - FT diff1 = val - node->high_value(); - FT diff2 = val - node->low_value(); - if (diff1 + diff2 < FT(0.0)) { + number_of_internal_nodes_visited++; + int new_cut_dim=node->cutting_dimension(); + FT new_rd,dst = dists[new_cut_dim]; + FT val = *(query_point_it + new_cut_dim); + FT diff1 = val - node->upper_low_value(); + FT diff2 = val - node->lower_high_value(); + if (diff1 + diff2 < FT(0.0)) { + diff1 = val - node->upper_high_value(); new_rd= - Orthogonal_distance_instance.new_distance(copy_rd,dst,diff1,new_cut_dim); - - CGAL_assertion(new_rd >= copy_rd); - Node_with_distance *Lower_Child = - new Node_with_distance(node->lower(), copy_rd, dists); - PriorityQueue.push(Lower_Child); - N=node->upper(); + Orthogonal_distance_instance.new_distance(copy_rd,dst,diff1,new_cut_dim); + Node_with_distance *Lower_Child = + new Node_with_distance(node->lower(), copy_rd, dists); + PriorityQueue.push(Lower_Child); + N=node->upper(); dists[new_cut_dim] = diff1; - copy_rd=new_rd; - - } - else { // compute new distance - new_rd=Orthogonal_distance_instance.new_distance(copy_rd,dst,diff2,new_cut_dim); - CGAL_assertion(new_rd >= copy_rd); - Node_with_distance *Upper_Child = - new Node_with_distance(node->upper(), copy_rd, dists); - PriorityQueue.push(Upper_Child); - N=node->lower(); + copy_rd=new_rd; + + } + else { // compute new distance + diff2 = val - node->lower_low_value(); + new_rd=Orthogonal_distance_instance.new_distance(copy_rd,dst,diff2,new_cut_dim); + Node_with_distance *Upper_Child = + new Node_with_distance(node->upper(), copy_rd, dists); + PriorityQueue.push(Upper_Child); + N=node->lower(); dists[new_cut_dim] = diff2; - copy_rd=new_rd; - } - } - // n is a leaf + copy_rd=new_rd; + } + } + // n is a leaf typename Tree::Leaf_node_const_handle node = static_cast(N); - number_of_leaf_nodes_visited++; - if (node->size() > 0) { - for (typename Tree::iterator it=node->begin(); it != node->end(); it++) { - number_of_items_visited++; - FT distance_to_query_point= - Orthogonal_distance_instance.transformed_distance(query_point,*it); - Point_with_transformed_distance *NN_Candidate= - new Point_with_transformed_distance(*it,distance_to_query_point); - Item_PriorityQueue.push(NN_Candidate); - } - // old top of PriorityQueue has been processed, - // hence update rd - - if (!(PriorityQueue.empty())) { - rd = CGAL::cpp11::get<1>(*PriorityQueue.top()); - next_neighbour_found = - (multiplication_factor*rd < - Item_PriorityQueue.top()->second); - } - else // priority queue empty => last neighbour found - { - next_neighbour_found=true; - } - - number_of_neighbours_computed++; - } + number_of_leaf_nodes_visited++; + if (node->size() > 0) { + for (typename Tree::iterator it=node->begin(); it != node->end(); it++) { + number_of_items_visited++; + FT distance_to_query_point= + Orthogonal_distance_instance.transformed_distance(query_point,*it); + Point_with_transformed_distance *NN_Candidate= + new Point_with_transformed_distance(*it,distance_to_query_point); + Item_PriorityQueue.push(NN_Candidate); + } + // old top of PriorityQueue has been processed, + // hence update rd + + if (!(PriorityQueue.empty())) { + rd = CGAL::cpp11::get<1>(*PriorityQueue.top()); + next_neighbour_found = + (multiplication_factor*rd < + Item_PriorityQueue.top()->second); + } + else // priority queue empty => last neighbour found + { + next_neighbour_found=true; + } + + number_of_neighbours_computed++; + } } // next_neighbour_found or priority queue is empty // in the latter case also the item priority quee is empty } }; // class Iterator_implementaion - - + + public: class iterator; typedef iterator const_iterator; // constructor - Orthogonal_incremental_neighbor_search(const Tree& tree, - const Query_item& q, FT Eps = FT(0.0), - bool search_nearest=true, const Distance& tr=Distance()) + Orthogonal_incremental_neighbor_search(const Tree& tree, + const Query_item& q, FT Eps = FT(0.0), + bool search_nearest=true, const Distance& tr=Distance()) : m_tree(tree),m_query(q),m_dist(tr),m_Eps(Eps),m_search_nearest(search_nearest) {} - iterator + iterator begin() const { return iterator(m_tree,m_query,m_dist,m_Eps,m_search_nearest); } - iterator + iterator end() const { return iterator(); } - std::ostream& - statistics(std::ostream& s) + std::ostream& + statistics(std::ostream& s) { begin()->statistics(s); return s; @@ -490,24 +489,24 @@ namespace CGAL { public: // default constructor - iterator() + iterator() : Ptr_implementation(0) {} - int - the_number_of_items_visited() + int + the_number_of_items_visited() { return Ptr_implementation->number_of_items_visited; } // constructor - iterator(const Tree& tree,const Query_item& q, const Distance& tr=Distance(), FT eps=FT(0.0), - bool search_nearest=true) - : Ptr_implementation(new Iterator_implementation(tree, q, tr, eps, search_nearest)) - {} + iterator(const Tree& tree,const Query_item& q, const Distance& tr=Distance(), FT eps=FT(0.0), + bool search_nearest=true) + : Ptr_implementation(new Iterator_implementation(tree, q, tr, eps, search_nearest)) + {} // copy constructor - iterator(const iterator& Iter) + iterator(const iterator& Iter) { Ptr_implementation = Iter.Ptr_implementation; if (Ptr_implementation != 0) Ptr_implementation->reference_count++; @@ -523,25 +522,25 @@ namespace CGAL { if (Ptr_implementation != 0) Ptr_implementation->reference_count++; } return *this; - } - - - const Point_with_transformed_distance& - operator* () const + } + + + const Point_with_transformed_distance& + operator* () const { - return *(*Ptr_implementation); + return *(*Ptr_implementation); } - + // -> operator const Point_with_transformed_distance* - operator-> () const + operator-> () const { - return &*(*Ptr_implementation); + return &*(*Ptr_implementation); } // prefix operator - iterator& - operator++() + iterator& + operator++() { ++(*Ptr_implementation); return *this; @@ -549,47 +548,47 @@ namespace CGAL { // postfix operator Object_wrapper - operator++(int) + operator++(int) { - return (*Ptr_implementation)++; + return (*Ptr_implementation)++; } - bool - operator==(const iterator& It) const + bool + operator==(const iterator& It) const { if ( - ((Ptr_implementation == 0) || - Ptr_implementation->Item_PriorityQueue.empty()) && - ((It.Ptr_implementation == 0) || - It.Ptr_implementation->Item_PriorityQueue.empty()) - ) - return true; + ((Ptr_implementation == 0) || + Ptr_implementation->Item_PriorityQueue.empty()) && + ((It.Ptr_implementation == 0) || + It.Ptr_implementation->Item_PriorityQueue.empty()) + ) + return true; // else return (Ptr_implementation == It.Ptr_implementation); } - bool - operator!=(const iterator& It) const + bool + operator!=(const iterator& It) const { return !(*this == It); } - std::ostream& - statistics (std::ostream& s) + std::ostream& + statistics (std::ostream& s) { - Ptr_implementation->statistics(s); + Ptr_implementation->statistics(s); return s; } - ~iterator() + ~iterator() { if (Ptr_implementation != 0) { - Ptr_implementation->reference_count--; - if (Ptr_implementation->reference_count==0) { - delete Ptr_implementation; - Ptr_implementation = 0; - } + Ptr_implementation->reference_count--; + if (Ptr_implementation->reference_count==0) { + delete Ptr_implementation; + Ptr_implementation = 0; + } } } @@ -600,17 +599,17 @@ namespace CGAL { const Tree& m_tree; Query_item m_query; Distance m_dist; - FT m_Eps; + FT m_Eps; bool m_search_nearest; - }; // class + }; // class template - void swap (typename Orthogonal_incremental_neighbor_search::iterator& x, - typename Orthogonal_incremental_neighbor_search::iterator& y) + void swap (typename Orthogonal_incremental_neighbor_search::iterator& x, + typename Orthogonal_incremental_neighbor_search::iterator& y) { - typename Orthogonal_incremental_neighbor_search::iterator::Iterator_implementation *tmp = x.Ptr_implementation; x.Ptr_implementation = y.Ptr_implementation; -- cgit v1.2.3 From aa6960f50b6a9e20e5361b4dc87ac03a33dab1fc Mon Sep 17 00:00:00 2001 From: fgodi Date: Fri, 25 Nov 2016 15:06:20 +0000 Subject: splitters.h added git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1787 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 751f595daf4fb8a53a3a4aada2f591418ddf909b --- .../include/gudhi/CGAL/Splitters.h | 313 +++++++++++++++++++++ 1 file changed, 313 insertions(+) create mode 100644 src/Bottleneck_distance/include/gudhi/CGAL/Splitters.h (limited to 'src') diff --git a/src/Bottleneck_distance/include/gudhi/CGAL/Splitters.h b/src/Bottleneck_distance/include/gudhi/CGAL/Splitters.h new file mode 100644 index 00000000..e58a593d --- /dev/null +++ b/src/Bottleneck_distance/include/gudhi/CGAL/Splitters.h @@ -0,0 +1,313 @@ +// Copyright (c) 2002-2011 Utrecht University (The Netherlands). +// 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 () + +// Defines rules used for constructing a split node. That is, it implements, +// in several ways, the concept +// Boxtree_splitter. + +#ifndef CGAL_SPLITTERS_H +#define CGAL_SPLITTERS_H + +#include +#include + +namespace CGAL { + + template + class Splitter_base { + private: + unsigned int the_bucket_size; + FT the_aspect_ratio; + + public: + //default bucket_size should be 10 + Splitter_base(unsigned int bucket_size = 10, + FT aspect_ratio = FT(3)) + : the_bucket_size(bucket_size), + the_aspect_ratio(aspect_ratio) + {} + + FT + aspect_ratio() const + { + return the_aspect_ratio; + } + + unsigned int + bucket_size() const + { + return the_bucket_size; + } + + }; + + + template > + class Median_of_max_spread + : public Splitter_base + { + + typedef Splitter_base Base; + public: + typedef typename SearchTraits::FT FT; + typedef Point_container Container; + typedef Separator_ Separator; + + Median_of_max_spread() + : Base() + {} + + Median_of_max_spread(unsigned int bucket_size) + : Base(bucket_size) + {} + + void + operator() (Separator& sep, + Container& c0, + Container& c1) const + { + sep=Separator(c0.max_tight_span_coord(),FT(0)); + sep.set_cutting_value(c0.median(sep.cutting_dimension())); + c0.split(c1,sep,true); + } + }; + + template > + class Fair + : public Splitter_base + { + + typedef Splitter_base Base; + public: + typedef typename SearchTraits::FT FT; + typedef Point_container Container; + typedef Separator_ Separator; + + Fair() + : Base() + {} + + Fair(unsigned int bucket_size, + FT aspect_ratio=FT(3)) + : Base(bucket_size, aspect_ratio) + {} + + void + operator()(Separator& sep, Container& c0, Container& c1) const + { + // find legal cut with max spread + sep=Separator(c0.max_tight_span_coord_balanced(this->aspect_ratio()), + FT(0)); + sep.set_cutting_value(c0.balanced_fair(sep.cutting_dimension(), + this->aspect_ratio())); + c0.split(c1,sep); + } + }; + + template > + class Sliding_fair + : public Splitter_base + { + + typedef Splitter_base Base; + + public: + typedef typename SearchTraits::FT FT; + typedef Point_container Container; + typedef Separator_ Separator; + + Sliding_fair() + : Base() + {} + + Sliding_fair(unsigned int bucket_size, + FT aspect_ratio=FT(3)) + : Base(bucket_size, aspect_ratio) + {} + + void + operator() (Separator& sep, Container& c0, Container& c1) const + { + // find legal cut with max spread + + sep = Separator(c0.max_tight_span_coord_balanced(this->aspect_ratio()), + FT(0)); + + sep.set_cutting_value(c0.balanced_sliding_fair(sep.cutting_dimension(), + this->aspect_ratio())); + c0.split(c1,sep,true); + } + }; + + + template > + class Sliding_midpoint + : public Splitter_base + { + + typedef Splitter_base Base; + + public: + typedef typename SearchTraits::FT FT; + typedef Point_container Container; + typedef Separator_ Separator; + + Sliding_midpoint() + : Base() + {} + + Sliding_midpoint(unsigned int bucket_size) + : Base(bucket_size) + {} + + void + operator()(Separator& sep, Container& c0, Container& c1) const + { + CGAL_assertion(c0.is_valid()); + CGAL_assertion(c1.is_valid()); + int cutdim = c0.max_span_coord(); + + //Bugfix: avoid linear tree in degenerated cases + if(c0.tight_bounding_box().min_coord(cutdim) != c0.tight_bounding_box().max_coord(cutdim)){ + sep = Separator(cutdim, + (c0.max_span_upper() + c0.max_span_lower())/FT(2)); + } + else{ + cutdim = c0.max_tight_span_coord(); + sep = Separator(cutdim, + (c0.max_tight_span_upper() + c0.max_tight_span_lower())/FT(2)); + } + + FT max_span_lower = + c0.tight_bounding_box().min_coord(cutdim); + + CGAL_assertion(max_span_lower >= c0.bounding_box().min_coord(cutdim)); + FT max_span_upper = + c0.tight_bounding_box().max_coord(cutdim); + + CGAL_assertion(max_span_upper <= c0.bounding_box().max_coord(cutdim)); + if (max_span_upper <= sep.cutting_value()) { + sep.set_cutting_value(max_span_upper); + }; + if (max_span_lower >= sep.cutting_value()) { + sep.set_cutting_value(max_span_lower); + }; + c0.split(c1,sep,true); + } + }; + + template > + class Median_of_rectangle + : public Splitter_base + { + + typedef Splitter_base Base; + + public: + typedef typename SearchTraits::FT FT; + typedef Point_container Container; + typedef Separator_ Separator; + + + Median_of_rectangle() + : Base() + {} + + Median_of_rectangle(unsigned int bucket_size) + : Base(bucket_size) + {} + + void + operator() (Separator& sep, Container& c0, Container& c1) const + { + sep = Separator(c0.max_span_coord(),FT(0)); + sep.set_cutting_value(c0.median(sep.cutting_dimension())); + c0.split(c1,sep,true); + } + }; + + template > + class Midpoint_of_max_spread + : public Splitter_base + { + typedef Splitter_base Base; + + public: + typedef typename SearchTraits::FT FT; + typedef Point_container Container; + typedef Separator_ Separator; + + + Midpoint_of_max_spread() + : Base() + {} + + Midpoint_of_max_spread(unsigned int bucket_size) + : Base(bucket_size) + {} + + void + operator()(Separator& sep, Container& c0, Container& c1) const + { + sep = Separator(c0.max_tight_span_coord(), + (c0.max_tight_span_upper() + c0.max_tight_span_lower())/FT(2)); + c0.split(c1,sep); + } + }; + + template > + class Midpoint_of_rectangle + : public Splitter_base + { + + typedef Splitter_base Base; + public: + typedef typename SearchTraits::FT FT; + typedef Point_container Container; + typedef Separator_ Separator; + + + Midpoint_of_rectangle() + : Base() + {} + + Midpoint_of_rectangle(unsigned int bucket_size) + : Base(bucket_size) + {} + + void + operator()(Separator& sep, Container& c0, Container& c1) const + { + sep = Separator(c0.max_span_coord(), + (c0.max_span_upper() + c0.max_span_lower())/FT(2)); + c0.split(c1,sep); + } + + }; + +} // namespace CGAL +#endif // CGAL_SPLITTERS -- cgit v1.2.3 From e9dd788438bff7289ddff1e0ade2de0f031a2f9b Mon Sep 17 00:00:00 2001 From: fgodi Date: Mon, 28 Nov 2016 09:57:43 +0000 Subject: Bug fix git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1789 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: f2c3ef0dab1a0d80cfcf0018da83dd2b6b9a9ef1 --- .../include/gudhi/CGAL/Kd_tree.h | 14 +- .../include/gudhi/CGAL/Kd_tree_node.h | 2 +- .../include/gudhi/CGAL/Splitters.h | 313 --------------------- .../include/gudhi/Neighbors_finder.h | 63 +++-- .../include/gudhi/Persistence_diagrams_graph.h | 2 +- .../include/gudhi/Planar_neighbors_finder.h | 156 ---------- .../test/bottleneck_unit_test.cpp | 30 -- 7 files changed, 48 insertions(+), 532 deletions(-) delete mode 100644 src/Bottleneck_distance/include/gudhi/CGAL/Splitters.h delete mode 100644 src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h (limited to 'src') diff --git a/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree.h b/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree.h index dbdf5259..f085b0da 100644 --- a/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree.h +++ b/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree.h @@ -392,24 +392,26 @@ public: bool success = remove_(p, 0, false, 0, false, root(), equal_to_p); CGAL_assertion(success); - removed_ |= success; + // Do not set the flag is the tree has been cleared. + if(is_built()) + removed_ |= success; } private: template bool remove_(const Point_d& p, - Internal_node_handle grandparent, bool islower, - Internal_node_handle parent, bool islower2, + Internal_node_handle grandparent, bool parent_islower, + Internal_node_handle parent, bool islower, Node_handle node, Equal const& equal_to_p) { // Recurse to locate the point if (!node->is_leaf()) { Internal_node_handle newparent = static_cast(node); // FIXME: This should be if(xcutting_dimension()] <= newparent->cutting_value()) { - if (remove_(p, parent, islower2, newparent, true, newparent->lower(), equal_to_p)) + if (remove_(p, parent, islower, newparent, true, newparent->lower(), equal_to_p)) return true; } //if (traits().construct_cartesian_const_iterator_d_object()(p)[newparent->cutting_dimension()] >= newparent->cutting_value()) - return remove_(p, parent, islower2, newparent, false, newparent->upper(), equal_to_p); + return remove_(p, parent, islower, newparent, false, newparent->upper(), equal_to_p); CGAL_assertion(false); // Point was not found } @@ -431,7 +433,7 @@ private: return false; } else if (grandparent) { Node_handle brother = islower ? parent->upper() : parent->lower(); - if (islower2) + if (parent_islower) grandparent->set_lower(brother); else grandparent->set_upper(brother); diff --git a/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree_node.h b/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree_node.h index 49b0c022..909ee260 100644 --- a/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree_node.h +++ b/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree_node.h @@ -21,7 +21,7 @@ #ifndef CGAL_KD_TREE_NODE_H #define CGAL_KD_TREE_NODE_H -#include "Splitters.h" +#include "CGAL/Splitters.h" #include #include diff --git a/src/Bottleneck_distance/include/gudhi/CGAL/Splitters.h b/src/Bottleneck_distance/include/gudhi/CGAL/Splitters.h deleted file mode 100644 index e58a593d..00000000 --- a/src/Bottleneck_distance/include/gudhi/CGAL/Splitters.h +++ /dev/null @@ -1,313 +0,0 @@ -// Copyright (c) 2002-2011 Utrecht University (The Netherlands). -// 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 () - -// Defines rules used for constructing a split node. That is, it implements, -// in several ways, the concept -// Boxtree_splitter. - -#ifndef CGAL_SPLITTERS_H -#define CGAL_SPLITTERS_H - -#include -#include - -namespace CGAL { - - template - class Splitter_base { - private: - unsigned int the_bucket_size; - FT the_aspect_ratio; - - public: - //default bucket_size should be 10 - Splitter_base(unsigned int bucket_size = 10, - FT aspect_ratio = FT(3)) - : the_bucket_size(bucket_size), - the_aspect_ratio(aspect_ratio) - {} - - FT - aspect_ratio() const - { - return the_aspect_ratio; - } - - unsigned int - bucket_size() const - { - return the_bucket_size; - } - - }; - - - template > - class Median_of_max_spread - : public Splitter_base - { - - typedef Splitter_base Base; - public: - typedef typename SearchTraits::FT FT; - typedef Point_container Container; - typedef Separator_ Separator; - - Median_of_max_spread() - : Base() - {} - - Median_of_max_spread(unsigned int bucket_size) - : Base(bucket_size) - {} - - void - operator() (Separator& sep, - Container& c0, - Container& c1) const - { - sep=Separator(c0.max_tight_span_coord(),FT(0)); - sep.set_cutting_value(c0.median(sep.cutting_dimension())); - c0.split(c1,sep,true); - } - }; - - template > - class Fair - : public Splitter_base - { - - typedef Splitter_base Base; - public: - typedef typename SearchTraits::FT FT; - typedef Point_container Container; - typedef Separator_ Separator; - - Fair() - : Base() - {} - - Fair(unsigned int bucket_size, - FT aspect_ratio=FT(3)) - : Base(bucket_size, aspect_ratio) - {} - - void - operator()(Separator& sep, Container& c0, Container& c1) const - { - // find legal cut with max spread - sep=Separator(c0.max_tight_span_coord_balanced(this->aspect_ratio()), - FT(0)); - sep.set_cutting_value(c0.balanced_fair(sep.cutting_dimension(), - this->aspect_ratio())); - c0.split(c1,sep); - } - }; - - template > - class Sliding_fair - : public Splitter_base - { - - typedef Splitter_base Base; - - public: - typedef typename SearchTraits::FT FT; - typedef Point_container Container; - typedef Separator_ Separator; - - Sliding_fair() - : Base() - {} - - Sliding_fair(unsigned int bucket_size, - FT aspect_ratio=FT(3)) - : Base(bucket_size, aspect_ratio) - {} - - void - operator() (Separator& sep, Container& c0, Container& c1) const - { - // find legal cut with max spread - - sep = Separator(c0.max_tight_span_coord_balanced(this->aspect_ratio()), - FT(0)); - - sep.set_cutting_value(c0.balanced_sliding_fair(sep.cutting_dimension(), - this->aspect_ratio())); - c0.split(c1,sep,true); - } - }; - - - template > - class Sliding_midpoint - : public Splitter_base - { - - typedef Splitter_base Base; - - public: - typedef typename SearchTraits::FT FT; - typedef Point_container Container; - typedef Separator_ Separator; - - Sliding_midpoint() - : Base() - {} - - Sliding_midpoint(unsigned int bucket_size) - : Base(bucket_size) - {} - - void - operator()(Separator& sep, Container& c0, Container& c1) const - { - CGAL_assertion(c0.is_valid()); - CGAL_assertion(c1.is_valid()); - int cutdim = c0.max_span_coord(); - - //Bugfix: avoid linear tree in degenerated cases - if(c0.tight_bounding_box().min_coord(cutdim) != c0.tight_bounding_box().max_coord(cutdim)){ - sep = Separator(cutdim, - (c0.max_span_upper() + c0.max_span_lower())/FT(2)); - } - else{ - cutdim = c0.max_tight_span_coord(); - sep = Separator(cutdim, - (c0.max_tight_span_upper() + c0.max_tight_span_lower())/FT(2)); - } - - FT max_span_lower = - c0.tight_bounding_box().min_coord(cutdim); - - CGAL_assertion(max_span_lower >= c0.bounding_box().min_coord(cutdim)); - FT max_span_upper = - c0.tight_bounding_box().max_coord(cutdim); - - CGAL_assertion(max_span_upper <= c0.bounding_box().max_coord(cutdim)); - if (max_span_upper <= sep.cutting_value()) { - sep.set_cutting_value(max_span_upper); - }; - if (max_span_lower >= sep.cutting_value()) { - sep.set_cutting_value(max_span_lower); - }; - c0.split(c1,sep,true); - } - }; - - template > - class Median_of_rectangle - : public Splitter_base - { - - typedef Splitter_base Base; - - public: - typedef typename SearchTraits::FT FT; - typedef Point_container Container; - typedef Separator_ Separator; - - - Median_of_rectangle() - : Base() - {} - - Median_of_rectangle(unsigned int bucket_size) - : Base(bucket_size) - {} - - void - operator() (Separator& sep, Container& c0, Container& c1) const - { - sep = Separator(c0.max_span_coord(),FT(0)); - sep.set_cutting_value(c0.median(sep.cutting_dimension())); - c0.split(c1,sep,true); - } - }; - - template > - class Midpoint_of_max_spread - : public Splitter_base - { - typedef Splitter_base Base; - - public: - typedef typename SearchTraits::FT FT; - typedef Point_container Container; - typedef Separator_ Separator; - - - Midpoint_of_max_spread() - : Base() - {} - - Midpoint_of_max_spread(unsigned int bucket_size) - : Base(bucket_size) - {} - - void - operator()(Separator& sep, Container& c0, Container& c1) const - { - sep = Separator(c0.max_tight_span_coord(), - (c0.max_tight_span_upper() + c0.max_tight_span_lower())/FT(2)); - c0.split(c1,sep); - } - }; - - template > - class Midpoint_of_rectangle - : public Splitter_base - { - - typedef Splitter_base Base; - public: - typedef typename SearchTraits::FT FT; - typedef Point_container Container; - typedef Separator_ Separator; - - - Midpoint_of_rectangle() - : Base() - {} - - Midpoint_of_rectangle(unsigned int bucket_size) - : Base(bucket_size) - {} - - void - operator()(Separator& sep, Container& c0, Container& c1) const - { - sep = Separator(c0.max_span_coord(), - (c0.max_span_upper() + c0.max_span_lower())/FT(2)); - c0.split(c1,sep); - } - - }; - -} // namespace CGAL -#endif // CGAL_SPLITTERS diff --git a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h index 20b47d0b..f2d9abb2 100644 --- a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h +++ b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h @@ -23,8 +23,18 @@ #ifndef NEIGHBORS_FINDER_H_ #define NEIGHBORS_FINDER_H_ +// Inclusion order is important for CGAL patch +#include "CGAL/Kd_tree_node.h" +#include "CGAL/Kd_tree.h" +#include "CGAL/Orthogonal_incremental_neighbor_search.h" + +#include +#include + +#include +#include + #include -#include namespace Gudhi { @@ -38,6 +48,13 @@ namespace bottleneck_distance { * \ingroup bottleneck_distance */ class Neighbors_finder { + + 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. */ Neighbors_finder(double r); @@ -50,10 +67,8 @@ public: private: const double r; - Planar_neighbors_finder planar_neighbors_f; + Kd_tree kd_t; 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 @@ -80,46 +95,44 @@ private: }; inline Neighbors_finder::Neighbors_finder(double r) : - r(r), planar_neighbors_f(r), projections_f() { } + r(r), kd_t(), 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); + kd_t.insert(G::get_v_point(v_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.empty()) + 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)) + projections_f.erase(tmp); + } + else if (projections_f.count(c) && (G::distance(u_point_index, c) <= r)){ //Is the query point near to its projection ? tmp = c; - else + projections_f.erase(tmp); + } + else{ //Is the query point near to a V point in the plane ? - tmp = planar_neighbors_f.pull_near(u_point_index); - remove(tmp); + 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(); + tmp = it->first.point_index; + kd_t.remove(G::get_v_point(tmp)); + } return tmp; } inline std::vector Neighbors_finder::pull_all_near(int u_point_index) { - std::vector all_pull(planar_neighbors_f.pull_all_near(u_point_index)); + std::vector all_pull; int last_pull = pull_near(u_point_index); while (last_pull != null_point_index()) { all_pull.emplace_back(last_pull); diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h index 8242ce2b..fd17bf4a 100644 --- a/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h +++ b/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h @@ -65,7 +65,7 @@ private: static Internal_point get_u_point(int u_point_index); static Internal_point get_v_point(int v_point_index); - friend class Planar_neighbors_finder; + friend class Neighbors_finder; }; /** \internal \typedef \brief Shorter alias */ diff --git a/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h deleted file mode 100644 index c1f4d908..00000000 --- a/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h +++ /dev/null @@ -1,156 +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: Francois Godi - * - * Copyright (C) 2015 INRIA (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 PLANAR_NEIGHBORS_FINDER_H_ -#define PLANAR_NEIGHBORS_FINDER_H_ - -// Inclusion order is important for CGAL patch -#include "CGAL/Kd_tree_node.h" -#include "CGAL/Kd_tree.h" -#include "CGAL/Orthogonal_incremental_neighbor_search.h" - -#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. */ - std::vector 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 Planar_neighbors_finder { - - 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. */ - Planar_neighbors_finder(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::vector pull_all_near(int u_point_index); - -private: - double r; - std::set contents; - Kd_tree kd_t; -}; - - -/** \internal \brief Constructor taking the near distance definition as parameter. */ -inline Planar_neighbors_finder::Planar_neighbors_finder(double r_) - : r(r_), contents(), kd_t() {} - - -/** \internal \brief A point added will be possibly pulled. */ -inline void Planar_neighbors_finder::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 Planar_neighbors_finder::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 ? */ -inline bool Planar_neighbors_finder::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 Planar_neighbors_finder::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; - if(!contains(tmp)) - std::cout << "!! A kd_tree returns a point (Point_index:" << tmp << ") previously removed !!" << std::endl; - remove(tmp); - return tmp; -} - -inline std::vector Planar_neighbors_finder::pull_all_near(int u_point_index) { - std::vector all_pull; - 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 // PLANAR_NEIGHBORS_FINDER_H_ diff --git a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp index 31ba18ad..7edfa062 100644 --- a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp +++ b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp @@ -89,36 +89,6 @@ 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 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) -- cgit v1.2.3 From cc1e554f26765bf9993079bef608d9bc4a3308c8 Mon Sep 17 00:00:00 2001 From: fgodi Date: Mon, 28 Nov 2016 14:15:22 +0000 Subject: graph no longer static git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1790 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 6bbb8dfaffd09a81ccafac6919e073ed74b9c7e6 --- .../concept/Persistence_diagram.h | 4 +- src/Bottleneck_distance/include/gudhi/Bottleneck.h | 22 +++--- .../include/gudhi/Construct_coord_iterator.h | 42 ---------- .../include/gudhi/Graph_matching.h | 18 +++-- .../include/gudhi/Internal_point.h | 18 ++++- .../include/gudhi/Neighbors_finder.h | 36 +++++---- .../test/bottleneck_unit_test.cpp | 92 ++++++++++++---------- 7 files changed, 107 insertions(+), 125 deletions(-) delete mode 100644 src/Bottleneck_distance/include/gudhi/Construct_coord_iterator.h (limited to 'src') diff --git a/src/Bottleneck_distance/concept/Persistence_diagram.h b/src/Bottleneck_distance/concept/Persistence_diagram.h index fe13e859..2ca10094 100644 --- a/src/Bottleneck_distance/concept/Persistence_diagram.h +++ b/src/Bottleneck_distance/concept/Persistence_diagram.h @@ -41,8 +41,8 @@ struct Diagram_point{ */ struct Persistence_Diagram { - const_iterator begin(); - const_iterator end(); + iterator begin(); + iterator end(); }; } // namespace bottleneck_distance diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h index bb0a13d2..52de30be 100644 --- a/src/Bottleneck_distance/include/gudhi/Bottleneck.h +++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h @@ -31,14 +31,14 @@ namespace bottleneck_distance { template double compute_exactly(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2) { - G::initialize(diag1, diag2, 0.); - std::vector sd(G::sorted_distances()); + Persistence_graph g(diag1, diag2, 0.); + std::vector sd(g.sorted_distances()); int idmin = 0; int idmax = sd.size() - 1; - // alpha can be modified, this will change the complexity + // alpha can change the complexity double alpha = pow(sd.size(), 0.25); - Graph_matching m; - Graph_matching biggest_unperfect; + Graph_matching m(g); + Graph_matching biggest_unperfect(g); while (idmin != idmax) { int step = static_cast((idmax - idmin) / alpha); m.set_r(sd.at(idmin + step)); @@ -64,14 +64,14 @@ template double compute(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e=0.) { if(e == 0.) return compute_exactly(diag1, diag2); - G::initialize(diag1, diag2, e); - int in = G::diameter()/e + 1; + Persistence_graph g(diag1, diag2, e); + int in = g.diameter_bound()/e + 1; 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; + // alpha can change the complexity + double alpha = pow(in, 0.10); + Graph_matching m(g); + Graph_matching biggest_unperfect(g); while (idmin != idmax) { int step = static_cast((idmax - idmin) / alpha); m.set_r(e*(idmin + step)); diff --git a/src/Bottleneck_distance/include/gudhi/Construct_coord_iterator.h b/src/Bottleneck_distance/include/gudhi/Construct_coord_iterator.h deleted file mode 100644 index 0959dd03..00000000 --- a/src/Bottleneck_distance/include/gudhi/Construct_coord_iterator.h +++ /dev/null @@ -1,42 +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: Francois Godi - * - * Copyright (C) 2015 INRIA (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::bottleneck_distance::Internal_point Internal_point; - -struct Construct_coord_iterator { - typedef const double* result_type; - const double* operator()(const Internal_point& p) const - { return p.vec; } - const double* operator()(const Internal_point& p, int) const - { return 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 index fa20b2a2..10b7073a 100644 --- a/src/Bottleneck_distance/include/gudhi/Graph_matching.h +++ b/src/Bottleneck_distance/include/gudhi/Graph_matching.h @@ -36,7 +36,7 @@ namespace bottleneck_distance { class Graph_matching { public: /** \internal \brief Constructor constructing an empty matching. */ - explicit Graph_matching(); + explicit Graph_matching(Persistence_graph &g); /** \internal \brief Copy operator. */ Graph_matching& operator=(const Graph_matching& m); /** \internal \brief Is the matching perfect ? */ @@ -47,6 +47,7 @@ public: void set_r(double r); private: + Persistence_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; @@ -61,13 +62,14 @@ private: void update(std::vector & 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) +inline Graph_matching::Graph_matching(Persistence_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) unmatched_in_u.emplace_back(u_point_index); } inline Graph_matching& Graph_matching::operator=(const Graph_matching& m) { + g = m.g; r = m.r; v_to_u = m.v_to_u; unmatched_in_u = m.unmatched_in_u; @@ -83,7 +85,7 @@ inline bool Graph_matching::multi_augment() { return false; Layered_neighbors_finder layered_nf(layering()); int max_depth = layered_nf.vlayers_number()*2 - 1; - double rn = sqrt(G::size()); + 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; @@ -130,10 +132,10 @@ inline bool Graph_matching::augment(Layered_neighbors_finder & layered_nf, int u inline Layered_neighbors_finder 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) + Neighbors_finder nf(g, r); + for (int v_point_index = 0; v_point_index < g.size(); ++v_point_index) nf.add(v_point_index); - Layered_neighbors_finder layered_nf(r); + Layered_neighbors_finder layered_nf(g, 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) { diff --git a/src/Bottleneck_distance/include/gudhi/Internal_point.h b/src/Bottleneck_distance/include/gudhi/Internal_point.h index 78aad470..1a050d48 100644 --- a/src/Bottleneck_distance/include/gudhi/Internal_point.h +++ b/src/Bottleneck_distance/include/gudhi/Internal_point.h @@ -35,7 +35,7 @@ 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; } + Internal_point(double x, double y, int p_i) { 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 ]; } @@ -44,7 +44,7 @@ struct Internal_point { { return point_index==p.point_index; } - bool operator!=(const Internal_point& p) const { return ! (*this == p); } + bool operator!=(const Internal_point& p) const { return !(*this == p); } }; inline int null_point_index() { @@ -55,4 +55,18 @@ inline int null_point_index() { } // namespace Gudhi +namespace CGAL { + +typedef Gudhi::bottleneck_distance::Internal_point Internal_point; + +struct Construct_coord_iterator { + typedef const double* result_type; + const double* operator()(const Internal_point& p) const + { return p.vec; } + const double* operator()(const Internal_point& p, int) const + { return p.vec+2; } +}; + +} //namespace CGAL + #endif // INTERNAL_POINT_H_ diff --git a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h index f2d9abb2..f28e21a2 100644 --- a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h +++ b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h @@ -31,8 +31,8 @@ #include #include -#include -#include +#include +#include #include @@ -57,7 +57,7 @@ class Neighbors_finder { public: /** \internal \brief Constructor taking the near distance definition as parameter. */ - Neighbors_finder(double r); + Neighbors_finder(const Persistence_graph& g, 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. */ @@ -66,6 +66,7 @@ public: std::vector pull_all_near(int u_point_index); private: + const Persistence_graph& g; const double r; Kd_tree kd_t; std::unordered_set projections_f; @@ -81,7 +82,7 @@ private: class Layered_neighbors_finder { public: /** \internal \brief Constructor taking the near distance definition as parameter. */ - Layered_neighbors_finder(double r); + Layered_neighbors_finder(const Persistence_graph& g, 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. */ @@ -90,43 +91,44 @@ public: int vlayers_number() const; private: + const Persistence_graph& g; const double r; std::vector> neighbors_finder; }; -inline Neighbors_finder::Neighbors_finder(double r) : - r(r), kd_t(), projections_f() { } +inline Neighbors_finder::Neighbors_finder(const Persistence_graph& g, double r) : + g(g), r(r), kd_t(), projections_f() { } inline void Neighbors_finder::add(int v_point_index) { - if (G::on_the_v_diagonal(v_point_index)) + if (g.on_the_v_diagonal(v_point_index)) projections_f.emplace(v_point_index); else - kd_t.insert(G::get_v_point(v_point_index)); + kd_t.insert(g.get_v_point(v_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.empty()){ + 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(); projections_f.erase(tmp); } - else if (projections_f.count(c) && (G::distance(u_point_index, c) <= r)){ + else if (projections_f.count(c) && (g.distance(u_point_index, c) <= r)){ //Is the query point near to its projection ? tmp = c; projections_f.erase(tmp); } else{ //Is the query point near to a V point in the plane ? - Internal_point u_point = G::get_u_point(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) + if(it==search.end() || g.distance(u_point_index, it->first.point_index) > r) return null_point_index(); tmp = it->first.point_index; - kd_t.remove(G::get_v_point(tmp)); + kd_t.remove(g.get_v_point(tmp)); } return tmp; } @@ -141,12 +143,12 @@ inline std::vector Neighbors_finder::pull_all_near(int u_point_index) { return all_pull; } -inline Layered_neighbors_finder::Layered_neighbors_finder(double r) : - r(r), neighbors_finder() { } +inline Layered_neighbors_finder::Layered_neighbors_finder(const Persistence_graph& g, double r) : + g(g), 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.emplace_back(std::shared_ptr(new Neighbors_finder(g, r))); neighbors_finder.at(vlayer)->add(v_point_index); } diff --git a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp index 7edfa062..2237b073 100644 --- a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp +++ b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp @@ -34,11 +34,13 @@ int n1 = 81; // a natural number >0 int n2 = 180; // a natural number >0 double upper_bound = 406.43; // any real >0 + +std::uniform_real_distribution unif(0.,upper_bound); +std::default_random_engine re; +std::vector< std::pair > v1, v2; + 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); @@ -49,83 +51,87 @@ BOOST_AUTO_TEST_CASE(persistence_diagrams_graph){ double b = unif(re); v2.emplace_back(std::min(a,b), std::max(a,b)); } - G::initialize(v1, v2, 0.); - std::vector d(G::sorted_distances()); + Persistence_graph g(v1, v2, 0.); + 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.