GISASSimulation Class Reference

Main class to run a Grazing-Incidence Small-Angle Scattering simulation. More...

Inheritance diagram for GISASSimulation:

Collaboration diagram for GISASSimulation:

Public Member Functions
	GISASSimulation ()
	GISASSimulation (const Beam &beam, const IDetector &detector)
	GISASSimulation (const Beam &beam, const MultiLayer &sample, const IDetector &detector)
	~GISASSimulation ()
void	accept (INodeVisitor *visitor) const override
	Calls the INodeVisitor's visit method. More...
void	addMask (const IShape2D &shape, bool mask_value=true)
	Adds mask of given shape to the stack of detector masks. More...
void	addParameterDistribution (const ParameterDistribution &par_distr)
void	addParameterDistribution (const std::string &param_name, const IDistribution1D &distribution, size_t nbr_samples, double sigma_factor=0.0, const RealLimits &limits=RealLimits())
const IBackground *	background () const
Beam &	beam ()
const Beam &	beam () const
GISASSimulation *	clone () const override
SimulationResult	convertData (const OutputData< double > &data, bool put_masked_areas_to_zero=true)
	Convert user data to SimulationResult object for later drawing in various axes units. More...
int	copyNumber (const INode *node) const
	Returns copyNumber of child, which takes into account existence of children with same name. More...
ParameterPool *	createParameterTree () const
	Creates new parameter pool, with all local parameters and those of its children. More...
IDetector &	detector ()
const IDetector &	detector () const
IDetector2D &	detector2D ()
const IDetector2D &	detector2D () const
std::string	displayName () const
	Returns display name, composed from the name of node and it's copy number. More...
std::vector< const INode * >	getChildren () const
	Returns a vector of children. More...
IDetector *	getDetector ()
const IDetector *	getDetector () const
const DistributionHandler &	getDistributionHandler () const
const std::string &	getName () const
SimulationOptions &	getOptions ()
const SimulationOptions &	getOptions () const
Instrument &	instrument ()
const Instrument &	instrument () const
size_t	intensityMapSize () const override
	Returns the total number of the intensity values in the simulation result. More...
void	maskAll ()
	Put the mask for all detector channels (i.e. exclude whole detector from the analysis) More...
virtual void	onChange ()
	Action to be taken in inherited class when a parameter has changed. More...
RealParameter *	parameter (const std::string &name) const
	Returns parameter with given 'name'. More...
ParameterPool *	parameterPool () const
	Returns pointer to the parameter pool. More...
std::string	parametersToString () const
	Returns multiline string representing available parameters. More...
INode *	parent ()
const INode *	parent () const
void	prepareSimulation () override
	Put into a clean state for running a simulation. More...
std::vector< const INode * >	progeny () const
	Returns a vector of all descendants. More...
void	registerChild (INode *node)
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	removeParameter (const std::string &name)
void	removeVector (const std::string &base_name)
SimulationResult	result () const override
	Returns the results of the simulation in a format that supports unit conversion and export to numpy arrays. More...
void	runMPISimulation ()
	Run a simulation in a MPI environment. More...
void	runSimulation ()
	Run a simulation, possibly averaged over parameter distributions. More...
const MultiLayer *	sample () const
void	setBackground (const IBackground &bg)
void	setBeamParameters (double wavelength, double alpha_i, double phi_i)
	Sets beam parameters from here (forwarded to Instrument) More...
void	setDetector (const IDetector2D &detector)
	Sets the detector (axes can be overwritten later) More...
void	setDetectorParameters (size_t n_phi, double phi_min, double phi_max, size_t n_alpha, double alpha_min, double alpha_max)
	Sets spherical detector parameters using angle ranges. More...
void	setDetectorResolutionFunction (const IResolutionFunction2D &resolution_function)
void	setInstrument (const Instrument &instrument_)
void	setName (const std::string &name)
void	setOptions (const SimulationOptions &options)
void	setParameterValue (const std::string &name, double value)
virtual void	setParent (const INode *newParent)
void	setRegionOfInterest (double xlow, double ylow, double xup, double yup)
	Sets rectangular region of interest with lower left and upper right corners defined. More...
void	setSample (const MultiLayer &sample)
	The MultiLayer object will not be owned by the ISimulation object. More...
void	setSampleBuilder (const std::shared_ptr< ISampleBuilder > &sample_builder)
void	setTerminalProgressMonitor ()
	Initializes a progress monitor that prints to stdout. More...
void	setVectorValue (const std::string &base_name, kvector_t value)
void	subscribe (ProgressHandler::Callback_t inform)
virtual void	transferToCPP ()
	Used for Python overriding of clone (see swig/tweaks.py) More...
virtual std::string	treeToString () const
	Returns multiline string representing tree structure below the node. More...

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
void	addBackgroundIntensity (size_t start_ind, size_t n_elements) override
void	addDataToCache (double weight) override
std::vector< SimulationElement >	generateSimulationElements (const Beam &beam)
	Generate simulation elements for given beam. More...
std::unique_ptr< IComputation >	generateSingleThreadedComputation (size_t start, size_t n_elements) override
	Generate a single threaded computation for a given range of simulation elements. More...
virtual void	initUnitConverter ()
void	moveDataFromCache () override
void	normalize (size_t start_ind, size_t n_elements) override
	Normalize the detector counts to beam intensity, to solid angle, and to exposure angle. More...
size_t	numberOfSimulationElements () const override
	Gets the number of elements this simulation needs to calculate. More...
const SimulationOptions &	options () const
ProgressHandler &	progress ()
virtual void	transferResultsToIntensityMap ()
	Creates the appropriate data structure (e.g. More...
virtual void	updateIntensityMap ()

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

Private Member Functions
	GISASSimulation (const GISASSimulation &other)
void	initialize ()
void	initSimulationElementVector () override
	Initializes the vector of ISimulation elements. More...
std::vector< double >	rawResults () const override
void	runSingleSimulation (size_t batch_start, size_t batch_size, double weight=1.0)
	Runs a single simulation with fixed parameter values. More...
void	setRawResults (const std::vector< double > &raw_data) override
virtual void	validateParametrization (const ParameterDistribution &) const
	Checks the distribution validity for simulation. More...

