diff --git a/App/inc/TestMesoCrystal2.h b/App/inc/TestMesoCrystal2.h
deleted file mode 100644
index db8519714db4f7cfcb0aea24258d0880befa1632..0000000000000000000000000000000000000000
--- a/App/inc/TestMesoCrystal2.h
+++ /dev/null
@@ -1,92 +0,0 @@
-// ************************************************************************** //
-//
-// BornAgain: simulate and fit scattering at grazing incidence
-//
-//! @file App/inc/TestMesoCrystal2.h
-//! @brief Defines class TestMesoCrystal2.
-//
-//! Homepage: apps.jcns.fz-juelich.de/BornAgain
-//! License: GNU General Public License v3 or higher (see COPYING)
-//! @copyright Forschungszentrum Jülich GmbH 2013
-//! @authors Scientific Computing Group at MLZ Garching
-//! @authors C. Durniak, G. Pospelov, W. Van Herck, J. Wuttke
-//
-// ************************************************************************** //
-
-#ifndef TESTMESOCRYSTAL2_H
-#define TESTMESOCRYSTAL2_H
-
-#include "IApplicationTest.h"
-#include "Types.h"
-#include "OutputData.h"
-#include "ISampleBuilder.h"
-
-class Simulation;
-class ISample;
-class MesoCrystal;
-class IFormFactor;
-class Lattice;
-class FitSuite;
-
-//! Simulation and fit of 3D ordered particle assemblies.
-
-class TestMesoCrystal2 : public IApplicationTest
-{
-public:
- typedef std::vector<std::vector<std::string > > fixplan_t; // to hold sets of fit parameters to fix/release
-
- TestMesoCrystal2();
- virtual ~TestMesoCrystal2();
-
- virtual void execute();
-
- class SampleBuilder : public ISampleBuilder
- {
- public:
- SampleBuilder();
- virtual ~SampleBuilder(){}
-
- virtual ISample *buildSample() const;
- protected:
- //! Initializes pool parameters
- virtual void init_parameters();
- private:
-// MesoCrystal *createMesoCrystal(double particle_radius, complex_t n_particle, const IFormFactor *p_meso_form_factor) const;
-// const Lattice *createLattice(double stacking_radius) const;
- MesoCrystal *createMesoCrystal(double stacking_radius_a, double stacking_radius_c, complex_t n_particle, const IFormFactor *p_meso_form_factor) const;
- const Lattice *createLattice(double stacking_radius_a, double stacking_radius_c) const;
- double m_meso_radius;
- double m_surface_filling_ratio;
- double m_meso_height;
- double m_sigma_meso_height;
- double m_sigma_meso_radius;
- double m_lattice_length_a;
- double m_lattice_length_c;
- double m_nanoparticle_radius;
- double m_sigma_nanoparticle_radius;
- double m_sigma_lattice_length_a;
- double m_roughness;
- };
-
- void draw_results(); // plot fit results
- void run_fit(); // run fit
-
- void fitsuite_setup(int nconfig);
- void fitsuite_config1();
- void fitsuite_config2();
- void fitsuite_config3();
- void fitsuite_config4();
-
-private:
- void initializeRealData();
- void initializeSimulation(const OutputData<double> *output_data=0);
-
- OutputData<double> *m_real_data;
- SampleBuilder_t m_sample_builder;
- Simulation *m_simulation;
- FitSuite *m_fitSuite;
-};
-
-#endif // TESTMESOCRYSTAL2_H
-
-
diff --git a/App/inc/TestMiscellaneous.h b/App/inc/TestMiscellaneous.h
index 189bd7e12b7ba6c65b1640965b4e2789e4324e72..1b4d49e1c69dd398d9c7b6b688fc8040a671a5c8 100644
--- a/App/inc/TestMiscellaneous.h
+++ b/App/inc/TestMiscellaneous.h
@@ -40,9 +40,6 @@ public:
//! test of fast sin function approximation
void test_FastSin();
- //! test of reading of OutputData from ASCII file
- void test_OutputDataIOFactory();
-
//! test kvector container
void test_KVectorContainer();
diff --git a/App/src/ApplicationTestFactory.cpp b/App/src/ApplicationTestFactory.cpp
index 24c0c72db8840f53529727645cb239c83b845599..c2d8ef538a68b00fa82b1dddc416adfb6b637cb9 100644
--- a/App/src/ApplicationTestFactory.cpp
+++ b/App/src/ApplicationTestFactory.cpp
@@ -30,7 +30,6 @@
#include "TestIsGISAXS13.h"
#include "TestIsGISAXS5.h"
#include "TestMesoCrystal1.h"
-#include "TestMesoCrystal2.h"
#include "TestMiscellaneous.h"
#include "TestMultiLayerRoughness.h"
#include "TestPerformance.h"
@@ -188,10 +187,6 @@ void RegisterApplicationTests(ApplicationTestFactory *p_test_factory)
"mesocrystal1",
IFactoryCreateFunction<TestMesoCrystal1, IApplicationTest>,
"functional test: mesocrystal");
- p_test_factory->registerItem(
- "mesocrystal2",
- IFactoryCreateFunction<TestMesoCrystal2, IApplicationTest>,
- "functional test: mesocrystal fit");
p_test_factory->registerItem(
"roottree",
IFactoryCreateFunction<TestRootTree, IApplicationTest>,
diff --git a/App/src/TestMesoCrystal1.cpp b/App/src/TestMesoCrystal1.cpp
index b51b5e6ee3071754b1fca129919d6a526e1c154b..5a24468684ba9770d7bcca21adb09a91b730d397 100644
--- a/App/src/TestMesoCrystal1.cpp
+++ b/App/src/TestMesoCrystal1.cpp
@@ -29,13 +29,11 @@ void TestMesoCrystal1::execute()
simulation->setProgramOptions(mp_options);
// loading reference data
- std::string filename = Utils::FileSystem::GetReferenceDataDir()+ "mesocrystal01_reference.int.gz";
+ std::string filename = Utils::FileSystem::GetReferenceDataDir()
+ + "mesocrystal01_reference.int.gz";
- OutputData<double> *reference = IntensityDataIOFactory::readIntensityData(filename);
-
- // setting detector axis as in reference data
- //simulation->setDetectorParameters(*reference);
- //simulation->getSampleBuilder()->setParameterValue("nphi_rotations", 180.);
+ OutputData<double> *reference =
+ IntensityDataIOFactory::readIntensityData(filename);
simulation->runSimulation();
simulation->normalize();
@@ -59,7 +57,7 @@ void TestMesoCrystal1::execute()
IsGISAXSTools::drawOutputDataComparisonResults(
*data, *reference, "found", "found params", 100, 1e6);
- IntensityDataIOFactory::writeIntensityData(*data,"test_mesocrystal1.txt");
+ IntensityDataIOFactory::writeIntensityData(*data,"test_mesocrystal1.int");
delete data;
delete simulation;
diff --git a/App/src/TestMesoCrystal2.cpp b/App/src/TestMesoCrystal2.cpp
deleted file mode 100644
index 7f5cd288eb46d595c34e4ad746bdd34c9976b2bc..0000000000000000000000000000000000000000
--- a/App/src/TestMesoCrystal2.cpp
+++ /dev/null
@@ -1,714 +0,0 @@
-// ************************************************************************** //
-//
-// BornAgain: simulate and fit scattering at grazing incidence
-//
-//! @file App/src/TestMesoCrystal2.cpp
-//! @brief Implements class TestMesoCrystal2.
