Minor changed in beam tracing

CMake/cmt-ulib.spec.in

@@ -1,116 +0,0 @@
-Summary: Cosmic Muon Tomography core libraries
-Name: cmt-ulib
-Version: @PKGVERSION@
-Release: @PKGRELEASE@%{?dist}
-License: EUROPEAN UNION PUBLIC LICENCE v. 1.2
-Vendor: INFN
-URL: https://github.com/OpenCMT/uLib
-Group: Development/Libraries
-BuildArch: %{_arch}
-%if %{?rhel}%{!?rhel:0} >= 8
-BuildRequires: cmake
-%else
-BuildRequires: cmake3
-%endif
-BuildRequires: doxygen
-BuildRequires: boost-devel
-BuildRequires: eigen3-devel
-BuildRequires: vtk-devel
-BuildRequires: readline-devel
-BuildRequires: pcl-devel
-BuildRequires: root-geom
-BuildRequires: root-genvector
-BuildRequires: root-smatrix
-BuildRequires: root-montecarlo-eg
-BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
-AutoReqProv: yes
-Source: %{name}-%{version}.tar.gz
-
-%description
-This package contains the base toolkit library for Cosmic Muon Tomography reconstruction,
-analysis and imaging software Developed by University of Padova and INFN Sezione di Padova  Italy
-
-%global _ulibpkgname mutom
-%global _ulibcmakedir %{_libdir}/cmake/%{_ulibpkgname}
-
-%prep
-%setup -c
-rm -rf %{buildroot}
-mkdir -p %{buildroot}
-
-%build
-mkdir %{_builddir}/%{name}-%{version}/build
-cd %{_builddir}/%{name}-%{version}/build
-%cmake -DCMAKE_INSTALL_PREFIX=%{buildroot}%{_prefix} \
-       -DCMAKE_BUILD_TYPE=RelWithDebInfo \
-       -DPACKAGE_NAME=%{_ulibpkgname} \
-       -DPACKAGE_INSTALL_LIB_DIR=%{buildroot}%{_libdir} \
-       -DPACKAGE_INSTALL_INC_DIR=%{buildroot}%{_includedir}/%{_ulibpkgname} \
-       -DPACKAGE_INSTALL_CMAKE_DIR=%{buildroot}%{_ulibcmakedir} \
-       -DNODOXYGEN=ON \
-       %{_builddir}/%{name}-%{version}
-make %{?_smp_mflags}
-
-%install
-cd %{_builddir}/%{name}-%{version}/build
-make install
-sed -i 's|%{buildroot}/usr|%{_prefix}|g' %{buildroot}%{_ulibcmakedir}/uLibTargets.cmake
-sed -i 's|%{buildroot}/usr|%{_prefix}|g' %{buildroot}%{_ulibcmakedir}/uLibTargets-relwithdebinfo.cmake
-
-%clean
-rm -rf %{buildroot}
-
-%files
-%defattr(-,root,root)
-%{_libdir}/libmutom*.so.0.2
-%{_libdir}/uLibRootDict_rdict.pcm
-
-%package devel
-Summary: Cosmic Muon Tomography core libraries, development files
-Requires: %{name}
-Requires: boost-devel
-Requires: eigen3-devel
-Requires: vtk-devel
-Requires: readline-devel
-Requires: pcl-devel
-Requires: root-geom
-Requires: root-genvector
-Requires: root-smatrix
-Requires: root-montecarlo-eg
-
-
-%description devel
-This package contains the base toolkit library for Cosmic Muon Tomography reconstruction,
-analysis and imaging software Developed by University of Padova and INFN Sezione di Padova  Italy
-
-%files devel
-%defattr(-,root,root)
-%dir %{_ulibcmakedir}
-/usr/bin/uLib_config
-%{_libdir}/libmutom*.so
-%{_ulibcmakedir}/*.cmake
-%dir %{_includedir}/%{_ulibpkgname}
-%dir %{_includedir}/%{_ulibpkgname}/Core
-%dir %{_includedir}/%{_ulibpkgname}/Math
-%dir %{_includedir}/%{_ulibpkgname}/Root
-%dir %{_includedir}/%{_ulibpkgname}/Detectors
-%dir %{_includedir}/%{_ulibpkgname}/Vtk
-%{_includedir}/%{_ulibpkgname}/*.h
-%{_includedir}/%{_ulibpkgname}/Core/*.h
-%{_includedir}/%{_ulibpkgname}/Math/*.h
-%{_includedir}/%{_ulibpkgname}/Math/*.hpp
-%{_includedir}/%{_ulibpkgname}/Root/*.h
-%{_includedir}/%{_ulibpkgname}/Detectors/*.h
-%{_includedir}/%{_ulibpkgname}/Vtk/*.h
-
-
-
-
-
-
-
-
-%changelog
-* Tue Dec 04 2018 Paolo Andreetto <paolo.andreetto@pd.infn.it> - 0.2.1-1
-- Repackaging for CentOS 7
-

