add first python bindings

fix mismatch Origin - Position

.clangd

@@ -0,0 +1,52 @@
+CompileFlags:
+  CompilationDatabase: build
+  Add: 
+    - -I/home/rigoni/devel/cmt/ulib/src
+    - -isystem/home/share/micromamba/envs/mutom/include
+    - -isystem/home/share/micromamba/envs/mutom/include/eigen3
+    - -isystem/home/share/micromamba/envs/mutom/targets/x86_64-linux/include
+    - -isystem/home/share/micromamba/envs/mutom/lib/gcc/x86_64-conda-linux-gnu/14.3.0/include/c++
+    - -isystem/isystem/home/share/micromamba/envs/mutom/lib/gcc/x86_64-conda-linux-gnu/14.3.0/include/c++/x86_64-conda-linux-gnu
+    - -isystem/home/share/micromamba/envs/mutom/x86_64-conda-linux-gnu/sysroot/usr/include
+    - "--gcc-toolchain=/home/share/micromamba/envs/mutom"
+    - -D_ULIB_DETAIL_SIGNAL_EMIT
+    - -DUSE_CUDA
+    - -std=c++17
+    - "-D__host__="
+    - "-D__device__="
+    - "-D__global__="
+    - "-D__constant__="
+    - "-D__shared__="
+    - "-D__align__(x)="
+    - "-D__forceinline__=inline"
+    - "-D__launch_bounds__(x)="
+
+Diagnostics:
+  UnusedIncludes: None
+  MissingIncludes: None
+
+---
+If:
+  PathExclude: [/home/rigoni/devel/cmt/ulib/src/.*]
+Diagnostics:
+  Suppress: ["*"]
+
+---
+If:
+  PathMatch: [.*\.cu, .*/src/Math/testing/VoxRaytracerTest.cpp, .*/src/Math/VoxRaytracer.cpp, .*/src/Math/VoxImage.cpp]
+CompileFlags:
+  Add: 
+    - "-x"
+    - "cuda"
+    - "--cuda-path=/home/share/micromamba/envs/mutom"
+    - "--cuda-gpu-arch=sm_61"
+    - "--gcc-toolchain=/home/share/micromamba/envs/mutom"
+    - "-L/home/share/micromamba/envs/mutom/lib"
+    - "-lcudart"
+    - "-lcuda"
+    - "-U__host__"
+    - "-U__device__"
+    - "-U__global__"
+    - "-U__constant__"
+    - "-U__shared__"
+    - "-U__forceinline__"

.gitignore

@@ -0,0 +1,7 @@
+CMakeFiles/
+build/
+.cache/
+build_warnings*.log
+final_build.log
+cmake_configure.log
+compile_commands.json

.vscode/settings.json

@@ -0,0 +1,32 @@
+{
+    "clangd.fallbackFlags": [
+        "-I/home/rigoni/devel/cmt/ulib/src",
+        "-isystem/home/share/micromamba/envs/mutom/include",
+        "-isystem/home/share/micromamba/envs/mutom/include/eigen3",
+        "-isystem/home/share/micromamba/envs/mutom/targets/x86_64-linux/include",
+        "-isystem/home/share/micromamba/envs/mutom/lib/gcc/x86_64-conda-linux-gnu/14.3.0/include/c++",
+        "-isystem/home/share/micromamba/envs/mutom/lib/gcc/x86_64-conda-linux-gnu/14.3.0/include/c++/x86_64-conda-linux-gnu",
+        "-isystem/home/share/micromamba/envs/mutom/x86_64-conda-linux-gnu/sysroot/usr/include",
+        "--gcc-toolchain=/home/share/micromamba/envs/mutom",
+        "-D__host__=",
+        "-D__device__=",
+        "-D__global__=",
+        "-D__constant__=",
+        "-D__shared__=",
+        "-DUSE_CUDA",
+        "-D__CUDACC__"
+    ],
+    "clangd.semanticHighlighting.enable": true,
+    "clangd.arguments": [
+        "--compile-commands-dir=build",
+        "--query-driver=/home/share/micromamba/envs/mutom/bin/g++,/home/share/micromamba/envs/mutom/bin/gcc,/home/share/micromamba/envs/mutom/bin/nvcc",
+        "--suppress-system-warnings",
+        "--all-scopes-completion",
+        "--completion-style=detailed",
+        "--header-insertion=never",
+        "-j=4",
+        "--pch-storage=memory",
+        "--background-index",
+        "--log=verbose"
+    ]
+}

CMake/uLibCommon.cmake

@@ -15,16 +15,16 @@ set(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin CACHE PATH "build path for
 mark_as_advanced(EXECUTABLE_OUTPUT_PATH)
 
 ## Install directories ##
-set(PACKAGE_INSTALL_BIN_DIR bin CACHE PATH "Installation directory for executables")
-set(PACKAGE_INSTALL_LIB_DIR lib/${PACKAGE_NAME} CACHE PATH "Installation directory for libraries")
-set(PACKAGE_INSTALL_INC_DIR include/${PACKAGE_NAME} CACHE PATH "Installation directory for headers")
-set(PACKAGE_INSTALL_DATA_DIR share/${PACKAGE_NAME} CACHE PATH "Installation directory for data files")
+set(INSTALL_BIN_DIR bin CACHE PATH "Installation directory for executables")
+set(INSTALL_LIB_DIR lib/${PACKAGE_NAME} CACHE PATH "Installation directory for libraries")
+set(INSTALL_INC_DIR include/${PACKAGE_NAME} CACHE PATH "Installation directory for headers")
+set(INSTALL_DATA_DIR share/${PACKAGE_NAME} CACHE PATH "Installation directory for data files")
 if(WIN32 AND NOT CYGWIN)
  set(DEF_INSTALL_CMAKE_DIR CMake)
 else()
  set(DEF_INSTALL_CMAKE_DIR lib/cmake/${PACKAGE_NAME})
 endif()
-set(PACKAGE_INSTALL_CMAKE_DIR ${DEF_INSTALL_CMAKE_DIR} CACHE PATH "Installation directory for CMake files")
+set(INSTALL_CMAKE_DIR ${DEF_INSTALL_CMAKE_DIR} CACHE PATH "Installation directory for CMake files")
 
 # Make relative paths absolute (needed later on)
 foreach(p LIB BIN INC DATA CMAKE)
@@ -58,7 +58,7 @@ endif()
 set(CMAKE_CXX_WARNING_OPTION "" CACHE STRING "Warning level -WAll to verbose all warnings")
 set(CMAKE_VERBOSE_MAKEFILE FALSE CACHE STRING "Verbose compile output switch")
 
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++0x ${CMAKE_CXX_WARNING_OPTION}")
+# set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++0x ${CMAKE_CXX_WARNING_OPTION}")
 
 
 

CMake/uLibConfigHeader.cmake

@@ -16,12 +16,6 @@ set(BOOST_PP_VARIADICS ON)
 message(STATUS "PROJECT NAME = ${PROJECT_NAME}")
 message(STATUS "PACKAGE VERSION = ${PACKAGE_VERSION}")
 message(STATUS "PACKAGE NAME = ${PACKAGE_NAME}")
-execute_process(COMMAND "svnversion"
-                WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
-                OUTPUT_VARIABLE SVN_REVISION
-                OUTPUT_STRIP_TRAILING_WHITESPACE )
-
-message(STATUS "SVN REVISION = ${SVN_REVISION}")
 
 CHECK_INCLUDE_FILES(inittypes.h HAVE_INITTYPES_H)
 CHECK_INCLUDE_FILES(stdbool.h HAVE_STDBOOL_H)

CMake/uLibFindDependencies.cmake

@@ -13,7 +13,7 @@ set(Boost_USE_STATIC_LIBS OFF)
 set(Boost_USE_MULTITHREADED ON)
 set(Boost_USE_STATIC_RUNTIME OFF)
 
-find_package(Boost 1.45.0 COMPONENTS serialization signals program_options REQUIRED)
+find_package(Boost 1.45.0 COMPONENTS program_options REQUIRED)
 if(Boost_FOUND)
  set(HAVE_BOOST true)
 endif(Boost_FOUND)
@@ -75,36 +75,36 @@ endif(ULIB_USE_VTK)
 
 
 ## GEANT ##
-option(ULIB_USE_GEANT4 "Activate use of GEANT Integration" ON)
-message(STATUS "## GEANT 4 ##")
-#include(FindGEANT4) # disabled using system finder
-find_package(Geant4)
-set(GEANT4_FOUND Geant4_DIR)
-if(GEANT4_FOUND AND ULIB_USE_GEANT4)
- message(STATUS "Looking for Geant4... - Geant4 found in ${Geant4_DIR}")
- set(HAVE_GEANT4 true)
- include_directories(${Geant4_INCLUDE_DIRS})         # Add -I type paths
- add_definitions(${Geant4_DEFINITIONS})              # Add -D type defs
- debug_package(Geant4)
-endif(GEANT4_FOUND AND ULIB_USE_GEANT4)
+#option(ULIB_USE_GEANT4 "Activate use of GEANT Integration" ON)
+#message(STATUS "## GEANT 4 ##")
+##include(FindGEANT4) # disabled using system finder
+#find_package(Geant4)
+#set(GEANT4_FOUND Geant4_DIR)
+#if(GEANT4_FOUND AND ULIB_USE_GEANT4)
+# message(STATUS "Looking for Geant4... - Geant4 found in ${Geant4_DIR}")
+# set(HAVE_GEANT4 true)
+# include_directories(${Geant4_INCLUDE_DIRS})         # Add -I type paths
+# add_definitions(${Geant4_DEFINITIONS})              # Add -D type defs
+# debug_package(Geant4)
+#endif(GEANT4_FOUND AND ULIB_USE_GEANT4)
 
 ## QT4 ##
-option(ULIB_USE_QT4 "Activate use of Qt Framework" ON)
-if(ULIB_USE_QT4)
- message(STATUS "## QT4 ##")
- find_package(Qt4)
-# include_directories(${Qt4_INCLUDE_DIRS})
-# debug(Qt4_INCLUDE_DIRS)
-endif(ULIB_USE_QT4)
+#option(ULIB_USE_QT4 "Activate use of Qt Framework" ON)
+#if(ULIB_USE_QT4)
+# message(STATUS "## QT4 ##")
+# find_package(Qt4)
+## include_directories(${Qt4_INCLUDE_DIRS})
+## debug(Qt4_INCLUDE_DIRS)
+#endif(ULIB_USE_QT4)
 
 ## QT5 ##
-option(ULIB_USE_QT5 "Activate use of Qt Framework" ON)
-if(ULIB_USE_QT5)
- message(STATUS "## QT5 ##")
- find_package(Qt5Widgets)
-# include_directories(${Qt5_INCLUDE_DIRS})
-# debug(Qt5_INCLUDE_DIRS)
-endif(ULIB_USE_QT5)
+#option(ULIB_USE_QT5 "Activate use of Qt Framework" ON)
+#if(ULIB_USE_QT5)
+# message(STATUS "## QT5 ##")
+# find_package(Qt5Widgets)
+## include_directories(${Qt5_INCLUDE_DIRS})
+## debug(Qt5_INCLUDE_DIRS)
+#endif(ULIB_USE_QT5)
 
 ## READLINE ##
 message(STATUS "## READLINE ##")

CMake/uLibGenerateDoc.cmake

@@ -0,0 +1,97 @@
+find_package(Doxygen)
+
+set(doxydirlist "")
+foreach(modname ${ULIB_SELECTED_MODULES})
+    set(doxydirlist "${CMAKE_CURRENT_SOURCE_DIR}/src/${modname} ${doxydirlist}")
+endforeach(modname)
+
+file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/doxygen.cfg
+     "PROJECT_NAME=${CMAKE_PROJECT_NAME}-${PACKAGE_VERSION}\n"
+     "OUTPUT_DIRECTORY=${CMAKE_CURRENT_BINARY_DIR}\n"
+     "CREATE_SUBDIRS=NO\n"
+     "OUTPUT_LANGUAGE=English\n"
+     "BRIEF_MEMBER_DESC=YES\n"
+     "REPEAT_BRIEF=YES\n"
+     "ALWAYS_DETAILED_SEC=NO\n"
+     "INLINE_INHERITED_MEMB=NO\n"
+     "STRIP_FROM_INC_PATH=${CMAKE_CURRENT_SOURCE_DIR}/src\n"
+     "FULL_PATH_NAMES=YES\n"
+     "STRIP_FROM_PATH=${CMAKE_CURRENT_SOURCE_DIR}/src\n"
+     "SHORT_NAMES=NO\n"
+     "MULTILINE_CPP_IS_BRIEF=NO\n"
+     "INHERIT_DOCS=YES\n"
+     "DISTRIBUTE_GROUP_DOC=NO\n"
+     "OPTIMIZE_OUTPUT_FOR_C=YES\n"
+     "SUBGROUPING=YES\n"
+     "EXTRACT_ALL=YES\n"
+     "EXTRACT_PRIVATE=NO\n"
+     "EXTRACT_STATIC=NO\n"
+     "EXTRACT_LOCAL_CLASSES=YES\n"
+     "EXTRACT_LOCAL_METHODS=NO\n"
+     "HIDE_UNDOC_MEMBERS=NO\n"
+     "HIDE_UNDOC_CLASSES=NO\n"
+     "HIDE_FRIEND_COMPOUNDS=NO\n"
+     "HIDE_IN_BODY_DOCS=NO\n"
+     "INTERNAL_DOCS=NO\n"
+     "CASE_SENSE_NAMES=NO\n"
+     "HIDE_SCOPE_NAMES=NO\n"
+     "SHOW_INCLUDE_FILES=YES\n"
+     "INLINE_INFO=YES\n"
+     "SORT_MEMBER_DOCS=YES\n"
+     "SORT_BRIEF_DOCS=NO\n"
+     "SORT_BY_SCOPE_NAME=NO\n"
+     "GENERATE_TODOLIST=YES\n"
+     "GENERATE_TESTLIST=YES\n"
+     "GENERATE_BUGLIST=YES\n"
+     "GENERATE_DEPRECATEDLIST=YES\n"
+     "MAX_INITIALIZER_LINES=30\n"
+     "SHOW_USED_FILES=YES\n"
+     "QUIET=YES\n"
+     "WARNINGS=NO\n"
+     "WARN_IF_UNDOCUMENTED=YES\n"
+     "WARN_IF_DOC_ERROR=YES\n"
+     "WARN_FORMAT=\"$file:$line: $text\"\n"
+     "INPUT=${doxydirlist}\n"
+     "FILE_PATTERNS=*.h *.hpp\n"
+     "ENABLE_PREPROCESSING=YES\n"
+     "MACRO_EXPANSION=YES\n"
+     "RECURSIVE=YES\n"
+     "EXCLUDE_SYMLINKS=NO\n"
+     "FILTER_SOURCE_FILES=NO\n"
+     "SOURCE_BROWSER=NO\n"
+     "INLINE_SOURCES=NO\n"
+     "STRIP_CODE_COMMENTS=YES\n"
+     "REFERENCED_BY_RELATION=YES\n"
+     "REFERENCES_RELATION=YES\n"
+     "VERBATIM_HEADERS=YES\n"
+     "ALPHABETICAL_INDEX=YES\n"
+     "COLS_IN_ALPHA_INDEX=5\n"
+     "GENERATE_HTML=YES\n"
+     "HTML_OUTPUT=html\n"
+     "HTML_FILE_EXTENSION=.html\n"
+     "GENERATE_HTMLHELP=NO\n"
+     "BINARY_TOC=NO\n"
+     "TOC_EXPAND=NO\n"
+     "DISABLE_INDEX=NO\n"
+     "ENUM_VALUES_PER_LINE=4\n"
+     "GENERATE_TREEVIEW=YES\n"
+     "TREEVIEW_WIDTH=250\n"
+     "GENERATE_LATEX=NO\n"
+     "GENERATE_RTF=NO\n"
+     "GENERATE_MAN=NO\n"
+     "GENERATE_XML=NO\n"
+     "GENERATE_AUTOGEN_DEF=NO\n"
+     "GENERATE_PERLMOD=NO\n")
+
+option(NODOXYGEN "Disable the creation of the API documentation")
+if(NODOXYGEN OR (NOT DOXYGEN_FOUND))
+    message("Doxygen is disabled or not installed")
+else(NODOXYGEN OR (NOT DOXYGEN_FOUND))
+    add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/html/index.html
+                       COMMAND doxygen ${CMAKE_CURRENT_BINARY_DIR}/doxygen.cfg)
+
+    add_custom_target(doxygen ALL DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/html/index.html)
+
+    install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/html
+            DESTINATION share/doc/${PACKAGE_NAME})
+endif(NODOXYGEN OR (NOT DOXYGEN_FOUND))

CMake/uLibTargetMacros.cmake

@@ -30,24 +30,26 @@ macro(uLib_add_shared_library name)
   set_target_properties(${mname} PROPERTIES
                         VERSION ${PROJECT_VERSION}
                         SOVERSION ${PROJECT_SOVERSION}
-                      INTERFACE_LINK_LIBRARIES "${LIBRARIES}"
-                      LINK_INTERFACE_LIBRARIES "${LIBRARIES}"          ## <- ok for cmake from  2.12 ?
-                      IMPORTED_LINK_INTERFACE_LIBRARIES "${LIBRARIES}" ## <- breaks cmake after 2.11 ?
+#                       INTERFACE_LINK_LIBRARIES "${LIBRARIES}"
+#                       LINK_INTERFACE_LIBRARIES "${LIBRARIES}"          ## <- ok for cmake from  2.12 ?
+#                       IMPORTED_LINK_INTERFACE_LIBRARIES "${LIBRARIES}" ## <- breaks cmake after 2.11 ?
 #                       PUBLIC_HEADER ""
   )
   debug(LIBRARIES)
 
+  target_link_libraries(${mname} ${LIBRARIES})
+
   install(TARGETS ${mname}
          EXPORT "${PROJECT_NAME}Targets"
-         RUNTIME DESTINATION ${PACKAGE_INSTALL_BIN_DIR} COMPONENT bin
-         LIBRARY DESTINATION ${PACKAGE_INSTALL_LIB_DIR} COMPONENT lib
-  #         PUBLIC_HEADER DESTINATION ${PACKAGE_INSTALL_INC_DIR} COMPONENT dev
+         RUNTIME DESTINATION ${INSTALL_BIN_DIR} COMPONENT bin
+         LIBRARY DESTINATION ${INSTALL_LIB_DIR} COMPONENT lib
+  #         PUBLIC_HEADER DESTINATION ${INSTALL_INC_DIR} COMPONENT dev
   )
  endif(SOURCES)
 
  if(HEADERS)
   foreach(header ${HEADERS})
-   install(FILES ${header} DESTINATION ${PACKAGE_INSTALL_INC_DIR}/${name})
+   install(FILES ${header} DESTINATION ${INSTALL_INC_DIR}/${name})
   endforeach(header)
   endif(HEADERS)
 
@@ -68,7 +70,7 @@ macro(uLib_add_target name)
 
     install(TARGETS ${name}
             EXPORT "${PROJECT_NAME}Targets"
-            RUNTIME DESTINATION ${PACKAGE_INSTALL_BIN_DIR} COMPONENT bin
+            RUNTIME DESTINATION ${INSTALL_BIN_DIR} COMPONENT bin
            )
 ENDMACRO(uLib_add_target)
 
@@ -80,24 +82,18 @@ ENDMACRO(uLib_add_target)
 # TESTS and LIBRARIES must be defined
 macro(uLib_add_tests name)
     foreach(tn ${TESTS})
-  add_executable(${tn} EXCLUDE_FROM_ALL ${tn}.cpp)
-  add_test(${tn} ${tn})
+        add_executable(${tn} ${tn}.cpp)
+        add_test(NAME ${tn} COMMAND ${tn})
 
-  # adds dependencies to all selected modules in uLib
-  #  foreach(module ${ULIB_SELECTED_MODULES})
-  #   add_dependencies(${tn} ${project_name}${module})
-  #  endforeach(module)
-
-  # adds libraries dependencies
-  foreach(library ${LIBRARIES})
-   target_link_libraries(${tn} ${library})
-  endforeach(library)
+        target_link_libraries(${tn} ${LIBRARIES})
 
     endforeach(tn)
 
     # custom target to compile all tests
     add_custom_target(all-${name}-tests)
+    if(TESTS)
         add_dependencies(all-${name}-tests ${TESTS})
+    endif()
 endmacro(uLib_add_tests name)
 
 

CMakeLists.txt

@@ -3,20 +3,35 @@
 ##### CMAKE LISTS ##############################################################
 ################################################################################
 
-cmake_minimum_required (VERSION 2.6)
+cmake_minimum_required (VERSION 3.26)
+if(POLICY CMP0167)
+    cmake_policy(SET CMP0167 NEW)
+endif()
 
-execute_process(COMMAND "clear")
-message("//////////////////////////////////////////////////////////////////////")
-message("/////////////////// CMAKE PJOJECT CONFIGURATION //////////////////////")
-message("//////////////////////////////////////////////////////////////////////")
 
 ## -------------------------------------------------------------------------- ##
 
 project(uLib)
 
+# CUDA Toolkit seems to be missing locally. Toggle ON if nvcc is made available.
+option(USE_CUDA "Enable CUDA support" ON)
+if(USE_CUDA)
+    set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -allow-unsupported-compiler")
+    set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} --expt-relaxed-constexpr")
+    set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -Wno-deprecated-gpu-targets")
+    set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -Xcudafe \"--diag_suppress=20012\"")
+    set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -Xcudafe \"--diag_suppress=20014\"")
+    set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -Xcudafe \"--diag_suppress=20015\"")
+    find_package(CUDAToolkit REQUIRED)
+    enable_language(CUDA)
+    set(CMAKE_CUDA_ARCHITECTURES 61)
+    include_directories(${CMAKE_CUDA_TOOLKIT_INCLUDE_DIRECTORIES})
+    add_compile_definitions(USE_CUDA)
+endif()
+
 # The version number.
 set(PROJECT_VERSION_MAJOR 0)
-set(PROJECT_VERSION_MINOR 2)
+set(PROJECT_VERSION_MINOR 6)
 set(PROJECT_VERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}")
 set(PROJECT_SOVERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}")
 
@@ -31,207 +46,250 @@ set(PACKAGE_AUTHOR "Andrea Rigoni Garola <andrea.rigoni@pd.infn.it>")
 
 set(ULIB_CMAKE_DIR "${PROJECT_SOURCE_DIR}/CMake")
 set(CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/CMake" ${CMAKE_MODULE_PATH})
-message(STATUS "Module path: ${CMAKE_MODULE_PATH}")
-
-include(uLibMacros)
-include(uLibDebugMacro)
-include(uLibTargetMacros)
-include(uLibGenerateRMake)
-
-
+message(STATUS "Project name = ${PROJECT_NAME}")
+message(STATUS "Package name = ${PACKAGE_NAME}")
+message(STATUS "Package version = ${PACKAGE_VERSION}")
+message(STATUS "Module path = ${CMAKE_MODULE_PATH}")
 
 ## GLOBALS ------------------------------------------------------------------ ##
 
-include(uLibCommon)
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ") ## Add flags here ##
+# -- move to GnuInstallDirs
+# ref: https://cmake.org/cmake/help/latest/module/GNUInstallDirs.html
+include(GNUInstallDirs)
+set(INSTALL_INC_DIR ${CMAKE_INSTALL_INCLUDEDIR}/${PACKAGE_NAME}
+    CACHE PATH "Location of header files (.../include)" )
+set(INSTALL_ETC_DIR ${CMAKE_INSTALL_SYSCONFDIR}/${PACKAGE_NAME}
+    CACHE PATH "Location of configuration files (.../etc)" )
+set(INSTALL_BIN_DIR ${CMAKE_INSTALL_BINDIR}/${PACKAGE_NAME}
+    CACHE PATH "Location of executable files (.../bin)" )
+set(INSTALL_LIB_DIR ${CMAKE_INSTALL_LIBDIR}
+    CACHE PATH "Location of library files (.../lib)" )
+set(INSTALL_CMAKE_DIR ${CMAKE_INSTALL_LIBDIR}/cmake/${PACKAGE_NAME}
+    CACHE PATH "Location of cmake files (.../lib/cmake)" )   
+set(INSTALL_DATA_DIR ${CMAKE_INSTALL_DATADIR}/${PACKAGE_NAME}
+    CACHE PATH "Location of data files (.../share)" )
 
+
+
+
+set(SRC_DIR ${PROJECT_SOURCE_DIR}/src)
+
+# this is used to be exported in build target 
+# ( to compile against build directory instead of install )
+set(ULIB_SOURCE_DIR ${PROJECT_SOURCE_DIR})
+
+if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+    message(STATUS "Setting build type to 'Release' as none was specified.")
+    set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose the type of build." FORCE)
+    set(CMAKE_EXE_LINKER_FLAGS "-Wl,--no-as-needed")
+    # Set the possible values of build type for cmake-gui
+    set_property(CACHE CMAKE_BUILD_TYPE PROPERTY 
+               STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
+endif()
+
+set(CMAKE_CXX_WARNING_OPTION "" 
+    CACHE STRING "Warning level -WAll to verbose all warnings")
+set(CMAKE_VERBOSE_MAKEFILE FALSE
+    CACHE STRING "Verbose compile output switch")
+
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_WARNING_OPTION}")
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -UULIB_SERIALIZATION_ON -Wno-cpp")
+
+# CTEST framework
+include(CTest)
 enable_testing()
 
+
 ## FIND PACKAGES ------------------------------------------------------------ ##
 
-include(uLibFindDependencies)
+set(Boost_USE_STATIC_LIBS OFF)
+set(Boost_USE_MULTITHREADED ON)
+set(Boost_USE_STATIC_RUNTIME OFF)
+message(STATUS "CMAKE_PREFIX_PATH is ${CMAKE_PREFIX_PATH}")
 
+find_package(Boost 1.45.0 COMPONENTS program_options serialization unit_test_framework REQUIRED)
+include_directories(${Boost_INCLUDE_DIRS})
+
+find_package(Eigen3 CONFIG REQUIRED)
+get_target_property(EIGEN3_INCLUDE_DIRS Eigen3::Eigen INTERFACE_INCLUDE_DIRECTORIES)
+include_directories(${EIGEN3_INCLUDE_DIRS})
+
+find_package(ROOT CONFIG REQUIRED)
+include(${ROOT_USE_FILE})
+
+find_package(VTK REQUIRED)
+# include(${VTK_USE_FILE})
+
+find_package(pybind11 REQUIRED)
+
+
+option(CENTOS_SUPPORT "VTK definitions for CentOS" OFF)
+if(CENTOS_SUPPORT)
+    find_package(VTK CONFIG REQUIRED)
+    include(${VTK_USE_FILE})
+else()
+    find_package(VTK REQUIRED
+                     COMPONENTS CommonColor
+                                CommonCore
+                                FiltersCore
+                                FiltersModeling
+                                FiltersSources
+                                IOLegacy
+                                IOXML
+                                IOXMLParser
+                                ImagingCore
+                                InteractionStyle
+                                InteractionWidgets
+                                RenderingAnnotation
+                                RenderingContextOpenGL2
+                                RenderingCore
+                                RenderingFreeType
+                                RenderingGL2PSOpenGL2
+                                RenderingOpenGL2
+                                RenderingVolumeOpenGL2)
+endif()
+
+set(CMAKE_REQUIRED_INCLUDES CMAKE_REQUIRED_INCLUDES math.h)
+set(CMAKE_REQUIRED_LIBRARIES CMAKE_REQUIRED_LIBRARIES m)
 
 ## CONFIG ------------------------------------------------------------------- ##
 
-include(uLibConfigHeader)
+set(BOOST_PP_VARIADICS ON)
+
+include(CheckIncludeFiles)
+include(CheckFunctionExists)
+include(CheckSymbolExists)
+
+CHECK_INCLUDE_FILES(inittypes.h HAVE_INITTYPES_H)
+CHECK_INCLUDE_FILES(stdbool.h HAVE_STDBOOL_H)
+CHECK_INCLUDE_FILES(stdint.h HAVE_STDINT_H)
+CHECK_INCLUDE_FILES(stdlib.h HAVE_STDLIB_H)
+CHECK_INCLUDE_FILES(dlfcn.h HAVE_DLFCN_H)
+CHECK_INCLUDE_FILES(malloc.h HAVE_MALLOC_H)
+CHECK_FUNCTION_EXISTS(malloc HAVE_MALLOC)
+CHECK_INCLUDE_FILES(memory.h HAVE_MEMORY_H)
+CHECK_INCLUDE_FILES(math.h HAVE_MATH_H)
+CHECK_FUNCTION_EXISTS(fsetround HAVE_FSETROUND)
+CHECK_FUNCTION_EXISTS(floor HAVE_FLOOR)
+CHECK_FUNCTION_EXISTS(pow HAVE_POW)
+CHECK_FUNCTION_EXISTS(sqrt HAVE_SQRT)
+CHECK_FUNCTION_EXISTS(strdup HAVE_STRDUP)
+CHECK_FUNCTION_EXISTS(strstr HAVE_STRSTR)
+CHECK_INCLUDE_FILES(strings.h HAVE_STRINGS_H)
+CHECK_INCLUDE_FILES(string.h HAVE_STRING_H)
+CHECK_INCLUDE_FILES(sys/stat.h HAVE_SYS_STAT_H)
+CHECK_INCLUDE_FILES(sys/types.h HAVE_SYS_TYPES_H)
+CHECK_INCLUDE_FILES(unistd.h HAVE_UNISTD_H)
+CHECK_INCLUDE_FILES(assert.h HAVE_ASSERT_H)
+
+configure_file("${PROJECT_SOURCE_DIR}/CMakeConfig.in.h"
+               "${PROJECT_BINARY_DIR}/config.h")
+
+install(FILES "${PROJECT_BINARY_DIR}/config.h"
+        DESTINATION ${INSTALL_INC_DIR})
 
 ## ADD LIBRARIES SUBDIRECTORIES --------------------------------------------- ##
 
-## select modules ##
-set(ULIB_SELECTED_MODULES
-      ltk
-      Core
-      Math
-      Detectors
-      Root
-)
+include_directories(${PROJECT_BINARY_DIR})
+include_directories(${SRC_DIR})
 
 ## uLib_add_shared_library puts names there
 set(ULIB_SHARED_LIBRARIES)
+## select modules ##
+set(ULIB_SELECTED_MODULES)
 
-if(ULIB_USE_VTK)
- LIST(APPEND ULIB_SELECTED_MODULES Vtk)
-endif(ULIB_USE_VTK)
+include_directories(${SRC_DIR}/Core)
+add_subdirectory(${SRC_DIR}/Core)
 
-## this gets ulib modules into a variable ##
-function(uLib_modules result)
- set(out)
- foreach(module ${ULIB_SELECTED_MODULES})
-  list(APPEND out ${PACKAGE_LIBPREFIX}${module})
- endforeach(module)
- set(${result} "${out}" PARENT_SCOPE)
-endfunction()
+include_directories(${SRC_DIR}/Math)
+add_subdirectory(${SRC_DIR}/Math)
 
+include_directories(${SRC_DIR}/Detectors)
+add_subdirectory(${SRC_DIR}/Detectors)
 
-## ENTERING MODULES SUBDIRECTORIES ##
-message("/////////// SELECTED MODULES //////////////")
-foreach(module ${ULIB_SELECTED_MODULES})
- message(STATUS "adding module: ${module}")
- set( uLib-module ${module})
- include_directories(${SRC_DIR}/${module})
- add_subdirectory(${SRC_DIR}/${module})
-endforeach(module)
+include_directories(${SRC_DIR}/Root)
+add_subdirectory(${SRC_DIR}/Root)
 
-## SINGLE LIBRARY LINKING ## (work in progress ... )
-option(ULIB_SINGLELIBRARY "Link everything to a single library" OFF)
-if(ULIB_SINGLELIBRARY) 
-# set(modgrp)
-# foreach(module ${ULIB_SELECTED_MODULES})
-#  set(grpn srcgrp_${module})
-#  list(APPEND modgrp ${grpn})
-# endforeach(module)
-# add_library(${project_name} SHARED ${srcgrp_Core})
-endif(ULIB_SINGLELIBRARY)
+include_directories(${SRC_DIR}/Vtk)
+add_subdirectory(${SRC_DIR}/Vtk)
+
+add_subdirectory(${SRC_DIR}/Python)
+
+#add_subdirectory("${SRC_DIR}/utils/make_recipe")
+
+## Documentation and packages
+
+#include(uLibGenerateDoc)
 
 ## UTILITIES ##
-add_subdirectory("${SRC_DIR}/utils/make_recipe")
-
-
-## PKG CONFIG compatible file ----------------------------------------------- ##
-
-set(PKGCONFIG_FILE_ENABLE OFF CACHE BOOL "enable pkg-config file")
-if(PKGCONFIG_FILE_ENABLE)
-message("/////////// PKG-CONFIG DISTILLER //////////////")
-set(PKGCONFIG_FILE_DESTDIR "/lib/pkgconfig/" CACHE PATH "destination path for pkg-config file")
-set(PKGCONFIG_LIBS)
-
-message(STATUS "[cflags] ${CMAKE_C_FLAGS}")
-message(STATUS "[cxxflags] ${CMAKE_CXX_FLAGS}")
-
-foreach(module ${ULIB_SHARED_LIBRARIES})
-set(PKGCONFIG_LIBS "${PKGCONFIG_LIBS} ${CMAKE_LINK_LIBRARY_FLAG}${module}")
-endforeach(module)
-message(STATUS "[libs] ${PKGCONFIG_LIBS}")
-
-set(PKGCONFIG_FLAGS)
-#add_custom_target(Dummy)
-
-# add the executable
-uLib_add_target(Dummy test.cpp)
-target_link_libraries(Dummy ${PACKAGE_LIBPREFIX}Core)
-target_link_libraries(Dummy ${Boost_SERIALIZATION_LIBRARY})
-target_link_libraries(Dummy ${Boost_SIGNALS_LIBRARY})
-target_link_libraries(Dummy ${Boost_PROGRAM_OPTIONS_LIBRARY})
-target_link_libraries(Dummy ${Geant4_LIBRARIES})
-target_link_libraries(Dummy ${ROOT_LIBRARIES})
-target_link_libraries(Dummy ${VTK_LIBRARIES})
-
-get_gcc_compile_flags(Dummy, gcc_flags_list)
-foreach(item ${gcc_flags_list})
- message(STATUS "[gcc cflags] ${item}")
- set(PKGCONFIG_FLAGS "${PKGCONFIG_FLAGS} ${item}")
-endforeach(item)
-message(STATUS "[includes] ${PKGCONFIG_FLAGS}")
-
-get_gcc_link_flags(Dummy, gcc_flags_list)
-foreach(item ${gcc_flags_list})
- message(STATUS "[gcc libs] ${item}")
-endforeach(item)
-
-configure_file(
-  "${PROJECT_SOURCE_DIR}/CMakePkgConfig.pc.in"
-  "${PROJECT_BINARY_DIR}/libmutom-${PACKAGE_VERSION}.pc"
-  )
-INSTALL_FILES(${PKGCONFIG_FILE_DESTDIR} FILES ${PROJECT_BINARY_DIR}/libmutom-${PACKAGE_VERSION}.pc)
-
-message("///////////////////////////////////////////")
-endif(PKGCONFIG_FILE_ENABLE)
-
-
-
+#add_subdirectory("${SRC_DIR}/utils/make_recipe")
 
 
 ## INSTALLS AND EXPORTS ----------------------------------------------------- ##
 
-#export(PACKAGE uLib)
-export(PACKAGE ULIB)
-export(TARGETS ${ULIB_SHARED_LIBRARIES} ${ULIB_EXPORTED_TARGETS}
-       FILE "${PROJECT_BINARY_DIR}/uLibTargets.cmake"    )
-#export(TARGETS ${ULIB_EXPORTED_TARGETS}
-#       FILE "${PROJECT_BINARY_DIR}/uLibExeTargets.cmake" )
+#export(PACKAGE ULIB)
+#export(TARGETS ${ULIB_SHARED_LIBRARIES} ${ULIB_EXPORTED_TARGETS}
+#       FILE "${PROJECT_BINARY_DIR}/uLibTargets.cmake"    )
 
 
 # Create the FooBarConfig.cmake and FooBarConfigVersion files
-file(RELATIVE_PATH REL_INCLUDE_DIR "${PACKAGE_INSTALL_CMAKE_DIR}"
-   "${PACKAGE_INSTALL_INC_DIR}")
+# file(RELATIVE_PATH REL_INCLUDE_DIR "${INSTALL_CMAKE_DIR}"
+#    "${INSTALL_INC_DIR}")
+
 # ... for the build tree
-set(CONF_INCLUDE_DIRS "${PROJECT_SOURCE_DIR}/src" "${PROJECT_BINARY_DIR}")
-configure_file(uLibConfig.cmake.in
-  "${PROJECT_BINARY_DIR}/uLibConfig.cmake" @ONLY)
+#set(CONF_INCLUDE_DIRS "${PROJECT_SOURCE_DIR}/src" "${PROJECT_BINARY_DIR}")
+#configure_file(uLibConfig.cmake.in 
+#               "${PROJECT_BINARY_DIR}/uLibConfig.cmake" @ONLY)
+
 # ... for the install tree
 set(CONF_INCLUDE_DIRS "\${ULIB_CMAKE_DIR}/${REL_INCLUDE_DIR}")
-configure_file(uLibConfig.cmake.in
-  "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/uLibConfig.cmake" @ONLY)
+# [ removed for the configure_config_file ]
+# configure_file(uLibConfig.cmake.in
+#                "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/uLibConfig.cmake"
+#                @ONLY)
+
 # ... for both
 configure_file(uLibConfigVersion.cmake.in
                 "${PROJECT_BINARY_DIR}/uLibConfigVersion.cmake" @ONLY)
 
-# Install the FooBarConfig.cmake and FooBarConfigVersion.cmake
-install(FILES
-  "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/uLibConfig.cmake"
-  "${PROJECT_BINARY_DIR}/uLibConfigVersion.cmake"
-  DESTINATION "${PACKAGE_INSTALL_CMAKE_DIR}" COMPONENT dev)
 
-# Install the export set for use with the install-tree
-install(EXPORT "${PROJECT_NAME}Targets" DESTINATION
-  "${PACKAGE_INSTALL_CMAKE_DIR}" COMPONENT dev)
-
-install(FILES ${PROJECT_SOURCE_DIR}/ulib.h DESTINATION ${PACKAGE_INSTALL_INC_DIR})
-
-
-
-## dummy main executable ---------------------------------------------------- ##
-
-message("Sara's debug....")
-message(${ROOT_LIBRARIES})
-
-# add the executable
-add_executable(Coretest test.cpp)
-target_link_libraries(Coretest ${PACKAGE_LIBPREFIX}Core)
-#target_link_libraries(Coretest ${Boost_SERIALIZATION_LIBRARY})
-#target_link_libraries(Coretest ${Boost_SIGNALS_LIBRARY})
-#target_link_libraries(Coretest ${Boost_PROGRAM_OPTIONS_LIBRARY})
-#target_link_libraries(Coretest ${Geant4_LIBRARIES})
-target_link_libraries(Coretest ${ROOT_LIBRARIES})
-target_link_libraries(Coretest ${VTK_LIBRARIES})
-
-#message( "---------------------------------------------------------------------" )
-#execute_process(COMMAND
-#                "ls"
-##                "cmake --find-package -DNAME=uLib -DLANGUAGE=C -DCOMPILER_ID=GNU -DMODE=COMPILE"
-#                )
-#message( "---------------------------------------------------------------------" )
-
-## -------------------------------------------------------------------------- ##
-
-
-# TODO clean also subdirectories
-add_custom_target(clean-cmake-files
-   COMMAND ${CMAKE_COMMAND} -P ${ULIB_CMAKE_DIR}/clean-all.cmake
+# from CMake 3.x configure file shall be created using a dedicated function
+# see: https://cmake.org/cmake/help/latest/module/CMakePackageConfigHelpers.html
+#
+include(CMakePackageConfigHelpers)
+configure_package_config_file(uLibConfig.cmake.in
+                              "${PROJECT_BINARY_DIR}/uLibConfig.cmake"
+                              INSTALL_DESTINATION ${INSTALL_CMAKE_DIR}
+                              PATH_VARS 
+                                INSTALL_LIB_DIR 
+                                INSTALL_INC_DIR 
+                                INSTALL_BIN_DIR 
+                                INSTALL_CMAKE_DIR 
+                                INSTALL_ETC_DIR 
+                                INSTALL_DATA_DIR
+                                ULIB_SOURCE_DIR
+                                ULIB_SHARED_LIBRARIES
+                              # NO_SET_AND_CHECK_MACRO
+                              # NO_CHECK_REQUIRED_COMPONENTS_MACRO
                               )
 
+install(FILES "${PROJECT_BINARY_DIR}/uLibConfig.cmake"
+              "${PROJECT_BINARY_DIR}/uLibConfigVersion.cmake"
+        DESTINATION "${INSTALL_CMAKE_DIR}"
+        COMPONENT dev)
 
 
+# this is a special target file for the build tree
+# it is used also to identify if we are using a build direcory
+# to link a project against uLib. see: uLibConfig.cmake ( IF )
+export (TARGETS ${ULIB_SHARED_LIBRARIES}
+        FILE "${PROJECT_BINARY_DIR}/uLibTargets-build.cmake"
+        # NAMESPACE "uLib::"
+)        
 
+# Install the export set for use with the install-tree
+install(EXPORT "uLibTargets"
+        FILE "uLibTargets.cmake"
+        DESTINATION "${INSTALL_CMAKE_DIR}"
+        COMPONENT dev)
 

CMakeUserPresets.json

@@ -0,0 +1,9 @@
+{
+    "version": 4,
+    "vendor": {
+        "conan": {}
+    },
+    "include": [
+        "build/CMakePresets.json"
+    ]
+}

Jenkinsfile

@@ -0,0 +1,35 @@
+pipeline {
+
+    agent {
+        docker {
+            image 'infnpd/cmt-environment:1.1-centos7'
+            args '-u 0:0'
+            label 'DOCKER'
+        }
+    }
+
+    environment {
+        NEXUS_PD_CREDS = credentials('jenkins-nexus-pd-creds')
+        NEXUS_PD_URL = 'https://cld-smact-02.pd.infn.it/artifacts/repository/muotom/devel/centos7/x86_64/'
+    }
+
+    stages {
+
+        stage('Build') {
+
+            steps {
+                sh "mkdir build && cd build && cmake -DNODOXYGEN=ON .. && make rpm"
+            }
+
+        }
+        stage('Deploy') {
+
+            steps {
+                sh "find . -name '*.x86_64.rpm' curl -v -k --user '${NEXUS_PD_CREDS_USR}:${NEXUS_PD_CREDS_PSW}' --upload-file '{}' ${NEXUS_PD_URL} ';'"
+            }
+
+        }
+
+    }
+
+}

README.md

@@ -0,0 +1,63 @@
+# uLib
+
+[![DOI](https://zenodo.org/badge/36926725.svg)](https://zenodo.org/badge/latestdoi/36926725)
+
+base toolkit library
+
+CMT Cosmic Muon Tomography reconstruction, analysis and imaging software
+Developed by University of Padova and INFN Sezione di Padova  Italy
+
+## Build Instructions
+
+This project relies on `conan` (v2) for dependency management (Eigen3, Boost) and `cmake` for configuration. VTK is provided through the micromamba/conda-forge environment.
+
+### Prerequisites
+
+This project requires a `conda` or `micromamba` environment containing the necessary global tools like **ROOT**, **VTK**, and **Conan** (v2). We provide a `condaenv.yml` file to quickly build this environment.
+
+#### Installing Micromamba (Optional)
+
+If you do not have `conda` installed, `micromamba` is a fast and lightweight alternative. You can install it on Linux via:
+
+```bash
+"${SHELL}" <(curl -L micro.mamba.pm/install.sh)
+```
+
+#### Creating the Environment
+
+You can create and activate the environment using either `micromamba` or `conda`.
+
+**Using Micromamba:**
+```bash
+micromamba env create -f condaenv.yml
+micromamba activate mutom
+```
+
+**Using Conda:**
+```bash
+conda env create -f condaenv.yml
+conda activate mutom
+```
+
+### Configure and Build
+
+1. **Configure Conan profile (if you haven't yet on your machine):**
+```bash
+conan profile detect
+```
+
+2. **Install Conan dependencies:**
+```bash
+conan install . --output-folder=build --build=missing
+```
+
+3. **Configure the project with CMake:**
+```bash
+cmake --preset conan-release
+```
+*(Alternatively: `cd build && cmake .. -DCMAKE_TOOLCHAIN_FILE=conan_toolchain.cmake -DCMAKE_BUILD_TYPE=Release`)*
+
+4. **Build the project:**
+```bash
+cmake --build build -j10
+```

build.log

@@ -0,0 +1,36 @@
+make: Entering directory '/home/rigoni/devel/cmt/ulib/build'
+[ 30%] Building CXX object src/Math/CMakeFiles/mutomMath.dir/VoxImage.cpp.o
+[ 30%] Building CXX object src/Math/CMakeFiles/mutomMath.dir/TriangleMesh.cpp.o
+[ 30%] Building CXX object src/Core/CMakeFiles/mutomCore.dir/Options.cpp.o
+[ 30%] Building CXX object src/Math/CMakeFiles/mutomMath.dir/Dense.cpp.o
+[ 30%] Building CXX object src/Math/CMakeFiles/mutomMath.dir/StructuredGrid.cpp.o
+[ 30%] Building CXX object src/Math/CMakeFiles/mutomMath.dir/VoxRaytracer.cpp.o
+[ 30%] Building CXX object src/Math/CMakeFiles/mutomMath.dir/StructuredData.cpp.o
+[ 30%] Building CXX object src/Math/CMakeFiles/mutomMath.dir/Structured2DGrid.cpp.o
+[ 30%] Building CXX object src/Math/CMakeFiles/mutomMath.dir/Structured4DGrid.cpp.o
+[ 33%] Linking CXX shared library libmutomCore.so
+[ 33%] Built target mutomCore
+[ 36%] Linking CXX shared library libmutomMath.so
+[ 36%] Built target mutomMath
+[ 63%] Building CXX object src/Vtk/CMakeFiles/mutomVtk.dir/vtkContainerBox.cpp.o
+[ 63%] Building CXX object src/Vtk/CMakeFiles/mutomVtk.dir/uLibVtkInterface.cxx.o
+[ 63%] Building CXX object src/Vtk/CMakeFiles/mutomVtk.dir/vtkStructuredGrid.cpp.o
+[ 63%] Building CXX object src/Vtk/CMakeFiles/mutomVtk.dir/vtkMuonScatter.cxx.o
+[ 63%] Building CXX object src/Vtk/CMakeFiles/mutomVtk.dir/uLibVtkViewer.cpp.o
+[ 63%] Generating mutomRootDict.cxx, libmutomRootDict_rdict.pcm, libmutomRootDict.rootmap
+[ 63%] Building CXX object src/Vtk/CMakeFiles/mutomVtk.dir/vtkVoxImage.cpp.o
+[ 63%] Building CXX object src/Vtk/CMakeFiles/mutomVtk.dir/vtkVoxRaytracerRepresentation.cpp.o
+[ 90%] Building CXX object src/Root/CMakeFiles/mutomRoot.dir/muCastorSkinHit.cpp.o
+[ 90%] Building CXX object src/Root/CMakeFiles/mutomRoot.dir/muCastorHit.cpp.o
+[ 90%] Building CXX object src/Root/CMakeFiles/mutomRoot.dir/muCastorMCTrack.cpp.o
+[ 90%] Building CXX object src/Root/CMakeFiles/mutomRoot.dir/muCastorInfo.cpp.o
+[ 90%] Building CXX object src/Root/CMakeFiles/mutomRoot.dir/RootMuonScatter.cpp.o
+[ 90%] Building CXX object src/Root/CMakeFiles/mutomRoot.dir/muCastorPrimaryVertex.cpp.o
+[ 90%] Building CXX object src/Root/CMakeFiles/mutomRoot.dir/muCastorMuDetDIGI.cpp.o
+[ 90%] Building CXX object src/Root/CMakeFiles/mutomRoot.dir/SkinDetectorWriter.cpp.o
+[ 93%] Building CXX object src/Root/CMakeFiles/mutomRoot.dir/mutomRootDict.cxx.o
+[ 96%] Linking CXX shared library libmutomVtk.so
+[ 96%] Built target mutomVtk
+[100%] Linking CXX shared library libmutomRoot.so
+[100%] Built target mutomRoot
+make: Leaving directory '/home/rigoni/devel/cmt/ulib/build'

conanfile.txt

@@ -0,0 +1,8 @@
+[requires]
+eigen/3.4.0
+boost/1.83.0
+pybind11/3.0.2
+
+[generators]
+CMakeDeps
+CMakeToolchain

condaenv.yml

@@ -0,0 +1,10 @@
+name: mutom
+channels:
+  - conda-forge
+dependencies:
+  - compiler-rt
+  - make
+  - cmake
+  - conan
+  - root
+  - vtk

docs/usage/usage.md

@@ -0,0 +1,60 @@
+# Usage and Installation Guide
+
+## Requirements
+
+### Compiling with CUDA Support
+
+The library supports running VoxImage filtering operations directly on CUDA cores via transparent RAM/VRAM memory transfers.
+
+By default, the `CMakeLists.txt` build system sets `USE_CUDA=ON` and will attempt to locate `nvcc` and the NVIDIA CUDA Toolkit. If the toolkit is missing, `CMake` will fail unless you explicitly configure the project with `-DUSE_CUDA=OFF`.
+
+### 1. Installing CUDA Environment via Micromamba
+
+If you are developing inside an isolated Conda/Micromamba environment (e.g., `mutom`), you can inject the CUDA compilers directly into your environment rather than relying on global system dependencies:
+
+```bash
+# Add the conda-forge channel if not already available
+micromamba config append channels conda-forge
+
+# Install nvcc and the necessary CUDA toolkit components
+micromamba install cuda-nvcc
+```
+
+Verify your installation:
+
+```bash
+nvcc --version
+```
+
+### 2. Building the Project
+
+Configure and compile the project using standard CMake flows:
+
+```bash
+mkdir -p build && cd build
+
+# Configure CMake
+# (Optional) Explicitly toggle CUDA: cmake -DUSE_CUDA=ON ..
+cmake ..
+
+# Compile the project and tests
+make -j $(nproc)
+```
+
+### 3. Validating CUDA Support
+
+You can verify that the CUDA kernels are launching correctly and allocating device memory through `DataAllocator` by running the mathematical unit tests.
+
+```bash
+# From the build directory
+./src/Math/testing/VoxImageFilterTest
+
+# Output should show:
+# "Data correctly stayed in VRAM after CUDA execution!"
+```
+
+## How It Works Under The Hood
+
+The `DataAllocator<T>` container automatically wraps memory allocations to transparently map to CPU RAM, or GPU VRAM. Standard iteration automatically pulls data backwards using implicit `MoveToRAM()` calls. 
+
+Filters using `#ifdef USE_CUDA` explicitly dictate `<buffer>.MoveToVRAM()` allocating directly on device bounds seamlessly. Fallbacks to Host compute iterations handle themselves automatically. Chaining specific filters together safely chains continuous VRAM operations avoiding costly Host copies in between iterations.

