add filters in python bindings

.gitignore

@@ -5,3 +5,10 @@ build_warnings*.log
 final_build.log
 cmake_configure.log
 compile_commands.json
+
+dist/
+build_python/
+src/Python/uLib/*.so*
+src/Python/uLib/*.pyd
+src/Python/uLib/*.pyc
+src/Python/uLib/__pycache__

build_python.py

@@ -0,0 +1,47 @@
+import os
+import subprocess
+import sys
+import shutil
+
+def build(setup_kwargs):
+    """
+    Build the C++ extension using CMake.
+    This function is called by poetry-core during the build process.
+    The binary is placed directly inside the uLib directory in src/Python.
+    """
+    # Root of the whole project where this build_extension.py is located
+    project_root = os.path.abspath(os.path.dirname(__file__))
+    
+    # Where the extension should go
+    package_dir = os.path.join(project_root, "src/Python/uLib")
+    
+    # Ensure package directory exists
+    os.makedirs(package_dir, exist_ok=True)
+    
+    # Temporary build directory
+    build_temp = os.path.join(project_root, "build_python")
+    os.makedirs(build_temp, exist_ok=True)
+
+    print(f"--- Running CMake build in {build_temp} ---")
+    print(f"Project root: {project_root}")
+    print(f"Target binary dir: {package_dir}")
+
+    # CMake configuration
+    cmake_args = [
+        f"-DCMAKE_LIBRARY_OUTPUT_DIRECTORY={package_dir}",
+        f"-DPYTHON_EXECUTABLE={sys.executable}",
+        "-DCMAKE_BUILD_TYPE=Release",
+        "-DUSE_CUDA=OFF", 
+        "-G", "Unix Makefiles",
+    ]
+
+    # Use micromamba to ensure Boost and VTK are found during the build
+    subprocess.check_call(["cmake", project_root] + cmake_args, cwd=build_temp)
+    subprocess.check_call(["cmake", "--build", ".", "--parallel", "--target", "uLib_python"], cwd=build_temp)
+    
+    # Ensure the package is found by poetry during the wheel creation process.
+    # Return setup_kwargs for poetry-core.
+    return setup_kwargs
+
+if __name__ == "__main__":
+    build({})

poetry.lock

@@ -0,0 +1,7 @@
+# This file is automatically @generated by Poetry 2.3.1 and should not be changed by hand.
+package = []
+
+[metadata]
+lock-version = "2.1"
+python-versions = ">=3.9"
+content-hash = "db9b4c08b159b17b239e26c67ead7c37b82d9f9eb06550245ae3134c095f98f7"

pyproject.toml

@@ -0,0 +1,15 @@
+[tool.poetry]
+name = "uLib"
+version = "0.6.0"
+description = "CMT Cosmic Muon Tomography project uLib python bindings"
+authors = ["Andrea Rigoni Garola <andrea.rigoni@pd.infn.it>"]
+readme = "README.md"
+packages = [{ include = "uLib", from = "src/Python" }]
+build = "build_python.py"
+
+[tool.poetry.dependencies]
+python = ">=3.9"
+
+[build-system]
+requires = ["poetry-core>=2.0.0", "pybind11>=2.6.0", "cmake>=3.12"]
+build-backend = "poetry.core.masonry.api"

src/Core/CMakeLists.txt

@@ -1,7 +1,36 @@
 
-set(HEADERS Archives.h Array.h Collection.h DataAllocator.h Debug.h Export.h Function.h Macros.h Mpl.h Object.h Options.h Serializable.h Signal.h Singleton.h SmartPointer.h StaticInterface.h StringReader.h Types.h Uuid.h Vector.h)
+set(HEADERS 
+    Archives.h 
+    Array.h 
+    Collection.h 
+    DataAllocator.h 
+    Debug.h 
+    Export.h 
+    Function.h 
+    Macros.h 
+    Mpl.h 
+    Object.h 
+    Options.h 
+    Serializable.h 
+    Signal.h 
+    Singleton.h 
+    SmartPointer.h 
+    StaticInterface.h 
+    StringReader.h 
+    Types.h 
+    Uuid.h 
+    Vector.h
+)
 
-set(SOURCES Archives.cpp Debug.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::program_options Boost::serialization)
 

src/Core/Vector.h

@@ -117,6 +117,10 @@ bool operator!=(const MetaAllocator<T> &, const MetaAllocator<U> &) {
   return false;
 }
 
+
+
+
+
 // Vector Implemetation ... wraps std::vector
 template <typename T> class Vector : public std::vector<T, MetaAllocator<T>> {
   typedef std::vector<T, MetaAllocator<T>> BaseClass;
@@ -136,6 +140,7 @@ public:
   Vector(unsigned int size) : BaseClass(size) {}
   Vector(unsigned int size, T &value) : BaseClass(size, value) {}
   Vector() : BaseClass(0) {}
+  Vector(std::initializer_list<T> init) : BaseClass(init) {}
 
   inline VectorCommaInit operator<<(T scalar) {
     return VectorCommaInit(this, scalar);
@@ -274,6 +279,11 @@ public:
     this->MoveToRAM();
     return BaseClass::insert(pos, std::move(x));
   }
+  template <typename InputIt>
+  iterator insert(const_iterator pos, InputIt first, InputIt last) {
+    this->MoveToRAM();
+    return BaseClass::insert(pos, first, last);
+  }
   iterator erase(const_iterator pos) {
     this->MoveToRAM();
     return BaseClass::erase(pos);

src/Core/test_meta_allocator.cpp

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

src/Math/Dense.h

@@ -47,6 +47,7 @@
 #ifndef ULIB_DENSEMATRIX_H
 #define ULIB_DENSEMATRIX_H
 
+// #include <Eigen/src/Core/Matrix.h>
 #include <stdlib.h>
 
 #include <Eigen/Dense>
@@ -114,6 +115,21 @@ typedef unsigned long Scalarul;
 typedef float Scalarf;
 typedef double Scalard;
 
+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::Vector2f Vector2f;
+typedef Eigen::Vector3f Vector3f;
+typedef Eigen::Vector4f Vector4f;
+
+typedef Eigen::Matrix<double, 1, 1> Vector1d;
+typedef Eigen::Vector2d Vector2d;
+typedef Eigen::Vector3d Vector3d;
+typedef Eigen::Vector4d Vector4d;
+
 typedef Eigen::Matrix<int, 1, 1> Matrix1i;
 typedef Eigen::Matrix2i Matrix2i;
 typedef Eigen::Matrix3i Matrix3i;
@@ -124,15 +140,15 @@ typedef Eigen::Matrix2f Matrix2f;
 typedef Eigen::Matrix3f Matrix3f;
 typedef Eigen::Matrix4f Matrix4f;
 
-typedef Eigen::Matrix<int, 1, 1> Vector1i;
+typedef Eigen::Matrix<double, 1, 1> Matrix1d;
-typedef Eigen::Vector2i Vector2i;
+typedef Eigen::Matrix2d Matrix2d;
-typedef Eigen::Vector3i Vector3i;
+typedef Eigen::Matrix3d Matrix3d;
-typedef Eigen::Vector4i Vector4i;
+typedef Eigen::Matrix4d Matrix4d;
+
+typedef Eigen::MatrixXi MatrixXi;
+typedef Eigen::MatrixXf MatrixXf;
+typedef Eigen::MatrixXd MatrixXd;
 