-//
-//! Homepage: apps.jcns.fz-juelich.de/BornAgain
-//! License: GNU General Public License v3 or higher (see COPYING)
-//! @copyright Forschungszentrum Jülich GmbH 2013
-//! @authors Scientific Computing Group at MLZ Garching
-//! @authors C. Durniak, G. Pospelov, W. Van Herck, J. Wuttke
-//
-// ************************************************************************** //
-
-#include "TestMesoCrystal2.h"
-#include "AttLimits.h"
-#include "Crystal.h"
-#include "DrawHelper.h"
-#include "FitStrategyAdjustParameters.h"
-#include "FitSuite.h"
-#include "FitSuiteObserverFactory.h"
-#include "FormFactorDecoratorDebyeWaller.h"
-#include "FormFactors.h"
-#include "Simulation.h"
-#include "IInterferenceFunction.h"
-#include "InterferenceFunctionNone.h"
-#include "IntensityDataFunctions.h"
-#include "IsGISAXSTools.h"
-#include "LatticeBasis.h"
-#include "Materials.h"
-#include "MathFunctions.h"
-#include "MesoCrystal.h"
-#include "MinimizerFactory.h"
-#include "MultiLayer.h"
-#include "FileSystem.h"
-#include "IntensityDataIOFactory.h"
-#include "OutputDataReader.h"
-#include "OutputDataFunctions.h"
-#include "ParticleLayout.h"
-#include "ProgramOptions.h"
-#include "ResolutionFunction2DSimple.h"
-#include "SampleFactory.h"
-#include "TRange.h"
-#include "Units.h"
-#include "Utils.h"
-
-#include "TCanvas.h"
-#include "TH2D.h"
-#include <boost/assign/list_of.hpp>
-
-
-/* ************************************************************************* */
-// TestMesoCrystal2 member definitions
-/* ************************************************************************* */
-TestMesoCrystal2::TestMesoCrystal2()
- : m_real_data(0)
- , m_sample_builder(new SampleBuilder)
- , m_simulation(0)
- , m_fitSuite(0)
-{
-}
-
-
-TestMesoCrystal2::~TestMesoCrystal2()
-{
- delete m_real_data;
- delete m_simulation;
- delete m_fitSuite;
-}
-
-
-void TestMesoCrystal2::execute()
-{
-
- //run_fit();
- draw_results();
-}
-
-
-
-// ----------------------------------------------------------------------------
-// draw fit results
-// ----------------------------------------------------------------------------
-void TestMesoCrystal2::draw_results()
-{
- initializeRealData();
- initializeSimulation(m_real_data);
-
- ParameterPool *pool = m_sample_builder->createParameterTree();
-// pool->setMatchedParametersValue("*/lattice_length_a", 6.2e+00); // 6.2
-// pool->setMatchedParametersValue("*/lattice_length_c", 6.2e+00); // 6.2
-// pool->setMatchedParametersValue("*/nanoparticle_radius", 5.7e+00); // 5.7
-// pool->setMatchedParametersValue("*/sigma_nanoparticle_radius", 1.0e-01); // 0.1
-// pool->setMatchedParametersValue("*/meso_height", 200); // 0.1
-// pool->setMatchedParametersValue("*/meso_radius", 1000); // 0.1
-// pool->setMatchedParametersValue("*/sigma_meso_height", 20); // 0.1
-// pool->setMatchedParametersValue("*/sigma_meso_radius", 100); // 0.1
-// pool->setMatchedParametersValue("*/sigma_lattice_length_a", 1.0); // 1.5
-// pool->setMatchedParametersValue("*/surface_filling_ratio", 0.2); // 0.25
-// pool->setMatchedParametersValue("*/roughness", 1.0); // 1.0
-// m_simulation->setBeamIntensity(8e+12);
-// m_simulation->runSimulation();
-// m_simulation->normalize();
-
-// IsGISAXSTools::drawOutputDataComparisonResults(*m_simulation->getOutputData(), *m_real_data, "initial", "initial params", 100, 1e6, 100);
-
- m_sample_builder->setParameterValue("lattice_length_c", 6.5677e+00); // 6.2
- m_sample_builder->setParameterValue("lattice_length_a", 6.2091e+00); // 6.2
- m_sample_builder->setParameterValue("nanoparticle_radius", 4.6976e+00); // 5.7
- m_sample_builder->setParameterValue("sigma_nanoparticle_radius", 3.6720e-01); // 0.1
- m_sample_builder->setParameterValue("meso_height", 1.1221e+02); // 0.1
- m_sample_builder->setParameterValue("meso_radius", 9.4567e+02); // 0.1
- m_sample_builder->setParameterValue("sigma_meso_height", 1.3310e+00); // 0.1
- m_sample_builder->setParameterValue("sigma_meso_radius", 1.3863e+00); // 0.1
- m_sample_builder->setParameterValue("sigma_lattice_length_a", 1.1601e+00); // 1.5
- m_sample_builder->setParameterValue("surface_filling_ratio", 1.7286e-01); // 0.25
- m_sample_builder->setParameterValue("roughness", 2.8746e+01); // 1.0
- m_simulation->setBeamIntensity(5.0090e+12);
- std::cout << *pool << std::endl;
- m_simulation->runSimulation();
- m_simulation->normalize();
-
-// IsGISAXSTools::drawOutputDataComparisonResults(
-// *m_simulation->getOutputData(), *m_real_data,
-// "found", "found params", 100, 1e6, 100);
-
-// TCanvas *c1 = new TCanvas("meso_real_data","meso_real_data",1024, 768);
-// c1->cd();
-// gPad->SetLogz();
-// gPad->SetRightMargin(0.12);
-// gPad->SetLeftMargin(0.125);
-// TH2D *hist_real = IsGISAXSTools::getOutputDataTH2D(
-// *m_real_data, "real_data");
-// hist_real->SetMinimum(100);
-// hist_real->SetMaximum(1e6);
-// hist_real->GetYaxis()->SetTitleOffset(1.35);
-// hist_real->DrawCopy("CONT4 Z");
-
- TCanvas *c2 = new TCanvas("meso_simul_data","meso_simul_data",1024, 768);
- c2->cd();
- gPad->SetLogz();
- gPad->SetRightMargin(0.12);
- gPad->SetLeftMargin(0.125);
- TH2D *hist_simu = IsGISAXSTools::getOutputDataTH2D(
- *m_simulation->getOutputData(), "simul_data");
-// hist_simu->SetMinimum(100);
-// hist_simu->SetMaximum(1e6);
- hist_simu->GetYaxis()->SetTitleOffset(1.35);
- hist_simu->DrawCopy("CONT4 Z");
-
-// OutputDataIOFactory::writeIntensityData(
-// *m_simulation->getOutputData(), "meso_simul.txt");
-}
-
-
-
-
-/* ************************************************************************* */
-//
-/* ************************************************************************* */
-void TestMesoCrystal2::run_fit()
-{
- initializeRealData();
-
- TCanvas *c1 = DrawHelper::createAndRegisterCanvas("c1_test_meso_crystal", "mesocrystal");
- c1->cd(); gPad->SetLogz();
- gPad->SetRightMargin(0.115);
- gPad->SetLeftMargin(0.115);
- IsGISAXSTools::setMinimum(100.);
- IsGISAXSTools::setMaximum(1e7);
- IsGISAXSTools::drawOutputDataInPad(*m_real_data, "CONT4 Z", "experiment");
- c1->Update();
-
- // initializing simulation using real data
- initializeSimulation(m_real_data);
-
- // setting fitSuite
- m_fitSuite = new FitSuite();
- m_fitSuite->getFitObjects()->setSimulationNormalize(true);
-
- int fitconfig = (*mp_options)["fitconfig"].as<int>();
- fitsuite_setup(fitconfig);
-
- m_fitSuite->attachObserver( FitSuiteObserverFactory::createPrintObserver() );
- m_fitSuite->attachObserver( FitSuiteObserverFactory::createDrawObserver() );
- m_fitSuite->attachObserver( FitSuiteObserverFactory::createTreeObserver() );
