UCL · KrisThielemans · Feb 6, 2025 · Sep 30, 2024 · Sep 30, 2024 · Feb 4, 2025
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -30,7 +30,6 @@ option(BUILD_SHARED_LIBS
 if (LLN_FOUND)
   set(HAVE_ECAT ON)
   message(STATUS "ECAT support enabled.")
-  include_directories(${LLN_INCLUDE_DIRS})
 else()
   message(STATUS "ECAT support disabled.")
 endif()
@@ -52,7 +51,6 @@ endif()
 if ((NOT DISABLE_HDF5) AND HDF5_FOUND)
   set(HAVE_HDF5 ON)
   message(STATUS "HDF5 support enabled.")
-  include_directories(${HDF5_INCLUDE_DIRS})
 else()
   message(STATUS "HDF5 support disabled.")
 endif()
@@ -120,7 +118,6 @@ endif()
 
 if (STIR_MPI)
   find_package(MPI REQUIRED)
-  include_directories(${MPI_CXX_INCLUDE_PATH})  
   # we add MPI_CXX_COMPILE_FLAGS for all files
   add_definitions(${MPI_CXX_COMPILE_FLAGS} -DMPICH_IGNORE_CXX_SEEK)
   # However, currently we decide to add  MPI_CXX_LINK_FLAGS only to those programs that need it,

diff --git a/src/IO/CMakeLists.txt b/src/IO/CMakeLists.txt
@@ -77,6 +77,7 @@ endif()
 include(stir_lib_target)
 
 if (LLN_FOUND)
+  target_include_directories(IO PUBLIC ${LLN_INCLUDE_DIRS})
   target_link_libraries(IO PUBLIC ${LLN_LIBRARIES})
 endif()
 
@@ -90,6 +91,7 @@ if (CERN_ROOT_FOUND)
 endif()
 
 if (HAVE_HDF5)
+  target_include_directories(IO PUBLIC ${HDF5_INCLUDE_DIRS})
   target_link_libraries(IO PUBLIC ${HDF5_CXX_LIBRARIES})
 endif()
 

diff --git a/src/buildblock/CMakeLists.txt b/src/buildblock/CMakeLists.txt
@@ -135,9 +135,9 @@ if (LLN_FOUND)
   target_link_libraries(buildblock PUBLIC ${LLN_LIBRARIES})
 endif()
 
-if (RDF_FOUND)
-  # TODO cannot do this as it creates circular dependencies
-  # target_link_libraries(buildblock PUBLIC local_IO_GE)
+if (HAVE_HDF5)
+  # for GEHDF5, TODO remove once IO dependency added or GEHDF5Wrapper no longer includes H5Cpp.h
+  target_include_directories(buildblock PRIVATE ${HDF5_INCLUDE_DIRS})
 endif()
 
 # TODO currently needed as filters need fourier

diff --git a/src/cmake/STIRConfig.cmake.in b/src/cmake/STIRConfig.cmake.in
@@ -102,17 +102,13 @@ if (@HDF5_FOUND@)
     find_package(HDF5 @HDF5_VERSION@ QUIET COMPONENTS C CXX)
   endif()
   find_package(HDF5 @HDF5_VERSION@ REQUIRED COMPONENTS CXX )
-  include_directories(${HDF5_INCLUDE_DIRS})
 
   set(STIR_BUILT_WITH_HDF5 TRUE)
 endif()
 
 if (@LLN_FOUND@)
   set(HAVE_ECAT ON)
   message(STATUS "ECAT support in STIR enabled.")
-  # need to add this as stir_ecat7.h etc rely on it
-  # would be better to add it to STIR_INCLUDE_DIRS (TODO)
-  include_directories("@LLN_INCLUDE_DIRS@")
   set(STIR_BUILT_WITH_LLN_MATRIX TRUE)
 endif()
 

diff --git a/src/data_buildblock/CMakeLists.txt b/src/data_buildblock/CMakeLists.txt
@@ -36,3 +36,8 @@ endif()
 include(stir_lib_target)
 
 target_link_libraries(${dir} PUBLIC buildblock)
+
+if (HAVE_HDF5)
+  # for GEHDF5, TODO remove once IO dependency added or GEHDF5Wrapper no longer includes H5Cpp.h
+  target_include_directories(data_buildblock PRIVATE ${HDF5_INCLUDE_DIRS})
+endif()
diff --git a/src/display/CMakeLists.txt b/src/display/CMakeLists.txt
@@ -45,7 +45,7 @@ include(stir_lib_target)
 
