diff --git a/App/src/TestFittingModule2.cpp b/App/src/TestFittingModule2.cpp
index 0588b382932a3fa10a1921e217ef80468fb65a83..2cbba913b13dee02288445daadc1f333868ece9b 100644
--- a/App/src/TestFittingModule2.cpp
+++ b/App/src/TestFittingModule2.cpp
@@ -55,12 +55,14 @@ TestFittingModule2::TestFittingModule2()
// setting up fitSuite
m_fitSuite = new FitSuite();
- m_fitSuite->setMinimizer( MinimizerFactory::createMinimizer("Minuit2", "Combined") );
- //m_fitSuite->setMinimizer( MinimizerFactory::createMinimizer("Fumili") );
- m_fitSuite->attachObserver( FitSuiteObserverFactory::createPrintObserver() );
- m_fitSuite->attachObserver( FitSuiteObserverFactory::createDrawObserver() );
- m_fitSuite->attachObserver( FitSuiteObserverFactory::createTreeObserver() );
-
+ m_fitSuite->setMinimizer(
+ MinimizerFactory::createMinimizer("Minuit2", "Combined") );
+ m_fitSuite->attachObserver(
+ FitSuiteObserverFactory::createPrintObserver() );
+ m_fitSuite->attachObserver(
+ FitSuiteObserverFactory::createDrawObserver() );
+ m_fitSuite->attachObserver(
+ FitSuiteObserverFactory::createTreeObserver() );
}
@@ -89,90 +91,94 @@ void TestFittingModule2::execute()
//fit_example_mask();
}
+//! Basic fit example.
-/* ************************************************************************* */
-// basic fit example
-/* ************************************************************************* */
void TestFittingModule2::fit_example_basics()
{
initializeSimulation();
initializeRealData();
- m_fitSuite->addFitParameter("*SampleBuilder/m_cylinder_height", 5*Units::nanometer, 1*Units::nanometer, AttLimits::lowerLimited(0.01) );
- m_fitSuite->addFitParameter("*SampleBuilder/m_cylinder_radius", 6*Units::nanometer, 1*Units::nanometer, AttLimits::lowerLimited(0.01) );
- m_fitSuite->addFitParameter("*SampleBuilder/m_prism3_half_side", 5*Units::nanometer, 1*Units::nanometer, AttLimits::lowerLimited(0.01) );
- m_fitSuite->addFitParameter("*SampleBuilder/m_prism3_height", 6*Units::nanometer, 1*Units::nanometer, AttLimits::lowerLimited(0.01) );
-// m_fitSuite->addFitParameter("*SampleBuilder/m_cylinder_height", 12*Units::nanometer, 1*Units::nanometer, AttLimits::lowerLimited(0.01) );
-// m_fitSuite->addFitParameter("*SampleBuilder/m_cylinder_radius", 2*Units::nanometer, 1*Units::nanometer, AttLimits::lowerLimited(0.01) );
-// m_fitSuite->addFitParameter("*SampleBuilder/m_prism3_half_side", 12*Units::nanometer, 1*Units::nanometer, AttLimits::lowerLimited(0.01) );
-// m_fitSuite->addFitParameter("*SampleBuilder/m_prism3_height", 2*Units::nanometer, 1*Units::nanometer, AttLimits::lowerLimited(0.01) );
- m_fitSuite->addFitParameter("*SampleBuilder/m_cylinder_ratio", 0.2, 0.1, AttLimits::fixed());
+ m_fitSuite->addFitParameter("*SampleBuilder/m_cylinder_height",
+ 5*Units::nanometer, 1*Units::nanometer,
+ AttLimits::lowerLimited(0.01) );
+ m_fitSuite->addFitParameter("*SampleBuilder/m_cylinder_radius",
+ 6*Units::nanometer, 1*Units::nanometer,
+ AttLimits::lowerLimited(0.01) );
+ m_fitSuite->addFitParameter("*SampleBuilder/m_prism3_half_side",
+ 5*Units::nanometer, 1*Units::nanometer,
+ AttLimits::lowerLimited(0.01) );
+ m_fitSuite->addFitParameter("*SampleBuilder/m_prism3_height",
+ 6*Units::nanometer, 1*Units::nanometer,
+ AttLimits::lowerLimited(0.01) );
+ m_fitSuite->addFitParameter("*SampleBuilder/m_cylinder_ratio",
+ 0.2, 0.1,
+ AttLimits::fixed());
m_fitSuite->addSimulationAndRealData(*mp_simulation, *mp_real_data);
m_fitSuite->runFit();
-
}
+//! Fit example with chi2 module adjustment.
