algorithm chain for ram-vram

.agents/rules/micromamba.md

@@ -0,0 +1,7 @@
+---
+trigger: always_on
+---
+
+build in build directory using always micromamba "mutom" env.
+build with make flag -j$(nproc).
+

.gitattributes

@@ -0,0 +1,2 @@
+*.vtk filter=lfs diff=lfs merge=lfs -text
+*.vti filter=lfs diff=lfs merge=lfs -text

CLAUDE.md

@@ -0,0 +1,90 @@
+
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Build Commands
+
+```bash
+# Activate the conda environment (required before any build/run)
+export MAMBA_EXE="/home/share/micromamba/bin/micromamba"
+export MAMBA_ROOT_PREFIX="/home/share/micromamba"
+eval "$(/home/share/micromamba/bin/micromamba shell hook --shell bash)"
+micromamba activate mutom
+
+# Configure (from repo root, using Conan preset)
+cmake --preset conan-release
+
+# Build everything
+cmake --build build -j$(nproc)
+
+# Build a specific target
+cmake --build build --target gcompose -j$(nproc)
+
+# Run tests
+cmake --build build --target test
+# or
+ctest --test-dir build
+
+# Run a single test binary (example)
+./build/src/Core/testing/CoreTest
+
+# Run the gcompose GUI app
+./build/app/gcompose/gcompose
+```
+
+First-time setup (if `build/` does not exist):
+```bash
+conan profile detect
+conan install . --output-folder=build --build=missing
+cmake --preset conan-release
+```
+
+## Architecture
+
+**uLib** is a C++ framework for Cosmic Muon Tomography (CMT), structured as layered shared libraries:
+
+```
+mutomCore  →  mutomMath  →  mutomDetectors  →  mutomGeant
+                                              ↘
+                                           mutomVtk  →  gcompose (Qt6 GUI app)
+                                           mutomRoot
+```
+
+### Core Object Model (`src/Core/`)
+- All framework objects inherit from `uLib::Object`
+- **Property system**: `Property<T>` wraps member pointers with change notification via `PropertyChanged` signal
+- **Signal/slot**: `uLib::Object::connect(sender, &Sender::Signal, callback)` — resembles Qt but works for non-QObject classes
+- **Serialization**: Boost archives (`xml_oarchive`, `text_oarchive`, `hrt_oarchive`); `hrp<T>` marks fields as "human-readable properties"
+- `ObjectsContext` is a container owning a list of `Object*` pointers; signals `ObjectAdded`/`ObjectRemoved`
+
+### VTK Layer (`src/Vtk/`)
+- `Puppet` (inherits `uLib::Object`): wraps a VTK `vtkProp` for rendering. Has `GetContent()` returning the underlying domain object. Display-only properties are registered via `ULIB_ACTIVATE_DISPLAY_PROPERTIES` macro.
+- `Viewport`: base class managing the VTK renderer, picking, selection logic. Maintains `m_Puppets` vector and `m_ObjectToPuppet` map.
+- `QViewport` (inherits `QWidget` + `Viewport`): Qt-embedded VTK widget. Emits Qt signal `puppetSelected(Puppet*)` on click-selection via `OnSelectionChanged`.
+- `vtkObjectsContext`: wraps `ObjectsContext`, creating/destroying `Puppet`s as objects come/go. Emits `PuppetAdded`/`PuppetRemoved`.
+- Display properties: `serialize_display()` + `display_properties_archive` registers selected `hrp<T>` fields as `PropertyBase*` in the puppet's `m_DisplayProperties`. `PropertyEditor::setObject(obj, displayOnly=true)` shows only those.
+
+### gcompose GUI App (`app/gcompose/src/`)
+- `MainPanel`: top-level widget. Owns `ContextPanel` (left) and `ViewportPane` (right). Wires together viewport↔context selection via signals.
+- `ContextPanel`: tree view of `ObjectsContext`. Emits `objectSelected(Object*)`. Contains an embedded `PropertiesPanel`.
+- `PropertiesPanel`: shows `uLib::Object` properties via `PropertyEditor`.
+- `ViewportPane`: embeds `QViewport` + a slide-out "Display Properties" panel (`PropertyEditor` in display-only mode).
+- `PropertyEditor`: populates widgets from `Object::GetProperties()` (all) or `Puppet::GetDisplayProperties()` (display-only mode).
+
+### Selection Sync Flow
+```
+Viewport click  →  Viewport::SelectPuppet()  →  QViewport::OnSelectionChanged()
+                →  emit puppetSelected(p)
+                →  MainPanel: contextPanel->selectObject(p->GetContent())  [updates tree + PropertiesPanel]
+                →  MainPanel: firstPane->setObject(p)  [updates Display Properties panel]
+
+ContextPanel tree click  →  emit objectSelected(obj)
+                →  MainPanel: viewport->SelectPuppet(puppet)  [visual selection in VTK]
+                →  MainPanel: firstPane->setObject(puppet)  [updates Display Properties panel]
+```
+
+### Key Patterns
+- **Two signal systems coexist**: Qt signals (`Q_OBJECT`, `connect(...)`) for GUI; `uLib::Object::connect(...)` for domain signals.
+- **Display properties** flow: `Puppet::serialize_display()` → `display_properties_archive` → `RegisterDisplayProperty()` → `PropertyEditor(displayOnly=true)`. Must call `ULIB_ACTIVATE_DISPLAY_PROPERTIES` in the puppet constructor.
+- **Puppet ↔ Object map**: `Viewport::m_ObjectToPuppet` allows lookup by domain object; `vtkObjectsContext::GetPuppet(obj)` does the same.

CMake/uLibTargetMacros.cmake

@@ -84,6 +84,7 @@ macro(uLib_add_tests name)
     foreach(tn ${TESTS})
         add_executable(${tn} ${tn}.cpp)
         add_test(NAME ${tn} COMMAND ${tn})
+        set_tests_properties(${tn} PROPERTIES ENVIRONMENT "CTEST_PROJECT_NAME=uLib;QT_QPA_PLATFORM=offscreen")
 
         target_link_libraries(${tn} ${LIBRARIES})
 

CMakeLists.txt

@@ -21,7 +21,7 @@ endif()
 project(uLib)
 
 # CUDA Toolkit seems to be missing locally. Toggle ON if nvcc is made available.
-option(USE_CUDA "Enable CUDA support" ON)
+option(USE_CUDA "Enable CUDA support" OFF)
 if(USE_CUDA)
     set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -allow-unsupported-compiler")
     set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} --expt-relaxed-constexpr")
@@ -103,6 +103,7 @@ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_WARNING_OPTION}")
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -UULIB_SERIALIZATION_ON -Wno-cpp")
 
 # CTEST framework
+set(CTEST_PROJECT_NAME "uLib")
 include(CTest)
 enable_testing()
 
@@ -114,7 +115,7 @@ set(Boost_USE_MULTITHREADED ON)
 set(Boost_USE_STATIC_RUNTIME OFF)
 message(STATUS "CMAKE_PREFIX_PATH is ${CMAKE_PREFIX_PATH}")
 
-find_package(HDF5 REQUIRED CONFIG)
+find_package(HDF5 REQUIRED)
 
 find_package(Boost 1.45.0 COMPONENTS program_options serialization unit_test_framework REQUIRED)
 include_directories(${Boost_INCLUDE_DIRS})

Testing/Temporary/CTestCostData.txt

@@ -0,0 +1 @@
+---

Testing/Temporary/LastTest.log

@@ -0,0 +1,3 @@
+Start testing: Mar 25 18:59 UTC
+----------------------------------------------------------
+End testing: Mar 25 18:59 UTC

app/gcompose/src/ContextModel.cpp

@@ -14,10 +14,25 @@ void ContextModel::setContext(uLib::ObjectsContext* context) {
     beginResetModel();
     m_rootContext = context;
     if (m_rootContext) {
-        uLib::Object::connect(m_rootContext, &uLib::Object::Updated, [this]() {
+        auto refresh = [this]() {
             this->beginResetModel();
             this->endResetModel();
+        };
+
+        uLib::Object::connect(m_rootContext, &uLib::Object::Updated, refresh);
+        uLib::Object::connect(m_rootContext, &uLib::ObjectsContext::ObjectAdded, [this, refresh](uLib::Object* obj) {
+            uLib::Object::connect(obj, &uLib::Object::Updated, refresh);
+            refresh();
         });
+        uLib::Object::connect(m_rootContext, &uLib::ObjectsContext::ObjectRemoved, [this, refresh](uLib::Object* obj) {
+            // Disconnect would be good here but not strictly required if refresh handles it
+            refresh();
+        });
+
+        // Connect existing objects
+        for (auto* obj : m_rootContext->GetObjects()) {
+            uLib::Object::connect(obj, &uLib::Object::Updated, refresh);
+        }
     }
     endResetModel();
 }

app/gcompose/src/ContextPanel.cpp

@@ -92,3 +92,27 @@ void ContextPanel::onSelectionChanged(const QItemSelection& selected, const QIte
     emit objectSelected(target);
     m_propertiesPanel->setObject(target);
 }
+
+void ContextPanel::selectObject(uLib::Object* obj) {
+    if (!obj) {
+        clearSelection();
+        return;
+    }
+    
+    for (int i = 0; i < m_model->rowCount(); ++i) {
+        QModelIndex idx = m_model->index(i, 0);
+        if (idx.internalPointer() == obj) {
+            QSignalBlocker blocker(m_treeView->selectionModel());
+            m_treeView->selectionModel()->select(idx, QItemSelectionModel::ClearAndSelect | QItemSelectionModel::Rows);
+            m_treeView->scrollTo(idx);
+            m_propertiesPanel->setObject(obj); // Explicitly update properties too
+            return;
+        }
+    }
+}
+
+void ContextPanel::clearSelection() {
+    QSignalBlocker blocker(m_treeView->selectionModel());
+    m_treeView->selectionModel()->clearSelection();
+    m_propertiesPanel->setObject(nullptr);
+}

app/gcompose/src/ContextPanel.h

@@ -20,6 +20,8 @@ public:
     ~ContextPanel();
 
     void setContext(uLib::ObjectsContext* context);
+    void selectObject(uLib::Object* obj);
+    void clearSelection();
 
 signals:
     void objectSelected(uLib::Object* obj);

app/gcompose/src/MainPanel.cpp

@@ -14,7 +14,10 @@
 #include <QMenu>
 #include <QAction>
 #include <QApplication>
+#include <QFileDialog>
+#include <QFileInfo>
 #include "StyleManager.h"
+#include "Math/VoxImage.h"
 
 MainPanel::MainPanel(QWidget* parent) : QWidget(parent), m_context(nullptr), m_mainVtkContext(nullptr) {
     this->setObjectName("MainPanel");
@@ -41,6 +44,8 @@ MainPanel::MainPanel(QWidget* parent) : QWidget(parent), m_context(nullptr), m_m
     auto* fileMenu = new QMenu(btnFile);
     fileMenu->addAction("Open", this, &MainPanel::onOpen);
     fileMenu->addAction("Save", this, &MainPanel::onSave);
+    fileMenu->addAction("Save As", this, &MainPanel::onSaveAs);
+    fileMenu->addAction("Exit", this, &MainPanel::onExit);
     btnFile->setMenu(fileMenu);
 
     // Theme Menu Button
@@ -52,7 +57,7 @@ MainPanel::MainPanel(QWidget* parent) : QWidget(parent), m_context(nullptr), m_m
     btnTheme->setMenu(themeMenu);
 
     // New Menu Button
-    auto* btnNew = new QPushButton("New", menuPanel);
+    auto* btnNew = new QPushButton("Add", menuPanel);
     btnNew->setObjectName("MenuButton");
     auto* newMenu = new QMenu(btnNew);
     
@@ -122,6 +127,17 @@ void MainPanel::setContext(uLib::ObjectsContext* context) {
             m_mainVtkContext = new uLib::Vtk::vtkObjectsContext(context);
             // viewport->AddPuppet(*m_mainVtkContext); // redundant
 
+            auto syncSelection = [this](uLib::Vtk::Puppet* p) {
+                if (!p) {
+                    m_contextPanel->clearSelection();
+                    m_firstPane->setObject(nullptr);
+                } else {
+                    m_contextPanel->selectObject(p->GetContent());
+                    m_firstPane->setObject(p);
+                }
+            };
+            connect(viewport, &uLib::Vtk::QViewport::puppetSelected, syncSelection);
+
             uLib::Object::connect(m_mainVtkContext, &uLib::Vtk::vtkObjectsContext::PuppetAdded, [this](uLib::Vtk::Puppet* p) {
                 if (p) {
                     auto panes = this->findChildren<ViewportPane*>();
@@ -177,13 +193,49 @@ void MainPanel::onCreateObject(const std::string& className) {
 }
 
 void MainPanel::onOpen() {
-    // Placeholder for open logic
+    QString fileName = QFileDialog::getOpenFileName(this, "Open File", "", 
+        "VTK/VTI Images (*.vtk *.vti);;All Files (*.*)");
+    
+    if (fileName.isEmpty()) return;
+
+    QFileInfo info(fileName);
+    QString ext = info.suffix().toLower();
+
+    if (ext == "vti" || ext == "vtk") {
+        auto* obj = uLib::ObjectFactory::Instance().Create("VoxImage");
+        auto* vox = dynamic_cast<uLib::Abstract::VoxImage*>(obj);
+        if (vox) {
+            bool success = false;
+            if (ext == "vti") {
+                success = vox->ImportFromVti(fileName.toStdString().c_str());
+            } else {
+                success = vox->ImportFromVtk(fileName.toStdString().c_str());
+            }
+
+            if (success) {
+                obj->SetInstanceName(info.fileName().toStdString());
+                m_context->AddObject(obj);
+            } else {
+                delete obj;
+            }
+        } else {
+            delete obj;
+        }
+    }
 }
 
 void MainPanel::onSave() {
     // Placeholder for save logic
 }
 
+void MainPanel::onSaveAs() {
+    // Placeholder for save as logic
+}
+
+void MainPanel::onExit() {
+    qApp->quit();
+}
+
 void MainPanel::onDarkTheme() {
     StyleManager::applyStyle(qApp, "dark");
 }

app/gcompose/src/MainPanel.h

@@ -27,6 +27,9 @@ public:
 private slots:
     void onOpen();
     void onSave();
+    void onSaveAs();
+    void onExit();
+
     void onDarkTheme();
     void onBrightTheme();
     

app/gcompose/src/PropertyWidgets.cpp

@@ -1,6 +1,13 @@
 #include "PropertyWidgets.h"
 #include <QSignalBlocker>
+#include <QRegularExpression>
+#include <QRegularExpressionMatch>
+#include <QComboBox>
+#include <QCheckBox>
 #include "Vtk/uLibVtkInterface.h"
+#include "Math/Units.h"
+#include "Math/Dense.h"
+#include "Settings.h"
 
 namespace uLib {
 namespace Qt {
@@ -9,63 +16,181 @@ PropertyWidgetBase::PropertyWidgetBase(PropertyBase* prop, QWidget* parent)
     : QWidget(parent), m_BaseProperty(prop) {
     m_Layout = new QHBoxLayout(this);
     m_Layout->setContentsMargins(4, 2, 4, 2);
-    m_Label = new QLabel(QString::fromStdString(prop->GetName()), this);
-    m_Label->setMinimumWidth(100);
+    
+    std::string unit = prop->GetUnits();
+    QString labelText = QString::fromStdString(prop->GetName());
+    if (!unit.empty()) {
+        auto dim = Settings::Instance().IdentifyDimension(unit);
+        std::string pref = Settings::Instance().GetPreferredUnit(dim);
+        if (!pref.empty()) {
+            labelText += " [" + QString::fromStdString(pref) + "]";
+        } else {
+            labelText += " [" + QString::fromStdString(unit) + "]";
+        }
+    }
+    
+    m_Label = new QLabel(labelText, this);
+    m_Label->setMinimumWidth(120);
     m_Layout->addWidget(m_Label);
 }
-PropertyWidgetBase::~PropertyWidgetBase() {}
+PropertyWidgetBase::~PropertyWidgetBase() {
+    m_Connection.disconnect();
+}
+
+// Helper for unit parsing
+double parseWithUnits(const QString& text, double* factorOut, QString* suffixOut) {
+    static QRegularExpression re("^\\s*([-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?)\\s*(_?[a-zA-Z]+)?\\s*$");
+    QRegularExpressionMatch match = re.match(text);
+    if (!match.hasMatch()) return 0.0;
+
+    double num = match.captured(1).toDouble();
+    QString unit = match.captured(3);
+    double factor = 1.0;
+
+    if (!unit.isEmpty()) {
+        QString u = unit.startsWith('_') ? unit.mid(1) : unit;
+        if (u == "m") factor = CLHEP::meter;
+        else if (u == "cm") factor = CLHEP::centimeter;
+        else if (u == "mm") factor = CLHEP::millimeter;
+        else if (u == "um") factor = CLHEP::micrometer;
+        else if (u == "nm") factor = CLHEP::nanometer;
+        else if (u == "km") factor = CLHEP::kilometer;
+        else if (u == "deg") factor = CLHEP::degree;
+        else if (u == "rad") factor = CLHEP::radian;
+        else if (u == "ns") factor = CLHEP::nanosecond;
+        else if (u == "s") factor = CLHEP::second;
+        else if (u == "ms") factor = CLHEP::millisecond;
+        else if (u == "MeV") factor = CLHEP::megaelectronvolt;
+        else if (u == "eV") factor = CLHEP::electronvolt;
+        else if (u == "keV") factor = CLHEP::kiloelectronvolt;
+        else if (u == "GeV") factor = CLHEP::gigaelectronvolt;
+        else if (u == "TeV") factor = CLHEP::teraelectronvolt;
+        if (suffixOut) *suffixOut = u;
+    } else if (suffixOut) {
+        // Reuse previous suffix if none provided, or empty
+    }
+
+    if (factorOut) *factorOut = factor;
+    return num * factor;
+}
+
+// UnitLineEdit implementation
+UnitLineEdit::UnitLineEdit(QWidget* parent) : QLineEdit(parent), m_Value(0), m_Factor(1.0), m_Suffix(""), m_IsInteger(false) {
+    connect(this, &QLineEdit::editingFinished, this, &UnitLineEdit::onEditingFinished);
+}
+
+void UnitLineEdit::setUnits(const QString& suffix, double factor) {
+    m_Suffix = suffix;
+    m_Factor = factor;
+    updateText();
+}
+
+void UnitLineEdit::setValue(double val) {
+    if (m_Value != val) {
+        m_Value = val;
+        // Suffix heuristic ONLY if it was mm and no explicit unit was given?
+        // Actually, if m_Suffix is empty or we have a specific one, we should respect it.
+        // The original code had a heuristic, but it's better to let property decide.
+        // Let's keep it ONLY if m_Suffix was mm (legacy behavior)
+        if (!m_IsInteger && m_Suffix == "mm" && std::abs(val) >= 1000.0) { m_Suffix = "m"; m_Factor = CLHEP::meter; }
+        updateText();
+    }
+}
+
+void UnitLineEdit::onEditingFinished() {
+    double factor = m_Factor;
+    QString suffix = m_Suffix;
+    double parsedVal = parseWithUnits(text(), &factor, &suffix);
+    if (!suffix.isEmpty()) {
+        m_Suffix = suffix;
+        m_Factor = factor;
+    }
+    if (m_IsInteger) {
+        parsedVal = std::round(parsedVal);
+    }
+    
+    if (m_Value != parsedVal) {
+        m_Value = parsedVal;
+        emit valueManualChanged(m_Value);
+    }
+    updateText();
+}
+
+void UnitLineEdit::updateText() {
+    QSignalBlocker blocker(this);
+    QString s;
+    if (m_IsInteger) {
+        s = QString::number((int)m_Value);
+        if (s.isEmpty()) s = "0";
+    } else {
+        double displayVal = m_Value / m_Factor;
+        s = QString::number(displayVal, 'g', 6);
+        if (!s.contains('.') && !s.contains('e')) {
+            s += ".0";
+        }
+    }
+    setText(s);
+}
+
+void UnitLineEdit::setIntegerOnly(bool integerOnly) {
+    m_IsInteger = integerOnly;
+    updateText();
+}
 
 DoublePropertyWidget::DoublePropertyWidget(Property<double>* prop, QWidget* parent)
     : PropertyWidgetBase(prop, parent), m_Prop(prop) {
-    m_SpinBox = new QDoubleSpinBox(this);
-    m_SpinBox->setRange(-1000000.0, 1000000.0);
-    m_SpinBox->setValue(prop->Get());
-    m_Layout->addWidget(m_SpinBox, 1);
-    connect(m_SpinBox, static_cast<void(QDoubleSpinBox::*)(double)>(&QDoubleSpinBox::valueChanged),
-            [this](double val){ if (m_Prop->Get() != val) m_Prop->Set(val); });
-    uLib::Object::connect(m_Prop, &Property<double>::PropertyChanged, [this](){
-        if (m_SpinBox->value() != m_Prop->Get()) {
-            QSignalBlocker blocker(m_SpinBox);
-            m_SpinBox->setValue(m_Prop->Get());
+    m_Edit = new UnitLineEdit(this);
+    std::string unit = prop->GetUnits();
+    if (!unit.empty()) {
+        auto dim = Settings::Instance().IdentifyDimension(unit);
+        std::string pref = Settings::Instance().GetPreferredUnit(dim);
+        double factor = Settings::Instance().GetUnitFactor(pref);
+        m_Edit->setUnits(QString::fromStdString(pref), factor);
     }
+    m_Edit->setValue(prop->Get());
+    m_Layout->addWidget(m_Edit, 1);
+    connect(m_Edit, &UnitLineEdit::valueManualChanged, [this](double val){ m_Prop->Set(val); });
+    m_Connection = uLib::Object::connect(m_Prop, &Property<double>::PropertyChanged, [this](){
+        m_Edit->setValue(m_Prop->Get());
     });
 }
-DoublePropertyWidget::~DoublePropertyWidget() {}
 
 FloatPropertyWidget::FloatPropertyWidget(Property<float>* prop, QWidget* parent)
     : PropertyWidgetBase(prop, parent), m_Prop(prop) {
-    m_SpinBox = new QDoubleSpinBox(this);
-    m_SpinBox->setRange(-1000000.0, 1000000.0);
-    m_SpinBox->setDecimals(3);
-    m_SpinBox->setValue(prop->Get());
-    m_Layout->addWidget(m_SpinBox, 1);
-    connect(m_SpinBox, static_cast<void(QDoubleSpinBox::*)(double)>(&QDoubleSpinBox::valueChanged),
-            [this](double val){ if (m_Prop->Get() != (float)val) m_Prop->Set((float)val); });
-    uLib::Object::connect(m_Prop, &Property<float>::PropertyChanged, [this](){
-        if (m_SpinBox->value() != (double)m_Prop->Get()) {
-            QSignalBlocker blocker(m_SpinBox);
-            m_SpinBox->setValue((double)m_Prop->Get());
+    m_Edit = new UnitLineEdit(this);
+    std::string unit = prop->GetUnits();
+    if (!unit.empty()) {
+        auto dim = Settings::Instance().IdentifyDimension(unit);
+        std::string pref = Settings::Instance().GetPreferredUnit(dim);
+        double factor = Settings::Instance().GetUnitFactor(pref);
+        m_Edit->setUnits(QString::fromStdString(pref), factor);
     }
+    m_Edit->setValue(prop->Get());
+    m_Layout->addWidget(m_Edit, 1);
+    connect(m_Edit, &UnitLineEdit::valueManualChanged, [this](double val){ m_Prop->Set((float)val); });
+    m_Connection = uLib::Object::connect(m_Prop, &Property<float>::PropertyChanged, [this](){
+        m_Edit->setValue((double)m_Prop->Get());
     });
 }
-FloatPropertyWidget::~FloatPropertyWidget() {}
 
 IntPropertyWidget::IntPropertyWidget(Property<int>* prop, QWidget* parent)
     : PropertyWidgetBase(prop, parent), m_Prop(prop) {
-    m_SpinBox = new QSpinBox(this);
-    m_SpinBox->setRange(-1000000, 1000000);
-    m_SpinBox->setValue(prop->Get());
-    m_Layout->addWidget(m_SpinBox, 1);
-    connect(m_SpinBox, static_cast<void(QSpinBox::*)(int)>(&QSpinBox::valueChanged),
-            [this](int val){ if (m_Prop->Get() != val) m_Prop->Set(val); });
-    uLib::Object::connect(m_Prop, &Property<int>::PropertyChanged, [this](){
-        if (m_SpinBox->value() != m_Prop->Get()) {
-            QSignalBlocker blocker(m_SpinBox);
-            m_SpinBox->setValue(m_Prop->Get());
+    m_Edit = new UnitLineEdit(this);
+    m_Edit->setIntegerOnly(true);
+    std::string unit = prop->GetUnits();
+    if (!unit.empty()) {
+        auto dim = Settings::Instance().IdentifyDimension(unit);
+        std::string pref = Settings::Instance().GetPreferredUnit(dim);
+        double factor = Settings::Instance().GetUnitFactor(pref);
+        m_Edit->setUnits(QString::fromStdString(pref), factor);
     }
+    m_Edit->setValue(prop->Get());
+    m_Layout->addWidget(m_Edit, 1);
+    connect(m_Edit, &UnitLineEdit::valueManualChanged, [this](double val){ m_Prop->Set((int)val); });
+    m_Connection = uLib::Object::connect(m_Prop, &Property<int>::PropertyChanged, [this](){
+        m_Edit->setValue((double)m_Prop->Get());
     });
 }
-IntPropertyWidget::~IntPropertyWidget() {}
 
 BoolPropertyWidget::BoolPropertyWidget(Property<bool>* prop, QWidget* parent)
     : PropertyWidgetBase(prop, parent), m_Prop(prop) {
@@ -73,7 +198,7 @@ BoolPropertyWidget::BoolPropertyWidget(Property<bool>* prop, QWidget* parent)
     m_CheckBox->setChecked(prop->Get());
     m_Layout->addWidget(m_CheckBox, 1);
     connect(m_CheckBox, &QCheckBox::toggled, [this](bool val){ if (m_Prop->Get() != val) m_Prop->Set(val); });
-    uLib::Object::connect(m_Prop, &Property<bool>::PropertyChanged, [this](){
+    m_Connection = uLib::Object::connect(m_Prop, &Property<bool>::PropertyChanged, [this](){
         if (m_CheckBox->isChecked() != m_Prop->Get()) {
             QSignalBlocker blocker(m_CheckBox);
             m_CheckBox->setChecked(m_Prop->Get());
@@ -91,7 +216,7 @@ StringPropertyWidget::StringPropertyWidget(Property<std::string>* prop, QWidget*
         std::string val = m_LineEdit->text().toStdString();
         if (m_Prop->Get() != val) m_Prop->Set(val);
     });
-    uLib::Object::connect(m_Prop, &Property<std::string>::PropertyChanged, [this](){
+    m_Connection = uLib::Object::connect(m_Prop, &Property<std::string>::PropertyChanged, [this](){
         if (m_LineEdit->text().toStdString() != m_Prop->Get()) {
             QSignalBlocker blocker(m_LineEdit);
             m_LineEdit->setText(QString::fromStdString(m_Prop->Get()));
@@ -100,6 +225,57 @@ StringPropertyWidget::StringPropertyWidget(Property<std::string>* prop, QWidget*
 }
 StringPropertyWidget::~StringPropertyWidget() {}
 
+class GroupHeaderWidget : public QWidget {
+public:
+    GroupHeaderWidget(const QString& name, QWidget* parent = nullptr) : QWidget(parent) {
+        auto* layout = new QVBoxLayout(this);
+        layout->setContentsMargins(0, 8, 0, 4);
+        auto* line = new QFrame(this);
+        line->setFrameShape(QFrame::HLine);
+        line->setFrameShadow(QFrame::Sunken);
+        line->setStyleSheet("color: #555;");
+        layout->addWidget(line);
+        auto* label = new QLabel(name, this);
+        QFont font = label->font();
+        font.setBold(true);
+        font.setPointSize(font.pointSize() + 1);
+        label->setFont(font);
+        label->setStyleSheet("color: #aaa; text-transform: uppercase;");
+        layout->addWidget(label);
+    }
+};
+
+class EnumPropertyWidget : public PropertyWidgetBase {
+    PropertyBase* m_Prop;
+    QComboBox* m_Combo;
+public:
+    EnumPropertyWidget(PropertyBase* prop, QWidget* parent)
+        : PropertyWidgetBase(prop, parent), m_Prop(prop) {
+        m_Combo = new QComboBox(this);
+        const auto& labels = prop->GetEnumLabels();
+        for (const auto& label : labels) {
+            m_Combo->addItem(QString::fromStdString(label));
+        }
+
+        // Get initial value
+        if (auto* p = dynamic_cast<Property<int>*>(prop)) {
+            m_Combo->setCurrentIndex(p->Get());
+            connect(m_Combo, &QComboBox::currentIndexChanged, [p](int index){
+                p->Set(index);
+            });
+            // Store connection in base m_Connection so it's auto-disconnected on destruction.
+            m_Connection = uLib::Object::connect(p, &Property<int>::PropertyChanged, [this, p](){
+                if (m_Combo->currentIndex() != p->Get()) {
+                    QSignalBlocker blocker(m_Combo);
+                    m_Combo->setCurrentIndex(p->Get());
+                }
+            });
+        }
+
+        m_Layout->addWidget(m_Combo, 1);
+    }
+};
+
 PropertyEditor::PropertyEditor(QWidget* parent) : QWidget(parent), m_Object(nullptr) {
     m_MainLayout = new QVBoxLayout(this);
     m_MainLayout->setContentsMargins(0, 0, 0, 0);
@@ -126,6 +302,22 @@ PropertyEditor::PropertyEditor(QWidget* parent) : QWidget(parent), m_Object(null
     registerFactory<std::string>([](PropertyBase* p, QWidget* parent){
         return new StringPropertyWidget(static_cast<Property<std::string>*>(p), parent);
     });
+    
+    // Register EnumProperty specifically (needs to check type since it holds Property<int> but is EnumProperty)
+    m_Factories[std::type_index(typeid(EnumProperty))] = [](PropertyBase* p, QWidget* parent) {
+        return new EnumPropertyWidget(p, parent);
+    };
+
+    // Vector Registration
+    registerFactory<Vector2i>([](PropertyBase* p, QWidget* parent){ return new VectorPropertyWidget<Vector2i, 2>(static_cast<Property<Vector2i>*>(p), parent); });
+    registerFactory<Vector2f>([](PropertyBase* p, QWidget* parent){ return new VectorPropertyWidget<Vector2f, 2>(static_cast<Property<Vector2f>*>(p), parent); });
+    registerFactory<Vector2d>([](PropertyBase* p, QWidget* parent){ return new VectorPropertyWidget<Vector2d, 2>(static_cast<Property<Vector2d>*>(p), parent); });
+    registerFactory<Vector3i>([](PropertyBase* p, QWidget* parent){ return new VectorPropertyWidget<Vector3i, 3>(static_cast<Property<Vector3i>*>(p), parent); });
+    registerFactory<Vector3f>([](PropertyBase* p, QWidget* parent){ return new VectorPropertyWidget<Vector3f, 3>(static_cast<Property<Vector3f>*>(p), parent); });
+    registerFactory<Vector3d>([](PropertyBase* p, QWidget* parent){ return new VectorPropertyWidget<Vector3d, 3>(static_cast<Property<Vector3d>*>(p), parent); });
+    registerFactory<Vector4i>([](PropertyBase* p, QWidget* parent){ return new VectorPropertyWidget<Vector4i, 4>(static_cast<Property<Vector4i>*>(p), parent); });
+    registerFactory<Vector4f>([](PropertyBase* p, QWidget* parent){ return new VectorPropertyWidget<Vector4f, 4>(static_cast<Property<Vector4f>*>(p), parent); });
+    registerFactory<Vector4d>([](PropertyBase* p, QWidget* parent){ return new VectorPropertyWidget<Vector4d, 4>(static_cast<Property<Vector4d>*>(p), parent); });
 }
 
 PropertyEditor::~PropertyEditor() {}
@@ -147,15 +339,51 @@ void PropertyEditor::setObject(::uLib::Object* obj, bool displayOnly) {
         }
     }
 
+    // Group properties by their group string
+    std::map<std::string, std::vector<::uLib::PropertyBase*>> groupedProps;
+    std::vector<std::string> groupOrder;
+    
     for (auto* prop : *props) {
+        std::string group = prop->GetGroup();
+        if (groupedProps.find(group) == groupedProps.end()) {
+            groupOrder.push_back(group);
+        }
+        groupedProps[group].push_back(prop);
+    }
+
+    for (const auto& groupName : groupOrder) {
+        if (!groupName.empty()) {
+            m_ContainerLayout->addWidget(new GroupHeaderWidget(QString::fromStdString(groupName), m_Container));
+        }
+
+        for (auto* prop : groupedProps[groupName]) {
+            QWidget* widget = nullptr;
+            
+            // Priority 1: Check if it provides enum labels
+            if (!prop->GetEnumLabels().empty()) {
+                widget = new EnumPropertyWidget(prop, m_Container);
+            } else {
+                // Priority 2: Standard factory lookup
                 auto it = m_Factories.find(prop->GetTypeIndex());
                 if (it != m_Factories.end()) {
-            QWidget* widget = it->second(prop, m_Container);
-            m_ContainerLayout->addWidget(widget);
+                    widget = it->second(prop, m_Container);
                 } else {
-            QWidget* fallback = new PropertyWidgetBase(prop, m_Container);
-            fallback->layout()->addWidget(new QLabel("(Read-only: " + QString::fromStdString(prop->GetValueAsString()) + ")"));
-            m_ContainerLayout->addWidget(fallback);
+                    // Debug info for unknown types
+                    std::cout << "PropertyEditor: No factory for " << prop->GetQualifiedName() 
+                              << " (Type: " << prop->GetTypeName() << ")" << std::endl;
+
+                    widget = new PropertyWidgetBase(prop, m_Container);
+                    widget->layout()->addWidget(new QLabel("(Read-only: " + QString::fromStdString(prop->GetValueAsString()) + ")"));
+                }
+            }
+
+            if (widget) {
+                if (!groupName.empty()) {
+                    // Indent grouped properties
+                    widget->setContentsMargins(16, 0, 0, 0);
+                }
+                m_ContainerLayout->addWidget(widget);
+            }
         }
     }
     m_ContainerLayout->addStretch(1);

app/gcompose/src/PropertyWidgets.h

@@ -5,8 +5,6 @@
 #include <QLabel>
 #include <QHBoxLayout>
 #include <QVBoxLayout>
-#include <QDoubleSpinBox>
-#include <QSpinBox>
 #include <QLineEdit>
 #include <QCheckBox>
 #include <QScrollArea>
@@ -16,10 +14,15 @@
 
