Code cleanup in isgisaxs1, preparing for isgisaxs14

App/App.pro

@@ -44,6 +44,7 @@ SOURCES += \
     src/TestIsGISAXS11.cpp \
     src/TestIsGISAXS12.cpp \
     src/TestIsGISAXS13.cpp \
+    src/TestIsGISAXS14.cpp \
     src/TestIsGISAXS15.cpp \
     src/TestIsGISAXS2.cpp \
     src/TestIsGISAXS3.cpp \
@@ -99,6 +100,7 @@ HEADERS += \
     inc/TestIsGISAXS11.h \
     inc/TestIsGISAXS12.h \
     inc/TestIsGISAXS13.h \
+    inc/TestIsGISAXS14.h \
     inc/TestIsGISAXS15.h \
     inc/TestIsGISAXS2.h \
     inc/TestIsGISAXS3.h \
@@ -123,9 +125,6 @@ CONFIG(DEBUG_FPE) {
     SOURCES += src/fp_exception_glibc_extension.c
 }
 
-
-
-
 # additional locations
 LOCATIONS = ./inc $${FUNCTIONAL_TESTS}/IsGISAXS01
 INCLUDEPATH += $${LOCATIONS}

App/inc/StandardSamples.h

@@ -14,7 +14,7 @@ ISample *MultilayerOffspecTestcase1a();
 ISample *MultilayerOffspecTestcase1b();
 ISample *MultilayerOffspecTestcase2a();
 ISample *MultilayerOffspecTestcase2b();
-ISample *IsGISAXS1_CylinderAndPrism();
+//ISample *IsGISAXS1_CylinderAndPrism();
 ISample *IsGISAXS2_CylindersMixture();
 ISample *IsGISAXS3_CylinderDWBA();
 ISample *IsGISAXS3_CylinderBA();
@@ -28,6 +28,7 @@ ISample *IsGISAXS9_Pyramid();
 ISample *IsGISAXS9_RotatedPyramid();
 ISample *IsGISAXS10_CylindersParacrystal1D();
 ISample *IsGISAXS11_CoreShellParticles();
+ISample *IsGISAXS14_LayeredSpheresOnGradedInterface();
 ISample *IsGISAXS15_SSCA();
 ISample *MesoCrystal1();
 ISample *MesoCrystal2();

App/inc/TestIsGISAXS1.h

@@ -23,7 +23,7 @@
 class TestIsGISAXS1 : public IFunctionalTest
 {
 public:
-    TestIsGISAXS1() { }
+    TestIsGISAXS1();
     virtual ~TestIsGISAXS1() { }
 
     virtual void execute();

App/inc/TestIsGISAXS14.h

+#ifndef TESTISGISAXS14_H
+#define TESTISGISAXS14_H
+// ********************************************************************
+// * The BornAgain project                                            *
+// * Simulation of neutron and x-ray scattering at grazing incidence  *
+// *                                                                  *
+// * LICENSE AND DISCLAIMER                                           *
+// * Lorem ipsum dolor sit amet, consectetur adipiscing elit.  Mauris *
+// * eget quam orci. Quisque  porta  varius  dui,  quis  posuere nibh *
+// * mollis quis. Mauris commodo rhoncus porttitor.                   *
+// ********************************************************************
+//! @file   TestIsGISAXS14.h
+//! @brief  Definition of TestIsGISAXS14 class for IsGISAXS validation
+//! @author Scientific Computing Group at FRM II
+//! @date   Jan 28, 2013
+
+#include "IFunctionalTest.h"
+
+//- -------------------------------------------------------------------
+//! @class TestIsGISAXS14
+//! @brief Comparison with IsGISAXS ex-14: multi layered sphere on graded interface
+//- -------------------------------------------------------------------
+class TestIsGISAXS14 : public IFunctionalTest
+{
+public:
+    TestIsGISAXS14();
+    virtual ~TestIsGISAXS14() {}
+    virtual void execute();
+    virtual void finalise();
+};
+
+#endif // TESTISGISAXS14_H

