Description

Simulation of radiation depth profile.

Holds an instrument and sample model. Computes radiation intensity as function of incoming glancing angle and penetration depth. Scattered rays are neglected. Only refraction, reflection and attenuation of the incoming beam are accounted for.

Definition at line 37 of file DepthProbeSimulation.h.

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Public Member Functions
	DepthProbeSimulation (const MultiLayer &sample)

	~DepthProbeSimulation () override

void	addMask (const IShape2D &shape, bool mask_value=true)
	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. More...

void	addParameterDistribution (const ParameterDistribution &par_distr)

void	addParameterDistribution (ParameterDistribution::WhichParameter whichParameter, const IDistribution1D &distribution, size_t nbr_samples, double sigma_factor=0.0, const RealLimits &limits=RealLimits())

const IAxis *	alphaAxis () const
	Returns a pointer to incident angle axis. More...

const IBackground *	background () const

Beam &	beam ()

const Beam &	beam () const

void	checkNodeArgs () const
	Raises exception if a parameter value is invalid. More...

std::string	className () const final
	Returns the class name, to be hard-coded in each leaf class that inherits from INode. More...

ICoordSystem *	createCoordSystem () const override

IDetector &	detector ()

const IDetector &	detector () const

bool	force_polarized () const override
	Force polarized computation even in absence of sample magnetization or external fields. More...

const IDetector *	getDetector () const

const std::vector< ParameterDistribution > &	getDistributions () 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...

std::vector< const INode * >	nodeChildren () const override
	Returns all children. More...

std::vector< const INode * >	nodeOffspring () const
	Returns all descendants. More...

SimulationOptions &	options ()

const SimulationOptions &	options () const

virtual std::vector< ParaMeta >	parDefs () const
	Returns the parameter definitions, to be hard-coded in each leaf class. 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	setRegionOfInterest (double xlow, double ylow, double xup, double yup)
	Sets rectangular region of interest with lower left and upper right corners defined. More...

void	setTerminalProgressMonitor ()
	Initializes a progress monitor that prints to stdout. More...

void	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. More...

SimulationResult	simulate ()
	Run a simulation, and return the result. More...

void	subscribe (const std::function< bool(size_t)> &inform)

std::string	unitOfParameter (ParameterDistribution::WhichParameter which) const

const IAxis *	zAxis () const
	Returns a pointer to z-position axis. More...

Protected Member Functions
virtual void	initCoordSystem ()

void	initDistributionHandler () override
	init callbacks for setting the parameter values More...

ProgressHandler &	progress ()

virtual void	updateIntensityMap ()

Protected Attributes
std::unique_ptr< Beam >	m_beam

std::unique_ptr< IDetector >	m_detector

DistributionHandler	m_distribution_handler

std::vector< double >	m_P

Private Member Functions
void	addBackgroundIntensity (size_t start_ind, size_t n_elements) override

void	addDataToCache (double weight) override

void	checkCache () const

std::unique_ptr< IComputation >	createComputation (const reSample &re_sample, size_t start, size_t n_elements) override
	Generate a single threaded computation for a given range of simulation elements. More...

std::unique_ptr< Datafield >	createIntensityData () const
	Creates intensity data from simulation elements. More...

std::vector< DepthProbeElement >	generateElements (const Beam &beam)
	Generate simulation elements for given beam. More...

double	incidentAngle (size_t index) const

void	initElementVector () 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	numberOfElements () const override
	Gets the number of elements this simulation needs to calculate. More...

SimulationResult	pack_result () override
	Sets m_result. More...

void	prepareSimulation () override
	Put into a clean state for running a simulation. More...

void	runSingleSimulation (const reSample &re_sample, size_t batch_start, size_t batch_size, double weight=1.0)
	Runs a single simulation with fixed parameter values. If desired, the simulation is run in several threads. 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	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::shared_ptr< IBackground >	m_background

std::vector< std::valarray< double > >	m_cache

std::unique_ptr< DetectorContext >	m_detector_context

std::vector< DepthProbeElement >	m_eles

std::shared_ptr< SimulationOptions >	m_options

std::shared_ptr< ProgressHandler >	m_progress

std::shared_ptr< MultiLayer >	m_sample

std::unique_ptr< IAxis >	m_z_axis

Constructor & Destructor Documentation

◆ DepthProbeSimulation()

DepthProbeSimulation::DepthProbeSimulation ( const MultiLayer & sample )

Definition at line 38 of file DepthProbeSimulation.cpp.

     : ISimulation2D(sample)
 {
     // allow for negative inclinations in the beam of specular simulation
     // it is required for proper averaging in the case of divergent beam
     beam().setInclinationLimits(RealLimits::limited(-M_PI_2, M_PI_2));
 }

References ISimulation2D::beam(), RealLimits::limited(), M_PI_2, and Beam::setInclinationLimits().