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(neighbors_finder) { - Neighbors_finder nf(1.); + Persistence_graph g(v1, v2, 0.); + Neighbors_finder nf(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.)); + BOOST_CHECK((v_point_index_1 == -1) || (g.distance(n2/2,v_point_index_1)<=1.)); std::vector 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) { - Layered_neighbors_finder lnf(1.); + Persistence_graph g(v1, v2, 0.); + Layered_neighbors_finder lnf(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.)); + 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) { - Graph_matching m1; + Persistence_graph g(v1, v2, 0.); + Graph_matching m1(g); m1.set_r(0.); int e = 0; while (m1.multi_augment()) ++e; + BOOST_CHECK(e > 0); BOOST_CHECK(e <= 2*sqrt(2*(n1+n2))); Graph_matching m2 = m1; BOOST_CHECK(!m2.multi_augment()); -- cgit v1.2.3 From b0c33669d948f25c413a67991f8ae03e854892a8 Mon Sep 17 00:00:00 2001 From: fgodi Date: Mon, 28 Nov 2016 15:25:08 +0000 Subject: compute and compute_exactly merged git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1791 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 89fbffc2e07d6d842746ba185a99f483cfec90a7 --- src/Bottleneck_distance/test/bottleneck_chrono.cpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'src') diff --git a/src/Bottleneck_distance/test/bottleneck_chrono.cpp b/src/Bottleneck_distance/test/bottleneck_chrono.cpp index a7440ecd..8e823897 100644 --- a/src/Bottleneck_distance/test/bottleneck_chrono.cpp +++ b/src/Bottleneck_distance/test/bottleneck_chrono.cpp @@ -34,7 +34,7 @@ int main(){ std::ofstream objetfichier; objetfichier.open("results.csv", std::ios::out); - int n = 1200; + for(int n = 400; n<=2000; 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; @@ -57,5 +57,6 @@ int main(){ 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 7449716dca77dd81759d024ae1e9dbfcfeb202e7 Mon Sep 17 00:00:00 2001 From: fgodi Date: Mon, 28 Nov 2016 15:25:17 +0000 Subject: compute and compute_exactly merged git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1792 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 7c4e66f5449759f7d99319ca14989b2d74e96e20 --- src/Bottleneck_distance/include/gudhi/Bottleneck.h | 62 +++------------------- .../include/gudhi/Neighbors_finder.h | 4 +- 2 files changed, 9 insertions(+), 57 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h index 52de30be..59df655e 100644 --- a/src/Bottleneck_distance/include/gudhi/Bottleneck.h +++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h @@ -29,32 +29,6 @@ namespace Gudhi { namespace bottleneck_distance { -template -double compute_exactly(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2) { - Persistence_graph g(diag1, diag2, 0.); - std::vector sd(g.sorted_distances()); - int idmin = 0; - int idmax = sd.size() - 1; - // alpha can change the complexity - double alpha = pow(sd.size(), 0.25); - Graph_matching m(g); - Graph_matching biggest_unperfect(g); - 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); -} - /** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams. * If the last parameter e is not 0 (default value if not explicited), you get an additive e-approximation. * @@ -62,19 +36,19 @@ double compute_exactly(const Persistence_diagram1 &diag1, const Persistence_diag */ template double compute(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e=0.) { - if(e == 0.) - return compute_exactly(diag1, diag2); Persistence_graph g(diag1, diag2, e); - int in = g.diameter_bound()/e + 1; + std::vector sd; + if(e == 0.) + sd = g.sorted_distances(); int idmin = 0; - int idmax = in; + int idmax = e==0. ? sd.size() - 1 : g.diameter_bound()/e + 1; // alpha can change the complexity - double alpha = pow(in, 0.10); + double alpha = pow(idmax, 0.25); Graph_matching m(g); Graph_matching biggest_unperfect(g); while (idmin != idmax) { int step = static_cast((idmax - idmin) / alpha); - m.set_r(e*(idmin + step)); + m.set_r(e == 0. ? sd.at(idmin + step) : e*(idmin + step)); while (m.multi_augment()); //The above while compute a maximum matching (according to the r setted before) if (m.perfect()) { @@ -85,7 +59,7 @@ double compute(const Persistence_diagram1 &diag1, const Persistence_diagram2 &di idmin = idmin + step + 1; } } - return e*(idmin); + return e == 0. ? sd.at(idmin) : e*(idmin); } @@ -95,25 +69,3 @@ double compute(const Persistence_diagram1 &diag1, const Persistence_diagram2 &di } // namespace Gudhi #endif // BOTTLENECK_H_ - -/* Dichotomic version -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; -} */ - diff --git a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h index f28e21a2..90ddabef 100644 --- a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h +++ b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h @@ -122,8 +122,8 @@ inline int Neighbors_finder::pull_near(int u_point_index) { else{ //Is the query point near to a V point in the plane ? 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)); + std::array w = { {1., 1.} }; + K_neighbor_search search(kd_t, u_point, 0., true, Distance(0, 2, w.begin(), w.end())); auto it = search.begin(); if(it==search.end() || g.distance(u_point_index, it->first.point_index) > r) return null_point_index(); -- cgit v1.2.3 From 6e5bfd760a6635acbaf19723bf4b883df7f2a416 Mon Sep 17 00:00:00 2001 From: fgodi Date: Mon, 28 Nov 2016 15:56:42 +0000 Subject: rm of a renamed file git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1793 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 422fa0b96831f83c82e47cc6bfe50b9289e5356c --- .../include/gudhi/Persistence_diagrams_graph.h | 162 --------------------- 1 file changed, 162 deletions(-) delete mode 100644 src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h (limited to 'src') diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h deleted file mode 100644 index fd17bf4a..00000000 --- a/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h +++ /dev/null @@ -1,162 +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: Francois Godi - * - * Copyright (C) 2015 INRIA (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 PERSISTENCE_DIAGRAMS_GRAPH_H_ -#define PERSISTENCE_DIAGRAMS_GRAPH_H_ - -#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::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 Neighbors_finder; -}; - -/** \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(std::get<0>(*it), std::get<1>(*it), u.size())); - for (auto it = diag2.cbegin(); it != diag2.cend(); ++it) - if (it->second - it->first > e) - v.push_back(Internal_point(std::get<0>(*it), std::get<1>(*it), 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::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)); - return std::vector(sorted_distances.begin(),sorted_distances.end()); -} - -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(auto it = u.cbegin(); it != u.cend(); it++) - max = std::max(max,it->y()); - for(auto it = v.cbegin(); it != v.cend(); it++) - max = std::max(max,it->y()); - return max; -} - -} // namespace bottleneck_distance - -} // namespace Gudhi - -#endif // PERSISTENCE_DIAGRAMS_GRAPH_H_ -- cgit v1.2.3 From 0cf9b8901ed858cba7ac16fcd5a65e631dc22782 Mon Sep 17 00:00:00 2001 From: fgodi Date: Mon, 28 Nov 2016 16:22:49 +0000 Subject: missing file added git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1794 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: f2cbc4b7bfa7ee7d6ea70c7318786f1c1684c37d --- .../include/gudhi/Persistence_graph.h | 155 +++++++++++++++++++++ 1 file changed, 155 insertions(+) create mode 100644 src/Bottleneck_distance/include/gudhi/Persistence_graph.h (limited to 'src') diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h new file mode 100644 index 00000000..a4ea6968 --- /dev/null +++ b/src/Bottleneck_distance/include/gudhi/Persistence_graph.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: Francois Godi + * + * Copyright (C) 2015 INRIA (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 PERSISTENCE_GRAPH_H_ +#define PERSISTENCE_GRAPH_H_ + +#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_graph { +public: + /** \internal \brief Initializer taking 2 Point (concept) ranges as parameters. */ + template + Persistence_graph(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 ? */ + bool on_the_u_diagonal(int u_point_index) const; + /** \internal \brief Is the given point from V the projection of a point in U ? */ + bool on_the_v_diagonal(int v_point_index) const; + /** \internal \brief Given a point from V, returns the corresponding (projection or projector) point in U. */ + int corresponding_point_in_u(int v_point_index) const; + /** \internal \brief Given a point from U, returns the corresponding (projection or projector) point in V. */ + int corresponding_point_in_v(int u_point_index) const; + /** \internal \brief Given a point from U and a point from V, returns the distance between those points. */ + double distance(int u_point_index, int v_point_index) const; + /** \internal \brief Returns size = |U| = |V|. */ + int size() const; + /** \internal \brief Returns the O(n^2) sorted distances between the points. */ + std::vector sorted_distances() const; + /** \internal \brief Returns an upper bound of the diameter of the convex hull */ + double diameter_bound() const; + /** \internal \brief Returns the corresponding internal point */ + Internal_point get_u_point(int u_point_index) const; + /** \internal \brief Returns the corresponding internal point */ + Internal_point get_v_point(int v_point_index) const; + +private: + std::vector u; + std::vector v; +}; + +template +Persistence_graph::Persistence_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.push_back(Internal_point(std::get<0>(*it), std::get<1>(*it), u.size())); + for (auto it = diag2.cbegin(); it != diag2.cend(); ++it) + if (it->second - it->first > e) + v.push_back(Internal_point(std::get<0>(*it), std::get<1>(*it), v.size())); + if (u.size() < v.size()) + swap(u, v); +} + +inline bool Persistence_graph::on_the_u_diagonal(int u_point_index) const { + return u_point_index >= static_cast (u.size()); +} + +inline bool Persistence_graph::on_the_v_diagonal(int v_point_index) const { + return v_point_index >= static_cast (v.size()); +} + +inline int Persistence_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_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_graph::distance(int u_point_index, int v_point_index) const { + 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 Persistence_graph::size() const { + return static_cast (u.size() + v.size()); +} + +inline std::vector Persistence_graph::sorted_distances() const { + // 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)); + return std::vector(sorted_distances.begin(),sorted_distances.end()); +} + +inline Internal_point Persistence_graph::get_u_point(int u_point_index) const { + 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 Persistence_graph::get_v_point(int v_point_index) const { + 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 Persistence_graph::diameter_bound() const { + double max = 0.; + for(auto it = u.cbegin(); it != u.cend(); it++) + max = std::max(max,it->y()); + for(auto it = v.cbegin(); it != v.cend(); it++) + max = std::max(max,it->y()); + return max; +} + +} // namespace bottleneck_distance + +} // namespace Gudhi + +#endif // PERSISTENCE_GRAPH_H_ -- cgit v1.2.3 From 759b53891e1572df0ea0562828fcd88d8f8f3031 Mon Sep 17 00:00:00 2001 From: fgodi Date: Tue, 29 Nov 2016 09:00:07 +0000 Subject: basic example, infinity git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1797 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 23432677e7f1628dda596e9ba31138fc5063a608 --- .../concept/Persistence_diagram.h | 3 +- src/Bottleneck_distance/example/CMakeLists.txt | 3 +- .../example/bottleneck_basic_example.cpp | 48 ++++++++++++++ .../example/bottleneck_example.cpp | 77 ---------------------- .../example/bottleneck_read_file_example.cpp | 77 ++++++++++++++++++++++ .../include/gudhi/Persistence_graph.h | 5 +- .../test/bottleneck_unit_test.cpp | 4 +- 7 files changed, 134 insertions(+), 83 deletions(-) create mode 100644 src/Bottleneck_distance/example/bottleneck_basic_example.cpp delete mode 100644 src/Bottleneck_distance/example/bottleneck_example.cpp create mode 100644 src/Bottleneck_distance/example/bottleneck_read_file_example.cpp (limited to 'src') diff --git a/src/Bottleneck_distance/concept/Persistence_diagram.h b/src/Bottleneck_distance/concept/Persistence_diagram.h index 2ca10094..d55f5573 100644 --- a/src/Bottleneck_distance/concept/Persistence_diagram.h +++ b/src/Bottleneck_distance/concept/Persistence_diagram.h @@ -27,7 +27,8 @@ namespace Gudhi { namespace bottleneck_distance { -/** \brief Concept of persistence diagram point. get<0>() must return the birth of the component and get<1>() its death. +/** \brief Concept of Diagram_point. get<0>() must return the birth of the corresponding component and get<1>() its death. + * If the component stay alive, get<1>() must return std::numeric_limits::infinity(). * * \ingroup bottleneck_distance */ diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt index 6f3204f6..cd53ccfc 100644 --- a/src/Bottleneck_distance/example/CMakeLists.txt +++ b/src/Bottleneck_distance/example/CMakeLists.txt @@ -6,7 +6,8 @@ project(Bottleneck_distance_examples) if(CGAL_FOUND) if (NOT CGAL_VERSION VERSION_LESS 4.8.0) if (EIGEN3_FOUND) - add_executable (bottleneck_example bottleneck_example.cpp) + add_executable (bottleneck_read_file_example bottleneck_read_file_example.cpp) + add_executable (bottleneck_basic_example bottleneck_basic_example.cpp) endif() endif () endif() diff --git a/src/Bottleneck_distance/example/bottleneck_basic_example.cpp b/src/Bottleneck_distance/example/bottleneck_basic_example.cpp new file mode 100644 index 00000000..95548579 --- /dev/null +++ b/src/Bottleneck_distance/example/bottleneck_basic_example.cpp @@ -0,0 +1,48 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Authors: Francois Godi, small modifications by Pawel Dlotko + * + * Copyright (C) 2015 INRIA (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 + +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); + v1.emplace_back(3., std::numeric_limits::infinity()); + + v2.emplace_back(2.8, 4.45); + v2.emplace_back(9.5, 14.1); + v2.emplace_back(3.2, std::numeric_limits::infinity()); + + + double b = Gudhi::bottleneck_distance::compute(v1, v2); + + std::cout << "Bottleneck distance = " << b << std::endl; + + b = Gudhi::bottleneck_distance::compute(v1, v2, 0.1); + + std::cout << "Approx bottleneck distance = " << b << std::endl; + +} diff --git a/src/Bottleneck_distance/example/bottleneck_example.cpp b/src/Bottleneck_distance/example/bottleneck_example.cpp deleted file mode 100644 index 28e458a5..00000000 --- a/src/Bottleneck_distance/example/bottleneck_example.cpp +++ /dev/null @@ -1,77 +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. - * - * Authors: Francois Godi, small modifications by Pawel Dlotko - * - * Copyright (C) 2015 INRIA (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 CGAL_HAS_THREADS - -#include -#include -#include -#include -#include - -std::vector< std::pair > read_diagram_from_file( const char* filename ) -{ - std::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"; - } - - 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 - -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 tolerance is : " << tolerance << std::endl; -} diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp new file mode 100644 index 00000000..4a503e4c --- /dev/null +++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp @@ -0,0 +1,77 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Authors: Francois Godi, small modifications by Pawel Dlotko + * + * Copyright (C) 2015 INRIA (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 CGAL_HAS_THREADS + +#include +#include +#include +#include +#include + +std::vector< std::pair > read_diagram_from_file( const char* filename ) +{ + std::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"; + } + + 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 + +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 tolerance is : " << tolerance << std::endl; +} diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h index a4ea6968..506dba52 100644 --- a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h +++ b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h @@ -74,10 +74,10 @@ Persistence_graph::Persistence_graph(const Persistence_diagram1 &diag1, : u(), v() { for (auto it = diag1.cbegin(); it != diag1.cend(); ++it) - if (it->second - it->first > e) + if (it->second != std::numeric_limits::infinity() && it->second - it->first > e) u.push_back(Internal_point(std::get<0>(*it), std::get<1>(*it), u.size())); for (auto it = diag2.cbegin(); it != diag2.cend(); ++it) - if (it->second - it->first > e) + if (it->second != std::numeric_limits::infinity() && it->second - it->first > e) v.push_back(Internal_point(std::get<0>(*it), std::get<1>(*it), v.size())); if (u.size() < v.size()) swap(u, v); @@ -120,6 +120,7 @@ inline std::vector Persistence_graph::sorted_distances() const { 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)); + sorted_distances.emplace(std::numeric_limits::infinity()); return std::vector(sorted_distances.begin(),sorted_distances.end()); } diff --git a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp index 2237b073..84101274 100644 --- a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp +++ b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp @@ -39,7 +39,7 @@ std::uniform_real_distribution unif(0.,upper_bound); std::default_random_engine re; std::vector< std::pair > v1, v2; -BOOST_AUTO_TEST_CASE(persistence_diagrams_graph){ +BOOST_AUTO_TEST_CASE(persistence_graph){ // Random construction for (int i = 0; i < n1; i++) { double a = unif(re); @@ -70,7 +70,7 @@ BOOST_AUTO_TEST_CASE(persistence_diagrams_graph){ // BOOST_CHECK(g.size()==(n1+n2)); // - BOOST_CHECK((int) d.size() <= (n1+n2)*(n1+n2) - n1*n2 + 1); + BOOST_CHECK((int) d.size() <= (n1+n2)*(n1+n2) - n1*n2 + 2); 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); -- cgit v1.2.3 From 6d1bfe69ea473088eb2ca3ede626a2accaa58205 Mon Sep 17 00:00:00 2001 From: fgodi Date: Tue, 29 Nov 2016 10:51:43 +0000 Subject: better gestion of infinite points git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1798 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 28cca4bf35541a677fe08d5f0a8b89dfe9017962 --- src/Bottleneck_distance/include/gudhi/Bottleneck.h | 8 ++-- .../include/gudhi/Persistence_graph.h | 38 ++++++++++++------- src/Bottleneck_distance/test/bottleneck_chrono.cpp | 2 +- .../test/bottleneck_unit_test.cpp | 43 +++++++++++----------- 4 files changed, 53 insertions(+), 38 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h index 59df655e..20225e80 100644 --- a/src/Bottleneck_distance/include/gudhi/Bottleneck.h +++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h @@ -37,17 +37,19 @@ namespace bottleneck_distance { template double compute(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e=0.) { Persistence_graph g(diag1, diag2, e); + if(!g.alive_match()) + return std::numeric_limits::infinity(); std::vector sd; if(e == 0.) sd = g.sorted_distances(); - int idmin = 0; - int idmax = e==0. ? sd.size() - 1 : g.diameter_bound()/e + 1; + long idmin = 0; + long idmax = e==0. ? sd.size() - 1 : g.diameter_bound()/e + 1; // alpha can change the complexity double alpha = pow(idmax, 0.25); Graph_matching m(g); Graph_matching biggest_unperfect(g); while (idmin != idmax) { - int step = static_cast((idmax - idmin) / alpha); + long step = static_cast((idmax - idmin) / alpha); m.set_r(e == 0. ? sd.at(idmin + step) : e*(idmin + step)); while (m.multi_augment()); //The above while compute a maximum matching (according to the r setted before) diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h index 506dba52..ebd3adaf 100644 --- a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h +++ b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h @@ -24,7 +24,7 @@ #define PERSISTENCE_GRAPH_H_ #include -#include +#include #include namespace Gudhi { @@ -39,7 +39,7 @@ namespace bottleneck_distance { */ class Persistence_graph { public: - /** \internal \brief Initializer taking 2 Point (concept) ranges as parameters. */ + /** \internal \brief Constructor taking 2 Persistence_Diagrams (concept) as parameters. */ template Persistence_graph(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 ? */ @@ -54,9 +54,11 @@ public: double distance(int u_point_index, int v_point_index) const; /** \internal \brief Returns size = |U| = |V|. */ int size() const; + /** \internal \brief Is there as many infinite points (alive components) in both diagrams ? */ + bool alive_match() const; /** \internal \brief Returns the O(n^2) sorted distances between the points. */ std::vector sorted_distances() const; - /** \internal \brief Returns an upper bound of the diameter of the convex hull */ + /** \internal \brief Returns an upper bound for the diameter of the convex hull of all non infinite points */ double diameter_bound() const; /** \internal \brief Returns the corresponding internal point */ Internal_point get_u_point(int u_point_index) const; @@ -66,18 +68,23 @@ public: private: std::vector u; std::vector v; + int alive_count; }; template Persistence_graph::Persistence_graph(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e) - : u(), v() + : u(), v(), alive_count(0) { for (auto it = diag1.cbegin(); it != diag1.cend(); ++it) - if (it->second != std::numeric_limits::infinity() && it->second - it->first > e) + if(it->second == std::numeric_limits::infinity()) + alive_count++; + else if (it->second - it->first > e) u.push_back(Internal_point(std::get<0>(*it), std::get<1>(*it), u.size())); for (auto it = diag2.cbegin(); it != diag2.cend(); ++it) - if (it->second != std::numeric_limits::infinity() && it->second - it->first > e) + if(it->second == std::numeric_limits::infinity()) + alive_count--; + else if (it->second - it->first > e) v.push_back(Internal_point(std::get<0>(*it), std::get<1>(*it), v.size())); if (u.size() < v.size()) swap(u, v); @@ -113,15 +120,20 @@ inline int Persistence_graph::size() const { return static_cast (u.size() + v.size()); } +inline bool Persistence_graph::alive_match() const{ + return alive_count==0; +} + inline std::vector Persistence_graph::sorted_distances() const { - // could be optimized - std::set sorted_distances; - sorted_distances.emplace(0.); - for (int u_point_index = 0; u_point_index < size(); ++u_point_index) + std::vector distances; + distances.push_back(0.); + for (int u_point_index = 0; u_point_index < size(); ++u_point_index){ + distances.push_back(distance(u_point_index, corresponding_point_in_v(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)); - sorted_distances.emplace(std::numeric_limits::infinity()); - return std::vector(sorted_distances.begin(),sorted_distances.end()); + distances.push_back(distance(u_point_index, v_point_index)); + } + std::sort(distances.begin(), distances.end()); + return distances; } inline Internal_point Persistence_graph::get_u_point(int u_point_index) const { diff --git a/src/Bottleneck_distance/test/bottleneck_chrono.cpp b/src/Bottleneck_distance/test/bottleneck_chrono.cpp index 8e823897..8bd41104 100644 --- a/src/Bottleneck_distance/test/bottleneck_chrono.cpp +++ b/src/Bottleneck_distance/test/bottleneck_chrono.cpp @@ -52,7 +52,7 @@ 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, 0.0001); + double b = compute(v1,v2, 0.00001); 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 84101274..2e67d436 100644 --- a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp +++ b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp @@ -70,25 +70,25 @@ BOOST_AUTO_TEST_CASE(persistence_graph){ // BOOST_CHECK(g.size()==(n1+n2)); // - BOOST_CHECK((int) d.size() <= (n1+n2)*(n1+n2) - n1*n2 + 2); - 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((int) d.size() == (n1+n2)*(n1+n2) + n1 + n2 + 1); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(0,0))>0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(0,n1-1))>0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(0,n1))>0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(0,n2-1))>0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(0,n2))>0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(0,(n1+n2)-1))>0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(n1,0))>0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(n1,n1-1))>0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(n1,n1))>0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(n1,n2-1))>0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(n1,n2))>0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(n1,(n1+n2)-1))>0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance((n1+n2)-1,0))>0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance((n1+n2)-1,n1-1))>0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance((n1+n2)-1,n1))>0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance((n1+n2)-1,n2-1))>0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance((n1+n2)-1,n2))>0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance((n1+n2)-1,(n1+n2)-1))>0); } BOOST_AUTO_TEST_CASE(neighbors_finder) { @@ -146,7 +146,7 @@ BOOST_AUTO_TEST_CASE(graph_matching) { 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::uniform_real_distribution unif2(upper_bound/10000.,upper_bound/100.); std::default_random_engine re; std::vector< std::pair > v1, v2; for (int i = 0; i < n1; i++) { @@ -162,5 +162,6 @@ BOOST_AUTO_TEST_CASE(global){ v2.emplace_back(std::max(a,b),std::max(a,b)+y); } BOOST_CHECK(compute(v1, v2) <= upper_bound/100.); - BOOST_CHECK(compute(v1, v2, upper_bound/1000.) <= upper_bound/100. + upper_bound/1000.); + BOOST_CHECK(compute(v1, v2, upper_bound/10000.) <= upper_bound/100. + upper_bound/10000.); + BOOST_CHECK(std::abs(compute(v1, v2) - compute(v1, v2, upper_bound/10000.)) <= upper_bound/10000.); } -- cgit v1.2.3 From 004dac98fde448065a1697ea696a67153ccdb77e Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 30 Nov 2016 21:39:44 +0000 Subject: Add tan_test for test purpose git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/tangential_test@1807 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 85200e0b013cc119aead9556e97db877b3421064 --- src/Tangential_complex/example/CMakeLists.txt | 6 +++ src/Tangential_complex/example/tan_test.cpp | 54 ++++++++++++++++++++++ .../include/gudhi/Tangential_complex/config.h | 3 +- 3 files changed, 61 insertions(+), 2 deletions(-) create mode 100644 src/Tangential_complex/example/tan_test.cpp (limited to 'src') diff --git a/src/Tangential_complex/example/CMakeLists.txt b/src/Tangential_complex/example/CMakeLists.txt index a75ccd5b..76ba0a32 100644 --- a/src/Tangential_complex/example/CMakeLists.txt +++ b/src/Tangential_complex/example/CMakeLists.txt @@ -8,9 +8,12 @@ if(CGAL_FOUND) target_link_libraries(Tangential_complex_example_basic ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY}) add_executable( Tangential_complex_example_with_perturb example_with_perturb.cpp ) target_link_libraries(Tangential_complex_example_with_perturb ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY}) + add_executable( tan_test tan_test.cpp ) + target_link_libraries(tan_test ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY}) if (TBB_FOUND) target_link_libraries(Tangential_complex_example_basic ${TBB_LIBRARIES}) target_link_libraries(Tangential_complex_example_with_perturb ${TBB_LIBRARIES}) + target_link_libraries(tan_test ${TBB_LIBRARIES}) endif(TBB_FOUND) add_test(Tangential_complex_example_basic @@ -18,6 +21,9 @@ if(CGAL_FOUND) add_test(Tangential_complex_example_with_perturb ${CMAKE_CURRENT_BINARY_DIR}/Tangential_complex_example_with_perturb) + + add_test(tan_test + ${CMAKE_CURRENT_BINARY_DIR}/tan_test) endif(EIGEN3_FOUND) endif(NOT CGAL_VERSION VERSION_LESS 4.8.0) endif(CGAL_FOUND) diff --git a/src/Tangential_complex/example/tan_test.cpp b/src/Tangential_complex/example/tan_test.cpp new file mode 100644 index 00000000..afb9f13c --- /dev/null +++ b/src/Tangential_complex/example/tan_test.cpp @@ -0,0 +1,54 @@ +#include +#include + +#include +#include + +#include +#include + +namespace tc = Gudhi::tangential_complex; + +typedef CGAL::Epick_d Kernel; +typedef Kernel::FT FT; +typedef Kernel::Point_d Point; +typedef Kernel::Vector_d Vector; +typedef tc::Tangential_complex< +Kernel, CGAL::Dynamic_dimension_tag, +CGAL::Parallel_tag> TC; + +int main(void) { + const int INTRINSIC_DIM = 1; + + // Generate points on a 2-sphere + std::vector points; + // [[0, 0], [1, 0], [0, 1], [1, 1]] + std::vector point = {0.0, 0.0}; + points.push_back(Point(point.size(), point.begin(), point.end())); + point = {1.0, 0.0}; + points.push_back(Point(point.size(), point.begin(), point.end())); + point = {0.0, 1.0}; + points.push_back(Point(point.size(), point.begin(), point.end())); + point = {1.0, 1.0}; + points.push_back(Point(point.size(), point.begin(), point.end())); + + Kernel k; + for (int i = 0; i < 100; i++) { + + // Compute the TC + TC tc(points, INTRINSIC_DIM, k); + tc.compute_tangential_complex(); + TC::Num_inconsistencies num_inc = tc.number_of_inconsistent_simplices(); + std::cout << "TC vertices = " << tc.number_of_vertices() << " - simplices = " << num_inc.num_simplices << + " - inconsistencies = " << num_inc.num_inconsistent_simplices << std::endl; + + tc.fix_inconsistencies_using_perturbation(10.0, 60.0); + // Export the TC into a Simplex_tree + Gudhi::Simplex_tree<> stree; + tc.create_complex(stree); + std::cout << "ST vertices = " << stree.num_vertices() << " - simplices = " << stree.num_simplices() << std::endl; + + } + + return 0; +} diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex/config.h b/src/Tangential_complex/include/gudhi/Tangential_complex/config.h index 98a1b14f..ffefcd6b 100644 --- a/src/Tangential_complex/include/gudhi/Tangential_complex/config.h +++ b/src/Tangential_complex/include/gudhi/Tangential_complex/config.h @@ -26,8 +26,7 @@ #include // ========================= Debugging & profiling ============================= -#define GUDHI_TC_PROFILING -#define DEBUG_TRACES +// #define GUDHI_TC_PROFILING // #define GUDHI_TC_VERY_VERBOSE // #define GUDHI_TC_PERFORM_EXTRA_CHECKS // #define GUDHI_TC_SHOW_DETAILED_STATS_FOR_INCONSISTENCIES -- cgit v1.2.3 From 3e2c4df7d6ac217f09d3aff6d238e71de8229e5b Mon Sep 17 00:00:00 2001 From: fgodi Date: Mon, 5 Dec 2016 15:42:42 +0000 Subject: review prise en compte git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1821 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 4c24c2bebc49c70d0502ffdb1f23e451d17a3b88 --- .../include/gudhi/Internal_point.h | 16 +++++++--------- .../include/gudhi/Neighbors_finder.h | 12 ++++++------ .../include/gudhi/Persistence_graph.h | 20 ++++++++++++-------- 3 files changed, 25 insertions(+), 23 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/include/gudhi/Internal_point.h b/src/Bottleneck_distance/include/gudhi/Internal_point.h index 1a050d48..27a59d3f 100644 --- a/src/Bottleneck_distance/include/gudhi/Internal_point.h +++ b/src/Bottleneck_distance/include/gudhi/Internal_point.h @@ -51,14 +51,6 @@ inline int null_point_index() { return -1; } -} // namespace bottleneck_distance - -} // namespace Gudhi - -namespace CGAL { - -typedef Gudhi::bottleneck_distance::Internal_point Internal_point; - struct Construct_coord_iterator { typedef const double* result_type; const double* operator()(const Internal_point& p) const @@ -67,6 +59,12 @@ struct Construct_coord_iterator { { return p.vec+2; } }; -} //namespace CGAL +} // namespace bottleneck_distance + +} // namespace Gudhi + + + + #endif // INTERNAL_POINT_H_ diff --git a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h index 90ddabef..e6acafc6 100644 --- a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h +++ b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h @@ -26,7 +26,7 @@ // Inclusion order is important for CGAL patch #include "CGAL/Kd_tree_node.h" #include "CGAL/Kd_tree.h" -#include "CGAL/Orthogonal_incremental_neighbor_search.h" +#include "CGAL/Orthogonal_k_neighbor_search.h" #include #include @@ -50,9 +50,9 @@ namespace bottleneck_distance { class Neighbors_finder { typedef CGAL::Dimension_tag<2> D; - typedef CGAL::Search_traits Traits; + typedef CGAL::Search_traits Traits; typedef CGAL::Weighted_Minkowski_distance Distance; - typedef CGAL::Orthogonal_incremental_neighbor_search K_neighbor_search; + typedef CGAL::Orthogonal_k_neighbor_search K_neighbor_search; typedef K_neighbor_search::Tree Kd_tree; public: @@ -93,7 +93,7 @@ public: private: const Persistence_graph& g; const double r; - std::vector> neighbors_finder; + std::vector> neighbors_finder; }; inline Neighbors_finder::Neighbors_finder(const Persistence_graph& g, double r) : @@ -123,7 +123,7 @@ inline int Neighbors_finder::pull_near(int u_point_index) { //Is the query point near to a V point in the plane ? Internal_point u_point = g.get_u_point(u_point_index); std::array w = { {1., 1.