 #include "Core/Property.h"
 #include "Core/Object.h"
+#include "Core/Signal.h"
+#include "Math/Dense.h"
+#include "Settings.h"
 
 namespace uLib {
 namespace Qt {
 
+double parseWithUnits(const QString& text, double* factorOut = nullptr, QString* suffixOut = nullptr);
+
 class PropertyWidgetBase : public QWidget {
     Q_OBJECT
 public:
@@ -31,36 +34,111 @@ protected:
     PropertyBase* m_BaseProperty;
     QHBoxLayout* m_Layout;
     QLabel* m_Label;
+    // Stores the uLib signal connection so it can be disconnected on destruction,
+    // preventing use-after-free when PropertyEditor::clear() deletes widgets.
+    Connection m_Connection;
+};
+
+class UnitLineEdit : public QLineEdit {
+    Q_OBJECT
+public:
+    UnitLineEdit(QWidget* parent = nullptr);
+    void setValue(double val);
+    void setUnits(const QString& suffix, double factor = 1.0);
+    double getValue() const { return m_Value; }
+    void setIntegerOnly(bool b);
+
+signals:
+    void valueManualChanged(double val);
+
+private slots:
+    void onEditingFinished();
+
+private:
+    void updateText();
+    double m_Value;
+    double m_Factor;
+    QString m_Suffix;
+    bool m_IsInteger;
 };
 
 class DoublePropertyWidget : public PropertyWidgetBase {
     Q_OBJECT
 public:
     DoublePropertyWidget(Property<double>* prop, QWidget* parent = nullptr);
-    virtual ~DoublePropertyWidget();
 private:
     Property<double>* m_Prop;
-    QDoubleSpinBox* m_SpinBox;
+    UnitLineEdit* m_Edit;
 };
 
 class FloatPropertyWidget : public PropertyWidgetBase {
     Q_OBJECT
 public:
     FloatPropertyWidget(Property<float>* prop, QWidget* parent = nullptr);
-    virtual ~FloatPropertyWidget();
 private:
     Property<float>* m_Prop;
-    QDoubleSpinBox* m_SpinBox;
+    UnitLineEdit* m_Edit;
 };
 
 class IntPropertyWidget : public PropertyWidgetBase {
     Q_OBJECT
 public:
     IntPropertyWidget(Property<int>* prop, QWidget* parent = nullptr);
-    virtual ~IntPropertyWidget();
 private:
     Property<int>* m_Prop;
-    QSpinBox* m_SpinBox;
+    UnitLineEdit* m_Edit;
+};
+
+template <typename VecT, int Size>
+class VectorPropertyWidget : public PropertyWidgetBase {
+public:
+    VectorPropertyWidget(Property<VecT>* prop, QWidget* parent = nullptr)
+        : PropertyWidgetBase(prop, parent), m_Prop(prop) {
+        
+        std::string unit = prop->GetUnits();
+        double factor = 1.0;
+        QString prefSuffix;
+        if (!unit.empty()) {
+            auto dim = Settings::Instance().IdentifyDimension(unit);
+            std::string pref = Settings::Instance().GetPreferredUnit(dim);
+            factor = Settings::Instance().GetUnitFactor(pref);
+            prefSuffix = QString::fromStdString(pref);
+        }
+
+        for (int i = 0; i < Size; ++i) {
+            m_Edits[i] = new UnitLineEdit(this);
+            if (std::is_integral<typename VecT::Scalar>::value) {
+                m_Edits[i]->setIntegerOnly(true);
+            }
+            if (!prefSuffix.isEmpty()) {
+               m_Edits[i]->setUnits(prefSuffix, factor);
+            }
+            m_Layout->addWidget(m_Edits[i], 1);
+            
+            connect(m_Edits[i], &UnitLineEdit::valueManualChanged, [this, i](double val){
+                VecT v = m_Prop->Get();
+                v(i) = (typename VecT::Scalar)val;
+                if (m_Prop->Get() != v) m_Prop->Set(v);
+            });
+        }
+        updateEdits();
+        m_Connection = uLib::Object::connect(m_Prop, &Property<VecT>::PropertyChanged, [this](){
+            updateEdits();
+        });
+    }
+    ~VectorPropertyWidget() { m_Connection.disconnect(); }
+
+private:
+    void updateEdits() {
+        VecT v = m_Prop->Get();
+        for (int i = 0; i < Size; ++i) {
+            if (!m_Edits[i]->hasFocus()) {
+                m_Edits[i]->setValue((double)v(i));
+            }
+        }
+    }
+    Property<VecT>* m_Prop;
+    UnitLineEdit* m_Edits[Size];
 };
 
 class BoolPropertyWidget : public PropertyWidgetBase {

app/gcompose/src/Settings.h

@@ -0,0 +1,75 @@
+#ifndef GCOMPOSE_SETTINGS_H
+#define GCOMPOSE_SETTINGS_H
+
+#include <string>
+#include <map>
+#include "Math/Units.h"
+
+namespace uLib {
+namespace Qt {
+
+class Settings {
+public:
+    static Settings& Instance() {
+        static Settings instance;
+        return instance;
+    }
+
+    enum Dimension {
+        Length,
+        Angle,
+        Energy,
+        Time,
+        Dimensionless
+    };
+
+    void SetPreferredUnit(Dimension dim, const std::string& unit) {
+        m_PreferredUnits[dim] = unit;
+    }
+
+    std::string GetPreferredUnit(Dimension dim) const {
+        auto it = m_PreferredUnits.find(dim);
+        if (it != m_PreferredUnits.end()) return it->second;
+        
+        switch(dim) {
+            case Length: return "mm";
+            case Angle: return "deg";
+            case Energy: return "MeV";
+            case Time: return "ns";
+            default: return "";
+        }
+    }
+
+    double GetUnitFactor(const std::string& unit) const {
+        if (unit == "m") return CLHEP::meter;
+        if (unit == "cm") return CLHEP::centimeter;
+        if (unit == "mm") return CLHEP::millimeter;
+        if (unit == "um") return CLHEP::micrometer;
+        if (unit == "deg") return CLHEP::degree;
+        if (unit == "rad") return CLHEP::radian;
+        if (unit == "ns") return CLHEP::nanosecond;
+        if (unit == "s") return CLHEP::second;
+        if (unit == "ms") return CLHEP::millisecond;
+        if (unit == "MeV") return CLHEP::megaelectronvolt;
+        if (unit == "GeV") return CLHEP::gigaelectronvolt;
+        if (unit == "eV") return CLHEP::electronvolt;
+        return 1.0;
+    }
+
+    Dimension IdentifyDimension(const std::string& unit) const {
+        if (unit == "m" || unit == "cm" || unit == "mm" || unit == "um" || unit == "nm") return Length;
+        if (unit == "deg" || unit == "rad") return Angle;
+        if (unit == "MeV" || unit == "GeV" || unit == "eV" || unit == "keV" || unit == "TeV") return Energy;
+        if (unit == "ns" || unit == "s" || unit == "ms" || unit == "us") return Time;
+        return Dimensionless;
+    }
+
+private:
+    Settings() {}
+    std::map<Dimension, std::string> m_PreferredUnits;
+};
+
+} // namespace Qt
+} // namespace uLib
+
+#endif

app/gcompose/src/ViewportPane.cpp

@@ -46,23 +46,25 @@ ViewportPane::ViewportPane(QWidget* parent) : QWidget(parent), m_viewport(nullpt
 
     m_layout->addWidget(m_titleBar);
 
-    // Main horizontal container for viewport and display panel
-    QWidget* mainArea = new QWidget(this);
-    QHBoxLayout* hLayout = new QHBoxLayout(mainArea);
-    hLayout->setContentsMargins(0, 0, 0, 0);
-    hLayout->setSpacing(0);
-    m_layout->addWidget(mainArea);
+    // Main area with splitter for viewport and display panel
+    m_areaSplitter = new QSplitter(Qt::Horizontal, this);
+    m_areaSplitter->setObjectName("ViewportAreaSplitter");
+    m_layout->addWidget(m_areaSplitter, 1);
 
     // Viewport will be added here via setViewport
-    m_viewport = new uLib::Vtk::QViewport(mainArea);
-    hLayout->addWidget(m_viewport);
+    m_viewport = new uLib::Vtk::QViewport(m_areaSplitter);
+    m_areaSplitter->addWidget(m_viewport);
 
     // Display Panel (Overlay/Slide-out)
-    m_displayPanel = new QFrame(mainArea);
+    m_displayPanel = new QFrame(m_areaSplitter);
     m_displayPanel->setObjectName("DisplayPropertiesPanel");
-    m_displayPanel->setFixedWidth(250);
+    m_displayPanel->setMinimumWidth(150);
     m_displayPanel->hide();
     
+    m_areaSplitter->addWidget(m_displayPanel);
+    m_areaSplitter->setStretchFactor(0, 1);
+    m_areaSplitter->setStretchFactor(1, 0);
+    
     QVBoxLayout* panelLayout = new QVBoxLayout(m_displayPanel);
     panelLayout->setContentsMargins(5, 5, 5, 5);
     
@@ -73,8 +75,6 @@ ViewportPane::ViewportPane(QWidget* parent) : QWidget(parent), m_viewport(nullpt
     m_displayEditor = new uLib::Qt::PropertyEditor(m_displayPanel);
     panelLayout->addWidget(m_displayEditor);
 
-    hLayout->addWidget(m_displayPanel);
-
     connect(m_toggleBtn, &QPushButton::toggled, this, &ViewportPane::toggleDisplayPanel);
     connect(m_titleBar, &QWidget::customContextMenuRequested, this, &ViewportPane::showContextMenu);
     connect(closeBtn, &QToolButton::clicked, this, &ViewportPane::onCloseRequested);
@@ -85,7 +85,15 @@ ViewportPane::ViewportPane(QWidget* parent) : QWidget(parent), m_viewport(nullpt
 ViewportPane::~ViewportPane() {}
 
 void ViewportPane::toggleDisplayPanel() {
-    m_displayPanel->setVisible(m_toggleBtn->isChecked());
+    bool visible = m_toggleBtn->isChecked();
+    m_displayPanel->setVisible(visible);
+    if (visible && m_areaSplitter->sizes().value(1, 0) == 0) {
+        QList<int> sizes = m_areaSplitter->sizes();
+        int total = sizes[0] + sizes[1];
+        sizes[1] = 250;
+        sizes[0] = total - 250;
+        m_areaSplitter->setSizes(sizes);
+    }
 }
 
 void ViewportPane::setObject(uLib::Object* obj) {
@@ -107,15 +115,14 @@ void ViewportPane::setObject(uLib::Object* obj) {
 
 void ViewportPane::setViewport(QWidget* viewport, const QString& title) {
     if (m_viewport) {
-        m_viewport->parentWidget()->layout()->removeWidget(m_viewport);
         delete m_viewport;
     }
     m_viewport = viewport;
     m_titleLabel->setText(title);
 
     m_viewport->setSizePolicy(QSizePolicy::Expanding, QSizePolicy::Expanding);
-    auto* mainAreaLayout = static_cast<QHBoxLayout*>(m_displayPanel->parentWidget()->layout());
-    mainAreaLayout->insertWidget(0, m_viewport);
+    m_areaSplitter->insertWidget(0, m_viewport);
+    m_areaSplitter->setStretchFactor(0, 1);
 }
 
 void ViewportPane::addVtkViewport() {

app/gcompose/src/ViewportPane.h

@@ -10,6 +10,7 @@ namespace uLib {
     namespace Qt { class PropertyEditor; }
 }
 
+class QSplitter;
 class QVBoxLayout;
 class QLabel;
 
@@ -39,6 +40,7 @@ private:
     QVBoxLayout* m_layout;
     QWidget* m_titleBar;
     QLabel* m_titleLabel;
+    QSplitter* m_areaSplitter;
     QWidget* m_viewport;
 
     // Display Properties Overlay

app/gcompose/src/main.cpp

@@ -9,7 +9,7 @@
 #include "HEP/Detectors/DetectorChamber.h"
 #include "Vtk/HEP/Detectors/vtkDetectorChamber.h"
 
-#include <Vtk/vtkContainerBox.h>
+#include <Vtk/Math/vtkContainerBox.h>
 #include <Vtk/vtkQViewport.h>
 
 #include "Core/ObjectsContext.h"

docs/algorithms/algoritm.md

@@ -0,0 +1,338 @@
+# Algorithm Infrastructure
+
+## Overview
+
+An algorithm in the uLib infrastructure is a class for containing a functional that can be dynamically loaded into memory as a plug-in.
+It derives from the base `Object` class (`Core/Object.h`) and therefore can contain properties that define the serialization of operating parameters or the implementation of widgets for interactive parameter manipulation.
+
+The algorithm class is designed to be inserted into an `AlgorithmTask`, a class for managing the execution of scheduled operations. A task contains `Run` and `Stop` methods to start and stop execution. A task can be configured to work in two modes:
+
+- **Cyclic mode**: the algorithm is executed periodically with a configurable cycle time.
+- **Asynchronous mode**: the task waits for a trigger before each execution. Triggers can come from the uLib signal-slot system (`Object::connect`) or from a condition variable as defined in the monitor pattern (`Core/Monitor.h`).
+
+The algorithm is defined as a template class on two types `T_enc` and `T_dec`. The encoder is a type for data input or another algorithm that is chained with this one and outputs data in a compatible format. The decoder is the type of data output or a downstream algorithm compatible with it.
+
+## Class Hierarchy
+
+```
+Object (Core/Object.h)
+  |
+  +-- Algorithm<T_enc, T_dec>        (Core/Algorithm.h)
+  |     |
+  |     +-- VoxImageFilter<VoxelT, CrtpImplT>  (Math/VoxImageFilter.h)
+  |           |
+  |           +-- VoxFilterAlgorithmLinear       (Math/VoxImageFilterLinear.hpp)
+  |           +-- VoxFilterAlgorithmMedian       (Math/VoxImageFilterMedian.hpp)
+  |           +-- VoxFilterAlgorithmAbtrim       (Math/VoxImageFilterABTrim.hpp)
+  |           +-- VoxFilterAlgorithmSPR          (Math/VoxImageFilterABTrim.hpp)
+  |           +-- VoxFilterAlgorithmThreshold    (Math/VoxImageFilterThreshold.hpp)
+  |           +-- VoxFilterAlgorithmBilateral    (Math/VoxImageFilterBilateral.hpp)
+  |           +-- VoxFilterAlgorithmBilateralTrim(Math/VoxImageFilterBilateral.hpp)
+  |           +-- VoxFilterAlgorithm2ndStat      (Math/VoxImageFilter2ndStat.hpp)
+  |           +-- VoxFilterAlgorithmCustom        (Math/VoxImageFilterCustom.hpp)
+  |
+  +-- Thread (Core/Threads.h)
+        |
+        +-- AlgorithmTask<T_enc, T_dec>  (Core/Algorithm.h)
+```
+
+## Algorithm (`Core/Algorithm.h`)
+
+### Template Parameters
+
+```cpp
+template <typename T_enc, typename T_dec>
+class Algorithm : public Object;
+```
+
+- **`T_enc`** (Encoder): the input data type. Can be a raw data type or a pointer to a data structure. When chaining algorithms, the upstream algorithm's `T_dec` must be compatible with this algorithm's `T_enc`.
+- **`T_dec`** (Decoder): the output data type. Produced by `Process()` and consumed by the next algorithm in the chain.
+
+### Core Interface
+
+| Method | Description |
+|--------|-------------|
+| `virtual T_dec Process(const T_enc& input) = 0` | Pure virtual. Implement the algorithm logic here. |
+| `T_dec operator()(const T_enc& input)` | Calls `Process()`. Enables functional syntax: `result = alg(data)`. |
+
+### Algorithm Chaining
+
+Algorithms can be linked in processing pipelines via encoder/decoder pointers:
+
+```cpp
+Algorithm* upstream;    // SetEncoder() / GetEncoder()
+Algorithm* downstream;  // SetDecoder() / GetDecoder()
+```
+
+This allows building chains like:
+
+```
+[RawData] --> AlgorithmA --> AlgorithmB --> [Result]
+               encoder         decoder
+```
+
+### Signals
+
+| Signal | Emitted when |
+|--------|-------------|
+| `Started()` | The algorithm begins processing (caller responsibility). |
+| `Finished()` | The algorithm completes processing (caller responsibility). |
+
+### Device Preference (CUDA)
+
+Algorithms report their preferred execution device via `GetPreferredDevice()`:
+
+| Method | Description |
+|--------|-------------|
+| `virtual MemoryDevice GetPreferredDevice() const` | Returns `RAM` or `VRAM`. Subclasses override. |
+| `void SetPreferredDevice(MemoryDevice dev)` | Manually set the device preference. |
+| `bool IsGPU() const` | Shorthand for `GetPreferredDevice() == VRAM`. |
+
+GPU-based algorithms are responsible for calling `cudaDeviceSynchronize()` inside their `Process()` implementation before returning, so that results are available to the caller or downstream algorithm.
+
+### Example: Defining a Custom Algorithm
+
+```cpp
+class MyFilter : public Algorithm<VoxImage<Voxel>*, VoxImage<Voxel>*> {
+public:
+    const char* GetClassName() const override { return "MyFilter"; }
+
+    VoxImage<Voxel>* Process(VoxImage<Voxel>* const& image) override {
+        // ... filter the image in-place ...
+        return image;
+    }
+};
+```
+
+## AlgorithmTask (`Core/Algorithm.h`)
+
+`AlgorithmTask` manages the execution of an `Algorithm` within a scheduled, threaded context. It inherits from `Thread` (`Core/Threads.h`) and uses `Mutex` (`Core/Monitor.h`) for synchronization.
+
+### Template Parameters
+
+```cpp
+template <typename T_enc, typename T_dec>
+class AlgorithmTask : public Thread;
+```
+
+Must match the `Algorithm<T_enc, T_dec>` it manages.
+
+### Configuration
+
+| Method | Description |
+|--------|-------------|
+| `void SetAlgorithm(AlgorithmType* alg)` | Set the algorithm to execute. |
+| `void SetMode(Mode mode)` | `Cyclic` or `Async`. |
+| `void SetCycleTime(int ms)` | Period for cyclic mode (milliseconds). |
+
+### Execution Modes
+
+#### Cyclic Mode
+
+The algorithm's `Process()` is called periodically. The cycle waits on a `condition_variable_any` with timeout, so `Stop()` can interrupt immediately without waiting for the full cycle.
+
+```cpp
+AlgorithmTask<int, int> task;
+task.SetAlgorithm(&myAlgorithm);
+task.SetMode(AlgorithmTask<int, int>::Cyclic);
+task.SetCycleTime(100);  // every 100ms
+task.Run(inputData);
+// ... later ...
+task.Stop();
+```
+
+#### Asynchronous Mode
+
+The task thread blocks on a condition variable until `Notify()` is called. Each notification triggers exactly one `Process()` invocation.
+
+```cpp
+task.SetMode(AlgorithmTask<int, int>::Async);
+task.Run(inputData);
+
+// Trigger manually:
+task.Notify();
+
+// Or connect to a signal:
+task.ConnectTrigger(sender, &SenderClass::DataReady);
+// Now each emission of DataReady() triggers one Process() call.
+```
+
+### Lifecycle
+
+| Method | Description |
+|--------|-------------|
+| `void Run(const T_enc& input)` | Starts the background thread with the given input. |
+| `void Stop()` | Requests stop and joins the thread. |
+| `bool IsRunning()` | Inherited from `Thread`. |
+
+### Signals
+
+| Signal | Emitted when |
+|--------|-------------|
+| `Stopped()` | The task thread has completed (after last `Process()` and before thread exit). |
+
+### Signal-Slot Triggering
+
+`ConnectTrigger()` connects any uLib `Object` signal to the task's `Notify()` method:
+
+```cpp
+task.ConnectTrigger(detector, &Detector::EventReady);
+```
+
+This uses the uLib signal system (`Core/Signal.h`), not Qt signals. The connection is type-safe and works with the `Object::connect` infrastructure.
+
+## VoxImageFilter (`Math/VoxImageFilter.h`)
+
+`VoxImageFilter` specializes `Algorithm` for kernel-based volumetric image filtering. It uses CRTP (Curiously Recurring Template Pattern) so that concrete filters provide their `Evaluate()` method without virtual dispatch overhead in the inner loop.
+
+### Template Parameters
+
+```cpp
+template <typename VoxelT, typename CrtpImplT>
+class VoxImageFilter : public Abstract::VoxImageFilter,
+                       public Algorithm<VoxImage<VoxelT>*, VoxImage<VoxelT>*>;
+```
+
+- **`VoxelT`**: the voxel data type (must satisfy `Interface::Voxel` — requires `.Value` and `.Count` fields).
+- **`CrtpImplT`**: the concrete filter subclass. Must implement:
+  ```cpp
+  float Evaluate(const VoxImage<VoxelT>& buffer, int index);
+  ```
+
+### How It Works
+
+1. `Process(image)` creates a read-only buffer copy of the input image.
+2. For each voxel in parallel (OpenMP), it calls `CrtpImplT::Evaluate(buffer, index)`.
+3. `Evaluate()` reads from the buffer using the kernel offsets and writes the result.
+4. The filtered image is returned (in-place modification).
+
+```
+Process(image)
+  |
+  +-- buffer = copy of image (read-only snapshot)
+  |
+  +-- #pragma omp parallel for
+  |     for each voxel i:
+  |       image[i].Value = CrtpImplT::Evaluate(buffer, i)
+  |
+  +-- return image
+```
+
+### Kernel System
+
+The `Kernel<VoxelT>` class stores convolution weights and precomputed index offsets:
+
+| Method | Description |
+|--------|-------------|
+| `SetKernelNumericXZY(values)` | Set kernel weights from a flat vector (XZY order). |
+| `SetKernelSpherical(shape)` | Set weights via a radial function `f(distance^2)`. |
+| `SetKernelWeightFunction(shape)` | Set weights via a 3D position function `f(Vector3f)`. |
+
+### CUDA Support
+
+Concrete filters can override `Process()` with a CUDA implementation:
+
+```cpp
+#if defined(USE_CUDA) && defined(__CUDACC__)
+VoxImage<VoxelT>* Process(VoxImage<VoxelT>* const& image) override {
+    if (this->GetPreferredDevice() == MemoryDevice::VRAM) {
+        // Launch CUDA kernel, synchronize, return
+    } else {
+        return BaseClass::Process(image);  // CPU fallback
+    }
+}
+#endif
+```
+
+The base class `GetPreferredDevice()` automatically returns `VRAM` when the image or kernel data resides on the GPU, enabling transparent device dispatch.
+
+Filters with CUDA implementations: `VoxFilterAlgorithmLinear`, `VoxFilterAlgorithmAbtrim`, `VoxFilterAlgorithmSPR`.
+
+### Concrete Filters
+
+| Filter | File | Description |
+|--------|------|-------------|
+| `VoxFilterAlgorithmLinear` | `VoxImageFilterLinear.hpp` | Weighted linear convolution (FIR filter). CUDA-enabled. |
+| `VoxFilterAlgorithmMedian` | `VoxImageFilterMedian.hpp` | Median filter with kernel-weighted sorting. |
+| `VoxFilterAlgorithmAbtrim` | `VoxImageFilterABTrim.hpp` | Alpha-beta trimmed mean filter. CUDA-enabled. |
+| `VoxFilterAlgorithmSPR` | `VoxImageFilterABTrim.hpp` | Robespierre filter: trimmed mean applied only to outlier voxels. CUDA-enabled. |
+| `VoxFilterAlgorithmThreshold` | `VoxImageFilterThreshold.hpp` | Binary threshold filter. |
+| `VoxFilterAlgorithmBilateral` | `VoxImageFilterBilateral.hpp` | Edge-preserving bilateral filter (intensity-weighted Gaussian). |
+| `VoxFilterAlgorithmBilateralTrim` | `VoxImageFilterBilateral.hpp` | Bilateral filter with alpha-beta trimming. |
+| `VoxFilterAlgorithm2ndStat` | `VoxImageFilter2ndStat.hpp` | Local variance (second-order statistic). |
+| `VoxFilterAlgorithmCustom` | `VoxImageFilterCustom.hpp` | User-supplied evaluation function via function pointer. |
+
+### Example: Using a Filter with AlgorithmTask
+
+```cpp
+// Create filter and configure kernel
+VoxFilterAlgorithmLinear<Voxel> filter(Vector3i(3, 3, 3));
+std::vector<float> weights(27, 1.0f);  // uniform 3x3x3
+filter.SetKernelNumericXZY(weights);
+
+// Direct use
+filter.SetImage(&image);
+filter.Run();
+
+// Or via Algorithm interface
+VoxImage<Voxel>* result = filter.Process(&image);
+
+// Or scheduled in a task
+AlgorithmTask<VoxImage<Voxel>*, VoxImage<Voxel>*> task;
+task.SetAlgorithm(&filter);
+task.SetMode(AlgorithmTask<VoxImage<Voxel>*, VoxImage<Voxel>*>::Cyclic);
+task.SetCycleTime(500);
+task.Run(&image);
+```
+
+## Structural Benefits
+
+### 1. Uniform Processing Interface
+
+Every algorithm — from a simple threshold to a GPU-accelerated convolution — exposes the same `Process(input) -> output` interface. Client code does not need to know the concrete type:
+
+```cpp
+Algorithm<VoxImage<Voxel>*, VoxImage<Voxel>*>* alg = &anyFilter;
+alg->Process(&image);
+```
+
+### 2. Pipeline Composition
+
+The encoder/decoder chaining allows building data processing pipelines where each stage transforms data and passes it to the next. Type safety is enforced at compile time through template parameters.
+
+### 3. Scheduled and Event-Driven Execution
+
+`AlgorithmTask` decouples the algorithm from its execution schedule. The same algorithm can be:
+- Called directly (`Process()`)
+- Run periodically (Cyclic mode for monitoring/acquisition)
+- Triggered by events (Async mode for reactive processing)
+
+### 4. Transparent CPU/GPU Dispatch
+
+The `MemoryDevice` preference and `GetPreferredDevice()` virtual allow the same algorithm interface to dispatch to CPU or GPU implementations. The `DataAllocator` transparently manages RAM/VRAM transfers, and concrete filters override `Process()` with CUDA kernels when data is on the GPU.
+
+### 5. Integration with the Object System
+
+Since `Algorithm` inherits from `Object`, algorithms gain:
+- **Properties**: serializable parameters via the `Property<T>` system, enabling persistent configuration and GUI widget generation.
+- **Signals**: `Started`/`Finished` notifications for connecting to monitoring or logging.
+- **Serialization**: save/load algorithm configuration via Boost archives.
+- **Instance naming**: `SetInstanceName()` for runtime identification in contexts.
+
+### 6. CRTP Performance for Inner Loops
+
+`VoxImageFilter` uses CRTP to dispatch to `Evaluate()` without virtual function overhead. The per-voxel evaluation runs at full speed inside OpenMP parallel loops, while the outer `Process()` method remains virtual for polymorphic use through the Algorithm interface.
+
+## Dependencies
+
+```
+Core/Object.h          — base class, properties, signals, serialization
+Core/Signal.h          — signal-slot connection infrastructure
+Core/Monitor.h         — Mutex, condition variables, ULIB_MUTEX_LOCK
+Core/Threads.h         — Thread base class for AlgorithmTask
+Core/DataAllocator.h   — MemoryDevice enum, RAM/VRAM data management
+Math/VoxImage.h        — volumetric image container
+Math/VoxImageFilter.h  — kernel-based filter framework
+```
+
+

src/Core/Algorithm.h

@@ -0,0 +1,263 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// CMT Cosmic Muon Tomography project //////////////////////////////////////////
+////////////////////////////////////////////////////////////////////////////////
+
+  Copyright (c) 2014, Universita' degli Studi di Padova, INFN sez. di Padova
+  All rights reserved
+
+  Authors: Andrea Rigoni Garola < andrea.rigoni@pd.infn.it >
+
+  ------------------------------------------------------------------
+  This library is free software;  you  can  redistribute  it  and/or
+  modify it  under the  terms  of  the  GNU  Lesser  General  Public
+  License as published  by  the  Free  Software  Foundation;  either
+  version 3.0 of the License, or (at your option) any later version.
+
+  This library is  distributed in  the hope that it will  be useful,
+  but  WITHOUT ANY WARRANTY;  without  even  the implied warranty of
+  MERCHANTABILITY  or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+  Lesser General Public License for more details.
+
+  You should have received a copy of  the GNU Lesser General  Public
+  License along with this library.
+
+//////////////////////////////////////////////////////////////////////////////*/
+
+#ifndef U_CORE_ALGORITHM_H
+#define U_CORE_ALGORITHM_H
+
+#include <atomic>
+#include <chrono>
+#include <condition_variable>
+
+#include "Core/Object.h"
+#include "Core/Monitor.h"
+#include "Core/Threads.h"
+#include "Core/DataAllocator.h"
+
+namespace uLib {
+
+////////////////////////////////////////////////////////////////////////////////
+//// ALGORITHM /////////////////////////////////////////////////////////////////
+////////////////////////////////////////////////////////////////////////////////
+
+/**
+ * @brief Algorithm is a template class for containing a functional that can be
+ * dynamically loaded as a plug-in. It derives from Object and supports
+ * properties for serialization and interactive parameter widgets.
+ *
+ * Algorithms are responsible for their own GPU synchronization: if Process()
+ * launches CUDA kernels, it must call cudaDeviceSynchronize() before returning
+ * so that the result is available to the caller or downstream algorithm.
+ *
+ * @tparam T_enc Encoder type: the input data type, or a chained algorithm
+ *               whose output is compatible with this algorithm's input.
+ * @tparam T_dec Decoder type: the output data type, or a chained algorithm
+ *               whose input is compatible with this algorithm's output.
+ */
+template <typename T_enc, typename T_dec>
+class Algorithm : public Object {
+public:
+    using EncoderType = T_enc;
+    using DecoderType = T_dec;
+
+    Algorithm()
+        : Object()
+        , m_Encoder(nullptr)
+        , m_Decoder(nullptr)
+        , m_PreferredDevice(MemoryDevice::RAM)
+    {}
+    virtual ~Algorithm() = default;
+
+    virtual const char* GetClassName() const override { return "Algorithm"; }
+
+    // Processing ///////////////////////////////////////////////////////////////
+
+    /**
+     * @brief Process input data and produce output.
+     * Override this in subclasses to implement the algorithm logic.
+     * GPU-based implementations must synchronize before returning.
+     */
+    virtual T_dec Process(const T_enc& input) = 0;
+
+    /** @brief Operator form of Process for functional chaining. */
+    T_dec operator()(const T_enc& input) { return Process(input); }
+
+    // Chaining /////////////////////////////////////////////////////////////////
+
+    void SetEncoder(Algorithm* enc) { m_Encoder = enc; }
+    Algorithm* GetEncoder() const { return m_Encoder; }
+
+    void SetDecoder(Algorithm* dec) { m_Decoder = dec; }
+    Algorithm* GetDecoder() const { return m_Decoder; }
+
+    // Device preference ////////////////////////////////////////////////////////
+
+    /**
+     * @brief Returns the preferred memory device for this algorithm.
+     * CUDA-capable algorithms should override to return VRAM when their
+     * data resides on the GPU.
+     */
+    virtual MemoryDevice GetPreferredDevice() const { return m_PreferredDevice; }
+    void SetPreferredDevice(MemoryDevice dev) { m_PreferredDevice = dev; }
+
+    /** @brief Returns true if this algorithm prefers GPU execution. */
+    bool IsGPU() const { return GetPreferredDevice() == MemoryDevice::VRAM; }
+
+    // Signals //////////////////////////////////////////////////////////////////
+
+signals:
+    virtual void Started() { ULIB_SIGNAL_EMIT(Algorithm::Started); }
+    virtual void Finished() { ULIB_SIGNAL_EMIT(Algorithm::Finished); }
+
+protected:
+    Algorithm* m_Encoder;
+    Algorithm* m_Decoder;
+    MemoryDevice m_PreferredDevice;
+};
+
+
+////////////////////////////////////////////////////////////////////////////////
+//// ALGORITHM TASK ////////////////////////////////////////////////////////////
+////////////////////////////////////////////////////////////////////////////////
+
+/**
+ * @brief AlgorithmTask manages the execution of an Algorithm within a
+ * scheduled context. Uses uLib::Thread for execution and uLib::Mutex for
+ * synchronization.
+ *
+ * Two execution modes:
+ *  - Cyclic:  executes Process() periodically with configurable cycle time.
+ *  - Async:   waits for Notify() or a connected signal before each execution.
+ *
+ * GPU synchronization is the algorithm's responsibility (see Algorithm::Process).
+ */
+template <typename T_enc, typename T_dec>
+class AlgorithmTask : public Thread {
+public:
+    using AlgorithmType = Algorithm<T_enc, T_dec>;
+
+    enum Mode { Cyclic, Async };
+
+    AlgorithmTask()
+        : Thread()
+        , m_Algorithm(nullptr)
+        , m_Mode(Cyclic)
+        , m_CycleTime_ms(1000)
+        , m_StopRequested(false)
+        , m_Triggered(false)
+    {}
+
+    virtual ~AlgorithmTask() { Stop(); }
+
+    virtual const char* GetClassName() const override { return "AlgorithmTask"; }
+
+    // Configuration ////////////////////////////////////////////////////////////
+
+    void SetAlgorithm(AlgorithmType* alg) { m_Algorithm = alg; }
+    AlgorithmType* GetAlgorithm() const { return m_Algorithm; }
+
+    void SetMode(Mode mode) { m_Mode = mode; }
+    Mode GetMode() const { return m_Mode; }
+
+    void SetCycleTime(int milliseconds) { m_CycleTime_ms = milliseconds; }
+    int GetCycleTime() const { return m_CycleTime_ms; }
+
+    // Lifecycle ////////////////////////////////////////////////////////////////
+
+    /**
+     * @brief Start the task execution in a separate thread (via Thread::Start).
+     * In Cyclic mode, the algorithm is executed periodically.
+     * In Async mode, call Notify() or connect a signal to trigger execution.
+     */
+    void Run(const T_enc& input) {
+        if (IsRunning()) return;
+        m_StopRequested.store(false);
+        m_Triggered.store(false);
+        m_Input = input;
+        Start();
+    }
+
+    /** @brief Stop the task execution and join the thread. */
+    void Stop() {
+        m_StopRequested.store(true);
+        ULIB_MUTEX_LOCK(m_WaitMutex, -1) {
+            m_Condition.notify_all();
+        }
+        if (IsJoinable()) Join();
+    }
+
+    // Async triggering /////////////////////////////////////////////////////////
+
+    /**
+     * @brief Notify the task to execute one iteration (Async mode).
+     * Can be called from a signal-slot connection or externally.
+     */
+    void Notify() {
+        m_Triggered.store(true);
+        ULIB_MUTEX_LOCK(m_WaitMutex, -1) {
+            m_Condition.notify_one();
+        }
+    }
+
+    /**
+     * @brief Connect an Object signal to trigger async execution.
+     * Usage: task.ConnectTrigger(sender, &SenderClass::SomeSignal);
+     */
+    template <typename Func1>
+    Connection ConnectTrigger(typename FunctionPointer<Func1>::Object* sender, Func1 sigf) {
+        return Object::connect(sender, sigf, [this]() { Notify(); });
+    }
+
+    // Signals //////////////////////////////////////////////////////////////////
+
+signals:
+    virtual void Stopped() { ULIB_SIGNAL_EMIT(AlgorithmTask::Stopped); }
+
+protected:
+    /** @brief Thread entry point — dispatches to cyclic or async loop. */
+    void Run() override {
+        if (m_Mode == Cyclic)
+            RunCyclic();
+        else
+            RunAsync();
+        Stopped();
+    }
+
+private:
+    void RunCyclic() {
+        while (!m_StopRequested.load()) {
+            if (m_Algorithm) m_Algorithm->Process(m_Input);
+            std::unique_lock<std::timed_mutex> lock(m_WaitMutex.GetNative());
+            m_Condition.wait_for(lock,
+                std::chrono::milliseconds(m_CycleTime_ms),
+                [this]() { return m_StopRequested.load(); });
+        }
+    }
+
+    void RunAsync() {
+        while (!m_StopRequested.load()) {
+            std::unique_lock<std::timed_mutex> lock(m_WaitMutex.GetNative());
+            m_Condition.wait(lock, [this]() {
+                return m_StopRequested.load() || m_Triggered.load();
+            });
+            if (m_StopRequested.load()) break;
+            m_Triggered.store(false);
+            if (m_Algorithm) m_Algorithm->Process(m_Input);
+        }
+    }
+
+    AlgorithmType* m_Algorithm;
+    Mode m_Mode;
+    int m_CycleTime_ms;
+    T_enc m_Input;
+
+    std::atomic<bool> m_StopRequested;
+    std::atomic<bool> m_Triggered;
+    Mutex m_WaitMutex;
+    std::condition_variable_any m_Condition;
+};
+
+} // namespace uLib
+
+#endif // U_CORE_ALGORITHM_H

src/Core/CMakeLists.txt

@@ -1,5 +1,6 @@
 
 set(HEADERS
+    Algorithm.h
     Archives.h
     Array.h
     Collection.h 
@@ -19,6 +20,8 @@ set(HEADERS
     SmartPointer.h 
     StaticInterface.h 
     StringReader.h 
+    Threads.h
+    Monitor.h
     Types.h 
     Uuid.h 
     Vector.h
@@ -34,9 +37,14 @@ set(SOURCES
     Serializable.cpp 
     Signal.cpp 
     Uuid.cpp
+    Threads.cpp
 )
 
