feat: add condaenv.yml for environment setup and update README.md with detailed build instructions.

fix mismatch Origin - Position

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(INSTALL_BIN_DIR bin CACHE PATH "Installation directory for executables")
-set(PACKAGE_INSTALL_LIB_DIR lib/${PACKAGE_NAME} CACHE PATH "Installation directory for libraries")
+set(INSTALL_LIB_DIR lib/${PACKAGE_NAME} CACHE PATH "Installation directory for libraries")
-set(PACKAGE_INSTALL_INC_DIR include/${PACKAGE_NAME} CACHE PATH "Installation directory for headers")
+set(INSTALL_INC_DIR include/${PACKAGE_NAME} CACHE PATH "Installation directory for headers")
-set(PACKAGE_INSTALL_DATA_DIR share/${PACKAGE_NAME} CACHE PATH "Installation directory for data files")
+set(INSTALL_DATA_DIR share/${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/uLibTargetMacros.cmake

@@ -41,15 +41,15 @@ macro(uLib_add_shared_library name)
 
   install(TARGETS ${mname}
          EXPORT "${PROJECT_NAME}Targets"
-         RUNTIME DESTINATION ${PACKAGE_INSTALL_BIN_DIR} COMPONENT bin
+         RUNTIME DESTINATION ${INSTALL_BIN_DIR} COMPONENT bin
-         LIBRARY DESTINATION ${PACKAGE_INSTALL_LIB_DIR} COMPONENT lib
+         LIBRARY DESTINATION ${INSTALL_LIB_DIR} COMPONENT lib
-  #         PUBLIC_HEADER DESTINATION ${PACKAGE_INSTALL_INC_DIR} COMPONENT dev
+  #         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)
 
@@ -70,7 +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)
 

CMakeLists.txt

@@ -3,7 +3,7 @@
 ##### CMAKE LISTS ##############################################################
 ################################################################################
 
-cmake_minimum_required (VERSION 2.6)
+cmake_minimum_required (VERSION 3.26)
 
 ## -------------------------------------------------------------------------- ##
 
@@ -11,7 +11,7 @@ project(uLib)
 
 # The version number.
 set(PROJECT_VERSION_MAJOR 0)
-set(PROJECT_VERSION_MINOR 5)
+set(PROJECT_VERSION_MINOR 6)
 set(PROJECT_VERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}")
 set(PROJECT_SOVERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}")
 
@@ -33,19 +33,31 @@ message(STATUS "Module path = ${CMAKE_MODULE_PATH}")
 
 ## GLOBALS ------------------------------------------------------------------ ##
 
-set(PACKAGE_INSTALL_BIN_DIR ${CMAKE_INSTALL_PREFIX}/bin 
+# -- move to GnuInstallDirs
-    CACHE PATH "Installation directory for executables")
+# ref: https://cmake.org/cmake/help/latest/module/GNUInstallDirs.html
-set(PACKAGE_INSTALL_LIB_DIR ${CMAKE_INSTALL_PREFIX}/lib/
+include(GNUInstallDirs)
-    CACHE PATH "Installation directory for libraries")
+set(INSTALL_INC_DIR ${CMAKE_INSTALL_INCLUDEDIR}/${PACKAGE_NAME}
-set(PACKAGE_INSTALL_INC_DIR ${CMAKE_INSTALL_PREFIX}/include/${PACKAGE_NAME}
+    CACHE PATH "Location of header files (.../include)" )
-    CACHE PATH "Installation directory for headers")
+set(INSTALL_ETC_DIR ${CMAKE_INSTALL_SYSCONFDIR}/${PACKAGE_NAME}
-set(PACKAGE_INSTALL_DATA_DIR ${CMAKE_INSTALL_PREFIX}/share/${PACKAGE_NAME}
+    CACHE PATH "Location of configuration files (.../etc)" )
-    CACHE PATH "Installation directory for data files")
+set(INSTALL_BIN_DIR ${CMAKE_INSTALL_BINDIR}/${PACKAGE_NAME}
-set(PACKAGE_INSTALL_CMAKE_DIR ${CMAKE_INSTALL_PREFIX}/lib/cmake/${PACKAGE_NAME}
+    CACHE PATH "Location of executable files (.../bin)" )
-    CACHE PATH "Installation directory for CMake files")
+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)
@@ -60,25 +72,34 @@ set(CMAKE_CXX_WARNING_OPTION ""
 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} ${CMAKE_CXX_WARNING_OPTION}")
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -UULIB_SERIALIZATION_ON")
 