-/* ************************************************************************* */
-// fit example with chi2 module adjustment
-/* ************************************************************************* */
void TestFittingModule2::fit_example_chimodule()
{
initializeSimulation();
initializeRealData();
- m_fitSuite->addFitParameter("*SampleBuilder/m_cylinder_height", 4*Units::nanometer, 0.01*Units::nanometer, AttLimits::lowerLimited(0.01) );
- m_fitSuite->addFitParameter("*SampleBuilder/m_cylinder_radius", 6*Units::nanometer, 0.01*Units::nanometer, AttLimits::lowerLimited(0.01) );
- m_fitSuite->addFitParameter("*SampleBuilder/m_prism3_half_side", 4*Units::nanometer, 0.01*Units::nanometer, AttLimits::lowerLimited(0.01) );
- m_fitSuite->addFitParameter("*SampleBuilder/m_prism3_height", 6*Units::nanometer, 0.01*Units::nanometer, AttLimits::lowerLimited(0.01) );
- m_fitSuite->addFitParameter("*SampleBuilder/m_cylinder_ratio", 0.2, 0.1, AttLimits::fixed());
- //m_fitSuite->addFitParameter("*Normalizer/scale", 1, 0.01*Units::nanometer, AttLimits::limited(0.9,1.1) );
-
+ m_fitSuite->addFitParameter("*SampleBuilder/m_cylinder_height",
+ 4*Units::nanometer, 0.01*Units::nanometer,
+ AttLimits::lowerLimited(0.01) );
+ m_fitSuite->addFitParameter("*SampleBuilder/m_cylinder_radius",
+ 6*Units::nanometer, 0.01*Units::nanometer,
+ AttLimits::lowerLimited(0.01) );
+ m_fitSuite->addFitParameter("*SampleBuilder/m_prism3_half_side",
+ 4*Units::nanometer, 0.01*Units::nanometer,
+ AttLimits::lowerLimited(0.01) );
+ m_fitSuite->addFitParameter("*SampleBuilder/m_prism3_height",
+ 6*Units::nanometer, 0.01*Units::nanometer,
+ AttLimits::lowerLimited(0.01) );
+ m_fitSuite->addFitParameter("*SampleBuilder/m_cylinder_ratio",
+ 0.2, 0.1,
+ AttLimits::fixed());
// setting up fitSuite
ChiSquaredModule chiModule;
- //chiModule.setChiSquaredFunction( SquaredFunctionDefault() );
-// chiModule.setChiSquaredFunction( SquaredFunctionWhichOnlyWorks() ); // it works only with resolution function, without it fit doesn't converge
chiModule.setChiSquaredFunction( SquaredFunctionWithSystematicError() );
chiModule.setOutputDataNormalizer( OutputDataSimpleNormalizer() );
- //chiModule.setIntensityFunction( IntensityFunctionLog() );
- m_fitSuite->addSimulationAndRealData(*mp_simulation, *mp_real_data, chiModule);
+ m_fitSuite->addSimulationAndRealData(
+ *mp_simulation, *mp_real_data, chiModule);
- for(FitSuiteParameters::iterator it = m_fitSuite->getFitParameters()->begin(); it!=m_fitSuite->getFitParameters()->end(); ++it) {
+ for(FitSuiteParameters::iterator it =
+ m_fitSuite->getFitParameters()->begin();
+ it!=m_fitSuite->getFitParameters()->end(); ++it)
std::cout << (*it) << std::endl;
- }
-
m_fitSuite->runFit();
-
}
-/* ************************************************************************* */
-// fit example with strategies
-/* ************************************************************************* */
+//! Fit example with strategies.
