OffSpecSimulation Class Reference

Inheritance diagram for OffSpecSimulation:

Collaboration diagram for OffSpecSimulation:

Public Member Functions
	OffSpecSimulation ()
	~OffSpecSimulation () final
OffSpecSimulation *	clone () const override
void	accept (INodeVisitor *visitor) const final
void	prepareSimulation () final
SimulationResult	result () const override
void	setBeamParameters (double wavelength, const IAxis &alpha_axis, double phi_i)
const IAxis *	beamAxis () const
std::unique_ptr< IUnitConverter >	createUnitConverter () const
size_t	intensityMapSize () const override
void	setDetectorParameters (size_t n_phi, double phi_min, double phi_max, size_t n_alpha, double alpha_min, double alpha_max)
void	setDetector (const IDetector2D &detector)
void	removeMasks ()
void	addMask (const IShape2D &shape, bool mask_value=true)
void	maskAll ()
void	setRegionOfInterest (double xlow, double ylow, double xup, double yup)
void	runSimulation ()
void	runMPISimulation ()
void	setInstrument (const Instrument &instrument_)
const Instrument &	instrument () const
Instrument &	instrument ()
void	setBeamIntensity (double intensity)
double	getBeamIntensity () const
void	setBeamPolarization (const kvector_t bloch_vector)
void	setDetectorResolutionFunction (const IResolutionFunction2D &resolution_function)
void	removeDetectorResolutionFunction ()
void	setAnalyzerProperties (const kvector_t direction, double efficiency, double total_transmission)
void	setSample (const MultiLayer &sample)
const MultiLayer *	sample () const
void	setSampleBuilder (const std::shared_ptr< ISampleBuilder > &sample_builder)
void	setBackground (const IBackground &bg)
const IBackground *	background () const
void	addParameterDistribution (const std::string &param_name, const IDistribution1D &distribution, size_t nbr_samples, double sigma_factor=0.0, const RealLimits &limits=RealLimits())
void	addParameterDistribution (const ParameterDistribution &par_distr)
const DistributionHandler &	getDistributionHandler () const
void	setOptions (const SimulationOptions &options)
const SimulationOptions &	getOptions () const
SimulationOptions &	getOptions ()
void	subscribe (ProgressHandler::Callback_t inform)
void	setTerminalProgressMonitor ()
std::vector< const INode * >	getChildren () const
SimulationResult	convertData (const OutputData< double > &data, bool put_masked_areas_to_zero=true)
virtual void	transferToCPP ()
virtual std::string	treeToString () const
void	registerChild (INode *node)
virtual void	setParent (const INode *newParent)
const INode *	parent () const
INode *	parent ()
int	copyNumber (const INode *node) const
std::string	displayName () const
ParameterPool *	createParameterTree () const
ParameterPool *	parameterPool () const
std::string	parametersToString () const
RealParameter &	registerParameter (const std::string &name, double *parpointer)
void	registerVector (const std::string &base_name, kvector_t *p_vec, const std::string &units="nm")
void	setParameterValue (const std::string &name, double value)
void	setVectorValue (const std::string &base_name, kvector_t value)
RealParameter *	parameter (const std::string &name) const
virtual void	onChange ()
void	removeParameter (const std::string &name)
void	removeVector (const std::string &base_name)
void	setName (const std::string &name)
const std::string &	getName () const

Static Public Member Functions
static std::string	XComponentName (const std::string &base_name)
static std::string	YComponentName (const std::string &base_name)
static std::string	ZComponentName (const std::string &base_name)

Protected Member Functions
virtual void	initUnitConverter ()
std::unique_ptr< IComputation >	generateSingleThreadedComputation (size_t start, size_t n_elements) override
std::vector< SimulationElement >	generateSimulationElements (const Beam &beam)
void	normalize (size_t start_ind, size_t n_elements) override
void	addBackgroundIntensity (size_t start_ind, size_t n_elements) override
void	addDataToCache (double weight) override
void	moveDataFromCache () override
const SimulationOptions &	options () const
ProgressHandler &	progress ()

Protected Attributes
std::vector< SimulationElement >	m_sim_elements
std::vector< double >	m_cache
const size_t	m_NP
std::vector< double >	m_P

Private Member Functions
	OffSpecSimulation (const OffSpecSimulation &other)
void	initSimulationElementVector () override
void	validateParametrization (const ParameterDistribution &par_distr) const override
void	transferResultsToIntensityMap () override
void	updateIntensityMap () override
size_t	numberOfSimulationElements () const final
void	transferDetectorImage (size_t index)
void	checkInitialization () const
void	initialize ()
std::vector< double >	rawResults () const override
void	setRawResults (const std::vector< double > &raw_data) override
void	runSingleSimulation (size_t batch_start, size_t batch_size, double weight=1.0)

Private Attributes
std::unique_ptr< IAxis >	mP_alpha_i_axis
OutputData< double >	m_intensity_map
std::unique_ptr< DetectorContext >	m_detector_context
SimulationOptions	m_options
ProgressHandler	m_progress
SampleProvider	m_sample_provider
DistributionHandler	m_distribution_handler
Instrument	m_instrument
std::unique_ptr< IBackground >	m_background
const INode *	m_parent {nullptr}
std::string	m_name
std::unique_ptr< ParameterPool >	m_pool

Detailed Description

Main class to run an off-specular simulation.

Definition at line 26 of file OffSpecSimulation.h.

Constructor & Destructor Documentation

OffSpecSimulation() [1/2]

OffSpecSimulation::OffSpecSimulation

(

)

Definition at line 25 of file OffSpecSimulation.cpp.

{
    initialize();
}

References initialize().

Referenced by clone().

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~OffSpecSimulation()

OffSpecSimulation::~OffSpecSimulation ( )

inlinefinal

Definition at line 30 of file OffSpecSimulation.h.

{}

OffSpecSimulation() [2/2]

OffSpecSimulation::OffSpecSimulation ( const OffSpecSimulation &  other )

private

Definition at line 82 of file OffSpecSimulation.cpp.

                                                                   : Simulation2D(other)
{
    if (other.mP_alpha_i_axis)
        mP_alpha_i_axis.reset(other.mP_alpha_i_axis->clone());
    m_intensity_map.copyFrom(other.m_intensity_map);
    initialize();
}

References OutputData< T >::copyFrom(), initialize(), m_intensity_map, and mP_alpha_i_axis.

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Member Function Documentation

clone()

OffSpecSimulation* OffSpecSimulation::clone ( ) const

inlineoverridevirtual

Implements Simulation2D.

Definition at line 32 of file OffSpecSimulation.h.

{ return new OffSpecSimulation(*this); }

References OffSpecSimulation().

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accept()

void OffSpecSimulation::accept ( INodeVisitor *  visitor ) const

inlinefinalvirtual

Calls the INodeVisitor's visit method.

Implements INode.

Definition at line 34 of file OffSpecSimulation.h.

{ visitor->visit(this); }

prepareSimulation()

void OffSpecSimulation::prepareSimulation ( )

finalvirtual

Put into a clean state for running a simulation.

Reimplemented from Simulation.

Definition at line 30 of file OffSpecSimulation.cpp.

{
    checkInitialization();
    Simulation2D::prepareSimulation();
}

References checkInitialization(), and Simulation2D::prepareSimulation().

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result()

SimulationResult OffSpecSimulation::result ( ) const

overridevirtual

Returns the results of the simulation in a format that supports unit conversion and export to numpy arrays.

Implements Simulation.

Definition at line 42 of file OffSpecSimulation.cpp.

{
    auto data = std::unique_ptr<OutputData<double>>(m_intensity_map.clone());
    OffSpecularConverter converter(instrument().detector2D(), instrument().getBeam(),
                                   *mP_alpha_i_axis);
    return SimulationResult(*data, converter);
}

References OutputData< T >::clone(), Simulation::instrument(), m_intensity_map, and mP_alpha_i_axis.

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setBeamParameters()

void OffSpecSimulation::setBeamParameters	(	double	wavelength,
		const IAxis &	alpha_axis,
		double	phi_i
	)

Sets beam parameters from here (forwarded to Instrument)

Definition at line 50 of file OffSpecSimulation.cpp.

{
    mP_alpha_i_axis.reset(alpha_axis.clone());
    if (alpha_axis.size() < 1)
        throw Exceptions::ClassInitializationException("OffSpecSimulation::prepareSimulation() "
                                                       "-> Error. Incoming alpha range size < 1.");
    const double alpha_zero = alpha_axis.getMin();
    instrument().setBeamParameters(wavelength, alpha_zero, phi_i);
    updateIntensityMap();
}

References IAxis::clone(), IAxis::getMin(), Simulation::instrument(), mP_alpha_i_axis, Instrument::setBeamParameters(), IAxis::size(), updateIntensityMap(), and anonymous_namespace{SlicedCylindersBuilder.cpp}::wavelength().

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beamAxis()

const IAxis * OffSpecSimulation::beamAxis

(

)

const

Returns axis of the beam.

Definition at line 61 of file OffSpecSimulation.cpp.

{
    return mP_alpha_i_axis.get();
}

References mP_alpha_i_axis.

Referenced by createUnitConverter(), and SimulationToPython::defineOffSpecBeam().

createUnitConverter()

std::unique_ptr< IUnitConverter > OffSpecSimulation::createUnitConverter

(

)

const

Definition at line 66 of file OffSpecSimulation.cpp.

{
    const IAxis* axis = beamAxis();
    if (!axis)
        throw std::runtime_error("Error in OffSpecSimulation::createUnitConverter:"
                                 " missing inclination angle axis");
    return std::make_unique<OffSpecularConverter>(instrument().detector2D(), instrument().getBeam(),
                                                  *axis);
}

References beamAxis(), and Simulation::instrument().

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intensityMapSize()

size_t OffSpecSimulation::intensityMapSize ( ) const

overridevirtual

Returns the total number of the intensity values in the simulation result.

Implements Simulation.

Definition at line 76 of file OffSpecSimulation.cpp.

{
    checkInitialization();
    return mP_alpha_i_axis->size() * instrument().getDetectorAxis(1).size();
}

References checkInitialization(), Instrument::getDetectorAxis(), Simulation::instrument(), mP_alpha_i_axis, and IAxis::size().

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initSimulationElementVector()

void OffSpecSimulation::initSimulationElementVector ( )

overrideprivatevirtual

Initializes the vector of Simulation elements.

Implements Simulation.

Definition at line 90 of file OffSpecSimulation.cpp.

{
    m_sim_elements.clear();
    Beam beam = instrument().getBeam();
    const double wavelength = beam.getWavelength();
    const double phi_i = beam.getPhi();
 
    for (size_t i = 0; i < mP_alpha_i_axis->size(); ++i) {
        // Incoming angle by convention defined as positive:
        double alpha_i = mP_alpha_i_axis->getBin(i).getMidPoint();
        double total_alpha = alpha_i;
        beam.setCentralK(wavelength, total_alpha, phi_i);
        auto sim_elements_i = generateSimulationElements(beam);
        m_sim_elements.insert(m_sim_elements.end(), std::make_move_iterator(sim_elements_i.begin()),
                              std::make_move_iterator(sim_elements_i.end()));
    }
    if (m_cache.empty())
        m_cache.resize(m_sim_elements.size(), 0.0);
}

References Simulation2D::generateSimulationElements(), Instrument::getBeam(), Beam::getPhi(), Beam::getWavelength(), Simulation::instrument(), Simulation2D::m_cache, Simulation2D::m_sim_elements, mP_alpha_i_axis, Beam::setCentralK(), and anonymous_namespace{SlicedCylindersBuilder.cpp}::wavelength().

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validateParametrization()

void OffSpecSimulation::validateParametrization ( const ParameterDistribution &  par_distr ) const

overrideprivatevirtual

Checks the distribution validity for simulation.

Reimplemented from Simulation.

Definition at line 110 of file OffSpecSimulation.cpp.

{
    const bool zero_mean = par_distr.getDistribution()->getMean() == 0.0;
    if (zero_mean)
        return;
 
    std::unique_ptr<ParameterPool> parameter_pool(createParameterTree());
    const std::vector<RealParameter*> names =
        parameter_pool->getMatchedParameters(par_distr.getMainParameterName());
    for (const auto par : names)
        if (par->getName().find("InclinationAngle") != std::string::npos && !zero_mean)
            throw std::runtime_error("Error in OffSpecSimulation: parameter distribution of "
                                     "beam inclination angle should have zero mean.");
}

References INode::createParameterTree(), ParameterDistribution::getDistribution(), ParameterDistribution::getMainParameterName(), and IDistribution1D::getMean().

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transferResultsToIntensityMap()

void OffSpecSimulation::transferResultsToIntensityMap ( )

overrideprivatevirtual

Creates the appropriate data structure (e.g.

2D intensity map) from the calculated SimulationElement objects

Reimplemented from Simulation.

Definition at line 125 of file OffSpecSimulation.cpp.

{
    checkInitialization();
    const IAxis& phi_axis = instrument().getDetectorAxis(0);
    size_t phi_f_size = phi_axis.size();
    if (phi_f_size * m_intensity_map.getAllocatedSize() != m_sim_elements.size())
        throw Exceptions::RuntimeErrorException(
            "OffSpecSimulation::transferResultsToIntensityMap: "
            "intensity map size does not conform to number of calculated intensities");
    for (size_t i = 0; i < mP_alpha_i_axis->size(); ++i)
        transferDetectorImage(i);
}

References checkInitialization(), OutputData< T >::getAllocatedSize(), Instrument::getDetectorAxis(), Simulation::instrument(), m_intensity_map, Simulation2D::m_sim_elements, mP_alpha_i_axis, IAxis::size(), and transferDetectorImage().

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updateIntensityMap()

void OffSpecSimulation::updateIntensityMap ( )

overrideprivatevirtual

Default implementation only adds the detector axes.

Reimplemented from Simulation.

Definition at line 138 of file OffSpecSimulation.cpp.

{
    m_intensity_map.clear();
    if (mP_alpha_i_axis)
        m_intensity_map.addAxis(*mP_alpha_i_axis);
    size_t detector_dimension = instrument().getDetectorDimension();
    if (detector_dimension == 2)
        m_intensity_map.addAxis(instrument().getDetectorAxis(1));
    m_intensity_map.setAllTo(0.);
}

References OutputData< T >::addAxis(), OutputData< T >::clear(), Instrument::getDetectorDimension(), Simulation::instrument(), m_intensity_map, mP_alpha_i_axis, and OutputData< T >::setAllTo().

Referenced by setBeamParameters().

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numberOfSimulationElements()

size_t OffSpecSimulation::numberOfSimulationElements ( ) const

finalprivatevirtual

Gets the number of elements this simulation needs to calculate.

Implements Simulation.

Definition at line 36 of file OffSpecSimulation.cpp.

{
    checkInitialization();
    return Simulation2D::numberOfSimulationElements() * mP_alpha_i_axis->size();
}

References checkInitialization(), mP_alpha_i_axis, and Simulation2D::numberOfSimulationElements().

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transferDetectorImage()

void OffSpecSimulation::transferDetectorImage ( size_t  index )

private

Normalize, apply detector resolution and transfer detector image corresponding to alpha_i = mp_alpha_i_axis->getBin(index)

Definition at line 149 of file OffSpecSimulation.cpp.

{
    OutputData<double> detector_image;
    size_t detector_dimension = instrument().getDetectorDimension();
    for (size_t dim = 0; dim < detector_dimension; ++dim)
        detector_image.addAxis(instrument().getDetectorAxis(dim));
    size_t detector_size = detector_image.getAllocatedSize();
    for (size_t i = 0; i < detector_size; ++i)
        detector_image[i] = m_sim_elements[index * detector_size + i].getIntensity();
    instrument().applyDetectorResolution(&detector_image);
    size_t y_axis_size = instrument().getDetectorAxis(1).size();
    for (size_t i = 0; i < detector_size; ++i)
        m_intensity_map[index * y_axis_size + i % y_axis_size] += detector_image[i];
}

References OutputData< T >::addAxis(), Instrument::applyDetectorResolution(), OutputData< T >::getAllocatedSize(), Instrument::getDetectorAxis(), Instrument::getDetectorDimension(), Simulation::instrument(), m_intensity_map, Simulation2D::m_sim_elements, and IAxis::size().

Referenced by transferResultsToIntensityMap().

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checkInitialization()

void OffSpecSimulation::checkInitialization ( ) const

private

Check correct number of axes.

Definition at line 164 of file OffSpecSimulation.cpp.

{
    if (!mP_alpha_i_axis || mP_alpha_i_axis->size() < 1)
        throw Exceptions::ClassInitializationException("OffSpecSimulation::checkInitialization() "
                                                       "Incoming alpha range not configured.");
    if (instrument().getDetectorDimension() != 2)
        throw Exceptions::RuntimeErrorException(
            "OffSpecSimulation::checkInitialization: detector is not two-dimensional");
}

References Simulation::instrument(), and mP_alpha_i_axis.

Referenced by intensityMapSize(), numberOfSimulationElements(), prepareSimulation(), and transferResultsToIntensityMap().

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initialize()

void OffSpecSimulation::initialize ( )

private

Definition at line 174 of file OffSpecSimulation.cpp.

{
    setName("OffSpecSimulation");
}

References IParameterized::setName().

Referenced by OffSpecSimulation().

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setDetectorParameters()

void Simulation2D::setDetectorParameters ( size_t  n_phi, double  phi_min, double  phi_max, size_t  n_alpha, double  alpha_min, double  alpha_max  )

inherited

Sets spherical detector parameters using angle ranges.

Parameters

n_phi	number of phi-axis bins
phi_min	low edge of first phi-bin
phi_max	upper edge of last phi-bin
n_alpha	number of alpha-axis bins
alpha_min	low edge of first alpha-bin
alpha_max	upper edge of last alpha-bin

Definition at line 64 of file Simulation2D.cpp.

{
    instrument().detector2D().setDetectorParameters(n_x, x_min, x_max, n_y, y_min, y_max);
    updateIntensityMap();
}

References Instrument::detector2D(), Simulation::instrument(), IDetector2D::setDetectorParameters(), and Simulation::updateIntensityMap().

Referenced by StandardSimulations::BasicGISAS(), StandardSimulations::ExtraLongWavelengthGISAS(), StandardSimulations::GISASWithMasks(), StandardSimulations::MaxiGISAS(), StandardSimulations::MiniGISAS(), StandardSimulations::MiniGISAS_v2(), StandardSimulations::MiniGISASFit(), StandardSimulations::MiniGISASSpecularPeak(), and StandardSimulations::SphericalDetWithRoi().

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setDetector()

void Simulation2D::setDetector ( const IDetector2D &  detector )

inherited

Sets the detector (axes can be overwritten later)

Definition at line 71 of file Simulation2D.cpp.

{
    instrument().setDetector(detector);
    initUnitConverter();
}

References Simulation2D::initUnitConverter(), Simulation::instrument(), and Instrument::setDetector().

Referenced by StandardSimulations::IsGISAXSSimulation1(), StandardSimulations::IsGISAXSSimulation2(), StandardSimulations::RectDetectorGeneric(), StandardSimulations::RectDetectorPerpToDirectBeam(), StandardSimulations::RectDetectorPerpToReflectedBeam(), StandardSimulations::RectDetectorPerpToReflectedBeamDpos(), and StandardSimulations::RectDetectorPerpToSample().

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removeMasks()

void Simulation2D::removeMasks ( )

inherited

removes all masks from the detector

Definition at line 32 of file Simulation2D.cpp.

{
    instrument().detector2D().removeMasks();
}

References Instrument::detector2D(), Simulation::instrument(), and IDetector2D::removeMasks().

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addMask()

void Simulation2D::addMask ( const IShape2D &  shape, bool  mask_value = true  )

inherited

Adds mask of given shape to the stack of detector masks.

The mask value 'true' means that the channel will be excluded from the simulation. The mask which is added last has priority.

Parameters

shape	The shape of mask (Rectangle, Polygon, Line, Ellipse)
mask_value	The value of mask

Definition at line 37 of file Simulation2D.cpp.

{
    instrument().detector2D().addMask(shape, mask_value);
}

References IDetector2D::addMask(), Instrument::detector2D(), and Simulation::instrument().

Referenced by StandardSimulations::GISASWithMasks(), StandardSimulations::RectDetWithRoi(), and StandardSimulations::SphericalDetWithRoi().

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maskAll()

void Simulation2D::maskAll ( )

inherited

Put the mask for all detector channels (i.e. exclude whole detector from the analysis)

Definition at line 42 of file Simulation2D.cpp.

{
    instrument().detector2D().maskAll();
}

References Instrument::detector2D(), Simulation::instrument(), and IDetector2D::maskAll().

Referenced by StandardSimulations::GISASWithMasks().

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setRegionOfInterest()

void Simulation2D::setRegionOfInterest ( double  xlow, double  ylow, double  xup, double  yup  )

inherited

Sets rectangular region of interest with lower left and upper right corners defined.

Definition at line 47 of file Simulation2D.cpp.

{
    instrument().detector2D().setRegionOfInterest(xlow, ylow, xup, yup);
}

References Instrument::detector2D(), Simulation::instrument(), and IDetector2D::setRegionOfInterest().

Referenced by StandardSimulations::RectDetWithRoi(), and StandardSimulations::SphericalDetWithRoi().

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initUnitConverter()

virtual void Simulation2D::initUnitConverter ( )

inlineprotectedvirtualinherited

Definition at line 69 of file Simulation2D.h.

{}

Referenced by Simulation2D::setDetector().

generateSingleThreadedComputation()

std::unique_ptr< IComputation > Simulation2D::generateSingleThreadedComputation ( size_t  start, size_t  n_elements  )

overrideprotectedvirtualinherited

Generate a single threaded computation for a given range of simulation elements.

Parameters

start	Index of the first element to include into computation
n_elements	Number of elements to process

Implements Simulation.

Definition at line 77 of file Simulation2D.cpp.

{
    ASSERT(start < m_sim_elements.size() && start + n_elements <= m_sim_elements.size());
    const auto& begin = m_sim_elements.begin() + static_cast<long>(start);
    return std::make_unique<DWBAComputation>(*sample(), options(), progress(), begin,
                                             begin + static_cast<long>(n_elements));
}

References ASSERT, Simulation2D::m_sim_elements, Simulation::options(), Simulation::progress(), and Simulation::sample().

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generateSimulationElements()

std::vector< SimulationElement > Simulation2D::generateSimulationElements ( const Beam &  beam )

protectedinherited

Generate simulation elements for given beam.

Definition at line 86 of file Simulation2D.cpp.

{
    const double wavelength = beam.getWavelength();
    const double alpha_i = -beam.getAlpha(); // Defined to be always positive in Beam
    const double phi_i = beam.getPhi();
    const Eigen::Matrix2cd beam_polarization = beam.getPolarization();
 
    const IDetector2D& detector = instrument().detector2D();
    const Eigen::Matrix2cd analyzer_operator = detector.detectionProperties().analyzerOperator();
    const size_t spec_index = detector.indexOfSpecular(beam);
 
    const size_t N = m_detector_context->numberOfSimulationElements();
 
    std::vector<SimulationElement> result;
    result.reserve(N);
    for (size_t element_index = 0; element_index < N; ++element_index) {
        SimulationElement element(wavelength, alpha_i, phi_i,
                                  m_detector_context->createPixel(element_index));
        element.setPolarization(beam_polarization);
        element.setAnalyzerOperator(analyzer_operator);
        if (m_detector_context->detectorIndex(element_index) == spec_index)
            element.setSpecular(true);
        result.emplace_back(std::move(element));
    }
    return result;
}

References DetectionProperties::analyzerOperator(), IDetector::detectionProperties(), Instrument::detector2D(), Beam::getAlpha(), Beam::getPhi(), Beam::getPolarization(), Beam::getWavelength(), IDetector2D::indexOfSpecular(), Simulation::instrument(), Simulation2D::m_detector_context, Simulation::result(), SimulationElement::setAnalyzerOperator(), SimulationElement::setPolarization(), SimulationElement::setSpecular(), and anonymous_namespace{SlicedCylindersBuilder.cpp}::wavelength().

Referenced by GISASSimulation::initSimulationElementVector(), and initSimulationElementVector().

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normalize()

void Simulation2D::normalize ( size_t  start_ind, size_t  n_elements  )

overrideprotectedvirtualinherited

Normalize the detector counts to beam intensity, to solid angle, and to exposure angle.

Parameters

start_ind	Index of the first element to operate on
n_elements	Number of elements to process

Implements Simulation.

Definition at line 113 of file Simulation2D.cpp.

{
    const double beam_intensity = getBeamIntensity();
    if (beam_intensity == 0.0)
        return; // no normalization when beam intensity is zero
    for (size_t i = start_ind, stop_point = start_ind + n_elements; i < stop_point; ++i) {
        SimulationElement& element = m_sim_elements[i];
        double sin_alpha_i = std::abs(std::sin(element.getAlphaI()));
        if (sin_alpha_i == 0.0)
            sin_alpha_i = 1.0;
        const double solid_angle = element.getSolidAngle();
        element.setIntensity(element.getIntensity() * beam_intensity * solid_angle / sin_alpha_i);
    }
}

References SimulationElement::getAlphaI(), Simulation::getBeamIntensity(), SimulationElement::getIntensity(), SimulationElement::getSolidAngle(), Simulation2D::m_sim_elements, and SimulationElement::setIntensity().

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addBackgroundIntensity()

void Simulation2D::addBackgroundIntensity ( size_t  start_ind, size_t  n_elements  )

overrideprotectedvirtualinherited

Implements Simulation.

