refactor: migrate voxel data storage to DataAllocator for CUDA

fix mismatch Origin - Position

.gitignore

@@ -0,0 +1,3 @@
+CMakeFiles/
+build/
+.cache/

.vscode/settings.json

@@ -0,0 +1,8 @@
+{
+    "clangd.fallbackFlags": [
+        "-I${workspaceFolder}/src",
+        "-I/home/share/micromamba/envs/mutom/include",
+        "-I/home/rigoni/.conan2/p/eigen5481853932f72/p/include/eigen3"
+    ],
+    "clangd.semanticHighlighting.enable": true
+}

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

@@ -28,26 +28,28 @@ macro(uLib_add_shared_library name)
   set(ULIB_SHARED_LIBRARIES ${shared} PARENT_SCOPE)
   source_group("${project_name}\\${name}" FILES ${SOURCES})
   set_target_properties(${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 ?
-#                      PUBLIC_HEADER ""
+                        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 ?
+#                       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)
 
@@ -79,25 +81,17 @@ 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})
+    foreach(tn ${TESTS})
+        add_executable(${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)
+        target_link_libraries(${tn} ${LIBRARIES})
 
-  # adds libraries dependencies
-  foreach(library ${LIBRARIES})
-   target_link_libraries(${tn} ${library})
-  endforeach(library)
+    endforeach(tn)
 
- endforeach(tn)
-
- # custom target to compile all tests
- add_custom_target(all-${name}-tests)
- add_dependencies(all-${name}-tests ${TESTS})
+    # custom target to compile all tests
+    add_custom_target(all-${name}-tests)
+    add_dependencies(all-${name}-tests ${TESTS})
 endmacro(uLib_add_tests name)
 
 

CMakeLists.txt

@@ -3,20 +3,22 @@
 ##### CMAKE LISTS ##############################################################
 ################################################################################
 
-cmake_minimum_required (VERSION 2.6)
-
-execute_process(COMMAND "clear")
-message("//////////////////////////////////////////////////////////////////////")
-message("/////////////////// CMAKE PJOJECT CONFIGURATION //////////////////////")
-message("//////////////////////////////////////////////////////////////////////")
+cmake_minimum_required (VERSION 3.26)
 
 ## -------------------------------------------------------------------------- ##
 
 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)
+    enable_language(CUDA)
+    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 +33,246 @@ 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(${VTK_USE_FILE})
+
+
+
+option(CENTOS_SUPPORT "VTK definitions for CentOS" OFF)
+if(CENTOS_SUPPORT)
+    find_package(VTK CONFIG REQUIRED)
+    include(${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}/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 ${PACKAGE_INSTALL_INC_DIR})
+                "${PROJECT_BINARY_DIR}/uLibConfigVersion.cmake" @ONLY)
 
 
+# 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
+                              )
 
-## 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 ${VTK_LIBRARIES})
-
-#message( "---------------------------------------------------------------------" )
-#execute_process(COMMAND
-#                "ls"
-##                "cmake --find-package -DNAME=uLib -DLANGUAGE=C -DCOMPILER_ID=GNU -DMODE=COMPILE"
-#                )
-#message( "---------------------------------------------------------------------" )
-
-## -------------------------------------------------------------------------- ##
+install(FILES "${PROJECT_BINARY_DIR}/uLibConfig.cmake"
+              "${PROJECT_BINARY_DIR}/uLibConfigVersion.cmake"
+        DESTINATION "${INSTALL_CMAKE_DIR}"
+        COMPONENT dev)
 
 
-# TODO clean also subdirectories
-add_custom_target(clean-cmake-files
-   COMMAND ${CMAKE_COMMAND} -P ${ULIB_CMAKE_DIR}/clean-all.cmake
+# 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 +1,7 @@
+[requires]
+eigen/3.4.0
+boost/1.83.0
+
+[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/CMakeLists.txt

@@ -1,46 +1,28 @@
 
-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 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)
 
-uLib_add_shared_library(${uLib-module})
-add_subdirectory(testing)
+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 ${PROJECT_SOVERSION})
+target_link_libraries(${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/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

@@ -23,95 +23,85 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
 #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 {
-        // 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 {
-    }
-    guid_initializer const & export_guid() const {
-        BOOST_STATIC_WARNING(boost::is_polymorphic< T >::value);
-        // note: exporting an abstract base class will have no effect
-        // and cannot be used to instantitiate serialization code
-        // (one might be using this in a DLL to instantiate code)
-        //BOOST_STATIC_WARNING(! boost::serialization::is_abstract< T >::value);
-        export_guid(boost::serialization::is_abstract< T >());
-        return *this;
-    }
+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(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
+    // and cannot be used to instantitiate serialization code
+    // (one might be using this in a DLL to instantiate code)
+    // BOOST_STATIC_WARNING(! boost::serialization::is_abstract< T >::value);
+    export_guid(boost::serialization::is_abstract<T>());
+    return *this;
+  }
 };
 
-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 > {                                  \
-        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();             \
-    }}}}                                                     \
-/**/
+#define ULIB_CLASS_EXPORT_IMPLEMENT(T)                                         \
+  namespace uLib {                                                             \
+  namespace Archive {                                                          \
+  namespace detail {                                                           \
+  namespace extra_detail {                                                     \
+  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();                                                      \
+  }                                                                            \
+  }                                                                            \
+  }                                                                            \
+  }                                                                            \
+  /**/
 
 #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

@@ -23,178 +23,128 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
-
-
 #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::PackageName = PACKAGE_NAME;
 const char *Version::VersionNumber = PACKAGE_VERSION;
-const char *Version::Release       = "x"; //SVN_REVISION;
-
+const char *Version::Release = "x"; // SVN_REVISION;
 
 ////////////////////////////////////////////////////////////////////////////////
 // Object Private //
 
 class ObjectPrivate {
 public:
+  struct Signal {
+    GenericMFPtr sigptr;
+    std::string sigstr;
+    SignalBase *signal;
+  };
 
-    struct Signal {
-        GenericMFPtr  sigptr;
-        std::string   sigstr;
-        SignalBase   *signal;
-    };
+  struct Slot {
+    GenericMFPtr sloptr;
+    std::string slostr;
+  };
 
-    struct Slot {
-        GenericMFPtr sloptr;
-        std::string  slostr;
-    };
-
-
-    Vector<Signal> sigv;
-    Vector<Slot>   slov;
+  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) {
+  // should lock to be tread safe //
+  memcpy(d, copy.d, sizeof(ObjectPrivate));
+  // ERROR! does not copy parameters ... <<<< FIXXXXX
 }
 
-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) {
+  Archive::xml_oarchive ar(os);
+  ar << boost::serialization::make_nvp("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) {
+  Archive::xml_iarchive ar(is);
+  ar >> boost::serialization::make_nvp("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)
-{   
-    Archive::xml_oarchive ar(os);
-    ObjectPropable::serialize(ar,0);
+void Object::SaveConfig(std::ostream &os, int version) {
+  Archive::xml_oarchive ar(os);
 }
 
-void Object::LoadConfig(std::istream &is, int version)
-{
-    if(!props()) this->init_properties();
-    Archive::xml_iarchive ar(is);
-    ObjectPropable::serialize(ar,0);
+void Object::LoadConfig(std::istream &is, int version) {
+  Archive::xml_iarchive ar(is);
 }
 
-
-
-
-
-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++)
-    {
-        o << "  signal:[ " << itr->sigstr << " ]\n";
-    }
-    o << "--------------------------------------\n\n";
+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++) {
+    o << "  signal:[ " << itr->sigstr << " ]\n";
+  }
+  o << "--------------------------------------\n\n";
 }
 
-
-bool Object::addSignalImpl(SignalBase *sig, GenericMFPtr fptr, const char *name)
-{
-    ObjectPrivate::Signal s = {fptr,std::string(name),sig};
-    d->sigv.push_back(s);
+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)
-{
-    ObjectPrivate::Slot s = {fptr,std::string(name)};
-    d->slov.push_back(s);
+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)
-    {
-        if(d->sigv[i].sigptr == fptr)
-            return d->sigv[i].signal;
-    }
-    return NULL;
+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
-{
-    std::string in(name);
-    for(int i=0; i<d->sigv.size(); ++i)
-    {
-        if(d->sigv[i].sigstr == in)
-            return d->sigv[i].signal;
-    }
-    return NULL;
+SignalBase *Object::findSignalImpl(const char *name) const {
+  std::string in(name);
+  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
-{
-    std::string in(name);
-    for(int i=0; i<d->slov.size(); ++i)
-    {
-        if(d->slov[i].slostr == in)
-            return &d->slov[i].sloptr;
-    }
-    return NULL;
+GenericMFPtr *Object::findSlotImpl(const char *name) const {
+  std::string in(name);
+  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

@@ -23,200 +23,185 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
 #ifndef U_CORE_OBJECT_H
 #define U_CORE_OBJECT_H
 
 #include <iostream>
 
 // WARNING: COPILE ERROR if this goes after mpl/vector //
-//#include "Core/Vector.h"
+// #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;
-    static const char *VersionNumber;
-    static const char *Release;
+  static const char *PackageName;
+  static const char *VersionNumber;
+  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;
-    //    void PrintName() { std::cout << "Ob name: " << name << "\n"; }
+  //    std::string name;
+  //    void PrintName() { std::cout << "Ob name: " << name << "\n"; }
 
-    Object();
-    Object(const Object &copy);
-    ~Object();
+  Object();
+  Object(const Object &copy);
+  ~Object();
 
-    ////////////////////////////////////////////////////////////////////////////
-    // PARAMETERS //
+  ////////////////////////////////////////////////////////////////////////////
+  // PARAMETERS //
 
-    // FIXX !!!
-    virtual void DeepCopy(const Object &copy);
+  // FIXX !!!
+  virtual void DeepCopy(const Object &copy);
 
+  ////////////////////////////////////////////////////////////////////////////
+  // SERIALIZATION //
 
-    ////////////////////////////////////////////////////////////////////////////
-    // SERIALIZATION //
+  template <class ArchiveT>
+  void serialize(ArchiveT &ar, const unsigned int version) {}
+  template <class ArchiveT>
+  void save_override(ArchiveT &ar, const unsigned int version) {}
 
-    template <class ArchiveT> void serialize(ArchiveT &ar, const unsigned int version)    {
-                ObjectPropable::serialize(ar,version);
+  void SaveConfig(std::ostream &os, int version = 0);
+  void LoadConfig(std::istream &is, int version = 0);
+
+  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) {
+    //        // NOT WORKING YET //
+    //        1) find slot pointer from name
+    //        SignalBase   *sig = ob1->findSignal(signal_name);
+    //        GenericMFPtr *slo = receiver->findSlot(slot_name);
+    //        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) {
+    SignalBase *sigb = sender->findOrAddSignal(sigf);
+    ConnectSignal<typename FunctionPointer<Func1>::SignalSignature>(sigb, slof,
+                                                                    receiver);
+    return true;
+  }
+
+  template <typename FuncT>
+  static inline bool connect(SignalBase *sigb, FuncT slof, Object *receiver) {
+    ConnectSignal<typename FunctionPointer<FuncT>::SignalSignature>(sigb, slof,
+                                                                    receiver);
+    return true;
+  }
+
+  template <typename FuncT>
+  inline
+      typename Signal<typename FunctionPointer<FuncT>::SignalSignature>::type *
+      addSignal(FuncT fun, const char *name) {
+    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) {
+    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;
+    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;
+    SignalBase *sig = findSignalImpl(GenericMFPtr(fptr));
+    if (!sig) {
+      sig = NewSignal(fptr);
+      addSignalImpl(sig, fptr, "signal_name_to_be_implemented");
     }
-    template <class ArchiveT> void save_override(ArchiveT &ar,const unsigned int version) {}
+    return (SigT *)sig;
+  }
 
-    void SaveConfig(std::ostream &os, int version = 0);
-    void LoadConfig(std::istream &is, int version = 0);
+  inline SignalBase *findSignal(const char *name) const {
+    return findSignalImpl(name);
+  }
 
-    static void SaveXml(std::ostream &os, Object &ob);
-    static void LoadXml(std::istream &is, Object &ob);
+  inline GenericMFPtr *findSlot(const char *name) const {
+    return findSlotImpl(name);
+  }
 
+  void PrintSelf(std::ostream &o) const;
 
-
-    ////////////////////////////////////////////////////////////////////////////
-    // SIGNALS //
-
-    // Qt4 style connector //
-    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);
-        //        GenericMFPtr *slo = receiver->findSlot(slot_name);
-        //        if(sig && slo)
-        //            return Object::connect(sig,slo->operator ()(),receiver);
-        //        else 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)
-    {
-        SignalBase *sigb = sender->findOrAddSignal(sigf);
-        typedef boost::signals2::signal<typename FunctionPointer<Func2>::SignalSignature> SigT;
-        ConnectSignal(sigb,slof,receiver);
-    }
-
-    template <typename FuncT>
-    static inline bool connect(SignalBase *sigb, FuncT slof, Object *receiver) {
-        ConnectSignal(sigb,slof,receiver);
-    }
-
-
-    template< typename FuncT >
-    inline typename Signal<typename FunctionPointer<FuncT>::SignalSignature>::type *
-    addSignal(FuncT fun, const char *name) {
-        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 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;
-        SignalBase *sig = findSignalImpl(GenericMFPtr(fptr));
-        if(!sig) {
-            sig = NewSignal(fptr);
-            addSignalImpl(sig,fptr,"signal_name_to_be_implemented");
-        }
-        return (SigT *)sig;
-    }
-
-
-    inline SignalBase *
-    findSignal(const char *name) const
-    {
-        return findSignalImpl(name);
-    }
-
-    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);
-    bool addSlotImpl(GenericMFPtr fptr, const char *name);
-    SignalBase   *findSignalImpl(const GenericMFPtr &fptr) const;
-    SignalBase   *findSignalImpl(const char *name) const;
-    GenericMFPtr *findSlotImpl(const char *name) const;
+  bool addSignalImpl(SignalBase *sig, GenericMFPtr fptr, const char *name);
+  bool addSlotImpl(GenericMFPtr fptr, const char *name);
+  SignalBase *findSignalImpl(const GenericMFPtr &fptr) const;
+  SignalBase *findSignalImpl(const char *name) const;
+  GenericMFPtr *findSlotImpl(const char *name) const;
 
-    friend class boost::serialization::access;
-    friend class ObjectPrivate;
-    class ObjectPrivate *d;
+  friend class boost::serialization::access;
+  friend class ObjectPrivate;
+  class ObjectPrivate *d;
 };
 
-
-
-} // uLib
+} // namespace uLib
 
 ////////////////////////////////////////////////////////////////////////////////
 
-//std::ostream & operator << (std::ostream &os, uLib::Object &ob);
-//std::ostream & operator << (std::ostream &os, uLib::Object *ob);
-//std::istream & operator >> (std::istream &is, uLib::Object &ob);
-
+// std::ostream & operator << (std::ostream &os, uLib::Object &ob);
+// 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>
 
@@ -48,26 +43,22 @@ TODO:
 #include <boost/mpl/remove_if.hpp>
 #include <boost/serialization/nvp.hpp>
 
-//#include <boost/archive/xml_iarchive.hpp>
-//#include <boost/archive/xml_oarchive.hpp>
-//#include <boost/archive/text_iarchive.hpp>
-//#include <boost/archive/text_oarchive.hpp>
-//#include "boost/archive/polymorphic_iarchive.hpp"
-//#include "boost/archive/polymorphic_oarchive.hpp"
+// #include <boost/archive/xml_iarchive.hpp>
+// #include <boost/archive/xml_oarchive.hpp>
+// #include <boost/archive/text_iarchive.hpp>
+// #include <boost/archive/text_oarchive.hpp>
+// #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"
 
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
@@ -80,63 +71,47 @@ namespace serialization {
 // ACCESS 2 //
 template <class T> struct access2 {};
 
-
 // NON FUNZIONA ... SISTEMARE !!!! // ------------------------------------------
-template<class T>
-class hrp :
-        public wrapper_traits<const hrp< T > >
-{
-    const char *m_name;
-    T *m_value;
-    std::string *m_str;
+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) {}
+  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;
-    }
+  const char *name() const { return this->m_name; }
 
-
-    template<class Archivex>
-    void save( Archivex & ar, const unsigned int /* file_version */) const {
-        ////        ar.operator<<(const_value());
-        //        std::stringstream ss;
-        //        uLib::Archive::hrt_oarchive har(ss);
-        //        har << make_nvp(m_name,*m_value);
-        //        //        (*m_str) = ss.str();
-        ////        ar.operator << (make_nvp(m_name, ss.str());
-    }
-    template<class Archivex>
-    void load( Archivex & ar, const unsigned int /* file_version */) {
-//        ar.operator>>(value());
-    }
-    BOOST_SERIALIZATION_SPLIT_MEMBER()
+  template <class Archivex>
+  void save(Archivex &ar, const unsigned int /* file_version */) const {
+    ////        ar.operator<<(const_value());
+    //        std::stringstream ss;
+    //        uLib::Archive::hrt_oarchive har(ss);
+    //        har << make_nvp(m_name,*m_value);
+    //        //        (*m_str) = ss.str();
+    ////        ar.operator << (make_nvp(m_name, ss.str());
+  }
+  template <class Archivex>
+  void load(Archivex &ar, const unsigned int /* file_version */) {
+    //        ar.operator>>(value());
+  }
+  BOOST_SERIALIZATION_SPLIT_MEMBER()
 };
 
-
-template<class T>
+template <class T>
 inline
 #ifndef BOOST_NO_FUNCTION_TEMPLATE_ORDERING
-const
+    const
 #endif
-hrp< T > make_hrp(const char * name, T & t){
-    return hrp< T >(name, t);
+    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
 
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
@@ -151,9 +126,7 @@ 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 _AR_OP(r, data, elem) data &BOOST_SERIALIZATION_BASE_OBJECT_NVP(elem);
 
 #define NVP(data) BOOST_SERIALIZATION_NVP(data)
 
@@ -166,51 +139,53 @@ namespace uLib {
 // SO LEAVE ULIB_CFG_INTRUSIVE_SERIALIZATION NOT DEFINED
 
 #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 _AR_(_name)                     _ULIB_DETAIL_INTRUSIVE_AR_(_name)
+#define ULIB_SERIALIZABLE_OBJECT _ULIB_DETAIL_INTRUSIVE_SERIALIZABLE_OBJECT
+#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) \
-                                            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) \
-                                            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 AR(_name)                        _ULIB_DETAIL_UNINTRUSIVE_AR_(_name)
-#  define HR(_name)                        _ULIB_DETAIL_UNINTRUSIVE_AR_(_name)
+#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)                            \
+  ULIB_CLASS_EXPORT_OBJECT_KEY(_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;
 