-typedef Eigen::Matrix<float, 1, 1> Vector1f;
-typedef Eigen::Vector2f Vector2f;
-typedef Eigen::Vector3f Vector3f;
-typedef Eigen::Vector4f Vector4f;
 
 ////////////////////////////////////////////////////////////////////////////////
 // Vector String interaction ///////////////////////////////////////////////////
@@ -175,7 +191,7 @@ std::string VectorxT_ToString(const Eigen::Matrix<T, size, 1> &vec) {
 // }
 
 template <typename T, int size>
-void operator>>(std::string &str, Eigen::Matrix<T, size, 1> &vec) {
+void operator >> (std::string &str, Eigen::Matrix<T, size, 1> &vec) {
   VectorxT_StringTo(vec, str);
 }
 
@@ -188,6 +204,9 @@ public:
   typedef Eigen::Matrix<Scalarf, 4, 1> BaseClass;
 
   _HPoint3f() : BaseClass(0, 0, 0, p) {}
+  _HPoint3f(int rows, int cols) : BaseClass() {
+    this->operator()(3) = p;
+  }
   _HPoint3f(float x, float y, float z) : BaseClass(x, y, z, p) {}
   _HPoint3f(Vector3f &in) : BaseClass(in.homogeneous()) {
     this->operator()(3) = p;

src/Math/VoxImage.h

@@ -70,8 +70,8 @@ public:
 
   int ImportFromVti(const char *file, bool density_type = 0);
 
-protected:
   virtual ~VoxImage() {}
+protected:
   VoxImage(const Vector3i &size) : BaseClass(size) {}
 };
 
@@ -90,7 +90,8 @@ struct Voxel {
 } // namespace Interface
 
 struct Voxel {
-  Scalarf Value;
+  Scalarf Value = 0.0f;
+  Scalari Count = 0;
 };
 
 ////////////////////////////////////////////////////////////////////////////////

src/Math/VoxImageFilterABTrim.hpp

@@ -36,7 +36,7 @@
 
 namespace uLib {
 
-#ifdef USE_CUDA
+#if defined(USE_CUDA) && defined(__CUDACC__)
 template <typename VoxelT>
 __global__ void ABTrimFilterKernel(const VoxelT *in, VoxelT *out,
                                    const VoxelT *kernel, int vox_size,
@@ -108,7 +108,7 @@ public:
     mBtrim = 0;
   }
 
-#ifdef USE_CUDA
+#if defined(USE_CUDA) && defined(__CUDACC__)
   void Run() {
     if (this->m_Image->Data().GetDevice() == MemoryDevice::VRAM ||
         this->m_KernelData.Data().GetDevice() == MemoryDevice::VRAM) {
@@ -206,7 +206,7 @@ public:
     mBtrim = 0;
   }
 
-#ifdef USE_CUDA
+#if defined(USE_CUDA) && defined(__CUDACC__)
   void Run() {
     if (this->m_Image->Data().GetDevice() == MemoryDevice::VRAM ||
         this->m_KernelData.Data().GetDevice() == MemoryDevice::VRAM) {

src/Math/VoxImageFilterLinear.hpp

@@ -36,7 +36,7 @@
 
 namespace uLib {
 
-#ifdef USE_CUDA
+#if defined(USE_CUDA) && defined(__CUDACC__)
 template <typename VoxelT>
 __global__ void LinearFilterKernel(const VoxelT *in, VoxelT *out,
                                    const VoxelT *kernel, int vox_size,
@@ -66,7 +66,7 @@ public:
   typedef VoxImageFilter<VoxelT, VoxFilterAlgorithmLinear<VoxelT>> BaseClass;
   VoxFilterAlgorithmLinear(const Vector3i &size) : BaseClass(size) {}
 
-#ifdef USE_CUDA
+#if defined(USE_CUDA) && defined(__CUDACC__)
   void Run() {
     if (this->m_Image->Data().GetDevice() == MemoryDevice::VRAM ||
         this->m_KernelData.Data().GetDevice() == MemoryDevice::VRAM) {

src/Python/CMakeLists.txt

@@ -4,10 +4,11 @@ set(SOURCES
     module.cpp
     core_bindings.cpp
     math_bindings.cpp
+    math_filters_bindings.cpp
 )
 
 # Use pybind11 to add the python module
-pybind11_add_module(uLib_python module.cpp core_bindings.cpp math_bindings.cpp)
+pybind11_add_module(uLib_python module.cpp core_bindings.cpp math_bindings.cpp math_filters_bindings.cpp)
 
 # Link against our C++ libraries
 target_link_libraries(uLib_python PRIVATE
@@ -22,6 +23,14 @@ target_include_directories(uLib_python PRIVATE
     ${PROJECT_BINARY_DIR}
 )
 
+# Install uLib_python within the uLib install target
+install(TARGETS uLib_python
+        EXPORT "${PROJECT_NAME}Targets"
+        RUNTIME DESTINATION ${INSTALL_BIN_DIR} COMPONENT bin
+        LIBRARY DESTINATION ${INSTALL_LIB_DIR} COMPONENT lib
+        ARCHIVE DESTINATION ${INSTALL_LIB_DIR} COMPONENT lib
+)
+
 # --- Python Tests ---------------------------------------------------------- #
 
 if(BUILD_TESTING)
@@ -30,15 +39,20 @@ if(BUILD_TESTING)
     add_test(NAME pybind_general
              COMMAND ${Python3_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/testing/pybind_test.py)
     set_tests_properties(pybind_general PROPERTIES 
-                         ENVIRONMENT "PYTHONPATH=$<TARGET_FILE_DIR:uLib_python>")
+                         ENVIRONMENT "PYTHONPATH=$<TARGET_FILE_DIR:uLib_python>:${PROJECT_SOURCE_DIR}/src/Python")
 
     add_test(NAME pybind_core 
              COMMAND ${Python3_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/testing/core_pybind_test.py)
     set_tests_properties(pybind_core PROPERTIES 
-                         ENVIRONMENT "PYTHONPATH=$<TARGET_FILE_DIR:uLib_python>")
+                         ENVIRONMENT "PYTHONPATH=$<TARGET_FILE_DIR:uLib_python>:${PROJECT_SOURCE_DIR}/src/Python")
 
     add_test(NAME pybind_math 
              COMMAND ${Python3_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/testing/math_pybind_test.py)
     set_tests_properties(pybind_math PROPERTIES 
-                         ENVIRONMENT "PYTHONPATH=$<TARGET_FILE_DIR:uLib_python>")
+                         ENVIRONMENT "PYTHONPATH=$<TARGET_FILE_DIR:uLib_python>:${PROJECT_SOURCE_DIR}/src/Python")
+
+    add_test(NAME pybind_math_filters 
+             COMMAND ${Python3_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/testing/math_filters_test.py)
+    set_tests_properties(pybind_math_filters PROPERTIES 
+                         ENVIRONMENT "PYTHONPATH=$<TARGET_FILE_DIR:uLib_python>:${PROJECT_SOURCE_DIR}/src/Python")
 endif()

src/Python/math_bindings.cpp

@@ -1,6 +1,9 @@
 #include <pybind11/pybind11.h>
 #include <pybind11/eigen.h>
 #include <pybind11/stl.h>
+#include <pybind11/stl_bind.h>
+
+#include <pybind11/numpy.h>
 
 #include "Math/Dense.h"
 #include "Math/Transform.h"
@@ -13,13 +16,224 @@
 #include "Math/TriangleMesh.h"
 #include "Math/VoxRaytracer.h"
 #include "Math/Accumulator.h"
+#include "Math/VoxImage.h"
 
 namespace py = pybind11;
 using namespace uLib;
 