-set(LIBRARIES Boost::program_options Boost::serialization)
+set(LIBRARIES 
+    Boost::program_options 
+    Boost::serialization
+    OpenMP::OpenMP_CXX
+)
 
 set(libname ${PACKAGE_LIBPREFIX}Core)
 set(ULIB_SHARED_LIBRARIES ${ULIB_SHARED_LIBRARIES} ${libname} PARENT_SCOPE)

src/Core/DataAllocator.h

@@ -52,6 +52,7 @@ public:
       else
         m_RamData = static_cast<T *>(::operator new(m_Size * sizeof(T)));
     }
+    // std::cout << "DataAllocator Constructor: ptr=" << m_RamData << " size=" << m_Size << " own=" << m_OwnsObjects << std::endl;
   }
 
   DataAllocator(const DataAllocator<T> &other)
@@ -63,8 +64,13 @@ public:
           m_RamData = new T[m_Size];
         else
           m_RamData = static_cast<T *>(::operator new(m_Size * sizeof(T)));
+        
+        if (m_OwnsObjects) {
+            std::copy(other.m_RamData, other.m_RamData + m_Size, m_RamData);
+        } else {
             std::memcpy(m_RamData, other.m_RamData, m_Size * sizeof(T));
         }
+      }
 #ifdef USE_CUDA
       if (other.m_VramData) {
         cudaMalloc((void **)&m_VramData, m_Size * sizeof(T));
@@ -73,14 +79,17 @@ public:
       }
 #endif
     }
+    // std::cout << "DataAllocator CopyConstructor: from=" << other.m_RamData << " to=" << m_RamData << " size=" << m_Size << " own=" << m_OwnsObjects << std::endl;
   }
 
   ~DataAllocator() {
+    // std::cout << "DataAllocator Destructor: ptr=" << m_RamData << " size=" << m_Size << " own=" << m_OwnsObjects << std::endl;
     if (m_RamData) {
       if (m_OwnsObjects)
         delete[] m_RamData;
       else
         ::operator delete(m_RamData);
+      m_RamData = nullptr;
     }
 #ifdef USE_CUDA
     if (m_VramData) {
@@ -91,6 +100,13 @@ public:
 
   DataAllocator &operator=(const DataAllocator &other) {
     if (this != &other) {
+      if (m_Size == other.m_Size && m_OwnsObjects != other.m_OwnsObjects) {
+          // Ownership changed but size is same: we must force reallocation
+          // to avoid using the wrong delete operator later.
+          size_t oldSize = m_Size;
+          m_Size = 0; 
+          resize(oldSize); // This will free the old buffer with the OLD ownership
+      }
       m_OwnsObjects = other.m_OwnsObjects;
       resize(other.m_Size);
       m_Device = other.m_Device;
@@ -101,8 +117,12 @@ public:
           else
             m_RamData = static_cast<T *>(::operator new(m_Size * sizeof(T)));
         }
+        if (m_OwnsObjects) {
+            std::copy(other.m_RamData, other.m_RamData + m_Size, m_RamData);
+        } else {
             std::memcpy(m_RamData, other.m_RamData, m_Size * sizeof(T));
         }
+      }
 #ifdef USE_CUDA
       if (other.m_VramData) {
         if (!m_VramData)
@@ -112,6 +132,7 @@ public:
       }
 #endif
     }
+    // std::cout << "DataAllocator AssigmentOp: otherPtr=" << other.m_RamData << " thisPtr=" << m_RamData << " size=" << m_Size << " own=" << m_OwnsObjects << std::endl;
     return *this;
   }
 
@@ -152,6 +173,8 @@ public:
     if (m_Size == size)
       return;
 
+    // std::cout << "DataAllocator Resize: from=" << m_Size << " to=" << size << " ptr=" << m_RamData << " own=" << m_OwnsObjects << std::endl;
+
     T *newRam = nullptr;
     T *newVram = nullptr;
 
@@ -162,8 +185,12 @@ public:
         newRam = static_cast<T *>(::operator new(size * sizeof(T)));
 
       if (m_RamData) {
+        if (m_OwnsObjects) {
+            std::copy(m_RamData, m_RamData + std::min(m_Size, size), newRam);
+        } else {
             std::memcpy(newRam, m_RamData, std::min(m_Size, size) * sizeof(T));
         }
+      }
 
 #ifdef USE_CUDA
       cudaMalloc((void **)&newVram, size * sizeof(T));

src/Core/Monitor.h

@@ -0,0 +1,215 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// CMT Cosmic Muon Tomography project //////////////////////////////////////////
+////////////////////////////////////////////////////////////////////////////////
+
+  Copyright (c) 2014, Universita' degli Studi di Padova, INFN sez. di Padova
+  All rights reserved
+
+  Authors: Andrea Rigoni Garola < andrea.rigoni@pd.infn.it >
+
+  ------------------------------------------------------------------
+  This library is free software;  you  can  redistribute  it  and/or
+  modify it  under the  terms  of  the  GNU  Lesser  General  Public
+  License as published  by  the  Free  Software  Foundation;  either
+  version 3.0 of the License, or (at your option) any later version.
+
+  This library is  distributed in  the hope that it will  be useful,
+  but  WITHOUT ANY WARRANTY;  without  even  the implied warranty of
+  MERCHANTABILITY  or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+  Lesser General Public License for more details.
+
+  You should have received a copy of  the GNU Lesser General  Public
+  License along with this library.
+
+//////////////////////////////////////////////////////////////////////////////*/
+
+#ifndef U_CORE_MONITOR_H
+#define U_CORE_MONITOR_H
+
+#include <mutex>
+#include <condition_variable>
+#include <chrono>
+#include <utility>
+
+namespace uLib {
+
+/**
+ * @brief Mutex class wraps std::timed_mutex and is used for thread synchronization.
+ */
+class Mutex {
+public:
+  Mutex() = default;
+  ~Mutex() = default;
+
+  /** @brief Locks the mutex, blocking if necessary. */
+  void Lock() { m_Mutex.lock(); }
+
+  /** @brief Unlocks the mutex. */
+  void Unlock() { m_Mutex.unlock(); }
+
+  /** @brief Tries to lock the mutex without blocking. */
+  bool TryLock() { return m_Mutex.try_lock(); }
+
+  /** @brief Tries to lock the mutex within a timeout in milliseconds. */
+  bool TryLockFor(int timeout_ms) {
+      if (timeout_ms < 0) { Lock(); return true; }
+      return m_Mutex.try_lock_for(std::chrono::milliseconds(timeout_ms));
+  }
+
+  /** @brief RAII helper for scoped locking. */
+  class ScopedLock {
+  public:
+    ScopedLock(Mutex &mutex) : m_Mutex(mutex) { m_Mutex.Lock(); }
+    ~ScopedLock() { m_Mutex.Unlock(); }
+  private:
+    Mutex &m_Mutex;
+    // Non-copyable
+    ScopedLock(const ScopedLock&) = delete;
+    ScopedLock& operator=(const ScopedLock&) = delete;
+  };
+
+  /** @brief Returns the underlying std::timed_mutex. */
+  std::timed_mutex& GetNative() { return m_Mutex; }
+
+private:
+  std::timed_mutex m_Mutex;
+  // Non-copyable
+  Mutex(const Mutex &) = delete;
+  Mutex &operator=(const Mutex &) = delete;
+};
+
+namespace detail {
+
+/** @brief Internal implementation for the ULIB_MUTEX_LOCK macros. */
+class ScopedTimedLock {
+public:
+    ScopedTimedLock(Mutex& mutex, int timeout_ms) 
+        : m_RawMutex(nullptr), m_MutexWrapper(&mutex), m_Locked(false) {
+        m_Locked = m_MutexWrapper->TryLockFor(timeout_ms);
+    }
+    
+    ScopedTimedLock(std::timed_mutex& mutex, int timeout_ms) 
+        : m_RawMutex(&mutex), m_MutexWrapper(nullptr), m_Locked(false) {
+        if (timeout_ms < 0) { m_RawMutex->lock(); m_Locked = true; }
+        else m_Locked = m_RawMutex->try_lock_for(std::chrono::milliseconds(timeout_ms));
+    }
+
+    ~ScopedTimedLock() {
+        if (m_Locked) {
+            if (m_RawMutex) m_RawMutex->unlock();
+            else if (m_MutexWrapper) m_MutexWrapper->Unlock();
+        }
+    }
+    
+    operator bool() const { return m_Locked; }
+    void unlock() { if (m_Locked) { 
+        if (m_RawMutex) m_RawMutex->unlock();
+        else if (m_MutexWrapper) m_MutexWrapper->Unlock();
+        m_Locked = false; 
+    } }
+
+private:
+    std::timed_mutex* m_RawMutex = nullptr;
+    Mutex* m_MutexWrapper = nullptr;
+    bool m_Locked;
+    
+    // Non-copyable/movable to be safe in the 'for' loop
+    ScopedTimedLock(const ScopedTimedLock&) = delete;
+    ScopedTimedLock& operator=(const ScopedTimedLock&) = delete;
+    ScopedTimedLock(ScopedTimedLock&&) = default; 
+};
+
+inline ScopedTimedLock makeScopedMutexLock(Mutex& mutex, int timeout_ms) {
+    return ScopedTimedLock(mutex, timeout_ms);
+}
+
+inline ScopedTimedLock makeScopedMutexLock(std::timed_mutex& mutex, int timeout_ms) {
+    return ScopedTimedLock(mutex, timeout_ms);
+}
+
+} // namespace detail
+
+/**
+ * @brief Macro for block-scoped locking of a static mutex.
+ * @param timeout Timeout in ms (-1 for infinite).
+ */
+#define ULIB_STATIC_LOCK(timeout) \
+    static std::timed_mutex __ulib_static_mutex; \
+    for (auto __ulib_lock = uLib::detail::makeScopedMutexLock(__ulib_static_mutex, timeout); \
+         __ulib_lock; \
+         __ulib_lock.unlock())
+
+/**
+ * @brief Macro for block-scoped locking of a provided mutex.
+ * @param mutex The uLib::Mutex or std::timed_mutex to lock.
+ * @param timeout Timeout in ms (-1 for infinite).
+ */
+#define ULIB_MUTEX_LOCK(mutex, timeout) \
+    for (auto __ulib_lock = uLib::detail::makeScopedMutexLock(mutex, timeout); \
+         __ulib_lock; \
+         __ulib_lock.unlock())
+
+/**
+ * @brief RecursiveMutex class wraps std::recursive_timed_mutex.
+ */
+class RecursiveMutex {
+public:
+  RecursiveMutex() = default;
+  ~RecursiveMutex() = default;
+
+  /** @brief Locks the mutex, blocking if necessary. */
+  void Lock() { m_Mutex.lock(); }
+
+  /** @brief Unlocks the mutex. */
+  void Unlock() { m_Mutex.unlock(); }
+
+  /** @brief Tries to lock the mutex without blocking. */
+  bool TryLock() { return m_Mutex.try_lock(); }
+
+  /** @brief Tries to lock the mutex within a timeout in milliseconds. */
+  bool TryLockFor(int timeout_ms) {
+      if (timeout_ms < 0) { Lock(); return true; }
+      return m_Mutex.try_lock_for(std::chrono::milliseconds(timeout_ms));
+  }
+
+  /** @brief RAII helper for scoped locking. */
+  class ScopedLock {
+  public:
+    ScopedLock(RecursiveMutex &mutex) : m_Mutex(mutex) { m_Mutex.Lock(); }
+    ~ScopedLock() { m_Mutex.Unlock(); }
+  private:
+    RecursiveMutex &m_Mutex;
+    ScopedLock(const ScopedLock&) = delete;
+    ScopedLock& operator=(const ScopedLock&) = delete;
+  };
+
+private:
+  std::recursive_timed_mutex m_Mutex;
+  RecursiveMutex(const RecursiveMutex &) = delete;
+  RecursiveMutex &operator=(const RecursiveMutex &) = delete;
+};
+
+/**
+ * @brief Monitor class provides a base for objects that need thread-safe access.
+ */
+template <typename T>
+class Monitor {
+protected:
+  T* m_Resource;
+  Mutex m_Mutex;
+
+public:
+  Monitor(T* resource) : m_Resource(resource) {}
+  virtual ~Monitor() { delete m_Resource; }
+
+  /** @brief Thread-safe access to the resource through a lambda. */
+  template <typename F>
+  auto Access(F f) -> decltype(f(*m_Resource)) {
+    Mutex::ScopedLock lock(m_Mutex);
+    return f(*m_Resource);
+  }
+};
+
+} // namespace uLib
+
+#endif // U_CORE_MONITOR_H

src/Core/Object.cpp

@@ -61,21 +61,26 @@ public:
   };
   
   std::string m_InstanceName;
-  Vector<Signal> sigv;
-  Vector<Slot> slov;
+  std::vector<Signal> sigv;
+  std::vector<Slot> slov;
   std::vector<PropertyBase*> m_Properties;
   std::vector<PropertyBase*> m_DynamicProperties;
+  bool m_SignalsBlocked;
 };
 
 // Implementations of Property methods
 void Object::RegisterProperty(PropertyBase* prop) {
-    if (prop) d->m_Properties.push_back(prop);
+    if (prop) {
+        d->m_Properties.push_back(prop);
+    }
 }
 
 void Object::RegisterDynamicProperty(PropertyBase* prop) {
     if (prop) {
+        for (auto* existing : d->m_DynamicProperties) {
+            if (existing == prop) return;
+        }
         d->m_DynamicProperties.push_back(prop);
-        d->m_Properties.push_back(prop);
     }
 }
 
@@ -83,6 +88,16 @@ const std::vector<PropertyBase*>& Object::GetProperties() const {
     return d->m_Properties;
 }
 
+PropertyBase* Object::GetProperty(const std::string& name) const {
+    for (auto* p : d->m_Properties) {
+        if (p->GetName() == name || p->GetQualifiedName() == name) return p;
+    }
+    for (auto* p : d->m_DynamicProperties) {
+        if (p->GetName() == name || p->GetQualifiedName() == name) return p;
+    }
+    return nullptr;
+}
+
 // In Object.h, the template serialize needs to be updated to call property serialization.
 // However, since Object::serialize is a template in the header, we might need a helper here.
 
@@ -113,9 +128,27 @@ template void Object::serialize(Archive::log_archive &, const unsigned int);
 ////////////////////////////////////////////////////////////////////////////////
 // OBJECT IMPLEMENTATION
 
-Object::Object() : d(new ObjectPrivate) {}
+Object::Object() : d(new ObjectPrivate) {
+    d->m_SignalsBlocked = false;
+}
+Object::Object(const Object &copy) : d(new ObjectPrivate) {
+    if (copy.d) {
+        d->m_InstanceName = copy.d->m_InstanceName;
+        d->m_SignalsBlocked = copy.d->m_SignalsBlocked;
+    }
+}
 
-Object::Object(const Object &copy) : d(new ObjectPrivate(*copy.d)) {}
+Object& Object::operator=(const Object &other) {
+    // Intentionally does NOT share 'd'. Each Object owns its own ObjectPrivate.
+    // Without this, the compiler-generated operator= would copy the 'd' pointer,
+    // causing two objects to share the same ObjectPrivate. When both are
+    // destroyed, 'd' would be deleted twice, corrupting the heap.
+    if (this != &other && other.d) {
+        d->m_InstanceName = other.d->m_InstanceName;
+        d->m_SignalsBlocked = other.d->m_SignalsBlocked;
+    }
+    return *this;
+}
 
 Object::~Object() {
     for (auto* p : d->m_DynamicProperties) {
@@ -125,9 +158,12 @@ Object::~Object() {
 }
 
 void Object::DeepCopy(const Object &copy) {
-  // should lock to be tread safe //
-  memcpy(d, copy.d, sizeof(ObjectPrivate));
-  // ERROR! does not copy parameters ... <<<< FIXXXXX
+    if (this == &copy) return;
+    if (copy.d) d->m_InstanceName = copy.d->m_InstanceName;
+    std::cout << "Object DeepCopy: from d=" << copy.d << " to d=" << d << std::endl;
+    // Note: signals, slots and properties are intentionally not copied 
+    // to maintain instance uniquely and avoid duplicate registrations.
+    this->Updated();
 }
 
 void Object::SaveXml(std::ostream &os, Object &ob) {
@@ -151,9 +187,8 @@ void Object::LoadConfig(std::istream &is, int version) {
 
 void Object::PrintSelf(std::ostream &o) const {
   o << "OBJECT signals: ------------------\n";
-  Vector<ObjectPrivate::Signal>::Iterator itr;
-  for (itr = d->sigv.begin(); itr < d->sigv.end(); itr++) {
-    o << "  signal:[ " << itr->sigstr << " ]\n";
+  for (const auto& sig : d->sigv) {
+    o << "  signal:[ " << sig.sigstr << " ]\n";
   }
   o << "--------------------------------------\n\n";
 }
@@ -206,6 +241,16 @@ void Object::SetInstanceName(const std::string& name) {
   this->Updated();
 }
  
+bool Object::blockSignals(bool block) {
+  bool old = d->m_SignalsBlocked;
+  d->m_SignalsBlocked = block;
+  return old;
+}
+ 
+bool Object::signalsBlocked() const {
+  return d->m_SignalsBlocked;
+}
+
 // std::ostream &
 // operator << (std::ostream &os, uLib::Object &ob)
 // {

src/Core/Object.h

@@ -75,18 +75,25 @@ public:
 
   Object();
   Object(const Object &copy);
-  ~Object();
+  virtual ~Object();
 
   virtual const char * GetClassName() const { return "Object"; }
 
   const std::string& GetInstanceName() const;
   void SetInstanceName(const std::string& name);
   
+  /** @brief Temporarily blocks all signal emissions from this object. Returns previous state. */
+  bool blockSignals(bool block);
+  
+  /** @brief Checks if signals are currently blocked. */
+  bool signalsBlocked() const;
+
   ////////////////////////////////////////////////////////////////////////////
   // PROPERTIES //
   void RegisterProperty(PropertyBase* prop);
   void RegisterDynamicProperty(PropertyBase* prop);
   const std::vector<PropertyBase*>& GetProperties() const;
+  PropertyBase* GetProperty(const std::string& name) const;
 
   ////////////////////////////////////////////////////////////////////////////
   // PARAMETERS //
@@ -138,24 +145,22 @@ public:
 
   // Qt5 style connector //
   template <typename Func1, typename Func2>
-  static bool
+  static Connection
   connect(typename FunctionPointer<Func1>::Object *sender, Func1 sigf,
           typename FunctionPointer<Func2>::Object *receiver, Func2 slof) {
     SignalBase *sigb = sender->findOrAddSignal(sigf);
-    ConnectSignal<typename FunctionPointer<Func1>::SignalSignature>(sigb, slof,
+    return ConnectSignal<typename FunctionPointer<Func1>::SignalSignature>(sigb, slof,
                                                                     receiver);
-    return true;
   }
 
   // Lambda/Function object connector //
   template <typename Func1, typename SlotT>
-  static bool connect(typename FunctionPointer<Func1>::Object *sender,
+  static Connection connect(typename FunctionPointer<Func1>::Object *sender,
                       Func1 sigf, SlotT slof) {
     SignalBase *sigb = sender->findOrAddSignal(sigf);
     typedef typename FunctionPointer<Func1>::SignalSignature SigSignature;
     typedef typename Signal<SigSignature>::type SigT;
-    reinterpret_cast<SigT *>(sigb)->connect(slof);
-    return true;
+    return reinterpret_cast<SigT *>(sigb)->connect(slof);
   }
 
   template <typename Func1, typename Func2>
@@ -167,10 +172,9 @@ public:
   }
 
   template <typename FuncT>
-  static inline bool connect(SignalBase *sigb, FuncT slof, Object *receiver) {
-    ConnectSignal<typename FunctionPointer<FuncT>::SignalSignature>(sigb, slof,
+  static inline Connection connect(SignalBase *sigb, FuncT slof, Object *receiver) {
+    return ConnectSignal<typename FunctionPointer<FuncT>::SignalSignature>(sigb, slof,
                                                                     receiver);
-    return true;
   }
 
   template <typename FuncT>
@@ -224,10 +228,7 @@ public:
 
   void PrintSelf(std::ostream &o) const;
 
-  inline const Object &operator=(const Object &copy) {
-    this->DeepCopy(copy);
-    return *this;
-  }
+  Object &operator=(const Object &other);
 
 private:
   bool addSignalImpl(SignalBase *sig, GenericMFPtr fptr, const char *name);

src/Core/ObjectsContext.h

@@ -20,13 +20,13 @@ public:
      * @brief Adds an object to the context.
      * @param obj Pointer to the object to add.
      */
-    void AddObject(Object* obj);
+    virtual void AddObject(Object* obj);
 
     /**
      * @brief Removes an object from the context.
      * @param obj Pointer to the object to remove.
      */
-    void RemoveObject(Object* obj);
+    virtual void RemoveObject(Object* obj);
 
     /**
      * @brief Clears all objects from the context.

src/Core/Property.h

@@ -2,11 +2,16 @@
 #define U_CORE_PROPERTY_H
 
 #include <string>
+#include <vector>
 #include <sstream>
 #include <typeinfo>
 #include <typeindex> // Added
 #include <boost/serialization/nvp.hpp>
 #include <boost/lexical_cast.hpp>
+#include <vector>
+#include <boost/type_traits/is_class.hpp>
+#include <boost/mpl/bool.hpp>
+#include <boost/serialization/serialization.hpp>
 #include "Core/Archives.h"
 #include "Core/Signal.h"
 #include "Core/Object.h"
@@ -23,6 +28,18 @@ public:
   virtual const char* GetTypeName() const = 0;
   virtual std::string GetValueAsString() const = 0;
   virtual std::type_index GetTypeIndex() const = 0; // Added
+  virtual const std::string& GetUnits() const = 0;
+  virtual void SetUnits(const std::string& units) = 0;
+  virtual const std::vector<std::string>& GetEnumLabels() const {
+      static std::vector<std::string> empty;
+      return empty;
+  }
+  virtual const std::string& GetGroup() const = 0;
+  virtual void SetGroup(const std::string& group) = 0;
+  std::string GetQualifiedName() const {
+      if (GetGroup().empty()) return GetName();
+      return GetGroup() + "." + GetName();
+  }
 
   // Signal support
   signals:
@@ -45,16 +62,16 @@ template <typename T>
 class Property : public PropertyBase {
 public:
   // PROXY: Use an existing variable as back-end storage
-  Property(Object* owner, const std::string& name, T* valuePtr)
-    : m_owner(owner), m_name(name), m_value(valuePtr), m_own(false) {
+  Property(Object* owner, const std::string& name, T* valuePtr, const std::string& units = "", const std::string& group = "")
+    : m_owner(owner), m_name(name), m_units(units), m_group(group), m_value(valuePtr), m_own(false) {
       if (m_owner) {
           m_owner->RegisterProperty(this);
       }
   }
 
   // MANAGED: Create and own internal storage
-  Property(Object* owner, const std::string& name, const T& defaultValue = T())
-    : m_owner(owner), m_name(name), m_value(new T(defaultValue)), m_own(true) {
+  Property(Object* owner, const std::string& name, const T& defaultValue = T(), const std::string& units = "", const std::string& group = "")
+    : m_owner(owner), m_name(name), m_units(units), m_group(group), m_value(new T(defaultValue)), m_own(true) {
       if (m_owner) {
           m_owner->RegisterProperty(this);
       }
@@ -68,6 +85,10 @@ public:
   virtual const std::string& GetName() const override { return m_name; }
   virtual const char* GetTypeName() const override { return typeid(T).name(); }
   virtual std::type_index GetTypeIndex() const override { return std::type_index(typeid(T)); }
+  virtual const std::string& GetUnits() const override { return m_units; }
+  virtual void SetUnits(const std::string& units) override { m_units = units; }
+  virtual const std::string& GetGroup() const override { return m_group; }
+  virtual void SetGroup(const std::string& group) override { m_group = group; }
 
   
   std::string GetValueAsString() const override {
@@ -118,6 +139,8 @@ public:
 
 private:
   std::string m_name;
+  std::string m_units;
+  std::string m_group;
   T* m_value;
   bool m_own;
   Object* m_owner;
@@ -135,6 +158,22 @@ typedef Property<float>         FloatProperty;
 typedef Property<double>        DoubleProperty;
 typedef Property<Bool_t>      BoolProperty;
 
+/**
+ * @brief Property specialized for enumerations, providing labels for GUI representations.
+ */
+class EnumProperty : public Property<int> {
+public:
+  EnumProperty(Object* owner, const std::string& name, int* valuePtr, const std::vector<std::string>& labels, const std::string& units = "", const std::string& group = "")
+    : Property<int>(owner, name, valuePtr, units, group), m_Labels(labels) {}
+
+  const std::vector<std::string>& GetEnumLabels() const override { return m_Labels; }
+  const char* GetTypeName() const override { return "Enum"; }
+  virtual std::type_index GetTypeIndex() const override { return std::type_index(typeid(EnumProperty)); }
+
+private:
+  std::vector<std::string> m_Labels;
+};
+
 /**
  * @brief Macro to simplify property declaration within a class.
  * Usage: ULIB_PROPERTY(float, Width, 1.0f)
@@ -184,25 +223,53 @@ public:
         boost::archive::detail::common_oarchive<property_register_archive>(boost::archive::no_header),
         m_Object(obj) {}
     
+    std::string GetCurrentGroup() const {
+        std::string group;
+        for (const auto& g : m_GroupStack) {
+            if (!group.empty()) group += ".";
+            group += g;
+        }
+        return group;
+    }
+
     // Core logic: encounter HRP -> Create Dynamic Property
     template<class T>
     void save_override(const boost::serialization::hrp<T> &t) {
         if (m_Object) {
-            // We use const_cast because we are just creating a proxy to the member
-            m_Object->RegisterDynamicProperty(
-                new Property<T>(m_Object, t.name(), &const_cast<boost::serialization::hrp<T>&>(t).value())
-            );
+            Property<T>* p = new Property<T>(m_Object, t.name(), &const_cast<boost::serialization::hrp<T>&>(t).value(), t.units() ? t.units() : "", GetCurrentGroup());
+            m_Object->RegisterDynamicProperty(p);
+        }
+    }
+
+    template<class T>
+    void save_override(const boost::serialization::hrp_enum<T> &t) {
+        if (m_Object) {
+            EnumProperty* p = new EnumProperty(m_Object, t.name(), (int*)&const_cast<boost::serialization::hrp_enum<T>&>(t).value(), t.labels(), t.units() ? t.units() : "", GetCurrentGroup());
+            m_Object->RegisterDynamicProperty(p);
         }
     }
 
     // Handle standard NVPs by recursing (important for base classes)
     template<class T>
     void save_override(const boost::serialization::nvp<T> &t) {
-        boost::archive::detail::common_oarchive<property_register_archive>::save_override(t.const_value());
+        if (t.name()) m_GroupStack.push_back(t.name());
+        this->save_helper(t.const_value(), typename boost::is_class<T>::type());
+        if (t.name()) m_GroupStack.pop_back();
     }
 
-    // Ignore everything else
-    template<class T> void save_override(const T &t) {}
+    // Recursion for nested classes, ignore primitives
+    template<class T>
+    void save_override(const T &t) {
+        this->save_helper(t, typename boost::is_class<T>::type());
+    }
+
+    template<class T>
+    void save_helper(const T &t, boost::mpl::true_) {
+        boost::serialization::serialize_adl(*this, const_cast<T&>(t), 0);
+    }
+
+    template<class T>
+    void save_helper(const T &t, boost::mpl::false_) {}
 
     // Required attribute overrides for common_oarchive
     void save_override(const boost::archive::object_id_type & t) {}
@@ -213,6 +280,9 @@ public:
     void save_override(const boost::archive::class_id_reference_type & t) {}
     void save_override(const boost::archive::class_name_type & t) {}
     void save_override(const boost::archive::tracking_type & t) {}
+
+private:
+    std::vector<std::string> m_GroupStack;
 };
 
 /**

src/Core/Serializable.h

@@ -75,12 +75,14 @@ template <class T> struct access2 {};
 template <class T>
 class hrp : public boost::serialization::wrapper_traits<hrp<T>> {
   const char *m_name;
+  const char *m_units;
   T &m_value;
 
 public:
-  explicit hrp(const char *name_, T &t) : m_name(name_), m_value(t) {}
+  explicit hrp(const char *name_, T &t, const char* units_ = nullptr) : m_name(name_), m_units(units_), m_value(t) {}
 
   const char *name() const { return this->m_name; }
+  const char *units() const { return this->m_units; }
   T &value() { return this->m_value; }
   const T &const_value() const { return this->m_value; }
 
@@ -98,11 +100,46 @@ public:
 };
 
 template <class T>
-inline hrp<T> make_hrp(const char *name, T &t) {
-  return hrp<T>(name, t);
+inline hrp<T> make_hrp(const char *name, T &t, const char* units = nullptr) {
+  return hrp<T>(name, t, units);
+}
+
+template <class T>
+class hrp_enum : public boost::serialization::wrapper_traits<hrp_enum<T>> {
+  const char *m_name;
+  const char *m_units;
+  T &m_value;
+  std::vector<std::string> m_labels;
+
+public:
+  explicit hrp_enum(const char *name_, T &t, const std::vector<std::string>& labels, const char* units_ = nullptr) 
+    : m_name(name_), m_units(units_), m_value(t), m_labels(labels) {}
+
+  const char *name() const { return this->m_name; }
+  const char *units() const { return this->m_units; }
+  T &value() { return this->m_value; }
+  const std::vector<std::string>& labels() const { return m_labels; }
+
+  BOOST_SERIALIZATION_SPLIT_MEMBER()
+
+  template <class Archivex>
+  void save(Archivex &ar, const unsigned int /* version */) const {
+    ar << boost::serialization::make_nvp(m_name, m_value);
+  }
+
+  template <class Archivex>
+  void load(Archivex &ar, const unsigned int /* version */) {
+    ar >> boost::serialization::make_nvp(m_name, m_value);
+  }
+};
+
+template <class T>
+inline hrp_enum<T> make_hrp_enum(const char *name, T &t, const std::vector<std::string>& labels, const char* units = nullptr) {
+  return hrp_enum<T>(name, t, labels, units);
 }
 
 #define HRP(name) boost::serialization::make_hrp(BOOST_PP_STRINGIZE(name), name)
+#define HRPU(name, units) boost::serialization::make_hrp(BOOST_PP_STRINGIZE(name), name, units)
 
 } // namespace serialization
 } // namespace boost

src/Core/Signal.h

@@ -31,6 +31,8 @@
 #include <boost/signals2/signal.hpp>
 #include <boost/signals2/signal_type.hpp>
 #include <boost/signals2/slot.hpp>
+#include <boost/signals2/connection.hpp>
+#include <boost/signals2/shared_connection_block.hpp>
 
 #include "Function.h"
 #include <boost/bind/bind.hpp>
@@ -63,9 +65,11 @@ using namespace boost::placeholders;
 
 #define _ULIB_DETAIL_SIGNAL_EMIT(_name, ...)                                   \
   do {                                                                         \
+    if (!this->signalsBlocked()) {                                             \
         BOOST_AUTO(sig, this->findOrAddSignal(&_name));                        \
         if (sig)                                                               \
           sig->operator()(__VA_ARGS__);                                        \
+    }                                                                          \
   } while (0)
 