-#define ULIB_SERIALIZE_ACCESS                                        \
-    friend class boost::serialization::access;                       \
-    template <class T> friend class boost::serialization::access2;
+#define ULIB_CLASS_EXPORT_KEY(_FullNamespaceClass)                             \
+  BOOST_CLASS_EXPORT_KEY(_FullNamespaceClass)
 
-#define ULIB_CLASS_EXPORT_KEY(_FullNamespaceClass)                   \
-    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>)
-
-
-#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)
+#define ULIB_CLASS_EXPORT_OBJECT_KEY(_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)
 
 /** 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)
 
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
@@ -220,38 +195,57 @@ namespace uLib {
 ////////////////////////////////////////////////////////////////////////////////
 // INTRUSIVE SERIALIZATION ( NOT WORKING YET !! ) //
 
-#define _ULIB_DETAIL_INTRUSIVE_AR_(name) ar & BOOST_SERIALIZATION_NVP(name);
+#define _ULIB_DETAIL_INTRUSIVE_AR_(name) ar &BOOST_SERIALIZATION_NVP(name);
 
-#define _ULIB_DETAIL_INTRUSIVE_SERIALIZE_FUNC(Class,Archive) \
-    template void Class::serialize(Archive &ar,const unsigned int);
+#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_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);
-
-#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));   \
-    _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__))) \
-    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)
+#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);
 
+#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));        \
+    _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__)))                  \
+  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)
 
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
@@ -261,152 +255,171 @@ 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)
+#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)
 
 // 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); }; }}
-
-#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) { \
-    serialize_parents(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)
-
-#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) { \
-    serialize_parents(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)
-
-
-#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); }}
-
-#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__))); \
-    /* 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*/  \
-    serialize_parents(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)
-
-
-
+#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);                     \
+  };                                                                           \
+  }                                                                            \
+  }
 
+#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) {          \
+    serialize_parents(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)
 
+#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) {          \
+    serialize_parents(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)
 
+#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);                     \
+  };                                                                           \
+  }                                                                            \
+  }
 
+#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__)));                   \
+  /* 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();                                                          \
+  }                                                                            \
+  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);                              \
+  }                                                                            \
+  }                                                                            \
+  }                                                                            \
+  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_AR_(name)                                     \
+  boost::serialization::make_nvp(BOOST_PP_STRINGIZE(name), ob.name)
 
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 
-
-
 namespace detail {
 
 struct Serializable {
 
-    /**
-     * Serializable trait to check if an object type is 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> {};
-
-    /**
-     * IsA Serializable Implementation Template
-     */
-    template <class T>
-    struct IsA : serializable_trait<T> {};
-
-    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));
-        }
-    };
+  /**
+   * Serializable trait to check if an object type is 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> {};
 
+  /**
+   * IsA Serializable Implementation Template
+   */
+  template <class T> struct IsA : serializable_trait<T> {};
 
+  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));
+    }
+  };
 };
 
-
-} // detail
-
-
-
-
+} // namespace detail
 
 struct Serializable {
-    friend class boost::serialization::access;
-    template <class T> friend class boost::serialization::access2;
-    virtual ~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;
 
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
@@ -48,12 +46,15 @@
 #define slots
 #define signals /*virtual void init_signals();*/ public
 #define emit
-#define SLOT(a)     BOOST_STRINGIZE(a)
-#define SIGNAL(a)   BOOST_STRINGIZE(a)
+#define SLOT(a) BOOST_STRINGIZE(a)
+#define SIGNAL(a) BOOST_STRINGIZE(a)
 
-#define _ULIB_DETAIL_SIGNAL_EMIT(_name,...)                       \
-        static BOOST_AUTO(sig,this->findOrAddSignal(&_name));     \
-        sig->operator()(__VA_ARGS__);
+#define _ULIB_DETAIL_SIGNAL_EMIT(_name, ...)                                   \
+  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:
@@ -66,103 +67,101 @@
  * // cast automatico //
  * 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 {
-    typedef boost::signals2::signal<T> type;
+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;
-        reinterpret_cast<SigT*>(sigb)->connect(slof);
-    }
+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;
-        reinterpret_cast<SigT*>(sigb)->connect(boost::bind(slof,receiver));
-    }
+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;
-        reinterpret_cast<SigT*>(sigb)->connect(boost::bind(slof,receiver,_1));
-    }
+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
 
@@ -33,244 +31,182 @@
 
 #include <boost/preprocessor.hpp>
 
-#include <ltk/ltktypes.h>
+// #include <ltk/ltktypes.h>
 
 #include "Core/Macros.h"
 #include "Core/Mpl.h"
 
-
-
-
-
-
-
 namespace uLib {
 
-
 ////////////////////////////////////////////////////////////////////////////////
 
 namespace detail {
 
 struct TypeIntrospection {
 
-    // BOOST IMPL  //
-    BOOST_MPL_HAS_XXX_TRAIT_DEF(type_info)
+  // BOOST IMPL  //
+  BOOST_MPL_HAS_XXX_TRAIT_DEF(type_info)
 
-    // SFINAE IMPL //
-    /*
-    template <typename T>
-    struct has_type_info {
-        typedef char yes[1];
-        typedef char no[2];
-        template <typename U> static yes& test(typename U::type_info::BaseList*);
-        template <typename   > static no&  test(...);
-        //        struct apply {
-        static const bool value = sizeof(test<T>(0)) == sizeof(yes);
-        typedef boost::mpl::bool_<value> type;
-        //        };
-    };
-    */    
+  // SFINAE IMPL //
+  /*
+  template <typename T>
+  struct has_type_info {
+      typedef char yes[1];
+      typedef char no[2];
+      template <typename U> static yes& test(typename U::type_info::BaseList*);
+      template <typename   > static no&  test(...);
+      //        struct apply {
+      static const bool value = sizeof(test<T>(0)) == sizeof(yes);
+      typedef boost::mpl::bool_<value> type;
+      //        };
+  };
+  */
 
-    /** IsA Introspectable Object Implementation Template */
-    template <class T>
-    struct IsIntrospectable : has_type_info<T> {};
+  /** IsA Introspectable Object Implementation Template */
+  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 access {
+    typedef typename T::type_info type_info;
+  };
+
+  template <typename T> struct child_first_impl {
+
+    template <class T1, bool cond> struct lambda_CFList_f {
+      typedef mpl::vector<T1> type;
     };
 
-    template <typename T>
-    struct child_first_impl {
-
-        template <class T1, bool cond>
-        struct lambda_CFList_f {
-            typedef mpl::vector<T1> type;
-        };
-
-        template <class T1>
-        struct lambda_CFList_f<T1,true> {
-            //            typedef typename T1::type_info::CFList type;
-            typedef typename access<T1>::type_info::CFList type;
-        };
-
-        template <class T1>
-        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;
-
-        /** 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;
-
-        /** Add This Class to final CFList sequence */
-        typedef typename mpl::copy< Childs
-                                  , mpl::back_inserter< mpl::vector<T> >
-                                  >::type type;
+    template <class T1> struct lambda_CFList_f<T1, true> {
+      //            typedef typename T1::type_info::CFList type;
+      typedef typename access<T1>::type_info::CFList type;
     };
 
+    template <class T1>
+    struct lambda_CFList : lambda_CFList_f<T1, has_type_info<T1>::value> {};
 
-    /**
-     * 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 {};
+    /** Transforms all Base Type into proper CFList */
+    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;
 
+    /** Add This Class to final CFList sequence */
+    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 {};
 };
 
-
-
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 // TYPE ADAPTERS // FINIRE !!!
 
-//#define _REPETITION_V(vz,vn,vdata)
-
-
-//template < class TypeList >
-//class TypeAdapterInputInterface {
-//    virtual ~TypeAdapterInputInterface() {}
-//public:
-
+// #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 bool             Bool_t;      //Boolean (0=false, 1=true) (bool)
+// 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 ---------------------------------------------------------
 #ifndef BIT
-#define BIT(n)       (1ULL << (n))
+#define BIT(n) (1ULL << (n))
 #endif
 
 #ifndef SETBIT
-#define SETBIT(n,i)  ((n) |= BIT(i))
+#define SETBIT(n, i) ((n) |= BIT(i))
 #endif
 
 #ifndef CLRBIT
-#define CLRBIT(n,i)  ((n) &= ~BIT(i))
+#define CLRBIT(n, i) ((n) &= ~BIT(i))
 #endif
 
 #ifndef TESTBIT
-#define TESTBIT(n,i) ((Bool_t)(((n) & BIT(i)) != 0))
+#define TESTBIT(n, i) ((Bool_t)(((n) & BIT(i)) != 0))
 #endif
 
-
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 // TYPE INTROSPECTION FOR OBJECTS //
 
-
-
-#define uLibTypeMacro(thisClass,...) \
-    \
-    /* Friendship detail for accessing introspection */ \
-    template <typename> friend class uLib::detail::TypeIntrospection::access;       \
-    \
-    /* type info structure*/ public: \
-    /* in GCC 4.8 must be public or dynamic_cast wont work */ \
-    struct type_info { \
-      /*WARNING: -std=c++0x required for this! */ \
-      constexpr static const char *name = BOOST_PP_STRINGIZE(thisClass);            \
-      typedef BOOST_PP_VARIADIC_ELEM(0,__VA_ARGS__) BaseClass;                      \
-      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; \
-    }; \
-    \
-    public: \
-    typedef type_info::BaseClass BaseClass; \
-    virtual const char *type_name() const { return type_info::name; } \
-    /* Object Props fwd declaration*/ \
-    struct ObjectProps; \
-    /**/
-
+#define uLibTypeMacro(thisClass, ...)                                          \
+                                                                               \
+  /* Friendship detail for accessing introspection */                          \
+  template <typename> friend class uLib::detail::TypeIntrospection::access;    \
+                                                                               \
+/* type info structure*/ public:                                               \
+  /* in GCC 4.8 must be public or dynamic_cast wont work */                    \
+  struct type_info {                                                           \
+    /*WARNING: -std=c++0x required for this! */                                \
+    constexpr static const char *name = BOOST_PP_STRINGIZE(thisClass);         \
+    typedef BOOST_PP_VARIADIC_ELEM(0, __VA_ARGS__) BaseClass;                  \
+    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;                                                                \
+  };                                                                           \
+                                                                               \
+public:                                                                        \
+  typedef type_info::BaseClass BaseClass;                                      \
+  virtual const char *type_name() const { return type_info::name; }            \
+  /**/
 
 /**
  * TypeList inheritance introspection
  */
 struct TypeIntrospection {
-    template <typename T>
-    struct child_first : detail::TypeIntrospection::child_first<T> {};
-
+  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

@@ -29,6 +29,7 @@
 #define U_CORE_UUID_H
 
 #include <iostream>
+#include <vector>
 
 #include <boost/uuid/uuid.hpp>
 #include <boost/uuid/name_generator.hpp>
@@ -36,7 +37,6 @@
 #include <boost/uuid/uuid_io.hpp>
 
 #include "Core/Mpl.h"
-#include "Core/Vector.h"
 #include "Core/Object.h"
 
 
@@ -127,7 +127,7 @@ public:
 
 private:
     IDGen_t gen;
-    Vector<RegisterEntry> m_registry;
+    std::vector<RegisterEntry> m_registry;
 
 };
 

src/Core/testing/CMakeLists.txt

@@ -16,18 +16,17 @@ set( TESTS
         SerializeTest
         SerializeDreadDiamondTest
         DreadDiamondParameters
-        ObjectPropableTest
         UuidTest
         TypeIntrospectionTraversal
         OptionsTest
+        PingPongTest
 )
 
 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"
 
@@ -37,78 +34,43 @@
 
 using namespace uLib;
 
-
-
-
-
-
-
-struct A :  Object {
-    uLibTypeMacro(A,Object)
-    A() : numa(5552368) {}
-    int numa;
+struct A : Object {
+  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) {}
-    int numb;
+  uLibTypeMacro(B, Object) B() : numb(5552369) {}
+  int numb;
 };
 
 ULIB_SERIALIZABLE_OBJECT(B)
-ULIB_SERIALIZE_OBJECT(B,Object) { ar & AR(numb); }
-
+ULIB_SERIALIZE_OBJECT(B, Object) { ar &AR(numb); }
 
 struct C : B {
-    uLibTypeMacro(C,B)
-    C() : numc(5552370) {}
-    int numc;
+  uLibTypeMacro(C, B) C() : numc(5552370) {}
+  int numc;
 };
 
 ULIB_SERIALIZABLE_OBJECT(C)
-ULIB_SERIALIZE_OBJECT(C,B) { ar & AR(numc); }
+ULIB_SERIALIZE_OBJECT(C, B) { ar &AR(numc); }
 
-struct D : A,B {
-    uLibTypeMacro(D,A,B)
+struct D : A, B {
+  uLibTypeMacro(D, A, B)
 
-    D() : numd(5552371) {}
-    int numd;
+      D()
+      : numd(5552371) {}
+  int numd;
 };
 
 ULIB_SERIALIZABLE_OBJECT(D)
-ULIB_SERIALIZE_OBJECT(D,A,B) { ar & AR(numd); }
+ULIB_SERIALIZE_OBJECT(D, A, B) { ar &AR(numd); }
 
+int main() {
+  A o;
 
-
-main() {
-    A o; o.init_properties();
-
-    Archive::xml_oarchive(std::cout) << NVP(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;
 
-
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
@@ -46,63 +41,51 @@ using namespace uLib;
 
 struct V3f {
 
-    float x,y,z;
-    V3f()
-    { x = y = z =0; }
+  float x, y, z;
+  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) {
-    Archive::hrt_oarchive(o) << v;
-    return o;
+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) {
-    Archive::hrt_iarchive(is) >> v;
-    return is;
+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 //
+  // testing human readble archive with simple serializable structure //
 
-    V3f v1(1,2,3),v2,v3,v4;
-    std::cout << "v    --> " << v1 << "\n";
+  V3f v1(1, 2, 3), v2, v3, v4;
+  std::cout << "v    --> " << v1 << "\n";
 
-    std::stringstream ss; ss << v1;
-    std::cout << "ss.v --> " << ss.str() << "\n";
+  std::stringstream ss;
+  ss << v1;
+  std::cout << "ss.v --> " << ss.str() << "\n";
 
-    Archive::hrt_iarchive ar(ss); ar >> v2;
-    std::cout << "v2   --> " << v2 << "\n";
+  Archive::hrt_iarchive ar(ss);
+  ar >> v2;
+  std::cout << "v2   --> " << v2 << "\n";
 
-    std::stringstream("<2 3 4>") >> v3;
-    std::cout << "v3   --> " << v3 << "\n";
+  std::stringstream("<2 3 4>") >> v3;
+  std::cout << "v3   --> " << v3 << "\n";
 
-    //    std::cout << "insert V3f string to parse: "; std::cin >> v4;
-    //    std::cout << "v4   --> " << v4 << "\n";
-    return (1);
+  //    std::cout << "insert V3f string to parse: "; std::cin >> v4;
+  //    std::cout << "v4   --> " << v4 << "\n";
+  return (1);
 }
 
-
-
-
-
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
@@ -110,140 +93,72 @@ 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() {
-        std::string p_a;
-    };
+  void init_properties();
+  std::string p_a;
+
+  uLibRefMacro(a, int);
 
-    uLibRefMacro (a,int);
 private:
-    int m_a;
+  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";
+ULIB_SERIALIZE_OBJECT(A, Object) {
+  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";
-    {
-        std::ifstream file("test.xml");
-        Archive::xml_iarchive(file) >> NVP(a);
-    }
+  {
+    std::ofstream file("test.xml");
+    Archive::xml_oarchive(file) << NVP(a);
+  }
+  a.a() = 0;
+  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" );
+  Archive::xml_oarchive(std::cout) << NVP(a);
+  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";
-    {
-        // ERRORE FIX !
-        //        std::ifstream file("test.xml");
-        //        Archive::hrt_iarchive(file) >> NVP(a);
-    }
+  {
+    std::ofstream file("test.xml");
+    Archive::hrt_oarchive(file) << NVP(a);
+  }
+  a.a() = 0;
+  a.p_a = "zero string";
+  {
+    // ERRORE FIX !
+    //        std::ifstream file("test.xml");
+    //        Archive::hrt_iarchive(file) >> NVP(a);
+  }
 
-    Archive::hrt_oarchive(std::cout) << NVP(a);
-    return ( a.a() == 5552368 && a.$$.p_a == "A property string" );
+  Archive::hrt_oarchive(std::cout) << NVP(a);
+  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);
+  BEGIN_TESTING(Serialize Test);
 
-    TEST1( test_V3f() );
-    TEST1( testing_xml_class() );
-    //    testing_hrt_class(); ///// << ERRORE in HRT with properties
-    TEST1( testing_mu() );
+  TEST1(test_V3f());
+  TEST1(testing_xml_class());
+  //    testing_hrt_class(); ///// << ERRORE in HRT with properties
 
-    END_TESTING;
+  END_TESTING;
 }
-
-
-
-
-
-
-
-
-
-
-
-
-

src/Core/testing/SignalTest.cpp

@@ -23,93 +23,63 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
 #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 V0();
 
+  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";
-    }
+  void PrintNumber(int n) {
+    std::cout << "Ob3 is printing number: " << n << "\n";
+  }
 };
 
-
-
-
 int main() {
-    BEGIN_TESTING(Signals);
+  BEGIN_TESTING(Signals);
 
-    Ob1 ob1;
-    Ob2 ob2;
-    Ob3 ob3;
+  Ob1 ob1;
+  Ob2 ob2;
+  Ob3 ob3;
 
-    Object::connect(&ob1,&Ob1::V0,&ob2,&Ob2::PrintV0);
-    Object::connect(&ob1,&Ob1::V0,&ob3,&Ob3::PrintV0);
-    Object::connect(&ob1,&Ob1::V1,&ob3,&Ob3::PrintNumber);
+  Object::connect(&ob1, &Ob1::V0, &ob2, &Ob2::PrintV0);
+  Object::connect(&ob1, &Ob1::V0, &ob3, &Ob3::PrintV0);
+  Object::connect(&ob1, &Ob1::V1, &ob3, &Ob3::PrintNumber);
 