+
void TestFittingModule2::fit_example_strategies()
{
initializeSimulation();
initializeRealData();
- m_fitSuite->addFitParameter("*SampleBuilder/m_cylinder_height", 12*Units::nanometer, 1*Units::nanometer, AttLimits::lowerLimited(0.01) );
- m_fitSuite->addFitParameter("*SampleBuilder/m_cylinder_radius", 2*Units::nanometer, 1*Units::nanometer, AttLimits::lowerLimited(0.01) );
- m_fitSuite->addFitParameter("*SampleBuilder/m_prism3_half_side", 12*Units::nanometer, 1*Units::nanometer, AttLimits::lowerLimited(0.01) );
- m_fitSuite->addFitParameter("*SampleBuilder/m_prism3_height", 2*Units::nanometer, 1*Units::nanometer, AttLimits::lowerLimited(0.01) );
- m_fitSuite->addFitParameter("*SampleBuilder/m_cylinder_ratio", 0.2, 0.1, AttLimits::fixed());
-
- // Applying fit strategy: fixing/releasing parameters
-// FitSuiteStrategyAdjustParameters *strategy0 = new FitSuiteStrategyAdjustParameters("strategy0");
-// strategy0->fix_all().release("*SampleBuilder/m_cylinder_ratio");
-// m_fitSuite->addFitStrategy(strategy0);
-// FitSuiteStrategyAdjustParameters *strategy1 = new FitSuiteStrategyAdjustParameters("strategy1");
-// strategy1->release_all().fix("*SampleBuilder/m_cylinder_ratio");
-// m_fitSuite->addFitStrategy(strategy1);
-// FitSuiteStrategyAdjustParameters *strategy2 = new FitSuiteStrategyAdjustParameters("strategy2");
-// strategy2->release_all();
-// m_fitSuite->addFitStrategy(strategy2);
+ m_fitSuite->addFitParameter("*SampleBuilder/m_cylinder_height",
+ 12*Units::nanometer, 1*Units::nanometer,
+ AttLimits::lowerLimited(0.01) );
+ m_fitSuite->addFitParameter("*SampleBuilder/m_cylinder_radius",
+ 2*Units::nanometer, 1*Units::nanometer,
+ AttLimits::lowerLimited(0.01) );
+ m_fitSuite->addFitParameter("*SampleBuilder/m_prism3_half_side",
+ 12*Units::nanometer, 1*Units::nanometer,
+ AttLimits::lowerLimited(0.01) );
+ m_fitSuite->addFitParameter("*SampleBuilder/m_prism3_height",
+ 2*Units::nanometer, 1*Units::nanometer,
+ AttLimits::lowerLimited(0.01) );
+ m_fitSuite->addFitParameter("*SampleBuilder/m_cylinder_ratio",
+ 0.2, 0.1,
+ AttLimits::fixed());
// Applying fit strategy: resizing real data
m_fitSuite->addFitStrategy(new FitSuiteStrategyAdjustData(3));
@@ -180,26 +186,25 @@ void TestFittingModule2::fit_example_strategies()
m_fitSuite->addFitStrategy(new FitSuiteStrategyAdjustData(1));
m_fitSuite->addFitStrategy(new FitSuiteStrategyDefault());
- // Applying fit strategy: disturbing data to get out of local minima
- //m_fitSuite->addFitStrategy(new FitSuiteStrategyBootstrap());
-
m_fitSuite->addSimulationAndRealData(*mp_simulation, *mp_real_data);
- m_fitSuite->setMinimizer( MinimizerFactory::createMinimizer("Minuit2", "Migrad") );
+ m_fitSuite->setMinimizer(
+ MinimizerFactory::createMinimizer("Minuit2", "Migrad") );
m_fitSuite->runFit();
}
-// ----------------------------------------------------------------------------
-// fit example with data masking
-// ----------------------------------------------------------------------------
+//! Fit example with data masking.