 /**
@@ -90,6 +94,7 @@ namespace uLib {
 // TODO ...
 
 typedef boost::signals2::signal_base SignalBase;
+typedef boost::signals2::connection Connection;
 
 template <typename T> struct Signal {
   typedef boost::signals2::signal<T> type;
@@ -104,57 +109,57 @@ struct ConnectSignal {};
 
 template <typename FuncT, typename SigSignature>
 struct ConnectSignal<FuncT, SigSignature, 0> {
-  static void connect(SignalBase *sigb, FuncT slof,
+  static Connection connect(SignalBase *sigb, FuncT slof,
                       typename FunctionPointer<FuncT>::Object *receiver) {
     typedef typename Signal<SigSignature>::type SigT;
-    reinterpret_cast<SigT *>(sigb)->connect(slof);
+    return reinterpret_cast<SigT *>(sigb)->connect(slof);
   }
 };
 
 template <typename FuncT, typename SigSignature>
 struct ConnectSignal<FuncT, SigSignature, 1> {
-  static void connect(SignalBase *sigb, FuncT slof,
+  static Connection connect(SignalBase *sigb, FuncT slof,
                       typename FunctionPointer<FuncT>::Object *receiver) {
     typedef typename Signal<SigSignature>::type SigT;
-    reinterpret_cast<SigT *>(sigb)->connect(boost::bind(slof, receiver));
+    return reinterpret_cast<SigT *>(sigb)->connect(boost::bind(slof, receiver));
   }
 };
 
 template <typename FuncT, typename SigSignature>
 struct ConnectSignal<FuncT, SigSignature, 2> {
-  static void connect(SignalBase *sigb, FuncT slof,
+  static Connection connect(SignalBase *sigb, FuncT slof,
                       typename FunctionPointer<FuncT>::Object *receiver) {
     typedef typename Signal<SigSignature>::type SigT;
-    reinterpret_cast<SigT *>(sigb)->connect(boost::bind(slof, receiver, _1));
+    return reinterpret_cast<SigT *>(sigb)->connect(boost::bind(slof, receiver, _1));
   }
 };
 
 template <typename FuncT, typename SigSignature>
 struct ConnectSignal<FuncT, SigSignature, 3> {
-  static void connect(SignalBase *sigb, FuncT slof,
+  static Connection connect(SignalBase *sigb, FuncT slof,
                       typename FunctionPointer<FuncT>::Object *receiver) {
     typedef typename Signal<SigSignature>::type SigT;
-    reinterpret_cast<SigT *>(sigb)->connect(
+    return reinterpret_cast<SigT *>(sigb)->connect(
         boost::bind(slof, receiver, _1, _2));
   }
 };
 
 template <typename FuncT, typename SigSignature>
 struct ConnectSignal<FuncT, SigSignature, 4> {
-  static void connect(SignalBase *sigb, FuncT slof,
+  static Connection connect(SignalBase *sigb, FuncT slof,
                       typename FunctionPointer<FuncT>::Object *receiver) {
     typedef typename Signal<SigSignature>::type SigT;
-    reinterpret_cast<SigT *>(sigb)->connect(
+    return reinterpret_cast<SigT *>(sigb)->connect(
         boost::bind(slof, receiver, _1, _2, _3));
   }
 };
 
 template <typename FuncT, typename SigSignature>
 struct ConnectSignal<FuncT, SigSignature, 5> {
-  static void connect(SignalBase *sigb, FuncT slof,
+  static Connection connect(SignalBase *sigb, FuncT slof,
                       typename FunctionPointer<FuncT>::Object *receiver) {
     typedef typename Signal<SigSignature>::type SigT;
-    reinterpret_cast<SigT *>(sigb)->connect(
+    return reinterpret_cast<SigT *>(sigb)->connect(
         boost::bind(slof, receiver, _1, _2, _3, _4));
   }
 };
@@ -167,9 +172,9 @@ template <typename FuncT> SignalBase *NewSignal(FuncT f) {
 }
 
 template <typename SigSignature, typename FuncT>
-void ConnectSignal(SignalBase *sigb, FuncT slof,
+Connection ConnectSignal(SignalBase *sigb, FuncT slof,
                    typename FunctionPointer<FuncT>::Object *receiver) {
-  detail::ConnectSignal<FuncT, SigSignature,
+  return detail::ConnectSignal<FuncT, SigSignature,
                          FunctionPointer<FuncT>::arity>::connect(sigb, slof,
                                                                  receiver);
 }

src/Core/Threads.cpp

@@ -0,0 +1,202 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// 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 "Threads.h"
+#include <chrono>
+
+#ifdef _OPENMP
+#include <omp.h>
+#endif
+
+#ifdef __linux__
+#include <pthread.h>
+#include <sched.h>
+#endif
+
+namespace uLib {
+
+Thread::Thread() : m_Running(false) {}
+
+Thread::~Thread() {
+  if (m_Thread.joinable()) {
+    m_Thread.detach();
+  }
+}
+
+void Thread::Start() {
+  Mutex::ScopedLock lock(m_ThreadMutex);
+  if (m_Running) return;
+  
+  m_Running = true;
+  m_Thread = std::thread(&Thread::ThreadEntryPoint, this);
+}
+
+void Thread::Join() {
+  if (m_Thread.joinable()) {
+    m_Thread.join();
+  }
+}
+
+void Thread::Detach() {
+  if (m_Thread.joinable()) {
+    m_Thread.detach();
+  }
+}
+
+bool Thread::IsJoinable() const {
+  return m_Thread.joinable();
+}
+
+bool Thread::IsRunning() const {
+  return m_Running;
+}
+
+void Thread::Run() {
+  // Override in subclasses
+}
+
+void Thread::ThreadEntryPoint() {
+  this->Run();
+  m_Running = false;
+}
+
+void Thread::Sleep(int milliseconds) {
+  std::this_thread::sleep_for(std::chrono::milliseconds(milliseconds));
+}
+
+void Thread::Yield() {
+  std::this_thread::yield();
+}
+
+void Thread::SetAffinity(int cpu) {
+#ifdef __linux__
+  if (m_Thread.joinable()) {
+    cpu_set_t cpuset;
+    CPU_ZERO(&cpuset);
+    CPU_SET(cpu, &cpuset);
+    pthread_setaffinity_np(m_Thread.native_handle(), sizeof(cpu_set_t), &cpuset);
+  }
+#endif
+}
+
+void Thread::SetAffinity(const std::vector<int>& cpus) {
+#ifdef __linux__
+  if (m_Thread.joinable()) {
+    cpu_set_t cpuset;
+    CPU_ZERO(&cpuset);
+    for (int cpu : cpus) {
+        CPU_SET(cpu, &cpuset);
+    }
+    pthread_setaffinity_np(m_Thread.native_handle(), sizeof(cpu_set_t), &cpuset);
+  }
+#endif
+}
+
+void Thread::SetNumThreads(int n) {
+#ifdef _OPENMP
+  omp_set_num_threads(n);
+#endif
+}
+
+int Thread::GetNumThreads() {
+#ifdef _OPENMP
+  return omp_get_max_threads();
+#else
+  return 1;
+#endif
+}
+
+int Thread::GetThreadNum() {
+#ifdef _OPENMP
+  return omp_get_thread_num();
+#else
+  return 0;
+#endif
+}
+
+// Team Implementation //
+
+Team::Team(int num_threads) : m_Size(num_threads), m_UseOpenMP(false) {
+#ifdef _OPENMP
+  m_UseOpenMP = true;
+  if (m_Size > 0) omp_set_num_threads(m_Size);
+  else m_Size = omp_get_max_threads();
+#else
+  if (m_Size <= 0) m_Size = 1;
+#endif
+}
+
+Team::~Team() {
+  Wait();
+}
+
+void Team::Run(Task* task) {
+  if (!task) return;
+#ifdef _OPENMP
+  if (m_UseOpenMP) {
+    #pragma omp task
+    task->Execute();
+    return;
+  }
+#endif
+  // Fallback to synchronous execution if no OpenMP
+  task->Execute();
+}
+
+void Team::Wait() {
+#ifdef _OPENMP
+  if (m_UseOpenMP) {
+    #pragma omp taskwait
+  }
+#endif
+}
+
+void Team::SetSize(int n) {
+  m_Size = n;
+#ifdef _OPENMP
+  if (m_UseOpenMP) omp_set_num_threads(m_Size);
+#endif
+}
+
+void Team::SetAffinity(const std::vector<int>& cpus) {
+  if (cpus.empty()) return;
+#ifdef __linux__
+#ifdef _OPENMP
+  if (m_UseOpenMP) {
+    #pragma omp parallel
+    {
+      int tid = omp_get_thread_num();
+      int cpu = cpus[tid % cpus.size()];
+      cpu_set_t cpuset;
+      CPU_ZERO(&cpuset);
+      CPU_SET(cpu, &cpuset);
+      pthread_setaffinity_np(pthread_self(), sizeof(cpu_set_t), &cpuset);
+    }
+  }
+#endif
+#endif
+}
+
+} // namespace uLib

src/Core/Threads.h

@@ -0,0 +1,147 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// CMT Cosmic Muon Tomography project //////////////////////////////////////////
+////////////////////////////////////////////////////////////////////////////////
+
+  Copyright (c) 2014, Universita' degli Studi di Padova, INFN sez. di Padova
+  All rights reserved
+
+  Authors: Andrea Rigoni Garola < andrea.rigoni@pd.infn.it >
+
+  ------------------------------------------------------------------
+  This library is free software;  you  can  redistribute  it  and/or
+  modify it  under the  terms  of  the  GNU  Lesser  General  Public
+  License as published  by  the  Free  Software  Foundation;  either
+  version 3.0 of the License, or (at your option) any later version.
+
+  This library is  distributed in  the hope that it will  be useful,
+  but  WITHOUT ANY WARRANTY;  without  even  the implied warranty of
+  MERCHANTABILITY  or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+  Lesser General Public License for more details.
+
+  You should have received a copy of  the GNU Lesser General  Public
+  License along with this library.
+
+//////////////////////////////////////////////////////////////////////////////*/
+
+#ifndef U_CORE_THREADS_H
+#define U_CORE_THREADS_H
+
+#include <thread>
+#include <functional>
+#include <atomic>
+#include <vector>
+#include <deque>
+#include "Core/Monitor.h"
+#include "Core/Object.h"
+
+namespace uLib {
+
+/**
+ * @brief Thread class wraps std::thread and provides a common interface.
+ */
+class Thread : public Object {
+public:
+  Thread();
+  virtual ~Thread();
+
+  /** @brief Starts the thread by calling Run(). */
+  void Start();
+
+  /** @brief Joins the thread. */
+  void Join();
+
+  /** @brief Detaches the thread. */
+  void Detach();
+
+  /** @brief Returns true if the thread is currently joinable. */
+  bool IsJoinable() const;
+  
+  /** @brief Returns true if the thread is currently running. */
+  bool IsRunning() const;
+
+  /** @brief The entry point for the thread. Override this in subclasses. */
+  virtual void Run();
+
+  /** @brief Static helper to sleep the current thread. */
+  static void Sleep(int milliseconds);
+
+  /** @brief Static helper to yield the current thread. */
+  static void Yield();
+
+  /** @brief Returns the native handle of the thread. */
+  std::thread::native_handle_type GetNativeHandle() { return m_Thread.native_handle(); }
+
+  /** @brief Sets CPU affinity for the thread. (Linux only) */
+  void SetAffinity(int cpu);
+  
+  /** @brief Sets CPU affinity for the thread using a list of CPUs. (Linux only) */
+  void SetAffinity(const std::vector<int>& cpus);
+
+  // OpenMP Support //
+  
+  /** @brief Sets the number of threads for OpenMP parallel regions. */
+  static void SetNumThreads(int n);
+  
+  /** @brief Returns the number of threads for OpenMP parallel regions. */
+  static int GetNumThreads();
+
+  /** @brief Returns the ID of the current thread in an OpenMP parallel region. */
+  static int GetThreadNum();
+
+protected:
+  // Internal thread entry point
+  void ThreadEntryPoint();
+
+  std::thread m_Thread;
+  std::atomic<bool> m_Running;
+  mutable Mutex m_ThreadMutex;
+};
+
+/**
+ * @brief Task class wraps a function call to be executed by a Team.
+ */
+class Task : public Object {
+public:
+  Task(std::function<void()> func) : m_Func(func) {}
+  virtual ~Task() = default;
+
+  /** @brief Executes the task. */
+  virtual void Execute() { if (m_Func) m_Func(); }
+
+protected:
+  std::function<void()> m_Func;
+};
+
+/**
+ * @brief Team class manages a group of threads and can execute Tasks.
+ * This is designed to be compatible with OpenMP tasks and teams.
+ */
+class Team : public Object {
+public:
+  Team(int num_threads = -1);
+  virtual ~Team();
+
+  /** @brief Runs a task within the team. Uses OpenMP task if available. */
+  void Run(Task* task);
+
+  /** @brief Waits for all tasks in the team to finish. */
+  void Wait();
+
+  /** @brief Sets the number of threads for this team. */
+  void SetSize(int n);
+
+  /** @brief Returns the number of threads in the team. */
+  int GetSize() const { return m_Size; }
+
+  /** @brief Sets CPU affinity for all threads in the team. */
+  void SetAffinity(const std::vector<int>& cpus);
+
+protected:
+  int m_Size;
+  bool m_UseOpenMP;
+  std::vector<Thread*> m_Threads;
+};
+
+} // namespace uLib
+
+#endif // U_CORE_THREADS_H

src/Core/testing/AffinityTest.cpp

@@ -0,0 +1,65 @@
+#include "Core/Threads.h"
+#include <iostream>
+#include <vector>
+#include <cassert>
+
+#ifdef __linux__
+#include <pthread.h>
+#include <sched.h>
+#endif
+
+using namespace uLib;
+
+void TestThreadAffinity() {
+    std::cout << "Testing Thread Affinity..." << std::endl;
+#ifdef __linux__
+    Thread t;
+    t.Start();
+    t.SetAffinity(0); // Bind to CPU 0
+    
+    cpu_set_t cpuset;
+    CPU_ZERO(&cpuset);
+    pthread_getaffinity_np(t.GetNativeHandle(), sizeof(cpu_set_t), &cpuset);
+    assert(CPU_ISSET(0, &cpuset));
+    
+    t.Join();
+    std::cout << "  Passed (Thread bound to CPU 0)." << std::endl;
+#else
+    std::cout << "  Affinity not supported on this OS, skipping." << std::endl;
+#endif
+}
+
+void TestTeamAffinity() {
+    std::cout << "Testing Team Affinity..." << std::endl;
+#ifdef __linux__
+#ifdef _OPENMP
+    Team team(2);
+    std::vector<int> cpus = {0, 1};
+    team.SetAffinity(cpus);
+    
+    // We check affinity inside a parallel region
+    #pragma omp parallel
+    {
+        cpu_set_t cpuset;
+        CPU_ZERO(&cpuset);
+        pthread_getaffinity_np(pthread_self(), sizeof(cpu_set_t), &cpuset);
+        int tid = Thread::GetThreadNum();
+        int expected_cpu = cpus[tid % cpus.size()];
+        assert(CPU_ISSET(expected_cpu, &cpuset));
+    }
+    std::cout << "  Passed (Team threads bound correctly)." << std::endl;
+#endif
+#else
+    std::cout << "  Affinity not supported on this OS, skipping." << std::endl;
+#endif
+}
+
+// Helper to get native handle if needed (oops, I forgot to add it to Thread class)
+// I'll add GetNativeHandle() to Thread class in Threads.h
+
+int main() {
+    TestThreadAffinity();
+    TestTeamAffinity();
+    std::cout << "All Affinity tests finished!" << std::endl;
+    return 0;
+}

src/Core/testing/AlgorithmTest.cpp

@@ -0,0 +1,206 @@
+#include "Core/Algorithm.h"
+#include <iostream>
+#include <atomic>
+#include <cassert>
+
+using namespace uLib;
+
+////////////////////////////////////////////////////////////////////////////////
+// Test algorithms
+
+class DoubleAlgorithm : public Algorithm<int, int> {
+public:
+    const char* GetClassName() const override { return "DoubleAlgorithm"; }
+    int Process(const int& input) override {
+        m_CallCount++;
+        return input * 2;
+    }
+    std::atomic<int> m_CallCount{0};
+};
+
+class StringifyAlgorithm : public Algorithm<int, std::string> {
+public:
+    const char* GetClassName() const override { return "StringifyAlgorithm"; }
+    std::string Process(const int& input) override {
+        return std::to_string(input);
+    }
+};
+
+// Signal source to test ConnectTrigger
+class TriggerSource : public Object {
+public:
+    const char* GetClassName() const override { return "TriggerSource"; }
+signals:
+    virtual void DataReady() { ULIB_SIGNAL_EMIT(TriggerSource::DataReady); }
+};
+
+////////////////////////////////////////////////////////////////////////////////
+// Tests
+
+void TestBasicProcess() {
+    std::cout << "Testing basic Algorithm::Process..." << std::endl;
+    DoubleAlgorithm alg;
+    assert(alg.Process(5) == 10);
+    assert(alg.Process(-3) == -6);
+    assert(alg.Process(0) == 0);
+    std::cout << "  Passed." << std::endl;
+}
+
+void TestOperatorCall() {
+    std::cout << "Testing Algorithm::operator()..." << std::endl;
+    DoubleAlgorithm alg;
+    assert(alg(7) == 14);
+    assert(alg(0) == 0);
+    std::cout << "  Passed." << std::endl;
+}
+
+void TestEncoderDecoderChain() {
+    std::cout << "Testing encoder/decoder chain pointers..." << std::endl;
+    DoubleAlgorithm a, b;
+    a.SetDecoder(&b);
+    b.SetEncoder(&a);
+    assert(a.GetDecoder() == &b);
+    assert(b.GetEncoder() == &a);
+    assert(a.GetEncoder() == nullptr);
+    assert(b.GetDecoder() == nullptr);
+    std::cout << "  Passed." << std::endl;
+}
+
+void TestAlgorithmSignals() {
+    std::cout << "Testing Algorithm signals..." << std::endl;
+    DoubleAlgorithm alg;
+    bool started = false;
+    bool finished = false;
+    Object::connect(&alg, &DoubleAlgorithm::Started, [&]() { started = true; });
+    Object::connect(&alg, &DoubleAlgorithm::Finished, [&]() { finished = true; });
+    alg.Started();
+    alg.Finished();
+    assert(started);
+    assert(finished);
+    std::cout << "  Passed." << std::endl;
+}
+
+void TestCyclicTask() {
+    std::cout << "Testing AlgorithmTask cyclic mode (Thread-based)..." << std::endl;
+    DoubleAlgorithm alg;
+    AlgorithmTask<int, int> task;
+    task.SetAlgorithm(&alg);
+    task.SetMode(AlgorithmTask<int, int>::Cyclic);
+    task.SetCycleTime(50);
+
+    assert(!task.IsRunning());
+    task.Run(5);
+
+    // Let it run for ~200ms -> expect ~4 cycles
+    Thread::Sleep(220);
+    task.Stop();
+
+    assert(!task.IsRunning());
+    int count = alg.m_CallCount.load();
+    std::cout << "  Cyclic iterations: " << count << std::endl;
+    assert(count >= 3 && count <= 6);
+    std::cout << "  Passed." << std::endl;
+}
+
+void TestAsyncTask() {
+    std::cout << "Testing AlgorithmTask async mode (Mutex + condition_variable)..." << std::endl;
+    DoubleAlgorithm alg;
+    AlgorithmTask<int, int> task;
+    task.SetAlgorithm(&alg);
+    task.SetMode(AlgorithmTask<int, int>::Async);
+
+    task.Run(42);
+    Thread::Sleep(50); // let the thread start and wait
+
+    // Trigger 3 notifications
+    for (int i = 0; i < 3; ++i) {
+        task.Notify();
+        Thread::Sleep(30);
+    }
+
+    task.Stop();
+    int count = alg.m_CallCount.load();
+    std::cout << "  Async invocations: " << count << std::endl;
+    assert(count == 3);
+    std::cout << "  Passed." << std::endl;
+}
+
+void TestConnectTrigger() {
+    std::cout << "Testing AlgorithmTask::ConnectTrigger (signal-slot async)..." << std::endl;
+    DoubleAlgorithm alg;
+    AlgorithmTask<int, int> task;
+    task.SetAlgorithm(&alg);
+    task.SetMode(AlgorithmTask<int, int>::Async);
+
+    TriggerSource source;
+    task.ConnectTrigger(&source, &TriggerSource::DataReady);
+
+    task.Run(10);
+    Thread::Sleep(50);
+
+    // Emit signal 3 times
+    for (int i = 0; i < 3; ++i) {
+        source.DataReady();
+        Thread::Sleep(30);
+    }
+
+    task.Stop();
+    int count = alg.m_CallCount.load();
+    std::cout << "  Signal-triggered invocations: " << count << std::endl;
+    assert(count == 3);
+    std::cout << "  Passed." << std::endl;
+}
+
+void TestTaskStoppedSignal() {
+    std::cout << "Testing AlgorithmTask Stopped signal..." << std::endl;
+    DoubleAlgorithm alg;
+    AlgorithmTask<int, int> task;
+    task.SetAlgorithm(&alg);
+    task.SetMode(AlgorithmTask<int, int>::Cyclic);
+    task.SetCycleTime(20);
+
+    std::atomic<bool> stopped{false};
+    Object::connect(&task, &AlgorithmTask<int, int>::Stopped,
+                    [&]() { stopped.store(true); });
+
+    task.Run(1);
+    Thread::Sleep(50);
+    task.Stop();
+    Thread::Sleep(50);
+
+    assert(stopped.load());
+    std::cout << "  Passed." << std::endl;
+}
+
+void TestClassName() {
+    std::cout << "Testing GetClassName..." << std::endl;
+    DoubleAlgorithm alg;
+    AlgorithmTask<int, int> task;
+    assert(std::string(alg.GetClassName()) == "DoubleAlgorithm");
+    assert(std::string(task.GetClassName()) == "AlgorithmTask");
+    std::cout << "  Passed." << std::endl;
+}
+
+void TestDifferentTypes() {
+    std::cout << "Testing Algorithm with different enc/dec types..." << std::endl;
+    StringifyAlgorithm alg;
+    assert(alg.Process(42) == "42");
+    assert(alg.Process(-1) == "-1");
+    assert(alg(100) == "100");
+    std::cout << "  Passed." << std::endl;
+}
+
+int main() {
+    TestBasicProcess();
+    TestOperatorCall();
+    TestEncoderDecoderChain();
+    TestAlgorithmSignals();
+    TestDifferentTypes();
+    TestCyclicTask();
+    TestAsyncTask();
+    TestConnectTrigger();
+    TestTaskStoppedSignal();
+    TestClassName();
+    std::cout << "All Algorithm tests passed!" << std::endl;
+    return 0;
+}

src/Core/testing/CMakeLists.txt

@@ -23,6 +23,13 @@ set( TESTS
         VectorMetaAllocatorTest
         PropertyTypesTest
         HRPTest
+        PropertyGroupingTest
+        MutexTest
+        ThreadsTest
+        OpenMPTest
+        TeamTest
+        AffinityTest
+        AlgorithmTest
 )
 
 set(LIBRARIES
@@ -31,6 +38,7 @@ set(LIBRARIES
        Boost::serialization
        Boost::program_options
        ${ROOT_LIBRARIES}
+       OpenMP::OpenMP_CXX
 )
 uLib_add_tests(Core)
 

src/Core/testing/MutexTest.cpp

@@ -0,0 +1,109 @@
+#include "Core/Monitor.h"
+#include <iostream>
+#include <chrono>
+#include <thread>
+#include <vector>
+#include <cassert>
+
+using namespace uLib;
+
+void TestBasicLock() {
+    std::cout << "Testing basic Mutex Lock/Unlock..." << std::endl;
+    Mutex m;
+    m.Lock();
+    m.Unlock();
+    assert(m.TryLock());
+    m.Unlock();
+    std::cout << "  Passed." << std::endl;
+}
+
+void TestScopedLock() {
+    std::cout << "Testing Mutex::ScopedLock..." << std::endl;
+    Mutex m;
+    {
+        Mutex::ScopedLock lock(m);
+        assert(!m.TryLock());
+    }
+    assert(m.TryLock());
+    m.Unlock();
+    std::cout << "  Passed." << std::endl;
+}
+
+void TestTimedLock() {
+    std::cout << "Testing Mutex TryLockFor..." << std::endl;
+    Mutex m;
+    m.Lock();
+    auto start = std::chrono::steady_clock::now();
+    bool locked = m.TryLockFor(100);
+    auto end = std::chrono::steady_clock::now();
+    auto diff = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
+    
+    assert(!locked);
+    assert(diff >= 100);
+    m.Unlock();
+    std::cout << "  Passed (waited " << diff << "ms)." << std::endl;
+}
+
+void TestMacros() {
+    std::cout << "Testing ULIB_STATIC_LOCK and ULIB_MUTEX_LOCK macros..." << std::endl;
+    
+    int counter = 0;
+    auto task = [&]() {
+        for(int i=0; i<500; ++i) {
+            ULIB_STATIC_LOCK(-1) {
+                counter++;
+            }
+        }
+    };
+    
+    std::vector<std::thread> threads;
+    for(int i=0; i<4; ++i) threads.emplace_back(task);
+    for(auto& t : threads) t.join();
+    
+    assert(counter == 2000);
+    
+    Mutex m;
+    int counter2 = 0;
+    ULIB_MUTEX_LOCK(m, -1) {
+        counter2++;
+    }
+    assert(counter2 == 1);
+    
+    std::cout << "  Passed." << std::endl;
+}
+
+void TestMonitor() {
+    std::cout << "Testing Monitor pattern..." << std::endl;
+    struct Resource {
+        int value = 0;
+        void increment() { value++; }
+    };
+    
+    Monitor<Resource> monitor(new Resource());
+    
+    auto task = [&]() {
+        for(int i=0; i<1000; ++i) {
+            monitor.Access([](Resource& r) {
+                r.increment();
+            });
+        }
+    };
+    
+    std::vector<std::thread> threads;
+    for(int i=0; i<5; ++i) threads.emplace_back(task);
+    for(auto& t : threads) t.join();
+    
+    int final_value = monitor.Access([](Resource& r) { return r.value; });
+    assert(final_value == 5000);
+    std::cout << "  Passed (final value: " << final_value << ")." << std::endl;
+}
+
+int main() {
+    TestBasicLock();
+    TestScopedLock();
+    TestTimedLock();
+    TestMacros();
+    TestMonitor();
+    std::cout << "All Mutex and Monitor tests passed!" << std::endl;
+    return 0;
+}

src/Core/testing/OpenMPTest.cpp

@@ -0,0 +1,47 @@
+#include "Core/Threads.h"
+#include <iostream>
+#include <cassert>
+
+#ifdef _OPENMP
+#include <omp.h>
+#endif
+
+using namespace uLib;
+
+class OpenMPThread : public Thread {
+public:
+    void Run() override {
+#ifdef _OPENMP
+        Thread::SetNumThreads(2);
+        int max = Thread::GetNumThreads();
+        std::cout << "  OpenMP max threads in uLib::Thread: " << max << std::endl;
+        
+        int shared_counter = 0;
+        #pragma omp parallel reduction(+:shared_counter)
+        {
+            shared_counter += 1;
+        }
+        std::cout << "  Parallel region executed with " << shared_counter << " threads." << std::endl;
+        assert(shared_counter <= max);
+#else
+        std::cout << "  OpenMP not available, skipping parallel check." << std::endl;
+        assert(Thread::GetNumThreads() == 1);
+#endif
+    }
+};
+
+int main() {
+    std::cout << "Testing OpenMP compatibility..." << std::endl;
+#ifdef _OPENMP
+    std::cout << "  OpenMP is AVAILABLE." << std::endl;
+#else
+    std::cout << "  OpenMP is NOT available." << std::endl;
+#endif
+
+    OpenMPThread t;
+    t.Start();
+    t.Join();
+
+    std::cout << "OpenMP compatibility test finished!" << std::endl;
+    return 0;
+}

src/Core/testing/PropertyGroupingTest.cpp

@@ -0,0 +1,78 @@
+#include <iostream>
+#include <vector>
+#include <string>
+#include <cassert>
+#include "Core/Object.h"
+#include "Core/Property.h"
+
+using namespace uLib;
+
+struct Nested {
+    float x = 1.0f;
+    float y = 2.0f;
+
+    ULIB_SERIALIZE_ACCESS
+    template<class Archive>
+    void serialize(Archive & ar, const unsigned int version) {
+        ar & HRP(x);
+        ar & HRP(y);
+    }
+};
+
+class GroupObject : public Object {
+    uLibTypeMacro(GroupObject, Object)
+public:
+    Nested position;
+    Nested orientation;
+    float weight = 50.0f;
+
+    ULIB_SERIALIZE_ACCESS
+    template<class Archive>
+    void serialize(Archive & ar, const unsigned int version) {
+        ar & boost::serialization::make_nvp("Position", position);
+        ar & boost::serialization::make_nvp("Orientation", orientation);
+        ar & HRP(weight);
+    }
+};
+
+int main() {
+    std::cout << "Testing Property Grouping..." << std::endl;
+
+    GroupObject obj;
+    ULIB_ACTIVATE_PROPERTIES(obj);
+
+    auto props = obj.GetProperties();
+    std::cout << "Registered " << props.size() << " properties." << std::endl;
+
+    for (auto* p : props) {
+        std::cout << "Prop: " << p->GetName() 
+                  << " Group: " << p->GetGroup() 
+                  << " Qualified: " << p->GetQualifiedName() << std::endl;
+    }
+
+    // Check if nested properties are registered
+    PropertyBase* p1 = obj.GetProperty("Position.x");
+    PropertyBase* p2 = obj.GetProperty("Position.y");
+    PropertyBase* p3 = obj.GetProperty("Orientation.x");
+    PropertyBase* p4 = obj.GetProperty("Orientation.y");
+    PropertyBase* p5 = obj.GetProperty("weight");
+
+    assert(p1 != nullptr && "Position.x not found");
+    assert(p2 != nullptr && "Position.y not found");
+    assert(p3 != nullptr && "Orientation.x not found");
+    assert(p4 != nullptr && "Orientation.y not found");
+    assert(p5 != nullptr && "weight not found");
+
+    assert(p1->GetGroup() == "Position");
+    assert(p2->GetGroup() == "Position");
+    assert(p3->GetGroup() == "Orientation");
+    assert(p4->GetGroup() == "Orientation");
+    assert(p5->GetGroup() == "");
+
+    assert(p1->GetQualifiedName() == "Position.x");
+    assert(p5->GetQualifiedName() == "weight");
+
+    std::cout << "Property Grouping Tests PASSED!" << std::endl;
+
+    return 0;
+}

src/Core/testing/TeamTest.cpp

@@ -0,0 +1,40 @@
+#include "Core/Threads.h"
+#include <iostream>
+#include <atomic>
+#include <cassert>
+#include <vector>
+
+using namespace uLib;
+
+void TestTaskTeam() {
+    std::cout << "Testing Task and Team..." << std::endl;
+    
+    std::atomic<int> counter(0);
+    auto task_func = [&]() {
+        counter++;
+        Thread::Sleep(10);
+    };
+    
+    Team team(4);
+    std::cout << "  Team size: " << team.GetSize() << std::endl;
+
+#ifdef _OPENMP
+    #pragma omp parallel
+    #pragma omp single
+#endif
+    {
+        for (int i = 0; i < 20; ++i) {
+            team.Run(new Task(task_func));
+        }
+        team.Wait();
+    }
+    
+    assert(counter == 20);
+    std::cout << "  Passed (counter: " << counter << ")." << std::endl;
+}
+
+int main() {
+    TestTaskTeam();
+    std::cout << "All Team tests passed!" << std::endl;
+    return 0;
+}

src/Core/testing/ThreadsTest.cpp

@@ -0,0 +1,72 @@
+#include "Core/Threads.h"
+#include <iostream>
+#include <atomic>
+#include <cassert>
+
+using namespace uLib;
+
+class MyThread : public Thread {
+public:
+    MyThread() : counter(0) {}
+    void Run() override {
+        for (int i = 0; i < 5; ++i) {
+            counter++;
+            Thread::Sleep(10);
+        }
+    }
+    std::atomic<int> counter;
+};
+
+void TestBasicThread() {
+    std::cout << "Testing basic Thread lifecycle..." << std::endl;
+    MyThread t;
+    assert(!t.IsRunning());
+    t.Start();
+    assert(t.IsRunning());
+    t.Join();
+    assert(!t.IsRunning());
+    assert(t.counter == 5);
+    std::cout << "  Passed." << std::endl;
+}
+
+void TestThreadDetach() {
+    std::cout << "Testing Thread Detach..." << std::endl;
+    std::atomic<bool> done(false);
+    
+    // Using a lambda or a simple subclass
+    class DetachedThread : public Thread {
+    public:
+        DetachedThread(std::atomic<bool>& d) : m_done(d) {}
+        void Run() override {
+            Thread::Sleep(50);
+            m_done = true;
+        }
+        std::atomic<bool>& m_done;
+    };
+    
+    {
+        DetachedThread* t = new DetachedThread(done);
+        t->Start();
+        t->Detach();
+        // The thread object 't' is still alive here, 
+        // but it will be destroyed soon if we delete it.
+        // For a detached thread using members, we MUST keep it alive.
+        
+        int wait_count = 0;
+        while(!done && wait_count < 20) {
+            Thread::Sleep(10);
+            wait_count++;
+        }
+        delete t;
+    }
+    
+    assert(done);
+    std::cout << "  Passed." << std::endl;
+}
+
+int main() {
+    TestBasicThread();
+    TestThreadDetach();
+    std::cout << "All Thread tests passed!" << std::endl;
+    return 0;
+}

src/HEP/Geant/ActionInitialization.cpp

@@ -13,6 +13,15 @@ ActionInitialization::ActionInitialization(EmitterPrimary *emitter, SimulationCo
 
 ActionInitialization::~ActionInitialization() {}
   
+// Lightweight wrapper to avoid double-free in Geant4 EventManager
+class SteppingActionWrapper : public G4UserSteppingAction {
+public:
+  SteppingActionWrapper(SteppingAction *real) : m_Real(real) {}
+  virtual void UserSteppingAction(const G4Step* step) override { m_Real->UserSteppingAction(step); }
+private:
+  SteppingAction *m_Real;
+};
+
 void ActionInitialization::BuildForMaster() const {}
 
 void ActionInitialization::Build() const {
@@ -23,8 +32,10 @@ void ActionInitialization::Build() const {
   }
   