-    //  not working yet
-    //    Object::connect(&ob1,SIGNAL(V0(),&ob2,SLOT(PrintV0())
+  //  not working yet
+  //    Object::connect(&ob1,SIGNAL(V0(),&ob2,SLOT(PrintV0())
 
-    ob1.PrintSelf(std::cout);
+  ob1.PrintSelf(std::cout);
 
-    emit ob1.V0();
-    emit ob1.V1(5552368);
+  emit ob1.V0();
+  emit ob1.V1(5552368);
 
-    END_TESTING;
+  END_TESTING;
 }
-
-

src/Core/testing/StaticInterfaceTest.cpp

@@ -23,90 +23,73 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
-
 #include <iostream>
 
 #include "testing-prototype.h"
 #include <Core/StaticInterface.h>
 
-
-
 namespace uLib {
 
 //// INTERFACE TO COMPLEX CLASS /////
 
 namespace Interface {
 struct Test {
-    MAKE_TRAITS
-    template<class Self> void check_structural() {
-        uLibCheckFunction(Self,test,bool,int,float);
-        uLibCheckMember(Self,testmemb,int);
-    }
+  MAKE_TRAITS
+  template <class Self> void check_structural() {
+    uLibCheckFunction(Self, test, bool, int, float);
+    uLibCheckMember(Self, testmemb, int);
+  }
 };
-}
+} // namespace Interface
 
 struct Test {
-    bool test(int i, float f){}
-    int testmemb;
+  bool test(int i, float f) { return true; }
+  int testmemb;
 };
 
-
-
 //// INTERFAC TO SIMPLE CLASS ///////////
 
 namespace Interface {
 struct Simple {
-    MAKE_TRAITS
-    template<class Self> void check_structural() {
-        uLibCheckMember(Self,memb1,int);
-        uLibCheckMember(Self,memb2,float);
-    }
+  MAKE_TRAITS
+  template <class Self> void check_structural() {
+    uLibCheckMember(Self, memb1, int);
+    uLibCheckMember(Self, memb2, float);
+  }
 };
-}
+} // namespace Interface
 
 struct Simple {
-    int memb1;
-    float memb2;
+  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;
-        t.test(i,f);
-    }
+  UseTest() {
+    Interface::IsA<T, Interface::Test>();
+    T t;
+    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() {
+  BEGIN_TESTING(Static Interface);
 
+  uLib::UseTest<uLib::Test> u;
+
+  uLib::UseSimple<uLib::Simple> s;
+
+  END_TESTING;
 }
-
-int main()
-{
-    BEGIN_TESTING(Static Interface);
-
-
-
-    uLib::UseTest<uLib::Test> u;
-
-    uLib::UseSimple<uLib::Simple> s;
-
-    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})
-add_subdirectory(testing)
+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"
 
@@ -37,32 +36,31 @@ 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;
-    Vector2f m_Position;
-    Vector2f m_Slope;
-    Vector2f m_PositionError;
-    Vector2f m_SlopeError;
-    int      m_HitsNumber;
+protected:
+    Vector2f            m_Position;
+    Vector2f            m_Slope;
+    Vector2f            m_PositionError;
+    Vector2f            m_SlopeError;
+    int                 m_HitsNumber;
     DetectorChamber::ID m_Idv;
 };
 
 
 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 @@
-#-------------------------------------------------
-#
-# Project created by QtCreator 2012-08-30T18:59:53
-#
-#-------------------------------------------------
-
-QT       += core gui
-
-TARGET = QVTKViewport2
-TEMPLATE = app
-
-
-SOURCES += main.cpp\
-        vtkviewport.cpp
-
-HEADERS  += vtkviewport.h
-
-FORMS    += vtkviewport.ui

src/Gui/Qt/QVTKViewport2/QVTKViewport2.pro.user

@@ -1,453 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE QtCreatorProject>
-<!-- Written by Qt Creator 2.4.1, 2012-09-03T09:43:56. -->
-<qtcreator>
- <data>
-  <variable>ProjectExplorer.Project.ActiveTarget</variable>
-  <value type="int">0</value>
- </data>
- <data>
-  <variable>ProjectExplorer.Project.EditorSettings</variable>
-  <valuemap type="QVariantMap">
-   <value type="bool" key="EditorConfiguration.AutoIndent">true</value>
-   <value type="bool" key="EditorConfiguration.AutoSpacesForTabs">false</value>
-   <valuemap type="QVariantMap" key="EditorConfiguration.CodeStyle.0">
-    <value type="QString" key="language">Cpp</value>
-    <valuemap type="QVariantMap" key="value">
-     <value type="QString" key="CurrentPreferences">CppGlobal</value>
-    </valuemap>
-   </valuemap>
-   <valuemap type="QVariantMap" key="EditorConfiguration.CodeStyle.1">
-    <value type="QString" key="language">QmlJS</value>
-    <valuemap type="QVariantMap" key="value">
-     <value type="QString" key="CurrentPreferences">QmlJSGlobal</value>
-    </valuemap>
-   </valuemap>
-   <value type="int" key="EditorConfiguration.CodeStyle.Count">2</value>
-   <value type="QByteArray" key="EditorConfiguration.Codec">System</value>
-   <value type="bool" key="EditorConfiguration.ConstrainTooltips">false</value>
-   <value type="int" key="EditorConfiguration.IndentSize">4</value>
-   <value type="bool" key="EditorConfiguration.MouseNavigation">true</value>
-   <value type="int" key="EditorConfiguration.PaddingMode">1</value>
-   <value type="bool" key="EditorConfiguration.ScrollWheelZooming">true</value>
-   <value type="int" key="EditorConfiguration.SmartBackspaceBehavior">0</value>
-   <value type="bool" key="EditorConfiguration.SpacesForTabs">true</value>
-   <value type="int" key="EditorConfiguration.TabKeyBehavior">1</value>
-   <value type="int" key="EditorConfiguration.TabSize">8</value>
-   <value type="bool" key="EditorConfiguration.UseGlobal">true</value>
-   <value type="int" key="EditorConfiguration.Utf8BomBehavior">1</value>
-   <value type="bool" key="EditorConfiguration.addFinalNewLine">true</value>
-   <value type="bool" key="EditorConfiguration.cleanIndentation">true</value>
-   <value type="bool" key="EditorConfiguration.cleanWhitespace">true</value>
-   <value type="bool" key="EditorConfiguration.inEntireDocument">false</value>
-  </valuemap>
- </data>
- <data>
-  <variable>ProjectExplorer.Project.PluginSettings</variable>
-  <valuemap type="QVariantMap"/>
- </data>
- <data>
-  <variable>ProjectExplorer.Project.Target.0</variable>
-  <valuemap type="QVariantMap">
-   <value type="QString" key="ProjectExplorer.ProjectConfiguration.DefaultDisplayName">Desktop</value>
-   <value type="QString" key="ProjectExplorer.ProjectConfiguration.DisplayName">Desktop</value>
-   <value type="QString" key="ProjectExplorer.ProjectConfiguration.Id">Qt4ProjectManager.Target.DesktopTarget</value>
-   <value type="int" key="ProjectExplorer.Target.ActiveBuildConfiguration">0</value>
-   <value type="int" key="ProjectExplorer.Target.ActiveDeployConfiguration">0</value>
-   <value type="int" key="ProjectExplorer.Target.ActiveRunConfiguration">0</value>
-   <valuemap type="QVariantMap" key="ProjectExplorer.Target.BuildConfiguration.0">
-    <value type="QString" key="ProjectExplorer.BuildCOnfiguration.ToolChain">ProjectExplorer.ToolChain.Gcc:/usr/bin/g++.x86-linux-generic-elf-64bit.gdb</value>
-    <valuemap type="QVariantMap" key="ProjectExplorer.BuildConfiguration.BuildStepList.0">
-     <valuemap type="QVariantMap" key="ProjectExplorer.BuildStepList.Step.0">
-      <value type="QString" key="ProjectExplorer.ProjectConfiguration.DefaultDisplayName">qmake</value>
-      <value type="QString" key="ProjectExplorer.ProjectConfiguration.DisplayName"></value>
-      <value type="QString" key="ProjectExplorer.ProjectConfiguration.Id">QtProjectManager.QMakeBuildStep</value>
-      <value type="bool" key="QtProjectManager.QMakeBuildStep.LinkQmlDebuggingLibrary">false</value>
-      <value type="bool" key="QtProjectManager.QMakeBuildStep.LinkQmlDebuggingLibraryAuto">true</value>
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-  <variable>ProjectExplorer.Project.Updater.EnvironmentId</variable>
-  <value type="QString">{f8bb0047-7f6e-45df-9cc8-e746abebf883}</value>
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-  <variable>ProjectExplorer.Project.Updater.FileVersion</variable>
-  <value type="int">10</value>
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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

@@ -1,50 +1,61 @@
 
-# HEADERS
-set(HEADERS
-                                ContainerBox.h
-                                Dense.h
-                                Geometry.h
-                                Transform.h
-                                StructuredData.h
-                                StructuredGrid.h
-                                VoxImage.h
-                                VoxRaytracer.h
-                                Utils.h
-                                VoxImageFilter.h
-                                VoxImageFilter.hpp
-                                VoxImageFilterLinear.hpp
-                                VoxImageFilterMedian.hpp
-                                VoxImageFilterABTrim.hpp
-                                VoxImageFilterBilateral.hpp
-                                VoxImageFilterThreshold.hpp
-                                VoxImageFilter2ndStat.hpp
-                                VoxImageFilterCustom.hpp
-                                Accumulator.h
-                                TriangleMesh.h
-                                BitCode.h
-)
+set(HEADERS ContainerBox.h
+            Dense.h
+            Geometry.h
+            Transform.h
+            StructuredData.h
+            StructuredGrid.h
+            VoxImage.h
+            VoxRaytracer.h
+            Utils.h
+            VoxImageFilter.h
+            VoxImageFilter.hpp
+            VoxImageFilterLinear.hpp
+            VoxImageFilterMedian.hpp
+            VoxImageFilterABTrim.hpp
+            VoxImageFilterBilateral.hpp
+            VoxImageFilterThreshold.hpp
+            VoxImageFilter2ndStat.hpp
+            VoxImageFilterCustom.hpp
+            Accumulator.h
+            TriangleMesh.h
+            BitCode.h
+            Structured2DGrid.h
+            Structured4DGrid.h)
+
+set(SOURCES VoxRaytracer.cpp
+            StructuredData.cpp
+            StructuredGrid.cpp
+            VoxImage.cpp
+            TriangleMesh.cpp
+            Dense.cpp
+            Structured2DGrid.cpp
+            Structured4DGrid.cpp)
+
+set(LIBRARIES Eigen3::Eigen
+              ${ROOT_LIBRARIES}
+              ${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 ${PROJECT_SOVERSION})
+target_link_libraries(${libname} ${LIBRARIES})
 
 
-# SOURCES
-set(SOURCES
-                VoxRaytracer.cpp
-                StructuredData.cpp
-                StructuredGrid.cpp
-                VoxImage.cpp
-                TriangleMesh.cpp
-                Dense.cpp
-)
+install(TARGETS ${libname}
+        EXPORT "${PROJECT_NAME}Targets"
+        RUNTIME DESTINATION ${INSTALL_BIN_DIR} COMPONENT bin
+        LIBRARY DESTINATION ${INSTALL_LIB_DIR} COMPONENT lib)
 
-set(LIBRARIES
-       ${Boost_SERIALIZATION_LIBRARY}
-       ${Boost_SIGNALS_LIBRARY}
-       ${Boost_PROGRAM_OPTIONS_LIBRARY}
-       ${Eigen_LIBRARY}
-       ${ROOT_LIBRARIES}
-       ${PACKAGE_LIBPREFIX}Core
-       ${PACKAGE_LIBPREFIX}Math
-)
+install(FILES ${HEADERS} DESTINATION ${INSTALL_INC_DIR}/Math)
 
+if(BUILD_TESTING)
+  include(uLibTargetMacros)
+  add_subdirectory(testing)
+endif()
 
-uLib_add_shared_library(${uLib-module})
-add_subdirectory(testing)

src/Math/DataAllocator.h

@@ -0,0 +1,232 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// 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()
+      : m_Size(0), m_RamData(nullptr), m_VramData(nullptr),
+        m_Device(MemoryDevice::RAM) {}
+
+  DataAllocator(size_t size)
+      : m_Size(size), m_RamData(new T[size]()), m_VramData(nullptr),
+        m_Device(MemoryDevice::RAM) {}
+
+  DataAllocator(const DataAllocator<T> &other)
+      : m_Size(other.m_Size), m_RamData(nullptr), m_VramData(nullptr),
+        m_Device(other.m_Device) {
+    if (m_Size > 0) {
+      if (other.m_RamData) {
+        m_RamData = new T[m_Size];
+        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) {
+      delete[] m_RamData;
+    }
+#ifdef USE_CUDA
+    if (m_VramData) {
+      cudaFree(m_VramData);
+    }
+#endif
+  }
+
+  DataAllocator &operator=(const DataAllocator &other) {
+    if (this != &other) {
+      resize(other.m_Size);
+      m_Device = other.m_Device;
+      if (other.m_RamData) {
+        if (!m_RamData)
+          m_RamData = new T[m_Size];
+        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)
+      m_RamData = new T[m_Size]();
+#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) {
+      newRam = new T[size]();
+      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)
+      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;
+};
+
+} // namespace uLib
+
+#endif // U_MATH_DATAALLOCATOR_H

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
 
 ////////////////////////////////////////////////////////////////////////////////
 
@@ -87,194 +82,179 @@ void serialize(Archive & ar, ::Eigen::Matrix<Scalar, RowsAtCompileTime, ColsAtCo
 // this is needed by boost::lexical_cast to cope with Eigens Vectors ///////////
 namespace Eigen {
 template <typename T, int size>
-std::istream & operator >> (std::istream &is, Eigen::Matrix<T,size,1> &vec) {
-    std::string str;
-    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);
-    }
-    return is;
+std::istream &operator>>(std::istream &is, Eigen::Matrix<T, size, 1> &vec) {
+  std::string str;
+  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);
+  }
+  return is;
 }
 template <typename T, int size>
-std::ostream & operator << (std::ostream &os, const Eigen::Matrix<T,size,1> &vec) {
-    os << vec.transpose();
-    return os;
+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;
-typedef long          Scalarl;
+typedef int Scalari;
+typedef unsigned int Scalarui;
+typedef long Scalarl;
 typedef unsigned long Scalarul;
-typedef float         Scalarf;
-typedef double        Scalard;
+typedef float Scalarf;
+typedef double Scalard;
 
-
-
-typedef Eigen::Matrix<int,1,1> Matrix1i;
+typedef Eigen::Matrix<int, 1, 1> Matrix1i;
 typedef Eigen::Matrix2i Matrix2i;
 typedef Eigen::Matrix3i Matrix3i;
 typedef Eigen::Matrix4i Matrix4i;
 
-typedef Eigen::Matrix<float,1,1> Matrix1f;
+typedef Eigen::Matrix<float, 1, 1> Matrix1f;
 typedef Eigen::Matrix2f Matrix2f;
 typedef Eigen::Matrix3f Matrix3f;
 typedef Eigen::Matrix4f Matrix4f;
 
-typedef Eigen::Matrix<int,1,1> Vector1i;
+typedef Eigen::Matrix<int, 1, 1> Vector1i;
 typedef Eigen::Vector2i Vector2i;
 typedef Eigen::Vector3i Vector3i;
 typedef Eigen::Vector4i Vector4i;
 
-typedef Eigen::Matrix<float,1,1> Vector1f;
+typedef Eigen::Matrix<float, 1, 1> Vector1f;
 typedef Eigen::Vector2f Vector2f;
 typedef Eigen::Vector3f Vector3f;
 typedef Eigen::Vector4f Vector4f;
 
-
-
-
 ////////////////////////////////////////////////////////////////////////////////
 // Vector String interaction ///////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 
 /*! Given a string consisting of a series of doubles with some
-*  delimiter, return an Eigen::Vector populated with those
-*  values, in the same order as they are given in the string.
-*
-*  \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
-*
-*/
+ *  delimiter, return an Eigen::Vector populated with those
+ *  values, in the same order as they are given in the string.
+ *
+ *  \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
+ *
+ */
 template <typename T, int size>
-void VectorxT_StringTo(Eigen::Matrix<T,size,1> &vec, std::string str, const char *delim = " ,;\t\n") {
-    std::vector<std::string> strvec;
+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::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);
 
-    for( unsigned int i=0; i<size; i++) {
-        vec(i) = boost::lexical_cast<T>(strvec[i]);
-    }
+  for (unsigned int i = 0; i < size; i++) {
+    vec(i) = boost::lexical_cast<T>(strvec[i]);
+  }
 }
 
 template <typename T, int size>
-std::string VectorxT_ToString(const Eigen::Matrix<T,size,1> &vec) {
-    std::stringstream sst;
-    sst << vec.transpose();
-    return sst.str();
+std::string VectorxT_ToString(const Eigen::Matrix<T, size, 1> &vec) {
+  std::stringstream sst;
+  sst << vec.transpose();
+  return sst.str();
 }
 
-
-//template <typename T, int size>
-//Eigen::Matrix<T,size,1> & operator >> (std::istream &is, Eigen::Matrix<T,size,1> &vec) {
-//}
+// template <typename T, int size>
+// Eigen::Matrix<T,size,1> & operator >> (std::istream &is,
+// Eigen::Matrix<T,size,1> &vec) {
+// }
 
 template <typename T, int size>
-void operator>> (std::string& str, Eigen::Matrix<T,size,1> &vec){
-    VectorxT_StringTo(vec,str);
+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;
+  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) {}
+  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)
-    { }
-
-    // This method allows to assign Eigen expressions to Vector3H
-    template<typename OtherDerived>
-    inline _HPoint3f<p> & operator= (const Eigen::MatrixBase <OtherDerived>& other)
-    {
-        this->BaseClass::operator=(other);
-        return *this;
-    }
+  // This constructor allows to construct MyVectorType from Eigen expressions
+  template <typename OtherDerived>
+  inline _HPoint3f(const Eigen::MatrixBase<OtherDerived> &other)
+      : BaseClass(other) {}
 
+  // This method allows to assign Eigen expressions to Vector3H
+  template <typename OtherDerived>
+  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
-{
-    HPoint3f origin;
-    HVector3f direction;
+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() << "]) ";
-    return stream;
+inline std::ostream &operator<<(std::ostream &stream, const HLine3f &line) {
+  stream << "HLine3f(" << "pt[" << line.origin.transpose() << "] , dr["
+         << line.direction.transpose() << "]) ";
+  return stream;
 }
 