-#enable_testing()
+# CTEST framework
+enable_testing()
+
 
 ## FIND PACKAGES ------------------------------------------------------------ ##
 
 set(Boost_USE_STATIC_LIBS OFF)
 set(Boost_USE_MULTITHREADED ON)
 set(Boost_USE_STATIC_RUNTIME OFF)
+message(STATUS "CMAKE_PREFIX_PATH is ${CMAKE_PREFIX_PATH}")
 find_package(Boost 1.45.0 COMPONENTS program_options REQUIRED)
 include_directories(${Boost_INCLUDE_DIRS})
 
 find_package(Eigen3 CONFIG REQUIRED)
-include(${EIGEN3_USE_FILE})
+get_target_property(EIGEN3_INCLUDE_DIRS Eigen3::Eigen INTERFACE_INCLUDE_DIRECTORIES)
+include_directories(${EIGEN3_INCLUDE_DIRS})
 
 find_package(ROOT CONFIG REQUIRED)
 include(${ROOT_USE_FILE})
 
+find_package(VTK REQUIRED)
+# include(${VTK_USE_FILE})
+
+
+
 option(CENTOS_SUPPORT "VTK definitions for CentOS" OFF)
 if(CENTOS_SUPPORT)
     find_package(VTK CONFIG REQUIRED)
@@ -142,7 +163,7 @@ configure_file("${PROJECT_SOURCE_DIR}/CMakeConfig.in.h"
                "${PROJECT_BINARY_DIR}/config.h")
 
 install(FILES "${PROJECT_BINARY_DIR}/config.h"
-        DESTINATION ${PACKAGE_INSTALL_INC_DIR})
+        DESTINATION ${INSTALL_INC_DIR})
 
 ## ADD LIBRARIES SUBDIRECTORIES --------------------------------------------- ##
 
@@ -187,8 +208,8 @@ add_subdirectory(${SRC_DIR}/Vtk)
 
 
 # Create the FooBarConfig.cmake and FooBarConfigVersion files
-file(RELATIVE_PATH REL_INCLUDE_DIR "${PACKAGE_INSTALL_CMAKE_DIR}"
+# file(RELATIVE_PATH REL_INCLUDE_DIR "${INSTALL_CMAKE_DIR}"
-   "${PACKAGE_INSTALL_INC_DIR}")
+#    "${INSTALL_INC_DIR}")
 
 # ... for the build tree
 #set(CONF_INCLUDE_DIRS "${PROJECT_SOURCE_DIR}/src" "${PROJECT_BINARY_DIR}")
@@ -197,21 +218,53 @@ file(RELATIVE_PATH REL_INCLUDE_DIR "${PACKAGE_INSTALL_CMAKE_DIR}"
 
 # ... for the install tree
 set(CONF_INCLUDE_DIRS "\${ULIB_CMAKE_DIR}/${REL_INCLUDE_DIR}")
-configure_file(uLibConfig.cmake.in
+# [ removed for the configure_config_file ]
-               "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/uLibConfig.cmake"
+# configure_file(uLibConfig.cmake.in
-               @ONLY)
+#                "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/uLibConfig.cmake"
+#                @ONLY)
 
 # ... for both
 configure_file(uLibConfigVersion.cmake.in
-               "${PROJECT_BINARY_DIR}/uLibConfigVersion.cmake" @ONLY)
+                "${PROJECT_BINARY_DIR}/uLibConfigVersion.cmake" @ONLY)
 
-install(FILES "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/uLibConfig.cmake"
+
+# from CMake 3.x configure file shall be created using a dedicated function
+# see: https://cmake.org/cmake/help/latest/module/CMakePackageConfigHelpers.html
+#
+include(CMakePackageConfigHelpers)
+configure_package_config_file(uLibConfig.cmake.in
+                              "${PROJECT_BINARY_DIR}/uLibConfig.cmake"
+                              INSTALL_DESTINATION ${INSTALL_CMAKE_DIR}
+                              PATH_VARS 
+                                INSTALL_LIB_DIR 
+                                INSTALL_INC_DIR 
+                                INSTALL_BIN_DIR 
+                                INSTALL_CMAKE_DIR 
+                                INSTALL_ETC_DIR 
+                                INSTALL_DATA_DIR
+                                ULIB_SOURCE_DIR
+                                ULIB_SHARED_LIBRARIES
+                              # NO_SET_AND_CHECK_MACRO
+                              # NO_CHECK_REQUIRED_COMPONENTS_MACRO
+                              )
+
+install(FILES "${PROJECT_BINARY_DIR}/uLibConfig.cmake"
               "${PROJECT_BINARY_DIR}/uLibConfigVersion.cmake"
-        DESTINATION "${PACKAGE_INSTALL_CMAKE_DIR}"
+        DESTINATION "${INSTALL_CMAKE_DIR}"
         COMPONENT dev)
 
+
+# this is a special target file for the build tree
+# it is used also to identify if we are using a build direcory
+# to link a project against uLib. see: uLibConfig.cmake ( IF )
+export (TARGETS ${ULIB_SHARED_LIBRARIES}
+        FILE "${PROJECT_BINARY_DIR}/uLibTargets-build.cmake"
+        # NAMESPACE "uLib::"
+)        
+
 # Install the export set for use with the install-tree
-install(EXPORT "${PROJECT_NAME}Targets"
+install(EXPORT "uLibTargets"
-        DESTINATION "${PACKAGE_INSTALL_CMAKE_DIR}"
+        FILE "uLibTargets.cmake"
+        DESTINATION "${INSTALL_CMAKE_DIR}"
         COMPONENT dev)
 

CMakeUserPresets.json

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

README.md

@@ -7,3 +7,57 @@ 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
+```

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

src/Core/CMakeLists.txt

@@ -18,10 +18,10 @@ target_link_libraries(${libname} ${LIBRARIES})
 
 install(TARGETS ${libname}
         EXPORT "${PROJECT_NAME}Targets"
-        RUNTIME DESTINATION ${PACKAGE_INSTALL_BIN_DIR} COMPONENT bin
+        RUNTIME DESTINATION ${INSTALL_BIN_DIR} COMPONENT bin
-        LIBRARY DESTINATION ${PACKAGE_INSTALL_LIB_DIR} COMPONENT lib)
+        LIBRARY DESTINATION ${INSTALL_LIB_DIR} COMPONENT lib)
 
-install(FILES ${HEADERS} DESTINATION ${PACKAGE_INSTALL_INC_DIR}/Core)
+install(FILES ${HEADERS} DESTINATION ${INSTALL_INC_DIR}/Core)
 
 
 

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/Detectors/CMakeLists.txt

@@ -2,5 +2,6 @@ set(HEADERS MuonScatter.h MuonError.h MuonEvent.h)
 
 set(ULIB_SELECTED_MODULES ${ULIB_SELECTED_MODULES} Detectors PARENT_SCOPE)
 
+
 install(FILES ${HEADERS}
-        DESTINATION ${PACKAGE_INSTALL_INC_DIR}/Detectors)
+        DESTINATION ${INSTALL_INC_DIR}/Detectors)

src/Math/BitCode.h

@@ -27,6 +27,8 @@
 #ifndef U_MATH_BITCODE_H
 #define U_MATH_BITCODE_H
 
+#include <iostream>
+
 #include <boost/static_assert.hpp>
 #include <boost/type_traits.hpp>
 #include <boost/mpl/vector_c.hpp>
@@ -34,6 +36,7 @@
 
 #include <Math/Dense.h>
 
+
 namespace uLib {
 
 

src/Math/CMakeLists.txt

@@ -1,3 +1,4 @@
+
 set(HEADERS ContainerBox.h
             Dense.h
             Geometry.h
@@ -31,8 +32,9 @@ set(SOURCES VoxRaytracer.cpp
             Structured2DGrid.cpp
             Structured4DGrid.cpp)
 
-set(LIBRARIES ${Eigen_LIBRARY}
+set(LIBRARIES Eigen3::Eigen
-              ${ROOT_LIBRARIES})
+              ${ROOT_LIBRARIES}
+              ${VTK_LIBRARIES})
 
 set(libname ${PACKAGE_LIBPREFIX}Math)
 set(ULIB_SHARED_LIBRARIES ${ULIB_SHARED_LIBRARIES} ${libname} PARENT_SCOPE)
@@ -44,10 +46,15 @@ set_target_properties(${libname} PROPERTIES
                       SOVERSION ${PROJECT_SOVERSION})
 target_link_libraries(${libname} ${LIBRARIES})
 
+
 install(TARGETS ${libname}
         EXPORT "${PROJECT_NAME}Targets"
-        RUNTIME DESTINATION ${PACKAGE_INSTALL_BIN_DIR} COMPONENT bin
+        RUNTIME DESTINATION ${INSTALL_BIN_DIR} COMPONENT bin
-        LIBRARY DESTINATION ${PACKAGE_INSTALL_LIB_DIR} COMPONENT lib)
+        LIBRARY DESTINATION ${INSTALL_LIB_DIR} COMPONENT lib)
 
-install(FILES ${HEADERS} DESTINATION ${PACKAGE_INSTALL_INC_DIR}/Math)
+install(FILES ${HEADERS} DESTINATION ${INSTALL_INC_DIR}/Math)
+
+# TESTING
+# include(uLibTargetMacros)
+# add_subdirectory(testing)
 

src/Math/Dense.h

@@ -139,7 +139,6 @@ typedef Eigen::Vector4f Vector4f;
 
 
 
-
 ////////////////////////////////////////////////////////////////////////////////
 // Vector String interaction ///////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////

src/Math/Transform.h

@@ -110,6 +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/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 / norm);
-                this->SetValue(idx,tmp_val*1E-6);
             }
         }
     }

src/Math/VoxImage.h

@@ -56,8 +56,18 @@ public:
     virtual void SetDims(const Vector3i &size) = 0;
 
     void ExportToVtk(const char *file, bool density_type = 0);
+
+    // use this function to export to VTK binary format
+    void ExportToVti (const char *file, bool density_type = 0, bool compressed = 0);
+    
+    // this function has been deprecated in favor of ExportToVti
+    // but it is kept for backward compatibility and because it 
+    // does not depend on vtk library
     void ExportToVtkXml(const char *file, bool density_type = 0);
-    int ImportFromVtk(const char *file);
+
+    int ImportFromVtk(const char *file, bool density_type = 0);
+
+    int ImportFromVti(const char *file, bool density_type = 0);
 
 protected:
 

src/Math/testing/CMakeLists.txt

@@ -19,4 +19,4 @@ set(LIBRARIES
        ${PACKAGE_LIBPREFIX}Math
 )
 
-uLib_add_tests(${uLib-module})
+uLib_add_tests(Math)

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/Root/CMakeLists.txt

@@ -42,7 +42,7 @@ list(APPEND SOURCES ${rDictName}.cxx)
 set(R_ARTIFACTS ${CMAKE_CURRENT_BINARY_DIR}/lib${rDictName}_rdict.pcm
                 ${CMAKE_CURRENT_BINARY_DIR}/lib${rDictName}.rootmap)
 install(FILES ${R_ARTIFACTS}
-        DESTINATION ${PACKAGE_INSTALL_LIB_DIR})
+        DESTINATION ${INSTALL_LIB_DIR})
 
 set(libname ${PACKAGE_LIBPREFIX}Root)
 set(ULIB_SHARED_LIBRARIES ${ULIB_SHARED_LIBRARIES} ${libname} PARENT_SCOPE)
@@ -51,14 +51,15 @@ 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})
+                      SOVERSION ${PROJECT_SOVERSION}
+                      CXX_STANDARD 17)
 target_link_libraries(${libname} ${LIBRARIES})
 
 install(TARGETS ${libname}
         EXPORT "${PROJECT_NAME}Targets"
-        RUNTIME DESTINATION ${PACKAGE_INSTALL_BIN_DIR} COMPONENT bin
+        RUNTIME DESTINATION ${INSTALL_BIN_DIR} COMPONENT bin
-        LIBRARY DESTINATION ${PACKAGE_INSTALL_LIB_DIR} COMPONENT lib)
+        LIBRARY DESTINATION ${INSTALL_LIB_DIR} COMPONENT lib)
 