   SteppingAction *sa = new SteppingAction(m_Context);
-  SetUserAction(static_cast<G4UserSteppingAction*>(sa));
+  // EventManager will delete sa via this slot
   SetUserAction(static_cast<G4UserEventAction*>(sa));
+  // EventManager will delete the wrapper, leaving sa alive to be deleted once.
+  SetUserAction(new SteppingActionWrapper(sa));
 }
 
 } // namespace Geant

src/HEP/Geant/DetectorActionInitialization.cpp

@@ -18,6 +18,14 @@ DetectorActionInitialization::DetectorActionInitialization(EmitterPrimary *emitt
 
 DetectorActionInitialization::~DetectorActionInitialization() {}
   
+class DetectorSteppingActionWrapper : public G4UserSteppingAction {
+public:
+  DetectorSteppingActionWrapper(DetectorSteppingAction *real) : m_Real(real) {}
+  virtual void UserSteppingAction(const G4Step* step) override { m_Real->UserSteppingAction(step); }
+private:
+  DetectorSteppingAction *m_Real;
+};
+
 void DetectorActionInitialization::BuildForMaster() const {}
 
 void DetectorActionInitialization::Build() const {
@@ -34,8 +42,10 @@ void DetectorActionInitialization::Build() const {
   if (m_Output) {
     DetectorSteppingAction *sa = new DetectorSteppingAction(m_Output, m_Planes);
     sa->SetVerbosity(m_Verbosity);
-    SetUserAction(static_cast<G4UserSteppingAction*>(sa));
+    // EventManager will delete sa via the Event slot
     SetUserAction(static_cast<G4UserEventAction*>(sa));
+    // EventManager will delete the wrapper, leaving sa alive for the other deletion.
+    SetUserAction(new DetectorSteppingActionWrapper(sa));
   }
 }
 

src/HEP/Geant/Scene.cpp

@@ -46,7 +46,7 @@ static void CheckGeant4Environment() {
 
 class SceneImpl {
 public:
-  SceneImpl() : m_RunManager(G4RunManagerFactory::CreateRunManager(G4RunManagerType::Default)),
+  SceneImpl() : m_RunManager(G4RunManagerFactory::CreateRunManager(G4RunManagerType::Serial)),
                 m_Emitter(nullptr),
                 m_InitCalled(false) {
     m_RunManager->SetUserInitialization(new PhysicsList);
@@ -102,6 +102,7 @@ void Scene::AddSolid(Solid *solid, Solid *parent) {
 
 const Solid* Scene::GetWorld() const { return d->m_World; }
 ContainerBox* Scene::GetWorldBox() const { return &d->m_WorldBox; }
+const Vector<Solid*>& Scene::GetSolids() const { return d->m_Solids; }
 
 void Scene::ConstructWorldBox(const Vector3f &size, const char *material) {
   d->m_WorldBox.Scale(size);

src/HEP/Geant/Scene.h

@@ -58,6 +58,9 @@ public:
   
   ContainerBox* GetWorldBox() const;
 
+  /// Get the list of solids in the scene
+  const Vector<Solid*>& GetSolids() const;
+
   /// Set the primary generator (emitter) for the simulation.
   /// The Scene does NOT take ownership of the emitter.
   void SetEmitter(EmitterPrimary *emitter);

src/HEP/Geant/Solid.cpp

@@ -151,6 +151,7 @@ TessellatedSolid::TessellatedSolid(const char *name)
     }
 
 void TessellatedSolid::SetMesh(TriangleMesh &mesh) {
+  this->m_Mesh = mesh;
   G4TessellatedSolid *ts = this->m_Solid;
   for (int i = 0; i < mesh.Triangles().size(); ++i) {
     const Vector3i &trg = mesh.Triangles().at(i);
@@ -165,6 +166,9 @@ void TessellatedSolid::SetMesh(TriangleMesh &mesh) {
   }
 }
 
+void TessellatedSolid::Update() {
+}
+
 
 
 

src/HEP/Geant/Solid.h

@@ -94,10 +94,13 @@ public:
   uLibGetMacro(Solid, G4TessellatedSolid *) 
   virtual G4VSolid* GetG4Solid() const override { return (G4VSolid*)m_Solid; }
   
+  const TriangleMesh& GetMesh() const { return m_Mesh; }
+
 public slots:
   void Update();
 
 private : 
+  TriangleMesh        m_Mesh;
   G4TessellatedSolid *m_Solid;
 };
 
@@ -126,6 +129,12 @@ private:
   G4Box *m_Solid;
 };
 
+
+
+
+
+
+
 } // namespace Geant
 } // namespace uLib
 

src/Math/Assembly.cpp

@@ -0,0 +1,146 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// 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 >
+
+//////////////////////////////////////////////////////////////////////////////*/
+
+#include "Math/Assembly.h"
+#include "Math/ContainerBox.h"
+#include "Math/Cylinder.h"
+
+#include <limits>
+#include <algorithm>
+#include <cstring>
+
+namespace uLib {
+
+Assembly::Assembly()
+    : ObjectsContext(),
+      AffineTransform(),
+      m_BBoxMin(Vector3f::Zero()),
+      m_BBoxMax(Vector3f::Zero()),
+      m_ShowBoundingBox(false),
+      m_GroupSelection(true) {}
+
+Assembly::Assembly(const Assembly &copy)
+    : ObjectsContext(copy),
+      AffineTransform(copy),
+      m_BBoxMin(copy.m_BBoxMin),
+      m_BBoxMax(copy.m_BBoxMax),
+      m_ShowBoundingBox(copy.m_ShowBoundingBox),
+      m_GroupSelection(copy.m_GroupSelection) {}
+
+Assembly::~Assembly() {}
+
+void Assembly::AddObject(Object *obj) {
+    if (auto *at = dynamic_cast<AffineTransform *>(obj)) {
+        at->SetParent(this);
+    }
+    ObjectsContext::AddObject(obj);
+}
+
+void Assembly::RemoveObject(Object *obj) {
+    if (auto *at = dynamic_cast<AffineTransform *>(obj)) {
+        if (at->GetParent() == this)
+            at->SetParent(nullptr);
+    }
+    ObjectsContext::RemoveObject(obj);
+}
+
+void Assembly::ComputeBoundingBox() {
+    const auto &objects = this->GetObjects();
+    if (objects.empty()) {
+        m_BBoxMin = Vector3f::Zero();
+        m_BBoxMax = Vector3f::Zero();
+        return;
+    }
+
+    float inf = std::numeric_limits<float>::max();
+    m_BBoxMin = Vector3f(inf, inf, inf);
+    m_BBoxMax = Vector3f(-inf, -inf, -inf);
+
+    Matrix4f invAsm = this->GetWorldMatrix().inverse();
+
+    for (Object *obj : objects) {
+        if (auto *box = dynamic_cast<ContainerBox *>(obj)) {
+            // ContainerBox: wm is matrix from unit cube [0,1] to assembly base
+            Matrix4f m = invAsm * box->GetWorldMatrix();
+            for (int i = 0; i < 8; ++i) {
+                float x = (i & 1) ? 1.0f : 0.0f;
+                float y = (i & 2) ? 1.0f : 0.0f;
+                float z = (i & 4) ? 1.0f : 0.0f;
+                Vector4f corner = m * Vector4f(x, y, z, 1.0f);
+                for (int a = 0; a < 3; ++a) {
+                    m_BBoxMin(a) = std::min(m_BBoxMin(a), corner(a));
+                    m_BBoxMax(a) = std::max(m_BBoxMax(a), corner(a));
+                }
+            }
+        } else if (auto *cyl = dynamic_cast<Cylinder *>(obj)) {
+            // Cylinder: centered [-1, 1] radial, [-0.5, 0.5] height
+            Matrix4f m = invAsm * cyl->GetWorldMatrix();
+            for (int i = 0; i < 8; ++i) {
+                float x = (i & 1) ? 1.0f : -1.0f;
+                float y = (i & 2) ? 0.5f : -0.5f;
+                float z = (i & 4) ? 1.0f : -1.0f;
+                Vector4f corner = m * Vector4f(x, y, z, 1.0f);
+                for (int a = 0; a < 3; ++a) {
+                    m_BBoxMin(a) = std::min(m_BBoxMin(a), corner(a));
+                    m_BBoxMax(a) = std::max(m_BBoxMax(a), corner(a));
+                }
+            }
+        } else if (auto *subAsm = dynamic_cast<Assembly *>(obj)) {
+            // Recursive AABB for nested assemblies
+            subAsm->ComputeBoundingBox();
+            Vector3f subMin, subMax;
+            subAsm->GetBoundingBox(subMin, subMax);
+            Matrix4f m = invAsm * subAsm->GetWorldMatrix();
+            for (int i = 0; i < 8; ++i) {
+                float x = (i & 1) ? subMax(0) : subMin(0);
+                float y = (i & 2) ? subMax(1) : subMin(1);
+                float z = (i & 4) ? subMax(2) : subMin(2);
+                Vector4f corner = m * Vector4f(x, y, z, 1.0f);
+                for (int a = 0; a < 3; ++a) {
+                    m_BBoxMin(a) = std::min(m_BBoxMin(a), corner(a));
+                    m_BBoxMax(a) = std::max(m_BBoxMax(a), corner(a));
+                }
+            }
+        }
+    }
+}
+
+void Assembly::GetBoundingBox(Vector3f &bbMin, Vector3f &bbMax) const {
+    bbMin = m_BBoxMin;
+    bbMax = m_BBoxMax;
+}
+
+ContainerBox Assembly::GetBoundingBoxAsContainer() const {
+    ContainerBox bb;
+    Vector3f size = m_BBoxMax - m_BBoxMin;
+    bb.SetSize(size);
+    bb.SetPosition(m_BBoxMin);
+    return bb;
+}
+
+void Assembly::SetShowBoundingBox(bool show) {
+    m_ShowBoundingBox = show;
+    this->Updated();
+}
+
+bool Assembly::GetShowBoundingBox() const {
+    return m_ShowBoundingBox;
+}
+
+void Assembly::SetGroupSelection(bool group) {
+    m_GroupSelection = group;
+}
+
+bool Assembly::GetGroupSelection() const {
+    return m_GroupSelection;
+}
+
+} // namespace uLib

src/Math/Assembly.h

@@ -0,0 +1,109 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// CMT Cosmic Muon Tomography project //////////////////////////////////////////
+////////////////////////////////////////////////////////////////////////////////
+
+  Copyright (c) 2014, Universita' degli Studi di Padova, INFN sez. di Padova
+  All rights reserved
+
+  Authors: Andrea Rigoni Garola < andrea.rigoni@pd.infn.it >
+
+  ------------------------------------------------------------------
+  This library is free software;  you  can  redistribute  it  and/or
+  modify it  under the  terms  of  the  GNU  Lesser  General  Public
+  License as published  by  the  Free  Software  Foundation;  either
+  version 3.0 of the License, or (at your option) any later version.
+
+  This library is  distributed in  the hope that it will  be useful,
+  but  WITHOUT ANY WARRANTY;  without  even  the implied warranty of
+  MERCHANTABILITY  or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+  Lesser General Public License for more details.
+
+  You should have received a copy of  the GNU Lesser General  Public
+  License along with this library.
+
+//////////////////////////////////////////////////////////////////////////////*/
+
+#ifndef U_ASSEMBLY_H
+#define U_ASSEMBLY_H
+
+#include "Core/ObjectsContext.h"
+#include "Math/ContainerBox.h"
+#include "Math/Transform.h"
+
+namespace uLib {
+
+/**
+ * @brief Assembly groups geometric objects (ContainerBox, Cylinder, etc.)
+ * under a common transformation.
+ *
+ * Assembly derives from ObjectsContext so objects can be added/removed
+ * dynamically. It also inherits AffineTransform to provide a group-level
+ * transformation that is applied on top of each child's own transform.
+ *
+ * A bounding box is automatically computed from all contained objects and
+ * can be queried or shown/hidden through the VTK puppet.
+ */
+class Assembly : public ObjectsContext, public AffineTransform {
+public:
+    virtual const char *GetClassName() const override { return "Assembly"; }
+
+    Assembly();
+    Assembly(const Assembly &copy);
+    virtual ~Assembly();
+
+    virtual void AddObject(Object* obj) override;
+    virtual void RemoveObject(Object* obj) override;
+
+    /**
+     * @brief Recomputes the axis-aligned bounding box enclosing all children.
+     * Stores the result internally.
+     */
+    void ComputeBoundingBox();
+
+    /**
+     * @brief Returns the bounding box as min/max corners (in assembly-local
+     * coordinates).
+     */
+    void GetBoundingBox(Vector3f &bbMin, Vector3f &bbMax) const;
+
+    /**
+     * @brief Returns the bounding box as a ContainerBox (positioned
+     * at bbMin, sized bbMax-bbMin, parented to this transform).
+     */
+    ContainerBox GetBoundingBoxAsContainer() const;
+
+    /**
+     * @brief Controls whether the bounding box wireframe should be shown
+     * in the viewer (used by the VTK puppet).
+     */
+    void SetShowBoundingBox(bool show);
+    bool GetShowBoundingBox() const;
+    
+    /**
+     * @brief Controls selection behavior.
+     * If true (default), clicking any child within the assembly will select 
+     * the assembly itself. If false, individual children can be picked.
+     */
+    void SetGroupSelection(bool group);
+    bool GetGroupSelection() const;
+
+signals:
+    virtual void Updated() override {
+        if (m_InUpdated) return;  // break signal recursion
+        m_InUpdated = true;
+        this->ComputeBoundingBox();
+        ULIB_SIGNAL_EMIT(Assembly::Updated);
+        m_InUpdated = false;
+    }
+
+private:
+    Vector3f m_BBoxMin;
+    Vector3f m_BBoxMax;
+    bool     m_ShowBoundingBox;
+    bool     m_GroupSelection;
+    bool     m_InUpdated = false;
+};
+
+} // namespace uLib
+
+#endif // U_ASSEMBLY_H

src/Math/CMakeLists.txt

@@ -1,5 +1,7 @@
 
 set(HEADERS ContainerBox.h
+            Cylinder.h
+            Assembly.h
             Dense.h
             Geometry.h
             Transform.h
@@ -32,6 +34,7 @@ set(SOURCES VoxRaytracer.cpp
             VoxImage.cpp
             TriangleMesh.cpp
             QuadMesh.cpp
+            Assembly.cpp
             Dense.cpp
             Structured2DGrid.cpp
             Structured4DGrid.cpp
@@ -70,4 +73,3 @@ if(BUILD_TESTING)
   include(uLibTargetMacros)
   add_subdirectory(testing)
 endif()
-

src/Math/ContainerBox.h

@@ -51,10 +51,8 @@ class ContainerBox : public AffineTransform, public Object {
 public:
   ////////////////////////////////////////////////////////////////////////////
   // PROPERTIES //
-  Property<float> Width;
-  Property<float> Height;
-  Property<float> Depth;
-
+  Property<Vector3f> p_Size;
+  Property<Vector3f> p_Origin;
   virtual const char * GetClassName() const { return "ContainerBox"; }
 
   /**
@@ -63,12 +61,10 @@ public:
    */
   ContainerBox()
       : m_LocalT(this), // BaseClass is Parent of m_LocalTransform
-        Width(this, "Width", 1.0f),
-        Height(this, "Height", 1.0f),
-        Depth(this, "Depth", 1.0f) {
-    Object::connect(&Width, &Property<float>::PropertyChanged, this, &ContainerBox::SyncSize);
-    Object::connect(&Height, &Property<float>::PropertyChanged, this, &ContainerBox::SyncSize);
-    Object::connect(&Depth, &Property<float>::PropertyChanged, this, &ContainerBox::SyncSize);
+        p_Size(this, "Size", Vector3f(1.0f, 1.0f, 1.0f)),
+        p_Origin(this, "Origin", Vector3f(0.0f, 0.0f, 0.0f)) {
+    Object::connect(&p_Size, &Property<Vector3f>::PropertyChanged, this, &ContainerBox::SyncSize);
+    Object::connect(&p_Origin, &Property<Vector3f>::PropertyChanged, this, &ContainerBox::SyncOrigin);
   }
 
   /**
@@ -77,12 +73,11 @@ public:
    */
   ContainerBox(const Vector3f &size)
       : m_LocalT(this),
-        Width(this, "Width", size(0)),
-        Height(this, "Height", size(1)),
-        Depth(this, "Depth", size(2)) {
-    Object::connect(&Width, &Property<float>::PropertyChanged, this, &ContainerBox::SyncSize);
-    Object::connect(&Height, &Property<float>::PropertyChanged, this, &ContainerBox::SyncSize);
-    Object::connect(&Depth, &Property<float>::PropertyChanged, this, &ContainerBox::SyncSize);
+        p_Size(this, "Size", size),
+        p_Origin(this, "Origin", Vector3f(0.0f, 0.0f, 0.0f)) {
+    Object::connect(&p_Size, &Property<Vector3f>::PropertyChanged, this, &ContainerBox::SyncSize);
+    Object::connect(&p_Origin, &Property<Vector3f>::PropertyChanged, this, &ContainerBox::SyncOrigin);
+    this->SetSize(size);
   }
 
   /**
@@ -90,22 +85,23 @@ public:
    * @param copy The ContainerBox instance to copy from.
    */
   ContainerBox(const ContainerBox &copy)
-      : m_LocalT(this), // BaseClass is Parent of m_LocalTransform
+      : m_LocalT(copy.m_LocalT), // Copy local transform state
         AffineTransform(copy),
-        Width(this, "Width", copy.Width),
-        Height(this, "Height", copy.Height),
-        Depth(this, "Depth", copy.Depth) {
-    Object::connect(&Width, &Property<float>::PropertyChanged, this, &ContainerBox::SyncSize);
-    Object::connect(&Height, &Property<float>::PropertyChanged, this, &ContainerBox::SyncSize);
-    Object::connect(&Depth, &Property<float>::PropertyChanged, this, &ContainerBox::SyncSize);
-    this->SetOrigin(copy.GetOrigin());
+        p_Size(this, "Size", copy.p_Size),
+        p_Origin(this, "Origin", copy.p_Origin) {
+    m_LocalT.SetParent(this); // Reset parent to the new object
+    Object::connect(&p_Size, &Property<Vector3f>::PropertyChanged, this, &ContainerBox::SyncSize);
+    Object::connect(&p_Origin, &Property<Vector3f>::PropertyChanged, this, &ContainerBox::SyncOrigin);
   }
 
   /**
    * @brief Sets the box origin relative to its coordinate system.
    * @param v The origin position vector.
    */
-  void SetOrigin(const Vector3f &v) { m_LocalT.SetPosition(v); }
+  void SetOrigin(const Vector3f &v) { 
+    p_Origin = v;
+    m_LocalT.SetPosition(v); 
+  }
 
   /**
    * @brief Gets the box origin relative to its coordinate system.
@@ -119,9 +115,7 @@ public:
    * @param v The size vector (width, height, depth).
    */
   void SetSize(const Vector3f &v) {
-    Width = v(0);
-    Height = v(1);
-    Depth = v(2);
+    p_Size = v;
     Vector3f pos = this->GetOrigin();
     m_LocalT = AffineTransform(this); // regenerate local transform
     m_LocalT.Scale(v);
@@ -213,11 +207,17 @@ signals:
   // signal to emit when the box is updated //
   virtual void Updated() override { ULIB_SIGNAL_EMIT(ContainerBox::Updated); }
 
-private:
+private slots:
   void SyncSize() {
-      this->SetSize(Vector3f(Width, Height, Depth));
+      this->SetSize(p_Size);
   }
 
+  void SyncOrigin() {
+      this->SetOrigin(p_Origin);
+  }
+
+
+private:
   AffineTransform m_LocalT;
 };
 

src/Math/Cylinder.h

@@ -34,32 +34,32 @@
 namespace uLib {
 
 /**
- * @brief Represents a cylindrical volume centered in the base circle.
+ * @brief Represents a cylindrical volume.
  * 
- * Cylinder inherits from AffineTransform, which defines its parent
- * coordinate system. It contains an internal local transformation (m_LocalT)
- * that defines the cylinder's actual volume (radius and height) 
- * relative to the emitter's origin (base circle center).
+ * The cylinder orientation is defined by the Axis property (0=X, 1=Y, 2=Z).
+ * By default, it is aligned with the Y axis (Axis=1).
  */
 class Cylinder : public AffineTransform, public Object {
-    typedef AffineTransform BaseClass;
 
 public:
+    uLibTypeMacro(Cylinder, Object)
 
-    virtual const char * GetClassName() const { return "Cylinder"; }
+    virtual const char * GetClassName() const override { return "Cylinder"; }
 
     /**
-     * @brief Default constructor.
-     * Initializes with radius 1 and height 1.
+     * @brief Default constructor. Aligns with Y by default.
      */
-    Cylinder() : m_LocalT(this), m_Radius(1.0), m_Height(1.0) {
+    Cylinder() : m_LocalT(this), Radius(1.0), Height(1.0), Axis(1) {
+        ULIB_ACTIVATE_PROPERTIES(*this);
         UpdateLocalMatrix();
     }
 
     /**
      * @brief Constructor with radius and height.
      */
-    Cylinder(float radius, float height) : m_LocalT(this), m_Radius(radius), m_Height(height) {
+    Cylinder(float radius, float height, int axis = 1) 
+        : m_LocalT(this), Radius(radius), Height(height), Axis(axis) {
+        ULIB_ACTIVATE_PROPERTIES(*this);
         UpdateLocalMatrix();
     }
 
@@ -67,75 +67,115 @@ public:
      * @brief Copy constructor.
      */
     Cylinder(const Cylinder &copy)
-        : m_LocalT(this), AffineTransform(copy) {
-        this->SetRadius(copy.GetRadius());
-        this->SetHeight(copy.GetHeight());
+        : m_LocalT(this), AffineTransform(copy), Radius(copy.Radius), Height(copy.Height), Axis(copy.Axis) {
+        ULIB_ACTIVATE_PROPERTIES(*this);
+        this->UpdateLocalMatrix();
+    }
+
+    /**
+     * @brief Serialization template for property registration and persistence.
+     */
+    template <class ArchiveT>
+    void serialize(ArchiveT & ar, const unsigned int version) {
+        ar & HRP(Radius);
+        ar & HRP(Height);
+        ar & HRP(Axis);
     }
 
     /** Sets the radius of the cylinder */
     inline void SetRadius(float r) { 
-        m_Radius = r; 
+        Radius = r; 
         UpdateLocalMatrix(); 
     }
     
     /** Gets the radius of the cylinder */
-    inline float GetRadius() const { return m_Radius; }
+    inline float GetRadius() const { return Radius; }
 
     /** Sets the height of the cylinder */
     inline void SetHeight(float h) { 
-        m_Height = h; 
+        Height = h; 
         UpdateLocalMatrix(); 
     }
     
     /** Gets the height of the cylinder */
-    inline float GetHeight() const { return m_Height; }
+    inline float GetHeight() const { return Height; }
+
+    /** Sets the main axis (0=X, 1=Y, 2=Z) */
+    inline void SetAxis(int axis) {
+        Axis = axis;
+        UpdateLocalMatrix();
+    }
+
+    /** Gets the main axis */
+    inline int GetAxis() const { return Axis; }
 
     /**
-     * @brief Returns the world transformation matrix of the cylinder's volume.
+     * @brief Returns the world transformation matrix.
      */
     Matrix4f GetWorldMatrix() const { return m_LocalT.GetWorldMatrix(); }
 
     /**
-     * @brief Returns the local transformation matrix of the cylinder's volume.
+     * @brief Returns the local transformation matrix.
      */
     Matrix4f GetLocalMatrix() const { return m_LocalT.GetMatrix(); }
 
     /**
      * @brief Transforms local cylindrical coordinates to world space.
-     * @param r Local radius (absolute).
-     * @param theta Local angle in radians.
-     * @param z Local height (absolute, relative to base circle).
-     * @return Transformed point in world space.
+     * @param r Local radius.
+     * @param theta Local angle in radians (around main axis).
+     * @param h Local height along main axis.
      */
-    inline Vector4f GetWorldPoint(float r, float theta, float z) const {
-        return BaseClass::GetWorldMatrix() * Vector4f(r * std::cos(theta), r * std::sin(theta), z, 1.0f);
+    inline Vector4f GetWorldPoint(float r, float theta, float h) const {
+        Vector3f p;
+        if (Axis == 0) p = Vector3f(h, r * std::cos(theta), r * std::sin(theta));
+        else if (Axis == 1) p = Vector3f(r * std::cos(theta), h, r * std::sin(theta));
+        else p = Vector3f(r * std::cos(theta), r * std::sin(theta), h);
+        
+        return AffineTransform::GetWorldMatrix() * Vector4f(p.x(), p.y(), p.z(), 1.0f);
     }
 
     /**
      * @brief Transforms a world point to cylindrical local space.
-     * @return Vector3f(r, theta, z)
+     * @return Vector3f(r, theta, h)
      */
     inline Vector3f GetCylindricalLocal(const Vector4f &world_v) const {
-        Vector4f local_v = BaseClass::GetWorldMatrix().inverse() * world_v;
-        float r = std::sqrt(local_v.x() * local_v.x() + local_v.y() * local_v.y());
-        float theta = std::atan2(local_v.y(), local_v.x());
-        return Vector3f(r, theta, local_v.z());
+        Vector4f local_v = AffineTransform::GetWorldMatrix().inverse() * world_v;
+        float r, theta, h;
+        if (Axis == 0) {
+            h = local_v.x();
+            r = std::sqrt(local_v.y() * local_v.y() + local_v.z() * local_v.z());
+            theta = std::atan2(local_v.z(), local_v.y());
+        } else if (Axis == 1) {
+            h = local_v.y();
+            r = std::sqrt(local_v.x() * local_v.x() + local_v.z() * local_v.z());
+            theta = std::atan2(local_v.z(), local_v.x());
+        } else {
+            h = local_v.z();
+            r = std::sqrt(local_v.x() * local_v.x() + local_v.y() * local_v.y());
+            theta = std::atan2(local_v.y(), local_v.x());
+        }
+        return Vector3f(r, theta, h);
     }
 
 signals:
-    /** Signal emitted when the cylinder geometry or transform is updated */
-    virtual void Updated() override { ULIB_SIGNAL_EMIT(Cylinder::Updated); }
-
-private:
-    /** Recalculates the internal local matrix based on radius and height */
-    void UpdateLocalMatrix() {
-        m_LocalT = AffineTransform(this); // BaseClass is parent
-        m_LocalT.Scale(Vector3f(m_Radius, m_Radius, m_Height));
-        this->Updated();
+    /** Signal emitted when properties change */
+    virtual void Updated() override { 
+        this->UpdateLocalMatrix();
+        ULIB_SIGNAL_EMIT(Cylinder::Updated); 
     }
 
-    float m_Radius;
-    float m_Height;
+private:
+    /** Recalculates the internal local matrix based on dimensions and axis */
+    void UpdateLocalMatrix() {
+        m_LocalT = AffineTransform(this);
+        if (Axis == 0) m_LocalT.Scale(Vector3f(Height, Radius, Radius));
+        else if (Axis == 1) m_LocalT.Scale(Vector3f(Radius, Height, Radius));
+        else m_LocalT.Scale(Vector3f(Radius, Radius, Height));
+    }
+
+    float Radius;
+    float Height;
+    int Axis;
     AffineTransform m_LocalT;
 };
 

src/Math/QuadMesh.h

@@ -52,7 +52,9 @@ public:
     Vector3f GetPoint(const Id_t id) const;
 
     inline std::vector<Vector3f> & Points() { return this->m_Points; }
+    inline const std::vector<Vector3f> & Points() const { return this->m_Points; }
     inline std::vector<Vector4i> & Quads() { return this->m_Quads; }
+    inline const std::vector<Vector4i> & Quads() const { return this->m_Quads; }
 
     const Vector4i & GetQuad(const Id_t id) const { return m_Quads.at(id); }
     Vector3f GetNormal(const Id_t id) const;

src/Math/Transform.h

@@ -69,6 +69,8 @@ public:
         m_Parent(NULL)
     {}
 
+    virtual ~AffineTransform() {}
+
     AffineTransform(AffineTransform *parent) :
         m_T(Matrix4f::Identity()),
         m_Parent(parent)

src/Math/TriangleMesh.h

@@ -55,7 +55,9 @@ public:
     Vector3f GetPoint(const Id_t id) const;
 
     inline std::vector<Vector3f> & Points() { return this->m_Points; }
+    inline const std::vector<Vector3f> & Points() const { return this->m_Points; }
     inline std::vector<Vector3i> & Triangles() { return this->m_Triangles; }
+    inline const std::vector<Vector3i> & Triangles() const { return this->m_Triangles; }
 
     const Vector3i & GetTriangle(const Id_t id) const { return m_Triangles.at(id); }
     Vector3f GetNormal(const Id_t id) const;

src/Math/VoxImage.h

@@ -109,8 +109,20 @@ public:
 
   VoxImage(const Vector3i &size);
 
-  VoxImage(const VoxImage<T> &copy) : BaseClass(copy) {
-    this->m_Data = copy.m_Data;
+  // Use compiler-generated copy constructor and assignment operator
+
+  VoxImage<T>& operator=(const VoxImage<T>& other) {
+    if (this != &other) {
+      // Copy the base class non-virtual parts (dims, spacing, position, etc.)
+      // WITHOUT going through the virtual SetDims chain (which would call
+      // m_Data.resize() THEN DataAllocator::operator= will resize again → double-free).
+      // Instead, directly copy DataAllocator and update the StructuredGrid state.
+      this->m_Data = other.m_Data;
+      StructuredGrid::SetDims(other.GetDims());
+      this->SetSpacing(other.GetSpacing());
+      this->SetPosition(other.GetPosition());
+    }
+    return *this;
   }
 
   inline DataAllocator<T> &Data() { return this->m_Data; }

src/Math/VoxImageFilter.h

@@ -27,12 +27,16 @@
 #define VOXIMAGEFILTER_H
 
 #include "Core/StaticInterface.h"
+#include "Core/Algorithm.h"
 #include "Math/Dense.h"
 
 #include "Math/VoxImage.h"
 
 namespace uLib {
 
+////////////////////////////////////////////////////////////////////////////////
+// Kernel shape interface (static check for operator()(float) and operator()(Vector3f))
+
 namespace Interface {
 struct VoxImageFilterShape {
   template <class Self> void check_structural() {
@@ -42,63 +46,95 @@ struct VoxImageFilterShape {
 };
 } // namespace Interface
 
+////////////////////////////////////////////////////////////////////////////////
+// Forward declaration
+
 template <typename VoxelT> class Kernel;
 
+////////////////////////////////////////////////////////////////////////////////
+// Abstract interface (type-erased, used by python bindings)
+
 namespace Abstract {
 class VoxImageFilter {
 public:
   virtual void Run() = 0;
-
   virtual void SetImage(Abstract::VoxImage *image) = 0;
-
 protected:
   virtual ~VoxImageFilter() {}
 };
 } // namespace Abstract
 
-template <typename VoxelT, typename AlgorithmT>
-class VoxImageFilter : public Abstract::VoxImageFilter, public Object {
+////////////////////////////////////////////////////////////////////////////////
+// VoxImageFilter — kernel-based voxel filter using CRTP + Algorithm
+//
+// Template parameters:
+//   VoxelT     — voxel data type (must satisfy Interface::Voxel)
+//   CrtpImplT  — concrete filter subclass (CRTP), must provide:
+//                 float Evaluate(const VoxImage<VoxelT>& buffer, int index)
+//
+// Inherits Algorithm<VoxImage<VoxelT>*, VoxImage<VoxelT>*> so that filters
+// can be used with AlgorithmTask for scheduled/async execution, and chained
+// via encoder/decoder.
 
