From 9e84d43535c14a0fe7ef44524a3520391ae9fa6c Mon Sep 17 00:00:00 2001
From: Gennady Pospelov <g.pospelov@fz-juelich.de>
Date: Thu, 12 Dec 2013 15:46:43 +0100
Subject: [PATCH] ThreadInfo is cloned now in Simulation, ThreadInfo is exposed
to python
---
App/src/TestMiscellaneous.cpp | 33 ++++++++-----
Core/Algorithms/src/Simulation.cpp | 1 +
Core/PythonAPI/inc/PythonCoreList.h | 1 +
Core/PythonAPI/inc/ThreadInfo.pypp.h | 11 +++++
Core/PythonAPI/src/PythonModule.cpp | 2 +
Core/PythonAPI/src/ThreadInfo.pypp.cpp | 49 +++++++++++++++++++
Core/python_module.pri | 2 +
.../FitSpheresInHexLattice.py | 8 +--
.../FitSpheresInHexLattice_builder.py | 5 +-
dev-tools/python-bindings/MakePyCore.py | 1 +
10 files changed, 95 insertions(+), 18 deletions(-)
create mode 100644 Core/PythonAPI/inc/ThreadInfo.pypp.h
create mode 100644 Core/PythonAPI/src/ThreadInfo.pypp.cpp
diff --git a/App/src/TestMiscellaneous.cpp b/App/src/TestMiscellaneous.cpp
index 45216c2827e..96bd138b020 100644
--- a/App/src/TestMiscellaneous.cpp
+++ b/App/src/TestMiscellaneous.cpp
@@ -91,10 +91,11 @@ void TestMiscellaneous::test_FunctionalTestRegistry()
MaterialManager::getHomogeneousMaterial("Substrate", 6e-6, 2e-8);
const IMaterial *particle_material = MaterialManager::getHomogeneousMaterial("Particle", 6e-4, 2e-8);
- Layer air_layer;
- air_layer.setMaterial(p_air_material);
- Layer substrate_layer;
- substrate_layer.setMaterial(p_substrate_material);
+ FormFactorFullSphere ff_cyl(5.0*Units::nanometer);
+ Particle particle(particle_material, ff_cyl);
+
+ ParticleDecoration particle_decoration;
+ particle_decoration.addParticle(particle);
Lattice2DIFParameters lattice_params;
lattice_params.m_length_1 = 10.0*Units::nanometer; // L1
@@ -106,16 +107,14 @@ void TestMiscellaneous::test_FunctionalTestRegistry()
new InterferenceFunction2DLattice(lattice_params);
FTDistribution2DCauchy pdf(10.0*Units::nanometer, 10.0*Units::nanometer);
p_interference_function->setProbabilityDistribution(pdf);
-
- // particles
- ParticleDecoration particle_decoration;
- FormFactorFullSphere ff_cyl(5.0*Units::nanometer);
- Particle particle(particle_material, ff_cyl);
- particle_decoration.addParticle(particle);
particle_decoration.addInterferenceFunction(p_interference_function);
+
+ Layer air_layer(p_air_material);
air_layer.setDecoration(particle_decoration);
+ Layer substrate_layer(p_substrate_material, 0);
+
multi_layer->addLayer(air_layer);
multi_layer->addLayer(substrate_layer);
@@ -135,12 +134,22 @@ void TestMiscellaneous::test_FunctionalTestRegistry()
// ----
simulation->runSimulation();
OutputData<double> *real_data = simulation->getIntensityData();
+ double noise_factor(0.1);
+ for(size_t i=0; i<real_data->getAllocatedSize(); ++i) {
+ double amplitude = (*real_data)[i];
+ double sigma = noise_factor*std::sqrt(amplitude);
+ double noisy_amplitude = MathFunctions::GenerateNormalRandom(amplitude, sigma);
+ if(noisy_amplitude < 0) noisy_amplitude = 0.0;
+ (*real_data)[i] = noisy_amplitude;
+ }
FitSuite *fit_suite = new FitSuite();
fit_suite->addSimulationAndRealData(*simulation, *real_data);
fit_suite->initPrint(10);
- fit_suite->addFitParameter("*2DLattice/length_*", 8.0*Units::nanometer, 0.01*Units::nanometer, AttLimits::lowerLimited(0.01));