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)

CMake/uLibGenerateRPMS.cmake

@@ -1,34 +0,0 @@
-# Target for RPMs creation
-
-set(PKGREL 1 CACHE STRING "Package build number")
-set(ITEMS_FOR_SOURCE AUTHORS
-                     CMakeConfig.in.h
-                     CMakePkgConfig.pc.in
-                     test.cpp
-                     uLibConfig.cmake.in
-                     uLib.creator
-                     ulib.h
-                     vtk_test.cpp
-                     CMake
-                     CMakeLists.txt
-                     Jenkinsfile
-                     src
-                     uLib.config
-                     uLibConfigVersion.cmake.in
-                     uLib.files
-                     uLib.includes)
-
-add_custom_target(rpm
-                  COMMAND mkdir -p ${CMAKE_CURRENT_BINARY_DIR}/rpmbuild/BUILD
-                                   ${CMAKE_CURRENT_BINARY_DIR}/rpmbuild/RPMS
-                                   ${CMAKE_CURRENT_BINARY_DIR}/rpmbuild/SOURCES
-                                   ${CMAKE_CURRENT_BINARY_DIR}/rpmbuild/SPECS
-                                   ${CMAKE_CURRENT_BINARY_DIR}/rpmbuild/SRPMS
-                  COMMAND tar -zcf ${CMAKE_CURRENT_BINARY_DIR}/rpmbuild/SOURCES/cmt-ulib-${PACKAGE_VERSION}.tar.gz ${ITEMS_FOR_SOURCE}
-                  COMMAND sed -e 's|@PKGVERSION@|${PACKAGE_VERSION}|g'
-                              -e 's|@PKGRELEASE@|${PKGREL}|g'
-                              CMake/cmt-ulib.spec.in > ${CMAKE_CURRENT_BINARY_DIR}/rpmbuild/SPECS/cmt-ulib.spec
-                  COMMAND QA_SKIP_BUILD_ROOT=1 rpmbuild -ba --define '_topdir ${CMAKE_CURRENT_BINARY_DIR}/rpmbuild'
-                          ${CMAKE_CURRENT_BINARY_DIR}/rpmbuild/SPECS/cmt-ulib.spec
-                  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
-

CMakeLists.txt

@@ -11,7 +11,7 @@ project(uLib)
 
 # The version number.
 set(PROJECT_VERSION_MAJOR 0)
-set(PROJECT_VERSION_MINOR 2)
+set(PROJECT_VERSION_MINOR 4)
 set(PROJECT_VERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}")
 set(PROJECT_SOVERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}")
 
@@ -26,130 +26,169 @@ 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}")
+message(STATUS "Project name = ${PROJECT_NAME}")
-
+message(STATUS "Package name = ${PACKAGE_NAME}")
-include(uLibMacros)
+message(STATUS "Package version = ${PACKAGE_VERSION}")
-include(uLibDebugMacro)
+message(STATUS "Module path = ${CMAKE_MODULE_PATH}")
-include(uLibTargetMacros)
-#include(uLibGenerateRMake)
-
 
 ## GLOBALS ------------------------------------------------------------------ ##
 
-include(uLibCommon)
+set(PACKAGE_INSTALL_BIN_DIR ${CMAKE_INSTALL_PREFIX}/bin 
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ") ## Add flags here ##
+    CACHE PATH "Installation directory for executables")
+set(PACKAGE_INSTALL_LIB_DIR ${CMAKE_INSTALL_PREFIX}/lib/
+    CACHE PATH "Installation directory for libraries")
+set(PACKAGE_INSTALL_INC_DIR ${CMAKE_INSTALL_PREFIX}/include/${PACKAGE_NAME}
+    CACHE PATH "Installation directory for headers")
+set(PACKAGE_INSTALL_DATA_DIR ${CMAKE_INSTALL_PREFIX}/share/${PACKAGE_NAME}
+    CACHE PATH "Installation directory for data files")
+set(PACKAGE_INSTALL_CMAKE_DIR ${CMAKE_INSTALL_PREFIX}/lib/cmake/${PACKAGE_NAME}
+    CACHE PATH "Installation directory for CMake files")
 
-enable_testing()
+set(SRC_DIR ${PROJECT_SOURCE_DIR}/src)
+
+if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+    message(STATUS "Setting build type to 'Release' as none was specified.")
+    set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose the type of build." FORCE)
+    set(CMAKE_EXE_LINKER_FLAGS "-Wl,--no-as-needed")
+    # Set the possible values of build type for cmake-gui
+    set_property(CACHE CMAKE_BUILD_TYPE PROPERTY 
+               STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
+endif()
+
+set(CMAKE_CXX_WARNING_OPTION "" 
+    CACHE STRING "Warning level -WAll to verbose all warnings")
+set(CMAKE_VERBOSE_MAKEFILE FALSE
+    CACHE STRING "Verbose compile output switch")
+
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++0x ${CMAKE_CXX_WARNING_OPTION}")
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -UULIB_SERIALIZATION_ON")
+
+#enable_testing()
 