Private Attributes
std::unique_ptr< IBackground >	m_background
std::unique_ptr< DetectorContext >	m_detector_context
DistributionHandler	m_distribution_handler
Instrument	m_instrument
std::string	m_name
SimulationOptions	m_options
const INode *	m_parent {nullptr}
std::unique_ptr< ParameterPool >	m_pool
	parameter pool (kind of pointer-to-implementation) More...
ProgressHandler	m_progress
SampleProvider	m_sample_provider

Detailed Description

Main class to run a Grazing-Incidence Small-Angle Scattering simulation.

Definition at line 27 of file GISASSimulation.h.

Constructor & Destructor Documentation

GISASSimulation() [1/4]

GISASSimulation::GISASSimulation	(	const Beam &	beam,
		const MultiLayer &	sample,
		const IDetector &	detector
	)

Definition at line 19 of file GISASSimulation.cpp.

    : ISimulation2D(beam, sample, detector)
{
    initialize();
}

References initialize().

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GISASSimulation() [2/4]

GISASSimulation::GISASSimulation	(	const Beam &	beam,
		const IDetector &	detector
	)

Definition at line 27 of file GISASSimulation.cpp.

    : ISimulation2D(beam, detector)
{
    initialize();
}

References initialize().

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GISASSimulation() [3/4]

GISASSimulation::GISASSimulation

(

)

Definition at line 34 of file GISASSimulation.cpp.

{
    initialize();
}

References initialize().

Referenced by clone().

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~GISASSimulation()

GISASSimulation::~GISASSimulation ( )

inline

Definition at line 34 of file GISASSimulation.h.

{}

GISASSimulation() [4/4]

GISASSimulation::GISASSimulation ( const GISASSimulation &  other )

private

Definition at line 39 of file GISASSimulation.cpp.

                                                             : ISimulation2D(other)
{
    initialize();
}

References initialize().

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Member Function Documentation

accept()

void GISASSimulation::accept ( INodeVisitor *  visitor ) const

inlineoverridevirtual

Calls the INodeVisitor's visit method.

Implements INode.

Definition at line 38 of file GISASSimulation.h.

{ visitor->visit(this); }

References INodeVisitor::visit().

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addBackgroundIntensity()

void ISimulation2D::addBackgroundIntensity ( size_t  start_ind, size_t  n_elements  )

overrideprotectedvirtualinherited

Implements ISimulation.

Definition at line 151 of file ISimulation2D.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.intensity()));
    }
}

References ISimulation::background(), SimulationElement::intensity(), ISimulation2D::m_sim_elements, and SimulationElement::setIntensity().

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addDataToCache()

void ISimulation2D::addDataToCache ( double  weight )

overrideprotectedvirtualinherited

Implements ISimulation.

Definition at line 161 of file ISimulation2D.cpp.

{
    if (m_sim_elements.size() != m_cache.size())
        throw std::runtime_error("Error in ISimulation2D::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].intensity() * weight;
}

References ISimulation2D::m_cache, and ISimulation2D::m_sim_elements.

addMask()

void ISimulation2D::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 60 of file ISimulation2D.cpp.

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

References IDetector2D::addMask(), and ISimulation2D::detector2D().

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

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addParameterDistribution() [1/2]

void ISimulation::addParameterDistribution ( const ParameterDistribution &  par_distr )

inherited

Definition at line 272 of file ISimulation.cpp.

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

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

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addParameterDistribution() [2/2]

void ISimulation::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 264 of file ISimulation.cpp.

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

Referenced by StandardSimulations::MiniGISASBeamDivergence(), and TransformToDomain::setBeamDistribution().

background()

const IBackground* ISimulation::background ( ) const

inlineinherited

Definition at line 74 of file ISimulation.h.

{ return m_background.get(); }

References ISimulation::m_background.

Referenced by DepthProbeSimulation::addBackgroundIntensity(), ISimulation2D::addBackgroundIntensity(), SpecularSimulation::addBackgroundIntensity(), and TransformFromDomain::setBackground().

beam() [1/2]

Beam& ISimulation::beam ( )

inlineinherited

Definition at line 58 of file ISimulation.h.

{ return m_instrument.beam(); }

References Instrument::beam(), and ISimulation::m_instrument.

Referenced by StandardSimulations::BasicGISAS00(), StandardSimulations::BasicPolarizedGISAS(), DepthProbeSimulation::createUnitConverter(), OffSpecularSimulation::createUnitConverter(), DepthProbeSimulation::generateSimulationElements(), ISimulation2D::generateSimulationElements(), DepthProbeSimulation::initialize(), DepthProbeSimulation::initSimulationElementVector(), initSimulationElementVector(), OffSpecularSimulation::initSimulationElementVector(), StandardSimulations::MaxiGISAS00(), StandardSimulations::MiniGISASPolarizationMM(), StandardSimulations::MiniGISASPolarizationMP(), StandardSimulations::MiniGISASPolarizationPM(), StandardSimulations::MiniGISASPolarizationPP(), DepthProbeSimulation::normalize(), ISimulation2D::normalize(), SpecularSimulation::normalize(), OffSpecularSimulation::result(), DepthProbeSimulation::setBeamParameters(), TransformFromDomain::setGISASBeamItem(), TransformFromDomain::setOffSpecularBeamItem(), and TransformFromDomain::setSpecularBeamItem().

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beam() [2/2]

const Beam& ISimulation::beam ( ) const

inlineinherited

Definition at line 59 of file ISimulation.h.