App/src/FunctionalTestFactory.cpp

@@ -16,6 +16,7 @@
 #include "TestIsGISAXS11.h"
 #include "TestIsGISAXS12.h"
 #include "TestIsGISAXS13.h"
+#include "TestIsGISAXS14.h"
 #include "TestIsGISAXS15.h"
 #include "TestConvolution.h"
 #include "TestDetectorResolution.h"
@@ -73,6 +74,8 @@ FunctionalTestFactory::FunctionalTestFactory() : m_benchmark(0)
                  "functional test: isgisaxs ex-12 (constrained fit example)");
     registerItem("isgisaxs13",  IFactoryCreateFunction<TestIsGISAXS13, IFunctionalTest>,
                  "functional test: isgisaxs ex-13 (simulated annealing fit)");
+    registerItem("isgisaxs14",  IFactoryCreateFunction<TestIsGISAXS14, IFunctionalTest>,
+                 "functional test: isgisaxs ex-14 (multilayered sphere on graded interface)");
     registerItem("isgisaxs15",  IFactoryCreateFunction<TestIsGISAXS15, IFunctionalTest>,
                  "functional test: isgisaxs ex-15 (size-spacing correlation approximation)");
     registerItem("convolution", IFactoryCreateFunction<TestConvolution, IFunctionalTest>,

App/src/SampleFactory.cpp

@@ -26,7 +26,7 @@ SampleFactory::SampleFactory()
     registerItem("MultilayerOffspecTestcase2b", StandardSamples::MultilayerOffspecTestcase2b);
 
     // IsGISAXS1 example: cylinder and prism
-    registerItem("IsGISAXS1_CylinderAndPrism", StandardSamples::IsGISAXS1_CylinderAndPrism);
+    //registerItem("IsGISAXS1_CylinderAndPrism", StandardSamples::IsGISAXS1_CylinderAndPrism);
 
     // IsGISAXS2 example: mixture of cylindrical particles with two size distribution
     registerItem("IsGISAXS2_CylindersMixture", StandardSamples::IsGISAXS2_CylindersMixture);
@@ -57,6 +57,9 @@ SampleFactory::SampleFactory()
     // IsGISAXS11 example: core shell parallelepipeds
     registerItem("IsGISAXS11_CoreShellParticle", StandardSamples::IsGISAXS11_CoreShellParticles);
 
+    // IsGISAXS14 example: layered sphere on graded interface
+    registerItem("IsGISAXS14_LayeredSpheresOnGradedInterface", StandardSamples::IsGISAXS14_LayeredSpheresOnGradedInterface);
+
     // IsGISAXS15 example: Size-Spacing Correlation Approximation
     registerItem("IsGISAXS15_SSCA", StandardSamples::IsGISAXS15_SSCA);
 

App/src/StandardSamples.cpp

@@ -350,35 +350,31 @@ ISample *StandardSamples::MultilayerOffspecTestcase2b()
 //
 
 
-
-
-
-
 /* ************************************************************************* */
 // IsGISAXS1 functional test: cylinder and prism
 /* ************************************************************************* */
-ISample *StandardSamples::IsGISAXS1_CylinderAndPrism()
-{
-    MultiLayer *p_multi_layer = new MultiLayer();
-    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::instance().addHomogeneousMaterial("Air", n_air);
-    const IMaterial *p_substrate_material = MaterialManager::instance().addHomogeneousMaterial("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(5*Units::nanometer, 5*Units::nanometer)),0.0, 0.5);
-    particle_decoration.addParticle(new Particle(n_particle, new FormFactorPrism3(5*Units::nanometer, 5*Units::nanometer)), 0.0, 0.5);
-    particle_decoration.addInterferenceFunction(new InterferenceFunctionNone());
-    LayerDecorator air_layer_decorator(air_layer, particle_decoration);
+//ISample *StandardSamples::IsGISAXS1_CylinderAndPrism()
+//{
+//    MultiLayer *p_multi_layer = new MultiLayer();
+//    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::instance().addHomogeneousMaterial("Air", n_air);
+//    const IMaterial *p_substrate_material = MaterialManager::instance().addHomogeneousMaterial("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(5*Units::nanometer, 5*Units::nanometer)),0.0, 0.5);
+//    particle_decoration.addParticle(new Particle(n_particle, new FormFactorPrism3(5*Units::nanometer, 5*Units::nanometer)), 0.0, 0.5);
+//    particle_decoration.addInterferenceFunction(new InterferenceFunctionNone());
+//    LayerDecorator air_layer_decorator(air_layer, particle_decoration);
 
