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(-) (limited to 'src') 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 From a63010aba4fedd80fc9076c9e10e9afce7a0755f Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Wed, 16 Nov 2022 14:34:11 +0100 Subject: Always include Hera's directory --- src/cmake/modules/GUDHI_submodules.cmake | 2 ++ src/python/setup.py.in | 4 +--- 2 files changed, 3 insertions(+), 3 deletions(-) (limited to 'src') diff --git a/src/cmake/modules/GUDHI_submodules.cmake b/src/cmake/modules/GUDHI_submodules.cmake index c844386d..9ede852d 100644 --- a/src/cmake/modules/GUDHI_submodules.cmake +++ b/src/cmake/modules/GUDHI_submodules.cmake @@ -1,3 +1,5 @@ # For those who dislike bundled dependencies, this indicates where to find a preinstalled Hera. set(HERA_INTERNAL_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/hera/include) set(HERA_INCLUDE_DIR ${HERA_INTERNAL_INCLUDE_DIR} CACHE PATH "Directory where one can find hera/{wasserstein.h,bottleneck.h}") +# since everything is cleanly under include/hera/, there is no harm always including it +include_directories(${HERA_INCLUDE_DIR}) diff --git a/src/python/setup.py.in b/src/python/setup.py.in index 1ecbe985..af921894 100644 --- a/src/python/setup.py.in +++ b/src/python/setup.py.in @@ -27,7 +27,7 @@ extra_compile_args=[@GUDHI_PYTHON_EXTRA_COMPILE_ARGS@] extra_link_args=[@GUDHI_PYTHON_EXTRA_LINK_ARGS@] libraries=[@GUDHI_PYTHON_LIBRARIES@] library_dirs=[@GUDHI_PYTHON_LIBRARY_DIRS@] -include_dirs = [numpy_get_include(), '@CMAKE_CURRENT_SOURCE_DIR@/gudhi/', @GUDHI_PYTHON_INCLUDE_DIRS@] +include_dirs = [numpy_get_include(), '@CMAKE_CURRENT_SOURCE_DIR@/gudhi/', '@HERA_INCLUDE_DIR@', @GUDHI_PYTHON_INCLUDE_DIRS@] runtime_library_dirs=[@GUDHI_PYTHON_RUNTIME_LIBRARY_DIRS@] # Create ext_modules list from module list @@ -48,8 +48,6 @@ ext_modules = cythonize(ext_modules, compiler_directives={'language_level': '3'} for module in pybind11_modules: my_include_dirs = include_dirs + [pybind11.get_include(False), pybind11.get_include(True)] - if module.startswith('hera/'): - my_include_dirs = ['@HERA_INCLUDE_DIR@'] + my_include_dirs ext_modules.append(Extension( 'gudhi.' + module.replace('/', '.'), sources = [source_dir + module + '.cc'], -- cgit v1.2.3 From ae423409b495166a52f473e387f031db7996b371 Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Wed, 16 Nov 2022 14:57:04 +0100 Subject: Declare variable even on the error path. --- src/Nerve_GIC/include/gudhi/GIC.h | 1 + 1 file changed, 1 insertion(+) (limited to 'src') diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h index 3f9f0dc5..560f7d6c 100644 --- a/src/Nerve_GIC/include/gudhi/GIC.h +++ b/src/Nerve_GIC/include/gudhi/GIC.h @@ -1238,6 +1238,7 @@ class Cover_complex { #elif defined GUDHI_GIC_USE_HERA double db = hera::bottleneckDistExact(this->PD, Cboot.PD); #else + double db; throw std::logic_error("This function requires CGAL or Hera for the bottleneck distance."); #endif if (verbose) std::clog << db << std::endl; -- cgit v1.2.3 From b7277485f6aa568f65abc9dbbe8d9420fad9575c Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Wed, 16 Nov 2022 15:11:24 +0100 Subject: Update the path for Hera --- src/Nerve_GIC/include/gudhi/GIC.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'src') diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h index 560f7d6c..047fba61 100644 --- a/src/Nerve_GIC/include/gudhi/GIC.h +++ b/src/Nerve_GIC/include/gudhi/GIC.h @@ -20,9 +20,9 @@ #if __has_include() # define GUDHI_GIC_USE_CGAL 1 # include -#elif __has_include() +#elif __has_include() # define GUDHI_GIC_USE_HERA 1 -# include +# include #endif #include -- cgit v1.2.3 From 99cb6c464b103a05cddd65fa88a9c341f1b384bc Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Fri, 25 Nov 2022 11:51:49 +0100 Subject: Remove redundant include --- src/python/setup.py.in | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'src') diff --git a/src/python/setup.py.in b/src/python/setup.py.in index af921894..6eb0db42 100644 --- a/src/python/setup.py.in +++ b/src/python/setup.py.in @@ -27,7 +27,7 @@ extra_compile_args=[@GUDHI_PYTHON_EXTRA_COMPILE_ARGS@] extra_link_args=[@GUDHI_PYTHON_EXTRA_LINK_ARGS@] libraries=[@GUDHI_PYTHON_LIBRARIES@] library_dirs=[@GUDHI_PYTHON_LIBRARY_DIRS@] -include_dirs = [numpy_get_include(), '@CMAKE_CURRENT_SOURCE_DIR@/gudhi/', '@HERA_INCLUDE_DIR@', @GUDHI_PYTHON_INCLUDE_DIRS@] +include_dirs = [numpy_get_include(), '@CMAKE_CURRENT_SOURCE_DIR@/gudhi/', @GUDHI_PYTHON_INCLUDE_DIRS@] runtime_library_dirs=[@GUDHI_PYTHON_RUNTIME_LIBRARY_DIRS@] # Create ext_modules list from module list -- cgit v1.2.3