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◆ ~DepthProbeSimulation()

DepthProbeSimulation::~DepthProbeSimulation ( )

overridedefault

Member Function Documentation

◆ addBackgroundIntensity()

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

overrideprivatevirtual

Implements ISimulation.

Definition at line 219 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 226 of file DepthProbeSimulation.cpp.

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

References checkCache(), m_cache, and m_eles.

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◆ 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 56 of file ISimulation2D.cpp.

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

References IDetector::addMask(), and ISimulation2D::detector().

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◆ addParameterDistribution() [1/2]

void ISimulation::addParameterDistribution ( const ParameterDistribution & par_distr )

inherited

Definition at line 231 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	(	ParameterDistribution::WhichParameter	whichParameter,
		const IDistribution1D &	distribution,
		size_t	nbr_samples,
		double	sigma_factor = `0.0`,
		const RealLimits &	limits = `RealLimits()`
	)

inherited

Definition at line 222 of file ISimulation.cpp.

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

◆ alphaAxis()

const IAxis * DepthProbeSimulation::alphaAxis ( ) const

Returns a pointer to incident angle axis.

Definition at line 75 of file DepthProbeSimulation.cpp.

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

References m_alpha_axis.

Referenced by createIntensityData(), generateElements(), numberOfElements(), and validityCheck().

◆ background()

const IBackground* ISimulation::background ( ) const

inlineinherited

Definition at line 76 of file ISimulation.h.

76 { return m_background.get(); }

ISimulation::m_background

std::shared_ptr< IBackground > m_background

Definition: ISimulation.h:137

References ISimulation::m_background.

Referenced by addBackgroundIntensity(), ISimulation2D::addBackgroundIntensity(), and SpecularSimulation::addBackgroundIntensity().

◆ beam() [1/2]

Beam& ISimulation2D::beam ( )

inlineinherited

Definition at line 57 of file ISimulation2D.h.

57 { return *m_beam; }

ISimulation2D::m_beam

std::unique_ptr< Beam > m_beam

Definition: ISimulation2D.h:98

References ISimulation2D::m_beam.

Referenced by DepthProbeSimulation(), createCoordSystem(), OffspecSimulation::createCoordSystem(), ScatteringSimulation::createCoordSystem(), generateElements(), ISimulation2D::generateElements(), ISimulation2D::initDistributionHandler(), initElementVector(), OffspecSimulation::initElementVector(), ScatteringSimulation::initElementVector(), normalize(), ISimulation2D::normalize(), setBeamParameters(), and OffspecSimulation::setBeamParameters().

◆ beam() [2/2]

const Beam& ISimulation2D::beam ( ) const

inlineinherited

Definition at line 62 of file ISimulation2D.h.

62 { return *m_beam; }

References ISimulation2D::m_beam.

◆ checkCache()

void DepthProbeSimulation::checkCache ( ) const

private

Definition at line 186 of file DepthProbeSimulation.cpp.

 {
     if (m_eles.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_eles.

Referenced by addDataToCache(), and moveDataFromCache().

◆ checkNodeArgs()

void INode::checkNodeArgs ( ) const

inherited

Raises exception if a parameter value is invalid.

Definition at line 27 of file INode.cpp.

 {
     size_t nP = m_P.size();
     if (parDefs().size() != nP) {
         std::cerr << "BUG in class " << className() << std::endl;
         std::cerr << "#m_P = " << nP << std::endl;
         std::cerr << "#PDf = " << parDefs().size() << std::endl;
         for (const ParaMeta& pm : parDefs())
             std::cerr << "  PDf: " << pm.name << std::endl;
         ASSERT(0);
     }
     ASSERT(parDefs().size() == nP);
     for (size_t i = 0; i < nP; ++i) {
         const ParaMeta pm = parDefs()[i];
  
         RealLimits limits = RealLimits::limitless();
         if (pm.vMin == -INF) {
             ASSERT(pm.vMax == +INF);
             // nothing to do
         } else if (pm.vMax == +INF) {
             ASSERT(pm.vMin == 0);
             limits = RealLimits::nonnegative();
         } else {
             limits = RealLimits::limited(pm.vMin, pm.vMax);
         }
         limits.check(pm.name, m_P[i]);
     }
 }

References ASSERT, RealLimits::check(), INode::className(), INF, RealLimits::limited(), RealLimits::limitless(), INode::m_P, ParaMeta::name, RealLimits::nonnegative(), INode::parDefs(), ParaMeta::vMax, and ParaMeta::vMin.

