Doxygen comments ...

Core/Samples/inc/MultiLayer.h

@@ -17,7 +17,6 @@
 #define MULTILAYER_H
 
 #include <vector>
-#include "ICompositeSample.h"
 #include "Layer.h"
 #include "LayerInterface.h"
 #include "LayerRoughness.h"

Core/Samples/inc/ParticleDecoration.h

@@ -20,34 +20,40 @@
 #include "Particle.h"
 #include "ParticleInfo.h"
 #include "IInterferenceFunction.h"
-#include "Transform3D.h"
 
 //! Decorator class that adds particles to ISample objects
 
 class ParticleDecoration : public IDecoration
 {
  public:
-	ParticleDecoration();
-    ParticleDecoration(Particle *p_particle, double depth=0.0, double abundance=1.0);
-    ParticleDecoration(const Particle &p_particle, double depth=0.0, double abundance=1.0);
+    ParticleDecoration();
+    ParticleDecoration(
+        Particle *p_particle, double depth=0.0, double abundance=1.0);
+    ParticleDecoration(
+        const Particle &p_particle, double depth=0.0, double abundance=1.0);
     virtual ~ParticleDecoration();
 
-	/// Clone decoration
-	virtual ParticleDecoration *clone() const;
+    virtual ParticleDecoration *clone() const;
 
-    /// add particle giving depth and transformation
-    void addParticle(Particle *p_particle, Geometry::Transform3D *p_transform=0, double depth=0, double abundance=1.0);
-    void addParticle(const Particle &particle, const Geometry::Transform3D &transform, double depth=0, double abundance=1.0);
+    //! add particle giving depth and transformation
+    void addParticle(
+        Particle *p_particle, Geometry::Transform3D *p_transform=0,
+        double depth=0, double abundance=1.0);
+    void addParticle(
+        const Particle &particle, const Geometry::Transform3D &transform,
+        double depth=0, double abundance=1.0);
 
-    /// add particle giving depth
-    void addParticle(const Particle &particle, double depth=0.0, double abundance=1.0);
-    void addParticle(Particle *p_particle, double depth=0.0, double abundance=1.0);
+    //! add particle giving depth
+    void addParticle(
+        const Particle &particle, double depth=0.0, double abundance=1.0);
+    void addParticle(
+        Particle *p_particle, double depth=0.0, double abundance=1.0);
 
-    /// Add particle info
+    //! Add particle info
     void addParticleInfo(const ParticleInfo &info);
 
-	/// Get number of particles
-	virtual size_t getNumberOfParticles() const { return m_particles.size(); }
+    //! Get number of particles
+    virtual size_t getNumberOfParticles() const { return m_particles.size(); }
 
     /// get information about particle with index
     virtual const ParticleInfo *getParticleInfo(size_t index) const;
@@ -56,24 +62,26 @@ class ParticleDecoration : public IDecoration
     double getAbundanceFractionOfParticle(size_t index) const;
 
     //! get number of interference functions
-    virtual size_t getNumberOfInterferenceFunctions() const {
-        return m_interference_functions.size();
-    }
+    virtual size_t getNumberOfInterferenceFunctions() const
+    { return m_interference_functions.size(); }
 
     //! get interference functions
-    virtual SafePointerVector<IInterferenceFunction> getInterferenceFunctions() const {
-        return m_interference_functions;
-    }
+    virtual SafePointerVector<IInterferenceFunction>
+        getInterferenceFunctions() const
+    { return m_interference_functions; }
+
+    //! Add interference function
+    void addInterferenceFunction(
+        IInterferenceFunction* p_interference_function);
 
-    /// Add interference function
-    void addInterferenceFunction(IInterferenceFunction* p_interference_function);
-    void addInterferenceFunction(const IInterferenceFunction &interference_function);
+    void addInterferenceFunction(
+        const IInterferenceFunction &interference_function);
 
-    /// Get interference function with index
+    //! Get interference function with index
     const IInterferenceFunction* getInterferenceFunction(size_t index) const;
 
  private:
-    //! adding particle information with simultaneous registration in parent class
+    //! Add particle information with simultaneous registration in parent class.
     void addAndRegisterParticleInfo(ParticleInfo *child)
     {
         m_total_abundance += child->getAbundance();
@@ -81,7 +89,7 @@ class ParticleDecoration : public IDecoration
         registerChild(child);
     }
 
-    //! adding interference function with simultaneous registration in parent class
+    //! Add interference function with simultaneous registration in parent class
     void addAndRegisterInterferenceFunction(IInterferenceFunction *child)
     {
         m_interference_functions.push_back(child);
@@ -90,9 +98,11 @@ class ParticleDecoration : public IDecoration
 
     //TODO: replace with SafePointerVector
     std::vector<ParticleInfo *> m_particles;
-    ///< Vector of the types of particles
+
+    //! Vector of the types of particles
     SafePointerVector<IInterferenceFunction> m_interference_functions;
-    ///< Currently only a scalar interference function (instead of matrix)
+
+    //! Currently only a scalar interference function (instead of matrix)
     double m_total_abundance;
 };
 

