diff --git a/App/src/TestIsGISAXS12.cpp b/App/src/TestIsGISAXS12.cpp
index 7709e17a176fa90198cbbba16729df401dadcc25..fdc74005c7e899a2cee234d89d382b4b7695235b 100644
--- a/App/src/TestIsGISAXS12.cpp
+++ b/App/src/TestIsGISAXS12.cpp
@@ -36,8 +36,6 @@
#include "ParticleBuilder.h"
#include "ParticleLayout.h"
#include "ResolutionFunction2DSimple.h"
-#include "StochasticGaussian.h"
-#include "StochasticSampledParameter.h"
#include "Units.h"
#include "Utils.h"
#include "FileSystem.h"
@@ -260,9 +258,9 @@ void TestIsGISAXS12::run_isgisaxs_fit()
hreal->DrawCopy();
hsimul->DrawCopy("same");
if(i_set==0) {
- leg1->AddEntry(hreal,"BornAgain data","lp");
- leg1->AddEntry(hsimul,"BornAgain simul","lp");
- }
+ leg1->AddEntry(hreal,"BornAgain data","lp");
+ leg1->AddEntry(hsimul,"BornAgain simul","lp");
+ }
}
c2->cd(1); leg1->Draw();
c2->cd(2); leg1->Draw();
@@ -501,10 +499,8 @@ ISample *TestIsGISAXS12::TestSampleBuilder::buildSample() const
double sigma1 = radius1*m_dispersion_radius1;
double sigma2 = radius2*m_dispersion_radius2;
int nfwhm(2); // to have xmin=average-nfwhm*FWHM, xmax=average+nfwhm*FWHM (nfwhm = xR/2, where xR is what is defined in isgisaxs *.inp file)
- StochasticDoubleGaussian sg1(radius1, sigma1);
- StochasticDoubleGaussian sg2(radius2, sigma2);
- StochasticSampledParameter par1(sg1, nbins, nfwhm);
- StochasticSampledParameter par2(sg2, nbins, nfwhm);
+ DistributionGaussian gauss1(radius1, sigma1);
+ DistributionGaussian gauss2(radius2, sigma2);
ParticleLayout particle_layout;
InterferenceFunction1DParaCrystal *p_interference_function =
@@ -516,9 +512,11 @@ ISample *TestIsGISAXS12::TestSampleBuilder::buildSample() const
// building nano particles
ParticleBuilder builder;
- builder.setPrototype(cylinder1,"/Particle/FormFactorCylinder/radius", par1, particle_probability1);
+ builder.setPrototype(cylinder1,"/Particle/FormFactorCylinder/radius", gauss1,
+ nbins, nfwhm, particle_probability1);
builder.plantParticles(particle_layout);
- builder.setPrototype(cylinder2,"/Particle/FormFactorCylinder/radius", par2, particle_probability2);
+ builder.setPrototype(cylinder2,"/Particle/FormFactorCylinder/radius", gauss2,
+ nbins, nfwhm, particle_probability2);
builder.plantParticles(particle_layout);
air_layer.addLayout(particle_layout);
diff --git a/App/src/TestIsGISAXS5.cpp b/App/src/TestIsGISAXS5.cpp
index 3e596220c38376454ba2103d2abf458445cb539e..c2a3a4b0c302b921c478b3d8ed49c72a61308e92 100644
--- a/App/src/TestIsGISAXS5.cpp
+++ b/App/src/TestIsGISAXS5.cpp
@@ -35,8 +35,6 @@
#include "ParticleBuilder.h"
#include "ParticleLayout.h"
#include "ResolutionFunction2DSimple.h"
-#include "StochasticGaussian.h"
-#include "StochasticSampledParameter.h"
#include "Units.h"
#include "Utils.h"
@@ -206,9 +204,9 @@ void TestIsGISAXS5::run_isgisaxs_fit()
hreal->DrawCopy();
hsimul->DrawCopy("same");
if(i_set==0) {
- leg1->AddEntry(hreal,"BornAgain data","lp");
- leg1->AddEntry(hsimul,"BornAgain simul","lp");
- }
+ leg1->AddEntry(hreal,"BornAgain data","lp");
+ leg1->AddEntry(hsimul,"BornAgain simul","lp");
+ }
}
c2->cd(1); leg1->Draw();
c2->cd(2); leg1->Draw();
@@ -292,8 +290,7 @@ ISample *TestIsGISAXS5::SampleBuilder::buildSample() const
int nbins=20;
double sigma = m_particle_radius*m_dispersion_radius;
int nfwhm(2); // to have xmin=average-nfwhm*FWHM, xmax=average+nfwhm*FWHM (nfwhm = xR/2, where xR is what is defined in isgisaxs *.inp file)
- StochasticDoubleGaussian sg(m_particle_radius, sigma);
- StochasticSampledParameter stochastic_parameter(sg, nbins, nfwhm);
+ DistributionGaussian gauss(m_particle_radius, sigma);
