diff options
author | MathieuCarriere <mathieu.carriere3@gmail.com> | 2022-12-06 09:16:26 +0100 |
---|---|---|
committer | MathieuCarriere <mathieu.carriere3@gmail.com> | 2022-12-06 09:16:26 +0100 |
commit | b259223b14827b0536934f23b662fba1a64bb866 (patch) | |
tree | 17e13d54f7c2bd5a0dea66a7d0cc5d03693e2d6b | |
parent | 7304fa44b91da85fc6ba013bc3be1839badfdb83 (diff) | |
parent | a82da7efd8ef465c4dbbc6fe72bf94f67f3bb639 (diff) |
Merge branch 'master' of https://github.com/GUDHI/gudhi-devel into perslay
-rw-r--r-- | .circleci/config.yml | 94 | ||||
-rw-r--r-- | biblio/bibliography.bib | 2 | ||||
-rw-r--r-- | biblio/test/test_biblio.tex | 7 | ||||
-rw-r--r-- | biblio/test/test_gudhi_citation.tex | 7 | ||||
-rw-r--r-- | src/Doxyfile.in | 1 | ||||
-rw-r--r-- | src/Nerve_GIC/example/CMakeLists.txt | 34 | ||||
-rw-r--r-- | src/Nerve_GIC/include/gudhi/GIC.h | 18 | ||||
-rw-r--r-- | src/Nerve_GIC/test/CMakeLists.txt | 17 | ||||
-rw-r--r-- | src/Nerve_GIC/utilities/CMakeLists.txt | 36 | ||||
-rw-r--r-- | src/cmake/modules/GUDHI_submodules.cmake | 2 | ||||
-rw-r--r-- | src/cmake/modules/GUDHI_user_version_target.cmake | 7 | ||||
-rw-r--r-- | src/python/CMakeLists.txt | 56 | ||||
-rw-r--r-- | src/python/gudhi/simplex_tree.pxd | 3 | ||||
-rw-r--r-- | src/python/gudhi/simplex_tree.pyx | 11 | ||||
-rw-r--r-- | src/python/setup.py.in | 2 |
15 files changed, 199 insertions, 98 deletions
diff --git a/.circleci/config.yml b/.circleci/config.yml index e2df5c87..958ec994 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -10,6 +10,11 @@ jobs: steps: - checkout - run: + name: Checkout submodules + command: | + git submodule sync + git submodule update --init + - run: name: Build and test examples command: | mkdir build @@ -24,6 +29,11 @@ jobs: steps: - checkout - run: + name: Checkout submodules + command: | + git submodule sync + git submodule update --init + - run: name: Build and test unitary tests command: | mkdir build @@ -38,6 +48,11 @@ jobs: steps: - checkout - run: + name: Checkout submodules + command: | + git submodule sync + git submodule update --init + - run: name: Build and test utilities command: | mkdir build @@ -52,10 +67,13 @@ jobs: steps: - checkout - run: + name: Checkout submodules + command: | + git submodule sync + git submodule update --init + - run: name: Build and test python module. Generates and tests the python documentation command: | - git submodule init - git submodule update mkdir build cd build cmake -DWITH_GUDHI_THIRD_PARTY=OFF -DUSER_VERSION_DIR=version .. @@ -64,6 +82,7 @@ jobs: cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 -DWITH_GUDHI_REMOTE_TEST=ON . cd python python3 setup.py build_ext --inplace + ctest --output-on-failure make sphinx cp -R sphinx /tmp/sphinx python3 setup.py install @@ -83,10 +102,13 @@ jobs: steps: - checkout - run: + name: Checkout submodules + command: | + git submodule sync + git submodule update --init + - run: name: Generates the C++ documentation with doxygen command: | - git submodule init - git submodule update mkdir build cd build cmake -DWITH_GUDHI_THIRD_PARTY=OFF -DUSER_VERSION_DIR=version .. @@ -104,6 +126,26 @@ jobs: path: /tmp/doxygen destination: doxygen + bibliography: + docker: + - image: gudhi/doxygen_for_gudhi:latest + steps: + - checkout + - run: + name: Checkout submodules + command: | + git submodule sync + git submodule update --init + - run: + name: Test the LaTeX bibliography files + command: | + mkdir build + cd build + cmake -DWITH_GUDHI_THIRD_PARTY=OFF -DUSER_VERSION_DIR=version .. + cd biblio/test + latexmk -pdf -interaction=nonstopmode test_biblio.tex + latexmk -pdf -interaction=nonstopmode test_gudhi_citation.tex + ### With all