src/Core/Archives.h

@@ -23,14 +23,12 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
 #ifndef U_CORE_ARCHIVES_H
 #define U_CORE_ARCHIVES_H
 
-
 #include <boost/archive/detail/basic_pointer_iserializer.hpp>
 #include <boost/archive/detail/basic_pointer_oserializer.hpp>
+#include <iostream>
 
 #include <boost/archive/text_iarchive.hpp>
 #include <boost/archive/text_oarchive.hpp>
@@ -40,25 +38,20 @@
 
 #include <boost/archive/detail/register_archive.hpp>
 
-#include <boost/archive/polymorphic_iarchive.hpp>
-#include <boost/archive/polymorphic_oarchive.hpp>
 #include <boost/archive/detail/polymorphic_iarchive_route.hpp>
 #include <boost/archive/detail/polymorphic_oarchive_route.hpp>
+#include <boost/archive/polymorphic_iarchive.hpp>
+#include <boost/archive/polymorphic_oarchive.hpp>
 
 #include <boost/archive/polymorphic_text_oarchive.hpp>
 
 #include "StringReader.h"
 
-
-
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 // FWD DECLARATIONS OF ARCHIVES //
 
-
-
-
 namespace uLib {
 namespace Archive {
 
@@ -68,40 +61,36 @@ class text_iarchive;
 class text_oarchive;
 class log_archive;
 
-
-}
-}
-
+} // namespace Archive
+} // namespace uLib
 
 namespace boost {
 namespace archive {
 namespace detail {
 template <class ArchiveImplementation> class polymorphic_oarchive_route;
 template <class ArchiveImplementation> class polymorphic_iarchive_route;
-}
-}
-}
+} // namespace detail
+} // namespace archive
+} // namespace boost
 
 namespace boost {
 namespace serialization {
 template <typename T> struct hrp;
 }
-}
-
+} // namespace boost
 
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 // ARCHIVES REGISTRATION //
 
-
 namespace uLib {
 namespace Archive {
 namespace detail {
 struct adl_tag {};
-}
-}
-}
+} // namespace detail
+} // namespace Archive
+} // namespace uLib
 
 namespace boost {
 namespace archive {
@@ -110,10 +99,11 @@ namespace detail {
 // in overload resolution with the functions declared by
 // BOOST_SERIALIZATION_REGISTER_ARCHIVE, below.
 template <class Serializable>
-void instantiate_ptr_serialization(Serializable*, int, uLib::Archive::detail::adl_tag ) {}
-}
-}
-}
+void instantiate_ptr_serialization(Serializable *, int,
+                                   uLib::Archive::detail::adl_tag) {}
+} // namespace detail
+} // namespace archive
+} // namespace boost
 
 // The function declaration generated by this macro never actually
 // gets called, but its return type gets instantiated, and that's
@@ -121,23 +111,24 @@ void instantiate_ptr_serialization(Serializable*, int, uLib::Archive::detail::ad
 // Archive and any exported Serializable type.  See also:
 // boost/serialization/export.hpp
 #define ULIB_SERIALIZATION_REGISTER_ARCHIVE(_Archive)                          \
-namespace boost { namespace archive { namespace detail {                \
+  namespace boost {                                                            \
+  namespace archive {                                                          \
+  namespace detail {                                                           \
                                                                                \
   template <class Serializable>                                                \
-BOOST_DEDUCED_TYPENAME _ptr_serialization_support<_Archive, Serializable>::type  \
-instantiate_ptr_serialization( Serializable*, _Archive*, uLib::Archive::detail::adl_tag ); }}}
-
-
-
-
-
+  BOOST_DEDUCED_TYPENAME                                                       \
+      _ptr_serialization_support<_Archive, Serializable>::type                 \
+      instantiate_ptr_serialization(Serializable *, _Archive *,                \
+                                    uLib::Archive::detail::adl_tag);           \
+  }                                                                            \
+  }                                                                            \
+  }
 
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 // ARCHIVES IO INTERFACES //
 
-
 namespace boost {
 namespace archive {
 namespace detail {
@@ -145,11 +136,10 @@ namespace detail {
 /**
  * Custom implementation of boost interface_iarchive to add new operators
  */
-template<class Archive>
-class uLib_interface_iarchive
-{
+template <class Archive> class uLib_interface_iarchive {
 protected:
   uLib_interface_iarchive() {};
+
 public:
   /////////////////////////////////////////////////////////
   // archive public interface
@@ -157,54 +147,40 @@ public:
   typedef mpl::bool_<false> is_saving;
 
   // return a pointer to the most derived class
-    Archive * This(){
-        return static_cast<Archive *>(this);
-    }
+  Archive *This() { return static_cast<Archive *>(this); }
 
   template <class T>
-    const basic_pointer_iserializer *
-    register_type(T * = NULL){
-        const basic_pointer_iserializer & bpis =
-            boost::serialization::singleton<
-                pointer_iserializer<Archive, T>
-            >::get_const_instance();
+  const basic_pointer_iserializer *register_type(T * = NULL) {
+    const basic_pointer_iserializer &bpis = boost::serialization::singleton<
+        pointer_iserializer<Archive, T>>::get_const_instance();
     this->This()->register_basic_serializer(bpis.get_basic_serializer());
     return &bpis;
   }
-    template<class T>
-    Archive & operator>>(T & t){
-        this->This()->load_override(t, 0);
+  template <class T> Archive &operator>>(T &t) {
+    this->This()->load_override(t);
     return *this->This();
   }
 
   // the & operator
-    template<class T>
-    Archive & operator&(T & t){
-        return *(this->This()) >> t;
-    }
+  template <class T> Archive &operator&(T &t) { return *(this->This()) >> t; }
 
   // the == operator
-    template <class T>
-    Archive & operator == (T & t) {
-        return this->operator &(t);
-    }
+  template <class T> Archive &operator==(T &t) { return this->operator&(t); }
 
   // the != operator for human readable access
-    template <class T>
-    Archive & operator != (T & t) {
+  template <class T> Archive &operator!=(T &t) {
     std::cerr << std::flush << "cauch string: " << t << "\n"; // REMOVE THIS !
     return *this->This();
   }
 };
 
-
 /**
  * Custom implementation of boost interface_oarchive to add new operators
  */
-template <class Archive>
-class uLib_interface_oarchive {
+template <class Archive> class uLib_interface_oarchive {
 protected:
   uLib_interface_oarchive() {};
+
 public:
   /////////////////////////////////////////////////////////
   // archive public interface
@@ -212,32 +188,25 @@ public:
   typedef mpl::bool_<true> is_saving;
 
   // return a pointer to the most derived class
-    Archive * This(){
-        return static_cast<Archive *>(this);
-    }
+  Archive *This() { return static_cast<Archive *>(this); }
 
   template <class T>
-    const basic_pointer_oserializer *
-    register_type(const T * = NULL){
-        const basic_pointer_oserializer & bpos =
-            boost::serialization::singleton<
-                pointer_oserializer<Archive, T>
-            >::get_const_instance();
+  const basic_pointer_oserializer *register_type(const T * = NULL) {
+    const basic_pointer_oserializer &bpos = boost::serialization::singleton<
+        pointer_oserializer<Archive, T>>::get_const_instance();
     this->This()->register_basic_serializer(bpos.get_basic_serializer());
     return &bpos;
   }
 
-    template<class T>
-    Archive & operator<<(T & t){
+  template <class T> Archive &operator<<(T &t) {
     // to get access you must redefine save_override by typing
     // "using save_override" in archive impl
-        this->This()->save_override(t, 0);
+    this->This()->save_override(t);
     return *this->This();
   }
 
   // the & operator
-    template<class T>
-    Archive & operator&(T & t){
+  template <class T> Archive &operator&(T &t) {
 #ifndef BOOST_NO_FUNCTION_TEMPLATE_ORDERING
     return *this->This() << const_cast<const T &>(t);
 #else
@@ -246,45 +215,38 @@ public:
   }
 
   // the == operator
-    template <class T>
-    Archive & operator == (T & t) {
-        return this->operator &(t);
-    }
+  template <class T> Archive &operator==(T &t) { return this->operator&(t); }
 
   // the != operator for human readable access
-    template <class T>
-    Archive & operator != (T & t) {
+  template <class T> Archive &operator!=(T &t) {
     std::cerr << std::flush << "cauch string: " << t << "\n"; // REMOVE THIS !
     return *this->This();
   }
 };
 
-
-
 // DECLARE INTERFACE SPECIALIZATIONS ///////////////////////////////////////////
 // With this declarations all uLib archive Implementation will use their own
 // extended interface //
 
 template <>
-class interface_iarchive        <uLib::Archive::xml_iarchive> : public
-        uLib_interface_iarchive <uLib::Archive::xml_iarchive> {};
+class interface_iarchive<uLib::Archive::xml_iarchive>
+    : public uLib_interface_iarchive<uLib::Archive::xml_iarchive> {};
 
 template <>
-class interface_oarchive        <uLib::Archive::xml_oarchive> : public
-        uLib_interface_oarchive <uLib::Archive::xml_oarchive> {};
+class interface_oarchive<uLib::Archive::xml_oarchive>
+    : public uLib_interface_oarchive<uLib::Archive::xml_oarchive> {};
 
 template <>
-class interface_iarchive        <uLib::Archive::text_iarchive> : public
-        uLib_interface_iarchive <uLib::Archive::text_iarchive> {};
+class interface_iarchive<uLib::Archive::text_iarchive>
+    : public uLib_interface_iarchive<uLib::Archive::text_iarchive> {};
 
 template <>
-class interface_oarchive        <uLib::Archive::text_oarchive> : public
-        uLib_interface_oarchive <uLib::Archive::text_oarchive> {};
+class interface_oarchive<uLib::Archive::text_oarchive>
+    : public uLib_interface_oarchive<uLib::Archive::text_oarchive> {};
 
 template <>
-class interface_oarchive        <uLib::Archive::log_archive> : public
-        uLib_interface_oarchive <uLib::Archive::log_archive> {};
-
+class interface_oarchive<uLib::Archive::log_archive>
+    : public uLib_interface_oarchive<uLib::Archive::log_archive> {};
 
 //// Veritical repetition macro // FINIRE !!!!!!!!!!!!!!!!!!!!!!!!!
 // #define _DECL_INTERFACE_ARCHIVE_V(vz,vn,vdata)           \
@@ -299,22 +261,9 @@ class interface_oarchive        <uLib::Archive::log_archive> : public
 // #undef  _INERIT_NOFOLD_H
 // #undef  _INERIT_NOFOLD_V
 
-
-} // detail
-} // archive
-} // boost
-
-
-
-
-
-
-
-
-
-
-
-
+} // namespace detail
+} // namespace archive
+} // namespace boost
 
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
@@ -332,8 +281,8 @@ namespace archive {
 
 // template<class Archive>
 // inline void load_const_override(Archive & ar, const char *t ){
-//    typedef typename mpl::identity<detail::load_non_pointer_type<Archive> >::type typex;
-//    typex::invoke(ar, t);
+//     typedef typename mpl::identity<detail::load_non_pointer_type<Archive>
+//     >::type typex; typex::invoke(ar, t);
 // }
 
 // template<class Archive, class T>
@@ -360,45 +309,36 @@ namespace archive {
 //     typex::invoke(ar, t);
 // }
 
-
-
-}
-}
-
-
-
+} // namespace archive
+} // namespace boost
 
 namespace uLib {
 
 namespace Archive {
 
-
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 // POLYMORPHIC //
 
-
 // class polymorphic_iarchive :
 //         public boost::archive::polymorphic_iarchive {
 
 // public:
 //     void load_override(const char *t, BOOST_PFTO int)
 //     {
-//        boost::archive::load_const_override(* this->This(), const_cast<char*>(t));
+//         boost::archive::load_const_override(* this->This(),
+//         const_cast<char*>(t));
 //     }
 
 //};
 
-
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 // XML //
 
-class xml_iarchive :
-    public boost::archive::xml_iarchive_impl<xml_iarchive>
-{
+class xml_iarchive : public boost::archive::xml_iarchive_impl<xml_iarchive> {
   typedef xml_iarchive Archive;
   typedef boost::archive::xml_iarchive_impl<Archive> base;
 
@@ -406,36 +346,34 @@ class xml_iarchive :
   friend class boost::archive::detail::interface_iarchive<Archive>;
   friend class boost::archive::basic_xml_iarchive<Archive>;
   friend class boost::archive::load_access;
+
 public:
-    xml_iarchive(std::istream & is, unsigned int flags = 0) :
-        xml_iarchive_impl<xml_iarchive>(is, flags)
-    {}
+  xml_iarchive(std::istream &is, unsigned int flags = 0)
+      : xml_iarchive_impl<xml_iarchive>(is, flags) {}
 
   using basic_xml_iarchive::load_override;
 
   // Anything not an attribute should be a name value pair as nvp or hrp
-    typedef boost::archive::detail::common_iarchive<Archive> detail_common_iarchive;
+  typedef boost::archive::detail::common_iarchive<Archive>
+      detail_common_iarchive;
   template <class T>
   void load_override(
 #ifndef BOOST_NO_FUNCTION_TEMPLATE_ORDERING
       const
 #endif
-        boost::serialization::hrp< T > & t,
-        int v
-    ){
+      boost::serialization::hrp<T> &t) {
     this->This()->load_start(t.name());
-        this->detail_common_iarchive::load_override(t.value(), 0);
+    this->detail_common_iarchive::load_override(t.value());
     //        t.stov();
     this->This()->load_end(t.name());
   }
 
-
   // class_name_type can't be handled here as it depends upon the
   // char type used by the stream.  So require the derived implementation.
   // derived in this case is xml_iarchive_impl or base ..
   using base::load_override;
 
-    void load_override(const char *str, int v) {
+  void load_override(const char *str) {
     //        StringReader sr(basic_text_iprimitive::is);
     //        sr >> str;
   }
@@ -448,33 +386,23 @@ public:
 //> polymorphic_xml_iarchive;
 
 template <class ArchiveImpl>
-struct polymorphic_iarchive_route :
-        boost::archive::detail::polymorphic_iarchive_route<ArchiveImpl>
-{
-    virtual void load(const char * t){
-        ArchiveImpl::load(t);
-    }
+struct polymorphic_iarchive_route
+    : boost::archive::detail::polymorphic_iarchive_route<ArchiveImpl> {
+  virtual void load(const char *t) { ArchiveImpl::load(t); }
 };
 
-
-class polymorphic_xml_iarchive :
-        public  polymorphic_iarchive_route< boost::archive::xml_iarchive_impl<xml_iarchive> >
-{
+class polymorphic_xml_iarchive
+    : public polymorphic_iarchive_route<
+          boost::archive::xml_iarchive_impl<xml_iarchive>> {
   // give serialization implementation access to this class
   //    friend class boost::archive::detail::interface_iarchive<Archive>;
   //    friend class boost::archive::basic_xml_iarchive<Archive>;
   //    friend class boost::archive::load_access;
 public:
-    virtual void load_override(const char *str, int v) {
-        ;
-    }
+  virtual void load_override(const char *str) { ; }
 };
 
-
-
-class xml_oarchive :
-    public boost::archive::xml_oarchive_impl<xml_oarchive>
-{
+class xml_oarchive : public boost::archive::xml_oarchive_impl<xml_oarchive> {
   typedef xml_oarchive Archive;
   typedef boost::archive::xml_oarchive_impl<Archive> base;
 
@@ -482,10 +410,10 @@ class xml_oarchive :
   friend class boost::archive::detail::interface_oarchive<Archive>;
   friend class boost::archive::basic_xml_oarchive<Archive>;
   friend class boost::archive::save_access;
+
 public:
-    xml_oarchive(std::ostream & os, unsigned int flags = 0) :
-        boost::archive::xml_oarchive_impl<xml_oarchive>(os, flags)
-    {}
+  xml_oarchive(std::ostream &os, unsigned int flags = 0)
+      : boost::archive::xml_oarchive_impl<xml_oarchive>(os, flags) {}
 
   // example of implementing save_override for const char* //
   //    void save_override(const char *t, int) {
@@ -495,22 +423,21 @@ public:
   using basic_xml_oarchive::save_override;
 
   // special treatment for name-value pairs.
-    typedef boost::archive::detail::common_oarchive<Archive> detail_common_oarchive;
+  typedef boost::archive::detail::common_oarchive<Archive>
+      detail_common_oarchive;
   template <class T>
   void save_override(
 #ifndef BOOST_NO_FUNCTION_TEMPLATE_ORDERING
       const
 #endif
-        ::boost::serialization::hrp< T > & t,
-        int v
-    ){
+      ::boost::serialization::hrp<T> &t) {
     this->This()->save_start(t.name());
     //        t.vtos();
-//        this->detail_common_oarchive::save_override(t.const_value(), 0);
+    //        this->detail_common_oarchive::save_override(t.const_value());
     this->This()->save_end(t.name());
   }
 
-    void save_override(const char *str, int v) {
+  void save_override(const char *str) {
     // Do not save any human decoration string //
     //        basic_text_oprimitive::save(str);
   }
@@ -527,9 +454,7 @@ public:
 ////////////////////////////////////////////////////////////////////////////////
 // TEXT //
 
-class text_iarchive :
-    public boost::archive::text_iarchive_impl<text_iarchive>
-{
+class text_iarchive : public boost::archive::text_iarchive_impl<text_iarchive> {
   typedef text_iarchive Archive;
   typedef boost::archive::text_iarchive_impl<Archive> base;
 
@@ -537,21 +462,21 @@ class text_iarchive :
   friend class boost::archive::detail::interface_iarchive<Archive>;
   friend class boost::archive::basic_text_iarchive<Archive>;
   friend class boost::archive::load_access;
+
 public:
-    text_iarchive(std::istream & is, unsigned int flags = 0) :
-        text_iarchive_impl<Archive>(is, flags)
-    {}
+  text_iarchive(std::istream &is, unsigned int flags = 0)
+      : text_iarchive_impl<Archive>(is, flags) {}
 
   using basic_text_iarchive::load_override;
 
-    void load_override(boost::archive::object_id_type & t, int)               {}
+  void load_override(boost::archive::object_id_type &t) {}
 
   // class_name_type can't be handled here as it depends upon the
   // char type used by the stream.  So require the derived implementation.
   // derived in this case is xml_iarchive_impl or base ..
   using base::load_override;
 
-    void load_override(const char *str, int v) {
+  void load_override(const char *str) {
     StringReader sr(basic_text_iprimitive::is);
     sr >> str;
   }
@@ -565,11 +490,7 @@ typedef text_iarchive naked_text_iarchive;
 // naked_text_iarchive
 //> polymorphic_text_iarchive;
 
-
-
-class text_oarchive :
-    public boost::archive::text_oarchive_impl<text_oarchive>
-{
+class text_oarchive : public boost::archive::text_oarchive_impl<text_oarchive> {
   typedef text_oarchive Archive;
   typedef boost::archive::text_oarchive_impl<Archive> base;
 
@@ -577,16 +498,14 @@ class text_oarchive :
   friend class boost::archive::detail::interface_oarchive<Archive>;
   friend class boost::archive::basic_text_oarchive<Archive>;
   friend class boost::archive::save_access;
+
 public:
-    text_oarchive(std::ostream & os, unsigned int flags = 0) :
-        boost::archive::text_oarchive_impl<Archive>(os, flags)
-    {}
+  text_oarchive(std::ostream &os, unsigned int flags = 0)
+      : boost::archive::text_oarchive_impl<Archive>(os, flags) {}
 
   using basic_text_oarchive::save_override;
 
-    void save_override(const char *str, int v) {
-        basic_text_oprimitive::save(str);
-    }
+  void save_override(const char *str) { basic_text_oprimitive::save(str); }
 
   ~text_oarchive() {}
 };
@@ -595,15 +514,12 @@ public:
 // boost::archive::text_oarchive_impl<text_oarchive>
 //> polymorphic_text_oarchive;
 
-
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 // SIMPLE HUMAN READABLE TEXT //
 
-class hrt_iarchive :
-    public boost::archive::text_iarchive_impl<hrt_iarchive>
-{
+class hrt_iarchive : public boost::archive::text_iarchive_impl<hrt_iarchive> {
   typedef hrt_iarchive Archive;
   typedef boost::archive::text_iarchive_impl<Archive> base;
 
@@ -611,29 +527,29 @@ class hrt_iarchive :
   friend class boost::archive::detail::interface_iarchive<Archive>;
   friend class boost::archive::basic_text_iarchive<Archive>;
   friend class boost::archive::load_access;
+
 public:
-    hrt_iarchive(std::istream & is, unsigned int flags = 0) :
-        base(is, flags | boost::archive::no_header )
-    {}
+  hrt_iarchive(std::istream &is, unsigned int flags = 0)
+      : base(is, flags | boost::archive::no_header) {}
 
   using basic_text_iarchive::load_override;
 
   // hide all archive props //
-    void load_override( boost::archive::object_id_type & t, int)         {}
-    void load_override( boost::archive::object_reference_type & t, int)  {}
-    void load_override( boost::archive::version_type & t, int)           {}
-    void load_override( boost::archive::class_id_type & t, int)          {}
-    void load_override( boost::archive::class_id_optional_type & t, int) {}
-    void load_override( boost::archive::class_id_reference_type & t, int){}
-    void load_override( boost::archive::class_name_type & t, int)        {}
-    void load_override( boost::archive::tracking_type & t, int)          {}
+  void load_override(boost::archive::object_id_type &t) {}
+  void load_override(boost::archive::object_reference_type &t) {}
+  void load_override(boost::archive::version_type &t) {}
+  void load_override(boost::archive::class_id_type &t) {}
+  void load_override(boost::archive::class_id_optional_type &t) {}
+  void load_override(boost::archive::class_id_reference_type &t) {}
+  void load_override(boost::archive::class_name_type &t) {}
+  void load_override(boost::archive::tracking_type &t) {}
 
   // class_name_type can't be handled here as it depends upon the
   // char type used by the stream.  So require the derived implementation.
   // derived in this case is xml_iarchive_impl or base ..
   using base::load_override;
 
-    void load_override(const char *str, int v) {
+  void load_override(const char *str) {
     StringReader sr(basic_text_iprimitive::is);
     sr >> str;
   }
@@ -641,10 +557,7 @@ public:
   ~hrt_iarchive() {};
 };
 
-
-class hrt_oarchive :
-        public boost::archive::text_oarchive_impl<hrt_oarchive>
-    {
+class hrt_oarchive : public boost::archive::text_oarchive_impl<hrt_oarchive> {
   typedef hrt_oarchive Archive;
   typedef boost::archive::text_oarchive_impl<Archive> base;
 
@@ -652,33 +565,27 @@ class hrt_oarchive :
   friend class boost::archive::detail::interface_oarchive<Archive>;
   friend class boost::archive::basic_text_oarchive<Archive>;
   friend class boost::archive::save_access;
+
 public:
-        hrt_oarchive(std::ostream & os, unsigned int flags = 0) :
-            base(os, flags | boost::archive::no_header )
-        {}
+  hrt_oarchive(std::ostream &os, unsigned int flags = 0)
+      : base(os, flags | boost::archive::no_header) {}
 
   using basic_text_oarchive::save_override;
 
-        void save_override(const boost::archive::object_id_type & t, int)         {}
-        void save_override(const boost::archive::object_reference_type & t, int)  {}
-        void save_override(const boost::archive::version_type & t, int)           {}
-        void save_override(const boost::archive::class_id_type & t, int)          {}
-        void save_override(const boost::archive::class_id_optional_type & t, int) {}
-        void save_override(const boost::archive::class_id_reference_type & t, int){}
-        void save_override(const boost::archive::class_name_type & t, int)        {}
-        void save_override(const boost::archive::tracking_type & t, int)          {}
+  void save_override(const boost::archive::object_id_type &t) {}
+  void save_override(const boost::archive::object_reference_type &t) {}
+  void save_override(const boost::archive::version_type &t) {}
+  void save_override(const boost::archive::class_id_type &t) {}
+  void save_override(const boost::archive::class_id_optional_type &t) {}
+  void save_override(const boost::archive::class_id_reference_type &t) {}
+  void save_override(const boost::archive::class_name_type &t) {}
+  void save_override(const boost::archive::tracking_type &t) {}
 
-
-        void save_override(const char *str, int v) {
-            basic_text_oprimitive::save(str);
-        }
+  void save_override(const char *str) { basic_text_oprimitive::save(str); }
 
   ~hrt_oarchive() {}
 };
 
-
-
-
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
@@ -690,8 +597,7 @@ class hrt_oarchive :
 // any serializable class.  Intended to be useful as a debugging aid.
 class log_archive :
     /* protected ? */
-    public boost::archive::xml_oarchive_impl<log_archive>
-{
+    public boost::archive::xml_oarchive_impl<log_archive> {
   typedef boost::archive::xml_oarchive_impl<log_archive> base;
   typedef log_archive Archive;
   // give serialization implementation access to this clas
@@ -700,66 +606,52 @@ class log_archive :
   friend class boost::archive::save_access;
 
 public:
-
-    void save_override(const char *str, int v) {
+  void save_override(const char *str) {
     // Do not save any human decoration string //
     //        basic_text_oprimitive::save(str);
   }
 
-    template<class T>
-    void save_override(T & t, BOOST_PFTO int){
-        base::save_override(boost::serialization::make_nvp(NULL, t), 0);
+  template <class T> void save_override(T &t) {
+    base::save_override(boost::serialization::make_nvp(NULL, t));
   }
 
   // activate this if you want to trap non nvp objects //
   //    template<class T>
-    //    void save_override(T & t, BOOST_PFTO int)
+  //    void save_override(T & t)
   //    {
   //        BOOST_MPL_ASSERT((boost::serialization::is_wrapper< T >));
-    //        //        this->detail_common_oarchive::save_override(t, 0);
+  //        //        this->detail_common_oarchive::save_override(t);
   //    }
 
-    template<class T>
-    void save_override(const boost::serialization::nvp<T> & t, int){
-        base::save_override(t, 0);
+  template <class T> void save_override(const boost::serialization::nvp<T> &t) {
+    base::save_override(t);
   }
 
-
   // specific overrides for attributes - not name value pairs so we
   // want to trap them before the above "fall through"
   // since we don't want to see these in the output - make them no-ops.
-    void save_override(const boost::archive::object_id_type & t, int)         {}
-    void save_override(const boost::archive::object_reference_type & t, int)  {}
-    void save_override(const boost::archive::version_type & t, int)           {}
-    void save_override(const boost::archive::class_id_type & t, int)          {}
-    void save_override(const boost::archive::class_id_optional_type & t, int) {}
-    void save_override(const boost::archive::class_id_reference_type & t, int){}
-    void save_override(const boost::archive::class_name_type & t, int)        {}
-    void save_override(const boost::archive::tracking_type & t, int)          {}
-
+  void save_override(const boost::archive::object_id_type &t) {}
+  void save_override(const boost::archive::object_reference_type &t) {}
+  void save_override(const boost::archive::version_type &t) {}
+  void save_override(const boost::archive::class_id_type &t) {}
+  void save_override(const boost::archive::class_id_optional_type &t) {}
+  void save_override(const boost::archive::class_id_reference_type &t) {}
+  void save_override(const boost::archive::class_name_type &t) {}
+  void save_override(const boost::archive::tracking_type &t) {}
 
 public:
-    log_archive(std::ostream & os, unsigned int flags = 0) :
-        boost::archive::xml_oarchive_impl<log_archive>(
-            os,
-            flags | boost::archive::no_header
-        )
-    {}
+  log_archive(std::ostream &os, unsigned int flags = 0)
+      : boost::archive::xml_oarchive_impl<log_archive>(
+            os, flags | boost::archive::no_header) {}
 };
 
 // typedef boost::archive::detail::polymorphic_oarchive_route<
 // boost::archive::xml_oarchive_impl<log_archive>
 //> polymorphic_log_archive;
 
+} // namespace Archive
 
-
-
-} // Archive
-
-
-
-} // uLib
-
+} // namespace uLib
 
 ULIB_SERIALIZATION_REGISTER_ARCHIVE(uLib::Archive::xml_iarchive)
 ULIB_SERIALIZATION_REGISTER_ARCHIVE(uLib::Archive::xml_oarchive)
@@ -775,7 +667,4 @@ ULIB_SERIALIZATION_REGISTER_ARCHIVE(uLib::Archive::log_archive)
 // ULIB_SERIALIZATION_REGISTER_ARCHIVE(uLib::Archive::polymorphic_text_oarchive)
 // ULIB_SERIALIZATION_REGISTER_ARCHIVE(uLib::Archive::polymorphic_log_archive)
 
-
-
-
 #endif // U_CORE_ARCHIVES_H

src/Core/CMakeLists.txt

@@ -1,46 +1,32 @@
 
-set(HEADERS
-                                Archives.h
-                                Array.h
-                                Collection.h
-                                Debug.h
-                                Export.h
-                                Function.h
-                                Macros.h
-                                Mpl.h
-                                Object.h
-                                ObjectProps.h
-                                Options.h
-                                Serializable.h
-                                Signal.h
-                                Singleton.h
-                                SmartPointer.h
-                                StaticInterface.h
-                                StringReader.h
-                                Types.h
-                                Uuid.h
-                                Vector.h
-                                CommaInitializer.h
-                                Timer.h
-)
+set(HEADERS Archives.h Array.h Collection.h DataAllocator.h Debug.h Export.h Function.h Macros.h Mpl.h Object.h Options.h Serializable.h Signal.h Singleton.h SmartPointer.h StaticInterface.h StringReader.h Types.h Uuid.h Vector.h)
 
-SET(SOURCES
-                Archives.cpp
-                Object.cpp
-                Options.cpp
-                Serializable.cpp
-                Signal.cpp
-                Uuid.cpp
-)
+set(SOURCES Archives.cpp Debug.cpp Object.cpp Options.cpp Serializable.cpp Signal.cpp Uuid.cpp)
 
-set(LIBRARIES
-       ${Boost_SERIALIZATION_LIBRARY}
-       ${Boost_SIGNALS_LIBRARY}
-       ${Boost_PROGRAM_OPTIONS_LIBRARY}
-       ${ROOT_LIBRARIES}
-       ${PACKAGE_LIBPREFIX}Core
-       ${PACKAGE_LIBPREFIX}Math
-)
+set(LIBRARIES Boost::program_options Boost::serialization)
 
-uLib_add_shared_library(${uLib-module})
+set(libname ${PACKAGE_LIBPREFIX}Core)
+set(ULIB_SHARED_LIBRARIES ${ULIB_SHARED_LIBRARIES} ${libname} PARENT_SCOPE)
+set(ULIB_SELECTED_MODULES ${ULIB_SELECTED_MODULES} Core PARENT_SCOPE)
+
+add_library(${libname} SHARED ${SOURCES})
+set_target_properties(${libname} PROPERTIES
+                      VERSION ${PROJECT_VERSION}
+                      SOVERSION ${PROJECT_SOVERSION})
+if(USE_CUDA)
+  set(LIBRARIES ${LIBRARIES} CUDA::cudart)
+endif()
+
+target_link_libraries(${libname} ${LIBRARIES})
+
+install(TARGETS ${libname}
+        EXPORT "${PROJECT_NAME}Targets"
+        RUNTIME DESTINATION ${INSTALL_BIN_DIR} COMPONENT bin
+        LIBRARY DESTINATION ${INSTALL_LIB_DIR} COMPONENT lib)
+
+install(FILES ${HEADERS} DESTINATION ${INSTALL_INC_DIR}/Core)
+
+if(BUILD_TESTING)
+  include(uLibTargetMacros)
   add_subdirectory(testing)
+endif()

src/Core/DataAllocator.h

@@ -0,0 +1,259 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// CMT Cosmic Muon Tomography project //////////////////////////////////////////
+////////////////////////////////////////////////////////////////////////////////
+
+  Copyright (c) 2014, Universita' degli Studi di Padova, INFN sez. di Padova
+  All rights reserved
+
+  Authors: Andrea Rigoni Garola < andrea.rigoni@pd.infn.it >
+
+  ------------------------------------------------------------------
+  This library is free software;  you  can  redistribute  it  and/or
+  modify it  under the  terms  of  the  GNU  Lesser  General  Public
+  License as published  by  the  Free  Software  Foundation;  either
+  version 3.0 of the License, or (at your option) any later version.
+
+  This library is  distributed in  the hope that it will  be useful,
+  but  WITHOUT ANY WARRANTY;  without  even  the implied warranty of
+  MERCHANTABILITY  or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+  Lesser General Public License for more details.
+
+  You should have received a copy of  the GNU Lesser General  Public
+  License along with this library.
+
+//////////////////////////////////////////////////////////////////////////////*/
+
+#ifndef U_MATH_DATAALLOCATOR_H
+#define U_MATH_DATAALLOCATOR_H
+
+#include <algorithm>
+#include <cstring>
+#include <iostream>
+#include <stdexcept>
+#include <vector>
+
+#ifdef USE_CUDA
+#include <cuda_runtime.h>
+#endif
+
+namespace uLib {
+
+enum class MemoryDevice { RAM, VRAM };
+
+template <typename T> class DataAllocator {
+public:
+  DataAllocator(size_t size = 0, bool owns_objects = true)
+      : m_Size(size), m_RamData(nullptr), m_VramData(nullptr),
+        m_Device(MemoryDevice::RAM), m_OwnsObjects(owns_objects) {
+    if (m_Size > 0) {
+      if (m_OwnsObjects)
+        m_RamData = new T[m_Size]();
+      else
+        m_RamData = static_cast<T *>(::operator new(m_Size * sizeof(T)));
+    }
+  }
+
+  DataAllocator(const DataAllocator<T> &other)
+      : m_Size(other.m_Size), m_RamData(nullptr), m_VramData(nullptr),
+        m_Device(other.m_Device), m_OwnsObjects(other.m_OwnsObjects) {
+    if (m_Size > 0) {
+      if (other.m_RamData) {
+        if (m_OwnsObjects)
+          m_RamData = new T[m_Size];
+        else
+          m_RamData = static_cast<T *>(::operator new(m_Size * sizeof(T)));
+        std::memcpy(m_RamData, other.m_RamData, m_Size * sizeof(T));
+      }
+#ifdef USE_CUDA
+      if (other.m_VramData) {
+        cudaMalloc((void **)&m_VramData, m_Size * sizeof(T));
+        cudaMemcpy(m_VramData, other.m_VramData, m_Size * sizeof(T),
+                   cudaMemcpyDeviceToDevice);
+      }
+#endif
+    }
+  }
+
+  ~DataAllocator() {
+    if (m_RamData) {
+      if (m_OwnsObjects)
+        delete[] m_RamData;
+      else
+        ::operator delete(m_RamData);
+    }
+#ifdef USE_CUDA
+    if (m_VramData) {
+      cudaFree(m_VramData);
+    }
+#endif
+  }
+
+  DataAllocator &operator=(const DataAllocator &other) {
+    if (this != &other) {
+      m_OwnsObjects = other.m_OwnsObjects;
+      resize(other.m_Size);
+      m_Device = other.m_Device;
+      if (other.m_RamData) {
+        if (!m_RamData) {
+          if (m_OwnsObjects)
+            m_RamData = new T[m_Size];
+          else
+            m_RamData = static_cast<T *>(::operator new(m_Size * sizeof(T)));
+        }
+        std::memcpy(m_RamData, other.m_RamData, m_Size * sizeof(T));
+      }
+#ifdef USE_CUDA
+      if (other.m_VramData) {
+        if (!m_VramData)
+          cudaMalloc((void **)&m_VramData, m_Size * sizeof(T));
+        cudaMemcpy(m_VramData, other.m_VramData, m_Size * sizeof(T),
+                   cudaMemcpyDeviceToDevice);
+      }
+#endif
+    }
+    return *this;
+  }
+
+  void MoveToRAM() {
+    if (m_Device == MemoryDevice::RAM)
+      return;
+    if (!m_RamData && m_Size > 0) {
+      if (m_OwnsObjects)
+        m_RamData = new T[m_Size]();
+      else
+        m_RamData = static_cast<T *>(::operator new(m_Size * sizeof(T)));
+    }
+#ifdef USE_CUDA
+    if (m_VramData && m_Size > 0) {
+      cudaMemcpy(m_RamData, m_VramData, m_Size * sizeof(T),
+                 cudaMemcpyDeviceToHost);
+    }
+#endif
+    m_Device = MemoryDevice::RAM;
+  }
+
+  void MoveToVRAM() {
+    if (m_Device == MemoryDevice::VRAM)
+      return;
+#ifdef USE_CUDA
+    if (!m_VramData && m_Size > 0) {
+      cudaMalloc((void **)&m_VramData, m_Size * sizeof(T));
+    }
+    if (m_RamData && m_Size > 0) {
+      cudaMemcpy(m_VramData, m_RamData, m_Size * sizeof(T),
+                 cudaMemcpyHostToDevice);
+    }
+#endif
+    m_Device = MemoryDevice::VRAM;
+  }
+
+  void resize(size_t size) {
+    if (m_Size == size)
+      return;
+
+    T *newRam = nullptr;
+    T *newVram = nullptr;
+
+    if (size > 0) {
+      if (m_OwnsObjects)
+        newRam = new T[size]();
+      else
+        newRam = static_cast<T *>(::operator new(size * sizeof(T)));
+
+      if (m_RamData) {
+        std::memcpy(newRam, m_RamData, std::min(m_Size, size) * sizeof(T));
+      }
+
+#ifdef USE_CUDA
+      cudaMalloc((void **)&newVram, size * sizeof(T));
+      if (m_VramData) {
+        cudaMemcpy(newVram, m_VramData, std::min(m_Size, size) * sizeof(T),
+                   cudaMemcpyDeviceToDevice);
+      }
+#endif
+    }
+
+    if (m_RamData) {
+      if (m_OwnsObjects)
+        delete[] m_RamData;
+      else
+        ::operator delete(m_RamData);
+    }
+#ifdef USE_CUDA
+    if (m_VramData)
+      cudaFree(m_VramData);
+#endif
+
+    m_Size = size;
+    m_RamData = newRam;
+    m_VramData = newVram;
+  }
+
+  size_t size() const { return m_Size; }
+
+  T &at(size_t index) {
+    MoveToRAM();
+    if (index >= m_Size)
+      throw std::out_of_range("Index out of range");
+    return m_RamData[index];
+  }
+
+  const T &at(size_t index) const {
+    const_cast<DataAllocator *>(this)->MoveToRAM();
+    if (index >= m_Size)
+      throw std::out_of_range("Index out of range");
+    return m_RamData[index];
+  }
+
+  T &operator[](size_t index) {
+    MoveToRAM();
+    return m_RamData[index];
+  }
+
+  const T &operator[](size_t index) const {
+    const_cast<DataAllocator *>(this)->MoveToRAM();
+    return m_RamData[index];
+  }
+
+  T *data() { return (m_Device == MemoryDevice::RAM) ? m_RamData : m_VramData; }
+  const T *data() const {
+    return (m_Device == MemoryDevice::RAM) ? m_RamData : m_VramData;
+  }
+
+  T *GetRAMData() { return m_RamData; }
+  const T *GetRAMData() const { return m_RamData; }
+
+  T *GetVRAMData() { return m_VramData; }
+  const T *GetVRAMData() const { return m_VramData; }
+
+  MemoryDevice GetDevice() const { return m_Device; }
+
+  // Iterator support for RAM operations
+  T *begin() {
+    MoveToRAM();
+    return m_RamData;
+  }
+  T *end() {
+    MoveToRAM();
+    return m_RamData + m_Size;
+  }
+  const T *begin() const {
+    const_cast<DataAllocator *>(this)->MoveToRAM();
+    return m_RamData;
+  }
+  const T *end() const {
+    const_cast<DataAllocator *>(this)->MoveToRAM();
+    return m_RamData + m_Size;
+  }
+
+private:
+  size_t m_Size;
+  T *m_RamData;
+  T *m_VramData;
+  MemoryDevice m_Device;
+  bool m_OwnsObjects;
+};
+
+} // namespace uLib
+
+#endif // U_MATH_DATAALLOCATOR_H

src/Core/Debug.h

@@ -29,12 +29,11 @@
 #define U_CORE_DEBUG_H
 
 
-
-#include "ltk/ltkdebug.h"
+#include <vector>
 #include "Macros.h"
 #include "Types.h"
 #include "Mpl.h"
-#include "Vector.h"
+#include "SmartPointer.h"
 
 #include <boost/any.hpp>
 #include <TObject.h>
@@ -128,8 +127,8 @@ public:
     }
 
 private:
-    Vector<DItem>     m_v;
-    Vector<Adapter>   m_a;
+    std::vector<DItem>     m_v;
+    std::vector<Adapter>   m_a;
 };
 
 

src/Core/Export.h

@@ -23,60 +23,51 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
 #ifndef U_CORE_EXPORT_H
 #define U_CORE_EXPORT_H
 
-#include <utility>
 #include <cstddef> // NULL
 #include <iostream>
+#include <utility>
 
 #include <boost/config.hpp>
-#include <boost/static_assert.hpp>
 #include <boost/preprocessor/stringize.hpp>
+#include <boost/static_assert.hpp>
 #include <boost/type_traits/is_polymorphic.hpp>
 
-#include <boost/mpl/assert.hpp>
 #include <boost/mpl/and.hpp>
-#include <boost/mpl/not.hpp>
+#include <boost/mpl/assert.hpp>
 #include <boost/mpl/bool.hpp>
+#include <boost/mpl/not.hpp>
 
-#include <boost/serialization/extended_type_info.hpp> // for guid_defined only
-#include <boost/serialization/static_warning.hpp>
 #include <boost/serialization/assume_abstract.hpp>
+#include <boost/serialization/extended_type_info.hpp> // for guid_defined only
 #include <boost/serialization/force_include.hpp>
 #include <boost/serialization/singleton.hpp>
+#include <boost/serialization/static_warning.hpp>
 
 #include <boost/archive/detail/register_archive.hpp>
 
-
 #include "Core/Archives.h"
 
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 
-
-
 namespace uLib {
 namespace Archive {
 namespace detail {
 namespace extra_detail {
 
-template<class T>
-struct guid_initializer
-{
-    void export_guid(mpl::false_) const {
+template <class T> struct guid_initializer {
+  void export_guid(boost::mpl::false_) const {
     // generates the statically-initialized objects whose constructors
     // register the information allowing serialization of T objects
     // through pointers to their base classes.
-        boost::archive::detail::
-                instantiate_ptr_serialization((T*)0, 0,
-                                              uLib::Archive::detail::adl_tag());
-    }
-    void export_guid(mpl::true_) const {
+    boost::archive::detail::instantiate_ptr_serialization(
+        (T *)0, 0, uLib::Archive::detail::adl_tag());
   }
+  void export_guid(boost::mpl::true_) const {}
   guid_initializer const &export_guid() const {
     BOOST_STATIC_WARNING(boost::is_polymorphic<T>::value);
     // note: exporting an abstract base class will have no effect
@@ -88,30 +79,29 @@ struct guid_initializer
   }
 };
 
-template<typename T>
-struct init_guid;
+template <typename T> struct init_guid;
 
-} // anonymous
+} // namespace extra_detail
 } // namespace detail
 } // namespace Archive
 } // namespace uLib
 
-
-
 #define ULIB_CLASS_EXPORT_IMPLEMENT(T)                                         \
   namespace uLib {                                                             \
   namespace Archive {                                                          \
   namespace detail {                                                           \
   namespace extra_detail {                                                     \
-    template<>                                               \
-    struct init_guid< T > {                                  \
+  template <> struct init_guid<T> {                                            \
     static guid_initializer<T> const &g;                                       \
   };                                                                           \
   guid_initializer<T> const &init_guid<T>::g =                                 \
       ::boost::serialization::singleton<                                       \
-            guid_initializer< T >                            \
-        >::get_mutable_instance().export_guid();             \
-    }}}}                                                     \
+          guid_initializer<T>>::get_mutable_instance()                         \
+          .export_guid();                                                      \
+  }                                                                            \
+  }                                                                            \
+  }                                                                            \
+  }                                                                            \
   /**/
 
 #endif // EXPORT_H

src/Core/Makefile.am

@@ -14,7 +14,6 @@ library_include_HEADERS = 	\
                                 Macros.h \
                                 Mpl.h \
                                 Object.h \
-                                ObjectProps.h \
                                 Options.h \
                                 Serializable.h \
                                 Signal.h \

src/Core/Object.cpp

@@ -23,38 +23,29 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
-
-
 #include "config.h"
 
 #include "Object.h"
 #include "Vector.h"
 
-#include "boost/archive/polymorphic_xml_oarchive.hpp"
-#include "boost/archive/polymorphic_xml_iarchive.hpp"
-#include "boost/archive/polymorphic_text_oarchive.hpp"
-#include "boost/archive/polymorphic_text_iarchive.hpp"
-#include "boost/archive/polymorphic_binary_oarchive.hpp"
 #include "boost/archive/polymorphic_binary_iarchive.hpp"
-
-
+#include "boost/archive/polymorphic_binary_oarchive.hpp"
+#include "boost/archive/polymorphic_text_iarchive.hpp"
+#include "boost/archive/polymorphic_text_oarchive.hpp"
+#include "boost/archive/polymorphic_xml_iarchive.hpp"
+#include "boost/archive/polymorphic_xml_oarchive.hpp"
 
 namespace uLib {
 
-
 const char *Version::PackageName = PACKAGE_NAME;
 const char *Version::VersionNumber = PACKAGE_VERSION;
 const char *Version::Release = "x"; // SVN_REVISION;
 
-
 ////////////////////////////////////////////////////////////////////////////////
 // Object Private //
 
 class ObjectPrivate {
 public:
-
   struct Signal {
     GenericMFPtr sigptr;
     std::string sigstr;
@@ -66,135 +57,94 @@ public:
     std::string slostr;
   };
 
-
   Vector<Signal> sigv;
   Vector<Slot> slov;
 };
 
-
-
-
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 // OBJECT IMPLEMENTATION
 
+Object::Object() : d(new ObjectPrivate) {}
 
+Object::Object(const Object &copy) : d(new ObjectPrivate(*copy.d)) {}
 
-Object::Object() :
-    d(new ObjectPrivate)
-{}
+Object::~Object() { delete d; }
 
-Object::Object(const Object &copy) :
-    ObjectPropable(copy),
-    d(new ObjectPrivate(*copy.d))
-{}
-
-Object::~Object() {
-    delete d;
-}
-
-void Object::DeepCopy(const Object &copy)
-{
+void Object::DeepCopy(const Object &copy) {
   // should lock to be tread safe //
   memcpy(d, copy.d, sizeof(ObjectPrivate));
   // ERROR! does not copy parameters ... <<<< FIXXXXX
 }
 
-
-
-
-
-void Object::SaveXml(std::ostream &os, Object &ob)
-{
+void Object::SaveXml(std::ostream &os, Object &ob) {
   Archive::xml_oarchive ar(os);
   ar << boost::serialization::make_nvp("Object", ob);
 }
 
-void Object::LoadXml(std::istream &is, Object &ob)
-{
+void Object::LoadXml(std::istream &is, Object &ob) {
   Archive::xml_iarchive ar(is);
   ar >> boost::serialization::make_nvp("Object", ob);
 }
 
-
 // FINIRE
-void Object::SaveConfig(std::ostream &os, int version)
-{   
+void Object::SaveConfig(std::ostream &os, int version) {
   Archive::xml_oarchive ar(os);
-    ObjectPropable::serialize(ar,0);
 }
 
-void Object::LoadConfig(std::istream &is, int version)
-{
-    if(!props()) this->init_properties();
+void Object::LoadConfig(std::istream &is, int version) {
   Archive::xml_iarchive ar(is);
-    ObjectPropable::serialize(ar,0);
 }
 
-
-
-
-
-void Object::PrintSelf(std::ostream &o) const
-{
+void Object::PrintSelf(std::ostream &o) const {
   o << "OBJECT signals: ------------------\n";
   Vector<ObjectPrivate::Signal>::Iterator itr;
-    for(itr = d->sigv.begin(); itr<d->sigv.end(); itr++)
-    {
+  for (itr = d->sigv.begin(); itr < d->sigv.end(); itr++) {
     o << "  signal:[ " << itr->sigstr << " ]\n";
   }
   o << "--------------------------------------\n\n";
 }
 
-
-bool Object::addSignalImpl(SignalBase *sig, GenericMFPtr fptr, const char *name)
-{
+bool Object::addSignalImpl(SignalBase *sig, GenericMFPtr fptr,
+                           const char *name) {
   ObjectPrivate::Signal s = {fptr, std::string(name), sig};
   d->sigv.push_back(s);
+  return true;
 }
 
-bool Object::addSlotImpl(GenericMFPtr fptr, const char *name)
-{
+bool Object::addSlotImpl(GenericMFPtr fptr, const char *name) {
   ObjectPrivate::Slot s = {fptr, std::string(name)};
   d->slov.push_back(s);
+  return true;
 }
 
-SignalBase *Object::findSignalImpl(const GenericMFPtr &fptr) const
-{
-    for(int i=0; i<d->sigv.size(); ++i)
-    {
+SignalBase *Object::findSignalImpl(const GenericMFPtr &fptr) const {
+  for (int i = 0; i < d->sigv.size(); ++i) {
     if (d->sigv[i].sigptr == fptr)
       return d->sigv[i].signal;
   }
   return NULL;
 }
 
-SignalBase *Object::findSignalImpl(const char *name) const
-{
+SignalBase *Object::findSignalImpl(const char *name) const {
   std::string in(name);
-    for(int i=0; i<d->sigv.size(); ++i)
-    {
+  for (int i = 0; i < d->sigv.size(); ++i) {
     if (d->sigv[i].sigstr == in)
       return d->sigv[i].signal;
   }
   return NULL;
 }
 
-GenericMFPtr *Object::findSlotImpl(const char *name) const
-{
+GenericMFPtr *Object::findSlotImpl(const char *name) const {
   std::string in(name);
-    for(int i=0; i<d->slov.size(); ++i)
-    {
+  for (int i = 0; i < d->slov.size(); ++i) {
     if (d->slov[i].slostr == in)
       return &d->slov[i].sloptr;
   }
   return NULL;
 }
 
-
-
-
 // std::ostream &
 // operator << (std::ostream &os, uLib::Object &ob)
 // {
@@ -218,10 +168,4 @@ GenericMFPtr *Object::findSlotImpl(const char *name) const
 //     return is;
 // }
 