- fit_suite->addFitParameter("*/FormFactorFullSphere/radius", 8.0*Units::nanometer, 0.01*Units::nanometer, AttLimits::lowerLimited(0.01));
+// fit_suite->addFitParameter("*2DLattice/length_*", 8.0*Units::nanometer, 0.01*Units::nanometer, AttLimits::lowerLimited(0.01));
+// fit_suite->addFitParameter("*/FormFactorFullSphere/radius", 8.0*Units::nanometer, 0.01*Units::nanometer, AttLimits::lowerLimited(0.01));
+ fit_suite->addFitParameter("*2DLattice/length_*", 8.0*Units::nanometer, 0.01*Units::nanometer, AttLimits::limited(4., 12.));
+ fit_suite->addFitParameter("*/FormFactorFullSphere/radius", 8.0*Units::nanometer, 0.01*Units::nanometer, AttLimits::limited(4., 12.));
fit_suite->runFit();
diff --git a/Core/Algorithms/src/Simulation.cpp b/Core/Algorithms/src/Simulation.cpp
index 266e68f9c9f..ae93487c7e0 100644
--- a/Core/Algorithms/src/Simulation.cpp
+++ b/Core/Algorithms/src/Simulation.cpp
@@ -47,6 +47,7 @@ Simulation::Simulation(const Simulation& other)
, mp_sample_builder(other.mp_sample_builder)
, m_instrument(other.m_instrument)
, m_sim_params(other.m_sim_params)
+, m_thread_info(other.m_thread_info)
, m_intensity_map()
, m_polarization_output()
, m_is_normalized(other.m_is_normalized)
diff --git a/Core/PythonAPI/inc/PythonCoreList.h b/Core/PythonAPI/inc/PythonCoreList.h
index 4ec09c90d50..1c0b4fe6091 100644
--- a/Core/PythonAPI/inc/PythonCoreList.h
+++ b/Core/PythonAPI/inc/PythonCoreList.h
@@ -81,6 +81,7 @@
#include "StochasticDoubleGate.h"
#include "StochasticGaussian.h"
#include "StochasticSampledParameter.h"
+#include "ThreadInfo.h"
#include "Types.h"
#include "Units.h"
#include "BAVersion.h"
diff --git a/Core/PythonAPI/inc/ThreadInfo.pypp.h b/Core/PythonAPI/inc/ThreadInfo.pypp.h
new file mode 100644
index 00000000000..52dc1d0a16e
--- /dev/null
+++ b/Core/PythonAPI/inc/ThreadInfo.pypp.h
@@ -0,0 +1,11 @@
+// This file has been generated by Py++.
+
+// BornAgain: simulate and fit scattering at grazing incidence
+//! @brief automatically generated boost::python code for PythonCoreAPI
+
+#ifndef ThreadInfo_hpp__pyplusplus_wrapper
+#define ThreadInfo_hpp__pyplusplus_wrapper
+
+void register_ThreadInfo_class();
+
+#endif//ThreadInfo_hpp__pyplusplus_wrapper
diff --git a/Core/PythonAPI/src/PythonModule.cpp b/Core/PythonAPI/src/PythonModule.cpp
index 08a156af7a1..ea93bdd1d65 100644
--- a/Core/PythonAPI/src/PythonModule.cpp
+++ b/Core/PythonAPI/src/PythonModule.cpp
@@ -19,6 +19,7 @@
#include "AxisDouble.pypp.h"
#include "IAxis.pypp.h"
#include "Layer.pypp.h"
+#include "ThreadInfo.pypp.h"
#include "IFormFactor.pypp.h"
#include "IObservable.pypp.h"
#include "FormFactorParallelepiped.pypp.h"
@@ -189,6 +190,7 @@ BOOST_PYTHON_MODULE(libBornAgainCore){
register_StochasticDoubleGate_class();
register_StochasticDoubleGaussian_class();
register_StochasticSampledParameter_class();
+ register_ThreadInfo_class();
register_global_variables();
register_free_functions();
diff --git a/Core/PythonAPI/src/ThreadInfo.pypp.cpp b/Core/PythonAPI/src/ThreadInfo.pypp.cpp
new file mode 100644
index 00000000000..e76bda361f6
--- /dev/null
+++ b/Core/PythonAPI/src/ThreadInfo.pypp.cpp
@@ -0,0 +1,49 @@
+// This file has been generated by Py++.