-install(FILES ${HEADERS} DESTINATION ${PACKAGE_INSTALL_INC_DIR}/Root)
+install(FILES ${HEADERS} DESTINATION ${INSTALL_INC_DIR}/Root)
 
 

src/Vtk/CMakeLists.txt

@@ -14,7 +14,7 @@ set(SOURCES uLibVtkInterface.cxx
             vtkVoxRaytracerRepresentation.cpp
             vtkVoxImage.cpp)
 
-set(LIBRARIES ${Eigen_LIBRARY}
+set(LIBRARIES Eigen3::Eigen
               ${ROOT_LIBRARIES}
               ${VTK_LIBRARIES}
               ${PACKAGE_LIBPREFIX}Math)
@@ -31,8 +31,8 @@ target_link_libraries(${libname} ${LIBRARIES})
 
 install(TARGETS ${libname}
         EXPORT "${PROJECT_NAME}Targets"
-        RUNTIME DESTINATION ${PACKAGE_INSTALL_BIN_DIR} COMPONENT bin
+        RUNTIME DESTINATION ${INSTALL_BIN_DIR} COMPONENT bin
-        LIBRARY DESTINATION ${PACKAGE_INSTALL_LIB_DIR} COMPONENT lib)
+        LIBRARY DESTINATION ${INSTALL_LIB_DIR} COMPONENT lib)
 
-install(FILES ${HEADERS} DESTINATION ${PACKAGE_INSTALL_INC_DIR}/Vtk)
+install(FILES ${HEADERS} DESTINATION ${INSTALL_INC_DIR}/Vtk)
 

src/Vtk/uLibVtkInterface.cxx

@@ -37,7 +37,7 @@
 #endif
 
 
-#include <vtkConfigure.h>
+#include <vtkVersion.h>
 #include <vtkProp.h>
 #include <vtkActor.h>
 #include <vtkSmartPointer.h>

src/Vtk/vtkContainerBox.cpp

@@ -65,6 +65,7 @@ vtkContainerBox::~vtkContainerBox()
 vtkPolyData *vtkContainerBox::GetPolyData() const
 {
     // TODO
+    return NULL;
 }
 
 void vtkContainerBox::InstallPipe()

src/Vtk/vtkMuonScatter.h

@@ -28,7 +28,7 @@
 #ifndef VTKMUONSCATTER_H
 #define VTKMUONSCATTER_H
 
-#include <vtkConfigure.h>
+#include <vtkVersion.h>
 #include <vtkSmartPointer.h>
 #include <vtkSphereSource.h>
 #include <vtkAppendPolyData.h>

src/Vtk/vtkVoxImage.h

@@ -28,11 +28,11 @@
 #ifndef U_VTKVOXIMAGE_H
 #define U_VTKVOXIMAGE_H
 
-#include "vtk/vtkVolume.h"
+#include <vtkVolume.h>
-#include "vtk/vtkImageData.h"
+#include <vtkImageData.h>
-#include "vtk/vtkXMLImageDataReader.h"
+#include <vtkXMLImageDataReader.h>
-#include "vtk/vtkXMLImageDataWriter.h"
+#include <vtkXMLImageDataWriter.h>
-#include "vtk/vtkCubeSource.h"
+#include <vtkCubeSource.h>
 