-    p_multi_layer->addLayer(air_layer_decorator);
-    p_multi_layer->addLayer(substrate_layer);
-    return p_multi_layer;
-}
+//    p_multi_layer->addLayer(air_layer_decorator);
+//    p_multi_layer->addLayer(substrate_layer);
+//    return p_multi_layer;
+//}
 
 
 /* ************************************************************************* */
@@ -801,6 +797,33 @@ ISample *StandardSamples::IsGISAXS11_CoreShellParticles()
     return p_multi_layer;
 }
 
+/* ************************************************************************* */
+// IsGISAXS14 functional test: layered sphere on graded interface
+/* ************************************************************************* */
+ISample *StandardSamples::IsGISAXS14_LayeredSpheresOnGradedInterface()
+{
+    MultiLayer *p_multi_layer = new MultiLayer();
+    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-5, 2e-8);
+    const IMaterial *p_air_material = MaterialManager::instance().addHomogeneousMaterial("Air10", n_air);
+    const IMaterial *p_substrate_material = MaterialManager::instance().addHomogeneousMaterial("Substrate10", n_substrate);
+    Layer air_layer;
+    air_layer.setMaterial(p_air_material);
+    Layer substrate_layer;
+    substrate_layer.setMaterial(p_substrate_material);
+    IInterferenceFunction *p_interference_function = new InterferenceFunction1DParaCrystal(15.0*Units::nanometer,5*Units::nanometer, 1e7*Units::nanometer);
+    ParticleDecoration particle_decoration(new Particle(n_particle, new FormFactorSphere(5*Units::nanometer, 5*Units::nanometer)));
+    particle_decoration.addInterferenceFunction(p_interference_function);
+    //    particle_decoration.setTotalParticleSurfaceDensity(1.0/(20.0*Units::nanometer*20.0*Units::nanometer));
+    LayerDecorator air_layer_decorator(air_layer, particle_decoration);
+
+    p_multi_layer->addLayer(air_layer_decorator);
+    p_multi_layer->addLayer(substrate_layer);
+
+    return p_multi_layer;
+}
+
 /* ************************************************************************* */
 // IsGISAXS15 functional test: size-spacing correlation approximation
 /* ************************************************************************* */

App/src/TestIsGISAXS1.cpp

 #include "TestIsGISAXS1.h"
+#include "IsGISAXS01.h"
 #include "IsGISAXSTools.h"
-#include "Units.h"
-#include "Utils.h"
-#include "MultiLayer.h"
-#include "GISASExperiment.h"
-#include "FormFactors.h"
-#include "SampleFactory.h"
-#include "DrawHelper.h"
-#include "TCanvas.h"
-#include "TH2.h"
-#include "TStyle.h"
 #include "OutputDataIOFactory.h"
+#include "Utils.h"
 
-#include "IsGISAXS01.h"
 #include <fstream>
 
 
-
-void TestIsGISAXS1::execute()
+TestIsGISAXS1::TestIsGISAXS1() : IFunctionalTest("TestIsGISAXS1")
 {
-//    MultiLayer *sample = dynamic_cast<MultiLayer *>(SampleFactory::instance().createItem("IsGISAXS1_CylinderAndPrism"));
-
-//    GISASExperiment experiment(mp_options);
-//    experiment.setSample(*sample);
-//    experiment.setDetectorParameters(100,-1.0*Units::degree, 1.0*Units::degree, 100, 0.0*Units::degree, 2.0*Units::degree, true);
-//    experiment.setBeamParameters(1.0*Units::angstrom, -0.2*Units::degree, 0.0*Units::degree);
-//    experiment.runSimulation();
+    setOutputPath(Utils::FileSystem::GetHomePath()+"./Examples/IsGISAXS_examples/ex-1/" );
+}
 
-//    FunctionalTests::IsGISAXS01 test;
 
+void TestIsGISAXS1::execute()
+{
     FunctionalTests::IsGISAXS01 test;
     test.run();
 
-    OutputDataIOFactory::writeOutputData(*test.getOutputData(), Utils::FileSystem::GetHomePath()+"./Examples/IsGISAXS_examples/ex-1/this_2-types-of-islands-ewald.ima");
+    OutputDataIOFactory::writeOutputData(*test.getOutputData(), getOutputPath()+"this_2-types-of-islands-ewald.ima");
 }
 
 
 void TestIsGISAXS1::finalise()
 {
-    std::string isgi_file(Utils::FileSystem::GetHomePath()+"./Examples/IsGISAXS_examples/ex-1/isgi_2-types-of-islands-ewald.ima.gz");
-    std::string this_file(Utils::FileSystem::GetHomePath()+"./Examples/IsGISAXS_examples/ex-1/this_2-types-of-islands-ewald.ima");
+    std::string isgi_file(getOutputPath()+"isgi_2-types-of-islands-ewald.ima.gz");
+    std::string this_file(getOutputPath()+"this_2-types-of-islands-ewald.ima");
 