third parties, except CGAL and Eigen @@ -114,6 +156,11 @@ jobs: steps: - checkout - run: + name: Checkout submodules + command: | + git submodule sync + git submodule update --init + - run: name: Build and test examples without cgal and eigen command: | mkdir build @@ -128,6 +175,11 @@ jobs: steps: - checkout - run: + name: Checkout submodules + command: | + git submodule sync + git submodule update --init + - run: name: Build and test unitary tests without cgal and eigen command: | mkdir build @@ -142,6 +194,11 @@ jobs: steps: - checkout - run: + name: Checkout submodules + command: | + git submodule sync + git submodule update --init + - run: name: Build and test utilities without cgal and eigen command: | mkdir build @@ -156,10 +213,13 @@ jobs: steps: - checkout - run: + name: Checkout submodules + command: | + git submodule sync + git submodule update --init + - run: name: Build and test python module without cgal and eigen command: | - git submodule init - git submodule update mkdir build cd build cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 .. @@ -176,6 +236,11 @@ jobs: steps: - checkout - run: + name: Checkout submodules + command: | + git submodule sync + git submodule update --init + - run: name: Build and test examples without cgal command: | mkdir build @@ -190,6 +255,11 @@ jobs: steps: - checkout - run: + name: Checkout submodules + command: | + git submodule sync + git submodule update --init + - run: name: Build and test unitary tests without cgal command: | mkdir build @@ -204,6 +274,11 @@ jobs: steps: - checkout - run: + name: Checkout submodules + command: | + git submodule sync + git submodule update --init + - run: name: Build and test utilities without cgal command: | mkdir build @@ -218,10 +293,13 @@ jobs: steps: - checkout - run: + name: Checkout submodules + command: | + git submodule sync + git submodule update --init + - run: name: Build and test python module without cgal command: | - git submodule init - git submodule update mkdir build cd build cmake -DCMAKE_BUILD_TYPE=Release -DEIGEN3_INCLUDE_DIR=/eigen-3.3.9 -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 .. diff --git a/biblio/bibliography.bib b/biblio/bibliography.bib index 0a3ef43d..d8472ad0 100644 --- a/biblio/bibliography.bib +++ b/biblio/bibliography.bib @@ -1090,7 +1090,7 @@ language={English} @ARTICLE{Reininghaus_Huber_ALL_PSSK, author = {J. Reininghaus and S. Huber and U. Bauer and R. Kwitt}, title = {A Stable Multi-Scale Kernel for Topological Machine Learning.}, - journal = {Proc. 2015 IEEE Conf. Comp. Vision & Pat. Rec. (CVPR '15)}, + journal = {Proc. 2015 IEEE Conf. Comp. Vision \& Pat. Rec. (CVPR '15)}, year = {2015} } diff --git a/biblio/test/test_biblio.tex b/biblio/test/test_biblio.tex new file mode 100644 index 00000000..97dee9ed --- /dev/null +++ b/biblio/test/test_biblio.tex @@ -0,0 +1,7 @@ +\documentclass{article} +\usepackage{hyperref} +\bibliographystyle{plainurl} +\begin{document} +\nocite{*} +\bibliography{../bibliography} +\end{document}
\ No newline at end of file diff --git a/biblio/test/test_gudhi_citation.tex b/biblio/test/test_gudhi_citation.tex new file mode 100644 index 00000000..5fb2d33d --- /dev/null +++ b/biblio/test/test_gudhi_citation.tex @@ -0,0 +1,7 @@ +\documentclass{article} +\usepackage{hyperref} +\bibliographystyle{plainurl} +\begin{document} +\nocite{*} +\bibliography{../how_to_cite_gudhi} +\end{document}
