DepthProbeSimulation Class Reference

Inheritance diagram for DepthProbeSimulation:

Collaboration diagram for DepthProbeSimulation:

Public Member Functions
	DepthProbeSimulation ()
	~DepthProbeSimulation () override
void	accept (INodeVisitor *visitor) const final
	Calls the INodeVisitor's visit method. 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
DepthProbeSimulation *	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...
std::unique_ptr< IUnitConverter >	createUnitConverter () const
IDetector &	detector ()
const IDetector &	detector () const
std::string	displayName () const
	Returns display name, composed from the name of node and it's copy number. More...
const IAxis *	getAlphaAxis () const
	Returns a pointer to incident angle axis. 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
const IAxis *	getZAxis () const
	Returns a pointer to z-position axis. More...
Instrument &	instrument ()
const Instrument &	instrument () const
size_t	intensityMapSize () const override
	Returns the total number of the intensity values in the simulation result. 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
virtual void	prepareSimulation ()
	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 lambda, int nbins, double alpha_i_min, double alpha_i_max, const IFootprintFactor *beam_shape=nullptr)
	Sets beam parameters with alpha_i of the beam defined in the range. 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	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	setZSpan (size_t n_bins, double z_min, double z_max)
	Set z positions for intensity calculations. More...
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
const SimulationOptions &	options () const
ProgressHandler &	progress ()
virtual void	transferResultsToIntensityMap ()
	Creates the appropriate data structure (e.g. More...
virtual void	updateIntensityMap ()

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

Private Member Functions
	DepthProbeSimulation (const DepthProbeSimulation &other)
void	addBackgroundIntensity (size_t start_ind, size_t n_elements) override
void	addDataToCache (double weight) override
void	checkCache () const
std::unique_ptr< OutputData< double > >	createIntensityData () const
	Creates intensity data from simulation elements. More...
std::vector< DepthProbeElement >	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...
double	incidentAngle (size_t index) const
void	initialize ()
	Initializes simulation. More...
void	initSimulationElementVector () override
	Initializes the vector of ISimulation elements. More...
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...
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	setBeamParameters (double lambda, const IAxis &alpha_axis, const IFootprintFactor *beam_shape)
	Sets beam parameters with alpha_i of the beam defined in the range. More...
void	setRawResults (const std::vector< double > &raw_data) override
void	validateParametrization (const ParameterDistribution &par_distr) const override
	Checks the distribution validity for simulation. More...
void	validityCheck () const
	Checks if simulation data is ready for retrieval. More...

Private Attributes
std::unique_ptr< IAxis >	m_alpha_axis
std::unique_ptr< IBackground >	m_background
std::vector< std::valarray< double > >	m_cache
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
std::vector< DepthProbeElement >	m_sim_elements
std::unique_ptr< IAxis >	m_z_axis

Detailed Description

Definition at line 33 of file DepthProbeSimulation.h.

Constructor & Destructor Documentation

DepthProbeSimulation() [1/2]

DepthProbeSimulation::DepthProbeSimulation

(

)

Definition at line 32 of file DepthProbeSimulation.cpp.

                                           : ISimulation()
{
    initialize();
}

References initialize().

Referenced by clone().

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~DepthProbeSimulation()

DepthProbeSimulation::~DepthProbeSimulation ( )

overridedefault

DepthProbeSimulation() [2/2]

DepthProbeSimulation::DepthProbeSimulation ( const DepthProbeSimulation &  other )

private

Definition at line 100 of file DepthProbeSimulation.cpp.

    : ISimulation(other), m_sim_elements(other.m_sim_elements), m_cache(other.m_cache)
{
    if (other.m_alpha_axis)
        m_alpha_axis.reset(other.m_alpha_axis->clone());
    if (other.m_z_axis)
        m_z_axis.reset(other.m_z_axis->clone());
    for (auto iter = m_sim_elements.begin(); iter != m_sim_elements.end(); ++iter)
        iter->setZPositions(m_alpha_axis.get());
    initialize();
}

References initialize(), m_alpha_axis, m_sim_elements, and m_z_axis.