-
-
-
-} // uLib
-
-
-
+} // namespace uLib

src/Core/Object.h

@@ -23,8 +23,6 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
 #ifndef U_CORE_OBJECT_H
 #define U_CORE_OBJECT_H
 
@@ -33,28 +31,25 @@
 // WARNING: COPILE ERROR if this goes after mpl/vector //
 // #include "Core/Vector.h"
 
-#include "Core/Types.h"
 #include "Core/Debug.h"
+#include "Core/Types.h"
 
 #include "Core/Function.h"
 #include "Core/Signal.h"
 
 #include "Core/Mpl.h"
 #include "Core/Serializable.h"
-#include "Core/ObjectProps.h"
 #include "Core/Uuid.h"
 
 namespace boost {
 namespace archive {
 class polymorphic_iarchive;
 class polymorphic_oarchive;
-} // archive
-} // boost
-
+} // namespace archive
+} // namespace boost
 
 namespace uLib {
 
-
 class Version {
 public:
   static const char *PackageName;
@@ -62,23 +57,14 @@ public:
   static const char *Release;
 };
 
-
-
-
-
-
 ////////////////////////////////////////////////////////////////////////////////
 //// OBJECT ////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 
-
-
 /**
  * @brief Object class is the object base implementation for uLib Framework.
  */
-class Object : public ObjectPropable
-{
-
+class Object {
 
 public:
   //    std::string name;
@@ -94,14 +80,13 @@ public:
   // FIXX !!!
   virtual void DeepCopy(const Object &copy);
 
-
   ////////////////////////////////////////////////////////////////////////////
   // SERIALIZATION //
 
-    template <class ArchiveT> void serialize(ArchiveT &ar, const unsigned int version)    {
-                ObjectPropable::serialize(ar,version);
-    }
-    template <class ArchiveT> void save_override(ArchiveT &ar,const unsigned int version) {}
+  template <class ArchiveT>
+  void serialize(ArchiveT &ar, const unsigned int version) {}
+  template <class ArchiveT>
+  void save_override(ArchiveT &ar, const unsigned int version) {}
 
   void SaveConfig(std::ostream &os, int version = 0);
   void LoadConfig(std::istream &is, int version = 0);
@@ -109,13 +94,12 @@ public:
   static void SaveXml(std::ostream &os, Object &ob);
   static void LoadXml(std::istream &is, Object &ob);
 
-
-
   ////////////////////////////////////////////////////////////////////////////
   // SIGNALS //
 
   // Qt4 style connector //
-    static bool connect(const Object *ob1, const char *signal_name, const Object *receiver, const char *slot_name) {
+  static bool connect(const Object *ob1, const char *signal_name,
+                      const Object *receiver, const char *slot_name) {
     //        // NOT WORKING YET //
     //        1) find slot pointer from name
     //        SignalBase   *sig = ob1->findSignal(signal_name);
@@ -123,51 +107,60 @@ public:
     //        if(sig && slo)
     //            return Object::connect(sig,slo->operator ()(),receiver);
     //        else return false;
+    return false;
   }
 
   // Qt5 style connector //
   template <typename Func1, typename Func2>
-    static bool connect( typename FunctionPointer<Func1>::Object *sender,   Func1 sigf,
-                         typename FunctionPointer<Func2>::Object *receiver, Func2 slof)
-    {
+  static bool
+  connect(typename FunctionPointer<Func1>::Object *sender, Func1 sigf,
+          typename FunctionPointer<Func2>::Object *receiver, Func2 slof) {
     SignalBase *sigb = sender->findOrAddSignal(sigf);
-        typedef boost::signals2::signal<typename FunctionPointer<Func2>::SignalSignature> SigT;
-        ConnectSignal(sigb,slof,receiver);
+    ConnectSignal<typename FunctionPointer<Func1>::SignalSignature>(sigb, slof,
+                                                                    receiver);
+    return true;
   }
 
   template <typename FuncT>
   static inline bool connect(SignalBase *sigb, FuncT slof, Object *receiver) {
-        ConnectSignal(sigb,slof,receiver);
+    ConnectSignal<typename FunctionPointer<FuncT>::SignalSignature>(sigb, slof,
+                                                                    receiver);
+    return true;
   }
 
-
   template <typename FuncT>
-    inline typename Signal<typename FunctionPointer<FuncT>::SignalSignature>::type *
+  inline
+      typename Signal<typename FunctionPointer<FuncT>::SignalSignature>::type *
       addSignal(FuncT fun, const char *name) {
-        typedef typename Signal<typename FunctionPointer<FuncT>::SignalSignature>::type SigT;
+    typedef
+        typename Signal<typename FunctionPointer<FuncT>::SignalSignature>::type
+            SigT;
     SignalBase *sig = NewSignal(fun);
     addSignalImpl(sig, fun, name);
     return (SigT *)sig;
   }
 
-    template< typename FuncT>
-    inline bool addSlot(FuncT fun, const char *name) {
-        this->addSlotImpl(GenericMFPtr(fun),name);
+  template <typename FuncT> inline bool addSlot(FuncT fun, const char *name) {
+    return this->addSlotImpl(GenericMFPtr(fun), name);
   }
 
   template <typename FuncT>
-    inline typename Signal<typename FunctionPointer<FuncT>::SignalSignature>::type *
-    findSignal(FuncT fptr)
-    {
-        typedef typename Signal<typename FunctionPointer<FuncT>::SignalSignature>::type SigT;
+  inline
+      typename Signal<typename FunctionPointer<FuncT>::SignalSignature>::type *
+      findSignal(FuncT fptr) {
+    typedef
+        typename Signal<typename FunctionPointer<FuncT>::SignalSignature>::type
+            SigT;
     return (SigT *)findSignalImpl(GenericMFPtr(fptr));
   }
 
   template <typename FuncT>
-    inline typename Signal<typename FunctionPointer<FuncT>::SignalSignature>::type *
-    findOrAddSignal(FuncT fptr)
-    {
-        typedef typename Signal<typename FunctionPointer<FuncT>::SignalSignature>::type SigT;
+  inline
+      typename Signal<typename FunctionPointer<FuncT>::SignalSignature>::type *
+      findOrAddSignal(FuncT fptr) {
+    typedef
+        typename Signal<typename FunctionPointer<FuncT>::SignalSignature>::type
+            SigT;
     SignalBase *sig = findSignalImpl(GenericMFPtr(fptr));
     if (!sig) {
       sig = NewSignal(fptr);
@@ -176,25 +169,20 @@ public:
     return (SigT *)sig;
   }
 
-
-    inline SignalBase *
-    findSignal(const char *name) const
-    {
+  inline SignalBase *findSignal(const char *name) const {
     return findSignalImpl(name);
   }
 
-    inline GenericMFPtr *
-    findSlot(const char *name) const
-    {
+  inline GenericMFPtr *findSlot(const char *name) const {
     return findSlotImpl(name);
   }
 
-
   void PrintSelf(std::ostream &o) const;
 
-    inline const Object& operator = (const Object &copy)
-    { this->DeepCopy(copy); return *this; }
-
+  inline const Object &operator=(const Object &copy) {
+    this->DeepCopy(copy);
+    return *this;
+  }
 
 private:
   bool addSignalImpl(SignalBase *sig, GenericMFPtr fptr, const char *name);
@@ -208,9 +196,7 @@ private:
   class ObjectPrivate *d;
 };
 
-
-
-} // uLib
+} // namespace uLib
 
 ////////////////////////////////////////////////////////////////////////////////
 
@@ -218,5 +204,4 @@ private:
 // std::ostream & operator << (std::ostream &os, uLib::Object *ob);
 // std::istream & operator >> (std::istream &is, uLib::Object &ob);
 
-
 #endif // U_OBJECT_H

src/Core/ObjectProps.h

@@ -1,278 +0,0 @@
-/*//////////////////////////////////////////////////////////////////////////////
-// CMT Cosmic Muon Tomography project //////////////////////////////////////////
-////////////////////////////////////////////////////////////////////////////////
-
-  Copyright (c) 2014, Universita' degli Studi di Padova, INFN sez. di Padova
-  All rights reserved
-
-  Authors: Andrea Rigoni Garola < andrea.rigoni@pd.infn.it >
-
-  ------------------------------------------------------------------
-  This library is free software;  you  can  redistribute  it  and/or
-  modify it  under the  terms  of  the  GNU  Lesser  General  Public
-  License as published  by  the  Free  Software  Foundation;  either
-  version 3.0 of the License, or (at your option) any later version.
-
-  This library is  distributed in  the hope that it will  be useful,
-  but  WITHOUT ANY WARRANTY;  without  even  the implied warranty of
-  MERCHANTABILITY  or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-  Lesser General Public License for more details.
-
-  You should have received a copy of  the GNU Lesser General  Public
-  License along with this library.
-
-//////////////////////////////////////////////////////////////////////////////*/
-
-
-
-#ifndef U_OBJECTPROPS_H
-#define U_OBJECTPROPS_H
-
-
-
-#include <boost/algorithm/string/replace.hpp>
-
-#include <Core/Mpl.h>
-#include <Core/Types.h>
-
-
-
-////////////////////////////////////////////////////////////////////////////////
-////////////////////////////////////////////////////////////////////////////////
-////////////////////////////////////////////////////////////////////////////////
-// MACROS //
-
-
-#define ULIB_props() \
-    public: struct ObjectProps;		                               \
-    virtual void init_properties();                                \
-    inline struct ObjectProps &p() { /* static const unsigned int offset = props_offset(this); */ \
-    /* NON FUNZIA!  return * (struct ObjectProps *)(reinterpret_cast<char*>(props())+offset);  */ \
-    return *props()->ptr<ObjectProps>(); }                                                        \
-    typedef uLib::mpl::bool_<true>::type propable_trait;                                          \
-    public: struct DLL_PUBLIC ObjectProps
-
-#define properties() ULIB_props()
-
-#define default(vlaue)
-
-#define $$ p()
-
-#define $(_name) props_ref<_name>()
-
-#define $_init()                                                               \
-    if(props(this)) return;                                                    \
-    props_new(this);                                                           \
-    uLib::detail::ObjectProps::initializer::init_object_baselist(this);
-
-
-
-////////////////////////////////////////////////////////////////////////////////
-////////////////////////////////////////////////////////////////////////////////
-////////////////////////////////////////////////////////////////////////////////
-
-
-namespace boost {
-namespace serialization {
-class access;
-}
-}
-
-
-namespace uLib {
-
-namespace detail {
-
-struct ObjectProps {
-
-    /** Define a trait has_member to find if an Object is Propable*/
-    BOOST_MPL_HAS_XXX_TRAIT_DEF(propable_trait)
-
-    /** IsA ProbapleObject Implementation Template */
-    template <class T>
-    struct IsA : has_propable_trait<T> {};
-
-    /** Lambda to get Props member type */
-    template <class T>
-    struct props_type {
-        typedef typename T::ObjectProps type;
-    };
-
-    template <typename T>
-    struct get_props {
-
-        /** CFList has result but this method check for has BaseList */
-        typedef typename detail::TypeIntrospection::child_first<T>::type CFTypeList;
-
-        /** Filter List items that have not Propable feature */
-        typedef typename mpl::filter_view< CFTypeList, IsA<mpl::_> >::type FilteredCFTypeList;
-
-        /** Get Props from each Parent in Seq */
-        typedef typename mpl::transform_view< FilteredCFTypeList, props_type<mpl::_> >::type type;
-
-
-        // qui sotto ho un problema che ho temporaneamente tamponato          //
-        // ovvero ho usato child_first_impl per ottenere la lista delle basi  //
-        // vorrei farlo facendo un pop_back ma non va forse perche il tipo    //
-        // non e' corretto. //
-
-        /** Get Parent list from CFTypeList */
-        typedef typename detail::TypeIntrospection::child_first_impl<T>::Childs CFBaseList;
-
-        /** Filter Parents that have not Propable feature */
-        typedef typename mpl::filter_view< CFBaseList, IsA<mpl::_> >::type FilteredCFBaseList;
-    };
-
-
-
-    // TODO: convert to pp const value,
-    // (non so se sia possibile con il dinamic casting intanto funziona cosi' )
-    template <typename T1, typename T2>
-    static unsigned int measure_offset(T1 base, T2 derived) {
-        return reinterpret_cast<char*>(derived) - reinterpret_cast<char*>(base);
-    }
-
-    struct initializer {
-
-        template <class _ObjectT>
-        struct lambda_init_object {
-            _ObjectT *o;
-            lambda_init_object(_ObjectT *o) : o(o) {}
-            template<class T> void operator()(T) {
-                o->T::init_properties();
-            }
-        };
-
-
-        /**
-         * This calls the internal init_properties() virtual function for each
-         * object parent defined in BaseList only if it is propable
-         */
-        template <class T>
-        static void init_object_baselist(T *o) {
-            typedef typename uLib::detail::ObjectProps::get_props<T>::FilteredCFBaseList CFBaseList;
-            mpl::for_each<CFBaseList>(lambda_init_object<T>(o));
-        }
-
-        /**
-         * This calls the internal init_properties() virtual function only if
-         * object is propable ( implementation if not propable )
-         */
-        template <class T>
-        static
-        typename boost::enable_if<mpl::not_<IsA<T> >,void>::type
-        init_object(T *o) {
-            ; // do nothing //
-        }
-
-        /**
-         * This calls the internal init_properties() virtual function only if
-         * object is propable ( implementation if propable )
-         */
-        template <class T>
-        static
-        typename boost::enable_if<IsA<T>,void>::type
-        init_object(T *o) {
-            o->init_properties();
-        }
-
-    };
-
-    template <class ThisClass, class Archive>
-    struct serialize_baselist {
-        ThisClass & m_object;
-        Archive   & m_ar;
-        serialize_baselist(ThisClass &o, Archive &ar) : m_object(o), m_ar(ar) {}
-        template <class T> void operator()(T &o) {
-            // T is taken fron get_props<BaseList>::FilteredPList types to get
-            // type_info_name that is the type name defined by Type macro
-            typedef typename props_type<T>::type PType;
-            std::string name(TypeIntrospection::access<T>::type_info::name);
-            boost::algorithm::replace_all(name,"::","_");
-            m_ar & boost::serialization::make_nvp(
-                        name.c_str() ,
-                        boost::serialization::base_object<PType>(m_object));
-        }
-    };
-
-};
-
-} // detail
-
-
-
-
-
-struct ObjectPropsBase {
-    virtual ~ObjectPropsBase() {}
-    virtual ObjectPropsBase *copy() = 0;
-
-    template <class T> inline T *ptr() { return dynamic_cast<T*>(this); }
-
-    template<class ArchiveT> void serialize(ArchiveT &ar, const unsigned int version) {}
-};
-
-
-
-template <class T>
-struct ObjectPropsImpl :
-        ObjectPropsBase,
-        ULIB_MPL_INHERIT_NOFOLD_SEQ(typename uLib::detail::ObjectProps::get_props<T>::type)
-{    
-    typedef ObjectPropsImpl<T> ThisClass;
-    typedef typename uLib::detail::ObjectProps::get_props<T>::type CFList;
-    typedef typename uLib::detail::ObjectProps::get_props<T>::FilteredCFTypeList FilteredCFTypeList;
-    ObjectPropsBase *copy() { return new ThisClass(*this); }
-
-    template<class ArchiveT> void serialize(ArchiveT &ar, const unsigned int version) {
-        boost::serialization::void_cast_register<ThisClass,ObjectPropsBase>();
-        mpl::for_each<FilteredCFTypeList>(detail::ObjectProps::serialize_baselist<ThisClass,ArchiveT>(*this,ar));
-    }
-};
-
-
-class ObjectPropable {
-
-    ObjectPropsBase *m_props;
-    friend class uLib::detail::ObjectProps;
-    friend class boost::serialization::access;
-public:
-    ObjectPropable() : m_props(NULL) {}
-    ObjectPropable(const ObjectPropable &c) { if(c.m_props) m_props = c.m_props->copy(); else m_props = NULL; }
-    ~ObjectPropable() { if(m_props) delete m_props; }
-
-
-    template <class T> inline typename T::ObjectProps&  props_ref() const { if(m_props) return *m_props->ptr<typename T::ObjectProps>(); else exit(1); }
-    template <class T> inline typename T::ObjectProps*  props(T *ptr = NULL) const { if(m_props) return m_props->ptr<typename T::ObjectProps>(); else return NULL; }
-protected:
-    ObjectPropsBase *props() const { return m_props; }
-    template <class T> inline void props_new(T* ptr = NULL) { if(!m_props) m_props = new ObjectPropsImpl<T>; }
-
-    /** NOT working dynamic cache casting */
-    template <class T> inline unsigned int props_offset(T *ptr) const
-    { if(m_props) return detail::ObjectProps::measure_offset(m_props,m_props->ptr<T>()); else return -1; }
-
-
-    template<class ArchiveT> void serialize(ArchiveT &ar, const unsigned int version) {
-        if(m_props) ar & boost::serialization::make_nvp("properties",m_props);
-    }
-
-public:
-    /**
-     * ObjectPropable is not directly propable itself to prevent Basclass
-     * duplication in inherit_nofold. And for the same reason ANY VIRTUAL BASE
-     * SHOULD NOT BE PROPABLE
-     */
-    virtual void init_properties() {}
-
-};
-
-} // uLib
-
-
-
-
-
-
-
-#endif // U_OBJECTPROPS_H

src/Core/Options.cpp

@@ -31,6 +31,9 @@
 
 #include <boost/program_options.hpp>
 
+#include <boost/property_tree/ptree.hpp>
+#include <boost/property_tree/ini_parser.hpp>
+
 
 //class boost::program_options::error_with_option_name;
 //template<> boost::program_options::typed_value<int> boost::program_options::value<int>();
@@ -74,6 +77,23 @@ void Options::parse_config_file(const char *fname)
     }
 }
 
+void Options::save_config_file(const char *fname) {
+    std::ofstream os;
+    os.open(fname);
+    
+    using boost::property_tree::ptree;
+
+    ptree root;
+
+
+    std::cout << m_configuration << "\n";
+    std::cout << m_global << "\n";
+
+    write_ini( std::cout, root );
+
+}
+
+
 bool Options::count(const char *str) const
 {
     return (m_vm.count(str));

src/Core/Options.h

@@ -160,6 +160,8 @@ public:
 
     void parse_config_file(const char *fname);
 
+    void save_config_file(const char *fname);
+
     template <typename T>
     static inline boost::program_options::typed_value<T>* value(T *v, T dvalue) {
         boost::program_options::typed_value<T> *r = boost::program_options::value<T>(v);

src/Core/Serializable.h

@@ -23,8 +23,6 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
 #ifndef U_SERIALIZABLE_H
 #define U_SERIALIZABLE_H
 
@@ -38,9 +36,6 @@ TODO:
 
 */
 
-
-
-
 #include <boost/serialization/access.hpp>
 #include <boost/serialization/export.hpp>
 
@@ -55,19 +50,15 @@ TODO:
 // #include "boost/archive/polymorphic_iarchive.hpp"
 // #include "boost/archive/polymorphic_oarchive.hpp"
 
-#include <boost/preprocessor/comma_if.hpp>
-#include <boost/preprocessor/repeat.hpp>
-#include <boost/preprocessor/inc.hpp>
 #include <boost/preprocessor/cat.hpp>
+#include <boost/preprocessor/comma_if.hpp>
+#include <boost/preprocessor/inc.hpp>
+#include <boost/preprocessor/repeat.hpp>
 #include <boost/preprocessor/tuple/to_seq.hpp>
 
-
-#include "Core/Mpl.h"
-#include "Core/ObjectProps.h"
 #include "Core/Archives.h"
 #include "Core/Export.h"
-
-
+#include "Core/Mpl.h"
 
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
@@ -80,25 +71,17 @@ namespace serialization {
 // ACCESS 2 //
 template <class T> struct access2 {};
 
-
 // NON FUNZIONA ... SISTEMARE !!!! // ------------------------------------------
-template<class T>
-class hrp :
-        public wrapper_traits<const hrp< T > >
-{
+template <class T> class hrp : public wrapper_traits<const hrp<T>> {
   const char *m_name;
   T *m_value;
   std::string *m_str;
 
 public:
-    explicit hrp(const char * name_, T &t) :
-        m_str(new std::string),
-        m_name(name_), m_value(&t) {}
-
-    const char * name() const {
-        return this->m_name;
-    }
+  explicit hrp(const char *name_, T &t)
+      : m_str(new std::string), m_name(name_), m_value(&t) {}
 
+  const char *name() const { return this->m_name; }
 
   template <class Archivex>
   void save(Archivex &ar, const unsigned int /* file_version */) const {
@@ -116,7 +99,6 @@ public:
   BOOST_SERIALIZATION_SPLIT_MEMBER()
 };
 
-
 template <class T>
 inline
 #ifndef BOOST_NO_FUNCTION_TEMPLATE_ORDERING
@@ -126,17 +108,10 @@ hrp< T > make_hrp(const char * name, T & t){
   return hrp<T>(name, t);
 }
 
-#define HRP(name) \
-    boost::serialization::make_hrp(BOOST_PP_STRINGIZE(name), name)
-
-
-} // serialization
-} // boost
-
-
-
-
+#define HRP(name) boost::serialization::make_hrp(BOOST_PP_STRINGIZE(name), name)
 
+} // namespace serialization
+} // namespace boost
 
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
@@ -151,8 +126,6 @@ hrp< T > make_hrp(const char * name, T & t){
 
 namespace uLib {
 
-
-
 #define _AR_OP(r, data, elem) data &BOOST_SERIALIZATION_BASE_OBJECT_NVP(elem);
 
 #define NVP(data) BOOST_SERIALIZATION_NVP(data)
@@ -167,22 +140,25 @@ namespace uLib {
 
 #ifdef ULIB_CFG_INTRUSIVE_SERIALIZATION_OBJECT
 #define ULIB_SERIALIZABLE_OBJECT _ULIB_DETAIL_INTRUSIVE_SERIALIZABLE_OBJECT
-#  define ULIB_SERIALIZE_OBJECT(_Ob,...)  _ULIB_DETAIL_INTRUSIVE_SERIALIZE_OBJECT(_Ob,__VA_ARGS__)
+#define ULIB_SERIALIZE_OBJECT(_Ob, ...)                                        \
+  _ULIB_DETAIL_INTRUSIVE_SERIALIZE_OBJECT(_Ob, __VA_ARGS__)
 #define _AR_(_name) _ULIB_DETAIL_INTRUSIVE_AR_(_name)
 #else
-#  define ULIB_SERIALIZABLE(_Ob)           _ULIB_DETAIL_UNINTRUSIVE_SERIALIZABLE(_Ob) \
+#define ULIB_SERIALIZABLE(_Ob)                                                 \
+  _ULIB_DETAIL_UNINTRUSIVE_SERIALIZABLE(_Ob)                                   \
   ULIB_CLASS_EXPORT_KEY(_Ob)
 #define ULIB_SERIALIZE(_Ob, ...) _ULIB_DETAIL_UNINTRUSIVE_SERIALIZE(_Ob)
-#  define ULIB_SERIALIZE_DERIVED(_Ob,...)  _ULIB_DETAIL_UNINTRUSIVE_SERIALIZE_DERIVED(_Ob,__VA_ARGS__)
-#  define ULIB_SERIALIZABLE_OBJECT(_Ob)    _ULIB_DETAIL_UNINTRUSIVE_SERIALIZABLE_OBJECT(_Ob) \
+#define ULIB_SERIALIZE_DERIVED(_Ob, ...)                                       \
+  _ULIB_DETAIL_UNINTRUSIVE_SERIALIZE_DERIVED(_Ob, __VA_ARGS__)
+#define ULIB_SERIALIZABLE_OBJECT(_Ob)                                          \
+  _ULIB_DETAIL_UNINTRUSIVE_SERIALIZABLE_OBJECT(_Ob)                            \
   ULIB_CLASS_EXPORT_OBJECT_KEY(_Ob)
-#  define ULIB_SERIALIZE_OBJECT(_Ob,...)   _ULIB_DETAIL_UNINTRUSIVE_SERIALIZE_OBJECT(_Ob,__VA_ARGS__)
-#  define ULIB_SERIALIZE_OBJECT_PROPS(_Ob) _ULIB_DETAIL_UNINTRUSIVE_SERIALIZE_PROPS(_Ob)
+#define ULIB_SERIALIZE_OBJECT(_Ob, ...)                                        \
+  _ULIB_DETAIL_UNINTRUSIVE_SERIALIZE_OBJECT(_Ob, __VA_ARGS__)
 #define AR(_name) _ULIB_DETAIL_UNINTRUSIVE_AR_(_name)
 #define HR(_name) _ULIB_DETAIL_UNINTRUSIVE_AR_(_name)
 #endif
 
-
 #define ULIB_SERIALIZE_ACCESS                                                  \
   friend class boost::serialization::access;                                   \
   template <class T> friend class boost::serialization::access2;
@@ -191,26 +167,25 @@ namespace uLib {
   BOOST_CLASS_EXPORT_KEY(_FullNamespaceClass)
 
 #define ULIB_CLASS_EXPORT_OBJECT_KEY(_FullNamespaceClass)                      \
-    BOOST_CLASS_EXPORT_KEY(_FullNamespaceClass)                      \
-    BOOST_CLASS_EXPORT_KEY(_FullNamespaceClass::ObjectProps)         \
-    BOOST_CLASS_EXPORT_KEY(uLib::ObjectPropsImpl<_FullNamespaceClass>)
-
+  BOOST_CLASS_EXPORT_KEY(_FullNamespaceClass)
 
 #define _SERIALIZE_IMPL_SEQ                                                                   \
-    (uLib::Archive::text_iarchive) \
-    (uLib::Archive::text_oarchive) \
-    (uLib::Archive::hrt_iarchive)  \
-    (uLib::Archive::hrt_oarchive)  \
-    (uLib::Archive::xml_iarchive)  \
-    (uLib::Archive::xml_oarchive)  \
-    (uLib::Archive::log_archive)
-
+  (uLib::Archive::text_iarchive)(uLib::Archive::text_oarchive)(                               \
+      uLib::Archive::                                                                         \
+          hrt_iarchive)(uLib::Archive::                                                       \
+                            hrt_oarchive)(uLib::Archive::                                     \
+                                              xml_iarchive)(uLib::Archive::                   \
+                                                                xml_oarchive)(uLib::Archive:: \
+                                                                                  log_archive)
 
 /** Solving virtual class check problem */
-#define _ULIB_DETAIL_SPECIALIZE_IS_VIRTUAL_BASE(_Base,_Derived)    namespace boost{ template<> struct is_virtual_base_of<_Base,_Derived>: public boost::mpl::true_ {}; }
-#define _ULIB_DETAIL_SPECIALIZE_IS_VIRTUAL_BASE_OP(r,data,elem) _ULIB_DETAIL_SPECIALIZE_IS_VIRTUAL_BASE(elem,data)
-
-
+#define _ULIB_DETAIL_SPECIALIZE_IS_VIRTUAL_BASE(_Base, _Derived)               \
+  namespace boost {                                                            \
+  template <>                                                                  \
+  struct is_virtual_base_of<_Base, _Derived> : public boost::mpl::true_ {};    \
+  }
+#define _ULIB_DETAIL_SPECIALIZE_IS_VIRTUAL_BASE_OP(r, data, elem)              \
+  _ULIB_DETAIL_SPECIALIZE_IS_VIRTUAL_BASE(elem, data)
 
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
@@ -225,33 +200,52 @@ namespace uLib {
 #define _ULIB_DETAIL_INTRUSIVE_SERIALIZE_FUNC(Class, Archive)                  \
   template void Class::serialize(Archive &ar, const unsigned int);
 
-#define _ULIB_DETAIL_INTRUSIVE_SERIALIZE_FUNC_OP(r,data,elem) _ULIB_DETAIL_INTRUSIVE_SERIALIZE_FUNC(data,elem);
+#define _ULIB_DETAIL_INTRUSIVE_SERIALIZE_FUNC_OP(r, data, elem)                \
+  _ULIB_DETAIL_INTRUSIVE_SERIALIZE_FUNC(data, elem);
 
 #define _ULIB_DETAIL_INTRUSIVE_SERIALIZABLE_OBJECT                             \
   typedef boost::mpl::bool_<true> serializable;                                \
-    typedef boost::mpl::remove_if< TypeList, IsUnSerializable >::type SerilizableTypeList;       \
-    void PrintSerializableListId() { boost::mpl::for_each<SerilizableTypeList>(PrintTypeId()); } \
-    template <class ArchiveT> void serialize(ArchiveT &ar,const unsigned int version);           \
-    template <class ArchiveT> void serialize_parents(ArchiveT &ar,const unsigned int version);   \
-    template <class ArchiveT> void save_override(ArchiveT &ar,const unsigned int version);
+  typedef boost::mpl::remove_if<TypeList, IsUnSerializable>::type              \
+      SerilizableTypeList;                                                     \
+  void PrintSerializableListId() {                                             \
+    boost::mpl::for_each<SerilizableTypeList>(PrintTypeId());                  \
+  }                                                                            \
+  template <class ArchiveT>                                                    \
+  void serialize(ArchiveT &ar, const unsigned int version);                    \
+  template <class ArchiveT>                                                    \
+  void serialize_parents(ArchiveT &ar, const unsigned int version);            \
+  template <class ArchiveT>                                                    \
+  void save_override(ArchiveT &ar, const unsigned int version);
 
 #define _ULIB_DETAIL_INTRUSIVE_SERIALIZE_OBJECT(_Ob, ...)                      \
-    template <class ArchiveT> void _Ob::serialize(ArchiveT &ar, const unsigned int version) { \
-    boost::serialization::void_cast_register<_Ob,_Ob::BaseClass>(static_cast<_Ob *>(NULL),static_cast<_Ob::BaseClass *>(NULL));   \
+  template <class ArchiveT>                                                    \
+  void _Ob::serialize(ArchiveT &ar, const unsigned int version) {              \
+    boost::serialization::void_cast_register<_Ob, _Ob::BaseClass>(             \
+        static_cast<_Ob *>(NULL), static_cast<_Ob::BaseClass *>(NULL));        \
     _Ob::serialize_parents(ar, version);                                       \
-    _Ob::save_override(ar,version); }\
-    template <class ArchiveT> void _Ob::serialize_parents(ArchiveT &ar, const unsigned int v) { \
-    BOOST_PP_SEQ_FOR_EACH(_AR_OP,ar,BOOST_PP_TUPLE_TO_SEQ((__VA_ARGS__))); } \
-    BOOST_PP_SEQ_FOR_EACH(_ULIB_DETAIL_INTRUSIVE_SERIALIZE_FUNC_OP,_Ob,_SERIALIZE_IMPL_SEQ)\
-    BOOST_PP_SEQ_FOR_EACH(_ULIB_DETAIL_SPECIALIZE_IS_VIRTUAL_BASE_OP,_Ob,BOOST_PP_TUPLE_TO_SEQ((__VA_ARGS__))) \
+    _Ob::save_override(ar, version);                                           \
+  }                                                                            \
+  template <class ArchiveT>                                                    \
+  void _Ob::serialize_parents(ArchiveT &ar, const unsigned int v) {            \
+    BOOST_PP_SEQ_FOR_EACH(_AR_OP, ar, BOOST_PP_TUPLE_TO_SEQ((__VA_ARGS__)));   \
+  }                                                                            \
+  BOOST_PP_SEQ_FOR_EACH(_ULIB_DETAIL_INTRUSIVE_SERIALIZE_FUNC_OP, _Ob,         \
+                        _SERIALIZE_IMPL_SEQ)                                   \
+  BOOST_PP_SEQ_FOR_EACH(_ULIB_DETAIL_SPECIALIZE_IS_VIRTUAL_BASE_OP, _Ob,       \
+                        BOOST_PP_TUPLE_TO_SEQ((__VA_ARGS__)))                  \
   ULIB_CLASS_EXPORT_IMPLEMENT(_Ob)                                             \
   namespace boost {                                                            \
   namespace serialization {                                                    \
-    template<class ArchiveT> inline void load_construct_data(ArchiveT & ar, _Ob *o, const unsigned int file_version) \
-    { ::new(o)_Ob(); o->init_parameters(); } }}\
-    template <class ArchiveT> void _Ob::save_override(ArchiveT &ar, const unsigned int version)
-
-
+  template <class ArchiveT>                                                    \
+  inline void load_construct_data(ArchiveT &ar, _Ob *o,                        \
+                                  const unsigned int file_version) {           \
+    ::new (o) _Ob();                                                           \
+    o->init_parameters();                                                      \
+  }                                                                            \
+  }                                                                            \
+  }                                                                            \
+  template <class ArchiveT>                                                    \
+  void _Ob::save_override(ArchiveT &ar, const unsigned int version)
 
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
@@ -261,96 +255,134 @@ namespace uLib {
 ////////////////////////////////////////////////////////////////////////////////
 // UNINTRUSIVE SERIALIZATION
 
-#define _UNAR_OP(r,data,elem) ar&boost::serialization::make_nvp(BOOST_PP_STRINGIZE(elem),boost::serialization::base_object<elem>(ob));
+#define _UNAR_OP(r, data, elem)                                                \
+  ar &boost::serialization::make_nvp(                                          \
+      BOOST_PP_STRINGIZE(elem), boost::serialization::base_object<elem>(ob));
 
 #define _ULIB_DETAIL_UNINTRUSIVE_SERIALIZE_FUNC(Class, Archive)                \
-    template void boost::serialization::serialize(Archive &ar, Class &ob, const unsigned int i);
-
-#define _ULIB_DETAIL_UNINTRUSIVE_SERIALIZE_FUNC_OP(r,data,elem) _ULIB_DETAIL_UNINTRUSIVE_SERIALIZE_FUNC(data,elem)
+  template void boost::serialization::serialize(Archive &ar, Class &ob,        \
+                                                const unsigned int i);
 
+#define _ULIB_DETAIL_UNINTRUSIVE_SERIALIZE_FUNC_OP(r, data, elem)              \
+  _ULIB_DETAIL_UNINTRUSIVE_SERIALIZE_FUNC(data, elem)
 
 // NOTE: becouse of BOOST_PP_VARIADIC_SIZE issue of some boost macro has two
 // different implementation
 
 #define _ULIB_DETAIL_UNINTRUSIVE_SERIALIZABLE(_Ob)                             \
-    namespace boost { namespace serialization { \
-    template <class ArchiveT> void serialize         (ArchiveT &ar, _Ob &ob, const unsigned int version); \
-    template <class ArchiveT> void serialize_parents (ArchiveT &ar, _Ob &ob, const unsigned int version); \
-    template <> struct access2< _Ob > { template <class ArchiveT> static void save_override (ArchiveT &ar, _Ob &ob, const unsigned int version); }; }}
+  namespace boost {                                                            \
+  namespace serialization {                                                    \
+  template <class ArchiveT>                                                    \
+  void serialize(ArchiveT &ar, _Ob &ob, const unsigned int version);           \
+  template <class ArchiveT>                                                    \
+  void serialize_parents(ArchiveT &ar, _Ob &ob, const unsigned int version);   \
+  template <> struct access2<_Ob> {                                            \
+    template <class ArchiveT>                                                  \
+    static void save_override(ArchiveT &ar, _Ob &ob,                           \
+                              const unsigned int version);                     \
+  };                                                                           \
+  }                                                                            \
+  }
 
 #define _ULIB_DETAIL_UNINTRUSIVE_SERIALIZE(_Ob)                                \
-    namespace boost { namespace serialization { \
-    template <class ArchiveT> void serialize_parents(ArchiveT &ar, _Ob &ob, const unsigned int v) {} \
-    template <class ArchiveT> void serialize  (ArchiveT &ar, _Ob &ob, const unsigned int version) { \
+  namespace boost {                                                            \
+  namespace serialization {                                                    \
+  template <class ArchiveT>                                                    \
+  void serialize_parents(ArchiveT &ar, _Ob &ob, const unsigned int v) {}       \
+  template <class ArchiveT>                                                    \
+  void serialize(ArchiveT &ar, _Ob &ob, const unsigned int version) {          \
     serialize_parents(ar, ob, version);                                        \
-    access2< _Ob >::save_override(ar,ob,version); } }}\
+    access2<_Ob>::save_override(ar, ob, version);                              \
+  }                                                                            \
+  }                                                                            \
+  }                                                                            \
   ULIB_CLASS_EXPORT_IMPLEMENT(_Ob)                                             \
-    BOOST_PP_SEQ_FOR_EACH(_ULIB_DETAIL_UNINTRUSIVE_SERIALIZE_FUNC_OP,_Ob,_SERIALIZE_IMPL_SEQ)\
-    template <class ArchiveT> void boost::serialization::access2< _Ob >::save_override(ArchiveT &ar, _Ob &ob, const unsigned int version)
+  BOOST_PP_SEQ_FOR_EACH(_ULIB_DETAIL_UNINTRUSIVE_SERIALIZE_FUNC_OP, _Ob,       \
+                        _SERIALIZE_IMPL_SEQ)                                   \
+  template <class ArchiveT>                                                    \
+  void boost::serialization::access2<_Ob>::save_override(                      \
+      ArchiveT &ar, _Ob &ob, const unsigned int version)
 
 #define _ULIB_DETAIL_UNINTRUSIVE_SERIALIZE_DERIVED(_Ob, ...)                   \
-    namespace boost { namespace serialization { \
-    template <class ArchiveT> void serialize_parents(ArchiveT &ar, _Ob &ob, const unsigned int v) { \
-    BOOST_PP_IF(BOOST_PP_VARIADIC_SIZE((__VA_ARGS__)),BOOST_PP_SEQ_FOR_EACH(_UNAR_OP,ob,BOOST_PP_TUPLE_TO_SEQ((__VA_ARGS__)));,) } \
-    template <class ArchiveT> void serialize  (ArchiveT &ar, _Ob &ob, const unsigned int version) { \
+  namespace boost {                                                            \
+  namespace serialization {                                                    \
+  template <class ArchiveT>                                                    \
+  void serialize_parents(ArchiveT &ar, _Ob &ob, const unsigned int v) {        \
+    BOOST_PP_IF(BOOST_PP_VARIADIC_SIZE((__VA_ARGS__)),                         \
+                BOOST_PP_SEQ_FOR_EACH(_UNAR_OP, ob,                            \
+                                      BOOST_PP_TUPLE_TO_SEQ((__VA_ARGS__)));   \
+                , )                                                            \
+  }                                                                            \
+  template <class ArchiveT>                                                    \
+  void serialize(ArchiveT &ar, _Ob &ob, const unsigned int version) {          \
     serialize_parents(ar, ob, version);                                        \
-    access2< _Ob >::save_override    (ar,ob,version); } }}\
+    access2<_Ob>::save_override(ar, ob, version);                              \
+  }                                                                            \
+  }                                                                            \
+  }                                                                            \
   ULIB_CLASS_EXPORT_IMPLEMENT(_Ob)                                             \
-    BOOST_PP_SEQ_FOR_EACH(_ULIB_DETAIL_UNINTRUSIVE_SERIALIZE_FUNC_OP,_Ob,_SERIALIZE_IMPL_SEQ) \
-    BOOST_PP_SEQ_FOR_EACH(_ULIB_DETAIL_SPECIALIZE_IS_VIRTUAL_BASE_OP,_Ob,BOOST_PP_TUPLE_TO_SEQ((__VA_ARGS__))) \
-    template <class ArchiveT> void boost::serialization::access2< _Ob >::save_override(ArchiveT &ar, _Ob &ob, const unsigned int version)
-
+  BOOST_PP_SEQ_FOR_EACH(_ULIB_DETAIL_UNINTRUSIVE_SERIALIZE_FUNC_OP, _Ob,       \
+                        _SERIALIZE_IMPL_SEQ)                                   \
+  BOOST_PP_SEQ_FOR_EACH(_ULIB_DETAIL_SPECIALIZE_IS_VIRTUAL_BASE_OP, _Ob,       \
+                        BOOST_PP_TUPLE_TO_SEQ((__VA_ARGS__)))                  \
+  template <class ArchiveT>                                                    \
+  void boost::serialization::access2<_Ob>::save_override(                      \
+      ArchiveT &ar, _Ob &ob, const unsigned int version)
 
 #define _ULIB_DETAIL_UNINTRUSIVE_SERIALIZABLE_OBJECT(_Ob)                      \
-    namespace boost { namespace serialization { \
-    template <class ArchiveT> void serialize         (ArchiveT &ar, _Ob &ob, const unsigned int version); \
-    template <class ArchiveT> void serialize_parents (ArchiveT &ar, _Ob &ob, const unsigned int version); \
-    template <> struct access2< _Ob > { template <class ArchiveT> static void save_override (ArchiveT &ar, _Ob &ob, const unsigned int version); }; \
-    template <class ArchiveT> void serialize         (ArchiveT &ar, class _Ob::ObjectProps &ob, const unsigned int version); \
-    template <class ArchiveT> void save_override     (ArchiveT &ar, class _Ob::ObjectProps &ob, const unsigned int version); }}
+  namespace boost {                                                            \
+  namespace serialization {                                                    \
+  template <class ArchiveT>                                                    \
+  void serialize(ArchiveT &ar, _Ob &ob, const unsigned int version);           \
+  template <class ArchiveT>                                                    \
+  void serialize_parents(ArchiveT &ar, _Ob &ob, const unsigned int version);   \
+  template <> struct access2<_Ob> {                                            \
+    template <class ArchiveT>                                                  \
+    static void save_override(ArchiveT &ar, _Ob &ob,                           \
+                              const unsigned int version);                     \
+  };                                                                           \
+  }                                                                            \
+  }
 
 #define _ULIB_DETAIL_UNINTRUSIVE_SERIALIZE_OBJECT(_Ob, ...)                    \
-    namespace boost { namespace serialization { \
-    template <class ArchiveT> void serialize_parents(ArchiveT &ar, _Ob &ob, const unsigned int v) { \
-    /* PP  serialize */ BOOST_PP_SEQ_FOR_EACH(_UNAR_OP,ob,BOOST_PP_TUPLE_TO_SEQ((__VA_ARGS__))); \
+  namespace boost {                                                            \
+  namespace serialization {                                                    \
+  template <class ArchiveT>                                                    \
+  void serialize_parents(ArchiveT &ar, _Ob &ob, const unsigned int v) {        \
+    /* PP  serialize */ BOOST_PP_SEQ_FOR_EACH(                                 \
+        _UNAR_OP, ob, BOOST_PP_TUPLE_TO_SEQ((__VA_ARGS__)));                   \
   /* MPL serialize */ /*uLib::mpl::for_each<_Ob::BaseList>(uLib::detail::Serializable::serialize_baseobject<_Ob,ArchiveT>(ob,ar) );*/ }                                                          \
-    template<class ArchiveT> inline void load_construct_data(ArchiveT & ar, _Ob *ob, const unsigned int file_version) { \
-    ::new(ob)_Ob(); uLib::detail::ObjectProps::initializer::init_object(ob); } \
-    template <class ArchiveT> void serialize  (ArchiveT &ar, _Ob &ob, const unsigned int version) { \
-    void_cast_register<_Ob,_Ob::BaseClass>(static_cast<_Ob *>(NULL),static_cast<_Ob::BaseClass *>(NULL)); /*fix*/  \
+  template <class ArchiveT>                                                    \
+  inline void load_construct_data(ArchiveT &ar, _Ob *ob,                       \
+                                  const unsigned int file_version) {           \
+    ::new (ob) _Ob();                                                          \
+  }                                                                            \
+  template <class ArchiveT>                                                    \
+  void serialize(ArchiveT &ar, _Ob &ob, const unsigned int version) {          \
+    void_cast_register<_Ob, _Ob::BaseClass>(                                   \
+        static_cast<_Ob *>(NULL),                                              \
+        static_cast<_Ob::BaseClass *>(NULL)); /*fix*/                          \
     serialize_parents(ar, ob, version);                                        \
-    access2< _Ob >::save_override    (ar,ob,version); } }}\
+    access2<_Ob>::save_override(ar, ob, version);                              \
+  }                                                                            \
+  }                                                                            \
+  }                                                                            \
   ULIB_CLASS_EXPORT_IMPLEMENT(_Ob)                                             \
-    BOOST_PP_SEQ_FOR_EACH(_ULIB_DETAIL_SPECIALIZE_IS_VIRTUAL_BASE_OP,_Ob,BOOST_PP_TUPLE_TO_SEQ((__VA_ARGS__))) \
-    BOOST_PP_SEQ_FOR_EACH(_ULIB_DETAIL_UNINTRUSIVE_SERIALIZE_FUNC_OP,_Ob,_SERIALIZE_IMPL_SEQ)\
-    template <class ArchiveT> void boost::serialization::access2< _Ob >::save_override(ArchiveT &ar, _Ob &ob, const unsigned int version)
-
-#define _ULIB_DETAIL_UNINTRUSIVE_SERIALIZE_PROPS(_Ob) \
-    namespace boost { namespace serialization { \
-    template <class ArchiveT> void serialize  (ArchiveT &ar, _Ob::ObjectProps &ob, const unsigned int version) { \
-    save_override    (ar,ob,version); } }}\
-    BOOST_PP_SEQ_FOR_EACH(_ULIB_DETAIL_UNINTRUSIVE_SERIALIZE_FUNC_OP,_Ob::ObjectProps,_SERIALIZE_IMPL_SEQ)\
-    ULIB_CLASS_EXPORT_IMPLEMENT(_Ob::ObjectProps) \
-    ULIB_CLASS_EXPORT_IMPLEMENT(uLib::ObjectPropsImpl<_Ob>) \
-    template <class ArchiveT> void boost::serialization::save_override(ArchiveT &ar, _Ob::ObjectProps &ob, const unsigned int version)
-
-
-#define _ULIB_DETAIL_UNINTRUSIVE_AR_(name) boost::serialization::make_nvp(BOOST_PP_STRINGIZE(name),ob.name)
-
-
-
-
-
-
-
+  BOOST_PP_SEQ_FOR_EACH(_ULIB_DETAIL_SPECIALIZE_IS_VIRTUAL_BASE_OP, _Ob,       \
+                        BOOST_PP_TUPLE_TO_SEQ((__VA_ARGS__)))                  \
+  BOOST_PP_SEQ_FOR_EACH(_ULIB_DETAIL_UNINTRUSIVE_SERIALIZE_FUNC_OP, _Ob,       \
+                        _SERIALIZE_IMPL_SEQ)                                   \
+  template <class ArchiveT>                                                    \
+  void boost::serialization::access2<_Ob>::save_override(                      \
+      ArchiveT &ar, _Ob &ob, const unsigned int version)
 
+#define _ULIB_DETAIL_UNINTRUSIVE_AR_(name)                                     \
+  boost::serialization::make_nvp(BOOST_PP_STRINGIZE(name), ob.name)
 
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 
-
-
 namespace detail {
 
 struct Serializable {
@@ -360,53 +392,34 @@ struct Serializable {
    * This only works if UNINTRUSIVE SERIALIZATION is applyed; in intrusive
    * cases a has_serialize trait should be implemented
    */
-    template <class T>
-    struct serializable_trait : mpl::bool_<false> {};
+  template <class T> struct serializable_trait : mpl::bool_<false> {};
 
   /**
    * IsA Serializable Implementation Template
    */
-    template <class T>
-    struct IsA : serializable_trait<T> {};
+  template <class T> struct IsA : serializable_trait<T> {};
 
-    template <class ThisClass, class Archive>
-    struct serialize_baseobject {
+  template <class ThisClass, class Archive> struct serialize_baseobject {
     ThisClass &m_object;
     Archive &m_ar;
     serialize_baseobject(ThisClass &o, Archive &ar) : m_object(o), m_ar(ar) {}
     template <class T> void operator()(T &o) {
       m_ar &boost::serialization::make_nvp(
-                        typeid(T).name() ,
-                        boost::serialization::base_object<T>(m_object));
+          typeid(T).name(), boost::serialization::base_object<T>(m_object));
     }
   };
-
-
 };
 
-
-} // detail
-
-
-
-
+} // namespace detail
 
 struct Serializable {
   friend class boost::serialization::access;
   template <class T> friend class boost::serialization::access2;
   virtual ~Serializable() {}
+
 protected:
 };
 
-
-
-
-
-} // uLib
-
-
-
-
-
+} // namespace uLib
 
 #endif // U_SERIALIZABLE_H

src/Core/Signal.h

@@ -23,21 +23,19 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
 #ifndef U_CORE_SIGNAL_H
 #define U_CORE_SIGNAL_H
 
 #include <boost/typeof/typeof.hpp>
 
 #include <boost/signals2/signal.hpp>
-#include <boost/signals2/slot.hpp>
 #include <boost/signals2/signal_type.hpp>
+#include <boost/signals2/slot.hpp>
 
 #include "Function.h"
+#include <boost/bind/bind.hpp>
 
-
-
+using namespace boost::placeholders;
 
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
@@ -52,8 +50,11 @@
 #define SIGNAL(a) BOOST_STRINGIZE(a)
 
 #define _ULIB_DETAIL_SIGNAL_EMIT(_name, ...)                                   \
-        static BOOST_AUTO(sig,this->findOrAddSignal(&_name));     \
-        sig->operator()(__VA_ARGS__);
+  do {                                                                         \
+    BOOST_AUTO(sig, this->findOrAddSignal(&_name));                            \
+    if (sig)                                                                   \
+      sig->operator()(__VA_ARGS__);                                            \
+  } while (0)
 
 /**
  * Utility macro to implement signal emission implementa una delle seguenti:
@@ -67,102 +68,100 @@
  * static BOOST_AUTO(sig,this->findOrAddSignal(&Ob1::V0));
  *   sig->operator()();
  */
-#define ULIB_SIGNAL_EMIT(_name,...) _ULIB_DETAIL_SIGNAL_EMIT(_name,__VA_ARGS__)
-
+#define ULIB_SIGNAL_EMIT(_name, ...)                                           \
+  _ULIB_DETAIL_SIGNAL_EMIT(_name, __VA_ARGS__)
 
 namespace uLib {
 
-
 // A boost::signal wrapper structure ///////////////////////////////////////////
 
 // TODO ...
 
 typedef boost::signals2::signal_base SignalBase;
 
-template <typename T>
-struct Signal {
+template <typename T> struct Signal {
   typedef boost::signals2::signal<T> type;
 };
 
-
-
 ////////////////////////////////////////////////////////////////////////////////
 
-
 namespace detail {
 
-
-template <typename FuncT, int arity>
+template <typename FuncT, typename SigSignature, int arity>
 struct ConnectSignal {};
 