{ return m_instrument.beam(); }

References Instrument::beam(), and ISimulation::m_instrument.

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clone()

GISASSimulation* GISASSimulation::clone ( ) const

inlineoverridevirtual

Implements ISimulation2D.

Definition at line 36 of file GISASSimulation.h.

{ return new GISASSimulation(*this); }

References GISASSimulation().

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convertData()

SimulationResult ISimulation::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 308 of file ISimulation.cpp.

{
    auto converter = UnitConverterUtils::createConverter(*this);
    auto roi_data = UnitConverterUtils::createOutputData(*converter, converter->defaultUnits());
 
    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(), ISimulation::detector(), SimulationAreaIterator::detectorIndex(), OutputData< T >::getRawDataVector(), IDetector::iterate(), and SimulationAreaIterator::roiIndex().

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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 94 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(), IParametricComponent::getName(), and INode::parent().

Referenced by INode::displayName().

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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 IParametricComponent.

Definition at line 126 of file INode.cpp.

{
    std::unique_ptr<ParameterPool> result(new ParameterPool);
 
    for (const INode* child : progeny()) {
        const std::string path = NodeUtils::nodePath(child, parent()) + "/";
        child->parameterPool()->copyToExternalPool(path, result.get());
    }
 
    return result.release();
}

References NodeUtils::nodePath(), INode::parent(), and INode::progeny().

Referenced by ISimulation::runSimulation(), DepthProbeSimulation::validateParametrization(), OffSpecularSimulation::validateParametrization(), and SpecularSimulation::validateParametrization().

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detector() [1/2]

IDetector& ISimulation::detector ( )

inlineinherited

Definition at line 63 of file ISimulation.h.

{ return m_instrument.detector(); }

References Instrument::detector(), and ISimulation::m_instrument.

Referenced by SpecularSimulation::SpecularSimulation(), StandardSimulations::BasicGISAS00(), StandardSimulations::BasicPolarizedGISAS(), OffSpecularSimulation::checkInitialization(), ISimulation::convertData(), ISimulation2D::generateSimulationElements(), ISimulation2D::generateSingleThreadedComputation(), SpecularSimulation::generateSingleThreadedComputation(), intensityMapSize(), OffSpecularSimulation::intensityMapSize(), StandardSimulations::MaxiGISAS00(), StandardSimulations::MiniGISASPolarizationMM(), StandardSimulations::MiniGISASPolarizationMP(), StandardSimulations::MiniGISASPolarizationPM(), StandardSimulations::MiniGISASPolarizationPP(), prepareSimulation(), SpecularSimulation::prepareSimulation(), result(), DepthProbeSimulation::setBeamParameters(), ISimulation2D::setDetector(), ISimulation::setDetectorResolutionFunction(), SpecularSimulation::setScan(), OffSpecularSimulation::transferDetectorImage(), OffSpecularSimulation::transferResultsToIntensityMap(), and OffSpecularSimulation::updateIntensityMap().

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detector() [2/2]

const IDetector& ISimulation::detector ( ) const

inlineinherited

Definition at line 64 of file ISimulation.h.

{ return m_instrument.detector(); }

References Instrument::detector(), and ISimulation::m_instrument.

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detector2D() [1/2]

IDetector2D & ISimulation2D::detector2D ( )

inherited

Definition at line 38 of file ISimulation2D.cpp.

{
    ASSERT(getDetector());
    IDetector2D* p = dynamic_cast<IDetector2D*>(getDetector());
    ASSERT(p);
    return *p;
}

References ASSERT, and ISimulation::getDetector().

Referenced by ISimulation2D::addMask(), OffSpecularSimulation::createUnitConverter(), ISimulation2D::generateSimulationElements(), ISimulation2D::maskAll(), ISimulation2D::prepareSimulation(), OffSpecularSimulation::result(), ISimulation2D::setDetectorParameters(), and ISimulation2D::setRegionOfInterest().

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detector2D() [2/2]

const IDetector2D & ISimulation2D::detector2D ( ) const

inherited

Definition at line 46 of file ISimulation2D.cpp.

{
    ASSERT(getDetector());
    const IDetector2D* p = dynamic_cast<const IDetector2D*>(getDetector());
    ASSERT(p);
    return *p;
}

References ASSERT, and ISimulation::getDetector().

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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 115 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(), IParametricComponent::getName(), and INode::m_parent.

Referenced by NodeUtils::nodePath().

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generateSimulationElements()

std::vector< SimulationElement > ISimulation2D::generateSimulationElements ( const Beam &  beam )

protectedinherited

Generate simulation elements for given beam.

Definition at line 111 of file ISimulation2D.cpp.

{
    const double wavelength = beam.wavelength();
    const double alpha_i = -beam.direction().alpha(); // Defined to be always positive in Beam
    const double phi_i = beam.direction().phi();
    const Eigen::Matrix2cd beam_polarization = beam.getPolarization();
 
    const IDetector2D& detector = 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), beam_polarization,
                                  analyzer_operator,
                                  m_detector_context->detectorIndex(element_index) == spec_index);
        result.emplace_back(std::move(element));
    }
    return result;
}

References Direction::alpha(), DetectionProperties::analyzerOperator(), ISimulation::beam(), IDetector::detectionProperties(), ISimulation::detector(), ISimulation2D::detector2D(), Beam::direction(), Beam::getPolarization(), ISimulation2D::m_detector_context, Direction::phi(), ISimulation::result(), and Beam::wavelength().

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

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generateSingleThreadedComputation()

std::unique_ptr< IComputation > ISimulation2D::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 ISimulation.