+PYBIND11_MAKE_OPAQUE(uLib::Vector<Scalari>);
+PYBIND11_MAKE_OPAQUE(uLib::Vector<Scalarui>);
+PYBIND11_MAKE_OPAQUE(uLib::Vector<Scalarl>);
+PYBIND11_MAKE_OPAQUE(uLib::Vector<Scalarul>);
+PYBIND11_MAKE_OPAQUE(uLib::Vector<Scalarf>);
+PYBIND11_MAKE_OPAQUE(uLib::Vector<Scalard>);
+
+PYBIND11_MAKE_OPAQUE(uLib::Vector<Vector3f>);
+PYBIND11_MAKE_OPAQUE(uLib::Vector<Vector3i>);
+PYBIND11_MAKE_OPAQUE(uLib::Vector<Vector4f>);
+PYBIND11_MAKE_OPAQUE(uLib::Vector<Vector4i>);
+PYBIND11_MAKE_OPAQUE(uLib::Vector<Vector3d>);
+PYBIND11_MAKE_OPAQUE(uLib::Vector<Vector4d>);
+
+PYBIND11_MAKE_OPAQUE(uLib::Vector<Voxel>);
+PYBIND11_MAKE_OPAQUE(uLib::Vector<VoxRaytracer::RayData::Element>);
+
+template <typename MatrixType>
+void bind_eigen_type(py::module_ &m, const char *name) {
+    using Scalar = typename MatrixType::Scalar;
+    constexpr bool is_vector = MatrixType::IsVectorAtCompileTime;
+
+    // Default constructor (zeros)
+    m.def(name, []() -> MatrixType {
+        if constexpr (MatrixType::RowsAtCompileTime == Eigen::Dynamic || MatrixType::ColsAtCompileTime == Eigen::Dynamic) {
+            return MatrixType(); // Empty dynamic matrix
+        } else {
+            return MatrixType::Zero(); // Zero static matrix
+        }
+    });
+
+    // Specialized constructor for dynamic matrices
+    if constexpr (MatrixType::RowsAtCompileTime == Eigen::Dynamic || MatrixType::ColsAtCompileTime == Eigen::Dynamic) {
+        m.def(name, [](int rows, int cols) -> MatrixType {
+            MatrixType mat;
+            mat.setZero(rows, cols);
+            return mat;
+        });
+    }
+
+    // Initialize from list
+    m.def(name, [](py::list l) -> MatrixType {
+        MatrixType mat;
+        if constexpr (is_vector) {
+            mat.setZero(l.size());
+            for (size_t i = 0; i < l.size(); ++i) {
+                mat(i) = l[i].cast<Scalar>();
+            }
+        } else {
+            int rows = MatrixType::RowsAtCompileTime == Eigen::Dynamic ? (int)std::sqrt(l.size()) : MatrixType::RowsAtCompileTime;
+            int cols = MatrixType::ColsAtCompileTime == Eigen::Dynamic ? (int)std::sqrt(l.size()) : MatrixType::ColsAtCompileTime;
+            mat.setZero(rows, cols);
+            for (size_t i = 0; i < (size_t)l.size(); ++i) {
+                mat(i / cols, i % cols) = l[i].cast<Scalar>();
+            }
+        }
+        return mat;
+    });
+
+    // Initialize from py::array
+    m.def(name, [](py::array_t<Scalar, py::array::c_style | py::array::forcecast> arr) -> MatrixType {
+        auto buf = arr.request();
+        MatrixType mat;
+        if constexpr (is_vector) {
+            mat.setZero(buf.size);
+            Scalar* ptr = static_cast<Scalar*>(buf.ptr);
+            for (ssize_t i = 0; i < buf.size; ++i) mat(i) = ptr[i];
+        } else {
+            int rows = buf.shape.size() > 0 ? (int)buf.shape[0] : 1;
+            int cols = buf.shape.size() > 1 ? (int)buf.shape[1] : 1;
+            mat.setZero(rows, cols);
+            Scalar* ptr = static_cast<Scalar*>(buf.ptr);
+            for (int i = 0; i < rows; ++i) {
+                for (int j = 0; j < cols; ++j) {
+                    mat(i, j) = ptr[i * cols + j];
+                }
+            }
+        }
+        return mat;
+    });
+}
+
 void init_math(py::module_ &m) {
 