\ No newline at end of file diff --git a/src/Doxyfile.in b/src/Doxyfile.in index 1ec190d9..d5664a49 100644 --- a/src/Doxyfile.in +++ b/src/Doxyfile.in @@ -700,7 +700,6 @@ LAYOUT_FILE = # search path. See also \cite for info how to create references. CITE_BIB_FILES = @CMAKE_SOURCE_DIR@/biblio/bibliography.bib \ - @CMAKE_SOURCE_DIR@/biblio/how_to_cite_cgal.bib \ @CMAKE_SOURCE_DIR@/biblio/how_to_cite_gudhi.bib #--------------------------------------------------------------------------- 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 $<TARGET_FILE:CoordGIC> + "${CMAKE_CURRENT_BINARY_DIR}/tore3D_1307.off" "0") - add_test(NAME Nerve_GIC_example_CoordGIC COMMAND $<TARGET_FILE:CoordGIC> - "${CMAKE_CURRENT_BINARY_DIR}/tore3D_1307.off" "0") - - add_test(NAME Nerve_GIC_example_FuncGIC COMMAND $<TARGET_FILE:FuncGIC> - "${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 $<TARGET_FILE:FuncGIC> + "${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..047fba61 100644 --- a/src/Nerve_GIC/include/gudhi/GIC.h +++ b/src/Nerve_GIC/include/gudhi/GIC.h @@ -17,6 +17,14 @@ #include <mutex> #endif +#if __has_include(<CGAL/version.h>) +# define GUDHI_GIC_USE_CGAL 1 +# include <gudhi/Bottleneck.h> +#elif __has_include(<hera/bottleneck.h>) +# define GUDHI_GIC_USE_HERA 1 +# include <hera/bottleneck.h> +#endif + #include <gudhi/Debug_utils.h> #include <gudhi/graph_simplicial_complex.h> #include <gudhi/reader_utils.h> @@ -25,7 +33,6 @@ #include <gudhi/Points_off_io.h> #include <gudhi/distance_functions.h> #include <gudhi/Persistent_cohomology.h> -#include <gudhi/Bottleneck.h> #include <boost/config.hpp> #include <boost/graph/graph_traits.hpp> @@ -35,8 +42,6 @@ #include <boost/graph/subgraph.hpp> #include <boost/graph/graph_utility.hpp> -#include <CGAL/version.h> // for CGAL_VERSION_NR - #include <iostream> #include <vector> #include <map> @@ -1228,7 +1233,14 @@ 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 + double db; + 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 $<TARGET_FILE:Nerve> + "human.off" "2" "10" "0.3") - add_test(NAME Nerve_GIC_utilities_nerve COMMAND $<TARGET_FILE:Nerve> - "human.off" "2" "10" "0.3") +add_test(NAME Nerve_GIC_utilities_VoronoiGIC COMMAND $<TARGET_FILE:VoronoiGIC> + "human.off" "100") - add_test(NAME Nerve_GIC_utilities_VoronoiGIC COMMAND $<TARGET_FILE:VoronoiGIC> - "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/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/cmake/modules/GUDHI_user_version_target.cmake b/src/cmake/modules/GUDHI_user_version_target.cmake index 2144ff6f..b9bf1414 100644 --- a/src/cmake/modules/GUDHI_user_version_target.cmake +++ b/src/cmake/modules/GUDHI_user_version_target.cmake @@ -18,14 +18,17 @@ add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E string(TIMESTAMP GUDHI_VERSION_YEAR "%Y") configure_file(${CMAKE_SOURCE_DIR}/biblio/how_to_cite_gudhi.bib.in "${CMAKE_CURRENT_BINARY_DIR}/biblio/how_to_cite_gudhi.bib" @ONLY) file(COPY "${CMAKE_SOURCE_DIR}/biblio/bibliography.bib" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/biblio/") +file(COPY "${CMAKE_SOURCE_DIR}/biblio/test" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/biblio") # append cgal citation inside bibliography - sphinx cannot deal with more than one bib file file(READ "${CMAKE_SOURCE_DIR}/biblio/how_to_cite_cgal.bib" CGAL_CITATION_CONTENT) file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/biblio/bibliography.bib" "${CGAL_CITATION_CONTENT}") -# Copy biblio directory for user version +# Copy biblio files for user version add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E - copy_directory ${CMAKE_CURRENT_BINARY_DIR}/biblio ${GUDHI_USER_VERSION_DIR}/biblio) + copy ${CMAKE_CURRENT_BINARY_DIR}/biblio/bibliography.bib ${GUDHI_USER_VERSION_DIR}/biblio/bibliography.bib) +add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E + copy ${CMAKE_CURRENT_BINARY_DIR}/biblio/how_to_cite_gudhi.bib ${GUDHI_USER_VERSION_DIR}/biblio/how_to_cite_gudhi.bib) add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/README.md ${GUDHI_USER_VERSION_DIR}/README.md) diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt index 0b86f1bb..198d0c65 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt @@ -163,10 +163,10 @@ if(PYTHONINTERP_FOUND) set(GUDHI_PYBIND11_MODULES "${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 diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd index f86f1232..5309c6fa 100644 --- a/src/python/gudhi/simplex_tree.pxd +++ b/src/python/gudhi/simplex_tree.pxd @@ -56,7 +56,8 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": int upper_bound_dimension() nogil bool find_simplex(vector[int] simplex) nogil bool insert(vector[int] simplex, double filtration) nogil - void insert_matrix(double* filtrations, int n, int stride0, int stride1, double max_filtration) nogil + void insert_matrix(double* filtrations, int n, int stride0, int stride1, double max_filtration) nogil except + + void insert_batch_vertices(vector[int] v, double f) nogil except + vector[pair[vector[int], double]] get_star(vector[int] simplex) nogil vector[pair[vector[int], double]] get_cofaces(vector[int] simplex, int dimension) nogil void expansion(int max_dim) nogil except + diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx index 18215d2f..4cf176f5 100644 --- a/src/python/gudhi/simplex_tree.pyx +++ b/src/python/gudhi/simplex_tree.pyx @@ -12,6 +12,7 @@ from libc.stdint cimport intptr_t, int32_t, int64_t import numpy as np cimport gudhi.simplex_tree cimport cython +from numpy.math cimport INFINITY __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" @@ -239,7 +240,7 @@ cdef class SimplexTree: @staticmethod @cython.boundscheck(False) - def create_from_array(filtrations, double max_filtration=np.inf): + def create_from_array(filtrations, double max_filtration=INFINITY): """Creates a new, empty complex and inserts vertices and edges. The vertices are numbered from 0 to n-1, and the filtration values are encoded in the array, with the diagonal representing the vertices. It is the caller's responsibility to ensure that this defines a filtration, which can be achieved with either:: @@ -281,6 +282,8 @@ cdef class SimplexTree: .. seealso:: :func:`insert_batch` """ + # Without this, it could be slow if we end up inserting vertices in a bad order (flat_map). + self.get_ptr().insert_batch_vertices(np.unique(np.stack((edges.row, edges.col))), INFINITY) # TODO: optimize this? for edge in zip(edges.row, edges.col, edges.data): self.get_ptr().insert((edge[0], edge[1]), edge[2]) @@ -303,8 +306,7 @@ cdef class SimplexTree: :param filtrations: the filtration values. :type filtrations: numpy.array of shape (n,) """ - # This may be slow if we end up inserting vertices in a bad order (flat_map). - # We could first insert the vertices from np.unique(vertex_array), or leave it to the caller. + cdef vector[int] vertices = np.unique(vertex_array) cdef Py_ssize_t k = vertex_array.shape[0] cdef Py_ssize_t n = vertex_array.shape[1] assert filtrations.shape[0] == n, 'inconsistent sizes for vertex_array and filtrations' @@ -312,6 +314,9 @@ cdef class SimplexTree: cdef Py_ssize_t j cdef vector[int] v with nogil: + # Without this, it could be slow if we end up inserting vertices in a bad order (flat_map). + # NaN currently does the wrong thing + self.get_ptr().insert_batch_vertices(vertices, INFINITY) for i in range(n): for j in range(k): v.push_back(vertex_array[j, i]) diff --git a/src/python/setup.py.in b/src/python/setup.py.in index 1ecbe985..6eb0db42 100644 --- a/src/python/setup.py.in +++ b/src/python/setup.py.in @@ -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'], |