Tests/FunctionalTests/TestCore/IsGISAXS01/IsGISAXS01.cpp

@@ -26,12 +26,14 @@ FunctionalTests::IsGISAXS01::IsGISAXS01()
 
 void FunctionalTests::IsGISAXS01::run()
 {
-    // ---------------------
-    // building sample
-    // ---------------------
+    // ------------
+    // Build sample
+    // ------------
     MultiLayer multi_layer;
-    const IMaterial *p_air_material = MaterialManager::getHomogeneousMaterial("Air", 1.0, 0.0);
-    const IMaterial *p_substrate_material = MaterialManager::getHomogeneousMaterial("Substrate", 1.0-6e-6, 2e-8);
+    const IMaterial *p_air_material =
+        MaterialManager::getHomogeneousMaterial("Air", 1., 0.);
+    const IMaterial *p_substrate_material =
+        MaterialManager::getHomogeneousMaterial("Substrate", 1-6e-6, 2e-8);
     Layer air_layer;
     air_layer.setMaterial(p_air_material);
     Layer substrate_layer;
@@ -39,8 +41,16 @@ void FunctionalTests::IsGISAXS01::run()
 
     ParticleDecoration particle_decoration;
     complex_t n_particle(1.0-6e-4, 2e-8);
-    particle_decoration.addParticle(new Particle(n_particle, new FormFactorCylinder(5*Units::nanometer, 5*Units::nanometer)), 0.0, 0.5);
-    particle_decoration.addParticle(new Particle(n_particle, new FormFactorPrism3(5*Units::nanometer, 5*Units::nanometer)), 0.0, 0.5);
+    particle_decoration.addParticle(
+        new Particle(n_particle,
+                     new FormFactorCylinder(5*Units::nanometer,
+                                            5*Units::nanometer)),
+        0.0, 0.5);
+    particle_decoration.addParticle(
+        new Particle(n_particle,
+                     new FormFactorPrism3(5*Units::nanometer,
+                                          5*Units::nanometer)),
+        0.0, 0.5);
     particle_decoration.addInterferenceFunction(new InterferenceFunctionNone());
 
     LayerDecorator air_layer_decorator(air_layer, particle_decoration);
@@ -48,22 +58,25 @@ void FunctionalTests::IsGISAXS01::run()
     multi_layer.addLayer(air_layer_decorator);
     multi_layer.addLayer(substrate_layer);
 
-    // ---------------------
-    // building simulation
-    // ---------------------
+    // ----------------
+    // Build simulation
+    // ----------------
     Simulation simulation;
-    simulation.setDetectorParameters(100,-1.0*Units::degree, 1.0*Units::degree, 100, 0.0*Units::degree, 2.0*Units::degree, true);
-    simulation.setBeamParameters(1.0*Units::angstrom, -0.2*Units::degree, 0.0*Units::degree);
-
-    // ---------------------
-    // running simulation
-    // ---------------------
+    simulation.setDetectorParameters(
+        100,-1.0*Units::degree, 1.0*Units::degree, 100,
+        0.0*Units::degree, 2.0*Units::degree, true);
+    simulation.setBeamParameters(
+        1.0*Units::angstrom, -0.2*Units::degree, 0.0*Units::degree);
+
+    // --------------
+    // Run simulation
+    // --------------
     simulation.setSample(multi_layer);
     simulation.runSimulation();
 
-    // ---------------------
-    // copying data
-    // ---------------------
+    // ------------
+    // Copy results
+    // ------------
     m_result = simulation.getOutputDataClone();
 }
 
@@ -72,25 +85,30 @@ int FunctionalTests::IsGISAXS01::analyseResults()
 {
     const double threshold(1e-10);
 
-    // retrieving reference data
-    std::string filename = Utils::FileSystem::GetHomePath() + "/Tests/FunctionalTests/TestCore/IsGISAXS01/isgisaxs01_reference.ima.gz";
-    OutputData<double > *reference = OutputDataIOFactory::getOutputData(filename);
+    // Retrieve reference data.
+    std::string filename =
+        Utils::FileSystem::GetHomePath() +
+        "/Tests/FunctionalTests/TestCore/IsGISAXS01/isgisaxs01_reference.ima.gz";
+    OutputData<double > *reference =
+        OutputDataIOFactory::getOutputData(filename);
 
-    // calculating average relative difference
+    // Calculating average relative difference.
     *m_result -= *reference;
     *m_result /= *reference;
-
     double diff(0);
-    for(OutputData<double>::const_iterator it=m_result->begin(); it!=m_result->end(); ++it) {
+    for(OutputData<double>::const_iterator it =
+            m_result->begin(); it!=m_result->end(); ++it) {
         diff+= std::fabs(*it);
     }
     diff /= m_result->getAllocatedSize();
 
+    // Assess result.
     bool status_ok(true);
     if( diff > threshold || std::isnan(diff) ) status_ok=false;
     delete reference;
 
-    std::cout << m_name << " " << m_description << " " << (status_ok ? "[OK]" : "[FAILED]") << std::endl;
+    std::cout << m_name << " " << m_description << " " <<
+        (status_ok ? "[OK]" : "[FAILED]") << std::endl;
     return (int)status_ok;
 }
 

Tests/FunctionalTests/TestCore/IsGISAXS01/IsGISAXS01.h

 #ifndef FUNCTIONALTESTS_ISGISAXS01_H
 #define FUNCTIONALTESTS_ISGISAXS01_H
 
-
 #include <string>
 #include "OutputData.h"