From 9920ebf573304c19dd18389ddcff3e677a8bc92a Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Tue, 15 Nov 2022 15:50:18 +0100 Subject: Fall back to Hera's bottleneck without CGAL Once we move to Hera 2, we could just add it to include_directories and not bother adding it specifically for 3 python files + some tests and examples. [skip ci] --- src/Nerve_GIC/example/CMakeLists.txt | 34 +++++++++------------ src/Nerve_GIC/include/gudhi/GIC.h | 17 +++++++++-- src/Nerve_GIC/test/CMakeLists.txt | 17 +++++------ src/Nerve_GIC/utilities/CMakeLists.txt | 36 ++++++++++------------ src/python/CMakeLists.txt | 56 +++++++++++++++++----------------- 5 files changed, 80 insertions(+), 80 deletions(-) diff --git a/src/Nerve_GIC/example/CMakeLists.txt b/src/Nerve_GIC/example/CMakeLists.txt index 4b0f4677..9faf1f3b 100644 --- a/src/Nerve_GIC/example/CMakeLists.txt +++ b/src/Nerve_GIC/example/CMakeLists.txt @@ -1,25 +1,21 @@ project(Nerve_GIC_examples) -if (NOT CGAL_VERSION VERSION_LESS 4.11.0) +add_executable ( CoordGIC CoordGIC.cpp ) +add_executable ( FuncGIC FuncGIC.cpp ) - add_executable ( CoordGIC CoordGIC.cpp ) - add_executable ( FuncGIC FuncGIC.cpp ) +if (TBB_FOUND) + target_link_libraries(CoordGIC ${TBB_LIBRARIES}) + target_link_libraries(FuncGIC ${TBB_LIBRARIES}) +endif() - if (TBB_FOUND) - target_link_libraries(CoordGIC ${TBB_LIBRARIES}) - target_link_libraries(FuncGIC ${TBB_LIBRARIES}) - endif() +# Copy files for not to pollute sources when testing +file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +file(COPY "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +file(COPY "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - # Copy files for not to pollute sources when testing - file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - file(COPY "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - file(COPY "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +add_test(NAME Nerve_GIC_example_CoordGIC COMMAND $ + "${CMAKE_CURRENT_BINARY_DIR}/tore3D_1307.off" "0") - add_test(NAME Nerve_GIC_example_CoordGIC COMMAND $ - "${CMAKE_CURRENT_BINARY_DIR}/tore3D_1307.off" "0") - - add_test(NAME Nerve_GIC_example_FuncGIC COMMAND $ - "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat.off" - "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat_PCA1") - -endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) +add_test(NAME Nerve_GIC_example_FuncGIC COMMAND $ + "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat.off" + "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat_PCA1") diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h index 1b1f9323..3f9f0dc5 100644 --- a/src/Nerve_GIC/include/gudhi/GIC.h +++ b/src/Nerve_GIC/include/gudhi/GIC.h @@ -17,6 +17,14 @@ #include #endif +#if __has_include() +# define GUDHI_GIC_USE_CGAL 1 +# include +#elif __has_include() +# define GUDHI_GIC_USE_HERA 1 +# include +#endif + #include #include #include @@ -25,7 +33,6 @@ #include #include #include -#include #include #include @@ -35,8 +42,6 @@ #include #include -#include // for CGAL_VERSION_NR - #include #include #include @@ -1228,7 +1233,13 @@ class Cover_complex { Cboot.set_cover_from_function(); Cboot.find_simplices(); Cboot.compute_PD(); +#ifdef GUDHI_GIC_USE_CGAL double db = Gudhi::persistence_diagram::bottleneck_distance(this->PD, Cboot.PD); +#elif defined GUDHI_GIC_USE_HERA + double db = hera::bottleneckDistExact(this->PD, Cboot.PD); +#else + throw std::logic_error("This function requires CGAL or Hera for the bottleneck distance."); +#endif if (verbose) std::clog << db << std::endl; distribution.push_back(db); } diff --git a/src/Nerve_GIC/test/CMakeLists.txt b/src/Nerve_GIC/test/CMakeLists.txt index 567bf43f..e012a178 100644 --- a/src/Nerve_GIC/test/CMakeLists.txt +++ b/src/Nerve_GIC/test/CMakeLists.txt @@ -1,15 +1,12 @@ project(Graph_induced_complex_tests) -if (NOT CGAL_VERSION VERSION_LESS 4.11.0) - include(GUDHI_boost_test) +include(GUDHI_boost_test) - add_executable ( Nerve_GIC_test_unit test_GIC.cpp ) - if (TBB_FOUND) - target_link_libraries(Nerve_GIC_test_unit ${TBB_LIBRARIES}) - endif() +add_executable ( Nerve_GIC_test_unit test_GIC.cpp ) +if (TBB_FOUND) + target_link_libraries(Nerve_GIC_test_unit ${TBB_LIBRARIES}) +endif() - file(COPY data DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +file(COPY data DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - gudhi_add_boost_test(Nerve_GIC_test_unit) - -endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) +gudhi_add_boost_test(Nerve_GIC_test_unit) diff --git a/src/Nerve_GIC/utilities/CMakeLists.txt b/src/Nerve_GIC/utilities/CMakeLists.txt index 65a08d9a..4521a992 100644 --- a/src/Nerve_GIC/utilities/CMakeLists.txt +++ b/src/Nerve_GIC/utilities/CMakeLists.txt @@ -1,27 +1,23 @@ project(Nerve_GIC_examples) -if (NOT CGAL_VERSION VERSION_LESS 4.11.0) +add_executable ( Nerve Nerve.cpp ) +add_executable ( VoronoiGIC VoronoiGIC.cpp ) - add_executable ( Nerve Nerve.cpp ) - add_executable ( VoronoiGIC VoronoiGIC.cpp ) +if (TBB_FOUND) + target_link_libraries(Nerve ${TBB_LIBRARIES}) + target_link_libraries(VoronoiGIC ${TBB_LIBRARIES}) +endif() - if (TBB_FOUND) - target_link_libraries(Nerve ${TBB_LIBRARIES}) - target_link_libraries(VoronoiGIC ${TBB_LIBRARIES}) - endif() +file(COPY KeplerMapperVisuFromTxtFile.py km.