From 741b8433d5a5b19fd00f6eaee6a813b763960a2b Mon Sep 17 00:00:00 2001
From: pospelov <pospelov@fz-juelich.de>
Date: Fri, 5 Oct 2012 18:44:19 +0200
Subject: [PATCH] FitSuite, part II
---
App/inc/ROOTMinimizer.h | 13 +-
App/src/ROOTMinimizer.cpp | 47 ++++++-
App/src/TestMesoCrystal2.cpp | 65 +++++++--
Core/Algorithms/inc/Experiment.h | 7 +
Core/Algorithms/src/Experiment.cpp | 11 ++
Core/Core.pro | 4 +-
Core/Samples/inc/ICompositeSample.h | 4 +
Core/Samples/inc/ISample.h | 5 +-
Core/Samples/inc/ParameterPool.h | 14 +-
Core/Samples/src/ISample.cpp | 10 +-
Core/Samples/src/ParameterPool.cpp | 17 +--
Core/Tools/inc/FitMultiParameter.h | 6 +
Core/Tools/inc/FitParameter.h | 37 +++++-
Core/Tools/inc/FitSuite.h | 34 ++++-
Core/Tools/inc/{Minimizer.h => IMinimizer.h} | 27 ++--
Core/Tools/src/FitMultiParameter.cpp | 8 ++
Core/Tools/src/FitParameter.cpp | 15 ++-
Core/Tools/src/FitSuite.cpp | 131 ++++++++++++++++++-
Core/Tools/src/IMinimizer.cpp | 5 +
Core/Tools/src/Minimizer.cpp | 5 -
20 files changed, 402 insertions(+), 63 deletions(-)
rename Core/Tools/inc/{Minimizer.h => IMinimizer.h} (61%)
create mode 100644 Core/Tools/src/IMinimizer.cpp
delete mode 100644 Core/Tools/src/Minimizer.cpp
diff --git a/App/inc/ROOTMinimizer.h b/App/inc/ROOTMinimizer.h
index 36e4115236c..bfdaa229725 100644
--- a/App/inc/ROOTMinimizer.h
+++ b/App/inc/ROOTMinimizer.h
@@ -14,25 +14,32 @@
//! @author Scientific Computing Group at FRM II
//! @date 05.10.2012
-#include "Minimizer.h"
+#include "IMinimizer.h"
#include "OutputData.h"
+#include <string>
// from ROOT
#include "Math/Minimizer.h"
#include "Math/Factory.h"
-#include <string>
+#include "Math/Functor.h"
+
//- -------------------------------------------------------------------
//! @class FitSuite
//! @brief Wrapper for ROOT minimizers to interface with our FitSuite
//- -------------------------------------------------------------------
-class ROOTMinimizer : public Minimizer
+class ROOTMinimizer : public IMinimizer
{
public:
ROOTMinimizer(const std::string &minimizer_name, const std::string &algo_type);
virtual ~ROOTMinimizer();
+ virtual void setVariable(int i, const FitParameter *par) ;
+ virtual void setFunction(boost::function<double(const double *)> fcn, int ndim=1);
+ virtual void minimize();
+
private:
ROOT::Math::Minimizer *m_root_minimizer;
+ ROOT::Math::Functor *m_fcn;
};
#endif // ROOTMINIMIZER_H
diff --git a/App/src/ROOTMinimizer.cpp b/App/src/ROOTMinimizer.cpp
index c6cc4cdf01b..9a04fbfc3c3 100644
--- a/App/src/ROOTMinimizer.cpp
+++ b/App/src/ROOTMinimizer.cpp
@@ -1,12 +1,57 @@
#include "ROOTMinimizer.h"
+#include "Exceptions.h"
-ROOTMinimizer::ROOTMinimizer(const std::string &minimizer_name, const std::string &algo_type)
+
+ROOTMinimizer::ROOTMinimizer(const std::string &minimizer_name, const std::string &algo_type) : m_fcn(0)
{
m_root_minimizer = ROOT::Math::Factory::CreateMinimizer(minimizer_name.c_str(), algo_type.c_str() );
+ if( m_root_minimizer == 0 ) {
+ throw NullPointerException("ROOTMinimizer::ROOTMinimizer() -> Error! Can't build minimizer");
+ }
}
ROOTMinimizer::~ROOTMinimizer()
{
delete m_root_minimizer;
+ delete m_fcn;
+}
+
+
+//void ROOTMinimizer::setVariable(int i, const std::string &name, double value, double step)
+//{
+// m_root_minimizer->SetVariable(i, name.c_str(), value, step);
+//}
+
+void ROOTMinimizer::setVariable(int i, const FitParameter *par)
+{
+ if(par->hasDoubleBound() ) {
+ m_root_minimizer->SetLimitedVariable(i, par->getName().c_str(), par->getValue(), par->getStep(), par->getLowerLimit(), par->getUpperLimit());
+ } else if(par->hasLowerLimit() && !par->hasUpperLimit() ) {
+ m_root_minimizer->SetLowerLimitedVariable(i, par->getName().c_str(), par->getValue(), par->getStep(), par->getLowerLimit());
+ } else if( par->hasUpperLimit() && !par->hasLowerLimit() ) {
+ m_root_minimizer->SetUpperLimitedVariable(i, par->getName().c_str(), par->getValue(), par->getStep(), par->getUpperLimit());
+ } else if( !par->hasUpperLimit() && !par->hasLowerLimit() ) {
+ m_root_minimizer->SetVariable(i, par->getName().c_str(), par->getValue(), par->getStep());
+ } else {
+ throw LogicErrorException("ROOTMinimizer::setVariable() -> I wish I knew how I got there...");
+ }
+}
+
+
+
+void ROOTMinimizer::minimize()
+{
+ m_root_minimizer->Minimize();
+}
+
+
+/* ************************************************************************* */
+// set fcn function for minimizer
+/* ************************************************************************* */
+void ROOTMinimizer::setFunction(boost::function<double(const double *)> fcn, int ndim)
+{
+ m_fcn = new ROOT::Math::Functor(fcn, ndim);
+ m_root_minimizer->SetFunction(*m_fcn);
}
+
diff --git a/App/src/TestMesoCrystal2.cpp b/App/src/TestMesoCrystal2.cpp
index f9420cbf9ae..41b65b76a00 100644
--- a/App/src/TestMesoCrystal2.cpp