-
- m_fitSuite->runFit();
-
- for(FitSuiteParameters::iterator it = m_fitSuite->getFitParameters()->begin(); it!=m_fitSuite->getFitParameters()->end(); ++it) {
- std::cout << (*it) << std::endl;
- }
-}
-
-
-// ----------------------------------------------------------------------------
-// initialize real data
-// ----------------------------------------------------------------------------
-void TestMesoCrystal2::initializeRealData()
-{
- delete m_real_data;
- //std::string file_name = Utils::FileSystem::GetHomePath()+"Examples/MesoCrystals/ex02_fitspheres/004_230_P144_im_full_qyqz.txt.gz";
- //std::string file_name = Utils::FileSystem::GetHomePath()+"Examples/MesoCrystals/ex02_fitspheres/004_230_P144_im_full_phitheta.txt.gz";
- //std::string file_name = "dev-tools/tmp-examples/MesoCrystals/ex02_fitspheres/004_230_P144_im_full_phitheta.txt.gz";
- //std::string file_name = "../support/input/001_ElisabethJosten/2013.01.03/004_230_P144_im_full_phitheta.txt.gz";
- std::string file_name = Utils::FileSystem::GetReferenceDataDir() + "mesocrystal1_reference_v2_nphi180.txt.gz";
-
- m_real_data = IntensityDataIOFactory::readIntensityData(file_name);
- //Mask *mask1 = OutputDataFunctions::CreateRectangularMask(*m_real_data, 0.025, 0.003, 0.051, 0.0375);
- Mask *mask1 = OutputDataFunctions::CreateRectangularMask(*m_real_data, 0.0, 0.015, 0.09, 0.020);
- m_real_data->setMask(*mask1);
-
-
- // OutputData<double > *real_data_half = doubleBinSize(*real_data);
- // OutputData<double > *real_data_quarter = doubleBinSize(*real_data_half);
- // OutputData<double > *real_data_eighth = doubleBinSize(*real_data_quarter);
-}
-
-
-// ----------------------------------------------------------------------------
-// run appropriate FitSuite configuration
-// ----------------------------------------------------------------------------
-void TestMesoCrystal2::fitsuite_setup(int nconfig)
-{
- switch(nconfig) {
- case 1:
- fitsuite_config1();
- break;
- case 2:
- fitsuite_config2();
- break;
- case 3:
- fitsuite_config3();
- break;
- case 4:
- fitsuite_config4();
- break;
- default:
- throw LogicErrorException("TestMesoCrystal2::fitsuite_setup() -> Error! Can't setup FitSuite");
- break;
- }
-}
-
-
-
-// ----------------------------------------------------------------------------
-// FitSuite configuration #3
-// * Mask on fit data
-// * Several fit iterations with different set of fixed released parameters
-// * ChiSquaredModule with normalizer
-// ----------------------------------------------------------------------------
-void TestMesoCrystal2::fitsuite_config4()
-{
- m_fitSuite->setMinimizer( MinimizerFactory::createMinimizer("Minuit2", "Combined") );
-// m_fitSuite->setMinimizer( MinimizerFactory::createMinimizer("Minuit2", "Fumili") );
-
- m_fitSuite->getAttributes().setStepFactor(0.01);
- m_fitSuite->addFitParameter("*/lattice_length_a", 6.2091e+00*Units::nanometer, AttLimits::limited(4.0*Units::nanometer, 8.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/lattice_length_c", 6.5677e+00*Units::nanometer, AttLimits::limited(4.0*Units::nanometer, 8.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/nanoparticle_radius", 4.6976e+00*Units::nanometer, AttLimits::limited(4.0*Units::nanometer, 8.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/sigma_nanoparticle_radius", 3.6720e-01*Units::nanometer, AttLimits::limited(0.01*Units::nanometer, 2.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/meso_height", 1.1221e+02*Units::nanometer, AttLimits::limited(10.0*Units::nanometer, 2000.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/meso_radius", 9.4567e+02*Units::nanometer, AttLimits::limited(10.0*Units::nanometer, 5000.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/sigma_meso_height", 1.3310e+00*Units::nanometer, AttLimits::limited(1.0*Units::nanometer, 200.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/sigma_meso_radius", 1.3863e+00*Units::nanometer, AttLimits::limited(1.0*Units::nanometer, 500.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/sigma_lattice_length_a", 1.1601e+00*Units::nanometer, AttLimits::limited(0.01*Units::nanometer, 4.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/surface_filling_ratio", 1.7286e-01, AttLimits::limited(0.05, 0.5) );
- m_fitSuite->addFitParameter("*/roughness", 2.8746e+01*Units::nanometer, AttLimits::limited(0.01*Units::nanometer, 50.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*Beam/intensity", 5.0090e+12, AttLimits::limited(8e11, 8e13) );
-
- fixplan_t fixplan;
- fixplan.push_back(boost::assign::list_of("*Beam/intensity")("*/lattice_length_a")("*/lattice_length_c")("*/nanoparticle_radius"));
- fixplan.push_back(boost::assign::list_of("*Beam/intensity")("*/meso_height")("*/meso_radius"));
- fixplan.push_back(boost::assign::list_of("*Beam/intensity")("*/surface_filling_ratio")("*/roughness"));
- fixplan.push_back(boost::assign::list_of("*Beam/intensity")("*/sigma_lattice_length_a")("*/sigma_nanoparticle_radius")("*/sigma_meso_height")("*/sigma_meso_radius"));
-
- // here we are fixing specific parameters before fit
- for( size_t i_plan=0; i_plan<fixplan.size(); ++i_plan) {
- std::ostringstream ostr;
- ostr << "strategy" <<i_plan;
- FitStrategyAdjustParameters *strategy = new FitStrategyAdjustParameters(ostr.str());
- strategy->fix_all();
- for(size_t i_par=0; i_par<fixplan[i_plan].size(); ++i_par) {
- strategy->release(fixplan[i_plan][i_par]);
- }
- m_fitSuite->addFitStrategy(strategy);
- }
- FitStrategyAdjustParameters *strategy_all = new FitStrategyAdjustParameters("strategy_all");
- strategy_all->release_all();
- m_fitSuite->addFitStrategy(strategy_all);
-
- // fitpreserve=1 - preserve original values
- // fitpreserve=0 - return always to previous fit values
- for(FitSuiteStrategies::iterator it = m_fitSuite->getFitStrategies()->begin(); it!= m_fitSuite->getFitStrategies()->end(); ++it) {
- FitStrategyAdjustParameters *strategy = dynamic_cast<FitStrategyAdjustParameters *>( (*it) );
- assert(strategy);
- strategy->setPreserveOriginalValues( (*mp_options)["fitpreserve"].as<int>() );
- }
-
-// Mask *mask1 = OutputDataFunctions::CreateRectangularMask(*m_real_data, 0.041, 0.003, 0.051, 0.03);
- Mask *mask1 = OutputDataFunctions::CreateRectangularMask(*m_real_data, 0.025, 0.003, 0.051, 0.0375);
- m_real_data->setMask(*mask1);
-// IntensityDataHelper::setRectangularMask(*m_real_data, 0.025, 0.003, 0.051, 0.0375);
-
- ChiSquaredModule chiModule;
-// chiModule.setChiSquaredFunction( SquaredFunctionDefault() );
