Merge branch 'master' of bitbucket.org:glavaux/cosmotool
This commit is contained in:
Guilhem Lavaux
commit
5e7437b7d4
@ -13,14 +13,20 @@ set(NumPy_FIND_REQUIRED TRUE)
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include(${CMAKE_SOURCE_DIR}/FindPyLibs.cmake)
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include(${CMAKE_SOURCE_DIR}/FindNumPy.cmake)
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get_git_head_revision(HEAD GIT_VER)
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option(BUILD_SHARED_LIBS "Build shared libraries." OFF)
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option(BUILD_STATIC_LIBS "Build static libraries." ON)
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option(ENABLE_SHARP "Enable SHARP support." ON)
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option(INTERNAL_HDF5 "Build internal version of HDF5" OFF)
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option(INTERNAL_NETCDF "Build internal version of NETCDF" OFF)
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option(INTERNAL_BOOST "Build internal version of BOOST" OFF)
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option(USE_GIT_VERSION "Use GIT version to pad version number" OFF)
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option(YORICK_SUPPORT "Add for pleasant yorick support" ON)
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option(BUILD_PYTHON "Build the python modules" ON)
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IF(USE_GIT_VERSION)
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get_git_head_revision(HEAD GIT_VER)
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SET(EXTRA_VERSION "-${GIT_VER}")
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ENDIF(USE_GIT_VERSION)
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#IF(NOT BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS)
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# SET(CosmoTool_local CosmoTool_static)
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@ -32,13 +38,15 @@ MESSAGE(STATUS "Using the target ${CosmoTool_local} to build python module")
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include(${CMAKE_SOURCE_DIR}/external/external_build.cmake)
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IF(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4")
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SET(FOUND_NETCDF4 1)
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FILE(WRITE ${CMAKE_BINARY_DIR}/src/ctool_netcdf_ver.hpp "#define NETCDFCPP4 1")
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ELSE(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4")
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SET(FOUND_NETCDF3 1)
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FILE(WRITE ${CMAKE_BINARY_DIR}/src/ctool_netcdf_ver.hpp "#undef NETCDFCPP4")
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ENDIF(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4")
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IF(YORICK_SUPPORT)
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IF(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4")
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SET(FOUND_NETCDF4 1)
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FILE(WRITE ${CMAKE_BINARY_DIR}/src/ctool_netcdf_ver.hpp "#define NETCDFCPP4 1")
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ELSE(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4")
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SET(FOUND_NETCDF3 1)
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FILE(WRITE ${CMAKE_BINARY_DIR}/src/ctool_netcdf_ver.hpp "#undef NETCDFCPP4")
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ENDIF(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4")
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ENDIF(YORICK_SUPPORT)
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find_program(CYTHON cython)
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@ -48,7 +56,7 @@ endif(HDF5_ROOTDIR)
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find_package(HDF5 COMPONENTS CXX HL)
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set(NETCDF_FIND_REQUIRED TRUE)
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set(NETCDF_FIND_REQUIRED ${YORICK_SUPPORT})
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set(GSL_FIND_REQUIRED TRUE)
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FIND_PACKAGE_HANDLE_STANDARD_ARGS(NetCDF DEFAULT_MSG NETCDF_LIBRARY NETCDFCPP_LIBRARY NETCDF_INCLUDE_PATH)
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FIND_PACKAGE_HANDLE_STANDARD_ARGS(GSL DEFAULT_MSG GSL_LIBRARY GSLCBLAS_LIBRARY GSL_INCLUDE_PATH)
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@ -60,14 +68,16 @@ SET(CPACK_PACKAGE_VENDOR "Guilhem Lavaux")
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SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENCE_CeCILL_V2")
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SET(CPACK_PACKAGE_VERSION_MAJOR "1")
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SET(CPACK_PACKAGE_VERSION_MINOR "0")
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SET(CPACK_PACKAGE_VERSION_PATCH "0-${GIT_VER}")
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SET(CPACK_PACKAGE_INSTALL_DIRECTORY "CosmoToolbox-${GalaxExplorer_VERSION_MAJOR}.${GalaxExplorer_VERSION_MINOR}")
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SET(CPACK_PACKAGE_VERSION_PATCH "0${EXTRA_VERSION}")
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SET(CPACK_PACKAGE_INSTALL_DIRECTORY "CosmoToolbox-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}")
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SET(CPACK_STRIP_FILES "lib/libCosmoTool.so")
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SET(CPACK_SOURCE_IGNORE_FILES
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"/CVS/;/\\\\.git/;/\\\\.svn/;\\\\.swp$;\\\\.#;/#;.*~;cscope.*;/CMakeFiles/;.*\\\\.cmake;Makefile")
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add_subdirectory(src)
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add_subdirectory(sample)
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add_subdirectory(python)
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if(BUILD_PYTHON)
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add_subdirectory(python)
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endif(BUILD_PYTHON)
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include(CPack)