Definition at line 128 of file Simulation2D.cpp.

{
    if (!background())
        return;
    for (size_t i = start_ind, stop_point = start_ind + n_elements; i < stop_point; ++i) {
        SimulationElement& element = m_sim_elements[i];
        element.setIntensity(background()->addBackground(element.getIntensity()));
    }
}

References Simulation::background(), SimulationElement::getIntensity(), Simulation2D::m_sim_elements, and SimulationElement::setIntensity().

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addDataToCache()

void Simulation2D::addDataToCache ( double  weight )

overrideprotectedvirtualinherited

Implements Simulation.

Definition at line 138 of file Simulation2D.cpp.

{
    if (m_sim_elements.size() != m_cache.size())
        throw std::runtime_error("Error in Simulation2D::addDataToCache(double): cache size"
                                 " not the same as element size");
    for (unsigned i = 0; i < m_sim_elements.size(); i++)
        m_cache[i] += m_sim_elements[i].getIntensity() * weight;
}

References Simulation2D::m_cache, and Simulation2D::m_sim_elements.

moveDataFromCache()

void Simulation2D::moveDataFromCache ( )

overrideprotectedvirtualinherited

Implements Simulation.

Definition at line 147 of file Simulation2D.cpp.

{
    ASSERT(!m_cache.empty());
    if (!m_cache.empty()) {
        for (unsigned i = 0; i < m_sim_elements.size(); i++)
            m_sim_elements[i].setIntensity(m_cache[i]);
        m_cache.clear();
    }
}

References ASSERT, Simulation2D::m_cache, and Simulation2D::m_sim_elements.

rawResults()

std::vector< double > Simulation2D::rawResults ( ) const

overrideprivatevirtualinherited

Implements Simulation.

Definition at line 157 of file Simulation2D.cpp.

{
    std::vector<double> result;
    result.resize(m_sim_elements.size());
    for (unsigned i = 0; i < m_sim_elements.size(); ++i)
        result[i] = m_sim_elements[i].getIntensity();
    return result;
}

References Simulation2D::m_sim_elements, and Simulation::result().

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setRawResults()

void Simulation2D::setRawResults ( const std::vector< double > &  raw_data )

overrideprivatevirtualinherited

Implements Simulation.

Definition at line 166 of file Simulation2D.cpp.

{
    initSimulationElementVector();
    if (raw_data.size() != m_sim_elements.size())
        throw std::runtime_error("Simulation2D::setRawResults: size of vector passed as "
                                 "argument doesn't match number of elements in this simulation");
    for (unsigned i = 0; i < raw_data.size(); i++)
        m_sim_elements[i].setIntensity(raw_data[i]);
    transferResultsToIntensityMap();
}

References Simulation::initSimulationElementVector(), Simulation2D::m_sim_elements, and Simulation::transferResultsToIntensityMap().

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runSimulation()

void Simulation::runSimulation ( )

inherited

Run a simulation, possibly averaged over parameter distributions.

Run simulation with possible averaging over parameter distributions.

Definition at line 200 of file Simulation.cpp.

{
    prepareSimulation();
 
    const size_t total_size = numberOfSimulationElements();
    size_t param_combinations = m_distribution_handler.getTotalNumberOfSamples();
 
    m_progress.reset();
    m_progress.setExpectedNTicks(param_combinations * total_size);
 
    // restrict calculation to current batch
    const size_t n_batches = m_options.getNumberOfBatches();
    const size_t current_batch = m_options.getCurrentBatch();
 
    const size_t batch_start = getStartIndex(n_batches, current_batch, total_size);
    const size_t batch_size = getNumberOfElements(n_batches, current_batch, total_size);
    if (batch_size == 0)
        return;
 
    std::unique_ptr<ParameterPool> param_pool(createParameterTree());
    for (size_t index = 0; index < param_combinations; ++index) {
        double weight = m_distribution_handler.setParameterValues(param_pool.get(), index);
        runSingleSimulation(batch_start, batch_size, weight);
    }
    m_distribution_handler.setParameterToMeans(param_pool.get());
    moveDataFromCache();
    transferResultsToIntensityMap();
}

References INode::createParameterTree(), SimulationOptions::getCurrentBatch(), SimulationOptions::getNumberOfBatches(), anonymous_namespace{Simulation.cpp}::getNumberOfElements(), anonymous_namespace{Simulation.cpp}::getStartIndex(), DistributionHandler::getTotalNumberOfSamples(), Simulation::m_distribution_handler, Simulation::m_options, Simulation::m_progress, Simulation::moveDataFromCache(), Simulation::numberOfSimulationElements(), Simulation::prepareSimulation(), ProgressHandler::reset(), Simulation::runSingleSimulation(), ProgressHandler::setExpectedNTicks(), DistributionHandler::setParameterToMeans(), DistributionHandler::setParameterValues(), and Simulation::transferResultsToIntensityMap().

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runMPISimulation()

void Simulation::runMPISimulation ( )

inherited

Run a simulation in a MPI environment.

Definition at line 229 of file Simulation.cpp.

{
    MPISimulation ompi;
    ompi.runSimulation(this);
}

References MPISimulation::runSimulation().

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setInstrument()

void Simulation::setInstrument ( const Instrument &  instrument_ )

inherited

Definition at line 235 of file Simulation.cpp.

{
    m_instrument = instrument_;
    updateIntensityMap();
}

References Simulation::m_instrument, and Simulation::updateIntensityMap().

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instrument() [1/2]

const Instrument& Simulation::instrument ( ) const

inlineinherited

Definition at line 55 of file Simulation.h.

{ return m_instrument; }

References Simulation::m_instrument.

Referenced by Simulation2D::addMask(), checkInitialization(), Simulation::convertData(), DepthProbeSimulation::createUnitConverter(), createUnitConverter(), SimulationToPython::defineDetector(), SimulationToPython::defineDetectorPolarizationAnalysis(), SimulationToPython::defineDetectorResolutionFunction(), SimulationToPython::defineGISASBeam(), SimulationToPython::defineMasks(), SimulationToPython::defineOffSpecBeam(), SimulationToPython::defineSpecularScan(), Simulation2D::generateSimulationElements(), Simulation::getBeamIntensity(), Simulation::getChildren(), DepthProbeSimulation::initialize(), SpecularSimulation::initialize(), DepthProbeSimulation::initSimulationElementVector(), GISASSimulation::initSimulationElementVector(), initSimulationElementVector(), SpecularSimulation::initSimulationElementVector(), GISASSimulation::intensityMapSize(), intensityMapSize(), Simulation2D::maskAll(), DepthProbeSimulation::normalize(), SpecularSimulation::normalize(), GISASSimulation::prepareSimulation(), Simulation2D::prepareSimulation(), SpecularSimulation::prepareSimulation(), Simulation::removeDetectorResolutionFunction(), Simulation2D::removeMasks(), GISASSimulation::result(), result(), Simulation::setAnalyzerProperties(), Simulation::setBeamIntensity(), DepthProbeSimulation::setBeamParameters(), setBeamParameters(), GISASSimulation::setBeamParameters(), Simulation::setBeamPolarization(), Simulation2D::setDetector(), Simulation2D::setDetectorParameters(), Simulation::setDetectorResolutionFunction(), Simulation2D::setRegionOfInterest(), SpecularSimulation::setScan(), transferDetectorImage(), transferResultsToIntensityMap(), and updateIntensityMap().

instrument() [2/2]

Instrument& Simulation::instrument ( )

inlineinherited

Definition at line 56 of file Simulation.h.

{ return m_instrument; }

References Simulation::m_instrument.

setBeamIntensity()

void Simulation::setBeamIntensity ( double  intensity )

inherited

Definition at line 173 of file Simulation.cpp.

{
    instrument().setBeamIntensity(intensity);
}

References Simulation::instrument(), and Instrument::setBeamIntensity().

Referenced by StandardSimulations::GISASWithMasks().

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getBeamIntensity()

double Simulation::getBeamIntensity ( ) const

inherited

Definition at line 178 of file Simulation.cpp.

{
    return instrument().getBeamIntensity();
}

References Instrument::getBeamIntensity(), and Simulation::instrument().

Referenced by DepthProbeSimulation::normalize(), Simulation2D::normalize(), and SpecularSimulation::normalize().

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setBeamPolarization()

void Simulation::setBeamPolarization ( const kvector_t  bloch_vector )

inherited

Sets the beam polarization according to the given Bloch vector.

Definition at line 184 of file Simulation.cpp.

{
    instrument().setBeamPolarization(bloch_vector);
}

References Simulation::instrument(), and Instrument::setBeamPolarization().