 ## FIND PACKAGES ------------------------------------------------------------ ##
 
-include(uLibFindDependencies)
+set(Boost_USE_STATIC_LIBS OFF)
+set(Boost_USE_MULTITHREADED ON)
+set(Boost_USE_STATIC_RUNTIME OFF)
+find_package(Boost 1.45.0 COMPONENTS program_options REQUIRED)
+include_directories(${Boost_INCLUDE_DIRS})
 
+find_package(Eigen3 CONFIG REQUIRED)
+include(${EIGEN3_USE_FILE})
+
+find_package(ROOT CONFIG REQUIRED)
+include(${ROOT_USE_FILE})
+
+find_package(VTK CONFIG REQUIRED)
+include(${VTK_USE_FILE})
+
+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 ${PACKAGE_INSTALL_INC_DIR})
 
 ## ADD LIBRARIES SUBDIRECTORIES --------------------------------------------- ##
 
-## select modules ##
+include_directories(${PROJECT_BINARY_DIR})
-set(ULIB_SELECTED_MODULES
+include_directories(${SRC_DIR})
-      Core
-      Math
-      Detectors
-      Root
-)
 
 ## uLib_add_shared_library puts names there
 set(ULIB_SHARED_LIBRARIES)
+## select modules ##
+set(ULIB_SELECTED_MODULES)
 
-if(ULIB_USE_VTK)
+include_directories(${SRC_DIR}/Core)
- LIST(APPEND ULIB_SELECTED_MODULES Vtk)
+add_subdirectory(${SRC_DIR}/Core)
-endif(ULIB_USE_VTK)
+
+include_directories(${SRC_DIR}/Math)
+add_subdirectory(${SRC_DIR}/Math)
+
+include_directories(${SRC_DIR}/Detectors)
+add_subdirectory(${SRC_DIR}/Detectors)
+
+include_directories(${SRC_DIR}/Root)
+add_subdirectory(${SRC_DIR}/Root)
+
+include_directories(${SRC_DIR}/Vtk)
+add_subdirectory(${SRC_DIR}/Vtk)
+
+#add_subdirectory("${SRC_DIR}/utils/make_recipe")
 
 ## Documentation and packages
 
-include(uLibGenerateRPMS)
+#include(uLibGenerateDoc)
-include(uLibGenerateDoc)
-
-## 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()
-
-
-## 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)
 
 ## UTILITIES ##
-add_subdirectory("${SRC_DIR}/utils/make_recipe")
+#add_subdirectory("${SRC_DIR}/utils/make_recipe")
 
 
 ## INSTALLS AND EXPORTS ----------------------------------------------------- ##
 
-#export(PACKAGE uLib)
+#export(PACKAGE ULIB)
-export(PACKAGE ULIB)
+#export(TARGETS ${ULIB_SHARED_LIBRARIES} ${ULIB_EXPORTED_TARGETS}
-export(TARGETS ${ULIB_SHARED_LIBRARIES} ${ULIB_EXPORTED_TARGETS}
+#       FILE "${PROJECT_BINARY_DIR}/uLibTargets.cmake"    )
-       FILE "${PROJECT_BINARY_DIR}/uLibTargets.cmake"    )
-#export(TARGETS ${ULIB_EXPORTED_TARGETS}
-#       FILE "${PROJECT_BINARY_DIR}/uLibExeTargets.cmake" )
 
 
 # Create the FooBarConfig.cmake and FooBarConfigVersion files
 file(RELATIVE_PATH REL_INCLUDE_DIR "${PACKAGE_INSTALL_CMAKE_DIR}"
    "${PACKAGE_INSTALL_INC_DIR}")
+
 # ... for the build tree
-set(CONF_INCLUDE_DIRS "${PROJECT_SOURCE_DIR}/src" "${PROJECT_BINARY_DIR}")
+#set(CONF_INCLUDE_DIRS "${PROJECT_SOURCE_DIR}/src" "${PROJECT_BINARY_DIR}")
-configure_file(uLibConfig.cmake.in
+#configure_file(uLibConfig.cmake.in 
-  "${PROJECT_BINARY_DIR}/uLibConfig.cmake" @ONLY)
+#               "${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}${CMAKE_FILES_DIRECTORY}/uLibConfig.cmake" @ONLY)
+               "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/uLibConfig.cmake"
+               @ONLY)
+
 # ... for both
 configure_file(uLibConfigVersion.cmake.in
                "${PROJECT_BINARY_DIR}/uLibConfigVersion.cmake" @ONLY)
 