-template <typename FuncT>
-struct ConnectSignal< FuncT, 0 > {
-    static void connect(SignalBase *sigb, FuncT slof, typename FunctionPointer<FuncT>::Object *receiver) {
-        typedef typename Signal<typename FunctionPointer<FuncT>::SignalSignature>::type SigT;
+template <typename FuncT, typename SigSignature>
+struct ConnectSignal<FuncT, SigSignature, 0> {
+  static void connect(SignalBase *sigb, FuncT slof,
+                      typename FunctionPointer<FuncT>::Object *receiver) {
+    typedef typename Signal<SigSignature>::type SigT;
     reinterpret_cast<SigT *>(sigb)->connect(slof);
   }
 };
 
-template <typename FuncT>
-struct ConnectSignal< FuncT, 1 > {
-    static void connect(SignalBase *sigb, FuncT slof, typename FunctionPointer<FuncT>::Object *receiver) {
-        typedef typename Signal<typename FunctionPointer<FuncT>::SignalSignature>::type SigT;
+template <typename FuncT, typename SigSignature>
+struct ConnectSignal<FuncT, SigSignature, 1> {
+  static void connect(SignalBase *sigb, FuncT slof,
+                      typename FunctionPointer<FuncT>::Object *receiver) {
+    typedef typename Signal<SigSignature>::type SigT;
     reinterpret_cast<SigT *>(sigb)->connect(boost::bind(slof, receiver));
   }
 };
 
-template <typename FuncT>
-struct ConnectSignal< FuncT, 2 > {
-    static void connect(SignalBase *sigb, FuncT slof, typename FunctionPointer<FuncT>::Object *receiver) {
-        typedef typename Signal<typename FunctionPointer<FuncT>::SignalSignature>::type SigT;
+template <typename FuncT, typename SigSignature>
+struct ConnectSignal<FuncT, SigSignature, 2> {
+  static void connect(SignalBase *sigb, FuncT slof,
+                      typename FunctionPointer<FuncT>::Object *receiver) {
+    typedef typename Signal<SigSignature>::type SigT;
     reinterpret_cast<SigT *>(sigb)->connect(boost::bind(slof, receiver, _1));
   }
 };
 
-template <typename FuncT>
-struct ConnectSignal< FuncT, 3 > {
-    static void connect(SignalBase *sigb, FuncT slof,  typename FunctionPointer<FuncT>::Object *receiver) {
-        typedef typename Signal<typename FunctionPointer<FuncT>::SignalSignature>::type SigT;
-        reinterpret_cast<SigT*>(sigb)->connect(boost::bind(slof,receiver,_1,_2));
+template <typename FuncT, typename SigSignature>
+struct ConnectSignal<FuncT, SigSignature, 3> {
+  static void connect(SignalBase *sigb, FuncT slof,
+                      typename FunctionPointer<FuncT>::Object *receiver) {
+    typedef typename Signal<SigSignature>::type SigT;
+    reinterpret_cast<SigT *>(sigb)->connect(
+        boost::bind(slof, receiver, _1, _2));
   }
 };
 
-template <typename FuncT>
-struct ConnectSignal< FuncT, 4 > {
-    static void connect(SignalBase *sigb, FuncT slof,  typename FunctionPointer<FuncT>::Object *receiver) {
-        typedef typename Signal<typename FunctionPointer<FuncT>::SignalSignature>::type SigT;
-        reinterpret_cast<SigT*>(sigb)->connect(boost::bind(slof,receiver,_1,_2,_3));
+template <typename FuncT, typename SigSignature>
+struct ConnectSignal<FuncT, SigSignature, 4> {
+  static void connect(SignalBase *sigb, FuncT slof,
+                      typename FunctionPointer<FuncT>::Object *receiver) {
+    typedef typename Signal<SigSignature>::type SigT;
+    reinterpret_cast<SigT *>(sigb)->connect(
+        boost::bind(slof, receiver, _1, _2, _3));
   }
 };
 
-template <typename FuncT>
-struct ConnectSignal< FuncT, 5 > {
-    static void connect(SignalBase *sigb, FuncT slof,  typename FunctionPointer<FuncT>::Object *receiver) {
-        typedef typename Signal<typename FunctionPointer<FuncT>::SignalSignature>::type SigT;
-        reinterpret_cast<SigT*>(sigb)->connect(boost::bind(slof,receiver,_1,_2,_3,_4));
+template <typename FuncT, typename SigSignature>
+struct ConnectSignal<FuncT, SigSignature, 5> {
+  static void connect(SignalBase *sigb, FuncT slof,
+                      typename FunctionPointer<FuncT>::Object *receiver) {
+    typedef typename Signal<SigSignature>::type SigT;
+    reinterpret_cast<SigT *>(sigb)->connect(
+        boost::bind(slof, receiver, _1, _2, _3, _4));
   }
 };
 
+} // namespace detail
 
-} // detail
-
-
-
-template <typename FuncT>
-SignalBase *NewSignal(FuncT f) {
-    // seems to work wow !
-    return new Signal<void()>::type;
+template <typename FuncT> SignalBase *NewSignal(FuncT f) {
+  return new
+      typename Signal<typename FunctionPointer<FuncT>::SignalSignature>::type;
 }
 
-template <typename FuncT>
-void ConnectSignal(SignalBase *sigb, FuncT slof, typename FunctionPointer<FuncT>::Object *receiver)
-{
-    detail::ConnectSignal< FuncT, FunctionPointer<FuncT>::arity >::connect(sigb,slof,receiver);
+template <typename SigSignature, typename FuncT>
+void ConnectSignal(SignalBase *sigb, FuncT slof,
+                   typename FunctionPointer<FuncT>::Object *receiver) {
+  detail::ConnectSignal<FuncT, SigSignature,
+                        FunctionPointer<FuncT>::arity>::connect(sigb, slof,
+                                                                receiver);
 }
 
-
-
-
-} // uLib
+} // namespace uLib
 
 #endif // SIGNAL_H

src/Core/StringReader.h

@@ -31,7 +31,6 @@
 #include <istream>
 #include <algorithm>
 
-#include "Core/Vector.h"
 #include <boost/lexical_cast.hpp>
 #include <boost/algorithm/string.hpp>
 

src/Core/Types.h

@@ -23,8 +23,6 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
 #ifndef U_CORE_TYPES_H
 #define U_CORE_TYPES_H
 
@@ -33,20 +31,13 @@
 
 #include <boost/preprocessor.hpp>
 
-#include <ltk/ltktypes.h>
+// #include <ltk/ltktypes.h>
 
 #include "Core/Macros.h"
 #include "Core/Mpl.h"
 
-
-
-
-
-
-
 namespace uLib {
 
-
 ////////////////////////////////////////////////////////////////////////////////
 
 namespace detail {
@@ -72,23 +63,19 @@ struct TypeIntrospection {
   */
 
   /** IsA Introspectable Object Implementation Template */
-    template <class T>
-    struct IsIntrospectable : has_type_info<T> {};
+  template <class T> struct IsIntrospectable : has_type_info<T> {};
 
   template <typename T> struct access {
     typedef typename T::type_info type_info;
   };
 
-    template <typename T>
-    struct child_first_impl {
+  template <typename T> struct child_first_impl {
 
-        template <class T1, bool cond>
-        struct lambda_CFList_f {
+    template <class T1, bool cond> struct lambda_CFList_f {
       typedef mpl::vector<T1> type;
     };
 
-        template <class T1>
-        struct lambda_CFList_f<T1,true> {
+    template <class T1> struct lambda_CFList_f<T1, true> {
       //            typedef typename T1::type_info::CFList type;
       typedef typename access<T1>::type_info::CFList type;
     };
@@ -97,39 +84,28 @@ struct TypeIntrospection {
     struct lambda_CFList : lambda_CFList_f<T1, has_type_info<T1>::value> {};
 
     /** Transforms all Base Type into proper CFList */
-        typedef typename mpl::transform_view < typename access<T>::type_info::BaseList
-                                             , lambda_CFList<mpl::_>
-                                             >::type CFListSeq;
+    typedef
+        typename mpl::transform_view<typename access<T>::type_info::BaseList,
+                                     lambda_CFList<mpl::_>>::type CFListSeq;
 
     /** Folds each CFList into a new sequence */
-        typedef typename mpl::fold< CFListSeq
-                                  , mpl::vector<>
-                                  , mpl::copy< mpl::_1
-                                             , mpl::back_inserter<mpl::_2>
-                                             >
-                                  >::type Childs;
+    typedef typename mpl::fold<
+        CFListSeq, mpl::vector<>,
+        mpl::copy<mpl::_1, mpl::back_inserter<mpl::_2>>>::type Childs;
 
     /** Add This Class to final CFList sequence */
-        typedef typename mpl::copy< Childs
-                                  , mpl::back_inserter< mpl::vector<T> >
-                                  >::type type;
+    typedef typename mpl::copy<Childs, mpl::back_inserter<mpl::vector<T>>>::type
+        type;
   };
 
-
   /**
    * Tests if T has a member called type_info then compile type CFList
    */
   template <typename T>
-    struct child_first : mpl::if_< has_type_info<T>
-                                 , child_first_impl<T>
-                                 , mpl::vector<>
-                                 >::type {};
-
-
+  struct child_first
+      : mpl::if_<has_type_info<T>, child_first_impl<T>, mpl::vector<>>::type {};
 };
 
-
-
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
@@ -137,34 +113,30 @@ struct TypeIntrospection {
 
 // #define _REPETITION_V(vz,vn,vdata)
 
-
 // template < class TypeList >
 // class TypeAdapterInputInterface {
 //     virtual ~TypeAdapterInputInterface() {}
 // public:
 
-
-
 //    virtual void operator()(int val)         {}
 //    virtual void operator()(std::string val) {}
 //};
 
-
-
-
-
-
-
-} // detail ////////////////////////////////////////////////////////////////////
-
+} // namespace detail
 
 #define CONSTEXPR BOOST_CONSTEXPR
 
-
-typedef ltk::Real_t      Real_t;
-typedef ltk::Id_t        Id_t;
-//typedef ltk::Size_t      Size_t;
-typedef ltk::Pointer_t   Pointer_t;
+// typedef ltk::Real_t      Real_t;
+#ifndef LTK_DOUBLE_PRECISION
+typedef float Real_t;
+#else
+typedef double Real_t;
+#endif
+// typedef ltk::Id_t        Id_t;
+typedef id_t Id_t;
+////typedef ltk::Size_t      Size_t;
+// typedef ltk::Pointer_t   Pointer_t;
+typedef void *Pointer_t;
 typedef bool Bool_t; // Boolean (0=false, 1=true) (bool)
 
 //--- bit manipulation ---------------------------------------------------------
@@ -184,14 +156,11 @@ typedef bool             Bool_t;      //Boolean (0=false, 1=true) (bool)
 #define TESTBIT(n, i) ((Bool_t)(((n) & BIT(i)) != 0))
 #endif
 
-
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 // TYPE INTROSPECTION FOR OBJECTS //
 
-
-
 #define uLibTypeMacro(thisClass, ...)                                          \
                                                                                \
   /* Friendship detail for accessing introspection */                          \
@@ -206,71 +175,38 @@ typedef bool             Bool_t;      //Boolean (0=false, 1=true) (bool)
     typedef thisClass ThisClass;                                               \
     typedef uLib::mpl::vector<__VA_ARGS__, thisClass> TypeList;                \
     typedef uLib::mpl::vector<__VA_ARGS__> BaseList;                           \
-      typedef uLib::detail::TypeIntrospection::child_first<ThisClass>::type CFList; \
+    typedef uLib::detail::TypeIntrospection::child_first<ThisClass>::type      \
+        CFList;                                                                \
   };                                                                           \
                                                                                \
 public:                                                                        \
   typedef type_info::BaseClass BaseClass;                                      \
   virtual const char *type_name() const { return type_info::name; }            \
-    /* Object Props fwd declaration*/ \
-    struct ObjectProps; \
   /**/
 
-
 /**
  * TypeList inheritance introspection
  */
 struct TypeIntrospection {
   template <typename T>
   struct child_first : detail::TypeIntrospection::child_first<T> {};
-
 };
 
-
-
-
-
-
 // SISTEMARE //
 struct PrintTypeId {
-    template <class T>
-    void operator()(T) const
-    { std::cout << typeid(T).name() << std::endl; }
+  template <class T> void operator()(T) const {
+    std::cout << typeid(T).name() << std::endl;
+  }
 
-    template <typename SeqT>
-    static void PrintMplSeq(SeqT *p = NULL) { boost::mpl::for_each<SeqT>(PrintTypeId()); }
+  template <typename SeqT> static void PrintMplSeq(SeqT *p = NULL) {
+    boost::mpl::for_each<SeqT>(PrintTypeId());
+  }
 
-    template <typename Class>
-    static void PrintType(Class *p = NULL) { std::cout << typeid(Class).name() << std::endl; }
+  template <typename Class> static void PrintType(Class *p = NULL) {
+    std::cout << typeid(Class).name() << std::endl;
+  }
 };
 
-
-
-
-
-
-
-} // uLib
+} // namespace uLib
 
 #endif // U_CORE_TYPES_H
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-

src/Core/Uuid.h

@@ -23,59 +23,42 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
 #ifndef U_CORE_UUID_H
 #define U_CORE_UUID_H
 
 #include <iostream>
+#include <vector>
 
-#include <boost/uuid/uuid.hpp>
 #include <boost/uuid/name_generator.hpp>
 #include <boost/uuid/random_generator.hpp>
+#include <boost/uuid/uuid.hpp>
 #include <boost/uuid/uuid_io.hpp>
 
 #include "Core/Mpl.h"
-#include "Core/Vector.h"
 #include "Core/Object.h"
 
-
 namespace uLib {
 
-
-
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 // Object Registration //
 
-
 typedef boost::uuids::uuid uuid_t;
 
 extern uuid_t uLib_dns_uuid;
 
-template < typename T >
-class type_id : public boost::uuids::uuid {
+template <typename T> class type_id : public boost::uuids::uuid {
 public:
-    type_id() :
-        m_size(sizeof(T)),
-        uuid(boost::uuids::name_generator(uLib_dns_uuid)(typeid(T).name()))
-    {
-        std::cout << "Request for register new type\n" <<
-                     "name: " << typeid(T).name() << "\n" <<
-                     "uuid: " << to_string(*this) << "\n";
+  type_id()
+      : m_size(sizeof(T)),
+        uuid(boost::uuids::name_generator(uLib_dns_uuid)(typeid(T).name())) {
+    std::cout << "Request for register new type\n"
+              << "name: " << typeid(T).name() << "\n"
+              << "uuid: " << to_string(*this) << "\n";
   }
 
-    explicit type_id(boost::uuids::uuid const& u)
-            : boost::uuids::uuid(u) {}
-
-    operator boost::uuids::uuid() {
-        return static_cast<boost::uuids::uuid&>(*this);
-    }
-
-    operator boost::uuids::uuid() const {
-        return static_cast<boost::uuids::uuid const&>(*this);
-    }
+  explicit type_id(boost::uuids::uuid const &u) : boost::uuids::uuid(u) {}
 
   unsigned int size() const { return m_size; }
 
@@ -83,9 +66,6 @@ private:
   unsigned int m_size;
 };
 
-
-
-
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
@@ -95,21 +75,20 @@ namespace detail {
 
 class TypeRegister {
   typedef boost::uuids::name_generator IDGen_t;
+
 public:
   struct RegisterEntry {
     uuid_t id;
     int size;
   };
 
-    TypeRegister(uuid_t const &dns) :
-        gen(dns) {}
+  TypeRegister(uuid_t const &dns) : gen(dns) {}
 
-
-    template< typename T >
-    RegisterEntry * AddType(T *t = NULL) {
+  template <typename T> RegisterEntry *AddType(T *t = NULL) {
     RegisterEntry en = {gen(typeid(T).name()), sizeof(T)};
     for (int i = 0; i < m_registry.size(); ++i)
-            if(en.id == m_registry[i].id) return &(m_registry[i]);
+      if (en.id == m_registry[i].id)
+        return &(m_registry[i]);
     m_registry.push_back(en);
     return &m_registry.back();
   }
@@ -117,24 +96,17 @@ public:
   void PrintSelf(std::ostream &o) {
     std::cout << "RegisterController: \n";
     for (int i = 0; i < m_registry.size(); ++i)
-            o << "type [" << i << "]: "
-              << to_string(m_registry[i].id) << " "
+      o << "type [" << i << "]: " << to_string(m_registry[i].id) << " "
         << m_registry[i].size << "\n";
     o << "\n";
   }
 
-
-
 private:
   IDGen_t gen;
-    Vector<RegisterEntry> m_registry;
-
+  std::vector<RegisterEntry> m_registry;
 };
 
-} // detail
-
-
-
+} // namespace detail
 
 class TypeRegister : public detail::TypeRegister {
 public:
@@ -148,16 +120,11 @@ private:
   static TypeRegister *s_Instance; // Singleton instance
 };
 
-
-
-
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 // OBJECT REGISTER //
 
-
-
-} // uLib
+} // namespace uLib
 
 #endif // UUID_H

src/Core/Vector.h

@@ -23,33 +23,115 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
 #ifndef U_CORE_VECTOR_H
 #define U_CORE_VECTOR_H
 
-#include <vector>
 #include <iostream>
+#include <map>
+#include <mutex>
+#include <vector>
+
+#include <Core/DataAllocator.h>
 
-#include <Core/StaticInterface.h>
-#include <Core/SmartPointer.h>
 #include <Core/CommaInitializer.h>
-
+#include <Core/SmartPointer.h>
+#include <Core/StaticInterface.h>
 
 namespace uLib {
 
+// MetaAllocator Implementation ...
+template <typename T> class MetaAllocator {
+public:
+  using value_type = T;
+  using pointer = T *;
+  using const_pointer = const T *;
+  using reference = T &;
+  using const_reference = const T &;
+  using size_type = std::size_t;
+  using difference_type = std::ptrdiff_t;
+
+  template <class U> struct rebind {
+    using other = MetaAllocator<U>;
+  };
+
+  MetaAllocator() noexcept = default;
+
+  template <class U>
+  constexpr MetaAllocator(const MetaAllocator<U> &) noexcept {}
+
+  T *allocate(std::size_t n) {
+    if (n == 0)
+      return nullptr;
+
+    DataAllocator<T> *da = new DataAllocator<T>(n, false);
+    T *ptr = da->GetRAMData();
+
+    std::lock_guard<std::mutex> lock(GetMutex());
+    GetAllocationMap()[ptr] = da;
+    return ptr;
+  }
+
+  void deallocate(T *p, std::size_t /*n*/) noexcept {
+    if (!p)
+      return;
+
+    std::lock_guard<std::mutex> lock(GetMutex());
+    auto &map = GetAllocationMap();
+    auto it = map.find(p);
+    if (it != map.end()) {
+      delete it->second;
+      map.erase(it);
+    }
+  }
+
+  static DataAllocator<T> *GetDataAllocator(T *p) {
+    if (!p)
+      return nullptr;
+    std::lock_guard<std::mutex> lock(GetMutex());
+    auto &map = GetAllocationMap();
+    auto it = map.find(p);
+    if (it != map.end()) {
+      return it->second;
+    }
+    return nullptr;
+  }
+
+private:
+  static std::map<T *, DataAllocator<T> *> &GetAllocationMap() {
+    static std::map<T *, DataAllocator<T> *> allocMap;
+    return allocMap;
+  }
+
+  static std::mutex &GetMutex() {
+    static std::mutex mtx;
+    return mtx;
+  }
+};
+
+template <class T, class U>
+bool operator==(const MetaAllocator<T> &, const MetaAllocator<U> &) {
+  return true;
+}
+template <class T, class U>
+bool operator!=(const MetaAllocator<T> &, const MetaAllocator<U> &) {
+  return false;
+}
+
 // Vector Implemetation ... wraps std::vector
-template <typename T>
-class Vector : public std::vector<T, std::allocator<T> >
-{    
-    typedef std::vector< T,std::allocator<T> > BaseClass;
-    typedef std::allocator<T> Allocator;
+template <typename T> class Vector : public std::vector<T, MetaAllocator<T>> {
+  typedef std::vector<T, MetaAllocator<T>> BaseClass;
+  typedef MetaAllocator<T> Allocator;
+
 public:
   typedef T TypeData;
   typedef __gnu_cxx::__normal_iterator<T *, BaseClass> Iterator;
   typedef __gnu_cxx::__normal_iterator<const T *, BaseClass> ConstIterator;
 
   typedef CommaInitializer<Vector<T>, T> VectorCommaInit;
+  typedef typename BaseClass::iterator iterator;
+  typedef typename BaseClass::const_iterator const_iterator;
+  typedef typename BaseClass::size_type size_type;
+  typedef typename BaseClass::reference reference;
 
   Vector(unsigned int size) : BaseClass(size) {}
   Vector(unsigned int size, T &value) : BaseClass(size, value) {}
@@ -59,23 +141,187 @@ public:
     return VectorCommaInit(this, scalar);
   }
 
+  void MoveToVRAM() {
+    if (auto alloc = MetaAllocator<T>::GetDataAllocator(BaseClass::data())) {
+      alloc->MoveToVRAM();
+    }
+  }
+
+  void MoveToRAM() {
+    if (auto alloc = MetaAllocator<T>::GetDataAllocator(BaseClass::data())) {
+      alloc->MoveToRAM();
+    }
+  }
+
+  T *GetVRAMData() {
+    if (auto alloc = MetaAllocator<T>::GetDataAllocator(BaseClass::data())) {
+      return alloc->GetVRAMData();
+    }
+    return nullptr;
+  }
+
+  const T *GetVRAMData() const {
+    if (auto alloc = MetaAllocator<T>::GetDataAllocator(
+            const_cast<T *>(BaseClass::data()))) {
+      return alloc->GetVRAMData();
+    }
+    return nullptr;
+  }
+
   inline void PrintSelf(std::ostream &o);
 
+  // Overrides for auto-sync //
+  T &operator[](size_t i) {
+    this->MoveToRAM();
+    return BaseClass::operator[](i);
+  }
+  const T &operator[](size_t i) const {
+    const_cast<Vector *>(this)->MoveToRAM();
+    return BaseClass::operator[](i);
+  }
+  T &at(size_t i) {
+    this->MoveToRAM();
+    return BaseClass::at(i);
+  }
+  const T &at(size_t i) const {
+    const_cast<Vector *>(this)->MoveToRAM();
+    return BaseClass::at(i);
+  }
+  T &front() {
+    this->MoveToRAM();
+    return BaseClass::front();
+  }
+  const T &front() const {
+    const_cast<Vector *>(this)->MoveToRAM();
+    return BaseClass::front();
+  }
+  T &back() {
+    this->MoveToRAM();
+    return BaseClass::back();
+  }
+  const T &back() const {
+    const_cast<Vector *>(this)->MoveToRAM();
+    return BaseClass::back();
+  }
+  T *data() noexcept {
+    this->MoveToRAM();
+    return BaseClass::data();
+  }
+  const T *data() const noexcept {
+    const_cast<Vector *>(this)->MoveToRAM();
+    return BaseClass::data();
+  }
+  Iterator begin() noexcept {
+    this->MoveToRAM();
+    return BaseClass::begin();
+  }
+  ConstIterator begin() const noexcept {
+    const_cast<Vector *>(this)->MoveToRAM();
+    return BaseClass::begin();
+  }
+  Iterator end() noexcept {
+    this->MoveToRAM();
+    return BaseClass::end();
+  }
+  ConstIterator end() const noexcept {
+    const_cast<Vector *>(this)->MoveToRAM();
+    return BaseClass::end();
+  }
+  auto rbegin() noexcept {
+    this->MoveToRAM();
+    return BaseClass::rbegin();
+  }
+  auto rbegin() const noexcept {
+    const_cast<Vector *>(this)->MoveToRAM();
+    return BaseClass::rbegin();
+  }
+  auto rend() noexcept {
+    this->MoveToRAM();
+    return BaseClass::rend();
+  }
+  auto rend() const noexcept {
+    const_cast<Vector *>(this)->MoveToRAM();
+    return BaseClass::rend();
+  }
+
+  void push_back(const T &x) {
+    this->MoveToRAM();
+    BaseClass::push_back(x);
+  }
+  void push_back(T &&x) {
+    this->MoveToRAM();
+    BaseClass::push_back(std::move(x));
+  }
+  template <typename... Args> reference emplace_back(Args &&...args) {
+    this->MoveToRAM();
+    return BaseClass::emplace_back(std::forward<Args>(args)...);
+  }
+  void pop_back() {
+    this->MoveToRAM();
+    BaseClass::pop_back();
+  }
+
+  template <typename... Args>
+  iterator emplace(const_iterator pos, Args &&...args) {
+    this->MoveToRAM();
+    return BaseClass::emplace(pos, std::forward<Args>(args)...);
+  }
+  iterator insert(const_iterator pos, const T &x) {
+    this->MoveToRAM();
+    return BaseClass::insert(pos, x);
+  }
+  iterator insert(const_iterator pos, T &&x) {
+    this->MoveToRAM();
+    return BaseClass::insert(pos, std::move(x));
+  }
+  iterator erase(const_iterator pos) {
+    this->MoveToRAM();
+    return BaseClass::erase(pos);
+  }
+  iterator erase(const_iterator first, const_iterator last) {
+    this->MoveToRAM();
+    return BaseClass::erase(first, last);
+  }
+
+  void resize(size_t n) {
+    this->MoveToRAM();
+    BaseClass::resize(n);
+  }
+  void resize(size_t n, const T &x) {
+    this->MoveToRAM();
+    BaseClass::resize(n, x);
+  }
+  void reserve(size_t n) {
+    this->MoveToRAM();
+    BaseClass::reserve(n);
+  }
+  void clear() noexcept {
+    this->MoveToRAM();
+    BaseClass::clear();
+  }
+  template <typename InputIt> void assign(InputIt first, InputIt last) {
+    this->MoveToRAM();
+    BaseClass::assign(first, last);
+  }
+  void assign(size_type count, const T &value) {
+    this->MoveToRAM();
+    BaseClass::assign(count, value);
+  }
+
   void remove_element(unsigned int index) {
+    this->MoveToRAM();
     std::swap(this->at(index), this->back());
     this->pop_back();
   }
 
   void remove_element(T &t) {
+    this->MoveToRAM();
     std::swap(t, this->back());
     this->pop_back();
   }
-
 };
 
-template<typename T>
-void Vector<T>::PrintSelf(std::ostream &o)
-{
+template <typename T> void Vector<T>::PrintSelf(std::ostream &o) {
   o << " *** uLib Vector *** \n";
   o << " n. of items = " << this->size() << "\n";
   for (int i = 0; i < this->size(); ++i)
@@ -98,36 +344,30 @@ std::ofstream & operator << (std::ofstream &o, const Vector<T> &v) {
   return o;
 }
 
-
-template < typename T >
-std::istream & operator >> (std::istream &is, Vector<T> &v) {
+template <typename T> std::istream &operator>>(std::istream &is, Vector<T> &v) {
   T value;
   while (is >> value) {
-        if(is.fail()) v.push_back(0);
-        else v.push_back( value );
+    if (is.fail())
+      v.push_back(0);
+    else
+      v.push_back(value);
   }
   return is;
 }
 
-
-
 // Smart pointer Vector Implementation //
 
-
-template <typename T>
-class SmartVector : public SmartPointer< Vector<T> > {
+template <typename T> class SmartVector : public SmartPointer<Vector<T>> {
   typedef SmartPointer<Vector<T>> Base;
-public:
 
+public:
   SmartVector() : Base(new Vector<T>()) {}
   SmartVector(const SmartVector &copy) : Base(copy) {}
   SmartVector(unsigned int size) : Base(new Vector<T>((int)size)) {}
 
   virtual ~SmartVector() {}
 
-  T& operator[](int p) {
-      return Base::get()->at(p);
-  }
+  T &operator[](int p) { return Base::get()->at(p); }
 
   void swap_elements(unsigned int first, unsigned int second) {
     std::swap(Base::get()->at(first), Base::get()->at(second));
@@ -144,35 +384,25 @@ public:
   }
 };
 
-
-
-
 // ------ Utils ------------------------------------------------------------- //
 
-
-
 // RIFARE con iteratore !
 template <typename _Tp, class _CmpT>
-inline const unsigned long
-VectorSplice(const _Tp &_it, const _Tp &_end, const float value, _CmpT _comp)
-{
+inline unsigned long VectorSplice(const _Tp &_it, const _Tp &_end,
+                                  const float value, _CmpT _comp) {
   _Tp it = _it;
   _Tp end = _end - 1;
-    for(it; it != end;)
-    {
-        if (_comp(*it,value))       ++it;
-        else if(_comp(*end,value))  std::swap(*it,*end--);
-        else                        --end;
+  for (; it != end;) {
+    if (_comp(*it, value))
+      ++it;
+    else if (_comp(*end, value))
+      std::swap(*it, *end--);
+    else
+      --end;
   }
   return it - _it;
 }
 
-
-
-} // uLib
-
-
-
-
+} // namespace uLib
 
 #endif // VECTOR_H

src/Core/test_meta_allocator.cpp

@@ -0,0 +1,31 @@
+#include <Core/Vector.h>
+#include <iostream>
+
+int main() {
+  uLib::Vector<int> v;
+  v.push_back(1);
+  v.push_back(2);
+  v.push_back(3);
+
+  std::cout << "RAM Vector elements: ";
+  for (int i = 0; i < v.size(); ++i) {
+    std::cout << v[i] << " ";
+  }
+  std::cout << std::endl;
+
+#ifdef USE_CUDA
+  std::cout << "Moving to VRAM..." << std::endl;
+  v.MoveToVRAM();
+  int *vram_ptr = v.GetVRAMData();
+  if (vram_ptr) {
+    std::cout << "Successfully got VRAM pointer!" << std::endl;
+  } else {
+    std::cout << "Failed to get VRAM pointer!" << std::endl;
+  }
+
+  std::cout << "Moving back to RAM..." << std::endl;
+  v.MoveToRAM();
+#endif
+
+  return 0;
+}

src/Core/testing/CMakeLists.txt

@@ -8,7 +8,7 @@ set( TESTS
         ObjectCopyTest
         StaticInterfaceTest
         CommaInitTest
-        DebugTTreeDumpTest
+        # DebugTTreeDumpTest
         BoostTest
         BoostAccumulatorTest
         PropertiesTest
@@ -16,18 +16,18 @@ set( TESTS
         SerializeTest
         SerializeDreadDiamondTest
         DreadDiamondParameters
-        ObjectPropableTest
         UuidTest
         TypeIntrospectionTraversal
         OptionsTest
+        PingPongTest
+        VectorMetaAllocatorTest
 )
 
 set(LIBRARIES
        ${PACKAGE_LIBPREFIX}Core
        ${PACKAGE_LIBPREFIX}Math
-       ${Boost_SERIALIZATION_LIBRARY}
-       ${Boost_SIGNALS_LIBRARY}
-       ${Boost_PROGRAM_OPTIONS_LIBRARY}
+       Boost::serialization
+       Boost::program_options
        ${ROOT_LIBRARIES}
 )
-uLib_add_tests(${uLib-module})
+uLib_add_tests(Core)

src/Core/testing/Makefile.am

@@ -19,7 +19,6 @@ TESTS = SmartPointerTest \
 	SerializeTest \
 	SerializeDreadDiamondTest \
 	DreadDiamondParameters \
-	ObjectPropableTest \
 	TypeIntrospectionTraversal \
         OptionsTest
 

src/Core/testing/ObjectPropableTest.cpp

@@ -1,237 +0,0 @@
-/*//////////////////////////////////////////////////////////////////////////////
-// CMT Cosmic Muon Tomography project //////////////////////////////////////////
-////////////////////////////////////////////////////////////////////////////////
-
-  Copyright (c) 2014, Universita' degli Studi di Padova, INFN sez. di Padova
-  All rights reserved
-
-  Authors: Andrea Rigoni Garola < andrea.rigoni@pd.infn.it >
-
-  ------------------------------------------------------------------
-  This library is free software;  you  can  redistribute  it  and/or
-  modify it  under the  terms  of  the  GNU  Lesser  General  Public
-  License as published  by  the  Free  Software  Foundation;  either
-  version 3.0 of the License, or (at your option) any later version.
-
-  This library is  distributed in  the hope that it will  be useful,
-  but  WITHOUT ANY WARRANTY;  without  even  the implied warranty of
-  MERCHANTABILITY  or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-  Lesser General Public License for more details.
-
-  You should have received a copy of  the GNU Lesser General  Public
-  License along with this library.
-
-//////////////////////////////////////////////////////////////////////////////*/
-
-
-
-#include <iostream>
-#include <fstream>
-#include <typeinfo>
-#include <string>
-
-
-#include "Core/Types.h"
-#include "Core/Object.h"
-#include "Core/ObjectProps.h"
-#include "Core/StringReader.h"
-#include "Math/Dense.h"
-
-#include "boost/archive/text_oarchive.hpp"
-#include "boost/archive/text_iarchive.hpp"
-
-
-#include "testing-prototype.h"
-
-
-
-
-using namespace uLib;
-
-
-
-////////////////////////////////////////////////////////////////////////////////
-////////////////////////////////////////////////////////////////////////////////
-////////////////////////////////////////////////////////////////////////////////
-// STRUCTURES //
-
-
-struct A : virtual Object {
-
-    uLibTypeMacro(A, Object)
-
-    properties() {
-        int      p_a;
-        Vector3f p_3f;
-    };
-
-    int m_a;
-};
-
-void A::init_properties() {
-    $_init();
-    $$.p_a   = 0;
-    $$.p_3f << 1,2,3;
-}
-
-ULIB_SERIALIZABLE_OBJECT(A)
-ULIB_SERIALIZE_OBJECT(A, Object) { ar & AR(m_a); }
-ULIB_SERIALIZE_OBJECT_PROPS(A)   { ar & AR(p_a) & AR(p_3f); }
-
-
-
-
-struct B : A {
-    uLibTypeMacro(B,A)
-
-    properties() {
-        std::string p;
-    };
-
-    B() : m_b(324) {}
-
-    int m_b;
-};
-
-
-void B::init_properties() {
-    $_init();
-    $$.p = "ciao";
-}
-
-ULIB_SERIALIZABLE_OBJECT(B)
-ULIB_SERIALIZE_OBJECT(B,A)     { ar & AR(m_b); }
-ULIB_SERIALIZE_OBJECT_PROPS(B) { ar & AR(p);   }
-
-
-
-struct C {
-    int m_c;    
-    std::string m_str;
-};
-
-ULIB_SERIALIZABLE(C)
-ULIB_SERIALIZE(C) { ar & AR(m_c) & AR(m_str); }
-
-
-
-struct D : virtual Object, B {
-    uLibTypeMacro(D,Object,B)
-
-    properties() {
-        C p_c;
-    };
-};
-
-void D::init_properties() {
-    $_init();
-    $$.p_c.m_c = 1234;
-}
-
-ULIB_SERIALIZABLE_OBJECT(D)
-ULIB_SERIALIZE_OBJECT(D,Object) {}
-ULIB_SERIALIZE_OBJECT_PROPS(D) {
- ar & AR(p_c);
-}
-
-
-
-class E : public C, public D {
-    uLibTypeMacro(E,D,C)
-public:
-        E() : m_Ea(5552368) {}
-        int m_Ea;
-};
-
-ULIB_SERIALIZABLE_OBJECT(E)
-ULIB_SERIALIZE_OBJECT(E,C,D) {
-    ar & AR(m_Ea);
-}
-
-
-
-
-////////////////////////////////////////////////////////////////////////////////
-////////////////////////////////////////////////////////////////////////////////
-////////////////////////////////////////////////////////////////////////////////
-// TESTS //
-
-
-int test_xml_direct() {
-    // TEST ARCHIVE SAVE AND LOAD direct //
-    E o; o.init_properties();
-    o.$$.p_c.m_str = "works";
-    {
-        std::ofstream file("test.xml");
-        Archive::xml_oarchive ar(file);
-        ar << NVP(o);
-    }
-    o.$$.p_c.m_str = "hola";
-    {
-        std::ifstream file("test.xml");
-        Archive::xml_iarchive ar(file);
-        ar >> NVP(o);
-    }
-    std::cout << o.$$.p_c.m_str << "\n";
-    return ( o.$$.p_c.m_str == "works" );
-}
-
-
-int test_xml_pointer() {
-    // TEST ARCHIVE SAVE AND LOAD from pointer //
-    E *o = new E; o->init_properties();
-    o->$$.p_c.m_str = "works";
-    {
-        std::ofstream file("test.xml");
-        Archive::xml_oarchive ar(file);
-        ar << NVP(o);
-    }
-    o->$$.p_c.m_str = "hola";
-    {
-        std::ifstream file("test.xml");
-        Archive::xml_iarchive ar(file);
-        ar >> NVP(o);
-    }
-    std::cout << o->$$.p_c.m_str << "\n";
-    return ( o->$$.p_c.m_str == "works" );
-}
-
-
-int test_xml_objsave() {
-    // TEST SELF SAVE
-    E o; o.init_properties();
-    o.$(B).p = "works";
-    {
-        std::ofstream file("test.xml");
-        Object::SaveXml(file,o);
-    }
-    o.$(B).p = "hola";
-    {
-        std::ifstream file("test.xml");
-        Object::LoadXml(file,o);
-    }
-
-    std::cout << o.$(B).p << "\n";
-    return ( o.$(B).p == "works" );
-}
-
-
-
-
-////////////////////////////////////////////////////////////////////////////////
-////////////////////////////////////////////////////////////////////////////////
-////////////////////////////////////////////////////////////////////////////////
-// MAIN //
-
-int main()
-{
-    BEGIN_TESTING(PropableTest);
-
-    TEST1( test_xml_direct()  );
-    TEST1( test_xml_pointer() );
-    TEST1( test_xml_objsave() );
-
-    END_TESTING;
-}
-
-

src/Core/testing/PingPongTest.cpp

@@ -0,0 +1,52 @@
+#include "Core/Object.h"
+#include "Core/Signal.h"
+#include "testing-prototype.h"
+#include <iostream>
+
+using namespace uLib;
+
+class Ping : public Object {
+public:
+signals:
+  void PingSignal(int count);
+public slots:
+  void OnPong(int count) {
+    std::cout << "Ping received Pong " << count << std::endl;
+    if (count > 0)
+      ULIB_SIGNAL_EMIT(Ping::PingSignal, count - 1);
+  }
+};
+
+void Ping::PingSignal(int count) { ULIB_SIGNAL_EMIT(Ping::PingSignal, count); }
+
+class Pong : public Object {
+public:
+signals:
+  void PongSignal(int count);
+public slots:
+  void OnPing(int count) {
+    std::cout << "Pong received Ping " << count << std::endl;
+    if (count > 0)
+      ULIB_SIGNAL_EMIT(Pong::PongSignal, count - 1);
+  }
+};
+
+void Pong::PongSignal(int count) { ULIB_SIGNAL_EMIT(Pong::PongSignal, count); }
+
+int main() {
+  BEGIN_TESTING(PingPong);
+  Ping ping;
+  Pong pong;
+
+  std::cout << "Connecting ping to pong" << std::endl;
+  Object::connect(&ping, &Ping::PingSignal, &pong, &Pong::OnPing);
+
+  std::cout << "Connecting pong to ping" << std::endl;
+  Object::connect(&pong, &Pong::PongSignal, &ping, &Ping::OnPong);
+
+  std::cout << "Emitting PingSignal(5)" << std::endl;
+  ping.PingSignal(5);
+
+  END_TESTING;
+  return 0;
+}

src/Core/testing/SerializeDreadDiamondTest.cpp

@@ -23,13 +23,10 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
-
-#include <iostream>
 #include <fstream>
-#include <typeinfo>
+#include <iostream>
 #include <string>
+#include <typeinfo>
 
 #include "Core/Object.h"
 
@@ -37,37 +34,24 @@
 
 using namespace uLib;
 
-
-
-
-
-
-
 struct A : Object {
-    uLibTypeMacro(A,Object)
-    A() : numa(5552368) {}
+  uLibTypeMacro(A, Object) A() : numa(5552368) {}
   int numa;
 };
 
-
 ULIB_SERIALIZABLE_OBJECT(A)
-ULIB_SERIALIZE_OBJECT(A,Object) {
-   ar & AR(numa);
-}
+ULIB_SERIALIZE_OBJECT(A, Object) { ar &AR(numa); }
 
 struct B : virtual Object {
-    uLibTypeMacro(B,Object)
-    B() : numb(5552369) {}
+  uLibTypeMacro(B, Object) B() : numb(5552369) {}
   int numb;
 };
 
 ULIB_SERIALIZABLE_OBJECT(B)
 ULIB_SERIALIZE_OBJECT(B, Object) { ar &AR(numb); }
 
-
 struct C : B {
-    uLibTypeMacro(C,B)
-    C() : numc(5552370) {}
+  uLibTypeMacro(C, B) C() : numc(5552370) {}
   int numc;
 };
 
@@ -77,38 +61,16 @@ ULIB_SERIALIZE_OBJECT(C,B) { ar & AR(numc); }
 struct D : A, B {
   uLibTypeMacro(D, A, B)
 
-    D() : numd(5552371) {}
+      D()
+      : numd(5552371) {}
   int numd;
 };
 
 ULIB_SERIALIZABLE_OBJECT(D)
 ULIB_SERIALIZE_OBJECT(D, A, B) { ar &AR(numd); }
 
-
-
-main() {
-    A o; o.init_properties();
+int main() {
+  A o;
 
   Archive::xml_oarchive(std::cout) << NVP(o);
-
 }
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-

src/Core/testing/SerializeTest.cpp

@@ -23,21 +23,16 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
-
-#include <iostream>
 #include <fstream>
+#include <iostream>
 
-#include "Core/Object.h"
 #include "Core/Archives.h"
-#include "ParticlePhysics/MuonTomography/MuonScatter.h"
+#include "Core/Object.h"
 
 #include "testing-prototype.h"
 
 using namespace uLib;
 
-
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
@@ -47,48 +42,40 @@ using namespace uLib;
 struct V3f {
 
   float x, y, z;
-    V3f()
-    { x = y = z =0; }
+  V3f() { x = y = z = 0; }
 
-    V3f(float x, float y, float z) :
-        x(x), y(y), z(z) {}
+  V3f(float x, float y, float z) : x(x), y(y), z(z) {}
 
-    template <class Archive>
-    void serialize (Archive &ar,unsigned int v) {
-        ar
-                & "<" & NVP(x) & NVP(y) & NVP(z) & ">";
+  template <class Archive> void serialize(Archive &ar, unsigned int v) {
+    ar & "<" & NVP(x) & NVP(y) & NVP(z) & ">";
   }
 };
 
 ULIB_CLASS_EXPORT_KEY(V3f);
 ULIB_CLASS_EXPORT_IMPLEMENT(V3f);
 
-
-inline std::ostream &
-operator <<(std::ostream &o, const V3f &v) {
+inline std::ostream &operator<<(std::ostream &o, const V3f &v) {
   Archive::hrt_oarchive(o) << v;
   return o;
 }
 
-inline std::istream &
-operator >>(std::istream &is, V3f &v) {
+inline std::istream &operator>>(std::istream &is, V3f &v) {
   Archive::hrt_iarchive(is) >> v;
   return is;
 }
 
-
-
-
 int test_V3f() {
   // testing human readble archive with simple serializable structure //
 
   V3f v1(1, 2, 3), v2, v3, v4;
   std::cout << "v    --> " << v1 << "\n";
 
-    std::stringstream ss; ss << v1;
+  std::stringstream ss;
+  ss << v1;
   std::cout << "ss.v --> " << ss.str() << "\n";
 
-    Archive::hrt_iarchive ar(ss); ar >> v2;
+  Archive::hrt_iarchive ar(ss);
+  ar >> v2;
   std::cout << "v2   --> " << v2 << "\n";
 
   std::stringstream("<2 3 4>") >> v3;
@@ -99,10 +86,6 @@ int test_V3f() {
   return (1);
 }
 
-
-
-
-
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
@@ -110,70 +93,56 @@ int test_V3f() {
 // OBJECT SERIALIZATION //
 
 class A : public virtual Object {
-    uLibTypeMacro(A,Object)
-    ULIB_SERIALIZE_ACCESS
-public:
-    A() : m_a(5552368) {}
+uLibTypeMacro(A, Object) ULIB_SERIALIZE_ACCESS public : A() : m_a(5552368) {}
 
-    properties() {
+  void init_properties();
   std::string p_a;
-    };
 
   uLibRefMacro(a, int);
+
 private:
   int m_a;
 };
 
-void A::init_properties() {
-    $_init();
-    $$.p_a = "A property string";
-}
+void A::init_properties() { p_a = "A property string"; }
 
 ULIB_SERIALIZABLE_OBJECT(A)
 ULIB_SERIALIZE_OBJECT(A, Object) {
-    ar
-            & "Object A : "
-            & "--> m_a = " & AR(m_a)
-            & "\n";
+  ar & "Object A : " & "--> m_a = " & AR(m_a) & "\n" & "Object A properties: " &
+      "---> p_a = " & AR(p_a) & "\n";
 }
 
-ULIB_SERIALIZE_OBJECT_PROPS(A) {
-    ar
-            & "Object A properties: "
-            & "---> p_a = " & AR(p_a) & "\n";
-}
-
-
-
 int testing_xml_class() {
 
-    A a; a.init_properties();
+  A a;
+  a.init_properties();
 
   {
     std::ofstream file("test.xml");
     Archive::xml_oarchive(file) << NVP(a);
   }
   a.a() = 0;
-    a.$$.p_a = "zero string";
+  a.p_a = "zero string";
   {
     std::ifstream file("test.xml");
     Archive::xml_iarchive(file) >> NVP(a);
   }
 
   Archive::xml_oarchive(std::cout) << NVP(a);
-    return ( a.a() == 5552368 && a.$$.p_a == "A property string" );
+  return (a.a() == 5552368 && a.p_a == "A property string");
 }
 
 int testing_hrt_class() {
 
-    A a; a.init_properties();
+  A a;
+  a.init_properties();
 
   {
     std::ofstream file("test.xml");
     Archive::hrt_oarchive(file) << NVP(a);
   }
   a.a() = 0;
-    a.$$.p_a = "zero string";
+  a.p_a = "zero string";
   {
     // ERRORE FIX !
     //        std::ifstream file("test.xml");
@@ -181,69 +150,15 @@ int testing_hrt_class() {
   }
 
   Archive::hrt_oarchive(std::cout) << NVP(a);
-    return ( a.a() == 5552368 && a.$$.p_a == "A property string" );
+  return (a.a() == 5552368 && a.p_a == "A property string");
 }
 
-
-
-
-
-
-////////////////////////////////////////////////////////////////////////////////
-////////////////////////////////////////////////////////////////////////////////
-////////////////////////////////////////////////////////////////////////////////
-////////////////////////////////////////////////////////////////////////////////
-// MUON SCATTER EXAMPLE //
-
-int testing_mu()
-{     
-     std::stringstream ss;
-
-     MuonScatter mu;
-     mu.SetMomentumIn(555);
-     mu.SetMomentumOut(2368);
-     {
-         std::ofstream file("test.txt");
-         file << mu;
-     }
-
-     mu.SetMomentumIn(0);
-     mu.SetMomentumOut(0);
-     {
-         std::ifstream file("test.txt");
-         file >> mu;
-     }
-
-     std::cout << mu << "\n";
-
-
-}
-
-
-
-
-
-
 int main() {
   BEGIN_TESTING(Serialize Test);
 
   TEST1(test_V3f());
   TEST1(testing_xml_class());
   //    testing_hrt_class(); ///// << ERRORE in HRT with properties
-    TEST1( testing_mu() );
 
   END_TESTING;
 }
-
-
-
-
-
-
-
-
-
-
-
-
-

src/Core/testing/SignalTest.cpp

@@ -23,73 +23,45 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
 #include <iostream>
 #include <typeinfo>
 
-
-#include "testing-prototype.h"
-#include "Core/Types.h"
 #include "Core/Object.h"
 #include "Core/Signal.h"
-
+#include "Core/Types.h"
+#include "testing-prototype.h"
 
 using namespace uLib;
 
-
-
-
 class Ob1 : public Object {
 public:
-
-
 signals:
   void V0();
 
-    int V1(int a);
-
+  void V1(int a);
 };
 
-
-
-
 // should be done by moc //
-void Ob1::V0() {
-    ULIB_SIGNAL_EMIT(Ob1::V0);
-}
-
-int Ob1::V1(int a) {
-    ULIB_SIGNAL_EMIT(Ob1::V1,a);
-}
-
-
-
+void Ob1::V0() { ULIB_SIGNAL_EMIT(Ob1::V0); }
 
+void Ob1::V1(int a) { ULIB_SIGNAL_EMIT(Ob1::V1, a); }
 
 class Ob2 : public Object {
 
 public slots:
-    void PrintV0() {
-        std::cout << "Ob2 prints V0\n" << std::flush;
-    }
+  void PrintV0() { std::cout << "Ob2 prints V0\n" << std::flush; }
 };
 
 class Ob3 : public Object {
 
 public slots:
-    void PrintV0() {
-        std::cout << "Ob3 prints V0\n" << std::flush;
-    }
+  void PrintV0() { std::cout << "Ob3 prints V0\n" << std::flush; }
 
   void PrintNumber(int n) {
     std::cout << "Ob3 is printing number: " << n << "\n";
   }
 };
 
-
-
-
 int main() {
   BEGIN_TESTING(Signals);
 
@@ -111,5 +83,3 @@ int main() {
 
   END_TESTING;
 }
-
-

src/Core/testing/StaticInterfaceTest.cpp

@@ -23,16 +23,11 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
-
 #include <iostream>
 
 #include "testing-prototype.h"
 #include <Core/StaticInterface.h>
 
-
-
 namespace uLib {
 
 //// INTERFACE TO COMPLEX CLASS /////
@@ -45,15 +40,13 @@ struct Test {
     uLibCheckMember(Self, testmemb, int);
   }
 };
-}
+} // namespace Interface
 
 struct Test {
-    bool test(int i, float f){}
+  bool test(int i, float f) { return true; }
   int testmemb;
 };
 
-
-
 //// INTERFAC TO SIMPLE CLASS ///////////
 
 namespace Interface {
@@ -64,49 +57,39 @@ struct Simple {
     uLibCheckMember(Self, memb2, float);
   }
 };
-}
+} // namespace Interface
 
 struct Simple {
   int memb1;
   float memb2;
 };
 
-
 /////////////////////////
 
-template <class T>
-class UseTest {
+template <class T> class UseTest {
 public:
   UseTest() {
     Interface::IsA<T, Interface::Test>();
     T t;
-        int i; float f;
+    int i;
+    float f;
     t.test(i, f);
   }
 };
 
-template <class T>
-class UseSimple {
+template <class T> class UseSimple {
 public:
-    UseSimple() {
-        Interface::IsA<T,Interface::Simple>();
-    }
+  UseSimple() { Interface::IsA<T, Interface::Simple>(); }
 };
 
+} // namespace uLib
 
-
-}
-
-int main()
-{
+int main() {
   BEGIN_TESTING(Static Interface);
 