Referenced by BarGauss::BarGauss(), BarLorentz::BarLorentz(), Bipyramid4::Bipyramid4(), Box::Box(), CantellatedCube::CantellatedCube(), Cone::Cone(), ConstantBackground::ConstantBackground(), CosineRippleBox::CosineRippleBox(), CosineRippleGauss::CosineRippleGauss(), CosineRippleLorentz::CosineRippleLorentz(), Cylinder::Cylinder(), DistributionCosine::DistributionCosine(), DistributionGate::DistributionGate(), DistributionGaussian::DistributionGaussian(), DistributionLogNormal::DistributionLogNormal(), DistributionLorentz::DistributionLorentz(), DistributionTrapezoid::DistributionTrapezoid(), Dodecahedron::Dodecahedron(), EllipsoidalCylinder::EllipsoidalCylinder(), FootprintGauss::FootprintGauss(), FootprintSquare::FootprintSquare(), FuzzySphere::FuzzySphere(), GaussSphere::GaussSphere(), HemiEllipsoid::HemiEllipsoid(), HollowSphere::HollowSphere(), HorizontalCylinder::HorizontalCylinder(), Icosahedron::Icosahedron(), LongBoxGauss::LongBoxGauss(), LongBoxLorentz::LongBoxLorentz(), PlatonicOctahedron::PlatonicOctahedron(), PlatonicTetrahedron::PlatonicTetrahedron(), Prism3::Prism3(), Prism6::Prism6(), Profile1DCauchy::Profile1DCauchy(), Profile1DCosine::Profile1DCosine(), Profile1DGate::Profile1DGate(), Profile1DGauss::Profile1DGauss(), Profile1DTriangle::Profile1DTriangle(), Profile1DVoigt::Profile1DVoigt(), Profile2DCauchy::Profile2DCauchy(), Profile2DCone::Profile2DCone(), Profile2DGate::Profile2DGate(), Profile2DGauss::Profile2DGauss(), Profile2DVoigt::Profile2DVoigt(), Pyramid2::Pyramid2(), Pyramid3::Pyramid3(), Pyramid4::Pyramid4(), Pyramid6::Pyramid6(), RotationEuler::RotationEuler(), RotationX::RotationX(), RotationY::RotationY(), RotationZ::RotationZ(), SawtoothRippleBox::SawtoothRippleBox(), SawtoothRippleGauss::SawtoothRippleGauss(), SawtoothRippleLorentz::SawtoothRippleLorentz(), Sphere::Sphere(), Spheroid::Spheroid(), TruncatedCube::TruncatedCube(), TruncatedSphere::TruncatedSphere(), and TruncatedSpheroid::TruncatedSpheroid().

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◆ className()

std::string DepthProbeSimulation::className ( ) const

inlinefinalvirtual

Returns the class name, to be hard-coded in each leaf class that inherits from INode.

Implements INode.

Definition at line 42 of file DepthProbeSimulation.h.

42 { return "DepthProbeSimulation"; }

◆ createComputation()

std::unique_ptr< IComputation > DepthProbeSimulation::createComputation	(	const reSample &	re_sample,
		size_t	start,
		size_t	n_elements
	)

overrideprivatevirtual

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

Parameters

re_sample	Preprocessed version of our sample
start	Index of the first element to include into computation
n_elements	Number of elements to process

Implements ISimulation.

Definition at line 164 of file DepthProbeSimulation.cpp.

 {
     ASSERT(start < m_eles.size() && start + n_elements <= m_eles.size());
     const auto& begin = m_eles.begin() + static_cast<long>(start);
     return std::make_unique<DepthProbeComputation>(re_sample, options(), progress(), begin,
                                                    begin + static_cast<long>(n_elements));
 }

References ASSERT, m_eles, ISimulation::options(), and ISimulation::progress().

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◆ createCoordSystem()

ICoordSystem * DepthProbeSimulation::createCoordSystem ( ) const

overridevirtual

Implements ISimulation.

Definition at line 100 of file DepthProbeSimulation.cpp.

 {
     OwningVector<IAxis> axes({m_alpha_axis->clone(), m_z_axis->clone()});
     return new DepthProbeCoordinates(axes, beam().direction(), beam().wavelength());
 }

References ISimulation2D::beam(), m_alpha_axis, and m_z_axis.

Referenced by pack_result().

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◆ createIntensityData()

std::unique_ptr< Datafield > DepthProbeSimulation::createIntensityData ( ) const

private

Creates intensity data from simulation elements.

Definition at line 247 of file DepthProbeSimulation.cpp.

 {
     auto frame = new Frame({alphaAxis()->clone(), zAxis()->clone()});
  
     std::vector<double> out(frame->size());
     size_t iout = 0;
     for (size_t i = 0, size = m_eles.size(); i < size; ++i)
         for (const double v: m_eles[i].getIntensities())
             out[iout++] = v;
  
     return std::unique_ptr<Datafield>(new Datafield(frame, out));
 }

References alphaAxis(), IAxis::clone(), m_eles, and zAxis().