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +# Copy files for not to pollute sources when testing +file(COPY "${CMAKE_SOURCE_DIR}/data/points/human.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - file(COPY KeplerMapperVisuFromTxtFile.py km.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - # Copy files for not to pollute sources when testing - file(COPY "${CMAKE_SOURCE_DIR}/data/points/human.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +add_test(NAME Nerve_GIC_utilities_nerve COMMAND $ + "human.off" "2" "10" "0.3") - add_test(NAME Nerve_GIC_utilities_nerve COMMAND $ - "human.off" "2" "10" "0.3") +add_test(NAME Nerve_GIC_utilities_VoronoiGIC COMMAND $ + "human.off" "100") - add_test(NAME Nerve_GIC_utilities_VoronoiGIC COMMAND $ - "human.off" "100") - - install(TARGETS Nerve DESTINATION bin) - install(TARGETS VoronoiGIC DESTINATION bin) - install(FILES KeplerMapperVisuFromTxtFile.py km.py km.py.COPYRIGHT DESTINATION bin) - -endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) +install(TARGETS Nerve DESTINATION bin) +install(TARGETS VoronoiGIC DESTINATION bin) +install(FILES KeplerMapperVisuFromTxtFile.py km.py km.py.COPYRIGHT DESTINATION bin) diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt index 32ec13bd..8bf176fc 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt @@ -163,10 +163,10 @@ if(PYTHONINTERP_FOUND) set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'clustering/_tomato', ") set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'hera/wasserstein', ") set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'hera/bottleneck', ") + set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'nerve_gic', ") if (NOT CGAL_VERSION VERSION_LESS 4.11.0) set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'datasets/generators/_points', ") set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'bottleneck', ") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'nerve_gic', ") endif () if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'subsampling', ") @@ -432,38 +432,38 @@ if(PYTHONINTERP_FOUND) ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py") add_gudhi_py_test(test_bottleneck_distance) + endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) - # Cover complex - file(COPY ${CMAKE_SOURCE_DIR}/data/points/human.off DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat.off DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - add_test(NAME cover_complex_nerve_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/nerve_of_a_covering.py" - -f human.off -c 2 -r 10 -g 0.3) + # Cover complex + file(COPY ${CMAKE_SOURCE_DIR}/data/points/human.off DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat.off DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + add_test(NAME cover_complex_nerve_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/nerve_of_a_covering.py" + -f human.off -c 2 -r 10 -g 0.3) - add_test(NAME cover_complex_coordinate_gic_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/coordinate_graph_induced_complex.py" - -f human.off -c 0 -v) + add_test(NAME cover_complex_coordinate_gic_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/coordinate_graph_induced_complex.py" + -f human.off -c 0 -v) - add_test(NAME cover_complex_functional_gic_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/functional_graph_induced_complex.py" - -o lucky_cat.off - -f lucky_cat_PCA1 -v) + add_test(NAME cover_complex_functional_gic_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/functional_graph_induced_complex.py" + -o lucky_cat.off + -f lucky_cat_PCA1 -v) - add_test(NAME cover_complex_voronoi_gic_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/voronoi_graph_induced_complex.py" - -f human.off -n 700 -v) + add_test(NAME cover_complex_voronoi_gic_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/voronoi_graph_induced_complex.py" + -f human.off -n 700 -v) - add_gudhi_py_test(test_cover_complex) - endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) + add_gudhi_py_test(test_cover_complex) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0) # Alpha -- cgit v1.2.3