-
-
   uLib::UseTest<uLib::Test> u;
 
   uLib::UseSimple<uLib::Simple> s;
 
   END_TESTING;
 }
-

src/Core/testing/VectorMetaAllocatorTest.cpp

@@ -0,0 +1,71 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// CMT Cosmic Muon Tomography project //////////////////////////////////////////
+////////////////////////////////////////////////////////////////////////////////
+
+  Copyright (c) 2014, Universita' degli Studi di Padova, INFN sez. di Padova
+  All rights reserved
+
+  Authors: Andrea Rigoni Garola < andrea.rigoni@pd.infn.it >
+
+//////////////////////////////////////////////////////////////////////////////*/
+
+#include "testing-prototype.h"
+#include <Core/Vector.h>
+
+int main() {
+  BEGIN_TESTING(VectorMetaAllocator);
+
+  uLib::Vector<int> v;
+  std::cout << "Pushing elements...\n";
+  v << 1, 2, 3, 4, 5;
+
+  std::cout << "Initial RAM contents: ";
+  for (size_t i = 0; i < v.size(); ++i) {
+    std::cout << v[i] << " ";
+    if (v[i] != (int)(i + 1)) {
+      std::cout << "\nError: Value mismatch at index " << i << "\n";
+      exit(1);
+    }
+  }
+  std::cout << "\n";
+
+#ifdef USE_CUDA
+  std::cout << "Moving to VRAM...\n";
+  v.MoveToVRAM();
+
+  int *vram_ptr = v.GetVRAMData();
+  if (vram_ptr) {
+    std::cout << "Successfully obtained VRAM pointer: " << vram_ptr << "\n";
+  } else {
+    std::cout << "Error: Failed to obtain VRAM pointer!\n";
+    exit(1);
+  }
+
+  std::cout << "Moving back to RAM...\n";
+  v.MoveToRAM();
+
+  std::cout << "RAM contents after VRAM trip: ";
+  for (size_t i = 0; i < v.size(); ++i) {
+    std::cout << v[i] << " ";
+    if (v[i] != (int)(i + 1)) {
+      std::cout << "\nError: Data corrupted after RAM->VRAM->RAM trip at index "
+                << i << "\n";
+      exit(1);
+    }
+  }
+  std::cout << "\n";
+#else
+  std::cout << "USE_CUDA not defined, skipping VRAM tests.\n";
+#endif
+
+  std::cout << "Scaling vector...\n";
+  for (size_t i = 0; i < v.size(); ++i)
+    v[i] *= 10;
+
+  std::cout << "Final contents: ";
+  for (size_t i = 0; i < v.size(); ++i)
+    std::cout << v[i] << " ";
+  std::cout << "\n";
+
+  END_TESTING;
+}

src/Core/testing/VectorTest.cpp

@@ -23,53 +23,40 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
-#include <Core/Vector.h>
 #include "testing-prototype.h"
+#include <Core/Vector.h>
 
 #include <algorithm>
 
-template < typename T >
-struct __Cmp {
-    bool operator()(const T &data, const float value) {
-        return data <= value;
-    }
+template <typename T> struct __Cmp {
+  bool operator()(const T &data, const float value) { return data <= value; }
 };
 
-
-
-
 template <typename _Tp, typename _CmpT>
-inline const unsigned long
-VectorSplice(const _Tp &_it, const _Tp &_end, const float value, _CmpT _comp)
-  {
+inline const unsigned long VectorSplice(const _Tp &_it, const _Tp &_end,
+                                        const float value, _CmpT _comp) {
 
   _Tp it = _it;
   _Tp end = _end - 1;
-    for(it; it != end; )
-    {
-        if ( _comp(*it, value) ) it++;
-        else if( _comp(*end, value) )
-        {
+  for (it; it != end;) {
+    if (_comp(*it, value))
+      it++;
+    else if (_comp(*end, value)) {
       std::swap(*it, *end--);
-        }
-        else --end;
+    } else
+      --end;
   }
   return it - _it;
 }
 
-
-int main()
-{
+int main() {
   BEGIN_TESTING(Vector);
 
   uLib::Vector<float> v;
-    v << 5,4,3,2,6,1,2,3,65,7,32,23,4,3,45,4,34,3,4,4,3,3,4,2,2,3;
+  v << 5, 4, 3, 2, 6, 1, 2, 3, 65, 7, 32, 23, 4, 3, 45, 4, 34, 3, 4, 4, 3, 3, 4,
+      2, 2, 3;
 
-
-
-    int id = VectorSplice(v.begin(),v.end(),3,__Cmp<float>());
+  int id = ::VectorSplice(v.begin(), v.end(), 3, __Cmp<float>());
 
   std::cout << "id: " << id << "\n";
   std::cout << "vector: ";
@@ -78,7 +65,5 @@ int main()
   std::cout << std::endl;
   //    std::sort(v.begin(),v.end(),LT<float>());
 
-
   END_TESTING;
 }
-

src/Detectors/CMakeLists.txt

@@ -1,38 +1,12 @@
-# HEADERS
-set(HEADERS
-                                DetectorChamber.h
-                                ExperimentFitEvent.h
-                                GeantEvent.h
-                                HitMC.h
-                                MuonScatter.h
-                                MuonEvent.h
-                                MuonError.h
-                                ChamberHitEvent.h
-                                Hit.h
-                                LinearFit.h
-                                Solid.h
-                                Matter.h
-                                Scene.h
-)
+set(HEADERS MuonScatter.h MuonError.h MuonEvent.h)
+
+set(ULIB_SELECTED_MODULES ${ULIB_SELECTED_MODULES} Detectors PARENT_SCOPE)
 
 
-# SOURCES
-set(SOURCES
-                Solid.cpp
-                Scene.cpp
-)
+install(FILES ${HEADERS}
+        DESTINATION ${INSTALL_INC_DIR}/Detectors)
 
-set(LIBRARIES
-       ${Boost_SERIALIZATION_LIBRARY}
-       ${Boost_SIGNALS_LIBRARY}
-       ${Boost_PROGRAM_OPTIONS_LIBRARY}
-       ${Eigen_LIBRARY}
-       ${Geant4_LIBRARIES}
-       ${ROOT_LIBRARIES}
-       ${PACKAGE_LIBPREFIX}Core
-       ${PACKAGE_LIBPREFIX}Math
-       ${PACKAGE_LIBPREFIX}Detectors
-)
-
-uLib_add_shared_library(${uLib-module})
+if(BUILD_TESTING)
+  include(uLibTargetMacros)
   add_subdirectory(testing)
+endif()

src/Detectors/HitMC.h

@@ -28,7 +28,6 @@
 #ifndef U_HITMC_H
 #define U_HITMC_H
 
-#include "Core/Macros.h"
 #include "Math/Dense.h"
 #include "Hit.h"
 
@@ -43,10 +42,10 @@ public:
         DeltaRay
     };
 
-    uLibConstRefMacro(Position,HPoint3f)
-    uLibGetMacro(Type, enum Type)
+    inline const HPoint3f & Position() const { return this->m_Position; }
+    inline enum Type GetType() const { return this->m_Type; }
 
-private:
+protected:
     HPoint3f  m_Position;
     enum Type m_Type;
 };
@@ -54,8 +53,8 @@ private:
 
 class HitMC : public HitMCData {
 public:
-    uLibRefMacro(Position,HPoint3f)
-    uLibSetMacro(Type, enum Type)
+    inline HPoint3f & Position() { return this->m_Position; }
+    inline void SetType(enum Type name) { this->m_Type = name; }
 };
 
 

src/Detectors/LinearFit.h

@@ -28,7 +28,6 @@
 #ifndef U_LINEARFIT_H
 #define U_LINEARFIT_H
 
-#include "Core/Macros.h"
 #include "Math/Dense.h"
 #include "ChamberDetector.h"
 
@@ -37,15 +36,14 @@ namespace uLib {
 
 class LinearFitData {
 public:
-    uLibConstRefMacro(Position,Vector2f)
-    uLibConstRefMacro(Slope,Vector2f)
-    uLibConstRefMacro(PositionError,Vector2f)
-    uLibConstRefMacro(SlopeError,Vector2f)
-    uLibGetMacro(HitsNumber,int)
-    uLibGetMacro(Idv,ChamberDetector::ID)
+    inline const Vector2f & Position() const { return this->m_Position; }
+    inline const Vector2f & Slope() const { return this->m_Slope; }
+    inline const Vector2f & PositionError() const { return this->m_PositionError; }
+    inline const Vector2f & SlopeError() const { return this->m_SlopeError; }
+    inline int GetHitsNumber() const { return this->m_HitsNumber; }
+    inline ChamberDetector::ID GetIdv() const { return this->m_Idv; }
 
-private:
-        friend class LinearFit;
+protected:
     Vector2f            m_Position;
     Vector2f            m_Slope;
     Vector2f            m_PositionError;
@@ -57,12 +55,12 @@ private:
 
 class LinearFit : public LinearFitData {
 public:
-    uLibRefMacro(Position,Vector2f)
-    uLibRefMacro(Slope,Vector2f)
-    uLibRefMacro(PositionError,Vector2f)
-    uLibRefMacro(SlopeError,Vector2f)
-    uLibSetMacro(HitsNumber,int)
-    uLibSetMacro(Idv,ChamberDetector::ID)
+    inline Vector2f & Position() { return this->m_Position; }
+    inline Vector2f & Slope() { return this->m_Slope; }
+    inline Vector2f & PositionError() { return this->m_PositionError; }
+    inline Vector2f & SlopeError() { return this->m_SlopeError; }
+    inline void SetHitsNumber(int name) { this->m_HitsNumber = name; }
+    inline void SetIdv(ChamberDetector::ID name) { this->m_Idv = name; }
 };
 
 

src/Detectors/MuonError.h

@@ -28,18 +28,16 @@
 #ifndef U_MUONERROR_H
 #define U_MUONERROR_H
 
-#include "Core/Macros.h"
 #include "Math/Dense.h"
 
 namespace uLib {
 
 
 class MuonErrorData {
-    friend class MuonError;
 public:
-    uLibConstRefMacro(Theta,Scalarf)
-    uLibConstRefMacro(Phi,Scalarf)
-private:
+    inline const Scalarf & Theta() const { return this->m_Theta; }
+    inline const Scalarf & Phi() const { return this->m_Phi; }
+protected:
     Scalarf m_Theta;
     Scalarf m_Phi;
 };
@@ -47,8 +45,8 @@ private:
 
 class MuonError  : public MuonErrorData {
 public:
-    uLibRefMacro(Theta,Scalarf)
-    uLibRefMacro(Phi,Scalarf)
+    inline Scalarf & Theta() { return this->m_Theta; }
+    inline Scalarf & Phi() { return this->m_Phi; }
 };
 
 

src/Detectors/MuonEvent.h

@@ -28,20 +28,18 @@
 #ifndef U_MUONEVENT_H
 #define U_MUONEVENT_H
 
-#include "Core/Macros.h"
 #include "Math/Dense.h"
 
 namespace uLib {
 
 
 class MuonEventData {
-    friend class MuonEvent;
 public:
-    uLibConstRefMacro(LineIn,HLine3f)
-    uLibConstRefMacro(LineOut,HLine3f)
-    uLibGetMacro(Momentum,Scalarf)
+    inline const HLine3f & LineIn() const { return this->m_LineIn; }
+    inline const HLine3f & LineOut() const { return this->m_LineOut; }
+    inline Scalarf GetMomentum() const { return this->m_Momentum; }
 
-private:
+protected:
     HLine3f  m_LineIn;
     HLine3f  m_LineOut;
     Scalarf  m_Momentum;
@@ -50,9 +48,9 @@ private:
 
 class MuonEvent  : public MuonEventData {
 public:
-    uLibRefMacro(LineIn,HLine3f)
-    uLibRefMacro(LineOut,HLine3f)
-    uLibRefMacro(Momentum,Scalarf)
+    inline HLine3f & LineIn() { return this->m_LineIn; }
+    inline HLine3f & LineOut() { return this->m_LineOut; }
+    inline Scalarf & Momentum() { return this->m_Momentum; }
 
 };
 

src/Detectors/MuonScatter.h

@@ -29,7 +29,6 @@
 #ifndef U_MUONSCATTER_H
 #define U_MUONSCATTER_H
 
-#include "Core/Macros.h"
 #include "Math/Dense.h"
 
 namespace uLib {
@@ -37,20 +36,21 @@ namespace uLib {
 
 class MuonScatter {
 public:
-    uLibConstRefMacro(LineIn,HLine3f)
-    uLibConstRefMacro(ErrorIn,HError3f)
-    uLibConstRefMacro(LineOut,HLine3f)
-    uLibConstRefMacro(ErrorOut,HError3f)
+    inline const HLine3f & LineIn() const { return this->m_LineIn; }
+    inline const HError3f & ErrorIn() const { return this->m_ErrorIn; }
+    inline const HLine3f & LineOut() const { return this->m_LineOut; }
+    inline const HError3f & ErrorOut() const { return this->m_ErrorOut; }
 
-    uLibRefMacro(LineIn,HLine3f)
-    uLibRefMacro(ErrorIn,HError3f)
-    uLibRefMacro(LineOut,HLine3f)
-    uLibRefMacro(ErrorOut,HError3f)
-    uLibSetMacro(Momentum,Scalarf)
-    uLibSetMacro(MomentumPrime,Scalarf)
+    inline HLine3f & LineIn() { return this->m_LineIn; }
+    inline HError3f & ErrorIn() { return this->m_ErrorIn; }
+    inline HLine3f & LineOut() { return this->m_LineOut; }
+    inline HError3f & ErrorOut() { return this->m_ErrorOut; }
 
-    uLibGetMacro(Momentum,Scalarf)
-    uLibGetMacro(MomentumPrime,Scalarf)
+    inline void SetMomentum(Scalarf name) { this->m_Momentum = name; }
+    inline void SetMomentumPrime(Scalarf name) { this->m_MomentumPrime = name; }
+
+    inline Scalarf GetMomentum() const { return this->m_Momentum; }
+    inline Scalarf GetMomentumPrime() const { return this->m_MomentumPrime; }
 
 protected:
     HLine3f  m_LineIn;

src/Detectors/testing/CMakeLists.txt

@@ -1,18 +1,15 @@
 # TESTS
 set( TESTS
-            GDMLSolidTest
+#            GDMLSolidTest
             HierarchicalEncodingTest
 )
 
-#set(LIBRARIES
-#       ${PACKAGE_LIBPREFIX}Core
-#       ${PACKAGE_LIBPREFIX}Math
-#       ${PACKAGE_LIBPREFIX}Detectors
-#       ${Boost_SERIALIZATION_LIBRARY}
-#       ${Boost_SIGNALS_LIBRARY}
-#       ${Boost_PROGRAM_OPTIONS_LIBRARY}
-#       ${Eigen_LIBRARY}
-#       ${Geant4_LIBRARIES}
-#       ${ROOT_LIBRARIES}
-#)
-uLib_add_tests(${uLib-module})
+set(LIBRARIES
+       ${PACKAGE_LIBPREFIX}Core
+       ${PACKAGE_LIBPREFIX}Math
+       Boost::serialization
+       Boost::program_options
+       Eigen3::Eigen
+       ${ROOT_LIBRARIES}
+)
+uLib_add_tests(Detectors)

src/Gui/Qt/QVTKViewport2/Makefile.am

@@ -1,35 +0,0 @@
-# SUBDIRS = .
-
-include $(top_srcdir)/Common.am
-
-DISTSOURCES        = vtkviewport.cpp main.cpp
-DISTHEADERS_MOC    =
-DISTHEADERS_NO_MOC = 
-FORMS              = vtkviewport.ui 
-
-FORMHEADERS = $(FORMS:.ui=.h)
-MOC_CC = $(FORMS:.ui=.moc.cpp) $(DISTHEADERS_MOC:.h=.moc.cpp)
-
-bin_PROGRAMS    = QTVtkViewport
-
-BUILT_SOURCES = $(FORMHEADERS) $(MOC_CC)
-CLEANFILES    = $(BUILT_SOURCES)
-
-EXTRA_DIST                   = $(FORMS)
-QTVtkViewport_SOURCES        = $(DISTSOURCES) $(DISTHEADERS_MOC) $(DISTHEADERS_NO_MOC)
-nodist_QTVtkViewport_SOURCES = $(MOC_CC)
-
-QTVtkViewport_LDADD = $(top_srcdir)/libmutom.la
-
-
-.ui.h: $(FORMS)
-	$(UIC) -o ui_$@ $<
-
-.ui.hpp: $(FORMS_HPP)
-	$(UIC) -o $@ $<
-
-.h.moc.cpp:
-	$(MOC) -o $@ $<
-
-
-SUFFIXES = .h .ui .moc.cpp

src/Gui/Qt/QVTKViewport2/QVTKViewport2.pro

@@ -1,18 +0,0 @@
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-#
-# Project created by QtCreator 2012-08-30T18:59:53
-#
-#-------------------------------------------------
-
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-
-TARGET = QVTKViewport2
-TEMPLATE = app
-
-
-SOURCES += main.cpp\
-        vtkviewport.cpp
-
-HEADERS  += vtkviewport.h
-
-FORMS    += vtkviewport.ui

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src/Gui/Qt/QVTKViewport2/main.cpp

@@ -1,38 +0,0 @@
-/*//////////////////////////////////////////////////////////////////////////////
-// CMT Cosmic Muon Tomography project //////////////////////////////////////////
-////////////////////////////////////////////////////////////////////////////////
-
-  Copyright (c) 2014, Universita' degli Studi di Padova, INFN sez. di Padova
-  All rights reserved
-
-  Authors: Andrea Rigoni Garola < andrea.rigoni@pd.infn.it >
-
-  ------------------------------------------------------------------
-  This library is free software;  you  can  redistribute  it  and/or
-  modify it  under the  terms  of  the  GNU  Lesser  General  Public
-  License as published  by  the  Free  Software  Foundation;  either
-  version 3.0 of the License, or (at your option) any later version.
-
-  This library is  distributed in  the hope that it will  be useful,
-  but  WITHOUT ANY WARRANTY;  without  even  the implied warranty of
-  MERCHANTABILITY  or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-  Lesser General Public License for more details.
-
-  You should have received a copy of  the GNU Lesser General  Public
-  License along with this library.
-
-//////////////////////////////////////////////////////////////////////////////*/
-
-
-
-#include <QtGui/QApplication>
-#include "vtkviewport.h"
-
-int main(int argc, char *argv[])
-{
-    QApplication a(argc, argv);
-    VtkViewport w;
-    w.show();
-    
-    return a.exec();
-}

src/Gui/Qt/QVTKViewport2/vtkviewport.cpp

@@ -1,41 +0,0 @@
-/*//////////////////////////////////////////////////////////////////////////////
-// CMT Cosmic Muon Tomography project //////////////////////////////////////////
-////////////////////////////////////////////////////////////////////////////////
-
-  Copyright (c) 2014, Universita' degli Studi di Padova, INFN sez. di Padova
-  All rights reserved
-
-  Authors: Andrea Rigoni Garola < andrea.rigoni@pd.infn.it >
-
-  ------------------------------------------------------------------
-  This library is free software;  you  can  redistribute  it  and/or
-  modify it  under the  terms  of  the  GNU  Lesser  General  Public
-  License as published  by  the  Free  Software  Foundation;  either
-  version 3.0 of the License, or (at your option) any later version.
-
-  This library is  distributed in  the hope that it will  be useful,
-  but  WITHOUT ANY WARRANTY;  without  even  the implied warranty of
-  MERCHANTABILITY  or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-  Lesser General Public License for more details.
-
-  You should have received a copy of  the GNU Lesser General  Public
-  License along with this library.
-
-//////////////////////////////////////////////////////////////////////////////*/
-
-
-
-#include "vtkviewport.h"
-#include "ui_vtkviewport.h"
-
-VtkViewport::VtkViewport(QWidget *parent) :
-    QWidget(parent),
-    ui(new Ui::VtkViewport)
-{
-    ui->setupUi(this);
-}
-
-VtkViewport::~VtkViewport()
-{
-    delete ui;
-}

src/Gui/Qt/QVTKViewport2/vtkviewport.h

@@ -1,49 +0,0 @@
-/*//////////////////////////////////////////////////////////////////////////////
-// CMT Cosmic Muon Tomography project //////////////////////////////////////////
-////////////////////////////////////////////////////////////////////////////////
-
-  Copyright (c) 2014, Universita' degli Studi di Padova, INFN sez. di Padova
-  All rights reserved
-
-  Authors: Andrea Rigoni Garola < andrea.rigoni@pd.infn.it >
-
-  ------------------------------------------------------------------
-  This library is free software;  you  can  redistribute  it  and/or
-  modify it  under the  terms  of  the  GNU  Lesser  General  Public
-  License as published  by  the  Free  Software  Foundation;  either
-  version 3.0 of the License, or (at your option) any later version.
-
-  This library is  distributed in  the hope that it will  be useful,
-  but  WITHOUT ANY WARRANTY;  without  even  the implied warranty of
-  MERCHANTABILITY  or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-  Lesser General Public License for more details.
-
-  You should have received a copy of  the GNU Lesser General  Public
-  License along with this library.
-
-//////////////////////////////////////////////////////////////////////////////*/
-
-
-
-#ifndef VTKVIEWPORT_H
-#define VTKVIEWPORT_H
-
-#include <QWidget>
-
-namespace Ui {
-class VtkViewport;
-}
-
-class VtkViewport : public QWidget
-{
-    Q_OBJECT
-    
-public:
-    explicit VtkViewport(QWidget *parent = 0);
-    ~VtkViewport();
-    
-private:
-    Ui::VtkViewport *ui;
-};
-
-#endif // VTKVIEWPORT_H

src/Gui/Qt/QVTKViewport2/vtkviewport.ui

@@ -1,32 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>VtkViewport</class>
- <widget class="QWidget" name="VtkViewport">
-  <property name="geometry">
-   <rect>
-    <x>0</x>
-    <y>0</y>
-    <width>580</width>
-    <height>536</height>
-   </rect>
-  </property>
-  <property name="windowTitle">
-   <string>Form</string>
-  </property>
-  <widget class="QLabel" name="label">
-   <property name="geometry">
-    <rect>
-     <x>140</x>
-     <y>170</y>
-     <width>161</width>
-     <height>41</height>
-    </rect>
-   </property>
-   <property name="text">
-    <string>Hello World !</string>
-   </property>
-  </widget>
- </widget>
- <resources/>
- <connections/>
-</ui>

src/Math/Accumulator.h

@@ -28,7 +28,8 @@
 #ifndef U_DATABINNING_H
 #define U_DATABINNING_H
 
-#include "Core/Vector.h"
+#include <vector>
+
 #include "Dense.h"
 
 
@@ -69,7 +70,7 @@ public:
     void AddPass() { m_Means.push_back( Tmean(0,0) ); }
 
 private:
-    Vector< Tmean > m_Means;
+    std::vector< Tmean > m_Means;
 };
 
 

src/Math/BitCode.h

@@ -27,15 +27,16 @@
 #ifndef U_MATH_BITCODE_H
 #define U_MATH_BITCODE_H
 
+#include <iostream>
+
 #include <boost/static_assert.hpp>
 #include <boost/type_traits.hpp>
-//#include <Core/CommaInitializer.h>
-#include <Math/Dense.h>
-
-#include <Core/Mpl.h>
 #include <boost/mpl/vector_c.hpp>
 #include <boost/mpl/set_c.hpp>
 
+#include <Math/Dense.h>
+
+
 namespace uLib {
 
 
@@ -237,9 +238,9 @@ public:
 //        std::cout << boost::mpl::at_c< BitSet,1 >::type::value << "\n";
     }
 
-    int Get(unsigned short field) const {
-        return boost::mpl::at_c< BitSet, field >::type::value;
-    }
+//    int Get(unsigned short field) const {
+//        return boost::mpl::at_c< BitSet, field >::type::value;
+//    }
 };
 
 

src/Math/CMakeLists.txt

@@ -1,7 +1,5 @@
 
-# HEADERS
-set(HEADERS
-                                ContainerBox.h
+set(HEADERS ContainerBox.h
             Dense.h
             Geometry.h
             Transform.h
@@ -22,29 +20,48 @@ set(HEADERS
             Accumulator.h
             TriangleMesh.h
             BitCode.h
-)
+            Structured2DGrid.h
+            Structured4DGrid.h)
 
-
-# SOURCES
-set(SOURCES
-                VoxRaytracer.cpp
+set(SOURCES VoxRaytracer.cpp
             StructuredData.cpp
             StructuredGrid.cpp
             VoxImage.cpp
             TriangleMesh.cpp
             Dense.cpp
-)
+            Structured2DGrid.cpp
+            Structured4DGrid.cpp)
 
-set(LIBRARIES
-       ${Boost_SERIALIZATION_LIBRARY}
-       ${Boost_SIGNALS_LIBRARY}
-       ${Boost_PROGRAM_OPTIONS_LIBRARY}
-       ${Eigen_LIBRARY}
+set(LIBRARIES Eigen3::Eigen
               ${ROOT_LIBRARIES}
-       ${PACKAGE_LIBPREFIX}Core
-       ${PACKAGE_LIBPREFIX}Math
-)
+              ${VTK_LIBRARIES})
+
+set(libname ${PACKAGE_LIBPREFIX}Math)
+set(ULIB_SHARED_LIBRARIES ${ULIB_SHARED_LIBRARIES} ${libname} PARENT_SCOPE)
+set(ULIB_SELECTED_MODULES ${ULIB_SELECTED_MODULES} Math PARENT_SCOPE)
+
+add_library(${libname} SHARED ${SOURCES})
+set_target_properties(${libname} PROPERTIES
+                      VERSION ${PROJECT_VERSION}
+                      SOVERSION ${PROJECT_SOVERSION}
+                      CXX_STANDARD 17
+                      CUDA_STANDARD 17)
+target_link_libraries(${libname} ${LIBRARIES})
+
+if(USE_CUDA)
+    set_source_files_properties(VoxRaytracer.cpp VoxImage.cpp PROPERTIES LANGUAGE CUDA)
+endif()
 
 
-uLib_add_shared_library(${uLib-module})
+install(TARGETS ${libname}
+        EXPORT "${PROJECT_NAME}Targets"
+        RUNTIME DESTINATION ${INSTALL_BIN_DIR} COMPONENT bin
+        LIBRARY DESTINATION ${INSTALL_LIB_DIR} COMPONENT lib)
+
+install(FILES ${HEADERS} DESTINATION ${INSTALL_INC_DIR}/Math)
+
+if(BUILD_TESTING)
+  include(uLibTargetMacros)
   add_subdirectory(testing)
+endif()
+

src/Math/Dense.cpp

@@ -27,8 +27,8 @@
 
 
 #include "Dense.h"
-#include "Core/Archives.h"
 
+#ifdef ULIB_SERIALIZATION_ON
 ULIB_SERIALIZE(uLib::HPoint3f) {
     ar & boost::serialization::make_nvp(NULL,boost::serialization::base_object<uLib::HPoint3f::BaseClass,uLib::HPoint3f>(ob));
 }
@@ -48,5 +48,5 @@ ULIB_SERIALIZE(uLib::HError3f) {
     ar
             & "HLine -> ( poserr: " & AR(position_error) & "; direrr: " & AR(direction_error) & ") ";
 }
-
+#endif // ULIB_SERIALIZATION_ON
 

src/Math/Dense.h

@@ -23,9 +23,6 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
-
 /*
  * <one line to give the program's name and a brief idea of what it does.>
  * Copyright (C) 2012  Andrea Rigoni Garola <andrea@pcimg05>
@@ -47,17 +44,12 @@
  *
  */
 
-
 #ifndef ULIB_DENSEMATRIX_H
 #define ULIB_DENSEMATRIX_H
 
 #include <stdlib.h>
 
 #include <Eigen/Dense>
-#include "Core/Types.h"
-#include "Core/Serializable.h"
-
-
 
 //// BOOST SERIALIZATION ///////////////////////////////////////////////////////
 
@@ -65,20 +57,23 @@
 #include <boost/algorithm/string/split.hpp>
 #include <boost/algorithm/string/trim.hpp>
 #include <boost/lexical_cast.hpp>
-#include <boost/serialization/string.hpp>
 #include <boost/serialization/array.hpp>
-
+#include <boost/serialization/string.hpp>
 
 namespace boost {
 namespace serialization {
 
-template<class Archive, class Scalar, int RowsAtCompileTime, int ColsAtCompileTime>
-void serialize(Archive & ar, ::Eigen::Matrix<Scalar, RowsAtCompileTime, ColsAtCompileTime> & m, const unsigned int /*version*/) {
-    ar & boost::serialization::make_array(m.data(), RowsAtCompileTime * ColsAtCompileTime);
+template <class Archive, class Scalar, int RowsAtCompileTime,
+          int ColsAtCompileTime>
+void serialize(Archive &ar,
+               ::Eigen::Matrix<Scalar, RowsAtCompileTime, ColsAtCompileTime> &m,
+               const unsigned int /*version*/) {
+  ar &boost::serialization::make_array(m.data(),
+                                       RowsAtCompileTime * ColsAtCompileTime);
 }
 
-} //  serialization
-} //  boost
+} // namespace serialization
+} // namespace boost
 
 ////////////////////////////////////////////////////////////////////////////////
 
@@ -92,23 +87,25 @@ std::istream & operator >> (std::istream &is, Eigen::Matrix<T,size,1> &vec) {
   for (unsigned int i = 0; i < size; i++) {
     is >> std::skipws;
     is >> str;
-        if(is.fail()) vec(i) = 0;
-        else vec(i) = boost::lexical_cast<T>(str);
+    if (is.fail())
+      vec(i) = 0;
+    else
+      vec(i) = boost::lexical_cast<T>(str);
   }
   return is;
 }
 template <typename T, int size>
-std::ostream & operator << (std::ostream &os, const Eigen::Matrix<T,size,1> &vec) {
+std::ostream &operator<<(std::ostream &os,
+                         const Eigen::Matrix<T, size, 1> &vec) {
   os << vec.transpose();
   return os;
 }
-} // Eigen
+} // namespace Eigen
 ////////////////////////////////////////////////////////////////////////////////
 
-
-
 namespace uLib {
 
+typedef id_t Id_t;
 
 typedef int Scalari;
 typedef unsigned int Scalarui;
@@ -117,8 +114,6 @@ typedef unsigned long Scalarul;
 typedef float Scalarf;
 typedef double Scalard;
 
-
-
 typedef Eigen::Matrix<int, 1, 1> Matrix1i;
 typedef Eigen::Matrix2i Matrix2i;
 typedef Eigen::Matrix3i Matrix3i;
@@ -139,9 +134,6 @@ typedef Eigen::Vector2f Vector2f;
 typedef Eigen::Vector3f Vector3f;
 typedef Eigen::Vector4f Vector4f;
 
-
-
-
 ////////////////////////////////////////////////////////////////////////////////
 // Vector String interaction ///////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
@@ -152,15 +144,18 @@ typedef Eigen::Vector4f Vector4f;
  *
  *  \param vec A double vector to be populated with the results
  *  \param str A string to be parsed as a series of doubles.
-*  \param delim Delimiters of the text (a typical default is " ," for comma and space-delimited text
+ *  \param delim Delimiters of the text (a typical default is " ," for comma and
+ * space-delimited text
  *
  */
 template <typename T, int size>
-void VectorxT_StringTo(Eigen::Matrix<T,size,1> &vec, std::string str, const char *delim = " ,;\t\n") {
+void VectorxT_StringTo(Eigen::Matrix<T, size, 1> &vec, std::string str,
+                       const char *delim = " ,;\t\n") {
   std::vector<std::string> strvec;
 
   boost::algorithm::trim_if(str, boost::algorithm::is_any_of(delim));
-    boost::algorithm::split(strvec,str,boost::algorithm::is_any_of(delim), boost::algorithm::token_compress_on);
+  boost::algorithm::split(strvec, str, boost::algorithm::is_any_of(delim),
+                          boost::algorithm::token_compress_on);
 
   for (unsigned int i = 0; i < size; i++) {
     vec(i) = boost::lexical_cast<T>(strvec[i]);
@@ -174,9 +169,9 @@ std::string VectorxT_ToString(const Eigen::Matrix<T,size,1> &vec) {
   return sst.str();
 }
 
-
 // template <typename T, int size>
-//Eigen::Matrix<T,size,1> & operator >> (std::istream &is, Eigen::Matrix<T,size,1> &vec) {
+// Eigen::Matrix<T,size,1> & operator >> (std::istream &is,
+// Eigen::Matrix<T,size,1> &vec) {
 // }
 
 template <typename T, int size>
@@ -184,97 +179,82 @@ void operator>> (std::string& str, Eigen::Matrix<T,size,1> &vec){
   VectorxT_StringTo(vec, str);
 }
 
-
 ////////////////////////////////////////////////////////////////////////////////
 //////   HOMOGENEOUS VECTORS  //////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 
-template <bool p>
-class _HPoint3f : public Eigen::Matrix< Scalarf,4,1 > {
+template <bool p> class _HPoint3f : public Eigen::Matrix<Scalarf, 4, 1> {
 public:
   typedef Eigen::Matrix<Scalarf, 4, 1> BaseClass;
 
-    _HPoint3f<p>() : BaseClass(0,0,0,p) {}
-    _HPoint3f<p>(float x,float y,float z) : BaseClass(x,y,z,p) {}
-    _HPoint3f<p>(Vector3f &in) : BaseClass(in.homogeneous()) { this->operator()(3) = p; }
+  _HPoint3f() : BaseClass(0, 0, 0, p) {}
+  _HPoint3f(float x, float y, float z) : BaseClass(x, y, z, p) {}
+  _HPoint3f(Vector3f &in) : BaseClass(in.homogeneous()) {
+    this->operator()(3) = p;
+  }
 
   void operator delete(void *_p, size_t _s) {}
 
   // This constructor allows to construct MyVectorType from Eigen expressions
   template <typename OtherDerived>
-    inline _HPoint3f<p>(const Eigen::MatrixBase<OtherDerived>& other)
-        : BaseClass(other)
-    { }
+  inline _HPoint3f(const Eigen::MatrixBase<OtherDerived> &other)
+      : BaseClass(other) {}
 
   // This method allows to assign Eigen expressions to Vector3H
   template <typename OtherDerived>
-    inline _HPoint3f<p> & operator= (const Eigen::MatrixBase <OtherDerived>& other)
-    {
+  inline _HPoint3f &operator=(const Eigen::MatrixBase<OtherDerived> &other) {
     this->BaseClass::operator=(other);
     return *this;
   }
-
 };
 typedef _HPoint3f<false> HVector3f;
 typedef _HPoint3f<true> HPoint3f;
 
-
-
-
 ////////////////////////////////////////////////////////////////////////////////
 //////   HOMOGENEOUS LINE     //////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 
-
-struct _HLine3f
-{
+struct _HLine3f {
   HPoint3f origin;
   HVector3f direction;
 };
 typedef struct _HLine3f HLine3f;
 
-inline std::ostream&
-operator<< (std::ostream& stream, const HLine3f &line) {
-    stream << "HLine3f(" << "pt[" << line.origin.transpose() <<"] , dr[" << line.direction.transpose() << "]) ";
+inline std::ostream &operator<<(std::ostream &stream, const HLine3f &line) {
+  stream << "HLine3f(" << "pt[" << line.origin.transpose() << "] , dr["
+         << line.direction.transpose() << "]) ";
   return stream;
 }
 
-
-
-
-struct _HError3f
-{
+struct _HError3f {
   HVector3f position_error;
   HVector3f direction_error;
 };
 typedef struct _HError3f HError3f;
 
-inline std::ostream&
-operator<< (std::ostream& stream, const HError3f &err) {
-    stream << "HError3f(" << "ept[" << err.position_error.transpose() <<"] , edr[" << err.direction_error.transpose() << "]) ";
+inline std::ostream &operator<<(std::ostream &stream, const HError3f &err) {
+  stream << "HError3f(" << "ept[" << err.position_error.transpose()
+         << "] , edr[" << err.direction_error.transpose() << "]) ";
   return stream;
 }
 
-
-}
-
+} // namespace uLib
 
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 // SERIALIZTION //
 
+#ifdef ULIB_SERIALIZATION_ON
+#include "Core/Serializable.h"
+
 ULIB_SERIALIZABLE(uLib::HPoint3f)
 
 ULIB_SERIALIZABLE(uLib::HVector3f)
 
-
 ULIB_SERIALIZABLE(uLib::HLine3f)
 
 ULIB_SERIALIZABLE(uLib::HError3f)
-
-
-
-
+#endif // ULIB_SERIALIZATION_ON
 
 #endif // U_DENSEMATRIX_H

src/Math/Geometry.h

@@ -28,7 +28,6 @@
 #ifndef U_GEOMETRY_H
 #define U_GEOMETRY_H
 
-#include "Core/Object.h"
 #include "Math/Dense.h"
 #include "Math/Transform.h"
 

src/Math/Quote.h

@@ -32,11 +32,11 @@
 
 namespace uLib {
 
-class Quote : public Vector2f {
+class Quote : public Vector2f
+{
 public:
 
-
-    uLibRefMacro(Offset,Scalarf);
+    inline Scalarf& Offset() { return this->m_Offset; }
 
 private:
     Scalarf m_Offset;

src/Math/Structured2DGrid.cpp

@@ -0,0 +1,130 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// CMT Cosmic Muon Tomography project //////////////////////////////////////////
+////////////////////////////////////////////////////////////////////////////////
+
+  Copyright (c) 2014, Universita' degli Studi di Padova, INFN sez. di Padova
+  All rights reserved
+
+  Authors: Sara Vanini < sara.vanini@pd.infn.it >
+
+  ------------------------------------------------------------------
+  This library is free software;  you  can  redistribute  it  and/or
+  modify it  under the  terms  of  the  GNU  Lesser  General  Public
+  License as published  by  the  Free  Software  Foundation;  either
+  version 3.0 of the License, or (at your option) any later version.
+
+  This library is  distributed in  the hope that it will  be useful,
+  but  WITHOUT ANY WARRANTY;  without  even  the implied warranty of
+  MERCHANTABILITY  or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+  Lesser General Public License for more details.
+
+  You should have received a copy of  the GNU Lesser General  Public
+  License along with this library.
+
+//////////////////////////////////////////////////////////////////////////////*/
+
+
+
+#include "Structured2DGrid.h"
+
+using namespace uLib;
+
+//_____________________________________________________________
+Structured2DGrid::Structured2DGrid()
+{
+    // reset uni-dim space
+    m_Dims = Vector2i(0,0);
+    m_Origin = Vector2f(0.,0.);
+    m_Increments = Vector2i(0,0);
+    m_binW = Vector2f(1.,1.);
+    m_debug = true;
+}
+
+
+//_____________________________________________________________
+void Structured2DGrid::SetDims(const Vector2i &size)
+{
+    this->m_Dims = size;
+
+    // set increments
+    this->m_Increments[0] = 1;
+    this->m_Increments[1] = m_Dims[0];
+   }
+
+//_____________________________________________________________
+void Structured2DGrid::SetPhysicalSpace(const Vector2f &origin, const Vector2f &spacing)
+{
+    m_Origin = origin;
+    m_binW = spacing;
+
+    m_uni2phys_T = Translation<float,2>(m_Origin) * Scaling(m_binW);
+    m_phys2uni_T = m_uni2phys_T.matrix().inverse();
+
+    return;
+}
+
+
+//_____________________________________________________________
+bool Structured2DGrid::IsInsideBounds(const Vector2f &pt) const
+{
+    Vector2i pLoc = this->PhysicsToUnitSpace(pt);
+    return this->IsInsideGrid(pLoc);
+}
+
+
+//_____________________________________________________________
+Vector2i Structured2DGrid::UnMap(int index) const
+{
+    Vector2i v( 0,0 );
+    Vector2i iv = m_Increments;
+
+    int id = 0;
+    for(int k=0; k<2; ++k) {
+        int inc = iv.maxCoeff(&id);
+        v(id) = index / inc;
+        index -= v(id) * inc;
+        iv(id) = 0;
+    }
+    return v;
+}
+
+//_____________________________________________________________
+bool Structured2DGrid::IsInsideGrid(const Vector2i &v) const
+{
+    int vok = 1;
+    vok *= (v(0) >= 0 && v(0) < m_Dims[0]);
+    vok *= (v(1) >= 0 && v(1) < m_Dims[1]);
+
+    return vok;
+}
+
+
+//_____________________________________________________________
+Vector2i Structured2DGrid::PhysicsToUnitSpace(const Vector2f &pt) const
+{
+    Vector2i out;
+    Vector2f pLoc = m_phys2uni_T * pt;
+
+    out << (int)floor(pLoc(0)),
+                (int)floor(pLoc(1));
+
+    return out;
+}
+
+//_____________________________________________________________
+Vector2f Structured2DGrid::UnitToPhysicsSpace(const Vector2i &ind) const
+{
+    Vector2f p;
+    p = m_uni2phys_T * ind.cast<float>();
+
+    return p;
+}
+
+//_____________________________________________________________
+void Structured2DGrid::PrintSelf(std::ostream &o)
+{
+    o << "uLib Structured Data 2D: \n"
+      << "dim     = " << this->GetDims().transpose() << "\n"
+      << "spacing = " << this->GetSpacing().transpose() << "\n";
+}
+

src/Math/Structured2DGrid.h

@@ -0,0 +1,74 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// CMT Cosmic Muon Tomography project //////////////////////////////////////////
+////////////////////////////////////////////////////////////////////////////////
+
+  Copyright (c) 2014, Universita' degli Studi di Padova, INFN sez. di Padova
+  All rights reserved
+
+  Authors: Sara Vanini < sara.vanini@pd.infn.it >
+
+  ------------------------------------------------------------------
+  This library is free software;  you  can  redistribute  it  and/or
+  modify it  under the  terms  of  the  GNU  Lesser  General  Public
+  License as published  by  the  Free  Software  Foundation;  either
+  version 3.0 of the License, or (at your option) any later version.
+
+  This library is  distributed in  the hope that it will  be useful,
+  but  WITHOUT ANY WARRANTY;  without  even  the implied warranty of
+  MERCHANTABILITY  or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+  Lesser General Public License for more details.
+
+  You should have received a copy of  the GNU Lesser General  Public
+  License along with this library.
+
+//////////////////////////////////////////////////////////////////////////////*/
+
+#ifndef Structured2DGrid_H
+#define Structured2DGrid_H
+
+#include "Math/Dense.h"
+
+#include <Eigen/Dense>
+#include <Eigen/Geometry>
+
+using namespace Eigen;
+
+namespace uLib {
+
+class Structured2DGrid {
+public:
+
+    Structured2DGrid();
+
+    /// unit-space
+    void SetDims(const Vector2i &size);
+    inline Vector2i GetDims() {return m_Dims; }
+    bool IsInsideGrid(const Vector2i &v) const;
+    inline int Map(Vector2i index) const  { return (m_Increments.transpose() * index);}
+    Vector2i UnMap(int index) const;
+
+    /// physics-space
+    void SetPhysicalSpace(const Vector2f &origin, const Vector2f &spacing);
+    inline Vector2f GetSpacing() const {    return m_binW; }
+    inline Vector2f GetOrigin() const {    return m_Origin; }
+    bool IsInsideBounds(const Vector2f &pt) const;
+
+    /// operations
+    Vector2i PhysicsToUnitSpace(const Vector2f &pt) const;
+    Vector2f UnitToPhysicsSpace(const Vector2i &ind) const;
+    void PrintSelf(std::ostream &o);
+    void SetDebug(bool debug){ m_debug = debug; };
+
+private:
+    Vector2i m_Dims;
+    Vector2i m_Increments;
+    Vector2f m_binW;
+    Vector2f m_Origin;
+    bool m_debug;
+
+     Transform<float, 2, Eigen::Affine>  m_uni2phys_T;
+     Transform<float, 2, Eigen::Affine>  m_phys2uni_T;
+};
+}
+
+#endif // Structured2DGrid_H

src/Math/Structured4DGrid.cpp

@@ -0,0 +1,136 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// CMT Cosmic Muon Tomography project //////////////////////////////////////////
+////////////////////////////////////////////////////////////////////////////////
+
+  Copyright (c) 2014, Universita' degli Studi di Padova, INFN sez. di Padova
+  All rights reserved
+
+  Authors: Andrea Rigoni Garola < andrea.rigoni@pd.infn.it >
+
+  ------------------------------------------------------------------
+  This library is free software;  you  can  redistribute  it  and/or
+  modify it  under the  terms  of  the  GNU  Lesser  General  Public
+  License as published  by  the  Free  Software  Foundation;  either
+  version 3.0 of the License, or (at your option) any later version.
+
+  This library is  distributed in  the hope that it will  be useful,
+  but  WITHOUT ANY WARRANTY;  without  even  the implied warranty of
+  MERCHANTABILITY  or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+  Lesser General Public License for more details.
+
+  You should have received a copy of  the GNU Lesser General  Public
+  License along with this library.
+
+//////////////////////////////////////////////////////////////////////////////*/
+
+
+
+#include "Structured4DGrid.h"
+
+using namespace uLib;
+
+//_____________________________________________________________
+Structured4DGrid::Structured4DGrid()
+{
+    // reset uni-dim space
+    m_Dims = Vector4i(0,0,0,0);
+    m_Origin = Vector4f(0.,0.,0.,0.);
+    m_Increments = Vector4i(0,0,0,0);
+    m_binW = Vector4f(1.,1.,1.,1.);
+    m_debug = true;
+}
+
+
+//_____________________________________________________________
+void Structured4DGrid::SetDims(const Vector4i &size)
+{
+    this->m_Dims = size;
+
+    // set increments
+    this->m_Increments[0] = 1;
+    this->m_Increments[1] = m_Dims[0];
+    this->m_Increments[2] = m_Dims[0] * m_Dims[1];
+    this->m_Increments[3] = m_Dims[0] * m_Dims[1] * m_Dims[2];
+
+}
+
+//_____________________________________________________________
+void Structured4DGrid::SetPhysicalSpace(const Vector4f &origin, const Vector4f &spacing)
+{
+    m_Origin = origin;
+    m_binW = spacing;
+
+    m_uni2phys_T = Translation<float,4>(m_Origin) * Scaling(m_binW);
+    m_phys2uni_T = m_uni2phys_T.matrix().inverse();
+
+    return;
+}
+
+
+//_____________________________________________________________
+bool Structured4DGrid::IsInsideBounds(const Vector4f &pt) const
+{
+    Vector4i pLoc = this->PhysicsToUnitSpace(pt);
+    return this->IsInsideGrid(pLoc);
+}
+
+
+//_____________________________________________________________
+Vector4i Structured4DGrid::UnMap(int index) const
+{
+    Vector4i v( 0,0,0, 0 );
+    Vector4i iv = m_Increments;
+
+    int id = 0;
+    for(int k=0; k<4; ++k) {
+        int inc = iv.maxCoeff(&id);
+        v(id) = index / inc;
+        index -= v(id) * inc;
+        iv(id) = 0;
+    }
+    return v;
+}
+
+//_____________________________________________________________
+bool Structured4DGrid::IsInsideGrid(const Vector4i &v) const
+{
+    int vok = 1;
+    vok *= (v(0) >= 0 && v(0) < m_Dims[0]);
+    vok *= (v(1) >= 0 && v(1) < m_Dims[1]);
+    vok *= (v(2) >= 0 && v(2) < m_Dims[2]);
+    vok *= (v(3) >= 0 && v(3) < m_Dims[3]);
+    return vok;
+}
+
+
+//_____________________________________________________________
+Vector4i Structured4DGrid::PhysicsToUnitSpace(const Vector4f &pt) const
+{
+    Vector4i out;
+    Vector4f pLoc = m_phys2uni_T * pt;
+
+    out << (int)floor(pLoc(0)),
+                (int)floor(pLoc(1)),
+                (int)floor(pLoc(2)),
+                (int)floor(pLoc(3));
+
+    return out;
+}
+
+//_____________________________________________________________
+Vector4f Structured4DGrid::UnitToPhysicsSpace(const Vector4i &ind) const
+{
+    Vector4f p;
+    p = m_uni2phys_T * ind.cast<float>();
+
+    return p;
+}
+
+//_____________________________________________________________
+void Structured4DGrid::PrintSelf(std::ostream &o)
+{
+    o << "uLib Structured Data 4D: \n"
+      << "dim     = " << this->GetDims().transpose() << "\n"
+      << "spacing = " << this->GetSpacing().transpose() << "\n";
+}
+

src/Math/Structured4DGrid.h

@@ -0,0 +1,74 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// CMT Cosmic Muon Tomography project //////////////////////////////////////////
+////////////////////////////////////////////////////////////////////////////////
+
+  Copyright (c) 2014, Universita' degli Studi di Padova, INFN sez. di Padova
+  All rights reserved
+
+  Authors: Andrea Rigoni Garola < andrea.rigoni@pd.infn.it >
+
+  ------------------------------------------------------------------
+  This library is free software;  you  can  redistribute  it  and/or
+  modify it  under the  terms  of  the  GNU  Lesser  General  Public
+  License as published  by  the  Free  Software  Foundation;  either
+  version 3.0 of the License, or (at your option) any later version.
+
+  This library is  distributed in  the hope that it will  be useful,
+  but  WITHOUT ANY WARRANTY;  without  even  the implied warranty of
+  MERCHANTABILITY  or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+  Lesser General Public License for more details.
+
+  You should have received a copy of  the GNU Lesser General  Public
+  License along with this library.
+
+//////////////////////////////////////////////////////////////////////////////*/
+
+#ifndef Structured4DGrid_H
+#define Structured4DGrid_H
+
+#include "Math/Dense.h"
+
+#include <Eigen/Dense>
+#include <Eigen/Geometry>
+
+using namespace Eigen;
+
+namespace uLib {
+
+class Structured4DGrid {
+public:
+
+    Structured4DGrid();
+
+    /// unit-space
+    void SetDims(const Vector4i &size);
+    inline Vector4i GetDims() {return m_Dims; }
+    bool IsInsideGrid(const Vector4i &v) const;
+    inline int Map(Vector4i index) const  { return (m_Increments.transpose() * index);}
+    Vector4i UnMap(int index) const;
+
+    /// physics-space
+    void SetPhysicalSpace(const Vector4f &origin, const Vector4f &spacing);
+    inline Vector4f GetSpacing() const {    return m_binW; }
+    inline Vector4f GetOrigin() const {    return m_Origin; }
+    bool IsInsideBounds(const Vector4f &pt) const;
+
+    /// operations
+    Vector4i PhysicsToUnitSpace(const Vector4f &pt) const;
+    Vector4f UnitToPhysicsSpace(const Vector4i &ind) const;
+    void PrintSelf(std::ostream &o);
+    void SetDebug(bool debug){ m_debug = debug; };
+
+private:
+    Vector4i m_Dims;
+    Vector4i m_Increments;
+    Vector4f m_binW;
+    Vector4f m_Origin;
+    bool m_debug;
+
+     Transform<float, 4, Eigen::Affine>  m_uni2phys_T;
+     Transform<float, 4, Eigen::Affine>  m_phys2uni_T;
+};
+}
+
+#endif // Structured4DGrid_H

src/Math/StructuredData.h

@@ -28,15 +28,12 @@
 #ifndef STRUCTUREDDATA_H
 #define STRUCTUREDDATA_H
 
-#include "Core/Macros.h"
-#include "Core/Object.h"
 #include "Math/Dense.h"
 
 namespace uLib {
 
-class StructuredData : public Object {
+class StructuredData {
 public:
-    typedef Object BaseClass;
     enum _Order
     {
         CustomOrder = 0,
@@ -53,22 +50,23 @@ public:
     StructuredData(const Vector3i &size);
 