     OutputData<double> *isgi_data = OutputDataIOFactory::getOutputData(isgi_file);
     OutputData<double> *our_data = OutputDataIOFactory::getOutputData(this_file);
 
-    TCanvas *c1 = DrawHelper::instance().createAndRegisterCanvas("TestIsGISAXS1_c1", "Two particles mean DWBA Formfactor");
-
-    c1->Divide(2,2);
-
-    IsGISAXSTools::setMinimum(1.);
-    // our calculations
-    c1->cd(1); gPad->SetLogz();
-    IsGISAXSTools::drawOutputDataInPad(*our_data, "CONT4 Z", "Our mean FF");
-
-    // isgisaxs data
-    c1->cd(2); gPad->SetLogz();
-    IsGISAXSTools::drawOutputDataInPad(*isgi_data, "CONT4 Z", "IsGisaxs mean FF");
-
-    // difference
-    c1->cd(3);
-    IsGISAXSTools::setMinimum(-0.0001);
-    IsGISAXSTools::setMaximum(0.0001);
-    IsGISAXSTools::drawOutputDataRelativeDifference2D(*our_data, *isgi_data, "CONT4 Z", "2D Difference map");
-
-    // difference
-    c1->cd(4);
-    IsGISAXSTools::resetMinimumAndMaximum();
-    IsGISAXSTools::setMinimum(1);
-    IsGISAXSTools::drawOutputDataDifference1D(*our_data, *isgi_data, "", "Difference spectra");
+    IsGISAXSTools::drawOutputDataComparisonResults(*our_data, *isgi_data, "TestIsGISAXS1_c1", "Two particles mean DWBA Formfactor");
 
     delete isgi_data;
     delete our_data;
-
 }
-
-
-
-
-//void TestIsGISAXS1::execute()
-//{
-//    MultiLayer *sample = dynamic_cast<MultiLayer *>(SampleFactory::instance().createItem("IsGISAXS1_CylinderAndPrism"));
-
-//    GISASExperiment experiment(mp_options);
-//    experiment.setSample(*sample);
-//    experiment.setDetectorParameters(100,-1.0*Units::degree, 1.0*Units::degree, 100, 0.0*Units::degree, 2.0*Units::degree, true);
-//    experiment.setBeamParameters(1.0*Units::angstrom, -0.2*Units::degree, 0.0*Units::degree);
-//    experiment.runSimulation();
-
-//    OutputDataIOFactory::writeOutputData(*experiment.getOutputData(), Utils::FileSystem::GetHomePath()+"./Examples/IsGISAXS_examples/ex-1/this_2-types-of-islands-ewald.ima");
-//}
-
-
-//void TestIsGISAXS1::finalise()
-//{
-//    std::string isgi_file(Utils::FileSystem::GetHomePath()+"./Examples/IsGISAXS_examples/ex-1/isgi_2-types-of-islands-ewald.ima.gz");
-//    std::string this_file(Utils::FileSystem::GetHomePath()+"./Examples/IsGISAXS_examples/ex-1/this_2-types-of-islands-ewald.ima");
-
-//    OutputData<double> *isgi_data = OutputDataIOFactory::getOutputData(isgi_file);
-//    OutputData<double> *our_data = OutputDataIOFactory::getOutputData(this_file);
-
-//    TCanvas *c1 = DrawHelper::instance().createAndRegisterCanvas("TestIsGISAXS1_c1", "Two particles mean DWBA Formfactor");
-
-//    c1->Divide(2,2);
-
-//    IsGISAXSTools::setMinimum(1.);
-//    // our calculations
-//    c1->cd(1); gPad->SetLogz();
-//    IsGISAXSTools::drawOutputDataInPad(*our_data, "CONT4 Z", "Our mean FF");
-
-//    // isgisaxs data
-//    c1->cd(2); gPad->SetLogz();
-//    IsGISAXSTools::drawOutputDataInPad(*isgi_data, "CONT4 Z", "IsGisaxs mean FF");
-
-//    // difference
-//    c1->cd(3);
-//    IsGISAXSTools::setMinimum(-0.0001);
-//    IsGISAXSTools::setMaximum(0.0001);
-//    IsGISAXSTools::drawOutputDataRelativeDifference2D(*our_data, *isgi_data, "CONT4 Z", "2D Difference map");
-
-//    // difference
-//    c1->cd(4);
-//    IsGISAXSTools::resetMinimumAndMaximum();
-//    IsGISAXSTools::setMinimum(1);
-//    IsGISAXSTools::drawOutputDataDifference1D(*our_data, *isgi_data, "", "Difference spectra");
-
-//    delete isgi_data;
-//    delete our_data;
-
-//}
-
-