- //chiModule.setChiSquaredFunction( SquaredFunctionWhichOnlyWorks() ); // it works only with resolution function, without it fit doesn't converge
- chiModule.setChiSquaredFunction( new SquaredFunctionMeanSquaredError() );
- //chiModule.setOutputDataNormalizer( OutputDataSimpleNormalizer(1.0,0) );
-
- m_fitSuite->addSimulationAndRealData(*m_simulation, *m_real_data, chiModule);
-// m_fitSuite->addSimulationAndRealData(*m_simulation, *m_real_data);
-
-}
-
-
-// ----------------------------------------------------------------------------
-// FitSuite configuration #3
-// * Mask on fit data
-// * Several fit iterations with different set of fixed released parameters
-// * ChiSquaredModule with normalizer
-// ----------------------------------------------------------------------------
-void TestMesoCrystal2::fitsuite_config3()
-{
- m_fitSuite->setMinimizer( MinimizerFactory::createMinimizer("Minuit2", "Combined") );
-// m_fitSuite->setMinimizer( MinimizerFactory::createMinimizer("Minuit2", "Fumili") );
-
- m_fitSuite->getAttributes().setStepFactor(0.01);
- m_fitSuite->addFitParameter("*/lattice_length_a", 6.2*Units::nanometer, AttLimits::limited(4.0*Units::nanometer, 8.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/lattice_length_c", 6.2*Units::nanometer, AttLimits::limited(4.0*Units::nanometer, 8.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/nanoparticle_radius", 5.7*Units::nanometer, AttLimits::limited(4.0*Units::nanometer, 8.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/sigma_nanoparticle_radius", 0.1*Units::nanometer, AttLimits::limited(0.01*Units::nanometer, 2.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/meso_height", 200.0*Units::nanometer, AttLimits::limited(10.0*Units::nanometer, 2000.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/meso_radius", 1000.0*Units::nanometer, AttLimits::limited(10.0*Units::nanometer, 5000.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/sigma_meso_height", 20.0*Units::nanometer, AttLimits::limited(1.0*Units::nanometer, 200.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/sigma_meso_radius", 100.0*Units::nanometer, AttLimits::limited(1.0*Units::nanometer, 500.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/sigma_lattice_length_a", 1.0*Units::nanometer, AttLimits::limited(0.01*Units::nanometer, 4.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/surface_filling_ratio", 0.2, AttLimits::limited(0.05, 0.5) );
- m_fitSuite->addFitParameter("*/roughness", 1.0*Units::nanometer, AttLimits::limited(0.01*Units::nanometer, 50.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*Beam/intensity", 8e12, AttLimits::limited(8e11, 8e13) );
-
- fixplan_t fixplan;
- fixplan.push_back(boost::assign::list_of("*Beam/intensity")("*/lattice_length_a")("*/lattice_length_c")("*/nanoparticle_radius"));
- fixplan.push_back(boost::assign::list_of("*Beam/intensity")("*/meso_height")("*/meso_radius"));
- fixplan.push_back(boost::assign::list_of("*Beam/intensity")("*/surface_filling_ratio")("*/roughness"));
- fixplan.push_back(boost::assign::list_of("*Beam/intensity")("*/sigma_lattice_length_a")("*/sigma_nanoparticle_radius")("*/sigma_meso_height")("*/sigma_meso_radius"));
-
- // here we are fixing specific parameters before fit
- for( size_t i_plan=0; i_plan<fixplan.size(); ++i_plan) {
- std::ostringstream ostr;
- ostr << "strategy" <<i_plan;
- FitStrategyAdjustParameters *strategy = new FitStrategyAdjustParameters(ostr.str());
- strategy->fix_all();
- for(size_t i_par=0; i_par<fixplan[i_plan].size(); ++i_par) {
- strategy->release(fixplan[i_plan][i_par]);
- }
- m_fitSuite->addFitStrategy(strategy);
- }
- FitStrategyAdjustParameters *strategy_all = new FitStrategyAdjustParameters("strategy_all");
- strategy_all->release_all();
- m_fitSuite->addFitStrategy(strategy_all);
-
- // fitpreserve=1 - preserve original values
- // fitpreserve=0 - return always to previous fit values
- for(FitSuiteStrategies::iterator it = m_fitSuite->getFitStrategies()->begin(); it!= m_fitSuite->getFitStrategies()->end(); ++it) {
- FitStrategyAdjustParameters *strategy = dynamic_cast<FitStrategyAdjustParameters *>( (*it) );
- assert(strategy);
- strategy->setPreserveOriginalValues( (*mp_options)["fitpreserve"].as<int>() );
- }
-
-// Mask *mask1 = OutputDataFunctions::CreateRectangularMask(*m_real_data, 0.041, 0.003, 0.051, 0.03);
- Mask *mask1 = OutputDataFunctions::CreateRectangularMask(*m_real_data, 0.025, 0.003, 0.051, 0.0375);
- m_real_data->setMask(*mask1);
-
- ChiSquaredModule chiModule;
-// chiModule.setChiSquaredFunction( SquaredFunctionDefault() );
- //chiModule.setChiSquaredFunction( SquaredFunctionWhichOnlyWorks() ); // it works only with resolution function, without it fit doesn't converge
- chiModule.setChiSquaredFunction( new SquaredFunctionSystematicError() );
- //chiModule.setOutputDataNormalizer( OutputDataSimpleNormalizer(1.0,0) );
-
- m_fitSuite->addSimulationAndRealData(*m_simulation, *m_real_data, chiModule);
-// m_fitSuite->addSimulationAndRealData(*m_simulation, *m_real_data);
-
-}
-
-
-// ----------------------------------------------------------------------------
-// FitSuite configuration #2
-// * Mask on fit data
-// * Several fit iterations with different set of fixed released parameters
-// * ChiSquaredModule with normalizer
-// ----------------------------------------------------------------------------
-void TestMesoCrystal2::fitsuite_config2()
-{
- m_fitSuite->setMinimizer( MinimizerFactory::createMinimizer("Minuit2", "Combined") );
-
- m_fitSuite->getAttributes().setStepFactor(0.01);
- m_fitSuite->addFitParameter("*/lattice_length_a", 6.2*Units::nanometer, AttLimits::limited(4.0*Units::nanometer, 8.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/nanoparticle_radius", 5.7*Units::nanometer, AttLimits::limited(2.0*Units::nanometer, 8.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/sigma_nanoparticle_radius", 0.1*Units::nanometer, AttLimits::limited(0.01*Units::nanometer, 2.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/meso_height", 500.0*Units::nanometer, AttLimits::limited(100.0*Units::nanometer, 2000.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/meso_radius", 1000.0*Units::nanometer, AttLimits::limited(100.0*Units::nanometer, 5000.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/sigma_meso_height", 5.0*Units::nanometer, AttLimits::limited(10.0*Units::nanometer, 200.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/sigma_meso_radius", 50.0*Units::nanometer, AttLimits::limited(10.0*Units::nanometer, 500.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/sigma_lattice_length_a", 1.5*Units::nanometer, AttLimits::limited(0.01*Units::nanometer, 4.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/surface_filling_ratio", 0.25, AttLimits::limited(0.1, 0.4) );