+template <typename VoxelT, typename CrtpImplT>
+class VoxImageFilter : public Abstract::VoxImageFilter,
+                       public Algorithm<VoxImage<VoxelT>*, VoxImage<VoxelT>*> {
 public:
 
   virtual const char* GetClassName() const { return "VoxImageFilter"; }
 
   VoxImageFilter(const Vector3i &size);
 
+  // Algorithm interface ////////////////////////////////////////////////////////
+
+  /**
+   * @brief Process implements Algorithm::Process.
+   * Applies the filter in-place on the input image and returns it.
+   */
+  VoxImage<VoxelT>* Process(VoxImage<VoxelT>* const& image) override;
+
+  /**
+   * @brief Run implements Abstract::VoxImageFilter::Run.
+   * Calls Process on the current image.
+   */
   void Run();
 
+  // Device awareness ///////////////////////////////////////////////////////////
+
+  /** @brief Returns VRAM if image or kernel data is on GPU, RAM otherwise. */
+  MemoryDevice GetPreferredDevice() const override {
+    if (m_Image && m_Image->Data().GetDevice() == MemoryDevice::VRAM)
+      return MemoryDevice::VRAM;
+    if (m_KernelData.ConstData().GetDevice() == MemoryDevice::VRAM)
+      return MemoryDevice::VRAM;
+    return MemoryDevice::RAM;
+  }
+
+  // Kernel setup ///////////////////////////////////////////////////////////////
+
   void SetKernelNumericXZY(const std::vector<float> &numeric);
-
   void SetKernelSpherical(float (*shape)(float));
-
   template <class ShapeT> void SetKernelSpherical(ShapeT shape);
-
   void SetKernelWeightFunction(float (*shape)(const Vector3f &));
-
   template <class ShapeT> void SetKernelWeightFunction(ShapeT shape);
 
-  inline const Kernel<VoxelT> &GetKernelData() const {
-    return this->m_KernelData;
-  }
-  inline Kernel<VoxelT> &GetKernelData() { return this->m_KernelData; }
+  // Accessors //////////////////////////////////////////////////////////////////
 
-  inline VoxImage<VoxelT> *GetImage() const { return this->m_Image; }
+  const Kernel<VoxelT> &GetKernelData() const { return m_KernelData; }
+  Kernel<VoxelT> &GetKernelData() { return m_KernelData; }
 
+  VoxImage<VoxelT> *GetImage() const { return m_Image; }
   void SetImage(Abstract::VoxImage *image);
 
 protected:
-  float Convolve(const VoxImage<VoxelT> &buffer, int index); // remove //
-
   void SetKernelOffset();
-
   float Distance2(const Vector3i &v);
 
-  // protected members for algorithm access //
   Kernel<VoxelT> m_KernelData;
   VoxImage<VoxelT> *m_Image;
 
 private:
-  AlgorithmT *t_Algoritm;
+  CrtpImplT *m_CrtpImpl;
 };
 
 } // namespace uLib

src/Math/VoxImageFilter.hpp

@@ -33,7 +33,9 @@
 
 namespace uLib {
 
-// KERNEL //////////////////////////////////////////////////////////////////////
+////////////////////////////////////////////////////////////////////////////////
+//// KERNEL ////////////////////////////////////////////////////////////////////
+////////////////////////////////////////////////////////////////////////////////
 
 template <typename T> class Kernel : public StructuredData {
   typedef StructuredData BaseClass;
@@ -41,13 +43,12 @@ template <typename T> class Kernel : public StructuredData {
 public:
   Kernel(const Vector3i &size);
 
-  inline T &operator[](const Vector3i &id) { return m_Data[Map(id)]; }
-  inline T &operator[](const int &id) { return m_Data[id]; }
-  inline int GetCenterData() const;
+  T &operator[](const Vector3i &id) { return m_Data[Map(id)]; }
+  T &operator[](const int &id) { return m_Data[id]; }
+  int GetCenterData() const;
 
-  inline DataAllocator<T> &Data() { return this->m_Data; }
-
-  inline const DataAllocator<T> &ConstData() const { return this->m_Data; }
+  DataAllocator<T> &Data() { return m_Data; }
+  const DataAllocator<T> &ConstData() const { return m_Data; }
 
   void PrintSelf(std::ostream &o) const;
 
@@ -60,12 +61,14 @@ Kernel<T>::Kernel(const Vector3i &size) : BaseClass(size), m_Data(size.prod()) {
   Interface::IsA<T, Interface::Voxel>();
 }
 
-template <typename T> inline int Kernel<T>::GetCenterData() const {
+template <typename T>
+int Kernel<T>::GetCenterData() const {
   static int center = Map(this->GetDims() / 2);
   return center;
 }
 
-template <typename T> void Kernel<T>::PrintSelf(std::ostream &o) const {
+template <typename T>
+void Kernel<T>::PrintSelf(std::ostream &o) const {
   o << " Filter Kernel Dump [XZ_Y]: \n";
   Vector3i index;
   o << "\n Value: \n\n"
@@ -96,26 +99,42 @@ template <typename T> void Kernel<T>::PrintSelf(std::ostream &o) const {
   }
 }
 
+////////////////////////////////////////////////////////////////////////////////
+//// VOXIMAGEFILTER IMPLEMENTATION /////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
 
-#define _TPL_ template <typename VoxelT, typename AlgorithmT>
-#define _TPLT_ VoxelT, AlgorithmT
+template <typename VoxelT, typename CrtpImplT>
+VoxImageFilter<VoxelT, CrtpImplT>::VoxImageFilter(const Vector3i &size)
+    : m_KernelData(size)
+    , m_Image(nullptr)
+    , m_CrtpImpl(static_cast<CrtpImplT *>(this))
+{}
 
-_TPL_
-VoxImageFilter<_TPLT_>::VoxImageFilter(const Vector3i &size)
-    : m_KernelData(size), t_Algoritm(static_cast<AlgorithmT *>(this)) {}
-
-_TPL_
-void VoxImageFilter<_TPLT_>::Run() {
+template <typename VoxelT, typename CrtpImplT>
+VoxImage<VoxelT>* VoxImageFilter<VoxelT, CrtpImplT>::Process(
+    VoxImage<VoxelT>* const& image) {
+  if (m_Image != image) SetImage(image);
   VoxImage<VoxelT> buffer = *m_Image;
 #pragma omp parallel for
   for (int i = 0; i < m_Image->Data().size(); ++i)
-    m_Image->operator[](i).Value = this->t_Algoritm->Evaluate(buffer, i);
+    m_Image->operator[](i).Value = m_CrtpImpl->Evaluate(buffer, i);
 #pragma omp barrier
+  return m_Image;
 }
 
-_TPL_
-void VoxImageFilter<_TPLT_>::SetKernelOffset() {
+template <typename VoxelT, typename CrtpImplT>
+void VoxImageFilter<VoxelT, CrtpImplT>::Run() {
+  Process(m_Image);
+}
+
+template <typename VoxelT, typename CrtpImplT>
+void VoxImageFilter<VoxelT, CrtpImplT>::SetImage(Abstract::VoxImage *image) {
+  m_Image = reinterpret_cast<VoxImage<VoxelT> *>(image);
+  SetKernelOffset();
+}
+
+template <typename VoxelT, typename CrtpImplT>
+void VoxImageFilter<VoxelT, CrtpImplT>::SetKernelOffset() {
   Vector3i id(0, 0, 0);
   for (int z = 0; z < m_KernelData.GetDims()(2); ++z) {
     for (int x = 0; x < m_KernelData.GetDims()(0); ++x) {
@@ -127,10 +146,10 @@ void VoxImageFilter<_TPLT_>::SetKernelOffset() {
   }
 }
 
-_TPL_
-float VoxImageFilter<_TPLT_>::Distance2(const Vector3i &v) {
+template <typename VoxelT, typename CrtpImplT>
+float VoxImageFilter<VoxelT, CrtpImplT>::Distance2(const Vector3i &v) {
   Vector3i tmp = v;
-  const Vector3i &dim = this->m_KernelData.GetDims();
+  const Vector3i &dim = m_KernelData.GetDims();
   Vector3i center = dim / 2;
   tmp = tmp - center;
   center = center.cwiseProduct(center);
@@ -140,12 +159,9 @@ float VoxImageFilter<_TPLT_>::Distance2(const Vector3i &v) {
                  0.25 * (3 - (dim(0) % 2) - (dim(1) % 2) - (dim(2) % 2)));
 }
 
-_TPL_
-void VoxImageFilter<_TPLT_>::SetKernelNumericXZY(
+template <typename VoxelT, typename CrtpImplT>
+void VoxImageFilter<VoxelT, CrtpImplT>::SetKernelNumericXZY(
     const std::vector<float> &numeric) {
-  // set data order //
-  StructuredData::Order order = m_KernelData.GetDataOrder();
-  // m_KernelData.SetDataOrder(StructuredData::XZY);
   Vector3i id;
   int index = 0;
   for (int y = 0; y < m_KernelData.GetDims()(1); ++y) {
@@ -156,38 +172,39 @@ void VoxImageFilter<_TPLT_>::SetKernelNumericXZY(
       }
     }
   }
-  // m_KernelData.SetDataOrder(order);
 }
 
-_TPL_
-void VoxImageFilter<_TPLT_>::SetKernelSpherical(float (*shape)(float)) {
+template <typename VoxelT, typename CrtpImplT>
+void VoxImageFilter<VoxelT, CrtpImplT>::SetKernelSpherical(
+    float (*shape)(float)) {
   Vector3i id;
   for (int y = 0; y < m_KernelData.GetDims()(1); ++y) {
     for (int z = 0; z < m_KernelData.GetDims()(2); ++z) {
       for (int x = 0; x < m_KernelData.GetDims()(0); ++x) {
         id << x, y, z;
-        m_KernelData[id].Value = shape(this->Distance2(id));
+        m_KernelData[id].Value = shape(Distance2(id));
       }
     }
   }
 }
 
-_TPL_ template <class ShapeT>
-void VoxImageFilter<_TPLT_>::SetKernelSpherical(ShapeT shape) {
+template <typename VoxelT, typename CrtpImplT>
+template <class ShapeT>
+void VoxImageFilter<VoxelT, CrtpImplT>::SetKernelSpherical(ShapeT shape) {
   Interface::IsA<ShapeT, Interface::VoxImageFilterShape>();
   Vector3i id;
   for (int y = 0; y < m_KernelData.GetDims()(1); ++y) {
     for (int z = 0; z < m_KernelData.GetDims()(2); ++z) {
       for (int x = 0; x < m_KernelData.GetDims()(0); ++x) {
         id << x, y, z;
-        m_KernelData[id].Value = shape(this->Distance2(id));
+        m_KernelData[id].Value = shape(Distance2(id));
       }
     }
   }
 }
 
-_TPL_
-void VoxImageFilter<_TPLT_>::SetKernelWeightFunction(
+template <typename VoxelT, typename CrtpImplT>
+void VoxImageFilter<VoxelT, CrtpImplT>::SetKernelWeightFunction(
     float (*shape)(const Vector3f &)) {
   const Vector3i &dim = m_KernelData.GetDims();
   Vector3i id;
@@ -195,20 +212,19 @@ void VoxImageFilter<_TPLT_>::SetKernelWeightFunction(
   for (int y = 0; y < dim(1); ++y) {
     for (int z = 0; z < dim(2); ++z) {
       for (int x = 0; x < dim(0); ++x) {
-        // get voxels centroid coords from kernel center //
         id << x, y, z;
         pt << id(0) - dim(0) / 2 + 0.5 * !(dim(0) % 2),
             id(1) - dim(1) / 2 + 0.5 * !(dim(1) % 2),
             id(2) - dim(2) / 2 + 0.5 * !(dim(2) % 2);
-        // compute function using given shape //
         m_KernelData[id].Value = shape(pt);
       }
     }
   }
 }
 
-_TPL_ template <class ShapeT>
-void VoxImageFilter<_TPLT_>::SetKernelWeightFunction(ShapeT shape) {
+template <typename VoxelT, typename CrtpImplT>
+template <class ShapeT>
+void VoxImageFilter<VoxelT, CrtpImplT>::SetKernelWeightFunction(ShapeT shape) {
   Interface::IsA<ShapeT, Interface::VoxImageFilterShape>();
   const Vector3i &dim = m_KernelData.GetDims();
   Vector3i id;
@@ -216,45 +232,16 @@ void VoxImageFilter<_TPLT_>::SetKernelWeightFunction(ShapeT shape) {
   for (int y = 0; y < dim(1); ++y) {
     for (int z = 0; z < dim(2); ++z) {
       for (int x = 0; x < dim(0); ++x) {
-        // get voxels centroid coords from kernel center //
         id << x, y, z;
         pt << id(0) - dim(0) / 2 + 0.5 * !(dim(0) % 2),
             id(1) - dim(1) / 2 + 0.5 * !(dim(1) % 2),
             id(2) - dim(2) / 2 + 0.5 * !(dim(2) % 2);
-        // compute function using given shape //
         m_KernelData[id].Value = shape(pt);
       }
     }
   }
 }
 
-_TPL_
-void VoxImageFilter<_TPLT_>::SetImage(Abstract::VoxImage *image) {
-  this->m_Image = reinterpret_cast<VoxImage<VoxelT> *>(image);
-  this->SetKernelOffset();
-}
-
-_TPL_
-float VoxImageFilter<_TPLT_>::Convolve(const VoxImage<VoxelT> &buffer,
-                                       int index) {
-  const DataAllocator<VoxelT> &vbuf = buffer.ConstData();
-  const DataAllocator<VoxelT> &vker = m_KernelData.ConstData();
-  int vox_size = vbuf.size();
-  int ker_size = vker.size();
-  int pos;
-  float conv = 0, ksum = 0;
-  for (int ik = 0; ik < ker_size; ++ik) {
-    pos = index + vker[ik].Count - vker[m_KernelData.GetCenterData()].Count;
-    pos = (pos + vox_size) % vox_size;
-    conv += vbuf[pos].Value * vker[ik].Value;
-    ksum += vker[ik].Value;
-  }
-  return conv / ksum;
-}
-
-#undef _TPLT_
-#undef _TPL_
-
 } // namespace uLib
 
 #endif // VOXIMAGEFILTER_HPP

src/Math/VoxImageFilterABTrim.hpp

@@ -109,7 +109,8 @@ public:
   }
 
 #if defined(USE_CUDA) && defined(__CUDACC__)
-  void Run() {
+  VoxImage<VoxelT>* Process(VoxImage<VoxelT>* const& image) override {
+    if (this->m_Image != image) this->SetImage(image);
     if (this->m_Image->Data().GetDevice() == MemoryDevice::VRAM ||
         this->m_KernelData.Data().GetDevice() == MemoryDevice::VRAM) {
 
@@ -136,8 +137,9 @@ public:
           d_img_in, d_img_out, d_kernel, vox_size, ker_size, center_count,
           mAtrim, mBtrim);
       cudaDeviceSynchronize();
+      return this->m_Image;
     } else {
-      BaseClass::Run();
+      return BaseClass::Process(image);
     }
   }
 #endif
@@ -207,7 +209,8 @@ public:
   }
 
 #if defined(USE_CUDA) && defined(__CUDACC__)
-  void Run() {
+  VoxImage<VoxelT>* Process(VoxImage<VoxelT>* const& image) override {
+    if (this->m_Image != image) this->SetImage(image);
     if (this->m_Image->Data().GetDevice() == MemoryDevice::VRAM ||
         this->m_KernelData.Data().GetDevice() == MemoryDevice::VRAM) {
 
@@ -234,8 +237,9 @@ public:
           d_img_in, d_img_out, d_kernel, vox_size, ker_size, center_count,
           mAtrim, mBtrim);
       cudaDeviceSynchronize();
+      return this->m_Image;
     } else {
-      BaseClass::Run();
+      return BaseClass::Process(image);
     }
   }
 #endif

src/Math/VoxImageFilterCustom.hpp

@@ -30,8 +30,6 @@
 #include "VoxImageFilter.h"
 #include <Math/Dense.h>
 
-#define likely(expr) __builtin_expect(!!(expr), 1)
-
 ////////////////////////////////////////////////////////////////////////////////
 /////  VOXIMAGE FILTER CUSTOM  /////////////////////////////////////////////////
 ////////////////////////////////////////////////////////////////////////////////
@@ -50,7 +48,7 @@ public:
       : BaseClass(size), m_CustomEvaluate(NULL) {}
 
   float Evaluate(const VoxImage<VoxelT> &buffer, int index) {
-    if (likely(m_CustomEvaluate)) {
+    if (m_CustomEvaluate) {
       const DataAllocator<VoxelT> &vbuf = buffer.ConstData();
       const DataAllocator<VoxelT> &vker = this->m_KernelData.ConstData();
       int vox_size = vbuf.size();

src/Math/VoxImageFilterLinear.hpp

@@ -67,7 +67,8 @@ public:
   VoxFilterAlgorithmLinear(const Vector3i &size) : BaseClass(size) {}
 
 #if defined(USE_CUDA) && defined(__CUDACC__)
-  void Run() {
+  VoxImage<VoxelT>* Process(VoxImage<VoxelT>* const& image) override {
+    if (this->m_Image != image) this->SetImage(image);
     if (this->m_Image->Data().GetDevice() == MemoryDevice::VRAM ||
         this->m_KernelData.Data().GetDevice() == MemoryDevice::VRAM) {
 
@@ -92,8 +93,9 @@ public:
       LinearFilterKernel<<<blocksPerGrid, threadsPerBlock>>>(
           d_img_in, d_img_out, d_kernel, vox_size, ker_size, center_count);
       cudaDeviceSynchronize();
+      return this->m_Image;
     } else {
-      BaseClass::Run();
+      return BaseClass::Process(image);
     }
   }
 #endif

src/Math/VoxImageFilterThreshold.hpp

@@ -23,8 +23,6 @@
 
 //////////////////////////////////////////////////////////////////////////////*/
 
-
-
 #ifndef VOXIMAGEFILTERTHRESHOLD_HPP
 #define VOXIMAGEFILTERTHRESHOLD_HPP
 
@@ -39,40 +37,24 @@
 namespace uLib {
 
 template <typename VoxelT>
-class VoxFilterAlgorithmThreshold :
-        public VoxImageFilter<VoxelT, VoxFilterAlgorithmThreshold<VoxelT> > {
+class VoxFilterAlgorithmThreshold
+    : public VoxImageFilter<VoxelT, VoxFilterAlgorithmThreshold<VoxelT>> {
 
   typedef VoxImageFilter<VoxelT, VoxFilterAlgorithmThreshold<VoxelT>> BaseClass;
-    //    ULIB_OBJECT_PARAMETERS(BaseClass) {
-    //        float threshold;
-    //    };
 
   float m_threshold;
 
 public:
-    VoxFilterAlgorithmThreshold(const Vector3i &size) : BaseClass(size)
-    {
-        //        init_parameters();
-        m_threshold = 0;
+  VoxFilterAlgorithmThreshold(const Vector3i &size)
+      : BaseClass(size), m_threshold(0) {}
+
+  void SetThreshold(float th) { m_threshold = th; }
+
+  float Evaluate(const VoxImage<VoxelT> &buffer, int index) {
+    return static_cast<float>(buffer.ConstData().at(index).Value >= m_threshold);
   }
-
-    inline void SetThreshold(float th) { m_threshold = th; }
-
-    float Evaluate(const VoxImage<VoxelT> &buffer, int index)
-    {
-        return static_cast<float>(buffer.ConstData().at(index).Value >=
-                                  //                                  parameters().threshold);
-                                  m_threshold );
-    }
-
 };
 
-//template <typename VoxelT>
-//inline void VoxFilterAlgorithmThreshold<VoxelT>::init_parameters()
-//{
-//    parameters().threshold = 0;
-//}
-
-}
+} // namespace uLib
 
 #endif // VOXIMAGEFILTERTHRESHOLD_HPP

src/Math/testing/AlgorithmCudaChainTest.cpp

@@ -0,0 +1,408 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// 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 "testing-prototype.h"
+
+#include "Core/Algorithm.h"
+#include "Math/VoxImage.h"
+#include "Math/VoxImageFilter.h"
+
+#include <iostream>
+#include <thread>
+#include <chrono>
+
+using namespace uLib;
+
+struct TestVoxel {
+  Scalarf Value;
+  unsigned int Count;
+};
+
+int main() {
+  BEGIN_TESTING(AlgorithmCudaChain);
+
+  ////////////////////////////////////////////////////////////////////////////
+  // TEST 1: Single filter — GetPreferredDevice reflects data location
+  ////////////////////////////////////////////////////////////////////////////
+  {
+    std::cout << "\n--- Test 1: GetPreferredDevice reflects data location ---\n";
+
+    VoxImage<TestVoxel> image(Vector3i(10, 10, 10));
+    image[Vector3i(5, 5, 5)].Value = 1;
+
+    VoxFilterAlgorithmLinear<TestVoxel> filter(Vector3i(3, 3, 3));
+    std::vector<float> weights(27, 1.0f);
+    filter.SetImage(&image);
+    filter.SetKernelNumericXZY(weights);
+
+    // Before VRAM move: should prefer RAM
+    TEST1(filter.GetPreferredDevice() == MemoryDevice::RAM);
+    TEST1(!filter.IsGPU());
+    std::cout << "  RAM mode: PreferredDevice=RAM, IsGPU=false  OK\n";
+
+    // Move image data to VRAM
+    image.Data().MoveToVRAM();
+
+    // After VRAM move: should prefer VRAM
+    TEST1(filter.GetPreferredDevice() == MemoryDevice::VRAM);
+    TEST1(filter.IsGPU());
+    std::cout << "  VRAM mode: PreferredDevice=VRAM, IsGPU=true  OK\n";
+
+    // Move back to RAM
+    image.Data().MoveToRAM();
+    TEST1(filter.GetPreferredDevice() == MemoryDevice::RAM);
+    std::cout << "  Back to RAM: PreferredDevice=RAM  OK\n";
+  }
+
+  ////////////////////////////////////////////////////////////////////////////
+  // TEST 2: Kernel data on VRAM also triggers GPU preference
+  ////////////////////////////////////////////////////////////////////////////
+  {
+    std::cout << "\n--- Test 2: Kernel on VRAM triggers GPU preference ---\n";
+
+    VoxImage<TestVoxel> image(Vector3i(8, 8, 8));
+    VoxFilterAlgorithmLinear<TestVoxel> filter(Vector3i(3, 3, 3));
+    std::vector<float> weights(27, 1.0f);
+    filter.SetImage(&image);
+    filter.SetKernelNumericXZY(weights);
+
+    TEST1(filter.GetPreferredDevice() == MemoryDevice::RAM);
+
+    // Only kernel on VRAM
+    filter.GetKernelData().Data().MoveToVRAM();
+    TEST1(filter.GetPreferredDevice() == MemoryDevice::VRAM);
+    std::cout << "  Kernel on VRAM: PreferredDevice=VRAM  OK\n";
+
+    filter.GetKernelData().Data().MoveToRAM();
+    TEST1(filter.GetPreferredDevice() == MemoryDevice::RAM);
+  }
+
+  ////////////////////////////////////////////////////////////////////////////
+  // TEST 3: Algorithm interface — Process through base pointer
+  ////////////////////////////////////////////////////////////////////////////
+  {
+    std::cout << "\n--- Test 3: Process through Algorithm base pointer ---\n";
+
+    VoxImage<TestVoxel> image(Vector3i(10, 10, 10));
+    image[Vector3i(5, 5, 5)].Value = 10;
+
+    VoxFilterAlgorithmLinear<TestVoxel> filter(Vector3i(3, 3, 3));
+    std::vector<float> weights(27, 1.0f);
+    filter.SetImage(&image);
+    filter.SetKernelNumericXZY(weights);
+
+    // Use through Algorithm base class pointer
+    Algorithm<VoxImage<TestVoxel>*, VoxImage<TestVoxel>*>* alg = &filter;
+
+    VoxImage<TestVoxel>* result = alg->Process(&image);
+    TEST1(result == &image);
+    std::cout << "  Process through base pointer returned correct image  OK\n";
+
+    // Verify filter actually ran (center voxel should be averaged)
+    // With uniform 3x3x3 kernel and single non-zero voxel at center,
+    // the center value should be 10/27 ≈ 0.37
+    TEST1(image[Vector3i(5, 5, 5)].Value < 10.0f);
+    std::cout << "  Filter modified voxel values  OK\n";
+  }
+
+  ////////////////////////////////////////////////////////////////////////////
+  // TEST 4: Encoder/decoder chain — two filters linked
+  ////////////////////////////////////////////////////////////////////////////
+  {
+    std::cout << "\n--- Test 4: Encoder/decoder chain ---\n";
+
+    VoxImage<TestVoxel> image(Vector3i(10, 10, 10));
+    image[Vector3i(5, 5, 5)].Value = 100;
+
+    // First filter: linear smoothing
+    VoxFilterAlgorithmLinear<TestVoxel> filter1(Vector3i(3, 3, 3));
+    std::vector<float> weights1(27, 1.0f);
+    filter1.SetImage(&image);
+    filter1.SetKernelNumericXZY(weights1);
+
+    // Second filter: threshold
+    VoxFilterAlgorithmThreshold<TestVoxel> filter2(Vector3i(1, 1, 1));
+    filter2.SetThreshold(0.5f);
+    filter2.SetImage(&image);
+    // 1x1x1 kernel with value 1
+    std::vector<float> weights2(1, 1.0f);
+    filter2.SetKernelNumericXZY(weights2);
+
+    // Chain: filter1 → filter2
+    filter1.SetDecoder(&filter2);
+    filter2.SetEncoder(&filter1);
+
+    TEST1(filter1.GetDecoder() == &filter2);
+    TEST1(filter2.GetEncoder() == &filter1);
+    std::cout << "  Chain linked: filter1 -> filter2  OK\n";
+
+    // Execute chain manually (encoder first, then decoder)
+    filter1.Process(&image);
+    float smoothed_center = image[Vector3i(5, 5, 5)].Value;
+    std::cout << "  After linear: center = " << smoothed_center << "\n";
+
+    filter2.Process(&image);
+    float thresholded_center = image[Vector3i(5, 5, 5)].Value;
+    std::cout << "  After threshold: center = " << thresholded_center << "\n";
+
+    // After threshold, values should be 0 or 1
+    TEST1(thresholded_center == 0.0f || thresholded_center == 1.0f);
+    std::cout << "  Chain execution produced valid results  OK\n";
+  }
+
+  ////////////////////////////////////////////////////////////////////////////
+  // TEST 5: CUDA chain — VRAM data through chained filters
+  ////////////////////////////////////////////////////////////////////////////
+  {
+    std::cout << "\n--- Test 5: VRAM data through chained filters ---\n";
+
+    VoxImage<TestVoxel> image(Vector3i(10, 10, 10));
+    image[Vector3i(5, 5, 5)].Value = 50;
+
+    VoxFilterAlgorithmLinear<TestVoxel> filter1(Vector3i(3, 3, 3));
+    std::vector<float> weights1(27, 1.0f);
+    filter1.SetImage(&image);
+    filter1.SetKernelNumericXZY(weights1);
+
+    VoxFilterAlgorithmAbtrim<TestVoxel> filter2(Vector3i(3, 3, 3));
+    std::vector<float> weights2(27, 1.0f);
+    filter2.SetImage(&image);
+    filter2.SetKernelNumericXZY(weights2);
+    filter2.SetABTrim(1, 1);
+
+    // Chain
+    filter1.SetDecoder(&filter2);
+    filter2.SetEncoder(&filter1);
+
+    // Move data to VRAM
+    image.Data().MoveToVRAM();
+    filter1.GetKernelData().Data().MoveToVRAM();
+    filter2.GetKernelData().Data().MoveToVRAM();
+
+    // Both filters should report VRAM preference
+    TEST1(filter1.GetPreferredDevice() == MemoryDevice::VRAM);
+    TEST1(filter2.GetPreferredDevice() == MemoryDevice::VRAM);
+    TEST1(filter1.IsGPU());
+    TEST1(filter2.IsGPU());
+    std::cout << "  Both filters detect VRAM preference  OK\n";
+
+    // Verify the chain's device consistency
+    auto* encoder = filter2.GetEncoder();
+    TEST1(encoder != nullptr);
+    TEST1(encoder->IsGPU());
+    std::cout << "  Encoder in chain also reports GPU  OK\n";
+
+#ifdef USE_CUDA
+    // With CUDA: filters execute on GPU via Process()
+    image.Data().MoveToRAM(); // reset for clean test
+    image[Vector3i(5, 5, 5)].Value = 50;
+    image.Data().MoveToVRAM();
+
+    filter1.Process(&image);
+    TEST1(image.Data().GetDevice() == MemoryDevice::VRAM);
+    std::cout << "  CUDA: data stays in VRAM after filter1  OK\n";
+
+    filter2.Process(&image);
+    TEST1(image.Data().GetDevice() == MemoryDevice::VRAM);
+    std::cout << "  CUDA: data stays in VRAM after filter2  OK\n";
+#else
+    // Without CUDA: verify Process still works via CPU fallback
+    image.Data().MoveToRAM();
+    image[Vector3i(5, 5, 5)].Value = 50;
+
+    filter1.GetKernelData().Data().MoveToRAM();
+    filter2.GetKernelData().Data().MoveToRAM();
+
+    filter1.Process(&image);
+    filter2.Process(&image);
+    std::cout << "  No CUDA: CPU fallback executed correctly  OK\n";
+#endif
+  }
+
+  ////////////////////////////////////////////////////////////////////////////
+  // TEST 6: AlgorithmTask with VRAM-aware filter
+  ////////////////////////////////////////////////////////////////////////////
+  {
+    std::cout << "\n--- Test 6: AlgorithmTask with VRAM-aware filter ---\n";
+
+    VoxImage<TestVoxel> image(Vector3i(8, 8, 8));
+    image[Vector3i(4, 4, 4)].Value = 20;
+
+    VoxFilterAlgorithmLinear<TestVoxel> filter(Vector3i(3, 3, 3));
+    std::vector<float> weights(27, 1.0f);
+    filter.SetImage(&image);
+    filter.SetKernelNumericXZY(weights);
+
+    // Set up task
+    AlgorithmTask<VoxImage<TestVoxel>*, VoxImage<TestVoxel>*> task;
+    task.SetAlgorithm(&filter);
+    task.SetMode(AlgorithmTask<VoxImage<TestVoxel>*, VoxImage<TestVoxel>*>::Cyclic);
+    task.SetCycleTime(50);
+
+    // Run task for a few cycles
+    task.Run(&image);
+    std::this_thread::sleep_for(std::chrono::milliseconds(200));
+    task.Stop();
+
+    // After cyclic execution, the filter should have smoothed values
+    TEST1(image[Vector3i(4, 4, 4)].Value < 20.0f);
+    std::cout << "  Task cyclic execution modified image  OK\n";
+    std::cout << "  Center value after smoothing: "
+              << image[Vector3i(4, 4, 4)].Value << "\n";
+  }
+
+  ////////////////////////////////////////////////////////////////////////////
+  // TEST 7: AlgorithmTask async with chained filters
+  ////////////////////////////////////////////////////////////////////////////
+  {
+    std::cout << "\n--- Test 7: AlgorithmTask async with filter ---\n";
+
+    VoxImage<TestVoxel> image(Vector3i(8, 8, 8));
+    image[Vector3i(4, 4, 4)].Value = 30;
+
+    VoxFilterAlgorithmLinear<TestVoxel> filter(Vector3i(3, 3, 3));
+    std::vector<float> weights(27, 1.0f);
+    filter.SetImage(&image);
+    filter.SetKernelNumericXZY(weights);
+
+    AlgorithmTask<VoxImage<TestVoxel>*, VoxImage<TestVoxel>*> task;
+    task.SetAlgorithm(&filter);
+    task.SetMode(AlgorithmTask<VoxImage<TestVoxel>*, VoxImage<TestVoxel>*>::Async);
+
+    float before = image[Vector3i(4, 4, 4)].Value;
+
+    task.Run(&image);
+
+    // Trigger one execution
+    task.Notify();
+    std::this_thread::sleep_for(std::chrono::milliseconds(100));
+
+    task.Stop();
+
+    float after = image[Vector3i(4, 4, 4)].Value;
+    TEST1(after < before);
+    std::cout << "  Async trigger: value " << before << " -> " << after << "  OK\n";
+  }
+
+  ////////////////////////////////////////////////////////////////////////////
+  // TEST 8: Device preference propagation in chain
+  ////////////////////////////////////////////////////////////////////////////
+  {
+    std::cout << "\n--- Test 8: Device preference propagation check ---\n";
+
+    VoxImage<TestVoxel> image(Vector3i(8, 8, 8));
+    image[Vector3i(4, 4, 4)].Value = 10;
+
+    VoxFilterAlgorithmLinear<TestVoxel> filterA(Vector3i(3, 3, 3));
+    VoxFilterAlgorithmAbtrim<TestVoxel> filterB(Vector3i(3, 3, 3));
+    VoxFilterAlgorithmThreshold<TestVoxel> filterC(Vector3i(1, 1, 1));
+
+    std::vector<float> w27(27, 1.0f);
+    std::vector<float> w1(1, 1.0f);
+
+    filterA.SetImage(&image);
+    filterA.SetKernelNumericXZY(w27);
+    filterB.SetImage(&image);
+    filterB.SetKernelNumericXZY(w27);
+    filterB.SetABTrim(1, 1);
+    filterC.SetImage(&image);
+    filterC.SetKernelNumericXZY(w1);
+    filterC.SetThreshold(0.1f);
+
+    // Chain: A → B → C
+    filterA.SetDecoder(&filterB);
+    filterB.SetEncoder(&filterA);
+    filterB.SetDecoder(&filterC);
+    filterC.SetEncoder(&filterB);
+
+    // All on RAM
+    TEST1(!filterA.IsGPU());
+    TEST1(!filterB.IsGPU());
+    TEST1(!filterC.IsGPU());
+    std::cout << "  All filters on RAM  OK\n";
+
+    // Move image to VRAM — filters A and B should detect it
+    image.Data().MoveToVRAM();
+    TEST1(filterA.IsGPU());
+    TEST1(filterB.IsGPU());
+    // filterC with 1x1x1 kernel doesn't have CUDA override, but still detects VRAM
+    TEST1(filterC.IsGPU());
+    std::cout << "  Image on VRAM: all filters report GPU  OK\n";
+
+    // Can walk the chain and check device consistency
+    auto* step = static_cast<Algorithm<VoxImage<TestVoxel>*, VoxImage<TestVoxel>*>*>(&filterA);
+    bool all_gpu = true;
+    while (step) {
+      if (!step->IsGPU()) all_gpu = false;
+      step = static_cast<Algorithm<VoxImage<TestVoxel>*, VoxImage<TestVoxel>*>*>(step->GetDecoder());
+    }
+    TEST1(all_gpu);
+    std::cout << "  Chain walk: all steps report GPU  OK\n";
+
+    image.Data().MoveToRAM();
+  }
+
+  ////////////////////////////////////////////////////////////////////////////
+  // TEST 9: Process through chain with Algorithm interface
+  ////////////////////////////////////////////////////////////////////////////
+  {
+    std::cout << "\n--- Test 9: Sequential chain processing via Algorithm interface ---\n";
+
+    VoxImage<TestVoxel> image(Vector3i(10, 10, 10));
+    // Set a pattern: single bright voxel
+    image[Vector3i(5, 5, 5)].Value = 100;
+
+    VoxFilterAlgorithmLinear<TestVoxel> filterA(Vector3i(3, 3, 3));
+    std::vector<float> w(27, 1.0f);
+    filterA.SetImage(&image);
+    filterA.SetKernelNumericXZY(w);
+
+    VoxFilterAlgorithmLinear<TestVoxel> filterB(Vector3i(3, 3, 3));
+    filterB.SetImage(&image);
+    filterB.SetKernelNumericXZY(w);
+
+    // Chain
+    filterA.SetDecoder(&filterB);
+    filterB.SetEncoder(&filterA);
+
+    // Process chain through base pointer
+    using AlgType = Algorithm<VoxImage<TestVoxel>*, VoxImage<TestVoxel>*>;
+    AlgType* chain = &filterA;
+
+    // Walk and process
+    AlgType* current = chain;
+    while (current) {
+      current->Process(&image);
+      current = static_cast<AlgType*>(current->GetDecoder());
+    }
+
+    // After two rounds of smoothing, the peak should be smaller than original
+    float final_val = image[Vector3i(5, 5, 5)].Value;
+    TEST1(final_val < 100.0f);
+    std::cout << "  Two-stage smoothing: peak = " << final_val << "  OK\n";
+  }
+
+  END_TESTING;
+}

src/Math/testing/CMakeLists.txt

@@ -16,6 +16,7 @@ set(TESTS
         QuadMeshTest
         BitCodeTest
         UnitsTest
+        AlgorithmCudaChainTest
 )
 
 set(LIBRARIES
@@ -28,6 +29,6 @@ set(LIBRARIES
 uLib_add_tests(Math)
 
 if(USE_CUDA)
-    set_source_files_properties(VoxImageTest.cpp VoxImageCopyTest.cpp VoxImageFilterTest.cpp VoxRaytracerTest.cpp VoxRaytracerTestExtended.cpp PROPERTIES LANGUAGE CUDA)
+    set_source_files_properties(VoxImageTest.cpp VoxImageCopyTest.cpp VoxImageFilterTest.cpp VoxRaytracerTest.cpp VoxRaytracerTestExtended.cpp AlgorithmCudaChainTest.cpp PROPERTIES LANGUAGE CUDA)
     set_source_files_properties(VoxRaytracerTest.cpp VoxRaytracerTestExtended.cpp PROPERTIES CXX_STANDARD 17 CUDA_STANDARD 17)
 endif()

src/Math/testing/CylinderTest.cpp

@@ -52,7 +52,7 @@ int main()
 
