diff options
Diffstat (limited to 'src/Bottleneck_distance')
5 files changed, 31 insertions, 23 deletions
diff --git a/src/Bottleneck_distance/benchmark/CMakeLists.txt b/src/Bottleneck_distance/benchmark/CMakeLists.txt index 170081ce..20a4e47b 100644 --- a/src/Bottleneck_distance/benchmark/CMakeLists.txt +++ b/src/Bottleneck_distance/benchmark/CMakeLists.txt @@ -1,9 +1,9 @@ cmake_minimum_required(VERSION 2.6) project(Bottleneck_distance_benchmark) -if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) +if (NOT CGAL_VERSION VERSION_LESS 4.8.1) add_executable ( bottleneck_chrono bottleneck_chrono.cpp ) if (TBB_FOUND) target_link_libraries(bottleneck_chrono ${TBB_LIBRARIES}) endif(TBB_FOUND) -endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) +endif(NOT CGAL_VERSION VERSION_LESS 4.8.1) diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt index dc1da31c..eac617db 100644 --- a/src/Bottleneck_distance/example/CMakeLists.txt +++ b/src/Bottleneck_distance/example/CMakeLists.txt @@ -1,30 +1,38 @@ cmake_minimum_required(VERSION 2.6) project(Bottleneck_distance_examples) -if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) +if (NOT CGAL_VERSION VERSION_LESS 4.8.1) add_executable (bottleneck_read_file_example bottleneck_read_file_example.cpp) add_executable (bottleneck_basic_example bottleneck_basic_example.cpp) - add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp) - target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_PROGRAM_OPTIONS_LIBRARY}) if (TBB_FOUND) target_link_libraries(bottleneck_read_file_example ${TBB_LIBRARIES}) target_link_libraries(bottleneck_basic_example ${TBB_LIBRARIES}) - target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES}) endif(TBB_FOUND) add_test(NAME Bottleneck_distance_example_basic COMMAND $<TARGET_FILE:bottleneck_basic_example>) - add_test(NAME Bottleneck_distance_example_alpha_rips_persistence_bottleneck - COMMAND $<TARGET_FILE:alpha_rips_persistence_bottleneck_distance> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.15" "-m" "0.12" "-d" "3" "-p" "3") - add_test(NAME Bottleneck_read_file_example COMMAND $<TARGET_FILE:bottleneck_read_file_example> "${CMAKE_SOURCE_DIR}/data/persistence_diagram/first.pers" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/second.pers") install(TARGETS bottleneck_read_file_example DESTINATION bin) install(TARGETS bottleneck_basic_example DESTINATION bin) - install(TARGETS alpha_rips_persistence_bottleneck_distance DESTINATION bin) +endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) + +# Eigen3 and CGAL > 4.7.0 is required for alpha complex +# CGAL > 4.8.1 is required for bottleneck distance => +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp) + target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_PROGRAM_OPTIONS_LIBRARY}) + + add_test(NAME Bottleneck_distance_example_alpha_rips_persistence_bottleneck + COMMAND $<TARGET_FILE:alpha_rips_persistence_bottleneck_distance> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.15" "-m" "0.12" "-d" "3" "-p" "3") + + install(TARGETS alpha_rips_persistence_bottleneck_distance DESTINATION bin) + if (TBB_FOUND) + target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES}) + endif(TBB_FOUND) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp index 1408681a..24d73c57 100644 --- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp +++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp @@ -25,21 +25,21 @@ #include <iostream> #include <vector> #include <utility> // for pair -#include <fstream> -#include <sstream> #include <string> +#include <limits> // for numeric_limits 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 the smallest positive double value). If you set the error bound to 0, be" << + " aware this version is exact but expensive. The program will now terminate \n"; return -1; } std::vector<std::pair<double, double>> diag1 = Gudhi::read_persistence_intervals_in_dimension(argv[1]); std::vector<std::pair<double, double>> diag2 = Gudhi::read_persistence_intervals_in_dimension(argv[2]); - double tolerance = 0.; + double tolerance = std::numeric_limits<double>::min(); if (argc == 4) { tolerance = atof(argv[3]); } diff --git a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h index bdc47578..a6b9b021 100644 --- a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h +++ b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h @@ -44,16 +44,16 @@ struct Square_query { typedef Internal_point Point_d; typedef double FT; bool contains(Point_d p) const { - return std::abs(p.x()-c.x())<=size && std::abs(p.y()-c.y())<=size; + return std::abs(p.x()-c.x()) <= size && std::abs(p.y()-c.y()) <= size; } - bool inner_range_intersects(CGAL::Kd_tree_rectangle<FT,D> const&r) const { + bool inner_range_intersects(CGAL::Kd_tree_rectangle<FT, D> const&r) const { return r.max_coord(0) >= c.x() - size && r.min_coord(0) <= c.x() + size && r.max_coord(1) >= c.y() - size && r.min_coord(1) <= c.y() + size; } - bool outer_range_contains(CGAL::Kd_tree_rectangle<FT,D> const&r) const { + bool outer_range_contains(CGAL::Kd_tree_rectangle<FT, D> const&r) const { return r.min_coord(0) >= c.x() - size && r.max_coord(0) <= c.x() + size && @@ -146,7 +146,7 @@ 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); auto neighbor = kd_t.search_any_point(Square_query{u_point, r}); - if(!neighbor) + if (!neighbor) return null_point_index(); tmp = neighbor->point_index; auto point = g.get_v_point(tmp); diff --git a/src/Bottleneck_distance/test/CMakeLists.txt b/src/Bottleneck_distance/test/CMakeLists.txt index a165d472..2676b82c 100644 --- a/src/Bottleneck_distance/test/CMakeLists.txt +++ b/src/Bottleneck_distance/test/CMakeLists.txt @@ -1,7 +1,7 @@ cmake_minimum_required(VERSION 2.6) project(Bottleneck_distance_tests) -if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) +if (NOT CGAL_VERSION VERSION_LESS 4.8.1) include(GUDHI_test_coverage) add_executable ( Bottleneck_distance_test_unit bottleneck_unit_test.cpp ) @@ -12,4 +12,4 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) gudhi_add_coverage_test(Bottleneck_distance_test_unit) -endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) +endif (NOT CGAL_VERSION VERSION_LESS 4.8.1) |