From 6a1697b9c721cc5567ed1a17605d1185a9aa2e70 Mon Sep 17 00:00:00 2001
From: Walter Van Herck <w.van.herck@fz-juelich.de>
Date: Mon, 29 Oct 2012 17:36:26 +0100
Subject: [PATCH] Added parameter registration, xi integration flag usage,
isgisaxs8 first sample initialization, debug symbols in release
---
App/src/FunctionalTestFactory.cpp | 5 +-
App/src/StandardSamples.cpp | 7 ++-
App/src/TestIsGISAXS8.cpp | 2 +
Core/Algorithms/inc/FTDistributions.h | 6 ++-
Core/Algorithms/src/FTDistributions.cpp | 9 ++++
.../inc/InterferenceFunction2DParaCrystal.h | 4 +-
.../src/InterferenceFunction2DParaCrystal.cpp | 46 ++++++++++++++++---
shared.pri | 2 +-
8 files changed, 70 insertions(+), 11 deletions(-)
diff --git a/App/src/FunctionalTestFactory.cpp b/App/src/FunctionalTestFactory.cpp
index 3f4c07c111a..2f28ae4ea1f 100644
--- a/App/src/FunctionalTestFactory.cpp
+++ b/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>,
diff --git a/App/src/StandardSamples.cpp b/App/src/StandardSamples.cpp
index 2bf149fe5e8..77a595d74b9 100644
--- a/App/src/StandardSamples.cpp
+++ b/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);
diff --git a/App/src/TestIsGISAXS8.cpp b/App/src/TestIsGISAXS8.cpp
index 0d0707664df..23c8861474b 100644
--- a/App/src/TestIsGISAXS8.cpp
+++ b/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");
diff --git a/Core/Algorithms/inc/FTDistributions.h b/Core/Algorithms/inc/FTDistributions.h
index 5dbc2a4cb91..d15a793cb41 100644
--- a/Core/Algorithms/inc/FTDistributions.h
+++ b/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_ */
diff --git a/Core/Algorithms/src/FTDistributions.cpp b/Core/Algorithms/src/FTDistributions.cpp
index 33de6450830..3a2420455df 100644
--- a/Core/Algorithms/src/FTDistributions.cpp
+++ b/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);
+}
diff --git a/Core/Samples/inc/InterferenceFunction2DParaCrystal.h b/Core/Samples/inc/InterferenceFunction2DParaCrystal.h
index bb7e144e286..809629a30da 100644
--- a/Core/Samples/inc/InterferenceFunction2DParaCrystal.h
+++ b/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];
diff --git a/Core/Samples/src/InterferenceFunction2DParaCrystal.cpp b/Core/Samples/src/InterferenceFunction2DParaCrystal.cpp
index b8696de3e1b..ad8469994ba 100644
--- a/Core/Samples/src/InterferenceFunction2DParaCrystal.cpp
+++ b/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(
diff --git a/shared.pri b/shared.pri
index eeef573c34d..f5b8c1263ac 100644
--- a/shared.pri
+++ b/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=:
--
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