ParticleLayout particle_layout;
InterferenceFunction1DParaCrystal *p_interference_function =
@@ -305,7 +302,8 @@ ISample *TestIsGISAXS5::SampleBuilder::buildSample() const
// building nano particles
ParticleBuilder builder;
- builder.setPrototype(cylinder,"/Particle/FormFactorCylinder/radius", stochastic_parameter);
+ builder.setPrototype(cylinder,"/Particle/FormFactorCylinder/radius", gauss,
+ nbins, nfwhm);
builder.plantParticles(particle_layout);
// making layer holding all whose nano particles
diff --git a/Core/Samples/inc/ParticleBuilder.h b/Core/Samples/inc/ParticleBuilder.h
index d81992ba2e7f35a51ca22ed13d994b84f24976f5..11ac7dc09f148008338fb022c6de0a1e9d012b88 100644
--- a/Core/Samples/inc/ParticleBuilder.h
+++ b/Core/Samples/inc/ParticleBuilder.h
@@ -17,7 +17,7 @@
#define PARTICLEBUILDER_H
#include "Particle.h"
-#include "IStochasticParameter.h"
+#include "Distributions.h"
#include "ParticleLayout.h"
//! @class ParticleBuilder
@@ -35,16 +35,21 @@ public:
//! @param name parameter name in the parameter pool of given prototype
//! @param parameter variation type
//! @param scale global scale factor for probabilities
- void setPrototype(const Particle& particle, std::string name, const StochasticParameter<double>& param, double scale=1.0);
+ void setPrototype(const Particle& particle, std::string name,
+ const IDistribution1D& param, size_t nbr_samples,
+ double sigma_factor=0.0, double scale=1.0);
//! plant particles in given decoration
- void plantParticles(ParticleLayout& decor);
+ void plantParticles(ParticleLayout& layout);
private:
- Particle *m_prototype; //!< prototype of the particle, all particles will be cloned from it
- std::string m_parameter_name; //!< name of parameter to variate
- StochasticParameter<double > *m_parameter;
- double m_scale; //!< global scale factor for probabilities
+ //! prototype of the particle, all particles will be cloned from it
+ Particle *mp_prototype;
+ std::string m_parameter_name; //!< name of parameter to vary
+ IDistribution1D *mp_distribution; //!< distribution for the parameter
+ size_t m_nbr_samples; //!< number of particles to be created
+ double m_sigma_factor; //!< range of parameter in FWHM
+ double m_scale; //!< global scale factor for probabilities
};
#endif // PARTICLEBUILDER_H
diff --git a/Core/Samples/src/ParticleBuilder.cpp b/Core/Samples/src/ParticleBuilder.cpp
index 605031a25232a59d66e512644a8a5aa948a41958..f4530febeb1442583195f9247b9f448c65403365 100644
--- a/Core/Samples/src/ParticleBuilder.cpp
+++ b/Core/Samples/src/ParticleBuilder.cpp
@@ -16,67 +16,78 @@
#include "ParticleBuilder.h"
#include "ParticleLayout.h"
#include "Numeric.h"
-#include "StochasticSampledParameter.h"
#include <numeric>
#include <algorithm>
-ParticleBuilder::ParticleBuilder() :
- m_prototype(0), m_parameter(0), m_scale(0)
+ParticleBuilder::ParticleBuilder()
+ : mp_prototype(0)
+ , mp_distribution(0)
+ , m_nbr_samples(0)
+ , m_sigma_factor(0.0)
+ , m_scale(0)
{
}
ParticleBuilder::~ParticleBuilder()
{
- delete m_prototype;
- delete m_parameter;
+ delete mp_prototype;
+ delete mp_distribution;
}
//! Sets prototype for particle production
-void ParticleBuilder::setPrototype(const Particle& particle, std::string name, const StochasticParameter<double>& param, double scale)
+void ParticleBuilder::setPrototype(const Particle &particle, std::string name,
+ const IDistribution1D ¶m, size_t nbr_samples, double sigma_factor,
+ double scale)
{
- delete m_prototype;
- m_prototype = particle.clone();
+ delete mp_prototype;
+ mp_prototype = particle.clone();
m_parameter_name = name;