 install(FILES "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/uLibConfig.cmake"
               "${PROJECT_BINARY_DIR}/uLibConfigVersion.cmake"
-              "${PROJECT_SOURCE_DIR}/CMake/FindReadLine.cmake"
-              "${PROJECT_SOURCE_DIR}/CMake/FindROOT.cmake"
-              "${PROJECT_SOURCE_DIR}/CMake/FindROOTv6.cmake"
-              "${PROJECT_SOURCE_DIR}/CMake/uLibCommon.cmake"
-              "${PROJECT_SOURCE_DIR}/CMake/uLibConfigHeader.cmake"
-              "${PROJECT_SOURCE_DIR}/CMake/uLibDebugMacro.cmake"
-              "${PROJECT_SOURCE_DIR}/CMake/uLibFindDependencies.cmake"
-              "${PROJECT_SOURCE_DIR}/CMake/uLibGenerateDoc.cmake"
-              "${PROJECT_SOURCE_DIR}/CMake/uLibGenerateRMake.cmake"
-              "${PROJECT_SOURCE_DIR}/CMake/uLibGenerateRPMS.cmake"
-              "${PROJECT_SOURCE_DIR}/CMake/uLibMacros.cmake"
-              "${PROJECT_SOURCE_DIR}/CMake/uLibTargetMacros.cmake"
         DESTINATION "${PACKAGE_INSTALL_CMAKE_DIR}"
         COMPONENT dev)
 
 # Install the export set for use with the install-tree
-install(EXPORT "${PROJECT_NAME}Targets" DESTINATION
+install(EXPORT "${PROJECT_NAME}Targets"
-  "${PACKAGE_INSTALL_CMAKE_DIR}" COMPONENT dev)
+        DESTINATION "${PACKAGE_INSTALL_CMAKE_DIR}"
-
+        COMPONENT dev)
-install(FILES ${PROJECT_SOURCE_DIR}/ulib.h DESTINATION ${PACKAGE_INSTALL_INC_DIR})
-
-
-# TODO clean also subdirectories
-add_custom_target(clean-cmake-files
-   COMMAND ${CMAKE_COMMAND} -P ${ULIB_CMAKE_DIR}/clean-all.cmake
-)
-
-
-
-
 

src/Core/CMakeLists.txt

@@ -1,41 +1,27 @@
 
-set(HEADERS
+set(HEADERS Options.h
-                                Archives.h
+            StaticInterface.h)
-                                Array.h
+
-                                Debug.h
+set(SOURCES Options.cpp)
-                                Export.h
+
-                                Function.h
+set(LIBRARIES ${Boost_PROGRAM_OPTIONS_LIBRARY})
-                                Macros.h
+
-                                Mpl.h
+set(libname ${PACKAGE_LIBPREFIX}Core)
-                                Object.h
+set(ULIB_SHARED_LIBRARIES ${ULIB_SHARED_LIBRARIES} ${libname} PARENT_SCOPE)
-                                ObjectProps.h
+set(ULIB_SELECTED_MODULES ${ULIB_SELECTED_MODULES} Core PARENT_SCOPE)
-                                Options.h
+
-                                Serializable.h
+add_library(${libname} SHARED ${SOURCES})
-                                Signal.h
+set_target_properties(${libname} PROPERTIES
-                                Singleton.h
+                      VERSION ${PROJECT_VERSION}
-                                SmartPointer.h
+                      SOVERSION ${PROJECT_SOVERSION})
-                                StaticInterface.h
+target_link_libraries(${libname} ${LIBRARIES})
-                                StringReader.h
+
-                                Types.h
+install(TARGETS ${libname}
-                                Uuid.h
+        EXPORT "${PROJECT_NAME}Targets"
-                                Timer.h
+        RUNTIME DESTINATION ${PACKAGE_INSTALL_BIN_DIR} COMPONENT bin
-)
+        LIBRARY DESTINATION ${PACKAGE_INSTALL_LIB_DIR} COMPONENT lib)
+
+install(FILES ${HEADERS} DESTINATION ${PACKAGE_INSTALL_INC_DIR}/Core)
 
-SET(SOURCES
-                Archives.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}
-)
 
-uLib_add_shared_library(${uLib-module})
-add_subdirectory(testing)

src/Detectors/CMakeLists.txt

@@ -1,37 +1,6 @@
-#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(SOURCES
-#                Solid.cpp
-#                Scene.cpp
-#)
-
-#set(LIBRARIES
-#       ${Boost_SERIALIZATION_LIBRARY}
-#       ${Boost_SIGNALS_LIBRARY}
-#       ${Boost_PROGRAM_OPTIONS_LIBRARY}
-#       ${Eigen_LIBRARY}
-#       ${Geant4_LIBRARIES}
-#       ${ROOT_LIBRARIES}
-#       ${PACKAGE_LIBPREFIX}Core
-#       ${PACKAGE_LIBPREFIX}Math
-#)
-
 set(HEADERS MuonScatter.h MuonError.h MuonEvent.h)
 
-uLib_add_shared_library(${uLib-module})
+set(ULIB_SELECTED_MODULES ${ULIB_SELECTED_MODULES} Detectors PARENT_SCOPE)
-add_subdirectory(testing)
+
+install(FILES ${HEADERS}
+        DESTINATION ${PACKAGE_INSTALL_INC_DIR}/Detectors)

src/Math/CMakeLists.txt

@@ -1,53 +1,53 @@
+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)
 