+
+// BornAgain: simulate and fit scattering at grazing incidence
+//! @brief automatically generated boost::python code for PythonCoreAPI
+
+#include "Macros.h"
+GCC_DIAG_OFF(unused-parameter);
+GCC_DIAG_OFF(missing-field-initializers);
+#include "boost/python.hpp"
+GCC_DIAG_ON(unused-parameter);
+GCC_DIAG_ON(missing-field-initializers);
+#include "PythonCoreList.h"
+#include "ThreadInfo.pypp.h"
+
+namespace bp = boost::python;
+
+void register_ThreadInfo_class(){
+
+ { //::ThreadInfo
+ typedef bp::class_< ThreadInfo > ThreadInfo_exposer_t;
+ ThreadInfo_exposer_t ThreadInfo_exposer = ThreadInfo_exposer_t( "ThreadInfo", bp::init< >() );
+ bp::scope ThreadInfo_scope( ThreadInfo_exposer );
+ { //::ThreadInfo::getBeginIndex
+
+ typedef int ( ::ThreadInfo::*getBeginIndex_function_type )( int ) ;
+
+ ThreadInfo_exposer.def(
+ "getBeginIndex"
+ , getBeginIndex_function_type( &::ThreadInfo::getBeginIndex )
+ , ( bp::arg("total_size") ) );
+
+ }
+ { //::ThreadInfo::getEndIndex
+
+ typedef int ( ::ThreadInfo::*getEndIndex_function_type )( int ) ;
+
+ ThreadInfo_exposer.def(
+ "getEndIndex"
+ , getEndIndex_function_type( &::ThreadInfo::getEndIndex )
+ , ( bp::arg("total_size") ) );
+
+ }
+ ThreadInfo_exposer.def_readwrite( "current_batch", &ThreadInfo::current_batch );
+ ThreadInfo_exposer.def_readwrite( "current_thread", &ThreadInfo::current_thread );
+ ThreadInfo_exposer.def_readwrite( "n_batches", &ThreadInfo::n_batches );
+ ThreadInfo_exposer.def_readwrite( "n_threads", &ThreadInfo::n_threads );
+ }
+
+}
diff --git a/Core/python_module.pri b/Core/python_module.pri
index ad5fb6536af..48b4a5b59c2 100644
--- a/Core/python_module.pri
+++ b/Core/python_module.pri
@@ -19,6 +19,7 @@ HEADERS += \
PythonAPI/inc/AxisDouble.pypp.h \
PythonAPI/inc/IAxis.pypp.h \
PythonAPI/inc/Layer.pypp.h \
+ PythonAPI/inc/ThreadInfo.pypp.h \
PythonAPI/inc/IFormFactor.pypp.h \
PythonAPI/inc/IObservable.pypp.h \
PythonAPI/inc/FormFactorParallelepiped.pypp.h \
@@ -142,6 +143,7 @@ SOURCES += \
PythonAPI/src/ParticleDecoration.pypp.cpp \
PythonAPI/src/FormFactorSphereGaussianRadius.pypp.cpp \
PythonAPI/src/IClusteredParticles.pypp.cpp \
+ PythonAPI/src/ThreadInfo.pypp.cpp \
PythonAPI/src/Particle.pypp.cpp \
PythonAPI/src/IObserver.pypp.cpp \
PythonAPI/src/Lattice.pypp.cpp \
diff --git a/Examples/python/fitting/ex003_FitSpheresInHexLattice/FitSpheresInHexLattice.py b/Examples/python/fitting/ex003_FitSpheresInHexLattice/FitSpheresInHexLattice.py
index 5f21ca044d7..7af3a83205a 100644
--- a/Examples/python/fitting/ex003_FitSpheresInHexLattice/FitSpheresInHexLattice.py
+++ b/Examples/python/fitting/ex003_FitSpheresInHexLattice/FitSpheresInHexLattice.py
