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

fix mismatch Origin - Position

CMakeLists.txt

@@ -84,11 +84,13 @@ enable_testing()
 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})

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/Math/CMakeLists.txt

@@ -32,7 +32,7 @@ set(SOURCES VoxRaytracer.cpp
             Structured2DGrid.cpp
             Structured4DGrid.cpp)
 
-set(LIBRARIES ${Eigen_LIBRARY}
+set(LIBRARIES Eigen3::Eigen
               ${ROOT_LIBRARIES}
               ${VTK_LIBRARIES})
 

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)

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/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>