Referenced by pack_result().

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◆ detector() [1/2]

IDetector& ISimulation2D::detector ( )

inlineinherited

Definition at line 58 of file ISimulation2D.h.

58 { return *m_detector; }

ISimulation2D::m_detector

std::unique_ptr< IDetector > m_detector

Definition: ISimulation2D.h:99

References ISimulation2D::m_detector.

Referenced by ISimulation2D::addMask(), OffspecSimulation::checkInitialization(), OffspecSimulation::createCoordSystem(), ISimulation2D::force_polarized(), ISimulation2D::generateElements(), OffspecSimulation::intensityMapSize(), ScatteringSimulation::intensityMapSize(), ISimulation2D::maskAll(), OffspecSimulation::pack_result(), ScatteringSimulation::pack_result(), ISimulation2D::prepareSimulation(), ScatteringSimulation::prepareSimulation(), ISimulation2D::setRegionOfInterest(), OffspecSimulation::transferDetectorImage(), and OffspecSimulation::updateIntensityMap().

◆ detector() [2/2]

const IDetector& ISimulation2D::detector ( ) const

inlineinherited

Definition at line 63 of file ISimulation2D.h.

63 { return *m_detector; }

References ISimulation2D::m_detector.

◆ force_polarized()

bool DepthProbeSimulation::force_polarized ( ) const

inlineoverridevirtual

Force polarized computation even in absence of sample magnetization or external fields.

Implements ISimulation.

Definition at line 61 of file DepthProbeSimulation.h.

61 { return false; }

◆ generateElements()

std::vector< DepthProbeElement > DepthProbeSimulation::generateElements ( const Beam & beam )

private

Generate simulation elements for given beam.

Definition at line 145 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 = alphaAxis()->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, zAxis());
         if (!alpha_limits.isInRange(result_angle))
             result.back().setCalculationFlag(false); // false = exclude from calculations
     }
     return result;
 }

References Direction::alpha(), alphaAxis(), ISimulation2D::beam(), Beam::direction(), incidentAngle(), IAxis::size(), Beam::wavelength(), and zAxis().

Referenced by initElementVector().

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◆ getDetector()

const IDetector* ISimulation2D::getDetector ( ) const

inlineinherited

Definition at line 64 of file ISimulation2D.h.

64 { return m_detector.get(); }

References ISimulation2D::m_detector.

Referenced by ScatteringSimulation::createCoordSystem().

◆ getDistributions()

const std::vector< ParameterDistribution > & ISimulation::getDistributions ( ) const

inherited

Definition at line 237 of file ISimulation.cpp.

 {
     return m_distribution_handler.getDistributions();
 }

References DistributionHandler::getDistributions(), and ISimulation::m_distribution_handler.

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◆ incidentAngle()

double DepthProbeSimulation::incidentAngle ( size_t index ) const

private

Definition at line 242 of file DepthProbeSimulation.cpp.

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

References m_alpha_axis.

Referenced by generateElements().

◆ initCoordSystem()

virtual void ISimulation2D::initCoordSystem ( )

inlineprotectedvirtualinherited

Definition at line 70 of file ISimulation2D.h.

70 {}

◆ initDistributionHandler()

void ISimulation2D::initDistributionHandler ( )

overrideprotectedvirtualinherited

init callbacks for setting the parameter values

Reimplemented from ISimulation.

Definition at line 159 of file ISimulation2D.cpp.

 {
     for (const auto& distribution : m_distribution_handler.getDistributions()) {
         const auto* dc = const_cast<ParameterDistribution*>(&distribution);
  
         switch (dc->whichParameter()) {
         case ParameterDistribution::BeamAzimuthalAngle:
             m_distribution_handler.defineCallbackForDistribution(
                 dc, [&](double d) { beam().setAzimuthalAngleGuarded(d); });
             break;
         case ParameterDistribution::BeamInclinationAngle:
             m_distribution_handler.defineCallbackForDistribution(
                 dc, [&](double d) { beam().setInclinationAngleGuarded(d); });
             break;
         case ParameterDistribution::BeamWavelength:
             m_distribution_handler.defineCallbackForDistribution(
                 dc, [&](double d) { beam().setWavelengthGuarded(d); });
             break;
         default:
             ASSERT(0);
         }
     }
 }

References ASSERT, ISimulation2D::beam(), ParameterDistribution::BeamAzimuthalAngle, ParameterDistribution::BeamInclinationAngle, ParameterDistribution::BeamWavelength, DistributionHandler::defineCallbackForDistribution(), DistributionHandler::getDistributions(), ISimulation::m_distribution_handler, Beam::setAzimuthalAngleGuarded(), Beam::setInclinationAngleGuarded(), and Beam::setWavelengthGuarded().