+++ b/App/src/TestMesoCrystal2.cpp
@@ -21,6 +21,9 @@
#include "OutputDataIOFactory.h"
#include "FitSuite.h"
#include "ROOTMinimizer.h"
+#include "SampleFactory.h"
+#include "FitMultiParameter.h"
+#include "TRange.h"
#include "TCanvas.h"
#include "TH2D.h"
@@ -46,16 +49,30 @@ void TestMesoCrystal2::execute()
{
initializeExperiment();
+// m_sample->walk_and_print();
+// ParameterPool *p_param_pool = m_sample->createParameterTree();
+// std::cout << *p_param_pool;
+// return;
+
m_experiment->runSimulation();
- IsGISAXSTools::drawLogOutputData(*(m_experiment->getOutputDataClone()), "c1_test_meso_crystal", "mesocrystal","CONT4 Z", "mesocrystal");
+ m_experiment->normalize();
+
+ OutputData<double > *m_real_data = m_experiment->getOutputDataClone();
+
+// IsGISAXSTools::setMinimum(1.);
+// IsGISAXSTools::drawLogOutputData(*(m_experiment->getOutputDataClone()), "c1_test_meso_crystal", "mesocrystal","CONT4 Z", "mesocrystal");
//mp_exact_data = experiment.getOutputDataClone();
- return;
+// return;
// setting fitSuite
FitSuite *fitSuite = new FitSuite();
-
fitSuite->setMinimizer( new ROOTMinimizer("Minuit2", "Migrad") );
fitSuite->setExperiment(m_experiment);
+ fitSuite->setRealData(*m_real_data);
+ //fitSuite->addFitParameter("*alpha",0.5, 0.1);
+ fitSuite->addFitParameter("*height",2.0, 0.1, TRange<double>(1.0, 10.0) );
+ fitSuite->runFit();
+
}
@@ -66,15 +83,19 @@ void TestMesoCrystal2::execute()
void TestMesoCrystal2::initializeExperiment()
{
delete m_experiment;
- initializeSample();
+ //initializeSample();
+
+ m_sample = SampleFactory::instance().createItem("IsGISAXS9_Pyramid");
+
m_experiment = new GISASExperiment();
m_experiment->setSample( m_sample );
- m_experiment->setDetectorParameters(100, 0.3*Units::degree, 0.073, 100 , -0.4*Units::degree, 0.066);
+ m_experiment->setDetectorParameters(200, 0.3*Units::degree, 0.073, 200, -0.4*Units::degree, 0.066);
m_experiment->setBeamParameters(1.77*Units::angstrom, -0.4*Units::degree, 0.0*Units::degree);
- m_experiment->setBeamIntensity(1e7);
+ m_experiment->setBeamIntensity(1e10);
}
+
/* ************************************************************************* */
//
/* ************************************************************************* */
@@ -91,8 +112,8 @@ void TestMesoCrystal2::initializeSample()
complex_t n_avg = std::sqrt(surface_filling_ratio*avg_n_squared_meso + 1.0 - surface_filling_ratio);
complex_t n_particle_adapted = std::sqrt(n_avg*n_avg + n_particle*n_particle - 1.0);
FormFactorCylinder ff_cyl(0.5*Units::micrometer, meso_width);
- double sigma_h = 40*Units::nanometer;
- double sigma_r = 120*Units::nanometer;
+ double sigma_h = 4*Units::nanometer;
+ double sigma_r = 50*Units::nanometer;
FormFactorDecoratorDebyeWaller ff_meso(ff_cyl.clone(), sigma_h*sigma_h/2.0, sigma_r*sigma_r/2.0);
// Create multilayer
@@ -112,12 +133,26 @@ void TestMesoCrystal2::initializeSample()
substrate_layer.setMaterial(p_substrate_material);
IInterferenceFunction *p_interference_funtion = new InterferenceFunctionNone();
ParticleDecoration particle_decoration;
- size_t n_max_phi_rotation_steps = 140;
+ size_t n_max_phi_rotation_steps = 180;
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;
+ // with optimization
+// TRange<double> phi_range(0.0, 2.0*M_PI/3.0);
+// TRange<double> z_range(0.0, 2.6);
+// double max_rho = 2.6;
+// std::vector<double> phi_angles = createLattice(6.1*Units::nanometer)->collectBraggAngles(n_max_phi_rotation_steps, max_rho, phi_range, z_range);
+// for (size_t i=0; i<phi_angles.size(); ++i) {
+// for (size_t j=0; j<n_alpha_rotation_steps; ++j) {
+// Geometry::RotateZ3D transform1(phi_angles[i]);
+// Geometry::RotateY3D transform2(alpha_start + j*alpha_step);
+// Geometry::Transform3D *p_total_transform = new Geometry::Transform3D(transform1*transform2);
+// particle_decoration.addParticle(createMesoCrystal(6.1*Units::nanometer,
+// n_particle_adapted, &ff_meso), p_total_transform, 0.2*Units::micrometer);
+// }
+// }
// without
double phi_step = 2.0*M_PI/3.0/n_max_phi_rotation_steps;
double phi_start = 0.0;
@@ -126,7 +161,7 @@ void TestMesoCrystal2::initializeSample()
Geometry::RotateZ3D transform1(phi_start + (double)i*phi_step);
Geometry::RotateY3D transform2(alpha_start + j*alpha_step);
Geometry::Transform3D *p_total_transform = new Geometry::Transform3D(transform1);
- particle_decoration.addParticle(createMesoCrystal(6.1*Units::nanometer,
+ particle_decoration.addParticle(createMesoCrystal(4.7*Units::nanometer,
n_particle_adapted, &ff_meso), p_total_transform, 0.5*Units::micrometer);
}
}
@@ -135,7 +170,7 @@ void TestMesoCrystal2::initializeSample()
particle_decoration.addInterferenceFunction(p_interference_funtion);
LayerDecorator avg_layer_decorator(avg_layer, particle_decoration);
- LayerRoughness roughness(0.5*Units::nanometer, 0.3, 500.0*Units::nanometer);