Definition at line 100 of file ISimulation2D.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);
    const auto polarized =
        this->detector().detectionProperties().analyzerDirection() != kvector_t{};
    return std::make_unique<DWBAComputation>(*sample(), options(), progress(), begin,
                                             begin + static_cast<long>(n_elements), polarized);
}

References DetectionProperties::analyzerDirection(), ASSERT, IDetector::detectionProperties(), ISimulation::detector(), ISimulation2D::m_sim_elements, ISimulation::options(), FormFactorPrecompute::polarized(), ISimulation::progress(), and ISimulation::sample().

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getChildren()

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

virtualinherited

Returns a vector of children.

Reimplemented from INode.

Definition at line 254 of file ISimulation.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(), ISimulation::instrument(), ISimulation::m_background, ISimulation::m_sample_provider, and ISimulation::result().

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getDetector() [1/2]

IDetector* ISimulation::getDetector ( )

inlineinherited

Definition at line 61 of file ISimulation.h.

{ return m_instrument.getDetector(); }

References Instrument::getDetector(), and ISimulation::m_instrument.

Referenced by ISimulation2D::detector2D(), TransformFromDomain::setDetector(), and TransformFromDomain::setDetectorMasks().

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getDetector() [2/2]

const IDetector* ISimulation::getDetector ( ) const

inlineinherited

Definition at line 62 of file ISimulation.h.

{ return m_instrument.getDetector(); }

References Instrument::getDetector(), and ISimulation::m_instrument.

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getDistributionHandler()

const DistributionHandler& ISimulation::getDistributionHandler ( ) const

inlineinherited

Definition at line 88 of file ISimulation.h.

{ return m_distribution_handler; }

References ISimulation::m_distribution_handler.

Referenced by TransformFromDomain::setGISASBeamItem().

getName()

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

inlineinherited

Definition at line 70 of file IParametricComponent.h.

{ return m_name; }

References IParametricComponent::m_name.

Referenced by Beam::Beam(), ConvolutionDetectorResolution::ConvolutionDetectorResolution(), IDetector::IDetector(), Instrument::Instrument(), IParametricComponent::IParametricComponent(), SampleBuilderNode::SampleBuilderNode(), Layer::clone(), INode::copyNumber(), IParametricComponent::createParameterTree(), IFormFactor::createSlicedFormFactor(), SampleToPython::defineInterferenceFunctions(), INode::displayName(), Beam::operator=(), SampleBuilderNode::operator=(), GUIObjectBuilder::populateInstrumentModel(), PyImportAssistant::populateModels(), GUIDomainSampleVisitor::populateSampleModel(), IParametricComponent::registerParameter(), IFormFactor::sliceFormFactor(), and GUIDomainSampleVisitor::visit().

getOptions() [1/2]

SimulationOptions& ISimulation::getOptions ( )

inlineinherited

Definition at line 92 of file ISimulation.h.

{ return m_options; }

References ISimulation::m_options.

getOptions() [2/2]

const SimulationOptions& ISimulation::getOptions ( ) const

inlineinherited

Definition at line 91 of file ISimulation.h.

{ return m_options; }

References ISimulation::m_options.

Referenced by StandardSimulations::MiniGISASMonteCarlo(), StandardSimulations::MiniGISASSpecularPeak(), GUIObjectBuilder::populateDocumentModel(), and TransformToDomain::setSimulationOptions().

initialize()

void GISASSimulation::initialize ( )

private

Definition at line 44 of file GISASSimulation.cpp.

{
    setName("GISASSimulation");
}

References IParametricComponent::setName().

Referenced by GISASSimulation().

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initSimulationElementVector()

void GISASSimulation::initSimulationElementVector ( )

overrideprivatevirtual

Initializes the vector of ISimulation elements.

Implements ISimulation.

Definition at line 81 of file GISASSimulation.cpp.

{
    m_sim_elements = generateSimulationElements(beam());
    if (m_cache.empty())
        m_cache.resize(m_sim_elements.size(), 0.0);
}

References ISimulation::beam(), ISimulation2D::generateSimulationElements(), ISimulation2D::m_cache, and ISimulation2D::m_sim_elements.

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initUnitConverter()

virtual void ISimulation2D::initUnitConverter ( )

inlineprotectedvirtualinherited

Definition at line 73 of file ISimulation2D.h.

{}

Referenced by ISimulation2D::setDetector().

instrument() [1/2]

Instrument& ISimulation::instrument ( )

inlineinherited

Definition at line 56 of file ISimulation.h.

{ return m_instrument; }

References ISimulation::m_instrument.

instrument() [2/2]

const Instrument& ISimulation::instrument ( ) const

inlineinherited

Definition at line 55 of file ISimulation.h.

{ return m_instrument; }

References ISimulation::m_instrument.

Referenced by SpecularSimulation::SpecularSimulation(), ISimulation::getChildren(), SpecularSimulation::initialize(), SpecularSimulation::initSimulationElementVector(), GUIObjectBuilder::populateInstrumentModel(), prepareSimulation(), SpecularSimulation::prepareSimulation(), result(), DepthProbeSimulation::setBeamParameters(), OffSpecularSimulation::setBeamParameters(), setBeamParameters(), ISimulation2D::setDetector(), and SpecularSimulation::setScan().

intensityMapSize()

size_t GISASSimulation::intensityMapSize ( ) const

overridevirtual

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

Implements ISimulation.

Definition at line 74 of file GISASSimulation.cpp.

{
    size_t result = 0;
    detector().iterate([&result](IDetector::const_iterator) { ++result; }, true);
    return result;
}

References ISimulation::detector(), IDetector::iterate(), and result().

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maskAll()

void ISimulation2D::maskAll ( )

inherited

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

Definition at line 65 of file ISimulation2D.cpp.

{
    detector2D().maskAll();
}

References ISimulation2D::detector2D(), and IDetector2D::maskAll().

Referenced by StandardSimulations::GISASWithMasks().

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moveDataFromCache()

void ISimulation2D::moveDataFromCache ( )

overrideprotectedvirtualinherited

Implements ISimulation.