+
void TestFittingModule2::fit_example_mask()
{
initializeSimulation();
initializeRealData();
- mp_simulation->setDetectorResolutionFunction(new ResolutionFunction2DSimple(0.0002, 0.0002));
+ mp_simulation->setDetectorResolutionFunction(
+ new ResolutionFunction2DSimple(0.0002, 0.0002));
- TCanvas *c1 = DrawHelper::createAndRegisterCanvas("c1_test_meso_crystal", "mesocrystal");
+ TCanvas *c1 = DrawHelper::createAndRegisterCanvas(
+ "c1_test_meso_crystal", "mesocrystal");
c1->cd(); gPad->SetLogz();
c1->Divide(2,2);
@@ -214,7 +219,8 @@ void TestFittingModule2::fit_example_mask()
const double minima[]={0.003, 0.003};
const double maxima[]={0.03, 0.03};
- Mask *mask1 = OutputDataFunctions::CreateRectangularMask(*mp_real_data, minima, maxima);
+ Mask *mask1 = OutputDataFunctions::CreateRectangularMask(
+ *mp_real_data, minima, maxima);
mp_real_data->setMask(*mask1);
c1->cd(2);
@@ -224,61 +230,66 @@ void TestFittingModule2::fit_example_mask()
IsGISAXSTools::drawOutputDataInPad(*mp_real_data, "COLZ", "real_data");
c1->Update();
- m_fitSuite->addFitParameter("*SampleBuilder/m_cylinder_height", 4*Units::nanometer, 1*Units::nanometer, AttLimits::lowerLimited(0.01) );
- m_fitSuite->addFitParameter("*SampleBuilder/m_cylinder_radius", 4*Units::nanometer, 1*Units::nanometer, AttLimits::lowerLimited(0.01) );
- m_fitSuite->addFitParameter("*SampleBuilder/m_prism3_half_side", 4*Units::nanometer, 1*Units::nanometer, AttLimits::lowerLimited(0.01) );
- m_fitSuite->addFitParameter("*SampleBuilder/m_prism3_height", 4*Units::nanometer, 1*Units::nanometer, AttLimits::lowerLimited(0.01) );
- m_fitSuite->addFitParameter("*SampleBuilder/m_cylinder_ratio", 0.2, 0.1, AttLimits::fixed());
-// m_fitSuite->addFitParameter("*Normalizer/scale", 1e10, 1, AttLimits::limited(0.1*1e10, 2.*1e10));
-// m_fitSuite->addFitParameter("*Normalizer/scale", 1e10, 1, AttLimits::limited(1e8, 1e12));
+ m_fitSuite->addFitParameter("*SampleBuilder/m_cylinder_height",
+ 4*Units::nanometer, 1*Units::nanometer,
+ AttLimits::lowerLimited(0.01) );
+ m_fitSuite->addFitParameter("*SampleBuilder/m_cylinder_radius",
+ 4*Units::nanometer, 1*Units::nanometer,
+ AttLimits::lowerLimited(0.01) );
+ m_fitSuite->addFitParameter("*SampleBuilder/m_prism3_half_side",
+ 4*Units::nanometer, 1*Units::nanometer,
+ AttLimits::lowerLimited(0.01) );
+ m_fitSuite->addFitParameter("*SampleBuilder/m_prism3_height",
+ 4*Units::nanometer, 1*Units::nanometer,
+ AttLimits::lowerLimited(0.01) );
+ m_fitSuite->addFitParameter("*SampleBuilder/m_cylinder_ratio",
+ 0.2, 0.1,
+ AttLimits::fixed());
ChiSquaredModule chiModule;
- //chiModule.setChiSquaredFunction( SquaredFunctionDefault() );
-// chiModule.setChiSquaredFunction( SquaredFunctionWhichOnlyWorks() ); // it works only with resolution function, without it fit doesn't converge
- //chiModule.setChiSquaredFunction( SquaredFunctionWithSystematicError() );
chiModule.setOutputDataNormalizer( OutputDataSimpleNormalizer(1.0,0) );
-
-
- m_fitSuite->addSimulationAndRealData(*mp_simulation, *mp_real_data, chiModule);
+ m_fitSuite->addSimulationAndRealData(
+ *mp_simulation, *mp_real_data, chiModule);
m_fitSuite->runFit();
-
}
+//! Initialize simulation.