-    // Math/Transform.h
+    // 1. Basic Eigen Types (Vectors and Matrices)
+    bind_eigen_type<Vector1f>(m, "Vector1f");
+    bind_eigen_type<Vector2f>(m, "Vector2f");
+    bind_eigen_type<Vector3f>(m, "Vector3f");
+    bind_eigen_type<Vector4f>(m, "Vector4f");
+    bind_eigen_type<Vector1i>(m, "Vector1i");
+    bind_eigen_type<Vector2i>(m, "Vector2i");
+    bind_eigen_type<Vector3i>(m, "Vector3i");
+    bind_eigen_type<Vector4i>(m, "Vector4i");
+    bind_eigen_type<Vector1d>(m, "Vector1d");
+    bind_eigen_type<Vector2d>(m, "Vector2d");
+    bind_eigen_type<Vector3d>(m, "Vector3d");
+    bind_eigen_type<Vector4d>(m, "Vector4d");
+
+    bind_eigen_type<Matrix2f>(m, "Matrix2f");
+    bind_eigen_type<Matrix3f>(m, "Matrix3f");
+    bind_eigen_type<Matrix4f>(m, "Matrix4f");
+    bind_eigen_type<Matrix2i>(m, "Matrix2i");
+    bind_eigen_type<Matrix3i>(m, "Matrix3i");
+    bind_eigen_type<Matrix4i>(m, "Matrix4i");
+    bind_eigen_type<Matrix2d>(m, "Matrix2d");
+    bind_eigen_type<Matrix3d>(m, "Matrix3d");
+    bind_eigen_type<Matrix4d>(m, "Matrix4d");
+
+    bind_eigen_type<MatrixXi>(m, "MatrixXi");
+    bind_eigen_type<MatrixXf>(m, "MatrixXf");
+    bind_eigen_type<MatrixXd>(m, "MatrixXd");
+
+    // 2. Homogeneous types
+    py::class_<HPoint3f>(m, "HPoint3f")
+        .def(py::init<>())
+        .def(py::init<float, float, float>())
+        .def(py::init<Vector3f &>());
+    py::class_<HVector3f>(m, "HVector3f")
+        .def(py::init<>())
+        .def(py::init<float, float, float>())
+        .def(py::init<Vector3f &>());
+    py::class_<HLine3f>(m, "HLine3f")
+        .def(py::init<>())
+        .def_readwrite("origin", &HLine3f::origin)
+        .def_readwrite("direction", &HLine3f::direction);
+    py::class_<HError3f>(m, "HError3f")
+        .def(py::init<>())
+        .def_readwrite("position_error", &HError3f::position_error)
+        .def_readwrite("direction_error", &HError3f::direction_error);
+
+    // 3. Dynamic Vectors (uLib::Vector)
+    py::bind_vector<uLib::Vector<Scalari>>(m, "Vector_i")
+        .def("MoveToVRAM", &uLib::Vector<Scalari>::MoveToVRAM)
+        .def("MoveToRAM", &uLib::Vector<Scalari>::MoveToRAM);
+    py::bind_vector<uLib::Vector<Scalarui>>(m, "Vector_ui")
+        .def("MoveToVRAM", &uLib::Vector<Scalarui>::MoveToVRAM)
+        .def("MoveToRAM", &uLib::Vector<Scalarui>::MoveToRAM);
+    py::bind_vector<uLib::Vector<Scalarl>>(m, "Vector_l")
+        .def("MoveToVRAM", &uLib::Vector<Scalarl>::MoveToVRAM)
+        .def("MoveToRAM", &uLib::Vector<Scalarl>::MoveToRAM);
+    py::bind_vector<uLib::Vector<Scalarul>>(m, "Vector_ul")
+        .def("MoveToVRAM", &uLib::Vector<Scalarul>::MoveToVRAM)
+        .def("MoveToRAM", &uLib::Vector<Scalarul>::MoveToRAM);
+    py::bind_vector<uLib::Vector<Scalarf>>(m, "Vector_f")
+        .def("MoveToVRAM", &uLib::Vector<Scalarf>::MoveToVRAM)
+        .def("MoveToRAM", &uLib::Vector<Scalarf>::MoveToRAM);
+    py::bind_vector<uLib::Vector<Scalard>>(m, "Vector_d")
+        .def("MoveToVRAM", &uLib::Vector<Scalard>::MoveToVRAM)
+        .def("MoveToRAM", &uLib::Vector<Scalard>::MoveToRAM);
+
+    py::bind_vector<uLib::Vector<Vector3f>>(m, "Vector_Vector3f")
+        .def("MoveToVRAM", &uLib::Vector<Vector3f>::MoveToVRAM)
+        .def("MoveToRAM", &uLib::Vector<Vector3f>::MoveToRAM);
+    py::bind_vector<uLib::Vector<Vector3i>>(m, "Vector_Vector3i")
+        .def("MoveToVRAM", &uLib::Vector<Vector3i>::MoveToVRAM)
+        .def("MoveToRAM", &uLib::Vector<Vector3i>::MoveToRAM);
+    py::bind_vector<uLib::Vector<Vector4f>>(m, "Vector_Vector4f")
+        .def("MoveToVRAM", &uLib::Vector<Vector4f>::MoveToVRAM)
+        .def("MoveToRAM", &uLib::Vector<Vector4f>::MoveToRAM);
+    py::bind_vector<uLib::Vector<Vector4i>>(m, "Vector_Vector4i")
+        .def("MoveToVRAM", &uLib::Vector<Vector4i>::MoveToVRAM)
+        .def("MoveToRAM", &uLib::Vector<Vector4i>::MoveToRAM);
+    py::bind_vector<uLib::Vector<Vector3d>>(m, "Vector_Vector3d")
+        .def("MoveToVRAM", &uLib::Vector<Vector3d>::MoveToVRAM)
+        .def("MoveToRAM", &uLib::Vector<Vector3d>::MoveToRAM);
+    py::bind_vector<uLib::Vector<Vector4d>>(m, "Vector_Vector4d")
+        .def("MoveToVRAM", &uLib::Vector<Vector4d>::MoveToVRAM)
+        .def("MoveToRAM", &uLib::Vector<Vector4d>::MoveToRAM);
+    py::bind_vector<uLib::Vector<Voxel>>(m, "Vector_Voxel")
+        .def("MoveToVRAM", &uLib::Vector<Voxel>::MoveToVRAM)
+        .def("MoveToRAM", &uLib::Vector<Voxel>::MoveToRAM);
+    py::bind_vector<uLib::Vector<VoxRaytracer::RayData::Element>>(m, "Vector_VoxRaytracerRayDataElement")
+        .def("MoveToVRAM", &uLib::Vector<VoxRaytracer::RayData::Element>::MoveToVRAM)
+        .def("MoveToRAM", &uLib::Vector<VoxRaytracer::RayData::Element>::MoveToRAM);
+
+    // 4. Accumulators
+    py::class_<Accumulator_Mean<float>>(m, "Accumulator_Mean_f")
+        .def(py::init<>())
+        .def("AddPass", &Accumulator_Mean<float>::AddPass)
+        .def("__call__", py::overload_cast<const float>(&Accumulator_Mean<float>::operator()))
+        .def("__call__", py::overload_cast<>(&Accumulator_Mean<float>::operator(), py::const_));
+
+    py::class_<Accumulator_Mean<double>>(m, "Accumulator_Mean_d")
+        .def(py::init<>())
+        .def("AddPass", &Accumulator_Mean<double>::AddPass)
+        .def("__call__", py::overload_cast<const double>(&Accumulator_Mean<double>::operator()))
+        .def("__call__", py::overload_cast<>(&Accumulator_Mean<double>::operator(), py::const_));
+
+    py::class_<Accumulator_ABTrim<float>>(m, "Accumulator_ABTrim_f")
+        .def(py::init<>())
+        .def("SetABTrim", &Accumulator_ABTrim<float>::SetABTrim)
+        .def("__iadd__", [](Accumulator_ABTrim<float> &self, float val) { self += val; return &self; })
+        .def("__call__", &Accumulator_ABTrim<float>::operator());
+
+    py::class_<Accumulator_ABTrim<double>>(m, "Accumulator_ABTrim_d")
+        .def(py::init<>())
+        .def("SetABTrim", &Accumulator_ABTrim<double>::SetABTrim)
+        .def("__iadd__", [](Accumulator_ABTrim<double> &self, double val) { self += val; return &self; })
+        .def("__call__", &Accumulator_ABTrim<double>::operator());
+
+    py::class_<Accumulator_ABClip<float>>(m, "Accumulator_ABClip_f")
+        .def(py::init<>())
+        .def("SetABTrim", &Accumulator_ABClip<float>::SetABTrim)
+        .def("__iadd__", [](Accumulator_ABClip<float> &self, float val) { self += val; return &self; })
+        .def("__call__", &Accumulator_ABClip<float>::operator());
+
+    py::class_<Accumulator_ABClip<double>>(m, "Accumulator_ABClip_d")
+        .def(py::init<>())
+        .def("SetABTrim", &Accumulator_ABClip<double>::SetABTrim)
+        .def("__iadd__", [](Accumulator_ABClip<double> &self, double val) { self += val; return &self; })
+        .def("__call__", &Accumulator_ABClip<double>::operator());
+
+    // 5. Core Math Structures
     py::class_<AffineTransform>(m, "AffineTransform")
         .def(py::init<>())
         .def("GetWorldMatrix", &AffineTransform::GetWorldMatrix)
@@ -34,13 +248,11 @@ void init_math(py::module_ &m) {
         .def("EulerYZYRotate", &AffineTransform::EulerYZYRotate)
         .def("FlipAxes", &AffineTransform::FlipAxes);
 
-    // Math/Geometry.h
     py::class_<Geometry, AffineTransform>(m, "Geometry")
         .def(py::init<>())
         .def("GetWorldPoint", py::overload_cast<const Vector4f &>(&Geometry::GetWorldPoint, py::const_))
         .def("GetLocalPoint", py::overload_cast<const Vector4f &>(&Geometry::GetLocalPoint, py::const_));
 
-    // Math/ContainerBox.h
     py::class_<ContainerBox, AffineTransform>(m, "ContainerBox")
         .def(py::init<>())
         .def("SetOrigin", &ContainerBox::SetOrigin)
@@ -51,7 +263,6 @@ void init_math(py::module_ &m) {
         .def("GetWorldPoint", py::overload_cast<const Vector4f &>(&ContainerBox::GetWorldPoint, py::const_))
         .def("GetLocalPoint", py::overload_cast<const Vector4f &>(&ContainerBox::GetLocalPoint, py::const_));
 