Definition at line 170 of file ISimulation2D.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, ISimulation2D::m_cache, and ISimulation2D::m_sim_elements.

normalize()

void ISimulation2D::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 ISimulation.

Definition at line 136 of file ISimulation2D.cpp.

{
    const double beam_intensity = beam().intensity();
    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) {
            element.setIntensity(0);
            continue;
        }
        const double solid_angle = element.solidAngle();
        element.setIntensity(element.intensity() * beam_intensity * solid_angle / sin_alpha_i);
    }
}

References ISimulation::beam(), SimulationElement::getAlphaI(), SimulationElement::intensity(), Beam::intensity(), ISimulation2D::m_sim_elements, SimulationElement::setIntensity(), and SimulationElement::solidAngle().

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numberOfSimulationElements()

size_t ISimulation2D::numberOfSimulationElements ( ) const

overrideprotectedvirtualinherited

Gets the number of elements this simulation needs to calculate.

Implements ISimulation.

Reimplemented in OffSpecularSimulation.

Definition at line 80 of file ISimulation2D.cpp.

{
    if (!m_detector_context)
        throw std::runtime_error("Error in numberOfSimulationElements(): no detector context");
    return m_detector_context->numberOfSimulationElements();
}

References ISimulation2D::m_detector_context.

Referenced by OffSpecularSimulation::numberOfSimulationElements().

onChange()

virtual void IParametricComponent::onChange ( )

inlinevirtualinherited

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

Reimplemented in IProfileRipple, Lattice3D, InterferenceFunction3DLattice, InterferenceFunction2DLattice, 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, and Lattice2D.

Definition at line 59 of file IParametricComponent.h.

{}

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

options()

const SimulationOptions& ISimulation::options ( ) const

inlineprotectedinherited

Definition at line 124 of file ISimulation.h.

{ return m_options; }

References ISimulation::m_options.

Referenced by DepthProbeSimulation::generateSingleThreadedComputation(), ISimulation2D::generateSingleThreadedComputation(), SpecularSimulation::generateSingleThreadedComputation(), and ISimulation::setOptions().

parameter()

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

inherited

Returns parameter with given 'name'.

Definition at line 86 of file IParametricComponent.cpp.

{
    return m_pool->parameter(name);
}

References IParametricComponent::m_pool, and RealSpace::Particles::name().

Referenced by DepthProbeSimulation::initialize(), SpecularSimulation::initialize(), Lattice3D::initialize(), IParticle::registerAbundance(), ParticleLayout::registerParticleDensity(), IParticle::registerPosition(), Layer::registerThickness(), Lattice2D::setRotationEnabled(), and DistributionLogNormal::setUnits().

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parameterPool()

ParameterPool* IParametricComponent::parameterPool ( ) const

inlineinherited

Returns pointer to the parameter pool.

Definition at line 39 of file IParametricComponent.h.

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

References IParametricComponent::m_pool.

Referenced by INode::INode(), IParametricComponent::IParametricComponent(), pyfmt2::argumentList(), SampleBuilderNode::borrow_builder_parameters(), SampleBuilderNode::reset(), and IDistribution1D::setUnits().

parametersToString()

std::string IParametricComponent::parametersToString ( ) const

inherited

Returns multiline string representing available parameters.

Definition at line 43 of file IParametricComponent.cpp.

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

References IParametricComponent::createParameterTree().

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parent() [1/2]

INode * INode::parent ( )

inherited

Definition at line 89 of file INode.cpp.

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

References INode::m_parent.

parent() [2/2]

const INode * INode::parent ( ) const

inherited

Definition at line 84 of file INode.cpp.

{
    return m_parent;
}

References INode::m_parent.

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

prepareSimulation()

void GISASSimulation::prepareSimulation ( )

overridevirtual

Put into a clean state for running a simulation.

Reimplemented from ISimulation.

Definition at line 49 of file GISASSimulation.cpp.

{
    if (detector().dimension() != 2)
        throw std::runtime_error("GISASSimulation::prepareSimulation() "
                                 "-> Error. The detector was not properly configured.");
    instrument().initDetector();
    ISimulation2D::prepareSimulation();
}

References ISimulation::detector(), Instrument::initDetector(), ISimulation::instrument(), and ISimulation2D::prepareSimulation().

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progeny()

std::vector< const INode * > INode::progeny ( ) const

inherited

Returns a vector of all descendants.

Definition at line 68 of file INode.cpp.

{
    std::vector<const INode*> result;
    result.push_back(this);
    for (const auto* child : getChildren()) {
        for (const auto* p : child->progeny())
            result.push_back(p);
    }
    return result;
}

References INode::getChildren().

Referenced by INode::createParameterTree(), and ParticleDistribution::generateParticles().

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progress()

ProgressHandler& ISimulation::progress ( )

inlineprotectedinherited

Definition at line 125 of file ISimulation.h.

{ return m_progress; }

References ISimulation::m_progress.

Referenced by DepthProbeSimulation::generateSingleThreadedComputation(), ISimulation2D::generateSingleThreadedComputation(), and SpecularSimulation::generateSingleThreadedComputation().

rawResults()

std::vector< double > ISimulation2D::rawResults ( ) const

overrideprivatevirtualinherited

Implements ISimulation.

Definition at line 180 of file ISimulation2D.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].intensity();
    return result;
}

References ISimulation2D::m_sim_elements, and ISimulation::result().

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registerChild()

void INode::registerChild ( INode *  node )

inherited

Definition at line 57 of file INode.cpp.

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

References ASSERT, and INode::setParent().

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

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registerParameter()

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

inherited

Definition at line 51 of file IParametricComponent.cpp.

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

References IParametricComponent::getName(), IParametricComponent::m_pool, RealSpace::Particles::name(), and IParametricComponent::onChange().