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◆ initElementVector()

void DepthProbeSimulation::initElementVector ( )

overrideprivatevirtual

Initializes the vector of ISimulation elements.

Implements ISimulation.

Definition at line 136 of file DepthProbeSimulation.cpp.

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

References ISimulation2D::beam(), generateElements(), m_cache, m_eles, and zAxis().

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◆ intensityMapSize()

size_t DepthProbeSimulation::intensityMapSize ( ) const

overridevirtual

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

Implements ISimulation.

Definition at line 91 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.

◆ maskAll()

void ISimulation2D::maskAll ( )

inherited

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

Definition at line 61 of file ISimulation2D.cpp.

 {
     detector().maskAll();
 }

References ISimulation2D::detector(), and IDetector::maskAll().

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◆ moveDataFromCache()

void DepthProbeSimulation::moveDataFromCache ( )

overrideprivatevirtual

Implements ISimulation.

Definition at line 233 of file DepthProbeSimulation.cpp.

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

References checkCache(), m_cache, and m_eles.

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◆ nodeChildren()

std::vector< const INode * > ISimulation2D::nodeChildren ( ) const

overridevirtualinherited

Returns all children.

Reimplemented from ISimulation.

Definition at line 42 of file ISimulation2D.cpp.

 {
     std::vector<const INode*> result = ISimulation::nodeChildren();
     result.push_back(m_beam.get());
     if (m_detector)
         result.push_back(m_detector.get());
     return result;
 }

References ISimulation2D::m_beam, ISimulation2D::m_detector, and ISimulation::nodeChildren().

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◆ nodeOffspring()

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

inherited

Returns all descendants.

Definition at line 61 of file INode.cpp.

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

References INode::nodeChildren().

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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 205 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_eles[i];
         const double alpha_i = -element.alphaI();
         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 ISimulation2D::beam(), IFootprintFactor::calculate(), Beam::footprintFactor(), Beam::intensity(), and m_eles.

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◆ numberOfElements()

size_t DepthProbeSimulation::numberOfElements ( ) const

overrideprivatevirtual

Gets the number of elements this simulation needs to calculate.

Implements ISimulation.

Definition at line 48 of file DepthProbeSimulation.cpp.

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

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

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◆ options() [1/2]

SimulationOptions & ISimulation::options ( )

inherited

Definition at line 123 of file ISimulation.cpp.

 {
     ASSERT(m_options);
     return *m_options;
 }

References ASSERT, and ISimulation::m_options.

◆ options() [2/2]

const SimulationOptions & ISimulation::options ( ) const

inherited

Definition at line 117 of file ISimulation.cpp.

 {
     ASSERT(m_options);
     return *m_options;
 }

References ASSERT, and ISimulation::m_options.

Referenced by createComputation(), ISimulation2D::createComputation(), SpecularSimulation::createComputation(), and ISimulation::simulate().

◆ pack_result()

SimulationResult DepthProbeSimulation::pack_result ( )

overrideprivatevirtual

Sets m_result.

Implements ISimulation.

Definition at line 53 of file DepthProbeSimulation.cpp.

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

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

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◆ parDefs()

virtual std::vector<ParaMeta> INode::parDefs ( ) const

inlinevirtualinherited

Returns the parameter definitions, to be hard-coded in each leaf class.

Reimplemented in ConstantBackground, GaussSphere, FuzzySphere, RotationEuler, RotationZ, RotationY, RotationX, Crystal, Layer, HexagonalLattice2D, SquareLattice2D, BasicLattice2D, LayerRoughness, TruncatedSpheroid, TruncatedSphere, TruncatedCube, Spheroid, Sphere, SawtoothRippleLorentz, SawtoothRippleGauss, SawtoothRippleBox, Pyramid6, Pyramid4, Pyramid3, Pyramid2, Prism6, Prism3, PlatonicTetrahedron, PlatonicOctahedron, LongBoxLorentz, LongBoxGauss, Icosahedron, HorizontalCylinder, HollowSphere, HemiEllipsoid, EllipsoidalCylinder, Dodecahedron, Cylinder, CosineRippleLorentz, CosineRippleGauss, CosineRippleBox, Cone, CantellatedCube, Box, Bipyramid4, BarLorentz, BarGauss, Profile2DVoigt, Profile2DCone, Profile2DGate, Profile2DGauss, Profile2DCauchy, Profile1DVoigt, Profile1DCosine, Profile1DTriangle, Profile1DGate, Profile1DGauss, Profile1DCauchy, MisesGaussPeakShape, MisesFisherGaussPeakShape, LorentzFisherPeakShape, GaussFisherPeakShape, IsotropicLorentzPeakShape, IsotropicGaussPeakShape, ParticleLayout, InterferenceTwin, InterferenceRadialParaCrystal, InterferenceHardDisk, Interference2DSuperLattice, Interference2DParaCrystal, Interference1DLattice, DistributionTrapezoid, DistributionCosine, DistributionLogNormal, DistributionGaussian, DistributionLorentz, DistributionGate, ResolutionFunction2DGaussian, PolFilter, FootprintSquare, and FootprintGauss.