-    // Math/StructuredData.h
     py::enum_<StructuredData::_Order>(m, "StructuredDataOrder")
         .value("CustomOrder", StructuredData::CustomOrder)
         .value("XYZ", StructuredData::XYZ)
@@ -74,7 +285,6 @@ void init_math(py::module_ &m) {
         .def("Map", &StructuredData::Map)
         .def("UnMap", &StructuredData::UnMap);
 
-    // Math/StructuredGrid.h
     py::class_<StructuredGrid, ContainerBox, StructuredData>(m, "StructuredGrid")
         .def(py::init<const Vector3i &>())
         .def("SetSpacing", &StructuredGrid::SetSpacing)
@@ -84,7 +294,6 @@ void init_math(py::module_ &m) {
             return self.Find(HPoint3f(pt));
         });
 
-    // Math/Structured2DGrid.h
     py::class_<Structured2DGrid>(m, "Structured2DGrid")
         .def(py::init<>())
         .def("SetDims", &Structured2DGrid::SetDims)
@@ -100,7 +309,6 @@ void init_math(py::module_ &m) {
         .def("UnitToPhysicsSpace", &Structured2DGrid::UnitToPhysicsSpace)
         .def("SetDebug", &Structured2DGrid::SetDebug);
 
-    // Math/Structured4DGrid.h
     py::class_<Structured4DGrid>(m, "Structured4DGrid")
         .def(py::init<>())
         .def("SetDims", &Structured4DGrid::SetDims)
@@ -116,7 +324,37 @@ void init_math(py::module_ &m) {
         .def("UnitToPhysicsSpace", &Structured4DGrid::UnitToPhysicsSpace)
         .def("SetDebug", &Structured4DGrid::SetDebug);
 
-    // Math/TriangleMesh.h
+    // 6. High-level Structures
+    py::class_<Voxel>(m, "Voxel")
+        .def(py::init<>())
+        .def_readwrite("Value", &Voxel::Value)
+        .def_readwrite("Count", &Voxel::Count);
+
+    py::class_<Abstract::VoxImage, StructuredGrid>(m, "AbstractVoxImage")
+        .def("GetValue", py::overload_cast<const Vector3i &>(&Abstract::VoxImage::GetValue, py::const_))
+        .def("GetValue", py::overload_cast<const int>(&Abstract::VoxImage::GetValue, py::const_))
+        .def("SetValue", py::overload_cast<const Vector3i &, float>(&Abstract::VoxImage::SetValue))
+        .def("SetValue", py::overload_cast<const int, float>(&Abstract::VoxImage::SetValue))
+        .def("ExportToVtk", &Abstract::VoxImage::ExportToVtk)
+        .def("ExportToVti", &Abstract::VoxImage::ExportToVti)
+        .def("ImportFromVtk", &Abstract::VoxImage::ImportFromVtk)
+        .def("ImportFromVti", &Abstract::VoxImage::ImportFromVti);
+
+    py::class_<VoxImage<Voxel>, Abstract::VoxImage>(m, "VoxImage")
+        .def(py::init<>())
+        .def(py::init<const Vector3i &>())
+        .def("Data", &VoxImage<Voxel>::Data, py::return_value_policy::reference_internal)
+        .def("InitVoxels", &VoxImage<Voxel>::InitVoxels)
+        .def("Abs", &VoxImage<Voxel>::Abs)
+        .def("clipImage", py::overload_cast<const Vector3i, const Vector3i>(&VoxImage<Voxel>::clipImage, py::const_))
+        .def("clipImage", py::overload_cast<const HPoint3f, const HPoint3f>(&VoxImage<Voxel>::clipImage, py::const_))
+        .def("clipImage", py::overload_cast<const float>(&VoxImage<Voxel>::clipImage, py::const_))
+        .def("maskImage", py::overload_cast<const HPoint3f, const HPoint3f, float>(&VoxImage<Voxel>::maskImage, py::const_))
+        .def("maskImage", py::overload_cast<const float, float, float>(&VoxImage<Voxel>::maskImage, py::const_), py::arg("threshold"), py::arg("belowValue") = 0, py::arg("aboveValue") = 0)
+        .def("fixVoxels", py::overload_cast<const float, float>(&VoxImage<Voxel>::fixVoxels, py::const_))
+        .def("__getitem__", py::overload_cast<unsigned int>(&VoxImage<Voxel>::operator[]))
+        .def("__getitem__", py::overload_cast<const Vector3i &>(&VoxImage<Voxel>::operator[]));
+
     py::class_<TriangleMesh>(m, "TriangleMesh")
         .def(py::init<>())
         .def("AddPoint", &TriangleMesh::AddPoint)
@@ -124,7 +362,6 @@ void init_math(py::module_ &m) {
         .def("Points", &TriangleMesh::Points, py::return_value_policy::reference_internal)
         .def("Triangles", &TriangleMesh::Triangles, py::return_value_policy::reference_internal);
 
-    // Math/VoxRaytracer.h
     py::class_<VoxRaytracer::RayData::Element>(m, "VoxRaytracerRayDataElement")
         .def(py::init<>())
         .def_readwrite("vox_id", &VoxRaytracer::RayData::Element::vox_id)
@@ -133,6 +370,7 @@ void init_math(py::module_ &m) {
     py::class_<VoxRaytracer::RayData>(m, "VoxRaytracerRayData")
         .def(py::init<>())
         .def("AppendRay", &VoxRaytracer::RayData::AppendRay)
+        .def("Data", py::overload_cast<>(&VoxRaytracer::RayData::Data), py::return_value_policy::reference_internal)
         .def("Count", &VoxRaytracer::RayData::Count)
         .def("TotalLength", &VoxRaytracer::RayData::TotalLength)
         .def("SetCount", &VoxRaytracer::RayData::SetCount)
@@ -140,13 +378,8 @@ void init_math(py::module_ &m) {
 
     py::class_<VoxRaytracer>(m, "VoxRaytracer")
         .def(py::init<StructuredGrid &>(), py::keep_alive<1, 2>())
-        .def("GetImage", &VoxRaytracer::GetImage, py::return_value_policy::reference_internal);
+        .def("GetImage", &VoxRaytracer::GetImage, py::return_value_policy::reference_internal)
-
+        .def("TraceLine", &VoxRaytracer::TraceLine)
-    // Math/Accumulator.h
+        .def("TraceBetweenPoints", &VoxRaytracer::TraceBetweenPoints);
-    py::class_<Accumulator_Mean<float>>(m, "Accumulator_Mean_f")
-        .def(py::init<>())
-        .def("AddPass", &Accumulator_Mean<float>::AddPass)
-        .def("__call__", py::overload_cast<const float>(&Accumulator_Mean<float>::operator()))
-        .def("__call__", py::overload_cast<>(&Accumulator_Mean<float>::operator(), py::const_));
 