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@ -1,7 +1,9 @@
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SET(tolink ${GSL_LIBRARIES} ${CosmoTool_local} ${CosmoTool_LIBS})
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include_directories(${CMAKE_SOURCE_DIR}/src)
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include_directories(${FFTW3_INCLUDE_DIRS}
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${EIGEN3_INCLUDE_DIRS} ${NETCDF_INCLUDE_PATH} ${GSL_INCLUDE_PATH})
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include_directories(${FFTW3_INCLUDE_DIRS} ${EIGEN3_INCLUDE_DIRS} ${GSL_INCLUDE_PATH})
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if(YORICK_SUPPORT)
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include_directories(${NETCDF_INCLUDE_PATH})
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endif(YORICK_SUPPORT)
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include_directories(${CMAKE_SOURCE_DIR}/sample)
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IF(SHARP_INCLUDE_PATH)
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@ -63,8 +65,10 @@ if (FFTW3_FOUND AND FFTW3F_FOUND AND EIGEN3_FOUND)
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IF (FFTW3_LIBRARY_FULL)
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SET(FFTW3_LIB ${FFTW3_LIB} ${FFTW3_LIBRARY_FULL})
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ENDIF (FFTW3_LIBRARY_FULL)
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add_executable(test_fft_calls test_fft_calls.cpp)
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target_link_libraries(test_fft_calls ${tolink} ${FFTW3_LIB})
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IF(YORICK_SUPPORT)
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add_executable(test_fft_calls test_fft_calls.cpp)
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target_link_libraries(test_fft_calls ${tolink} ${FFTW3_LIB})
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ENDIF(YORICK_SUPPORT)
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endif (FFTW3_FOUND AND FFTW3F_FOUND AND EIGEN3_FOUND)
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if (ENABLE_SHARP AND SHARP_LIBRARY AND SHARP_INCLUDE_PATH AND EIGEN3_FOUND)
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@ -81,15 +85,17 @@ target_link_libraries(test_cosmopower ${tolink})
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if (Boost_FOUND)
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include_directories(${Boost_INCLUDE_DIRS})
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add_executable(testSmooth testSmooth.cpp)
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target_link_libraries(testSmooth ${tolink})
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IF (YORICK_SUPPORT)
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add_executable(testSmooth testSmooth.cpp)
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target_link_libraries(testSmooth ${tolink})
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add_executable(simple3DFilter simple3DFilter.cpp)
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target_link_libraries(simple3DFilter ${tolink})
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add_executable(simple3DFilter simple3DFilter.cpp)
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target_link_libraries(simple3DFilter ${tolink})
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ENDIF (YORICK_SUPPORT)
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endif (Boost_FOUND)
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IF (ENABLE_OPENMP)
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IF (ENABLE_OPENMP AND YORICK_SUPPORT)
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add_executable(gadgetToDensity gadgetToDensity.cpp)
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target_link_libraries(gadgetToDensity ${tolink})
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ENDIF (ENABLE_OPENMP)
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ENDIF (ENABLE_OPENMP AND YORICK_SUPPORT)
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@ -15,13 +15,15 @@ SET(CosmoTool_SRCS
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IF (ENABLE_OPENMP)
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ENDIF (ENABLE_OPENMP)
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IF(FOUND_NETCDF3)
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IF (YORICK_SUPPORT)
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IF(FOUND_NETCDF3)
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SET(CosmoTool_SRCS ${CosmoTool_SRCS} yorick_nc3.cpp)
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ELSE(FOUND_NETCDF3)
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IF(FOUND_NETCDF4)
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ELSE(FOUND_NETCDF3)
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IF(FOUND_NETCDF4)
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SET(CosmoTool_SRCS ${CosmoTool_SRCS} yorick_nc4.cpp)
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ENDIF(FOUND_NETCDF4)
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ENDIF(FOUND_NETCDF3)
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ENDIF(FOUND_NETCDF4)
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ENDIF(FOUND_NETCDF3)
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ENDIF(YORICK_SUPPORT)
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if (HDF5_FOUND)
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@ -59,9 +61,13 @@ SET(CosmoTool_SRCS ${CosmoTool_SRCS}
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growthFactor.hpp
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)
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include_directories(${GSL_INCLUDE_PATH} ${NETCDF_INCLUDE_PATH} ${NETCDFCPP_INCLUDE_PATH} ${CMAKE_BINARY_DIR}/src)
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include_directories(${Boost_INCLUDE_DIRS} ${GSL_INCLUDE_PATH} ${CMAKE_BINARY_DIR}/src)
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set(CosmoTool_LIBS ${NETCDFCPP_LIBRARY} ${NETCDF_LIBRARY} ${GSL_LIBRARIES})
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set(CosmoTool_LIBS ${GSL_LIBRARIES})
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if(YORICK_SUPPORT)
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set(CosmoTool_LIBS ${CosmoTool_LIBS} ${NETCDFCPP_LIBRARY} ${NETCDF_LIBRARY} ${GSL_LIBRARIES})
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include_directories(${NETCDF_INCLUDE_PATH} ${NETCDFCPP_INCLUDE_PATH})