     StructuredData(const StructuredData &copy) :
-        BaseClass(copy),
         m_DataOrder(copy.m_DataOrder),
         m_Dims(copy.m_Dims),
         m_Increments(copy.m_Increments)
     {}
 
 
-    uLibGetMacro(Dims,Vector3i)
+    inline Vector3i GetDims() const { return this->m_Dims; }
 
     void SetDims(const Vector3i &size);
 
-    uLibGetSetMacro(Increments,Vector3i)
+    inline Vector3i GetIncrements() const { return this->m_Increments; }
+
+    inline void SetIncrements(Vector3i name) { this->m_Increments = name; }
 
     void SetDataOrder(Order order = YXZ);
 
-    uLibGetMacro(DataOrder,Order)
+    inline Order GetDataOrder() const { return this->m_DataOrder; }
 
     bool IsInsideGrid(const Vector3i &v) const;
 

src/Math/StructuredGrid.h

@@ -28,7 +28,6 @@
 #ifndef U_MATH_STRUCTUREDGRID_H
 #define U_MATH_STRUCTUREDGRID_H
 
-#include "Core/Object.h"
 #include "Math/ContainerBox.h"
 #include "Math/StructuredData.h"
 

src/Math/Transform.h

@@ -49,7 +49,6 @@
 #ifndef U_TRANSFORM_H
 #define U_TRANSFORM_H
 
-#include <Core/Macros.h>
 #include <Eigen/Geometry>
 
 
@@ -80,7 +79,10 @@ public:
     {}
 
     Eigen::Affine3f& GetTransform() { return m_T; }
-    uLibGetSetMacro(Parent,AffineTransform *)
+
+    inline AffineTransform *GetParent() const { return this->m_Parent; }
+
+    inline void SetParent(AffineTransform *name) { this->m_Parent = name; }
 
     inline void SetMatrix (Matrix4f &mat) { m_T.matrix() = mat; }
     inline Matrix4f& GetMatrix () { return m_T.matrix(); }
@@ -108,6 +110,17 @@ public:
 
     inline void Rotate(const Matrix3f &m) { this->m_T.rotate(m); }
 
+    inline void Rotate(const float angle, Vector3f axis)
+    {
+        axis.normalize(); // prehaps not necessary ( see eigens )
+        Eigen::AngleAxisf ax(angle,axis);
+        this->m_T.rotate(Eigen::Quaternion<float>(ax));
+    }
+
+    inline void Rotate(const Vector3f euler_axis) {
+        float angle = euler_axis.norm();
+        Rotate(angle,euler_axis);
+    }
 
     inline void PreRotate(const Matrix3f &m) { this->m_T.prerotate(m); }
 

src/Math/TriangleMesh.h

@@ -28,14 +28,14 @@
 #ifndef TRIANGLEMESH_H
 #define TRIANGLEMESH_H
 
-#include "Core/Object.h"
-#include "Core/Vector.h"
+#include <vector>
+
 #include "Math/Dense.h"
 
 namespace uLib {
 
-class TriangleMesh : public Object {
-
+class TriangleMesh
+{
 public:
     void PrintSelf(std::ostream &o);
 
@@ -44,12 +44,12 @@ public:
     void AddTriangle(const Id_t *id);
     void AddTriangle(const Vector3i &id);
 
-    uLibRefMacro(Points,Vector<Vector3f>)
-    uLibRefMacro(Triangles,Vector<Vector3i>)
+    inline std::vector<Vector3f> & Points() { return this->m_Points; }
+    inline std::vector<Vector3i> & Triangles() { return this->m_Triangles; }
 
 private:
-    Vector<Vector3f> m_Points;
-    Vector<Vector3i> m_Triangles;
+    std::vector<Vector3f> m_Points;
+    std::vector<Vector3i> m_Triangles;
 
 };
 

src/Math/VoxImage.cpp

@@ -30,6 +30,13 @@
 
 #include "VoxImage.h"
 
+#include <vtkSmartPointer.h>
+#include <vtkImageData.h>
+#include <vtkXMLImageDataReader.h>
+#include <vtkXMLImageDataWriter.h>
+#include <vtkStringArray.h>
+#include <vtkInformation.h>
+#include <vtkInformationStringKey.h>
 
 namespace uLib {
 
@@ -83,7 +90,103 @@ void Abstract::VoxImage::ExportToVtk (const char *file, bool density_type)
     printf("%s vtk file saved\n",file);
 }
 
-int Abstract::VoxImage::ImportFromVtk(const char *file)
+
+
+void Abstract::VoxImage::ExportToVti (const char *file, bool density_type, bool compressed)
+{
+    Abstract::VoxImage *voxels = this;
+
+    vtkSmartPointer<vtkImageData> image = vtkSmartPointer<vtkImageData>::New();
+    image->SetDimensions(voxels->GetDims()(0), voxels->GetDims()(1), voxels->GetDims()(2));
+    image->SetSpacing(voxels->GetSpacing()(0), voxels->GetSpacing()(1), voxels->GetSpacing()(2));
+    image->SetOrigin(voxels->GetPosition()(0), voxels->GetPosition()(1), voxels->GetPosition()(2));
+    image->AllocateScalars(VTK_FLOAT, 1);
+
+    float norm;
+    if (density_type) {
+        norm = 1;
+    } else norm = 1.E6;
+
+    int nx = voxels->GetDims()(0);
+    int ny = voxels->GetDims()(1);
+    int nz = voxels->GetDims()(2);
+
+    size_t npoints = nx*ny*nz;
+    float *scalar = static_cast<float*>(image->GetScalarPointer());
+
+    StructuredData unwrap(*voxels);
+    unwrap.SetDataOrder(StructuredData::XYZ); // move to XYZ order (VTK)
+    for (size_t i = 0; i < npoints; i++) {
+        Vector3i idx = unwrap.UnMap(i);
+        scalar[i] = static_cast<float>(voxels->GetValue(idx) * norm);
+    }
+
+    // Create a custom string key
+    static vtkInformationStringKey* ConfigNote =
+        vtkInformationStringKey::MakeKey("cmt.config", "Config");
+
+    // Attach metadata
+    vtkInformation *info = image->GetInformation();
+    info->Set(ConfigNote, 
+
+    "This image was generated with uLib\n"
+    "-----------------------------------\n"
+    "Author: Andrea Rigoni\n"
+    "Version: 0.1\n"
+    "Date: 2025\n"
+
+    );
+
+    // std::cout << info->Get(ConfigNote) << std::endl;
+    vtkSmartPointer<vtkXMLImageDataWriter> writer = vtkSmartPointer<vtkXMLImageDataWriter>::New();
+    writer->SetFileName(file);
+    writer->SetInputData(image);
+    if(compressed) {
+        writer->SetDataModeToBinary();
+        writer->SetCompressorTypeToZLib();
+    }
+    writer->Write();
+}
+
+
+int Abstract::VoxImage::ImportFromVti(const char *file, bool density_type) {
+    
+    vtkSmartPointer<vtkXMLImageDataReader> reader = vtkSmartPointer<vtkXMLImageDataReader>::New();
+    reader->SetFileName(file);
+    reader->Update();
+    vtkImageData *image = reader->GetOutput();
+    if(!image) return false;
+    
+    Abstract::VoxImage *voxels = this;
+    int nx = image->GetDimensions()[0];
+    int ny = image->GetDimensions()[1];
+    int nz = image->GetDimensions()[2];
+    
+    voxels->SetDims(Vector3i(nx,ny,nz));
+    voxels->SetSpacing(Vector3f(image->GetSpacing()[0],image->GetSpacing()[1],image->GetSpacing()[2]));
+    voxels->SetPosition(Vector3f(image->GetOrigin()[0],image->GetOrigin()[1],image->GetOrigin()[2]));
+
+    float norm;
+    if (density_type) {
+        norm = 1;
+    } else norm = 1.E6;
+
+    size_t npoints = nx*ny*nz;
+    float *scalar = static_cast<float*>(image->GetScalarPointer());
+
+    StructuredData wrap(*voxels);
+    wrap.SetDataOrder(StructuredData::XYZ);
+    for (size_t i = 0; i < npoints; i++) {
+        Vector3i idx = wrap.UnMap(i);
+        voxels->SetValue(idx, scalar[i] / norm);
+    }
+
+    return true;
+}
+
+
+
+int Abstract::VoxImage::ImportFromVtk(const char *file, bool density_type)
 {
     FILE * vtk_file = fopen(file, "r");
     if (!vtk_file) return false;
@@ -115,14 +218,18 @@ int Abstract::VoxImage::ImportFromVtk(const char *file)
     this->SetSpacing(Vector3f(sx,sy,sz));
     this->SetPosition(Vector3f(ox,oy,oz));
 
+    float norm;
+    if (density_type) {
+        norm = 1;
+    } else norm = 1.E6;
+
     for (int k = 0; k < dz; ++k) {
         for (int j = 0; j < dy; ++j) {
             for (int i = 0; i < dx; ++i) {
                 Vector3i idx(i, j, k);
                 float tmp_val;
                 fscanf(vtk_file, "%f", &tmp_val);
-                //this->SetValue(idx,fabs(tmp_val)*1E-6);
-                this->SetValue(idx,tmp_val*1E-6);
+                this->SetValue(idx,tmp_val / norm);
             }
         }
     }

src/Math/VoxImage.h

@@ -23,18 +23,18 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
 #ifndef U_MATH_VOXIMAGE_H
 #define U_MATH_VOXIMAGE_H
 
-#include "Core/Vector.h"
 #include "Core/StaticInterface.h"
 #include "Math/Dense.h"
 #include "Math/StructuredGrid.h"
 
 #include <iostream>
 #include <stdlib.h>
+#include <vector>
+
+#include <Core/DataAllocator.h>
 
 namespace uLib {
 
@@ -56,16 +56,26 @@ public:
   virtual void SetDims(const Vector3i &size) = 0;
 
   void ExportToVtk(const char *file, bool density_type = 0);
+
+  // use this function to export to VTK binary format
+  void ExportToVti(const char *file, bool density_type = 0,
+                   bool compressed = 0);
+
+  // this function has been deprecated in favor of ExportToVti
+  // but it is kept for backward compatibility and because it
+  // does not depend on vtk library
   void ExportToVtkXml(const char *file, bool density_type = 0);
-    int ImportFromVtk(const char *file);
+
+  int ImportFromVtk(const char *file, bool density_type = 0);
+
+  int ImportFromVti(const char *file, bool density_type = 0);
 
 protected:
-
   virtual ~VoxImage() {}
   VoxImage(const Vector3i &size) : BaseClass(size) {}
 };
 
-}
+} // namespace Abstract
 
 ////////////////////////////////////////////////////////////////////////////////
 //  VOXEL   ////////////////////////////////////////////////////////////////////
@@ -77,20 +87,17 @@ struct Voxel {
     uLibCheckMember(Self, Value, Scalarf);
   }
 };
-}
+} // namespace Interface
 
 struct Voxel {
   Scalarf Value;
 };
 
-
 ////////////////////////////////////////////////////////////////////////////////
 //  VOX IMAGE  /////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 
-
-template< typename T >
-class VoxImage :  public Abstract::VoxImage {
+template <typename T> class VoxImage : public Abstract::VoxImage {
 public:
   typedef Abstract::VoxImage BaseClass;
 
@@ -98,14 +105,12 @@ public:
 
   VoxImage(const Vector3i &size);
 
-    VoxImage(const VoxImage<T> &copy) :
-        BaseClass(copy)
-    {
+  VoxImage(const VoxImage<T> &copy) : BaseClass(copy) {
     this->m_Data = copy.m_Data;
   }
 
-    uLibRefMacro(Data,Vector<T>)
-    inline const Vector<T>& ConstData() const { return m_Data; }
+  inline DataAllocator<T> &Data() { return this->m_Data; }
+  inline const DataAllocator<T> &ConstData() const { return m_Data; }
 
   inline const T &At(int i) const { return m_Data.at(i); }
   inline const T &At(const Vector3i &id) const { return m_Data.at(Map(id)); }
@@ -116,9 +121,7 @@ public:
   inline Scalarf GetValue(const Vector3i &id) const {
     return this->At(id).Value;
   }
-    inline Scalarf GetValue(const int id) const {
-        return this->At(id).Value;
-    }
+  inline Scalarf GetValue(const int id) const { return this->At(id).Value; }
 
   inline void SetValue(const Vector3i &id, Scalarf value) {
     this->operator[](id).Value = value;
@@ -129,19 +132,26 @@ public:
 
   inline void SetDims(const Vector3i &size) {
     this->m_Data.resize(size.prod());
-        BaseClass::BaseClass::SetDims(size); // FIX horrible coding style !
+    StructuredGrid::SetDims(size);
   }
 
   inline VoxImage<T> clipImage(const Vector3i begin, const Vector3i end) const;
   inline VoxImage<T> clipImage(const HPoint3f begin, const HPoint3f end) const;
   inline VoxImage<T> clipImage(const float density) const;
-    inline VoxImage<T> clipImage(const float densityMin, const float densityMax) const;
+  inline VoxImage<T> clipImage(const float densityMin,
+                               const float densityMax) const;
 
-    inline VoxImage<T> maskImage(const HPoint3f begin, const HPoint3f end, float value) const;
-    inline VoxImage<T> maskImage(const float threshold, float belowValue=0, float aboveValue=0) const;
+  inline VoxImage<T> maskImage(const HPoint3f begin, const HPoint3f end,
+                               float value) const;
+  inline VoxImage<T> maskImage(const float threshold, float belowValue = 0,
+                               float aboveValue = 0) const;
   inline VoxImage<T> fixVoxels(const float threshold, float tolerance) const;
-    inline VoxImage<T> fixVoxels(const float threshold, float tolerance, const HPoint3f begin, const HPoint3f end) const;
-    inline VoxImage<T> fixVoxelsAroundPlane(const float threshold, float tolerance, const HPoint3f begin, const HPoint3f end, bool aboveAir) const;
+  inline VoxImage<T> fixVoxels(const float threshold, float tolerance,
+                               const HPoint3f begin, const HPoint3f end) const;
+  inline VoxImage<T> fixVoxelsAroundPlane(const float threshold,
+                                          float tolerance, const HPoint3f begin,
+                                          const HPoint3f end,
+                                          bool aboveAir) const;
   inline VoxImage<T> fixVoxels(const HPoint3f begin, const HPoint3f end) const;
   inline VoxImage<T> Abs() const;
 
@@ -168,8 +178,7 @@ public:
   }
 
   // MATH VoxImage Operators //
-    template <typename S>
-    void operator +=(VoxImage<S> &sibling) {
+  template <typename S> void operator+=(VoxImage<S> &sibling) {
     if (this->GetDims() != sibling.GetDims()) {
       // printf("Warning when adding VoxImages: I'm NOT doing it!\n");
       return;
@@ -179,8 +188,7 @@ public:
     }
   }
 
-    template <typename S>
-    void operator -=(VoxImage<S> &sibling) {
+  template <typename S> void operator-=(VoxImage<S> &sibling) {
     if (this->GetDims() != sibling.GetDims()) {
       // printf("Warning when subtracting VoxImages: I'm NOT doing it!\n");
       return;
@@ -190,8 +198,7 @@ public:
     }
   }
 
-    template <typename S>
-    void operator *=(VoxImage<S> &sibling) {
+  template <typename S> void operator*=(VoxImage<S> &sibling) {
     if (this->GetDims() != sibling.GetDims()) {
       // printf("Warning when multiplying VoxImages: I'm NOT doing it!\n");
       return;
@@ -201,8 +208,7 @@ public:
     }
   }
 
-    template <typename S>
-    void operator /=(VoxImage<S> &sibling) {
+  template <typename S> void operator/=(VoxImage<S> &sibling) {
     if (this->GetDims() != sibling.GetDims()) {
       // printf("Warning when dividing VoxImages: I'm NOT doing it!\n");
       return;
@@ -213,35 +219,32 @@ public:
   }
 
 private:
-    Vector<T> m_Data;
+  DataAllocator<T> m_Data;
 };
 
+template <typename T>
+VoxImage<T>::VoxImage() : m_Data(0), BaseClass(Vector3i(0, 0, 0)) {
+  Interface::IsA<T, Interface::Voxel>(); /* structural check for T */
+}
 
 template <typename T>
-VoxImage<T>::VoxImage() :
-    m_Data(0),
-    BaseClass(Vector3i(0,0,0))
-{ Interface::IsA <T,Interface::Voxel>(); /* structural check for T */ }
+VoxImage<T>::VoxImage(const Vector3i &size)
+    : m_Data(size.prod()), BaseClass(size) {
+  Interface::IsA<T, Interface::Voxel>(); /* structural check for T */
+}
 
 template <typename T>
-VoxImage<T>::VoxImage(const Vector3i &size) :
-    m_Data(size.prod()),
-    BaseClass(size)
-{ Interface::IsA <T,Interface::Voxel>(); /* structural check for T */ }
-
-
-template <typename T>
-VoxImage<T> VoxImage<T>::clipImage(const Vector3i begin, const Vector3i end) const
-{
+VoxImage<T> VoxImage<T>::clipImage(const Vector3i begin,
+                                   const Vector3i end) const {
   Vector3i dim = (end - begin) + Vector3i(1, 1, 1);
   VoxImage<T> out(*this);
   out.SetDims(dim);
-        out.SetPosition(this->GetPosition() + this->GetSpacing().cwiseProduct(begin.cast<float>()) );
+  out.SetPosition(this->GetPosition() +
+                  this->GetSpacing().cwiseProduct(begin.cast<float>()));
 
   for (uint x = 0; x < dim(0); ++x)
     for (uint y = 0; y < dim(1); ++y)
-                for(uint z = 0; z<dim(2); ++z )
-                {
+      for (uint z = 0; z < dim(2); ++z) {
         Vector3i id = Vector3i(x, y, z);
         out[id] = this->At(begin + id);
       }
@@ -249,16 +252,15 @@ VoxImage<T> VoxImage<T>::clipImage(const Vector3i begin, const Vector3i end) con
 }
 
 template <typename T>
-VoxImage<T> VoxImage<T>::clipImage(const HPoint3f begin, const HPoint3f end) const
-{
+VoxImage<T> VoxImage<T>::clipImage(const HPoint3f begin,
+                                   const HPoint3f end) const {
   Vector3i v1 = this->Find(begin);
   Vector3i v2 = this->Find(end);
   return this->clipImage(v1, v2);
 }
 
 template <typename T>
-VoxImage<T> VoxImage<T>::clipImage(const float density) const
-{
+VoxImage<T> VoxImage<T>::clipImage(const float density) const {
   Vector3i v1 = this->GetDims();
   Vector3i v2 = Vector3i(0, 0, 0);
   for (uint i = 0; i < this->m_Data.size(); ++i) {
@@ -272,8 +274,8 @@ VoxImage<T> VoxImage<T>::clipImage(const float density) const
 }
 
 template <typename T>
-VoxImage<T> VoxImage<T>::clipImage(const float densityMin, const float densityMax) const
-{
+VoxImage<T> VoxImage<T>::clipImage(const float densityMin,
+                                   const float densityMax) const {
   Vector3i v1 = this->GetDims();
   Vector3i v2 = Vector3i(0, 0, 0);
   for (uint i = 0; i < this->m_Data.size(); ++i) {
@@ -287,8 +289,8 @@ VoxImage<T> VoxImage<T>::clipImage(const float densityMin, const float densityMa
 }
 
 template <typename T>
-VoxImage<T> VoxImage<T>::maskImage(const HPoint3f begin, const HPoint3f end, float value) const
-{
+VoxImage<T> VoxImage<T>::maskImage(const HPoint3f begin, const HPoint3f end,
+                                   float value) const {
   VoxImage<T> out(*this);
   out.SetDims(this->GetDims());
   out.SetPosition(this->GetPosition());
@@ -309,9 +311,10 @@ VoxImage<T> VoxImage<T>::maskImage(const HPoint3f begin, const HPoint3f end, flo
 }
 
 template <typename T>
-VoxImage<T> VoxImage<T>::maskImage(const float threshold, float belowValue, float aboveValue) const
-{
-    std::cout << "VoxImage: maskImage, fixing voxels under threshold " << threshold;
+VoxImage<T> VoxImage<T>::maskImage(const float threshold, float belowValue,
+                                   float aboveValue) const {
+  std::cout << "VoxImage: maskImage, fixing voxels under threshold "
+            << threshold;
   if (belowValue)
     std::cout << " at value " << belowValue;
   else
@@ -322,7 +325,6 @@ VoxImage<T> VoxImage<T>::maskImage(const float threshold, float belowValue, floa
   else
     std::cout << "found";
 
-
   VoxImage<T> out(*this);
   out.SetDims(this->GetDims());
   out.SetPosition(this->GetPosition());
@@ -333,10 +335,11 @@ VoxImage<T> VoxImage<T>::maskImage(const float threshold, float belowValue, floa
       // voxels under threshold
       if (this->GetValue(i) <= threshold * 1.E-6) {
         if (belowValue) {
-                    //                std::cout << "vox " << i << ", " << this->GetValue(i);
-                    //                std::cout << " ----> set to " << -1.*belowValue*1.E-6 << std::endl;
-                    out.SetValue(i,-1.*belowValue*1.E-6);}
-                else
+          //                std::cout << "vox " << i << ", " <<
+          //                this->GetValue(i); std::cout << " ----> set to " <<
+          //                -1.*belowValue*1.E-6 << std::endl;
+          out.SetValue(i, -1. * belowValue * 1.E-6);
+        } else
           out.SetValue(i, -1. * this->GetValue(i));
       }
       // voxels over threshold
@@ -352,8 +355,8 @@ VoxImage<T> VoxImage<T>::maskImage(const float threshold, float belowValue, floa
 }
 
 template <typename T>
-VoxImage<T> VoxImage<T>::fixVoxels(const float threshold, float tolerance) const
-{
+VoxImage<T> VoxImage<T>::fixVoxels(const float threshold,
+                                   float tolerance) const {
   std::cout << "VoxImage: fixing voxels with value " << threshold << std::endl;
 
   VoxImage<T> out(*this);
@@ -364,16 +367,15 @@ VoxImage<T> VoxImage<T>::fixVoxels(const float threshold, float tolerance) const
     // voxels around threshold
     if (fabs(this->GetValue(i) - threshold * 1.E-6) < tolerance * 1.E-6) {
       //            std::cout << "vox " << i << ", " << this->GetValue(i);
-//            std::cout << " ----> set to " << -1.*this->GetValue(i) << std::endl;
+      //            std::cout << " ----> set to " << -1.*this->GetValue(i) <<
+      //            std::endl;
       out.SetValue(i, -1. * this->GetValue(i));
     }
   }
   return out;
 }
 
-template <typename T>
-VoxImage<T> VoxImage<T>::Abs() const
-{
+template <typename T> VoxImage<T> VoxImage<T>::Abs() const {
   std::cout << "VoxImage: set abs voxels value " << std::endl;
 
   VoxImage<T> out(*this);
@@ -387,8 +389,9 @@ VoxImage<T> VoxImage<T>::Abs() const
 }
 
 template <typename T>
-VoxImage<T> VoxImage<T>::fixVoxels( const float threshold, float tolerance, const HPoint3f begin, const HPoint3f end) const
-{
+VoxImage<T> VoxImage<T>::fixVoxels(const float threshold, float tolerance,
+                                   const HPoint3f begin,
+                                   const HPoint3f end) const {
   VoxImage<T> out(*this);
   out.SetDims(this->GetDims());
   out.SetPosition(this->GetPosition());
@@ -412,8 +415,8 @@ VoxImage<T> VoxImage<T>::fixVoxels( const float threshold, float tolerance, cons
 }
 
 template <typename T>
-VoxImage<T> VoxImage<T>::fixVoxels(const HPoint3f begin, const HPoint3f end) const
-{
+VoxImage<T> VoxImage<T>::fixVoxels(const HPoint3f begin,
+                                   const HPoint3f end) const {
   VoxImage<T> out(*this);
   out.SetDims(this->GetDims());
   out.SetPosition(this->GetPosition());
@@ -433,10 +436,11 @@ VoxImage<T> VoxImage<T>::fixVoxels(const HPoint3f begin, const HPoint3f end) con
   return out;
 }
 
-
 template <typename T>
-VoxImage<T> VoxImage<T>::fixVoxelsAroundPlane( const float threshold, float tolerance, const HPoint3f B, const HPoint3f E, bool aboveAir) const
-{
+VoxImage<T> VoxImage<T>::fixVoxelsAroundPlane(const float threshold,
+                                              float tolerance, const HPoint3f B,
+                                              const HPoint3f E,
+                                              bool aboveAir) const {
   VoxImage<T> out(*this);
   Vector3i dim = this->GetDims();
   out.SetDims(dim);
@@ -452,27 +456,30 @@ VoxImage<T> VoxImage<T>::fixVoxelsAroundPlane( const float threshold, float tole
 
         // B, E voxel position
         Vector3i iv(ix, iy, iz);
-                Vector3f v = Vector3f(iv.cast<float>().cwiseProduct(this->GetSpacing()));
+        Vector3f v =
+            Vector3f(iv.cast<float>().cwiseProduct(this->GetSpacing()));
         HPoint3f Bvox = Bcoll + HPoint3f(v);
         HPoint3f Evox = Bvox + this->GetSpacing().homogeneous();
         HPoint3f V = Bvox + 0.5 * (this->GetSpacing().homogeneous());
 
-                // if distance point (x0,y0) from line by points (x1,y1) and (x2,y2) is less than tolerance
+        // if distance point (x0,y0) from line by points (x1,y1) and (x2,y2) is
+        // less than tolerance
         float x1 = B[1];
         float y1 = B[2];
         float x2 = E[1];
         float y2 = E[2];
         float x0 = V[1];
         float y0 = V[2];
-                float dist = fabs( (x2-x1)*(y1-y0) - ((x1-x0)*(y2-y1))) / sqrt( (x2-x1)*(x2-x1)+((y2-y1)*(y2-y1)));
+        float dist = fabs((x2 - x1) * (y1 - y0) - ((x1 - x0) * (y2 - y1))) /
+                     sqrt((x2 - x1) * (x2 - x1) + ((y2 - y1) * (y2 - y1)));
         float distSign = (x2 - x1) * (y1 - y0) - ((x1 - x0) * (y2 - y1));
 
         // set voxel air value
         if (dist < tolerance) {
-                    //std::cout << "voxel " << iv << ", line " << dist << ", tolerance " << tolerance << std::endl;
+          // std::cout << "voxel " << iv << ", line " << dist << ", tolerance "
+          // << tolerance << std::endl;
           out.SetValue(ID, threshold * 1.E-6);
-                }
-                else
+        } else
           out.SetValue(ID, this->GetValue(ID));
 
         if ((distSign > 0 && aboveAir) || (distSign < 0 && !aboveAir))
@@ -481,13 +488,10 @@ VoxImage<T> VoxImage<T>::fixVoxelsAroundPlane( const float threshold, float tole
   return out;
 }
 
-
-template<typename T>
-void VoxImage<T>::InitVoxels(T t)
-{
+template <typename T> void VoxImage<T>::InitVoxels(T t) {
   std::fill(m_Data.begin(), m_Data.end(), t); // warning... stl function //
 }
 
-}
+} // namespace uLib
 
 #endif // VOXIMAGE_H

src/Math/VoxImageFilter.h

@@ -23,21 +23,16 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
 #ifndef VOXIMAGEFILTER_H
 #define VOXIMAGEFILTER_H
 
 #include "Core/StaticInterface.h"
-#include "Core/Object.h"
 #include "Math/Dense.h"
 
 #include "Math/VoxImage.h"
 
-
 namespace uLib {
 
-
 namespace Interface {
 struct VoxImageFilterShape {
   template <class Self> void check_structural() {
@@ -45,11 +40,10 @@ struct VoxImageFilterShape {
     uLibCheckFunction(Self, operator(), float, const Vector3f &);
   }
 };
-}
+} // namespace Interface
 
 template <typename VoxelT> class Kernel;
 
-
 namespace Abstract {
 class VoxImageFilter {
 public:
@@ -60,38 +54,36 @@ public:
 protected:
   virtual ~VoxImageFilter() {}
 };
-}
-
+} // namespace Abstract
 
 template <typename VoxelT, typename AlgorithmT>
-class VoxImageFilter : public Abstract::VoxImageFilter, public Object
-{   
+class VoxImageFilter : public Abstract::VoxImageFilter {
 
 public:
   VoxImageFilter(const Vector3i &size);
 
   void Run();
 
-    void SetKernelNumericXZY(const Vector<float> &numeric);
+  void SetKernelNumericXZY(const std::vector<float> &numeric);
 
   void SetKernelSpherical(float (*shape)(float));
 
-    template < class ShapeT >
-    void SetKernelSpherical( ShapeT shape );
+  template <class ShapeT> void SetKernelSpherical(ShapeT shape);
 
   void SetKernelWeightFunction(float (*shape)(const Vector3f &));
 
-    template < class ShapeT >
-    void SetKernelWeightFunction( ShapeT shape );
+  template <class ShapeT> void SetKernelWeightFunction(ShapeT shape);
 
-    uLibGetMacro(KernelData,Kernel<VoxelT>)
+  inline const Kernel<VoxelT> &GetKernelData() const {
+    return this->m_KernelData;
+  }
+  inline Kernel<VoxelT> &GetKernelData() { return this->m_KernelData; }
 
-    uLibGetMacro(Image,VoxImage<VoxelT> *)
+  inline VoxImage<VoxelT> *GetImage() const { return this->m_Image; }
 
   void SetImage(Abstract::VoxImage *image);
 
 protected:
-
   float Convolve(const VoxImage<VoxelT> &buffer, int index); // remove //
 
   void SetKernelOffset();
@@ -104,26 +96,18 @@ protected:
 
 private:
   AlgorithmT *t_Algoritm;
-
 };
 
-
-
-
-
-
-}
-
+} // namespace uLib
 
 #endif // VOXIMAGEFILTER_H
 
 #include "VoxImageFilter.hpp"
 
-#include "VoxImageFilterLinear.hpp"
-#include "VoxImageFilterThreshold.hpp"
-#include "VoxImageFilterMedian.hpp"
+#include "VoxImageFilter2ndStat.hpp"
 #include "VoxImageFilterABTrim.hpp"
 #include "VoxImageFilterBilateral.hpp"
-#include "VoxImageFilter2ndStat.hpp"
 #include "VoxImageFilterCustom.hpp"
-
+#include "VoxImageFilterLinear.hpp"
+#include "VoxImageFilterMedian.hpp"
+#include "VoxImageFilterThreshold.hpp"

src/Math/VoxImageFilter.hpp

@@ -23,24 +23,21 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
 #ifndef VOXIMAGEFILTER_HPP
 #define VOXIMAGEFILTER_HPP
 
-#include <Math/Dense.h>
 #include "Math/StructuredData.h"
 #include "Math/VoxImage.h"
 #include "VoxImageFilter.h"
+#include <Math/Dense.h>
 
 namespace uLib {
 
-
 // KERNEL //////////////////////////////////////////////////////////////////////
 
-template < typename T >
-class Kernel : public StructuredData {
+template <typename T> class Kernel : public StructuredData {
   typedef StructuredData BaseClass;
+
 public:
   Kernel(const Vector3i &size);
 
@@ -48,34 +45,27 @@ public:
   inline T &operator[](const int &id) { return m_Data[id]; }
   inline int GetCenterData() const;
 
-    uLibRefMacro(Data,Vector<T>)
+  inline DataAllocator<T> &Data() { return this->m_Data; }
 
-    inline const Vector<T>& ConstData() const { return this->m_Data; }
+  inline const DataAllocator<T> &ConstData() const { return this->m_Data; }
 
   void PrintSelf(std::ostream &o) const;
 
 private:
-    Vector<T> m_Data;
+  DataAllocator<T> m_Data;
 };
 
 template <typename T>
-Kernel<T>::Kernel(const Vector3i &size) :
-    BaseClass(size),
-    m_Data(size.prod())
-{
+Kernel<T>::Kernel(const Vector3i &size) : BaseClass(size), m_Data(size.prod()) {
   Interface::IsA<T, Interface::Voxel>();
 }
 
-template < typename T >
-inline int Kernel<T>::GetCenterData() const
-{
+template <typename T> inline int Kernel<T>::GetCenterData() const {
   static int center = Map(this->GetDims() / 2);
   return center;
 }
 
-template < typename T >
-void Kernel<T>::PrintSelf(std::ostream &o) const
-{
+template <typename T> void Kernel<T>::PrintSelf(std::ostream &o) const {
   o << " Filter Kernel Dump [XZ_Y]: \n";
   Vector3i index;
   o << "\n Value: \n\n"
@@ -86,8 +76,10 @@ void Kernel<T>::PrintSelf(std::ostream &o) const
       for (int x = 0; x < this->GetDims()(0); ++x) {
         index << x, y, z;
         o << m_Data[Map(index)].Value << " ";
-            } o << "\n";
-        } o << " --------------------------------------------------- \n";
+      }
+      o << "\n";
+    }
+    o << " --------------------------------------------------- \n";
   }
   o << "\n Offset: \n"
     << "------------------------------------------------- \n";
@@ -97,36 +89,24 @@ void Kernel<T>::PrintSelf(std::ostream &o) const
       for (int x = 0; x < this->GetDims()(0); ++x) {
         index << x, y, z;
         o << m_Data[Map(index)].Count << " ";
-            } o << "\n";
-        } o << " --------------------------------------------------- \n";
+      }
+      o << "\n";
+    }
+    o << " --------------------------------------------------- \n";
   }
 }
 
 ////////////////////////////////////////////////////////////////////////////////
 
-
-
-
-
-
-
-
 #define _TPL_ template <typename VoxelT, typename AlgorithmT>
 #define _TPLT_ VoxelT, AlgorithmT
 
-
+_TPL_
+VoxImageFilter<_TPLT_>::VoxImageFilter(const Vector3i &size)
+    : m_KernelData(size), t_Algoritm(static_cast<AlgorithmT *>(this)) {}
 
 _TPL_
-VoxImageFilter<_TPLT_>::VoxImageFilter(const Vector3i &size) :
-    m_KernelData(size),
-    t_Algoritm(static_cast<AlgorithmT *>(this))
-{
-
-}
-
-_TPL_
-void VoxImageFilter<_TPLT_>::Run()
-{
+void VoxImageFilter<_TPLT_>::Run() {
   VoxImage<VoxelT> buffer = *m_Image;
 #pragma omp parallel for
   for (int i = 0; i < m_Image->Data().size(); ++i)
@@ -135,8 +115,7 @@ void VoxImageFilter<_TPLT_>::Run()
 }
 
 _TPL_
-void VoxImageFilter<_TPLT_>::SetKernelOffset()
-{
+void VoxImageFilter<_TPLT_>::SetKernelOffset() {
   Vector3i id(0, 0, 0);
   for (int z = 0; z < m_KernelData.GetDims()(2); ++z) {
     for (int x = 0; x < m_KernelData.GetDims()(0); ++x) {
@@ -149,22 +128,21 @@ void VoxImageFilter<_TPLT_>::SetKernelOffset()
 }
 
 _TPL_
-float VoxImageFilter<_TPLT_>::Distance2(const Vector3i &v)
-{
+float VoxImageFilter<_TPLT_>::Distance2(const Vector3i &v) {
   Vector3i tmp = v;
   const Vector3i &dim = this->m_KernelData.GetDims();
   Vector3i center = dim / 2;
   tmp = tmp - center;
   center = center.cwiseProduct(center);
   tmp = tmp.cwiseProduct(tmp);
-    return (float)(tmp.sum()) / (float)( center.sum() + 0.25 *
-                                         (3 - (dim(0) % 2) - (dim(1) % 2) - (dim(2) % 2)));
+  return (float)(tmp.sum()) /
+         (float)(center.sum() +
+                 0.25 * (3 - (dim(0) % 2) - (dim(1) % 2) - (dim(2) % 2)));
 }
 
-
 _TPL_
-void VoxImageFilter<_TPLT_>::SetKernelNumericXZY(const Vector<float> &numeric)
-{
+void VoxImageFilter<_TPLT_>::SetKernelNumericXZY(
+    const std::vector<float> &numeric) {
   // set data order //
   StructuredData::Order order = m_KernelData.GetDataOrder();
   // m_KernelData.SetDataOrder(StructuredData::XZY);
@@ -182,8 +160,7 @@ void VoxImageFilter<_TPLT_>::SetKernelNumericXZY(const Vector<float> &numeric)
 }
 
 _TPL_
-void VoxImageFilter<_TPLT_>::SetKernelSpherical(float(* shape)(float))
-{
+void VoxImageFilter<_TPLT_>::SetKernelSpherical(float (*shape)(float)) {
   Vector3i id;
   for (int y = 0; y < m_KernelData.GetDims()(1); ++y) {
     for (int z = 0; z < m_KernelData.GetDims()(2); ++z) {
@@ -195,10 +172,8 @@ void VoxImageFilter<_TPLT_>::SetKernelSpherical(float(* shape)(float))
   }
 }
 
-
 _TPL_ template <class ShapeT>
-void VoxImageFilter<_TPLT_>::SetKernelSpherical(ShapeT shape)
-{
+void VoxImageFilter<_TPLT_>::SetKernelSpherical(ShapeT shape) {
   Interface::IsA<ShapeT, Interface::VoxImageFilterShape>();
   Vector3i id;
   for (int y = 0; y < m_KernelData.GetDims()(1); ++y) {
@@ -212,8 +187,8 @@ void VoxImageFilter<_TPLT_>::SetKernelSpherical(ShapeT shape)
 }
 
 _TPL_
-void VoxImageFilter<_TPLT_>::SetKernelWeightFunction(float (*shape)(const Vector3f &))
-{
+void VoxImageFilter<_TPLT_>::SetKernelWeightFunction(
+    float (*shape)(const Vector3f &)) {
   const Vector3i &dim = m_KernelData.GetDims();
   Vector3i id;
   Vector3f pt;
@@ -233,8 +208,7 @@ void VoxImageFilter<_TPLT_>::SetKernelWeightFunction(float (*shape)(const Vector
 }
 
 _TPL_ template <class ShapeT>
-void VoxImageFilter<_TPLT_>::SetKernelWeightFunction(ShapeT shape)
-{
+void VoxImageFilter<_TPLT_>::SetKernelWeightFunction(ShapeT shape) {
   Interface::IsA<ShapeT, Interface::VoxImageFilterShape>();
   const Vector3i &dim = m_KernelData.GetDims();
   Vector3i id;
@@ -254,22 +228,17 @@ void VoxImageFilter<_TPLT_>::SetKernelWeightFunction(ShapeT shape)
   }
 }
 
-
-
-
 _TPL_
-void VoxImageFilter<_TPLT_>::SetImage(Abstract::VoxImage *image)
-{
+void VoxImageFilter<_TPLT_>::SetImage(Abstract::VoxImage *image) {
   this->m_Image = reinterpret_cast<VoxImage<VoxelT> *>(image);
   this->SetKernelOffset();
 }
 
-
 _TPL_
-float VoxImageFilter<_TPLT_>::Convolve(const VoxImage<VoxelT> &buffer, int index)
-{
-    const Vector<VoxelT> &vbuf = buffer.ConstData();
-    const Vector<VoxelT> &vker = m_KernelData.ConstData();
+float VoxImageFilter<_TPLT_>::Convolve(const VoxImage<VoxelT> &buffer,
+                                       int index) {
+  const DataAllocator<VoxelT> &vbuf = buffer.ConstData();
+  const DataAllocator<VoxelT> &vker = m_KernelData.ConstData();
   int vox_size = vbuf.size();
   int ker_size = vker.size();
   int pos;
@@ -283,20 +252,9 @@ float VoxImageFilter<_TPLT_>::Convolve(const VoxImage<VoxelT> &buffer, int index
   return conv / ksum;
 }
 
-
-
 #undef _TPLT_
 #undef _TPL_
 
-
-
-
-
-
-
-}
-
-
-
+} // namespace uLib
 
 #endif // VOXIMAGEFILTER_HPP

src/Math/VoxImageFilter2ndStat.hpp

@@ -23,14 +23,12 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
 #ifndef VOXIMAGEFILTER2NDSTAT_HPP
 #define VOXIMAGEFILTER2NDSTAT_HPP
 
-#include <Math/Dense.h>
 #include "Math/VoxImage.h"
 #include "VoxImageFilter.h"
+#include <Math/Dense.h>
 
 ////////////////////////////////////////////////////////////////////////////////
 /////  VOXIMAGE FILTER ABTRIM  /////////////////////////////////////////////////
@@ -39,19 +37,16 @@
 namespace uLib {
 
 template <typename VoxelT>
-class VoxFilterAlgorithm2ndStat :
-        public VoxImageFilter<VoxelT, VoxFilterAlgorithm2ndStat<VoxelT> > {
+class VoxFilterAlgorithm2ndStat
+    : public VoxImageFilter<VoxelT, VoxFilterAlgorithm2ndStat<VoxelT>> {
 
 public:
   typedef VoxImageFilter<VoxelT, VoxFilterAlgorithm2ndStat<VoxelT>> BaseClass;
-    VoxFilterAlgorithm2ndStat(const Vector3i &size) :
-        BaseClass(size)
-    { }
+  VoxFilterAlgorithm2ndStat(const Vector3i &size) : BaseClass(size) {}
 
-    float Evaluate(const VoxImage<VoxelT> &buffer, int index)
-    {
-        const Vector<VoxelT> &vbuf = buffer.ConstData();
-        const Vector<VoxelT> &vker = this->m_KernelData.ConstData();
+  float Evaluate(const VoxImage<VoxelT> &buffer, int index) {
+    const DataAllocator<VoxelT> &vbuf = buffer.ConstData();
+    const DataAllocator<VoxelT> &vker = this->m_KernelData.ConstData();
     int vox_size = vbuf.size();
     int ker_size = vker.size();
     int pos;
@@ -59,7 +54,8 @@ public:
     // mean //
     float conv = 0, ksum = 0;
     for (int ik = 0; ik < ker_size; ++ik) {
-            pos = index + vker[ik].Count - vker[this->m_KernelData.GetCenterData()].Count;
+      pos = index + vker[ik].Count -
+            vker[this->m_KernelData.GetCenterData()].Count;
       pos = (pos + vox_size) % vox_size;
       conv += vbuf[pos].Value * vker[ik].Value;
       ksum += vker[ik].Value;
@@ -69,15 +65,14 @@ public:
     // rms //
     conv = 0;
     for (int ik = 0; ik < ker_size; ++ik) {
-            pos = index + vker[ik].Count - vker[this->m_KernelData.GetCenterData()].Count;
+      pos = index + vker[ik].Count -
+            vker[this->m_KernelData.GetCenterData()].Count;
       pos = (pos + vox_size) % vox_size;
       conv += pow((vbuf[pos].Value * vker[ik].Value) - mean, 2);
     }
     return conv / (vker.size() - 1);
   }
-
-
 };
 
-}
+} // namespace uLib
 #endif // VOXIMAGEFILTER2NDSTAT_HPP

src/Math/VoxImageFilterABTrim.hpp

@@ -23,14 +23,12 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
 #ifndef VOXIMAGEFILTERABTRIM_HPP
 #define VOXIMAGEFILTERABTRIM_HPP
 
-#include <Math/Dense.h>
 #include "Math/VoxImage.h"
 #include "VoxImageFilter.h"
+#include <Math/Dense.h>
 
 ////////////////////////////////////////////////////////////////////////////////
 /////  VOXIMAGE FILTER ABTRIM  /////////////////////////////////////////////////
@@ -38,38 +36,125 @@
 
 namespace uLib {
 
+#ifdef USE_CUDA
 template <typename VoxelT>
-class VoxFilterAlgorithmAbtrim :
-        public VoxImageFilter<VoxelT, VoxFilterAlgorithmAbtrim<VoxelT> > {
+__global__ void ABTrimFilterKernel(const VoxelT *in, VoxelT *out,
+                                   const VoxelT *kernel, int vox_size,
+                                   int ker_size, int center_count, int mAtrim,
+                                   int mBtrim) {
+  int index = blockIdx.x * blockDim.x + threadIdx.x;
+  if (index < vox_size) {
+    // Allocate space for sorting
+    extern __shared__ char shared_mem[];
+    VoxelT *mfh =
+        (VoxelT *)&shared_mem[threadIdx.x * ker_size * sizeof(VoxelT)];
 
-    struct KernelSortAscending
-    {
-        bool operator()(const VoxelT& e1, const VoxelT& e2)
-        { return e1.Value < e2.Value; }
+    for (int i = 0; i < ker_size; ++i) {
+      mfh[i].Count = i;
+    }
+
+    for (int ik = 0; ik < ker_size; ik++) {
+      int pos = index + kernel[ik].Count - center_count;
+      if (pos < 0) {
+        pos += vox_size * ((-pos / vox_size) + 1);
+      }
+      pos = pos % vox_size;
+      mfh[ik].Value = in[pos].Value;
+    }
+
+    // Simple bubble sort for small arrays
+    for (int i = 0; i < ker_size - 1; i++) {
+      for (int j = 0; j < ker_size - i - 1; j++) {
+        if (mfh[j].Value > mfh[j + 1].Value) {
+          VoxelT temp = mfh[j];
+          mfh[j] = mfh[j + 1];
+          mfh[j + 1] = temp;
+        }
+      }
+    }
+
+    float ker_sum = 0;
+    float fconv = 0;
+    for (int ik = 0; ik < mAtrim; ik++) {
+      ker_sum += kernel[mfh[ik].Count].Value;
+    }
+    for (int ik = mAtrim; ik < ker_size - mBtrim; ik++) {
+      fconv += mfh[ik].Value * kernel[mfh[ik].Count].Value;
+      ker_sum += kernel[mfh[ik].Count].Value;
+    }
+    for (int ik = ker_size - mBtrim; ik < ker_size; ik++) {
+      ker_sum += kernel[mfh[ik].Count].Value;
+    }
+
+    out[index].Value = fconv / ker_sum;
+  }
+}
+#endif
+
+template <typename VoxelT>
+class VoxFilterAlgorithmAbtrim
+    : public VoxImageFilter<VoxelT, VoxFilterAlgorithmAbtrim<VoxelT>> {
+
+  struct KernelSortAscending {
+    bool operator()(const VoxelT &e1, const VoxelT &e2) {
+      return e1.Value < e2.Value;
+    }
   };
 
 public:
   typedef VoxImageFilter<VoxelT, VoxFilterAlgorithmAbtrim<VoxelT>> BaseClass;
-    VoxFilterAlgorithmAbtrim(const Vector3i &size) :
-        BaseClass(size)
-    {
+  VoxFilterAlgorithmAbtrim(const Vector3i &size) : BaseClass(size) {
     mAtrim = 0;
     mBtrim = 0;
   }
 
-    float Evaluate(const VoxImage<VoxelT> &buffer, int index)
-    {
-        const Vector<VoxelT> &vbuf = buffer.ConstData();
-        const Vector<VoxelT> &vker = this->m_KernelData.ConstData();
+#ifdef USE_CUDA
+  void Run() {
+    if (this->m_Image->Data().GetDevice() == MemoryDevice::VRAM ||
+        this->m_KernelData.Data().GetDevice() == MemoryDevice::VRAM) {
+
+      this->m_Image->Data().MoveToVRAM();
+      this->m_KernelData.Data().MoveToVRAM();
+
+      VoxImage<VoxelT> buffer = *(this->m_Image);
+      buffer.Data().MoveToVRAM();
+
+      int vox_size = buffer.Data().size();
+      int ker_size = this->m_KernelData.Data().size();
+
+      VoxelT *d_img_out = this->m_Image->Data().GetVRAMData();
+      const VoxelT *d_img_in = buffer.Data().GetVRAMData();
+      const VoxelT *d_kernel = this->m_KernelData.Data().GetVRAMData();
+      int center_count =
+          this->m_KernelData[this->m_KernelData.GetCenterData()].Count;
+
+      int threadsPerBlock = 256;
+      int blocksPerGrid = (vox_size + threadsPerBlock - 1) / threadsPerBlock;
+      size_t shared_mem_size = threadsPerBlock * ker_size * sizeof(VoxelT);
+
+      ABTrimFilterKernel<<<blocksPerGrid, threadsPerBlock, shared_mem_size>>>(
+          d_img_in, d_img_out, d_kernel, vox_size, ker_size, center_count,
+          mAtrim, mBtrim);
+      cudaDeviceSynchronize();
+    } else {
+      BaseClass::Run();
+    }
+  }
+#endif
+
+  float Evaluate(const VoxImage<VoxelT> &buffer, int index) {
+    const DataAllocator<VoxelT> &vbuf = buffer.ConstData();
+    const DataAllocator<VoxelT> &vker = this->m_KernelData.ConstData();
     int vox_size = vbuf.size();
     int ker_size = vker.size();
     int pos;
 
-        Vector<VoxelT> mfh(ker_size);
+    std::vector<VoxelT> mfh(ker_size);
     for (int i = 0; i < ker_size; ++i)
       mfh[i].Count = i; // index key for ordering function
     for (int ik = 0; ik < ker_size; ik++) {
-            pos = index + vker[ik].Count - vker[this->m_KernelData.GetCenterData()].Count;
+      pos = index + vker[ik].Count -
+            vker[this->m_KernelData.GetCenterData()].Count;
       pos = (pos + vox_size) % vox_size;
       mfh[ik].Value = vbuf[pos].Value;
     }
@@ -89,50 +174,80 @@ public:
     return fconv / ker_sum;
   }
 
-    inline void SetABTrim(int a, int b) { mAtrim = a; mBtrim = b; }
+  inline void SetABTrim(int a, int b) {
+    mAtrim = a;
+    mBtrim = b;
+  }
 
 private:
   int mAtrim;
   int mBtrim;
 };
 
-
-
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 // Roberspierre Filter //
 
-
-
 template <typename VoxelT>
-class VoxFilterAlgorithmSPR :
-        public VoxImageFilter<VoxelT, VoxFilterAlgorithmSPR<VoxelT> > {
+class VoxFilterAlgorithmSPR
+    : public VoxImageFilter<VoxelT, VoxFilterAlgorithmSPR<VoxelT>> {
 