App/src/TestIsGISAXS14.cpp

+#include "TestIsGISAXS14.h"
+#include "IsGISAXSTools.h"
+#include "OutputDataIOFactory.h"
+#include "Utils.h"
+
+#include "GISASExperiment.h"
+#include "MultiLayer.h"
+#include "SampleFactory.h"
+#include "Units.h"
+
+#include <fstream>
+
+
+TestIsGISAXS14::TestIsGISAXS14() : IFunctionalTest("TestIsGISAXS14")
+{
+    setOutputPath(Utils::FileSystem::GetHomePath()+"./Examples/IsGISAXS_examples/ex-14/" );
+}
+
+
+void TestIsGISAXS14::execute()
+{
+    MultiLayer *sample = dynamic_cast<MultiLayer *>(SampleFactory::instance().createItem("IsGISAXS14_LayeredSpheresOnGradedInterface"));
+
+    GISASExperiment experiment(mp_options);
+    experiment.setSample(*sample);
+    experiment.setDetectorParameters(100, 0.0*Units::degree, 2.0*Units::degree, 100, 0.0*Units::degree, 2.0*Units::degree, true);
+    experiment.setBeamParameters(1.0*Units::angstrom, -0.2*Units::degree, 0.0*Units::degree);
+    experiment.runSimulation();
+    OutputDataIOFactory::writeOutputData(*experiment.getOutputDataClone(), getOutputPath() + "this_multilayer_sphere.ima");
+}
+
+
+void TestIsGISAXS14::finalise()
+{
+    std::string isgi_file(getOutputPath()+"isgi_normal_sphere.ima");
+    std::string this_file(getOutputPath()+"this_multilayer_sphere.ima");
+
+    OutputData<double> *isgi_data = OutputDataIOFactory::getOutputData(isgi_file);
+    OutputData<double> *our_data = OutputDataIOFactory::getOutputData(this_file);
+
+    IsGISAXSTools::drawOutputDataComparisonResults(*our_data, *isgi_data, "TestIsGISAXS14_c1", "Multilayered sphere on graded interface");
+
+    delete isgi_data;
+    delete our_data;
+}

Examples/IsGISAXS_examples/README

@@ -6,10 +6,21 @@ In each subdirectory, one finds:
 - isgi_*.ima files with simulated intensity produced by IsGISAXS
 
 List of examples:
-ex-1  2 types of particles (cylinder, prism3) on top of substrate. No interference function.
-ex-3  cylinder form factor
-ex-9  pyramid form factor
-ex-10 cylinders with interference on top of substrate
+ex-1   Mixture of cylinders and prisms without interference.
+ex-2   Two gaussian size cylinder distribution.
+ex-3   Cylinder formfactor in BA and DWBA.
+ex-4   1D and 2D paracrystal.
+ex-5   1D paracrystal fit example.
+ex-6   2D lattice with different disorders.
+ex-7   Mixture of different particles defined in morphology file.
+ex-8   2DDL paracrystal 
+ex-9   Rotated pyramids on top of substrate.
+ex-10  Cylinders with interference on top of substrate.
+ex-11  Core shell nano particles.
+ex-12  Constrained fit example: mixture of two cylinder types
+ex-13  Simulated annealing fit example.
+ex-14  Layered spheres on graded interface.
+ex-15  Size spacing correlation approximation
 
 Some notes:
 -Since polarization (x-ray) is not yet included in GISASFW, this feature should be disabled in IsGISAXS by returning 1._wp from function PolFac in Reflectivity_mod.f90