Fixed rotated mesocrystal form factors

App/src/TestMesoCrystal2.cpp

@@ -88,7 +88,6 @@ void TestMesoCrystal2::draw_results()
     initializeSimulation(m_real_data);
 
     ParameterPool *pool = m_sample_builder->createParameterTree();
-    std::cout << *pool << std::endl;
 //    pool->setMatchedParametersValue("*/lattice_length_a", 6.2e+00);           // 6.2
 //    pool->setMatchedParametersValue("*/lattice_length_c", 6.2e+00);           // 6.2
 //    pool->setMatchedParametersValue("*/nanoparticle_radius", 5.7e+00);        // 5.7
@@ -106,18 +105,19 @@ void TestMesoCrystal2::draw_results()
 
 //    IsGISAXSTools::drawOutputDataComparisonResults(*m_simulation->getOutputData(), *m_real_data, "initial", "initial params", 100, 1e6, 100);
 
-    pool->setMatchedParametersValue("*/lattice_length_a", 6.2091e+00);           // 6.2
-    pool->setMatchedParametersValue("*/lattice_length_c", 6.5677e+00);           // 6.2
-    pool->setMatchedParametersValue("*/nanoparticle_radius", 4.6976e+00);        // 5.7
-    pool->setMatchedParametersValue("*/sigma_nanoparticle_radius", 3.6720e-01);  // 0.1
-    pool->setMatchedParametersValue("*/meso_height", 1.1221e+02);  // 0.1
-    pool->setMatchedParametersValue("*/meso_radius", 9.4567e+02);  // 0.1
-    pool->setMatchedParametersValue("*/sigma_meso_height", 1.3310e+00);  // 0.1
-    pool->setMatchedParametersValue("*/sigma_meso_radius", 1.3863e+00);  // 0.1
-    pool->setMatchedParametersValue("*/sigma_lattice_length_a", 1.1601e+00);     // 1.5
-    pool->setMatchedParametersValue("*/surface_filling_ratio", 1.7286e-01);      // 0.25
-    pool->setMatchedParametersValue("*/roughness", 2.8746e+01);                      // 1.0
+    m_sample_builder->setMatchedParametersValue("*/lattice_length_a", 6.2091e+00);           // 6.2
+    m_sample_builder->setMatchedParametersValue("*/lattice_length_c", 6.5677e+00);           // 6.2
+    m_sample_builder->setMatchedParametersValue("*/nanoparticle_radius", 4.6976e+00);        // 5.7
+    m_sample_builder->setMatchedParametersValue("*/sigma_nanoparticle_radius", 3.6720e-01);  // 0.1
+    m_sample_builder->setMatchedParametersValue("*/meso_height", 1.1221e+02);  // 0.1
+    m_sample_builder->setMatchedParametersValue("*/meso_radius", 9.4567e+02);  // 0.1
+    m_sample_builder->setMatchedParametersValue("*/sigma_meso_height", 1.3310e+00);  // 0.1
+    m_sample_builder->setMatchedParametersValue("*/sigma_meso_radius", 1.3863e+00);  // 0.1
+    m_sample_builder->setMatchedParametersValue("*/sigma_lattice_length_a", 1.1601e+00);     // 1.5
+    m_sample_builder->setMatchedParametersValue("*/surface_filling_ratio", 1.7286e-01);      // 0.25
+    m_sample_builder->setMatchedParametersValue("*/roughness", 2.8746e+01);                      // 1.0
     m_simulation->setBeamIntensity(5.0090e+12);
+    std::cout << *pool << std::endl;
     m_simulation->runSimulation();
     m_simulation->normalize();
 
@@ -202,7 +202,7 @@ void TestMesoCrystal2::initializeRealData()
     delete m_real_data;
     //std::string file_name = Utils::FileSystem::GetHomePath()+"Examples/MesoCrystals/ex02_fitspheres/004_230_P144_im_full_qyqz.txt.gz";
     //std::string file_name = Utils::FileSystem::GetHomePath()+"Examples/MesoCrystals/ex02_fitspheres/004_230_P144_im_full_phitheta.txt.gz";
-    std::string file_name = Utils::FileSystem::GetHomePath()+"dev-tools/tmp-examples/MesoCrystals/ex02_fitspheres/004_230_P144_im_full_phitheta.txt.gz";
+    std::string file_name = "dev-tools/tmp-examples/MesoCrystals/ex02_fitspheres/004_230_P144_im_full_phitheta.txt.gz";
 
     m_real_data = OutputDataIOFactory::readIntensityData(file_name);
 

Core/Samples/src/MesoCrystal.cpp

@@ -43,14 +43,22 @@ MesoCrystal::~MesoCrystal()
 
 MesoCrystal* MesoCrystal::clone() const
 {
-    return new MesoCrystal(mp_particle_structure->clone(),
+    MesoCrystal *p_result = new MesoCrystal(mp_particle_structure->clone(),
             mp_meso_form_factor->clone());
+    if (mP_transform.get()) {
+        p_result->setTransform(mP_transform);
+    }
+    return p_result;
 }
 
 MesoCrystal* MesoCrystal::cloneInvertB() const
 {
-    return new MesoCrystal(mp_particle_structure->cloneInvertB(),
+    MesoCrystal *p_result = new MesoCrystal(mp_particle_structure->cloneInvertB(),
             mp_meso_form_factor->clone());
+    if (mP_transform.get()) {
+        p_result->setTransform(mP_transform);
+    }
+    return p_result;
 }
 
 void MesoCrystal::setAmbientMaterial(const IMaterial* p_material)
@@ -62,9 +70,18 @@ void MesoCrystal::setAmbientMaterial(const IMaterial* p_material)
 IFormFactor* MesoCrystal::createFormFactor(
         complex_t wavevector_scattering_factor) const
 {
-    return mp_particle_structure->createTotalFormFactor(
+    IFormFactor *p_result;
+    IFormFactor *p_crystal_ff = mp_particle_structure->createTotalFormFactor(
             *mp_meso_form_factor, mp_ambient_material,
             wavevector_scattering_factor);
+    if(mP_transform.get()) {
+        p_result = new FormFactorDecoratorTransformation(
+                p_crystal_ff, mP_transform);
+    }
+    else {
+        p_result = p_crystal_ff;
+    }
+    return p_result;
 }
 
 void MesoCrystal::setSimpleFormFactor(IFormFactor* p_form_factor)