- m_fitSuite->addFitParameter("*/roughness", 1.0*Units::nanometer, AttLimits::limited(0.01*Units::nanometer, 50.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*Beam/intensity", 8e12, AttLimits::limited(8e11, 8e13) );
-
- fixplan_t fixplan;
- fixplan.resize(7);
- fixplan[0] = boost::assign::list_of("*/lattice_length_a")("*/nanoparticle_radius");
- fixplan[1] = boost::assign::list_of("*/meso_height")("*/meso_radius");
- fixplan[2] = boost::assign::list_of("*Beam/intensity");
- fixplan[3] = boost::assign::list_of("*/surface_filling_ratio");
- fixplan[4] = boost::assign::list_of("*/roughness");
- fixplan[5] = boost::assign::list_of("*/sigma_lattice_length_a")("*/sigma_nanoparticle_radius");
- fixplan[6] = boost::assign::list_of("*/sigma_meso_height")("*/sigma_meso_radius");
-
- // here we are fixing specific parameters before fit
- for( size_t i_plan=0; i_plan<fixplan.size(); ++i_plan) {
- std::ostringstream ostr;
- ostr << "strategy" <<i_plan;
- FitStrategyAdjustParameters *strategy = new FitStrategyAdjustParameters(ostr.str());
- strategy->fix_all();
- strategy->setPreserveOriginalValues(true); // initial values of parameters will be restored after each fit
- for(size_t i_par=0; i_par<fixplan[i_plan].size(); ++i_par) {
- strategy->release(fixplan[i_plan][i_par]);
- }
- m_fitSuite->addFitStrategy(strategy);
- }
- FitStrategyAdjustParameters *strategy_all = new FitStrategyAdjustParameters("strategy_all");
- strategy_all->release_all();
- m_fitSuite->addFitStrategy(strategy_all);
-
- // fitpreserve=1 - preserve original values
- // fitpreserve=0 - return always to previous fit values
- for(FitSuiteStrategies::iterator it = m_fitSuite->getFitStrategies()->begin(); it!= m_fitSuite->getFitStrategies()->end(); ++it) {
- FitStrategyAdjustParameters *strategy = dynamic_cast<FitStrategyAdjustParameters *>( (*it) );
- assert(strategy);
- strategy->setPreserveOriginalValues( (*mp_options)["fitpreserve"].as<int>() );
- }
-
- Mask *mask1 = OutputDataFunctions::CreateRectangularMask(*m_real_data, 0.041, 0.003, 0.051, 0.03);
- m_real_data->setMask(*mask1);
-
-
-}
-
-
-// ----------------------------------------------------------------------------
-// FitSuite configuration #1
-// 7 fit iterations with different sets of fixed/release parameters
-// ----------------------------------------------------------------------------
-void TestMesoCrystal2::fitsuite_config1()
-{
-
- m_fitSuite->setMinimizer( MinimizerFactory::createMinimizer("Minuit2", "Combined") );
-
- m_fitSuite->addFitParameter("*/lattice_length_a", 6.2*Units::nanometer, AttLimits::limited(4.0*Units::nanometer, 8.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/nanoparticle_radius", 5.7*Units::nanometer, 1.0*Units::nanometer, AttLimits::limited(2.0*Units::nanometer, 8.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/sigma_nanoparticle_radius", 0.1*Units::nanometer, 0.05*Units::nanometer, AttLimits::limited(0.01*Units::nanometer, 2.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/meso_height", 500.0*Units::nanometer, 100.0*Units::nanometer, AttLimits::limited(100.0*Units::nanometer, 2000.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/meso_radius", 1000.0*Units::nanometer, 100.0*Units::nanometer, AttLimits::limited(100.0*Units::nanometer, 5000.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/sigma_meso_height", 5.0*Units::nanometer, 1.0*Units::nanometer, AttLimits::limited(10.0*Units::nanometer, 200.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/sigma_meso_radius", 50.0*Units::nanometer, 10.0*Units::nanometer, AttLimits::limited(10.0*Units::nanometer, 500.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/sigma_lattice_length_a", 1.5*Units::nanometer, 0.5*Units::nanometer, AttLimits::limited(0.01*Units::nanometer, 4.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*/surface_filling_ratio", 0.25, 0.1, AttLimits::limited(0.1, 0.4) );
- m_fitSuite->addFitParameter("*/roughness", 1.0*Units::nanometer, 0.1*Units::nanometer, AttLimits::limited(0.01*Units::nanometer, 50.0*Units::nanometer) );
- m_fitSuite->addFitParameter("*Beam/intensity", 8e12, 100, AttLimits::limited(8e11, 8e13) );
-
- fixplan_t fixplan;
- fixplan.resize(7);
- fixplan[0] = boost::assign::list_of("*/lattice_length_a")("*/nanoparticle_radius");
- fixplan[1] = boost::assign::list_of("*/meso_height")("*/meso_radius");
- fixplan[2] = boost::assign::list_of("*Beam/intensity");
- fixplan[3] = boost::assign::list_of("*/surface_filling_ratio");
- fixplan[4] = boost::assign::list_of("*/roughness");
- fixplan[5] = boost::assign::list_of("*/sigma_lattice_length_a")("*/sigma_nanoparticle_radius");
- fixplan[6] = boost::assign::list_of("*/sigma_meso_height")("*/sigma_meso_radius");
-
- // here we are fixing specific parameters before fit
- for( size_t i_plan=0; i_plan<fixplan.size(); ++i_plan) {
- std::ostringstream ostr;
- ostr << "strategy" <<i_plan;
- FitStrategyAdjustParameters *strategy = new FitStrategyAdjustParameters(ostr.str());
- strategy->fix_all();
- strategy->setPreserveOriginalValues(true); // initial values of parameters will be restored after each fit
- for(size_t i_par=0; i_par<fixplan[i_plan].size(); ++i_par) {
- strategy->release(fixplan[i_plan][i_par]);
- }
- m_fitSuite->addFitStrategy(strategy);
- }
- FitStrategyAdjustParameters *strategy_all = new FitStrategyAdjustParameters("strategy_all");
- strategy_all->release_all();
- m_fitSuite->addFitStrategy(strategy_all);
-
- // fitpreserve=1 - preserve original values
- // fitpreserve=0 - return always to previous fit values
- for(FitSuiteStrategies::iterator it = m_fitSuite->getFitStrategies()->begin(); it!= m_fitSuite->getFitStrategies()->end(); ++it) {
- FitStrategyAdjustParameters *strategy = dynamic_cast<FitStrategyAdjustParameters *>( (*it) );
- assert(strategy);
- strategy->setPreserveOriginalValues( (*mp_options)["fitpreserve"].as<int>() );
- }
-
- m_fitSuite->addSimulationAndRealData(*m_simulation, *m_real_data);
-
-}
-
-
-/* ************************************************************************* */
-//
-/* ************************************************************************* */
-void TestMesoCrystal2::initializeSimulation(const OutputData<double> *output_data)
-{
