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Hdf5Reader supporting reading into frame, ndarray and generic bytestream

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This commit is contained in:
mazzol_a
2025-05-26 09:06:47 +02:00
parent 6328369ce9
commit b94be4cbe8
5 changed files with 456 additions and 26 deletions
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26
CMakeLists.txt
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@ -62,6 +62,7 @@ option(AARE_FETCH_CATCH "Use FetchContent to download catch2" ON)
option(AARE_FETCH_JSON "Use FetchContent to download nlohmann::json" ON)
option(AARE_FETCH_ZMQ "Use FetchContent to download libzmq" ON)
option(AARE_FETCH_LMFIT "Use FetchContent to download lmfit" ON)
option(AARE_FETCH_HDF5 "Use FetchContent to download hdf5-devel" OFF)
#Convenience option to use system libraries only (no FetchContent)
@ -73,6 +74,7 @@ if(AARE_SYSTEM_LIBRARIES)
set(AARE_FETCH_CATCH OFF CACHE BOOL "Disabled FetchContent for catch2" FORCE)
set(AARE_FETCH_JSON OFF CACHE BOOL "Disabled FetchContent for nlohmann::json" FORCE)
set(AARE_FETCH_ZMQ OFF CACHE BOOL "Disabled FetchContent for libzmq" FORCE)
set(AARE_FETCH_HDF5 OFF CACHE BOOL "Disabled FetchContent for hdf5" FORCE)
# Still fetch lmfit when setting AARE_SYSTEM_LIBRARIES since this is not available
# on conda-forge
endif()
@ -219,6 +221,23 @@ else()
find_package(nlohmann_json 3.11.3 REQUIRED)
endif()
if(AARE_FETCH_HDF5)
message(FATAL_ERROR "Fetching HDF5 via FetchContent is not supported here. Please install it via your system.
For Ubuntu: sudo apt install libhdf5-dev
For Red Hat: sudo dnf install hdf5-devel
For MacOS: brew install hdf5")
else()
find_package(HDF5 QUIET COMPONENTS CXX)
if (HDF5_FOUND)
message(STATUS "Found HDF5: ${HDF5_INCLUDE_DIRS}")
else()
message(FATAL_ERROR "HDF5 was NOT found! Please install it via your system
For Ubuntu: sudo apt install libhdf5-dev
For Red Hat: sudo dnf install hdf5-devel
For MacOS: brew install hdf5")
endif()
endif()
include(GNUInstallDirs)
# If conda build, always set lib dir to 'lib'
@ -331,10 +350,6 @@ if(AARE_ASAN)
)
endif()
if(AARE_TESTS)
enable_testing()
add_subdirectory(tests)
@ -362,6 +377,7 @@ set(PUBLICHEADERS
include/aare/Frame.hpp
include/aare/GainMap.hpp
include/aare/geo_helpers.hpp
include/aare/Hdf5FileReader.hpp
include/aare/JungfrauDataFile.hpp
include/aare/NDArray.hpp
include/aare/NDView.hpp
@ -414,6 +430,7 @@ target_link_libraries(
PUBLIC
fmt::fmt
nlohmann_json::nlohmann_json
HDF5::HDF5
${STD_FS_LIB} # from helpers.cmake
PRIVATE
aare_compiler_flags
@ -441,6 +458,7 @@ if(AARE_TESTS)
${CMAKE_CURRENT_SOURCE_DIR}/src/Frame.test.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/geo_helpers.test.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/RawMasterFile.test.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/Hdf5FileReader.test.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/NDArray.test.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/NDView.test.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/ClusterFinder.test.cpp