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Member Function Documentation

accept()

void DepthProbeSimulation::accept ( INodeVisitor *  visitor ) const

inlinefinalvirtual

Calls the INodeVisitor's visit method.

Implements INode.

Definition at line 40 of file DepthProbeSimulation.h.

{ visitor->visit(this); }

addBackgroundIntensity()

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

overrideprivatevirtual

Implements ISimulation.

Definition at line 239 of file DepthProbeSimulation.cpp.

{
    if (background())
        throw std::runtime_error(
            "Error: nonzero background is not supported by DepthProbeSimulation");
}

References ISimulation::background().

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addDataToCache()

void DepthProbeSimulation::addDataToCache ( double  weight )

overrideprivatevirtual

Implements ISimulation.

Definition at line 246 of file DepthProbeSimulation.cpp.

{
    checkCache();
    for (size_t i = 0, size = m_sim_elements.size(); i < size; ++i)
        m_cache[i] += m_sim_elements[i].getIntensities() * weight;
}

References checkCache(), m_cache, and m_sim_elements.

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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 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(), createUnitConverter(), OffSpecularSimulation::createUnitConverter(), generateSimulationElements(), ISimulation2D::generateSimulationElements(), initialize(), initSimulationElementVector(), GISASSimulation::initSimulationElementVector(), OffSpecularSimulation::initSimulationElementVector(), StandardSimulations::MaxiGISAS00(), StandardSimulations::MiniGISASPolarizationMM(), StandardSimulations::MiniGISASPolarizationMP(), StandardSimulations::MiniGISASPolarizationPM(), StandardSimulations::MiniGISASPolarizationPP(), normalize(), ISimulation2D::normalize(), SpecularSimulation::normalize(), OffSpecularSimulation::result(), 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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checkCache()

void DepthProbeSimulation::checkCache ( ) const

private

Definition at line 193 of file DepthProbeSimulation.cpp.

{
    if (m_sim_elements.size() != m_cache.size())
        throw std::runtime_error("Error in DepthProbeSimulation: the sizes of simulation element "
                                 "vector and of its cache are different");
}

References m_cache, and m_sim_elements.

Referenced by addDataToCache(), and moveDataFromCache().

clone()

DepthProbeSimulation * DepthProbeSimulation::clone ( ) const

overridevirtual

Implements ISimulation.

Definition at line 39 of file DepthProbeSimulation.cpp.

{
    return new DepthProbeSimulation(*this);
}

References DepthProbeSimulation().

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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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createIntensityData()

std::unique_ptr< OutputData< double > > DepthProbeSimulation::createIntensityData ( ) const

private

Creates intensity data from simulation elements.

Definition at line 267 of file DepthProbeSimulation.cpp.

{
    std::unique_ptr<OutputData<double>> result = std::make_unique<OutputData<double>>();
    result->addAxis(*getAlphaAxis());
    result->addAxis(*getZAxis());
 
    std::vector<double> rawData;
    rawData.reserve(getAlphaAxis()->size() * getZAxis()->size());
    for (size_t i = 0, size = m_sim_elements.size(); i < size; ++i) {
        const std::valarray<double>& fixed_angle_result = m_sim_elements[i].getIntensities();
        rawData.insert(rawData.end(), std::begin(fixed_angle_result), std::end(fixed_angle_result));
    }
    result->setRawDataVector(rawData);
 
    return result;
}

References getAlphaAxis(), getZAxis(), m_sim_elements, result(), and IAxis::size().

Referenced by result().

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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(), validateParametrization(), OffSpecularSimulation::validateParametrization(), and SpecularSimulation::validateParametrization().

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createUnitConverter()

std::unique_ptr< IUnitConverter > DepthProbeSimulation::createUnitConverter

(

)

const

Definition at line 95 of file DepthProbeSimulation.cpp.