 }

src/Python/math_filters_bindings.cpp

@@ -0,0 +1,100 @@
+#include <pybind11/pybind11.h>
+#include <pybind11/eigen.h>
+#include <pybind11/stl.h>
+
+#include "Math/VoxImage.h"
+#include "Math/VoxImageFilter.h"
+#include "Math/VoxImageFilterLinear.hpp"
+#include "Math/VoxImageFilterABTrim.hpp"
+#include "Math/VoxImageFilterBilateral.hpp"
+#include "Math/VoxImageFilterThreshold.hpp"
+#include "Math/VoxImageFilterMedian.hpp"
+#include "Math/VoxImageFilter2ndStat.hpp"
+#include "Math/VoxImageFilterCustom.hpp"
+
+namespace py = pybind11;
+using namespace uLib;
+
+template <typename Algorithm>
+void bind_common_filter(py::class_<Algorithm, Abstract::VoxImageFilter> &cls) {
+    cls.def(py::init<const Vector3i &>())
+       .def("Run", &Algorithm::Run)
+       .def("SetKernelNumericXZY", &Algorithm::SetKernelNumericXZY)
+       .def("GetImage", &Algorithm::GetImage, py::return_value_policy::reference_internal)
+       .def("SetImage", &Algorithm::SetImage);
+}
+
+void init_math_filters(py::module_ &m) {
+
+    // Abstract::VoxImageFilter
+    py::class_<Abstract::VoxImageFilter, std::unique_ptr<Abstract::VoxImageFilter, py::nodelete>>(m, "AbstractVoxImageFilter")
+        .def("Run", &Abstract::VoxImageFilter::Run)
+        .def("SetImage", &Abstract::VoxImageFilter::SetImage);
+
+    // Helper macro to define standard bindings for a filter
+#define BIND_FILTER(ClassName) \
+    { \
+        auto cls = py::class_<ClassName<Voxel>, Abstract::VoxImageFilter>(m, #ClassName); \
+        bind_common_filter(cls); \
+    }
+
+    // VoxFilterAlgorithmLinear
+    {
+        auto cls = py::class_<VoxFilterAlgorithmLinear<Voxel>, Abstract::VoxImageFilter>(m, "VoxFilterAlgorithmLinear");
+        bind_common_filter(cls);
+    }
+
+    // VoxFilterAlgorithmAbtrim
+    {
+        auto cls = py::class_<VoxFilterAlgorithmAbtrim<Voxel>, Abstract::VoxImageFilter>(m, "VoxFilterAlgorithmAbtrim");
+        bind_common_filter(cls);
+        cls.def("SetABTrim", &VoxFilterAlgorithmAbtrim<Voxel>::SetABTrim);
+    }
+
+    // VoxFilterAlgorithmSPR
+    {
+        auto cls = py::class_<VoxFilterAlgorithmSPR<Voxel>, Abstract::VoxImageFilter>(m, "VoxFilterAlgorithmSPR");
+        bind_common_filter(cls);
+        cls.def("SetABTrim", &VoxFilterAlgorithmSPR<Voxel>::SetABTrim);
+    }
+
+    // VoxFilterAlgorithmBilateral
+    {
+        auto cls = py::class_<VoxFilterAlgorithmBilateral<Voxel>, Abstract::VoxImageFilter>(m, "VoxFilterAlgorithmBilateral");
+        bind_common_filter(cls);
+        cls.def("SetIntensitySigma", &VoxFilterAlgorithmBilateral<Voxel>::SetIntensitySigma);
+    }
+
+    // VoxFilterAlgorithmBilateralTrim
+    {
+        auto cls = py::class_<VoxFilterAlgorithmBilateralTrim<Voxel>, Abstract::VoxImageFilter>(m, "VoxFilterAlgorithmBilateralTrim");
+        bind_common_filter(cls);
+        cls.def("SetIntensitySigma", &VoxFilterAlgorithmBilateralTrim<Voxel>::SetIntensitySigma);
+        cls.def("SetABTrim", &VoxFilterAlgorithmBilateralTrim<Voxel>::SetABTrim);
+    }
+
+    // VoxFilterAlgorithmThreshold
+    {
+        auto cls = py::class_<VoxFilterAlgorithmThreshold<Voxel>, Abstract::VoxImageFilter>(m, "VoxFilterAlgorithmThreshold");
+        bind_common_filter(cls);
+        cls.def("SetThreshold", &VoxFilterAlgorithmThreshold<Voxel>::SetThreshold);
+    }
+
+    // VoxFilterAlgorithmMedian
+    {
+        auto cls = py::class_<VoxFilterAlgorithmMedian<Voxel>, Abstract::VoxImageFilter>(m, "VoxFilterAlgorithmMedian");
+        bind_common_filter(cls);
+    }
+
+    // VoxFilterAlgorithm2ndStat
+    {
+        auto cls = py::class_<VoxFilterAlgorithm2ndStat<Voxel>, Abstract::VoxImageFilter>(m, "VoxFilterAlgorithm2ndStat");
+        bind_common_filter(cls);
+    }
+
+    // VoxFilterAlgorithmCustom (Omit CustomEvaluate since it uses static function ptrs)
+    {
+        auto cls = py::class_<VoxFilterAlgorithmCustom<Voxel>, Abstract::VoxImageFilter>(m, "VoxFilterAlgorithmCustom");
+        bind_common_filter(cls);
+    }
+}

src/Python/module.cpp

@@ -4,6 +4,7 @@ namespace py = pybind11;
 
 void init_core(py::module_ &m);
 void init_math(py::module_ &m);
+void init_math_filters(py::module_ &m);
 
 PYBIND11_MODULE(uLib_python, m) {
     m.doc() = "Python bindings for uLib Core and Math libraries";
@@ -15,4 +16,5 @@ PYBIND11_MODULE(uLib_python, m) {
     // Math submodule
     py::module_ math = m.def_submodule("Math", "Math library bindings");
     init_math(math);
+    init_math_filters(math);
 }

src/Python/testing/core_pybind_test.py

@@ -3,11 +3,11 @@ import os
 import unittest
 import time
 
-import uLib_python
+import uLib
 
 class TestCoreOptions(unittest.TestCase):
     def test_options(self):
-        opt = uLib_python.Core.Options("Test Options")
+        opt = uLib.Core.Options("Test Options")
         
         # Test basic config file parsing
         with open("test_configuration.ini", "w") as f:
@@ -18,12 +18,12 @@ class TestCoreOptions(unittest.TestCase):
 
 class TestCoreObject(unittest.TestCase):
     def test_object(self):
-        obj = uLib_python.Core.Object()
+        obj = uLib.Core.Object()
         self.assertIsNotNone(obj)
 
 class TestCoreTimer(unittest.TestCase):
     def test_timer(self):
-        timer = uLib_python.Core.Timer()
+        timer = uLib.Core.Timer()
         timer.Start()
         time.sleep(0.1)
         val = timer.StopWatch()

