Merge branch 'master' of git.jcns.frm2:GISASFW

App/App.pro

@@ -129,14 +129,14 @@ CONFIG(JCNS) {
 exists($$(ROOTSYS)/bin/root-config){
   INCLUDEPATH += $$system($ROOTSYS/bin/root-config --incdir)
   #LIBS += $$system($ROOTSYS/bin/root-config --glibs)
-  LIBS += -L$$system($ROOTSYS/bin/root-config --libdir ) -lGui -lCore -lCint -lRIO -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -lpthread -lm -ldl
+  LIBS += -L$$system($ROOTSYS/bin/root-config --libdir ) -lGui -lCore -lCint -lRIO -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lMathMore -lMinuit2 -lThread -lpthread -lm -ldl
 
   MYROOTCINT = ${ROOTSYS}/bin/rootcint
 }
 # if it doesn't exist, try to do something
 !exists($$(ROOTSYS)/bin/root-config){
   INCLUDEPATH += /opt/local/include/root
-  LIBS +=  -L/opt/local/lib/root -lGui -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -lpthread -lm -ldl
+  LIBS +=  -L/opt/local/lib/root -lGui -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lMathMore -lMinuit2 -lThread -lpthread -lm -ldl
   MYROOTCINT = /opt/local/bin/rootcint
 }
 

App/inc/TestFittingModule.h

@@ -17,6 +17,9 @@
 #include "IFunctionalTest.h"
 #include "OutputData.h"
 #include "ISample.h"
+#include "ChiSquaredModule.h"
+#include "FitMultiParameter.h"
+#include "GISASExperiment.h"
 
 class TestFittingModule : public IFunctionalTest
 {
@@ -34,5 +37,12 @@ private:
     ISample *mp_sample;
 };
 
+namespace Fitting {
+extern GISASExperiment *p_experiment;
+extern ChiSquaredModule *p_chi_squared_module;
+extern std::vector<FitMultiParameter *> fit_params;
+double functionToMinimize(const double *p_params);
+}
+
 
 #endif /* TESTFITTINGMODULE_H_ */

App/src/TestFittingModule.cpp

@@ -11,6 +11,12 @@
 #include "NanoParticle.h"
 #include "FormFactors.h"
 
+#include "Math/GSLMinimizer.h"
+#include "Minuit2/Minuit2Minimizer.h"
+#include "Math/Functor.h"
+
+MultiLayer *gp_fit_sample = 0;
+
 TestFittingModule::TestFittingModule()
 : mp_exact_data(0)
 , mp_real_data(0)
@@ -32,6 +38,7 @@ void TestFittingModule::execute()
     // Generate exact sample simulation
     if (mp_exact_data) delete mp_exact_data;
     initializeSample();
+    gp_fit_sample = dynamic_cast<MultiLayer *>(mp_sample);
     GISASExperiment experiment;
     experiment.setSample(mp_sample);
     experiment.setDetectorParameters(100, 0.0*Units::degree, 2.0*Units::degree
@@ -41,6 +48,37 @@ void TestFittingModule::execute()
     mp_exact_data = experiment.getOutputDataClone();
     // Generate noisy version
     generateRealData(0.2);
+    // Perform the actual fitting
+    //   Initialize global data:
+    Fitting::p_experiment = &experiment;
+    ChiSquaredModule csm(*mp_real_data);
+    Fitting::p_chi_squared_module = &csm;
+    ParameterPool *p_param_pool = mp_sample->createParameterTree();
+    std::cout << *p_param_pool;
+    FitMultiParameter fmp1;
+    fmp1.addParameterFromPool("/multilayer/layer1/thickness", p_param_pool);
+    Fitting::fit_params.push_back(&fmp1);
+    //   Execute the fitting with ROOT:
+    ROOT::Minuit2::Minuit2Minimizer min ( ROOT::Minuit2::kMigrad );
+//    ROOT::Math::GSLMinimizer min;
+    min.SetMaxFunctionCalls(1000000);
+    min.SetMaxIterations(100000);
+    min.SetTolerance(0.001);
+
+    ROOT::Math::Functor f(&Fitting::functionToMinimize, 1);
+    double step[1] = { 5*Units::nanometer };
+    double variable[1] = { 12*Units::nanometer };
+
+    min.SetFunction(f);
+
+      // Set the free variables to be minimized!
+    min.SetVariable(0,"x",variable[0], step[0]);
+
+    min.Minimize();
+    mp_simulated_data = experiment.getOutputDataClone();
+
+    std::cout << "Layer thickness fit: " << min.X()[0] << " nanometer" << std::endl;
+
     IsGISAXSTools::drawLogOutputData(*mp_real_data, "c1_test_fitting", "fitting", "CONT4 Z");
 //    IsGISAXSTools::writeOutputDataToFile(*mp_real_data, Utils::FileSystem::GetHomePath()+"./Examples/IsGISAXS_examples/ex-10/para1dcyl.ima");
 }
@@ -67,12 +105,12 @@ void TestFittingModule::initializeSample()
             7*Units::nanometer, 1e7*Units::nanometer);
     NanoParticleDecoration particle_decoration(
                 new NanoParticle(n_particle, new FormFactorCylinder(5*Units::nanometer, 5*Units::nanometer)),
-                10*Units::nanometer, 1.0);
+                0*Units::nanometer, 1.0);
     particle_decoration.addInterferenceFunction(p_interference_funtion);
-    LayerDecorator layer_decorator(layer_layer, particle_decoration);
+    LayerDecorator layer_decorator(air_layer, particle_decoration);
 
-    p_multi_layer->addLayer(air_layer);
     p_multi_layer->addLayer(layer_decorator);
+    p_multi_layer->addLayer(layer_layer);
     p_multi_layer->addLayer(substrate_layer);
     mp_sample = p_multi_layer;
 }
@@ -95,3 +133,21 @@ void TestFittingModule::generateRealData(double noise_factor)
         mp_real_data->next() = random;
     }
 }
+
+GISASExperiment *Fitting::p_experiment = 0;
+ChiSquaredModule *Fitting::p_chi_squared_module = 0;
+std::vector<FitMultiParameter *> Fitting::fit_params;
+
+double Fitting::functionToMinimize(const double* p_params)
+{
+    for (size_t i=0; i<Fitting::fit_params.size(); ++i) {
+        std::cout << "param " << i+1 << ": " << p_params[i] << std::endl;
+        Fitting::fit_params[i]->setValue(p_params[i]);
+    }
+    std::cout << "thickness of layer 1: " << gp_fit_sample->getLayer(1)->getThickness() << std::endl;
+    Fitting::p_experiment->runSimulation();
+    const OutputData<double> *p_simulated_data = Fitting::p_experiment->getOutputData();
+    double chi_squared = Fitting::p_chi_squared_module->calculateChiSquared(p_simulated_data);
+    std::cout << "chi squared = " << chi_squared << std::endl;
+    return chi_squared;
+}

ThirdParty/gtest/gtest.pro

@@ -8,7 +8,7 @@ QT      -= gui core
 
 QMAKE_EXTENSION_SHLIB = so
 
-include($$PWD/../shared.pri)
+include($$PWD/../../shared.pri)
 
 mygtest = gtest-1.6.0