- delete m_simulation;
-
- m_simulation = new Simulation(mp_options);
- m_simulation->setSampleBuilder( m_sample_builder );
- m_simulation->setBeamParameters(1.77*Units::angstrom, 0.4*Units::degree, 0.0*Units::degree);
- m_simulation->setBeamIntensity(8e12);
- m_simulation->setDetectorResolutionFunction(new ResolutionFunction2DSimple(0.0002, 0.0002));
-
- if( !output_data ) {
- // initialize default detector
- m_simulation->setDetectorParameters(200, 0.3*Units::degree, 0.073, 200, -0.4*Units::degree, 0.066);
- } else {
- // if there is output_data as input parameter, build detector using output_data axises
- //const IAxis *axis0 = output_data->getAxis(0);
- //const IAxis *axis1 = output_data->getAxis(1);
- //std::cout << "Axis!!! " << axis0->getSize() << " " << axis0->getMin() << " " << axis0->getMax() << " " << axis1->getSize() << " " << axis1->getMin() << " " << axis1->getMax() << std::endl;
- //m_simulation->setDetectorParameters(axis0->getSize(), axis0->getMin(), axis0->getMax(), axis1->getSize(), axis1->getMin(), axis1->getMax());
- m_simulation->setDetectorParameters(*m_real_data);
- }
- m_simulation->printParameters();
-}
-
-
-
-/* ************************************************************************* */
-// MesoCrystalBuilder member definitions
-/* ************************************************************************* */
-TestMesoCrystal2::SampleBuilder::SampleBuilder()
-: m_meso_radius(1000.0*Units::nanometer)
-, m_surface_filling_ratio(0.25)
-, m_meso_height(500.0*Units::nanometer)
-, m_sigma_meso_height(5.0*Units::nanometer)
-, m_sigma_meso_radius(50.0*Units::nanometer)
-, m_lattice_length_a(6.2*Units::nanometer)
-, m_lattice_length_c(6.2*Units::nanometer)
-, m_nanoparticle_radius(5.7*Units::nanometer)
-, m_sigma_nanoparticle_radius(0.1*Units::nanometer)
-, m_sigma_lattice_length_a(1.5*Units::nanometer)
-, m_roughness(1.0*Units::nanometer)
-{
- init_parameters();
-}
-
-
-ISample* TestMesoCrystal2::SampleBuilder::buildSample() const
-{
- // create mesocrystal
- double surface_density = m_surface_filling_ratio/M_PI/m_meso_radius/m_meso_radius;
-// complex_t n_particle(1.0-1.55e-5, 1.37e-6); // data from Artur
- complex_t n_particle(1.0-2.84e-5, 4.7e-7); // data from http://henke.lbl.gov/optical_constants/getdb2.html
- complex_t avg_n_squared_meso = 0.7886*n_particle*n_particle + 0.2114;
- complex_t n_avg = std::sqrt(m_surface_filling_ratio*avg_n_squared_meso + 1.0 - m_surface_filling_ratio);
- complex_t n_particle_adapted = std::sqrt(n_avg*n_avg + n_particle*n_particle - 1.0);
- FormFactorCylinder ff_cyl(m_meso_radius, m_meso_height);
- FormFactorDecoratorDebyeWaller ff_meso(ff_cyl.clone(), m_sigma_meso_height*m_sigma_meso_height/2.0,
- m_sigma_meso_radius*m_sigma_meso_radius/2.0);
-
- // Create multilayer
- MultiLayer *p_multi_layer = new MultiLayer();
- complex_t n_air(1.0, 0.0);
- complex_t n_substrate(1.0-7.57e-6, 1.73e-7);
-
- HomogeneousMaterial air_material("Air", n_air);
- HomogeneousMaterial average_layer_material("Averagelayer", n_avg);
- HomogeneousMaterial substrate_material("Substrate", n_substrate);
- Layer air_layer;
- air_layer.setMaterial(air_material);
- Layer avg_layer;
- avg_layer.setMaterial(average_layer_material);
- avg_layer.setThickness(m_meso_height);
- Layer substrate_layer;
- substrate_layer.setMaterial(substrate_material);
- IInterferenceFunction *p_interference_funtion =
- new InterferenceFunctionNone();
- ParticleLayout particle_layout;
- size_t n_max_phi_rotation_steps = 1;
- size_t n_alpha_rotation_steps = 1;
-
-// double alpha_step = 5.0*Units::degree/n_alpha_rotation_steps;
-// double alpha_start = - (n_alpha_rotation_steps/2.0)*alpha_step;
-
- double phi_step = 2*M_PI/3.0/n_max_phi_rotation_steps;
- double phi_start = 0.0;
- for (size_t i=0; i<n_max_phi_rotation_steps; ++i) {
- for (size_t j=0; j<n_alpha_rotation_steps; ++j) {
- Geometry::Transform3D transform =
- Geometry::Transform3D::createRotateZ(phi_start + i*phi_step);
-// Geometry::Transform3D transform2 =
-// Geometry::Transform3D::createRotateY(alpha_start + j*alpha_step);
- particle_layout.addParticle(
- createMesoCrystal(
- m_lattice_length_a, m_lattice_length_c,
- n_particle_adapted, &ff_meso),
- transform, m_meso_height);
- }
- }
-
- particle_layout.setTotalParticleSurfaceDensity(surface_density);
- particle_layout.addInterferenceFunction(p_interference_funtion);
-
- avg_layer.addLayout(particle_layout);
-
- LayerRoughness roughness(m_roughness, 0.3, 500.0*Units::nanometer);
-
- p_multi_layer->addLayer(air_layer);
- p_multi_layer->addLayer(avg_layer);
- p_multi_layer->addLayerWithTopRoughness(substrate_layer, roughness);
-
-// std::cout << "Average layer index: " << n_avg << std::endl;
-// std::cout << "Adapted particle index: " << n_particle_adapted << std::endl;
-// std::cout << "Substrate layer index: " << n_substrate << std::endl;
-
- return p_multi_layer;
-}
-
-void TestMesoCrystal2::SampleBuilder::init_parameters()
-{
- clearParameterPool();
- registerParameter("meso_radius", &m_meso_radius);
- registerParameter("surface_filling_ratio", &m_surface_filling_ratio);
- registerParameter("meso_height", &m_meso_height);
- registerParameter("sigma_meso_height", &m_sigma_meso_height);
- registerParameter("sigma_meso_radius", &m_sigma_meso_radius);
- registerParameter("lattice_length_a", &m_lattice_length_a);
- registerParameter("lattice_length_c", &m_lattice_length_c);
- registerParameter("nanoparticle_radius", &m_nanoparticle_radius);
- registerParameter("sigma_nanoparticle_radius", &m_sigma_nanoparticle_radius);
- registerParameter("sigma_lattice_length_a", &m_sigma_lattice_length_a);
- registerParameter("roughness", &m_roughness);
-}
-
-//MesoCrystal* TestMesoCrystal2::SampleBuilder::createMesoCrystal(double stacking_radius, complex_t n_particle,
-// const IFormFactor* p_meso_form_factor) const
-//{
-// const Lattice *p_lat = createLattice(stacking_radius);
-// kvector_t bas_a = p_lat->getBasisVectorA();
-// kvector_t bas_b = p_lat->getBasisVectorB();
-// kvector_t bas_c = p_lat->getBasisVectorC();
-// Particle particle(n_particle, new FormFactorSphereGaussianRadius(m_nanoparticle_radius, m_sigma_nanoparticle_radius));
-// kvector_t position_0 = kvector_t(0.0, 0.0, 0.0);
-// kvector_t position_1 = 1.0/3.0*(2.0*bas_a + bas_b + bas_c);
-// kvector_t position_2 = 1.0/3.0*(bas_a + 2.0*bas_b + 2.0*bas_c);
-// std::vector<kvector_t> pos_vector;
-// pos_vector.push_back(position_0);
-// pos_vector.push_back(position_1);
-// pos_vector.push_back(position_2);