 #include <Math/VoxImage.h>
 

uLibConfig.cmake.in

@@ -1,15 +1,92 @@
-# - Config file for the FooBar package
+# - Config file for the ULib package
 # It defines the following variables
-#  FOOBAR_INCLUDE_DIRS - include directories for FooBar
+#  ULIB_INCLUDE_DIRS - include directories for ULib
-#  FOOBAR_LIBRARIES    - libraries to link against
+#  ULIB_LIBRARIES    - libraries to link against
-#  FOOBAR_EXECUTABLE   - the bar executable
+#  ULIB_EXECUTABLE   - the bar executable
+
+
+set(ULIB_VERSION @PROJECT_VERSION@)
+
+@PACKAGE_INIT@
+
+# Defines the include directories for the header files
+# PACKAGE_INCLUDE_INSTALL_DIR is replaced by configure_package_config_file
+# with the correct path for the installation.
+set(ULIB_INCLUDE_DIRS "${PACKAGE_INCLUDE_INSTALL_DIR}")
 
-# Compute paths
 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)
+# Search for the directory of exported build targets
-include("${ULIB_CMAKE_DIR}/uLibTargets.cmake")
+set(uLib_BUILD_TARGETS_FILE
+    "${ULIB_CMAKE_DIR}/uLibTargets-build.cmake"
+)
+
+# Search for the directory of installed targets
+set(uLib_INSTALL_TARGETS_FILE
+    "${ULIB_CMAKE_DIR}/uLibTargets.cmake"
+)
+
+# We use a logic based on the presence of the build target file
+# to determine if we are in a local build.
+if(EXISTS "${uLib_BUILD_TARGETS_FILE}")
+    message(STATUS " ++ Using uLib build targets")
+
+    include("${uLib_BUILD_TARGETS_FILE}")
+    set_and_check(ULIB_INCLUDE_DIRS "@ULIB_SOURCE_DIR@/src")
+    set_and_check(ULIB_LIBRARY_DIRS "${ULIB_CMAKE_DIR}")
+    set(ULIB_BUILD_DIR ${ULIB_CMAKE_DIR})
+
+    # Target that builds uLib inside its build directory
+    add_custom_target(uLib_dependency_target
+        COMMAND echo " --------------------------------- "
+        COMMAND echo " - Building uLib as a dependency - "
+        COMMAND echo " --------------------------------- "
+        COMMAND echo ""
+        COMMAND ${CMAKE_COMMAND} --build ${ULIB_BUILD_DIR}
+        COMMAND echo ""
+        WORKING_DIRECTORY ${ULIB_BUILD_DIR}
+    )
+
+    add_library(uLib_dependency INTERFACE)
+    add_dependencies(uLib_dependency uLib_dependency_target)
+    link_libraries(uLib_dependency)
+
+else()
+    message(STATUS " ++ Using uLib installed targets")
+
+    include("${uLib_INSTALL_TARGETS_FILE}")
+    set_and_check(ULIB_INCLUDE_DIRS "@PACKAGE_INSTALL_INC_DIR@")
+    set(ULIB_SYSCONFIG_DIR "@PACKAGE_INSTALL_ETC_DIR@")
+    set_and_check(ULIB_CMAKE_DIR "@PACKAGE_INSTALL_CMAKE_DIR@")
+    set_and_check(ULIB_LIBRARY_DIRS "@PACKAGE_INSTALL_LIB_DIR@")
+endif()
+
+# --- Add required packages from uLib ---
+# TODO: this should be selected if components are active
+#
+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 filesystem REQUIRED)
+include_directories(${Boost_INCLUDE_DIRS})
+link_libraries(${Boost_LIBRARIES})
+
+find_package(Eigen3 CONFIG REQUIRED)
+include(${EIGEN3_USE_FILE})
+
+find_package(ROOT CONFIG REQUIRED)
+include(${ROOT_USE_FILE})
+
+find_package(VTK REQUIRED)
+# include(${VTK_USE_FILE})
+
+
+
+link_directories("${ULIB_LIBRARY_DIRS}")
+set(ULIB_LIBRARIES "@ULIB_SHARED_LIBRARIES@")
+check_required_components(uLib)
+
+# Set the variable to indicate that the package has been found.
+set(uLib_FOUND TRUE)
+
 
-# These are IMPORTED targets created by FooBarTargets.cmake
-set(ULIB_LIBRARIES @ULIB_SHARED_LIBRARIES@)