Referenced by BasicLattice2D::BasicLattice2D(), Beam::Beam(), CylindersInBABuilder::CylindersInBABuilder(), DetectionProperties::DetectionProperties(), HexagonalLattice2D::HexagonalLattice2D(), IInterferenceFunction::IInterferenceFunction(), INode::INode(), InterferenceFunction1DLattice::InterferenceFunction1DLattice(), InterferenceFunction2DParaCrystal::InterferenceFunction2DParaCrystal(), InterferenceFunctionHardDisk::InterferenceFunctionHardDisk(), InterferenceFunctionRadialParaCrystal::InterferenceFunctionRadialParaCrystal(), InterferenceFunctionTwin::InterferenceFunctionTwin(), Lattice2D::Lattice2D(), LayerRoughness::LayerRoughness(), MultiLayer::MultiLayer(), ParticleDistribution::ParticleDistribution(), PlainMultiLayerBySLDBuilder::PlainMultiLayerBySLDBuilder(), ResolutionFunction2DGaussian::ResolutionFunction2DGaussian(), ResonatorBuilder::ResonatorBuilder(), SquareLattice2D::SquareLattice2D(), TriangularRippleBuilder::TriangularRippleBuilder(), IParticle::registerAbundance(), ParticleLayout::registerParticleDensity(), Layer::registerThickness(), IParametricComponent::registerVector(), ParticleLayout::registerWeight(), and Lattice2D::setRotationEnabled().

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registerVector()

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

inherited

Definition at line 57 of file IParametricComponent.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 ModelView::Utils::base_name(), IParametricComponent::registerParameter(), RealParameter::setUnit(), IParametricComponent::XComponentName(), IParametricComponent::YComponentName(), and IParametricComponent::ZComponentName().

Referenced by Beam::Beam(), DetectionProperties::DetectionProperties(), InterferenceFunctionTwin::InterferenceFunctionTwin(), MultiLayer::MultiLayer(), Lattice3D::initialize(), and IParticle::registerPosition().

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removeParameter()

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

inherited

Definition at line 91 of file IParametricComponent.cpp.

{
    m_pool->removeParameter(name);
}

References IParametricComponent::m_pool, and RealSpace::Particles::name().

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

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removeVector()

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

inherited

Definition at line 96 of file IParametricComponent.cpp.

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

References ModelView::Utils::base_name(), IParametricComponent::removeParameter(), IParametricComponent::XComponentName(), IParametricComponent::YComponentName(), and IParametricComponent::ZComponentName().

Referenced by IParticle::registerPosition().

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result()

SimulationResult GISASSimulation::result ( ) const

overridevirtual

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

Implements ISimulation.

Definition at line 58 of file GISASSimulation.cpp.

{
    const auto converter = UnitConverterUtils::createConverterForGISAS(instrument());
    const std::unique_ptr<OutputData<double>> data(
        detector().createDetectorIntensity(m_sim_elements));
    return SimulationResult(*data, *converter);
}

References UnitConverterUtils::createConverterForGISAS(), ISimulation::detector(), ISimulation::instrument(), and ISimulation2D::m_sim_elements.

Referenced by intensityMapSize().

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runMPISimulation()

void ISimulation::runMPISimulation ( )

inherited

Run a simulation in a MPI environment.

Definition at line 226 of file ISimulation.cpp.

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

References MPISimulation::runSimulation().

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runSimulation()

void ISimulation::runSimulation ( )

inherited

Run a simulation, possibly averaged over parameter distributions.

Run simulation with possible averaging over parameter distributions.

Definition at line 193 of file ISimulation.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;
 
    if(param_combinations == 1)
        runSingleSimulation(batch_start, batch_size, 1.);
    else{
        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(), DistributionHandler::getTotalNumberOfSamples(), ISimulation::m_distribution_handler, ISimulation::m_options, ISimulation::m_progress, ISimulation::moveDataFromCache(), ISimulation::numberOfSimulationElements(), ISimulation::prepareSimulation(), ProgressHandler::reset(), ISimulation::runSingleSimulation(), ProgressHandler::setExpectedNTicks(), DistributionHandler::setParameterToMeans(), DistributionHandler::setParameterValues(), and ISimulation::transferResultsToIntensityMap().

Referenced by JobWorker::start().

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runSingleSimulation()

void ISimulation::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 280 of file ISimulation.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(computations);
 
    normalize(batch_start, batch_size);
    addBackgroundIntensity(batch_start, batch_size);
    addDataToCache(weight);
}

References ISimulation::addBackgroundIntensity(), ISimulation::addDataToCache(), ASSERT, ISimulation::generateSingleThreadedComputation(), SimulationOptions::getNumberOfThreads(), ISimulation::initSimulationElementVector(), ISimulation::m_options, and ISimulation::normalize().

Referenced by ISimulation::runSimulation().

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sample()

const MultiLayer * ISimulation::sample ( ) const

inherited

Definition at line 238 of file ISimulation.cpp.

{
    return m_sample_provider.sample();
}

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

Referenced by ISimulation::ISimulation(), DepthProbeSimulation::generateSingleThreadedComputation(), ISimulation2D::generateSingleThreadedComputation(), SpecularSimulation::generateSingleThreadedComputation(), ISimulation::setSample(), and DepthProbeSimulation::validityCheck().

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setBackground()

void ISimulation::setBackground ( const IBackground &  bg )

inherited

Definition at line 248 of file ISimulation.cpp.

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

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

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

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setBeamParameters()

void GISASSimulation::setBeamParameters	(	double	wavelength,
		double	alpha_i,
		double	phi_i
	)

Sets beam parameters from here (forwarded to Instrument)

Definition at line 66 of file GISASSimulation.cpp.