+ LayerRoughness roughness(2.0*Units::nanometer, 0.3, 500.0*Units::nanometer);
p_multi_layer->addLayer(air_layer);
p_multi_layer->addLayer(avg_layer_decorator);
@@ -147,6 +182,10 @@ void TestMesoCrystal2::initializeSample()
m_sample = p_multi_layer;
+
+ 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;
}
MesoCrystal* TestMesoCrystal2::createMesoCrystal(double stacking_radius, complex_t n_particle, const IFormFactor* p_meso_form_factor)
@@ -155,8 +194,8 @@ MesoCrystal* TestMesoCrystal2::createMesoCrystal(double stacking_radius, complex
kvector_t bas_a = p_lat->getBasisVectorA();
kvector_t bas_b = p_lat->getBasisVectorB();
kvector_t bas_c = p_lat->getBasisVectorC();
- double sigma = 1.0*Units::nanometer;
- Particle particle(n_particle, new FormFactorSphereGaussianRadius(stacking_radius-1.0*Units::nanometer, sigma));
+ double sigma = 0.2*Units::nanometer;
+ Particle particle(n_particle, new FormFactorSphereGaussianRadius(stacking_radius-0.5*Units::nanometer, sigma));
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);
diff --git a/Core/Algorithms/inc/Experiment.h b/Core/Algorithms/inc/Experiment.h
index 2a14e34e473..0d174cb3fef 100644
--- a/Core/Algorithms/inc/Experiment.h
+++ b/Core/Algorithms/inc/Experiment.h
@@ -35,6 +35,10 @@ public:
/// Set the sample to be tested
void setSample(ISample *p_sample);
+ /// get the sample
+ ISample *getSample() { return mp_sample; }
+ const ISample *getSample() const { return mp_sample; }
+
/// Get data structure that contains the intensity map on the detector for all scan parameters
OutputData<double>* getOutputDataClone() const;
@@ -63,6 +67,9 @@ public:
const OutputData<double>* getOutputDataMask() const;
+ //! create combined parameter pool of the whole sample and experiment (if any)
+ virtual ParameterPool *createParameterTree() const;
+
protected:
/// Default implementation only adds the detector axes
virtual void updateIntensityMapAxes();
diff --git a/Core/Algorithms/src/Experiment.cpp b/Core/Algorithms/src/Experiment.cpp
index f7c7600cbde..46776a222dc 100644
--- a/Core/Algorithms/src/Experiment.cpp
+++ b/Core/Algorithms/src/Experiment.cpp
@@ -97,3 +97,14 @@ void Experiment::setOutputDataMask(size_t n_chunks_total, size_t n_chunk )
}
}
+
+
+/* ************************************************************************* */
+// create combined parameter pool of the whole sample and experiment (if any)
+/* ************************************************************************* */
+ParameterPool *Experiment::createParameterTree() const
+{
+ if(mp_sample == 0 ) throw NullPointerException("Experiment::createParameterTree() -> Error! Sample is absent");
+ return mp_sample->createParameterTree();
+}
+
diff --git a/Core/Core.pro b/Core/Core.pro
index 15c37992dc8..d9a009292f2 100644
--- a/Core/Core.pro
+++ b/Core/Core.pro
@@ -111,7 +111,7 @@ SOURCES += \
PythonAPI/src/PythonModule.cpp \
PythonAPI/src/PythonPlusplusHelper.cpp \
PythonAPI/src/PythonOutputData.cpp \
- Tools/src/Minimizer.cpp
+ Tools/src/IMinimizer.cpp
HEADERS += \
Algorithms/inc/Beam.h \
@@ -235,7 +235,7 @@ HEADERS += \
PythonAPI/inc/PythonModule.h \
PythonAPI/inc/PythonOutputData.h \
PythonAPI/inc/PythonPlusplusHelper.h \
- Tools/inc/Minimizer.h
+ Tools/inc/IMinimizer.h
INCLUDEPATH += ./Algorithms/inc ./FormFactors/inc/ ./Geometry/inc ./Samples/inc ./Tools/inc ./PythonAPI/inc
DEPENDPATH += ./Algorithms/inc ./FormFactors/inc/ ./Geometry/inc ./Samples/inc ./Tools/inc ./PythonAPI/inc
diff --git a/Core/Samples/inc/ICompositeSample.h b/Core/Samples/inc/ICompositeSample.h
index 80cec442393..592f3f19df8 100644
--- a/Core/Samples/inc/ICompositeSample.h
+++ b/Core/Samples/inc/ICompositeSample.h
@@ -31,11 +31,13 @@ public:
//! definition of container for registered children
typedef std::list<ISample *> samples_t;
typedef samples_t::iterator iterator_t;
+ typedef samples_t::const_iterator const_iterator_t;
ICompositeSample();
//! to confirm compound nature of given class
virtual ICompositeSample *getCompositeSample() { return this; }
+ virtual const ICompositeSample *getCompositeSample() const { return this; }
//! register child in the container
virtual void registerChild(ISample *sample);
@@ -46,6 +48,8 @@ public:
//! iteration over local registered children
iterator_t begin_shallow() { return m_samples.begin(); }
iterator_t end_shallow() { return m_samples.end(); }
+ const_iterator_t begin_shallow() const { return m_samples.begin(); }
+ const_iterator_t end_shallow() const { return m_samples.end(); }
//! size of children
virtual size_t size() const { return m_samples.size(); }
diff --git a/Core/Samples/inc/ISample.h b/Core/Samples/inc/ISample.h
index b36aeba266a..780a2672412 100644
--- a/Core/Samples/inc/ISample.h
+++ b/Core/Samples/inc/ISample.h
@@ -35,6 +35,7 @@ public:
//! return pointer to "this", if it is composite sample (to overload)
virtual ICompositeSample *getCompositeSample() { return 0; }
+ virtual const ICompositeSample *getCompositeSample() const { return 0; }
//! clone sample (to overload)
virtual ISample *clone() const;
@@ -43,7 +44,7 @@ public:
ParameterPool *getParameterPool() { return &m_parameters; }
//! create new parameter pool which contains all local parameter and parameters of children
- virtual ParameterPool *createParameterTree();
+ virtual ParameterPool *createParameterTree() const;
//! check if this sample (or one of its subsamples) contains elements requiring DWBA corrections and return an ISimulation to calculate this
virtual DWBASimulation *createDWBASimulation() const { return 0; }
@@ -62,7 +63,7 @@ protected:
virtual void init_parameters();
//! add parameters from local pool to external pool and call recursion over direct children
- virtual void addParametersToExternalPool(std::string path, ParameterPool *external_pool, int copy_number=-1);
+ virtual void addParametersToExternalPool(std::string path, ParameterPool *external_pool, int copy_number=-1) const;
ParameterPool m_parameters; //! parameter pool
};
diff --git a/Core/Samples/inc/ParameterPool.h b/Core/Samples/inc/ParameterPool.h
index b3a8c07304c..7beb0bf7135 100644
--- a/Core/Samples/inc/ParameterPool.h
+++ b/Core/Samples/inc/ParameterPool.h
@@ -52,10 +52,10 @@ public:
ParameterPool *clone();
//! clone with adding preffix to every parameter key
- ParameterPool *cloneWithPrefix(std::string prefix);
+ ParameterPool *cloneWithPrefix(const std::string &prefix);
//! copy parameters of given pool to the external pool while adding prefix to local parameter keys
- void copyToExternalPool(std::string prefix, ParameterPool *external_pool);
+ void copyToExternalPool(const std::string &prefix, ParameterPool *external_pool) const;
//! clear and delete parameter map
void clear();
@@ -64,10 +64,10 @@ public:
size_t size() const { return m_map.size(); }
//! main method to register data address in the pool
- bool registerParameter(std::string name, double *parpointer);
+ bool registerParameter(const std::string &name, double *parpointer);
//! add parameter to the pool
- bool addParameter(std::string name, RealPar par);
+ bool addParameter(const std::string &name, RealPar par);
//! access to parameter container
iterator_t begin() { return m_map.begin(); }
@@ -78,13 +78,13 @@ public:
const_iterator_t end() const { return m_map.end(); }
//! return parameter with given name
- RealPar getParameter(std::string name) const;
+ RealPar getParameter(const std::string &name) const;
//! set parameter value, return true in the case of success
- bool setParameterValue(std::string name, double value);
+ bool setParameterValue(const std::string &name, double value);
//! set parameter value, return number of changed parameters
- int setMatchedParametersValue(std::string wildcards, double value);
+ int setMatchedParametersValue(const std::string &wildcards, double value);
//! print parameter pool
friend std::ostream &operator<<(std::ostream &ostr, const ParameterPool &obj)
diff --git a/Core/Samples/src/ISample.cpp b/Core/Samples/src/ISample.cpp
index 8a243c0904a..dc6a370236a 100644
--- a/Core/Samples/src/ISample.cpp
+++ b/Core/Samples/src/ISample.cpp
@@ -56,7 +56,7 @@ void ISample::init_parameters()
// create new parameter pool which contains all local parameter and parameters of children
// user have to delete it
/* ************************************************************************* */
-ParameterPool *ISample::createParameterTree()
+ParameterPool *ISample::createParameterTree() const
{
ParameterPool *newpool = new ParameterPool;
std::string path("/");
@@ -68,7 +68,7 @@ ParameterPool *ISample::createParameterTree()
/* ************************************************************************* */
// add parameters from local pool to external pool and call recursion over direct children
/* ************************************************************************* */
-void ISample::addParametersToExternalPool(std::string path, ParameterPool *external_pool, int copy_number)
+void ISample::addParametersToExternalPool(std::string path, ParameterPool *external_pool, int copy_number) const
{
// adding trailing slash, if it is not already there
if( path[path.length()-1] != '/' ) path += "/";
@@ -82,19 +82,19 @@ void ISample::addParametersToExternalPool(std::string path, ParameterPool *exter
m_parameters.copyToExternalPool(path, external_pool);
// going through direct children of given sample and copy they parameters recursively
- ICompositeSample *sample = getCompositeSample();
+ const ICompositeSample *sample = getCompositeSample();
if( sample ) {
// Here we need some default mechanism to handle cases with many children with same name.
// Lets run through all direct children and save they names
Utils::StringUsageMap strUsageMap;
- for(ICompositeSample::iterator_t it=sample->begin_shallow(); it!=sample->end_shallow(); ++it) {
+ for(ICompositeSample::const_iterator_t it=sample->begin_shallow(); it!=sample->end_shallow(); ++it) {
strUsageMap.add( path +(*it)->getName() ); // saving children name
}
// Now we run through direct children again, and assign copy number for all children with same name
Utils::StringUsageMap strUsageMap2;
- for(ICompositeSample::iterator_t it=sample->begin_shallow(); it!=sample->end_shallow(); ++it) {
+ for(ICompositeSample::const_iterator_t it=sample->begin_shallow(); it!=sample->end_shallow(); ++it) {
std::string children_name = path +(*it)->getName();
strUsageMap2.add(children_name);
int ncopy = strUsageMap2[children_name]-1; // staring from 0
diff --git a/Core/Samples/src/ParameterPool.cpp b/Core/Samples/src/ParameterPool.cpp
index b11111fba6f..bd8736dbe4a 100644
--- a/Core/Samples/src/ParameterPool.cpp
+++ b/Core/Samples/src/ParameterPool.cpp
@@ -48,13 +48,13 @@ void ParameterPool::clear()
// Registering parameter with given name. Name should be different for each
// register.
/* ************************************************************************* */
-bool ParameterPool::registerParameter(std::string name, double *parameter_address)
+bool ParameterPool::registerParameter(const std::string &name, double *parameter_address)
{
RealPar par(parameter_address);
return addParameter(name, par);
}
-bool ParameterPool::addParameter(std::string name, RealPar par)
+bool ParameterPool::addParameter(const std::string &name, RealPar par)
{
parametermap_t::iterator it = m_map.find(name);
if( it!=m_map.end() ) {
@@ -79,7 +79,7 @@ ParameterPool *ParameterPool::clone()
/* ************************************************************************* */
// Clone method that adds a prefix to parameter's keys
/* ************************************************************************* */
-ParameterPool *ParameterPool::cloneWithPrefix(std::string prefix)
+ParameterPool *ParameterPool::cloneWithPrefix(const std::string &prefix)
{
ParameterPool *new_pool = new ParameterPool;
for(parametermap_t::iterator it=m_map.begin(); it!= m_map.end(); ++it)
@@ -93,20 +93,21 @@ ParameterPool *ParameterPool::cloneWithPrefix(std::string prefix)
// copy parameters of given pool to the external pool while adding prefix to
// local parameter keys
/* ************************************************************************* */
-void ParameterPool::copyToExternalPool(std::string prefix, ParameterPool *external_pool)
+void ParameterPool::copyToExternalPool(const std::string &prefix, ParameterPool *external_pool) const
{
- for(parametermap_t::iterator it=m_map.begin(); it!= m_map.end(); ++it) {
+ for(parametermap_t::const_iterator it=m_map.begin(); it!= m_map.end(); ++it) {
external_pool->addParameter(prefix+it->first, it->second);
}
}
/* ************************************************************************* */
-ParameterPool::RealPar ParameterPool::getParameter(std::string name) const
+ParameterPool::RealPar ParameterPool::getParameter(const std::string &name) const
{
parametermap_t::const_iterator it = m_map.find(name);
if( it!=m_map.end() ) {
return (*it).second;
} else {
+ std::cout << "ParameterPool::getParameter() -> Warning. No parameter with name '" << name << std::endl;
return RealPar(0);
}
}
@@ -114,7 +115,7 @@ ParameterPool::RealPar ParameterPool::getParameter(std::string name) const
/* ************************************************************************* */
// set parameter value
/* ************************************************************************* */
-bool ParameterPool::setParameterValue(std::string name, double value)
+bool ParameterPool::setParameterValue(const std::string &name, double value)
{
RealPar x = getParameter(name);
if( x.isNull() ) {
@@ -129,7 +130,7 @@ bool ParameterPool::setParameterValue(std::string name, double value)
/* ************************************************************************* */
// set parameter value
/* ************************************************************************* */
-int ParameterPool::setMatchedParametersValue(std::string wildcards, double value)
+int ParameterPool::setMatchedParametersValue(const std::string &wildcards, double value)
{
int npars(0);
for(iterator_t it=begin(); it!= end(); it++) {
diff --git a/Core/Tools/inc/FitMultiParameter.h b/Core/Tools/inc/FitMultiParameter.h
index 4a2bf284c56..75ad390d70b 100644
--- a/Core/Tools/inc/FitMultiParameter.h
+++ b/Core/Tools/inc/FitMultiParameter.h
@@ -33,6 +33,7 @@ public:
typedef std::vector<parameter_t > parametercoll_t;
FitMultiParameter();
+ FitMultiParameter(const std::string &name, double value, double step, double error=0.0);
virtual void setValue(double value)
{
@@ -55,6 +56,11 @@ public:
friend std::ostream &operator<<(std::ostream &ostr, const FitMultiParameter &m) { m.print(ostr); return ostr; }
protected:
+ // disabled copy constructor
+ FitMultiParameter(const FitMultiParameter &other);
+ // disabled assignment operator
+ FitMultiParameter &operator=(const FitMultiParameter &other);
+
//! print class
void print(std::ostream &ostr) const;
diff --git a/Core/Tools/inc/FitParameter.h b/Core/Tools/inc/FitParameter.h
index 7bbc74951ea..bc2581b91b4 100644
--- a/Core/Tools/inc/FitParameter.h
+++ b/Core/Tools/inc/FitParameter.h
@@ -27,15 +27,42 @@ class FitParameter : public INamed
{
public:
FitParameter();
+ FitParameter(const std::string &name, double value, double step, double error=0.0);
FitParameter(const FitParameter &other);
FitParameter &operator=(const FitParameter &other);
virtual ~FitParameter(){}
- //! return value of parameter
- virtual double getValue() const { return m_value;}
-
//! set value of parameter
virtual void setValue(double value) { m_value = value;}
+ //! get value of parameter
+ virtual double getValue() const { return m_value;}
+
+ //! set parameter step for minimizer
+ virtual void setStep(double value) { m_step = value; }
+ //! get parameter step for minimizer
+ virtual double getStep() const { return m_step;}
+
+ //! set lower and upper limits
+ virtual void setLimits(double xmin, double xmax) { setLowerLimit(xmin); setUpperLimit(xmax); }
+
+ //! set lower limit
+ virtual void setLowerLimit(double value) { m_lower_limit = value; m_has_lower_limit = true; }
+ //! get lower limit
+ double getLowerLimit() const { return m_lower_limit; }
+
+ //! set upper limit
+ virtual void setUpperLimit(double value) { m_upper_limit = value; m_has_upper_limit = true; }
+ //! get upper limit
+ double getUpperLimit() const { return m_upper_limit; }
+
+ //! if has lower limit
+ virtual bool hasLowerLimit() const { return m_has_lower_limit; }
+
+ //! if has upper limit
+ virtual bool hasUpperLimit() const { return m_has_upper_limit; }
+
+ //! if has upper limit
+ virtual bool hasDoubleBound() const { return (m_has_lower_limit && m_has_upper_limit); }
//! print class
friend std::ostream &operator<<(std::ostream &ostr, const FitParameter &m) { m.print(ostr); return ostr; }
@@ -45,9 +72,13 @@ protected:
void print(std::ostream &ostr) const;
double m_value; //! parameter value
+ double m_step; //! parameter step size
double m_error; //! parameter error
+ bool m_has_lower_limit; //! paramter has lower bound
+ bool m_has_upper_limit; //! paramter has upper bound
double m_lower_limit; //! minimum allowed value
double m_upper_limit; //! maximum allowed value
};
+
#endif // FITPARAMETER_H
diff --git a/Core/Tools/inc/FitSuite.h b/Core/Tools/inc/FitSuite.h
index 51bc7401643..a1c9f1ec682 100644
--- a/Core/Tools/inc/FitSuite.h
+++ b/Core/Tools/inc/FitSuite.h
@@ -16,8 +16,15 @@
#include "OutputData.h"
+#include "TRange.h"
+#include "FitMultiParameter.h"
+#include <string>
+
class Experiment;
-class Minimizer;
+class IMinimizer;
+class ParameterPool;
+class ChiSquaredModule;
+
//- -------------------------------------------------------------------
//! @class FitSuite
@@ -26,13 +33,34 @@ class Minimizer;
class FitSuite
{
public:
+ typedef std::vector<FitMultiParameter *> fitmultiparameters_t;
FitSuite();
+ virtual ~FitSuite();
void setExperiment(Experiment *experiment) { m_experiment = experiment; }
- void setMinimizer(Minimizer *minimizer) { m_minimizer = minimizer; }
+ void setMinimizer(IMinimizer *minimizer) { m_minimizer = minimizer; }
+
+ //! add fit parameter
+ FitMultiParameter *addFitParameter(const std::string &name, double value, double step, double error=0.0);
+ FitMultiParameter *addFitParameter(const std::string &name, double value, double step, const TRange<double> &range);
+
+ //! initialize fitting parameters
+ virtual void init_fit_parameters();
+
+ //! set real data
+ void setRealData(const OutputData<double> &data);
+
+ //! run fit
+ virtual void runFit();
+
+ //! function to minimize
+ double functionToMinimize(const double *pars_current_values);
+
private:
Experiment *m_experiment;
- Minimizer *m_minimizer;
+ IMinimizer *m_minimizer;
+ fitmultiparameters_t m_fit_params;
+ ChiSquaredModule *m_chi2_module;
};
#endif // FITSUITE_H
diff --git a/Core/Tools/inc/Minimizer.h b/Core/Tools/inc/IMinimizer.h
similarity index 61%
rename from Core/Tools/inc/Minimizer.h
rename to Core/Tools/inc/IMinimizer.h
index 7d3f0072794..15e40512d72 100644