Definition at line 51 of file INode.h.

51 { return {}; }

Referenced by INode::checkNodeArgs(), and IFormFactor::pythonConstructor().

◆ prepareSimulation()

void DepthProbeSimulation::prepareSimulation ( )

inlineoverrideprivatevirtual

Put into a clean state for running a simulation.

Implements ISimulation.

Definition at line 67 of file DepthProbeSimulation.h.

67 {}

◆ progress()

ProgressHandler & ISimulation::progress ( )

protectedinherited

Definition at line 129 of file ISimulation.cpp.

 {
     ASSERT(m_progress);
     return *m_progress;
 }

References ASSERT, and ISimulation::m_progress.

Referenced by createComputation(), ISimulation2D::createComputation(), and SpecularSimulation::createComputation().

◆ runSingleSimulation()

void ISimulation::runSingleSimulation	(	const reSample &	re_sample,
		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 245 of file ISimulation.cpp.

 {
     initElementVector();
  
     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) {
         const size_t thread_start = batch_start + startIndex(n_threads, i_thread, batch_size);
         const size_t thread_size = batchSize(n_threads, i_thread, batch_size);
         if (thread_size == 0)
             break;
         computations.emplace_back(createComputation(re_sample, 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::createComputation(), ISimulation::initElementVector(), ISimulation::m_options, and ISimulation::normalize().

Referenced by ISimulation::simulate().

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◆ sample()

const MultiLayer * ISimulation::sample ( ) const

inherited

Definition at line 191 of file ISimulation.cpp.

 {
     return m_sample.get();
 }

References ISimulation::m_sample.

Referenced by ISimulation::simulate(), and validityCheck().

◆ setBackground()

void ISimulation::setBackground ( const IBackground & bg )

inherited

Definition at line 196 of file ISimulation.cpp.

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

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

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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 107 of file DepthProbeSimulation.cpp.

 {
     if (lambda <= 0.0)
         throw std::runtime_error(
             "Error in DepthProbeSimulation::setBeamParameters: wavelength must be positive.");
     if (alpha_axis.min() < 0.0)
         throw std::runtime_error(
             "Error in DepthProbeSimulation::setBeamParameters: minimum value on "
             "angle axis is negative.");
     if (alpha_axis.min() >= alpha_axis.max())
         throw std::runtime_error(
             "Error in DepthProbeSimulation::setBeamParameters: alpha bounds are not sorted.");
     if (alpha_axis.size() == 0)
         throw std::runtime_error(
             "Error in DepthProbeSimulation::setBeamParameters: angle axis is empty");
  
     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
     beam().setWavelength(lambda);
     beam().setDirection({zero_alpha_i, zero_phi_i});
  
     if (beam_shape)
         beam().setFootprintFactor(*beam_shape);
 }

References ISimulation2D::beam(), IAxis::clone(), m_alpha_axis, IAxis::max(), IAxis::min(), Beam::setDirection(), Beam::setFootprintFactor(), Beam::setWavelength(), and IAxis::size().

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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 60 of file DepthProbeSimulation.cpp.

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

◆ 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 66 of file ISimulation2D.cpp.

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

References ISimulation2D::detector(), and IDetector::setRegionOfInterest().

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◆ setTerminalProgressMonitor()

void ISimulation::setTerminalProgressMonitor ( )

inherited

Initializes a progress monitor that prints to stdout.

Definition at line 142 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.

◆ 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 67 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.

◆ simulate()

SimulationResult ISimulation::simulate ( )

inherited

Run a simulation, and return the result.

Runs simulation with possible averaging over parameter distributions; returns result.

Definition at line 154 of file ISimulation.cpp.

 {
     if (!SampleUtils::Multilayer::ContainsCompatibleMaterials(*m_sample))
         throw std::runtime_error("Sample contains incompatible material definitions");
     gsl_set_error_handler_off();
  
     prepareSimulation();
  
     const auto re_sample = reSample::make(*sample(), options(), force_polarized());
  
     const size_t total_size = numberOfElements();
     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 = startIndex(n_batches, current_batch, total_size);
     const size_t batch_size = batchSize(n_batches, current_batch, total_size);
     ASSERT(batch_size);
  
     if (param_combinations == 1)
         runSingleSimulation(re_sample, batch_start, batch_size, 1.);
     else {
         initDistributionHandler();
         for (size_t index = 0; index < param_combinations; ++index) {
             double weight = m_distribution_handler.setParameterValues(index);
             runSingleSimulation(re_sample, batch_start, batch_size, weight);
         }
     }
     moveDataFromCache();
     return pack_result();
 }

References ASSERT, SampleUtils::Multilayer::ContainsCompatibleMaterials(), ISimulation::force_polarized(), DistributionHandler::getTotalNumberOfSamples(), ISimulation::initDistributionHandler(), ISimulation::m_distribution_handler, ISimulation::m_options, ISimulation::m_progress, ISimulation::m_sample, reSample::make(), ISimulation::moveDataFromCache(), ISimulation::numberOfElements(), ISimulation::options(), ISimulation::pack_result(), ISimulation::prepareSimulation(), ISimulation::runSingleSimulation(), ISimulation::sample(), and DistributionHandler::setParameterValues().

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◆ subscribe()

void ISimulation::subscribe ( const std::function< bool(size_t)> & inform )

inherited

Definition at line 135 of file ISimulation.cpp.

 {
     ASSERT(m_progress);
     m_progress->subscribe(inform);
 }

References ASSERT, and ISimulation::m_progress.

◆ unitOfParameter()

std::string ISimulation::unitOfParameter ( ParameterDistribution::WhichParameter which ) const

inherited

Definition at line 209 of file ISimulation.cpp.

 {
     switch (which) {
     case ParameterDistribution::BeamWavelength:
         return "nm";
     case ParameterDistribution::BeamAzimuthalAngle:
     case ParameterDistribution::BeamInclinationAngle:
         return "rad";
     default:
         throw std::runtime_error("ISimulation::unitOfParameter(): missing implementation");
     }
 }

References ParameterDistribution::BeamAzimuthalAngle, ParameterDistribution::BeamInclinationAngle, and ParameterDistribution::BeamWavelength.

◆ updateIntensityMap()

virtual void ISimulation::updateIntensityMap ( )

inlineprotectedvirtualinherited

Reimplemented in OffspecSimulation.

Definition at line 97 of file ISimulation.h.

97 {}

◆ validateParametrization()

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

overrideprivatevirtual

Checks the distribution validity for simulation.

Reimplemented from ISimulation.

Definition at line 193 of file DepthProbeSimulation.cpp.

 {
     const bool zero_mean = par_distr.getDistribution()->mean() == 0.0;
     if (zero_mean)
         return;
     /* TODO come back to this after refactoring of distribution handling
     if (par_distr.whichParameter() == ParameterDistribution::BeamInclinationAngle)
         throw std::runtime_error("Error in DepthProbeSimulation: parameter distribution of "
                                  "beam inclination angle should have zero mean.");
     */
 }

References ParameterDistribution::getDistribution(), and IDistribution1D::mean().

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◆ validityCheck()

void DepthProbeSimulation::validityCheck ( ) const

private

Checks if simulation data is ready for retrieval.

Definition at line 172 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_eles.size();
     if (data_size != alphaAxis()->size())
         throw std::runtime_error(
             "Error in DepthProbeSimulation::validityCheck: length of simulation "
             "element vector is not equal to the number of inclination angles");
 }

References alphaAxis(), m_eles, and ISimulation::sample().

Referenced by pack_result().

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◆ zAxis()

const IAxis * DepthProbeSimulation::zAxis ( ) const

Returns a pointer to z-position axis.

Definition at line 83 of file DepthProbeSimulation.cpp.

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

References m_z_axis.

Referenced by createIntensityData(), generateElements(), and initElementVector().

Member Data Documentation

◆ m_alpha_axis

std::unique_ptr<IAxis> DepthProbeSimulation::m_alpha_axis

private

Definition at line 115 of file DepthProbeSimulation.h.

Referenced by alphaAxis(), createCoordSystem(), incidentAngle(), intensityMapSize(), and setBeamParameters().

◆ m_background

std::shared_ptr<IBackground> ISimulation::m_background

privateinherited

Definition at line 137 of file ISimulation.h.

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

◆ m_beam

std::unique_ptr<Beam> ISimulation2D::m_beam

protectedinherited

Definition at line 98 of file ISimulation2D.h.

Referenced by ISimulation2D::ISimulation2D(), ISimulation2D::beam(), and ISimulation2D::nodeChildren().

◆ m_cache

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

private

Definition at line 118 of file DepthProbeSimulation.h.

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

◆ m_detector

std::unique_ptr<IDetector> ISimulation2D::m_detector

protectedinherited

Definition at line 99 of file ISimulation2D.h.

Referenced by ISimulation2D::ISimulation2D(), ISimulation2D::detector(), ISimulation2D::getDetector(), and ISimulation2D::nodeChildren().

◆ m_detector_context

std::unique_ptr<DetectorContext> ISimulation2D::m_detector_context

privateinherited

Definition at line 104 of file ISimulation2D.h.

Referenced by ISimulation2D::generateElements(), ISimulation2D::numberOfElements(), and ISimulation2D::prepareSimulation().

◆ m_distribution_handler

DistributionHandler ISimulation::m_distribution_handler

protectedinherited

Definition at line 104 of file ISimulation.h.

Referenced by ISimulation::addParameterDistribution(), ISimulation::getDistributions(), ISimulation2D::initDistributionHandler(), and ISimulation::simulate().

◆ m_eles

std::vector<DepthProbeElement> DepthProbeSimulation::m_eles

private

Definition at line 117 of file DepthProbeSimulation.h.

Referenced by addDataToCache(), checkCache(), createComputation(), createIntensityData(), initElementVector(), moveDataFromCache(), normalize(), and validityCheck().

◆ m_options

std::shared_ptr<SimulationOptions> ISimulation::m_options

privateinherited

Definition at line 135 of file ISimulation.h.

Referenced by ISimulation::options(), ISimulation::runSingleSimulation(), and ISimulation::simulate().

◆ m_P

std::vector<double> INode::m_P

protectedinherited

Definition at line 63 of file INode.h.

Referenced by IFootprintFactor::IFootprintFactor(), INode::checkNodeArgs(), IProfile1D::pythonConstructor(), IProfile2D::pythonConstructor(), IFormFactor::pythonConstructor(), Profile1DVoigt::pythonConstructor(), and Profile2DVoigt::pythonConstructor().

◆ m_progress

std::shared_ptr<ProgressHandler> ISimulation::m_progress

privateinherited

Definition at line 136 of file ISimulation.h.

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

◆ m_sample

std::shared_ptr<MultiLayer> ISimulation::m_sample

privateinherited

Definition at line 133 of file ISimulation.h.

Referenced by ISimulation::nodeChildren(), ISimulation::sample(), and ISimulation::simulate().

◆ m_z_axis

std::unique_ptr<IAxis> DepthProbeSimulation::m_z_axis

private

Definition at line 116 of file DepthProbeSimulation.h.

Referenced by createCoordSystem(), intensityMapSize(), setZSpan(), and zAxis().

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

/home/build/builds/o5h8MZZm/0/mlz/bornagain/Sim/Simulation/DepthProbeSimulation.h
/home/build/builds/o5h8MZZm/0/mlz/bornagain/Sim/Simulation/DepthProbeSimulation.cpp

Description

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ DepthProbeSimulation()

◆ ~DepthProbeSimulation()

Member Function Documentation

◆ addBackgroundIntensity()

◆ addDataToCache()

◆ addMask()

◆ addParameterDistribution() [1/2]

◆ addParameterDistribution() [2/2]

◆ alphaAxis()

◆ background()

◆ beam() [1/2]

◆ beam() [2/2]

◆ checkCache()

◆ checkNodeArgs()

◆ className()

◆ createComputation()

◆ createCoordSystem()

◆ createIntensityData()

◆ detector() [1/2]

◆ detector() [2/2]

◆ force_polarized()

◆ generateElements()

◆ getDetector()

◆ getDistributions()

◆ incidentAngle()

◆ initCoordSystem()

◆ initDistributionHandler()

◆ initElementVector()

◆ intensityMapSize()

◆ maskAll()

◆ moveDataFromCache()

◆ nodeChildren()

◆ nodeOffspring()

◆ normalize()

◆ numberOfElements()

◆ options() [1/2]

◆ options() [2/2]

◆ pack_result()

◆ parDefs()

◆ prepareSimulation()

◆ progress()

◆ runSingleSimulation()

◆ sample()

◆ setBackground()

◆ setBeamParameters() [1/2]

◆ setBeamParameters() [2/2]

◆ setRegionOfInterest()

◆ setTerminalProgressMonitor()

◆ setZSpan()

◆ simulate()

◆ subscribe()

◆ unitOfParameter()

◆ updateIntensityMap()

◆ validateParametrization()

◆ validityCheck()

◆ zAxis()

Member Data Documentation

◆ m_alpha_axis

◆ m_background

◆ m_beam

◆ m_cache

◆ m_detector

◆ m_detector_context

◆ m_distribution_handler

◆ m_eles

◆ m_options

◆ m_P

◆ m_progress

◆ m_sample

◆ m_z_axis