src/Python/testing/math_filters_test.py

@@ -0,0 +1,151 @@
+import unittest
+import numpy as np
+import os
+import sys
+
+# Ensure PYTHONPATH is correct if run from root
+sys.path.append(os.path.join(os.getcwd(), 'src', 'Python'))
+
+import uLib
+
+class TestMathFilters(unittest.TestCase):
+    def test_filter_creation(self):
+        # 1. Linear Filter
+        dims = [10, 10, 10]
+        v_dims = uLib.Math.Vector3i(dims)
+        
+        linear_filter = uLib.Math.VoxFilterAlgorithmLinear(v_dims)
+        self.assertIsNotNone(linear_filter)
+        
+        # 2. ABTrim Filter
+        abtrim_filter = uLib.Math.VoxFilterAlgorithmAbtrim(v_dims)
+        self.assertIsNotNone(abtrim_filter)
+        abtrim_filter.SetABTrim(1, 1)
+        
+        # 3. Bilateral Filter
+        bilat_filter = uLib.Math.VoxFilterAlgorithmBilateral(v_dims)
+        self.assertIsNotNone(bilat_filter)
+        bilat_filter.SetIntensitySigma(0.5)
+        
+        # 4. Threshold Filter
+        threshold_filter = uLib.Math.VoxFilterAlgorithmThreshold(v_dims)
+        self.assertIsNotNone(threshold_filter)
+        threshold_filter.SetThreshold(0.5)
+        
+        # 5. Median Filter
+        median_filter = uLib.Math.VoxFilterAlgorithmMedian(v_dims)
+        self.assertIsNotNone(median_filter)
+
+    def test_filter_run(self):
+        # Create image
+        dims = [10, 10, 10]
+        vox_img = uLib.Math.VoxImage(dims)
+        for i in range(10*10*10):
+            vox_img.SetValue(i, 1.0)
+        
+        # Linear filter
+        linear_filter = uLib.Math.VoxFilterAlgorithmLinear([3, 3, 3])
+        linear_filter.SetImage(vox_img)
+        
+        # Set kernel (simple 3x3x3 all ones)
+        # Weights are usually normalized in linear filter logic?
+        # Let's just test it runs.
+        linear_filter.SetKernelNumericXZY([1.0] * 27)
+        
+        # Run filter
+        linear_filter.Run()
+        
+        # Value should be 1.0 (mean of all 1.0 is 1.0)
+        self.assertAlmostEqual(vox_img.GetValue(0), 1.0)
+
+    def test_filter_run_abtrim(self):
+        # Create image
+        dims = [10, 10, 10]
+        vox_img = uLib.Math.VoxImage(dims)
+        for i in range(10*10*10):
+            vox_img.SetValue(i, 1.0)
+        
+        # ABTrim filter
+        abtrim_filter = uLib.Math.VoxFilterAlgorithmAbtrim([3, 3, 3])
+        abtrim_filter.SetImage(vox_img)
+        
+        # Set kernel (simple 3x3x3 all ones)
+        # Weights are usually normalized in linear filter logic?
+        # Let's just test it runs.
+        abtrim_filter.SetKernelNumericXZY([1.0] * 27)
+        
+        # Run filter
+        abtrim_filter.Run()
+        
+        # Value should be 1.0 (mean of all 1.0 is 1.0)
+        self.assertAlmostEqual(vox_img.GetValue(0), 1.0)
+
+    def test_filter_run_bilateral(self):
+        # Create image
+        dims = [10, 10, 10]
+        vox_img = uLib.Math.VoxImage(dims)
+        for i in range(10*10*10):
+            vox_img.SetValue(i, 1.0)
+        
+        # Bilateral filter
+        bilat_filter = uLib.Math.VoxFilterAlgorithmBilateral([3, 3, 3])
+        bilat_filter.SetImage(vox_img)
+        
+        # Set kernel (simple 3x3x3 all ones)
+        # Weights are usually normalized in linear filter logic?
+        # Let's just test it runs.
+        bilat_filter.SetKernelNumericXZY([1.0] * 27)
+        
+        # Run filter
+        bilat_filter.Run()
+        
+        # Value should be 1.0 (mean of all 1.0 is 1.0)
+        self.assertAlmostEqual(vox_img.GetValue(0), 1.0)
+
+    def test_filter_run_threshold(self):
+        # Create image
+        dims = [10, 10, 10]
+        vox_img = uLib.Math.VoxImage(dims)
+        for i in range(10*10*10):
+            vox_img.SetValue(i, 1.0)
+        
+        # Threshold filter
+        threshold_filter = uLib.Math.VoxFilterAlgorithmThreshold([3, 3, 3])
+        threshold_filter.SetImage(vox_img)
+        
+        # Set kernel (simple 3x3x3 all ones)
+        # Weights are usually normalized in linear filter logic?
+        # Let's just test it runs.
+        threshold_filter.SetKernelNumericXZY([1.0] * 27)
+        
+        # Run filter
+        threshold_filter.Run()
+        
+        # Value should be 1.0 (mean of all 1.0 is 1.0)
+        self.assertAlmostEqual(vox_img.GetValue(0), 1.0)
+
+    def test_filter_run_median(self):
+        # Create image
+        dims = [10, 10, 10]
+        vox_img = uLib.Math.VoxImage(dims)
+        for i in range(10*10*10):
+            vox_img.SetValue(i, 1.0)
+        
+        # Median filter
+        median_filter = uLib.Math.VoxFilterAlgorithmMedian([3, 3, 3])
+        median_filter.SetImage(vox_img)
+        
+        # Set kernel (simple 3x3x3 all ones)
+        # Weights are usually normalized in linear filter logic?
+        # Let's just test it runs.
+        median_filter.SetKernelNumericXZY([1.0] * 27)
+        
+        # Run filter
+        median_filter.Run()
+        
+        # Value should be 1.0 (mean of all 1.0 is 1.0)
+        self.assertAlmostEqual(vox_img.GetValue(0), 1.0)
+
+
+if __name__ == '__main__':
+    unittest.main()

src/Python/testing/math_pybind_test.py

@@ -3,16 +3,77 @@ import os
 import unittest
 import numpy as np
 
-import uLib_python
+import uLib
 
 def vector4f0(v, target):
     diff = np.array(v) - np.array(target)
     diff[3] = 0 # ignoring w
     return np.all(np.abs(diff) < 0.001)
 
+
+class TestMathMatrix(unittest.TestCase):
+
+    def test_matrix(self):
+        def check_1234(m2f):
+            self.assertEqual(m2f[0, 0], 1)
+            self.assertEqual(m2f[0, 1], 2)
+            self.assertEqual(m2f[1, 0], 3)
+            self.assertEqual(m2f[1, 1], 4)
+
+        m2f = uLib.Math.Matrix2f()
+        m2f[0, 0] = 1
+        m2f[0, 1] = 2
+        m2f[1, 0] = 3
+        m2f[1, 1] = 4
+        check_1234(m2f)
+
+        m2f = uLib.Math.Matrix2f([1, 2, 3, 4])
+        check_1234(m2f)
+
+        # m2f = uLib.Math.Matrix2f([[1, 2], [3, 4]])
+        # check_1234(m2f)
+
+        m2f = uLib.Math.Matrix2f(np.array([[1, 2], [3, 4]]))
+        check_1234(m2f)
+
+    def test_vector2(self):
+        v2f = uLib.Math.Vector2f()
+        v2f[0] = 1
+        v2f[1] = 2
+        self.assertEqual(v2f[0], 1)
+        self.assertEqual(v2f[1], 2)
+        
+        v2f = uLib.Math.Vector2f([1, 2])
+        self.assertEqual(v2f[0], 1)
+        self.assertEqual(v2f[1], 2)
+        
+        v2f = uLib.Math.Vector2f(np.array([1, 2]))
+        self.assertEqual(v2f[0], 1)
+        self.assertEqual(v2f[1], 2)
+    
+    def test_vector3(self):
+        v3f = uLib.Math.Vector3f()
+        v3f[0] = 1
+        v3f[1] = 2
+        v3f[2] = 3
+        self.assertEqual(v3f[0], 1)
+        self.assertEqual(v3f[1], 2)
+        self.assertEqual(v3f[2], 3)
+        
+        v3f = uLib.Math.Vector3f([1, 2, 3])
+        self.assertEqual(v3f[0], 1)
+        self.assertEqual(v3f[1], 2)
+        self.assertEqual(v3f[2], 3)
+        
+        v3f = uLib.Math.Vector3f(np.array([1, 2, 3]))
+        self.assertEqual(v3f[0], 1)
+        self.assertEqual(v3f[1], 2)
+        self.assertEqual(v3f[2], 3)
+    
+
 class TestMathGeometry(unittest.TestCase):
     def test_geometry(self):
-        Geo = uLib_python.Math.Geometry()
+        Geo = uLib.Math.Geometry()
         