{
    return std::make_unique<DepthProbeConverter>(beam(), *m_alpha_axis, *m_z_axis);
}

References ISimulation::beam(), m_alpha_axis, and m_z_axis.

Referenced by result().

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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(), GISASSimulation::intensityMapSize(), OffSpecularSimulation::intensityMapSize(), StandardSimulations::MaxiGISAS00(), StandardSimulations::MiniGISASPolarizationMM(), StandardSimulations::MiniGISASPolarizationMP(), StandardSimulations::MiniGISASPolarizationPM(), StandardSimulations::MiniGISASPolarizationPP(), GISASSimulation::prepareSimulation(), SpecularSimulation::prepareSimulation(), GISASSimulation::result(), 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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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< DepthProbeElement > DepthProbeSimulation::generateSimulationElements ( const Beam &  beam )

private

Generate simulation elements for given beam.

Definition at line 152 of file DepthProbeSimulation.cpp.

{
    std::vector<DepthProbeElement> result;
 
    const double wavelength = beam.wavelength();
    const double angle_shift = beam.direction().alpha();
 
    const size_t axis_size = getAlphaAxis()->size();
    result.reserve(axis_size);
    for (size_t i = 0; i < axis_size; ++i) {
        double result_angle = incidentAngle(i) + angle_shift;
        result.emplace_back(wavelength, -result_angle, getZAxis());
        if (!alpha_limits.isInRange(result_angle))
            result.back().setCalculationFlag(false); // false = exclude from calculations
    }
    return result;
}

References Direction::alpha(), ISimulation::beam(), Beam::direction(), getAlphaAxis(), getZAxis(), incidentAngle(), result(), IAxis::size(), and Beam::wavelength().

Referenced by initSimulationElementVector().

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generateSingleThreadedComputation()

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

overrideprivatevirtual

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 171 of file DepthProbeSimulation.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<DepthProbeComputation>(*sample(), options(), progress(), begin,
                                                   begin + static_cast<long>(n_elements));
}

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

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getAlphaAxis()

const IAxis * DepthProbeSimulation::getAlphaAxis

(

)

const

Returns a pointer to incident angle axis.

Definition at line 71 of file DepthProbeSimulation.cpp.

{
    if (!m_alpha_axis)
        throw std::runtime_error("Error in DepthProbeSimulation::getAlphaAxis: incident angle axis "
                                 "was not initialized.");
    return m_alpha_axis.get();
}

References m_alpha_axis.

Referenced by createIntensityData(), generateSimulationElements(), numberOfSimulationElements(), rawResults(), setRawResults(), and validityCheck().

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().

getZAxis()

const IAxis * DepthProbeSimulation::getZAxis

(

)

const

Returns a pointer to z-position axis.

Definition at line 79 of file DepthProbeSimulation.cpp.

{
    if (!m_z_axis)
        throw std::runtime_error("Error in DepthProbeSimulation::getZAxis: position axis "
                                 "was not initialized.");
    return m_z_axis.get();
}

References m_z_axis.

Referenced by createIntensityData(), generateSimulationElements(), initSimulationElementVector(), rawResults(), and setRawResults().

incidentAngle()

double DepthProbeSimulation::incidentAngle ( size_t  index ) const

private

Definition at line 262 of file DepthProbeSimulation.cpp.

{
    return m_alpha_axis->bin(index).center();
}

References m_alpha_axis.

Referenced by generateSimulationElements().

initialize()

void DepthProbeSimulation::initialize ( )

private

Initializes simulation.

Definition at line 215 of file DepthProbeSimulation.cpp.

{
    setName("DepthProbeSimulation");
 
    // allow for negative inclinations in the beam of specular simulation
    // it is required for proper averaging in the case of divergent beam
    auto inclination = beam().parameter("InclinationAngle");
    inclination->setLimits(RealLimits::limited(-M_PI_2, M_PI_2));
}

References ISimulation::beam(), RealLimits::limited(), M_PI_2, IParametricComponent::parameter(), RealParameter::setLimits(), and IParametricComponent::setName().