   // Test 1: Basic identity transformation and cylinder parameters
   {
-    Cylinder cyl(2.0, 10.0);
+    Cylinder cyl(2.0, 10.0, 2);
     std::cout << "Cyl R=" << cyl.GetRadius() << " H=" << cyl.GetHeight() << std::endl;
     std::cout << "Cyl World Matrix:\n" << cyl.GetWorldMatrix() << std::endl;
 
@@ -82,7 +82,7 @@ int main()
 
   // Test 2: Translation
   {
-    Cylinder cyl(1.0, 2.0);
+    Cylinder cyl(1.0, 2.0, 2);
     cyl.SetPosition(Vector3f(10, 20, 30));
     
     // Local base origin (0, 0, 0) -> World (10, 20, 30)
@@ -96,7 +96,7 @@ int main()
 
   // Test 3: Rotation and complex mapping
   {
-    Cylinder cyl(5.0, 20.0);
+    Cylinder cyl(5.0, 20.0, 2);
     cyl.SetPosition(Vector3f(1.0, 2.0, 3.0));
     // Rotate 90 degrees around X: Local Y becomes World Z, Local Z becomes World -Y
     cyl.Rotate(M_PI/2.0, Vector3f(1, 0, 0));

src/Python/math_bindings.cpp

@@ -432,9 +432,9 @@ void init_math(py::module_ &m) {
       .def("AddPoint", &TriangleMesh::AddPoint)
       .def("AddTriangle",
            py::overload_cast<const Vector3i &>(&TriangleMesh::AddTriangle))
-      .def("Points", &TriangleMesh::Points,
+      .def("Points", py::overload_cast<>(&TriangleMesh::Points),
            py::return_value_policy::reference_internal)
-      .def("Triangles", &TriangleMesh::Triangles,
+      .def("Triangles", py::overload_cast<>(&TriangleMesh::Triangles),
            py::return_value_policy::reference_internal)
       .def("GetTriangle", &TriangleMesh::GetTriangle)
       .def("GetNormal", &TriangleMesh::GetNormal);
@@ -444,9 +444,9 @@ void init_math(py::module_ &m) {
       .def("AddPoint", &QuadMesh::AddPoint)
       .def("AddQuad",
            py::overload_cast<const Vector4i &>(&QuadMesh::AddQuad))
-      .def("Points", &QuadMesh::Points,
+      .def("Points", py::overload_cast<>(&QuadMesh::Points),
            py::return_value_policy::reference_internal)
-      .def("Quads", &QuadMesh::Quads,
+      .def("Quads", py::overload_cast<>(&QuadMesh::Quads),
            py::return_value_policy::reference_internal)
       .def("GetQuad", &QuadMesh::GetQuad)
       .def("GetNormal", &QuadMesh::GetNormal);

src/Root/QCanvas.cpp

@@ -1,6 +1,7 @@
 #include "QCanvas.h"
 #include <iostream>
 #include <cstdio>
+#include <cstdlib>
 
 
 
@@ -40,8 +41,14 @@ QCanvas::QCanvas(QWidget *parent) : QWidget(parent), m_canvas(nullptr) {
     if (!gApplication) {
         static int argc = 1;
         static char* argv[] = {(char*)"App", nullptr};
+        if (std::getenv("CTEST_PROJECT_NAME")) {
+            static int bargc = 2;
+            static char* bargv[] = {(char*)"App", (char*)"-b", nullptr};
+            new TApplication("App", &bargc, bargv);
+        } else {
             new TApplication("App", &argc, argv);
         }
+    }
     
     // Create the TCanvas associated with this QWidget
     m_canvas = nullptr;

src/Root/testing/QCanvasTest.cpp

@@ -6,6 +6,7 @@
 #include <TCanvas.h>
 #include <TRandom.h>
 #include <TEnv.h>
+#include <cstdlib>
 #include "Root/QCanvas.h"
 
 int main(int argc, char **argv) {
@@ -37,10 +38,11 @@ int main(int argc, char **argv) {
     } else {
         std::cerr << "FAIL: Canvas is still NULL after show() and processEvents()" << std::endl;
     }
-
+    if (std::getenv("CTEST_PROJECT_NAME")) {
+        return 0;
+    }
     return app.exec();
 }
 #else
 int main() { return 0; }
 #endif
-

src/Vtk/CMakeLists.txt

@@ -1,6 +1,5 @@
 set(HEADERS uLibVtkInterface.h
             uLibVtkViewer.h
-            vtkContainerBox.h
             vtkHandlerWidget.h
             vtkQViewport.h
             vtkViewport.h
@@ -10,7 +9,6 @@ set(HEADERS uLibVtkInterface.h
 
 set(SOURCES uLibVtkInterface.cxx
             uLibVtkViewer.cpp
-            vtkContainerBox.cpp
             vtkHandlerWidget.cpp
             vtkQViewport.cpp
             vtkViewport.cpp

src/Vtk/HEP/Detectors/vtkDetectorChamber.h

@@ -34,7 +34,7 @@
 #include "HEP/Detectors/DetectorChamber.h"
 #include "Math/Dense.h"
 #include "Vtk/uLibVtkInterface.h"
-#include "Vtk/vtkContainerBox.h"
+#include "Vtk/Math/vtkContainerBox.h"
 #include <vtkActor.h>
 #include <vtkBoxWidget.h>
 #include <vtkTransformPolyDataFilter.h>

src/Vtk/HEP/Geant/CMakeLists.txt

@@ -5,11 +5,19 @@
 
 set(HEP_GEANT_SOURCES
     ${CMAKE_CURRENT_SOURCE_DIR}/vtkGeantEvent.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/vtkGeantSolid.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/vtkBoxSolid.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/vtkTessellatedSolid.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/vtkGeantScene.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/vtkEmitterPrimary.cpp
     PARENT_SCOPE)
 
 set(HEP_GEANT_HEADERS
     ${CMAKE_CURRENT_SOURCE_DIR}/vtkGeantEvent.h
+    ${CMAKE_CURRENT_SOURCE_DIR}/vtkGeantSolid.h
+    ${CMAKE_CURRENT_SOURCE_DIR}/vtkBoxSolid.h
+    ${CMAKE_CURRENT_SOURCE_DIR}/vtkTessellatedSolid.h
+    ${CMAKE_CURRENT_SOURCE_DIR}/vtkGeantScene.h
     ${CMAKE_CURRENT_SOURCE_DIR}/vtkEmitterPrimary.h
     PARENT_SCOPE)
 

src/Vtk/HEP/Geant/testing/CMakeLists.txt

@@ -1,6 +1,8 @@
 # TESTS
 set(TESTS
        vtkGeantEventTest
+       vtkGeantSceneTest
+       vtkSolidsTest
        vtkEmitterPrimaryTest
        vtkSkyPlaneEmitterPrimaryTest
        vtkCylinderEmitterPrimaryTest

src/Vtk/HEP/Geant/testing/vtkCylinderEmitterPrimaryTest.cpp

@@ -19,7 +19,7 @@
 #include "Vtk/uLibVtkViewer.h"
 #include "Vtk/HEP/Geant/vtkGeantEvent.h"
 #include "Vtk/HEP/Geant/vtkEmitterPrimary.h"
-#include "Vtk/vtkContainerBox.h"
+#include "Vtk/Math/vtkContainerBox.h"
 
 #include <vtkSmartPointer.h>
 #include <vtkCallbackCommand.h>

src/Vtk/HEP/Geant/testing/vtkEmitterPrimaryTest.cpp

@@ -8,7 +8,7 @@
 #include "Vtk/uLibVtkViewer.h"
 #include "Vtk/HEP/Geant/vtkGeantEvent.h"
 #include "Vtk/HEP/Geant/vtkEmitterPrimary.h"
-#include "Vtk/vtkContainerBox.h"
+#include "Vtk/Math/vtkContainerBox.h"
 #include "HEP/Detectors/DetectorChamber.h"
 #include "Vtk/HEP/Detectors/vtkDetectorChamber.h"
 

src/Vtk/HEP/Geant/testing/vtkGeantEventTest.cpp

@@ -18,7 +18,7 @@
 #include "Math/Units.h"
 #include "Vtk/uLibVtkViewer.h"
 #include "Vtk/HEP/Geant/vtkGeantEvent.h"
-#include "Vtk/vtkContainerBox.h"
+#include "Vtk/Math/vtkContainerBox.h"
 
 #include <vtkSmartPointer.h>
 #include <vtkCallbackCommand.h>

src/Vtk/HEP/Geant/testing/vtkGeantSceneTest.cpp

@@ -0,0 +1,65 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// 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 >
+
+//////////////////////////////////////////////////////////////////////////////*/
+
+#include "Geant/Solid.h"
+#include "HEP/Geant/Scene.h"
+#include "Math/ContainerBox.h"
+#include "Math/Dense.h"
+#include "Math/Units.h"
+#include "Vtk/uLibVtkViewer.h"
+#include "Vtk/HEP/Geant/vtkGeantScene.h"
+
+#include <vtkSmartPointer.h>
+#include <vtkRenderer.h>
+#include <vtkRenderWindow.h>
+
+#include <iostream>
+
+using namespace uLib;
+
+int main(int argc, char** argv) {
+    bool interactive = (argc > 1 && std::string(argv[1]) == "-i");
+
+    // 1. Setup Geant4 Scene
+    Geant::Scene scene;
+    scene.ConstructWorldBox(Vector3f(30_m, 30_m, 30_m), "G4_AIR");
+
+    // Add an iron cube inside the world
+    ContainerBox iron_box;
+    iron_box.Scale(Vector3f(10_m, 10_m, 10_m));
+    iron_box.SetPosition(Vector3f(-5_m, -5_m, -5_m));
+    Geant::BoxSolid* iron_cube = new Geant::BoxSolid("IronCube", &iron_box);
+    iron_cube->SetNistMaterial("G4_Fe");
+    iron_cube->Update();
+    scene.AddSolid(iron_cube);
+    scene.Initialize();
+
+    // 2. Build VTK scene representation
+    Vtk::Viewer viewer;
+    viewer.GetRenderer()->SetBackground(0.05, 0.05, 0.1);
+
+    Vtk::vtkGeantScene vtkScene(&scene);
+    vtkScene.AddToViewer(viewer);
+
+    std::cout << "==================================================" << std::endl;
+    std::cout << " vtkGeantScene Test" << std::endl;
+    std::cout << " World box + 1 iron cube displayed" << std::endl;
+    std::cout << "==================================================" << std::endl;
+
+    if (interactive) {
+        viewer.ZoomAuto();
+        viewer.Start();
+    } else {
+        std::cout << "Non-interactive test: scene initialized successfully" << std::endl;
+    }
+
+    return 0;
+}

src/Vtk/HEP/Geant/testing/vtkSkyPlaneEmitterPrimaryTest.cpp

@@ -8,7 +8,7 @@
 #include "Vtk/uLibVtkViewer.h"
 #include "Vtk/HEP/Geant/vtkGeantEvent.h"
 #include "Vtk/HEP/Geant/vtkEmitterPrimary.h"
-#include "Vtk/vtkContainerBox.h"
+#include "Vtk/Math/vtkContainerBox.h"
 #include "HEP/Detectors/DetectorChamber.h"
 #include "Vtk/HEP/Detectors/vtkDetectorChamber.h"
 

src/Vtk/HEP/Geant/testing/vtkSolidsTest.cpp

@@ -0,0 +1,84 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// 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 >
+
+//////////////////////////////////////////////////////////////////////////////*/
+
+#include "Vtk/HEP/Geant/vtkBoxSolid.h"
+#include "Vtk/HEP/Geant/vtkTessellatedSolid.h"
+#include "Vtk/uLibVtkViewer.h"
+#include "HEP/Geant/Solid.h"
+#include "Math/ContainerBox.h"
+#include "Math/TriangleMesh.h"
+#include "Math/Units.h"
+
+#include <vtkProperty.h>
+#include <vtkActor.h>
+
+using namespace uLib;
+
+int main(int argc, char** argv) {
+    bool interactive = (argc > 1 && std::string(argv[1]) == "-i");
+
+    // 1. Create a BoxSolid
+    ContainerBox box;
+    box.Scale(Vector3f(1_m, 2_m, 3_m));
+    Geant::BoxSolid gBox("MyBox", &box);
+    gBox.Update();
+
+    Vtk::vtkBoxSolid vtkBox(&gBox);
+
+    // 2. Create a TessellatedSolid
+    Geant::TessellatedSolid gTess("MyTess");
+    TriangleMesh mesh;
+    // Create a simple pyramid
+    mesh.Points().push_back(Vector3f(0, 0, 1_m));   // apex
+    mesh.Points().push_back(Vector3f(-1_m, -1_m, 0));
+    mesh.Points().push_back(Vector3f( 1_m, -1_m, 0));
+    mesh.Points().push_back(Vector3f( 1_m,  1_m, 0));
+    mesh.Points().push_back(Vector3f(-1_m,  1_m, 0));
+    
+    mesh.Triangles().push_back(Vector3i(1, 2, 0));
+    mesh.Triangles().push_back(Vector3i(2, 3, 0));
+    mesh.Triangles().push_back(Vector3i(3, 4, 0));
+    mesh.Triangles().push_back(Vector3i(4, 1, 0));
+    mesh.Triangles().push_back(Vector3i(1, 3, 2)); // base
+    mesh.Triangles().push_back(Vector3i(1, 4, 3)); // base
+    
+    gTess.SetMesh(mesh);
+    gTess.Update();
+
+    Vtk::vtkTessellatedSolid vtkTess(&gTess);
+
+    // 3. Visualization setup
+    Vtk::Viewer viewer;
+    vtkBox.AddToViewer(viewer);
+    vtkTess.AddToViewer(viewer);
+
+    // Color them differently
+    vtkActor::SafeDownCast(vtkBox.GetProp())->GetProperty()->SetColor(0.8, 0.2, 0.2); // Redish box
+    vtkActor::SafeDownCast(vtkTess.GetProp())->GetProperty()->SetColor(0.2, 0.8, 0.2); // Greenish tess
+    
+    // Position tessellated solid away from box
+    Matrix4f trans = Matrix4f::Identity();
+    trans.block<3,1>(0,3) = Vector3f(5_m, 0, 0);
+    gTess.SetTransform(trans);
+    vtkTess.Update();
+
+    std::cout << "..:: Testing vtkSolidsTest ::.." << std::endl;
+    std::cout << "Box and Tessellated solids initialized." << std::endl;
+
+    if (interactive) {
+        viewer.ZoomAuto();
+        viewer.Start();
+    } else {
+        std::cout << "Non-interactive test passed." << std::endl;
+    }
+
+    return 0;
+}

src/Vtk/HEP/Geant/vtkBoxSolid.cpp

@@ -0,0 +1,57 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// CMT Cosmic Muon Tomography project //////////////////////////////////////////
+////////////////////////////////////////////////////////////////////////////////
+
+  Copyright (c) 2014, Universita' degli Studi Padova, INFN sez. di Padova
+  All rights reserved
+
+  Authors: Andrea Rigoni Garola < andrea.rigoni@pd.infn.it >
+
+//////////////////////////////////////////////////////////////////////////////*/
+
+#include "vtkBoxSolid.h"
+#include <vtkCubeSource.h>
+#include <vtkPolyDataMapper.h>
+#include <vtkActor.h>
+
+namespace uLib {
+namespace Vtk {
+
+vtkBoxSolid::vtkBoxSolid(Geant::BoxSolid *content)
+    : vtkGeantSolid(content), m_BoxContent(content) {
+  // Re-run Update for box-specific pipe
+  this->Update();
+}
+
+vtkBoxSolid::~vtkBoxSolid() {}
+
+void vtkBoxSolid::Update() {
+  this->UpdateGeometry();
+  this->UpdateTransform();
+}
+
+void vtkBoxSolid::UpdateGeometry() {
+  if (!m_BoxContent || !m_BoxContent->GetObject()) {
+    // Fallback to base tessellation if no model object
+    vtkGeantSolid::UpdateGeometry();
+    return;
+  }
+
+  // Use the underlying ContainerBox for precise geometry
+  Vector3f size = m_BoxContent->GetObject()->GetSize();
+  
+  vtkNew<vtkCubeSource> cube;
+  cube->SetXLength(size(0));
+  cube->SetYLength(size(1));
+  cube->SetZLength(size(2));
+  cube->Update();
+
+  vtkPolyData *poly = GetPolyData();
+  if (poly) {
+      poly->ShallowCopy(cube->GetOutput());
+      poly->Modified();
+  }
+}
+
+} // namespace Vtk
+} // namespace uLib

src/Vtk/HEP/Geant/vtkBoxSolid.h

@@ -0,0 +1,52 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// CMT Cosmic Muon Tomography project //////////////////////////////////////////
+////////////////////////////////////////////////////////////////////////////////
+
+  Copyright (c) 2014, Universita' degli Studi di Padova, INFN sez. di Padova
+  All rights reserved
+
+  Authors: Andrea Rigoni Garola < andrea.rigoni@pd.infn.it >
+
+  ------------------------------------------------------------------
+  This library is free software;  you  can  redistribute  it  and/or
+  modify it  under the  terms  of  the  GNU  Lesser  General  Public
+  License as published  by  the  Free  Software  Foundation;  either
+  version 3.0 of the License, or (at your option) any later version.
+
+  This library is  distributed in  the hope that it will  be useful,
+  but  WITHOUT ANY WARRANTY;  without  even  the implied warranty of
+  MERCHANTABILITY  or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+  Lesser General Public License for more details.
+
+  You should have received a copy of  the GNU Lesser General  Public
+  License along with this library.
+
+//////////////////////////////////////////////////////////////////////////////*/
+
+#ifndef U_VTKBOXSOLID_H
+#define U_VTKBOXSOLID_H
+
+#include "vtkGeantSolid.h"
+
+namespace uLib {
+namespace Vtk {
+
+/**
+ * @brief VTK Puppet for visualizing a Geant::BoxSolid.
+ */
+class vtkBoxSolid : public vtkGeantSolid {
+public:
+  vtkBoxSolid(Geant::BoxSolid *content);
+  virtual ~vtkBoxSolid();
+
+  virtual void Update() override;
+  virtual void UpdateGeometry() override;
+
+protected:
+  Geant::BoxSolid *m_BoxContent;
+};
+
+} // namespace Vtk
+} // namespace uLib
+
+#endif // U_VTKBOXSOLID_H

src/Vtk/HEP/Geant/vtkGeantScene.cpp

@@ -0,0 +1,102 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// 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 "vtkGeantScene.h"
+#include "vtkGeantSolid.h"
+#include "vtkBoxSolid.h"
+#include "vtkTessellatedSolid.h"
+#include "Vtk/vtkViewport.h"
+
+namespace uLib {
+namespace Vtk {
+
+vtkGeantScene::vtkGeantScene(Geant::Scene *scene)
+    : m_Scene(scene), m_WorldPuppet(nullptr) {
+  if (!m_Scene)
+    return;
+
+  // 1. Create the world box wireframe puppet
+  ContainerBox *worldBox = m_Scene->GetWorldBox();
+  if (worldBox) {
+    m_WorldPuppet = new vtkContainerBox(worldBox);
+    m_WorldPuppet->SetRepresentation(Puppet::Wireframe);
+    m_WorldPuppet->ShowScaleMeasures(true);
+  }
+
+  // 2. Create puppets for each non-world solid
+  const Geant::Solid *world = m_Scene->GetWorld();
+  const Vector<Geant::Solid *> &solids = m_Scene->GetSolids();
+
+  for (Geant::Solid *solid : solids) {
+    // Skip the world volume itself — it's already shown as the wireframe box
+    if (solid == world)
+      continue;
+
+    // Only create a puppet if the solid has a valid G4VSolid
+    if (solid->GetG4Solid()) {
+      vtkGeantSolid *vtkSolid = nullptr;
+      if (auto *box = dynamic_cast<Geant::BoxSolid *>(solid)) {
+        vtkSolid = new vtkBoxSolid(box);
+      } else if (auto *tess = dynamic_cast<Geant::TessellatedSolid *>(solid)) {
+        vtkSolid = new vtkTessellatedSolid(tess);
+      } else {
+        vtkSolid = new vtkGeantSolid(solid);
+        vtkSolid->Update();
+      }
+      
+      if (vtkSolid) {
+        m_SolidPuppets.push_back(vtkSolid);
+      }
+    }
+  }
+}
+
+vtkGeantScene::~vtkGeantScene() {
+  delete m_WorldPuppet;
+  for (auto *p : m_SolidPuppets) {
+    delete p;
+  }
+}
+
+void vtkGeantScene::AddToViewer(Viewport &viewer) {
+  if (m_WorldPuppet) {
+    viewer.AddPuppet(*m_WorldPuppet);
+  }
+  for (auto *p : m_SolidPuppets) {
+    viewer.AddPuppet(*p);
+  }
+}
+
+void vtkGeantScene::RemoveFromViewer(Viewport &viewer) {
+  if (m_WorldPuppet) {
+    viewer.RemovePuppet(*m_WorldPuppet);
+  }
+  for (auto *p : m_SolidPuppets) {
+    viewer.RemovePuppet(*p);
+  }
+}
+
+} // namespace Vtk
+} // namespace uLib

src/Vtk/HEP/Geant/vtkGeantScene.h

@@ -0,0 +1,87 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// CMT Cosmic Muon Tomography project //////////////////////////////////////////
+////////////////////////////////////////////////////////////////////////////////
+
+  Copyright (c) 2014, Universita' degli Studi di Padova, INFN sez. di Padova
+  All rights reserved
+
+  Authors: Andrea Rigoni Garola < andrea.rigoni@pd.infn.it >
+
+  ------------------------------------------------------------------
+  This library is free software;  you  can  redistribute  it  and/or
+  modify it  under the  terms  of  the  GNU  Lesser  General  Public
+  License as published  by  the  Free  Software  Foundation;  either
+  version 3.0 of the License, or (at your option) any later version.
+
+  This library is  distributed in  the hope that it will  be useful,
+  but  WITHOUT ANY WARRANTY;  without  even  the implied warranty of
+  MERCHANTABILITY  or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+  Lesser General Public License for more details.
+
+  You should have received a copy of  the GNU Lesser General  Public
+  License along with this library.
+
+//////////////////////////////////////////////////////////////////////////////*/
+
+#ifndef U_VTKGEANTSCENE_H
+#define U_VTKGEANTSCENE_H
+
+#include "HEP/Geant/Scene.h"
+#include "uLibVtkInterface.h"
+#include "Vtk/Math/vtkContainerBox.h"
+
+#include <vector>
+#include <memory>
+
+namespace uLib {
+namespace Vtk {
+
+class vtkGeantSolid;
+
+/**
+ * @brief VTK Puppet representing the entire Geant::Scene.
+ *
+ * When constructed, it creates child puppets for the world box (as a
+ * vtkContainerBox wireframe) and for each non-world Solid in the scene
+ * (as vtkGeantSolid surfaces).
+ *
+ * Usage:
+ * @code
+ *   Geant::Scene scene;
+ *   scene.ConstructWorldBox(Vector3f(30_m, 30_m, 30_m), "G4_AIR");
+ *   // ... add solids ...
+ *   scene.Initialize();
+ *
+ *   Vtk::Viewer viewer;
+ *   Vtk::vtkGeantScene vtkScene(&scene);
+ *   vtkScene.AddToViewer(viewer);
+ *   viewer.Start();
+ * @endcode
+ */
+class vtkGeantScene : public Object {
+public:
+  vtkGeantScene(Geant::Scene *scene);
+  ~vtkGeantScene();
+
+  /// Add all puppets (world box + solids) to a viewer.
+  void AddToViewer(class Viewport &viewer);
+
+  /// Remove all puppets from viewport.
+  void RemoveFromViewer(class Viewport &viewer);
+
+  /// Get the world box puppet 
+  vtkContainerBox* GetWorldPuppet() const { return m_WorldPuppet; }
+
+  /// Get the solid puppets
+  const std::vector<vtkGeantSolid*>& GetSolidPuppets() const { return m_SolidPuppets; }
+
+private:
+  Geant::Scene             *m_Scene;
+  vtkContainerBox          *m_WorldPuppet;
+  std::vector<vtkGeantSolid*> m_SolidPuppets;
+};
+
+} // namespace Vtk
+} // namespace uLib
+
+#endif // U_VTKGEANTSCENE_H

src/Vtk/HEP/Geant/vtkGeantSolid.cpp

@@ -0,0 +1,165 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// 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 "vtkGeantSolid.h"
+
+#include <vtkActor.h>
+#include <vtkPolyData.h>
+#include <vtkPoints.h>
+#include <vtkCellArray.h>
+#include <vtkPolyDataMapper.h>
+#include <vtkProperty.h>
+#include <vtkSmartPointer.h>
+#include <vtkTransform.h>
+#include <vtkMatrix4x4.h>
+
+#include <Geant4/G4VSolid.hh>
+#include <Geant4/G4Polyhedron.hh>
+#include <Geant4/G4VPhysicalVolume.hh>
+
+namespace uLib {
+namespace Vtk {
+
+vtkGeantSolid::vtkGeantSolid(Content *content)
+    : m_SolidActor(vtkActor::New()), m_Content(content) {
+  this->InstallPipe();
+}
+
+vtkGeantSolid::~vtkGeantSolid() {
+  m_SolidActor->Delete();
+}
+
+vtkPolyData *vtkGeantSolid::GetPolyData() const {
+  if (!m_SolidActor || !m_SolidActor->GetMapper())
+    return NULL;
+  return vtkPolyData::SafeDownCast(m_SolidActor->GetMapper()->GetInput());
+}
+
+void vtkGeantSolid::Update() {
+  this->UpdateGeometry();
+  this->UpdateTransform();
+}
+
+void vtkGeantSolid::UpdateGeometry() {
+  if (!m_Content)
+    return;
+
+  G4VSolid *g4solid = m_Content->GetG4Solid();
+  if (!g4solid)
+    return;
+
+  // Get the polyhedron tessellation from Geant4
+  G4Polyhedron *polyhedron = g4solid->GetPolyhedron();
+  if (!polyhedron)
+    return;
+
+  vtkSmartPointer<vtkPoints> points = vtkSmartPointer<vtkPoints>::New();
+  vtkSmartPointer<vtkCellArray> polys = vtkSmartPointer<vtkCellArray>::New();
+
+  // Extract vertices
+  int nVertices = polyhedron->GetNoVertices();
+  for (int i = 1; i <= nVertices; ++i) {
+    G4Point3D vtx = polyhedron->GetVertex(i);
+    points->InsertNextPoint(vtx.x(), vtx.y(), vtx.z());
+  }
+
+  // Extract facets (polygons)
+  int nFacets = polyhedron->GetNoFacets();
+  for (int f = 1; f <= nFacets; ++f) {
+    G4int nEdges;
+    G4int iVertex[4]; // G4Polyhedron facets have at most 4 vertices
+    // GetNextFacet returns edges; for quads nEdges=4, for triangles nEdges=3
+    polyhedron->GetFacet(f, nEdges, iVertex);
+
+    vtkIdType ids[4];
+    for (int e = 0; e < nEdges; ++e) {
+      // G4Polyhedron vertices are 1-indexed; VTK expects 0-indexed
+      ids[e] = static_cast<vtkIdType>(std::abs(iVertex[e]) - 1);
+    }
+    polys->InsertNextCell(nEdges, ids);
+  }
+
+  vtkPolyData *polyData = GetPolyData();
+  if (polyData) {
+    polyData->SetPoints(points);
+    polyData->SetPolys(polys);
+    polyData->Modified();
+  }
+}
+
+void vtkGeantSolid::UpdateTransform() {
+  if (!m_Content || !m_SolidActor)
+    return;
+
+  // Apply the Geant4 transform (position/rotation) if placed
+  if (m_Content->GetPhysical()) {
+    auto *phys = m_Content->GetPhysical();
+    G4ThreeVector pos = phys->GetTranslation();
+    const G4RotationMatrix *rot = phys->GetRotation();
+
+    vtkSmartPointer<vtkTransform> transform = vtkSmartPointer<vtkTransform>::New();
+    transform->Identity();
+    transform->Translate(pos.x(), pos.y(), pos.z());
+
+    if (rot) {
+      // G4RotationMatrix stores the inverse of the rotation for placement
+      G4RotationMatrix invRot = rot->inverse();
+      double elements[16] = {
+        invRot.xx(), invRot.xy(), invRot.xz(), 0,
+        invRot.yx(), invRot.yy(), invRot.yz(), 0,
+        invRot.zx(), invRot.zy(), invRot.zz(), 0,
+        0, 0, 0, 1
+      };
+      vtkSmartPointer<vtkMatrix4x4> mat = vtkSmartPointer<vtkMatrix4x4>::New();
+      mat->DeepCopy(elements);
+      transform->Concatenate(mat);
+    }
+
+    m_SolidActor->SetUserTransform(transform);
+  }
+}
+
+void vtkGeantSolid::InstallPipe() {
+  vtkSmartPointer<vtkPolyData> polyData = vtkSmartPointer<vtkPolyData>::New();
+  vtkSmartPointer<vtkPolyDataMapper> mapper =
+      vtkSmartPointer<vtkPolyDataMapper>::New();
+  mapper->SetInputData(polyData);
+
+  m_SolidActor->SetMapper(mapper);
+
+  // Default look: semi-transparent blue surface
+  m_SolidActor->GetProperty()->SetColor(0.4, 0.6, 0.9);
+  m_SolidActor->GetProperty()->SetOpacity(0.3);
+  m_SolidActor->GetProperty()->SetAmbient(0.5);
+  m_SolidActor->GetProperty()->SetDiffuse(0.6);
+  m_SolidActor->GetProperty()->SetSpecular(0.2);
+  m_SolidActor->GetProperty()->SetEdgeVisibility(1);
+  m_SolidActor->GetProperty()->SetEdgeColor(0.2, 0.3, 0.5);
+
+  this->SetProp(m_SolidActor);
+}
+
+} // namespace Vtk
+} // namespace uLib

src/Vtk/HEP/Geant/vtkGeantSolid.h

@@ -0,0 +1,69 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// CMT Cosmic Muon Tomography project //////////////////////////////////////////
+////////////////////////////////////////////////////////////////////////////////
+
+  Copyright (c) 2014, Universita' degli Studi di Padova, INFN sez. di Padova
+  All rights reserved
+
+  Authors: Andrea Rigoni Garola < andrea.rigoni@pd.infn.it >
+
+  ------------------------------------------------------------------
+  This library is free software;  you  can  redistribute  it  and/or
+  modify it  under the  terms  of  the  GNU  Lesser  General  Public
+  License as published  by  the  Free  Software  Foundation;  either
+  version 3.0 of the License, or (at your option) any later version.
+
+  This library is  distributed in  the hope that it will  be useful,
+  but  WITHOUT ANY WARRANTY;  without  even  the implied warranty of
+  MERCHANTABILITY  or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+  Lesser General Public License for more details.
+
+  You should have received a copy of  the GNU Lesser General  Public
+  License along with this library.
+
+//////////////////////////////////////////////////////////////////////////////*/
+
+#ifndef U_VTKGEANTSOLID_H
+#define U_VTKGEANTSOLID_H
+
+#include "HEP/Geant/Solid.h"
+#include "uLibVtkInterface.h"
+#include "vtkPolydata.h"
+
+class vtkActor;
+
+namespace uLib {
+namespace Vtk {
+
+/**
+ * @brief VTK Puppet for visualizing a Geant::Solid.
+ *
+ * Renders the G4VSolid geometry as a tessellated polydata surface.
+ * Works with BoxSolid, TessellatedSolid, or any Solid that provides
+ * a valid G4VSolid via GetG4Solid().
+ */
+class vtkGeantSolid : public Puppet, public Polydata {
+  typedef Geant::Solid Content;
+
+public:
+  vtkGeantSolid(Content *content);
+  ~vtkGeantSolid();
+
+  virtual class vtkPolyData *GetPolyData() const override;
+
+  virtual void Update() override;
+
+  virtual void UpdateGeometry();
+  virtual void UpdateTransform();
+
+protected:
+  virtual void InstallPipe();
+
+  vtkActor *m_SolidActor;
+  Content  *m_Content;
+};
+
+} // namespace Vtk
+} // namespace uLib
+
+#endif // U_VTKGEANTSOLID_H

src/Vtk/HEP/Geant/vtkTessellatedSolid.cpp

@@ -0,0 +1,62 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// CMT Cosmic Muon Tomography project //////////////////////////////////////////
+////////////////////////////////////////////////////////////////////////////////
+
+  Copyright (c) 2014, Universita' degli Studi Padova, INFN sez. di Padova
+  All rights reserved
+
+  Authors: Andrea Rigoni Garola < andrea.rigoni@pd.infn.it >
+
+//////////////////////////////////////////////////////////////////////////////*/
+
+#include "vtkTessellatedSolid.h"
+
+#include <vtkPoints.h>
+#include <vtkCellArray.h>
+#include <vtkPolyData.h>
+
+namespace uLib {
+namespace Vtk {
+
+vtkTessellatedSolid::vtkTessellatedSolid(Geant::TessellatedSolid *content)
+    : vtkGeantSolid(content), m_TessContent(content) {
+  this->Update();
+}
+
+vtkTessellatedSolid::~vtkTessellatedSolid() {}
+
+void vtkTessellatedSolid::Update() {
+  this->UpdateGeometry();
+  this->UpdateTransform();
+}
+
+void vtkTessellatedSolid::UpdateGeometry() {
+  if (!m_TessContent || m_TessContent->GetMesh().Points().empty()) {
+    // Fallback to base tessellation if no model mesh
+    vtkGeantSolid::UpdateGeometry();
+    return;
+  }
+
+  const TriangleMesh &mesh = m_TessContent->GetMesh();
+  
+  vtkNew<vtkPoints> points;
+  for (const auto& pt : mesh.Points()) {
+    points->InsertNextPoint(pt(0), pt(1), pt(2));
+  }
+
+  vtkNew<vtkCellArray> polys;
+  for (const auto& trg : mesh.Triangles()) {
+    vtkIdType ids[3] = { (vtkIdType)trg(0), (vtkIdType)trg(1), (vtkIdType)trg(2) };
+    polys->InsertNextCell(3, ids);
+  }
+
+  vtkPolyData *poly = GetPolyData();
+  if (poly) {
+      poly->SetPoints(points);
+      poly->SetPolys(polys);
+      poly->Modified();
+  }
+}
+
+} // namespace Vtk
+} // namespace uLib

src/Vtk/HEP/Geant/vtkTessellatedSolid.h

@@ -0,0 +1,38 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// 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 >
+
+//////////////////////////////////////////////////////////////////////////////*/
+
+#ifndef U_VTKTESSELLATEDSOLID_H
+#define U_VTKTESSELLATEDSOLID_H
+
+#include "vtkGeantSolid.h"
+
+namespace uLib {
+namespace Vtk {
+
+/**
+ * @brief VTK Puppet for visualizing a Geant::TessellatedSolid.
+ */
+class vtkTessellatedSolid : public vtkGeantSolid {
+public:
+  vtkTessellatedSolid(Geant::TessellatedSolid *content);
+  virtual ~vtkTessellatedSolid();
+
+  virtual void Update() override;
+  virtual void UpdateGeometry() override;
+
+protected:
+  Geant::TessellatedSolid *m_TessContent;
+};
+
+} // namespace Vtk
+} // namespace uLib
+
+#endif // U_VTKTESSELLATEDSOLID_H

src/Vtk/Math/CMakeLists.txt

@@ -8,6 +8,9 @@ set(MATH_SOURCES
     ${CMAKE_CURRENT_SOURCE_DIR}/vtkTriangleMesh.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/vtkQuadMesh.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/vtkVoxImage.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/vtkContainerBox.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/vtkCylinder.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/vtkAssembly.cpp
     PARENT_SCOPE)
 
 set(MATH_HEADERS
@@ -16,6 +19,9 @@ set(MATH_HEADERS
     ${CMAKE_CURRENT_SOURCE_DIR}/vtkTriangleMesh.h
     ${CMAKE_CURRENT_SOURCE_DIR}/vtkQuadMesh.h
     ${CMAKE_CURRENT_SOURCE_DIR}/vtkVoxImage.h
+    ${CMAKE_CURRENT_SOURCE_DIR}/vtkContainerBox.h
+    ${CMAKE_CURRENT_SOURCE_DIR}/vtkCylinder.h
+    ${CMAKE_CURRENT_SOURCE_DIR}/vtkAssembly.h
     PARENT_SCOPE)
 
 if(BUILD_TESTING)

src/Vtk/Math/testing/CMakeLists.txt

@@ -5,7 +5,9 @@ set(TESTS
     vtkQuadMeshTest
     vtkVoxImageTest
     vtkVoxImageInteractiveTest
+    vtkContainerBoxTest
     vtkContainerBoxTest2
+    vtkAssemblyTest
 )
 
 set(LIBRARIES

src/Vtk/Math/testing/testing-prototype.h

@@ -0,0 +1,41 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// 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 <stdio.h>
+
+#include "Vtk/uLibVtkInterface.h"
+
+
+#define BEGIN_TESTING(name)                \
+static int _fail = 0;                      \
+printf("..:: Testing " #name " ::..\n");
+
+#define TEST1(val) _fail += (val)==0
+#define TEST0(val) _fail += (val)!=0
+#define END_TESTING return _fail;
+
+

src/Vtk/Math/testing/vtkAssemblyTest.cpp

@@ -0,0 +1,104 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// 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 >
+
+//////////////////////////////////////////////////////////////////////////////*/
+
+#include "Math/Assembly.h"
+#include "Math/ContainerBox.h"
+#include "Math/Cylinder.h"
+#include "Vtk/Math/vtkAssembly.h"
+#include "Vtk/vtkObjectsContext.h"
+#include "Vtk/uLibVtkViewer.h"
+#include "Math/Units.h"
+
+#include <vtkActor.h>
+#include <vtkProperty.h>
+#include <vtkPropCollection.h>
+
+#include <iostream>
+
+using namespace uLib;
+
+int main(int argc, char **argv) {
+    bool interactive = (argc > 1 && std::string(argv[1]) == "-i");
+
+    // ---- 1. Build model objects ----
+    ContainerBox box1;
+    box1.Scale(Vector3f(1_m, 2_m, 0.5_m));
+    box1.SetPosition(Vector3f(0, 0, 0));
+
+    ContainerBox box2;
+    box2.Scale(Vector3f(0.5_m, 0.5_m, 3_m));
+    box2.SetPosition(Vector3f(2_m, 0, 0));
+
+    Cylinder cyl(0.3_m, 1.5_m, 1);
+    cyl.SetPosition(Vector3f(0, 3_m, 0));
+
+    // ---- 2. Create an Assembly and add objects ----
+    Assembly assembly;
+    assembly.AddObject(&box1);
+    assembly.AddObject(&box2);
+    assembly.AddObject(&cyl);
+    assembly.SetShowBoundingBox(true);
+
+    // ---- 3. Apply a group transform ----
+    assembly.SetPosition(Vector3f(1_m, 1_m, 0));
+
+    // ---- 5. Visualize (create puppets to set properties) ----
+    Vtk::Assembly vtkAsm(&assembly);
+
+    Vtk::Viewer viewer;
+    vtkAsm.AddToViewer(viewer); // This triggers puppet creation via ConnectRenderer which eventually calls Puppet::GetProp
+    
+    // Explicitly update to ensure puppets exist and are added to assemblies
+    vtkAsm.Update();
+
+    // Use the child context to find child puppets and set colors
+    if (auto* childCtx = vtkAsm.GetChildrenContext()) {
+        auto setProps = [](Vtk::Puppet* p, float r, float g, float b) {
+            if (!p) return;
+            vtkPropCollection* props = p->GetProps();
+            props->InitTraversal();
+            for (int i=0; i < props->GetNumberOfItems(); ++i) {
+                if (auto* actor = vtkActor::SafeDownCast(props->GetNextProp())) {
+                    actor->GetProperty()->SetColor(r, g, b);
+                    actor->GetProperty()->SetRepresentationToSurface();
+                    actor->GetProperty()->SetOpacity(0.5);
+                }
+            }
+        };
+
+        setProps(childCtx->GetPuppet(&box1), 1.0, 0.0, 0.0); // Red
+        setProps(childCtx->GetPuppet(&box2), 0.0, 1.0, 0.0); // Green
+        setProps(childCtx->GetPuppet(&cyl),  0.0, 0.0, 1.0); // Blue
+    }
+
+    std::cout << "Puppets in viewport: " << viewer.getPuppets().size() << " (Expected 4: 1 assembly + 3 children)" << std::endl;
+
+    // ---- 4. Query the bounding box for terminal output ----
+    Vector3f bbMin, bbMax;
+    assembly.GetBoundingBox(bbMin, bbMax);
+    std::cout << "Assembly bounding box:" << std::endl;
+    std::cout << "  min = " << bbMin.transpose() << std::endl;
+    std::cout << "  max = " << bbMax.transpose() << std::endl;
+
+    std::cout << "==================================================\n";
+    std::cout << " vtkAssemblyTest\n";
+    std::cout << " 2 boxes + 1 cylinder grouped in an assembly\n";
+    std::cout << "==================================================" << std::endl;
+
+    if (interactive) {
+        viewer.ZoomAuto();
+        viewer.Start();
+    } else {
+        std::cout << "Non-interactive test passed." << std::endl;
+    }
+
+    return 0;
+}

src/Vtk/Math/testing/vtkContainerBoxTest.cpp

@@ -27,7 +27,7 @@
 
 #include "Math/ContainerBox.h"
 #include "Math/Units.h"
-#include "Vtk/vtkContainerBox.h"
+#include "Vtk/Math/vtkContainerBox.h"
 
 #include "testing-prototype.h"
 

src/Vtk/Math/testing/vtkContainerBoxTest2.cpp

@@ -8,7 +8,7 @@
 #include "Vtk/uLibVtkViewer.h"
 #include "Math/ContainerBox.h"
 #include "Math/Units.h"
-#include "Vtk/vtkContainerBox.h"
+#include "Vtk/Math/vtkContainerBox.h"
 #include <iostream>
 
 using namespace uLib;

src/Vtk/Math/vtkAssembly.cpp

@@ -0,0 +1,210 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// 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 >
+
+//////////////////////////////////////////////////////////////////////////////*/
+
+#include "vtkAssembly.h"       // uLib::Vtk::Assembly
+#include "Vtk/vtkObjectsContext.h"
+#include "Math/vtkDense.h"
+
+#include <vtkAssembly.h>       // VTK library ::vtkAssembly
+#include <vtkActor.h>
+#include <vtkCubeSource.h>
+#include <vtkPolyDataMapper.h>
+#include <vtkProperty.h>
+#include <vtkMatrix4x4.h>
+#include <vtkPropCollection.h>
+#include <vtkNew.h>
+#include <vtkProp3D.h>
+#include <vtkPoints.h>
+#include <vtkCellArray.h>
+#include <vtkPolyData.h>
+
+namespace uLib {
+namespace Vtk {
+
+// ------------------------------------------------------------------ //
+Assembly::Assembly(uLib::Assembly *content)
+    : m_Content(content),
+      m_ChildContext(nullptr),
+      m_BBoxActor(nullptr),
+      m_VtkAsm(nullptr),
+      m_InUpdate(false),
+      m_BlockUpdate(false) {
+    this->InstallPipe();
+    if (m_Content) {
+        Object::connect(m_Content, &uLib::Assembly::Updated,
+                        this, &Assembly::contentUpdate);
+    }
+}
+
+Assembly::~Assembly() {
+    delete m_ChildContext;
+    if (m_BBoxActor)  m_BBoxActor->Delete();
+    if (m_VtkAsm)     m_VtkAsm->Delete();
+}
+
+// ------------------------------------------------------------------ //
+void Assembly::InstallPipe() {
+    // 1. Create the VTK library assembly that groups everything
+    m_VtkAsm = ::vtkAssembly::New();
+    this->SetProp(m_VtkAsm);
+
+    // 2. Create the bounding-box wireframe actor
+    vtkNew<vtkCubeSource> cube;
+    cube->SetBounds(0, 1, 0, 1, 0, 1);
+    cube->Update();
+
+    vtkNew<vtkPolyDataMapper> mapper;
+    mapper->SetInputConnection(cube->GetOutputPort());
+
+    m_BBoxActor = vtkActor::New();
+    m_BBoxActor->SetMapper(mapper);
+    m_BBoxActor->GetProperty()->SetRepresentationToWireframe();
+    m_BBoxActor->GetProperty()->SetColor(1.0, 0.85, 0.0);   // gold wireframe
+    m_BBoxActor->GetProperty()->SetLineWidth(1.5);
+    m_BBoxActor->GetProperty()->SetOpacity(0.6);
+    m_BBoxActor->SetVisibility(m_Content ? m_Content->GetShowBoundingBox() : false);
+
+    m_VtkAsm->AddPart(m_BBoxActor);
+
+    // 3. Build a child-objects context (auto-creates puppets for each child)
+    if (m_Content) {
+        m_ChildContext = new vtkObjectsContext(m_Content);
+        // The vtkObjectsContext's own prop is already a ::vtkAssembly;
+        // nest it inside ours so everything moves together.
+        if (auto *childProp = vtkProp3D::SafeDownCast(m_ChildContext->GetProp()))
+            m_VtkAsm->AddPart(childProp);
+    }
+
+    // 4. Apply initial transform
+    this->UpdateTransform();
+    this->UpdateBoundingBox();
+}
+
+// ------------------------------------------------------------------ //
+void Assembly::contentUpdate() {
+    if (m_InUpdate) return;
+    m_InUpdate = true;
+
+    this->UpdateTransform();
+    this->UpdateBoundingBox();
+    if (m_ChildContext)
+        m_ChildContext->Update();
+
+    m_BlockUpdate = true;
+    Puppet::Update();
+    m_InUpdate = false;
+}
+
+// ------------------------------------------------------------------ //
+void Assembly::Update() {
+    if (m_InUpdate) return;
+    if (!m_Content || !m_VtkAsm) return;
+
+    if (m_BlockUpdate) {
+        m_BlockUpdate = false;
+        return;
+    }
+
+    m_InUpdate = true;
+
+    // Pull VTK transform back into the uLib model
+    vtkMatrix4x4* vmat = m_VtkAsm->GetUserMatrix();
+    if (vmat) {
+        Matrix4f transform = VtkToMatrix4f(vmat);
+        m_Content->SetMatrix(transform);
+    }
+
+    this->UpdateBoundingBox();
+    if (m_ChildContext)
+        m_ChildContext->Update();
+
+    m_Content->Updated(); // Notify change in model
+
+    m_InUpdate = false;
+}
+
+// ------------------------------------------------------------------ //
+void Assembly::UpdateTransform() {
+    if (!m_Content || !m_VtkAsm) return;
+
+    Matrix4f mat = m_Content->GetMatrix();
+    vtkNew<vtkMatrix4x4> vmat;
+    Matrix4fToVtk(mat, vmat);
+    m_VtkAsm->SetUserMatrix(vmat);
+    m_VtkAsm->Modified();
+}
+
+// ------------------------------------------------------------------ //
+void Assembly::UpdateBoundingBox() {
+    if (!m_Content || !m_BBoxActor) return;
+
+    m_BBoxActor->SetVisibility(m_Content->GetShowBoundingBox());
+
+    Vector3f bbMin, bbMax;
+    m_Content->GetBoundingBox(bbMin, bbMax);
+
+    // Avoid degenerate boxes
+    Vector3f size = bbMax - bbMin;
+    if (size.norm() < 1e-6f) return;
+
+    // Rebuild the corner segments to match the AABB
+    vtkNew<vtkPoints> points;
+    vtkNew<vtkCellArray> lines;
+
+    float bounds[2][3] = {
+        {bbMin(0), bbMin(1), bbMin(2)},
+        {bbMax(0), bbMax(1), bbMax(2)}
+    };
+
+    // Corner segment length: 10% of dimension
+    float len[3] = {
+        (bbMax(0) - bbMin(0)) * 0.1f,
+        (bbMax(1) - bbMin(1)) * 0.1f,
+        (bbMax(2) - bbMin(2)) * 0.1f
+    };
+
+    for (int i = 0; i < 8; ++i) {
+        float p[3];
+        p[0] = bounds[(i & 1) ? 1 : 0][0];
+        p[1] = bounds[(i & 2) ? 1 : 0][1];
+        p[2] = bounds[(i & 4) ? 1 : 0][2];
+
+        for (int axis = 0; axis < 3; ++axis) {
+            float p2[3] = {p[0], p[1], p[2]};
+            float delta = (i & (1 << axis)) ? -len[axis] : len[axis];
+            p2[axis] += delta;
+
+            vtkIdType id1 = points->InsertNextPoint(p);
+            vtkIdType id2 = points->InsertNextPoint(p2);
+            lines->InsertNextCell(2);
+            lines->InsertCellPoint(id1);
+            lines->InsertCellPoint(id2);
+        }
+    }
+
+    vtkNew<vtkPolyData> poly;
+    poly->SetPoints(points);
+    poly->SetLines(lines);
+
+    vtkNew<vtkPolyDataMapper> mapper;
+    mapper->SetInputData(poly);
+
+    m_BBoxActor->SetMapper(mapper);
+    m_BBoxActor->Modified();
+}
+
+// ------------------------------------------------------------------ //
+vtkObjectsContext *Assembly::GetChildrenContext() const {
+    return m_ChildContext;
+}
+
+} // namespace Vtk
+} // namespace uLib

src/Vtk/Math/vtkAssembly.h

@@ -0,0 +1,71 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// 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 >
+
+//////////////////////////////////////////////////////////////////////////////*/
+
+#ifndef U_VTK_ASSEMBLY_H
+#define U_VTK_ASSEMBLY_H
+
+#include "Math/Assembly.h"
+#include "uLibVtkInterface.h"
+
+class vtkActor;
+class vtkAssembly;  // VTK library forward declaration (must be before namespace)
+
+namespace uLib {
+namespace Vtk {
+
+class vtkObjectsContext; // forward
+
+/**
+ * @brief VTK Puppet for visualizing uLib::Assembly.
+ *
+ * Manages a VTK assembly (vtkAssembly from the VTK library) that groups
+ * all child puppets and applies the Assembly's AffineTransform. It also
+ * renders an optional bounding box wireframe computed from the Assembly's AABB.
+ *
+ * @note This class is uLib::Vtk::Assembly. It internally uses
+ *       the VTK library class vtkAssembly for grouping, but the two
+ *       are distinct.
+ */
+class Assembly : public Puppet {
+public:
+    virtual const char *GetClassName() const override { return "Vtk.Assembly"; }
+
+    Assembly(uLib::Assembly *content);
+    virtual ~Assembly();
+
+    /** @brief Updates the VTK representation from the model (model→VTK). */
+    virtual void Update() override;
+
+    virtual uLib::Object* GetContent() const override { return (uLib::Object*)m_Content; }
+
+    /** @brief Called when the model signals an update (model→VTK push). */
+    void contentUpdate();
+
+    /** @brief Returns the puppet managing child objects. */
+    vtkObjectsContext *GetChildrenContext() const;
+
+private:
+    void UpdateTransform();
+    void UpdateBoundingBox();
+    void InstallPipe();
+
+    uLib::Assembly     *m_Content;
+    vtkObjectsContext  *m_ChildContext;
+    vtkActor           *m_BBoxActor;
+    ::vtkAssembly      *m_VtkAsm; // VTK library assembly — NOT this class
+    bool                m_InUpdate;    // re-entrancy guard
+    bool                m_BlockUpdate; // block feedback from contentUpdate→Update
+};
+
+} // namespace Vtk
+} // namespace uLib
+
+#endif // U_VTK_ASSEMBLY_H

src/Vtk/Math/vtkContainerBox.cpp

@@ -47,18 +47,23 @@
 namespace uLib {
 namespace Vtk {
 
+struct ContainerBoxData {
+  vtkSmartPointer<vtkActor> m_Cube;
+  vtkSmartPointer<vtkActor> m_Axes;
+
+  ContainerBoxData() : m_Cube(vtkSmartPointer<vtkActor>::New()), m_Axes(vtkSmartPointer<vtkActor>::New()) {}
+  ~ContainerBoxData() {
+  }
+};
+
 vtkContainerBox::vtkContainerBox(vtkContainerBox::Content *content)
-    : m_Cube(vtkActor::New()), m_Axes(vtkActor::New()),
-      // m_Pivot(vtkActor::New()), 
-      m_Content(content) {
+    : d(new ContainerBoxData()), m_Content(content) {
   this->InstallPipe();
   Object::connect(m_Content, &Content::Updated, this, &vtkContainerBox::contentUpdate);
 }
 
 vtkContainerBox::~vtkContainerBox() {
-  m_Cube->Delete();
-  m_Axes->Delete();
-//   m_Pivot->Delete();
+  delete d;
 }
 
 vtkPolyData *vtkContainerBox::GetPolyData() const {
@@ -68,6 +73,7 @@ vtkPolyData *vtkContainerBox::GetPolyData() const {
 
 
 void vtkContainerBox::contentUpdate() {
+  RecursiveMutex::ScopedLock lock(this->m_UpdateMutex);
   if (!m_Content)
     return;
 
@@ -82,37 +88,45 @@ void vtkContainerBox::contentUpdate() {
     vmat = mat;
   }
 
-  m_Cube->SetUserMatrix(nullptr);
-  m_Axes->SetUserMatrix(nullptr);
+  d->m_Cube->SetUserMatrix(nullptr);
+  d->m_Axes->SetUserMatrix(nullptr);
 
   Matrix4f transform = m_Content->GetMatrix();
-  for (int i = 0; i < 4; ++i)
-    for (int j = 0; j < 4; ++j) {
-      vmat->SetElement(i, j, transform(i, j));
-    }
+  Matrix4fToVtk(transform, vmat);
 
   root->Modified();
+  m_BlockUpdate = true;
   Puppet::Update();
 }
 
 
 void vtkContainerBox::Update() {
+  RecursiveMutex::ScopedLock lock(this->m_UpdateMutex);
   if (!m_Content) return;
   
+  if (m_BlockUpdate) {
+    m_BlockUpdate = false;
+    return;
+  }
+
+  // Use Targeted Blocking: only block the feedback connection to this puppet
+  // boost::signals2::shared_connection_block block(m_Connection);
+
   vtkProp3D* assembly = vtkProp3D::SafeDownCast(this->GetProp());
   if (!assembly) return;
 
   vtkMatrix4x4* vmat = assembly->GetUserMatrix();
   if (!vmat) return;
+  
   Matrix4f transform = VtkToMatrix4f(vmat);
 
   // Update uLib model's affine transform
-  if (m_Content->GetParent()) {
-    Matrix4f localT = m_Content->GetParent()->GetWorldMatrix().inverse() * transform;
-    m_Content->SetMatrix(localT);
-  } else {
+  // if (m_Content->GetParent()) {
+  //   Matrix4f localT = m_Content->GetParent()->GetWorldMatrix().inverse() * transform;
+  //   m_Content->SetMatrix(localT);
+  // } else {
   m_Content->SetMatrix(transform);
-  }
+  // }
 
   m_Content->Updated(); // Notify change
 }
@@ -134,9 +148,9 @@ void vtkContainerBox::InstallPipe() {
   cube->SetBounds(0, 1, 0, 1, 0, 1);
   mapper->SetInputConnection(cube->GetOutputPort());
   mapper->Update();
-  m_Cube->SetMapper(mapper);
-  m_Cube->GetProperty()->SetRepresentationToWireframe();
-  m_Cube->GetProperty()->SetAmbient(0.7);
+  d->m_Cube->SetMapper(mapper);
+  d->m_Cube->GetProperty()->SetRepresentationToWireframe();
+  d->m_Cube->GetProperty()->SetAmbient(0.7);
 
   // AXES //
   vtkSmartPointer<vtkAxes> axes = vtkSmartPointer<vtkAxes>::New();
@@ -144,10 +158,10 @@ void vtkContainerBox::InstallPipe() {
   mapper = vtkSmartPointer<vtkPolyDataMapper>::New();
   mapper->SetInputConnection(axes->GetOutputPort());
   mapper->Update();
-  m_Axes->SetMapper(mapper);
-  m_Axes->GetProperty()->SetLineWidth(3);
-  m_Axes->GetProperty()->SetAmbient(0.4);
-  m_Axes->GetProperty()->SetSpecular(0);
+  d->m_Axes->SetMapper(mapper);
+  d->m_Axes->GetProperty()->SetLineWidth(3);
+  d->m_Axes->GetProperty()->SetAmbient(0.4);
+  d->m_Axes->GetProperty()->SetSpecular(0);
 
   // PIVOT //
   axes = vtkSmartPointer<vtkAxes>::New();
@@ -156,8 +170,8 @@ void vtkContainerBox::InstallPipe() {
   mapper->SetInputConnection(axes->GetOutputPort());
   mapper->Update();
   
-  this->SetProp(m_Cube);
-  this->SetProp(m_Axes);
+  this->SetProp(d->m_Cube);
+  this->SetProp(d->m_Axes);
   
   vtkProp3D* root = vtkProp3D::SafeDownCast(this->GetProp());
   if (root) {

src/Vtk/Math/vtkContainerBox.h

@@ -29,11 +29,15 @@
 #include "Math/ContainerBox.h"
 #include "uLibVtkInterface.h"
 #include "vtkPolydata.h"
-#include <vtkActor.h>
+#include <boost/signals2/connection.hpp>
+
+class vtkActor;
 
 namespace uLib {
 namespace Vtk {
 
+struct ContainerBoxData;
+
 class vtkContainerBox : public Puppet, public Polydata {
   typedef ContainerBox Content;
 
@@ -47,14 +51,14 @@ public:
 
   virtual void Update();
 
+  virtual uLib::Object* GetContent() const override { return (uLib::Object*)m_Content; }
+
 protected:
   virtual void InstallPipe();
 
-  vtkActor *m_Cube;
-  vtkActor *m_Axes;
-  // vtkActor *m_Pivot;
-
+  struct ContainerBoxData *d;
   Content                 *m_Content;
+  bool                     m_BlockUpdate = false;
 };
 
 } // namespace Vtk

src/Vtk/Math/vtkCylinder.cpp

@@ -0,0 +1,133 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// 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 "Vtk/Math/vtkCylinder.h"
+#include <vtkActor.h>
+#include <vtkAssembly.h>
+#include <vtkCylinderSource.h>
+#include <vtkMatrix4x4.h>
+#include <vtkPolyDataMapper.h>
+#include <vtkProperty.h>
+#include <vtkSmartPointer.h>
+#include <vtkTransform.h>
+#include "Math/vtkDense.h"
+
+namespace uLib {
+namespace Vtk {
+
+vtkCylinder::vtkCylinder(vtkCylinder::Content *content)
+    : m_Content(content), m_Actor(nullptr), m_VtkAsm(nullptr) {
+  this->InstallPipe();
+  Object::connect(m_Content, &Content::Updated, this, &vtkCylinder::contentUpdate);
+}
+
+vtkCylinder::~vtkCylinder() {
+  if (m_Actor) m_Actor->Delete();
+  if (m_VtkAsm) m_VtkAsm->Delete();
+}
+
+void vtkCylinder::contentUpdate() {
+  if (!m_Content)
+    return;
+
+  vtkProp3D* root = vtkProp3D::SafeDownCast(this->GetProp());
+  if (!root) return;
+
+  // 1. Placement (Position/Rotation/Model-level Scale) goes to the root prop
+  vtkMatrix4x4* vmat = root->GetUserMatrix();
+  if (!vmat) {
+    vtkNew<vtkMatrix4x4> mat;
+    root->SetUserMatrix(mat);
+    vmat = mat;
+  }
+  Matrix4f transform = m_Content->GetMatrix();
+  Matrix4fToVtk(transform, vmat);
+
+  // 2. Shape-local properties (Radius, Height, Axis alignment) go to the internal actor
+  vtkTransform* alignment = vtkTransform::SafeDownCast(m_Actor->GetUserTransform());
+  if (alignment) {
+      alignment->Identity();
+      alignment->PostMultiply();
+      
+      // Initial source is centered Y-cylinder (Radial XZ [-1,1], Height Y [-0.5, 0.5])
+      // Apply Radius and Height scaling
+      alignment->Scale(m_Content->GetRadius(), m_Content->GetHeight(), m_Content->GetRadius());
+
+      // Apply Axis alignment
+      int axis = m_Content->GetAxis();
+      if (axis == 0) alignment->RotateZ(-90); // Y -> X
+      else if (axis == 1) ;                   // Y -> Y (identity)
+      else if (axis == 2) alignment->RotateX(90);  // Y -> Z
+  }
+
+  root->Modified();
+  Puppet::Update();
+}
+
+void vtkCylinder::Update() {
+  if (!m_Content) return;
+
+  vtkProp3D* root = vtkProp3D::SafeDownCast(this->GetProp());
+  if (!root) return;
+
+  vtkMatrix4x4* vmat = root->GetUserMatrix();
+  if (!vmat) return;
+  
+  // Pull the placement matrix directly from VTK
+  Matrix4f transform = VtkToMatrix4f(vmat);
+  m_Content->SetMatrix(transform);
+
+  m_Content->Updated();
+}
+
+void vtkCylinder::InstallPipe() {
+  if (!m_Content)
+    return;
+
+  m_VtkAsm = ::vtkAssembly::New();
+  this->SetProp(m_VtkAsm);
+
+  vtkNew<vtkCylinderSource> cylinder;
+  cylinder->SetRadius(1.0);
+  cylinder->SetHeight(1.0);
+  cylinder->SetResolution(32);
+
+  m_Actor = vtkActor::New();
+  vtkNew<vtkTransform> alignment;
+  m_Actor->SetUserTransform(alignment);
+
+  vtkNew<vtkPolyDataMapper> mapper;
+  mapper->SetInputConnection(cylinder->GetOutputPort());
+  m_Actor->SetMapper(mapper);
+  m_Actor->GetProperty()->SetRepresentationToWireframe();
+  m_Actor->GetProperty()->SetAmbient(0.6);
+
+  m_VtkAsm->AddPart(m_Actor);
+
+  this->contentUpdate();
+}
+
+} // namespace Vtk
+} // namespace uLib

src/Vtk/Math/vtkCylinder.h

@@ -0,0 +1,71 @@
+/*//////////////////////////////////////////////////////////////////////////////
+// CMT Cosmic Muon Tomography project //////////////////////////////////////////
+////////////////////////////////////////////////////////////////////////////////
+
+  Copyright (c) 2014, Universita’ degli Studi di Padova, INFN sez. di Padova
+  All rights reserved
+
+  Authors: Andrea Rigoni Garola < andrea.rigoni@pd.infn.it >
+
+  ------------------------------------------------------------------
+  This library is free software;  you  can  redistribute  it  and/or
+  modify it  under the  terms  of  the  GNU  Lesser  General  Public
+  License as published  by  the  Free  Software  Foundation;  either
+  version 3.0 of the License, or (at your option) any later version.
+
+  This library is  distributed in  the hope that it will  be useful,
+  but  WITHOUT ANY WARRANTY;  without  even  the implied warranty of
+  MERCHANTABILITY  or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+  Lesser General Public License for more details.
+
+  You should have received a copy of  the GNU Lesser General  Public
+  License along with this library.
+
+//////////////////////////////////////////////////////////////////////////////*/
+
+#ifndef U_VTKCYLINDER_H
+#define U_VTKCYLINDER_H
+
+#include "Math/Cylinder.h"
+#include "Vtk/uLibVtkInterface.h"
+#include <vtkActor.h>
+class vtkAssembly;
+
+namespace uLib {
+namespace Vtk {
+
+/**
+ * @brief VTK representation of the uLib::Cylinder object.
+ *
+ * This class wraps a vtkCylinderSource and synchronizes it with the
+ * mathematical state of a Cylinder object. It manages the alignment
+ * between VTK's Y-centered cylinder and uLib's Z-based coordinate system.
+ */
+class vtkCylinder : public Puppet {
+  typedef Cylinder Content;
+
+public:
+  vtkCylinder(Content *content);
+  virtual ~vtkCylinder();
+
+  /** Synchronizes the VTK actor with the uLib model matrix */
+  virtual void contentUpdate();
+
+  /** Synchronizes the uLib model matrix with the VTK actor (e.g., after UI manipulation) */
+  virtual void Update();
+
+  virtual uLib::Object* GetContent() const override { return (uLib::Object*)m_Content; }
+
+protected:
+  /** Sets up the VTK visualization pipeline */
+  virtual void InstallPipe();
+
+  vtkActor *m_Actor;
+  ::vtkAssembly *m_VtkAsm;
+  Content *m_Content;
+};
+
+} // namespace Vtk
+} // namespace uLib
+
+#endif // U_VTKCYLINDER_H

src/Vtk/Math/vtkVoxImage.cpp

@@ -126,9 +126,11 @@ vtkVoxImage::vtkVoxImage(Content &content)
     : m_Content(content), m_Actor(vtkVolume::New()),
       m_Image(vtkImageData::New()), m_Outline(vtkCubeSource::New()),
       m_OutlineActor(vtkActor::New()),
-      m_Reader(NULL), m_Writer(NULL), writer_factor(1.E6) {
+      m_Reader(NULL), m_Writer(NULL), writer_factor(1.E6),
+      m_Window(40/1.E6), m_Level(20/1.E6), m_ShadingPreset(0) {
   GetContent();
   InstallPipe();
+  ULIB_ACTIVATE_DISPLAY_PROPERTIES;
 }
 
 vtkVoxImage::~vtkVoxImage() {
@@ -199,14 +201,15 @@ void vtkVoxImage::ReadFromXMLFile(const char *fname) {
 }
 
 void vtkVoxImage::setShadingPreset(int blendType) {
+  m_ShadingPreset = blendType;
   vtkSmartVolumeMapper *mapper = (vtkSmartVolumeMapper *)m_Actor->GetMapper();
   vtkVolumeProperty *property = m_Actor->GetProperty();
 
   static vtkColorTransferFunction *colorFun = vtkColorTransferFunction::New();
   static vtkPiecewiseFunction *opacityFun = vtkPiecewiseFunction::New();
 
-  float window = 40 / writer_factor;
-  float level = 20 / writer_factor;
+  float window = m_Window;
+  float level = m_Level;
 
   property->SetColor(colorFun);
   property->SetScalarOpacity(opacityFun);
@@ -281,13 +284,24 @@ void vtkVoxImage::SetRepresentation(Representation mode) {
     m_OutlineActor->SetVisibility(1);
   } else if (mode == Surface) {
     m_Actor->SetVisibility(1);
-    m_OutlineActor->SetVisibility(0);
+    m_OutlineActor->SetVisibility(1); // Keep outline visible as boundary
   } else {
       Puppet::SetRepresentation(mode);
   }
 }
 
+void vtkVoxImage::serialize_display(uLib::Archive::display_properties_archive & ar, const unsigned int version) {
+    // Call base class if it has display properties
+    Puppet::serialize_display(ar, version);
+    
+    // Use the member variables if they are available
+    ar & boost::serialization::make_hrp("Window", m_Window);
+    ar & boost::serialization::make_hrp("Level", m_Level);
+    ar & boost::serialization::make_hrp_enum("Shading", m_ShadingPreset, {"MIP", "Composite", "Composite Shaded", "MIP Bone", "MIP Hot", "Additive"});
+}
+
 void vtkVoxImage::Update() {
+  setShadingPreset(m_ShadingPreset);
   m_Actor->Update();
   m_Outline->SetBounds(m_Image->GetBounds());
   m_Outline->Update();

src/Vtk/Math/vtkVoxImage.h

@@ -65,7 +65,8 @@ public:
   void setShadingPreset(int blendType = 2);
   void SetRepresentation(Representation mode);
 
-  void Update();
+  void Update() override;
+  void serialize_display(uLib::Archive::display_properties_archive & ar, const unsigned int version = 0) override;
 
 protected:
   void InstallPipe();
@@ -84,6 +85,7 @@ private:
 
   float m_Window;
   float m_Level;
+  int m_ShadingPreset;
 };
 
 } // namespace Vtk

src/Vtk/testing/CMakeLists.txt

@@ -1,7 +1,6 @@
 # TESTS
 set(TESTS
         vtkViewerTest
-        vtkContainerBoxTest
         vtkHandlerWidget
         PuppetPropertyTest
         # vtkVoxImageTest