- delete m_parameter;
- m_parameter = param.clone();
+ delete mp_distribution;
+ mp_distribution = param.clone();
+ m_nbr_samples = nbr_samples;
+ m_sigma_factor = sigma_factor;
m_scale = scale;
}
//! plant particles in given decoration
-void ParticleBuilder::plantParticles(ParticleLayout& decor)
+void ParticleBuilder::plantParticles(ParticleLayout& layout)
{
- if( !m_prototype ) throw NullPointerException("ParticleBuilder::plantParticle() -> Error. No prototype is defined");
+ if( !mp_prototype ) throw NullPointerException(
+ "ParticleBuilder::plantParticle() -> Error. No prototype is defined");
- if( !m_parameter ) throw NullPointerException("ParticleBuilder::plantParticle() -> Error. No parameter is defined");
+ if( !mp_distribution ) throw NullPointerException(
+ "ParticleBuilder::plantParticle() -> Error. No distribution is defined");
- ParameterPool *pool = m_prototype->createParameterTree();
+ ParameterPool *pool = mp_prototype->createParameterTree();
- StochasticSampledParameter *sampled_parameter = dynamic_cast<StochasticSampledParameter *>(m_parameter);
- if( !sampled_parameter) {
- throw LogicErrorException("ParticleBuilder::plantParticle() -> Error. Not supported parameter type");
+ // generate parameter samples
+ std::vector<ParameterSample> samples =
+ mp_distribution->generateSamples(m_nbr_samples, m_sigma_factor);
+
+ // find maximum weight
+ double max_weight = 0.0;
+ for(std::vector<ParameterSample>::const_iterator it = samples.begin();
+ it != samples.end(); ++it) {
+ max_weight = std::max(max_weight, it->weight);
}
- // calculating sum of all weights, and maximum value
- std::vector<double> weights;
- for(size_t i=0; i<sampled_parameter->getNbins(); ++i) weights.push_back(sampled_parameter->probabilityBinDensity(i));
- double maximum_value = *std::max_element(weights.begin(), weights.end());
- double sum_of_weights = std::accumulate(weights.begin(), weights.end(), 0.0);
// loop over sampled parameter values
- for(size_t i=0; i<sampled_parameter->getNbins(); ++i) {
+ for(std::vector<ParameterSample>::const_iterator it = samples.begin();
+ it != samples.end(); ++it) {
- double weight = sampled_parameter->probabilityBinDensity(i);
- double value = sampled_parameter->getBinValue(i);
+ double weight = it->weight;
+ double value = it->value;
// changing value of the particle's parameter and making clone
pool->setParameterValue(m_parameter_name, value);
- Particle *particle = m_prototype->clone();
+ Particle *particle = mp_prototype->clone();
- if(weight/maximum_value > Numeric::probthreshold) { // isgisaxs way
- decor.addParticle(*particle, 0.0, weight/sum_of_weights*m_scale);
+ if(weight/max_weight > Numeric::probthreshold) { // isgisaxs way
+ layout.addParticle(*particle, 0.0, weight*m_scale);
}
delete particle;
diff --git a/Core/StandardSamples/IsGISAXS02Builder.cpp b/Core/StandardSamples/IsGISAXS02Builder.cpp
index 6df79cb3bfd77ce4d3685b325c96c5d60a54ddb1..94480d7359cc63258fc9d05e6aaf90f05d299032 100644
--- a/Core/StandardSamples/IsGISAXS02Builder.cpp
+++ b/Core/StandardSamples/IsGISAXS02Builder.cpp
@@ -18,11 +18,8 @@
#include "ParticleLayout.h"
#include "Materials.h"
#include "FormFactorCylinder.h"
-//#include "FormFactorPrism3.h"
#include "Units.h"
#include "InterferenceFunctionNone.h"
-#include "StochasticSampledParameter.h"
-#include "StochasticGaussian.h"
#include "ParticleBuilder.h"
@@ -73,17 +70,17 @@ ISample *IsGISAXS02Builder::buildSample() const
double sigma1 = m_radius1*m_sigma1_ratio;
double sigma2 = m_radius2*m_sigma2_ratio;