Referenced by DepthProbeSimulation().

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initSimulationElementVector()

void DepthProbeSimulation::initSimulationElementVector ( )

overrideprivatevirtual

Initializes the vector of ISimulation elements.

Implements ISimulation.

Definition at line 143 of file DepthProbeSimulation.cpp.

{
    m_sim_elements = generateSimulationElements(beam());
 
    if (!m_cache.empty())
        return;
    m_cache.resize(m_sim_elements.size(), std::valarray<double>(0.0, getZAxis()->size()));
}

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

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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(), GISASSimulation::prepareSimulation(), SpecularSimulation::prepareSimulation(), GISASSimulation::result(), setBeamParameters(), OffSpecularSimulation::setBeamParameters(), GISASSimulation::setBeamParameters(), ISimulation2D::setDetector(), and SpecularSimulation::setScan().

intensityMapSize()

size_t DepthProbeSimulation::intensityMapSize ( ) const

overridevirtual

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

Implements ISimulation.

Definition at line 87 of file DepthProbeSimulation.cpp.

{
    if (!m_z_axis || !m_alpha_axis)
        throw std::runtime_error("Error in DepthProbeSimulation::intensityMapSize: attempt to "
                                 "access non-initialized data.");
    return m_z_axis->size() * m_alpha_axis->size();
}

References m_alpha_axis, and m_z_axis.

moveDataFromCache()

void DepthProbeSimulation::moveDataFromCache ( )

overrideprivatevirtual

Implements ISimulation.

Definition at line 253 of file DepthProbeSimulation.cpp.

{
    checkCache();
    for (size_t i = 0, size = m_sim_elements.size(); i < size; ++i)
        m_sim_elements[i].setIntensities(std::move(m_cache[i]));
    m_cache.clear();
    m_cache.shrink_to_fit();
}

References checkCache(), m_cache, and m_sim_elements.

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normalize()

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

overrideprivatevirtual

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 225 of file DepthProbeSimulation.cpp.

{
    const double beam_intensity = beam().intensity();
    for (size_t i = start_ind, stop_point = start_ind + n_elements; i < stop_point; ++i) {
        auto& element = m_sim_elements[i];
        const double alpha_i = -element.getAlphaI();
        const auto footprint = beam().footprintFactor();
        double intensity_factor = beam_intensity;
        if (footprint != nullptr)
            intensity_factor = intensity_factor * footprint->calculate(alpha_i);
        element.setIntensities(element.getIntensities() * intensity_factor);
    }
}

References ISimulation::beam(), IFootprintFactor::calculate(), Beam::footprintFactor(), Beam::intensity(), and m_sim_elements.

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numberOfSimulationElements()

size_t DepthProbeSimulation::numberOfSimulationElements ( ) const

overrideprivatevirtual

Gets the number of elements this simulation needs to calculate.

Implements ISimulation.

Definition at line 44 of file DepthProbeSimulation.cpp.

{
    return getAlphaAxis()->size();
}

References getAlphaAxis(), and IAxis::size().

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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 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 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 ISimulation::prepareSimulation ( )

virtualinherited

Put into a clean state for running a simulation.

Reimplemented in SpecularSimulation, OffSpecularSimulation, ISimulation2D, and GISASSimulation.

Definition at line 182 of file ISimulation.cpp.

{
    m_sample_provider.updateSample();
    if (!MultiLayerUtils::ContainsCompatibleMaterials(*m_sample_provider.sample()))
        throw std::runtime_error(
            "Error in ISimulation::prepareSimulation(): non-default materials of"
            " several different types are used in the sample provided");
    gsl_set_error_handler_off();
}

References MultiLayerUtils::ContainsCompatibleMaterials(), ISimulation::m_sample_provider, SampleProvider::sample(), and SampleProvider::updateSample().