-// LatticeBasis basis(particle, pos_vector);
-
-// Crystal npc(basis, *p_lat);
-// delete p_lat;
-// double dw_factor = m_sigma_lattice_length_a*m_sigma_lattice_length_a/6.0;
-// npc.setDWFactor(dw_factor);
-// return new MesoCrystal(npc.clone(), p_meso_form_factor->clone());
-//}
-
-//const Lattice *TestMesoCrystal2::SampleBuilder::createLattice(double stacking_radius) const
-//{
-// Lattice *p_result = new Lattice(Lattice::createTrigonalLattice(stacking_radius*2.0, stacking_radius*2.0*2.3));
-// p_result->setSelectionRule(SimpleSelectionRule(-1, 1, 1, 3));
-// return p_result;
-//}
-
-MesoCrystal* TestMesoCrystal2::SampleBuilder::createMesoCrystal(double stacking_radius_a, double stacking_radius_c, complex_t n_particle,
- const IFormFactor* p_meso_form_factor) const
-{
- const Lattice *p_lat = createLattice(stacking_radius_a, stacking_radius_c);
- kvector_t bas_a = p_lat->getBasisVectorA();
- kvector_t bas_b = p_lat->getBasisVectorB();
- kvector_t bas_c = p_lat->getBasisVectorC();
-
- HomogeneousMaterial particle_material("Particle", n_particle);
-
- Particle particle(particle_material, FormFactorSphereGaussianRadius(m_nanoparticle_radius, m_sigma_nanoparticle_radius));
- kvector_t position_0 = kvector_t(0.0, 0.0, 0.0);
- kvector_t position_1 = 1.0/3.0*(2.0*bas_a + bas_b + bas_c);
- kvector_t position_2 = 1.0/3.0*(bas_a + 2.0*bas_b + 2.0*bas_c);
- std::vector<kvector_t> pos_vector;
- pos_vector.push_back(position_0);
- pos_vector.push_back(position_1);
- pos_vector.push_back(position_2);
- LatticeBasis basis(particle, pos_vector);
-
- Crystal npc(basis, *p_lat);
- delete p_lat;
- double dw_factor = m_sigma_lattice_length_a*m_sigma_lattice_length_a/6.0;
- npc.setDWFactor(dw_factor);
- return new MesoCrystal(npc.clone(), p_meso_form_factor->clone());
-}
-
-const Lattice *TestMesoCrystal2::SampleBuilder::createLattice(double stacking_radius_a, double stacking_radius_c) const
-{
- Lattice *p_result = new Lattice(Lattice::createTrigonalLattice(stacking_radius_a*2.0, stacking_radius_c*2.0*2.3));
- p_result->setSelectionRule(SimpleSelectionRule(-1, 1, 1, 3));
- return p_result;
-}
-
-
-
diff --git a/App/src/TestMiscellaneous.cpp b/App/src/TestMiscellaneous.cpp
index 2caab6b2587df4d352c0e0cf5eb5cc442cc5d555..ae2b9ebc7d599302822efd70cfed97e922afc42e 100644
--- a/App/src/TestMiscellaneous.cpp
+++ b/App/src/TestMiscellaneous.cpp
@@ -64,7 +64,6 @@ void TestMiscellaneous::execute()
//test_LogSystem();
//test_OutputDataTo2DArray();
//test_KVectorContainer();
- //test_OutputDataIOFactory();
//test_FastSin();
//test_FormFactor1();
//test_FormFactor();
@@ -260,26 +259,6 @@ void TestMiscellaneous::test_KVectorContainer()
}
}
-/* ************************************************************************* */
-// test of reading of OutputData from ASCII file
-/* ************************************************************************* */
-void TestMiscellaneous::test_OutputDataIOFactory()
-{
- std::string file_name = Utils::FileSystem::GetHomePath()
- +"Examples/MesoCrystals/ex02_fitspheres/004_230_P144_im_full_qyqz.txt.gz";
- OutputData<double > *data =
- IntensityDataIOFactory::readIntensityData(file_name);
-
- TCanvas *c1 = new TCanvas("c1","c1",800, 800);
- c1->cd(); gPad->SetRightMargin(0.14);
- gPad->SetLogz();
-
- TH2D *h2 = IsGISAXSTools::getOutputDataTH2D(*data, "xxx");
- h2->SetMinimum(100.);
- h2->Draw("CONT4 Z");
-}
-
-
/* ************************************************************************* */
// test of fast sin function approximation
/* ************************************************************************* */
diff --git a/App/src/TestPolarizedDWBA.cpp b/App/src/TestPolarizedDWBA.cpp
index 736818edec6e9a66759203aa4b7130e8aea828f6..7853da3f5f58cb94e02dfe3ff24f19ba8d3ec96b 100644
--- a/App/src/TestPolarizedDWBA.cpp
+++ b/App/src/TestPolarizedDWBA.cpp
@@ -37,43 +37,12 @@ void TestPolarizedDWBA::execute()
Simulation *simulation = sim_registry.createSimulation("magcyl2");
simulation->setProgramOptions(mp_options);
-
simulation->runSimulation();
simulation->normalize();
IsGISAXSTools::drawLogOutputDataPol(*simulation->getPolarizedOutputData(),
"c1_polDWBA", "Polarized DWBA", "CONT4 Z", "Polarized DWBA");
-// OutputDataIOFactory::writeIntensityData(*simulation->getPolarizedIntensityData(0,0),"magcyl2_reference_00.txt");
-// OutputDataIOFactory::writeIntensityData(*simulation->getPolarizedIntensityData(0,1),"magcyl2_reference_01.txt");
-// OutputDataIOFactory::writeIntensityData(*simulation->getPolarizedIntensityData(1,0),"magcyl2_reference_10.txt");
-// OutputDataIOFactory::writeIntensityData(*simulation->getPolarizedIntensityData(1,1),"magcyl2_reference_11.txt");
-
-
-// OutputData<double> *reference00 = OutputDataIOFactory::readIntensityData(Utils::FileSystem::GetReferenceDataDir()+ "magcyl2_reference_00.txt.gz");
-// OutputData<double> *reference01 = OutputDataIOFactory::readIntensityData(Utils::FileSystem::GetReferenceDataDir()+ "magcyl2_reference_01.txt.gz");
-// OutputData<double> *reference10 = OutputDataIOFactory::readIntensityData(Utils::FileSystem::GetReferenceDataDir()+ "magcyl2_reference_10.txt.gz");
-// OutputData<double> *reference11 = OutputDataIOFactory::readIntensityData(Utils::FileSystem::GetReferenceDataDir()+ "magcyl2_reference_11.txt.gz");
-
-// IsGISAXSTools::drawOutputDataComparisonResults(
-// *simulation->getPolarizedIntensityData(0,0), *reference00, "00", "found params");
-
-// IsGISAXSTools::drawOutputDataComparisonResults(
-// *simulation->getPolarizedIntensityData(0,1), *reference01, "01", "found params");
-
-// IsGISAXSTools::drawOutputDataComparisonResults(
-// *simulation->getPolarizedIntensityData(1,0), *reference10, "10", "found params");
-
-// IsGISAXSTools::drawOutputDataComparisonResults(
-// *simulation->getPolarizedIntensityData(1,1), *reference11, "11", "found params");
-
-
-// delete reference00;
-// delete reference01;
-// delete reference10;
-// delete reference11;
-
delete simulation;
-
}
diff --git a/Core/CMakeLists.txt b/Core/CMakeLists.txt
index 03b40f8c246b6e5a27f3d12c91c37ec6743e167d..baa08ef2687328eadcd90f56f2cc2ac5b8217c46 100644
--- a/Core/CMakeLists.txt
+++ b/Core/CMakeLists.txt
@@ -22,16 +22,16 @@ file(GLOB source_files
"FormFactors/src/*.cpp"
"Geometry/src/*.cpp"
"Samples/src/*.cpp"
- "StandardSamples/*.cpp"
+ "StandardSamples/*.cpp"
"Tools/src/*.cpp"
)
-file(GLOB include_files
+file(GLOB include_files
"Algorithms/inc/*.h"
"FormFactors/inc/*.h"
"Geometry/inc/*.h"
"Samples/inc/*.h"
- "StandardSamples/*.h"
+ "StandardSamples/*.h"
"Tools/inc/*.h"
)