{
    if (wavelength <= 0.0)
        throw std::runtime_error(
            "ISimulation::setBeamParameters() -> Error. Incoming wavelength <= 0.");
    instrument().setBeamParameters(wavelength, alpha_i, phi_i);
}

References ISimulation::instrument(), and Instrument::setBeamParameters().

Referenced by StandardSimulations::MiniGISASSpecularPeak().

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setDetector()

void ISimulation2D::setDetector ( const IDetector2D &  detector )

inherited

Sets the detector (axes can be overwritten later)

Definition at line 94 of file ISimulation2D.cpp.

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

References ISimulation::detector(), ISimulation2D::initUnitConverter(), ISimulation::instrument(), and Instrument::setDetector().

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setDetectorParameters()

void ISimulation2D::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 87 of file ISimulation2D.cpp.

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

References ISimulation2D::detector2D(), IDetector2D::setDetectorParameters(), and ISimulation::updateIntensityMap().

Referenced by StandardSimulations::MiniGISASFit().

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setDetectorResolutionFunction()

void ISimulation::setDetectorResolutionFunction ( const IResolutionFunction2D &  resolution_function )

inherited

Definition at line 177 of file ISimulation.cpp.

{
    detector().setResolutionFunction(resolution_function);
}

References ISimulation::detector(), and IDetector::setResolutionFunction().

Referenced by StandardSimulations::MiniGISASDetectorResolution().

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setInstrument()

void ISimulation::setInstrument ( const Instrument &  instrument_ )

inherited

Definition at line 158 of file ISimulation.cpp.

{
    m_instrument = instrument_;
    updateIntensityMap();
}

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

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setName()

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

inlineinherited

Definition at line 69 of file IParametricComponent.h.

{ m_name = name; }

References IParametricComponent::m_name, and RealSpace::Particles::name().

Referenced by BasicLattice2D::BasicLattice2D(), Beam::Beam(), ConvolutionDetectorResolution::ConvolutionDetectorResolution(), Crystal::Crystal(), DetectionProperties::DetectionProperties(), DistributionHandler::DistributionHandler(), FormFactorCoreShell::FormFactorCoreShell(), FormFactorCrystal::FormFactorCrystal(), FormFactorDecoratorMaterial::FormFactorDecoratorMaterial(), FormFactorDecoratorPositionFactor::FormFactorDecoratorPositionFactor(), FormFactorDecoratorRotation::FormFactorDecoratorRotation(), FormFactorWeighted::FormFactorWeighted(), HexagonalLattice2D::HexagonalLattice2D(), IDetector::IDetector(), 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(), Lattice3D::Lattice3D(), Layer::Layer(), LayerInterface::LayerInterface(), LayerRoughness::LayerRoughness(), MultiLayer::MultiLayer(), ParticleCoreShell::ParticleCoreShell(), ParticleDistribution::ParticleDistribution(), ParticleLayout::ParticleLayout(), RectangularDetector::RectangularDetector(), ResolutionFunction2DGaussian::ResolutionFunction2DGaussian(), SampleBuilderNode::SampleBuilderNode(), SphericalDetector::SphericalDetector(), SquareLattice2D::SquareLattice2D(), Layer::clone(), LayersWithAbsorptionBuilder::createSampleByIndex(), Basic2DParaCrystalBuilder::createSampleByIndex(), ParticleInVacuumBuilder::createSampleByIndex(), SimpleMagneticRotationBuilder::createSampleByIndex(), DepthProbeSimulation::initialize(), initialize(), OffSpecularSimulation::initialize(), SpecularSimulation::initialize(), SpecularDetector1D::initialize(), MesoCrystal::initialize(), Particle::initialize(), ParticleComposition::initialize(), Beam::operator=(), SampleBuilderNode::operator=(), SampleBuilderNode::reset(), and SampleBuilderNode::setSBN().

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setOptions()

void ISimulation::setOptions ( const SimulationOptions &  options )

inlineinherited

Definition at line 90 of file ISimulation.h.

{ m_options = options; }

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

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setParameterValue()

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

inherited

Definition at line 65 of file IParametricComponent.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 IParametricComponent::createParameterTree(), IParametricComponent::m_pool, RealSpace::Particles::name(), and ParameterPool::setMatchedParametersValue().

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

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setParent()

void INode::setParent ( const INode *  newParent )

virtualinherited

Reimplemented in SampleProvider.

Definition at line 79 of file INode.cpp.

{
    m_parent = newParent;
}

References INode::m_parent.

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

setRawResults()

void ISimulation2D::setRawResults ( const std::vector< double > &  raw_data )

overrideprivatevirtualinherited

Implements ISimulation.

Definition at line 189 of file ISimulation2D.cpp.

{
    initSimulationElementVector();
    if (raw_data.size() != m_sim_elements.size())
        throw std::runtime_error("ISimulation2D::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 ISimulation::initSimulationElementVector(), ISimulation2D::m_sim_elements, and ISimulation::transferResultsToIntensityMap().

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setRegionOfInterest()

void ISimulation2D::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 70 of file ISimulation2D.cpp.

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

References ISimulation2D::detector2D(), and IDetector2D::setRegionOfInterest().

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

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setSample()

void ISimulation::setSample ( const MultiLayer &  sample )

inherited

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

Definition at line 233 of file ISimulation.cpp.

{
    m_sample_provider.setSample(sample);
}

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

Referenced by ISimulation::ISimulation().

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setSampleBuilder()

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

inherited

Definition at line 243 of file ISimulation.cpp.

{
    m_sample_provider.setBuilder(sample_builder);
}

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

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setTerminalProgressMonitor()

void ISimulation::setTerminalProgressMonitor ( )

inherited

Initializes a progress monitor that prints to stdout.

Definition at line 166 of file ISimulation.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 ISimulation::m_progress, and ProgressHandler::subscribe().

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setVectorValue()

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

inherited

Definition at line 78 of file IParametricComponent.cpp.