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

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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 generateSingleThreadedComputation(), ISimulation2D::generateSingleThreadedComputation(), and SpecularSimulation::generateSingleThreadedComputation().

rawResults()

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

overrideprivatevirtual

Implements ISimulation.

Definition at line 284 of file DepthProbeSimulation.cpp.

{
    validityCheck();
    const size_t z_size = getZAxis()->size();
    const size_t alpha_size = getAlphaAxis()->size();
 
    std::vector<double> result;
    result.reserve(alpha_size * z_size);
    for (size_t i = 0; i < alpha_size; ++i) {
        if (m_sim_elements[i].size() != z_size)
            throw std::runtime_error("Error in DepthProbeSimulation::rawResults: simulation "
                                     "element size is not equal to the size of the position axis");
        const auto& intensities = m_sim_elements[i].getIntensities();
        result.insert(result.end(), std::begin(intensities), std::end(intensities));
    }
 
    return result;
}

References getAlphaAxis(), getZAxis(), m_sim_elements, result(), IAxis::size(), and validityCheck().

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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 DepthProbeSimulation::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 49 of file DepthProbeSimulation.cpp.

{
    validityCheck();
    auto data = createIntensityData();
    return SimulationResult(*data, *createUnitConverter());
}

References createIntensityData(), createUnitConverter(), and validityCheck().

Referenced by createIntensityData(), generateSimulationElements(), and rawResults().

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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(), generateSingleThreadedComputation(), ISimulation2D::generateSingleThreadedComputation(), SpecularSimulation::generateSingleThreadedComputation(), ISimulation::setSample(), and 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() [1/2]

void DepthProbeSimulation::setBeamParameters ( double  lambda, const IAxis &  alpha_axis, const IFootprintFactor *  beam_shape  )

private

Sets beam parameters with alpha_i of the beam defined in the range.

Definition at line 112 of file DepthProbeSimulation.cpp.

{
    if (lambda <= 0.0)
        throw std::runtime_error(
            "Error in DepthProbeSimulation::setBeamParameters: wavelength must be positive.");
    if (alpha_axis.lowerBound() < 0.0)
        throw std::runtime_error(
            "Error in DepthProbeSimulation::setBeamParameters: minimum value on "
            "angle axis is negative.");
    if (alpha_axis.lowerBound() >= alpha_axis.upperBound())
        throw std::runtime_error(
            "Error in DepthProbeSimulation::setBeamParameters: maximal value on "
            "angle axis is less or equal to the minimal one.");
    if (alpha_axis.size() == 0)
        throw std::runtime_error(
            "Error in DepthProbeSimulation::setBeamParameters: angle axis is empty");
 
    SpecularDetector1D detector(alpha_axis);
    instrument().setDetector(detector);
    m_alpha_axis.reset(alpha_axis.clone());
 
    // beam is initialized with zero-valued angles
    // Zero-valued incident alpha is required for proper
    // taking into account beam resolution effects
    instrument().setBeamParameters(lambda, zero_alpha_i, zero_phi_i);
 
    if (beam_shape)
        beam().setFootprintFactor(*beam_shape);
}

References ISimulation::beam(), IAxis::clone(), ISimulation::detector(), ISimulation::instrument(), IAxis::lowerBound(), m_alpha_axis, Instrument::setBeamParameters(), Instrument::setDetector(), Beam::setFootprintFactor(), IAxis::size(), and IAxis::upperBound().

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setBeamParameters() [2/2]

void DepthProbeSimulation::setBeamParameters	(	double	lambda,
		int	nbins,
		double	alpha_i_min,
		double	alpha_i_max,
		const IFootprintFactor *	beam_shape = nullptr
	)

Sets beam parameters with alpha_i of the beam defined in the range.

Definition at line 56 of file DepthProbeSimulation.cpp.

{
    FixedBinAxis axis("alpha_i", static_cast<size_t>(nbins), alpha_i_min, alpha_i_max);
    setBeamParameters(lambda, axis, beam_shape);
}

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(), initialize(), GISASSimulation::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 DepthProbeSimulation::setRawResults ( const std::vector< double > &  raw_data )

overrideprivatevirtual

Implements ISimulation.