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endif(YORICK_SUPPORT)
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if (HDF5_FOUND)
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set(CosmoTool_LIBS ${CosmoTool_LIBS} ${HDF5_CXX_LIBRARIES} ${HDF5_LIBRARIES})
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include_directories(${HDF5_INCLUDE_DIRS})
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@ -90,10 +90,31 @@ namespace CosmoTool {
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#undef HDF5_TYPE
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// Extent generator
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template<std::size_t r>
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struct hdf5_extent_gen {
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typedef typename boost::detail::multi_array::extent_gen<r> type;
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static inline type build(hsize_t *d)
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{
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return (hdf5_extent_gen<r-1>::build(d))[d[r-1]];
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}
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};
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template<>
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struct hdf5_extent_gen<0> {
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static inline boost::multi_array_types::extent_gen build(hsize_t *d)
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{
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return boost::extents;
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}
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};
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//!_______________________________________________________________________________________
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//!
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//! write_hdf5 multi_array
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//!
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//! \author Guilhem Lavaux (2014-2015)
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//! \author leo Goodstadt (04 March 2013)
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//!
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//!_______________________________________________________________________________________
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@ -216,24 +237,11 @@ namespace CosmoTool {
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class InvalidDimensions: virtual std::exception {
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};
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template<std::size_t r>
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struct hdf5_extent_gen {
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typedef typename boost::detail::multi_array::extent_gen<r> type;
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static inline type build(hsize_t *d)
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{
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return (hdf5_extent_gen<r-1>::build(d))[d[r-1]];
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}
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};
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template<>
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struct hdf5_extent_gen<0> {
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static inline boost::multi_array_types::extent_gen build(hsize_t *d)
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{
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return boost::extents;
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}
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};
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// ----------------------------------------------------------------------
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// Conditional resize support
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// If the Array type support resize then it is called. Otherwise
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// the dimensions are checked and lead to a failure if they are different
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template<typename Array> class array_has_resize {
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struct Fallback { int resize; };
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@ -282,11 +290,13 @@ namespace CosmoTool {
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hdf5_resize_array(ArrayType& data, std::vector<hsize_t>& dims) {
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hdf5_check_array(data, dims);
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}
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// ----------------------------------------------------------------------
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template<typename ArrayType, typename hdf5_data_type>
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void hdf5_read_array_typed(H5::CommonFG& fg, const std::string& data_set_name,
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ArrayType& data,
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const hdf5_data_type& datatype, bool auto_resize = true)
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ArrayType& data,
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const hdf5_data_type& datatype, bool auto_resize = true)
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{
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H5::DataSet dataset = fg.openDataSet(data_set_name);
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H5::DataSpace dataspace = dataset.getSpace();
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@ -311,8 +321,7 @@ namespace CosmoTool {
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{
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typedef typename ArrayType::element T;
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get_hdf5_data_type<T> hdf_data_type;
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hdf5_read_array_typed(fg, data_set_name, data, hdf_data_type.type(), auto_resize);
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hdf5_read_array_typed(fg, data_set_name, data, get_hdf5_data_type<T>::type(), auto_resize);
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}
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