} }; - K_neighbor_search search(kd_t, u_point, 0., true, Distance(0, 2, w.begin(), w.end())); + K_neighbor_search search(kd_t, u_point, 1, 0., true, Distance(0, 2, w.begin(), w.end())); auto it = search.begin(); if(it==search.end() || g.distance(u_point_index, it->first.point_index) > r) return null_point_index(); @@ -148,7 +148,7 @@ inline Layered_neighbors_finder::Layered_neighbors_finder(const Persistence_grap 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(g, r))); + neighbors_finder.emplace_back(std::unique_ptr(new Neighbors_finder(g, r))); neighbors_finder.at(vlayer)->add(v_point_index); } diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h index ebd3adaf..d31a4826 100644 --- a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h +++ b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h @@ -76,16 +76,18 @@ Persistence_graph::Persistence_graph(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e) : u(), v(), alive_count(0) { - for (auto it = diag1.cbegin(); it != diag1.cend(); ++it) - if(it->second == std::numeric_limits::infinity()) + for (auto it = std::begin(diag1); it != std::end(diag1); ++it){ + if(std::get<1>(*it) == std::numeric_limits::infinity()) alive_count++; - else if (it->second - it->first > e) + if (std::get<1>(*it) - std::get<0>(*it) > e) u.push_back(Internal_point(std::get<0>(*it), std::get<1>(*it), u.size())); - for (auto it = diag2.cbegin(); it != diag2.cend(); ++it) - if(it->second == std::numeric_limits::infinity()) + } + for (auto it = std::begin(diag2); it != std::end(diag2); ++it){ + if(std::get<1>(*it) == std::numeric_limits::infinity()) alive_count--; - else if (it->second - it->first > e) + if (std::get<1>(*it) - std::get<0>(*it) > e) v.push_back(Internal_point(std::get<0>(*it), std::get<1>(*it), v.size())); + } if (u.size() < v.size()) swap(u, v); } @@ -113,6 +115,8 @@ inline double Persistence_graph::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); + if(p_u.y() == p_v.y()) + return std::fabs(p_u.x() - p_v.x()); return std::max(std::fabs(p_u.x() - p_v.x()), std::fabs(p_u.y() - p_v.y())); } @@ -155,9 +159,9 @@ inline Internal_point Persistence_graph::get_v_point(int v_point_index) const { inline double Persistence_graph::diameter_bound() const { double max = 0.; for(auto it = u.cbegin(); it != u.cend(); it++) - max = std::max(max,it->y()); + max = std::max(max,it->y() == std::numeric_limits::infinity() ? it->x() : it->y()); for(auto it = v.cbegin(); it != v.cend(); it++) - max = std::max(max,it->y()); + max = std::max(max,it->y() == std::numeric_limits::infinity() ? it->x() : it->y()); return max; } -- cgit v1.2.3 From d0db67f8ff185a7698d2f6643d86e43955bab882 Mon Sep 17 00:00:00 2001 From: fgodi Date: Tue, 6 Dec 2016 16:20:10 +0000 Subject: infinite points separately computed git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1828 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 5d1cd63a1b8ff26feffce86a4febe2f42d52340d --- .../concept/Persistence_diagram.h | 16 ++++------- src/Bottleneck_distance/include/gudhi/Bottleneck.h | 11 +++++--- .../include/gudhi/Persistence_graph.h | 33 +++++++++++++--------- 3 files changed, 33 insertions(+), 27 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/concept/Persistence_diagram.h b/src/Bottleneck_distance/concept/Persistence_diagram.h index d55f5573..e4766628 100644 --- a/src/Bottleneck_distance/concept/Persistence_diagram.h +++ b/src/Bottleneck_distance/concept/Persistence_diagram.h @@ -27,24 +27,20 @@ namespace Gudhi { namespace bottleneck_distance { -/** \brief Concept of Diagram_point. get<0>() must return the birth of the corresponding component and get<1>() its death. - * If the component stay alive, get<1>() must return std::numeric_limits::infinity(). +/** \brief Concept of Diagram_point. std::get<0>(point) must return the birth of the corresponding component and std::get<1>(point) its death. + * A valid implementation of this concept is std::pair. + * Birth must be 0 or positive, death should be larger than birth, death can be std::numeric_limits::infinity() for components which stay alive. * * \ingroup bottleneck_distance */ -struct Diagram_point{ - double get(); -}; +struct Diagram_point; /** \brief Concept of persistence diagram. It's a range of Diagram_point. + * std::begin(diagram) and std::end(diagram) must return corresponding iterators. * * \ingroup bottleneck_distance */ -struct Persistence_Diagram -{ - iterator begin(); - iterator end(); -}; +struct Persistence_Diagram; } // namespace bottleneck_distance diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h index 20225e80..4a69fb96 100644 --- a/src/Bottleneck_distance/include/gudhi/Bottleneck.h +++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h @@ -24,12 +24,13 @@ #define BOTTLENECK_H_ #include +#include namespace Gudhi { namespace bottleneck_distance { -/** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams. +/** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams (see Concepts). * If the last parameter e is not 0 (default value if not explicited), you get an additive e-approximation. * * \ingroup bottleneck_distance @@ -37,7 +38,8 @@ namespace bottleneck_distance { template double compute(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e=0.) { Persistence_graph g(diag1, diag2, e); - if(!g.alive_match()) + double b = g.bottleneck_alive(); + if(b == std::numeric_limits::infinity()) return std::numeric_limits::infinity(); std::vector sd; if(e == 0.) @@ -45,7 +47,7 @@ double compute(const Persistence_diagram1 &diag1, const Persistence_diagram2 &di long idmin = 0; long idmax = e==0. ? sd.size() - 1 : g.diameter_bound()/e + 1; // alpha can change the complexity - double alpha = pow(idmax, 0.25); + double alpha = std::pow(idmax, 0.25); Graph_matching m(g); Graph_matching biggest_unperfect(g); while (idmin != idmax) { @@ -61,7 +63,8 @@ double compute(const Persistence_diagram1 &diag1, const Persistence_diagram2 &di idmin = idmin + step + 1; } } - return e == 0. ? sd.at(idmin) : e*(idmin); + b = std::max(b, e == 0. ? sd.at(idmin) : e*(idmin)); + return b; } diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h index d31a4826..8accb926 100644 --- a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h +++ b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h @@ -55,7 +55,7 @@ public: /** \internal \brief Returns size = |U| = |V|. */ int size() const; /** \internal \brief Is there as many infinite points (alive components) in both diagrams ? */ - bool alive_match() const; + double bottleneck_alive() const; /** \internal \brief Returns the O(n^2) sorted distances between the points. */ std::vector sorted_distances() const; /** \internal \brief Returns an upper bound for the diameter of the convex hull of all non infinite points */ @@ -68,26 +68,29 @@ public: private: std::vector u; std::vector v; - int alive_count; + std::vector u_alive; + std::vector v_alive; }; template Persistence_graph::Persistence_graph(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e) - : u(), v(), alive_count(0) + : u(), v(), u_alive(), v_alive() { for (auto it = std::begin(diag1); it != std::end(diag1); ++it){ if(std::get<1>(*it) == std::numeric_limits::infinity()) - alive_count++; - if (std::get<1>(*it) - std::get<0>(*it) > e) + u_alive.push_back(std::get<0>(*it)); + else if (std::get<1>(*it) - std::get<0>(*it) > e) u.push_back(Internal_point(std::get<0>(*it), std::get<1>(*it), u.size())); } for (auto it = std::begin(diag2); it != std::end(diag2); ++it){ if(std::get<1>(*it) == std::numeric_limits::infinity()) - alive_count--; - if (std::get<1>(*it) - std::get<0>(*it) > e) + v_alive.push_back(std::get<0>(*it)); + else if (std::get<1>(*it) - std::get<0>(*it) > e) v.push_back(Internal_point(std::get<0>(*it), std::get<1>(*it), v.size())); } + std::sort(u_alive.begin(), u_alive.end()); + std::sort(v_alive.begin(), v_alive.end()); if (u.size() < v.size()) swap(u, v); } @@ -115,8 +118,6 @@ inline double Persistence_graph::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); - if(p_u.y() == p_v.y()) - return std::fabs(p_u.x() - p_v.x()); return std::max(std::fabs(p_u.x() - p_v.x()), std::fabs(p_u.y() - p_v.y())); } @@ -124,8 +125,13 @@ inline int Persistence_graph::size() const { return static_cast (u.size() + v.size()); } -inline bool Persistence_graph::alive_match() const{ - return alive_count==0; +inline double Persistence_graph::bottleneck_alive() const{ + if(u_alive.size() != v_alive.size()) + return std::numeric_limits::infinity(); + double max = 0.; + for(auto it_u=u_alive.cbegin(), it_v=v_alive.cbegin();it_u != u_alive.cend();++it_u, ++it_v) + max = std::max(max, std::fabs(*it_u - *it_v)); + return max; } inline std::vector Persistence_graph::sorted_distances() const { @@ -159,12 +165,13 @@ inline Internal_point Persistence_graph::get_v_point(int v_point_index) const { inline double Persistence_graph::diameter_bound() const { double max = 0.; for(auto it = u.cbegin(); it != u.cend(); it++) - max = std::max(max,it->y() == std::numeric_limits::infinity() ? it->x() : it->y()); + max = std::max(max, it->y()); for(auto it = v.cbegin(); it != v.cend(); it++) - max = std::max(max,it->y() == std::numeric_limits::infinity() ? it->x() : it->y()); + max = std::max(max, it->y()); return max; } + } // namespace bottleneck_distance } // namespace Gudhi -- cgit v1.2.3 From 524652d3a8a46dd9749821ad2e7684937179d4eb Mon Sep 17 00:00:00 2001 From: fgodi Date: Tue, 6 Dec 2016 16:47:19 +0000 Subject: small modification git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1829 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: c4eeb9f4b467bdf23c8cd02b5aeac68170c9bcf9 --- .../include/gudhi/Persistence_graph.h | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h index 8accb926..f16a6c95 100644 --- a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h +++ b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h @@ -68,15 +68,16 @@ public: private: std::vector u; std::vector v; - std::vector u_alive; - std::vector v_alive; + double b_alive; }; template Persistence_graph::Persistence_graph(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e) - : u(), v(), u_alive(), v_alive() + : u(), v(), b_alive(0.) { + std::vector u_alive; + std::vector v_alive; for (auto it = std::begin(diag1); it != std::end(diag1); ++it){ if(std::get<1>(*it) == std::numeric_limits::infinity()) u_alive.push_back(std::get<0>(*it)); @@ -89,10 +90,14 @@ Persistence_graph::Persistence_graph(const Persistence_diagram1 &diag1, else if (std::get<1>(*it) - std::get<0>(*it) > e) v.push_back(Internal_point(std::get<0>(*it), std::get<1>(*it), v.size())); } - std::sort(u_alive.begin(), u_alive.end()); - std::sort(v_alive.begin(), v_alive.end()); if (u.size() < v.size()) swap(u, v); + std::sort(u_alive.begin(), u_alive.end()); + std::sort(v_alive.begin(), v_alive.end()); + if(u_alive.size() != v_alive.size()) + b_alive = std::numeric_limits::infinity(); + else for(auto it_u=u_alive.cbegin(), it_v=v_alive.cbegin();it_u != u_alive.cend();++it_u, ++it_v) + b_alive = std::max(b_alive, std::fabs(*it_u - *it_v)); } inline bool Persistence_graph::on_the_u_diagonal(int u_point_index) const { @@ -126,12 +131,7 @@ inline int Persistence_graph::size() const { } inline double Persistence_graph::bottleneck_alive() const{ - if(u_alive.size() != v_alive.size()) - return std::numeric_limits::infinity(); - double max = 0.; - for(auto it_u=u_alive.cbegin(), it_v=v_alive.cbegin();it_u != u_alive.cend();++it_u, ++it_v) - max = std::max(max, std::fabs(*it_u - *it_v)); - return max; + return b_alive; } inline std::vector Persistence_graph::sorted_distances() const { -- cgit v1.2.3 From f0e5330a88f9e89a887769ab79f6db6dd4e1c35a Mon Sep 17 00:00:00 2001 From: glisse Date: Mon, 12 Dec 2016 05:23:28 +0000 Subject: Boost bug https://svn.boost.org/trac/boost/ticket/12534 git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@1847 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 063ad9bf7bcf1163dc4935f8bdd93d6ea334609f --- src/GudhUI/gui/MainWindow.h | 3 +++ 1 file changed, 3 insertions(+) (limited to 'src') diff --git a/src/GudhUI/gui/MainWindow.h b/src/GudhUI/gui/MainWindow.h index c8c3fcf6..3fe0d720 100644 --- a/src/GudhUI/gui/MainWindow.h +++ b/src/GudhUI/gui/MainWindow.h @@ -26,6 +26,9 @@ // Workaround for moc-qt4 not parsing boost headers #include +// Workaround https://svn.boost.org/trac/boost/ticket/12534 +#include + #include #include "ui_main_window.h" #include "model/Model.h" -- cgit v1.2.3 From 12fa1bbb902bebb2ffc21482a25913ac7c49dc85 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 12 Dec 2016 10:04:42 +0000 Subject: Fix the bug, remove tan_test from examples and add a unitary test git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/tangential_test@1850 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 852570382d6f5713e534b49e7abf1e96a4a84076 --- CMakeLists.txt | 14 +++--- src/Tangential_complex/example/CMakeLists.txt | 5 -- src/Tangential_complex/example/tan_test.cpp | 54 -------------------- .../include/gudhi/Tangential_complex.h | 8 ++- .../test/test_tangential_complex.cpp | 57 ++++++++++++++++++++++ 5 files changed, 70 insertions(+), 68 deletions(-) delete mode 100644 src/Tangential_complex/example/tan_test.cpp (limited to 'src') diff --git a/CMakeLists.txt b/CMakeLists.txt index 005df6d7..78de6c09 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -73,13 +73,13 @@ else() set(Boost_USE_STATIC_RUNTIME OFF) # Find TBB package for parallel sort - not mandatory, just optional. - set(TBB_FIND_QUIETLY ON) - find_package(TBB) - if (TBB_FOUND) - include(${TBB_USE_FILE}) - message("TBB found in ${TBB_LIBRARY_DIRS}") - add_definitions(-DGUDHI_USE_TBB) - endif() + #set(TBB_FIND_QUIETLY ON) + #find_package(TBB) + #if (TBB_FOUND) + # include(${TBB_USE_FILE}) + # message("TBB found in ${TBB_LIBRARY_DIRS}") + # add_definitions(-DGUDHI_USE_TBB) + #endif() find_package(Eigen3 3.1.0) if (EIGEN3_FOUND) diff --git a/src/Tangential_complex/example/CMakeLists.txt b/src/Tangential_complex/example/CMakeLists.txt index 76ba0a32..32f6eebb 100644 --- a/src/Tangential_complex/example/CMakeLists.txt +++ b/src/Tangential_complex/example/CMakeLists.txt @@ -8,12 +8,9 @@ if(CGAL_FOUND) target_link_libraries(Tangential_complex_example_basic ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY}) add_executable( Tangential_complex_example_with_perturb example_with_perturb.cpp ) target_link_libraries(Tangential_complex_example_with_perturb ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY}) - add_executable( tan_test tan_test.cpp ) - target_link_libraries(tan_test ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY}) if (TBB_FOUND) target_link_libraries(Tangential_complex_example_basic ${TBB_LIBRARIES}) target_link_libraries(Tangential_complex_example_with_perturb ${TBB_LIBRARIES}) - target_link_libraries(tan_test ${TBB_LIBRARIES}) endif(TBB_FOUND) add_test(Tangential_complex_example_basic @@ -22,8 +19,6 @@ if(CGAL_FOUND) add_test(Tangential_complex_example_with_perturb ${CMAKE_CURRENT_BINARY_DIR}/Tangential_complex_example_with_perturb) - add_test(tan_test - ${CMAKE_CURRENT_BINARY_DIR}/tan_test) endif(EIGEN3_FOUND) endif(NOT CGAL_VERSION VERSION_LESS 4.8.0) endif(CGAL_FOUND) diff --git a/src/Tangential_complex/example/tan_test.cpp b/src/Tangential_complex/example/tan_test.cpp deleted file mode 100644 index afb9f13c..00000000 --- a/src/Tangential_complex/example/tan_test.cpp +++ /dev/null @@ -1,54 +0,0 @@ -#include -#include - -#include -#include - -#include -#include - -namespace tc = Gudhi::tangential_complex; - -typedef CGAL::Epick_d Kernel; -typedef Kernel::FT FT; -typedef Kernel::Point_d Point; -typedef Kernel::Vector_d Vector; -typedef tc::Tangential_complex< -Kernel, CGAL::Dynamic_dimension_tag, -CGAL::Parallel_tag> TC; - -int main(void) { - const int INTRINSIC_DIM = 1; - - // Generate points on a 2-sphere - std::vector points; - // [[0, 0], [1, 0], [0, 1], [1, 1]] - std::vector point = {0.0, 0.0}; - points.push_back(Point(point.size(), point.begin(), point.end())); - point = {1.0, 0.0}; - points.push_back(Point(point.size(), point.begin(), point.end())); - point = {0.0, 1.0}; - points.push_back(Point(point.size(), point.begin(), point.end())); - point = {1.0, 1.0}; - points.push_back(Point(point.size(), point.begin(), point.end())); - - Kernel k; - for (int i = 0; i < 100; i++) { - - // Compute the TC - TC tc(points, INTRINSIC_DIM, k); - tc.compute_tangential_complex(); - TC::Num_inconsistencies num_inc = tc.number_of_inconsistent_simplices(); - std::cout << "TC vertices = " << tc.number_of_vertices() << " - simplices = " << num_inc.num_simplices << - " - inconsistencies = " << num_inc.num_inconsistent_simplices << std::endl; - - tc.fix_inconsistencies_using_perturbation(10.0, 60.0); - // Export the TC into a Simplex_tree - Gudhi::Simplex_tree<> stree; - tc.create_complex(stree); - std::cout << "ST vertices = " << stree.num_vertices() << " - simplices = " << stree.num_simplices() << std::endl; - - } - - return 0; -} diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex.h b/src/Tangential_complex/include/gudhi/Tangential_complex.h index e748d3b7..90c164e2 100644 --- a/src/Tangential_complex/include/gudhi/Tangential_complex.h +++ b/src/Tangential_complex/include/gudhi/Tangential_complex.h @@ -1303,7 +1303,9 @@ class Tangential_complex { , bool normalize_basis = true , Orthogonal_space_basis *p_orth_space_basis = NULL ) { - unsigned int num_pts_for_pca = static_cast (std::pow(GUDHI_TC_BASE_VALUE_FOR_PCA, m_intrinsic_dim)); +// unsigned int num_pts_for_pca = static_cast (std::pow(GUDHI_TC_BASE_VALUE_FOR_PCA, m_intrinsic_dim)); + unsigned int num_pts_for_pca = (std::min)(static_cast (std::pow(GUDHI_TC_BASE_VALUE_FOR_PCA, m_intrinsic_dim)), + static_cast (m_points.size())); // Kernel functors typename K::Construct_vector_d constr_vec = @@ -1392,7 +1394,9 @@ class Tangential_complex { // on it. Note that most points are duplicated. Tangent_space_basis compute_tangent_space(const Simplex &s, bool normalize_basis = true) { - unsigned int num_pts_for_pca = static_cast (std::pow(GUDHI_TC_BASE_VALUE_FOR_PCA, m_intrinsic_dim)); +// unsigned int num_pts_for_pca = static_cast (std::pow(GUDHI_TC_BASE_VALUE_FOR_PCA, m_intrinsic_dim)); + unsigned int num_pts_for_pca = (std::min)(static_cast (std::pow(GUDHI_TC_BASE_VALUE_FOR_PCA, m_intrinsic_dim)), + static_cast (m_points.size())); // Kernel functors typename K::Construct_vector_d constr_vec = diff --git a/src/Tangential_complex/test/test_tangential_complex.cpp b/src/Tangential_complex/test/test_tangential_complex.cpp index f8b0d2fb..4c3dec3b 100644 --- a/src/Tangential_complex/test/test_tangential_complex.cpp +++ b/src/Tangential_complex/test/test_tangential_complex.cpp @@ -68,3 +68,60 @@ BOOST_AUTO_TEST_CASE(test_Spatial_tree_data_structure) { Gudhi::Simplex_tree<> stree; tc.create_complex(stree); } + +BOOST_AUTO_TEST_CASE(test_mini_tangential) { + typedef CGAL::Epick_d Kernel; + typedef Kernel::FT FT; + typedef Kernel::Point_d Point; + typedef Kernel::Vector_d Vector; + typedef tc::Tangential_complex TC; + + + const int INTRINSIC_DIM = 1; + + // Generate points on a 2-sphere + std::vector points; + // [[0, 0], [1, 0], [0, 1], [1, 1]] + std::vector point = {0.0, 0.0}; + points.push_back(Point(point.size(), point.begin(), point.end())); + point = {1.0, 0.0}; + points.push_back(Point(point.size(), point.begin(), point.end())); + point = {0.0, 1.0}; + points.push_back(Point(point.size(), point.begin(), point.end())); + point = {1.0, 1.0}; + points.push_back(Point(point.size(), point.begin(), point.end())); + std::cout << "points = " << points.size() << std::endl; + Kernel k; + + // Compute the TC + TC tc(points, INTRINSIC_DIM, k); + tc.compute_tangential_complex(); + TC::Num_inconsistencies num_inc = tc.number_of_inconsistent_simplices(); + std::cout << "TC vertices = " << tc.number_of_vertices() << " - simplices = " << num_inc.num_simplices << + " - inconsistencies = " << num_inc.num_inconsistent_simplices << std::endl; + + BOOST_CHECK(tc.number_of_vertices() == 4); + BOOST_CHECK(num_inc.num_simplices == 4); + BOOST_CHECK(num_inc.num_inconsistent_simplices == 2); + + // Export the TC into a Simplex_tree + Gudhi::Simplex_tree<> stree; + tc.create_complex(stree); + std::cout << "ST vertices = " << stree.num_vertices() << " - simplices = " << stree.num_simplices() << std::endl; + + BOOST_CHECK(stree.num_vertices() == 4); + BOOST_CHECK(stree.num_simplices() == 12); + + tc.fix_inconsistencies_using_perturbation(0.01, 30.0); + + BOOST_CHECK(tc.number_of_vertices() == 4); + BOOST_CHECK(num_inc.num_simplices == 4); + BOOST_CHECK(num_inc.num_inconsistent_simplices == 2); + + // Export the TC into a Simplex_tree + tc.create_complex(stree); + std::cout << "ST vertices = " << stree.num_vertices() << " - simplices = " << stree.num_simplices() << std::endl; + + BOOST_CHECK(stree.num_vertices() == 4); + BOOST_CHECK(stree.num_simplices() == 12); +} -- cgit v1.2.3 From 09150bdb2d0b7f55fd6014ca5fbd63fd002fafc9 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 12 Dec 2016 12:53:14 +0000 Subject: Fix max issue and remove (&tr == NULL) test git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/tangential_test@1852 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 932aa53773092c64f1d69ce0d4c0fdaf817b5b06 --- src/Tangential_complex/include/gudhi/Tangential_complex.h | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) (limited to 'src') diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex.h b/src/Tangential_complex/include/gudhi/Tangential_complex.h index 90c164e2..c9317a44 100644 --- a/src/Tangential_complex/include/gudhi/Tangential_complex.h +++ b/src/Tangential_complex/include/gudhi/Tangential_complex.h @@ -63,6 +63,7 @@ #include #include // for std::sqrt #include +#include // for std::size_t #ifdef GUDHI_USE_TBB #include @@ -82,7 +83,7 @@ using namespace internal; class Vertex_data { public: - Vertex_data(std::size_t data = std::numeric_limits::max()) + Vertex_data(std::size_t data = (std::numeric_limits::max)()) : m_data(data) { } operator std::size_t() { @@ -1048,7 +1049,7 @@ class Tangential_complex { #endif // GUDHI_USE_TBB bool is_infinite(Simplex const& s) const { - return *s.rbegin() == std::numeric_limits::max(); + return *s.rbegin() == (std::numeric_limits::max)(); } // Output: "triangulation" is a Regular Triangulation containing at least the @@ -1654,7 +1655,7 @@ class Tangential_complex { for (; it_point_idx != simplex.end(); ++it_point_idx) { std::size_t point_idx = *it_point_idx; // Don't check infinite simplices - if (point_idx == std::numeric_limits::max()) + if (point_idx == (std::numeric_limits::max)()) continue; Star const& star = m_stars[point_idx]; @@ -1693,7 +1694,7 @@ class Tangential_complex { for (; it_point_idx != s.end(); ++it_point_idx) { std::size_t point_idx = *it_point_idx; // Don't check infinite simplices - if (point_idx == std::numeric_limits::max()) + if (point_idx == (std::numeric_limits::max)()) continue; Star const& star = m_stars[point_idx]; @@ -1959,7 +1960,7 @@ class Tangential_complex { Triangulation const& tr = it_tr->tr(); Tr_vertex_handle center_vh = it_tr->center_vertex(); - if (&tr == NULL || tr.current_dimension() < m_intrinsic_dim) + if (tr.current_dimension() < m_intrinsic_dim) continue; // Color for this star -- cgit v1.2.3 From 454558fecf99cee350eb7d3f81a149c647805c16 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 12 Dec 2016 13:08:22 +0000 Subject: Use (std::numeric_limits::max) to fix Windows global min max git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/tangential_test@1853 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 970c2190f89a6f11712edc07c1980ce0cbdb486b --- src/Tangential_complex/benchmark/benchmark_tc.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'src') diff --git a/src/Tangential_complex/benchmark/benchmark_tc.cpp b/src/Tangential_complex/benchmark/benchmark_tc.cpp index 943fcb54..6d6dd548 100644 --- a/src/Tangential_complex/benchmark/benchmark_tc.cpp +++ b/src/Tangential_complex/benchmark/benchmark_tc.cpp @@ -161,7 +161,7 @@ typename Kernel, typename OutputIteratorPoints> bool load_points_from_file( const std::string &filename, OutputIteratorPoints points, - std::size_t only_first_n_points = std::numeric_limits::max()) { + std::size_t only_first_n_points = (std::numeric_limits::max)()) { typedef typename Kernel::Point_d Point; std::ifstream in(filename); @@ -196,7 +196,7 @@ bool load_points_and_tangent_space_basis_from_file( OutputIteratorPoints points, OutputIteratorTS tangent_spaces, int intrinsic_dim, - std::size_t only_first_n_points = std::numeric_limits::max()) { + std::size_t only_first_n_points = (std::numeric_limits::max)()) { typedef typename Kernel::Point_d Point; typedef typename Kernel::Vector_d Vector; -- cgit v1.2.3 From 8c1fdb043e58e6d5006d51c46cdf54b5de4613e7 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Mon, 12 Dec 2016 13:28:57 +0000 Subject: parenthesis for std::min because of Windows min global function git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/tangential_test@1854 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 4540b7f111515cbe8e9e53c78fc00111533306f1 --- src/Tangential_complex/include/gudhi/Tangential_complex.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'src') diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex.h b/src/Tangential_complex/include/gudhi/Tangential_complex.h index c9317a44..2d185a90 100644 --- a/src/Tangential_complex/include/gudhi/Tangential_complex.h +++ b/src/Tangential_complex/include/gudhi/Tangential_complex.h @@ -1905,7 +1905,7 @@ class Tangential_complex { #ifdef GUDHI_TC_EXPORT_ALL_COORDS_IN_OFF int num_coords = m_ambient_dim; #else - int num_coords = std::min(m_ambient_dim, 3); + int num_coords = (std::min)(m_ambient_dim, 3); #endif #ifdef GUDHI_TC_EXPORT_NORMALS -- cgit v1.2.3 From da92ae2f10d715b801f55f8f651fea8a4979f263 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 13 Dec 2016 10:28:07 +0000 Subject: Add example just for Mac test. To be removed. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/tangential_test@1861 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: be598143de42dba782462985515cbc77b0a51e8b --- src/Tangential_complex/example/CMakeLists.txt | 3 ++ src/Tangential_complex/example/example.cpp | 78 +++++++++++++++++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 src/Tangential_complex/example/example.cpp (limited to 'src') diff --git a/src/Tangential_complex/example/CMakeLists.txt b/src/Tangential_complex/example/CMakeLists.txt index 32f6eebb..291432b0 100644 --- a/src/Tangential_complex/example/CMakeLists.txt +++ b/src/Tangential_complex/example/CMakeLists.txt @@ -8,9 +8,12 @@ if(CGAL_FOUND) target_link_libraries(Tangential_complex_example_basic ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY}) add_executable( Tangential_complex_example_with_perturb example_with_perturb.cpp ) target_link_libraries(Tangential_complex_example_with_perturb ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY}) + add_executable( example example.cpp ) + target_link_libraries(example ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY}) if (TBB_FOUND) target_link_libraries(Tangential_complex_example_basic ${TBB_LIBRARIES}) target_link_libraries(Tangential_complex_example_with_perturb ${TBB_LIBRARIES}) + target_link_libraries(example ${TBB_LIBRARIES}) endif(TBB_FOUND) add_test(Tangential_complex_example_basic diff --git a/src/Tangential_complex/example/example.cpp b/src/Tangential_complex/example/example.cpp new file mode 100644 index 00000000..cd0f121f --- /dev/null +++ b/src/Tangential_complex/example/example.cpp @@ -0,0 +1,78 @@ +#include +#include + +#include +#include + +#include +#include + +namespace tc = Gudhi::tangential_complex; + + +int main(void) { + typedef CGAL::Epick_d Kernel; + typedef Kernel::FT FT; + typedef Kernel::Point_d Point; + typedef Kernel::Vector_d Vector; + typedef tc::Tangential_complex TC; + + + const int INTRINSIC_DIM = 1; + + // Generate points on a 2-sphere + std::vector points; + // [[0, 0], [1, 0], [0, 1], [1, 1]] + std::vector point = {0.0, 0.0}; + points.push_back(Point(point.size(), point.begin(), point.end())); + point = {1.0, 0.0}; + points.push_back(Point(point.size(), point.begin(), point.end())); + point = {0.0, 1.0}; + points.push_back(Point(point.size(), point.begin(), point.end())); + point = {1.0, 1.0}; + points.push_back(Point(point.size(), point.begin(), point.end())); + std::cout << "points = " << points.size() << std::endl; + Kernel k; + + // Compute the TC + TC tc(points, INTRINSIC_DIM, k); + tc.compute_tangential_complex(); + TC::Num_inconsistencies num_inc = tc.number_of_inconsistent_simplices(); + std::cout << "TC vertices = " << tc.number_of_vertices() << " - simplices = " << num_inc.num_simplices << + " - inconsistencies = " << num_inc.num_inconsistent_simplices << std::endl; + + // Export the TC into a Simplex_tree + Gudhi::Simplex_tree<> stree; + tc.create_complex(stree); + + std::cout << "********************************************************************\n"; + std::cout << "* The complex contains " << stree.num_simplices() << " simplices"; + std::cout << " - dimension " << stree.dimension() << " - filtration " << stree.filtration() << "\n"; + std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; + for (auto f_simplex : stree.filtration_simplex_range()) { + std::cout << " " << "[" << stree.filtration(f_simplex) << "] "; + for (auto vertex : stree.simplex_vertex_range(f_simplex)) { + std::cout << static_cast(vertex) << " "; + } + std::cout << std::endl; + } + + tc.fix_inconsistencies_using_perturbation(0.01, 30.0); + + // Export the TC into a Simplex_tree + tc.create_complex(stree); + + std::cout << "********************************************************************\n"; + std::cout << "* The complex contains " << stree.num_simplices() << " simplices\n"; + std::cout << " - dimension " << stree.dimension() << " - filtration " << stree.filtration() << "\n"; + std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; + for (auto f_simplex : stree.filtration_simplex_range()) { + std::cout << " " << "[" << stree.filtration(f_simplex) << "] "; + for (auto vertex : stree.simplex_vertex_range(f_simplex)) { + std::cout << static_cast(vertex) << " "; + } + std::cout << std::endl; + } + + return 0; +} -- cgit v1.2.3 From 0c277327bb7fbbc096825ed817458440930cca33 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 13 Dec 2016 11:53:31 +0000 Subject: Example modification git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/tangential_test@1863 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 0706eed9656c214bbabfa9a8da2f800c2afdf140 --- src/Tangential_complex/example/example.cpp | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) (limited to 'src') diff --git a/src/Tangential_complex/example/example.cpp b/src/Tangential_complex/example/example.cpp index cd0f121f..fa25ac53 100644 --- a/src/Tangential_complex/example/example.cpp +++ b/src/Tangential_complex/example/example.cpp @@ -43,7 +43,9 @@ int main(void) { // Export the TC into a Simplex_tree Gudhi::Simplex_tree<> stree; - tc.create_complex(stree); + int max_dim = tc.create_complex(stree); + stree.set_dimension(max_dim); + stree.initialize_filtration(); std::cout << "********************************************************************\n"; std::cout << "* The complex contains " << stree.num_simplices() << " simplices"; @@ -60,7 +62,9 @@ int main(void) { tc.fix_inconsistencies_using_perturbation(0.01, 30.0); // Export the TC into a Simplex_tree - tc.create_complex(stree); + max_dim = tc.create_complex(stree); + stree.set_dimension(max_dim); + stree.initialize_filtration(); std::cout << "********************************************************************\n"; std::cout << "* The complex contains " << stree.num_simplices() << " simplices\n"; -- cgit v1.2.3 From 1860c2f5e93b789fa14095668dc0b62d94dddfa5 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 13 Dec 2016 12:36:20 +0000 Subject: example point display git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/tangential_test@1864 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 1a97b8a9c1f7aff6cdeae8a2fa0eef911f4a5596 --- src/Tangential_complex/example/example.cpp | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) (limited to 'src') diff --git a/src/Tangential_complex/example/example.cpp b/src/Tangential_complex/example/example.cpp index fa25ac53..f740cb1c 100644 --- a/src/Tangential_complex/example/example.cpp +++ b/src/Tangential_complex/example/example.cpp @@ -41,6 +41,9 @@ int main(void) { std::cout << "TC vertices = " << tc.number_of_vertices() << " - simplices = " << num_inc.num_simplices << " - inconsistencies = " << num_inc.num_inconsistent_simplices << std::endl; + std::cout << "TC point[0] " << tc.get_point(0) << " - point[1] " << tc.get_point(1) << + " - point[2] " << tc.get_point(2) << " - point[3] " << tc.get_point(3) << std::endl; + // Export the TC into a Simplex_tree Gudhi::Simplex_tree<> stree; int max_dim = tc.create_complex(stree); @@ -67,7 +70,7 @@ int main(void) { stree.initialize_filtration(); std::cout << "********************************************************************\n"; - std::cout << "* The complex contains " << stree.num_simplices() << " simplices\n"; + std::cout << "* The complex contains " << stree.num_simplices() << " simplices"; std::cout << " - dimension " << stree.dimension() << " - filtration " << stree.filtration() << "\n"; std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; for (auto f_simplex : stree.filtration_simplex_range()) { -- cgit v1.2.3 From 9e8db290ff0b3f69f88fa5ed54482bfb6730ad9b Mon Sep 17 00:00:00 2001 From: skachano Date: Wed, 14 Dec 2016 14:03:59 +0000 Subject: Improved the documentation for choose_farthest_points git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/subsampling_and_spatialsearching@1869 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 08223b7d1788c73b0fb3fc7255a6386896b63626 --- .../include/gudhi/choose_n_farthest_points.h | 31 +++++++++++++++++++--- 1 file changed, 27 insertions(+), 4 deletions(-) (limited to 'src') diff --git a/src/Subsampling/include/gudhi/choose_n_farthest_points.h b/src/Subsampling/include/gudhi/choose_n_farthest_points.h index 40c7808d..43bf6402 100644 --- a/src/Subsampling/include/gudhi/choose_n_farthest_points.h +++ b/src/Subsampling/include/gudhi/choose_n_farthest_points.h @@ -48,15 +48,27 @@ namespace subsampling { * \brief Subsample by a greedy strategy of iteratively adding the farthest point from the * current chosen point set to the subsampling. * The iteration starts with the landmark `starting point`. + * \tparam Kernel must provide a type Kernel::Squared_distance_d which is a model of the + * concept Kernel_d::Squared_distance_d + * concept. + * \tparam Point_range Range whose value type is Kernel::Point_d. It must provide random-access + * via `operator[]` and the points should be stored contiguously in memory. + * \tparam OutputIterator Output iterator whose value type is Kernel::Point_d. * \details It chooses `final_size` points from a random access range `input_pts` and * outputs it in the output iterator `output_it`. + * @param[in] k A kernel object. + * @param[in] input_pts Const reference to the input points. + * @param[in] final_size The size of the subsample to compute. + * @param[in] starting_point The seed in the farthest point algorithm. + * @param[out] output_it The output iterator. * */ template < typename Kernel, -typename Point_container, +typename Point_range, typename OutputIterator> void choose_n_farthest_points(Kernel const &k, - Point_container const &input_pts, + Point_range const &input_pts, std::size_t final_size, std::size_t starting_point, OutputIterator output_it) { @@ -96,15 +108,26 @@ void choose_n_farthest_points(Kernel const &k, * \brief Subsample by a greedy strategy of iteratively adding the farthest point from the * current chosen point set to the subsampling. * The iteration starts with a random landmark. + * \tparam Kernel must provide a type Kernel::Squared_distance_d which is a model of the + * concept Kernel_d::Squared_distance_d + * concept. + * \tparam Point_range Range whose value type is Kernel::Point_d. It must provide random-access + * via `operator[]` and the points should be stored contiguously in memory. + * \tparam OutputIterator Output iterator whose value type is Kernel::Point_d. * \details It chooses `final_size` points from a random access range `input_pts` and * outputs it in the output iterator `output_it`. + * @param[in] k A kernel object. + * @param[in] input_pts Const reference to the input points. + * @param[in] final_size The size of the subsample to compute. + * @param[out] output_it The output iterator. * */ template < typename Kernel, -typename Point_container, +typename Point_range, typename OutputIterator> void choose_n_farthest_points(Kernel const& k, - Point_container const &input_pts, + Point_range const &input_pts, unsigned final_size, OutputIterator output_it) { // Choose randomly the first landmark -- cgit v1.2.3 From 5703e63889f239e11a6688cda43011cb27282d99 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 14 Dec 2016 15:24:13 +0000 Subject: example modif git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/tangential_test@1870 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 43cf0d0b91808445614a3dc3d51ee87679c1a5d1 --- src/Tangential_complex/example/example.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'src') diff --git a/src/Tangential_complex/example/example.cpp b/src/Tangential_complex/example/example.cpp index f740cb1c..a503091c 100644 --- a/src/Tangential_complex/example/example.cpp +++ b/src/Tangential_complex/example/example.cpp @@ -39,7 +39,7 @@ int main(void) { tc.compute_tangential_complex(); TC::Num_inconsistencies num_inc = tc.number_of_inconsistent_simplices(); std::cout << "TC vertices = " << tc.number_of_vertices() << " - simplices = " << num_inc.num_simplices << - " - inconsistencies = " << num_inc.num_inconsistent_simplices << std::endl; + " - inc simplices = " << num_inc.num_inconsistent_simplices << " - inc stars = " << num_inc.num_inconsistent_stars << std::endl; std::cout << "TC point[0] " << tc.get_point(0) << " - point[1] " << tc.get_point(1) << " - point[2] " << tc.get_point(2) << " - point[3] " << tc.get_point(3) << std::endl; -- cgit v1.2.3 From 42e91253237a19af47c9a721a7f119dccc89113a Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 14 Dec 2016 15:46:39 +0000 Subject: Add traces git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/tangential_test@1871 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: b37d7be6b0f2ecc5217180e7ce3b14ab338c2354 --- src/Tangential_complex/include/gudhi/Tangential_complex.h | 5 +++++ 1 file changed, 5 insertions(+) (limited to 'src') diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex.h b/src/Tangential_complex/include/gudhi/Tangential_complex.h index 2d185a90..fc368a5d 100644 --- a/src/Tangential_complex/include/gudhi/Tangential_complex.h +++ b/src/Tangential_complex/include/gudhi/Tangential_complex.h @@ -1364,6 +1364,11 @@ class Tangential_complex { eig.eigenvectors().col(j).data() + m_ambient_dim)); } } + for (auto v : tsb) { + for (int i = 0; i < 2; ++i) + std::cerr << coord(v, i) << ", "; + std::cerr << "\n"; + } if (p_orth_space_basis) { p_orth_space_basis->set_origin(i); -- cgit v1.2.3 From b1e6e79715f68498c04a88e7d2237ec478078d11 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 14 Dec 2016 16:00:37 +0000 Subject: Points perturb git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/tangential_test@1872 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: f194dac5b999169fdf29fbb9223f0ee9db9c12ba --- src/Tangential_complex/example/example.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'src') diff --git a/src/Tangential_complex/example/example.cpp b/src/Tangential_complex/example/example.cpp index a503091c..b7eb542b 100644 --- a/src/Tangential_complex/example/example.cpp +++ b/src/Tangential_complex/example/example.cpp @@ -25,9 +25,9 @@ int main(void) { // [[0, 0], [1, 0], [0, 1], [1, 1]] std::vector point = {0.0, 0.0}; points.push_back(Point(point.size(), point.begin(), point.end())); - point = {1.0, 0.0}; + point = {1.1, 0.0}; points.push_back(Point(point.size(), point.begin(), point.end())); - point = {0.0, 1.0}; + point = {0.2, 1.3}; points.push_back(Point(point.size(), point.begin(), point.end())); point = {1.0, 1.0}; points.push_back(Point(point.size(), point.begin(), point.end())); -- cgit v1.2.3 From 28b7623d0aed90abe58260861c85b20e43227216 Mon Sep 17 00:00:00 2001 From: cjamin Date: Wed, 14 Dec 2016 18:02:15 +0000 Subject: Bug fix for degenerate cases git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/tangential_test@1873 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a292246c5e85275ec8bbf293fa0157d6693121cf --- src/Tangential_complex/include/gudhi/Tangential_complex.h | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) (limited to 'src') diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex.h b/src/Tangential_complex/include/gudhi/Tangential_complex.h index fc368a5d..18919362 100644 --- a/src/Tangential_complex/include/gudhi/Tangential_complex.h +++ b/src/Tangential_complex/include/gudhi/Tangential_complex.h @@ -1131,7 +1131,7 @@ class Tangential_complex { Tr_vertex_handle vh = triangulation.insert_if_in_star(proj_pt, center_vertex); // Tr_vertex_handle vh = triangulation.insert(proj_pt); - if (vh != Tr_vertex_handle()) { + if (vh != Tr_vertex_handle() && vh->data() == (std::numeric_limits::max())) { #ifdef GUDHI_TC_VERY_VERBOSE ++num_inserted_points; #endif @@ -1293,6 +1293,8 @@ class Tangential_complex { if (index != i) incident_simplex.insert(index); } + GUDHI_CHECK(incident_simplex.size() == cur_dim_plus_1 - 1, + std::logic_error("update_star: wrong size of incident simplex")); star.push_back(incident_simplex); } } -- cgit v1.2.3 From 04f4501b35eaa2bd33393ef2445d038251ba1355 Mon Sep 17 00:00:00 2001 From: skachano Date: Wed, 14 Dec 2016 18:08:09 +0000 Subject: Added an example with a distance matrix for the farthest point algorithm git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/subsampling_and_spatialsearching@1874 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 340e465189dc7ec8f8706e60e2d8097b53bfd5a0 --- src/Subsampling/example/CMakeLists.txt | 1 + src/Subsampling/example/example_custom_kernel.cpp | 69 ++++++++++++++++++++++ .../include/gudhi/choose_n_farthest_points.h | 4 +- 3 files changed, 73 insertions(+), 1 deletion(-) create mode 100644 src/Subsampling/example/example_custom_kernel.cpp (limited to 'src') diff --git a/src/Subsampling/example/CMakeLists.txt b/src/Subsampling/example/CMakeLists.txt index 54349f0c..0fd3335c 100644 --- a/src/Subsampling/example/CMakeLists.txt +++ b/src/Subsampling/example/CMakeLists.txt @@ -6,6 +6,7 @@ if(CGAL_FOUND) if (EIGEN3_FOUND) add_executable(Subsampling_example_pick_n_random_points example_pick_n_random_points.cpp) add_executable(Subsampling_example_choose_n_farthest_points example_choose_n_farthest_points.cpp) + add_executable(Subsampling_example_custom_kernel example_custom_kernel.cpp) add_executable(Subsampling_example_sparsify_point_set example_sparsify_point_set.cpp) target_link_libraries(Subsampling_example_sparsify_point_set ${CGAL_LIBRARY}) diff --git a/src/Subsampling/example/example_custom_kernel.cpp b/src/Subsampling/example/example_custom_kernel.cpp new file mode 100644 index 00000000..05797ebe --- /dev/null +++ b/src/Subsampling/example/example_custom_kernel.cpp @@ -0,0 +1,69 @@ +#include + +#include +#include + +#include +#include + + +/* The class Kernel contains a distance function defined on the set of points {0,1,2,3} + * and computes a distance according to the matrix: + * 0 1 2 4 + * 1 0 4 2 + * 2 4 0 1 + * 4 2 1 0 + */ +class Kernel { +public: + typedef double FT; + typedef unsigned Point_d; + + // Class Squared_distance_d + class Squared_distance_d { + private: + std::vector> matrix_; + + public: + + Squared_distance_d() + { + matrix_.push_back(std::vector({0,1,2,4})); + matrix_.push_back(std::vector({1,0,4,2})); + matrix_.push_back(std::vector({2,4,0,1})); + matrix_.push_back(std::vector({4,2,1,0})); + } + + FT operator()(Point_d p1, Point_d p2) + { + return matrix_[p1][p2]; + } + }; + + // Constructor + Kernel() + {} + + // Object of type Squared_distance_d + Squared_distance_d squared_distance_d_object() const + { + return Squared_distance_d(); + } + +}; + +int main(void) { + typedef Kernel K; + typedef typename K::Point_d Point_d; + + K k; + std::vector points = {0,1,2,3}; + std::vector results; + + Gudhi::subsampling::choose_n_farthest_points(k, points, 2, std::back_inserter(results)); + std::cout << "Before sparsification: " << points.size() << " points.