--- a/Core/Tools/inc/Minimizer.h
+++ b/Core/Tools/inc/IMinimizer.h
@@ -1,5 +1,5 @@
-#ifndef MINIMIZER_H
-#define MINIMIZER_H
+#ifndef IMINIMIZER_H
+#define IMINIMIZER_H
// ********************************************************************
// * The BornAgain project *
// * Simulation of neutron and x-ray scattering at grazing incidence *
@@ -9,21 +9,30 @@
// * eget quam orci. Quisque porta varius dui, quis posuere nibh *
// * mollis quis. Mauris commodo rhoncus porttitor. *
// ********************************************************************
-//! @file Minimizer.h
+//! @file IMinimizer.h
//! @brief Definition of Minimizer class
//! @author Scientific Computing Group at FRM II
//! @date 05.10.2012
+#include "FitParameter.h"
+#include <boost/function.hpp>
+
+
//- -------------------------------------------------------------------
-//! @class Minimizer
-//! @brief Common wrapper for all kind minimizer's
+//! @class IMinimizer
+//! @brief Common interface for all kind minimizer's
//- -------------------------------------------------------------------
-class Minimizer
+class IMinimizer
{
public:
- Minimizer();
- virtual ~Minimizer(){}
+ IMinimizer();
+ virtual ~IMinimizer(){}
+
+ virtual void setVariable(int i, const FitParameter *par) = 0;
+ //virtual void setVariable(int i, const std::string &name, double value, double step) = 0;
+ virtual void minimize() = 0;
+ virtual void setFunction(boost::function<double(const double *)> fcn, int ndim=1) = 0;
};
-#endif // MINIMIZER_H
+#endif // IMINIMIZER_H
diff --git a/Core/Tools/src/FitMultiParameter.cpp b/Core/Tools/src/FitMultiParameter.cpp
index 709ca7f07ec..b79ee6e4f07 100644
--- a/Core/Tools/src/FitMultiParameter.cpp
+++ b/Core/Tools/src/FitMultiParameter.cpp
@@ -1,11 +1,19 @@
#include "FitMultiParameter.h"
#include "Utils.h"
+
FitMultiParameter::FitMultiParameter()
{
setName("FitMultiParameter");
}
+
+FitMultiParameter::FitMultiParameter(const std::string &name, double value, double step, double error) : FitParameter(name, value, step, error)
+{
+
+}
+
+
/* ************************************************************************* */
//! add real parameter to the collection
/* ************************************************************************* */
diff --git a/Core/Tools/src/FitParameter.cpp b/Core/Tools/src/FitParameter.cpp
index c2aa5581af8..426dc299222 100644
--- a/Core/Tools/src/FitParameter.cpp
+++ b/Core/Tools/src/FitParameter.cpp
@@ -2,17 +2,27 @@
#include <iostream>
-FitParameter::FitParameter() : m_value(0), m_error(0), m_lower_limit(0), m_upper_limit(0)
+FitParameter::FitParameter() : m_value(0), m_step(0), m_error(0),
+ m_has_lower_limit(false), m_has_upper_limit(false), m_lower_limit(0), m_upper_limit(0)
{
setName("FitParameter");
}
+FitParameter::FitParameter(const std::string &name, double value, double step, double error) : INamed(name), m_value(value), m_step(step), m_error(error),
+ m_has_lower_limit(false), m_has_upper_limit(false), m_lower_limit(0), m_upper_limit(0)
+{
+
+}
+
FitParameter::FitParameter(const FitParameter &other) : INamed(other)
{
setName("FitParameter");
m_value = other.m_value;
+ m_step = other.m_step;
m_error = other.m_error;
+ m_has_lower_limit = other.m_has_lower_limit;
+ m_has_upper_limit = other.m_has_upper_limit;
m_lower_limit = other.m_lower_limit;
m_upper_limit = other.m_upper_limit;
}
@@ -24,7 +34,10 @@ FitParameter &FitParameter::operator=(const FitParameter &other)
{
INamed::operator=(other);
m_value = other.m_value;
+ m_step = other.m_step;
m_error = other.m_error;
+ m_has_lower_limit = other.m_has_lower_limit;
+ m_has_upper_limit = other.m_has_upper_limit;
m_lower_limit = other.m_lower_limit;
m_upper_limit = other.m_upper_limit;
}
diff --git a/Core/Tools/src/FitSuite.cpp b/Core/Tools/src/FitSuite.cpp
index 6330d857923..d93d8d8a84c 100644
--- a/Core/Tools/src/FitSuite.cpp
+++ b/Core/Tools/src/FitSuite.cpp
@@ -1,5 +1,134 @@
#include "FitSuite.h"
+#include "Exceptions.h"
+#include "FitMultiParameter.h"
+#include "ParameterPool.h"
+#include "Experiment.h"
+#include "IMinimizer.h"
+#include "ChiSquaredModule.h"
-FitSuite::FitSuite() : m_experiment(0), m_minimizer(0)
+
+FitSuite::FitSuite() : m_experiment(0), m_minimizer(0), m_chi2_module(0)
+{
+}
+
+
+FitSuite::~FitSuite()
+{
+ for(fitmultiparameters_t::iterator it = m_fit_params.begin(); it!= m_fit_params.end(); ++it) {
+ delete (*it);
+ }
+ delete m_minimizer;
+ delete m_chi2_module;
+}
+
+
+/* ************************************************************************* */
+// add fit parameter
+/* ************************************************************************* */