         Geo.SetPosition([1, 1, 1])
         
@@ -27,7 +88,7 @@ class TestMathGeometry(unittest.TestCase):
         
 class TestMathContainerBox(unittest.TestCase):
     def test_container_box_local(self):
-        Cnt = uLib_python.Math.ContainerBox()
+        Cnt = uLib.Math.ContainerBox()
         Cnt.SetOrigin([-1, -1, -1])
         Cnt.SetSize([2, 2, 2])
         
@@ -35,7 +96,7 @@ class TestMathContainerBox(unittest.TestCase):
         self.assertTrue(np.allclose(size, [2, 2, 2]))
 
     def test_container_box_global(self):
-        Box = uLib_python.Math.ContainerBox()
+        Box = uLib.Math.ContainerBox()
         Box.SetPosition([1, 1, 1])
         Box.SetSize([2, 2, 2])
         
@@ -45,7 +106,7 @@ class TestMathContainerBox(unittest.TestCase):
 
 class TestMathStructuredGrid(unittest.TestCase):
     def test_structured_grid(self):
-        grid = uLib_python.Math.StructuredGrid([10, 10, 10])
+        grid = uLib.Math.StructuredGrid([10, 10, 10])
         grid.SetSpacing([1, 1, 1])
         
         spacing = grid.GetSpacing()
@@ -53,10 +114,76 @@ class TestMathStructuredGrid(unittest.TestCase):
 
 class TestMathAccumulator(unittest.TestCase):
     def test_accumulator_mean(self):
-        acc = uLib_python.Math.Accumulator_Mean_f()
+        acc = uLib.Math.Accumulator_Mean_f()
         acc(10.0)
         acc(20.0)
         self.assertAlmostEqual(acc(), 15.0)
 
+class TestMathNewTypes(unittest.TestCase):
+    def test_eigen_vectors(self):
+        v1f = uLib.Math.Vector1f()
+        v3d = uLib.Math.Vector3d()
+        m4f = uLib.Math.Matrix4f()
+        self.assertIsNotNone(v1f)
+        self.assertIsNotNone(v3d)
+        self.assertIsNotNone(m4f)
+
+    def test_ulib_vectors(self):
+        vi = uLib.Math.Vector_i()
+        vi.append(1)
+        vi.append(2)
+        self.assertEqual(len(vi), 2)
+        self.assertEqual(vi[0], 1)
+        self.assertEqual(vi[1], 2)
+        
+        vf = uLib.Math.Vector_f()
+        vf.append(1.5)
+        self.assertAlmostEqual(vf[0], 1.5)
+
+    def test_homogeneous(self):
+        p = uLib.Math.HPoint3f(1.0, 2.0, 3.0)
+        v = uLib.Math.HVector3f(0.0, 1.0, 0.0)
+        self.assertIsNotNone(p)
+        self.assertIsNotNone(v)
+
+    def test_vox_image(self):
+        img = uLib.Math.VoxImage([2, 2, 2])
+        self.assertEqual(img.GetDims()[0], 2)
+        img.SetValue([0, 0, 0], 10.5)
+        # Note: GetValue returns float, and there might be internal scaling (1.E-6 observed in code)
+        # Actually in VoxImage.h: GetValue(id) returns At(id).Value
+        # SetValue(id, value) sets At(id).Value = value
+        self.assertAlmostEqual(img.GetValue([0, 0, 0]), 10.5)
+
+class TestMathVoxRaytracer(unittest.TestCase):
+    def test_raytracer(self):
+        grid = uLib.Math.StructuredGrid([10, 10, 10])
+        grid.SetSpacing([1, 1, 1])
+        grid.SetOrigin([0, 0, 0])
+        
+        rt = uLib.Math.VoxRaytracer(grid)
+        self.assertIsNotNone(rt)
+        
+        # Test TraceBetweenPoints
+        p1 = np.array([0.5, 0.5, -1.0, 1.0], dtype=np.float32)
+        p2 = np.array([0.5, 0.5, 11.0, 1.0], dtype=np.float32)
+        data = rt.TraceBetweenPoints(p1, p2)
+        
+        self.assertGreater(data.Count(), 0)
+        self.assertAlmostEqual(data.TotalLength(), 10.0)
+        
+        # Check elements
+        elements = data.Data()
+        for i in range(data.Count()):
+            self.assertGreaterEqual(elements[i].vox_id, 0)
+            self.assertGreater(elements[i].L, 0)
+
+    def test_ray_data(self):
+        data = uLib.Math.VoxRaytracerRayData()
+        data.SetCount(10)
+        data.SetTotalLength(5.5)
+        self.assertEqual(data.Count(), 10)
+        self.assertAlmostEqual(data.TotalLength(), 5.5)
+
 if __name__ == '__main__':
     unittest.main()

src/Python/testing/pybind_test.py

@@ -1,42 +1,42 @@
 import sys
 import os
 
-import uLib_python
+import uLib
 
 def test_core():
     print("Testing Core module...")
-    obj = uLib_python.Core.Object()
+    obj = uLib.Core.Object()
     print("Core Object created:", obj)
     
-    timer = uLib_python.Core.Timer()
+    timer = uLib.Core.Timer()
     timer.Start()
     print("Core Timer started")
     
-    options = uLib_python.Core.Options("Test Options")
+    options = uLib.Core.Options("Test Options")
     print("Core Options created:", options)
 
 def test_math():
     print("Testing Math module...")
     
     # Test AffineTransform
-    transform = uLib_python.Math.AffineTransform()
+    transform = uLib.Math.AffineTransform()
     print("AffineTransform created")
     
     # Test Geometry
-    geom = uLib_python.Math.Geometry()
+    geom = uLib.Math.Geometry()
     print("Geometry created")
     
     # Test StructuredData
-    data = uLib_python.Math.StructuredData([10, 10, 10])
+    data = uLib.Math.StructuredData([10, 10, 10])
     print("StructuredData created with dims:", data.GetDims())
     
     # Test Structured2DGrid
-    grid2d = uLib_python.Math.Structured2DGrid()
+    grid2d = uLib.Math.Structured2DGrid()
     grid2d.SetDims([100, 100])
     print("Structured2DGrid created with dims:", grid2d.GetDims())
     
     # Test TriangleMesh
-    mesh = uLib_python.Math.TriangleMesh()
+    mesh = uLib.Math.TriangleMesh()
     print("TriangleMesh created")
     
     print("All tests passed successfully!")

src/Python/uLib/__init__.py

@@ -0,0 +1,7 @@
+try:
+    from .uLib_python import Core, Math
+except ImportError:
+    # Handle cases where the binary extension is not yet built
+    pass
+
+__all__ = ["Core", "Math"]

test.cpp

@@ -1,10 +0,0 @@
-
-#include "Core/Object.h"
-
-
-
-int main()
-{
-    uLib::Object obj;
-    return 0;
-}