Added parameter registration, xi integration flag usage, isgisaxs8 first...

Added parameter registration, xi integration flag usage, isgisaxs8 first sample initialization, debug symbols in release

App/src/FunctionalTestFactory.cpp

@@ -7,6 +7,7 @@
 #include "TestIsGISAXS2.h"
 #include "TestIsGISAXS3.h"
 #include "TestIsGISAXS4.h"
+#include "TestIsGISAXS8.h"
 #include "TestIsGISAXS9.h"
 #include "TestIsGISAXS10.h"
 #include "TestIsGISAXS11.h"
@@ -44,7 +45,9 @@ FunctionalTestFactory::FunctionalTestFactory() : m_benchmark(0)
     registerItem("isgisaxs3",   IFactoryCreateFunction<TestIsGISAXS3, IFunctionalTest>,
                  "functional test: isgisaxs ex-3 (cylinder FF)");
     registerItem("isgisaxs4",   IFactoryCreateFunction<TestIsGISAXS4, IFunctionalTest>,
-                 "functional test: isgisaxs ex-4 (paracrystal structure factors)");
+                 "functional test: isgisaxs ex-4 (paracrystal 1d structure factors)");
+    registerItem("isgisaxs8",   IFactoryCreateFunction<TestIsGISAXS8, IFunctionalTest>,
+                 "functional test: isgisaxs ex-8 (paracrystal lattice structure factors)");
     registerItem("isgisaxs9",   IFactoryCreateFunction<TestIsGISAXS9, IFunctionalTest>,
                  "functional test: isgisaxs ex-9 (rotated pyramid FF)");
     registerItem("isgisaxs10",  IFactoryCreateFunction<TestIsGISAXS10, IFunctionalTest>,

App/src/StandardSamples.cpp

@@ -456,7 +456,12 @@ ISample *StandardSamples::IsGISAXS8_2DDL_lattice()
     air_layer.setMaterial(p_air_material);
     Layer substrate_layer;
     substrate_layer.setMaterial(p_substrate_material);
-    IInterferenceFunction *p_interference_function = new InterferenceFunction1DParaCrystal(20.0*Units::nanometer,7*Units::nanometer, 1e3*Units::nanometer);
+    InterferenceFunction2DParaCrystal *p_interference_function = new InterferenceFunction2DParaCrystal(10.0*Units::nanometer, 10.0*Units::nanometer, M_PI/2.0,
+            0.0, 1e7*Units::nanometer);
+    p_interference_function->setDomainSizes(20.0*Units::micrometer, 20.0*Units::micrometer);
+    FTDistribution2DCauchy pdf1(0.5*Units::nanometer, 2.0*Units::nanometer);
+    FTDistribution2DCauchy pdf2(2.0*Units::nanometer, 0.5*Units::nanometer);
+    p_interference_function->setProbabilityDistributions(pdf1, pdf2);
     ParticleDecoration particle_decoration( new Particle(n_particle, new FormFactorCylinder(5*Units::nanometer, 5*Units::nanometer)));
     particle_decoration.addInterferenceFunction(p_interference_function);
     LayerDecorator air_layer_decorator(air_layer, particle_decoration);

App/src/TestIsGISAXS8.cpp

@@ -27,6 +27,8 @@ void TestIsGISAXS8::execute()
 
     // 2DDL_lattice
     p_sample = dynamic_cast<MultiLayer *>(SampleFactory::instance().createItem("IsGISAXS8_2DDL_lattice"));
+//    ParameterPool *p_pool = p_sample->createParameterTree();
+//    std::cout << (*p_pool);
     experiment.setSample(*p_sample);
     experiment.runSimulation();
     IsGISAXSTools::writeOutputDataToFile(*experiment.getOutputData(), m_data_path+"this_2DDL_lattice.ima");

Core/Algorithms/inc/FTDistributions.h

@@ -14,6 +14,8 @@
 //! @author Scientific Computing Group at FRM II
 //! @date   Oct 26, 2012
 
+#include "IParameterized.h"
+#include "ParameterPool.h"
 #include <cmath>
 
 class IFTDistribution1D
@@ -27,7 +29,7 @@ protected:
     double m_omega;
 };
 
-class IFTDistribution2D
+class IFTDistribution2D : public IParameterized
 {
 public:
     IFTDistribution2D(double omega_x, double omega_y) : m_omega_x(omega_x), m_omega_y(omega_y),
@@ -55,6 +57,8 @@ public:
     virtual FTDistribution2DCauchy *clone() const;
 
     virtual double evaluate(double qx, double qy) const;
+protected:
+    virtual void init_parameters();
 };
 
 #endif /* FTDISTRIBUTIONS_H_ */

Core/Algorithms/src/FTDistributions.cpp

@@ -3,6 +3,8 @@
 FTDistribution2DCauchy::FTDistribution2DCauchy(double omega_x, double omega_y)
 : IFTDistribution2D(omega_x, omega_y)
 {
+    setName("2DDistributionCauchy");
+    init_parameters();
 }
 
 FTDistribution2DCauchy* FTDistribution2DCauchy::clone() const
@@ -15,3 +17,10 @@ double FTDistribution2DCauchy::evaluate(double qx, double qy) const
     double sum_sq = qx*qx*m_omega_x*m_omega_x + qy*qy*m_omega_y*m_omega_y;
     return std::pow(1.0 + sum_sq, -1.5);
 }
+
+void FTDistribution2DCauchy::init_parameters()
+{
+    getParameterPool()->clear();
+    getParameterPool()->registerParameter("omega_x", &m_omega_x);
+    getParameterPool()->registerParameter("omega_y", &m_omega_y);
+}