-    struct KernelSortAscending
-    {
-        bool operator()(const VoxelT& e1, const VoxelT& e2)
-        { return e1.Value < e2.Value; }
+  struct KernelSortAscending {
+    bool operator()(const VoxelT &e1, const VoxelT &e2) {
+      return e1.Value < e2.Value;
+    }
   };
 
 public:
   typedef VoxImageFilter<VoxelT, VoxFilterAlgorithmSPR<VoxelT>> BaseClass;
-    VoxFilterAlgorithmSPR(const Vector3i &size) :
-        BaseClass(size)
-    {
+  VoxFilterAlgorithmSPR(const Vector3i &size) : BaseClass(size) {
     mAtrim = 0;
     mBtrim = 0;
   }
 
-    float Evaluate(const VoxImage<VoxelT> &buffer, int index)
-    {
-        const Vector<VoxelT> &vbuf = buffer.ConstData();
-        const Vector<VoxelT> &vker = this->m_KernelData.ConstData();
+#ifdef USE_CUDA
+  void Run() {
+    if (this->m_Image->Data().GetDevice() == MemoryDevice::VRAM ||
+        this->m_KernelData.Data().GetDevice() == MemoryDevice::VRAM) {
+
+      this->m_Image->Data().MoveToVRAM();
+      this->m_KernelData.Data().MoveToVRAM();
+
+      VoxImage<VoxelT> buffer = *(this->m_Image);
+      buffer.Data().MoveToVRAM();
+
+      int vox_size = buffer.Data().size();
+      int ker_size = this->m_KernelData.Data().size();
+
+      VoxelT *d_img_out = this->m_Image->Data().GetVRAMData();
+      const VoxelT *d_img_in = buffer.Data().GetVRAMData();
+      const VoxelT *d_kernel = this->m_KernelData.Data().GetVRAMData();
+      int center_count =
+          this->m_KernelData[this->m_KernelData.GetCenterData()].Count;
+
+      int threadsPerBlock = 256;
+      int blocksPerGrid = (vox_size + threadsPerBlock - 1) / threadsPerBlock;
+      size_t shared_mem_size = threadsPerBlock * ker_size * sizeof(VoxelT);
+
+      ABTrimFilterKernel<<<blocksPerGrid, threadsPerBlock, shared_mem_size>>>(
+          d_img_in, d_img_out, d_kernel, vox_size, ker_size, center_count,
+          mAtrim, mBtrim);
+      cudaDeviceSynchronize();
+    } else {
+      BaseClass::Run();
+    }
+  }
+#endif
+
+  float Evaluate(const VoxImage<VoxelT> &buffer, int index) {
+    const DataAllocator<VoxelT> &vbuf = buffer.ConstData();
+    const DataAllocator<VoxelT> &vker = this->m_KernelData.ConstData();
     int vox_size = vbuf.size();
     int ker_size = vker.size();
     int pos;
 
-        Vector<VoxelT> mfh(ker_size);
+    std::vector<VoxelT> mfh(ker_size);
     for (int i = 0; i < ker_size; ++i)
       mfh[i].Count = i; // index key for ordering function
     for (int ik = 0; ik < ker_size; ik++) {
@@ -145,8 +260,7 @@ public:
     std::sort(mfh.begin(), mfh.end(), KernelSortAscending());
     float spr = vbuf[index].Value;
     if ((mAtrim > 0 && spr <= mfh[mAtrim - 1].Value) ||
-                (mBtrim > 0 && spr >= mfh[ker_size - mBtrim].Value) )
-        {
+        (mBtrim > 0 && spr >= mfh[ker_size - mBtrim].Value)) {
       float ker_sum = 0;
       float fconv = 0;
       for (int ik = 0; ik < mAtrim; ik++)
@@ -159,21 +273,20 @@ public:
         ker_sum += vker[mfh[ik].Count].Value;
 
       return fconv / ker_sum;
-        }
-        else
+    } else
       return spr;
   }
 
-    inline void SetABTrim(int a, int b) { mAtrim = a; mBtrim = b; }
+  inline void SetABTrim(int a, int b) {
+    mAtrim = a;
+    mBtrim = b;
+  }
 
 private:
   int mAtrim;
   int mBtrim;
 };
 
-
-
-
-}
+} // namespace uLib
 
 #endif // VOXIMAGEFILTERABTRIM_HPP

src/Math/VoxImageFilterBilateral.hpp

@@ -23,14 +23,12 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
 #ifndef VOXIMAGEFILTERBILATERAL_HPP
 #define VOXIMAGEFILTERBILATERAL_HPP
 
-#include <Math/Dense.h>
 #include "Math/VoxImage.h"
 #include "VoxImageFilter.h"
+#include <Math/Dense.h>
 
 ////////////////////////////////////////////////////////////////////////////////
 /////  VOXIMAGE FILTER LINEAR  /////////////////////////////////////////////////
@@ -38,20 +36,18 @@
 
 namespace uLib {
 
-
 template <typename VoxelT>
-class VoxFilterAlgorithmBilateral :
-        public VoxImageFilter<VoxelT, VoxFilterAlgorithmBilateral<VoxelT> > {
+class VoxFilterAlgorithmBilateral
+    : public VoxImageFilter<VoxelT, VoxFilterAlgorithmBilateral<VoxelT>> {
 public:
   typedef VoxImageFilter<VoxelT, VoxFilterAlgorithmBilateral<VoxelT>> BaseClass;
   VoxFilterAlgorithmBilateral(const Vector3i &size) : BaseClass(size) {
     m_sigma = 1;
   }
 
-    float Evaluate(const VoxImage<VoxelT> &buffer, int index)
-    {
-        const Vector<VoxelT> &vbuf = buffer.ConstData();
-        const Vector<VoxelT> &vker = this->m_KernelData.ConstData();
+  float Evaluate(const VoxImage<VoxelT> &buffer, int index) {
+    const DataAllocator<VoxelT> &vbuf = buffer.ConstData();
+    const DataAllocator<VoxelT> &vker = this->m_KernelData.ConstData();
     int vox_size = vbuf.size();
     int ker_size = vker.size();
     int pos;
@@ -59,9 +55,11 @@ public:
     float gamma_smooth;
     for (int ik = 0; ik < ker_size; ++ik) {
       //            if (ik==this->m_KernelData.GetCenterData()) continue;
-            pos = index + vker[ik].Count - vker[this->m_KernelData.GetCenterData()].Count;
+      pos = index + vker[ik].Count -
+            vker[this->m_KernelData.GetCenterData()].Count;
       pos = (pos + vox_size) % vox_size;
-            gamma_smooth = compute_gauss( fabs(vbuf[index].Value - vbuf[pos].Value) * 1.E6 );
+      gamma_smooth =
+          compute_gauss(fabs(vbuf[index].Value - vbuf[pos].Value) * 1.E6);
       conv += vbuf[pos].Value * vker[ik].Value * gamma_smooth;
       ksum += vker[ik].Value * gamma_smooth;
     }
@@ -72,48 +70,47 @@ public:
 
 private:
   inline float compute_gauss(const float x) {
-        return 1/(sqrt(2*M_PI)* m_sigma) * exp(-0.5*(x*x)/(m_sigma*m_sigma));
+    return 1 / (sqrt(2 * M_PI) * m_sigma) *
+           exp(-0.5 * (x * x) / (m_sigma * m_sigma));
   }
 
   Scalarf m_sigma;
 };
 
-
 template <typename VoxelT>
-class VoxFilterAlgorithmBilateralTrim :
-        public VoxImageFilter<VoxelT, VoxFilterAlgorithmBilateralTrim<VoxelT> > {
+class VoxFilterAlgorithmBilateralTrim
+    : public VoxImageFilter<VoxelT, VoxFilterAlgorithmBilateralTrim<VoxelT>> {
 
   typedef std::pair<float, float> FPair;
 
-    struct KernelSortAscending
-    {
-        bool operator()(const FPair& e1, const FPair& e2)
-        { return e1.second < e2.second; }
+  struct KernelSortAscending {
+    bool operator()(const FPair &e1, const FPair &e2) {
+      return e1.second < e2.second;
+    }
   };
 
 public:
-    typedef VoxImageFilter<VoxelT, VoxFilterAlgorithmBilateralTrim<VoxelT> > BaseClass;
+  typedef VoxImageFilter<VoxelT, VoxFilterAlgorithmBilateralTrim<VoxelT>>
+      BaseClass;
   VoxFilterAlgorithmBilateralTrim(const Vector3i &size) : BaseClass(size) {
     m_sigma = 1;
     mAtrim = 0;
     mBtrim = 0;
   }
 
-    float Evaluate(const VoxImage<VoxelT> &buffer, int index)
-    {
-        const Vector<VoxelT> &vbuf = buffer.ConstData();
-        const Vector<VoxelT> &vker = this->m_KernelData.ConstData();
+  float Evaluate(const VoxImage<VoxelT> &buffer, int index) {
+    const DataAllocator<VoxelT> &vbuf = buffer.ConstData();
+    const DataAllocator<VoxelT> &vker = this->m_KernelData.ConstData();
     int img_size = vbuf.size();
     int ker_size = vker.size();
     int pos;
 
-
-
-        Vector<FPair> mfh(ker_size);
+    std::vector<FPair> mfh(ker_size);
     for (int i = 0; i < ker_size; ++i)
       mfh[i].first = vker[i].Value; // kernel value in first
     for (int ik = 0; ik < ker_size; ik++) {
-            pos = index + vker[ik].Count - vker[this->m_KernelData.GetCenterData()].Count;
+      pos = index + vker[ik].Count -
+            vker[this->m_KernelData.GetCenterData()].Count;
       pos = (pos + img_size) % img_size;
       mfh[ik].second = vbuf[pos].Value; // image value in second
     }
@@ -124,7 +121,8 @@ public:
     //        for (int ik = 0; ik < mAtrim; ik++)
     //            ksum += mfh[ik].first;
     for (int ik = mAtrim; ik < ker_size - mBtrim; ik++) {
-            gamma_smooth = compute_gauss( fabs(vbuf[index].Value - mfh[ik].second) * 1.E6 );
+      gamma_smooth =
+          compute_gauss(fabs(vbuf[index].Value - mfh[ik].second) * 1.E6);
       conv += mfh[ik].first * mfh[ik].second * gamma_smooth;
       ksum += mfh[ik].first * gamma_smooth;
     }
@@ -135,11 +133,15 @@ public:
   }
 
   inline void SetIntensitySigma(const float s) { m_sigma = s; }
-    inline void SetABTrim(int a, int b) { mAtrim = a; mBtrim = b; }
+  inline void SetABTrim(int a, int b) {
+    mAtrim = a;
+    mBtrim = b;
+  }
 
 private:
   inline float compute_gauss(const float x) {
-        return 1/(sqrt(2*M_PI)* m_sigma) * exp(-0.5*(x*x)/(m_sigma*m_sigma));
+    return 1 / (sqrt(2 * M_PI) * m_sigma) *
+           exp(-0.5 * (x * x) / (m_sigma * m_sigma));
   }
 
   Scalarf m_sigma;
@@ -147,6 +149,6 @@ private:
   int mBtrim;
 };
 
-}
+} // namespace uLib
 
 #endif // VOXIMAGEFILTERBILATERAL_HPP

src/Math/VoxImageFilterCustom.hpp

@@ -23,14 +23,14 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
 #ifndef VOXIMAGEFILTERCUSTOM_HPP
 #define VOXIMAGEFILTERCUSTOM_HPP
 
-#include <Math/Dense.h>
 #include "Math/VoxImage.h"
 #include "VoxImageFilter.h"
+#include <Math/Dense.h>
+
+#define likely(expr) __builtin_expect(!!(expr), 1)
 
 ////////////////////////////////////////////////////////////////////////////////
 /////  VOXIMAGE FILTER CUSTOM  /////////////////////////////////////////////////
@@ -39,50 +39,50 @@
 namespace uLib {
 
 template <typename VoxelT>
-class VoxFilterAlgorithmCustom :
-        public VoxImageFilter<VoxelT, VoxFilterAlgorithmCustom<VoxelT> > {
+class VoxFilterAlgorithmCustom
+    : public VoxImageFilter<VoxelT, VoxFilterAlgorithmCustom<VoxelT>> {
 
+  typedef float (*FunctionPt)(const std::vector<Scalarf> &);
 
-    typedef float (* FunctionPt)(const Vector<Scalarf> &);
 public:
   typedef VoxImageFilter<VoxelT, VoxFilterAlgorithmCustom<VoxelT>> BaseClass;
-    VoxFilterAlgorithmCustom(const Vector3i &size) :
-        BaseClass(size), m_CustomEvaluate(NULL)
-    {}
+  VoxFilterAlgorithmCustom(const Vector3i &size)
+      : BaseClass(size), m_CustomEvaluate(NULL) {}
 
-    float Evaluate(const VoxImage<VoxelT> &buffer, int index)
-    {
+  float Evaluate(const VoxImage<VoxelT> &buffer, int index) {
     if (likely(m_CustomEvaluate)) {
-            const Vector<VoxelT> &vbuf = buffer.ConstData();
-            const Vector<VoxelT> &vker = this->m_KernelData.ConstData();
+      const DataAllocator<VoxelT> &vbuf = buffer.ConstData();
+      const DataAllocator<VoxelT> &vker = this->m_KernelData.ConstData();
       int vox_size = vbuf.size();
       int ker_size = vker.size();
       int pos;
 
       float ker_sum = 0;
-            Vector<Scalarf> mfh(ker_size);
+      std::vector<Scalarf> mfh(ker_size);
       for (int ik = 0; ik < ker_size; ik++) {
-                pos = index + vker[ik].Count - vker[this->m_KernelData.GetCenterData()].Count;
+        pos = index + vker[ik].Count -
+              vker[this->m_KernelData.GetCenterData()].Count;
         pos = (pos + vox_size) % vox_size;
         mfh[ik] = vbuf[pos].Value * vker[ik].Value;
         ker_sum += vker[ik].Value;
       }
 
       return this->m_CustomEvaluate(mfh);
+    } else {
+      std::cerr << "Custom evaluate function is NULL \n"
+                << "No operation performed by filter.\n";
+      return 0;
     }
-        else
-            std::cerr << "Custom evaluate function is NULL \n" <<
-                         "No operation performed by filter.\n";
-
   }
 
-    uLibSetMacro(CustomEvaluate,FunctionPt)
+  inline void SetCustomEvaluate(FunctionPt funPt) {
+    this->m_CustomEvaluate = funPt;
+  }
 
 private:
   FunctionPt m_CustomEvaluate;
 };
 
-}
-
+} // namespace uLib
 
 #endif // VOXIMAGEFILTERCUSTOM_HPP

src/Math/VoxImageFilterLinear.hpp

@@ -23,14 +23,12 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
 #ifndef VOXIMAGEFILTERLINEAR_HPP
 #define VOXIMAGEFILTERLINEAR_HPP
 
-#include <Math/Dense.h>
 #include "Math/VoxImage.h"
 #include "VoxImageFilter.h"
+#include <Math/Dense.h>
 
 ////////////////////////////////////////////////////////////////////////////////
 /////  VOXIMAGE FILTER LINEAR  /////////////////////////////////////////////////
@@ -38,24 +36,78 @@
 
 namespace uLib {
 
+#ifdef USE_CUDA
+template <typename VoxelT>
+__global__ void LinearFilterKernel(const VoxelT *in, VoxelT *out,
+                                   const VoxelT *kernel, int vox_size,
+                                   int ker_size, int center_count) {
+  int index = blockIdx.x * blockDim.x + threadIdx.x;
+  if (index < vox_size) {
+    float conv = 0;
+    float ksum = 0;
+    for (int ik = 0; ik < ker_size; ++ik) {
+      int pos = index + kernel[ik].Count - center_count;
+      if (pos < 0) {
+        pos += vox_size * ((-pos / vox_size) + 1);
+      }
+      pos = pos % vox_size;
+      conv += in[pos].Value * kernel[ik].Value;
+      ksum += kernel[ik].Value;
+    }
+    out[index].Value = conv / ksum;
+  }
+}
+#endif
 
 template <typename VoxelT>
-class VoxFilterAlgorithmLinear :
-        public VoxImageFilter<VoxelT, VoxFilterAlgorithmLinear<VoxelT> > {
+class VoxFilterAlgorithmLinear
+    : public VoxImageFilter<VoxelT, VoxFilterAlgorithmLinear<VoxelT>> {
 public:
   typedef VoxImageFilter<VoxelT, VoxFilterAlgorithmLinear<VoxelT>> BaseClass;
   VoxFilterAlgorithmLinear(const Vector3i &size) : BaseClass(size) {}
 
-    float Evaluate(const VoxImage<VoxelT> &buffer, int index)
-    {
-        const Vector<VoxelT> &vbuf = buffer.ConstData();
-        const Vector<VoxelT> &vker = this->m_KernelData.ConstData();
+#ifdef USE_CUDA
+  void Run() {
+    if (this->m_Image->Data().GetDevice() == MemoryDevice::VRAM ||
+        this->m_KernelData.Data().GetDevice() == MemoryDevice::VRAM) {
+
+      this->m_Image->Data().MoveToVRAM();
+      this->m_KernelData.Data().MoveToVRAM();
+
+      VoxImage<VoxelT> buffer = *(this->m_Image);
+      buffer.Data().MoveToVRAM();
+
+      int vox_size = buffer.Data().size();
+      int ker_size = this->m_KernelData.Data().size();
+
+      VoxelT *d_img_out = this->m_Image->Data().GetVRAMData();
+      const VoxelT *d_img_in = buffer.Data().GetVRAMData();
+      const VoxelT *d_kernel = this->m_KernelData.Data().GetVRAMData();
+      int center_count =
+          this->m_KernelData[this->m_KernelData.GetCenterData()].Count;
+
+      int threadsPerBlock = 256;
+      int blocksPerGrid = (vox_size + threadsPerBlock - 1) / threadsPerBlock;
+
+      LinearFilterKernel<<<blocksPerGrid, threadsPerBlock>>>(
+          d_img_in, d_img_out, d_kernel, vox_size, ker_size, center_count);
+      cudaDeviceSynchronize();
+    } else {
+      BaseClass::Run();
+    }
+  }
+#endif
+
+  float Evaluate(const VoxImage<VoxelT> &buffer, int index) {
+    const DataAllocator<VoxelT> &vbuf = buffer.ConstData();
+    const DataAllocator<VoxelT> &vker = this->m_KernelData.ConstData();
     int vox_size = vbuf.size();
     int ker_size = vker.size();
     int pos;
     float conv = 0, ksum = 0;
     for (int ik = 0; ik < ker_size; ++ik) {
-            pos = index + vker[ik].Count - vker[this->m_KernelData.GetCenterData()].Count;
+      pos = index + vker[ik].Count -
+            vker[this->m_KernelData.GetCenterData()].Count;
       pos = (pos + vox_size) % vox_size;
       conv += vbuf[pos].Value * vker[ik].Value;
       ksum += vker[ik].Value;
@@ -64,6 +116,6 @@ public:
   }
 };
 
-}
+} // namespace uLib
 
 #endif // VOXIMAGEFILTERLINEAR_HPP

src/Math/VoxImageFilterMedian.hpp

@@ -23,14 +23,12 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
 #ifndef VOXIMAGEFILTERMEDIAN_HPP
 #define VOXIMAGEFILTERMEDIAN_HPP
 
-#include <Math/Dense.h>
 #include "Math/VoxImage.h"
 #include "VoxImageFilter.h"
+#include <Math/Dense.h>
 
 ////////////////////////////////////////////////////////////////////////////////
 /////  VOXIMAGE FILTER MEDIAN  /////////////////////////////////////////////////
@@ -39,23 +37,23 @@
 namespace uLib {
 
 template <typename VoxelT>
-class VoxFilterAlgorithmMedian :
-        public VoxImageFilter<VoxelT, VoxFilterAlgorithmMedian<VoxelT> > {
+class VoxFilterAlgorithmMedian
+    : public VoxImageFilter<VoxelT, VoxFilterAlgorithmMedian<VoxelT>> {
 public:
   typedef VoxImageFilter<VoxelT, VoxFilterAlgorithmMedian<VoxelT>> BaseClass;
   VoxFilterAlgorithmMedian(const Vector3i &size) : BaseClass(size) {}
 
-    float Evaluate(const VoxImage<VoxelT> &buffer, int index)
-    {
-        const Vector<VoxelT> &vbuf = buffer.ConstData();
-        const Vector<VoxelT> &vker = this->m_KernelData.ConstData();
+  float Evaluate(const VoxImage<VoxelT> &buffer, int index) {
+    const DataAllocator<VoxelT> &vbuf = buffer.ConstData();
+    const DataAllocator<VoxelT> &vker = this->m_KernelData.ConstData();
     int vox_size = vbuf.size();
     int ker_size = vker.size();
     int pos;
 
-        Vector<float> mfh(ker_size);
+    std::vector<float> mfh(ker_size);
     for (int ik = 0; ik < ker_size; ik++) {
-            pos = index + vker[ik].Count - vker[this->m_KernelData.GetCenterData()].Count;
+      pos = index + vker[ik].Count -
+            vker[this->m_KernelData.GetCenterData()].Count;
       pos = (pos + vox_size) % vox_size;
       mfh[ik] = vbuf[pos].Value * vker[ik].Value;
     }
@@ -63,13 +61,14 @@ public:
     pos = 0;
     // count zeroes in filter kernel to move it out of median //
     for (int i = 0; i < ker_size; ++i)
-            if (vker[i].Value == 0.0) pos++;
+      if (vker[i].Value == 0.0)
+        pos++;
     // median //
     pos += (ker_size - pos) / 2;
     return mfh[pos];
   }
 };
 
-}
+} // namespace uLib
 
 #endif // VOXIMAGEFILTERMEDIAN_HPP

src/Math/VoxImageFilterUser.cpp

@@ -26,7 +26,6 @@
 
 
 
-#include "Core/Vector.h"
 #include "Dense.h"
 #include "VoxImage.h"
 #include "VoxImageFilterUser.h"

src/Math/VoxRaytracer.cpp

@@ -23,11 +23,12 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
+#include <iostream>
 
-
-
-#include "VoxRaytracer.h"
 #include "Utils.h"
+#include "VoxRaytracer.h"
+
+#define unlikely(expr) __builtin_expect(!!(expr), 0)
 
 inline float fast_sign(float f) { return 1 - 2 * (f < 0); }
 
@@ -37,62 +38,56 @@ namespace uLib {
 ///// RAY DATA /////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 
-void VoxRaytracer::RayData::AddElement(Id_t id, float L)
-{
+void VoxRaytracer::RayData::AddElement(Id_t id, float L) {
+  if (m_Count >= m_Data.size()) {
+    size_t new_size = m_Data.size() == 0 ? 128 : m_Data.size() * 2;
+    m_Data.resize(new_size);
+  }
   Element el = {id, L};
-    m_Data.push_back(el);
+  m_Data[m_Count] = el;
+  m_Count++;
   m_TotalLength += L;
 }
 
-
-void VoxRaytracer::RayData::AppendRay(const VoxRaytracer::RayData &in)
-{
-    if (unlikely(!in.m_Data.size())) {
+void VoxRaytracer::RayData::AppendRay(const VoxRaytracer::RayData &in) {
+  if (unlikely(in.m_Count == 0)) {
     std::cout << "Warinig: PoCA on exit border!\n";
     return;
+  } else if (unlikely(m_Count == 0)) {
+    m_Data.resize(in.m_Count);
+    for (size_t i = 0; i < in.m_Count; ++i) {
+      m_Data[i] = in.m_Data[i];
     }
-    else if (unlikely(!m_Data.size())) {
-        m_Data = in.m_Data;
+    m_Count = in.m_Count;
+    m_TotalLength = in.m_TotalLength;
     std::cout << "Warinig: PoCA on entrance border!\n";
     return;
-    }
-    else {
+  } else {
     // Opzione 1) un voxel in piu' //
-        m_Data.reserve(m_Data.size() + in.m_Data.size());
-        m_Data.insert(m_Data.end(), in.m_Data.begin(), in.m_Data.end());
-        // Opzione 2) merge dei voxel nel poca.
-        //        RayData::Element &e1 = m_Data.back();
-        //        const RayData::Element &e2 = in.m_Data.front();
-        //        if(e1.vox_id == e2.vox_id)
-        //        {
-        //            m_Data.reserve(m_Data.size() + in.m_Data.size() - 1);
-        //            e1.L += e2.L; //fix//
-        //            m_Data.insert(m_Data.end(), in.m_Data.begin()+1, in.m_Data.end());
-        //        }
-        //        else {
-        //            m_Data.reserve(m_Data.size() + in.m_Data.size());
-        //            m_Data.insert(m_Data.end(), in.m_Data.begin(), in.m_Data.end());
-        //        }
+    if (in.m_Count > 0) {
+      if (m_Count + in.m_Count > m_Data.size()) {
+        m_Data.resize(m_Count + in.m_Count);
+      }
+      for (size_t i = 0; i < in.m_Count; ++i) {
+        m_Data[m_Count + i] = in.m_Data[i];
+      }
+      m_Count += in.m_Count;
+    }
     m_TotalLength += in.m_TotalLength;
   }
 }
 
-void VoxRaytracer::RayData::PrintSelf(std::ostream &o)
-{
+void VoxRaytracer::RayData::PrintSelf(std::ostream &o) {
   o << "Ray: total lenght " << m_TotalLength << "\n";
-    Vector<Element>::Iterator it;
-    for(it = m_Data.begin(); it < m_Data.end(); ++it)
-        o << "[ " << (*it).vox_id << ", " << (*it).L << "] \n";
+  for (size_t i = 0; i < m_Count; ++i)
+    o << "[ " << m_Data[i].vox_id << ", " << m_Data[i].L << "] \n";
 }
 
-
 ////////////////////////////////////////////////////////////////////////////////
 //// RAY TRACER ////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 
-
-bool VoxRaytracer::GetEntryPoint(const HLine3f &line, HPoint3f &pt)
-{
+bool VoxRaytracer::GetEntryPoint(const HLine3f &line, HPoint3f &pt) {
   Vector4f s = m_Image->GetLocalPoint(line.direction);
   pt = m_Image->GetLocalPoint(line.origin);
 
@@ -109,9 +104,9 @@ bool VoxRaytracer::GetEntryPoint(const HLine3f &line, HPoint3f &pt)
     offset(i) = (s(i) > 0) - (pt(i) - floor(pt(i)));
   offset = offset.cwiseProduct(L).cwiseAbs();
 
-    int id; float d;
-    for(int loop=0; loop<8; loop++)
-    {
+  int id;
+  float d;
+  for (int loop = 0; loop < 8; loop++) {
     int check_border = 0;
     for (int i = 0; i < 3; ++i) {
       check_border += pt(i) > 1;
@@ -130,7 +125,6 @@ bool VoxRaytracer::GetEntryPoint(const HLine3f &line, HPoint3f &pt)
 
     pt(id) = rintf(pt(id));
 
-
     offset.array() -= d;
     offset(id) = fabs(L(id));
   }
@@ -140,33 +134,38 @@ bool VoxRaytracer::GetEntryPoint(const HLine3f &line, HPoint3f &pt)
   return false;
 }
 
-bool VoxRaytracer::GetExitPoint(const HLine3f &line, HPoint3f &pt)
-{
+bool VoxRaytracer::GetExitPoint(const HLine3f &line, HPoint3f &pt) {
   HLine3f out = line;
   out.direction *= -1;
   return GetEntryPoint(out, pt);
 }
 
-
-VoxRaytracer::RayData VoxRaytracer::TraceBetweenPoints(const HPoint3f &in,
-                                                       const HPoint3f &out)
-const
-{
+VoxRaytracer::RayData
+VoxRaytracer::TraceBetweenPoints(const HPoint3f &in,
+                                 const HPoint3f &out) const {
   RayData ray;
+
+  // get the local points and the direction vector
+  // local to image means in the normalized voxel space where the size
+  // of the voxel is 1 in all dimensions
   Vector4f pt1 = m_Image->GetLocalPoint(in);
   Vector4f pt2 = m_Image->GetLocalPoint(out);
   Vector4f s = pt2 - pt1;
 
+  // l is the total length of the ray in normalized voxel space
   float l = s.head(3).norm();
+
+  // L is the length of the ray between two grid lines in grid
   Vector3f L(l / s(0), l / s(1), l / s(2));
 
-    // Vector3f scale; // FIXXX
+  // Vector3f scale; // TODO: FIX Scaling
   // scale << (m_Image->GetWorldMatrix() * Vector4f(1,0,0,0)).norm(),
   //          (m_Image->GetWorldMatrix() * Vector4f(0,1,0,0)).norm(),
   //          (m_Image->GetWorldMatrix() * Vector4f(0,0,1,0)).norm();
 
   Vector3f offset;
-    for(int i=0;i<3;++i) offset(i) = (s(i)>=0) - (pt1(i)-floor(pt1(i))) ;
+  for (int i = 0; i < 3; ++i)
+    offset(i) = (s(i) >= 0) - (pt1(i) - floor(pt1(i)));
   offset = offset.cwiseProduct(L).cwiseAbs();
   L = L.cwiseAbs();
 
@@ -178,24 +177,27 @@ const
   }
 
   //---- Otherwise, loop until ray is finished
-    int id; float d;	
+  int id;
+  float d;
   while (l > 0) {
 
+    // find which is the minimum of the offsets to the next grid line
+    // it will be also the actual normalized voxel ray length
     d = offset.minCoeff(&id);
 
+    // see if the voxel is inside the grid (we are still inside image)
     if (m_Image->IsInsideGrid(vid)) {
+      // add the voxel to the ray with mapping id and length scaled
       ray.AddElement(m_Image->Map(vid), d * m_scale(id));
     }
 
-      // nan check //
-      //        if(unlikely(!isFinite(d * scale(id)))) {
-      //            std:: cout << "NAN in raytracer\n";
-      //            exit(1);
-      //        }
-      
+    // move to the next voxel
     vid(id) += (int)fast_sign(s(id));
 
+    // update the remaining length
     l -= d;
+
+    // update the offsets
     offset.array() -= d;
     offset(id) = fmin(L(id), l);
   }
@@ -203,8 +205,7 @@ const
 }
 
 // 20150528 SV for absorbed muons
-VoxRaytracer::RayData VoxRaytracer::TraceLine(const HLine3f &line) const
-{
+VoxRaytracer::RayData VoxRaytracer::TraceLine(const HLine3f &line) const {
   RayData ray;
 
   Vector4f pt = m_Image->GetLocalPoint(line.origin);
@@ -220,18 +221,18 @@ VoxRaytracer::RayData VoxRaytracer::TraceLine(const HLine3f &line) const
   //          (m_Image->GetWorldMatrix() * Vector4f(0,1,0,0)).norm(),
   //          (m_Image->GetWorldMatrix() * Vector4f(0,0,1,0)).norm();
 
-    // offset is the fraction of the segment between grid lines when origin is insiede voxel
-    // cwiseAbs for having positive distances
+  // offset is the fraction of the segment between grid lines when origin is
+  // insiede voxel cwiseAbs for having positive distances
   Vector3f offset;
   for (int i = 0; i < 3; ++i)
     offset(i) = (s(i) >= 0) - (pt(i) - floor(pt(i)));
   offset = offset.cwiseProduct(L).cwiseAbs();
   L = L.cwiseAbs();
 
-    int id; float d;
+  int id;
+  float d;
   Vector3i vid = m_Image->Find(line.origin);
-    while(m_Image->IsInsideGrid(vid))
-    {
+  while (m_Image->IsInsideGrid(vid)) {
     // minimun coefficient of offset: id is the coordinate, d is the value
     // dependig on which grid line horizontal or vertical it is first intercept
     d = offset.minCoeff(&id);
@@ -248,4 +249,4 @@ VoxRaytracer::RayData VoxRaytracer::TraceLine(const HLine3f &line) const
   return ray;
 }
 
-}
+} // namespace uLib

src/Math/VoxRaytracer.h

@@ -23,15 +23,20 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
 #ifndef VOXRAYTRACER_H
 #define VOXRAYTRACER_H
 
+#include <Core/DataAllocator.h>
+#include <Core/Vector.h>
 #include <math.h>
+#include <vector>
 
-#include "Core/Vector.h"
 #include "Math/StructuredGrid.h"
+#include "Math/VoxImage.h"
+
+#ifdef USE_CUDA
+#include <cuda_runtime.h>
+#endif
 
 namespace uLib {
 
@@ -40,32 +45,41 @@ class VoxRaytracer {
 public:
   class RayData {
   public:
-        RayData() : m_TotalLength(0) {}
+    RayData() : m_TotalLength(0), m_Count(0) {}
 
-        typedef struct {
+    struct Element {
       Id_t vox_id;
       Scalarf L;
-        } Element;
+      ~Element() {}
+    };
 
     inline void AddElement(Id_t id, float L);
 
     void AppendRay(const RayData &in);
 
-        uLibConstRefMacro(Data,Vector<Element>)
-        uLibConstRefMacro(TotalLength,Scalarf)
+    inline uLib::Vector<Element> &Data() { return this->m_Data; }
+
+    inline const uLib::Vector<Element> &Data() const { return this->m_Data; }
+
+    inline size_t Count() const { return this->m_Count; }
+
+    inline const Scalarf &TotalLength() const { return this->m_TotalLength; }
+
+    inline void SetCount(size_t c) { this->m_Count = c; }
+
+    inline void SetTotalLength(Scalarf tl) { this->m_TotalLength = tl; }
 
     void PrintSelf(std::ostream &o);
 
   private:
-        Vector<Element> m_Data;
+    uLib::Vector<Element> m_Data;
     Scalarf m_TotalLength;
+    size_t m_Count;
   };
 
-
 public:
   VoxRaytracer(StructuredGrid &image) : m_Image(&image) {
-      m_scale <<
-	(m_Image->GetWorldMatrix() * Vector4f(1,0,0,0)).norm(),
+    m_scale << (m_Image->GetWorldMatrix() * Vector4f(1, 0, 0, 0)).norm(),
         (m_Image->GetWorldMatrix() * Vector4f(0, 1, 0, 0)).norm(),
         (m_Image->GetWorldMatrix() * Vector4f(0, 0, 1, 0)).norm();
   }
@@ -78,15 +92,32 @@ public:
 
   RayData TraceLine(const HLine3f &line) const;
 
-    uLibGetMacro(Image,StructuredGrid *)
+  inline StructuredGrid *GetImage() const { return this->m_Image; }
+
+#ifdef USE_CUDA
+  template <typename VoxelT>
+  void AccumulateLinesCUDA(const HLine3f *lines, size_t num_lines,
+                           VoxImage<VoxelT> &image);
+
+  void TraceLineCUDA(const HLine3f *lines, size_t num_lines, RayData *out_rays,
+                     int max_elements_per_ray = 128,
+                     float *kernel_time_ms = nullptr);
+
+  void TraceBetweenPointsCUDA(const HPoint3f *in_pts, const HPoint3f *out_pts,
+                              size_t num_lines, RayData *out_rays,
+                              int max_elements_per_ray = 128,
+                              float *kernel_time_ms = nullptr);
+#endif
 
 private:
   StructuredGrid *m_Image;
   Vector3f m_scale;
 };
 
-}
-
+} // namespace uLib
 
+#ifdef USE_CUDA
+#include "Math/VoxRaytracerCUDA.hpp"
+#endif
 
 #endif // VOXRAYTRACER_H

src/Math/VoxRaytracerCUDA.hpp

@@ -0,0 +1,548 @@
+#ifndef VOXRAYTRACERCUDA_H
+#define VOXRAYTRACERCUDA_H
+
+#ifdef USE_CUDA
+
+#include "Math/VoxImage.h"
+#include "Math/VoxRaytracer.h"
+#include <cuda_runtime.h>
+
+namespace uLib {
+
+#ifdef __CUDACC__
+template <typename VoxelT>
+__global__ void
+RaytraceAccumulateKernel(const float *lines_data, int num_lines,
+                         VoxelT *d_image, int dim0, int dim1, int dim2,
+                         const float *inv_world_matrix_data, float scale0,
+                         float scale1, float scale2) {
+  int idx = blockIdx.x * blockDim.x + threadIdx.x;
+  if (idx >= num_lines)
+    return;
+
+  const float *line_ptr = &lines_data[idx * 8];
+
+  float o_vec[4] = {line_ptr[0], line_ptr[1], line_ptr[2], line_ptr[3]};
+  float d_vec[4] = {line_ptr[4], line_ptr[5], line_ptr[6], line_ptr[7]};
+
+  float pt[4] = {0, 0, 0, 0};
+  float s[4] = {0, 0, 0, 0};
+
+  for (int i = 0; i < 4; ++i) {
+    for (int j = 0; j < 4; ++j) {
+      float m_val = inv_world_matrix_data[i + j * 4];
+      pt[i] += m_val * o_vec[j];
+      s[i] += m_val * d_vec[j];
+    }
+  }
+
+  float l = sqrtf(s[0] * s[0] + s[1] * s[1] + s[2] * s[2]);
+  if (l == 0)
+    return;
+
+  float L[3];
+  L[0] = l / s[0];
+  L[1] = l / s[1];
+  L[2] = l / s[2];
+
+  float offset[3];
+  for (int i = 0; i < 3; ++i) {
+    float fpt_i = floorf(pt[i]);
+    offset[i] = (s[i] >= 0) ? (1.0f - (pt[i] - fpt_i)) : (pt[i] - fpt_i);
+    offset[i] = fabsf(offset[i] * L[i]);
+    L[i] = fabsf(L[i]);
+  }
+
+  int id;
+  float d;
+  int vid[3] = {(int)floorf(pt[0]), (int)floorf(pt[1]), (int)floorf(pt[2])};
+
+  float scale_arr[3] = {scale0, scale1, scale2};
+
+  while (vid[0] >= 0 && vid[0] < dim0 && vid[1] >= 0 && vid[1] < dim1 &&
+         vid[2] >= 0 && vid[2] < dim2) {
+
+    d = offset[0];
+    id = 0;
+    if (offset[1] < d) {
+      d = offset[1];
+      id = 1;
+    }
+    if (offset[2] < d) {
+      d = offset[2];
+      id = 2;
+    }
+
+    float L_intersect = d * scale_arr[id];
+    size_t vox_index = vid[0] * dim1 * dim2 + vid[1] * dim2 + vid[2];
+
+    atomicAdd(&(d_image[vox_index].Value), L_intersect);
+
+    float sign_s = (s[id] >= 0) ? 1.0f : -1.0f;
+    vid[id] += (int)sign_s;
+
+    offset[0] -= d;
+    offset[1] -= d;
+    offset[2] -= d;
+    offset[id] = L[id];
+  }
+}
+#endif
+
+template <typename VoxelT>
+void VoxRaytracer::AccumulateLinesCUDA(const HLine3f *lines, size_t num_lines,
+                                       VoxImage<VoxelT> &image) {
+  if (num_lines == 0)
+    return;
+
+  image.Data().MoveToVRAM();
+
+  float *d_lines = nullptr;
+  size_t lines_size = num_lines * sizeof(HLine3f);
+  cudaMalloc(&d_lines, lines_size);
+  cudaMemcpy(d_lines, lines, lines_size, cudaMemcpyHostToDevice);
+  int threadsPerBlock = 256;
+  int blocksPerGrid = (num_lines + threadsPerBlock - 1) / threadsPerBlock;
+
+  Vector3i dims = image.GetDims();
+  Matrix4f inv_world_matrix = image.GetWorldMatrix().inverse();
+
+  float *d_inv_world;
+  cudaMalloc(&d_inv_world, 16 * sizeof(float));
+  cudaMemcpy(d_inv_world, inv_world_matrix.data(), 16 * sizeof(float),
+             cudaMemcpyHostToDevice);
+
+#ifdef __CUDACC__
+  RaytraceAccumulateKernel<<<blocksPerGrid, threadsPerBlock>>>(
+      d_lines, num_lines, image.Data().GetVRAMData(), dims(0), dims(1), dims(2),
+      d_inv_world, m_scale(0), m_scale(1), m_scale(2));
+  cudaDeviceSynchronize();
+
+  cudaError_t err = cudaGetLastError();
+  if (err != cudaSuccess) {
+    std::cerr << "CUDA Error in AccumulateLinesCUDA: "
+              << cudaGetErrorString(err) << std::endl;
+  }
+#else
+  std::cerr << "RaytraceAccumulateKernel requires NVCC!" << std::endl;
+#endif
+
+  cudaFree(d_lines);
+  cudaFree(d_inv_world);
+}
+
+#ifdef __CUDACC__
+
+__global__ void TraceBetweenPointsKernel(
+    const float *in_pts_data, const float *out_pts_data, int num_lines,
+    VoxRaytracer::RayData::Element **d_out_elements, size_t *d_out_counts,
+    float *d_out_lengths, int max_elements, int dim0, int dim1, int dim2,
+    const float *inv_world_matrix_data, float scale0, float scale1,
+    float scale2, int inc0, int inc1, int inc2) {
+  int idx = blockIdx.x * blockDim.x + threadIdx.x;
+  if (idx >= num_lines)
+    return;
+
+  VoxRaytracer::RayData::Element *ray_out = d_out_elements[idx];
+  size_t count = 0;
+  float tot_len = 0.0f;
+
+  const float *in_ptr = &in_pts_data[idx * 4];
+  const float *out_ptr = &out_pts_data[idx * 4];
+
+  float pt1[4] = {0, 0, 0, 0}, pt2[4] = {0, 0, 0, 0};
+  for (int i = 0; i < 4; ++i) {
+    for (int j = 0; j < 4; ++j) {
+      float m_val = inv_world_matrix_data[i + j * 4];
+      pt1[i] += m_val * in_ptr[j];
+      pt2[i] += m_val * out_ptr[j];
+    }
+  }
+
+  float s[4];
+  for (int i = 0; i < 4; ++i)
+    s[i] = pt2[i] - pt1[i];
+
+  float l = sqrtf(s[0] * s[0] + s[1] * s[1] + s[2] * s[2]);
+  if (l == 0) {
+    d_out_counts[idx] = count;
+    d_out_lengths[idx] = tot_len;
+    return;
+  }
+
+  float L[3];
+  L[0] = fabsf(l / s[0]);
+  L[1] = fabsf(l / s[1]);
+  L[2] = fabsf(l / s[2]);
+
+  float offset[3];
+  for (int i = 0; i < 3; ++i) {
+    float fpt_i = floorf(pt1[i]);
+    offset[i] = (s[i] >= 0) ? (1.0f - (pt1[i] - fpt_i)) : (pt1[i] - fpt_i);
+    offset[i] = fabsf(offset[i] * L[i]);
+  }
+
+  int vid[3] = {(int)floorf(pt1[0]), (int)floorf(pt1[1]), (int)floorf(pt1[2])};
+  int vid_out[3] = {(int)floorf(pt2[0]), (int)floorf(pt2[1]),
+                    (int)floorf(pt2[2])};
+
+  float scale_arr[3] = {scale0, scale1, scale2};
+
+  if (vid[0] == vid_out[0] && vid[1] == vid_out[1] && vid[2] == vid_out[2]) {
+    if (vid[0] >= 0 && vid[0] < dim0 && vid[1] >= 0 && vid[1] < dim1 &&
+        vid[2] >= 0 && vid[2] < dim2) {
+      if (count < max_elements) {
+        int map_id = vid[0] * inc0 + vid[1] * inc1 + vid[2] * inc2;
+        ray_out[count].vox_id = map_id;
+        ray_out[count].L = l;
+        tot_len += l;
+        count++;
+      }
+    }
+    d_out_counts[idx] = count;
+    d_out_lengths[idx] = tot_len;
+    return;
+  }
+
+  int id;
+  float d;
+  while (l > 0) {
+    d = offset[0];
+    id = 0;
+    if (offset[1] < d) {
+      d = offset[1];
+      id = 1;
+    }
+    if (offset[2] < d) {
+      d = offset[2];
+      id = 2;
+    }
+
+    if (vid[0] >= 0 && vid[0] < dim0 && vid[1] >= 0 && vid[1] < dim1 &&
+        vid[2] >= 0 && vid[2] < dim2) {
+      if (count < max_elements) {
+        int map_id = vid[0] * inc0 + vid[1] * inc1 + vid[2] * inc2;
+        ray_out[count].vox_id = map_id;
+        ray_out[count].L = d * scale_arr[id];
+        tot_len += d * scale_arr[id];
+        count++;
+      }
+    }
+
+    float sign_s = (s[id] >= 0) ? 1.0f : -1.0f;
+    vid[id] += (int)sign_s;
+
+    l -= d;
+
+    offset[0] -= d;
+    offset[1] -= d;
+    offset[2] -= d;
+    offset[id] = fminf(L[id], l);
+  }
+  d_out_counts[idx] = count;
+  d_out_lengths[idx] = tot_len;
+}
+
+__global__ void TraceLineKernel(const float *lines_data, int num_lines,
+                                VoxRaytracer::RayData::Element **d_out_elements,
+                                size_t *d_out_counts, float *d_out_lengths,
+                                int max_elements, int dim0, int dim1, int dim2,
+                                const float *inv_world_matrix_data,
+                                float scale0, float scale1, float scale2,
+                                int inc0, int inc1, int inc2) {
+  int idx = blockIdx.x * blockDim.x + threadIdx.x;
+  if (idx >= num_lines)
+    return;
+
+  VoxRaytracer::RayData::Element *ray_out = d_out_elements[idx];
+  size_t count = 0;
+  float tot_len = 0.0f;
+
+  const float *line_ptr = &lines_data[idx * 8];
+  float o_vec[4] = {line_ptr[0], line_ptr[1], line_ptr[2], line_ptr[3]};
+  float d_vec[4] = {line_ptr[4], line_ptr[5], line_ptr[6], line_ptr[7]};
+
+  float pt[4] = {0, 0, 0, 0}, s[4] = {0, 0, 0, 0};
+  for (int i = 0; i < 4; ++i) {
+    for (int j = 0; j < 4; ++j) {
+      float m_val = inv_world_matrix_data[i + j * 4];
+      pt[i] += m_val * o_vec[j];
+      s[i] += m_val * d_vec[j];
+    }
+  }
+
+  float l = sqrtf(s[0] * s[0] + s[1] * s[1] + s[2] * s[2]);
+  if (l == 0) {
+    d_out_counts[idx] = count;
+    d_out_lengths[idx] = tot_len;
+    return;
+  }
+
+  float L[3];
+  L[0] = fabsf(l / s[0]);
+  L[1] = fabsf(l / s[1]);
+  L[2] = fabsf(l / s[2]);
+
+  float offset[3];
+  for (int i = 0; i < 3; ++i) {
+    float fpt_i = floorf(pt[i]);
+    offset[i] = (s[i] >= 0) ? (1.0f - (pt[i] - fpt_i)) : (pt[i] - fpt_i);
+    offset[i] = fabsf(offset[i] * L[i]);
+  }
+
+  int id;
+  float d;
+  int vid[3] = {(int)floorf(pt[0]), (int)floorf(pt[1]), (int)floorf(pt[2])};
+  float scale_arr[3] = {scale0, scale1, scale2};
+
+  while (vid[0] >= 0 && vid[0] < dim0 && vid[1] >= 0 && vid[1] < dim1 &&
+         vid[2] >= 0 && vid[2] < dim2) {
+    d = offset[0];
+    id = 0;
+    if (offset[1] < d) {
+      d = offset[1];
+      id = 1;
+    }
+    if (offset[2] < d) {
+      d = offset[2];
+      id = 2;
+    }
+
+    if (count < max_elements) {
+      int map_id = vid[0] * inc0 + vid[1] * inc1 + vid[2] * inc2;
+      ray_out[count].vox_id = map_id;
+      ray_out[count].L = d * scale_arr[id];
+      tot_len += d * scale_arr[id];
+      count++;
+    }
+
+    float sign_s = (s[id] >= 0) ? 1.0f : -1.0f;
+    vid[id] += (int)sign_s;
+
+    offset[0] -= d;
+    offset[1] -= d;
+    offset[2] -= d;
+    offset[id] = L[id];
+  }
+  d_out_counts[idx] = count;
+  d_out_lengths[idx] = tot_len;
+}
+
+#endif // __CUDACC__
+
+inline void VoxRaytracer::TraceLineCUDA(const HLine3f *lines, size_t num_lines,
+                                        RayData *out_rays,
+                                        int max_elements_per_ray,
+                                        float *kernel_time_ms) {
+  if (num_lines == 0)
+    return;
+
+  float *d_lines = nullptr;
+  bool alloc_lines = false;
+
+  cudaPointerAttributes ptr_attr;
+  cudaPointerGetAttributes(&ptr_attr, lines);
+  if (ptr_attr.type == cudaMemoryTypeDevice) {
+    d_lines = (float *)lines;
+  } else {
+    alloc_lines = true;
+    size_t lines_size = num_lines * sizeof(HLine3f);
+    cudaMalloc(&d_lines, lines_size);
+    cudaMemcpy(d_lines, lines, lines_size, cudaMemcpyHostToDevice);
+  }
+
+  std::vector<RayData::Element *> h_out_elements(num_lines);
+  for (size_t i = 0; i < num_lines; ++i) {
+    out_rays[i].Data().resize(max_elements_per_ray);
+    out_rays[i].Data().MoveToVRAM();
+    h_out_elements[i] = out_rays[i].Data().GetVRAMData();
+  }
+
+  RayData::Element **d_out_elements;
+  cudaMalloc(&d_out_elements, num_lines * sizeof(RayData::Element *));
+  cudaMemcpy(d_out_elements, h_out_elements.data(),
+             num_lines * sizeof(RayData::Element *), cudaMemcpyHostToDevice);
+
+  size_t *d_out_counts;
+  float *d_out_lengths;
+  cudaMalloc(&d_out_counts, num_lines * sizeof(size_t));
+  cudaMalloc(&d_out_lengths, num_lines * sizeof(float));
+
+  int threadsPerBlock = 256;
+  int blocksPerGrid = (num_lines + threadsPerBlock - 1) / threadsPerBlock;
+
+  Vector3i dims = m_Image->GetDims();
+  Vector3i incs = m_Image->GetIncrements();
+  Matrix4f inv_world_matrix = m_Image->GetWorldMatrix().inverse();
+
+  float *d_inv_world;
+  cudaMalloc(&d_inv_world, 16 * sizeof(float));
+  cudaMemcpy(d_inv_world, inv_world_matrix.data(), 16 * sizeof(float),
+             cudaMemcpyHostToDevice);
+
+#ifdef __CUDACC__
+  cudaEvent_t start, stop;
+  if (kernel_time_ms) {
+    cudaEventCreate(&start);
+    cudaEventCreate(&stop);
+    cudaEventRecord(start);
+  }
+
+  TraceLineKernel<<<blocksPerGrid, threadsPerBlock>>>(
+      d_lines, num_lines, d_out_elements, d_out_counts, d_out_lengths,
+      max_elements_per_ray, dims(0), dims(1), dims(2), d_inv_world, m_scale(0),
+      m_scale(1), m_scale(2), incs(0), incs(1), incs(2));
+
+  if (kernel_time_ms) {
+    cudaEventRecord(stop);
+    cudaEventSynchronize(stop);
+    cudaEventElapsedTime(kernel_time_ms, start, stop);
+    cudaEventDestroy(start);
+    cudaEventDestroy(stop);
+  } else {
+    cudaDeviceSynchronize();
+  }
+
+  cudaError_t err = cudaGetLastError();
+  if (err != cudaSuccess) {
+    std::cerr << "CUDA Error in TraceLineCUDA: " << cudaGetErrorString(err)
+              << std::endl;
+  }
+#else
+  std::cerr << "TraceLineKernel requires NVCC!" << std::endl;
+#endif
+
+  std::vector<size_t> h_out_counts(num_lines);
+  std::vector<float> h_out_lengths(num_lines);
+  cudaMemcpy(h_out_counts.data(), d_out_counts, num_lines * sizeof(size_t),
+             cudaMemcpyDeviceToHost);
+  cudaMemcpy(h_out_lengths.data(), d_out_lengths, num_lines * sizeof(float),
+             cudaMemcpyDeviceToHost);
+
+  for (size_t i = 0; i < num_lines; ++i) {
+    out_rays[i].SetCount(h_out_counts[i]);
+    out_rays[i].SetTotalLength(h_out_lengths[i]);
+  }
+
+  if (alloc_lines) {
+    cudaFree(d_lines);
+  }
+  cudaFree(d_out_elements);
+  cudaFree(d_out_counts);
+  cudaFree(d_out_lengths);
+  cudaFree(d_inv_world);
+}
+
+inline void VoxRaytracer::TraceBetweenPointsCUDA(
+    const HPoint3f *in_pts, const HPoint3f *out_pts, size_t num_lines,
+    RayData *out_rays, int max_elements_per_ray, float *kernel_time_ms) {
+  if (num_lines == 0)
+    return;
+
+  float *d_in_pts = nullptr;
+  float *d_out_pts = nullptr;
+  bool alloc_pts = false;
+
+  cudaPointerAttributes ptr_attr;
+  cudaPointerGetAttributes(&ptr_attr, in_pts);
+  if (ptr_attr.type == cudaMemoryTypeDevice) {
+    d_in_pts = (float *)in_pts;
+    d_out_pts = (float *)out_pts;
+  } else {
+    alloc_pts = true;
+    size_t pts_size = num_lines * sizeof(HPoint3f);
+    cudaMalloc(&d_in_pts, pts_size);
+    cudaMalloc(&d_out_pts, pts_size);
+    cudaMemcpy(d_in_pts, in_pts, pts_size, cudaMemcpyHostToDevice);
+    cudaMemcpy(d_out_pts, out_pts, pts_size, cudaMemcpyHostToDevice);
+  }
+
+  std::vector<RayData::Element *> h_out_elements(num_lines);
+  for (size_t i = 0; i < num_lines; ++i) {
+    out_rays[i].Data().resize(max_elements_per_ray);
+    out_rays[i].Data().MoveToVRAM();
+    h_out_elements[i] = out_rays[i].Data().GetVRAMData();
+  }
+
+  RayData::Element **d_out_elements;
+  cudaMalloc(&d_out_elements, num_lines * sizeof(RayData::Element *));
+  cudaMemcpy(d_out_elements, h_out_elements.data(),
+             num_lines * sizeof(RayData::Element *), cudaMemcpyHostToDevice);
+
+  size_t *d_out_counts;
+  float *d_out_lengths;
+  cudaMalloc(&d_out_counts, num_lines * sizeof(size_t));
+  cudaMalloc(&d_out_lengths, num_lines * sizeof(float));
+
+  int threadsPerBlock = 256;
+  int blocksPerGrid = (num_lines + threadsPerBlock - 1) / threadsPerBlock;
+
+  Vector3i dims = m_Image->GetDims();
+  Vector3i incs = m_Image->GetIncrements();
+  Matrix4f inv_world_matrix = m_Image->GetWorldMatrix().inverse();
+
+  float *d_inv_world;
+  cudaMalloc(&d_inv_world, 16 * sizeof(float));
+  cudaMemcpy(d_inv_world, inv_world_matrix.data(), 16 * sizeof(float),
+             cudaMemcpyHostToDevice);
+
+#ifdef __CUDACC__
+  cudaEvent_t start, stop;
+  if (kernel_time_ms) {
+    cudaEventCreate(&start);
+    cudaEventCreate(&stop);
+    cudaEventRecord(start);
+  }
+
+  TraceBetweenPointsKernel<<<blocksPerGrid, threadsPerBlock>>>(
+      d_in_pts, d_out_pts, num_lines, d_out_elements, d_out_counts,
+      d_out_lengths, max_elements_per_ray, dims(0), dims(1), dims(2),
+      d_inv_world, m_scale(0), m_scale(1), m_scale(2), incs(0), incs(1),
+      incs(2));
+
+  if (kernel_time_ms) {
+    cudaEventRecord(stop);
+    cudaEventSynchronize(stop);
+    cudaEventElapsedTime(kernel_time_ms, start, stop);
+    cudaEventDestroy(start);
+    cudaEventDestroy(stop);
+  } else {
+    cudaDeviceSynchronize();
+  }
+
+  cudaError_t err = cudaGetLastError();
+  if (err != cudaSuccess) {
+    std::cerr << "CUDA Error in TraceBetweenPointsCUDA: "
+              << cudaGetErrorString(err) << std::endl;
+  }
+#else
+  std::cerr << "TraceBetweenPointsKernel requires NVCC!" << std::endl;
+#endif
+
+  std::vector<size_t> h_out_counts(num_lines);
+  std::vector<float> h_out_lengths(num_lines);
+  cudaMemcpy(h_out_counts.data(), d_out_counts, num_lines * sizeof(size_t),
+             cudaMemcpyDeviceToHost);
+  cudaMemcpy(h_out_lengths.data(), d_out_lengths, num_lines * sizeof(float),
+             cudaMemcpyDeviceToHost);
+
+  for (size_t i = 0; i < num_lines; ++i) {
+    out_rays[i].SetCount(h_out_counts[i]);
+    out_rays[i].SetTotalLength(h_out_lengths[i]);
+  }
+
+  if (alloc_pts) {
+    cudaFree(d_in_pts);
+    cudaFree(d_out_pts);
+  }
+  cudaFree(d_out_elements);
+  cudaFree(d_out_counts);
+  cudaFree(d_out_lengths);
+  cudaFree(d_inv_world);
+}
+
+} // namespace uLib
+
+#endif // USE_CUDA
+
+#endif // VOXRAYTRACERCUDA_H

src/Math/testing/AccumulatorTest.cpp

@@ -23,14 +23,12 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
-
 #include "Math/Accumulator.h"
 #include "testing-prototype.h"
 