-
-/* ************************************************************************* */
-// initializing simulation
-/* ************************************************************************* */
void TestFittingModule2::initializeSimulation()
{
- if( !mp_sample_builder ) {
- throw NullPointerException("TestFittingModule2::initializeSimulation() -> No sample builder defined");
- }
+ if( !mp_sample_builder )
+ throw NullPointerException(
+ "TestFittingModule2::initializeSimulation() -> "
+ "No sample builder defined");
delete mp_simulation;
mp_simulation = new Simulation(mp_options);
mp_simulation->setSampleBuilder(mp_sample_builder);
- mp_simulation->setDetectorParameters(100, 0.0*Units::degree, 2.0*Units::degree,100 , 0.0*Units::degree, 2.0*Units::degree);
- mp_simulation->setBeamParameters(1.0*Units::angstrom, -0.2*Units::degree, 0.0*Units::degree);
- //mp_simulation->setBeamIntensity(1e10);
+ mp_simulation->setDetectorParameters(
+ 100, 0.0*Units::degree, 2.0*Units::degree,
+ 100, 0.0*Units::degree, 2.0*Units::degree);
+ mp_simulation->setBeamParameters(
+ 1.0*Units::angstrom,
+ -0.2*Units::degree,
+ 0.0*Units::degree);
}
-/* ************************************************************************* */
-// initializing real data
-/* ************************************************************************* */
+//! Create noisy data (simulated experiment).
+
void TestFittingModule2::initializeRealData()
{
- if( !mp_simulation ) throw NullPointerException("TestFittingModule2::initializeRealData() -> Error! No simulation of sample defined ");
+ if( !mp_simulation )
+ throw NullPointerException(
+ "TestFittingModule2::initializeRealData() -> "
+ "Error! No simulation of sample defined ");
- // generating "real" data
mp_simulation->runSimulation();
- // mp_simulation->normalize();
- //m_fitSuite->getFitObjects()->setSimulationNormalize(true);
delete mp_real_data;
- mp_real_data = IsGISAXSTools::createNoisyData(*mp_simulation->getOutputData());
+ mp_real_data = IsGISAXSTools::createNoisyData(
+ *mp_simulation->getOutputData());
- // drawing data
+ // draw data
TCanvas *c1 = new TCanvas("c1","c1",640, 480);
c1->cd(); gPad->SetLogz();
TH2D *hist = IsGISAXSTools::getOutputDataTH2D( *mp_real_data, "real_data");
@@ -287,11 +298,10 @@ void TestFittingModule2::initializeRealData()
}
-/* ************************************************************************* */
// simple sample - mixture of cylinders and prisms on top of substrate
// builder via ISampleBuilder
// 5 fit parameters
-/* ************************************************************************* */
+
TestFittingModule2::SampleBuilder::SampleBuilder()
: m_cylinder_height(5.0*Units::nanometer)
, m_cylinder_radius(5.0*Units::nanometer)
@@ -309,15 +319,25 @@ ISample *TestFittingModule2::SampleBuilder::buildSample() const
complex_t n_air(1.0, 0.0);
complex_t n_substrate(1.0-6e-6, 2e-8);
complex_t n_particle(1.0-6e-4, 2e-8);
- const IMaterial *p_air_material = MaterialManager::getHomogeneousMaterial("Air", n_air);
- const IMaterial *p_substrate_material = MaterialManager::getHomogeneousMaterial("Substrate", n_substrate);
+ const IMaterial *p_air_material =
+ MaterialManager::getHomogeneousMaterial("Air", n_air);
+ const IMaterial *p_substrate_material =
+ MaterialManager::getHomogeneousMaterial("Substrate", n_substrate);
Layer air_layer;
air_layer.setMaterial(p_air_material);
Layer substrate_layer;
substrate_layer.setMaterial(p_substrate_material);
ParticleDecoration particle_decoration;
- particle_decoration.addParticle(new Particle(n_particle, new FormFactorCylinder(m_cylinder_height, m_cylinder_radius)),0.0, m_cylinder_ratio);
- particle_decoration.addParticle(new Particle(n_particle, new FormFactorPrism3(m_prism3_height, m_prism3_half_side)), 0.0, 1.0 - m_cylinder_ratio);
+ particle_decoration.addParticle(
+ new Particle(n_particle,
+ new FormFactorCylinder(m_cylinder_height,
+ m_cylinder_radius)),
+ 0.0, m_cylinder_ratio);
+ particle_decoration.addParticle(
+ new Particle(n_particle,
+ new FormFactorPrism3(m_prism3_height,
+ m_prism3_half_side)),
+ 0.0, 1.0 - m_cylinder_ratio);
particle_decoration.addInterferenceFunction(new InterferenceFunctionNone());
LayerDecorator air_layer_decorator(air_layer, particle_decoration);