Referenced by StandardSimulations::BasicGISAS00(), StandardSimulations::BasicPolarizedGISAS(), StandardSimulations::MaxiGISAS00(), StandardSimulations::MiniGISASPolarizationMM(), StandardSimulations::MiniGISASPolarizationMP(), StandardSimulations::MiniGISASPolarizationPM(), and StandardSimulations::MiniGISASPolarizationPP().

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setDetectorResolutionFunction()

void Simulation::setDetectorResolutionFunction ( const IResolutionFunction2D &  resolution_function )

inherited

Definition at line 156 of file Simulation.cpp.

{
    instrument().setDetectorResolutionFunction(resolution_function);
}

References Simulation::instrument(), and Instrument::setDetectorResolutionFunction().

Referenced by StandardSimulations::MiniGISASDetectorResolution().

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removeDetectorResolutionFunction()

void Simulation::removeDetectorResolutionFunction ( )

inherited

Definition at line 161 of file Simulation.cpp.

{
    instrument().removeDetectorResolution();
}

References Simulation::instrument(), and Instrument::removeDetectorResolution().

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setAnalyzerProperties()

void Simulation::setAnalyzerProperties ( const kvector_t  direction, double  efficiency, double  total_transmission  )

inherited

Sets the polarization analyzer characteristics of the detector.

Definition at line 167 of file Simulation.cpp.

{
    instrument().setAnalyzerProperties(direction, efficiency, total_transmission);
}

References Simulation::instrument(), and Instrument::setAnalyzerProperties().

Referenced by StandardSimulations::BasicGISAS00(), StandardSimulations::BasicPolarizedGISAS(), StandardSimulations::MaxiGISAS00(), StandardSimulations::MiniGISASPolarizationMM(), StandardSimulations::MiniGISASPolarizationMP(), StandardSimulations::MiniGISASPolarizationPM(), and StandardSimulations::MiniGISASPolarizationPP().

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setSample()

void Simulation::setSample ( const MultiLayer &  sample )

inherited

The MultiLayer object will not be owned by the Simulation object.

Definition at line 242 of file Simulation.cpp.

{
    m_sample_provider.setSample(sample);
}

References Simulation::m_sample_provider, Simulation::sample(), and SampleProvider::setSample().

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sample()

const MultiLayer * Simulation::sample ( ) const

inherited

Definition at line 247 of file Simulation.cpp.

{
    return m_sample_provider.sample();
}

References Simulation::m_sample_provider, and SampleProvider::sample().

Referenced by SimulationToPython::generateSimulationCode(), DepthProbeSimulation::generateSingleThreadedComputation(), Simulation2D::generateSingleThreadedComputation(), SpecularSimulation::generateSingleThreadedComputation(), Simulation::setSample(), and DepthProbeSimulation::validityCheck().

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setSampleBuilder()

void Simulation::setSampleBuilder ( const std::shared_ptr< ISampleBuilder > &  sample_builder )

inherited

Definition at line 252 of file Simulation.cpp.

{
    m_sample_provider.setBuilder(sample_builder);
}

References Simulation::m_sample_provider, and SampleProvider::setBuilder().

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setBackground()

void Simulation::setBackground ( const IBackground &  bg )

inherited

Definition at line 257 of file Simulation.cpp.

{
    m_background.reset(bg.clone());
    registerChild(m_background.get());
}

References IBackground::clone(), Simulation::m_background, and INode::registerChild().

Referenced by StandardSimulations::ConstantBackgroundGISAS(), and Simulation::Simulation().

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background()

const IBackground* Simulation::background ( ) const

inlineinherited

Definition at line 75 of file Simulation.h.

{ return m_background.get(); }

References Simulation::m_background.

Referenced by DepthProbeSimulation::addBackgroundIntensity(), Simulation2D::addBackgroundIntensity(), SpecularSimulation::addBackgroundIntensity(), and SimulationToPython::defineBackground().

addParameterDistribution() [1/2]

void Simulation::addParameterDistribution ( const std::string &  param_name, const IDistribution1D &  distribution, size_t  nbr_samples, double  sigma_factor = 0.0, const RealLimits &  limits = RealLimits()  )

inherited

Definition at line 273 of file Simulation.cpp.

{
    ParameterDistribution par_distr(param_name, distribution, nbr_samples, sigma_factor, limits);
    addParameterDistribution(par_distr);
}

Referenced by StandardSimulations::MiniGISASBeamDivergence().

addParameterDistribution() [2/2]

void Simulation::addParameterDistribution ( const ParameterDistribution &  par_distr )

inherited

Definition at line 281 of file Simulation.cpp.

{
    validateParametrization(par_distr);
    m_distribution_handler.addParameterDistribution(par_distr);
}

References DistributionHandler::addParameterDistribution(), Simulation::m_distribution_handler, and Simulation::validateParametrization().

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getDistributionHandler()

const DistributionHandler& Simulation::getDistributionHandler ( ) const

inlineinherited

Definition at line 89 of file Simulation.h.

{ return m_distribution_handler; }

References Simulation::m_distribution_handler.

Referenced by SimulationToPython::defineParameterDistributions().

setOptions()

void Simulation::setOptions ( const SimulationOptions &  options )

inlineinherited

Definition at line 91 of file Simulation.h.

{ m_options = options; }

References Simulation::m_options, and Simulation::options().

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getOptions() [1/2]

const SimulationOptions& Simulation::getOptions ( ) const

inlineinherited

Definition at line 92 of file Simulation.h.

{ return m_options; }

References Simulation::m_options.

Referenced by SimulationToPython::defineSimulationOptions(), StandardSimulations::MiniGISASMonteCarlo(), and StandardSimulations::MiniGISASSpecularPeak().

getOptions() [2/2]

SimulationOptions& Simulation::getOptions ( )

inlineinherited

Definition at line 93 of file Simulation.h.

{ return m_options; }

References Simulation::m_options.

subscribe()

void Simulation::subscribe ( ProgressHandler::Callback_t  inform )

inlineinherited

Definition at line 95 of file Simulation.h.

{ m_progress.subscribe(inform); }

References Simulation::m_progress, and ProgressHandler::subscribe().

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setTerminalProgressMonitor()

void Simulation::setTerminalProgressMonitor ( )

inherited

Initializes a progress monitor that prints to stdout.

Definition at line 145 of file Simulation.cpp.

{
    m_progress.subscribe([](size_t percentage_done) -> bool {
        if (percentage_done < 100)
            std::cout << std::setprecision(2) << "\r... " << percentage_done << "%" << std::flush;
        else // wipe out
            std::cout << "\r... 100%\n";
        return true;
    });
}

References Simulation::m_progress, and ProgressHandler::subscribe().

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getChildren()

std::vector< const INode * > Simulation::getChildren ( ) const

virtualinherited

Returns a vector of children (const).

Reimplemented from INode.

Definition at line 263 of file Simulation.cpp.

{
    std::vector<const INode*> result;
    result.push_back(&instrument());
    result << m_sample_provider.getChildren();
    if (m_background)
        result.push_back(m_background.get());
    return result;
}

References SampleProvider::getChildren(), Simulation::instrument(), Simulation::m_background, Simulation::m_sample_provider, and Simulation::result().

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convertData()

SimulationResult Simulation::convertData ( const OutputData< double > &  data, bool  put_masked_areas_to_zero = true  )

inherited

Convert user data to SimulationResult object for later drawing in various axes units.

User data will be cropped to the ROI defined in the simulation, amplitudes in areas corresponding to the masked areas of the detector will be set to zero.

Definition at line 317 of file Simulation.cpp.

{
    auto converter = UnitConverterUtils::createConverter(*this);
    auto roi_data = UnitConverterUtils::createOutputData(*converter, converter->defaultUnits());
 
    const IDetector& detector = instrument().detector();
 
    if (roi_data->hasSameDimensions(data)) {
        // data is already cropped to ROI
        if (put_masked_areas_to_zero) {
            detector.iterate(
                [&](IDetector::const_iterator it) {
                    (*roi_data)[it.roiIndex()] = data[it.roiIndex()];
                },
                /*visit_masked*/ false);
        } else {
            roi_data->setRawDataVector(data.getRawDataVector());
        }
 
    } else if (detHasSameDimensions(detector, data)) {
        // exp data has same shape as the detector, we have to put orig data to smaller roi map
        detector.iterate(
            [&](IDetector::const_iterator it) {
                (*roi_data)[it.roiIndex()] = data[it.detectorIndex()];
            },
            /*visit_masked*/ !put_masked_areas_to_zero);
 
    } else {
        throw std::runtime_error("FitObject::init_dataset() -> Error. Detector and exp data have "
                                 "different shape.");
    }
 
    return SimulationResult(*roi_data, *converter);
}

References UnitConverterUtils::createConverter(), UnitConverterUtils::createOutputData(), Instrument::detector(), SimulationAreaIterator::detectorIndex(), anonymous_namespace{Simulation.cpp}::detHasSameDimensions(), OutputData< T >::getRawDataVector(), Simulation::instrument(), IDetector::iterate(), and SimulationAreaIterator::roiIndex().