 #include <TRandom.h>
-
+#include <iostream>
+#include <vector>
 
 // #include <boost/accumulators/framework/accumulator_set.hpp>
 // #include <boost/accumulators/statistics/count.hpp>
@@ -44,60 +42,66 @@ int test_ABTrim() {
 
   acc.SetABTrim(1, 1);
 
-    Vector<float> v;
-    v << 1,5,5,5,300;
+  std::vector<float> v;
+  for (float tmpf : {1, 5, 5, 5, 300})
+    v.push_back(tmpf);
+  // v << 1,5,5,5,300;
 
-    for(Vector<float>::Iterator itr=v.begin(); itr<v.end(); itr++)
+  for (std::vector<float>::iterator itr = v.begin(); itr < v.end(); itr++)
     acc += *itr;
 
-    std::cout << "Accumulating  Trim(1,1) vector: "
-              << v << " ... out = " << acc() << "\n";
+  // TODO missing operator <<
+  // std::cout << "Accumulating  Trim(1,1) vector: "
+  //          << v << " ... out = " << acc() << "\n";
 
   return (acc() == 15.0);
-
 }
 
-
 int test_Mean() {
   Accumulator_Mean<float> mean;
   TRandom rnd;
   const int c = 10000000;
-    Vector<float> v;
+  std::vector<float> v;
   v.reserve(c);
-    for(int i=0;i<c;++i) v.push_back( rnd.Gaus(2000,5) );
+  for (int i = 0; i < c; ++i)
+    v.push_back(rnd.Gaus(2000, 5));
 
   float m = 0;
-    for(int i=0;i<c;++i) m += v[i];
+  for (int i = 0; i < c; ++i)
+    m += v[i];
   m /= c;
   std::cout << "simple mean: " << m << "\n";
 
-    for(int i=0;i<c;++i) mean(v[i]);
+  for (int i = 0; i < c; ++i)
+    mean(v[i]);
   std::cout << "mean pass: " << mean() << "\n";
   mean.AddPass();
-    for(int i=0;i<c;++i) mean(v[i]);
+  for (int i = 0; i < c; ++i)
+    mean(v[i]);
   std::cout << "mean pass: " << mean() << "\n";
   mean.AddPass();
-    for(int i=0;i<c;++i) mean(v[i]);
+  for (int i = 0; i < c; ++i)
+    mean(v[i]);
   std::cout << "mean pass: " << mean() << "\n";
   mean.AddPass();
-    for(int i=0;i<c;++i) mean(v[i]);
+  for (int i = 0; i < c; ++i)
+    mean(v[i]);
   std::cout << "mean pass: " << mean() << "\n";
   mean.AddPass();
-    for(int i=0;i<c;++i) mean(v[i]);
+  for (int i = 0; i < c; ++i)
+    mean(v[i]);
   std::cout << "mean pass: " << mean() << "\n";
   mean.AddPass();
-    for(int i=0;i<c;++i) mean(v[i]);
+  for (int i = 0; i < c; ++i)
+    mean(v[i]);
   std::cout << "mean pass: " << mean() << "\n";
   mean.AddPass();
-    for(int i=0;i<c;++i) mean(v[i]);
+  for (int i = 0; i < c; ++i)
+    mean(v[i]);
   std::cout << "mean pass: " << mean() << "\n";
-
-
+  return 1;
 }
 
-
-
-
 int main(void) {
   BEGIN_TESTING(Accumulator);
 

src/Math/testing/CMakeLists.txt

@@ -5,6 +5,7 @@ set(TESTS
         ContainerBoxTest
         VoxImageTest
         VoxRaytracerTest
+        VoxRaytracerTestExtended
         StructuredDataTest
         VoxImageFilterTest
         PolicyTest
@@ -14,5 +15,16 @@ set(TESTS
         BitCodeTest
 )
 
+set(LIBRARIES
+       ${PACKAGE_LIBPREFIX}Core
+       ${PACKAGE_LIBPREFIX}Math
+       Boost::serialization
+       Eigen3::Eigen
+)
 
-uLib_add_tests(${uLib-module})
+uLib_add_tests(Math)
+
+if(USE_CUDA)
+    set_source_files_properties(VoxImageTest.cpp VoxImageCopyTest.cpp VoxImageFilterTest.cpp VoxRaytracerTest.cpp VoxRaytracerTestExtended.cpp PROPERTIES LANGUAGE CUDA)
+    set_source_files_properties(VoxRaytracerTest.cpp VoxRaytracerTestExtended.cpp PROPERTIES CXX_STANDARD 17 CUDA_STANDARD 17)
+endif()

src/Math/testing/TriangleMeshTest.cpp

@@ -23,18 +23,14 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
-
 #include "testing-prototype.h"
 
 #include "Math/TriangleMesh.h"
-
+#include <iostream>
 
 using namespace uLib;
 
-int main()
-{
+int main() {
   BEGIN_TESTING(Triangle Mesh);
 
   TriangleMesh mesh;
@@ -45,7 +41,6 @@ int main()
 
   mesh.AddTriangle(Vector3i(0, 1, 2));
 
-
   mesh.PrintSelf(std::cout);
 
   END_TESTING;

src/Math/testing/VoxImageCopyTest.cpp

@@ -23,15 +23,12 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
 #include "testing-prototype.h"
 
 #include "Math/VoxImage.h"
 
 using namespace uLib;
 
-
 struct TestVoxel {
   Scalarf Value;
   unsigned int Count;
@@ -42,14 +39,13 @@ int main() {
 
   {
     VoxImage<TestVoxel> img(Vector3i(10, 10, 10));
-        TestVoxel zero = {0,0};
+    TestVoxel zero = {0.f, 0};
     img.InitVoxels(zero);
-        TestVoxel nonzero = {5.552368, 0};
+    TestVoxel nonzero = {5.552368f, 0};
     img[Vector3i(5, 1, 7)] = nonzero;
     img[img.Find(HPoint3f(3, 3, 3))].Value = 5.552369;
     TEST1(img.GetValue(Vector3i(5, 1, 7)) == 5.552368f);
 
-
     img.SetOrigin(Vector3f(4, 5, 6));
 
     std::cout << "\n";
@@ -63,15 +59,8 @@ int main() {
     TEST1(img.GetSpacing() == img2.GetSpacing());
 
     img2 = img;
-
   }
 
-
-
-
-
-
-
   std::cout << "returns " << _fail << "\n";
   END_TESTING;
 }

src/Math/testing/VoxImageFilterTest.cpp

@@ -23,17 +23,12 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
-
-#include "testing-prototype.h"
 #include "Math/StructuredGrid.h"
+#include "testing-prototype.h"
 
 #include "Math/VoxImage.h"
 #include "Math/VoxImageFilter.h"
 
-
-
 using namespace uLib;
 
 struct TestVoxel {
@@ -41,39 +36,30 @@ struct TestVoxel {
   unsigned int Count;
 };
 
-float GaussianShape(float d)
-{
+float GaussianShape(float d) {
   // normalized manually .. fix //
   return 4.5 * exp(-d * 4.5);
 }
 
-
 class GaussianShapeClass : public Interface::VoxImageFilterShape {
 public:
-    GaussianShapeClass(float sigma) :
-        m_sigma(sigma)
-    {}
+  GaussianShapeClass(float sigma) : m_sigma(sigma) {}
 
-    float operator ()(float d) {
-        return (1/m_sigma) * exp(-d/m_sigma);
-    }
+  float operator()(float d) { return (1 / m_sigma) * exp(-d / m_sigma); }
 
 private:
   float m_sigma;
 };
 
-
-static float MaxInVector(const Vector<float> &v)
-{
+static float MaxInVector(const std::vector<float> &v) {
   float max = 0;
   for (int i = 0; i < v.size(); ++i)
-        if(v.at(i) > max) max = v.at(i);
+    if (v.at(i) > max)
+      max = v.at(i);
   return max;
 }
 
-
-int main()
-{
+int main() {
   BEGIN_TESTING(VoxImageFilters);
 
   VoxImage<TestVoxel> image(Vector3i(20, 30, 40));
@@ -81,8 +67,6 @@ int main()
   // image[Vector3i(10,10,8)].Value = 1;
   image.ExportToVtk("test_filter_original.vtk", 0);
 
-
-
   ////////////////////////////////////////////////////////////////////////////
   ////////////////////////////////////////////////////////////////////////////
   ////////////////////////////////////////////////////////////////////////////
@@ -93,7 +77,7 @@ int main()
 
     VoxImage<TestVoxel> filtered = image;
 
-        Vector<float> values;
+    std::vector<float> values;
     for (int i = 0; i < filter.GetKernelData().GetDims().prod(); ++i) {
       values.push_back(1.);
       std::cout << values[i] << " ";
@@ -113,10 +97,6 @@ int main()
     filtered.ExportToVtk("filter_RPS_out.vtk", 0);
   }
 
-
-
-
-
   {
 
     VoxImage<TestVoxel> image(Vector3i(20, 30, 40));
@@ -124,11 +104,9 @@ int main()
     image[Vector3i(9, 10, 8)].Value = 2;
     image.ExportToVtk("test_filter_max_original.vtk", 0);
 
-
-
     VoxFilterAlgorithmCustom<TestVoxel> filter(Vector3i(3, 3, 4));
 
-        Vector<float> values;
+    std::vector<float> values;
     for (int i = 0; i < filter.GetKernelData().GetDims().prod(); ++i) {
       values.push_back(static_cast<float>(1));
     }
@@ -144,7 +122,92 @@ int main()
     image.ExportToVtk("test_filter_max.vtk", 0);
   }
 
+  ////////////////////////////////////////////////////////////////////////////
+  // CUDA Allocator Transfer Test //
+  {
+    VoxImage<TestVoxel> image(Vector3i(10, 10, 10));
+    image[Vector3i(5, 5, 5)].Value = 1;
 
+    VoxFilterAlgorithmLinear<TestVoxel> filter(Vector3i(3, 3, 3));
+
+    std::vector<float> values;
+    for (int i = 0; i < filter.GetKernelData().GetDims().prod(); ++i) {
+      values.push_back(1.0f);
+    }
+
+    filter.SetImage(&image);
+    filter.SetKernelNumericXZY(values);
+
+    // Move the kernel data and image data to VRAM to simulate CUDA transfer
+    filter.GetKernelData().Data().MoveToVRAM();
+    image.Data().MoveToVRAM();
+
+    // Validate devices
+    if (filter.GetKernelData().Data().GetDevice() != MemoryDevice::VRAM ||
+        image.Data().GetDevice() != MemoryDevice::VRAM) {
+#ifdef USE_CUDA
+      std::cerr << "Failed to move memory to VRAM." << std::endl;
+#else
+      std::cout << "DataAllocator correctly simulates VRAM without crashing."
+                << std::endl;
+#endif
+    }
+
+    // Run the filter; The fallback CPU filter will trigger MoveToRAM
+    // behind the scenes inside Convolve / Evaluate.
+    filter.Run();
+
+    // Assert it came back to RAM if evaluated on CPU
+    if (image.Data().GetDevice() != MemoryDevice::RAM) {
+#ifdef USE_CUDA
+      std::cout << "Data correctly stayed in VRAM after CUDA execution!"
+                << std::endl;
+#else
+      std::cout << "Data correctly stayed in RAM simulation." << std::endl;
+#endif
+    }
+
+    image.ExportToVtk("test_filter_cuda_transfer.vtk", 0);
+  }
+
+  ////////////////////////////////////////////////////////////////////////////
+  // CUDA ABTrim Allocator Transfer Test //
+  {
+    VoxImage<TestVoxel> image(Vector3i(10, 10, 10));
+    image[Vector3i(5, 5, 5)].Value = 10;
+    image[Vector3i(5, 5, 6)].Value = 2; // Test trimming
+
+    VoxFilterAlgorithmAbtrim<TestVoxel> filter(Vector3i(3, 3, 3));
+
+    std::vector<float> values;
+    for (int i = 0; i < filter.GetKernelData().GetDims().prod(); ++i) {
+      values.push_back(1.0f);
+    }
+
+    filter.SetImage(&image);
+    filter.SetKernelNumericXZY(values);
+    filter.SetABTrim(1, 1); // trim highest and lowest
+
+    // Move the kernel data and image data to VRAM to simulate CUDA transfer
+    filter.GetKernelData().Data().MoveToVRAM();
+    image.Data().MoveToVRAM();
+
+    // Run the filter
+    filter.Run();
+
+    // Ensure data stays on device if CUDA was toggled
+    if (image.Data().GetDevice() != MemoryDevice::RAM) {
+#ifdef USE_CUDA
+      std::cout << "ABTrim correctly stayed in VRAM after CUDA execution!"
+                << std::endl;
+#else
+      std::cout << "ABTrim Data correctly stayed in RAM simulation."
+                << std::endl;
+#endif
+    }
+
+    image.ExportToVtk("test_filter_abtrim_cuda_transfer.vtk", 0);
+  }
 
   END_TESTING;
 }

src/Math/testing/VoxImageTest.cpp

@@ -23,16 +23,12 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
-
-#include "testing-prototype.h"
-#include "Math/StructuredGrid.h"
 #include "Math/VoxImage.h"
+#include "Math/StructuredGrid.h"
+#include "testing-prototype.h"
 
 using namespace uLib;
 
-
 struct TestVoxel {
   Scalarf Value;
   unsigned int Count;
@@ -64,12 +60,11 @@ int main() {
     TEST1(img.GetWorldPoint(1, 1, 1) == HPoint3f(3, 5, 3));
   }
 
-
   {
     VoxImage<TestVoxel> img(Vector3i(10, 10, 10));
-        TestVoxel zero = {0,0};
+    TestVoxel zero = {0.f, 0};
     img.InitVoxels(zero);
-        TestVoxel nonzero = {5.552368, 0};
+    TestVoxel nonzero = {5.552368f, 0};
     img[Vector3i(5, 1, 7)] = nonzero;
     img[img.Find(HPoint3f(3, 3, 3))].Value = 5.552369;
     img.ExportToVtk("./test_vox_image.vtk", 0);
@@ -79,11 +74,12 @@ int main() {
 
   {
     VoxImage<TestVoxel> img(Vector3i(4, 4, 4));
-        TestVoxel zero = {0,0};
+    TestVoxel zero = {0.f, 0};
     img.InitVoxels(zero);
     img.SetSpacing(Vector3f(2, 2, 2));
     img.SetPosition(Vector3f(-4, -4, -4));
-        TEST1( img.GetWorldPoint(img.GetLocalPoint(HPoint3f(5,5,5))) == HPoint3f(5,5,5));
+    TEST1(img.GetWorldPoint(img.GetLocalPoint(HPoint3f(5, 5, 5))) ==
+          HPoint3f(5, 5, 5));
   }
 
   {
@@ -92,6 +88,19 @@ int main() {
     imgR.ExportToVtk("./read_and_saved.vtk");
   }
 
+  {
+    VoxImage<TestVoxel> img(Vector3i(4, 4, 4));
+    img.InitVoxels({0.f, 0});
+    for (int i = 0; i < 4; i++) {
+      for (int j = 0; j < 4; j++) {
+        for (int k = 0; k < 4; k++) {
+          img[Vector3i(i, j, k)] = {static_cast<float>(i + j + k), 0};
+        }
+      }
+    }
+    img.ExportToVti("./vti_saved.vti", 0, 1);
+    // img.ImportFromVtkXml("./test_vox_image.vti");
+  }
 
   {
     VoxImage<TestVoxel> img1(Vector3i(5, 5, 5));
@@ -100,8 +109,5 @@ int main() {
     TEST1(img1.GetDims() == img2.GetDims());
   }
 
-
-
-
   END_TESTING
 }

src/Math/testing/VoxRaytracerTest.cpp

@@ -23,18 +23,14 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
-
-#include "Math/StructuredGrid.h"
 #include "Math/VoxRaytracer.h"
+#include "Math/StructuredGrid.h"
 #include "testing-prototype.h"
+#include <iostream>
 
 using namespace uLib;
 
-
-int Vector4f0(Vector4f c)
-{
+int Vector4f0(Vector4f c) {
   c(3) = 0;
   if (fabs(c(0)) < 0.001 && fabs(c(1)) < 0.001 && fabs(c(2)) < 0.001)
     return 0;
@@ -50,11 +46,14 @@ int Vector4f0(Vector4f c)
 //     return out == 0;
 // }
 
-
 typedef VoxRaytracer Raytracer;
 
-int main()
-{
+struct TestVoxel {
+  float Value;
+  int Count;
+};
+
+int main() {
   BEGIN_TESTING(Math VoxRaytracer);
 
   StructuredGrid img(Vector3i(2, 2, 2));
@@ -93,21 +92,21 @@ int main()
     TEST1(ray.GetEntryPoint(line, pt));
     TEST1(pt == HPoint3f(-3, -3, -3));
 
-        Raytracer::RayData rdata = ray.TraceBetweenPoints(HPoint3f(-3,-3,-3), HPoint3f(3,3,3));
-        foreach (const Raytracer::RayData::Element &el, rdata.Data())
-        {
+    Raytracer::RayData rdata =
+        ray.TraceBetweenPoints(HPoint3f(-3, -3, -3), HPoint3f(3, 3, 3));
+    for (size_t i = 0; i < rdata.Count(); ++i) {
+      const Raytracer::RayData::Element &el = rdata.Data()[i];
       std::cout << " " << el.vox_id << " , " << el.L << "\n";
     }
   }
 
-
   {
     HPoint3f pt1(1, -0.5, 1);
     HPoint3f pt2(1, 4.5, 1);
     Raytracer rt(img);
 
     Raytracer::RayData ray = rt.TraceBetweenPoints(pt1, pt2);
-        TEST1( ray.Data().size() == 2 );
+    TEST1(ray.Count() == 2);
     TEST1(ray.Data().at(0).vox_id == 6);
     TEST1(ray.Data().at(1).vox_id == 7);
     ray.PrintSelf(std::cout);
@@ -119,7 +118,7 @@ int main()
     Raytracer rt(img);
 
     Raytracer::RayData ray = rt.TraceBetweenPoints(pt1, pt2);
-        TEST1( ray.Data().size() == 2 );
+    TEST1(ray.Count() == 2);
     TEST1(ray.Data().at(0).vox_id == 6);
     TEST1(ray.Data().at(1).vox_id == 4);
     ray.PrintSelf(std::cout);
@@ -131,7 +130,7 @@ int main()
     Raytracer rt(img);
 
     Raytracer::RayData ray = rt.TraceBetweenPoints(pt1, pt2);
-        TEST1( ray.Data().size() == 4 );
+    TEST1(ray.Count() == 4);
     TEST1(ray.Data().at(0).vox_id == 6);
     TEST1(ray.Data().at(1).vox_id == 4);
     TEST1(ray.Data().at(2).vox_id == 5);
@@ -139,13 +138,81 @@ int main()
     ray.PrintSelf(std::cout);
   }
 
-    END_TESTING
+#ifdef USE_CUDA
+  {
+    std::cout << "\n--- Testing CUDA Raytracer Accumulator ---\n";
+
+    Raytracer rt(img);
+
+    {
+      HPoint3f pt1(1, -0.5, 1);
+      HPoint3f pt2(1, 4.5, 1);
+      HPoint3f pts1[1] = {pt1};
+      HPoint3f pts2[1] = {pt2};
+      Raytracer::RayData ray_cuda[1];
+      rt.TraceBetweenPointsCUDA(pts1, pts2, 1, ray_cuda);
+      TEST1(ray_cuda[0].Count() == 2);
+      TEST1(ray_cuda[0].Data().at(0).vox_id == 6);
+      TEST1(ray_cuda[0].Data().at(1).vox_id == 7);
     }
 
+    {
+      HPoint3f pt1(5, 1, 1);
+      HPoint3f pt2(-3, 1, 1);
+      HPoint3f pts1[1] = {pt1};
+      HPoint3f pts2[1] = {pt2};
+      Raytracer::RayData ray_cuda[1];
+      rt.TraceBetweenPointsCUDA(pts1, pts2, 1, ray_cuda);
+      TEST1(ray_cuda[0].Count() == 2);
+      TEST1(ray_cuda[0].Data().at(0).vox_id == 6);
+      TEST1(ray_cuda[0].Data().at(1).vox_id == 4);
+    }
 
+    {
+      HPoint3f pt1(1, 1, 1);
+      HPoint3f pt2(-1, 3, -1);
+      HPoint3f pts1[1] = {pt1};
+      HPoint3f pts2[1] = {pt2};
+      Raytracer::RayData ray_cuda[1];
+      rt.TraceBetweenPointsCUDA(pts1, pts2, 1, ray_cuda);
+      TEST1(ray_cuda[0].Count() == 4);
+      TEST1(ray_cuda[0].Data().at(0).vox_id == 6);
+      TEST1(ray_cuda[0].Data().at(1).vox_id == 4);
+      TEST1(ray_cuda[0].Data().at(2).vox_id == 5);
+      TEST1(ray_cuda[0].Data().at(3).vox_id == 1);
+    }
 
+    VoxImage<TestVoxel> img_cuda(Vector3i(4, 4, 4));
+    img_cuda.SetSpacing(Vector3f(2, 2, 2));
+    img_cuda.SetPosition(Vector3f(-4, -4, -4));
 
+    Raytracer ray(img_cuda);
 
+    HLine3f line1;
+    line1.origin << -3, -3, -3, 1;
+    line1.direction << 1, 1, 1, 0;
 
+    HLine3f line2;
+    line2.origin << -3, -3, 1, 1;
+    line2.direction << 1, 1, -1, 0;
 
+    HLine3f lines[2] = {line1, line2};
+    // Execute CUDA kernel wrapper over target VoxImage mapped internally into
+    // VRAM
+    ray.AccumulateLinesCUDA(lines, 2, img_cuda);
 
+    // Validate device synchronization returned data correctly pulling back to
+    // host
+    TEST1(img_cuda.Data().GetDevice() !=
+          MemoryDevice::RAM); // Confirms VRAM executed
+
+    // Pull down checking values
+    float l_val = img_cuda[img_cuda.Find(Vector4f(-3, -3, -3, 1))].Value;
+    std::cout << "Accumulated Voxel test trace point length returned: " << l_val
+              << "\n";
+    TEST1(l_val > 0.1f);
+  }
+#endif
+
+  END_TESTING
+}

src/Math/testing/VoxRaytracerTestExtended.cpp

@@ -0,0 +1,211 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// CMT Cosmic Muon Tomography project //////////////////////////////////////////
+////////////////////////////////////////////////////////////////////////////////
+
+  Copyright (c) 2014, Universita' degli Studi di Padova, INFN sez. di Padova
+  All rights reserved
+
+  Authors: Andrea Rigoni Garola < andrea.rigoni@pd.infn.it >
+
+  ------------------------------------------------------------------
+  This library is free software;  you  can  redistribute  it  and/or
+  modify it  under the  terms  of  the  GNU  Lesser  General  Public
+  License as published  by  the  Free  Software  Foundation;  either
+  version 3.0 of the License, or (at your option) any later version.
+
+  This library is  distributed in  the hope that it will  be useful,
+  but  WITHOUT ANY WARRANTY;  without  even  the implied warranty of
+  MERCHANTABILITY  or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+  Lesser General Public License for more details.
+
+  You should have received a copy of  the GNU Lesser General  Public
+  License along with this library.
+
+//////////////////////////////////////////////////////////////////////////////*/
+
+#include "Math/StructuredGrid.h"
+#include "Math/VoxRaytracer.h"
+#include "testing-prototype.h"
+#include <chrono>
+#include <iostream>
+#include <random>
+
+using namespace uLib;
+
+typedef VoxRaytracer Raytracer;
+
+int main() {
+  BEGIN_TESTING(Math VoxRaytracer Extended Benchmark);
+
+  std::cout << "\n=============================================\n";
+  std::cout << "  VoxRaytracer CPU vs CUDA Benchmark Test\n";
+  std::cout << "=============================================\n\n";
+
+  // Create a 100x100x100 grid (1 million voxels)
+  StructuredGrid img(Vector3i(100, 100, 100));
+  img.SetSpacing(Vector3f(1.0f, 1.0f, 1.0f));
+  img.SetPosition(Vector3f(-50.0f, -50.0f, -50.0f));
+
+  Raytracer rt(img);
+
+  const size_t NUM_RAYS = 1000000;
+  std::cout << "Generating " << NUM_RAYS
+            << " random ray pairs across a 100x100x100 grid...\n";
+
+  std::vector<HPoint3f> in_pts(NUM_RAYS);
+  std::vector<HPoint3f> out_pts(NUM_RAYS);
+
+  // Use a fixed seed for reproducible tests
+  std::random_device rd;
+  std::mt19937 gen(rd());
+  // The grid spans from -50 to 50 on each axis
+  std::uniform_real_distribution<float> dist(-49.9f, 49.9f);
+  // Pick a random face for in/out to ensure rays cross the volume
+  std::uniform_int_distribution<int> face_dist(0, 5);
+
+  for (size_t i = 0; i < NUM_RAYS; ++i) {
+    HPoint3f p1, p2;
+    // Generate point 1 on a random face
+    int f1 = face_dist(gen);
+    p1(0) = (f1 == 0) ? -50.0f : (f1 == 1) ? 50.0f : dist(gen);
+    p1(1) = (f1 == 2) ? -50.0f : (f1 == 3) ? 50.0f : dist(gen);
+    p1(2) = (f1 == 4) ? -50.0f : (f1 == 5) ? 50.0f : dist(gen);
+    p1(3) = 1.0f;
+
+    // Generate point 2 on a different face
+    int f2;
+    do {
+      f2 = face_dist(gen);
+    } while (
+        f1 == f2 ||
+        f1 / 2 ==
+            f2 / 2); // Avoid same face or opposite face trivially if desired
+
+    p2(0) = (f2 == 0) ? -50.0f : (f2 == 1) ? 50.0f : dist(gen);
+    p2(1) = (f2 == 2) ? -50.0f : (f2 == 3) ? 50.0f : dist(gen);
+    p2(2) = (f2 == 4) ? -50.0f : (f2 == 5) ? 50.0f : dist(gen);
+    p2(3) = 1.0f;
+
+    in_pts[i] = p1;
+    out_pts[i] = p2;
+  }
+
+  std::vector<Raytracer::RayData> cpu_results(NUM_RAYS);
+
+  std::cout << "\nRunning CPU Raytracing...\n";
+  auto start_cpu = std::chrono::high_resolution_clock::now();
+
+  for (size_t i = 0; i < NUM_RAYS; ++i) {
+    cpu_results[i] = rt.TraceBetweenPoints(in_pts[i], out_pts[i]);
+  }
+
+  auto end_cpu = std::chrono::high_resolution_clock::now();
+  std::chrono::duration<double, std::milli> cpu_ms = end_cpu - start_cpu;
+  std::cout << "CPU Execution Time: " << cpu_ms.count() << " ms\n";
+
+#ifdef USE_CUDA
+  std::vector<Raytracer::RayData> cuda_results(NUM_RAYS);
+  int max_elements_per_ray =
+      400; // 100x100x100 grid max trace length usually ~300 items
+
+  std::cout << "\nPre-Allocating Data to VRAM...\n";
+  // Pre-allocate input and output points to VRAM
+  HPoint3f *d_in_pts;
+  HPoint3f *d_out_pts;
+  size_t pts_size = NUM_RAYS * sizeof(HPoint3f);
+  cudaMalloc(&d_in_pts, pts_size);
+  cudaMalloc(&d_out_pts, pts_size);
+  cudaMemcpy(d_in_pts, in_pts.data(), pts_size, cudaMemcpyHostToDevice);
+  cudaMemcpy(d_out_pts, out_pts.data(), pts_size, cudaMemcpyHostToDevice);
+
+  // Pre-allocate elements output arrays in VRAM via DataAllocator
+  for (size_t i = 0; i < NUM_RAYS; ++i) {
+    cuda_results[i].Data().resize(max_elements_per_ray);
+    cuda_results[i].Data().MoveToVRAM();
+  }
+
+  std::cout << "Running CUDA Raytracing...\n";
+  auto start_cuda = std::chrono::high_resolution_clock::now();
+
+  float kernel_time_ms = 0.0f;
+  rt.TraceBetweenPointsCUDA(d_in_pts, d_out_pts, NUM_RAYS, cuda_results.data(),
+                            max_elements_per_ray, &kernel_time_ms);
+
+  auto end_cuda = std::chrono::high_resolution_clock::now();
+  std::chrono::duration<double, std::milli> cuda_ms = end_cuda - start_cuda;
+
+  // Free explicit input pointers
+  cudaFree(d_in_pts);
+  cudaFree(d_out_pts);
+
+  // Also query memory usage info
+  size_t free_byte;
+  size_t total_byte;
+  cudaMemGetInfo(&free_byte, &total_byte);
+  double free_db = (double)free_byte / (1024.0 * 1024.0);
+  double total_db = (double)total_byte / (1024.0 * 1024.0);
+  double used_db = total_db - free_db;
+
+  std::cout << "CUDA Kernel Exec Time: " << kernel_time_ms << " ms\n";
+  std::cout << "CUDA Total Time (API): " << cuda_ms.count() << " ms\n";
+  std::cout << "CUDA Total Time Spdup: " << (cpu_ms.count() / cuda_ms.count())
+            << "x\n";
+  if (kernel_time_ms > 0.0f) {
+    std::cout << "CUDA Kernel Speedup  : " << (cpu_ms.count() / kernel_time_ms)
+              << "x\n";
+  }
+  std::cout << "CUDA VRAM Usage Est. : " << used_db << " MB out of " << total_db
+            << " MB total\n";
+
+  std::cout << "\nVerifying CUDA results against CPU...\n";
+  size_t mismatches = 0;
+  for (size_t i = 0; i < NUM_RAYS; ++i) {
+    const auto &cpu_ray = cpu_results[i];
+    const auto &cuda_ray = cuda_results[i];
+
+    if (cpu_ray.Count() != cuda_ray.Count() ||
+        std::abs(cpu_ray.TotalLength() - cuda_ray.TotalLength()) > 1e-3) {
+      if (mismatches < 5) {
+        std::cout << "Mismatch at ray " << i
+                  << ": CPU count=" << cpu_ray.Count()
+                  << ", len=" << cpu_ray.TotalLength()
+                  << " vs CUDA count=" << cuda_ray.Count()
+                  << ", len=" << cuda_ray.TotalLength() << "\n";
+      }
+      mismatches++;
+      continue;
+    }
+
+    // Check elements
+    for (size_t j = 0; j < cpu_ray.Count(); ++j) {
+      if (cpu_ray.Data()[j].vox_id != cuda_ray.Data()[j].vox_id ||
+          std::abs(cpu_ray.Data()[j].L - cuda_ray.Data()[j].L) > 1e-3) {
+        if (mismatches < 5) {
+          std::cout << "Mismatch at ray " << i << ", element " << j
+                    << ": CPU id=" << cpu_ray.Data()[j].vox_id
+                    << ", L=" << cpu_ray.Data()[j].L
+                    << " vs CUDA id=" << cuda_ray.Data()[j].vox_id
+                    << ", L=" << cuda_ray.Data()[j].L << "\n";
+        }
+        mismatches++;
+        break;
+      }
+    }
+  }
+
+  if (mismatches == 0) {
+    std::cout << "SUCCESS! All " << NUM_RAYS
+              << " rays perfectly match between CPU and CUDA.\n";
+  } else {
+    std::cout << "FAILED! " << mismatches << " rays contain mismatched data.\n";
+  }
+
+  TEST1(mismatches == 0);
+
+#else
+  std::cout << "\nUSE_CUDA is not defined. Skipping CUDA benchmarking.\n";
+#endif
+
+  std::cout << "=============================================\n";
+  END_TESTING
+}

src/Python/CMakeLists.txt

@@ -0,0 +1,44 @@
+set(HEADERS "")
+
+set(SOURCES
+    module.cpp
+    core_bindings.cpp
+    math_bindings.cpp
+)
+
+# Use pybind11 to add the python module
+pybind11_add_module(uLib_python module.cpp core_bindings.cpp math_bindings.cpp)
+
+# Link against our C++ libraries
+target_link_libraries(uLib_python PRIVATE
+    ${PACKAGE_LIBPREFIX}Core
+    ${PACKAGE_LIBPREFIX}Math
+)
+
+# Include directories from Core and Math are automatically handled if target_include_directories were set appropriately,
+# but we might need to manually include them if they aren't INTERFACE includes.
+target_include_directories(uLib_python PRIVATE
+    ${PROJECT_SOURCE_DIR}/src
+    ${PROJECT_BINARY_DIR}
+)
+
+# --- Python Tests ---------------------------------------------------------- #
+
+if(BUILD_TESTING)
+    find_package(Python3 COMPONENTS Interpreter REQUIRED)
+
+    add_test(NAME pybind_general
+             COMMAND ${Python3_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/testing/pybind_test.py)
+    set_tests_properties(pybind_general PROPERTIES 
+                         ENVIRONMENT "PYTHONPATH=$<TARGET_FILE_DIR:uLib_python>")
+
+    add_test(NAME pybind_core 
+             COMMAND ${Python3_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/testing/core_pybind_test.py)
+    set_tests_properties(pybind_core PROPERTIES 
+                         ENVIRONMENT "PYTHONPATH=$<TARGET_FILE_DIR:uLib_python>")
+
+    add_test(NAME pybind_math 
+             COMMAND ${Python3_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/testing/math_pybind_test.py)
+    set_tests_properties(pybind_math PROPERTIES 
+                         ENVIRONMENT "PYTHONPATH=$<TARGET_FILE_DIR:uLib_python>")
+endif()

src/Python/core_bindings.cpp

@@ -0,0 +1,30 @@
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+
+#include "Core/Object.h"
+#include "Core/Timer.h"
+#include "Core/Options.h"
+#include "Core/Uuid.h"
+
+namespace py = pybind11;
+using namespace uLib;
+
+void init_core(py::module_ &m) {
+    py::class_<Object, std::shared_ptr<Object>>(m, "Object")
+        .def(py::init<>())
+        .def("DeepCopy", &Object::DeepCopy);
+
+    py::class_<Timer>(m, "Timer")
+        .def(py::init<>())
+        .def("Start", &Timer::Start)
+        .def("StopWatch", &Timer::StopWatch);
+
+    py::class_<Options>(m, "Options")
+        .def(py::init<const char*>(), py::arg("str") = "Program options")
+        .def("parse_config_file", py::overload_cast<const char*>(&Options::parse_config_file))
+        .def("save_config_file", &Options::save_config_file)
+        .def("count", &Options::count);
+
+    py::class_<TypeRegister>(m, "TypeRegister")
+        .def_static("Controller", &TypeRegister::Controller, py::return_value_policy::reference_internal);
+}

src/Python/math_bindings.cpp

@@ -0,0 +1,152 @@
+#include <pybind11/pybind11.h>
+#include <pybind11/eigen.h>
+#include <pybind11/stl.h>
+
+#include "Math/Dense.h"
+#include "Math/Transform.h"
+#include "Math/Geometry.h"
+#include "Math/ContainerBox.h"
+#include "Math/StructuredData.h"
+#include "Math/StructuredGrid.h"
+#include "Math/Structured2DGrid.h"
+#include "Math/Structured4DGrid.h"
+#include "Math/TriangleMesh.h"
+#include "Math/VoxRaytracer.h"
+#include "Math/Accumulator.h"
+
+namespace py = pybind11;
+using namespace uLib;
+
+void init_math(py::module_ &m) {
+
+    // Math/Transform.h
+    py::class_<AffineTransform>(m, "AffineTransform")
+        .def(py::init<>())
+        .def("GetWorldMatrix", &AffineTransform::GetWorldMatrix)
+        .def("SetPosition", &AffineTransform::SetPosition)
+        .def("GetPosition", &AffineTransform::GetPosition)
+        .def("Translate", &AffineTransform::Translate)
+        .def("Scale", &AffineTransform::Scale)
+        .def("SetRotation", &AffineTransform::SetRotation)
+        .def("GetRotation", &AffineTransform::GetRotation)
+        .def("Rotate", py::overload_cast<const Matrix3f &>(&AffineTransform::Rotate))
+        .def("Rotate", py::overload_cast<const Vector3f>(&AffineTransform::Rotate))
+        .def("EulerYZYRotate", &AffineTransform::EulerYZYRotate)
+        .def("FlipAxes", &AffineTransform::FlipAxes);
+
+    // Math/Geometry.h
+    py::class_<Geometry, AffineTransform>(m, "Geometry")
+        .def(py::init<>())
+        .def("GetWorldPoint", py::overload_cast<const Vector4f &>(&Geometry::GetWorldPoint, py::const_))
+        .def("GetLocalPoint", py::overload_cast<const Vector4f &>(&Geometry::GetLocalPoint, py::const_));
+
+    // Math/ContainerBox.h
+    py::class_<ContainerBox, AffineTransform>(m, "ContainerBox")
+        .def(py::init<>())
+        .def("SetOrigin", &ContainerBox::SetOrigin)
+        .def("GetOrigin", &ContainerBox::GetOrigin)
+        .def("SetSize", &ContainerBox::SetSize)
+        .def("GetSize", &ContainerBox::GetSize)
+        .def("GetWorldMatrix", &ContainerBox::GetWorldMatrix)
+        .def("GetWorldPoint", py::overload_cast<const Vector4f &>(&ContainerBox::GetWorldPoint, py::const_))
+        .def("GetLocalPoint", py::overload_cast<const Vector4f &>(&ContainerBox::GetLocalPoint, py::const_));
+
+    // Math/StructuredData.h
+    py::enum_<StructuredData::_Order>(m, "StructuredDataOrder")
+        .value("CustomOrder", StructuredData::CustomOrder)
+        .value("XYZ", StructuredData::XYZ)
+        .value("XZY", StructuredData::XZY)
+        .value("YXZ", StructuredData::YXZ)
+        .value("YZX", StructuredData::YZX)
+        .value("ZXY", StructuredData::ZXY)
+        .value("ZYX", StructuredData::ZYX)
+        .export_values();
+
+    py::class_<StructuredData>(m, "StructuredData")
+        .def(py::init<const Vector3i &>())
+        .def("GetDims", &StructuredData::GetDims)
+        .def("SetDims", &StructuredData::SetDims)
+        .def("GetIncrements", &StructuredData::GetIncrements)
+        .def("SetIncrements", &StructuredData::SetIncrements)
+        .def("SetDataOrder", &StructuredData::SetDataOrder)
+        .def("GetDataOrder", &StructuredData::GetDataOrder)
+        .def("IsInsideGrid", &StructuredData::IsInsideGrid)
+        .def("Map", &StructuredData::Map)
+        .def("UnMap", &StructuredData::UnMap);
+
+    // Math/StructuredGrid.h
+    py::class_<StructuredGrid, ContainerBox, StructuredData>(m, "StructuredGrid")
+        .def(py::init<const Vector3i &>())
+        .def("SetSpacing", &StructuredGrid::SetSpacing)
+        .def("GetSpacing", &StructuredGrid::GetSpacing)
+        .def("IsInsideBounds", &StructuredGrid::IsInsideBounds)
+        .def("Find", [](StructuredGrid &self, Vector3f pt) {
+            return self.Find(HPoint3f(pt));
+        });
+
+    // Math/Structured2DGrid.h
+    py::class_<Structured2DGrid>(m, "Structured2DGrid")
+        .def(py::init<>())
+        .def("SetDims", &Structured2DGrid::SetDims)
+        .def("GetDims", &Structured2DGrid::GetDims)
+        .def("IsInsideGrid", &Structured2DGrid::IsInsideGrid)
+        .def("Map", &Structured2DGrid::Map)
+        .def("UnMap", &Structured2DGrid::UnMap)
+        .def("SetPhysicalSpace", &Structured2DGrid::SetPhysicalSpace)
+        .def("GetSpacing", &Structured2DGrid::GetSpacing)
+        .def("GetOrigin", &Structured2DGrid::GetOrigin)
+        .def("IsInsideBounds", &Structured2DGrid::IsInsideBounds)
+        .def("PhysicsToUnitSpace", &Structured2DGrid::PhysicsToUnitSpace)
+        .def("UnitToPhysicsSpace", &Structured2DGrid::UnitToPhysicsSpace)
+        .def("SetDebug", &Structured2DGrid::SetDebug);
+
+    // Math/Structured4DGrid.h
+    py::class_<Structured4DGrid>(m, "Structured4DGrid")
+        .def(py::init<>())
+        .def("SetDims", &Structured4DGrid::SetDims)
+        .def("GetDims", &Structured4DGrid::GetDims)
+        .def("IsInsideGrid", &Structured4DGrid::IsInsideGrid)
+        .def("Map", &Structured4DGrid::Map)
+        .def("UnMap", &Structured4DGrid::UnMap)
+        .def("SetPhysicalSpace", &Structured4DGrid::SetPhysicalSpace)
+        .def("GetSpacing", &Structured4DGrid::GetSpacing)
+        .def("GetOrigin", &Structured4DGrid::GetOrigin)
+        .def("IsInsideBounds", &Structured4DGrid::IsInsideBounds)
+        .def("PhysicsToUnitSpace", &Structured4DGrid::PhysicsToUnitSpace)
+        .def("UnitToPhysicsSpace", &Structured4DGrid::UnitToPhysicsSpace)
+        .def("SetDebug", &Structured4DGrid::SetDebug);
+
+    // Math/TriangleMesh.h
+    py::class_<TriangleMesh>(m, "TriangleMesh")
+        .def(py::init<>())
+        .def("AddPoint", &TriangleMesh::AddPoint)
+        .def("AddTriangle", py::overload_cast<const Vector3i &>(&TriangleMesh::AddTriangle))
+        .def("Points", &TriangleMesh::Points, py::return_value_policy::reference_internal)
+        .def("Triangles", &TriangleMesh::Triangles, py::return_value_policy::reference_internal);
+
+    // Math/VoxRaytracer.h
+    py::class_<VoxRaytracer::RayData::Element>(m, "VoxRaytracerRayDataElement")
+        .def(py::init<>())
+        .def_readwrite("vox_id", &VoxRaytracer::RayData::Element::vox_id)
+        .def_readwrite("L", &VoxRaytracer::RayData::Element::L);
+
+    py::class_<VoxRaytracer::RayData>(m, "VoxRaytracerRayData")
+        .def(py::init<>())
+        .def("AppendRay", &VoxRaytracer::RayData::AppendRay)
+        .def("Count", &VoxRaytracer::RayData::Count)
+        .def("TotalLength", &VoxRaytracer::RayData::TotalLength)
+        .def("SetCount", &VoxRaytracer::RayData::SetCount)
+        .def("SetTotalLength", &VoxRaytracer::RayData::SetTotalLength);
+
+    py::class_<VoxRaytracer>(m, "VoxRaytracer")
+        .def(py::init<StructuredGrid &>(), py::keep_alive<1, 2>())
+        .def("GetImage", &VoxRaytracer::GetImage, py::return_value_policy::reference_internal);
+
+    // Math/Accumulator.h
+    py::class_<Accumulator_Mean<float>>(m, "Accumulator_Mean_f")
+        .def(py::init<>())
+        .def("AddPass", &Accumulator_Mean<float>::AddPass)
+        .def("__call__", py::overload_cast<const float>(&Accumulator_Mean<float>::operator()))
+        .def("__call__", py::overload_cast<>(&Accumulator_Mean<float>::operator(), py::const_));
+
+}

src/Python/module.cpp

@@ -0,0 +1,18 @@
+#include <pybind11/pybind11.h>
+
+namespace py = pybind11;
+
+void init_core(py::module_ &m);
+void init_math(py::module_ &m);
+
+PYBIND11_MODULE(uLib_python, m) {
+    m.doc() = "Python bindings for uLib Core and Math libraries";
+    
+    // Core submodule
+    py::module_ core = m.def_submodule("Core", "Core library bindings");
+    init_core(core);
+
+    // Math submodule
+    py::module_ math = m.def_submodule("Math", "Math library bindings");
+    init_math(math);
+}