diff options
Diffstat (limited to 'src/Bottleneck_distance')
5 files changed, 35 insertions, 48 deletions
diff --git a/src/Bottleneck_distance/benchmark/CMakeLists.txt b/src/Bottleneck_distance/benchmark/CMakeLists.txt index c99e0373..170081ce 100644 --- a/src/Bottleneck_distance/benchmark/CMakeLists.txt +++ b/src/Bottleneck_distance/benchmark/CMakeLists.txt @@ -1,14 +1,9 @@ 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) - add_executable ( bottleneck_chrono bottleneck_chrono.cpp ) - if (TBB_FOUND) - target_link_libraries(bottleneck_chrono ${TBB_LIBRARIES}) - endif(TBB_FOUND) - endif () -endif() +if (NOT CGAL_WITH_EIGEN3_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) diff --git a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h index 5223678d..3998fe8d 100644 --- a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h +++ b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h @@ -35,9 +35,9 @@ namespace persistence_diagram { * * \section bottleneckdefinition Definition * - * The bottleneck distance measures the similarity between two persistence diagrams. It is 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. + * The bottleneck distance measures the similarity between two persistence diagrams. It is 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 On this picture, the red edges represent the matching. The bottleneck distance is the length of the longest edge. * diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt index 55f22c01..b0a19f8b 100644 --- a/src/Bottleneck_distance/example/CMakeLists.txt +++ b/src/Bottleneck_distance/example/CMakeLists.txt @@ -1,24 +1,20 @@ cmake_minimum_required(VERSION 2.6) project(Bottleneck_distance_examples) -# requires CGAL 4.8 -# cmake -DCGAL_DIR=~/workspace/CGAL-4.8 ../../.. -if(CGAL_FOUND) - if (NOT CGAL_VERSION VERSION_LESS 4.8.0) - add_executable (bottleneck_read_file_example bottleneck_read_file_example.cpp) - add_executable (bottleneck_basic_example bottleneck_basic_example.cpp) +if (NOT CGAL_WITH_EIGEN3_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_test(bottleneck_basic_example ${CMAKE_CURRENT_BINARY_DIR}/bottleneck_basic_example) + add_test(bottleneck_basic_example ${CMAKE_CURRENT_BINARY_DIR}/bottleneck_basic_example) - add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp) - target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_SYSTEM_LIBRARY} ${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(alpha_rips_persistence_bottleneck_distance ${CMAKE_CURRENT_BINARY_DIR}/alpha_rips_persistence_bottleneck_distance - ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -r 0.15 -m 0.12 -d 3 -p 3) + add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp) + target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_SYSTEM_LIBRARY} ${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(alpha_rips_persistence_bottleneck_distance ${CMAKE_CURRENT_BINARY_DIR}/alpha_rips_persistence_bottleneck_distance + ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -r 0.15 -m 0.12 -d 3 -p 3) - endif () -endif() +endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp index 6e9be97b..fd9f0858 100644 --- a/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp +++ b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp @@ -56,7 +56,7 @@ void program_options(int argc, char * argv[] , int & p , Filtration_value & min_persistence); -static inline std::pair<double, double> compute_root_square (std::pair<double, double> input) { +static inline std::pair<double, double> compute_root_square(std::pair<double, double> input) { return std::make_pair(std::sqrt(input.first), std::sqrt(input.second)); } diff --git a/src/Bottleneck_distance/test/CMakeLists.txt b/src/Bottleneck_distance/test/CMakeLists.txt index 3e61f4cf..3d8e1f95 100644 --- a/src/Bottleneck_distance/test/CMakeLists.txt +++ b/src/Bottleneck_distance/test/CMakeLists.txt @@ -11,19 +11,15 @@ if (GPROF_PATH) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") endif() -# requires CGAL 4.8 -# cmake -DCGAL_DIR=~/workspace/CGAL-4.8 ../../.. -if(CGAL_FOUND) - if (NOT CGAL_VERSION VERSION_LESS 4.8.0) - add_executable ( bottleneckUT bottleneck_unit_test.cpp ) - target_link_libraries(bottleneckUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) - if (TBB_FOUND) - target_link_libraries(bottleneckUT ${TBB_LIBRARIES}) - endif(TBB_FOUND) +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) + add_executable ( bottleneckUT bottleneck_unit_test.cpp ) + target_link_libraries(bottleneckUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(bottleneckUT ${TBB_LIBRARIES}) + endif(TBB_FOUND) - # 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) - endif () -endif() + # 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) +endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) |