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options()

const SimulationOptions& Simulation::options ( ) const

inlineprotectedinherited

Definition at line 120 of file Simulation.h.

{ return m_options; }

References Simulation::m_options.

Referenced by DepthProbeSimulation::generateSingleThreadedComputation(), Simulation2D::generateSingleThreadedComputation(), SpecularSimulation::generateSingleThreadedComputation(), and Simulation::setOptions().

progress()

ProgressHandler& Simulation::progress ( )

inlineprotectedinherited

Definition at line 121 of file Simulation.h.

{ return m_progress; }

References Simulation::m_progress.

Referenced by DepthProbeSimulation::generateSingleThreadedComputation(), Simulation2D::generateSingleThreadedComputation(), and SpecularSimulation::generateSingleThreadedComputation().

runSingleSimulation()

void Simulation::runSingleSimulation ( size_t  batch_start, size_t  batch_size, double  weight = 1.0  )

privateinherited

Runs a single simulation with fixed parameter values.

If desired, the simulation is run in several threads.

Definition at line 289 of file Simulation.cpp.

{
    initSimulationElementVector();
 
    const size_t n_threads = m_options.getNumberOfThreads();
    ASSERT(n_threads > 0);
 
    std::vector<std::unique_ptr<IComputation>> computations;
 
    for (size_t i_thread = 0; i_thread < n_threads;
         ++i_thread) { // Distribute computations by threads
        const size_t thread_start = batch_start + getStartIndex(n_threads, i_thread, batch_size);
        const size_t thread_size = getNumberOfElements(n_threads, i_thread, batch_size);
        if (thread_size == 0)
            break;
        computations.push_back(generateSingleThreadedComputation(thread_start, thread_size));
    }
    runComputations(std::move(computations));
 
    normalize(batch_start, batch_size);
    addBackgroundIntensity(batch_start, batch_size);
    addDataToCache(weight);
}

References Simulation::addBackgroundIntensity(), Simulation::addDataToCache(), ASSERT, Simulation::generateSingleThreadedComputation(), anonymous_namespace{Simulation.cpp}::getNumberOfElements(), SimulationOptions::getNumberOfThreads(), anonymous_namespace{Simulation.cpp}::getStartIndex(), Simulation::initSimulationElementVector(), Simulation::m_options, Simulation::normalize(), and anonymous_namespace{Simulation.cpp}::runComputations().

Referenced by Simulation::runSimulation().

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transferToCPP()

virtual void ICloneable::transferToCPP ( )

inlinevirtualinherited

Used for Python overriding of clone (see swig/tweaks.py)

Definition at line 34 of file ICloneable.h.

treeToString()

std::string INode::treeToString ( ) const

virtualinherited

Returns multiline string representing tree structure below the node.

Definition at line 53 of file INode.cpp.

{
    return NodeUtils::nodeToString(*this);
}

References NodeUtils::nodeToString().

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registerChild()

void INode::registerChild ( INode *  node )

inherited

Definition at line 58 of file INode.cpp.

{
    ASSERT(node);
    node->setParent(this);
}

References ASSERT, and INode::setParent().

Referenced by ParticleLayout::addAndRegisterAbstractParticle(), ParticleCoreShell::addAndRegisterCore(), MultiLayer::addAndRegisterInterface(), MultiLayer::addAndRegisterLayer(), ParticleCoreShell::addAndRegisterShell(), Layer::addLayout(), ParticleComposition::addParticlePointer(), Beam::Beam(), Crystal::Crystal(), IDetector::IDetector(), Simulation::initialize(), MesoCrystal::initialize(), Instrument::Instrument(), Beam::operator=(), Instrument::operator=(), Particle::Particle(), ParticleDistribution::ParticleDistribution(), IParticle::rotate(), ParticleLayout::setAndRegisterInterferenceFunction(), Simulation::setBackground(), InterferenceFunction1DLattice::setDecayFunction(), InterferenceFunction2DLattice::setDecayFunction(), Instrument::setDetector(), IDetector::setDetectorResolution(), Beam::setFootprintFactor(), Particle::setFormFactor(), InterferenceFunctionFinite3DLattice::setLattice(), InterferenceFunction2DLattice::setLattice(), InterferenceFunction2DParaCrystal::setLattice(), InterferenceFunction2DSuperLattice::setLattice(), InterferenceFunctionFinite2DLattice::setLattice(), InterferenceFunctionRadialParaCrystal::setProbabilityDistribution(), InterferenceFunction2DParaCrystal::setProbabilityDistributions(), ConvolutionDetectorResolution::setResolutionFunction(), IParticle::setRotation(), LayerInterface::setRoughness(), and InterferenceFunction2DSuperLattice::setSubstructureIFF().

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setParent()

void INode::setParent ( const INode *  newParent )

virtualinherited

Reimplemented in SampleProvider.

Definition at line 69 of file INode.cpp.

{
    m_parent = newParent;
}

References INode::m_parent.

Referenced by INode::registerChild(), SampleProvider::setBuilder(), and SampleProvider::setParent().

parent() [1/2]

const INode * INode::parent ( ) const

inherited

Definition at line 74 of file INode.cpp.

{
    return m_parent;
}

References INode::m_parent.

Referenced by INode::copyNumber(), INode::createParameterTree(), NodeUtils::nodePath(), Lattice2D::onChange(), SampleProvider::setBuilder(), SampleProvider::setParent(), and SampleProvider::setSample().

parent() [2/2]

INode * INode::parent ( )

inherited

Definition at line 79 of file INode.cpp.

{
    return const_cast<INode*>(m_parent);
}

References INode::m_parent.

copyNumber()

int INode::copyNumber ( const INode *  node ) const

inherited

Returns copyNumber of child, which takes into account existence of children with same name.

Definition at line 84 of file INode.cpp.

{
    if (node->parent() != this)
        return -1;
 
    int result(-1), count(0);
    for (auto child : getChildren()) {
 
        if (child == nullptr)
            throw std::runtime_error("INode::copyNumber() -> Error. Nullptr as child.");
 
        if (child == node)
            result = count;
 
        if (child->getName() == node->getName())
            ++count;
    }
 
    return count > 1 ? result : -1;
}

References INode::getChildren(), IParameterized::getName(), and INode::parent().

Referenced by INode::displayName().

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displayName()

std::string INode::displayName ( ) const

inherited

Returns display name, composed from the name of node and it's copy number.

Definition at line 105 of file INode.cpp.

{
    std::string result = getName();
    if (m_parent) {
        int index = m_parent->copyNumber(this);
        if (index >= 0)
            result = result + std::to_string(index);
    }
    return result;
}

References INode::copyNumber(), IParameterized::getName(), and INode::m_parent.

Referenced by NodeUtils::nodePath(), and anonymous_namespace{NodeUtils.cpp}::nodeString().

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createParameterTree()

ParameterPool * INode::createParameterTree ( ) const

virtualinherited

Creates new parameter pool, with all local parameters and those of its children.

Reimplemented from IParameterized.

Definition at line 116 of file INode.cpp.

{
    std::unique_ptr<ParameterPool> result(new ParameterPool);
 
    NodeIterator<PreorderStrategy> it(this);
    it.first();
    while (!it.isDone()) {
        const INode* child = it.getCurrent();
        const std::string path = NodeUtils::nodePath(*child, this->parent()) + "/";
        child->parameterPool()->copyToExternalPool(path, result.get());
        it.next();
    }
 
    return result.release();
}

References ParameterPool::copyToExternalPool(), NodeIterator< Strategy >::first(), NodeIterator< Strategy >::getCurrent(), NodeIterator< Strategy >::isDone(), NodeIterator< Strategy >::next(), NodeUtils::nodePath(), IParameterized::parameterPool(), and INode::parent().

Referenced by ParticleDistribution::generateParticles(), Simulation::runSimulation(), DepthProbeSimulation::validateParametrization(), validateParametrization(), and SpecularSimulation::validateParametrization().

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parameterPool()

ParameterPool* IParameterized::parameterPool ( ) const

inlineinherited

Returns pointer to the parameter pool.

Definition at line 38 of file IParameterized.h.

{ return m_pool.get(); } // has non-const usages!

References IParameterized::m_pool.