@@ -153,12 +153,12 @@ def run_fitting():
#fit_suite.setMinimizer( MinimizerFactory.createMinimizer("Minuit2","Scan"))
#fit_suite.setMinimizer( MinimizerFactory.createMinimizer("GSLSimAn"))
- #draw_observer = DrawObserver()
- #fit_suite.attachObserver(draw_observer)
+ draw_observer = DrawObserver()
+ fit_suite.attachObserver(draw_observer)
# setting fitting parameters with starting values
- fit_suite.addFitParameter("*2DLattice/length_*", 8.*nanometer, 0.01*nanometer, AttLimits.lowerLimited(0.01)) # this fit parameter will change both length_1 and length_2 simultaneously
- fit_suite.addFitParameter("*/FormFactorFullSphere/radius", 8.*nanometer, 0.01*nanometer, AttLimits.lowerLimited(0.01))
+ fit_suite.addFitParameter("*2DLattice/length_*", 8.*nanometer, 0.01*nanometer, AttLimits.limited(4., 12.)) # this fit parameter will change both length_1 and length_2 simultaneously
+ fit_suite.addFitParameter("*/FormFactorFullSphere/radius", 8.*nanometer, 0.01*nanometer, AttLimits.limited(4., 12.))
# running fit
fit_suite.runFit()
diff --git a/Examples/python/fitting/ex003_FitSpheresInHexLattice/FitSpheresInHexLattice_builder.py b/Examples/python/fitting/ex003_FitSpheresInHexLattice/FitSpheresInHexLattice_builder.py
index 74c0fccad0d..e3dd45fadaa 100644
--- a/Examples/python/fitting/ex003_FitSpheresInHexLattice/FitSpheresInHexLattice_builder.py
+++ b/Examples/python/fitting/ex003_FitSpheresInHexLattice/FitSpheresInHexLattice_builder.py
@@ -79,6 +79,7 @@ def get_simulation():
sim_params.me_if_approx = SimulationParameters.LMA
sim_params.me_lattice_type = SimulationParameters.LATTICE
simulation.setSimulationParameters(sim_params)
+ return simulation
def create_real_data():
@@ -174,8 +175,8 @@ def run_fitting():
fit_suite.attachObserver(draw_observer)
# setting fitting parameters with starting values
- fit_suite.addFitParameter("*radius", 8.*nanometer, 0.01*nanometer, AttLimits.lowerLimited(0.01))
- fit_suite.addFitParameter("*lattice_constant", 8.*nanometer, 0.01*nanometer, AttLimits.lowerLimited(0.01))
+ fit_suite.addFitParameter("*radius", 8.*nanometer, 0.01*nanometer, AttLimits.limited(4., 12.))
+ fit_suite.addFitParameter("*lattice_constant", 8.*nanometer, 0.01*nanometer, AttLimits.limited(4., 12.))
# running fit
fit_suite.runFit()
diff --git a/dev-tools/python-bindings/MakePyCore.py b/dev-tools/python-bindings/MakePyCore.py
index 6758655f22f..0adddedfb38 100644
--- a/dev-tools/python-bindings/MakePyCore.py
+++ b/dev-tools/python-bindings/MakePyCore.py
@@ -115,6 +115,7 @@ include_classes = [
"StochasticDoubleGaussian",
"StochasticParameter<double>",
"StochasticSampledParameter",
+ "ThreadInfo",
"cvector_t",
"kvector_t",
]
--
GitLab