int nfwhm(3); // to have xmin=average-nfwhm*FWHM, xmax=average+nfwhm*FWHM (nfwhm = xR/2, where xR is what is defined in isgisaxs *.inp file)
- StochasticDoubleGaussian sg1(m_radius1, sigma1);
- StochasticDoubleGaussian sg2(m_radius2, sigma2);
- StochasticSampledParameter par1(sg1, nbins, nfwhm);
- StochasticSampledParameter par2(sg2, nbins, nfwhm);
+ DistributionGaussian gauss1(m_radius1, sigma1);
+ DistributionGaussian gauss2(m_radius2, sigma2);
// building nano particles
ParticleBuilder builder;
- builder.setPrototype(cylinder1,"/Particle/FormFactorCylinder/radius", par1, 0.95);
+ builder.setPrototype(cylinder1,"/Particle/FormFactorCylinder/radius", gauss1,
+ nbins, nfwhm, 0.95);
builder.plantParticles(particle_layout);
- builder.setPrototype(cylinder2,"/Particle/FormFactorCylinder/radius", par2, 0.05);
+ builder.setPrototype(cylinder2,"/Particle/FormFactorCylinder/radius", gauss2,
+ nbins, nfwhm, 0.05);
builder.plantParticles(particle_layout);
particle_layout.addInterferenceFunction(new InterferenceFunctionNone());
diff --git a/Core/StandardSamples/IsGISAXS03Builder.cpp b/Core/StandardSamples/IsGISAXS03Builder.cpp
index e5949ca93d850be2f8817c2dfc740cc693efc317..23be06c91f90c17ba08621ad0f5c50152f0e89aa 100644
--- a/Core/StandardSamples/IsGISAXS03Builder.cpp
+++ b/Core/StandardSamples/IsGISAXS03Builder.cpp
@@ -20,8 +20,7 @@
#include "FormFactorCylinder.h"
#include "Units.h"
#include "InterferenceFunctionNone.h"
-#include "StochasticSampledParameter.h"
-#include "StochasticGaussian.h"
+#include "Distributions.h"
#include "ParticleBuilder.h"
@@ -144,11 +143,11 @@ ISample *IsGISAXS03BASizeBuilder::buildSample() const
FormFactorCylinder p_ff_cylinder( m_radius, m_height);
Particle nano_particle(particle_material, p_ff_cylinder);
// radius of nanoparticles will be sampled with gaussian probability
- int nbins(100), nfwhm(2);
- StochasticDoubleGaussian double_gaussian(m_radius, sigma);
- StochasticSampledParameter par(double_gaussian, nbins, nfwhm);
+ int n_samples(100), nfwhm(2);
+ DistributionGaussian gauss(m_radius, sigma);
ParticleBuilder builder;
- builder.setPrototype(nano_particle,"/Particle/FormFactorCylinder/radius", par);
+ builder.setPrototype(nano_particle,"/Particle/FormFactorCylinder/radius",
+ gauss, n_samples, nfwhm);
builder.plantParticles(particle_layout);
particle_layout.addInterferenceFunction(new InterferenceFunctionNone());
diff --git a/Core/StandardSamples/IsGISAXS15Builder.cpp b/Core/StandardSamples/IsGISAXS15Builder.cpp
index e85d1d2d1a6c7bda3a8768a3e99bac8d5d75db70..2925902c32556057f2c6db5ee2c355e1a1a1a0f1 100644
--- a/Core/StandardSamples/IsGISAXS15Builder.cpp
+++ b/Core/StandardSamples/IsGISAXS15Builder.cpp
@@ -20,8 +20,6 @@
#include "Units.h"
#include "InterferenceFunction1DParaCrystal.h"
#include "FormFactorCylinder.h"
-#include "StochasticGaussian.h"
-#include "StochasticSampledParameter.h"
#include "ParticleBuilder.h"
@@ -49,11 +47,10 @@ ISample *IsGISAXS15Builder::buildSample() const
FormFactorCylinder ff_cylinder(5.0*Units::nanometer, 5.0*Units::nanometer);
Particle particle_prototype(particle_material, ff_cylinder);
- StochasticDoubleGaussian sg(5.0*Units::nanometer, 1.25*Units::nanometer);
- StochasticSampledParameter stochastic_radius(sg,30, 2);
+ DistributionGaussian gauss(5.0*Units::nanometer, 1.25*Units::nanometer);
ParticleBuilder particle_builder;
particle_builder.setPrototype(particle_prototype,
- "/Particle/FormFactorCylinder/radius", stochastic_radius);
+ "/Particle/FormFactorCylinder/radius", gauss, 30, 2.0);
particle_builder.plantParticles(particle_layout);
// Set height of each particle to its radius (H/R fixed)