Referenced by pyfmt2::argumentList(), SampleBuilderNode::borrow_builder_parameters(), INode::createParameterTree(), INode::INode(), IParameterized::IParameterized(), anonymous_namespace{NodeUtils.cpp}::poolToString(), SampleBuilderNode::reset(), and IDistribution1D::setUnits().

parametersToString()

std::string IParameterized::parametersToString ( ) const

inherited

Returns multiline string representing available parameters.

Definition at line 40 of file IParameterized.cpp.

{
    std::ostringstream result;
    std::unique_ptr<ParameterPool> P_pool(createParameterTree());
    result << *P_pool << "\n";
    return result.str();
}

References IParameterized::createParameterTree().

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registerParameter()

RealParameter & IParameterized::registerParameter ( const std::string &  name, double *  parpointer  )

inherited

Definition at line 48 of file IParameterized.cpp.

{
    return m_pool->addParameter(
        new RealParameter(name, data, getName(), [&]() -> void { onChange(); }));
}

References IParameterized::getName(), IParameterized::m_pool, and IParameterized::onChange().

Referenced by BasicLattice::BasicLattice(), Beam::Beam(), CylindersInBABuilder::CylindersInBABuilder(), DetectionProperties::DetectionProperties(), HexagonalLattice::HexagonalLattice(), IInterferenceFunction::IInterferenceFunction(), INode::INode(), InterferenceFunction1DLattice::InterferenceFunction1DLattice(), InterferenceFunction2DParaCrystal::InterferenceFunction2DParaCrystal(), InterferenceFunctionHardDisk::InterferenceFunctionHardDisk(), InterferenceFunctionRadialParaCrystal::InterferenceFunctionRadialParaCrystal(), InterferenceFunctionTwin::InterferenceFunctionTwin(), Lattice2D::Lattice2D(), LayerRoughness::LayerRoughness(), MultiLayer::MultiLayer(), ParticleDistribution::ParticleDistribution(), PlainMultiLayerBySLDBuilder::PlainMultiLayerBySLDBuilder(), IParticle::registerAbundance(), ParticleLayout::registerParticleDensity(), Layer::registerThickness(), IParameterized::registerVector(), ParticleLayout::registerWeight(), ResolutionFunction2DGaussian::ResolutionFunction2DGaussian(), ResonatorBuilder::ResonatorBuilder(), Lattice2D::setRotationEnabled(), SquareLattice::SquareLattice(), and TriangularRippleBuilder::TriangularRippleBuilder().

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registerVector()

void IParameterized::registerVector ( const std::string &  base_name, kvector_t *  p_vec, const std::string &  units = "nm"  )

inherited

Definition at line 54 of file IParameterized.cpp.

{
    registerParameter(XComponentName(base_name), &((*p_vec)[0])).setUnit(units);
    registerParameter(YComponentName(base_name), &((*p_vec)[1])).setUnit(units);
    registerParameter(ZComponentName(base_name), &((*p_vec)[2])).setUnit(units);
}

References IParameterized::registerParameter(), RealParameter::setUnit(), IParameterized::XComponentName(), IParameterized::YComponentName(), and IParameterized::ZComponentName().

Referenced by Beam::Beam(), DetectionProperties::DetectionProperties(), InterferenceFunctionTwin::InterferenceFunctionTwin(), MultiLayer::MultiLayer(), Lattice::registerBasisVectors(), and IParticle::registerPosition().

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setParameterValue()

void IParameterized::setParameterValue ( const std::string &  name, double  value  )

inherited

Definition at line 62 of file IParameterized.cpp.

{
    if (name.find('*') == std::string::npos && name.find('/') == std::string::npos) {
        m_pool->setParameterValue(name, value);
    } else {
        std::unique_ptr<ParameterPool> P_pool{createParameterTree()};
        if (name.find('*') != std::string::npos)
            P_pool->setMatchedParametersValue(name, value);
        else
            P_pool->setParameterValue(name, value);
    }
}

References IParameterized::createParameterTree(), IParameterized::m_pool, and ParameterPool::setMatchedParametersValue().

Referenced by AsymRippleBuilder::buildSample(), and IParameterized::setVectorValue().

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setVectorValue()

void IParameterized::setVectorValue ( const std::string &  base_name, kvector_t  value  )

inherited

Definition at line 75 of file IParameterized.cpp.

{
    setParameterValue(XComponentName(base_name), value.x());
    setParameterValue(YComponentName(base_name), value.y());
    setParameterValue(ZComponentName(base_name), value.z());
}

References IParameterized::setParameterValue(), BasicVector3D< T >::x(), IParameterized::XComponentName(), BasicVector3D< T >::y(), IParameterized::YComponentName(), BasicVector3D< T >::z(), and IParameterized::ZComponentName().

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parameter()

RealParameter * IParameterized::parameter ( const std::string &  name ) const

inherited

Returns parameter with given 'name'.

Definition at line 83 of file IParameterized.cpp.

{
    return m_pool->parameter(name);
}

References IParameterized::m_pool.

Referenced by DepthProbeSimulation::initialize(), SpecularSimulation::initialize(), IParticle::registerAbundance(), Lattice::registerBasisVectors(), ParticleLayout::registerParticleDensity(), IParticle::registerPosition(), Layer::registerThickness(), Lattice2D::setRotationEnabled(), and DistributionLogNormal::setUnits().

onChange()

virtual void IParameterized::onChange ( )

inlinevirtualinherited

Action to be taken in inherited class when a parameter has changed.

Reimplemented in IProfileRipple, FormFactorSphereLogNormalRadius, FormFactorSphereGaussianRadius, FormFactorGaussSphere, ISawtoothRipple, ICosineRipple, IProfileRectangularRipple, FormFactorTruncatedSpheroid, FormFactorTruncatedSphere, FormFactorTruncatedCube, FormFactorTetrahedron, FormFactorPyramid, FormFactorPrism6, FormFactorPrism3, FormFactorLongBoxLorentz, FormFactorLongBoxGauss, FormFactorIcosahedron, FormFactorHollowSphere, FormFactorHemiEllipsoid, FormFactorFullSpheroid, FormFactorFullSphere, FormFactorEllipsoidalCylinder, FormFactorDodecahedron, FormFactorCylinder, FormFactorCuboctahedron, FormFactorCone6, FormFactorCone, FormFactorCantellatedCube, FormFactorBox, FormFactorAnisoPyramid, InterferenceFunction3DLattice, InterferenceFunction2DLattice, Lattice, and Lattice2D.

Definition at line 58 of file IParameterized.h.

{}

Referenced by Lattice2D::onChange(), and IParameterized::registerParameter().

removeParameter()

void IParameterized::removeParameter ( const std::string &  name )

inherited

Definition at line 88 of file IParameterized.cpp.

{
    m_pool->removeParameter(name);
}

References IParameterized::m_pool.

Referenced by IParticle::registerAbundance(), ParticleLayout::registerParticleDensity(), Layer::registerThickness(), IParameterized::removeVector(), and Lattice2D::setRotationEnabled().

removeVector()

void IParameterized::removeVector ( const std::string &  base_name )

inherited

Definition at line 93 of file IParameterized.cpp.

{
    removeParameter(XComponentName(base_name));
    removeParameter(YComponentName(base_name));
    removeParameter(ZComponentName(base_name));
}

References IParameterized::removeParameter(), IParameterized::XComponentName(), IParameterized::YComponentName(), and IParameterized::ZComponentName().

Referenced by IParticle::registerPosition().

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XComponentName()

std::string IParameterized::XComponentName ( const std::string &  base_name )

staticinherited

Definition at line 100 of file IParameterized.cpp.

{
    return base_name + "X";
}

Referenced by Lattice::registerBasisVectors(), IParticle::registerPosition(), IParameterized::registerVector(), IParameterized::removeVector(), and IParameterized::setVectorValue().

YComponentName()

std::string IParameterized::YComponentName ( const std::string &  base_name )

staticinherited

Definition at line 105 of file IParameterized.cpp.

{
    return base_name + "Y";
}

Referenced by IParameterized::registerVector(), IParameterized::removeVector(), and IParameterized::setVectorValue().

ZComponentName()

std::string IParameterized::ZComponentName ( const std::string &  base_name )

staticinherited

Definition at line 110 of file IParameterized.cpp.

{
    return base_name + "Z";
}

Referenced by IParameterized::registerVector(), IParameterized::removeVector(), and IParameterized::setVectorValue().

setName()

void IParameterized::setName ( const std::string &  name )

inlineinherited

Definition at line 68 of file IParameterized.h.

{ m_name = name; }

References IParameterized::m_name.