-
-
-
-struct _HError3f
-{
-    HVector3f position_error;
-    HVector3f direction_error;
+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() << "]) ";
-    return stream;
-}
-
-
+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
+#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 "Math/DataAllocator.h"
 
 namespace uLib {
 
@@ -46,26 +46,36 @@ namespace Abstract {
 
 class VoxImage : public uLib::StructuredGrid {
 public:
-    typedef uLib::StructuredGrid BaseClass;
+  typedef uLib::StructuredGrid BaseClass;
 
-    virtual float GetValue(const Vector3i &id) const = 0;
-    virtual float GetValue(const int id) const = 0;
-    virtual void SetValue(const Vector3i &id, float value) = 0;
-    virtual void SetValue(const int id, float value) = 0;
+  virtual float GetValue(const Vector3i &id) const = 0;
+  virtual float GetValue(const int id) const = 0;
+  virtual void SetValue(const Vector3i &id, float value) = 0;
+  virtual void SetValue(const int id, float value) = 0;
 
-    virtual void SetDims(const Vector3i &size) = 0;
+  virtual void SetDims(const Vector3i &size) = 0;
 
-    void ExportToVtk(const char *file, bool density_type = 0);
-    void ExportToVtkXml(const char *file, bool density_type = 0);
-    int ImportFromVtk(const char *file);
+  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, bool density_type = 0);
+
+  int ImportFromVti(const char *file, bool density_type = 0);
 
 protected:
-
-    virtual ~VoxImage() {}
-    VoxImage(const Vector3i &size) : BaseClass(size) {}
+  virtual ~VoxImage() {}
+  VoxImage(const Vector3i &size) : BaseClass(size) {}
 };
 
-}
+} // namespace Abstract
 
 ////////////////////////////////////////////////////////////////////////////////
 //  VOXEL   ////////////////////////////////////////////////////////////////////
@@ -73,421 +83,415 @@ protected:
 
 namespace Interface {
 struct Voxel {
-    template<class Self> void check_structural() {
-        uLibCheckMember(Self,Value, Scalarf);
-    }
+  template <class Self> void check_structural() {
+    uLibCheckMember(Self, Value, Scalarf);
+  }
 };
-}
+} // namespace Interface
 
 struct Voxel {
-    Scalarf      Value;
+  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;
+  typedef Abstract::VoxImage BaseClass;
 
-    VoxImage();
+  VoxImage();
 
-    VoxImage(const Vector3i &size);
+  VoxImage(const Vector3i &size);
 
-    VoxImage(const VoxImage<T> &copy) :
-        BaseClass(copy)
-    {
-        this->m_Data = copy.m_Data;
+  VoxImage(const VoxImage<T> &copy) : BaseClass(copy) {
+    this->m_Data = copy.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)); }
+  inline T &operator[](unsigned int i) { return m_Data[i]; }
+  inline T &operator[](const Vector3i &id) { return m_Data[Map(id)]; }
+
+  // this implements Abstract interface //
+  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 void SetValue(const Vector3i &id, Scalarf value) {
+    this->operator[](id).Value = value;
+  }
+  inline void SetValue(const int id, float value) {
+    this->operator[](id).Value = value;
+  }
+
+  inline void SetDims(const Vector3i &size) {
+    this->m_Data.resize(size.prod());
+    BaseClass::BaseClass::SetDims(size); // FIX horrible coding style !
+  }
+
+  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> 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 HPoint3f begin, const HPoint3f end) const;
+  inline VoxImage<T> Abs() const;
+
+  inline void SelectScalarfComponent(T &element, Scalarf *scalar);
+
+  inline void InitVoxels(T t);
+
+  // MATH OPERATORS //
+  inline void operator*=(Scalarf scalar) {
+    for (unsigned int i = 0; i < m_Data.size(); ++i)
+      m_Data[i].Value *= scalar;
+  }
+  inline void operator+=(Scalarf scalar) {
+    for (unsigned int i = 0; i < m_Data.size(); ++i)
+      m_Data[i].Value += scalar;
+  }
+  inline void operator/=(Scalarf scalar) {
+    for (unsigned int i = 0; i < m_Data.size(); ++i)
+      m_Data[i].Value /= scalar;
+  }
+  inline void operator-=(Scalarf scalar) {
+    for (unsigned int i = 0; i < m_Data.size(); ++i)
+      m_Data[i].Value -= scalar;
+  }
+
+  // MATH VoxImage Operators //
+  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;
+    } // WARNING! You must Warn the user!
+    for (unsigned int i = 0; i < m_Data.size(); ++i) {
+      m_Data[i].Value += sibling.At(i).Value;
     }
+  }
 
-    uLibRefMacro(Data,Vector<T>)
-    inline const Vector<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)); }
-    inline T& operator[](unsigned int i)     { return m_Data[i]; }
-    inline T& operator[](const Vector3i &id) { return m_Data[Map(id)]; }
-
-    // this implements Abstract interface //
-    inline Scalarf GetValue(const Vector3i &id) const {
-        return this->At(id).Value;
-    }
-    inline Scalarf GetValue(const int id) const {
-        return this->At(id).Value;
+  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;
+    } // WARNING! You must Warn the user!
+    for (unsigned int i = 0; i < m_Data.size(); ++i) {
+      m_Data[i].Value -= sibling.At(i).Value;
     }
+  }
 
-    inline void SetValue(const Vector3i &id, Scalarf value) {
-        this->operator [](id).Value = value;
-    }
-    inline void SetValue(const int id, float value) {
-        this->operator [](id).Value = value;
+  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;
+    } // WARNING! You must Warn the user!
+    for (unsigned int i = 0; i < m_Data.size(); ++i) {
+      m_Data[i].Value *= sibling.At(i).Value;
     }
+  }
 
-    inline void SetDims(const Vector3i &size) {
-        this->m_Data.resize(size.prod());
-        BaseClass::BaseClass::SetDims(size); // FIX horrible coding style !
-    }    
-
-    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> 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 HPoint3f begin, const HPoint3f end) const;
-    inline VoxImage<T> Abs() const;
-
-    inline void SelectScalarfComponent(T &element, Scalarf *scalar);
-
-    inline void InitVoxels(T t);
-
-    // MATH OPERATORS //
-    inline void operator *=(Scalarf scalar) {
-        for(unsigned int i = 0; i < m_Data.size(); ++i)
-            m_Data[i].Value *= scalar;
-    }
-    inline void operator +=(Scalarf scalar) {
-        for(unsigned int i = 0; i < m_Data.size(); ++i)
-            m_Data[i].Value += scalar;
-    }
-    inline void operator /=(Scalarf scalar) {
-        for(unsigned int i = 0; i < m_Data.size(); ++i)
-            m_Data[i].Value /= scalar;
-    }
-    inline void operator -=(Scalarf scalar) {
-        for(unsigned int i = 0; i < m_Data.size(); ++i)
-            m_Data[i].Value -= scalar;
-    }
-
-    // MATH VoxImage Operators //
-    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;
-        }// WARNING! You must Warn the user!
-        for(unsigned int i = 0; i < m_Data.size(); ++i) {
-            m_Data[i].Value += sibling.At(i).Value;
-        }
-    }
-
-    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;
-        }// WARNING! You must Warn the user!
-        for(unsigned int i = 0; i < m_Data.size(); ++i) {
-            m_Data[i].Value -= sibling.At(i).Value;
-        }
-    }
-
-    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;
-        }// WARNING! You must Warn the user!
-        for(unsigned int i = 0; i < m_Data.size(); ++i) {
-            m_Data[i].Value *= sibling.At(i).Value;
-        }
-    }
-
-    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;
-        }// WARNING! You must Warn the user!
-        for(unsigned int i = 0; i < m_Data.size(); ++i) {
-            m_Data[i].Value /= sibling.At(i).Value;
-        }
+  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;
+    } // WARNING! You must Warn the user!
+    for (unsigned int i = 0; i < m_Data.size(); ++i) {
+      m_Data[i].Value /= sibling.At(i).Value;
     }
+  }
 
 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(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
-{
-        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>()) );
-
-        for(uint x = 0; x<dim(0); ++x )
-            for(uint y = 0; y<dim(1); ++y )
-                for(uint z = 0; z<dim(2); ++z )
-                {
-                    Vector3i id = Vector3i(x,y,z);
-                    out[id] = this->At(begin + id);
-                }
-        return out;
+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<T>::clipImage(const HPoint3f begin, const HPoint3f end) const
-{
-    Vector3i v1 = this->Find(begin);
-    Vector3i v2 = this->Find(end);
-    return this->clipImage(v1,v2);
+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 float density) const
-{
-    Vector3i v1 = this->GetDims();
-    Vector3i v2 = Vector3i(0,0,0);
-    for(uint i=0; i< this->m_Data.size(); ++i) {
-        if( this->GetValue(i) >= density ) {
-            Vector3i id = this->UnMap(i);
-            v1 = v1.array().min(id.array());
-            v2 = v2.array().max(id.array());
-        }
+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>()));
+
+  for (uint x = 0; x < dim(0); ++x)
+    for (uint y = 0; y < dim(1); ++y)
+      for (uint z = 0; z < dim(2); ++z) {
+        Vector3i id = Vector3i(x, y, z);
+        out[id] = this->At(begin + id);
+      }
+  return out;
+}
+
+template <typename T>
+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 {
+  Vector3i v1 = this->GetDims();
+  Vector3i v2 = Vector3i(0, 0, 0);
+  for (uint i = 0; i < this->m_Data.size(); ++i) {
+    if (this->GetValue(i) >= density) {
+      Vector3i id = this->UnMap(i);
+      v1 = v1.array().min(id.array());
+      v2 = v2.array().max(id.array());
     }
-    return this->clipImage(v1,v2);
+  }
+  return this->clipImage(v1, v2);
 }
 
 template <typename T>
-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) {
-        if( this->GetValue(i) >= densityMin && this->GetValue(i) <= densityMax) {
-            Vector3i id = this->UnMap(i);
-            v1 = v1.array().min(id.array());
-            v2 = v2.array().max(id.array());
-        }
+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) {
+    if (this->GetValue(i) >= densityMin && this->GetValue(i) <= densityMax) {
+      Vector3i id = this->UnMap(i);
+      v1 = v1.array().min(id.array());
+      v2 = v2.array().max(id.array());
     }
-    return this->clipImage(v1,v2);
+  }
+  return this->clipImage(v1, v2);
 }
 
 template <typename T>
-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());
+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());
 
-    Vector3i voxB = this->Find(begin);
-    Vector3i voxE = this->Find(end);
+  Vector3i voxB = this->Find(begin);
+  Vector3i voxE = this->Find(end);
 
-    Vector3i ID;
+  Vector3i ID;
 
-    for(int ix=voxB(0); ix<voxE(0); ix++)
-        for(int iy=voxB(1); iy<voxE(1); iy++)
-            for(int iz=voxB(2); iz<voxE(2); iz++){
-                ID << ix,iy,iz;
-                out.SetValue(ID,value*1.E-6);
-            }
+  for (int ix = voxB(0); ix < voxE(0); ix++)
+    for (int iy = voxB(1); iy < voxE(1); iy++)
+      for (int iz = voxB(2); iz < voxE(2); iz++) {
+        ID << ix, iy, iz;
+        out.SetValue(ID, value * 1.E-6);
+      }
 
-    return out;
+  return out;
 }
 
 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;
-    if(belowValue)
-        std::cout << " at value " << belowValue;
-    else
-        std::cout << " at -value";
-    std::cout << ", voxels above threshold at value ";
-    if(aboveValue)
-        std::cout << aboveValue;
-    else
-        std::cout << "found";
+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
+    std::cout << " at -value";
+  std::cout << ", voxels above threshold at value ";
+  if (aboveValue)
+    std::cout << aboveValue;
+  else
+    std::cout << "found";
 
+  VoxImage<T> out(*this);
+  out.SetDims(this->GetDims());
+  out.SetPosition(this->GetPosition());
 
-    VoxImage<T> out(*this);
-    out.SetDims(this->GetDims());
-    out.SetPosition(this->GetPosition());
-
-    for(uint i=0; i< this->m_Data.size(); ++i) {
-        // skip negative voxels: they are already frozen
-        if( this->GetValue(i) >= 0 ){
-            // 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
-                    out.SetValue(i,-1.*this->GetValue(i));
-            }
-            // voxels over threshold
-            else{
-                if(aboveValue)
-                    out.SetValue(i,aboveValue*1.E-6);
-                else
-                    out.SetValue(i,this->GetValue(i));
-            }
-        }
+  for (uint i = 0; i < this->m_Data.size(); ++i) {
+    // skip negative voxels: they are already frozen
+    if (this->GetValue(i) >= 0) {
+      // 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
+          out.SetValue(i, -1. * this->GetValue(i));
+      }
+      // voxels over threshold
+      else {
+        if (aboveValue)
+          out.SetValue(i, aboveValue * 1.E-6);
+        else
+          out.SetValue(i, this->GetValue(i));
+      }
     }
-    return out;
+  }
+  return out;
 }
 
 template <typename T>
-VoxImage<T> VoxImage<T>::fixVoxels(const float threshold, float tolerance) const
-{
-    std::cout << "VoxImage: fixing voxels with value " << threshold << std::endl;
+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);
-    out.SetDims(this->GetDims());
-    out.SetPosition(this->GetPosition());
+  VoxImage<T> out(*this);
+  out.SetDims(this->GetDims());
+  out.SetPosition(this->GetPosition());
 
-    for(uint i=0; i< this->m_Data.size(); ++i) {
+  for (uint i = 0; i < this->m_Data.size(); ++i) {
+    // 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;
+      out.SetValue(i, -1. * this->GetValue(i));
+    }
+  }
+  return out;
+}
+
+template <typename T> VoxImage<T> VoxImage<T>::Abs() const {
+  std::cout << "VoxImage: set abs voxels value " << std::endl;
+
+  VoxImage<T> out(*this);
+  out.SetDims(this->GetDims());
+  out.SetPosition(this->GetPosition());
+
+  for (uint i = 0; i < this->m_Data.size(); ++i)
+    out.SetValue(i, fabs(this->GetValue(i)));
+
+  return out;
+}
+
+template <typename T>
+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());
+
+  Vector3i voxB = this->Find(begin);
+  Vector3i voxE = this->Find(end);
+
+  Vector3i ID;
+
+  for (int ix = voxB(0); ix < voxE(0); ix++)
+    for (int iy = voxB(1); iy < voxE(1); iy++)
+      for (int iz = voxB(2); iz < voxE(2); iz++) {
+        ID << ix, iy, iz;
         // 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;
-                out.SetValue(i,-1.*this->GetValue(i));
+        if (fabs(this->GetValue(ID) - threshold * 1.E-6) < tolerance * 1.E-6) {
+          out.SetValue(ID, -1. * this->GetValue(ID));
         }
-    }
-    return out;
+      }
+
+  return out;
 }
 
 template <typename T>
-VoxImage<T> VoxImage<T>::Abs() const
-{
-    std::cout << "VoxImage: set abs voxels value " << std::endl;
+VoxImage<T> VoxImage<T>::fixVoxels(const HPoint3f begin,
+                                   const HPoint3f end) const {
+  VoxImage<T> out(*this);
+  out.SetDims(this->GetDims());
+  out.SetPosition(this->GetPosition());
 
-    VoxImage<T> out(*this);
-    out.SetDims(this->GetDims());
-    out.SetPosition(this->GetPosition());
+  Vector3i voxB = this->Find(begin);
+  Vector3i voxE = this->Find(end);
 
-    for(uint i=0; i< this->m_Data.size(); ++i)
-        out.SetValue(i,fabs(this->GetValue(i)));
+  Vector3i ID;
 
-    return out;
+  for (int ix = voxB(0); ix < voxE(0); ix++)
+    for (int iy = voxB(1); iy < voxE(1); iy++)
+      for (int iz = voxB(2); iz < voxE(2); iz++) {
+        ID << ix, iy, iz;
+        // voxels around threshold
+        out.SetValue(ID, -1. * this->GetValue(ID));
+      }
+  return out;
 }
 
 template <typename T>
-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());
+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);
+  out.SetPosition(this->GetPosition());
 
-    Vector3i voxB = this->Find(begin);
-    Vector3i voxE = this->Find(end);
+  HPoint3f Bcoll = this->GetPosition().homogeneous();
 
-    Vector3i ID;
+  Vector3i ID;
+  for (int ix = 0; ix < dim(0); ix++)
+    for (int iy = 0; iy < dim(1); iy++)
+      for (int iz = 0; iz < dim(2); iz++) {
+        ID << ix, iy, iz;
 
-    for(int ix=voxB(0); ix<voxE(0); ix++)
-        for(int iy=voxB(1); iy<voxE(1); iy++)
-            for(int iz=voxB(2); iz<voxE(2); iz++){
-                ID << ix,iy,iz;
-                // voxels around threshold
-                if( fabs(this->GetValue(ID) - threshold*1.E-6) < tolerance*1.E-6 ){
-                    out.SetValue(ID,-1.*this->GetValue(ID));
-                }
-            }
+        // B, E voxel position
+        Vector3i iv(ix, iy, iz);
+        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());
 
-    return out;
+        // 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 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;
+          out.SetValue(ID, threshold * 1.E-6);
+        } else
+          out.SetValue(ID, this->GetValue(ID));
+
+        if ((distSign > 0 && aboveAir) || (distSign < 0 && !aboveAir))
+          out.SetValue(ID, threshold * 1.E-6);
+      }
+  return out;
 }
 
-template <typename T>
-VoxImage<T> VoxImage<T>::fixVoxels(const HPoint3f begin, const HPoint3f end) const
-{
-    VoxImage<T> out(*this);
-    out.SetDims(this->GetDims());
-    out.SetPosition(this->GetPosition());
-
-    Vector3i voxB = this->Find(begin);
-    Vector3i voxE = this->Find(end);
-
-    Vector3i ID;
-
-    for(int ix=voxB(0); ix<voxE(0); ix++)
-        for(int iy=voxB(1); iy<voxE(1); iy++)
-            for(int iz=voxB(2); iz<voxE(2); iz++){
-                ID << ix,iy,iz;
-                // voxels around threshold
-                out.SetValue(ID,-1.*this->GetValue(ID));
-            }
-    return out;
+template <typename T> void VoxImage<T>::InitVoxels(T t) {
+  std::fill(m_Data.begin(), m_Data.end(), t); // warning... stl function //
 }
 