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

References ModelView::Utils::base_name(), IParametricComponent::setParameterValue(), BasicVector3D< T >::x(), IParametricComponent::XComponentName(), BasicVector3D< T >::y(), IParametricComponent::YComponentName(), BasicVector3D< T >::z(), and IParametricComponent::ZComponentName().

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subscribe()

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

inlineinherited

Definition at line 94 of file ISimulation.h.

{ m_progress.subscribe(inform); }

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

Referenced by JobWorker::start().

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transferResultsToIntensityMap()

virtual void ISimulation::transferResultsToIntensityMap ( )

inlineprotectedvirtualinherited

Creates the appropriate data structure (e.g.

2D intensity map) from the calculated SimulationElement objects

Reimplemented in OffSpecularSimulation.

Definition at line 114 of file ISimulation.h.

{}

Referenced by ISimulation::runSimulation(), ISimulation2D::setRawResults(), and SpecularSimulation::setRawResults().

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 52 of file INode.cpp.

{
    return NodeUtils::nodeToString(this);
}

References NodeUtils::nodeToString().

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updateIntensityMap()

virtual void ISimulation::updateIntensityMap ( )

inlineprotectedvirtualinherited

Reimplemented in OffSpecularSimulation.

Definition at line 119 of file ISimulation.h.

{}

Referenced by ISimulation2D::setDetectorParameters(), and ISimulation::setInstrument().

validateParametrization()

virtual void ISimulation::validateParametrization ( const ParameterDistribution &  ) const

inlineprivatevirtualinherited

Checks the distribution validity for simulation.

Reimplemented in SpecularSimulation, OffSpecularSimulation, and DepthProbeSimulation.

Definition at line 139 of file ISimulation.h.

{}

Referenced by ISimulation::addParameterDistribution().

XComponentName()

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

staticinherited

Definition at line 103 of file IParametricComponent.cpp.

{
    return base_name + "X";
}

References ModelView::Utils::base_name().

Referenced by Lattice3D::initialize(), IParticle::registerPosition(), IParametricComponent::registerVector(), IParametricComponent::removeVector(), IParametricComponent::setVectorValue(), and VectorParameterTranslator::translate().

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YComponentName()

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

staticinherited

Definition at line 108 of file IParametricComponent.cpp.

{
    return base_name + "Y";
}

References ModelView::Utils::base_name().

Referenced by IParametricComponent::registerVector(), IParametricComponent::removeVector(), IParametricComponent::setVectorValue(), and VectorParameterTranslator::translate().

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ZComponentName()

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

staticinherited

Definition at line 113 of file IParametricComponent.cpp.

{
    return base_name + "Z";
}

References ModelView::Utils::base_name().

Referenced by IParametricComponent::registerVector(), IParametricComponent::removeVector(), IParametricComponent::setVectorValue(), and VectorParameterTranslator::translate().

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Member Data Documentation

m_background

std::unique_ptr<IBackground> ISimulation::m_background

privateinherited

Definition at line 161 of file ISimulation.h.

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

m_cache

std::vector<double> ISimulation2D::m_cache

protectedinherited

Definition at line 99 of file ISimulation2D.h.

Referenced by ISimulation2D::addDataToCache(), initSimulationElementVector(), OffSpecularSimulation::initSimulationElementVector(), and ISimulation2D::moveDataFromCache().

m_detector_context

std::unique_ptr<DetectorContext> ISimulation2D::m_detector_context

privateinherited

Definition at line 104 of file ISimulation2D.h.

Referenced by ISimulation2D::generateSimulationElements(), ISimulation2D::numberOfSimulationElements(), and ISimulation2D::prepareSimulation().

m_distribution_handler

DistributionHandler ISimulation::m_distribution_handler

privateinherited

Definition at line 159 of file ISimulation.h.

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

m_instrument

Instrument ISimulation::m_instrument

privateinherited

Definition at line 160 of file ISimulation.h.

Referenced by ISimulation::beam(), ISimulation::detector(), ISimulation::getDetector(), ISimulation::initialize(), ISimulation::instrument(), and ISimulation::setInstrument().

m_name

std::string IParametricComponent::m_name

privateinherited

Definition at line 73 of file IParametricComponent.h.

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

m_NP

const size_t INode::m_NP

protectedinherited

Definition at line 88 of file INode.h.

Referenced by INode::INode().

m_options

SimulationOptions ISimulation::m_options

privateinherited

Definition at line 156 of file ISimulation.h.

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

m_P

std::vector<double> INode::m_P

protectedinherited

Definition at line 89 of file INode.h.

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

m_parent

const INode* INode::m_parent {nullptr}

privateinherited

Definition at line 83 of file INode.h.

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

m_pool

std::unique_ptr<ParameterPool> IParametricComponent::m_pool

privateinherited

parameter pool (kind of pointer-to-implementation)

Definition at line 74 of file IParametricComponent.h.

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

m_progress

ProgressHandler ISimulation::m_progress

privateinherited

Definition at line 157 of file ISimulation.h.

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

m_sample_provider

SampleProvider ISimulation::m_sample_provider

privateinherited

Definition at line 158 of file ISimulation.h.

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

m_sim_elements

std::vector<SimulationElement> ISimulation2D::m_sim_elements

protectedinherited

Definition at line 98 of file ISimulation2D.h.

Referenced by ISimulation2D::addBackgroundIntensity(), ISimulation2D::addDataToCache(), ISimulation2D::generateSingleThreadedComputation(), initSimulationElementVector(), OffSpecularSimulation::initSimulationElementVector(), ISimulation2D::moveDataFromCache(), ISimulation2D::normalize(), ISimulation2D::rawResults(), result(), ISimulation2D::setRawResults(), OffSpecularSimulation::transferDetectorImage(), and OffSpecularSimulation::transferResultsToIntensityMap().

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

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