-# HEADERS
+set(SOURCES VoxRaytracer.cpp
-set(HEADERS
+            StructuredData.cpp
-                                ContainerBox.h
+            StructuredGrid.cpp
-                                Dense.h
+            VoxImage.cpp
-                                Geometry.h
+            TriangleMesh.cpp
-                                Transform.h
+            Dense.cpp
-                                StructuredData.h
+            Structured2DGrid.cpp
-                                StructuredGrid.h
+            Structured4DGrid.cpp)
-                                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(LIBRARIES ${Eigen_LIBRARY}
+              ${ROOT_LIBRARIES})
 
-# SOURCES
+set(libname ${PACKAGE_LIBPREFIX}Math)
-set(SOURCES
+set(ULIB_SHARED_LIBRARIES ${ULIB_SHARED_LIBRARIES} ${libname} PARENT_SCOPE)
-                VoxRaytracer.cpp
+set(ULIB_SELECTED_MODULES ${ULIB_SELECTED_MODULES} Math PARENT_SCOPE)
-                StructuredData.cpp
-                StructuredGrid.cpp
-                VoxImage.cpp
-                TriangleMesh.cpp
-                Dense.cpp
-                Structured2DGrid.cpp
-                Structured4DGrid.cpp
-)
 
-set(LIBRARIES
+add_library(${libname} SHARED ${SOURCES})
-       ${Boost_SERIALIZATION_LIBRARY}
+set_target_properties(${libname} PROPERTIES
-       ${Boost_SIGNALS_LIBRARY}
+                      VERSION ${PROJECT_VERSION}
-       ${Boost_PROGRAM_OPTIONS_LIBRARY}
+                      SOVERSION ${PROJECT_SOVERSION})
-       ${Eigen_LIBRARY}
+target_link_libraries(${libname} ${LIBRARIES})
-       ${ROOT_LIBRARIES}
-       ${PACKAGE_LIBPREFIX}Core
-)
 
+install(TARGETS ${libname}
+        EXPORT "${PROJECT_NAME}Targets"
+        RUNTIME DESTINATION ${PACKAGE_INSTALL_BIN_DIR} COMPONENT bin
+        LIBRARY DESTINATION ${PACKAGE_INSTALL_LIB_DIR} COMPONENT lib)
+
+install(FILES ${HEADERS} DESTINATION ${PACKAGE_INSTALL_INC_DIR}/Math)
 
-uLib_add_shared_library(${uLib-module})
-add_subdirectory(testing)

src/Math/VoxImageFilterCustom.hpp

@@ -28,11 +28,12 @@
 #ifndef VOXIMAGEFILTERCUSTOM_HPP
 #define VOXIMAGEFILTERCUSTOM_HPP
 
-#include "Core/Macros.h"
 #include <Math/Dense.h>
 #include "Math/VoxImage.h"
 #include "VoxImageFilter.h"
 
+#define likely(expr) __builtin_expect(!!(expr), 1)
+
 ////////////////////////////////////////////////////////////////////////////////
 /////  VOXIMAGE FILTER CUSTOM  /////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////

src/Math/VoxRaytracer.cpp

@@ -24,13 +24,12 @@
 //////////////////////////////////////////////////////////////////////////////*/
 
 
-
+#include <iostream>
+#include <unordered_map>
 
 #include "VoxRaytracer.h"
 #include "Utils.h"
 
-#include "Core/Macros.h"
-
 inline float fast_sign(float f) { return 1 - 2 * (f < 0); }
 
 namespace uLib {
@@ -49,16 +48,17 @@ void VoxRaytracer::RayData::AddElement(Id_t id, float L)
 
 void VoxRaytracer::RayData::AppendRay(const VoxRaytracer::RayData &in)
 {
-    if (unlikely(!in.m_Data.size())) {
+    if (!in.m_Data.size())
+    {
         std::cout << "Warinig: PoCA on exit border!\n";
-        return;
     }
-    else if (unlikely(!m_Data.size())) {
+    else if (!m_Data.size())
+    {
         m_Data = in.m_Data;
         std::cout << "Warinig: PoCA on entrance border!\n";
-        return;
     }
-    else {
+    else
+    {
         // Opzione 1) un voxel in piu' //
         m_Data.reserve(m_Data.size() + in.m_Data.size());
         m_Data.insert(m_Data.end(), in.m_Data.begin(), in.m_Data.end());
@@ -82,16 +82,22 @@ void VoxRaytracer::RayData::AppendRay(const VoxRaytracer::RayData &in)
 void VoxRaytracer::RayData::PrintSelf(std::ostream &o)
 {
     o << "Ray: total lenght " << m_TotalLength << "\n";
-    std::vector<Element>::iterator it;
+    for(std::vector<Element>::iterator it = m_Data.begin(); it < m_Data.end(); ++it)
-    for(it = m_Data.begin(); it < m_Data.end(); ++it)
+    {
         o << "[ " << (*it).vox_id << ", " << (*it).L << "] \n";
+    }
 }
 