\n"; + std::cout << "After sparsification: " << results.size() << " points.\n"; + std::cout << "Result table: {" << results[0] << "," << results[1] << "}\n"; + + return 0; +} diff --git a/src/Subsampling/include/gudhi/choose_n_farthest_points.h b/src/Subsampling/include/gudhi/choose_n_farthest_points.h index 43bf6402..b6b7ace3 100644 --- a/src/Subsampling/include/gudhi/choose_n_farthest_points.h +++ b/src/Subsampling/include/gudhi/choose_n_farthest_points.h @@ -52,6 +52,7 @@ namespace subsampling { * concept Kernel_d::Squared_distance_d * concept. + * It must also contain a public member 'squared_distance_d_object' of this type. * \tparam Point_range Range whose value type is Kernel::Point_d. It must provide random-access * via `operator[]` and the points should be stored contiguously in memory. * \tparam OutputIterator Output iterator whose value type is Kernel::Point_d. @@ -112,6 +113,7 @@ void choose_n_farthest_points(Kernel const &k, * concept Kernel_d::Squared_distance_d * concept. + * It must also contain a public member 'squared_distance_d_object' of this type. * \tparam Point_range Range whose value type is Kernel::Point_d. It must provide random-access * via `operator[]` and the points should be stored contiguously in memory. * \tparam OutputIterator Output iterator whose value type is Kernel::Point_d. @@ -133,7 +135,7 @@ void choose_n_farthest_points(Kernel const& k, // Choose randomly the first landmark std::random_device rd; std::mt19937 gen(rd()); - std::uniform_int_distribution<> dis(1, 6); + std::uniform_int_distribution<> dis(0, final_size); int starting_point = dis(gen); choose_n_farthest_points(k, input_pts, final_size, starting_point, output_it); } -- cgit v1.2.3 From c7cd528c7fa9a548dd47586ae258d33168e04a07 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 15 Dec 2016 09:27:42 +0000 Subject: Remove example.cpp Remove tangent traces in Tangential_complex.h Modify test_tangential_complex.cpp to make UT work git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/tangential_test@1875 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 1bd09671ca6f30c66cce7b48b382e1a8e4fbd3b5 --- src/Tangential_complex/example/CMakeLists.txt | 3 - src/Tangential_complex/example/example.cpp | 85 ---------------------- .../include/gudhi/Tangential_complex.h | 5 -- .../test/test_tangential_complex.cpp | 13 ++-- 4 files changed, 8 insertions(+), 98 deletions(-) delete mode 100644 src/Tangential_complex/example/example.cpp (limited to 'src') diff --git a/src/Tangential_complex/example/CMakeLists.txt b/src/Tangential_complex/example/CMakeLists.txt index 291432b0..32f6eebb 100644 --- a/src/Tangential_complex/example/CMakeLists.txt +++ b/src/Tangential_complex/example/CMakeLists.txt @@ -8,12 +8,9 @@ if(CGAL_FOUND) target_link_libraries(Tangential_complex_example_basic ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY}) add_executable( Tangential_complex_example_with_perturb example_with_perturb.cpp ) target_link_libraries(Tangential_complex_example_with_perturb ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY}) - add_executable( example example.cpp ) - target_link_libraries(example ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY}) if (TBB_FOUND) target_link_libraries(Tangential_complex_example_basic ${TBB_LIBRARIES}) target_link_libraries(Tangential_complex_example_with_perturb ${TBB_LIBRARIES}) - target_link_libraries(example ${TBB_LIBRARIES}) endif(TBB_FOUND) add_test(Tangential_complex_example_basic diff --git a/src/Tangential_complex/example/example.cpp b/src/Tangential_complex/example/example.cpp deleted file mode 100644 index b7eb542b..00000000 --- a/src/Tangential_complex/example/example.cpp +++ /dev/null @@ -1,85 +0,0 @@ -#include -#include - -#include -#include - -#include -#include - -namespace tc = Gudhi::tangential_complex; - - -int main(void) { - typedef CGAL::Epick_d Kernel; - typedef Kernel::FT FT; - typedef Kernel::Point_d Point; - typedef Kernel::Vector_d Vector; - typedef tc::Tangential_complex TC; - - - const int INTRINSIC_DIM = 1; - - // Generate points on a 2-sphere - std::vector points; - // [[0, 0], [1, 0], [0, 1], [1, 1]] - std::vector point = {0.0, 0.0}; - points.push_back(Point(point.size(), point.begin(), point.end())); - point = {1.1, 0.0}; - points.push_back(Point(point.size(), point.begin(), point.end())); - point = {0.2, 1.3}; - points.push_back(Point(point.size(), point.begin(), point.end())); - point = {1.0, 1.0}; - points.push_back(Point(point.size(), point.begin(), point.end())); - std::cout << "points = " << points.size() << std::endl; - Kernel k; - - // Compute the TC - TC tc(points, INTRINSIC_DIM, k); - tc.compute_tangential_complex(); - TC::Num_inconsistencies num_inc = tc.number_of_inconsistent_simplices(); - std::cout << "TC vertices = " << tc.number_of_vertices() << " - simplices = " << num_inc.num_simplices << - " - inc simplices = " << num_inc.num_inconsistent_simplices << " - inc stars = " << num_inc.num_inconsistent_stars << std::endl; - - std::cout << "TC point[0] " << tc.get_point(0) << " - point[1] " << tc.get_point(1) << - " - point[2] " << tc.get_point(2) << " - point[3] " << tc.get_point(3) << std::endl; - - // Export the TC into a Simplex_tree - Gudhi::Simplex_tree<> stree; - int max_dim = tc.create_complex(stree); - stree.set_dimension(max_dim); - stree.initialize_filtration(); - - std::cout << "********************************************************************\n"; - std::cout << "* The complex contains " << stree.num_simplices() << " simplices"; - std::cout << " - dimension " << stree.dimension() << " - filtration " << stree.filtration() << "\n"; - std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; - for (auto f_simplex : stree.filtration_simplex_range()) { - std::cout << " " << "[" << stree.filtration(f_simplex) << "] "; - for (auto vertex : stree.simplex_vertex_range(f_simplex)) { - std::cout << static_cast(vertex) << " "; - } - std::cout << std::endl; - } - - tc.fix_inconsistencies_using_perturbation(0.01, 30.0); - - // Export the TC into a Simplex_tree - max_dim = tc.create_complex(stree); - stree.set_dimension(max_dim); - stree.initialize_filtration(); - - std::cout << "********************************************************************\n"; - std::cout << "* The complex contains " << stree.num_simplices() << " simplices"; - std::cout << " - dimension " << stree.dimension() << " - filtration " << stree.filtration() << "\n"; - std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; - for (auto f_simplex : stree.filtration_simplex_range()) { - std::cout << " " << "[" << stree.filtration(f_simplex) << "] "; - for (auto vertex : stree.simplex_vertex_range(f_simplex)) { - std::cout << static_cast(vertex) << " "; - } - std::cout << std::endl; - } - - return 0; -} diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex.h b/src/Tangential_complex/include/gudhi/Tangential_complex.h index 18919362..6c0bbce6 100644 --- a/src/Tangential_complex/include/gudhi/Tangential_complex.h +++ b/src/Tangential_complex/include/gudhi/Tangential_complex.h @@ -1366,11 +1366,6 @@ class Tangential_complex { eig.eigenvectors().col(j).data() + m_ambient_dim)); } } - for (auto v : tsb) { - for (int i = 0; i < 2; ++i) - std::cerr << coord(v, i) << ", "; - std::cerr << "\n"; - } if (p_orth_space_basis) { p_orth_space_basis->set_origin(i); diff --git a/src/Tangential_complex/test/test_tangential_complex.cpp b/src/Tangential_complex/test/test_tangential_complex.cpp index 4c3dec3b..ebe5cdb4 100644 --- a/src/Tangential_complex/test/test_tangential_complex.cpp +++ b/src/Tangential_complex/test/test_tangential_complex.cpp @@ -98,11 +98,13 @@ BOOST_AUTO_TEST_CASE(test_mini_tangential) { tc.compute_tangential_complex(); TC::Num_inconsistencies num_inc = tc.number_of_inconsistent_simplices(); std::cout << "TC vertices = " << tc.number_of_vertices() << " - simplices = " << num_inc.num_simplices << - " - inconsistencies = " << num_inc.num_inconsistent_simplices << std::endl; + " - inc simplices = " << num_inc.num_inconsistent_simplices << + " - inc stars = " << num_inc.num_inconsistent_stars << std::endl; BOOST_CHECK(tc.number_of_vertices() == 4); BOOST_CHECK(num_inc.num_simplices == 4); - BOOST_CHECK(num_inc.num_inconsistent_simplices == 2); + BOOST_CHECK(num_inc.num_inconsistent_simplices == 0); + BOOST_CHECK(num_inc.num_inconsistent_stars == 0); // Export the TC into a Simplex_tree Gudhi::Simplex_tree<> stree; @@ -110,18 +112,19 @@ BOOST_AUTO_TEST_CASE(test_mini_tangential) { std::cout << "ST vertices = " << stree.num_vertices() << " - simplices = " << stree.num_simplices() << std::endl; BOOST_CHECK(stree.num_vertices() == 4); - BOOST_CHECK(stree.num_simplices() == 12); + BOOST_CHECK(stree.num_simplices() == 6); tc.fix_inconsistencies_using_perturbation(0.01, 30.0); BOOST_CHECK(tc.number_of_vertices() == 4); BOOST_CHECK(num_inc.num_simplices == 4); - BOOST_CHECK(num_inc.num_inconsistent_simplices == 2); + BOOST_CHECK(num_inc.num_inconsistent_simplices == 0); + BOOST_CHECK(num_inc.num_inconsistent_stars == 0); // Export the TC into a Simplex_tree tc.create_complex(stree); std::cout << "ST vertices = " << stree.num_vertices() << " - simplices = " << stree.num_simplices() << std::endl; BOOST_CHECK(stree.num_vertices() == 4); - BOOST_CHECK(stree.num_simplices() == 12); + BOOST_CHECK(stree.num_simplices() == 6); } -- cgit v1.2.3 From 72885b69e5fbe786f01b8275586281bb05198241 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 15 Dec 2016 09:41:12 +0000 Subject: Fix max issue on Windows git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/tangential_test@1876 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 957e2196a4a56308f76c0f55d182ffd3952eaf4e --- src/Tangential_complex/include/gudhi/Tangential_complex.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'src') diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex.h b/src/Tangential_complex/include/gudhi/Tangential_complex.h index 6c0bbce6..e7e50ce9 100644 --- a/src/Tangential_complex/include/gudhi/Tangential_complex.h +++ b/src/Tangential_complex/include/gudhi/Tangential_complex.h @@ -1131,7 +1131,7 @@ class Tangential_complex { Tr_vertex_handle vh = triangulation.insert_if_in_star(proj_pt, center_vertex); // Tr_vertex_handle vh = triangulation.insert(proj_pt); - if (vh != Tr_vertex_handle() && vh->data() == (std::numeric_limits::max())) { + if (vh != Tr_vertex_handle() && vh->data() == (std::numeric_limits::max)()) { #ifdef GUDHI_TC_VERY_VERBOSE ++num_inserted_points; #endif -- cgit v1.2.3 From 9906477eb45f16cfafe7186482f4c44606c575dc Mon Sep 17 00:00:00 2001 From: fgodi Date: Thu, 15 Dec 2016 10:00:19 +0000 Subject: namespace git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1877 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 0d15f01525272ec8bea7436fa18dbac213becf0a --- src/Bottleneck_distance/example/bottleneck_basic_example.cpp | 4 ++-- src/Bottleneck_distance/example/bottleneck_read_file_example.cpp | 2 +- src/Bottleneck_distance/include/gudhi/Bottleneck.h | 6 +++--- src/Bottleneck_distance/include/gudhi/Graph_matching.h | 4 ++-- src/Bottleneck_distance/include/gudhi/Internal_point.h | 4 ++-- src/Bottleneck_distance/include/gudhi/Neighbors_finder.h | 4 ++-- src/Bottleneck_distance/include/gudhi/Persistence_graph.h | 4 ++-- src/Bottleneck_distance/test/bottleneck_chrono.cpp | 6 +++--- src/Bottleneck_distance/test/bottleneck_unit_test.cpp | 8 ++++---- 9 files changed, 21 insertions(+), 21 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/example/bottleneck_basic_example.cpp b/src/Bottleneck_distance/example/bottleneck_basic_example.cpp index 95548579..78e00e57 100644 --- a/src/Bottleneck_distance/example/bottleneck_basic_example.cpp +++ b/src/Bottleneck_distance/example/bottleneck_basic_example.cpp @@ -37,11 +37,11 @@ int main() { v2.emplace_back(3.2, std::numeric_limits::infinity()); - double b = Gudhi::bottleneck_distance::compute(v1, v2); + double b = Gudhi::persistence_diagram::bottleneck_distance(v1, v2); std::cout << "Bottleneck distance = " << b << std::endl; - b = Gudhi::bottleneck_distance::compute(v1, v2, 0.1); + b = Gudhi::persistence_diagram::bottleneck_distance(v1, v2, 0.1); std::cout << "Approx bottleneck distance = " << b << std::endl; diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp index 4a503e4c..ceedccc5 100644 --- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp +++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp @@ -72,6 +72,6 @@ int main( int argc , char** argv ) { tolerance = atof( argv[3] ); } - double b = Gudhi::bottleneck_distance::compute(diag1, diag2, tolerance); + double b = Gudhi::persistence_diagram::bottleneck_distance(diag1, diag2, tolerance); std::cout << "The distance between the diagrams is : " << b << ". The tolerance is : " << tolerance << std::endl; } diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h index 4a69fb96..0c9e5ea8 100644 --- a/src/Bottleneck_distance/include/gudhi/Bottleneck.h +++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h @@ -28,7 +28,7 @@ namespace Gudhi { -namespace bottleneck_distance { +namespace persistence_diagram { /** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams (see Concepts). * If the last parameter e is not 0 (default value if not explicited), you get an additive e-approximation. @@ -36,7 +36,7 @@ namespace bottleneck_distance { * \ingroup bottleneck_distance */ template -double compute(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e=0.) { +double bottleneck_distance(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e=0.) { Persistence_graph g(diag1, diag2, e); double b = g.bottleneck_alive(); if(b == std::numeric_limits::infinity()) @@ -69,7 +69,7 @@ double compute(const Persistence_diagram1 &diag1, const Persistence_diagram2 &di -} // namespace bottleneck_distance +} // namespace persistence_diagram } // namespace Gudhi diff --git a/src/Bottleneck_distance/include/gudhi/Graph_matching.h b/src/Bottleneck_distance/include/gudhi/Graph_matching.h index 10b7073a..e9f455d7 100644 --- a/src/Bottleneck_distance/include/gudhi/Graph_matching.h +++ b/src/Bottleneck_distance/include/gudhi/Graph_matching.h @@ -27,7 +27,7 @@ namespace Gudhi { -namespace bottleneck_distance { +namespace persistence_diagram { /** \internal \brief Structure representing a graph matching. The graph is a Persistence_diagrams_graph. * @@ -172,7 +172,7 @@ inline void Graph_matching::update(std::vector& path) { } -} // namespace bottleneck_distance +} // namespace persistence_diagram } // namespace Gudhi diff --git a/src/Bottleneck_distance/include/gudhi/Internal_point.h b/src/Bottleneck_distance/include/gudhi/Internal_point.h index 27a59d3f..70342d0c 100644 --- a/src/Bottleneck_distance/include/gudhi/Internal_point.h +++ b/src/Bottleneck_distance/include/gudhi/Internal_point.h @@ -25,7 +25,7 @@ namespace Gudhi { -namespace bottleneck_distance { +namespace persistence_diagram { /** \internal \brief Returns the used index for encoding none of the points */ int null_point_index(); @@ -59,7 +59,7 @@ struct Construct_coord_iterator { { return p.vec+2; } }; -} // namespace bottleneck_distance +} // namespace persistence_diagram } // namespace Gudhi diff --git a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h index e6acafc6..792925b7 100644 --- a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h +++ b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h @@ -38,7 +38,7 @@ namespace Gudhi { -namespace bottleneck_distance { +namespace persistence_diagram { /** \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). @@ -162,7 +162,7 @@ inline int Layered_neighbors_finder::vlayers_number() const { return static_cast(neighbors_finder.size()); } -} // namespace bottleneck_distance +} // namespace persistence_diagram } // namespace Gudhi diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h index f16a6c95..2ee55995 100644 --- a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h +++ b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h @@ -29,7 +29,7 @@ namespace Gudhi { -namespace bottleneck_distance { +namespace persistence_diagram { /** \internal \brief Structure representing an euclidean bipartite graph containing @@ -172,7 +172,7 @@ inline double Persistence_graph::diameter_bound() const { } -} // namespace bottleneck_distance +} // namespace persistence_diagram } // namespace Gudhi diff --git a/src/Bottleneck_distance/test/bottleneck_chrono.cpp b/src/Bottleneck_distance/test/bottleneck_chrono.cpp index 8bd41104..f51714a2 100644 --- a/src/Bottleneck_distance/test/bottleneck_chrono.cpp +++ b/src/Bottleneck_distance/test/bottleneck_chrono.cpp @@ -25,7 +25,7 @@ #include #include -using namespace Gudhi::bottleneck_distance; +using namespace Gudhi::persistence_diagram; double upper_bound = 400.; // any real >0 @@ -34,7 +34,7 @@ int main(){ std::ofstream objetfichier; objetfichier.open("results.csv", std::ios::out); - for(int n = 400; n<=2000; n+=400){ + for(int n = 1000; n<=4000; n+=1000){ std::uniform_real_distribution unif1(0.,upper_bound); std::uniform_real_distribution unif2(upper_bound/1000.,upper_bound/100.); std::default_random_engine re; @@ -52,7 +52,7 @@ 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, 0.00001); + double b = bottleneck_distance(v1,v2, 0.00001); 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 2e67d436..fba1d369 100644 --- a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp +++ b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp @@ -28,7 +28,7 @@ #include #include -using namespace Gudhi::bottleneck_distance; +using namespace Gudhi::persistence_diagram; int n1 = 81; // a natural number >0 int n2 = 180; // a natural number >0 @@ -161,7 +161,7 @@ BOOST_AUTO_TEST_CASE(global){ if(i%3==0) v2.emplace_back(std::max(a,b),std::max(a,b)+y); } - BOOST_CHECK(compute(v1, v2) <= upper_bound/100.); - BOOST_CHECK(compute(v1, v2, upper_bound/10000.) <= upper_bound/100. + upper_bound/10000.); - BOOST_CHECK(std::abs(compute(v1, v2) - compute(v1, v2, upper_bound/10000.)) <= upper_bound/10000.); + BOOST_CHECK(bottleneck_distance(v1, v2, 0.) <= upper_bound/100.); + BOOST_CHECK(bottleneck_distance(v1, v2, upper_bound/10000.) <= upper_bound/100. + upper_bound/10000.); + BOOST_CHECK(std::abs(bottleneck_distance(v1, v2, 0.) - bottleneck_distance(v1, v2, upper_bound/10000.)) <= upper_bound/10000.); } -- cgit v1.2.3 From 47374e6d54a8b251e421681d25d2e585d0203d19 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 15 Dec 2016 11:00:56 +0000 Subject: Remove unused modifications git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/tangential_test@1878 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 1b3dafad298e0caa87825ce47f6e8ac3983206a0 --- CMakeLists.txt | 14 +++++++------- src/Tangential_complex/example/CMakeLists.txt | 1 - src/Tangential_complex/include/gudhi/Tangential_complex.h | 2 -- 3 files changed, 7 insertions(+), 10 deletions(-) (limited to 'src') diff --git a/CMakeLists.txt b/CMakeLists.txt index 78de6c09..005df6d7 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -73,13 +73,13 @@ else() set(Boost_USE_STATIC_RUNTIME OFF) # Find TBB package for parallel sort - not mandatory, just optional. - #set(TBB_FIND_QUIETLY ON) - #find_package(TBB) - #if (TBB_FOUND) - # include(${TBB_USE_FILE}) - # message("TBB found in ${TBB_LIBRARY_DIRS}") - # add_definitions(-DGUDHI_USE_TBB) - #endif() + set(TBB_FIND_QUIETLY ON) + find_package(TBB) + if (TBB_FOUND) + include(${TBB_USE_FILE}) + message("TBB found in ${TBB_LIBRARY_DIRS}") + add_definitions(-DGUDHI_USE_TBB) + endif() find_package(Eigen3 3.1.0) if (EIGEN3_FOUND) diff --git a/src/Tangential_complex/example/CMakeLists.txt b/src/Tangential_complex/example/CMakeLists.txt index 32f6eebb..a75ccd5b 100644 --- a/src/Tangential_complex/example/CMakeLists.txt +++ b/src/Tangential_complex/example/CMakeLists.txt @@ -18,7 +18,6 @@ if(CGAL_FOUND) add_test(Tangential_complex_example_with_perturb ${CMAKE_CURRENT_BINARY_DIR}/Tangential_complex_example_with_perturb) - endif(EIGEN3_FOUND) endif(NOT CGAL_VERSION VERSION_LESS 4.8.0) endif(CGAL_FOUND) diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex.h b/src/Tangential_complex/include/gudhi/Tangential_complex.h index e7e50ce9..65de2743 100644 --- a/src/Tangential_complex/include/gudhi/Tangential_complex.h +++ b/src/Tangential_complex/include/gudhi/Tangential_complex.h @@ -1306,7 +1306,6 @@ class Tangential_complex { , bool normalize_basis = true , Orthogonal_space_basis *p_orth_space_basis = NULL ) { -// unsigned int num_pts_for_pca = static_cast (std::pow(GUDHI_TC_BASE_VALUE_FOR_PCA, m_intrinsic_dim)); unsigned int num_pts_for_pca = (std::min)(static_cast (std::pow(GUDHI_TC_BASE_VALUE_FOR_PCA, m_intrinsic_dim)), static_cast (m_points.size())); @@ -1397,7 +1396,6 @@ class Tangential_complex { // on it. Note that most points are duplicated. Tangent_space_basis compute_tangent_space(const Simplex &s, bool normalize_basis = true) { -// unsigned int num_pts_for_pca = static_cast (std::pow(GUDHI_TC_BASE_VALUE_FOR_PCA, m_intrinsic_dim)); unsigned int num_pts_for_pca = (std::min)(static_cast (std::pow(GUDHI_TC_BASE_VALUE_FOR_PCA, m_intrinsic_dim)), static_cast (m_points.size())); -- cgit v1.2.3 From 93c82310194d5fc28979e86287f15dacddbaa5ba Mon Sep 17 00:00:00 2001 From: fgodi Date: Thu, 15 Dec 2016 16:24:35 +0000 Subject: small modifications git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1882 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 11247904405f3da37514e5cc4848c6971edb4254 --- src/Bottleneck_distance/include/gudhi/Bottleneck.h | 5 ++--- src/Bottleneck_distance/test/bottleneck_chrono.cpp | 3 ++- 2 files changed, 4 insertions(+), 4 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h index 0c9e5ea8..24a31ac1 100644 --- a/src/Bottleneck_distance/include/gudhi/Bottleneck.h +++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h @@ -46,12 +46,11 @@ double bottleneck_distance(const Persistence_diagram1 &diag1, const Persistence_ sd = g.sorted_distances(); long idmin = 0; long idmax = e==0. ? sd.size() - 1 : g.diameter_bound()/e + 1; - // alpha can change the complexity - double alpha = std::pow(idmax, 0.25); + double alpha = std::pow(g.size(), 1./5.); Graph_matching m(g); Graph_matching biggest_unperfect(g); while (idmin != idmax) { - long step = static_cast((idmax - idmin) / alpha); + long step = static_cast((idmax - idmin - 1)/alpha); m.set_r(e == 0. ? sd.at(idmin + step) : e*(idmin + step)); while (m.multi_augment()); //The above while compute a maximum matching (according to the r setted before) diff --git a/src/Bottleneck_distance/test/bottleneck_chrono.cpp b/src/Bottleneck_distance/test/bottleneck_chrono.cpp index f51714a2..dcf98460 100644 --- a/src/Bottleneck_distance/test/bottleneck_chrono.cpp +++ b/src/Bottleneck_distance/test/bottleneck_chrono.cpp @@ -51,8 +51,9 @@ int main(){ if(i%3==0) v2.emplace_back(std::max(a,b),std::max(a,b)+y); } + double epsilon = 0.0000000000000001; std::chrono::steady_clock::time_point start = std::chrono::steady_clock::now(); - double b = bottleneck_distance(v1,v2, 0.00001); + double b = bottleneck_distance(v1,v2, epsilon); 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 66d5bb10fcbaf75962004dfa34d8f2b8d5d23c0a Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 15 Dec 2016 16:30:50 +0000 Subject: Modify random and limit tests cases git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/subsampling_and_spatialsearching@1883 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 385f334f9358ae62c2ba6ec0d652ecfd52a052a7 --- .../include/gudhi/choose_n_farthest_points.h | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) (limited to 'src') diff --git a/src/Subsampling/include/gudhi/choose_n_farthest_points.h b/src/Subsampling/include/gudhi/choose_n_farthest_points.h index b6b7ace3..ea387bf9 100644 --- a/src/Subsampling/include/gudhi/choose_n_farthest_points.h +++ b/src/Subsampling/include/gudhi/choose_n_farthest_points.h @@ -73,10 +73,15 @@ void choose_n_farthest_points(Kernel const &k, std::size_t final_size, std::size_t starting_point, OutputIterator output_it) { - typename Kernel::Squared_distance_d sqdist = k.squared_distance_d_object(); - std::size_t nb_points = boost::size(input_pts); - assert(nb_points >= final_size); + if (final_size > nb_points) + final_size = nb_points; + + // Tests to the limit + if (final_size < 1) + return; + + typename Kernel::Squared_distance_d sqdist = k.squared_distance_d_object(); std::size_t current_number_of_landmarks = 0; // counter for landmarks const double infty = std::numeric_limits::infinity(); // infinity (see next entry) @@ -132,10 +137,14 @@ void choose_n_farthest_points(Kernel const& k, Point_range const &input_pts, unsigned final_size, OutputIterator output_it) { + // Tests to the limit + if ((final_size < 1) || (input_pts.size() == 0)) + return; + // Choose randomly the first landmark std::random_device rd; std::mt19937 gen(rd()); - std::uniform_int_distribution<> dis(0, final_size); + std::uniform_int_distribution<> dis(0, (input_pts.size() - 1)); int starting_point = dis(gen); choose_n_farthest_points(k, input_pts, final_size, starting_point, output_it); } -- cgit v1.2.3 From 07db62d323a2dabdc86ad6f1eb8edbc7b1bf26bb Mon Sep 17 00:00:00 2001 From: fgodi Date: Thu, 15 Dec 2016 16:51:19 +0000 Subject: small modifications git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1885 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 111fc4e381223fc2d4b6e6c71b61dd1552c7cc95 --- src/Bottleneck_distance/include/gudhi/Bottleneck.h | 2 +- src/Bottleneck_distance/test/bottleneck_chrono.cpp | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) (limited to 'src') diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h index 24a31ac1..bb1d6d38 100644 --- a/src/Bottleneck_distance/include/gudhi/Bottleneck.h +++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h @@ -49,7 +49,7 @@ double bottleneck_distance(const Persistence_diagram1 &diag1, const Persistence_ double alpha = std::pow(g.size(), 1./5.); Graph_matching m(g); Graph_matching biggest_unperfect(g); - while (idmin != idmax) { + while (idmax - idmin > epsilon) { long step = static_cast((idmax - idmin - 1)/alpha); m.set_r(e == 0. ? sd.at(idmin + step) : e*(idmin + step)); while (m.multi_augment()); diff --git a/src/Bottleneck_distance/test/bottleneck_chrono.cpp b/src/Bottleneck_distance/test/bottleneck_chrono.cpp index dcf98460..7a440aeb 100644 --- a/src/Bottleneck_distance/test/bottleneck_chrono.cpp +++ b/src/Bottleneck_distance/test/bottleneck_chrono.cpp @@ -51,6 +51,7 @@ int main(){ if(i%3==0) v2.emplace_back(std::max(a,b),std::max(a,b)+y); } + std::cout << std::numeric_limits::max() / std::numeric_limits::min() << std::endl; double epsilon = 0.0000000000000001; std::chrono::steady_clock::time_point start = std::chrono::steady_clock::now(); double b = bottleneck_distance(v1,v2, epsilon); -- cgit v1.2.3 From b93ea27ea392f49f85deee23526c9330a716093b Mon Sep 17 00:00:00 2001 From: fgodi Date: Thu, 15 Dec 2016 16:57:53 +0000 Subject: cancel commit of temporary testing code git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1886 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 03f3e6515fd74fd2ae8d1de6b7febb4af7607fb5 --- src/Bottleneck_distance/include/gudhi/Bottleneck.h | 2 +- src/Bottleneck_distance/test/bottleneck_chrono.cpp | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h index bb1d6d38..24a31ac1 100644 --- a/src/Bottleneck_distance/include/gudhi/Bottleneck.h +++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h @@ -49,7 +49,7 @@ double bottleneck_distance(const Persistence_diagram1 &diag1, const Persistence_ double alpha = std::pow(g.size(), 1./5.); Graph_matching m(g); Graph_matching biggest_unperfect(g); - while (idmax - idmin > epsilon) { + while (idmin != idmax) { long step = static_cast((idmax - idmin - 1)/alpha); m.set_r(e == 0. ? sd.at(idmin + step) : e*(idmin + step)); while (m.multi_augment()); diff --git a/src/Bottleneck_distance/test/bottleneck_chrono.cpp b/src/Bottleneck_distance/test/bottleneck_chrono.cpp index 7a440aeb..dcf98460 100644 --- a/src/Bottleneck_distance/test/bottleneck_chrono.cpp +++ b/src/Bottleneck_distance/test/bottleneck_chrono.cpp @@ -51,7 +51,6 @@ int main(){ if(i%3==0) v2.emplace_back(std::max(a,b),std::max(a,b)+y); } - std::cout << std::numeric_limits::max() / std::numeric_limits::min() << std::endl; double epsilon = 0.0000000000000001; std::chrono::steady_clock::time_point start = std::chrono::steady_clock::now(); double b = bottleneck_distance(v1,v2, epsilon); -- cgit v1.2.3 From 0df3c9bcca4345b8be27ca2fd90eb5137072740c Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 15 Dec 2016 20:50:56 +0000 Subject: New pairs in dimension function in Persistence cohomology git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@1887 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 76bc9a951d752a6ca0f62244012965b5b6597a17 --- .../include/gudhi/Persistent_cohomology.h | 15 ++++++ .../test/betti_numbers_unit_test.cpp | 57 ++++++++++++++++++++++ 2 files changed, 72 insertions(+) (limited to 'src') diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h index b31df6a4..d3a8acc0 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h @@ -690,6 +690,21 @@ class Persistent_cohomology { return persistent_pairs_; } + /** @brief Returns persistence pairs for a given dimension. + * @param[in] dimension Dimension to get the birth and death pairs from. + * @return A vector of persistence intervals (birth and death) on a fixed dimension. + */ + std::vector< std::pair< Filtration_value , Filtration_value > > + pairs_in_dimension( unsigned dimension ) { + std::vector< std::pair< Filtration_value , Filtration_value > > result; + for (auto pair : persistent_pairs_) { + if (cpx_->dimension( get<0>(pair)) == dimension ) { + result.push_back(std::pair(cpx_->filtration(get<0>(pair)), + cpx_->filtration(get<1>(pair)))); + } + } + return result; + } private: /* * Structure representing a cocycle. diff --git a/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp b/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp index 40221005..67dfcce4 100644 --- a/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp +++ b/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp @@ -84,6 +84,8 @@ BOOST_AUTO_TEST_CASE( plain_homology_betti_numbers ) // 2 1 0 inf // means that in Z/2Z-homology, the Betti numbers are b0=2 and b1=1. + std::cout << "BETTI NUMBERS" << std::endl; + BOOST_CHECK(pcoh.betti_number(0) == 2); BOOST_CHECK(pcoh.betti_number(1) == 1); BOOST_CHECK(pcoh.betti_number(2) == 0); @@ -93,6 +95,8 @@ BOOST_AUTO_TEST_CASE( plain_homology_betti_numbers ) BOOST_CHECK(bns[0] == 2); BOOST_CHECK(bns[1] == 1); BOOST_CHECK(bns[2] == 0); + + std::cout << "GET PERSISTENT PAIRS" << std::endl; // Custom sort and output persistence cmp_intervals_by_dim_then_length cmp(&st); @@ -115,6 +119,33 @@ BOOST_AUTO_TEST_CASE( plain_homology_betti_numbers ) BOOST_CHECK(st.dimension(get<0>(persistent_pairs[2])) == 0); BOOST_CHECK(st.filtration(get<0>(persistent_pairs[2])) == 0); BOOST_CHECK(get<1>(persistent_pairs[2]) == st.null_simplex()); + + std::cout << "PAIRS IN DIMENSION" << std::endl; + + auto pairs_in_dimension_0 = pcoh.pairs_in_dimension(0); + std::cout << "pairs_in_dimension_0.size() = " << pairs_in_dimension_0.size() << std::endl; + for (int i = 0; i < pairs_in_dimension_0.size(); i++) + std::cout << "pairs_in_dimension_0[" << i << "] = [" << pairs_in_dimension_0[i].first << "," << + pairs_in_dimension_0[i].second << "]" << std::endl; + BOOST_CHECK(pairs_in_dimension_0.size() == 2); + BOOST_CHECK(pairs_in_dimension_0[0].first == 0); + BOOST_CHECK(pairs_in_dimension_0[0].second == std::numeric_limits::infinity()); + BOOST_CHECK(pairs_in_dimension_0[1].first == 0); + BOOST_CHECK(pairs_in_dimension_0[1].second == std::numeric_limits::infinity()); + + + auto pairs_in_dimension_1 = pcoh.pairs_in_dimension(1); + std::cout << "pairs_in_dimension_1.size() = " << pairs_in_dimension_1.size() << std::endl; + for (int i = 0; i < pairs_in_dimension_1.size(); i++) + std::cout << "pairs_in_dimension_1[" << i << "] = [" << pairs_in_dimension_1[i].first << "," << + pairs_in_dimension_1[i].second << "]" << std::endl; + BOOST_CHECK(pairs_in_dimension_1.size() == 1); + BOOST_CHECK(pairs_in_dimension_1[0].first == 0); + BOOST_CHECK(pairs_in_dimension_1[0].second == std::numeric_limits::infinity()); + + auto pairs_in_dimension_2 = pcoh.pairs_in_dimension(2); + std::cout << "pairs_in_dimension_2.size() = " << pairs_in_dimension_2.size() << std::endl; + BOOST_CHECK(pairs_in_dimension_2.size() == 0); } using Simplex_tree = Gudhi::Simplex_tree<>; @@ -231,4 +262,30 @@ BOOST_AUTO_TEST_CASE( betti_numbers ) BOOST_CHECK(st.dimension(get<0>(persistent_pairs[2])) == 0); BOOST_CHECK(st.filtration(get<0>(persistent_pairs[2])) == 1); BOOST_CHECK(get<1>(persistent_pairs[2]) == st.null_simplex()); + + std::cout << "PAIRS IN DIMENSION" << std::endl; + + auto pairs_in_dimension_0 = pcoh.pairs_in_dimension(0); + std::cout << "pairs_in_dimension_0.size() = " << pairs_in_dimension_0.size() << std::endl; + for (int i = 0; i < pairs_in_dimension_0.size(); i++) + std::cout << "pairs_in_dimension_0[" << i << "] = [" << pairs_in_dimension_0[i].first << "," << + pairs_in_dimension_0[i].second << "]" << std::endl; + BOOST_CHECK(pairs_in_dimension_0.size() == 2); + BOOST_CHECK(pairs_in_dimension_0[0].first == 2); + BOOST_CHECK(pairs_in_dimension_0[0].second == std::numeric_limits::infinity()); + BOOST_CHECK(pairs_in_dimension_0[1].first == 1); + BOOST_CHECK(pairs_in_dimension_0[1].second == std::numeric_limits::infinity()); + + auto pairs_in_dimension_1 = pcoh.pairs_in_dimension(1); + std::cout << "pairs_in_dimension_1.size() = " << pairs_in_dimension_1.size() << std::endl; + for (int i = 0; i < pairs_in_dimension_1.size(); i++) + std::cout << "pairs_in_dimension_1[" << i << "] = [" << pairs_in_dimension_1[i].first << "," << + pairs_in_dimension_1[i].second << "]" << std::endl; + BOOST_CHECK(pairs_in_dimension_1.size() == 1); + BOOST_CHECK(pairs_in_dimension_1[0].first == 4); + BOOST_CHECK(pairs_in_dimension_1[0].second == std::numeric_limits::infinity()); + + auto pairs_in_dimension_2 = pcoh.pairs_in_dimension(2); + std::cout << "pairs_in_dimension_2.size() = " << pairs_in_dimension_2.size() << std::endl; + BOOST_CHECK(pairs_in_dimension_2.size() == 0); } -- cgit v1.2.3 From 251d5726f17275b0af8333440b21476751925e1b Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Thu, 15 Dec 2016 22:53:16 +0000 Subject: Fix after code review git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@1889 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 9ec3dcd290042159c313a83be3a3e8fb7bafa6e8 --- .../include/gudhi/Persistent_cohomology.h | 10 +- .../test/betti_numbers_unit_test.cpp | 102 ++++++++++----------- 2 files changed, 56 insertions(+), 56 deletions(-) (limited to 'src') diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h index d3a8acc0..c3a1535a 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h @@ -690,17 +690,17 @@ class Persistent_cohomology { return persistent_pairs_; } - /** @brief Returns persistence pairs for a given dimension. + /** @brief Returns persistence intervals for a given dimension. * @param[in] dimension Dimension to get the birth and death pairs from. * @return A vector of persistence intervals (birth and death) on a fixed dimension. */ std::vector< std::pair< Filtration_value , Filtration_value > > - pairs_in_dimension( unsigned dimension ) { + intervals_in_dimension(int dimension) { std::vector< std::pair< Filtration_value , Filtration_value > > result; - for (auto pair : persistent_pairs_) { + // auto && pair, to avoid unnecessary copying + for (auto && pair : persistent_pairs_) { if (cpx_->dimension( get<0>(pair)) == dimension ) { - result.push_back(std::pair(cpx_->filtration(get<0>(pair)), - cpx_->filtration(get<1>(pair)))); + result.emplace_back(cpx_->filtration(get<0>(pair)), cpx_->filtration(get<1>(pair))); } } return result; diff --git a/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp b/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp index 67dfcce4..b98a3765 100644 --- a/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp +++ b/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp @@ -120,32 +120,32 @@ BOOST_AUTO_TEST_CASE( plain_homology_betti_numbers ) BOOST_CHECK(st.filtration(get<0>(persistent_pairs[2])) == 0); BOOST_CHECK(get<1>(persistent_pairs[2]) == st.null_simplex()); - std::cout << "PAIRS IN DIMENSION" << std::endl; - - auto pairs_in_dimension_0 = pcoh.pairs_in_dimension(0); - std::cout << "pairs_in_dimension_0.size() = " << pairs_in_dimension_0.size() << std::endl; - for (int i = 0; i < pairs_in_dimension_0.size(); i++) - std::cout << "pairs_in_dimension_0[" << i << "] = [" << pairs_in_dimension_0[i].first << "," << - pairs_in_dimension_0[i].second << "]" << std::endl; - BOOST_CHECK(pairs_in_dimension_0.size() == 2); - BOOST_CHECK(pairs_in_dimension_0[0].first == 0); - BOOST_CHECK(pairs_in_dimension_0[0].second == std::numeric_limits::infinity()); - BOOST_CHECK(pairs_in_dimension_0[1].first == 0); - BOOST_CHECK(pairs_in_dimension_0[1].second == std::numeric_limits::infinity()); - - - auto pairs_in_dimension_1 = pcoh.pairs_in_dimension(1); - std::cout << "pairs_in_dimension_1.size() = " << pairs_in_dimension_1.size() << std::endl; - for (int i = 0; i < pairs_in_dimension_1.size(); i++) - std::cout << "pairs_in_dimension_1[" << i << "] = [" << pairs_in_dimension_1[i].first << "," << - pairs_in_dimension_1[i].second << "]" << std::endl; - BOOST_CHECK(pairs_in_dimension_1.size() == 1); - BOOST_CHECK(pairs_in_dimension_1[0].first == 0); - BOOST_CHECK(pairs_in_dimension_1[0].second == std::numeric_limits::infinity()); - - auto pairs_in_dimension_2 = pcoh.pairs_in_dimension(2); - std::cout << "pairs_in_dimension_2.size() = " << pairs_in_dimension_2.size() << std::endl; - BOOST_CHECK(pairs_in_dimension_2.size() == 0); + std::cout << "INTERVALS IN DIMENSION" << std::endl; + + auto intervals_in_dimension_0 = pcoh.intervals_in_dimension(0); + std::cout << "intervals_in_dimension_0.size() = " << intervals_in_dimension_0.size() << std::endl; + for (int i = 0; i < intervals_in_dimension_0.size(); i++) + std::cout << "intervals_in_dimension_0[" << i << "] = [" << intervals_in_dimension_0[i].first << "," << + intervals_in_dimension_0[i].second << "]" << std::endl; + BOOST_CHECK(intervals_in_dimension_0.size() == 2); + BOOST_CHECK(intervals_in_dimension_0[0].first == 0); + BOOST_CHECK(intervals_in_dimension_0[0].second == std::numeric_limits::infinity()); + BOOST_CHECK(intervals_in_dimension_0[1].first == 0); + BOOST_CHECK(intervals_in_dimension_0[1].second == std::numeric_limits::infinity()); + + + auto intervals_in_dimension_1 = pcoh.intervals_in_dimension(1); + std::cout << "intervals_in_dimension_1.size() = " << intervals_in_dimension_1.size() << std::endl; + for (int i = 0; i < intervals_in_dimension_1.size(); i++) + std::cout << "intervals_in_dimension_1[" << i << "] = [" << intervals_in_dimension_1[i].first << "," << + intervals_in_dimension_1[i].second << "]" << std::endl; + BOOST_CHECK(intervals_in_dimension_1.size() == 1); + BOOST_CHECK(intervals_in_dimension_1[0].first == 0); + BOOST_CHECK(intervals_in_dimension_1[0].second == std::numeric_limits::infinity()); + + auto intervals_in_dimension_2 = pcoh.intervals_in_dimension(2); + std::cout << "intervals_in_dimension_2.size() = " << intervals_in_dimension_2.size() << std::endl; + BOOST_CHECK(intervals_in_dimension_2.size() == 0); } using Simplex_tree = Gudhi::Simplex_tree<>; @@ -263,29 +263,29 @@ BOOST_AUTO_TEST_CASE( betti_numbers ) BOOST_CHECK(st.filtration(get<0>(persistent_pairs[2])) == 1); BOOST_CHECK(get<1>(persistent_pairs[2]) == st.null_simplex()); - std::cout << "PAIRS IN DIMENSION" << std::endl; - - auto pairs_in_dimension_0 = pcoh.pairs_in_dimension(0); - std::cout << "pairs_in_dimension_0.size() = " << pairs_in_dimension_0.size() << std::endl; - for (int i = 0; i < pairs_in_dimension_0.size(); i++) - std::cout << "pairs_in_dimension_0[" << i << "] = [" << pairs_in_dimension_0[i].first << "," << - pairs_in_dimension_0[i].second << "]" << std::endl; - BOOST_CHECK(pairs_in_dimension_0.size() == 2); - BOOST_CHECK(pairs_in_dimension_0[0].first == 2); - BOOST_CHECK(pairs_in_dimension_0[0].second == std::numeric_limits::infinity()); - BOOST_CHECK(pairs_in_dimension_0[1].first == 1); - BOOST_CHECK(pairs_in_dimension_0[1].second == std::numeric_limits::infinity()); - - auto pairs_in_dimension_1 = pcoh.pairs_in_dimension(1); - std::cout << "pairs_in_dimension_1.size() = " << pairs_in_dimension_1.size() << std::endl; - for (int i = 0; i < pairs_in_dimension_1.size(); i++) - std::cout << "pairs_in_dimension_1[" << i << "] = [" << pairs_in_dimension_1[i].first << "," << - pairs_in_dimension_1[i].second << "]" << std::endl; - BOOST_CHECK(pairs_in_dimension_1.size() == 1); - BOOST_CHECK(pairs_in_dimension_1[0].first == 4); - BOOST_CHECK(pairs_in_dimension_1[0].second == std::numeric_limits::infinity()); - - auto pairs_in_dimension_2 = pcoh.pairs_in_dimension(2); - std::cout << "pairs_in_dimension_2.size() = " << pairs_in_dimension_2.size() << std::endl; - BOOST_CHECK(pairs_in_dimension_2.size() == 0); + std::cout << "INTERVALS IN DIMENSION" << std::endl; + + auto intervals_in_dimension_0 = pcoh.intervals_in_dimension(0); + std::cout << "intervals_in_dimension_0.size() = " << intervals_in_dimension_0.size() << std::endl; + for (int i = 0; i < intervals_in_dimension_0.size(); i++) + std::cout << "intervals_in_dimension_0[" << i << "] = [" << intervals_in_dimension_0[i].first << "," << + intervals_in_dimension_0[i].second << "]" << std::endl; + BOOST_CHECK(intervals_in_dimension_0.size() == 2); + BOOST_CHECK(intervals_in_dimension_0[0].first == 2); + BOOST_CHECK(intervals_in_dimension_0[0].second == std::numeric_limits::infinity()); + BOOST_CHECK(intervals_in_dimension_0[1].first == 1); + BOOST_CHECK(intervals_in_dimension_0[1].second == std::numeric_limits::infinity()); + + auto intervals_in_dimension_1 = pcoh.intervals_in_dimension(1); + std::cout << "intervals_in_dimension_1.size() = " << intervals_in_dimension_1.size() << std::endl; + for (int i = 0; i < intervals_in_dimension_1.size(); i++) + std::cout << "intervals_in_dimension_1[" << i << "] = [" << intervals_in_dimension_1[i].first << "," << + intervals_in_dimension_1[i].second << "]" << std::endl; + BOOST_CHECK(intervals_in_dimension_1.size() == 1); + BOOST_CHECK(intervals_in_dimension_1[0].first == 4); + BOOST_CHECK(intervals_in_dimension_1[0].second == std::numeric_limits::infinity()); + + auto intervals_in_dimension_2 = pcoh.intervals_in_dimension(2); + std::cout << "intervals_in_dimension_2.size() = " << intervals_in_dimension_2.size() << std::endl; + BOOST_CHECK(intervals_in_dimension_2.size() == 0); } -- cgit v1.2.3 From b638f095644a1cda0fac00e1b11f19b6cec50473 Mon Sep 17 00:00:00 2001 From: fgodi Date: Fri, 16 Dec 2016 10:44:16 +0000 Subject: separation of exactly and approximate git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1895 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: db94c84c29afbb94c0b0710a53e6ee417a5618df --- src/Bottleneck_distance/include/gudhi/Bottleneck.h | 71 ++++++++++++++-------- .../include/gudhi/Persistence_graph.h | 8 +-- src/Bottleneck_distance/test/bottleneck_chrono.cpp | 2 +- 3 files changed, 50 insertions(+), 31 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h index 24a31ac1..c34ea933 100644 --- a/src/Bottleneck_distance/include/gudhi/Bottleneck.h +++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h @@ -30,43 +30,62 @@ namespace Gudhi { namespace persistence_diagram { -/** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams (see Concepts). - * If the last parameter e is not 0 (default value if not explicited), you get an additive e-approximation. - * - * \ingroup bottleneck_distance - */ -template -double bottleneck_distance(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e=0.) { - Persistence_graph g(diag1, diag2, e); - double b = g.bottleneck_alive(); - if(b == std::numeric_limits::infinity()) - return std::numeric_limits::infinity(); - std::vector sd; - if(e == 0.) - sd = g.sorted_distances(); - long idmin = 0; - long idmax = e==0. ? sd.size() - 1 : g.diameter_bound()/e + 1; - double alpha = std::pow(g.size(), 1./5.); +double bottleneck_distance_approx(Persistence_graph& g, double e) { + double b_lower_bound = 0.; + double b_upper_bound = g.diameter_bound(); + const double alpha = std::pow(g.size(), 1./5.); Graph_matching m(g); Graph_matching biggest_unperfect(g); - while (idmin != idmax) { - long step = static_cast((idmax - idmin - 1)/alpha); - m.set_r(e == 0. ? sd.at(idmin + step) : e*(idmin + step)); - while (m.multi_augment()); - //The above while compute a maximum matching (according to the r setted before) + while (b_upper_bound - b_lower_bound > 2*e) { + double step = b_lower_bound + (b_upper_bound - b_lower_bound)/alpha; + m.set_r(step); + while (m.multi_augment()); //compute a maximum matching (in the graph corresponding to the current r) if (m.perfect()) { - idmax = idmin + step; m = biggest_unperfect; + b_upper_bound = step; } else { biggest_unperfect = m; - idmin = idmin + step + 1; + b_lower_bound = step; } } - b = std::max(b, e == 0. ? sd.at(idmin) : e*(idmin)); - return b; + return (b_lower_bound + b_upper_bound)/2.; } +double bottleneck_distance_exact(Persistence_graph& g) { + std::vector sd = g.sorted_distances(); + long lower_bound_i = 0; + long upper_bound_i = sd.size()-1; + const double alpha = std::pow(g.size(), 1./5.); + Graph_matching m(g); + Graph_matching biggest_unperfect(g); + while (lower_bound_i != upper_bound_i) { + long step = lower_bound_i + static_cast((upper_bound_i - lower_bound_i - 1)/alpha); + m.set_r(sd.at(step)); + while (m.multi_augment()); //compute a maximum matching (in the graph corresponding to the current r) + if (m.perfect()) { + m = biggest_unperfect; + upper_bound_i = step; + } else { + biggest_unperfect = m; + lower_bound_i = step + 1; + } + } + return sd.at(lower_bound_i); +} +/** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams (see Concepts). + * If the last parameter e is not 0 (default value if not explicited), you get an additive e-approximation. + * + * \ingroup bottleneck_distance + */ +template +double bottleneck_distance(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e=0.) { + Persistence_graph g(diag1, diag2, e); + if(g.bottleneck_alive() == std::numeric_limits::infinity()) + return std::numeric_limits::infinity(); + double b = (e == 0. ? bottleneck_distance_exact(g) : bottleneck_distance_approx(g, e)); + return std::max(g.bottleneck_alive(),b); +} } // namespace persistence_diagram diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h index 2ee55995..45a4d586 100644 --- a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h +++ b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h @@ -96,7 +96,7 @@ Persistence_graph::Persistence_graph(const Persistence_diagram1 &diag1, std::sort(v_alive.begin(), v_alive.end()); if(u_alive.size() != v_alive.size()) b_alive = std::numeric_limits::infinity(); - else for(auto it_u=u_alive.cbegin(), it_v=v_alive.cbegin();it_u != u_alive.cend();++it_u, ++it_v) + else for(auto it_u=u_alive.cbegin(), it_v=v_alive.cbegin(); it_u != u_alive.cend(); ++it_u, ++it_v) b_alive = std::max(b_alive, std::fabs(*it_u - *it_v)); } @@ -136,7 +136,7 @@ inline double Persistence_graph::bottleneck_alive() const{ inline std::vector Persistence_graph::sorted_distances() const { std::vector distances; - distances.push_back(0.); + distances.push_back(0.); //for empty diagrams for (int u_point_index = 0; u_point_index < size(); ++u_point_index){ distances.push_back(distance(u_point_index, corresponding_point_in_v(u_point_index))); for (int v_point_index = 0; v_point_index < size(); ++v_point_index) @@ -150,7 +150,7 @@ inline Internal_point Persistence_graph::get_u_point(int u_point_index) const { 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; + double m = (projector.x() + projector.y()) / 2.; return Internal_point(m,m,u_point_index); } @@ -158,7 +158,7 @@ inline Internal_point Persistence_graph::get_v_point(int v_point_index) const { 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; + double m = (projector.x() + projector.y()) / 2.; return Internal_point(m,m,v_point_index); } diff --git a/src/Bottleneck_distance/test/bottleneck_chrono.cpp b/src/Bottleneck_distance/test/bottleneck_chrono.cpp index dcf98460..b46a19e4 100644 --- a/src/Bottleneck_distance/test/bottleneck_chrono.cpp +++ b/src/Bottleneck_distance/test/bottleneck_chrono.cpp @@ -51,7 +51,7 @@ int main(){ if(i%3==0) v2.emplace_back(std::max(a,b),std::max(a,b)+y); } - double epsilon = 0.0000000000000001; + double epsilon = std::numeric_limits::min(); std::chrono::steady_clock::time_point start = std::chrono::steady_clock::now(); double b = bottleneck_distance(v1,v2, epsilon); std::chrono::steady_clock::time_point end = std::chrono::steady_clock::now(); -- cgit v1.2.3 From 66c657a9b422474a1a151fea2ba711b377dce57f Mon Sep 17 00:00:00 2001 From: fgodi Date: Fri, 16 Dec 2016 12:19:22 +0000 Subject: modifs done git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1897 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: f1c2ac9389d5da7556a5c47e90c68572ae97450b --- src/Bottleneck_distance/include/gudhi/Bottleneck.h | 16 +++++++++++----- src/Bottleneck_distance/test/bottleneck_chrono.cpp | 2 +- 2 files changed, 12 insertions(+), 6 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h index c34ea933..d7e11a05 100644 --- a/src/Bottleneck_distance/include/gudhi/Bottleneck.h +++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h @@ -34,6 +34,12 @@ double bottleneck_distance_approx(Persistence_graph& g, double e) { double b_lower_bound = 0.; double b_upper_bound = g.diameter_bound(); const double alpha = std::pow(g.size(), 1./5.); + if(e < std::numeric_limits::epsilon() * alpha){ + e = std::numeric_limits::epsilon() * alpha; +#ifdef DEBUG_TRACES + std::cout << "Epsilon user given value is less than eps_min. Forced to eps_min by the application" << std::endl; +#endif // DEBUG_TRACES + } Graph_matching m(g); Graph_matching biggest_unperfect(g); while (b_upper_bound - b_lower_bound > 2*e) { @@ -73,18 +79,18 @@ double bottleneck_distance_exact(Persistence_graph& g) { return sd.at(lower_bound_i); } -/** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams (see Concepts). - * If the last parameter e is not 0 (default value if not explicited), you get an additive e-approximation. +/** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams (see concepts). + * If the last parameter e is not 0, you get an additive e-approximation, which is a lot faster to compute whatever is e. + * Thus, by default, e is a very small positive double, actually the smallest double possible such that the floating-point inaccuracies don't lead to a failure of the algorithm. * * \ingroup bottleneck_distance */ template -double bottleneck_distance(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e=0.) { +double bottleneck_distance(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e=std::numeric_limits::epsilon()) { Persistence_graph g(diag1, diag2, e); if(g.bottleneck_alive() == std::numeric_limits::infinity()) return std::numeric_limits::infinity(); - double b = (e == 0. ? bottleneck_distance_exact(g) : bottleneck_distance_approx(g, e)); - return std::max(g.bottleneck_alive(),b); + return std::max(g.bottleneck_alive(), e == 0. ? bottleneck_distance_exact(g) : bottleneck_distance_approx(g, e)); } } // namespace persistence_diagram diff --git a/src/Bottleneck_distance/test/bottleneck_chrono.cpp b/src/Bottleneck_distance/test/bottleneck_chrono.cpp index b46a19e4..1bff96f4 100644 --- a/src/Bottleneck_distance/test/bottleneck_chrono.cpp +++ b/src/Bottleneck_distance/test/bottleneck_chrono.cpp @@ -51,7 +51,7 @@ int main(){ if(i%3==0) v2.emplace_back(std::max(a,b),std::max(a,b)+y); } - double epsilon = std::numeric_limits::min(); + double epsilon = std::numeric_limits::epsilon(); std::chrono::steady_clock::time_point start = std::chrono::steady_clock::now(); double b = bottleneck_distance(v1,v2, epsilon); std::chrono::steady_clock::time_point end = std::chrono::steady_clock::now(); -- cgit v1.2.3 From 5cc424d34f304fad2a8b462156672e2af25ab756 Mon Sep 17 00:00:00 2001 From: fgodi Date: Fri, 16 Dec 2016 12:44:11 +0000 Subject: intro documentation git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1898 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 2aae46574350bb2240f83e183d471965c933fe0b --- src/Bottleneck_distance/doc/Intro_bottleneck_distance.h | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h index 1f443f7f..ebe1123b 100644 --- a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h +++ b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h @@ -35,12 +35,11 @@ namespace bottleneck_distance { * * \section bottleneckdefinition Definition * - * Bottleneck distance measures the similarity between two persistence diagrams. - * It's the shortest distance b for which there exists a perfect matching between - * the points of the two diagrams (and also all the points of the diagonal) such that + * The bottleneck distance measures the similarity between two persistence diagrams. It's the shortest distance b for which there exists a perfect matching between + * the points of the two diagrams (completed with all the points on the diagonal in order to ignore cardinality mismatchs) such that * any couple of matched points are at distance at most b. * - * \image html perturb_pd.png Bottleneck distance is the length of the longest edge on this picture. + * \image html perturb_pd.png On this picture, the red edges represent the matching. The bottleneck distance is the length of the longest edge. * */ /** @} */ // end defgroup bottleneck_distance -- cgit v1.2.3 From f1a8c07758aa66c3a95effd7a898e8a063b5f3ce Mon Sep 17 00:00:00 2001 From: fgodi Date: Fri, 16 Dec 2016 12:56:39 +0000 Subject: small modifications (doc) git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1899 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: e1a9e88af05611d3572830a719ca9ee0d042144e --- src/Bottleneck_distance/concept/Persistence_diagram.h | 2 +- src/Bottleneck_distance/test/bottleneck_chrono.cpp | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/concept/Persistence_diagram.h b/src/Bottleneck_distance/concept/Persistence_diagram.h index e4766628..2d841086 100644 --- a/src/Bottleneck_distance/concept/Persistence_diagram.h +++ b/src/Bottleneck_distance/concept/Persistence_diagram.h @@ -29,7 +29,7 @@ namespace bottleneck_distance { /** \brief Concept of Diagram_point. std::get<0>(point) must return the birth of the corresponding component and std::get<1>(point) its death. * A valid implementation of this concept is std::pair. - * Birth must be 0 or positive, death should be larger than birth, death can be std::numeric_limits::infinity() for components which stay alive. + * Death should be larger than birth, death can be std::numeric_limits::infinity() for components which stay alive. * * \ingroup bottleneck_distance */ diff --git a/src/Bottleneck_distance/test/bottleneck_chrono.cpp b/src/Bottleneck_distance/test/bottleneck_chrono.cpp index 1bff96f4..0a3bb012 100644 --- a/src/Bottleneck_distance/test/bottleneck_chrono.cpp +++ b/src/Bottleneck_distance/test/bottleneck_chrono.cpp @@ -51,9 +51,8 @@ int main(){ if(i%3==0) v2.emplace_back(std::max(a,b),std::max(a,b)+y); } - double epsilon = std::numeric_limits::epsilon(); std::chrono::steady_clock::time_point start = std::chrono::steady_clock::now(); - double b = bottleneck_distance(v1,v2, epsilon); + 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)); -- cgit v1.2.3 From c0ee17043a446279b63bd65482c82ebe207dc9d2 Mon Sep 17 00:00:00 2001 From: fgodi Date: Fri, 16 Dec 2016 12:57:35 +0000 Subject: small modifications git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1900 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 31538228069cb6ef867be8aac231f11b5c8689f6 --- src/Bottleneck_distance/concept/Persistence_diagram.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/concept/Persistence_diagram.h b/src/Bottleneck_distance/concept/Persistence_diagram.h index 2d841086..2706716b 100644 --- a/src/Bottleneck_distance/concept/Persistence_diagram.h +++ b/src/Bottleneck_distance/concept/Persistence_diagram.h @@ -33,14 +33,14 @@ namespace bottleneck_distance { * * \ingroup bottleneck_distance */ -struct Diagram_point; +typename Diagram_point; /** \brief Concept of persistence diagram. It's a range of Diagram_point. * std::begin(diagram) and std::end(diagram) must return corresponding iterators. * * \ingroup bottleneck_distance */ -struct Persistence_Diagram; +typename Persistence_Diagram; } // namespace bottleneck_distance -- cgit v1.2.3 From c8dbfc68cca3c5462226e5d953f721143fc645f0 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 16 Dec 2016 14:07:02 +0000 Subject: Fix cpplint and warnings git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@1902 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 24c5aacf579eb1ceb35c680770d5168524c4c84b --- .../include/gudhi/Persistent_cohomology.h | 3 +- .../test/betti_numbers_unit_test.cpp | 8 ++--- src/Subsampling/example/example_custom_kernel.cpp | 38 +++++++++------------- src/Subsampling/include/gudhi/sparsify_point_set.h | 2 -- src/common/include/gudhi/random_point_generators.h | 2 -- 5 files changed, 22 insertions(+), 31 deletions(-) (limited to 'src') diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h index c3a1535a..681de8c6 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h @@ -699,12 +699,13 @@ class Persistent_cohomology { std::vector< std::pair< Filtration_value , Filtration_value > > result; // auto && pair, to avoid unnecessary copying for (auto && pair : persistent_pairs_) { - if (cpx_->dimension( get<0>(pair)) == dimension ) { + if (cpx_->dimension(get<0>(pair)) == dimension) { result.emplace_back(cpx_->filtration(get<0>(pair)), cpx_->filtration(get<1>(pair))); } } return result; } + private: /* * Structure representing a cocycle. diff --git a/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp b/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp index b98a3765..0ed3fddf 100644 --- a/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp +++ b/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp @@ -124,7 +124,7 @@ BOOST_AUTO_TEST_CASE( plain_homology_betti_numbers ) auto intervals_in_dimension_0 = pcoh.intervals_in_dimension(0); std::cout << "intervals_in_dimension_0.size() = " << intervals_in_dimension_0.size() << std::endl; - for (int i = 0; i < intervals_in_dimension_0.size(); i++) + for (std::size_t i = 0; i < intervals_in_dimension_0.size(); i++) std::cout << "intervals_in_dimension_0[" << i << "] = [" << intervals_in_dimension_0[i].first << "," << intervals_in_dimension_0[i].second << "]" << std::endl; BOOST_CHECK(intervals_in_dimension_0.size() == 2); @@ -136,7 +136,7 @@ BOOST_AUTO_TEST_CASE( plain_homology_betti_numbers ) auto intervals_in_dimension_1 = pcoh.intervals_in_dimension(1); std::cout << "intervals_in_dimension_1.size() = " << intervals_in_dimension_1.size() << std::endl; - for (int i = 0; i < intervals_in_dimension_1.size(); i++) + for (std::size_t i = 0; i < intervals_in_dimension_1.size(); i++) std::cout << "intervals_in_dimension_1[" << i << "] = [" << intervals_in_dimension_1[i].first << "," << intervals_in_dimension_1[i].second << "]" << std::endl; BOOST_CHECK(intervals_in_dimension_1.size() == 1); @@ -267,7 +267,7 @@ BOOST_AUTO_TEST_CASE( betti_numbers ) auto intervals_in_dimension_0 = pcoh.intervals_in_dimension(0); std::cout << "intervals_in_dimension_0.size() = " << intervals_in_dimension_0.size() << std::endl; - for (int i = 0; i < intervals_in_dimension_0.size(); i++) + for (std::size_t i = 0; i < intervals_in_dimension_0.size(); i++) std::cout << "intervals_in_dimension_0[" << i << "] = [" << intervals_in_dimension_0[i].first << "," << intervals_in_dimension_0[i].second << "]" << std::endl; BOOST_CHECK(intervals_in_dimension_0.size() == 2); @@ -278,7 +278,7 @@ BOOST_AUTO_TEST_CASE( betti_numbers ) auto intervals_in_dimension_1 = pcoh.intervals_in_dimension(1); std::cout << "intervals_in_dimension_1.size() = " << intervals_in_dimension_1.size() << std::endl; - for (int i = 0; i < intervals_in_dimension_1.size(); i++) + for (std::size_t i = 0; i < intervals_in_dimension_1.size(); i++) std::cout << "intervals_in_dimension_1[" << i << "] = [" << intervals_in_dimension_1[i].first << "," << intervals_in_dimension_1[i].second << "]" << std::endl; BOOST_CHECK(intervals_in_dimension_1.size() == 1); diff --git a/src/Subsampling/example/example_custom_kernel.cpp b/src/Subsampling/example/example_custom_kernel.cpp index 05797ebe..f87ef0b3 100644 --- a/src/Subsampling/example/example_custom_kernel.cpp +++ b/src/Subsampling/example/example_custom_kernel.cpp @@ -7,7 +7,7 @@ #include -/* The class Kernel contains a distance function defined on the set of points {0,1,2,3} +/* The class Kernel contains a distance function defined on the set of points {0, 1, 2, 3} * and computes a distance according to the matrix: * 0 1 2 4 * 1 0 4 2 @@ -15,41 +15,35 @@ * 4 2 1 0 */ class Kernel { -public: + public: typedef double FT; typedef unsigned Point_d; // Class Squared_distance_d class Squared_distance_d { - private: + private: std::vector> matrix_; - - public: - Squared_distance_d() - { - matrix_.push_back(std::vector({0,1,2,4})); - matrix_.push_back(std::vector({1,0,4,2})); - matrix_.push_back(std::vector({2,4,0,1})); - matrix_.push_back(std::vector({4,2,1,0})); - } - - FT operator()(Point_d p1, Point_d p2) - { + public: + Squared_distance_d() { + matrix_.push_back(std::vector({0,1,2,4})); + matrix_.push_back(std::vector({1,0,4,2})); + matrix_.push_back(std::vector({2,4,0,1})); + matrix_.push_back(std::vector({4,2,1,0})); + } + + FT operator()(Point_d p1, Point_d p2) { return matrix_[p1][p2]; } }; // Constructor - Kernel() - {} + Kernel() {} // Object of type Squared_distance_d - Squared_distance_d squared_distance_d_object() const - { + Squared_distance_d squared_distance_d_object() const { return Squared_distance_d(); } - }; int main(void) { @@ -57,9 +51,9 @@ int main(void) { typedef typename K::Point_d Point_d; K k; - std::vector points = {0,1,2,3}; + std::vector points = {0, 1, 2, 3}; std::vector results; - + Gudhi::subsampling::choose_n_farthest_points(k, points, 2, std::back_inserter(results)); std::cout << "Before sparsification: " << points.size() << " points.\n"; std::cout << "After sparsification: " << results.size() << " points.\n"; diff --git a/src/Subsampling/include/gudhi/sparsify_point_set.h b/src/Subsampling/include/gudhi/sparsify_point_set.h index 7ff11b4c..507f8c79 100644 --- a/src/Subsampling/include/gudhi/sparsify_point_set.h +++ b/src/Subsampling/include/gudhi/sparsify_point_set.h @@ -64,8 +64,6 @@ sparsify_point_set( typedef typename Gudhi::spatial_searching::Kd_tree_search< Kernel, Point_range> Points_ds; - typename Kernel::Squared_distance_d sqdist = k.squared_distance_d_object(); - #ifdef GUDHI_SUBSAMPLING_PROFILING Gudhi::Clock t; #endif diff --git a/src/common/include/gudhi/random_point_generators.h b/src/common/include/gudhi/random_point_generators.h index 3050b7ea..c643a1e3 100644 --- a/src/common/include/gudhi/random_point_generators.h +++ b/src/common/include/gudhi/random_point_generators.h @@ -338,8 +338,6 @@ std::vector generate_points_on_3sphere_and_circle(std: std::vector points; points.reserve(num_points); - typename Kernel::Translated_point_d k_transl = - k.translated_point_d_object(); typename Kernel::Compute_coordinate_d k_coord = k.compute_coordinate_d_object(); for (std::size_t i = 0; i < num_points;) { -- cgit v1.2.3 From b6b00e19be498e039ac40368157b3b7e10da4a0b Mon Sep 17 00:00:00 2001 From: fgodi Date: Fri, 16 Dec 2016 15:36:20 +0000 Subject: git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1903 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: ab471ba8c17c17d4e52a5eaccb19ea36c5f278c8 --- src/Bottleneck_distance/include/gudhi/Bottleneck.h | 10 +++------- src/Bottleneck_distance/test/bottleneck_chrono.cpp | 2 +- 2 files changed, 4 insertions(+), 8 deletions(-) (limited to 'src') diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h index d7e11a05..42a0d444 100644 --- a/src/Bottleneck_distance/include/gudhi/Bottleneck.h +++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h @@ -34,16 +34,12 @@ double bottleneck_distance_approx(Persistence_graph& g, double e) { double b_lower_bound = 0.; double b_upper_bound = g.diameter_bound(); const double alpha = std::pow(g.size(), 1./5.); - if(e < std::numeric_limits::epsilon() * alpha){ - e = std::numeric_limits::epsilon() * alpha; -#ifdef DEBUG_TRACES - std::cout << "Epsilon user given value is less than eps_min. Forced to eps_min by the application" << std::endl; -#endif // DEBUG_TRACES - } Graph_matching m(g); Graph_matching biggest_unperfect(g); while (b_upper_bound - b_lower_bound > 2*e) { double step = b_lower_bound + (b_upper_bound - b_lower_bound)/alpha; + if(step <= b_lower_bound || step >= b_upper_bound) //Avoid precision problem + break; m.set_r(step); while (m.multi_augment()); //compute a maximum matching (in the graph corresponding to the current r) if (m.perfect()) { @@ -86,7 +82,7 @@ double bottleneck_distance_exact(Persistence_graph& g) { * \ingroup bottleneck_distance */ template -double bottleneck_distance(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e=std::numeric_limits::epsilon()) { +double bottleneck_distance(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e=std::numeric_limits::min()) { Persistence_graph g(diag1, diag2, e); if(g.bottleneck_alive() == std::numeric_limits::infinity()) return std::numeric_limits::infinity(); diff --git a/src/Bottleneck_distance/test/bottleneck_chrono.cpp b/src/Bottleneck_distance/test/bottleneck_chrono.cpp index 0a3bb012..a30d42b5 100644 --- a/src/Bottleneck_distance/test/bottleneck_chrono.cpp +++ b/src/Bottleneck_distance/test/bottleneck_chrono.cpp @@ -34,7 +34,7 @@ int main(){ std::ofstream objetfichier; objetfichier.open("results.csv", std::ios::out); - for(int n = 1000; n<=4000; n+=1000){ + for(int n = 1000; n<=10000; n+=1000){ std::uniform_real_distribution unif1(0.,upper_bound); std::uniform_real_distribution unif2(upper_bound/1000.,upper_bound/100.); std::default_random_engine re; -- cgit v1.2.3 From de0bdf55c16de11d47809dc6f347773b10cc3673 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 16 Dec 2016 16:11:45 +0000 Subject: Warning fixes git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@1905 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 7b7222ebe65fd01fde30f8ba527ebaee633fc87e --- src/Contraction/example/Garland_heckbert.cpp | 12 ++--- src/GudhUI/utils/Critical_points.h | 2 - src/GudhUI/utils/Is_manifold.h | 1 - src/GudhUI/utils/Vertex_collapsor.h | 1 - .../include/gudhi/choose_n_farthest_points.h | 3 +- .../include/gudhi/pick_n_random_points.h | 4 +- .../test/test_choose_n_farthest_points.cpp | 55 ++++++++++++++++++++-- .../include/gudhi/Tangential_complex.h | 10 +--- .../test/test_tangential_complex.cpp | 2 - src/common/include/gudhi/random_point_generators.h | 7 ++- 10 files changed, 63 insertions(+), 34 deletions(-) (limited to 'src') diff --git a/src/Contraction/example/Garland_heckbert.cpp b/src/Contraction/example/Garland_heckbert.cpp index 5347830c..4689519f 100644 --- a/src/Contraction/example/Garland_heckbert.cpp +++ b/src/Contraction/example/Garland_heckbert.cpp @@ -63,12 +63,10 @@ typedef Skeleton_blocker_contractor Complex_contractor; * the point minimizing the cost of the quadric. */ class GH_placement : public Gudhi::contraction::Placement_policy { - Complex& complex_; - public: typedef Gudhi::contraction::Placement_policy::Placement_type Placement_type; - GH_placement(Complex& complex) : complex_(complex) { } + GH_placement(Complex& complex) { } Placement_type operator()(const EdgeProfile& profile) const override { auto sum_quad(profile.v0().quadric); @@ -87,12 +85,10 @@ class GH_placement : public Gudhi::contraction::Placement_policy { * which expresses a squared distances with triangles planes. */ class GH_cost : public Gudhi::contraction::Cost_policy { - Complex& complex_; - public: typedef Gudhi::contraction::Cost_policy::Cost_type Cost_type; - GH_cost(Complex& complex) : complex_(complex) { } + GH_cost(Complex& complex) { } Cost_type operator()(EdgeProfile const& profile, boost::optional const& new_point) const override { Cost_type res; @@ -111,10 +107,8 @@ class GH_cost : public Gudhi::contraction::Cost_policy { * and we update them when contracting an edge (the quadric become the sum of both quadrics). */ class GH_visitor : public Gudhi::contraction::Contraction_visitor { - Complex& complex_; - public: - GH_visitor(Complex& complex) : complex_(complex) { } + GH_visitor(Complex& complex) { } // Compute quadrics for every vertex v // The quadric of v consists in the sum of quadric diff --git a/src/GudhUI/utils/Critical_points.h b/src/GudhUI/utils/Critical_points.h index 3021a5fe..b88293e9 100644 --- a/src/GudhUI/utils/Critical_points.h +++ b/src/GudhUI/utils/Critical_points.h @@ -105,8 +105,6 @@ template class Critical_points { if (link.empty()) return 0; - Edge_contractor contractor(link, link.num_vertices() - 1); - if (link.num_connected_components() > 1) // one than more CC -> not contractible return 0; diff --git a/src/GudhUI/utils/Is_manifold.h b/src/GudhUI/utils/Is_manifold.h index 0640ea47..6dd7898e 100644 --- a/src/GudhUI/utils/Is_manifold.h +++ b/src/GudhUI/utils/Is_manifold.h @@ -76,7 +76,6 @@ template class Is_manifold { bool is_k_sphere(Vertex_handle v, int k) { auto link = input_complex_.link(v); - Edge_contractor contractor(link, link.num_vertices() - 1); return (is_sphere_simplex(link) == k); } diff --git a/src/GudhUI/utils/Vertex_collapsor.h b/src/GudhUI/utils/Vertex_collapsor.h index 2b36cb3a..3f0e7ffd 100644 --- a/src/GudhUI/utils/Vertex_collapsor.h +++ b/src/GudhUI/utils/Vertex_collapsor.h @@ -80,7 +80,6 @@ template class Vertex_collapsor { if (link.empty()) return false; if (link.is_cone()) return true; if (link.num_connected_components() > 1) return false; - Edge_contractor contractor(link, link.num_vertices() - 1); return (link.num_vertices() == 1); } }; diff --git a/src/Subsampling/include/gudhi/choose_n_farthest_points.h b/src/Subsampling/include/gudhi/choose_n_farthest_points.h index ea387bf9..5e908090 100644 --- a/src/Subsampling/include/gudhi/choose_n_farthest_points.h +++ b/src/Subsampling/include/gudhi/choose_n_farthest_points.h @@ -145,7 +145,8 @@ void choose_n_farthest_points(Kernel const& k, std::random_device rd; std::mt19937 gen(rd()); std::uniform_int_distribution<> dis(0, (input_pts.size() - 1)); - int starting_point = dis(gen); + std::size_t starting_point = dis(gen); + choose_n_farthest_points(k, input_pts, final_size, starting_point, output_it); } diff --git a/src/Subsampling/include/gudhi/pick_n_random_points.h b/src/Subsampling/include/gudhi/pick_n_random_points.h index e89b2b2d..f0e3f1f1 100644 --- a/src/Subsampling/include/gudhi/pick_n_random_points.h +++ b/src/Subsampling/include/gudhi/pick_n_random_points.h @@ -57,7 +57,9 @@ void pick_n_random_points(Point_container const &points, #endif std::size_t nbP = boost::size(points); - assert(nbP >= final_size); + if (final_size > nbP) + final_size = nbP; + std::vector landmarks(nbP); std::iota(landmarks.begin(), landmarks.end(), 0); diff --git a/src/Subsampling/test/test_choose_n_farthest_points.cpp b/src/Subsampling/test/test_choose_n_farthest_points.cpp index d064899a..0bc0dff4 100644 --- a/src/Subsampling/test/test_choose_n_farthest_points.cpp +++ b/src/Subsampling/test/test_choose_n_farthest_points.cpp @@ -39,18 +39,65 @@ typedef CGAL::Epick_d K; typedef typename K::FT FT; typedef typename K::Point_d Point_d; -BOOST_AUTO_TEST_CASE(test_choose_farthest_point) { +typedef boost::mpl::list, CGAL::Epick_d>> list_of_tested_kernels; + +BOOST_AUTO_TEST_CASE_TEMPLATE(test_choose_farthest_point, Kernel, list_of_tested_kernels) { + typedef typename Kernel::FT FT; + typedef typename Kernel::Point_d Point_d; std::vector< Point_d > points, landmarks; // Add grid points (625 points) for (FT i = 0; i < 5; i += 1.0) for (FT j = 0; j < 5; j += 1.0) for (FT k = 0; k < 5; k += 1.0) - for (FT l = 0; l < 5; l += 1.0) - points.push_back(Point_d(std::vector({i, j, k, l}))); + for (FT l = 0; l < 5; l += 1.0) { + std::vector point({i, j, k, l}); + points.push_back(Point_d(point.begin(), point.end())); + } landmarks.clear(); - K k; + Kernel k; Gudhi::subsampling::choose_n_farthest_points(k, points, 100, std::back_inserter(landmarks)); BOOST_CHECK(landmarks.size() == 100); + for (auto landmark : landmarks) + { + // Check all landmarks are in points + BOOST_CHECK(std::find (points.begin(), points.end(), landmark) != points.end()); + } +} + +BOOST_AUTO_TEST_CASE_TEMPLATE(test_choose_farthest_point_limits, Kernel, list_of_tested_kernels) { + typedef typename Kernel::FT FT; + typedef typename Kernel::Point_d Point_d; + std::vector< Point_d > points, landmarks; + landmarks.clear(); + Kernel k; + // Choose -1 farthest points in an empty point cloud + Gudhi::subsampling::choose_n_farthest_points(k, points, -1, std::back_inserter(landmarks)); + BOOST_CHECK(landmarks.size() == 0); + landmarks.clear(); + // Choose 0 farthest points in an empty point cloud + Gudhi::subsampling::choose_n_farthest_points(k, points, 0, std::back_inserter(landmarks)); + BOOST_CHECK(landmarks.size() == 0); + landmarks.clear(); + // Choose 1 farthest points in an empty point cloud + Gudhi::subsampling::choose_n_farthest_points(k, points, 1, std::back_inserter(landmarks)); + BOOST_CHECK(landmarks.size() == 0); + landmarks.clear(); + + std::vector point({0.0, 0.0, 0.0, 0.0}); + points.push_back(Point_d(point.begin(), point.end())); + // Choose -1 farthest points in an empty point cloud + Gudhi::subsampling::choose_n_farthest_points(k, points, -1, std::back_inserter(landmarks)); + BOOST_CHECK(landmarks.size() == 1); + landmarks.clear(); + // Choose 0 farthest points in a one point cloud + Gudhi::subsampling::choose_n_farthest_points(k, points, 0, std::back_inserter(landmarks)); + BOOST_CHECK(landmarks.size() == 0); + landmarks.clear(); + // Choose 1 farthest points in a one point cloud + Gudhi::subsampling::choose_n_farthest_points(k, points, 1, std::back_inserter(landmarks)); + BOOST_CHECK(landmarks.size() == 1); + landmarks.clear(); + } diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex.h b/src/Tangential_complex/include/gudhi/Tangential_complex.h index 65de2743..cfc82eb1 100644 --- a/src/Tangential_complex/include/gudhi/Tangential_complex.h +++ b/src/Tangential_complex/include/gudhi/Tangential_complex.h @@ -1314,14 +1314,6 @@ class Tangential_complex { m_k.construct_vector_d_object(); typename K::Compute_coordinate_d coord = m_k.compute_coordinate_d_object(); - typename K::Squared_length_d sqlen = - m_k.squared_length_d_object(); - typename K::Scaled_vector_d scaled_vec = - m_k.scaled_vector_d_object(); - typename K::Scalar_product_d scalar_pdct = - m_k.scalar_product_d_object(); - typename K::Difference_of_vectors_d diff_vec = - m_k.difference_of_vectors_d_object(); #ifdef GUDHI_TC_USE_ANOTHER_POINT_SET_FOR_TANGENT_SPACE_ESTIM KNS_range kns_range = m_points_ds_for_tse.query_k_nearest_neighbors( @@ -2159,7 +2151,7 @@ class Tangential_complex { typedef std::vector Triangles; Triangles triangles; - std::size_t num_vertices = c.size(); + int num_vertices = static_cast(c.size()); // Do not export smaller dimension simplices if (num_vertices < m_intrinsic_dim + 1) continue; diff --git a/src/Tangential_complex/test/test_tangential_complex.cpp b/src/Tangential_complex/test/test_tangential_complex.cpp index ebe5cdb4..48156440 100644 --- a/src/Tangential_complex/test/test_tangential_complex.cpp +++ b/src/Tangential_complex/test/test_tangential_complex.cpp @@ -71,9 +71,7 @@ BOOST_AUTO_TEST_CASE(test_Spatial_tree_data_structure) { BOOST_AUTO_TEST_CASE(test_mini_tangential) { typedef CGAL::Epick_d Kernel; - typedef Kernel::FT FT; typedef Kernel::Point_d Point; - typedef Kernel::Vector_d Vector; typedef tc::Tangential_complex TC; diff --git a/src/common/include/gudhi/random_point_generators.h b/src/common/include/gudhi/random_point_generators.h index c643a1e3..2ec465ef 100644 --- a/src/common/include/gudhi/random_point_generators.h +++ b/src/common/include/gudhi/random_point_generators.h @@ -192,10 +192,9 @@ static void generate_uniform_points_on_torus_d(const Kernel &k, int dim, std::si double radius_noise_percentage = 0., std::vector current_point = std::vector()) { CGAL::Random rng; - if (current_point.size() == 2 * dim) { - *out++ = k.construct_point_d_object()( - static_cast (current_point.size()), - current_point.begin(), current_point.end()); + int point_size = static_cast(current_point.size()); + if (point_size == 2 * dim) { + *out++ = k.construct_point_d_object()(point_size, current_point.begin(), current_point.end()); } else { for (std::size_t slice_idx = 0; slice_idx < num_slices; ++slice_idx) { double radius_noise_ratio = 1.; -- cgit v1.2.3 From a07a50640eaa4006cd532c1ec166a527b9ee8920 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 16 Dec 2016 16:35:31 +0000 Subject: Fix cppcheck warnings git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@1906 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: abb0875f5cfe3b3d0ce738257efc3f4c0fb57adc --- src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h | 2 +- src/Subsampling/example/example_custom_kernel.cpp | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) (limited to 'src') diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h index 681de8c6..bc8099e6 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h @@ -110,7 +110,7 @@ class Persistent_cohomology { cell_pool_() { if (cpx_->num_simplices() > std::numeric_limits::max()) { // num_simplices must be strictly lower than the limit, because a value is reserved for null_key. - throw std::out_of_range ("The number of simplices is more than Simplex_key type numeric limit."); + throw std::out_of_range("The number of simplices is more than Simplex_key type numeric limit."); } Simplex_key idx_fil = 0; for (auto sh : cpx_->filtration_simplex_range()) { diff --git a/src/Subsampling/example/example_custom_kernel.cpp b/src/Subsampling/example/example_custom_kernel.cpp index f87ef0b3..25b5bf6c 100644 --- a/src/Subsampling/example/example_custom_kernel.cpp +++ b/src/Subsampling/example/example_custom_kernel.cpp @@ -26,10 +26,10 @@ class Kernel { public: Squared_distance_d() { - matrix_.push_back(std::vector({0,1,2,4})); - matrix_.push_back(std::vector({1,0,4,2})); - matrix_.push_back(std::vector({2,4,0,1})); - matrix_.push_back(std::vector({4,2,1,0})); + matrix_.push_back(std::vector({0, 1, 2, 4})); + matrix_.push_back(std::vector({1, 0, 4, 2})); + matrix_.push_back(std::vector({2, 4, 0, 1})); + matrix_.push_back(std::vector({4, 2, 1, 0})); } FT operator()(Point_d p1, Point_d p2) { -- cgit v1.2.3 From a0685fdfba0e6fb210468726ca45ce5dff8672ff Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 16 Dec 2016 16:36:31 +0000 Subject: Fix cppcheck warnings git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@1907 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: fa45fd8721733a07c8d218930e545ee590788de5 --- src/Alpha_complex/include/gudhi/Alpha_complex.h | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'src') diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index 9d5a9bad..1ff95c3d 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -193,17 +193,17 @@ class Alpha_complex { triangulation_ = new Delaunay_triangulation(point_dimension(*first)); std::vector point_cloud(first, last); - + // Creates a vector {0, 1, ..., N-1} std::vector indices(boost::counting_iterator(0), boost::counting_iterator(point_cloud.size())); - + typedef boost::iterator_property_map::iterator, CGAL::Identity_property_map> Point_property_map; typedef CGAL::Spatial_sort_traits_adapter_d Search_traits_d; - + CGAL::spatial_sort(indices.begin(), indices.end(), Search_traits_d(std::begin(point_cloud))); - + typename Delaunay_triangulation::Full_cell_handle hint; for (auto index : indices) { typename Delaunay_triangulation::Vertex_handle pos = triangulation_->insert(point_cloud[index], hint); -- cgit v1.2.3 From 64dd2a2b0eec1374ed23ca079f86b312125d03f7 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 4 Jan 2017 08:39:18 +0000 Subject: Move bottleneck_chrono in benchmark Add test in cmake for basic example Move CGAL gudhi patches for bottleneck in dedicated directory Fix cpplint syntax issue git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1920 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 24671facf791de93dc6fd94bb39ca7362bb22959 --- CMakeLists.txt | 1 + src/Bottleneck_distance/benchmark/CMakeLists.txt | 13 + .../benchmark/bottleneck_chrono.cpp | 62 ++ .../doc/Intro_bottleneck_distance.h | 7 +- src/Bottleneck_distance/example/CMakeLists.txt | 2 + .../example/bottleneck_basic_example.cpp | 26 +- .../example/bottleneck_read_file_example.cpp | 71 ++- src/Bottleneck_distance/include/gudhi/Bottleneck.h | 93 +-- .../include/gudhi/CGAL/Kd_tree.h | 582 ------------------- .../include/gudhi/CGAL/Kd_tree_node.h | 586 ------------------- .../CGAL/Orthogonal_incremental_neighbor_search.h | 621 --------------------- .../include/gudhi/Graph_matching.h | 220 ++++---- .../include/gudhi/Internal_point.h | 69 ++- .../include/gudhi/Neighbors_finder.h | 172 +++--- .../include/gudhi/Persistence_graph.h | 191 ++++--- src/Bottleneck_distance/test/CMakeLists.txt | 1 - src/Bottleneck_distance/test/bottleneck_chrono.cpp | 62 -- .../test/bottleneck_unit_test.cpp | 238 ++++---- src/Tangential_complex/benchmark/CMakeLists.txt | 9 - .../Bottleneck_distance_CGAL_patches.txt | 3 + src/common/include/gudhi_patches/CGAL/Kd_tree.h | 582 +++++++++++++++++++ .../include/gudhi_patches/CGAL/Kd_tree_node.h | 586 +++++++++++++++++++ .../CGAL/Orthogonal_incremental_neighbor_search.h | 621 +++++++++++++++++++++ .../Tangential_complex_CGAL_patches.txt | 82 +++ 24 files changed, 2504 insertions(+), 2396 deletions(-) create mode 100644 src/Bottleneck_distance/benchmark/CMakeLists.txt create mode 100644 src/Bottleneck_distance/benchmark/bottleneck_chrono.cpp delete mode 100644 src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree.h delete mode 100644 src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree_node.h delete mode 100644 src/Bottleneck_distance/include/gudhi/CGAL/Orthogonal_incremental_neighbor_search.h delete mode 100644 src/Bottleneck_distance/test/bottleneck_chrono.cpp create mode 100644 src/common/include/gudhi_patches/Bottleneck_distance_CGAL_patches.txt create mode 100644 src/common/include/gudhi_patches/CGAL/Kd_tree.h create mode 100644 src/common/include/gudhi_patches/CGAL/Kd_tree_node.h create mode 100644 src/common/include/gudhi_patches/CGAL/Orthogonal_incremental_neighbor_search.h create mode 100644 src/common/include/gudhi_patches/Tangential_complex_CGAL_patches.txt (limited to 'src') diff --git a/CMakeLists.txt b/CMakeLists.txt index d1a3c7bf..f949a803 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -158,6 +158,7 @@ else() add_subdirectory(src/Tangential_complex/benchmark) add_subdirectory(src/Bottleneck_distance/example) add_subdirectory(src/Bottleneck_distance/test) + add_subdirectory(src/Bottleneck_distance/benchmark) # data points generator add_subdirectory(data/points/generator) diff --git a/src/Bottleneck_distance/benchmark/CMakeLists.txt b/src/Bottleneck_distance/benchmark/CMakeLists.txt new file mode 100644 index 00000000..f70dd8ff --- /dev/null +++ b/src/Bottleneck_distance/benchmark/CMakeLists.txt @@ -0,0 +1,13 @@ +cmake_minimum_required(VERSION 2.6) +project(Bottleneck_distance_benchmark) + + +# requires CGAL 4.8 +# cmake -DCGAL_DIR=~/workspace/CGAL-4.8 ../../.. +if(CGAL_FOUND) + if (NOT CGAL_VERSION VERSION_LESS 4.8.0) + if (EIGEN3_FOUND) + add_executable ( bottleneck_chrono bottleneck_chrono.cpp ) + endif() + endif () +endif() diff --git a/src/Bottleneck_distance/benchmark/bottleneck_chrono.cpp b/src/Bottleneck_distance/benchmark/bottleneck_chrono.cpp new file mode 100644 index 00000000..456c570b --- /dev/null +++ b/src/Bottleneck_distance/benchmark/bottleneck_chrono.cpp @@ -0,0 +1,62 @@ +/* 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: Francois Godi + * + * Copyright (C) 2015 INRIA + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include +#include +#include +#include + +using namespace Gudhi::persistence_diagram; + + +double upper_bound = 400.; // any real > 0 + +int main() { + std::ofstream result_file; + result_file.open("results.csv", std::ios::out); + + for (int n = 1000; n <= 10000; n += 1000) { + 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)); + result_file << n << ";" << duration.count() << ";" << b << std::endl; + } + result_file.close(); +} diff --git a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h index ebe1123b..21187f9c 100644 --- a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h +++ b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h @@ -4,7 +4,7 @@ * * Author: François Godi * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2015 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -20,8 +20,8 @@ * along with this program. If not, see . */ -#ifndef DOC_BOTTLENECK_DISTANCE_H_ -#define DOC_BOTTLENECK_DISTANCE_H_ +#ifndef DOC_BOTTLENECK_DISTANCE_INTRO_BOTTLENECK_DISTANCE_H_ +#define DOC_BOTTLENECK_DISTANCE_INTRO_BOTTLENECK_DISTANCE_H_ // needs namespace for Doxygen to link on classes namespace Gudhi { @@ -48,3 +48,4 @@ namespace bottleneck_distance { } // namespace Gudhi +#endif // DOC_BOTTLENECK_DISTANCE_INTRO_BOTTLENECK_DISTANCE_H_ diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt index cd53ccfc..c66623e9 100644 --- a/src/Bottleneck_distance/example/CMakeLists.txt +++ b/src/Bottleneck_distance/example/CMakeLists.txt @@ -8,6 +8,8 @@ if(CGAL_FOUND) if (EIGEN3_FOUND) add_executable (bottleneck_read_file_example bottleneck_read_file_example.cpp) add_executable (bottleneck_basic_example bottleneck_basic_example.cpp) + + add_test(bottleneck_basic_example ${CMAKE_CURRENT_BINARY_DIR}/bottleneck_basic_example) endif() endif () endif() diff --git a/src/Bottleneck_distance/example/bottleneck_basic_example.cpp b/src/Bottleneck_distance/example/bottleneck_basic_example.cpp index 78e00e57..91a7302f 100644 --- a/src/Bottleneck_distance/example/bottleneck_basic_example.cpp +++ b/src/Bottleneck_distance/example/bottleneck_basic_example.cpp @@ -4,7 +4,7 @@ * * Authors: Francois Godi, small modifications by Pawel Dlotko * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2015 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -25,24 +25,24 @@ int main() { - std::vector< std::pair > v1, v2; + 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); - v1.emplace_back(3., std::numeric_limits::infinity()); + v1.emplace_back(2.7, 3.7); + v1.emplace_back(9.6, 14.); + v1.emplace_back(34.2, 34.974); + v1.emplace_back(3., std::numeric_limits::infinity()); - v2.emplace_back(2.8, 4.45); - v2.emplace_back(9.5, 14.1); - v2.emplace_back(3.2, std::numeric_limits::infinity()); + v2.emplace_back(2.8, 4.45); + v2.emplace_back(9.5, 14.1); + v2.emplace_back(3.2, std::numeric_limits::infinity()); - double b = Gudhi::persistence_diagram::bottleneck_distance(v1, v2); + double b = Gudhi::persistence_diagram::bottleneck_distance(v1, v2); - std::cout << "Bottleneck distance = " << b << std::endl; + std::cout << "Bottleneck distance = " << b << std::endl; - b = Gudhi::persistence_diagram::bottleneck_distance(v1, v2, 0.1); + b = Gudhi::persistence_diagram::bottleneck_distance(v1, v2, 0.1); - std::cout << "Approx bottleneck distance = " << b << std::endl; + std::cout << "Approx bottleneck distance = " << b << std::endl; } diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp index ceedccc5..4c74b66e 100644 --- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp +++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp @@ -4,7 +4,7 @@ * * Authors: Francois Godi, small modifications by Pawel Dlotko * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2015 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -28,49 +28,42 @@ #include #include -std::vector< std::pair > read_diagram_from_file( const char* filename ) -{ - std::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"; - } +std::vector< std::pair > read_diagram_from_file(const char* filename) { + std::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"; + } - 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 ) ); - } + 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 + } + in.close(); + return result; +} // read_diagram_from_file -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"; +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] ); + 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] ); + if (argc == 4) { + tolerance = atof(argv[3]); } double b = Gudhi::persistence_diagram::bottleneck_distance(diag1, diag2, tolerance); std::cout << "The distance between the diagrams is : " << b << ". The tolerance is : " << tolerance << std::endl; diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h index 42a0d444..2b7e4767 100644 --- a/src/Bottleneck_distance/include/gudhi/Bottleneck.h +++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h @@ -4,7 +4,7 @@ * * Author: Francois Godi * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2015 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -31,62 +31,65 @@ namespace Gudhi { namespace persistence_diagram { double bottleneck_distance_approx(Persistence_graph& g, double e) { - double b_lower_bound = 0.; - double b_upper_bound = g.diameter_bound(); - const double alpha = std::pow(g.size(), 1./5.); - Graph_matching m(g); - Graph_matching biggest_unperfect(g); - while (b_upper_bound - b_lower_bound > 2*e) { - double step = b_lower_bound + (b_upper_bound - b_lower_bound)/alpha; - if(step <= b_lower_bound || step >= b_upper_bound) //Avoid precision problem - break; - m.set_r(step); - while (m.multi_augment()); //compute a maximum matching (in the graph corresponding to the current r) - if (m.perfect()) { - m = biggest_unperfect; - b_upper_bound = step; - } else { - biggest_unperfect = m; - b_lower_bound = step; - } + double b_lower_bound = 0.; + double b_upper_bound = g.diameter_bound(); + const double alpha = std::pow(g.size(), 1. / 5.); + Graph_matching m(g); + Graph_matching biggest_unperfect(g); + while (b_upper_bound - b_lower_bound > 2 * e) { + double step = b_lower_bound + (b_upper_bound - b_lower_bound) / alpha; + if (step <= b_lower_bound || step >= b_upper_bound) // Avoid precision problem + break; + m.set_r(step); + while (m.multi_augment()); // compute a maximum matching (in the graph corresponding to the current r) + if (m.perfect()) { + m = biggest_unperfect; + b_upper_bound = step; + } else { + biggest_unperfect = m; + b_lower_bound = step; } - return (b_lower_bound + b_upper_bound)/2.; + } + return (b_lower_bound + b_upper_bound) / 2.; } double bottleneck_distance_exact(Persistence_graph& g) { - std::vector sd = g.sorted_distances(); - long lower_bound_i = 0; - long upper_bound_i = sd.size()-1; - const double alpha = std::pow(g.size(), 1./5.); - Graph_matching m(g); - Graph_matching biggest_unperfect(g); - while (lower_bound_i != upper_bound_i) { - long step = lower_bound_i + static_cast((upper_bound_i - lower_bound_i - 1)/alpha); - m.set_r(sd.at(step)); - while (m.multi_augment()); //compute a maximum matching (in the graph corresponding to the current r) - if (m.perfect()) { - m = biggest_unperfect; - upper_bound_i = step; - } else { - biggest_unperfect = m; - lower_bound_i = step + 1; - } + std::vector sd = g.sorted_distances(); + long lower_bound_i = 0; + long upper_bound_i = sd.size() - 1; + const double alpha = std::pow(g.size(), 1. / 5.); + Graph_matching m(g); + Graph_matching biggest_unperfect(g); + while (lower_bound_i != upper_bound_i) { + long step = lower_bound_i + static_cast ((upper_bound_i - lower_bound_i - 1) / alpha); + m.set_r(sd.at(step)); + while (m.multi_augment()); // compute a maximum matching (in the graph corresponding to the current r) + if (m.perfect()) { + m = biggest_unperfect; + upper_bound_i = step; + } else { + biggest_unperfect = m; + lower_bound_i = step + 1; } - return sd.at(lower_bound_i); + } + return sd.at(lower_bound_i); } /** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams (see concepts). - * If the last parameter e is not 0, you get an additive e-approximation, which is a lot faster to compute whatever is e. - * Thus, by default, e is a very small positive double, actually the smallest double possible such that the floating-point inaccuracies don't lead to a failure of the algorithm. + * If the last parameter e is not 0, you get an additive e-approximation, which is a lot faster to compute whatever is + * e. + * Thus, by default, e is a very small positive double, actually the smallest double possible such that the + * floating-point inaccuracies don't lead to a failure of the algorithm. * * \ingroup bottleneck_distance */ template -double bottleneck_distance(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e=std::numeric_limits::min()) { - Persistence_graph g(diag1, diag2, e); - if(g.bottleneck_alive() == std::numeric_limits::infinity()) - return std::numeric_limits::infinity(); - return std::max(g.bottleneck_alive(), e == 0. ? bottleneck_distance_exact(g) : bottleneck_distance_approx(g, e)); +double bottleneck_distance(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, + double e = std::numeric_limits::min()) { + Persistence_graph g(diag1, diag2, e); + if (g.bottleneck_alive() == std::numeric_limits::infinity()) + return std::numeric_limits::infinity(); + return std::max(g.bottleneck_alive(), e == 0. ? bottleneck_distance_exact(g) : bottleneck_distance_approx(g, e)); } } // namespace persistence_diagram diff --git a/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree.h b/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree.h deleted file mode 100644 index f085b0da..00000000 --- a/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree.h +++ /dev/null @@ -1,582 +0,0 @@ -// 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 "Kd_tree_node.h" - -#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->lower_low_val = c_low.tight_bounding_box().min_coord(cd); - nh->lower_high_val = c_low.tight_bounding_box().max_coord(cd); - } - else{ - nh->lower_low_val = nh->cutting_value(); - nh->lower_high_val = nh->cutting_value(); - } - if(!c.empty()){ - nh->upper_low_val = c.tight_bounding_box().min_coord(cd); - nh->upper_high_val = c.tight_bounding_box().max_coord(cd); - } - else{ - nh->upper_low_val = nh->cutting_value(); - nh->upper_high_val = nh->cutting_value(); - } - - CGAL_assertion(nh->cutting_value() >= nh->lower_low_val); - CGAL_assertion(nh->cutting_value() <= nh->upper_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() - { - // This function is not ready to be called when a tree already exists, one - // must call invalidate_built() first. - CGAL_assertion(!is_built()); - CGAL_assertion(!removed_); - 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(removed_){ - // Walk the tree to collect the remaining points. - // Writing directly to pts would likely work, but better be safe. - std::vector ptstmp; - //ptstmp.resize(root()->num_items()); - root()->tree_items(std::back_inserter(ptstmp)); - pts.swap(ptstmp); - removed_=false; - CGAL_assertion(is_built()); // the rest of the cleanup must happen - } - 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) - { - invalidate_built(); - pts.push_back(p); - } - - template - void - insert(InputIterator first, InputIterator beyond) - { - invalidate_built(); - pts.insert(pts.end(),first, beyond); - } - -private: - struct Equal_by_coordinates { - SearchTraits const* traits; - Point_d const* pp; - bool operator()(Point_d const&q) const { - typename SearchTraits::Construct_cartesian_const_iterator_d ccci=traits->construct_cartesian_const_iterator_d_object(); - return std::equal(ccci(*pp), ccci(*pp,0), ccci(q)); - } - }; - Equal_by_coordinates equal_by_coordinates(Point_d const&p){ - Equal_by_coordinates ret = { &traits(), &p }; - return ret; - } - -public: - void - remove(const Point_d& p) - { - remove(p, equal_by_coordinates(p)); - } - - template - void - remove(const Point_d& p, Equal const& equal_to_p) - { -#if 0 - // This code could have quadratic runtime. - if (!is_built()) { - std::vector::iterator pi = std::find(pts.begin(), pts.end(), p); - // Precondition: the point must be there. - CGAL_assertion (pi != pts.end()); - pts.erase(pi); - return; - } -#endif - bool success = remove_(p, 0, false, 0, false, root(), equal_to_p); - CGAL_assertion(success); - - // Do not set the flag is the tree has been cleared. - if(is_built()) - removed_ |= success; - } -private: - template - bool remove_(const Point_d& p, - Internal_node_handle grandparent, bool parent_islower, - Internal_node_handle parent, bool islower, - Node_handle node, Equal const& equal_to_p) { - // Recurse to locate the point - if (!node->is_leaf()) { - Internal_node_handle newparent = static_cast(node); - // FIXME: This should be if(xcutting_dimension()] <= newparent->cutting_value()) { - if (remove_(p, parent, islower, newparent, true, newparent->lower(), equal_to_p)) - return true; - } - //if (traits().construct_cartesian_const_iterator_d_object()(p)[newparent->cutting_dimension()] >= newparent->cutting_value()) - return remove_(p, parent, islower, newparent, false, newparent->upper(), equal_to_p); - - CGAL_assertion(false); // Point was not found - } - - // Actual removal - Leaf_node_handle lnode = static_cast(node); - if (lnode->size() > 1) { - iterator pi = std::find_if(lnode->begin(), lnode->end(), equal_to_p); - // FIXME: we should ensure this never happens - if (pi == lnode->end()) return false; - 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 (!equal_to_p(*lnode->begin())) { - // FIXME: we should ensure this never happens - return false; - } else if (grandparent) { - Node_handle brother = islower ? parent->upper() : parent->lower(); - if (parent_islower) - grandparent->set_lower(brother); - else - grandparent->set_upper(brother); - } else if (parent) { - tree_root = islower ? parent->upper() : parent->lower(); - } else { - clear(); - } - return true; - } - -public: - //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 diff --git a/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree_node.h b/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree_node.h deleted file mode 100644 index 909ee260..00000000 --- a/src/Bottleneck_distance/include/gudhi/CGAL/Kd_tree_node.h +++ /dev/null @@ -1,586 +0,0 @@ -// Copyright (c) 2002,2011 Utrecht University (The Netherlands). -// 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. -// -// $URL$ -// $Id$ -// -// -// Authors : Hans Tangelder () - -#ifndef CGAL_KD_TREE_NODE_H -#define CGAL_KD_TREE_NODE_H - -#include "CGAL/Splitters.h" - -#include -#include - -namespace CGAL { - - template - class Kd_tree; - - template < class TreeTraits, class Splitter, class UseExtendedNode > - class Kd_tree_node { - - friend class Kd_tree; - - typedef typename Kd_tree::Node_handle Node_handle; - typedef typename Kd_tree::Node_const_handle Node_const_handle; - typedef typename Kd_tree::Internal_node_handle Internal_node_handle; - typedef typename Kd_tree::Internal_node_const_handle Internal_node_const_handle; - typedef typename Kd_tree::Leaf_node_handle Leaf_node_handle; - typedef typename Kd_tree::Leaf_node_const_handle Leaf_node_const_handle; - typedef typename TreeTraits::Point_d Point_d; - - typedef typename TreeTraits::FT FT; - typedef typename Kd_tree::Separator Separator; - typedef typename Kd_tree::Point_d_iterator Point_d_iterator; - typedef typename Kd_tree::iterator iterator; - typedef typename Kd_tree::D D; - - bool leaf; - - public : - Kd_tree_node(bool leaf_) - :leaf(leaf_){} - - bool is_leaf() const{ - return leaf; - } - - std::size_t - num_items() const - { - if (is_leaf()){ - Leaf_node_const_handle node = - static_cast(this); - return node->size(); - } - else { - Internal_node_const_handle node = - static_cast(this); - return node->lower()->num_items() + node->upper()->num_items(); - } - } - - std::size_t - num_nodes() const - { - if (is_leaf()) return 1; - else { - Internal_node_const_handle node = - static_cast(this); - return node->lower()->num_nodes() + node->upper()->num_nodes(); - } - } - - int - depth(const int current_max_depth) const - { - if (is_leaf()){ - return current_max_depth; - } - else { - Internal_node_const_handle node = - static_cast(this); - return - (std::max)( node->lower()->depth(current_max_depth + 1), - node->upper()->depth(current_max_depth + 1)); - } - } - - int - depth() const - { - return depth(1); - } - - template - OutputIterator - tree_items(OutputIterator it) const { - if (is_leaf()) { - Leaf_node_const_handle node = - static_cast(this); - if (node->size()>0) - for (iterator i=node->begin(); i != node->end(); i++) - {*it=*i; ++it;} - } - else { - Internal_node_const_handle node = - static_cast(this); - it=node->lower()->tree_items(it); - it=node->upper()->tree_items(it); - } - return it; - } - - - boost::optional - any_tree_item() const { - boost::optional result = boost::none; - if (is_leaf()) { - Leaf_node_const_handle node = - static_cast(this); - if (node->size()>0){ - return boost::make_optional(*(node->begin())); - } - } - else { - Internal_node_const_handle node = - static_cast(this); - result = node->lower()->any_tree_item(); - if(! result){ - result = node->upper()->any_tree_item(); - } - } - return result; - } - - - void - indent(int d) const - { - for(int i = 0; i < d; i++){ - std::cout << " "; - } - } - - - void - print(int d = 0) const - { - if (is_leaf()) { - Leaf_node_const_handle node = - static_cast(this); - indent(d); - std::cout << "leaf" << std::endl; - if (node->size()>0) - for (iterator i=node->begin(); i != node->end(); i++) - {indent(d);std::cout << *i << std::endl;} - } - else { - Internal_node_const_handle node = - static_cast(this); - indent(d); - std::cout << "lower tree" << std::endl; - node->lower()->print(d+1); - indent(d); - std::cout << "separator: dim = " << node->cutting_dimension() << " val = " << node->cutting_value() << std::endl; - indent(d); - std::cout << "upper tree" << std::endl; - node->upper()->print(d+1); - } - } - - - template - OutputIterator - search(OutputIterator it, const FuzzyQueryItem& q, - Kd_tree_rectangle& b) const - { - if (is_leaf()) { - Leaf_node_const_handle node = - static_cast(this); - if (node->size()>0) - for (iterator i=node->begin(); i != node->end(); i++) - if (q.contains(*i)) - {*it++=*i;} - } - else { - Internal_node_const_handle node = - static_cast(this); - // after splitting b denotes the lower part of b - Kd_tree_rectangle b_upper(b); - b.split(b_upper, node->cutting_dimension(), - node->cutting_value()); - - if (q.outer_range_contains(b)) - it=node->lower()->tree_items(it); - else - if (q.inner_range_intersects(b)) - it=node->lower()->search(it,q,b); - if (q.outer_range_contains(b_upper)) - it=node->upper()->tree_items(it); - else - if (q.inner_range_intersects(b_upper)) - it=node->upper()->search(it,q,b_upper); - }; - return it; - } - - - template - boost::optional - search_any_point(const FuzzyQueryItem& q, - Kd_tree_rectangle& b) const - { - boost::optional result = boost::none; - if (is_leaf()) { - Leaf_node_const_handle node = - static_cast(this); - if (node->size()>0) - for (iterator i=node->begin(); i != node->end(); i++) - if (q.contains(*i)) - { result = *i; break; } - } - else { - Internal_node_const_handle node = - static_cast(this); - // after splitting b denotes the lower part of b - Kd_tree_rectangle b_upper(b); - b.split(b_upper, node->cutting_dimension(), - node->cutting_value()); - - if (q.outer_range_contains(b)){ - result = node->lower()->any_tree_item(); - }else{ - if (q.inner_range_intersects(b)){ - result = node->lower()->search_any_point(q,b); - } - } - if(result){ - return result; - } - if (q.outer_range_contains(b_upper)){ - result = node->upper()->any_tree_item(); - }else{ - if (q.inner_range_intersects(b_upper)) - result = node->upper()->search_any_point(q,b_upper); - } - } - return result; - } - - }; - - - template < class TreeTraits, class Splitter, class UseExtendedNode > - class Kd_tree_leaf_node : public Kd_tree_node< TreeTraits, Splitter, UseExtendedNode >{ - - friend class Kd_tree; - - typedef typename Kd_tree::iterator iterator; - typedef Kd_tree_node< TreeTraits, Splitter, UseExtendedNode> Base; - typedef typename TreeTraits::Point_d Point_d; - - private: - - // private variables for leaf nodes - boost::int32_t n; // denotes number of items in a leaf node - iterator data; // iterator to data in leaf node - - - public: - - // default constructor - Kd_tree_leaf_node() - {} - - Kd_tree_leaf_node(bool leaf_ ) - : Base(leaf_) - {} - - Kd_tree_leaf_node(bool leaf_,unsigned int n_ ) - : Base(leaf_), n(n_) - {} - - // members for all nodes - - // members for leaf nodes only - inline - unsigned int - size() const - { - return n; - } - - inline - iterator - begin() const - { - return data; - } - - inline - iterator - end() const - { - return data + n; - } - - inline - void - drop_last_point() - { - --n; - } - - }; //leaf node - - - - template < class TreeTraits, class Splitter, class UseExtendedNode> - class Kd_tree_internal_node : public Kd_tree_node< TreeTraits, Splitter, UseExtendedNode >{ - - friend class Kd_tree; - - typedef Kd_tree_node< TreeTraits, Splitter, UseExtendedNode> Base; - typedef typename Kd_tree::Node_handle Node_handle; - typedef typename Kd_tree::Node_const_handle Node_const_handle; - - typedef typename TreeTraits::FT FT; - typedef typename Kd_tree::Separator Separator; - - private: - - // private variables for internal nodes - boost::int32_t cut_dim; - FT cut_val; - Node_handle lower_ch, upper_ch; - - - // private variables for extended internal nodes - FT upper_low_val; - FT upper_high_val; - FT lower_low_val; - FT lower_high_val; - - - public: - - // default constructor - Kd_tree_internal_node() - {} - - Kd_tree_internal_node(bool leaf_) - : Base(leaf_) - {} - - - // members for internal node and extended internal node - - inline - Node_const_handle - lower() const - { - return lower_ch; - } - - inline - Node_const_handle - upper() const - { - return upper_ch; - } - - inline - Node_handle - lower() - { - return lower_ch; - } - - inline - Node_handle - upper() - { - return upper_ch; - } - - inline - void - set_lower(Node_handle nh) - { - lower_ch = nh; - } - - inline - void - set_upper(Node_handle nh) - { - upper_ch = nh; - } - - // inline Separator& separator() {return sep; } - // use instead - inline - void set_separator(Separator& sep){ - cut_dim = sep.cutting_dimension(); - cut_val = sep.cutting_value(); - } - - inline - FT - cutting_value() const - { - return cut_val; - } - - inline - int - cutting_dimension() const - { - return cut_dim; - } - - // members for extended internal node only - inline - FT - upper_low_value() const - { - return upper_low_val; - } - - inline - FT - upper_high_value() const - { - return upper_high_val; - } - - inline - FT - lower_low_value() const - { - return lower_low_val; - } - - inline - FT - lower_high_value() const - { - return lower_high_val; - } - - /*Separator& - separator() - { - return Separator(cutting_dimension,cutting_value); - }*/ - - - };//internal node - - template < class TreeTraits, class Splitter> - class Kd_tree_internal_node : public Kd_tree_node< TreeTraits, Splitter, Tag_false >{ - - friend class Kd_tree; - - typedef Kd_tree_node< TreeTraits, Splitter, Tag_false> Base; - typedef typename Kd_tree::Node_handle Node_handle; - typedef typename Kd_tree::Node_const_handle Node_const_handle; - - typedef typename TreeTraits::FT FT; - typedef typename Kd_tree::Separator Separator; - - private: - - // private variables for internal nodes - boost::uint8_t cut_dim; - FT cut_val; - - Node_handle lower_ch, upper_ch; - - public: - - // default constructor - Kd_tree_internal_node() - {} - - Kd_tree_internal_node(bool leaf_) - : Base(leaf_) - {} - - - // members for internal node and extended internal node - - inline - Node_const_handle - lower() const - { - return lower_ch; - } - - inline - Node_const_handle - upper() const - { - return upper_ch; - } - - inline - Node_handle - lower() - { - return lower_ch; - } - - inline - Node_handle - upper() - { - return upper_ch; - } - - inline - void - set_lower(Node_handle nh) - { - lower_ch = nh; - } - - inline - void - set_upper(Node_handle nh) - { - upper_ch = nh; - } - - // inline Separator& separator() {return sep; } - // use instead - - inline - void set_separator(Separator& sep){ - cut_dim = sep.cutting_dimension(); - cut_val = sep.cutting_value(); - } - - inline - FT - cutting_value() const - { - return cut_val; - } - - inline - int - cutting_dimension() const - { - return cut_dim; - } - - /* Separator& - separator() - { - return Separator(cutting_dimension,cutting_value); - }*/ - - - };//internal node - - - -} // namespace CGAL -#endif // CGAL_KDTREE_NODE_H diff --git a/src/Bottleneck_distance/include/gudhi/CGAL/Orthogonal_incremental_neighbor_search.h b/src/Bottleneck_distance/include/gudhi/CGAL/Orthogonal_incremental_neighbor_search.h deleted file mode 100644 index dbe707ed..00000000 --- a/src/Bottleneck_distance/include/gudhi/CGAL/Orthogonal_incremental_neighbor_search.h +++ /dev/null @@ -1,621 +0,0 @@ -// Copyright (c) 2002,2011 Utrecht University (The Netherlands). -// 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 () - -#ifndef CGAL_ORTHOGONAL_INCREMENTAL_NEIGHBOR_SEARCH -#define CGAL_ORTHOGONAL_INCREMENTAL_NEIGHBOR_SEARCH - -#include "CGAL/Kd_tree.h" - -#include -#include -#include -#include -#include -#include - -namespace CGAL { - - template ::type, - class Splitter_ = Sliding_midpoint, - class Tree_= Kd_tree > - class Orthogonal_incremental_neighbor_search { - - public: - typedef Splitter_ Splitter; - typedef Tree_ Tree; - typedef Distance_ Distance; - typedef typename SearchTraits::Point_d Point_d; - typedef typename Distance::Query_item Query_item; - typedef typename SearchTraits::FT FT; - typedef typename Tree::Point_d_iterator Point_d_iterator; - typedef typename Tree::Node_const_handle Node_const_handle; - - typedef std::pair Point_with_transformed_distance; - typedef CGAL::cpp11::tuple > Node_with_distance; - typedef std::vector Node_with_distance_vector; - typedef std::vector Point_with_transformed_distance_vector; - - template - struct Object_wrapper - { - T object; - Object_wrapper(const T& t):object(t){} - const T& operator* () const { return object; } - const T* operator-> () const { return &object; } - }; - - class Iterator_implementation { - SearchTraits traits; - public: - - int number_of_neighbours_computed; - int number_of_internal_nodes_visited; - int number_of_leaf_nodes_visited; - int number_of_items_visited; - - private: - - typedef std::vector Distance_vector; - - Distance_vector dists; - - Distance Orthogonal_distance_instance; - - FT multiplication_factor; - - Query_item query_point; - - FT distance_to_root; - - bool search_nearest_neighbour; - - FT rd; - - - class Priority_higher { - public: - - bool search_nearest; - - Priority_higher(bool search_the_nearest_neighbour) - : search_nearest(search_the_nearest_neighbour) - {} - - //highest priority is smallest distance - bool - operator() (Node_with_distance* n1, Node_with_distance* n2) const - { - return (search_nearest) ? (CGAL::cpp11::get<1>(*n1) > CGAL::cpp11::get<1>(*n2)) : (CGAL::cpp11::get<1>(*n2) > CGAL::cpp11::get<1>(*n1)); - } - }; - - class Distance_smaller { - - public: - - bool search_nearest; - - Distance_smaller(bool search_the_nearest_neighbour) - : search_nearest(search_the_nearest_neighbour) - {} - - //highest priority is smallest distance - bool operator() (Point_with_transformed_distance* p1, Point_with_transformed_distance* p2) const - { - return (search_nearest) ? (p1->second > p2->second) : (p2->second > p1->second); - } - }; - - - std::priority_queue PriorityQueue; - - public: - std::priority_queue Item_PriorityQueue; - - - public: - - int reference_count; - - - - // constructor - Iterator_implementation(const Tree& tree,const Query_item& q, const Distance& tr, - FT Eps=FT(0.0), bool search_nearest=true) - : traits(tree.traits()),number_of_neighbours_computed(0), number_of_internal_nodes_visited(0), - number_of_leaf_nodes_visited(0), number_of_items_visited(0), - Orthogonal_distance_instance(tr), multiplication_factor(Orthogonal_distance_instance.transformed_distance(FT(1.0)+Eps)), - query_point(q), search_nearest_neighbour(search_nearest), - PriorityQueue(Priority_higher(search_nearest)), Item_PriorityQueue(Distance_smaller(search_nearest)), - reference_count(1) - - - { - if (tree.empty()) return; - - typename SearchTraits::Construct_cartesian_const_iterator_d ccci=traits.construct_cartesian_const_iterator_d_object(); - int dim = static_cast(std::distance(ccci(q), ccci(q,0))); - - dists.resize(dim); - for(int i=0 ; i(*The_Root); - Compute_the_next_nearest_neighbour(); - } - else{ - distance_to_root= - Orthogonal_distance_instance.max_distance_to_rectangle(q, - tree.bounding_box(), dists); - Node_with_distance *The_Root = new Node_with_distance(tree.root(), - distance_to_root, dists); - PriorityQueue.push(The_Root); - - // rd is the distance of the top of the priority queue to q - rd=CGAL::cpp11::get<1>(*The_Root); - Compute_the_next_furthest_neighbour(); - } - - - } - - // * operator - const Point_with_transformed_distance& - operator* () const - { - return *(Item_PriorityQueue.top()); - } - - // prefix operator - Iterator_implementation& - operator++() - { - Delete_the_current_item_top(); - if(search_nearest_neighbour) - Compute_the_next_nearest_neighbour(); - else - Compute_the_next_furthest_neighbour(); - return *this; - } - - // postfix operator - Object_wrapper - operator++(int) - { - Object_wrapper result( *(Item_PriorityQueue.top()) ); - ++*this; - return result; - } - - // Print statistics of the general priority search process. - std::ostream& - statistics (std::ostream& s) const { - s << "Orthogonal priority search statistics:" - << std::endl; - s << "Number of internal nodes visited:" - << number_of_internal_nodes_visited << std::endl; - s << "Number of leaf nodes visited:" - << number_of_leaf_nodes_visited << std::endl; - s << "Number of items visited:" - << number_of_items_visited << std::endl; - s << "Number of neighbours computed:" - << number_of_neighbours_computed << std::endl; - return s; - } - - - //destructor - ~Iterator_implementation() - { - while (!PriorityQueue.empty()) { - Node_with_distance* The_top=PriorityQueue.top(); - PriorityQueue.pop(); - delete The_top; - } - while (!Item_PriorityQueue.empty()) { - Point_with_transformed_distance* The_top=Item_PriorityQueue.top(); - Item_PriorityQueue.pop(); - delete The_top; - } - } - - private: - - void - Delete_the_current_item_top() - { - Point_with_transformed_distance* The_item_top=Item_PriorityQueue.top(); - Item_PriorityQueue.pop(); - delete The_item_top; - } - - void - Compute_the_next_nearest_neighbour() - { - // compute the next item - bool next_neighbour_found=false; - if (!(Item_PriorityQueue.empty())) { - next_neighbour_found= - (multiplication_factor*rd > Item_PriorityQueue.top()->second); - } - typename SearchTraits::Construct_cartesian_const_iterator_d construct_it=traits.construct_cartesian_const_iterator_d_object(); - typename SearchTraits::Cartesian_const_iterator_d query_point_it = construct_it(query_point); - // otherwise browse the tree further - while ((!next_neighbour_found) && (!PriorityQueue.empty())) { - Node_with_distance* The_node_top=PriorityQueue.top(); - Node_const_handle N= CGAL::cpp11::get<0>(*The_node_top); - dists = CGAL::cpp11::get<2>(*The_node_top); - PriorityQueue.pop(); - delete The_node_top; - FT copy_rd=rd; - while (!(N->is_leaf())) { // compute new distance - typename Tree::Internal_node_const_handle node = - static_cast(N); - number_of_internal_nodes_visited++; - int new_cut_dim=node->cutting_dimension(); - FT new_rd,dst = dists[new_cut_dim]; - FT val = *(query_point_it + new_cut_dim); - FT diff1 = val - node->upper_low_value(); - FT diff2 = val - node->lower_high_value(); - if (diff1 + diff2 < FT(0.0)) { - new_rd= - Orthogonal_distance_instance.new_distance(copy_rd,dst,diff1,new_cut_dim); - - CGAL_assertion(new_rd >= copy_rd); - dists[new_cut_dim] = diff1; - Node_with_distance *Upper_Child = - new Node_with_distance(node->upper(), new_rd, dists); - PriorityQueue.push(Upper_Child); - dists[new_cut_dim] = dst; - N=node->lower(); - - } - else { // compute new distance - new_rd=Orthogonal_distance_instance.new_distance(copy_rd,dst,diff2,new_cut_dim); - CGAL_assertion(new_rd >= copy_rd); - dists[new_cut_dim] = diff2; - Node_with_distance *Lower_Child = - new Node_with_distance(node->lower(), new_rd, dists); - PriorityQueue.push(Lower_Child); - dists[new_cut_dim] = dst; - N=node->upper(); - } - } - // n is a leaf - typename Tree::Leaf_node_const_handle node = - static_cast(N); - number_of_leaf_nodes_visited++; - if (node->size() > 0) { - for (typename Tree::iterator it=node->begin(); it != node->end(); it++) { - number_of_items_visited++; - FT distance_to_query_point= - Orthogonal_distance_instance.transformed_distance(query_point,*it); - Point_with_transformed_distance *NN_Candidate= - new Point_with_transformed_distance(*it,distance_to_query_point); - Item_PriorityQueue.push(NN_Candidate); - } - // old top of PriorityQueue has been processed, - // hence update rd - - if (!(PriorityQueue.empty())) { - rd = CGAL::cpp11::get<1>(*PriorityQueue.top()); - next_neighbour_found = - (multiplication_factor*rd > - Item_PriorityQueue.top()->second); - } - else // priority queue empty => last neighbour found - { - next_neighbour_found=true; - } - - number_of_neighbours_computed++; - } - } // next_neighbour_found or priority queue is empty - // in the latter case also the item priority quee is empty - } - - - void - Compute_the_next_furthest_neighbour() - { - // compute the next item - bool next_neighbour_found=false; - if (!(Item_PriorityQueue.empty())) { - next_neighbour_found= - (rd < multiplication_factor*Item_PriorityQueue.top()->second); - } - typename SearchTraits::Construct_cartesian_const_iterator_d construct_it=traits.construct_cartesian_const_iterator_d_object(); - typename SearchTraits::Cartesian_const_iterator_d query_point_it = construct_it(query_point); - // otherwise browse the tree further - while ((!next_neighbour_found) && (!PriorityQueue.empty())) { - Node_with_distance* The_node_top=PriorityQueue.top(); - Node_const_handle N= CGAL::cpp11::get<0>(*The_node_top); - dists = CGAL::cpp11::get<2>(*The_node_top); - PriorityQueue.pop(); - delete The_node_top; - FT copy_rd=rd; - while (!(N->is_leaf())) { // compute new distance - typename Tree::Internal_node_const_handle node = - static_cast(N); - number_of_internal_nodes_visited++; - int new_cut_dim=node->cutting_dimension(); - FT new_rd,dst = dists[new_cut_dim]; - FT val = *(query_point_it + new_cut_dim); - FT diff1 = val - node->upper_low_value(); - FT diff2 = val - node->lower_high_value(); - if (diff1 + diff2 < FT(0.0)) { - diff1 = val - node->upper_high_value(); - new_rd= - Orthogonal_distance_instance.new_distance(copy_rd,dst,diff1,new_cut_dim); - Node_with_distance *Lower_Child = - new Node_with_distance(node->lower(), copy_rd, dists); - PriorityQueue.push(Lower_Child); - N=node->upper(); - dists[new_cut_dim] = diff1; - copy_rd=new_rd; - - } - else { // compute new distance - diff2 = val - node->lower_low_value(); - new_rd=Orthogonal_distance_instance.new_distance(copy_rd,dst,diff2,new_cut_dim); - Node_with_distance *Upper_Child = - new Node_with_distance(node->upper(), copy_rd, dists); - PriorityQueue.push(Upper_Child); - N=node->lower(); - dists[new_cut_dim] = diff2; - copy_rd=new_rd; - } - } - // n is a leaf - typename Tree::Leaf_node_const_handle node = - static_cast(N); - number_of_leaf_nodes_visited++; - if (node->size() > 0) { - for (typename Tree::iterator it=node->begin(); it != node->end(); it++) { - number_of_items_visited++; - FT distance_to_query_point= - Orthogonal_distance_instance.transformed_distance(query_point,*it); - Point_with_transformed_distance *NN_Candidate= - new Point_with_transformed_distance(*it,distance_to_query_point); - Item_PriorityQueue.push(NN_Candidate); - } - // old top of PriorityQueue has been processed, - // hence update rd - - if (!(PriorityQueue.empty())) { - rd = CGAL::cpp11::get<1>(*PriorityQueue.top()); - next_neighbour_found = - (multiplication_factor*rd < - Item_PriorityQueue.top()->second); - } - else // priority queue empty => last neighbour found - { - next_neighbour_found=true; - } - - number_of_neighbours_computed++; - } - } // next_neighbour_found or priority queue is empty - // in the latter case also the item priority quee is empty - } - }; // class Iterator_implementaion - - - - - - - - - - public: - class iterator; - typedef iterator const_iterator; - - // constructor - Orthogonal_incremental_neighbor_search(const Tree& tree, - const Query_item& q, FT Eps = FT(0.0), - bool search_nearest=true, const Distance& tr=Distance()) - : m_tree(tree),m_query(q),m_dist(tr),m_Eps(Eps),m_search_nearest(search_nearest) - {} - - iterator - begin() const - { - return iterator(m_tree,m_query,m_dist,m_Eps,m_search_nearest); - } - - iterator - end() const - { - return iterator(); - } - - std::ostream& - statistics(std::ostream& s) - { - begin()->statistics(s); - return s; - } - - - - - class iterator { - - public: - - typedef std::input_iterator_tag iterator_category; - typedef Point_with_transformed_distance value_type; - typedef Point_with_transformed_distance* pointer; - typedef const Point_with_transformed_distance& reference; - typedef std::size_t size_type; - typedef std::ptrdiff_t difference_type; - typedef int distance_type; - - //class Iterator_implementation; - Iterator_implementation *Ptr_implementation; - - - public: - - // default constructor - iterator() - : Ptr_implementation(0) - {} - - int - the_number_of_items_visited() - { - return Ptr_implementation->number_of_items_visited; - } - - // constructor - iterator(const Tree& tree,const Query_item& q, const Distance& tr=Distance(), FT eps=FT(0.0), - bool search_nearest=true) - : Ptr_implementation(new Iterator_implementation(tree, q, tr, eps, search_nearest)) - {} - - // copy constructor - iterator(const iterator& Iter) - { - Ptr_implementation = Iter.Ptr_implementation; - if (Ptr_implementation != 0) Ptr_implementation->reference_count++; - } - - iterator& operator=(const iterator& Iter) - { - if (Ptr_implementation != Iter.Ptr_implementation){ - if (Ptr_implementation != 0 && --(Ptr_implementation->reference_count)==0) { - delete Ptr_implementation; - } - Ptr_implementation = Iter.Ptr_implementation; - if (Ptr_implementation != 0) Ptr_implementation->reference_count++; - } - return *this; - } - - - const Point_with_transformed_distance& - operator* () const - { - return *(*Ptr_implementation); - } - - // -> operator - const Point_with_transformed_distance* - operator-> () const - { - return &*(*Ptr_implementation); - } - - // prefix operator - iterator& - operator++() - { - ++(*Ptr_implementation); - return *this; - } - - // postfix operator - Object_wrapper - operator++(int) - { - return (*Ptr_implementation)++; - } - - - bool - operator==(const iterator& It) const - { - if ( - ((Ptr_implementation == 0) || - Ptr_implementation->Item_PriorityQueue.empty()) && - ((It.Ptr_implementation == 0) || - It.Ptr_implementation->Item_PriorityQueue.empty()) - ) - return true; - // else - return (Ptr_implementation == It.Ptr_implementation); - } - - bool - operator!=(const iterator& It) const - { - return !(*this == It); - } - - std::ostream& - statistics (std::ostream& s) - { - Ptr_implementation->statistics(s); - return s; - } - - ~iterator() - { - if (Ptr_implementation != 0) { - Ptr_implementation->reference_count--; - if (Ptr_implementation->reference_count==0) { - delete Ptr_implementation; - Ptr_implementation = 0; - } - } - } - - - }; // class iterator - - //data members - const Tree& m_tree; - Query_item m_query; - Distance m_dist; - FT m_Eps; - bool m_search_nearest; - }; // class - - template - void swap (typename Orthogonal_incremental_neighbor_search::iterator& x, - typename Orthogonal_incremental_neighbor_search::iterator& y) - { - typename Orthogonal_incremental_neighbor_search::iterator::Iterator_implementation - *tmp = x.Ptr_implementation; - x.Ptr_implementation = y.Ptr_implementation; - y.Ptr_implementation = tmp; - } - -} // namespace CGAL - -#endif // CGAL_ORTHOGONAL_INCREMENTAL_NEIGHBOR_SEARCH_H diff --git a/src/Bottleneck_distance/include/gudhi/Graph_matching.h b/src/Bottleneck_distance/include/gudhi/Graph_matching.h index e9f455d7..253c89b4 100644 --- a/src/Bottleneck_distance/include/gudhi/Graph_matching.h +++ b/src/Bottleneck_distance/include/gudhi/Graph_matching.h @@ -4,7 +4,7 @@ * * Author: Francois Godi * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2015 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -34,141 +34,141 @@ namespace persistence_diagram { * \ingroup bottleneck_distance */ class Graph_matching { -public: - /** \internal \brief Constructor constructing an empty matching. */ - explicit Graph_matching(Persistence_graph &g); - /** \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: - Persistence_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. */ - Layered_neighbors_finder 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::vector & path); + public: + /** \internal \brief Constructor constructing an empty matching. */ + explicit Graph_matching(Persistence_graph &g); + /** \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: + Persistence_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. */ + Layered_neighbors_finder 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::vector & path); }; inline Graph_matching::Graph_matching(Persistence_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) - unmatched_in_u.emplace_back(u_point_index); + 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) { - g = m.g; - r = m.r; - v_to_u = m.v_to_u; - unmatched_in_u = m.unmatched_in_u; - return *this; + g = m.g; + 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(); + 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; + 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; + 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::vector 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; + // V vertices have at most one successor, thus when we backtrack from U we can directly pop_back 2 vertices. + std::vector 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 Layered_neighbors_finder 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) - nf.add(v_point_index); - Layered_neighbors_finder layered_nf(g, 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::vector 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(); + 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); + Layered_neighbors_finder layered_nf(g, 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::vector 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); + } } - return layered_nf; + // 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::vector& 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; - } + 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; + } } diff --git a/src/Bottleneck_distance/include/gudhi/Internal_point.h b/src/Bottleneck_distance/include/gudhi/Internal_point.h index 70342d0c..0b2d26fe 100644 --- a/src/Bottleneck_distance/include/gudhi/Internal_point.h +++ b/src/Bottleneck_distance/include/gudhi/Internal_point.h @@ -4,7 +4,7 @@ * * Author: Francois Godi * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2015 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -32,39 +32,60 @@ 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) { 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); } + double vec[2]; + int point_index; + + Internal_point() { } + + Internal_point(double x, double y, int p_i) { + 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); + } }; inline int null_point_index() { - return -1; + return -1; } struct Construct_coord_iterator { - typedef const double* result_type; - const double* operator()(const Internal_point& p) const - { return p.vec; } - const double* operator()(const Internal_point& p, int) const - { return p.vec+2; } + typedef const double* result_type; + + const double* operator()(const Internal_point& p) const { + return p.vec; + } + + const double* operator()(const Internal_point& p, int) const { + return p.vec + 2; + } }; } // namespace persistence_diagram } // namespace Gudhi - - - - #endif // INTERNAL_POINT_H_ diff --git a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h index 792925b7..96ece360 100644 --- a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h +++ b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h @@ -4,7 +4,7 @@ * * Author: Francois Godi * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2015 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -24,10 +24,9 @@ #define NEIGHBORS_FINDER_H_ // Inclusion order is important for CGAL patch -#include "CGAL/Kd_tree_node.h" -#include "CGAL/Kd_tree.h" -#include "CGAL/Orthogonal_k_neighbor_search.h" - +#include +#include +#include #include #include @@ -43,123 +42,126 @@ namespace persistence_diagram { /** \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. + * 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 { - - typedef CGAL::Dimension_tag<2> D; - typedef CGAL::Search_traits Traits; - typedef CGAL::Weighted_Minkowski_distance Distance; - typedef CGAL::Orthogonal_k_neighbor_search K_neighbor_search; - typedef K_neighbor_search::Tree Kd_tree; - -public: - /** \internal \brief Constructor taking the near distance definition as parameter. */ - Neighbors_finder(const Persistence_graph& g, 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::vector pull_all_near(int u_point_index); - -private: - const Persistence_graph& g; - const double r; - Kd_tree kd_t; - std::unordered_set projections_f; + typedef CGAL::Dimension_tag<2> D; + typedef CGAL::Search_traits Traits; + typedef CGAL::Weighted_Minkowski_distance Distance; + typedef CGAL::Orthogonal_k_neighbor_search K_neighbor_search; + typedef K_neighbor_search::Tree Kd_tree; + + public: + /** \internal \brief Constructor taking the near distance definition as parameter. */ + Neighbors_finder(const Persistence_graph& g, 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::vector pull_all_near(int u_point_index); + + private: + const Persistence_graph& g; + const double r; + Kd_tree kd_t; + std::unordered_set projections_f; }; /** \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. + * 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(const Persistence_graph& g, 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_graph& g; - const double r; - std::vector> neighbors_finder; + public: + /** \internal \brief Constructor taking the near distance definition as parameter. */ + Layered_neighbors_finder(const Persistence_graph& g, 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_graph& g; + const double r; + std::vector> neighbors_finder; }; inline Neighbors_finder::Neighbors_finder(const Persistence_graph& g, double r) : g(g), r(r), kd_t(), 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 - kd_t.insert(g.get_v_point(v_point_index)); + if (g.on_the_v_diagonal(v_point_index)) + projections_f.emplace(v_point_index); + else + kd_t.insert(g.get_v_point(v_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.empty()){ - //Any pair of projection is at distance 0 - tmp = *projections_f.cbegin(); - projections_f.erase(tmp); - } - else if (projections_f.count(c) && (g.distance(u_point_index, c) <= r)){ - //Is the query point near to its projection ? - tmp = c; - projections_f.erase(tmp); - } - else{ - //Is the query point near to a V point in the plane ? - Internal_point u_point = g.get_u_point(u_point_index); - std::array w = { {1., 1.} }; - K_neighbor_search search(kd_t, u_point, 1, 0., true, Distance(0, 2, w.begin(), w.end())); - auto it = search.begin(); - if(it==search.end() || g.distance(u_point_index, it->first.point_index) > r) - return null_point_index(); - tmp = it->first.point_index; - kd_t.remove(g.get_v_point(tmp)); - } - return tmp; + 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(); + projections_f.erase(tmp); + } else if (projections_f.count(c) && (g.distance(u_point_index, c) <= r)) { + // Is the query point near to its projection ? + tmp = c; + projections_f.erase(tmp); + } else { + // Is the query point near to a V point in the plane ? + Internal_point u_point = g.get_u_point(u_point_index); + std::array w = { + {1., 1.} + }; + K_neighbor_search search(kd_t, u_point, 1, 0., true, Distance(0, 2, w.begin(), w.end())); + auto it = search.begin(); + if (it == search.end() || g.distance(u_point_index, it->first.point_index) > r) + return null_point_index(); + tmp = it->first.point_index; + kd_t.remove(g.get_v_point(tmp)); + } + return tmp; } inline std::vector Neighbors_finder::pull_all_near(int u_point_index) { - std::vector all_pull; - 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; + std::vector all_pull; + 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(const Persistence_graph& g, double r) : g(g), 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::unique_ptr(new Neighbors_finder(g, r))); - neighbors_finder.at(vlayer)->add(v_point_index); + for (int l = neighbors_finder.size(); l <= vlayer; l++) + neighbors_finder.emplace_back(std::unique_ptr(new 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) { - if (static_cast (neighbors_finder.size()) <= vlayer) - return null_point_index(); - return neighbors_finder.at(vlayer)->pull_near(u_point_index); + 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()); + return static_cast (neighbors_finder.size()); } } // namespace persistence_diagram diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h index 45a4d586..3a4a5fec 100644 --- a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h +++ b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h @@ -4,7 +4,7 @@ * * Author: Francois Godi * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2015 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -31,147 +31,144 @@ namespace Gudhi { namespace persistence_diagram { - /** \internal \brief Structure representing an euclidean bipartite graph containing * the points from the two persistence diagrams (including the projections). * * \ingroup bottleneck_distance */ class Persistence_graph { -public: - /** \internal \brief Constructor taking 2 Persistence_Diagrams (concept) as parameters. */ - template - Persistence_graph(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 ? */ - bool on_the_u_diagonal(int u_point_index) const; - /** \internal \brief Is the given point from V the projection of a point in U ? */ - bool on_the_v_diagonal(int v_point_index) const; - /** \internal \brief Given a point from V, returns the corresponding (projection or projector) point in U. */ - int corresponding_point_in_u(int v_point_index) const; - /** \internal \brief Given a point from U, returns the corresponding (projection or projector) point in V. */ - int corresponding_point_in_v(int u_point_index) const; - /** \internal \brief Given a point from U and a point from V, returns the distance between those points. */ - double distance(int u_point_index, int v_point_index) const; - /** \internal \brief Returns size = |U| = |V|. */ - int size() const; - /** \internal \brief Is there as many infinite points (alive components) in both diagrams ? */ - double bottleneck_alive() const; - /** \internal \brief Returns the O(n^2) sorted distances between the points. */ - std::vector sorted_distances() const; - /** \internal \brief Returns an upper bound for the diameter of the convex hull of all non infinite points */ - double diameter_bound() const; - /** \internal \brief Returns the corresponding internal point */ - Internal_point get_u_point(int u_point_index) const; - /** \internal \brief Returns the corresponding internal point */ - Internal_point get_v_point(int v_point_index) const; - -private: - std::vector u; - std::vector v; - double b_alive; + public: + /** \internal \brief Constructor taking 2 Persistence_Diagrams (concept) as parameters. */ + template + Persistence_graph(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 ? */ + bool on_the_u_diagonal(int u_point_index) const; + /** \internal \brief Is the given point from V the projection of a point in U ? */ + bool on_the_v_diagonal(int v_point_index) const; + /** \internal \brief Given a point from V, returns the corresponding (projection or projector) point in U. */ + int corresponding_point_in_u(int v_point_index) const; + /** \internal \brief Given a point from U, returns the corresponding (projection or projector) point in V. */ + int corresponding_point_in_v(int u_point_index) const; + /** \internal \brief Given a point from U and a point from V, returns the distance between those points. */ + double distance(int u_point_index, int v_point_index) const; + /** \internal \brief Returns size = |U| = |V|. */ + int size() const; + /** \internal \brief Is there as many infinite points (alive components) in both diagrams ? */ + double bottleneck_alive() const; + /** \internal \brief Returns the O(n^2) sorted distances between the points. */ + std::vector sorted_distances() const; + /** \internal \brief Returns an upper bound for the diameter of the convex hull of all non infinite points */ + double diameter_bound() const; + /** \internal \brief Returns the corresponding internal point */ + Internal_point get_u_point(int u_point_index) const; + /** \internal \brief Returns the corresponding internal point */ + Internal_point get_v_point(int v_point_index) const; + + private: + std::vector u; + std::vector v; + double b_alive; }; template Persistence_graph::Persistence_graph(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e) - : u(), v(), b_alive(0.) -{ - std::vector u_alive; - std::vector v_alive; - for (auto it = std::begin(diag1); it != std::end(diag1); ++it){ - if(std::get<1>(*it) == std::numeric_limits::infinity()) - u_alive.push_back(std::get<0>(*it)); - else if (std::get<1>(*it) - std::get<0>(*it) > e) - u.push_back(Internal_point(std::get<0>(*it), std::get<1>(*it), u.size())); - } - for (auto it = std::begin(diag2); it != std::end(diag2); ++it){ - if(std::get<1>(*it) == std::numeric_limits::infinity()) - v_alive.push_back(std::get<0>(*it)); - else if (std::get<1>(*it) - std::get<0>(*it) > e) - v.push_back(Internal_point(std::get<0>(*it), std::get<1>(*it), v.size())); - } - if (u.size() < v.size()) - swap(u, v); - std::sort(u_alive.begin(), u_alive.end()); - std::sort(v_alive.begin(), v_alive.end()); - if(u_alive.size() != v_alive.size()) - b_alive = std::numeric_limits::infinity(); - else for(auto it_u=u_alive.cbegin(), it_v=v_alive.cbegin(); it_u != u_alive.cend(); ++it_u, ++it_v) - b_alive = std::max(b_alive, std::fabs(*it_u - *it_v)); + : u(), v(), b_alive(0.) { + std::vector u_alive; + std::vector v_alive; + for (auto it = std::begin(diag1); it != std::end(diag1); ++it) { + if (std::get<1>(*it) == std::numeric_limits::infinity()) + u_alive.push_back(std::get<0>(*it)); + else if (std::get<1>(*it) - std::get<0>(*it) > e) + u.push_back(Internal_point(std::get<0>(*it), std::get<1>(*it), u.size())); + } + for (auto it = std::begin(diag2); it != std::end(diag2); ++it) { + if (std::get<1>(*it) == std::numeric_limits::infinity()) + v_alive.push_back(std::get<0>(*it)); + else if (std::get<1>(*it) - std::get<0>(*it) > e) + v.push_back(Internal_point(std::get<0>(*it), std::get<1>(*it), v.size())); + } + if (u.size() < v.size()) + swap(u, v); + std::sort(u_alive.begin(), u_alive.end()); + std::sort(v_alive.begin(), v_alive.end()); + if (u_alive.size() != v_alive.size()) + b_alive = std::numeric_limits::infinity(); + else for (auto it_u = u_alive.cbegin(), it_v = v_alive.cbegin(); it_u != u_alive.cend(); ++it_u, ++it_v) + b_alive = std::max(b_alive, std::fabs(*it_u - *it_v)); } inline bool Persistence_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_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_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_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_graph::distance(int u_point_index, int v_point_index) const { - 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())); + 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 Persistence_graph::size() const { - return static_cast (u.size() + v.size()); + return static_cast (u.size() + v.size()); } -inline double Persistence_graph::bottleneck_alive() const{ - return b_alive; +inline double Persistence_graph::bottleneck_alive() const { + return b_alive; } inline std::vector Persistence_graph::sorted_distances() const { - std::vector distances; - distances.push_back(0.); //for empty diagrams - for (int u_point_index = 0; u_point_index < size(); ++u_point_index){ - distances.push_back(distance(u_point_index, corresponding_point_in_v(u_point_index))); - for (int v_point_index = 0; v_point_index < size(); ++v_point_index) - distances.push_back(distance(u_point_index, v_point_index)); - } - std::sort(distances.begin(), distances.end()); - return distances; + std::vector distances; + distances.push_back(0.); // for empty diagrams + for (int u_point_index = 0; u_point_index < size(); ++u_point_index) { + distances.push_back(distance(u_point_index, corresponding_point_in_v(u_point_index))); + for (int v_point_index = 0; v_point_index < size(); ++v_point_index) + distances.push_back(distance(u_point_index, v_point_index)); + } + std::sort(distances.begin(), distances.end()); + return distances; } inline Internal_point Persistence_graph::get_u_point(int u_point_index) const { - 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); + 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 Persistence_graph::get_v_point(int v_point_index) const { - 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); + 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 Persistence_graph::diameter_bound() const { - double max = 0.; - for(auto it = u.cbegin(); it != u.cend(); it++) - max = std::max(max, it->y()); - for(auto it = v.cbegin(); it != v.cend(); it++) - max = std::max(max, it->y()); - return max; + double max = 0.; + for (auto it = u.cbegin(); it != u.cend(); it++) + max = std::max(max, it->y()); + for (auto it = v.cbegin(); it != v.cend(); it++) + max = std::max(max, it->y()); + return max; } - } // namespace persistence_diagram } // namespace Gudhi diff --git a/src/Bottleneck_distance/test/CMakeLists.txt b/src/Bottleneck_distance/test/CMakeLists.txt index 13213075..a6979d3c 100644 --- a/src/Bottleneck_distance/test/CMakeLists.txt +++ b/src/Bottleneck_distance/test/CMakeLists.txt @@ -17,7 +17,6 @@ if(CGAL_FOUND) if (NOT CGAL_VERSION VERSION_LESS 4.8.0) if (EIGEN3_FOUND) 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 diff --git a/src/Bottleneck_distance/test/bottleneck_chrono.cpp b/src/Bottleneck_distance/test/bottleneck_chrono.cpp deleted file mode 100644 index a30d42b5..00000000 --- a/src/Bottleneck_distance/test/bottleneck_chrono.cpp +++ /dev/null @@ -1,62 +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: Francois Godi - * - * Copyright (C) 2015 INRIA (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::persistence_diagram; - - -double upper_bound = 400.; // any real >0 - -int main(){ - std::ofstream objetfichier; - objetfichier.open("results.csv", std::ios::out); - - for(int n = 1000; n<=10000; n+=1000){ - 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/Bottleneck_distance/test/bottleneck_unit_test.cpp b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp index fba1d369..e39613b3 100644 --- a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp +++ b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp @@ -4,7 +4,7 @@ * * Author: Francois Godi * - * Copyright (C) 2015 INRIA (France) + * Copyright (C) 2015 INRIA * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by @@ -30,138 +30,138 @@ using namespace Gudhi::persistence_diagram; -int n1 = 81; // a natural number >0 -int n2 = 180; // a natural number >0 -double upper_bound = 406.43; // any real >0 +int n1 = 81; // a natural number >0 +int n2 = 180; // a natural number >0 +double upper_bound = 406.43; // any real >0 -std::uniform_real_distribution unif(0.,upper_bound); +std::uniform_real_distribution unif(0., upper_bound); std::default_random_engine re; std::vector< std::pair > v1, v2; -BOOST_AUTO_TEST_CASE(persistence_graph){ - // Random construction - 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)); - } - Persistence_graph g(v1, v2, 0.); - 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))>0); - BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(0,n1-1))>0); - BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(0,n1))>0); - BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(0,n2-1))>0); - BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(0,n2))>0); - BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(0,(n1+n2)-1))>0); - BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(n1,0))>0); - BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(n1,n1-1))>0); - BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(n1,n1))>0); - BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(n1,n2-1))>0); - BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(n1,n2))>0); - BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(n1,(n1+n2)-1))>0); - BOOST_CHECK(std::count(d.begin(), d.end(), g.distance((n1+n2)-1,0))>0); - BOOST_CHECK(std::count(d.begin(), d.end(), g.distance((n1+n2)-1,n1-1))>0); - BOOST_CHECK(std::count(d.begin(), d.end(), g.distance((n1+n2)-1,n1))>0); - BOOST_CHECK(std::count(d.begin(), d.end(), g.distance((n1+n2)-1,n2-1))>0); - BOOST_CHECK(std::count(d.begin(), d.end(), g.distance((n1+n2)-1,n2))>0); - BOOST_CHECK(std::count(d.begin(), d.end(), g.distance((n1+n2)-1,(n1+n2)-1))>0); +BOOST_AUTO_TEST_CASE(persistence_graph) { + // Random construction + 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)); + } + Persistence_graph g(v1, v2, 0.); + 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)) > 0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(0, n1 - 1)) > 0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(0, n1)) > 0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(0, n2 - 1)) > 0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(0, n2)) > 0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(0, (n1 + n2) - 1)) > 0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(n1, 0)) > 0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(n1, n1 - 1)) > 0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(n1, n1)) > 0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(n1, n2 - 1)) > 0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(n1, n2)) > 0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance(n1, (n1 + n2) - 1)) > 0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance((n1 + n2) - 1, 0)) > 0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance((n1 + n2) - 1, n1 - 1)) > 0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance((n1 + n2) - 1, n1)) > 0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance((n1 + n2) - 1, n2 - 1)) > 0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance((n1 + n2) - 1, n2)) > 0); + BOOST_CHECK(std::count(d.begin(), d.end(), g.distance((n1 + n2) - 1, (n1 + n2) - 1)) > 0); } BOOST_AUTO_TEST_CASE(neighbors_finder) { - Persistence_graph g(v1, v2, 0.); - Neighbors_finder nf(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::vector 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); + Persistence_graph g(v1, v2, 0.); + Neighbors_finder nf(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::vector 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) { - Persistence_graph g(v1, v2, 0.); - Layered_neighbors_finder lnf(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); + Persistence_graph g(v1, v2, 0.); + Layered_neighbors_finder lnf(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) { - Persistence_graph g(v1, v2, 0.); - Graph_matching m1(g); - m1.set_r(0.); - int e = 0; - while (m1.multi_augment()) - ++e; - BOOST_CHECK(e > 0); - 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()); + Persistence_graph g(v1, v2, 0.); + Graph_matching m1(g); + m1.set_r(0.); + int e = 0; + while (m1.multi_augment()) + ++e; + BOOST_CHECK(e > 0); + 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/10000.,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, 0.) <= upper_bound/100.); - BOOST_CHECK(bottleneck_distance(v1, v2, upper_bound/10000.) <= upper_bound/100. + upper_bound/10000.); - BOOST_CHECK(std::abs(bottleneck_distance(v1, v2, 0.) - bottleneck_distance(v1, v2, upper_bound/10000.)) <= upper_bound/10000.); +BOOST_AUTO_TEST_CASE(global) { + std::uniform_real_distribution unif1(0., upper_bound); + std::uniform_real_distribution unif2(upper_bound / 10000., 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, 0.) <= upper_bound / 100.); + BOOST_CHECK(bottleneck_distance(v1, v2, upper_bound / 10000.) <= upper_bound / 100. + upper_bound / 10000.); + BOOST_CHECK(std::abs(bottleneck_distance(v1, v2, 0.) - bottleneck_distance(v1, v2, upper_bound / 10000.)) <= upper_bound / 10000.); } diff --git a/src/Tangential_complex/benchmark/CMakeLists.txt b/src/Tangential_complex/benchmark/CMakeLists.txt index 56dd8128..788c2b4d 100644 --- a/src/Tangential_complex/benchmark/CMakeLists.txt +++ b/src/Tangential_complex/benchmark/CMakeLists.txt @@ -1,15 +1,6 @@ cmake_minimum_required(VERSION 2.6) project(Tangential_complex_benchmark) -if (GCOVR_PATH) - # for gcovr to make coverage reports - Corbera Jenkins plugin - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage") -endif() -if (GPROF_PATH) - # for gprof to make coverage reports - Jenkins - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") -endif() - # need CGAL 4.8 if(CGAL_FOUND) if (NOT CGAL_VERSION VERSION_LESS 4.8.0) diff --git a/src/common/include/gudhi_patches/Bottleneck_distance_CGAL_patches.txt b/src/common/include/gudhi_patches/Bottleneck_distance_CGAL_patches.txt new file mode 100644 index 00000000..a588d113 --- /dev/null +++ b/src/common/include/gudhi_patches/Bottleneck_distance_CGAL_patches.txt @@ -0,0 +1,3 @@ +CGAL/Kd_tree.h +CGAL/Kd_tree_node.h +CGAL/Orthogonal_incremental_neighbor_search.h diff --git a/src/common/include/gudhi_patches/CGAL/Kd_tree.h b/src/common/include/gudhi_patches/CGAL/Kd_tree.h new file mode 100644 index 00000000..f085b0da --- /dev/null +++ b/src/common/include/gudhi_patches/CGAL/Kd_tree.h @@ -0,0 +1,582 @@ +// 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 "Kd_tree_node.h" + +#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->lower_low_val = c_low.tight_bounding_box().min_coord(cd); + nh->lower_high_val = c_low.tight_bounding_box().max_coord(cd); + } + else{ + nh->lower_low_val = nh->cutting_value(); + nh->lower_high_val = nh->cutting_value(); + } + if(!c.empty()){ + nh->upper_low_val = c.tight_bounding_box().min_coord(cd); + nh->upper_high_val = c.tight_bounding_box().max_coord(cd); + } + else{ + nh->upper_low_val = nh->cutting_value(); + nh->upper_high_val = nh->cutting_value(); + } + + CGAL_assertion(nh->cutting_value() >= nh->lower_low_val); + CGAL_assertion(nh->cutting_value() <= nh->upper_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() + { + // This function is not ready to be called when a tree already exists, one + // must call invalidate_built() first. + CGAL_assertion(!is_built()); + CGAL_assertion(!removed_); + 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(removed_){ + // Walk the tree to collect the remaining points. + // Writing directly to pts would likely work, but better be safe. + std::vector ptstmp; + //ptstmp.resize(root()->num_items()); + root()->tree_items(std::back_inserter(ptstmp)); + pts.swap(ptstmp); + removed_=false; + CGAL_assertion(is_built()); // the rest of the cleanup must happen + } + 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) + { + invalidate_built(); + pts.push_back(p); + } + + template + void + insert(InputIterator first, InputIterator beyond) + { + invalidate_built(); + pts.insert(pts.end(),first, beyond); + } + +private: + struct Equal_by_coordinates { + SearchTraits const* traits; + Point_d const* pp; + bool operator()(Point_d const&q) const { + typename SearchTraits::Construct_cartesian_const_iterator_d ccci=traits->construct_cartesian_const_iterator_d_object(); + return std::equal(ccci(*pp), ccci(*pp,0), ccci(q)); + } + }; + Equal_by_coordinates equal_by_coordinates(Point_d const&p){ + Equal_by_coordinates ret = { &traits(), &p }; + return ret; + } + +public: + void + remove(const Point_d& p) + { + remove(p, equal_by_coordinates(p)); + } + + template + void + remove(const Point_d& p, Equal const& equal_to_p) + { +#if 0 + // This code could have quadratic runtime. + if (!is_built()) { + std::vector::iterator pi = std::find(pts.begin(), pts.end(), p); + // Precondition: the point must be there. + CGAL_assertion (pi != pts.end()); + pts.erase(pi); + return; + } +#endif + bool success = remove_(p, 0, false, 0, false, root(), equal_to_p); + CGAL_assertion(success); + + // Do not set the flag is the tree has been cleared. + if(is_built()) + removed_ |= success; + } +private: + template + bool remove_(const Point_d& p, + Internal_node_handle grandparent, bool parent_islower, + Internal_node_handle parent, bool islower, + Node_handle node, Equal const& equal_to_p) { + // Recurse to locate the point + if (!node->is_leaf()) { + Internal_node_handle newparent = static_cast(node); + // FIXME: This should be if(xcutting_dimension()] <= newparent->cutting_value()) { + if (remove_(p, parent, islower, newparent, true, newparent->lower(), equal_to_p)) + return true; + } + //if (traits().construct_cartesian_const_iterator_d_object()(p)[newparent->cutting_dimension()] >= newparent->cutting_value()) + return remove_(p, parent, islower, newparent, false, newparent->upper(), equal_to_p); + + CGAL_assertion(false); // Point was not found + } + + // Actual removal + Leaf_node_handle lnode = static_cast(node); + if (lnode->size() > 1) { + iterator pi = std::find_if(lnode->begin(), lnode->end(), equal_to_p); + // FIXME: we should ensure this never happens + if (pi == lnode->end()) return false; + 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 (!equal_to_p(*lnode->begin())) { + // FIXME: we should ensure this never happens + return false; + } else if (grandparent) { + Node_handle brother = islower ? parent->upper() : parent->lower(); + if (parent_islower) + grandparent->set_lower(brother); + else + grandparent->set_upper(brother); + } else if (parent) { + tree_root = islower ? parent->upper() : parent->lower(); + } else { + clear(); + } + return true; + } + +public: + //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 diff --git a/src/common/include/gudhi_patches/CGAL/Kd_tree_node.h b/src/common/include/gudhi_patches/CGAL/Kd_tree_node.h new file mode 100644 index 00000000..909ee260 --- /dev/null +++ b/src/common/include/gudhi_patches/CGAL/Kd_tree_node.h @@ -0,0 +1,586 @@ +// Copyright (c) 2002,2011 Utrecht University (The Netherlands). +// 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. +// +// $URL$ +// $Id$ +// +// +// Authors : Hans Tangelder () + +#ifndef CGAL_KD_TREE_NODE_H +#define CGAL_KD_TREE_NODE_H + +#include "CGAL/Splitters.h" + +#include +#include + +namespace CGAL { + + template + class Kd_tree; + + template < class TreeTraits, class Splitter, class UseExtendedNode > + class Kd_tree_node { + + friend class Kd_tree; + + typedef typename Kd_tree::Node_handle Node_handle; + typedef typename Kd_tree::Node_const_handle Node_const_handle; + typedef typename Kd_tree::Internal_node_handle Internal_node_handle; + typedef typename Kd_tree::Internal_node_const_handle Internal_node_const_handle; + typedef typename Kd_tree::Leaf_node_handle Leaf_node_handle; + typedef typename Kd_tree::Leaf_node_const_handle Leaf_node_const_handle; + typedef typename TreeTraits::Point_d Point_d; + + typedef typename TreeTraits::FT FT; + typedef typename Kd_tree::Separator Separator; + typedef typename Kd_tree::Point_d_iterator Point_d_iterator; + typedef typename Kd_tree::iterator iterator; + typedef typename Kd_tree::D D; + + bool leaf; + + public : + Kd_tree_node(bool leaf_) + :leaf(leaf_){} + + bool is_leaf() const{ + return leaf; + } + + std::size_t + num_items() const + { + if (is_leaf()){ + Leaf_node_const_handle node = + static_cast(this); + return node->size(); + } + else { + Internal_node_const_handle node = + static_cast(this); + return node->lower()->num_items() + node->upper()->num_items(); + } + } + + std::size_t + num_nodes() const + { + if (is_leaf()) return 1; + else { + Internal_node_const_handle node = + static_cast(this); + return node->lower()->num_nodes() + node->upper()->num_nodes(); + } + } + + int + depth(const int current_max_depth) const + { + if (is_leaf()){ + return current_max_depth; + } + else { + Internal_node_const_handle node = + static_cast(this); + return + (std::max)( node->lower()->depth(current_max_depth + 1), + node->upper()->depth(current_max_depth + 1)); + } + } + + int + depth() const + { + return depth(1); + } + + template + OutputIterator + tree_items(OutputIterator it) const { + if (is_leaf()) { + Leaf_node_const_handle node = + static_cast(this); + if (node->size()>0) + for (iterator i=node->begin(); i != node->end(); i++) + {*it=*i; ++it;} + } + else { + Internal_node_const_handle node = + static_cast(this); + it=node->lower()->tree_items(it); + it=node->upper()->tree_items(it); + } + return it; + } + + + boost::optional + any_tree_item() const { + boost::optional result = boost::none; + if (is_leaf()) { + Leaf_node_const_handle node = + static_cast(this); + if (node->size()>0){ + return boost::make_optional(*(node->begin())); + } + } + else { + Internal_node_const_handle node = + static_cast(this); + result = node->lower()->any_tree_item(); + if(! result){ + result = node->upper()->any_tree_item(); + } + } + return result; + } + + + void + indent(int d) const + { + for(int i = 0; i < d; i++){ + std::cout << " "; + } + } + + + void + print(int d = 0) const + { + if (is_leaf()) { + Leaf_node_const_handle node = + static_cast(this); + indent(d); + std::cout << "leaf" << std::endl; + if (node->size()>0) + for (iterator i=node->begin(); i != node->end(); i++) + {indent(d);std::cout << *i << std::endl;} + } + else { + Internal_node_const_handle node = + static_cast(this); + indent(d); + std::cout << "lower tree" << std::endl; + node->lower()->print(d+1); + indent(d); + std::cout << "separator: dim = " << node->cutting_dimension() << " val = " << node->cutting_value() << std::endl; + indent(d); + std::cout << "upper tree" << std::endl; + node->upper()->print(d+1); + } + } + + + template + OutputIterator + search(OutputIterator it, const FuzzyQueryItem& q, + Kd_tree_rectangle& b) const + { + if (is_leaf()) { + Leaf_node_const_handle node = + static_cast(this); + if (node->size()>0) + for (iterator i=node->begin(); i != node->end(); i++) + if (q.contains(*i)) + {*it++=*i;} + } + else { + Internal_node_const_handle node = + static_cast(this); + // after splitting b denotes the lower part of b + Kd_tree_rectangle b_upper(b); + b.split(b_upper, node->cutting_dimension(), + node->cutting_value()); + + if (q.outer_range_contains(b)) + it=node->lower()->tree_items(it); + else + if (q.inner_range_intersects(b)) + it=node->lower()->search(it,q,b); + if (q.outer_range_contains(b_upper)) + it=node->upper()->tree_items(it); + else + if (q.inner_range_intersects(b_upper)) + it=node->upper()->search(it,q,b_upper); + }; + return it; + } + + + template + boost::optional + search_any_point(const FuzzyQueryItem& q, + Kd_tree_rectangle& b) const + { + boost::optional result = boost::none; + if (is_leaf()) { + Leaf_node_const_handle node = + static_cast(this); + if (node->size()>0) + for (iterator i=node->begin(); i != node->end(); i++) + if (q.contains(*i)) + { result = *i; break; } + } + else { + Internal_node_const_handle node = + static_cast(this); + // after splitting b denotes the lower part of b + Kd_tree_rectangle b_upper(b); + b.split(b_upper, node->cutting_dimension(), + node->cutting_value()); + + if (q.outer_range_contains(b)){ + result = node->lower()->any_tree_item(); + }else{ + if (q.inner_range_intersects(b)){ + result = node->lower()->search_any_point(q,b); + } + } + if(result){ + return result; + } + if (q.outer_range_contains(b_upper)){ + result = node->upper()->any_tree_item(); + }else{ + if (q.inner_range_intersects(b_upper)) + result = node->upper()->search_any_point(q,b_upper); + } + } + return result; + } + + }; + + + template < class TreeTraits, class Splitter, class UseExtendedNode > + class Kd_tree_leaf_node : public Kd_tree_node< TreeTraits, Splitter, UseExtendedNode >{ + + friend class Kd_tree; + + typedef typename Kd_tree::iterator iterator; + typedef Kd_tree_node< TreeTraits, Splitter, UseExtendedNode> Base; + typedef typename TreeTraits::Point_d Point_d; + + private: + + // private variables for leaf nodes + boost::int32_t n; // denotes number of items in a leaf node + iterator data; // iterator to data in leaf node + + + public: + + // default constructor + Kd_tree_leaf_node() + {} + + Kd_tree_leaf_node(bool leaf_ ) + : Base(leaf_) + {} + + Kd_tree_leaf_node(bool leaf_,unsigned int n_ ) + : Base(leaf_), n(n_) + {} + + // members for all nodes + + // members for leaf nodes only + inline + unsigned int + size() const + { + return n; + } + + inline + iterator + begin() const + { + return data; + } + + inline + iterator + end() const + { + return data + n; + } + + inline + void + drop_last_point() + { + --n; + } + + }; //leaf node + + + + template < class TreeTraits, class Splitter, class UseExtendedNode> + class Kd_tree_internal_node : public Kd_tree_node< TreeTraits, Splitter, UseExtendedNode >{ + + friend class Kd_tree; + + typedef Kd_tree_node< TreeTraits, Splitter, UseExtendedNode> Base; + typedef typename Kd_tree::Node_handle Node_handle; + typedef typename Kd_tree::Node_const_handle Node_const_handle; + + typedef typename TreeTraits::FT FT; + typedef typename Kd_tree::Separator Separator; + + private: + + // private variables for internal nodes + boost::int32_t cut_dim; + FT cut_val; + Node_handle lower_ch, upper_ch; + + + // private variables for extended internal nodes + FT upper_low_val; + FT upper_high_val; + FT lower_low_val; + FT lower_high_val; + + + public: + + // default constructor + Kd_tree_internal_node() + {} + + Kd_tree_internal_node(bool leaf_) + : Base(leaf_) + {} + + + // members for internal node and extended internal node + + inline + Node_const_handle + lower() const + { + return lower_ch; + } + + inline + Node_const_handle + upper() const + { + return upper_ch; + } + + inline + Node_handle + lower() + { + return lower_ch; + } + + inline + Node_handle + upper() + { + return upper_ch; + } + + inline + void + set_lower(Node_handle nh) + { + lower_ch = nh; + } + + inline + void + set_upper(Node_handle nh) + { + upper_ch = nh; + } + + // inline Separator& separator() {return sep; } + // use instead + inline + void set_separator(Separator& sep){ + cut_dim = sep.cutting_dimension(); + cut_val = sep.cutting_value(); + } + + inline + FT + cutting_value() const + { + return cut_val; + } + + inline + int + cutting_dimension() const + { + return cut_dim; + } + + // members for extended internal node only + inline + FT + upper_low_value() const + { + return upper_low_val; + } + + inline + FT + upper_high_value() const + { + return upper_high_val; + } + + inline + FT + lower_low_value() const + { + return lower_low_val; + } + + inline + FT + lower_high_value() const + { + return lower_high_val; + } + + /*Separator& + separator() + { + return Separator(cutting_dimension,cutting_value); + }*/ + + + };//internal node + + template < class TreeTraits, class Splitter> + class Kd_tree_internal_node : public Kd_tree_node< TreeTraits, Splitter, Tag_false >{ + + friend class Kd_tree; + + typedef Kd_tree_node< TreeTraits, Splitter, Tag_false> Base; + typedef typename Kd_tree::Node_handle Node_handle; + typedef typename Kd_tree::Node_const_handle Node_const_handle; + + typedef typename TreeTraits::FT FT; + typedef typename Kd_tree::Separator Separator; + + private: + + // private variables for internal nodes + boost::uint8_t cut_dim; + FT cut_val; + + Node_handle lower_ch, upper_ch; + + public: + + // default constructor + Kd_tree_internal_node() + {} + + Kd_tree_internal_node(bool leaf_) + : Base(leaf_) + {} + + + // members for internal node and extended internal node + + inline + Node_const_handle + lower() const + { + return lower_ch; + } + + inline + Node_const_handle + upper() const + { + return upper_ch; + } + + inline + Node_handle + lower() + { + return lower_ch; + } + + inline + Node_handle + upper() + { + return upper_ch; + } + + inline + void + set_lower(Node_handle nh) + { + lower_ch = nh; + } + + inline + void + set_upper(Node_handle nh) + { + upper_ch = nh; + } + + // inline Separator& separator() {return sep; } + // use instead + + inline + void set_separator(Separator& sep){ + cut_dim = sep.cutting_dimension(); + cut_val = sep.cutting_value(); + } + + inline + FT + cutting_value() const + { + return cut_val; + } + + inline + int + cutting_dimension() const + { + return cut_dim; + } + + /* Separator& + separator() + { + return Separator(cutting_dimension,cutting_value); + }*/ + + + };//internal node + + + +} // namespace CGAL +#endif // CGAL_KDTREE_NODE_H diff --git a/src/common/include/gudhi_patches/CGAL/Orthogonal_incremental_neighbor_search.h b/src/common/include/gudhi_patches/CGAL/Orthogonal_incremental_neighbor_search.h new file mode 100644 index 00000000..dbe707ed --- /dev/null +++ b/src/common/include/gudhi_patches/CGAL/Orthogonal_incremental_neighbor_search.h @@ -0,0 +1,621 @@ +// Copyright (c) 2002,2011 Utrecht University (The Netherlands). +// 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 () + +#ifndef CGAL_ORTHOGONAL_INCREMENTAL_NEIGHBOR_SEARCH +#define CGAL_ORTHOGONAL_INCREMENTAL_NEIGHBOR_SEARCH + +#include "CGAL/Kd_tree.h" + +#include +#include +#include +#include +#include +#include + +namespace CGAL { + + template ::type, + class Splitter_ = Sliding_midpoint, + class Tree_= Kd_tree > + class Orthogonal_incremental_neighbor_search { + + public: + typedef Splitter_ Splitter; + typedef Tree_ Tree; + typedef Distance_ Distance; + typedef typename SearchTraits::Point_d Point_d; + typedef typename Distance::Query_item Query_item; + typedef typename SearchTraits::FT FT; + typedef typename Tree::Point_d_iterator Point_d_iterator; + typedef typename Tree::Node_const_handle Node_const_handle; + + typedef std::pair Point_with_transformed_distance; + typedef CGAL::cpp11::tuple > Node_with_distance; + typedef std::vector Node_with_distance_vector; + typedef std::vector Point_with_transformed_distance_vector; + + template + struct Object_wrapper + { + T object; + Object_wrapper(const T& t):object(t){} + const T& operator* () const { return object; } + const T* operator-> () const { return &object; } + }; + + class Iterator_implementation { + SearchTraits traits; + public: + + int number_of_neighbours_computed; + int number_of_internal_nodes_visited; + int number_of_leaf_nodes_visited; + int number_of_items_visited; + + private: + + typedef std::vector Distance_vector; + + Distance_vector dists; + + Distance Orthogonal_distance_instance; + + FT multiplication_factor; + + Query_item query_point; + + FT distance_to_root; + + bool search_nearest_neighbour; + + FT rd; + + + class Priority_higher { + public: + + bool search_nearest; + + Priority_higher(bool search_the_nearest_neighbour) + : search_nearest(search_the_nearest_neighbour) + {} + + //highest priority is smallest distance + bool + operator() (Node_with_distance* n1, Node_with_distance* n2) const + { + return (search_nearest) ? (CGAL::cpp11::get<1>(*n1) > CGAL::cpp11::get<1>(*n2)) : (CGAL::cpp11::get<1>(*n2) > CGAL::cpp11::get<1>(*n1)); + } + }; + + class Distance_smaller { + + public: + + bool search_nearest; + + Distance_smaller(bool search_the_nearest_neighbour) + : search_nearest(search_the_nearest_neighbour) + {} + + //highest priority is smallest distance + bool operator() (Point_with_transformed_distance* p1, Point_with_transformed_distance* p2) const + { + return (search_nearest) ? (p1->second > p2->second) : (p2->second > p1->second); + } + }; + + + std::priority_queue PriorityQueue; + + public: + std::priority_queue Item_PriorityQueue; + + + public: + + int reference_count; + + + + // constructor + Iterator_implementation(const Tree& tree,const Query_item& q, const Distance& tr, + FT Eps=FT(0.0), bool search_nearest=true) + : traits(tree.traits()),number_of_neighbours_computed(0), number_of_internal_nodes_visited(0), + number_of_leaf_nodes_visited(0), number_of_items_visited(0), + Orthogonal_distance_instance(tr), multiplication_factor(Orthogonal_distance_instance.transformed_distance(FT(1.0)+Eps)), + query_point(q), search_nearest_neighbour(search_nearest), + PriorityQueue(Priority_higher(search_nearest)), Item_PriorityQueue(Distance_smaller(search_nearest)), + reference_count(1) + + + { + if (tree.empty()) return; + + typename SearchTraits::Construct_cartesian_const_iterator_d ccci=traits.construct_cartesian_const_iterator_d_object(); + int dim = static_cast(std::distance(ccci(q), ccci(q,0))); + + dists.resize(dim); + for(int i=0 ; i(*The_Root); + Compute_the_next_nearest_neighbour(); + } + else{ + distance_to_root= + Orthogonal_distance_instance.max_distance_to_rectangle(q, + tree.bounding_box(), dists); + Node_with_distance *The_Root = new Node_with_distance(tree.root(), + distance_to_root, dists); + PriorityQueue.push(The_Root); + + // rd is the distance of the top of the priority queue to q + rd=CGAL::cpp11::get<1>(*The_Root); + Compute_the_next_furthest_neighbour(); + } + + + } + + // * operator + const Point_with_transformed_distance& + operator* () const + { + return *(Item_PriorityQueue.top()); + } + + // prefix operator + Iterator_implementation& + operator++() + { + Delete_the_current_item_top(); + if(search_nearest_neighbour) + Compute_the_next_nearest_neighbour(); + else + Compute_the_next_furthest_neighbour(); + return *this; + } + + // postfix operator + Object_wrapper + operator++(int) + { + Object_wrapper result( *(Item_PriorityQueue.top()) ); + ++*this; + return result; + } + + // Print statistics of the general priority search process. + std::ostream& + statistics (std::ostream& s) const { + s << "Orthogonal priority search statistics:" + << std::endl; + s << "Number of internal nodes visited:" + << number_of_internal_nodes_visited << std::endl; + s << "Number of leaf nodes visited:" + << number_of_leaf_nodes_visited << std::endl; + s << "Number of items visited:" + << number_of_items_visited << std::endl; + s << "Number of neighbours computed:" + << number_of_neighbours_computed << std::endl; + return s; + } + + + //destructor + ~Iterator_implementation() + { + while (!PriorityQueue.empty()) { + Node_with_distance* The_top=PriorityQueue.top(); + PriorityQueue.pop(); + delete The_top; + } + while (!Item_PriorityQueue.empty()) { + Point_with_transformed_distance* The_top=Item_PriorityQueue.top(); + Item_PriorityQueue.pop(); + delete The_top; + } + } + + private: + + void + Delete_the_current_item_top() + { + Point_with_transformed_distance* The_item_top=Item_PriorityQueue.top(); + Item_PriorityQueue.pop(); + delete The_item_top; + } + + void + Compute_the_next_nearest_neighbour() + { + // compute the next item + bool next_neighbour_found=false; + if (!(Item_PriorityQueue.empty())) { + next_neighbour_found= + (multiplication_factor*rd > Item_PriorityQueue.top()->second); + } + typename SearchTraits::Construct_cartesian_const_iterator_d construct_it=traits.construct_cartesian_const_iterator_d_object(); + typename SearchTraits::Cartesian_const_iterator_d query_point_it = construct_it(query_point); + // otherwise browse the tree further + while ((!next_neighbour_found) && (!PriorityQueue.empty())) { + Node_with_distance* The_node_top=PriorityQueue.top(); + Node_const_handle N= CGAL::cpp11::get<0>(*The_node_top); + dists = CGAL::cpp11::get<2>(*The_node_top); + PriorityQueue.pop(); + delete The_node_top; + FT copy_rd=rd; + while (!(N->is_leaf())) { // compute new distance + typename Tree::Internal_node_const_handle node = + static_cast(N); + number_of_internal_nodes_visited++; + int new_cut_dim=node->cutting_dimension(); + FT new_rd,dst = dists[new_cut_dim]; + FT val = *(query_point_it + new_cut_dim); + FT diff1 = val - node->upper_low_value(); + FT diff2 = val - node->lower_high_value(); + if (diff1 + diff2 < FT(0.0)) { + new_rd= + Orthogonal_distance_instance.new_distance(copy_rd,dst,diff1,new_cut_dim); + + CGAL_assertion(new_rd >= copy_rd); + dists[new_cut_dim] = diff1; + Node_with_distance *Upper_Child = + new Node_with_distance(node->upper(), new_rd, dists); + PriorityQueue.push(Upper_Child); + dists[new_cut_dim] = dst; + N=node->lower(); + + } + else { // compute new distance + new_rd=Orthogonal_distance_instance.new_distance(copy_rd,dst,diff2,new_cut_dim); + CGAL_assertion(new_rd >= copy_rd); + dists[new_cut_dim] = diff2; + Node_with_distance *Lower_Child = + new Node_with_distance(node->lower(), new_rd, dists); + PriorityQueue.push(Lower_Child); + dists[new_cut_dim] = dst; + N=node->upper(); + } + } + // n is a leaf + typename Tree::Leaf_node_const_handle node = + static_cast(N); + number_of_leaf_nodes_visited++; + if (node->size() > 0) { + for (typename Tree::iterator it=node->begin(); it != node->end(); it++) { + number_of_items_visited++; + FT distance_to_query_point= + Orthogonal_distance_instance.transformed_distance(query_point,*it); + Point_with_transformed_distance *NN_Candidate= + new Point_with_transformed_distance(*it,distance_to_query_point); + Item_PriorityQueue.push(NN_Candidate); + } + // old top of PriorityQueue has been processed, + // hence update rd + + if (!(PriorityQueue.empty())) { + rd = CGAL::cpp11::get<1>(*PriorityQueue.top()); + next_neighbour_found = + (multiplication_factor*rd > + Item_PriorityQueue.top()->second); + } + else // priority queue empty => last neighbour found + { + next_neighbour_found=true; + } + + number_of_neighbours_computed++; + } + } // next_neighbour_found or priority queue is empty + // in the latter case also the item priority quee is empty + } + + + void + Compute_the_next_furthest_neighbour() + { + // compute the next item + bool next_neighbour_found=false; + if (!(Item_PriorityQueue.empty())) { + next_neighbour_found= + (rd < multiplication_factor*Item_PriorityQueue.top()->second); + } + typename SearchTraits::Construct_cartesian_const_iterator_d construct_it=traits.construct_cartesian_const_iterator_d_object(); + typename SearchTraits::Cartesian_const_iterator_d query_point_it = construct_it(query_point); + // otherwise browse the tree further + while ((!next_neighbour_found) && (!PriorityQueue.empty())) { + Node_with_distance* The_node_top=PriorityQueue.top(); + Node_const_handle N= CGAL::cpp11::get<0>(*The_node_top); + dists = CGAL::cpp11::get<2>(*The_node_top); + PriorityQueue.pop(); + delete The_node_top; + FT copy_rd=rd; + while (!(N->is_leaf())) { // compute new distance + typename Tree::Internal_node_const_handle node = + static_cast(N); + number_of_internal_nodes_visited++; + int new_cut_dim=node->cutting_dimension(); + FT new_rd,dst = dists[new_cut_dim]; + FT val = *(query_point_it + new_cut_dim); + FT diff1 = val - node->upper_low_value(); + FT diff2 = val - node->lower_high_value(); + if (diff1 + diff2 < FT(0.0)) { + diff1 = val - node->upper_high_value(); + new_rd= + Orthogonal_distance_instance.new_distance(copy_rd,dst,diff1,new_cut_dim); + Node_with_distance *Lower_Child = + new Node_with_distance(node->lower(), copy_rd, dists); + PriorityQueue.push(Lower_Child); + N=node->upper(); + dists[new_cut_dim] = diff1; + copy_rd=new_rd; + + } + else { // compute new distance + diff2 = val - node->lower_low_value(); + new_rd=Orthogonal_distance_instance.new_distance(copy_rd,dst,diff2,new_cut_dim); + Node_with_distance *Upper_Child = + new Node_with_distance(node->upper(), copy_rd, dists); + PriorityQueue.push(Upper_Child); + N=node->lower(); + dists[new_cut_dim] = diff2; + copy_rd=new_rd; + } + } + // n is a leaf + typename Tree::Leaf_node_const_handle node = + static_cast(N); + number_of_leaf_nodes_visited++; + if (node->size() > 0) { + for (typename Tree::iterator it=node->begin(); it != node->end(); it++) { + number_of_items_visited++; + FT distance_to_query_point= + Orthogonal_distance_instance.transformed_distance(query_point,*it); + Point_with_transformed_distance *NN_Candidate= + new Point_with_transformed_distance(*it,distance_to_query_point); + Item_PriorityQueue.push(NN_Candidate); + } + // old top of PriorityQueue has been processed, + // hence update rd + + if (!(PriorityQueue.empty())) { + rd = CGAL::cpp11::get<1>(*PriorityQueue.top()); + next_neighbour_found = + (multiplication_factor*rd < + Item_PriorityQueue.top()->second); + } + else // priority queue empty => last neighbour found + { + next_neighbour_found=true; + } + + number_of_neighbours_computed++; + } + } // next_neighbour_found or priority queue is empty + // in the latter case also the item priority quee is empty + } + }; // class Iterator_implementaion + + + + + + + + + + public: + class iterator; + typedef iterator const_iterator; + + // constructor + Orthogonal_incremental_neighbor_search(const Tree& tree, + const Query_item& q, FT Eps = FT(0.0), + bool search_nearest=true, const Distance& tr=Distance()) + : m_tree(tree),m_query(q),m_dist(tr),m_Eps(Eps),m_search_nearest(search_nearest) + {} + + iterator + begin() const + { + return iterator(m_tree,m_query,m_dist,m_Eps,m_search_nearest); + } + + iterator + end() const + { + return iterator(); + } + + std::ostream& + statistics(std::ostream& s) + { + begin()->statistics(s); + return s; + } + + + + + class iterator { + + public: + + typedef std::input_iterator_tag iterator_category; + typedef Point_with_transformed_distance value_type; + typedef Point_with_transformed_distance* pointer; + typedef const Point_with_transformed_distance& reference; + typedef std::size_t size_type; + typedef std::ptrdiff_t difference_type; + typedef int distance_type; + + //class Iterator_implementation; + Iterator_implementation *Ptr_implementation; + + + public: + + // default constructor + iterator() + : Ptr_implementation(0) + {} + + int + the_number_of_items_visited() + { + return Ptr_implementation->number_of_items_visited; + } + + // constructor + iterator(const Tree& tree,const Query_item& q, const Distance& tr=Distance(), FT eps=FT(0.0), + bool search_nearest=true) + : Ptr_implementation(new Iterator_implementation(tree, q, tr, eps, search_nearest)) + {} + + // copy constructor + iterator(const iterator& Iter) + { + Ptr_implementation = Iter.Ptr_implementation; + if (Ptr_implementation != 0) Ptr_implementation->reference_count++; + } + + iterator& operator=(const iterator& Iter) + { + if (Ptr_implementation != Iter.Ptr_implementation){ + if (Ptr_implementation != 0 && --(Ptr_implementation->reference_count)==0) { + delete Ptr_implementation; + } + Ptr_implementation = Iter.Ptr_implementation; + if (Ptr_implementation != 0) Ptr_implementation->reference_count++; + } + return *this; + } + + + const Point_with_transformed_distance& + operator* () const + { + return *(*Ptr_implementation); + } + + // -> operator + const Point_with_transformed_distance* + operator-> () const + { + return &*(*Ptr_implementation); + } + + // prefix operator + iterator& + operator++() + { + ++(*Ptr_implementation); + return *this; + } + + // postfix operator + Object_wrapper + operator++(int) + { + return (*Ptr_implementation)++; + } + + + bool + operator==(const iterator& It) const + { + if ( + ((Ptr_implementation == 0) || + Ptr_implementation->Item_PriorityQueue.empty()) && + ((It.Ptr_implementation == 0) || + It.Ptr_implementation->Item_PriorityQueue.empty()) + ) + return true; + // else + return (Ptr_implementation == It.Ptr_implementation); + } + + bool + operator!=(const iterator& It) const + { + return !(*this == It); + } + + std::ostream& + statistics (std::ostream& s) + { + Ptr_implementation->statistics(s); + return s; + } + + ~iterator() + { + if (Ptr_implementation != 0) { + Ptr_implementation->reference_count--; + if (Ptr_implementation->reference_count==0) { + delete Ptr_implementation; + Ptr_implementation = 0; + } + } + } + + + }; // class iterator + + //data members + const Tree& m_tree; + Query_item m_query; + Distance m_dist; + FT m_Eps; + bool m_search_nearest; + }; // class + + template + void swap (typename Orthogonal_incremental_neighbor_search::iterator& x, + typename Orthogonal_incremental_neighbor_search::iterator& y) + { + typename Orthogonal_incremental_neighbor_search::iterator::Iterator_implementation + *tmp = x.Ptr_implementation; + x.Ptr_implementation = y.Ptr_implementation; + y.Ptr_implementation = tmp; + } + +} // namespace CGAL + +#endif // CGAL_ORTHOGONAL_INCREMENTAL_NEIGHBOR_SEARCH_H diff --git a/src/common/include/gudhi_patches/Tangential_complex_CGAL_patches.txt b/src/common/include/gudhi_patches/Tangential_complex_CGAL_patches.txt new file mode 100644 index 00000000..5b9581a0 --- /dev/null +++ b/src/common/include/gudhi_patches/Tangential_complex_CGAL_patches.txt @@ -0,0 +1,82 @@ +CGAL/Regular_triangulation_traits_adapter.h +CGAL/Triangulation_ds_vertex.h +CGAL/Triangulation_data_structure.h +CGAL/transforming_pair_iterator.h +CGAL/NewKernel_d/static_int.h +CGAL/NewKernel_d/Cartesian_LA_functors.h +CGAL/NewKernel_d/Cartesian_change_FT.h +CGAL/NewKernel_d/Wrapper/Vector_d.h +CGAL/NewKernel_d/Wrapper/Hyperplane_d.h +CGAL/NewKernel_d/Wrapper/Ref_count_obj.h +CGAL/NewKernel_d/Wrapper/Cartesian_wrap.h +CGAL/NewKernel_d/Wrapper/Point_d.h +CGAL/NewKernel_d/Wrapper/Segment_d.h +CGAL/NewKernel_d/Wrapper/Weighted_point_d.h +CGAL/NewKernel_d/Wrapper/Sphere_d.h +CGAL/NewKernel_d/Cartesian_per_dimension.h +CGAL/NewKernel_d/Kernel_object_converter.h +CGAL/NewKernel_d/KernelD_converter.h +CGAL/NewKernel_d/Vector/sse2.h +CGAL/NewKernel_d/Vector/avx4.h +CGAL/NewKernel_d/Vector/determinant_of_vectors_small_dim_internal.h +CGAL/NewKernel_d/Vector/determinant_of_iterator_to_points_from_points.h +CGAL/NewKernel_d/Vector/determinant_of_points_from_vectors.h +CGAL/NewKernel_d/Vector/array.h +CGAL/NewKernel_d/Vector/determinant_of_iterator_to_points_from_iterator_to_vectors.h +CGAL/NewKernel_d/Vector/determinant_of_iterator_to_vectors_from_vectors.h +CGAL/NewKernel_d/Vector/determinant_of_vectors_small_dim.h +CGAL/NewKernel_d/Vector/vector.h +CGAL/NewKernel_d/Vector/v2int.h +CGAL/NewKernel_d/Vector/mix.h +CGAL/NewKernel_d/Cartesian_static_filters.h +CGAL/NewKernel_d/Cartesian_LA_base.h +CGAL/NewKernel_d/Lazy_cartesian.h +CGAL/NewKernel_d/Coaffine.h +CGAL/NewKernel_d/store_kernel.h +CGAL/NewKernel_d/Dimension_base.h +CGAL/NewKernel_d/Kernel_3_interface.h +CGAL/NewKernel_d/Cartesian_complete.h +CGAL/NewKernel_d/Cartesian_base.h +CGAL/NewKernel_d/Cartesian_filter_K.h +CGAL/NewKernel_d/functor_tags.h +CGAL/NewKernel_d/Filtered_predicate2.h +CGAL/NewKernel_d/functor_properties.h +CGAL/NewKernel_d/Define_kernel_types.h +CGAL/NewKernel_d/LA_eigen/LA.h +CGAL/NewKernel_d/LA_eigen/constructors.h +CGAL/NewKernel_d/Types/Aff_transformation.h +CGAL/NewKernel_d/Types/Sphere.h +CGAL/NewKernel_d/Types/Hyperplane.h +CGAL/NewKernel_d/Types/Line.h +CGAL/NewKernel_d/Types/Ray.h +CGAL/NewKernel_d/Types/Iso_box.h +CGAL/NewKernel_d/Types/Weighted_point.h +CGAL/NewKernel_d/Types/Segment.h +CGAL/NewKernel_d/Kernel_d_interface.h +CGAL/NewKernel_d/utils.h +CGAL/NewKernel_d/Kernel_2_interface.h +CGAL/NewKernel_d/Cartesian_filter_NT.h +CGAL/NewKernel_d/function_objects_cartesian.h +CGAL/Convex_hull.h +CGAL/Triangulation_ds_full_cell.h +CGAL/Regular_triangulation.h +CGAL/Epick_d.h +CGAL/transforming_iterator.h +CGAL/iterator_from_indices.h +CGAL/Delaunay_triangulation.h +CGAL/IO/Triangulation_off_ostream.h +CGAL/typeset.h +CGAL/Triangulation_full_cell.h +CGAL/Triangulation.h +CGAL/internal/Static_or_dynamic_array.h +CGAL/internal/Combination_enumerator.h +CGAL/internal/Triangulation/utilities.h +CGAL/internal/Triangulation/Triangulation_ds_iterators.h +CGAL/internal/Triangulation/Dummy_TDS.h +CGAL/argument_swaps.h +CGAL/Epeck_d.h +CGAL/determinant_of_vectors.h +CGAL/TDS_full_cell_default_storage_policy.h +CGAL/TDS_full_cell_mirror_storage_policy.h +CGAL/Triangulation_face.h +CGAL/Triangulation_vertex.h -- cgit v1.2.3 From 3b83c563f5a9992b2eb9a82738e6eebbe471b3e4 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 6 Jan 2017 13:58:04 +0000 Subject: Test of thread_local solution git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/thread_local_no_static@1932 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a1f31ab16d2a086d38d0d019bbdc59152f8e02e7 --- src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h | 3 +-- src/Simplex_tree/include/gudhi/Simplex_tree.h | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) (limited to 'src') diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h index bc8099e6..b3339b7d 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h @@ -300,8 +300,7 @@ class Persistent_cohomology { // with multiplicity. We used to sum the coefficients directly in // annotations_in_boundary by using a map, we now do it later. typedef std::pair annotation_t; - // Danger: not thread-safe! - static std::vector annotations_in_boundary; + thread_local std::vector annotations_in_boundary; annotations_in_boundary.clear(); int sign = 1 - 2 * (dim_sigma % 2); // \in {-1,1} provides the sign in the // alternate sum in the boundary. diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index 63e3f0e5..317bce23 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -1029,7 +1029,7 @@ class Simplex_tree { Dictionary_it next = siblings->members().begin(); ++next; - static std::vector > inter; // static, not thread-safe. + thread_local std::vector > inter; for (Dictionary_it s_h = siblings->members().begin(); s_h != siblings->members().end(); ++s_h, ++next) { Simplex_handle root_sh = find_vertex(s_h->first); -- cgit v1.2.3 From 4fc6491ae2ee7e02950bf4dc8c027210fb127f76 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Sat, 7 Jan 2017 14:09:55 +0000 Subject: Fix user version for patches Bad include type in CGAL/Orthogonal_incremental_neighbor_search.h git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@1935 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 1fc3888dd7af8624d3b501b32b76194215e0b7cf --- src/cmake/modules/GUDHI_user_version_target.txt | 15 +++++++++++++++ .../CGAL/Orthogonal_incremental_neighbor_search.h | 3 +-- 2 files changed, 16 insertions(+), 2 deletions(-) (limited to 'src') diff --git a/src/cmake/modules/GUDHI_user_version_target.txt b/src/cmake/modules/GUDHI_user_version_target.txt index 25db1c87..63301413 100644 --- a/src/cmake/modules/GUDHI_user_version_target.txt +++ b/src/cmake/modules/GUDHI_user_version_target.txt @@ -96,6 +96,21 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11) endif() endforeach() + # Patches + file(GLOB GUDHI_PATCHES_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/include/gudhi_patches/*) + + foreach(GUDHI_PATCHES_FILE ${GUDHI_PATCHES_FILES}) + get_filename_component(GUDHI_PATCHES_FILE_NAME ${GUDHI_PATCHES_FILE} NAME) + # GUDHI_PATCHES_FILE can be a file or a directory + if(IS_DIRECTORY ${GUDHI_PATCHES_FILE}) + add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E + copy_directory ${GUDHI_PATCHES_FILE} ${GUDHI_USER_VERSION_DIR}/include/gudhi/${GUDHI_PATCHES_FILE_NAME}) + else() + add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E + copy ${GUDHI_PATCHES_FILE} ${GUDHI_USER_VERSION_DIR}/include/gudhi/${GUDHI_PATCHES_FILE_NAME}) + endif() + endforeach() + # concept files file(GLOB GUDHI_CONCEPT_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/concept/*.h) diff --git a/src/common/include/gudhi_patches/CGAL/Orthogonal_incremental_neighbor_search.h b/src/common/include/gudhi_patches/CGAL/Orthogonal_incremental_neighbor_search.h index dbe707ed..e29ce14f 100644 --- a/src/common/include/gudhi_patches/CGAL/Orthogonal_incremental_neighbor_search.h +++ b/src/common/include/gudhi_patches/CGAL/Orthogonal_incremental_neighbor_search.h @@ -21,8 +21,7 @@ #ifndef CGAL_ORTHOGONAL_INCREMENTAL_NEIGHBOR_SEARCH #define CGAL_ORTHOGONAL_INCREMENTAL_NEIGHBOR_SEARCH -#include "CGAL/Kd_tree.h" - +#include #include #include #include -- cgit v1.2.3 From e3707de64413df06f83770a40ed8ba4ad9a69951 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Sat, 7 Jan 2017 14:30:09 +0000 Subject: Fix user version for gudhi patches git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@1936 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 462555b65b7b3c724a08d11e9b5a2776bf3a1bd8 --- src/cmake/modules/GUDHI_user_version_target.txt | 23 ++++------------------- 1 file changed, 4 insertions(+), 19 deletions(-) (limited to 'src') diff --git a/src/cmake/modules/GUDHI_user_version_target.txt b/src/cmake/modules/GUDHI_user_version_target.txt index 63301413..c91d5659 100644 --- a/src/cmake/modules/GUDHI_user_version_target.txt +++ b/src/cmake/modules/GUDHI_user_version_target.txt @@ -81,33 +81,18 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11) endif() endforeach() - # include files - file(GLOB GUDHI_INCLUDE_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/include/gudhi/*) + # include files and patches + file(GLOB GUDHI_INCLUDE_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/include/*) foreach(GUDHI_INCLUDE_FILE ${GUDHI_INCLUDE_FILES}) get_filename_component(GUDHI_INCLUDE_FILE_NAME ${GUDHI_INCLUDE_FILE} NAME) # GUDHI_INCLUDE_FILE can be a file or a directory if(IS_DIRECTORY ${GUDHI_INCLUDE_FILE}) add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy_directory ${GUDHI_INCLUDE_FILE} ${GUDHI_USER_VERSION_DIR}/include/gudhi/${GUDHI_INCLUDE_FILE_NAME}) + copy_directory ${GUDHI_INCLUDE_FILE} ${GUDHI_USER_VERSION_DIR}/include/${GUDHI_INCLUDE_FILE_NAME}) else() add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy ${GUDHI_INCLUDE_FILE} ${GUDHI_USER_VERSION_DIR}/include/gudhi/${GUDHI_INCLUDE_FILE_NAME}) - endif() - endforeach() - - # Patches - file(GLOB GUDHI_PATCHES_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/include/gudhi_patches/*) - - foreach(GUDHI_PATCHES_FILE ${GUDHI_PATCHES_FILES}) - get_filename_component(GUDHI_PATCHES_FILE_NAME ${GUDHI_PATCHES_FILE} NAME) - # GUDHI_PATCHES_FILE can be a file or a directory - if(IS_DIRECTORY ${GUDHI_PATCHES_FILE}) - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy_directory ${GUDHI_PATCHES_FILE} ${GUDHI_USER_VERSION_DIR}/include/gudhi/${GUDHI_PATCHES_FILE_NAME}) - else() - add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy ${GUDHI_PATCHES_FILE} ${GUDHI_USER_VERSION_DIR}/include/gudhi/${GUDHI_PATCHES_FILE_NAME}) + copy ${GUDHI_INCLUDE_FILE} ${GUDHI_USER_VERSION_DIR}/include/${GUDHI_INCLUDE_FILE_NAME}) endif() endforeach() -- cgit v1.2.3