Definition at line 303 of file DepthProbeSimulation.cpp.

{
    validityCheck();
    const size_t z_size = getZAxis()->size();
    const size_t alpha_size = getAlphaAxis()->size();
 
    if (raw_results.size() != z_size * alpha_size)
        throw std::runtime_error(
            "Error in DepthProbeSimulation::setRawResults: the vector to set is of invalid size");
 
    const double* raw_array = raw_results.data();
    for (size_t i = 0; i < alpha_size; ++i) {
        std::valarray<double> fixed_angle_result(raw_array, z_size);
        m_sim_elements[i].setIntensities(std::move(fixed_angle_result));
        raw_array += z_size;
    }
}

References getAlphaAxis(), getZAxis(), m_sim_elements, IAxis::size(), and validityCheck().

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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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setZSpan()

void DepthProbeSimulation::setZSpan	(	size_t	n_bins,
		double	z_min,
		double	z_max
	)

Set z positions for intensity calculations.

Negative z's correspond to the area under sample surface. The more negative z is, the deeper layer corresponds to it.

Definition at line 63 of file DepthProbeSimulation.cpp.

{
    if (z_max <= z_min)
        throw std::runtime_error("Error in DepthProbeSimulation::setZSpan: maximum on-axis value "
                                 "is less or equal to the minimum one");
    m_z_axis = std::make_unique<FixedBinAxis>("z", n_bins, z_min, z_max);
}

References m_z_axis.

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()

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

overrideprivatevirtual

Checks the distribution validity for simulation.

Reimplemented from ISimulation.

Definition at line 200 of file DepthProbeSimulation.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 DepthProbeSimulation: parameter distribution of "
                                     "beam inclination angle should have zero mean.");
}

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

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validityCheck()

void DepthProbeSimulation::validityCheck ( ) const

private

Checks if simulation data is ready for retrieval.

Definition at line 179 of file DepthProbeSimulation.cpp.

{
    const MultiLayer* current_sample = sample();
    if (!current_sample)
        throw std::runtime_error(
            "Error in DepthProbeSimulation::validityCheck: no sample found in the simulation.");
 
    const size_t data_size = m_sim_elements.size();
    if (data_size != getAlphaAxis()->size())
        throw std::runtime_error(
            "Error in DepthProbeSimulation::validityCheck: length of simulation "
            "element vector is not equal to the number of inclination angles");
}

References getAlphaAxis(), m_sim_elements, and ISimulation::sample().

Referenced by rawResults(), result(), and setRawResults().

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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_alpha_axis

std::unique_ptr<IAxis> DepthProbeSimulation::m_alpha_axis

private

Definition at line 119 of file DepthProbeSimulation.h.

Referenced by DepthProbeSimulation(), createUnitConverter(), getAlphaAxis(), incidentAngle(), intensityMapSize(), and setBeamParameters().

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<std::valarray<double> > DepthProbeSimulation::m_cache

private

Definition at line 122 of file DepthProbeSimulation.h.

Referenced by addDataToCache(), checkCache(), initSimulationElementVector(), and moveDataFromCache().

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<DepthProbeElement> DepthProbeSimulation::m_sim_elements

private

Definition at line 121 of file DepthProbeSimulation.h.

Referenced by DepthProbeSimulation(), addDataToCache(), checkCache(), createIntensityData(), generateSingleThreadedComputation(), initSimulationElementVector(), moveDataFromCache(), normalize(), rawResults(), setRawResults(), and validityCheck().

m_z_axis

std::unique_ptr<IAxis> DepthProbeSimulation::m_z_axis

private

Definition at line 120 of file DepthProbeSimulation.h.

Referenced by DepthProbeSimulation(), createUnitConverter(), getZAxis(), intensityMapSize(), and setZSpan().

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

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