@@ -111,7 +111,6 @@ endif()
# installation
# -----------------------------------------------
install (DIRECTORY ${CMAKE_SOURCE_DIR}/Examples/ DESTINATION ${destination_examples} COMPONENT Examples FILES_MATCHING PATTERN "*.py" )
-install (DIRECTORY ${CMAKE_SOURCE_DIR}/Examples/ DESTINATION ${destination_examples} COMPONENT Examples FILES_MATCHING PATTERN "refdata*.txt" )
install (DIRECTORY ${CMAKE_SOURCE_DIR}/Examples/ DESTINATION ${destination_examples} COMPONENT Examples FILES_MATCHING PATTERN "README")
install (DIRECTORY ${CMAKE_SOURCE_DIR}/Examples/cpp DESTINATION ${destination_examples} COMPONENT Examples)
# the line below copies the contains ${CMAKE_SOURCE_DIR}/bin to the bin folder of the final package
@@ -139,7 +138,7 @@ install (FILES ${include_files} DESTINATION ${destination_include} COMPONENT Hea
if(WIN32)
if(MSVC)
set(boost_suffix "-vc110-mt-1_55.dll")
- install(FILES
+ install(FILES
${CMAKE_LIBRARY_PATH}/boost_date_time${boost_suffix}
${CMAKE_LIBRARY_PATH}/boost_chrono${boost_suffix}
${CMAKE_LIBRARY_PATH}/boost_program_options${boost_suffix}
diff --git a/Doc/UserManual/AppendixListings.tex b/Doc/UserManual/AppendixListings.tex
index 18ff93b257beca4b37e76cf36c21eb81e9c499de..0591a5d38789f0b304ebfef98cdca1b0c17810a0 100755
--- a/Doc/UserManual/AppendixListings.tex
+++ b/Doc/UserManual/AppendixListings.tex
@@ -157,7 +157,7 @@ def run_fitting():
simulation = get_simulation()
simulation.setSample(sample)
- real_data = IntensityDataIOFactory.readIntensityData('refdata_fitcylinderprisms.txt')
+ real_data = IntensityDataIOFactory.readIntensityData('refdata_fitcylinderprisms.int.gz')
fit_suite = FitSuite()
fit_suite.addSimulationAndRealData(simulation, real_data)
diff --git a/Doc/UserManual/FittingExamples.tex b/Doc/UserManual/FittingExamples.tex
index 056758102a75fb51130937a2a9f3383e7fa46723..f6990b8a5b5d4eb969db7f19cbaf49883cb20efd 100755
--- a/Doc/UserManual/FittingExamples.tex
+++ b/Doc/UserManual/FittingExamples.tex
@@ -110,13 +110,13 @@ def run_fitting(): @\label{script2::run_fitting}@
simulation = get_simulation()
simulation.setSample(sample) @\label{script2::setup_simulation2}@
- real_data = IntensityDataIOFactory.readIntensityData('refdata_fitcylinderprisms.txt') @\label{script2::real_data}@
+ real_data = IntensityDataIOFactory.readIntensityData('refdata_fitcylinderprisms.int.gz') @\label{script2::real_data}@
\end{lstlisting}
Lines
~\ref{script2::setup_simulation1}-~\ref{script2::setup_simulation2}
generate the
sample and simulation description and assign the sample to the simulation.
-Our reference data are contained in the file \Code{'refdata\_fitcylinderprisms.txt'}.
+Our reference data are contained in the file \Code{'refdata\_fitcylinderprisms.int.gz'}.
This reference had been generated by adding noise
on the scattered intensity from a numerical sample with a fixed length of 5~nm for the four fitting
parameters (\textit{i.e.} the dimensions of the cylinders and prisms).
diff --git a/Examples/python/fitting/ex002_FitCylindersAndPrisms/FitCylindersPrisms_detailed.py b/Examples/python/fitting/ex002_FitCylindersAndPrisms/FitCylindersPrisms_detailed.py
index 339ae70485510b4500a63a7a1840a052c0c6bb52..c1caa63ef9ff2f87763ab5035c7e51b6d0a208d7 100644
--- a/Examples/python/fitting/ex002_FitCylindersAndPrisms/FitCylindersPrisms_detailed.py
+++ b/Examples/python/fitting/ex002_FitCylindersAndPrisms/FitCylindersPrisms_detailed.py
@@ -71,7 +71,7 @@ def get_sample(cylinder_height=1.0*nanometer,
def create_real_data():
"""
Generating "real" data by adding noise to the simulated data.
- This function has been used once to generate refdata_fitcylinderprisms.txt
+ This function has been used once to generate refdata_fitcylinderprisms.int
"""
# creating sample with set of parameters we will later try to find during the fit
sample = get_sample(5.0*nanometer, 5.0*nanometer, 5.0*nanometer, 5.0*nanometer)
diff --git a/GUI/externals/qt-manhattan-style/fancymainwindow.cpp b/GUI/externals/qt-manhattan-style/fancymainwindow.cpp
index 74908dd1ec8d9731d28223c0b72ae1d7d70023c0..7a69ac2dd7121117c0f8fadac9f1cfea623e8b56 100644
--- a/GUI/externals/qt-manhattan-style/fancymainwindow.cpp
+++ b/GUI/externals/qt-manhattan-style/fancymainwindow.cpp
@@ -106,7 +106,8 @@ QDockWidget *FancyMainWindow::addDockForWidget(QWidget *widget)
// Set an object name to be used in settings, derive from widget name
const QString objectName = widget->objectName();
if (objectName.isEmpty()) {
- dockWidget->setObjectName(QLatin1String("dockWidget") + QString::number(dockWidgets().size() + 1));
+ dockWidget->setObjectName(QLatin1String("dockWidget")
+ + QString::number(dockWidgets().size() + 1));
} else {
dockWidget->setObjectName(objectName + QLatin1String("DockWidget"));
}
@@ -124,9 +125,12 @@ QDockWidget *FancyMainWindow::addDockForWidget(QWidget *widget)
void FancyMainWindow::updateDockWidget(QDockWidget *dockWidget)
{
const QDockWidget::DockWidgetFeatures features =
- (d->m_locked) ? QDockWidget::DockWidgetClosable | QDockWidget::DockWidgetFloatable
- : QDockWidget::DockWidgetMovable | QDockWidget::DockWidgetClosable | QDockWidget::DockWidgetFloatable;
- if (dockWidget->property("managed_dockwidget").isNull()) { // for the debugger tool bar
+ (d->m_locked) ?
+ QDockWidget::DockWidgetClosable | QDockWidget::DockWidgetFloatable :
+ QDockWidget::DockWidgetMovable | QDockWidget::DockWidgetClosable
+ | QDockWidget::DockWidgetFloatable;
+ // for the debugger tool bar
+ if (dockWidget->property("managed_dockwidget").isNull()) {
QWidget *titleBarWidget = dockWidget->titleBarWidget();
if (d->m_locked && !titleBarWidget && !dockWidget->isFloating())
titleBarWidget = new QWidget(dockWidget);
@@ -164,7 +168,8 @@ void FancyMainWindow::setTrackingEnabled(bool enabled)
if (enabled) {
d->m_handleDockVisibilityChanges = true;
foreach (QDockWidget *dockWidget, dockWidgets())
- dockWidget->setProperty(dockWidgetActiveState, dockWidget->isVisible());
+ dockWidget->setProperty(dockWidgetActiveState,
+ dockWidget->isVisible());
} else {
d->m_handleDockVisibilityChanges = false;
}
@@ -243,7 +248,8 @@ QHash<QString, QVariant> FancyMainWindow::saveSettings() const
void FancyMainWindow::restoreSettings(const QHash<QString, QVariant> &settings)
{
- QByteArray ba = settings.value(QLatin1String(stateKeyC), QByteArray()).toByteArray();
+ QByteArray ba = settings.value(QLatin1String(stateKeyC),
+ QByteArray()).toByteArray();
if (!ba.isEmpty())
restoreState(ba, settingsVersion);
d->m_locked = settings.value(QLatin1String("Locked"), true).toBool();