-
-template <typename T>
-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);
-    out.SetPosition(this->GetPosition());
-
-    HPoint3f  Bcoll = this->GetPosition().homogeneous();
-
-    Vector3i ID;
-    for(int ix=0; ix<dim(0); ix++)
-        for(int iy=0; iy<dim(1); iy++)
-            for(int iz=0; iz<dim(2); iz++){
-                ID << ix,iy,iz;
-
-                // B, E voxel position
-                Vector3i iv(ix,iy,iz);
-                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
-                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 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;
-                    out.SetValue(ID,threshold*1.E-6);
-                }
-                else
-                    out.SetValue(ID,this->GetValue(ID));
-
-                if((distSign>0 && aboveAir) || (distSign<0 && !aboveAir)  )
-                    out.SetValue(ID,threshold*1.E-6);
-            }
-    return out;
-}
-
-
-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

@@ -23,107 +23,91 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
 #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() {
-        uLibCheckFunction(Self,operator(),float,float);
-        uLibCheckFunction(Self,operator(),float,const Vector3f&);
-    }
+  template <class Self> void check_structural() {
+    uLibCheckFunction(Self, operator(), float, float);
+    uLibCheckFunction(Self, operator(), float, const Vector3f &);
+  }
 };
-}
-
-template < typename VoxelT > class Kernel;
+} // namespace Interface
 
+template <typename VoxelT> class Kernel;
 
 namespace Abstract {
 class VoxImageFilter {
 public:
-    virtual void Run() = 0;
+  virtual void Run() = 0;
 
-    virtual void SetImage(Abstract::VoxImage *image) = 0;
+  virtual void SetImage(Abstract::VoxImage *image) = 0;
 
 protected:
-    virtual ~VoxImageFilter() {}
+  virtual ~VoxImageFilter() {}
 };
-}
+} // namespace Abstract
 
-
-template < typename VoxelT, typename AlgorithmT >
-class VoxImageFilter : public Abstract::VoxImageFilter, public Object
-{   
+template <typename VoxelT, typename AlgorithmT>
+class VoxImageFilter : public Abstract::VoxImageFilter {
 
 public:
-    VoxImageFilter(const Vector3i &size);
+  VoxImageFilter(const Vector3i &size);
 
-    void Run();
+  void Run();
 
-    void SetKernelNumericXZY(const Vector<float> &numeric);
+  void SetKernelNumericXZY(const std::vector<float> &numeric);
 
-    void SetKernelSpherical(float (*shape)(float));
+  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 &));
+  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);
+  void SetImage(Abstract::VoxImage *image);
 
 protected:
+  float Convolve(const VoxImage<VoxelT> &buffer, int index); // remove //
 
-    float Convolve(const VoxImage<VoxelT> &buffer, int index); // remove //
+  void SetKernelOffset();
 
-    void SetKernelOffset();
+  float Distance2(const Vector3i &v);
 
-    float Distance2(const Vector3i &v);
-
-    // protected members for algorithm access //
-    Kernel<VoxelT>    m_KernelData;
-    VoxImage<VoxelT> *m_Image;
+  // protected members for algorithm access //
+  Kernel<VoxelT> m_KernelData;
+  VoxImage<VoxelT> *m_Image;
 
 private:
-    AlgorithmT       *t_Algoritm;
-
+  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

@@ -23,280 +23,238 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
 #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 {
-    typedef StructuredData BaseClass;
+template <typename T> class Kernel : public StructuredData {
+  typedef StructuredData BaseClass;
+
 public:
-    Kernel(const Vector3i &size);
+  Kernel(const Vector3i &size);
 
-    inline T& operator[](const Vector3i &id) { return m_Data[Map(id)]; }
-    inline T& operator[](const int &id) { return m_Data[id]; }
-    inline int GetCenterData() const;
+  inline T &operator[](const Vector3i &id) { return m_Data[Map(id)]; }
+  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;
+  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())
-{
-    Interface::IsA<T,Interface::Voxel>();
+template <typename T>
+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
-{
-    static int center = Map(this->GetDims() / 2);
-    return center;
+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
-{
-    o << " Filter Kernel Dump [XZ_Y]: \n";
-    Vector3i index;
-    o << "\n Value: \n\n"
-      << "------------------------------------------------- \n";
-    for (int y = 0 ; y < this->GetDims()(1); ++y ) {
-        o << "[y=" << y << "]\n";
-        for (int z = 0 ; z < this->GetDims()(2); ++z ) {
-            for (int x = 0 ; x < this->GetDims()(0); ++x ) {
-                index << x,y,z;
-                o << m_Data[Map(index)].Value << " ";
-            } o << "\n";
-        } o << " --------------------------------------------------- \n";
+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"
+    << "------------------------------------------------- \n";
+  for (int y = 0; y < this->GetDims()(1); ++y) {
+    o << "[y=" << y << "]\n";
+    for (int z = 0; z < this->GetDims()(2); ++z) {
+      for (int x = 0; x < this->GetDims()(0); ++x) {
+        index << x, y, z;
+        o << m_Data[Map(index)].Value << " ";
+      }
+      o << "\n";
     }
-    o << "\n Offset: \n"
-      << "------------------------------------------------- \n";
-    for (int y = 0 ; y < this->GetDims()(1); ++y ) {
-        o << "[y=" << y << "]\n";
-        for (int z = 0 ; z < this->GetDims()(2); ++z ) {
-            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 Offset: \n"
+    << "------------------------------------------------- \n";
+  for (int y = 0; y < this->GetDims()(1); ++y) {
+    o << "[y=" << y << "]\n";
+    for (int z = 0; z < this->GetDims()(2); ++z) {
+      for (int x = 0; x < this->GetDims()(0); ++x) {
+        index << x, y, z;
+        o << m_Data[Map(index)].Count << " ";
+      }
+      o << "\n";
     }
+    o << " --------------------------------------------------- \n";
+  }
 }
 
 ////////////////////////////////////////////////////////////////////////////////
 
-
-
-
-
-
-
-
-#define _TPL_  template < typename VoxelT , typename AlgorithmT >
-#define _TPLT_ VoxelT,AlgorithmT
-
-
+#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))
-{
+VoxImageFilter<_TPLT_>::VoxImageFilter(const Vector3i &size)
+    : m_KernelData(size), t_Algoritm(static_cast<AlgorithmT *>(this)) {}
 
+_TPL_
+void VoxImageFilter<_TPLT_>::Run() {
+  VoxImage<VoxelT> buffer = *m_Image;
+#pragma omp parallel for
+  for (int i = 0; i < m_Image->Data().size(); ++i)
+    m_Image->operator[](i).Value = this->t_Algoritm->Evaluate(buffer, i);
+#pragma omp barrier
 }
 
 _TPL_
-void VoxImageFilter<_TPLT_>::Run()
-{
-    VoxImage<VoxelT> buffer = *m_Image;
-    #pragma omp parallel for
-    for(int i=0 ; i < m_Image->Data().size() ; ++i)
-        m_Image->operator [](i).Value = this->t_Algoritm->Evaluate(buffer,i);
-    #pragma omp barrier
-}
-
-_TPL_
-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 ) {
-            for( int y=0 ; y < m_KernelData.GetDims()(1); ++y ) {
-                id << x,y,z;
-                m_KernelData[id].Count = id.transpose() * m_Image->GetIncrements();
-            }
-        }
+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) {
+      for (int y = 0; y < m_KernelData.GetDims()(1); ++y) {
+        id << x, y, z;
+        m_KernelData[id].Count = id.transpose() * m_Image->GetIncrements();
+      }
     }
+  }
 }
 
 _TPL_
-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)));
+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)));
 }
 
-
 _TPL_
-void VoxImageFilter<_TPLT_>::SetKernelNumericXZY(const Vector<float> &numeric)
-{
-    // set data order //
-    StructuredData::Order order = m_KernelData.GetDataOrder();
-    //m_KernelData.SetDataOrder(StructuredData::XZY);
-    Vector3i id;
-    int index = 0;
-    for( int y=0 ; y < m_KernelData.GetDims()(1); ++y ) {
-        for( int z=0 ; z < m_KernelData.GetDims()(2); ++z ) {
-            for( int x=0 ; x < m_KernelData.GetDims()(0); ++x ) {
-                id << x,y,z;
-                m_KernelData[id].Value = numeric[index++];
-            }
-        }
+void VoxImageFilter<_TPLT_>::SetKernelNumericXZY(
+    const std::vector<float> &numeric) {
+  // set data order //
+  StructuredData::Order order = m_KernelData.GetDataOrder();
+  // m_KernelData.SetDataOrder(StructuredData::XZY);
+  Vector3i id;
+  int index = 0;
+  for (int y = 0; y < m_KernelData.GetDims()(1); ++y) {
+    for (int z = 0; z < m_KernelData.GetDims()(2); ++z) {
+      for (int x = 0; x < m_KernelData.GetDims()(0); ++x) {
+        id << x, y, z;
+        m_KernelData[id].Value = numeric[index++];
+      }
     }
-    //m_KernelData.SetDataOrder(order);
+  }
+  // m_KernelData.SetDataOrder(order);
 }
 
 _TPL_
-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 ) {
-            for( int x=0 ; x < m_KernelData.GetDims()(0); ++x ) {
-                id << x,y,z;
-                m_KernelData[id].Value = shape(this->Distance2(id));
-            }
-        }
+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) {
+      for (int x = 0; x < m_KernelData.GetDims()(0); ++x) {
+        id << x, y, z;
+        m_KernelData[id].Value = shape(this->Distance2(id));
+      }
     }
+  }
 }
 
-
 _TPL_ template <class ShapeT>
-void VoxImageFilter<_TPLT_>::SetKernelSpherical(ShapeT shape)
-{
-    Interface::IsA<ShapeT,Interface::VoxImageFilterShape>();
-    Vector3i id;
-    for( int y=0 ; y < m_KernelData.GetDims()(1); ++y ) {
-        for( int z=0 ; z < m_KernelData.GetDims()(2); ++z ) {
-            for( int x=0 ; x < m_KernelData.GetDims()(0); ++x ) {
-                id << x,y,z;
-                m_KernelData[id].Value = shape(this->Distance2(id));
-            }
-        }
+void VoxImageFilter<_TPLT_>::SetKernelSpherical(ShapeT shape) {
+  Interface::IsA<ShapeT, Interface::VoxImageFilterShape>();
+  Vector3i id;
+  for (int y = 0; y < m_KernelData.GetDims()(1); ++y) {
+    for (int z = 0; z < m_KernelData.GetDims()(2); ++z) {
+      for (int x = 0; x < m_KernelData.GetDims()(0); ++x) {
+        id << x, y, z;
+        m_KernelData[id].Value = shape(this->Distance2(id));
+      }
     }
+  }
 }
 
 _TPL_
-void VoxImageFilter<_TPLT_>::SetKernelWeightFunction(float (*shape)(const Vector3f &))
-{
-    const Vector3i &dim = m_KernelData.GetDims();
-    Vector3i id;
-    Vector3f pt;
-    for( int y=0 ; y < dim(1); ++y ) {
-        for( int z=0 ; z < dim(2); ++z ) {
-            for( int x=0 ; x < dim(0); ++x ) {
-                // get voxels centroid coords from kernel center //
-                id << x,y,z;
-                pt << id(0) - dim(0)/2 + 0.5 * !(dim(0) % 2),
-                      id(1) - dim(1)/2 + 0.5 * !(dim(1) % 2),
-                      id(2) - dim(2)/2 + 0.5 * !(dim(2) % 2);
-                // compute function using given shape //
-                m_KernelData[id].Value = shape(pt);
-            }
-        }
+void VoxImageFilter<_TPLT_>::SetKernelWeightFunction(
+    float (*shape)(const Vector3f &)) {
+  const Vector3i &dim = m_KernelData.GetDims();
+  Vector3i id;
+  Vector3f pt;
+  for (int y = 0; y < dim(1); ++y) {
+    for (int z = 0; z < dim(2); ++z) {
+      for (int x = 0; x < dim(0); ++x) {
+        // get voxels centroid coords from kernel center //
+        id << x, y, z;
+        pt << id(0) - dim(0) / 2 + 0.5 * !(dim(0) % 2),
+            id(1) - dim(1) / 2 + 0.5 * !(dim(1) % 2),
+            id(2) - dim(2) / 2 + 0.5 * !(dim(2) % 2);
+        // compute function using given shape //
+        m_KernelData[id].Value = shape(pt);
+      }
     }
+  }
 }
 
-_TPL_ template < class ShapeT >
-void VoxImageFilter<_TPLT_>::SetKernelWeightFunction(ShapeT shape)
-{
-    Interface::IsA<ShapeT,Interface::VoxImageFilterShape>();
-    const Vector3i &dim = m_KernelData.GetDims();
-    Vector3i id;
-    Vector3f pt;
-    for( int y=0 ; y < dim(1); ++y ) {
-        for( int z=0 ; z < dim(2); ++z ) {
-            for( int x=0 ; x < dim(0); ++x ) {
-                // get voxels centroid coords from kernel center //
-                id << x,y,z;
-                pt << id(0) - dim(0)/2 + 0.5 * !(dim(0) % 2),
-                      id(1) - dim(1)/2 + 0.5 * !(dim(1) % 2),
-                      id(2) - dim(2)/2 + 0.5 * !(dim(2) % 2);
-                // compute function using given shape //
-                m_KernelData[id].Value = shape(pt);
-            }
-        }
+_TPL_ template <class ShapeT>
+void VoxImageFilter<_TPLT_>::SetKernelWeightFunction(ShapeT shape) {
+  Interface::IsA<ShapeT, Interface::VoxImageFilterShape>();
+  const Vector3i &dim = m_KernelData.GetDims();
+  Vector3i id;
+  Vector3f pt;
+  for (int y = 0; y < dim(1); ++y) {
+    for (int z = 0; z < dim(2); ++z) {
+      for (int x = 0; x < dim(0); ++x) {
+        // get voxels centroid coords from kernel center //
+        id << x, y, z;
+        pt << id(0) - dim(0) / 2 + 0.5 * !(dim(0) % 2),
+            id(1) - dim(1) / 2 + 0.5 * !(dim(1) % 2),
+            id(2) - dim(2) / 2 + 0.5 * !(dim(2) % 2);
+        // compute function using given shape //
+        m_KernelData[id].Value = shape(pt);
+      }
     }
+  }
 }
 
-
-
-
 _TPL_
-void VoxImageFilter<_TPLT_>::SetImage(Abstract::VoxImage *image)
-{
-    this->m_Image = reinterpret_cast<VoxImage<VoxelT> *> (image);
-    this->SetKernelOffset();
+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();
-    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[m_KernelData.GetCenterData()].Count;
-        pos = (pos + vox_size) % vox_size;
-        conv += vbuf[pos].Value * vker[ik].Value;
-        ksum += vker[ik].Value;
-    }
-    return conv / ksum;
+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;
+  float conv = 0, ksum = 0;
+  for (int ik = 0; ik < ker_size; ++ik) {
+    pos = index + vker[ik].Count - vker[m_KernelData.GetCenterData()].Count;
+    pos = (pos + vox_size) % vox_size;
+    conv += vbuf[pos].Value * vker[ik].Value;
+    ksum += vker[ik].Value;
+  }
+  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  /////////////////////////////////////////////////
@@ -39,45 +37,42 @@
 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)
-    { }
+  typedef VoxImageFilter<VoxelT, VoxFilterAlgorithm2ndStat<VoxelT>> BaseClass;
+  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();
-        int vox_size = vbuf.size();
-        int ker_size = vker.size();
-        int pos;
+  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;
 
-        // 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 = (pos + vox_size) % vox_size;
-            conv += vbuf[pos].Value * vker[ik].Value;
-            ksum += vker[ik].Value;
-        }
-        float mean = conv / ksum;
-
-        // rms //
-        conv = 0;
-        for (int ik = 0; ik < ker_size; ++ik) {
-            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) ;
+    // 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 = (pos + vox_size) % vox_size;
+      conv += vbuf[pos].Value * vker[ik].Value;
+      ksum += vker[ik].Value;
     }
+    float mean = conv / ksum;
 
-
+    // rms //
+    conv = 0;
+    for (int ik = 0; ik < ker_size; ++ik) {
+      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  /////////////////////////////////////////////////
@@ -38,142 +36,257 @@
 
 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)
-    {
-        mAtrim = 0;
-        mBtrim = 0;
+  typedef VoxImageFilter<VoxelT, VoxFilterAlgorithmAbtrim<VoxelT>> BaseClass;
+  VoxFilterAlgorithmAbtrim(const Vector3i &size) : BaseClass(size) {
+    mAtrim = 0;
+    mBtrim = 0;
+  }
+
+#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;
+
+    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 = (pos + vox_size) % vox_size;
+      mfh[ik].Value = vbuf[pos].Value;
     }
 
-    float Evaluate(const VoxImage<VoxelT> &buffer, int index)
-    {
-        const Vector<VoxelT> &vbuf = buffer.ConstData();
-        const Vector<VoxelT> &vker = this->m_KernelData.ConstData();
-        int vox_size = vbuf.size();
-        int ker_size = vker.size();
-        int pos;
-
-        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 = (pos + vox_size) % vox_size;
-            mfh[ik].Value = vbuf[pos].Value;
-        }
-
-        std::sort(mfh.begin(), mfh.end(), KernelSortAscending());
-        float ker_sum = 0;
-        float fconv = 0;
-        for (int ik = 0; ik < mAtrim; ik++)
-            ker_sum += vker[ mfh[ik].Count ].Value;
-        for (int ik = mAtrim; ik < ker_size - mBtrim; ik++) {
-            fconv += mfh[ik].Value * vker[ mfh[ik].Count ].Value; // convloution //
-            ker_sum += vker[ mfh[ik].Count ].Value;
-        }
-        for (int ik = ker_size - mBtrim; ik < ker_size; ik++)
-            ker_sum += vker[ mfh[ik].Count ].Value;
-
-        return fconv / ker_sum;
+    std::sort(mfh.begin(), mfh.end(), KernelSortAscending());
+    float ker_sum = 0;
+    float fconv = 0;
+    for (int ik = 0; ik < mAtrim; ik++)
+      ker_sum += vker[mfh[ik].Count].Value;
+    for (int ik = mAtrim; ik < ker_size - mBtrim; ik++) {
+      fconv += mfh[ik].Value * vker[mfh[ik].Count].Value; // convloution //
+      ker_sum += vker[mfh[ik].Count].Value;
     }
+    for (int ik = ker_size - mBtrim; ik < ker_size; ik++)
+      ker_sum += vker[mfh[ik].Count].Value;
 