-
 ////////////////////////////////////////////////////////////////////////////////
 //// RAY TRACER ////////////////////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 
+VoxRaytracer::VoxRaytracer(StructuredGrid &image) : m_Image(&image)
+{
+    m_scale << (m_Image->GetWorldMatrix() * Vector4f(1,0,0,0)).norm(),
+               (m_Image->GetWorldMatrix() * Vector4f(0,1,0,0)).norm(),
+               (m_Image->GetWorldMatrix() * Vector4f(0,0,1,0)).norm();
+}
 
 bool VoxRaytracer::GetEntryPoint(const HLine3f &line, HPoint3f &pt)
 {
@@ -150,9 +156,7 @@ bool VoxRaytracer::GetExitPoint(const HLine3f &line, HPoint3f &pt)
 }
 
 
-VoxRaytracer::RayData VoxRaytracer::TraceBetweenPoints(const HPoint3f &in,
+VoxRaytracer::RayData VoxRaytracer::TraceBetweenPoints(const HPoint3f &in, const HPoint3f &out) const
-                                                       const HPoint3f &out)
-const
 {
     RayData ray;
     Vector4f pt1 = m_Image->GetLocalPoint(in);
@@ -162,53 +166,138 @@ const
     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))) ;
+    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)){
+    if (vid == m_Image->Find(out))
-      ray.AddElement(m_Image->Map(vid),s.norm());
+    {
-      return ray;
+        ray.AddElement(m_Image->Map(vid),s.norm());
+        return ray;
     }
 
     //---- Otherwise, loop until ray is finished
     int id; float d;
-    while(l>0){
+    while (l>0)
+    {
+        d = offset.minCoeff(&id);
 
-      d = offset.minCoeff(&id);
+        if (m_Image->IsInsideGrid(vid))
+        {
+            ray.AddElement(m_Image->Map(vid), d * m_scale(id));
+        }
 
-      if(m_Image->IsInsideGrid(vid)){
+        vid(id) += (int)fast_sign(s(id));
-	ray.AddElement(m_Image->Map(vid), d * m_scale(id) );
-      }
 
-      // nan check //
+        l -= d;
-      //        if(unlikely(!isFinite(d * scale(id)))) {
+        offset.array() -= d;
-      //            std:: cout << "NAN in raytracer\n";
+        offset(id) = fmin(L(id),l);
-      //            exit(1);
-      //        }
-
-      vid(id) += (int)fast_sign(s(id));
-
-      l -= d;
-      offset.array() -= d;
-      offset(id) = fmin(L(id),l);
     }
     return ray;
 }
 
+static int encode_v(Vector3i in)
+{
+    return ((in[0] + 1) << 4) + ((in[1] + 1) << 2) + in[2] + 1;
+}
+
+static Vector3i decode_v(int in)
+{
+    Vector3i result {
+     ((in & 48) >> 4) - 1,
+     ((in & 12) >> 2) - 1,
+     (in & 3) - 1
+    };
+    return result;
+}
+
+VoxRaytracer::RayData VoxRaytracer::BeamBetweenPoints(const HPoint3f &in, const HPoint3f &out, Vector3i thickness) const
+{
+    if (thickness[0] < 0) thickness[0] = 0;
+    if (thickness[1] < 0) thickness[1] = 0;
+    if (thickness[2] < 0) thickness[2] = 0;
+
+    Vector3i zero_v { 0, 0, 0 };
+
+    RayData ray = TraceBetweenPoints(in, out);
+    if (thickness == zero_v || ray.Data().size() == 0) return ray;
+
+    /*
+     * Calculate the forbidden relocations
+     */
+
+    std::unordered_map<int, int> ban_points(26);
+
+    Vector3i prevPos = m_Image->UnMap(ray.Data()[0].vox_id);
+    Vector3i currDir = zero_v;
+    int currLen = 1;
+
+    for (int k = 1; k < ray.Data().size(); k++)
+    {
+        Vector3i currPos = m_Image->UnMap(ray.Data()[k].vox_id);
+        Vector3i offset = currPos - prevPos;
+        prevPos = currPos;
+
+        if (k == 1) currDir = offset;
+
+        if (offset == currDir)
+        {
+            currLen++;
+            continue;
+        }
+
+        int enc_v = encode_v(currDir);
+        if (ban_points.find(enc_v) == ban_points.end())
+        {
+            ban_points.emplace(enc_v, currLen);
+        }
+        else if (currLen > ban_points[enc_v])
+        {
+            ban_points[enc_v] = currLen;
+        }
+
+        currDir = offset;
+        currLen = 2;
+    }
+
+    /*
+     * Calculate the beam section
+     */
+    std::vector<Vector3i> relocs;
+    relocs.push_back(zero_v);
+
+    /*
+     * Compose the beam
+     */
+    RayData beam;
+    for (auto iter : ray.Data())
+    {
+        Vector3i rPos = m_Image->UnMap(iter.vox_id);
+
+        for (Vector3i reloc : relocs)
+        {
+            Vector3i cPos = rPos + reloc;
+            if (!m_Image->IsInsideGrid(cPos)) continue;
+
+            beam.AddElement(m_Image->Map(cPos), iter.L);
+        }
+    }
+
+    return beam;
+}
+
+
+
 // 20150528 SV for absorbed muons
 VoxRaytracer::RayData VoxRaytracer::TraceLine(const HLine3f &line) const
 {
     RayData ray;
-
     Vector4f pt = m_Image->GetLocalPoint(line.origin);
     Vector4f s = m_Image->GetLocalPoint(line.direction);
 
@@ -250,4 +339,4 @@ VoxRaytracer::RayData VoxRaytracer::TraceLine(const HLine3f &line) const
     return ray;
 }
 
-}
+} //end of namespace uLib

src/Math/VoxRaytracer.h

@@ -38,7 +38,8 @@ namespace uLib {
 class VoxRaytracer {
 
 public:
-    class RayData {
+    class RayData
+    {
     public:
         RayData() : m_TotalLength(0) {}
 
@@ -62,14 +63,8 @@ public:
         Scalarf              m_TotalLength;
     };
 
-
+public:
- public:
+    VoxRaytracer(StructuredGrid &image);
- VoxRaytracer(StructuredGrid &image) : m_Image(&image) {
-      m_scale <<
-	(m_Image->GetWorldMatrix() * Vector4f(1,0,0,0)).norm(),
-	(m_Image->GetWorldMatrix() * Vector4f(0,1,0,0)).norm(),
-	(m_Image->GetWorldMatrix() * Vector4f(0,0,1,0)).norm();
-    }
 
     bool GetEntryPoint(const HLine3f &line, HPoint3f &pt);
 
@@ -77,6 +72,8 @@ public:
 
     RayData TraceBetweenPoints(const HPoint3f &in, const HPoint3f &out) const;
 
+    RayData BeamBetweenPoints(const HPoint3f &in, const HPoint3f &out, Vector3i thickness) const;
+
     RayData TraceLine(const HLine3f &line) const;
 
     inline StructuredGrid* GetImage() const { return this->m_Image; }

src/Root/CMakeLists.txt

@@ -1,55 +1,27 @@
-set(HEADERS
+set(HEADERS RootMathDense.h
- TestTObject.h
+            RootMuonScatter.h
- RootMathDense.h
+            RootHitRaw.h)
- RootMuonScatter.h
- RootHitRaw.h
- muBlastHit.h
- muBlastMCTrack.h
- muCastorMCTrack.h
- muCastorHit.h
- muCastorInfo.h
-)
 
-set(DICTIONARY_HEADERS
+set(SOURCES ${HEADERS} RootMuonScatter.cpp)
- TestTObject.h
- RootMathDense.h
- RootMuonScatter.h
- RootHitRaw.h
- muBlastHit.h
- muBlastMCTrack.h
- muCastorMCTrack.h
- muCastorHit.h
- muCastorInfo.h
-)
 
-SET(SOURCES
+set(LIBRARIES ${ROOT_LIBRARIES}
- TestTObject.cpp
+              ${PACKAGE_LIBPREFIX}Math)
- RootMuonScatter.cpp
- muBlastHit.cpp
- muBlastMCTrack.cpp
- muCastorMCTrack.cpp
- muCastorHit.cpp
- muCastorInfo.cpp
-)
 
-set(LIBRARIES
+set(libname ${PACKAGE_LIBPREFIX}Root)
-#       ${Boost_SERIALIZATION_LIBRARY}
+set(ULIB_SHARED_LIBRARIES ${ULIB_SHARED_LIBRARIES} ${libname} PARENT_SCOPE)
-#       ${Boost_SIGNALS_LIBRARY}
+set(ULIB_SELECTED_MODULES ${ULIB_SELECTED_MODULES} Root PARENT_SCOPE)
-#       ${Boost_PROGRAM_OPTIONS_LIBRARY}
-       ${ROOT_LIBRARIES}
-       ${PACKAGE_LIBPREFIX}Core
-       ${PACKAGE_LIBPREFIX}Math
-)
 
-include(FindROOTv6)
+add_library(${libname} SHARED ${SOURCES})
-root_generate_dictionary(uLibRootDict ${DICTIONARY_HEADERS} LINKDEF Linkdef.h)
+set_target_properties(${libname} PROPERTIES
-set_source_files_properties(uLibRootDict.cxx PROPERTIES GENERATED TRUE)
+                      VERSION ${PROJECT_VERSION}
-set_source_files_properties(uLibRootDict.h PROPERTIES GENERATED TRUE)
+                      SOVERSION ${PROJECT_SOVERSION})
-list(APPEND SOURCES     uLibRootDict.cxx)
+target_link_libraries(${libname} ${LIBRARIES})
+
+install(TARGETS ${libname}
+        EXPORT "${PROJECT_NAME}Targets"
+        RUNTIME DESTINATION ${PACKAGE_INSTALL_BIN_DIR} COMPONENT bin
+        LIBRARY DESTINATION ${PACKAGE_INSTALL_LIB_DIR} COMPONENT lib)
+
+install(FILES ${HEADERS} DESTINATION ${PACKAGE_INSTALL_INC_DIR}/Root)
 
-# TODO use a custom target linked to root_generate_dictionary
-install(FILES ${CMAKE_CURRENT_BINARY_DIR}/uLibRootDict_rdict.pcm
-        DESTINATION ${PACKAGE_INSTALL_LIB_DIR})
 
-uLib_add_shared_library(${uLib-module})
-add_subdirectory(testing)

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/muCastorMCTrack.h

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

src/Vtk/CMakeLists.txt

@@ -1,37 +1,38 @@
-set(HEADERS
+set(HEADERS uLibVtkInterface.h
-                          uLibVtkInterface.h
+            uLibVtkViewer.h
-                          uLibVtkViewer.h
+            vtkContainerBox.h
-                          vtkContainerBox.h
+            vtkMuonScatter.h
-                          vtkMuonScatter.h
+            vtkStructuredGrid.h
-                          vtkStructuredGrid.h
+            vtkVoxRaytracerRepresentation.h
-                          vtkVoxRaytracerRepresentation.h
+            vtkVoxImage.h)
-                          vtkVoxImage.h
-#                          vtkHLineRepresentation.h
-#			  vtkTriangleMesh.h
-)
 
-SET(SOURCES
+set(SOURCES uLibVtkInterface.cxx
-                uLibVtkInterface.cxx
+            uLibVtkViewer.cpp
-                uLibVtkViewer.cpp
+            vtkContainerBox.cpp
-                vtkContainerBox.cpp
+            vtkMuonScatter.cxx
-                vtkMuonScatter.cxx
+            vtkStructuredGrid.cpp
-                vtkStructuredGrid.cpp
+            vtkVoxRaytracerRepresentation.cpp
-                vtkVoxRaytracerRepresentation.cpp
+            vtkVoxImage.cpp)
-                vtkVoxImage.cpp
-)
 
-set(LIBRARIES
+set(LIBRARIES ${Eigen_LIBRARY}
-       ${Boost_SERIALIZATION_LIBRARY}
+              ${ROOT_LIBRARIES}
-       ${Boost_SIGNALS_LIBRARY}
+              ${VTK_LIBRARIES}
-       ${Boost_PROGRAM_OPTIONS_LIBRARY}
+              ${PACKAGE_LIBPREFIX}Math)
-       ${Eigen_LIBRARY}
-       ${ROOT_LIBRARIES}
-       ${Geant4_LIBRARIES}
-       ${VTK_LIBRARIES}
-       ${PACKAGE_LIBPREFIX}Core
-       ${PACKAGE_LIBPREFIX}Math
-)
 
-uLib_add_shared_library(${uLib-module})
+set(libname ${PACKAGE_LIBPREFIX}Vtk)
+set(ULIB_SHARED_LIBRARIES ${ULIB_SHARED_LIBRARIES} ${libname} PARENT_SCOPE)
+set(ULIB_SELECTED_MODULES ${ULIB_SELECTED_MODULES} Vtk PARENT_SCOPE)
+
+add_library(${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 ${PACKAGE_INSTALL_BIN_DIR} COMPONENT bin
+        LIBRARY DESTINATION ${PACKAGE_INSTALL_LIB_DIR} COMPONENT lib)
+
+install(FILES ${HEADERS} DESTINATION ${PACKAGE_INSTALL_INC_DIR}/Vtk)
 
-add_subdirectory(testing)

src/ltk/main.C

@@ -1,35 +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 "Object.h"
-
-
-int main()
-{
-  return 0;
-}

uLibConfig.cmake.in

@@ -9,11 +9,7 @@ get_filename_component(ULIB_CMAKE_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH)
 set(ULIB_INCLUDE_DIRS "@CONF_INCLUDE_DIRS@")
 
 # Our library dependencies (contains definitions for IMPORTED targets)
-# if(NOT TARGET foo AND NOT FooBar_BINARY_DIR)
+include("${ULIB_CMAKE_DIR}/uLibTargets.cmake")
-  include("${ULIB_CMAKE_DIR}/uLibTargets.cmake")
-# endif()
 
 # These are IMPORTED targets created by FooBarTargets.cmake
-# set(FOOBAR_LIBRARIES foo)
-# set(FOOBAR_EXECUTABLE bar)
 set(ULIB_LIBRARIES @ULIB_SHARED_LIBRARIES@)