+FitMultiParameter * FitSuite::addFitParameter(const std::string &name, double value, double step, double error)
+{
+ // making MultiFitParameter for later access to sample's parameters
+ FitMultiParameter *par = new FitMultiParameter(name, value, step, error);
+ m_fit_params.push_back( par );
+ return par;
+}
+
+FitMultiParameter * FitSuite::addFitParameter(const std::string &name, double value, double step, const TRange<double> &range)
{
+ // making MultiFitParameter for later access to sample's parameters
+ FitMultiParameter *par = new FitMultiParameter(name, value, step);
+ par->setLimits(range.getMin(), range.getMax() );
+ m_fit_params.push_back( par );
+ return par;
}
+
+
+
+
+/* ************************************************************************* */
+// linking defined FitMultiParameters with sample parameters from pool
+// initialising minimiser's fit parameters
+/* ************************************************************************* */
+void FitSuite::init_fit_parameters()
+{
+ if( !m_experiment ) throw NullPointerException("FitSuite::init_fit_parameters() -> Error! Experiment is absent.");
+ if( !m_minimizer ) throw NullPointerException("FitSuite::init_fit_parameters() -> Error! Minimizer is absent.");
+ if( m_fit_params.empty() ) throw NullPointerException("FitSuite::init_fit_parameters() -> Error! No fit parameters defined");
+
+ // Linking FitMultiParameters with sample parameters from parameter pool.
+ ParameterPool *pool = m_experiment->createParameterTree();
+ for(fitmultiparameters_t::iterator it = m_fit_params.begin(); it!= m_fit_params.end(); ++it) {
+ FitMultiParameter *par = (*it);
+ // name of FitMultiParameter is used to find in the pool links to sample's parameters
+ par->addMatchedParametersFromPool(par->getName(), pool);
+ }
+
+ // propagating fit parameters in the minimizer
+ int npar(0);
+ for(fitmultiparameters_t::iterator it = m_fit_params.begin(); it!= m_fit_params.end(); ++it) {
+ m_minimizer->setVariable(npar++, (*it) );
+ }
+
+ delete pool;
+}
+
+
+/* ************************************************************************* */
+// linking defined FitMultiParameters with sample parameters from pool
+// initialising minimiser's fit parameters
+/* ************************************************************************* */
+void FitSuite::setRealData(const OutputData<double> &data)
+{
+ delete m_chi2_module;
+ m_chi2_module = new ChiSquaredModule(data);
+}
+
+
+/* ************************************************************************* */
+// run fit
+/* ************************************************************************* */
+void FitSuite::runFit()
+{
+ if( !m_experiment || !m_minimizer || !m_chi2_module || m_fit_params.empty()) throw NullPointerException("FitSuite::runFit() -> Error! Something is wrong.");
+
+ m_experiment->getSample()->walk_and_print();
+
+ // initializing fit parameters
+ init_fit_parameters();
+
+ std::cout << m_fit_params[0]->getName() << std::endl;
+ m_fit_params[0]->setValue(999);
+ m_experiment->getSample()->walk_and_print();
+
+
+ // initializing minimizer with fcn function belonging to given class
+ m_minimizer->setFunction( std::bind1st(std::mem_fun(&FitSuite::functionToMinimize), this), m_fit_params.size() );
+
+ // run minimizer
+ m_minimizer->minimize();
+
+}
+
+
+/* ************************************************************************* */
+// function to minimize
+/* ************************************************************************* */
+double FitSuite::functionToMinimize(const double *pars_current_values)
+{
+ std::cout << " FitSuit::functionToMinimize() -> Info. We are here." << std::endl;
+
+ for(size_t i=0; i<m_fit_params.size(); ++i) {
+ std::cout << i << " " << pars_current_values[i] << std::endl;
+ m_fit_params[i]->setValue(pars_current_values[i]);
+ }
+
+ m_experiment->runSimulation();
+ m_experiment->normalize();
+
+ const OutputData<double> *p_simulated_data = m_experiment->getOutputData();
+ double chi_squared = m_chi2_module->calculateChiSquared(p_simulated_data);
+
+ std::cout << "chi squared = " << chi_squared << std::endl;
+ return chi_squared;
+}
+
diff --git a/Core/Tools/src/IMinimizer.cpp b/Core/Tools/src/IMinimizer.cpp
new file mode 100644
index 00000000000..223391c988b
--- /dev/null
+++ b/Core/Tools/src/IMinimizer.cpp
@@ -0,0 +1,5 @@
+#include "IMinimizer.h"
+
+IMinimizer::IMinimizer()
+{
+}
diff --git a/Core/Tools/src/Minimizer.cpp b/Core/Tools/src/Minimizer.cpp
deleted file mode 100644
index 12b9bd97d94..00000000000
--- a/Core/Tools/src/Minimizer.cpp
+++ /dev/null
@@ -1,5 +0,0 @@
-#include "Minimizer.h"
-
-Minimizer::Minimizer()
-{
-}
--
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