Referenced by BasicLattice::BasicLattice(), Beam::Beam(), Layer::clone(), ConvolutionDetectorResolution::ConvolutionDetectorResolution(), LayersWithAbsorptionBuilder::createSampleByIndex(), Basic2DParaCrystalBuilder::createSampleByIndex(), ParticleInVacuumBuilder::createSampleByIndex(), SimpleMagneticRotationBuilder::createSampleByIndex(), Crystal::Crystal(), DetectionProperties::DetectionProperties(), DistributionHandler::DistributionHandler(), FormFactorBAPol::FormFactorBAPol(), FormFactorCoreShell::FormFactorCoreShell(), FormFactorCrystal::FormFactorCrystal(), FormFactorDecoratorMaterial::FormFactorDecoratorMaterial(), FormFactorDecoratorPositionFactor::FormFactorDecoratorPositionFactor(), FormFactorDecoratorRotation::FormFactorDecoratorRotation(), FormFactorDWBA::FormFactorDWBA(), FormFactorDWBAPol::FormFactorDWBAPol(), FormFactorWeighted::FormFactorWeighted(), HexagonalLattice::HexagonalLattice(), IDetector::IDetector(), DepthProbeSimulation::initialize(), GISASSimulation::initialize(), initialize(), SpecularSimulation::initialize(), SpecularDetector1D::initialize(), MesoCrystal::initialize(), Particle::initialize(), ParticleComposition::initialize(), INode::INode(), Instrument::Instrument(), InterferenceFunction1DLattice::InterferenceFunction1DLattice(), InterferenceFunction2DLattice::InterferenceFunction2DLattice(), InterferenceFunction2DParaCrystal::InterferenceFunction2DParaCrystal(), InterferenceFunction2DSuperLattice::InterferenceFunction2DSuperLattice(), InterferenceFunction3DLattice::InterferenceFunction3DLattice(), InterferenceFunctionFinite2DLattice::InterferenceFunctionFinite2DLattice(), InterferenceFunctionFinite3DLattice::InterferenceFunctionFinite3DLattice(), InterferenceFunctionHardDisk::InterferenceFunctionHardDisk(), InterferenceFunctionNone::InterferenceFunctionNone(), InterferenceFunctionRadialParaCrystal::InterferenceFunctionRadialParaCrystal(), InterferenceFunctionTwin::InterferenceFunctionTwin(), ISampleBuilder::ISampleBuilder(), IsGISAXSDetector::IsGISAXSDetector(), Lattice::Lattice(), Layer::Layer(), LayerInterface::LayerInterface(), LayerRoughness::LayerRoughness(), MultiLayer::MultiLayer(), Beam::operator=(), SampleBuilderNode::operator=(), ParticleCoreShell::ParticleCoreShell(), ParticleDistribution::ParticleDistribution(), ParticleLayout::ParticleLayout(), RectangularDetector::RectangularDetector(), SampleBuilderNode::reset(), ResolutionFunction2DGaussian::ResolutionFunction2DGaussian(), SampleBuilderNode::SampleBuilderNode(), SampleBuilderNode::setSBN(), SphericalDetector::SphericalDetector(), and SquareLattice::SquareLattice().

getName()

const std::string& IParameterized::getName ( ) const

inlineinherited

Definition at line 69 of file IParameterized.h.

{ return m_name; }

References IParameterized::m_name.

Referenced by Beam::Beam(), Layer::clone(), IFormFactorBorn::computeSlicingEffects(), ConvolutionDetectorResolution::ConvolutionDetectorResolution(), INode::copyNumber(), IParameterized::createParameterTree(), IFormFactor::createSlicedFormFactor(), SampleToPython::defineFormFactors(), SampleToPython::defineInterferenceFunctions(), INode::displayName(), IDetector::IDetector(), Instrument::Instrument(), IParameterized::IParameterized(), Beam::operator=(), SampleBuilderNode::operator=(), anonymous_namespace{ParticleLayout.cpp}::particleDensityIsProvidedByInterference(), IParameterized::registerParameter(), SampleBuilderNode::SampleBuilderNode(), and IFormFactor::sliceFormFactor().

Member Data Documentation

mP_alpha_i_axis

std::unique_ptr<IAxis> OffSpecSimulation::mP_alpha_i_axis

private

Definition at line 84 of file OffSpecSimulation.h.

Referenced by beamAxis(), checkInitialization(), initSimulationElementVector(), intensityMapSize(), numberOfSimulationElements(), OffSpecSimulation(), result(), setBeamParameters(), transferResultsToIntensityMap(), and updateIntensityMap().

m_intensity_map

OutputData<double> OffSpecSimulation::m_intensity_map

private

Definition at line 85 of file OffSpecSimulation.h.

Referenced by OffSpecSimulation(), result(), transferDetectorImage(), transferResultsToIntensityMap(), and updateIntensityMap().

m_sim_elements

std::vector<SimulationElement> Simulation2D::m_sim_elements

protectedinherited

Definition at line 94 of file Simulation2D.h.

Referenced by Simulation2D::addBackgroundIntensity(), Simulation2D::addDataToCache(), Simulation2D::generateSingleThreadedComputation(), GISASSimulation::initSimulationElementVector(), initSimulationElementVector(), Simulation2D::moveDataFromCache(), Simulation2D::normalize(), Simulation2D::rawResults(), GISASSimulation::result(), Simulation2D::setRawResults(), transferDetectorImage(), and transferResultsToIntensityMap().

m_cache

std::vector<double> Simulation2D::m_cache

protectedinherited

Definition at line 95 of file Simulation2D.h.

Referenced by Simulation2D::addDataToCache(), GISASSimulation::initSimulationElementVector(), initSimulationElementVector(), and Simulation2D::moveDataFromCache().

m_detector_context

std::unique_ptr<DetectorContext> Simulation2D::m_detector_context

privateinherited

Definition at line 100 of file Simulation2D.h.

Referenced by Simulation2D::generateSimulationElements(), Simulation2D::numberOfSimulationElements(), and Simulation2D::prepareSimulation().

m_options

SimulationOptions Simulation::m_options

privateinherited

Definition at line 152 of file Simulation.h.

Referenced by Simulation::getOptions(), Simulation::options(), Simulation::runSimulation(), Simulation::runSingleSimulation(), and Simulation::setOptions().

m_progress

ProgressHandler Simulation::m_progress

privateinherited

Definition at line 153 of file Simulation.h.

Referenced by Simulation::progress(), Simulation::runSimulation(), Simulation::setTerminalProgressMonitor(), and Simulation::subscribe().

m_sample_provider

SampleProvider Simulation::m_sample_provider

privateinherited

Definition at line 154 of file Simulation.h.

Referenced by Simulation::getChildren(), Simulation::initialize(), Simulation::prepareSimulation(), Simulation::sample(), Simulation::setSample(), and Simulation::setSampleBuilder().

m_distribution_handler

DistributionHandler Simulation::m_distribution_handler

privateinherited

Definition at line 155 of file Simulation.h.

Referenced by Simulation::addParameterDistribution(), Simulation::getDistributionHandler(), and Simulation::runSimulation().

m_instrument

Instrument Simulation::m_instrument

privateinherited

Definition at line 156 of file Simulation.h.

Referenced by Simulation::initialize(), Simulation::instrument(), and Simulation::setInstrument().

m_background

std::unique_ptr<IBackground> Simulation::m_background

privateinherited

Definition at line 157 of file Simulation.h.

Referenced by Simulation::background(), Simulation::getChildren(), Simulation::setBackground(), and Simulation::Simulation().

m_parent

const INode* INode::m_parent {nullptr}

privateinherited

Definition at line 81 of file INode.h.

Referenced by INode::displayName(), INode::parent(), and INode::setParent().

m_NP

const size_t INode::m_NP

protectedinherited

Definition at line 86 of file INode.h.

Referenced by INode::INode().

m_P

std::vector<double> INode::m_P

protectedinherited

Definition at line 87 of file INode.h.

Referenced by INode::INode(), and IFootprintFactor::setWidthRatio().

m_name

std::string IParameterized::m_name

privateinherited

Definition at line 72 of file IParameterized.h.

Referenced by IParameterized::getName(), and IParameterized::setName().

m_pool

std::unique_ptr<ParameterPool> IParameterized::m_pool

privateinherited

parameter pool (kind of pointer-to-implementation)

Definition at line 73 of file IParameterized.h.

Referenced by IParameterized::createParameterTree(), IParameterized::parameter(), IParameterized::parameterPool(), IParameterized::registerParameter(), IParameterized::removeParameter(), and IParameterized::setParameterValue().

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The documentation for this class was generated from the following files:

• /home/www/ba/Core/Simulation/OffSpecSimulation.h
• /home/www/ba/Core/Simulation/OffSpecSimulation.cpp