 if( "${GRAPHICS}" STREQUAL "X")
 	find_package(Curses REQUIRED)
-	INCLUDE_DIRECTORIES(${X11_INCLUDE_DIR} ${CURSES_INCLUDE_DIR})
+	target_include_directories(${dir} PRIVATE ${X11_INCLUDE_DIR} ${CURSES_INCLUDE_DIR})
 	target_link_libraries(${dir} PUBLIC ${X11_LIBRARIES} ${CURSES_LIBRARY})
 endif()
 

diff --git a/src/include/stir/recon_buildblock/BinNormalisationFromGEHDF5.h b/src/include/stir/recon_buildblock/BinNormalisationFromGEHDF5.h
@@ -31,7 +31,6 @@
 #include "stir/data/SinglesRates.h"
 #include "stir/Scanner.h"
 #include "stir/Array.h"
-#include "stir/IO/GEHDF5Wrapper.h"
 #include <string>
 
 using std::string;
@@ -45,6 +44,8 @@ namespace GE
 namespace RDF_HDF5
 {
 
+class GEHDF5Wrapper;
+
 /*!
   \ingroup recon_buildblock
   \ingroup GE
@@ -135,7 +136,6 @@ class BinNormalisationFromGEHDF5
 
   string normalisation_GEHDF5_filename;
   shared_ptr<GEHDF5Wrapper> m_input_hdf5_sptr;
-  GEHDF5Wrapper h5data;
 };
 
 } // namespace RDF_HDF5

diff --git a/src/listmode_buildblock/CMakeLists.txt b/src/listmode_buildblock/CMakeLists.txt
@@ -58,3 +58,8 @@ endif()
 include(stir_lib_target)
 
 target_link_libraries(listmode_buildblock PUBLIC data_buildblock )
+
+if (HAVE_HDF5)
+  # for GEHDF5, TODO remove once IO dependency added or GEHDF5Wrapper no longer includes H5Cpp.h
+  target_include_directories(listmode_buildblock PRIVATE ${HDF5_INCLUDE_DIRS})
+endif()
diff --git a/src/recon_buildblock/BinNormalisationFromGEHDF5.cxx b/src/recon_buildblock/BinNormalisationFromGEHDF5.cxx
@@ -26,6 +26,7 @@
 */
 
 #include "stir/recon_buildblock/BinNormalisationFromGEHDF5.h"
+#include "stir/IO/GEHDF5Wrapper.h"
 #include "stir/DetectionPosition.h"
 #include "stir/DetectionPositionPair.h"
 #include "stir/shared_ptr.h"

diff --git a/src/recon_buildblock/CMakeLists.txt b/src/recon_buildblock/CMakeLists.txt
@@ -135,6 +135,7 @@ endif()
 include(stir_lib_target)
 
 if (STIR_MPI)
+  target_include_directories(recon_buildblock ${MPI_CXX_INCLUDE_PATH})
   target_link_libraries(recon_buildblock PUBLIC ${MPI_CXX_LIBRARIES})
 endif()
 
@@ -160,6 +161,11 @@ if (STIR_WITH_Parallelproj_PROJECTOR)
   endif()
 endif()
 
+if (HAVE_HDF5)
+  # for GEHDF5, TODO remove once IO dependency added or GEHDF5Wrapper no longer includes H5Cpp.h
+  target_include_directories(recon_buildblock PRIVATE ${HDF5_INCLUDE_DIRS})
+endif()
+
 if (STIR_WITH_CUDA)
   target_link_libraries(recon_buildblock PRIVATE CUDA::cudart)
 endif()
diff --git a/src/swig/CMakeLists.txt b/src/swig/CMakeLists.txt
@@ -211,7 +211,7 @@ if (BUILD_SWIG_MATLAB)
 
   SWIG_LINK_LIBRARIES(stirMATLAB PUBLIC ${STIR_LIBRARIES}  ${Matlab_LIBRARIES})
 
-  include_directories(${Matlab_INCLUDE_DIRS})
+  target_include_directories(${SWIG_MODULE_stirMATLAB_REAL_NAME} PUBLIC ${Matlab_INCLUDE_DIRS})
   # disabled, as currently set via add_definitions in main CMakeLists.txt
   #SET_SOURCE_FILES_PROPERTIES( ${swig_generated_file_fullname}
   #      PROPERTIES COMPILE_FLAGS "${MATLAB_CXXFLAGS}")