-    inline void SetABTrim(int a, int b) { mAtrim = a; mBtrim = b; }
+    return fconv / ker_sum;
+  }
+
+  inline void SetABTrim(int a, int b) {
+    mAtrim = a;
+    mBtrim = b;
+  }
 
 private:
-    int mAtrim;
-    int mBtrim;
+  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)
-    {
-        mAtrim = 0;
-        mBtrim = 0;
+  typedef VoxImageFilter<VoxelT, VoxFilterAlgorithmSPR<VoxelT>> BaseClass;
+  VoxFilterAlgorithmSPR(const Vector3i &size) : BaseClass(size) {
+    mAtrim = 0;
+    mBtrim = 0;
+  }
+
+#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;
+
+    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 = (pos + vox_size) % vox_size;
+      mfh[ik].Value = vbuf[pos].Value;
     }
 
-    float Evaluate(const VoxImage<VoxelT> &buffer, int index)
-    {
-        const Vector<VoxelT> &vbuf = buffer.ConstData();
-        const Vector<VoxelT> &vker = this->m_KernelData.ConstData();
-        int vox_size = vbuf.size();
-        int ker_size = vker.size();
-        int pos;
+    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)) {
+      float ker_sum = 0;
+      float fconv = 0;
+      for (int ik = 0; ik < mAtrim; ik++)
+        ker_sum += vker[mfh[ik].Count].Value;
+      for (int ik = mAtrim; ik < ker_size - mBtrim; ik++) {
+        fconv += mfh[ik].Value * vker[mfh[ik].Count].Value;
+        ker_sum += vker[mfh[ik].Count].Value;
+      }
+      for (int ik = ker_size - mBtrim; ik < ker_size; ik++)
+        ker_sum += vker[mfh[ik].Count].Value;
 
-        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 = (pos + vox_size) % vox_size;
-            mfh[ik].Value = vbuf[pos].Value;
-        }
+      return fconv / ker_sum;
+    } else
+      return spr;
+  }
 
-        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) )
-        {
-            float ker_sum = 0;
-            float fconv = 0;
-            for (int ik = 0; ik < mAtrim; ik++)
-                ker_sum += vker[ mfh[ik].Count ].Value;
-            for (int ik = mAtrim; ik < ker_size - mBtrim; ik++) {
-                fconv += mfh[ik].Value * vker[ mfh[ik].Count ].Value;
-                ker_sum += vker[ mfh[ik].Count ].Value;
-            }
-            for (int ik = ker_size - mBtrim; ik < ker_size; ik++)
-                ker_sum += vker[ mfh[ik].Count ].Value;
-
-            return fconv / ker_sum;
-        }
-        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;
+  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  /////////////////////////////////////////////////
@@ -38,115 +36,119 @@
 
 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;
-    }
+  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();
-        int vox_size = vbuf.size();
-        int ker_size = vker.size();
-        int pos;
-        float conv = 0, ksum = 0;
-        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 = (pos + vox_size) % vox_size;
-            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;
-        }
-        return conv / ksum;
+  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;
+    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 = (pos + vox_size) % vox_size;
+      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;
     }
+    return conv / ksum;
+  }
 
-    inline void SetIntensitySigma(const float s) { m_sigma = s; }
+  inline void SetIntensitySigma(const float s) { m_sigma = s; }
 
 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));
-    }
+  inline float compute_gauss(const float x) {
+    return 1 / (sqrt(2 * M_PI) * m_sigma) *
+           exp(-0.5 * (x * x) / (m_sigma * m_sigma));
+  }
 
-    Scalarf 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;
+  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;
-    VoxFilterAlgorithmBilateralTrim(const Vector3i &size) : BaseClass(size) {
-        m_sigma = 1;
-        mAtrim = 0;
-        mBtrim = 0;
+  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 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;
+
+    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 = (pos + img_size) % img_size;
+      mfh[ik].second = vbuf[pos].Value; // image value in second
     }
+    std::sort(mfh.begin(), mfh.end(), KernelSortAscending());
 
-    float Evaluate(const VoxImage<VoxelT> &buffer, int index)
-    {
-        const Vector<VoxelT> &vbuf = buffer.ConstData();
-        const Vector<VoxelT> &vker = this->m_KernelData.ConstData();
-        int img_size = vbuf.size();
-        int ker_size = vker.size();
-        int pos;
-
-
-
-        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 = (pos + img_size) % img_size;
-            mfh[ik].second = vbuf[pos].Value; // image value in second
-        }
-        std::sort(mfh.begin(), mfh.end(), KernelSortAscending());
-
-        float conv = 0, ksum = 0;
-        float gamma_smooth;
-        //        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 );
-            conv += mfh[ik].first * mfh[ik].second * gamma_smooth;
-            ksum += mfh[ik].first * gamma_smooth;
-        }
-        //        for (int ik = ker_size - mBtrim; ik < ker_size; ik++)
-        //            ksum += mfh[ik].first;
-
-        return conv / ksum;
+    float conv = 0, ksum = 0;
+    float gamma_smooth;
+    //        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);
+      conv += mfh[ik].first * mfh[ik].second * gamma_smooth;
+      ksum += mfh[ik].first * gamma_smooth;
     }
+    //        for (int ik = ker_size - mBtrim; ik < ker_size; ik++)
+    //            ksum += mfh[ik].first;
 
-    inline void SetIntensitySigma(const float s) { m_sigma = s; }
-    inline void SetABTrim(int a, int b) { mAtrim = a; mBtrim = b; }
+    return conv / ksum;
+  }
+
+  inline void SetIntensitySigma(const float s) { m_sigma = s; }
+  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));
-    }
+  inline float compute_gauss(const float x) {
+    return 1 / (sqrt(2 * M_PI) * m_sigma) *
+           exp(-0.5 * (x * x) / (m_sigma * m_sigma));
+  }
 
-    Scalarf m_sigma;
-    int mAtrim;
-    int mBtrim;
+  Scalarf m_sigma;
+  int mAtrim;
+  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)
-    {}
+  typedef VoxImageFilter<VoxelT, VoxFilterAlgorithmCustom<VoxelT>> BaseClass;
+  VoxFilterAlgorithmCustom(const Vector3i &size)
+      : BaseClass(size), m_CustomEvaluate(NULL) {}
 
-    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();
-            int vox_size = vbuf.size();
-            int ker_size = vker.size();
-            int pos;
+  float Evaluate(const VoxImage<VoxelT> &buffer, int index) {
+    if (likely(m_CustomEvaluate)) {
+      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);
-            for (int ik = 0; ik < ker_size; ik++) {
-                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";
+      float ker_sum = 0;
+      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 = (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;
     }
+  }
 
-    uLibSetMacro(CustomEvaluate,FunctionPt)
+  inline void SetCustomEvaluate(FunctionPt funPt) {
+    this->m_CustomEvaluate = funPt;
+  }
 
 private:
-    FunctionPt m_CustomEvaluate;
+  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  /////////////////////////////////////////////////
@@ -38,32 +36,86 @@
 
 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) {}
+  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();
-        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 = (pos + vox_size) % vox_size;
-            conv += vbuf[pos].Value * vker[ik].Value;
-            ksum += vker[ik].Value;
-        }
-        return conv / ksum;
+#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 = (pos + vox_size) % vox_size;
+      conv += vbuf[pos].Value * vker[ik].Value;
+      ksum += vker[ik].Value;
+    }
+    return conv / ksum;
+  }
 };
 
-}
+} // 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  /////////////////////////////////////////////////
@@ -39,37 +37,38 @@
 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) {}
+  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();
-        int vox_size = vbuf.size();
-        int ker_size = vker.size();
-        int pos;
+  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);
-        for (int ik = 0; ik < ker_size; ik++) {
-            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;
-        }
-        std::sort(mfh.begin(), mfh.end());
-        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++;
-        // median //
-        pos += (ker_size - pos) / 2;
-        return mfh[pos];
+    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 = (pos + vox_size) % vox_size;
+      mfh[ik] = vbuf[pos].Value * vker[ik].Value;
     }
+    std::sort(mfh.begin(), mfh.end());
+    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++;
+    // 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); }
 
@@ -37,215 +38,206 @@ namespace uLib {
 ///// RAY DATA /////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 
-void VoxRaytracer::RayData::AddElement(Id_t id, float L)
-{
-    Element el = {id, L};
-    m_Data.push_back(el);
-    m_TotalLength += L;
+void VoxRaytracer::RayData::AddElement(Id_t id, float L) {
+  Element el = {id, L};
+  m_Data.push_back(el);
+  m_TotalLength += L;
 }
 
-
-void VoxRaytracer::RayData::AppendRay(const VoxRaytracer::RayData &in)
-{
-    if (unlikely(!in.m_Data.size())) {
-        std::cout << "Warinig: PoCA on exit border!\n";
-        return;
-    }
-    else if (unlikely(!m_Data.size())) {
-        m_Data = in.m_Data;
-        std::cout << "Warinig: PoCA on entrance border!\n";
-        return;
-    }
-    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());
-        //        }
-        m_TotalLength += in.m_TotalLength;
+void VoxRaytracer::RayData::AppendRay(const VoxRaytracer::RayData &in) {
+  if (unlikely(!in.m_Data.size())) {
+    std::cout << "Warinig: PoCA on exit border!\n";
+    return;
+  } else if (unlikely(!m_Data.size())) {
+    m_Data = in.m_Data;
+    std::cout << "Warinig: PoCA on entrance border!\n";
+    return;
+  } else {
+    // Opzione 1) un voxel in piu' //
+    if (in.m_Data.size() > 0) {
+      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());
+    //        }
+    m_TotalLength += in.m_TotalLength;
+  }
 }
 
-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";
+void VoxRaytracer::RayData::PrintSelf(std::ostream &o) {
+  o << "Ray: total lenght " << m_TotalLength << "\n";
+  std::vector<Element>::iterator it;
+  for (it = m_Data.begin(); it < m_Data.end(); ++it)
+    o << "[ " << (*it).vox_id << ", " << (*it).L << "] \n";
 }
 
-
 ////////////////////////////////////////////////////////////////////////////////
 //// RAY TRACER ////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 
+bool VoxRaytracer::GetEntryPoint(const HLine3f &line, HPoint3f &pt) {
+  Vector4f s = m_Image->GetLocalPoint(line.direction);
+  pt = m_Image->GetLocalPoint(line.origin);
 
-bool VoxRaytracer::GetEntryPoint(const HLine3f &line, HPoint3f &pt)
-{
-    Vector4f s = m_Image->GetLocalPoint(line.direction);
-    pt = m_Image->GetLocalPoint(line.origin);
+  // Considers Structured grid dimensions //
+  Vector4f dims = m_Image->GetDims().homogeneous().cast<float>();
+  pt = pt.cwiseQuotient(dims);
+  s = s.cwiseQuotient(dims);
 
-    // Considers Structured grid dimensions //
-    Vector4f dims = m_Image->GetDims().homogeneous().cast<float>();
-    pt = pt.cwiseQuotient(dims);
-    s  = s.cwiseQuotient(dims);
+  float l = s.head(3).norm();
+  Vector3f L(l / s(0), l / s(1), l / s(2));
 
-    float l = s.head(3).norm();
-    Vector3f L(l/s(0), l/s(1), l/s(2));
+  Vector3f offset;
+  for (int i = 0; i < 3; ++i)
+    offset(i) = (s(i) > 0) - (pt(i) - floor(pt(i)));
+  offset = offset.cwiseProduct(L).cwiseAbs();
 
-    Vector3f offset;
-    for(int i=0;i<3;++i)
-        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 check_border = 0;
-        for ( int i=0; i<3 ;++i) {
-            check_border += pt(i) > 1;
-            check_border += pt(i) < 0;
-        }
-        if(check_border == 0) {
-            for(int i=0;i<3;++i)
-                pt(i) *= (float)dims(i);
-            pt = m_Image->GetWorldPoint(pt);
-            return true;
-        }
-
-       d = offset.minCoeff(&id);
-       for(int i=0; i<3; ++i)
-           pt(i) += d / L(i);
-
-       pt(id) = rintf(pt(id));
-
-
-       offset.array() -= d;
-       offset(id) = fabs(L(id));
+  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;
+      check_border += pt(i) < 0;
     }
-    for(int i=0;i<3;++i)
+    if (check_border == 0) {
+      for (int i = 0; i < 3; ++i)
         pt(i) *= (float)dims(i);
-    pt = m_Image->GetWorldPoint(pt);
-    return false;
-}
-
-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
-{
-    RayData ray;
-    Vector4f pt1 = m_Image->GetLocalPoint(in);
-    Vector4f pt2 = m_Image->GetLocalPoint(out);
-    Vector4f s = pt2 - pt1;
-
-    float l = s.head(3).norm();
-    Vector3f L(l/s(0), l/s(1), l/s(2));
-
-    // Vector3f scale; // FIXXX
-    // 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))) ;
-    offset = offset.cwiseProduct(L).cwiseAbs();
-    L = L.cwiseAbs();
-
-    //---- Check if the ray only crosses one voxel
-    Vector3i vid = m_Image->Find(in);
-    if(vid == m_Image->Find(out)){                  
-      ray.AddElement(m_Image->Map(vid),s.norm());
-      return ray;
+      pt = m_Image->GetWorldPoint(pt);
+      return true;
     }
 
-    //---- Otherwise, loop until ray is finished
-    int id; float d;	
-    while(l>0){
+    d = offset.minCoeff(&id);
+    for (int i = 0; i < 3; ++i)
+      pt(i) += d / L(i);
 
-      d = offset.minCoeff(&id);
+    pt(id) = rintf(pt(id));
 
-      if(m_Image->IsInsideGrid(vid)){
-	ray.AddElement(m_Image->Map(vid), d * m_scale(id) );
-      }
+    offset.array() -= d;
+    offset(id) = fabs(L(id));
+  }
+  for (int i = 0; i < 3; ++i)
+    pt(i) *= (float)dims(i);
+  pt = m_Image->GetWorldPoint(pt);
+  return false;
+}
 
-      // nan check //
-      //        if(unlikely(!isFinite(d * scale(id)))) {
-      //            std:: cout << "NAN in raytracer\n";
-      //            exit(1);
-      //        }
+bool VoxRaytracer::GetExitPoint(const HLine3f &line, HPoint3f &pt) {
+  HLine3f out = line;
+  out.direction *= -1;
+  return GetEntryPoint(out, pt);
+}
 
-      vid(id) += (int)fast_sign(s(id));
+VoxRaytracer::RayData
+VoxRaytracer::TraceBetweenPoints(const HPoint3f &in,
+                                 const HPoint3f &out) const {
+  RayData ray;
+  Vector4f pt1 = m_Image->GetLocalPoint(in);
+  Vector4f pt2 = m_Image->GetLocalPoint(out);
+  Vector4f s = pt2 - pt1;
 
-      l -= d;
-      offset.array() -= d;
-      offset(id) = fmin(L(id),l);
-    }
+  float l = s.head(3).norm();
+  Vector3f L(l / s(0), l / s(1), l / s(2));
+
+  // Vector3f scale; // FIXXX
+  // 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)));
+  offset = offset.cwiseProduct(L).cwiseAbs();
+  L = L.cwiseAbs();
+
+  //---- Check if the ray only crosses one voxel
+  Vector3i vid = m_Image->Find(in);
+  if (vid == m_Image->Find(out)) {
+    ray.AddElement(m_Image->Map(vid), s.norm());
     return ray;
+  }
+
+  //---- Otherwise, loop until ray is finished
+  int id;
+  float d;
+  while (l > 0) {
+
+    d = offset.minCoeff(&id);
+
+    if (m_Image->IsInsideGrid(vid)) {
+      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);
+    //        }
+
+    vid(id) += (int)fast_sign(s(id));
+
+    l -= d;
+    offset.array() -= d;
+    offset(id) = fmin(L(id), l);
+  }
+  return ray;
 }
 
 // 20150528 SV for absorbed muons
-VoxRaytracer::RayData VoxRaytracer::TraceLine(const HLine3f &line) const
-{
-    RayData ray;
+VoxRaytracer::RayData VoxRaytracer::TraceLine(const HLine3f &line) const {
+  RayData ray;
 
-    Vector4f pt = m_Image->GetLocalPoint(line.origin);
-    Vector4f s = m_Image->GetLocalPoint(line.direction);
+  Vector4f pt = m_Image->GetLocalPoint(line.origin);
+  Vector4f s = m_Image->GetLocalPoint(line.direction);
 
-    float l = s.head(3).norm();
-    // intersection between track and grid when spacing is +1
-    Vector3f L(l/s(0), l/s(1), l/s(2));
+  float l = s.head(3).norm();
+  // intersection between track and grid when spacing is +1
+  Vector3f L(l / s(0), l / s(1), l / s(2));
 
-    // RayTracer works with a grid of interspace +1
-    // Vector3f scale; // FIXXX
-    // 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();
+  // RayTracer works with a grid of interspace +1
+  // Vector3f scale; // FIXXX
+  // 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();
 
-    // 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();
+  // 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;
-    Vector3i vid = m_Image->Find(line.origin);
-    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);
+  int id;
+  float d;
+  Vector3i vid = m_Image->Find(line.origin);
+  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);
 
-        // add Lij to ray
-        ray.AddElement(m_Image->Map(vid), d * m_scale(id) );
+    // add Lij to ray
+    ray.AddElement(m_Image->Map(vid), d * m_scale(id));
 
-        // move to the next voxel
-        vid(id) += (int)fast_sign(s(id));
+    // move to the next voxel
+    vid(id) += (int)fast_sign(s(id));
 
-        offset.array() -= d;
-        offset(id) = L(id);
-    }
-    return ray;
+    offset.array() -= d;
+    offset(id) = L(id);
+  }
+  return ray;
 }
 
-}
+} // namespace uLib

src/Math/VoxRaytracer.h

@@ -29,8 +29,8 @@
 #define VOXRAYTRACER_H
 
 #include <math.h>
+#include <vector>
 
-#include "Core/Vector.h"
 #include "Math/StructuredGrid.h"
 
 namespace uLib {
@@ -51,14 +51,15 @@ public:
 
         void AppendRay ( const RayData &in);
 
-        uLibConstRefMacro(Data,Vector<Element>)
-        uLibConstRefMacro(TotalLength,Scalarf)
+        inline const std::vector<Element>& Data() const { return this->m_Data; }
+
+        inline const Scalarf& TotalLength() const { return this->m_TotalLength; }
 
         void PrintSelf(std::ostream &o);
 
     private:
-        Vector<Element> m_Data;
-        Scalarf         m_TotalLength;
+        std::vector<Element> m_Data;
+        Scalarf              m_TotalLength;
     };
 
 
@@ -78,7 +79,7 @@ public:
 
     RayData TraceLine(const HLine3f &line) const;
 
-    uLibGetMacro(Image,StructuredGrid *)
+    inline StructuredGrid* GetImage() const { return this->m_Image; }
 
 private:
     StructuredGrid *m_Image;

src/Math/testing/AccumulatorTest.cpp

@@ -23,86 +23,90 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
-
 #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>
-//#include <boost/accumulators/accumulators.hpp>
+// #include <boost/accumulators/framework/accumulator_set.hpp>
+// #include <boost/accumulators/statistics/count.hpp>
+// #include <boost/accumulators/accumulators.hpp>
 
 using namespace uLib;
 
 int test_ABTrim() {
 
-    Accumulator_ABTrim<float> acc;
+  Accumulator_ABTrim<float> acc;
 
-    acc.SetABTrim(1,1);
+  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++)
-        acc += *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";
-
-    return( acc() == 15.0 );
+  // 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;
-    v.reserve(c);
-    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];
-    m /= c;
-    std::cout << "simple mean: " << m << "\n";
-
-    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]);
-    std::cout << "mean pass: " << mean() << "\n";
-    mean.AddPass();
-    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]);
-    std::cout << "mean pass: " << mean() << "\n";
-    mean.AddPass();
-    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]);
-    std::cout << "mean pass: " << mean() << "\n";
-    mean.AddPass();
-    for(int i=0;i<c;++i) mean(v[i]);
-    std::cout << "mean pass: " << mean() << "\n";
+  Accumulator_Mean<float> mean;
+  TRandom rnd;
+  const int c = 10000000;
+  std::vector<float> v;
+  v.reserve(c);
+  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];
+  m /= c;
+  std::cout << "simple mean: " << m << "\n";
 
+  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]);
+  std::cout << "mean pass: " << mean() << "\n";
+  mean.AddPass();
+  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]);
+  std::cout << "mean pass: " << mean() << "\n";
+  mean.AddPass();
+  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]);
+  std::cout << "mean pass: " << mean() << "\n";
+  mean.AddPass();
+  for (int i = 0; i < c; ++i)
+    mean(v[i]);
+  std::cout << "mean pass: " << mean() << "\n";
+  return 1;
 }
 
-
-
-
 int main(void) {
-    BEGIN_TESTING(Accumulator);
+  BEGIN_TESTING(Accumulator);
 
-    //TEST1( test_ABTrim() );
-    test_Mean();
+  // TEST1( test_ABTrim() );
+  test_Mean();
 
-    END_TESTING;
+  END_TESTING;
 }

src/Math/testing/CMakeLists.txt

@@ -14,5 +14,15 @@ 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(VoxImageFilterTest.cpp PROPERTIES LANGUAGE CUDA)
+endif()

src/Math/testing/TriangleMeshTest.cpp

@@ -23,30 +23,25 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
-
 #include "testing-prototype.h"
 
 #include "Math/TriangleMesh.h"
-
+#include <iostream>
 
 using namespace uLib;
 
-int main()
-{
-    BEGIN_TESTING(Triangle Mesh);
+int main() {
+  BEGIN_TESTING(Triangle Mesh);
 
-    TriangleMesh mesh;
+  TriangleMesh mesh;
 
-    mesh.AddPoint(Vector3f(0,0,0));
-    mesh.AddPoint(Vector3f(0,1,0));
-    mesh.AddPoint(Vector3f(1,0,0));
+  mesh.AddPoint(Vector3f(0, 0, 0));
+  mesh.AddPoint(Vector3f(0, 1, 0));
+  mesh.AddPoint(Vector3f(1, 0, 0));
 
-    mesh.AddTriangle(Vector3i(0,1,2));
+  mesh.AddTriangle(Vector3i(0, 1, 2));
 
+  mesh.PrintSelf(std::cout);
 
-    mesh.PrintSelf(std::cout);
-
-    END_TESTING;
+  END_TESTING;
 }

src/Math/testing/VoxImageFilterTest.cpp

@@ -23,128 +23,191 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
-
-#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 {
-    Scalarf Value;
-    unsigned int Count;
+  Scalarf Value;
+  unsigned int Count;
 };
 
-float GaussianShape(float d)
-{
-    // normalized manually .. fix //
-    return 4.5 * exp(-d * 4.5);
+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;
+  float m_sigma;
 };
 
-
-static float MaxInVector(const Vector<float> &v)
-{
-    float max = 0;
-    for(int i=0; i<v.size(); ++i)
-        if(v.at(i) > max) max = v.at(i);
-    return max;
+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);
+  return max;
 }
 
+int main() {
+  BEGIN_TESTING(VoxImageFilters);
 
-int main()
-{
-    BEGIN_TESTING(VoxImageFilters);
+  VoxImage<TestVoxel> image(Vector3i(20, 30, 40));
+  image[Vector3i(10, 10, 10)].Value = 1;
+  // image[Vector3i(10,10,8)].Value = 1;
+  image.ExportToVtk("test_filter_original.vtk", 0);
 
-    VoxImage<TestVoxel> image(Vector3i(20,30,40));
-    image[Vector3i(10,10,10)].Value = 1;
-    //image[Vector3i(10,10,8)].Value = 1;
-    image.ExportToVtk("test_filter_original.vtk",0);
+  ////////////////////////////////////////////////////////////////////////////
+  ////////////////////////////////////////////////////////////////////////////
+  ////////////////////////////////////////////////////////////////////////////
+  // RPS //
 
+  {
+    VoxFilterAlgorithmSPR<TestVoxel> filter(Vector3i(2, 3, 4));
 
+    VoxImage<TestVoxel> filtered = image;
 
-    ////////////////////////////////////////////////////////////////////////////
-    ////////////////////////////////////////////////////////////////////////////
-    ////////////////////////////////////////////////////////////////////////////
-    // RPS //
+    std::vector<float> values;
+    for (int i = 0; i < filter.GetKernelData().GetDims().prod(); ++i) {
+      values.push_back(1.);
+      std::cout << values[i] << " ";
+    }
+    std::cout << "\n";
 
-    {
-        VoxFilterAlgorithmSPR<TestVoxel> filter(Vector3i(2,3,4));
+    filter.SetImage(&filtered);
 
-        VoxImage<TestVoxel> filtered = image;
+    filter.SetKernelNumericXZY(values);
 
-        Vector<float> values;
-        for(int i=0; i < filter.GetKernelData().GetDims().prod(); ++i) {
-            values.push_back(1.);
-            std::cout << values[i] << " ";
-        }
-        std::cout << "\n";
+    filter.SetABTrim(0, 2);
 
-        filter.SetImage(&filtered);
+    filter.GetKernelData().PrintSelf(std::cout);
 
-        filter.SetKernelNumericXZY(values);
+    filter.Run();
 
-        filter.SetABTrim(0,2);
+    filtered.ExportToVtk("filter_RPS_out.vtk", 0);
+  }
 
-        filter.GetKernelData().PrintSelf(std::cout);
+  {
 
-        filter.Run();
+    VoxImage<TestVoxel> image(Vector3i(20, 30, 40));
+    image[Vector3i(10, 10, 10)].Value = 1;
+    image[Vector3i(9, 10, 8)].Value = 2;
+    image.ExportToVtk("test_filter_max_original.vtk", 0);
 
-        filtered.ExportToVtk("filter_RPS_out.vtk",0);
+    VoxFilterAlgorithmCustom<TestVoxel> filter(Vector3i(3, 3, 4));
+
+    std::vector<float> values;
+    for (int i = 0; i < filter.GetKernelData().GetDims().prod(); ++i) {
+      values.push_back(static_cast<float>(1));
     }
 
+    filter.SetImage(&image);
 
+    filter.SetKernelNumericXZY(values);
 
+    filter.SetCustomEvaluate(MaxInVector);
 
+    filter.Run();
 
-    {
+    image.ExportToVtk("test_filter_max.vtk", 0);
+  }
 
-        VoxImage<TestVoxel> image(Vector3i(20,30,40));
-        image[Vector3i(10,10,10)].Value = 1;
-        image[Vector3i(9,10,8)].Value = 2;
-        image.ExportToVtk("test_filter_max_original.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));
 
-
-        VoxFilterAlgorithmCustom<TestVoxel> filter(Vector3i(3,3,4));
-
-        Vector<float> values;
-        for(int i=0; i < filter.GetKernelData().GetDims().prod(); ++i) {
-            values.push_back(static_cast<float>(1));
-        }
-
-        filter.SetImage(&image);
-
-        filter.SetKernelNumericXZY(values);
-
-        filter.SetCustomEvaluate(MaxInVector);
-
-        filter.Run();
-
-        image.ExportToVtk("test_filter_max.vtk",0);
+    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();
 
-    END_TESTING;
+    // 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

@@ -92,6 +92,20 @@ int main() {
         imgR.ExportToVtk("./read_and_saved.vtk");
     }
 
+    {
+        VoxImage<TestVoxel> img(Vector3i(4,4,4));
+        img.InitVoxels({0,0});
+        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)] = {i+j+k,0};
+                }
+            }
+        }
+        img.ExportToVti("./vti_saved.vti",0,1);
+        // img.ImportFromVtkXml("./test_vox_image.vti");
+    }
+
 
     {
         VoxImage<TestVoxel> img1(Vector3i(5,5,5));

src/Math/testing/VoxRaytracerTest.cpp

@@ -23,129 +23,114 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
-
-#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 )
+  if (fabs(c(0)) < 0.001 && fabs(c(1)) < 0.001 && fabs(c(2)) < 0.001)
     return 0;
   else
     return 1;
 }
 
-//bool Comapare(const  &t1, const T2 &t2)
+// bool Comapare(const  &t1, const T2 &t2)
 //{
-//    int out = 0;
-//    out += t1.vox_id != t2.vox_id;
-//    out += (fabs(t1.L) - fabs(t2.L)) > 0.001;
-//    return out == 0;
-//}
-
+//     int out = 0;
+//     out += t1.vox_id != t2.vox_id;
+//     out += (fabs(t1.L) - fabs(t2.L)) > 0.001;
+//     return out == 0;
+// }
 
 typedef VoxRaytracer Raytracer;
 
-int main()
-{
-    BEGIN_TESTING(Math VoxRaytracer);
+int main() {
+  BEGIN_TESTING(Math VoxRaytracer);
 
-    StructuredGrid img(Vector3i(2,2,2));
-    img.SetSpacing(Vector3f(2,2,2));
-    img.SetPosition(Vector3f(-2,0,-2));
+  StructuredGrid img(Vector3i(2, 2, 2));
+  img.SetSpacing(Vector3f(2, 2, 2));
+  img.SetPosition(Vector3f(-2, 0, -2));
 
-    {
-        HLine3f line;
-        line.origin << 0.1, 4.1, 0.1, 1;
-        line.direction << 0.1, -0.1, 0.1,0;
-        Raytracer rt(img);
-        HPoint3f pt;
-        TEST1( rt.GetEntryPoint(line,pt) );
-        TEST0( Vector4f0( pt - HPoint3f(0.2,4,0.2)  ) );
+  {
+    HLine3f line;
+    line.origin << 0.1, 4.1, 0.1, 1;
+    line.direction << 0.1, -0.1, 0.1, 0;
+    Raytracer rt(img);
+    HPoint3f pt;
+    TEST1(rt.GetEntryPoint(line, pt));
+    TEST0(Vector4f0(pt - HPoint3f(0.2, 4, 0.2)));
+  }
+
+  {
+    HLine3f line;
+    line.origin << 4, 0, 4, 1;
+    line.direction << -0.1, 0.1, -0.1, 0;
+    Raytracer rt(img);
+    HPoint3f pt;
+    TEST1(rt.GetEntryPoint(line, pt));
+    TEST0(Vector4f0(pt - HPoint3f(2, 2, 2)));
+  }
+
+  { // Test a point inside image //
+    StructuredGrid img(Vector3i(4, 4, 4));
+    img.SetSpacing(Vector3f(2, 2, 2));
+    img.SetPosition(Vector3f(-4, -4, -4));
+    Raytracer ray(img);
+    HPoint3f pt;
+    HLine3f line;
+    line.origin = HPoint3f(-3, -3, -3);
+    //        line.direction = HVector3f(1,1,1); //
+    TEST1(ray.GetEntryPoint(line, pt));
+    TEST1(pt == HPoint3f(-3, -3, -3));
+
+    Raytracer::RayData rdata =
+        ray.TraceBetweenPoints(HPoint3f(-3, -3, -3), HPoint3f(3, 3, 3));
+    for (const Raytracer::RayData::Element &el : rdata.Data()) {
+      std::cout << " " << el.vox_id << " , " << el.L << "\n";
     }
+  }
 
-    {
-        HLine3f line;
-        line.origin << 4,0,4, 1;
-        line.direction << -0.1, 0.1, -0.1, 0;
-        Raytracer rt(img);
-        HPoint3f pt;
-        TEST1( rt.GetEntryPoint(line,pt) );
-        TEST0( Vector4f0( pt - HPoint3f(2,2,2)  ) );
-    }
+  {
+    HPoint3f pt1(1, -0.5, 1);
+    HPoint3f pt2(1, 4.5, 1);
+    Raytracer rt(img);
 
-    {   // Test a point inside image //
-        StructuredGrid img(Vector3i(4,4,4));
-        img.SetSpacing(Vector3f(2,2,2));
-        img.SetPosition(Vector3f(-4,-4,-4));
-        Raytracer ray(img);
-        HPoint3f pt;
-        HLine3f  line;
-        line.origin = HPoint3f(-3,-3,-3);
-        //        line.direction = HVector3f(1,1,1); //
-        TEST1( ray.GetEntryPoint(line,pt) );
-        TEST1( pt == HPoint3f(-3,-3,-3) );
+    Raytracer::RayData ray = rt.TraceBetweenPoints(pt1, pt2);
+    TEST1(ray.Data().size() == 2);
+    TEST1(ray.Data().at(0).vox_id == 6);
+    TEST1(ray.Data().at(1).vox_id == 7);
+    ray.PrintSelf(std::cout);
+  }
 
-        Raytracer::RayData rdata = ray.TraceBetweenPoints(HPoint3f(-3,-3,-3), HPoint3f(3,3,3));
-        foreach (const Raytracer::RayData::Element &el, rdata.Data())
-        {
-            std::cout << " " << el.vox_id << " , " << el.L << "\n";
-        }
-    }
+  {
+    HPoint3f pt1(5, 1, 1);
+    HPoint3f pt2(-3, 1, 1);
+    Raytracer rt(img);
 
+    Raytracer::RayData ray = rt.TraceBetweenPoints(pt1, pt2);
+    TEST1(ray.Data().size() == 2);
+    TEST1(ray.Data().at(0).vox_id == 6);
+    TEST1(ray.Data().at(1).vox_id == 4);
+    ray.PrintSelf(std::cout);
+  }
 
-    {
-        HPoint3f pt1(1,-0.5,1);
-        HPoint3f pt2(1,4.5,1);
-        Raytracer rt(img);
+  {
+    HPoint3f pt1(1, 1, 1);
+    HPoint3f pt2(-1, 3, -1);
+    Raytracer rt(img);
 
-        Raytracer::RayData ray = rt.TraceBetweenPoints(pt1,pt2);
-        TEST1( ray.Data().size() == 2 );
-        TEST1( ray.Data().at(0).vox_id == 6 );
-        TEST1( ray.Data().at(1).vox_id == 7 );
-        ray.PrintSelf(std::cout);
-    }
+    Raytracer::RayData ray = rt.TraceBetweenPoints(pt1, pt2);
+    TEST1(ray.Data().size() == 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);
+    TEST1(ray.Data().at(3).vox_id == 1);
+    ray.PrintSelf(std::cout);
+  }
 
-    {
-        HPoint3f pt1(5,1,1);
-        HPoint3f pt2(-3,1,1);
-        Raytracer rt(img);
-
-        Raytracer::RayData ray = rt.TraceBetweenPoints(pt1,pt2);
-        TEST1( ray.Data().size() == 2 );
-        TEST1( ray.Data().at(0).vox_id == 6 );
-        TEST1( ray.Data().at(1).vox_id == 4 );
-        ray.PrintSelf(std::cout);
-    }
-
-    {
-        HPoint3f pt1(1,1,1);
-        HPoint3f pt2(-1,3,-1);
-        Raytracer rt(img);
-
-        Raytracer::RayData ray = rt.TraceBetweenPoints(pt1,pt2);
-        TEST1( ray.Data().size() == 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 );
-        TEST1( ray.Data().at(3).vox_id == 1 );
-        ray.PrintSelf(std::cout);
-    }
-
-    END_TESTING
+  END_TESTING
 }
-
-
-
-
-
-
-
-

src/Root/CMakeLists.txt

@@ -1,49 +1,68 @@
-set(HEADERS
- TestTObject.h
- RootMathDense.h
- RootMuonScatter.h
- RootHitRaw.h
- muBlastHit.h
- muBlastMCTrack.h
- muCastorMCTrack.h
- muCastorHit.h
-)
+set(HEADERS RootMathDense.h
+            RootMuonScatter.h
+            RootHitRaw.h
+            muCastorMCTrack.h
+            muCastorHit.h
+            muCastorInfo.h
+            muCastorSkinHit.h
+            muCastorPrimaryVertex.h
+            muCastorMuDetDIGI.h
+            SkinDetectorWriter.h)
 
-set(DICTIONARY_HEADERS
- TestTObject.h
- RootMathDense.h
- RootMuonScatter.h
- RootHitRaw.h
- muBlastHit.h
- muBlastMCTrack.h
- muCastorMCTrack.h
- muCastorHit.h
-)
+set(SOURCES ${HEADERS} RootMuonScatter.cpp
+                       muCastorMCTrack.cpp
+                       muCastorHit.cpp
+                       muCastorInfo.cpp
+                       muCastorSkinHit.cpp
+                       muCastorPrimaryVertex.cpp
+                       muCastorMuDetDIGI.cpp
+                       SkinDetectorWriter.cpp)
 
-SET(SOURCES
- TestTObject.cpp
- RootMuonScatter.cpp
- muBlastHit.cpp
- muBlastMCTrack.cpp
- muCastorMCTrack.cpp
- muCastorHit.cpp
-)
+set(DICTIONARY_HEADERS muCastorMCTrack.h
+                       muCastorHit.h
+                       muCastorInfo.h
+                       muCastorSkinHit.h
+                       muCastorPrimaryVertex.h
+                       muCastorMuDetDIGI.h
+                       SkinDetectorWriter.h)
 
-set(LIBRARIES
-#       ${Boost_SERIALIZATION_LIBRARY}
-#       ${Boost_SIGNALS_LIBRARY}
-#       ${Boost_PROGRAM_OPTIONS_LIBRARY}
-       ${ROOT_LIBRARIES}
-       ${PACKAGE_LIBPREFIX}Core
-       ${PACKAGE_LIBPREFIX}Math
-)
+set(LIBRARIES ${ROOT_LIBRARIES}
+              ${PACKAGE_LIBPREFIX}Math)
 
-include(FindROOTv6)
-root_generate_dictionary(uLibRootDict ${DICTIONARY_HEADERS} LINKDEF Linkdef.h)
-set_source_files_properties(uLibRootDict.cxx PROPERTIES GENERATED TRUE)
-set_source_files_properties(uLibRootDict.h PROPERTIES GENERATED TRUE)
-list(APPEND SOURCES     uLibRootDict.cxx)
+set(rDictName ${PACKAGE_LIBPREFIX}RootDict)
+root_generate_dictionary(${rDictName} ${DICTIONARY_HEADERS}
+                         LINKDEF Linkdef.h)
+set_source_files_properties(${rDictName}.cxx
+                            PROPERTIES GENERATED TRUE)
+set_source_files_properties(${rDictName}.h
+                            PROPERTIES GENERATED TRUE)
+list(APPEND SOURCES ${rDictName}.cxx)
 
+# TODO use a custom target linked to root_generate_dictionary
+set(R_ARTIFACTS ${CMAKE_CURRENT_BINARY_DIR}/lib${rDictName}_rdict.pcm
+                ${CMAKE_CURRENT_BINARY_DIR}/lib${rDictName}.rootmap)
+install(FILES ${R_ARTIFACTS}
+        DESTINATION ${INSTALL_LIB_DIR})
 
-uLib_add_shared_library(${uLib-module})
-add_subdirectory(testing)
+set(libname ${PACKAGE_LIBPREFIX}Root)
+set(ULIB_SHARED_LIBRARIES ${ULIB_SHARED_LIBRARIES} ${libname} PARENT_SCOPE)
+set(ULIB_SELECTED_MODULES ${ULIB_SELECTED_MODULES} Root PARENT_SCOPE)
+
+add_library(${libname} SHARED ${SOURCES})
+set_target_properties(${libname} PROPERTIES
+                      VERSION ${PROJECT_VERSION}
+                      SOVERSION ${PROJECT_SOVERSION}
+                      CXX_STANDARD 17)
+target_link_libraries(${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}/Root)
+
+if(BUILD_TESTING)
+  include(uLibTargetMacros)
+  add_subdirectory(testing)
+endif()

src/Root/Linkdef.h

@@ -23,8 +23,6 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
 #ifndef U_ROOT_LINKDEF_H
 #define U_ROOT_LINKDEF_H
 
@@ -35,49 +33,21 @@
 #pragma link off all functions;
 #pragma link C++ nestedclasses;
 
-#pragma link C++ class TestTObject+;
-
 using namespace ROOT::Mutom;
 
-#pragma link C++ class ROOT::Math::Cartesian2D<int>+;
-#pragma link C++ class ROOT::Math::Cartesian2D<float>+;
-#pragma link C++ class ROOT::Math::Cartesian2D<double>+;
-
-#pragma link C++ class ROOT::Math::Cartesian3D<int>+;
-#pragma link C++ class ROOT::Math::Cartesian3D<float>+;
-#pragma link C++ class ROOT::Math::Cartesian3D<double>+;
-
-#pragma link C++ class Vector2i+;
-#pragma link C++ class Vector2f+;
-#pragma link C++ class Vector2d+;
-
-#pragma link C++ class Vector3i+;
-#pragma link C++ class Vector3f+;
-#pragma link C++ class Vector3d+;
-
-#pragma link C++ typedef Matrix3i;
-#pragma link C++ typedef Matrix3f;
-#pragma link C++ typedef Matrix3d;
-
-#pragma link C++ class Line3f+;
-#pragma link C++ class Line3d+;
-
-#pragma link C++ class MuonTrack+;
-#pragma link C++ class MuonScatter+;
-#pragma link C++ function MuonScatter::p_mean() const;
+#pragma link C++ class ROOT::Math::Cartesian3D < int> + ;
+#pragma link C++ class ROOT::Math::Cartesian3D < float> + ;
+#pragma link C++ class ROOT::Math::Cartesian3D < double> + ;
 
 // #pragma link C++ class DetectorChamber+;
 
-#pragma link C++ class HitRaw+;
-#pragma link C++ function HitRaw::Chm() const;
-#pragma link C++ function HitRaw::Rob() const;
-#pragma link C++ function HitRaw::Tdc() const;
-#pragma link C++ function HitRaw::Ch() const;
-
-#pragma link C++ class  muBlastMCTrack+;
-#pragma link C++ class  muBlastHit+;
-#pragma link C++ class  muCastorMCTrack+;
-#pragma link C++ class  muCastorHit+;
+#pragma link C++ class muCastorMCTrack + ;
+#pragma link C++ class muCastorHit + ;
+#pragma link C++ class muCastorInfo + ;
+#pragma link C++ class muCastorSkinHit + ;
+#pragma link C++ class muCastorPrimaryVertex + ;
+#pragma link C++ class muCastorMuDetDIGI + ;
+#pragma link C++ class SkinDetectorWriter + ;
 
 #endif // __CINT__
 

src/Root/SkinDetectorWriter.cpp

@@ -0,0 +1,47 @@
+#include "SkinDetectorWriter.h"
+#include "muCastorSkinHit.h"
+#include "TVector3.h"
+
+SkinDetectorWriter::SkinDetectorWriter(string filename) :
+    t_file(nullptr),
+    t_tree(nullptr),
+    t_buffer(nullptr),
+    i_status(0)
+{
+    t_file = new TFile(filename.c_str(), "RECREATE");
+    t_tree = new TTree("muCastorMC", "muCastorMC");
+    t_buffer = new TClonesArray("muCastorSkinHit");
+
+    t_tree->Branch("CastorSkinHits", "TClonesArray", t_buffer, 32000, 99);
+
+    if (t_file->IsZombie()) i_status = 1;
+}
+
+SkinDetectorWriter::~SkinDetectorWriter()
+{}
+
+void SkinDetectorWriter::add(int detID, float p_x, float p_y, float p_z,
+                             float m_x, float m_y, float m_z)
+{
+    TClonesArray& ref = *t_buffer;
+    int size = ref.GetEntriesFast();
+
+    muCastorSkinHit* new_hit = new(ref[size]) muCastorSkinHit();
+    new_hit->SetDetID(detID);
+    new_hit->SetPdgCode(13);
+    new_hit->SetMotherID(-1);
+    new_hit->SetPos (TVector3(p_x, p_y, p_z));
+    new_hit->SetMom (TVector3(m_x, m_y, m_z));
+}
+
+void SkinDetectorWriter::write()
+{
+    if (t_tree->Fill() < 0) i_status = 2;
+    t_buffer->Delete();   // or t_buffer->Clear() ??
+}
+
+void SkinDetectorWriter::close()
+{
+    if (t_tree->Write() == 0) i_status = 3;
+    t_file->Close();
+}

src/Root/SkinDetectorWriter.h

@@ -0,0 +1,32 @@
+#ifndef SkinDetectorWriter_h
+#define SkinDetectorWriter_h
+
+#include <string>
+
+#include "TFile.h"
+#include "TTree.h"
+#include "TClonesArray.h"
+
+using std::string;
+
+class SkinDetectorWriter
+{
+public:
+    SkinDetectorWriter(string filename);
+    virtual ~SkinDetectorWriter();
+
+    void add(int detID, float p_x, float p_y, float p_z, float m_x, float m_y, float m_z);
+    int status() { return i_status; }
+    void write();
+    void close();
+
+private:
+    TFile* t_file;
+    TTree* t_tree;
+    TClonesArray* t_buffer;
+    int i_status;
+};
+
+
+
+#endif //SkinDetectorWriter_h

src/Root/muBlastMCTrack.h

@@ -9,6 +9,7 @@
 //         Martin Subieta   martin.subieta@ing.unibs.it
 //########################################
 
+#include <iostream>
 #include <vector>
 #include "TObject.h"
 #include "TParticle.h"

src/Root/muCastorInfo.cpp

@@ -0,0 +1,44 @@
+//------------------------------------------------
+// The Virtual Monte Carlo examples
+// Copyright (C) 2007, 2008 Ivana Hrivnacova
+// All rights reserved.
+//
+// For the licensing terms see geant4_vmc/LICENSE.
+// Contact: vmc@pcroot.cern.ch
+//-------------------------------------------------
+
+/// \file muCastorInfo.cxx 
+/// \brief Implementation of the muCastorInfo class 
+///
+/// \author G. Bonomi, A. Donzella - INFN
+
+#include <iostream>
+
+#include "muCastorInfo.h"
+
+/// \cond CLASSIMP
+ClassImp(muCastorInfo)
+/// \endcond
+
+using namespace std;
+
+//_____________________________________________________________________________
+muCastorInfo::muCastorInfo() 
+  : fMuGen(-1)
+{
+/// Default constructor
+}
+//_____________________________________________________________________________
+muCastorInfo::~muCastorInfo() 
+{
+/// Destructor
+}
+//_____________________________________________________________________________
+void muCastorInfo::Print(const Option_t* /*opt*/) const
+{
+/// Printing
+
+  cout << "  Generated muons: " << fMuGen 
+       << endl;
+}
+

src/Root/muCastorInfo.h

@@ -0,0 +1,44 @@
+#ifndef muCastor_RUN_H
+#define muCastor_RUN_H
+
+//------------------------------------------------
+// The Virtual Monte Carlo examples
+// Copyright (C) 2007, 2008 Ivana Hrivnacova
+// All rights reserved.
+//
+// For the licensing terms see geant4_vmc/LICENSE.
+// Contact: vmc@pcroot.cern.ch
+//-------------------------------------------------
+
+/// \file muCastorInfo.h
+/// \brief Definition of the muCastorInfo class 
+///
+/// \authors G. Bonomi, A. Donzella - INFN
+
+#include <TObject.h>
+#include <TVector3.h>
+
+class muCastorInfo : public TObject
+{
+  public:
+    muCastorInfo();
+    virtual ~muCastorInfo();
+
+    // methods
+    virtual void Print(const Option_t* option = "") const;
+
+    void SetMuGen  (Int_t muGen)  { fMuGen = muGen; };
+    void SetMuTrk  (Int_t muTrk)  { fMuTrk = muTrk; };
+
+    Int_t GetMuGen()   { return fMuGen; };
+
+  private:
+    Int_t      fMuGen;   // Generated muons
+    Int_t      fMuTrk;   // Tracked muons
+    
+  ClassDef(muCastorInfo,1) //muCastorInfo  
+};
+
+#endif //muCastor_RUN_H
+
+

src/Root/muCastorMCTrack.cpp

@@ -6,11 +6,9 @@
 //         Martin Subieta   martin.subieta@ing.unibs.it
 //******************************************************************************************
 
-#include <iostream>
-
-#include "Detectors/MuonScatter.h"
 #include <Root/muCastorMCTrack.h>
 #include <TClonesArray.h>
+#include <iostream>
 
 using namespace std;
 
@@ -32,8 +30,6 @@ uLib::MuonScatter &operator << (uLib::MuonScatter &mu, const muCastorMCTrack &bs
     return mu;
 }
 
-//namespace ROOT {
-//namespace Mutom {
 // -----   Default constructor   -------------------------------------------
 muCastorMCTrack::muCastorMCTrack()
 {
@@ -223,5 +219,3 @@ void muCastorMCTrack::Reset()
    fPntE       = 0;
 
 }
-//} // Mutom
-//} // ROOT

src/Root/muCastorMCTrack.h

@@ -9,20 +9,14 @@
 //         Martin Subieta   martin.subieta@ing.unibs.it
 //########################################
 
+#include <iostream>
 #include "vector"
 #include "TObject.h"
 #include "TParticle.h"
+#include "Detectors/MuonScatter.h"
 
 class TClonesArray;
 
-
-namespace uLib {
-class MuonScatter;
-}
-
-//namespace ROOT {
-//namespace Mutom {
-
 class muCastorMCTrack : public TObject
 {
 
@@ -89,8 +83,6 @@ public:
   ClassDef(muCastorMCTrack,1);
 
 };
-//} // Mutom
-//} // ROOT
 
 uLib::MuonScatter &operator << (uLib::MuonScatter &mu, const muCastorMCTrack &bsmu);
 #endif //muCastor_MCTRACK_H   

src/Root/muCastorMuDetDIGI.cpp

@@ -0,0 +1,41 @@
+/// \file muCastorMuDetDIGI.cxx 
+/// \brief Implementation of the muCastorMuDetDIGI class 
+//  This class build the DIGI for the scintillator detectors 
+/// \author G. Bonomi, M. Subieta - INFN
+
+#include <iostream>
+
+#include "muCastorMuDetDIGI.h"
+
+/// \cond CLASSIMP
+ClassImp(muCastorMuDetDIGI)
+/// \endcond
+
+using namespace std;
+
+//_____________________________________________________________________________
+muCastorMuDetDIGI::muCastorMuDetDIGI() :
+    fDetID(-1),
+    fLayID(-1),
+    fTubID(-1),
+    fDistMC(0.),
+    fDriftMC(0.),
+    fDist(0.),
+    fDrift(0.),
+    fEnergy(0.)
+{}
+
+//_____________________________________________________________________________
+muCastorMuDetDIGI::~muCastorMuDetDIGI() 
+{}
+
+//_____________________________________________________________________________
+void muCastorMuDetDIGI::Print(const Option_t* /*opt*/) const
+{
+    cout << "  DetID: " << fDetID
+         << "  LayID: " << fLayID
+         << "  TubID: " << fTubID
+         << "  energy deposit (keV): " << fEnergy
+         << endl;
+}
+

src/Root/muCastorMuDetDIGI.h

@@ -0,0 +1,75 @@
+#ifndef muCastor_MuDetDIGI_H
+#define muCastor_MuDetDIGI_H
+
+/// \file muCastorMuDetDIGI.h
+/// \brief Definition of the muCastorMuDetDIGI class 
+///
+/// \authors G. Bonomi, M. Subieta - INFN
+
+#include <TObject.h>
+
+class muCastorMuDetDIGI : public TObject
+{
+public:
+    muCastorMuDetDIGI();
+    virtual ~muCastorMuDetDIGI();
+
+    // -------> PUBLIC FUNCTIONS
+    virtual void Print(const Option_t* option = "") const;
+
+    // -------> SET METHODS
+
+    /// Set Det ID (Detector module)
+    void SetDetID(Int_t id)  { fDetID = id; };  
+
+    /// Set Layer ID (Layer [0,5])
+    void SetLayID(Int_t id)  { fLayID = id; };  
+
+    /// Set Tube ID (Tube inside each layer)
+    void SetTubID(Int_t id)  { fTubID = id; };  
+
+    void SetDistMC      (Double_t v)  { fDistMC = v; };
+    void SetDriftMC     (Double_t v)  { fDriftMC= v; };
+    void SetDist        (Double_t v)  { fDist   = v; };
+    void SetDrift       (Double_t v)  { fDrift  = v; };
+
+    // Set energy 
+    void SetEnergy(Double_t e)  { fEnergy = e; };
+
+    // -------> GET METHODS
+
+    /// \return The Module number
+    Int_t GetDetID() { return fDetID; };
+
+    /// \return The Layer number
+    Int_t GetLayID() { return fLayID; };
+
+    /// \return The Tube number
+    Int_t GetTubID() { return fTubID; };
+
+    Double_t GetDistMC()    { return fDistMC;   };
+    Double_t GetDriftMC()   { return fDriftMC;  };
+    Double_t GetDist()      { return fDist;     };
+    Double_t GetDrift()     { return fDrift;    };
+
+    /// \return Get energy
+    Double_t GetEnergy()   { return fEnergy; };
+
+
+    // -------> PRIVATE VARIABLES
+private:
+    Int_t      fDetID;      // Detector module ID 
+    Int_t      fLayID;      // Detector layer ID
+    Int_t      fTubID;      // Layer tube ID
+    Double_t   fDistMC;     // Minimum distance of particle tracks to the wire
+    Double_t   fDriftMC;    // Minimum drift time to the wire
+    Double_t   fDist;       // Minimum distance of particle tracks to the wire (with smearing)
+    Double_t   fDrift;      // Minimum drift time to the wire (with smearing)
+    Double_t   fEnergy;     // Energy released in the element
+
+    ClassDef(muCastorMuDetDIGI,1) //muCastorMuDetDIGI  
+};
+
+#endif //muCastorMuDetDIGI_H
+
+

src/Root/muCastorPrimaryVertex.cpp

@@ -0,0 +1,47 @@
+#include <iostream>
+#include <limits>
+
+#include "muCastorPrimaryVertex.h"
+
+/// \cond CLASSIMP
+ClassImp(muCastorPrimaryVertex)
+/// \endcond
+
+using namespace std;
+
+//_____________________________________________________________________________
+muCastorPrimaryVertex::muCastorPrimaryVertex() {
+/// Default constructor
+    Reset();
+}
+
+//_____________________________________________________________________________
+muCastorPrimaryVertex::~muCastorPrimaryVertex()
+{
+/// Destructor
+}
+
+//_____________________________________________________________________________
+void muCastorPrimaryVertex::Reset()
+{
+    fPdgCode    = 0;
+    fVx         = std::numeric_limits<double>::quiet_NaN();
+    fVy         = std::numeric_limits<double>::quiet_NaN();
+    fVz         = std::numeric_limits<double>::quiet_NaN();
+    fPx         = std::numeric_limits<double>::quiet_NaN();
+    fPy         = std::numeric_limits<double>::quiet_NaN();
+    fPz         = std::numeric_limits<double>::quiet_NaN();
+    fE          = std::numeric_limits<double>::quiet_NaN();
+}
+
+//_____________________________________________________________________________
+void muCastorPrimaryVertex::Print(const Option_t* /*opt*/) const
+{
+/// Printing
+
+  	cout << "  Primary particle PDG Code " << fPdgCode << endl; 
+	cout << "  Vertex: (" << fVx << ", " << fVy << ", " << fVz << ") cm" << endl;
+	cout << "  Mom: (" << fPx << ", " << fPy << ", " << fPz << ")  MeV/c" << endl;
+
+}
+