Core/Samples/inc/InterferenceFunction2DParaCrystal.h

@@ -21,7 +21,7 @@ class InterferenceFunction2DParaCrystal : public IInterferenceFunction
 {
 public:
     InterferenceFunction2DParaCrystal(double length_1, double length_2, double alpha_lattice, double xi=0.0, double corr_length=0.0);
-    virtual ~InterferenceFunction2DParaCrystal() {}
+    virtual ~InterferenceFunction2DParaCrystal();
     virtual InterferenceFunction2DParaCrystal *clone() const {
         InterferenceFunction2DParaCrystal *p_new = new InterferenceFunction2DParaCrystal(m_lattice_lengths[0], m_lattice_lengths[1], m_alpha_lattice, m_xi, m_corr_length);
         p_new->setDomainSizes(m_domain_sizes[0], m_domain_sizes[1]);
@@ -45,6 +45,8 @@ public:
 
     virtual double evaluate(const cvector_t &q) const;
 
+    //! add parameters from local pool to external pool and call recursion over direct children
+    virtual std::string addParametersToExternalPool(std::string path, ParameterPool *external_pool, int copy_number=-1) const;
 protected:
     void transformToPrincipalAxes(double qx, double qy, double gamma, double delta, double &q_pa_1, double &q_pa_2) const;
     double m_lattice_lengths[2];

Core/Samples/src/InterferenceFunction2DParaCrystal.cpp

@@ -31,6 +31,13 @@ InterferenceFunction2DParaCrystal::InterferenceFunction2DParaCrystal(double leng
     init_parameters();
 }
 
+InterferenceFunction2DParaCrystal::~InterferenceFunction2DParaCrystal()
+{
+    for (size_t i=0; i<2; ++i) {
+        if (m_pdfs[i]) delete m_pdfs[i];
+    }
+}
+
 void InterferenceFunction2DParaCrystal::setProbabilityDistributions(
         const IFTDistribution2D& pdf_1, const IFTDistribution2D& pdf_2)
 {
@@ -45,14 +52,36 @@ double InterferenceFunction2DParaCrystal::evaluate(const cvector_t &q) const
 {
     m_qx = q.x().real();
     m_qy = q.y().real();
-    std::binder1st<std::const_mem_fun1_t<double, InterferenceFunction2DParaCrystal, double> > f_base = std::bind1st(std::mem_fun(&InterferenceFunction2DParaCrystal::interferenceForXi), this);
-    gsl_function f;
-    f.function = &wrapFunctionForGSL;
-    f.params = &f_base;
-    double result = MathFunctions::Integrate1D(&f, 0.0, M_PI)/M_PI;
+    double result;
+    if (m_integrate_xi) {
+        std::binder1st<std::const_mem_fun1_t<double, InterferenceFunction2DParaCrystal, double> > f_base = std::bind1st(std::mem_fun(&InterferenceFunction2DParaCrystal::interferenceForXi), this);
+        gsl_function f;
+        f.function = &wrapFunctionForGSL;
+        f.params = &f_base;
+        result = MathFunctions::Integrate1D(&f, 0.0, M_PI)/M_PI;
+    }
+    else {
+        result = interferenceForXi(m_xi);
+    }
     return result;
 }
 
+std::string InterferenceFunction2DParaCrystal::addParametersToExternalPool(std::string path,
+        ParameterPool* external_pool, int copy_number) const
+{
+    // add own parameters
+    std::string  new_path = IParameterized::addParametersToExternalPool(path, external_pool, copy_number);
+
+    // add parameters of the probability density functions
+    if (m_pdfs[0]) {
+        m_pdfs[0]->addParametersToExternalPool(new_path, external_pool, 0);
+    }
+    if (m_pdfs[1]) {
+        m_pdfs[1]->addParametersToExternalPool(new_path, external_pool, 1);
+    }
+    return new_path;
+}
+
 void InterferenceFunction2DParaCrystal::transformToPrincipalAxes(double qx,
         double qy, double gamma, double delta, double& q_pa_1, double& q_pa_2) const
 {
@@ -63,8 +92,13 @@ void InterferenceFunction2DParaCrystal::transformToPrincipalAxes(double qx,
 void InterferenceFunction2DParaCrystal::init_parameters()
 {
     getParameterPool()->clear();
-//    getParameterPool()->registerParameter("peak_distance", &m_peak_distance);
+    getParameterPool()->registerParameter("lattice_length_1", &m_lattice_lengths[0]);
+    getParameterPool()->registerParameter("lattice_length_2", &m_lattice_lengths[1]);
+    getParameterPool()->registerParameter("lattice_angle", &m_alpha_lattice);
+    getParameterPool()->registerParameter("lattice_orientation", &m_xi);
     getParameterPool()->registerParameter("corr_length", &m_corr_length);
+    getParameterPool()->registerParameter("domain_size_1", &m_domain_sizes[0]);
+    getParameterPool()->registerParameter("domain_size_2", &m_domain_sizes[1]);
 }
 
 InterferenceFunction2DParaCrystal* InterferenceFunction2DParaCrystal::createSquare(

shared.pri

@@ -90,7 +90,7 @@ NumberOfSuchFiles=$$system(ls $${GENERAL_EXTERNALS_DIR}/lib/libboost_thread-mt*
 QMAKE_CXXFLAGS_DEBUG += -fdiagnostics-show-option # to find out in gcc which option control warning
 #QMAKE_CXXFLAGS_RELEASE += -O3 -ffast-math -msse3
 QMAKE_CXXFLAGS_RELEASE -= -O2
-QMAKE_CXXFLAGS_RELEASE += -O3  -ffast-math
+QMAKE_CXXFLAGS_RELEASE += -g -O3 -ffast-math
 # uncommenting line below produces non-stripped (very large) libraries
 #QMAKE_STRIP=: