diff options
author | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-01-04 08:39:18 +0000 |
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committer | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-01-04 08:39:18 +0000 |
commit | 64dd2a2b0eec1374ed23ca079f86b312125d03f7 (patch) | |
tree | f22c13edb5f6d2980c0af4ec21a6a9b8910990de /src/Bottleneck_distance/test | |
parent | 67c34d7b506efe6445a24380b3ad0743e09ef334 (diff) |
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
Diffstat (limited to 'src/Bottleneck_distance/test')
-rw-r--r-- | src/Bottleneck_distance/test/CMakeLists.txt | 1 | ||||
-rw-r--r-- | src/Bottleneck_distance/test/bottleneck_chrono.cpp | 62 | ||||
-rw-r--r-- | src/Bottleneck_distance/test/bottleneck_unit_test.cpp | 238 |
3 files changed, 119 insertions, 182 deletions
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 <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Bottleneck.h> -#include <chrono> -#include <fstream> -#include <random> - -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<double> unif1(0.,upper_bound); - std::uniform_real_distribution<double> unif2(upper_bound/1000.,upper_bound/100.); - std::default_random_engine re; - std::vector< std::pair<double, double> > 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<int,std::milli> millisecs_t; - millisecs_t duration(std::chrono::duration_cast<millisecs_t>(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<double> unif(0.,upper_bound); +std::uniform_real_distribution<double> unif(0., upper_bound); std::default_random_engine re; std::vector< std::pair<double, double> > 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<double> 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<double> 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<int> 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<int> 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<double> unif1(0.,upper_bound); - std::uniform_real_distribution<double> unif2(upper_bound/10000.,upper_bound/100.); - std::default_random_engine re; - std::vector< std::pair<double, double> > 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<double> unif1(0., upper_bound); + std::uniform_real_distribution<double> unif2(upper_bound / 10000., upper_bound / 100.); + std::default_random_engine re; + std::vector< std::pair<double, double> > 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.); } |