High-level driver for the alignment of Gaussian shapes against a set of reference shapes. More...

#include <GaussianShapeAlignment.hpp>

Public Types
typedef std::shared_ptr< GaussianShapeAlignment >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `GaussianShapeAlignment` instances. More...

typedef ResultList::const_iterator	ConstResultIterator
	A constant iterator over the alignment results. More...

typedef ResultList::iterator	ResultIterator
	A mutable iterator over the alignment results. More...

typedef boost::transform_iterator< GetShapeFunction, ShapeFunctionList::const_iterator >	ConstShapeIterator
	A constant iterator over the reference shapes. More...

typedef GaussianShapeFunctionAlignment::ColorFilterFunction	ColorFilterFunction
	Type of the function used to filter color (pharmacophore) features by type. More...

typedef GaussianShapeFunctionAlignment::ColorMatchFunction	ColorMatchFunction
	Type of the function used to decide whether two color features match. More...

typedef std::function< double(const AlignmentResult &)>	ScoringFunction
	Type of the function used to score an alignment result. More...

typedef std::function< bool(const AlignmentResult &, const AlignmentResult &)>	ResultCompareFunction
	Type of the function used to compare two alignment results. More...

Public Member Functions
	GaussianShapeAlignment ()
	Constructs the `GaussianShapeAlignment` instance. More...

	GaussianShapeAlignment (const GaussianShape &ref_shape)
	Constructs the `GaussianShapeAlignment` instance with ref_shape as the single reference shape. More...

	GaussianShapeAlignment (const GaussianShapeSet &ref_shapes)
	Constructs the `GaussianShapeAlignment` instance with the shapes in ref_shapes as the reference set. More...

	GaussianShapeAlignment (const GaussianShapeAlignment &alignment)=delete

	~GaussianShapeAlignment ()
	Destructor. More...

GaussianShapeAlignment &	operator= (const GaussianShapeAlignment &alignment)=delete

void	setOverlapFunction (GaussianShapeOverlapFunction &func)
	Specifies the Gaussian-shape overlap function used during alignment. More...

GaussianShapeOverlapFunction &	getOverlapFunction () const
	Returns the currently configured overlap function. More...

const FastGaussianShapeOverlapFunction &	getDefaultOverlapFunction () const
	Returns the built-in default overlap function. More...

FastGaussianShapeOverlapFunction &	getDefaultOverlapFunction ()
	Returns the built-in default overlap function. More...

void	setStartGenerator (GaussianShapeAlignmentStartGenerator &gen)
	Specifies the alignment-start generator used to seed the overlap optimization. More...

GaussianShapeAlignmentStartGenerator &	getStartGenerator () const
	Returns the currently configured alignment-start generator. More...

const PrincipalAxesAlignmentStartGenerator &	getDefaultStartGenerator () const
	Returns the built-in principal-axes alignment-start generator. More...

PrincipalAxesAlignmentStartGenerator &	getDefaultStartGenerator ()
	Returns the built-in principal-axes alignment-start generator. More...

void	setColorMatchFunction (const ColorMatchFunction &func)
	Specifies the function used to decide whether two color features match. More...

const ColorMatchFunction &	getColorMatchFunction () const
	Returns the currently configured color-match function. More...

void	setColorFilterFunction (const ColorFilterFunction &func)
	Specifies the function used to filter color features by type. More...

const ColorFilterFunction &	getColorFilterFunction () const
	Returns the currently configured color-filter function. More...

void	setResultCompareFunction (const ResultCompareFunction &func)
	Specifies the function used to compare two alignment results for sorting and filtering. More...

const ResultCompareFunction &	getResultCompareFunction () const
	Returns the currently configured result-compare function. More...

void	setScoringFunction (const ScoringFunction &func)
	Specifies the function used to score an alignment result. More...

const ScoringFunction &	getScoringFunction () const
	Returns the currently configured scoring function. More...

void	setResultSelectionMode (unsigned int mode)
	Sets the alignment-result selection mode (see namespace Shape::AlignmentResultSelectionMode). More...

unsigned int	getResultSelectionMode () const
	Returns the currently configured alignment-result selection mode. More...

void	calcSelfOverlaps (bool calc)
	Specifies whether shape self-overlaps shall be computed for the involved shapes. More...

bool	calcSelfOverlaps () const
	Tells whether shape self-overlaps are computed for the involved shapes. More...

void	calcColorSelfOverlaps (bool calc)
	Specifies whether color self-overlaps shall be computed for the involved shapes. More...

bool	calcColorSelfOverlaps () const
	Tells whether color self-overlaps are computed for the involved shapes. More...

void	calcColorOverlaps (bool calc)
	Specifies whether color overlaps shall be computed in addition to shape overlaps. More...

bool	calcColorOverlaps () const
	Tells whether color overlaps are computed in addition to shape overlaps. More...

void	performAlignment (bool perf_align)
	Specifies whether the actual alignment shall be performed (vs. only computing overlaps in the initial pose). More...

bool	performAlignment () const
	Tells whether the actual alignment is performed. More...

void	optimizeOverlap (bool optimize)
	Specifies whether the overlap shall be optimized iteratively after the initial alignment. More...

bool	optimizeOverlap () const
	Tells whether the overlap is optimized iteratively. More...

void	greedyOptimization (bool greedy)
	Specifies whether the overlap optimization shall use a greedy strategy that stops at the first local maximum. More...

bool	greedyOptimization () const
	Tells whether the overlap optimization uses a greedy strategy. More...

void	setMaxNumOptimizationIterations (std::size_t max_iter)
	Sets the maximum number of overlap-optimization iterations. More...

std::size_t	getMaxNumOptimizationIterations () const
	Returns the currently configured maximum number of overlap-optimization iterations. More...

void	setOptimizationStopGradient (double grad_norm)
	Sets the gradient norm at which the overlap optimization is stopped. More...

double	getOptimizationStopGradient () const
	Returns the currently configured overlap-optimization stop gradient. More...

void	setMaxOrder (std::size_t max_order)
	Sets the maximum order of the Gaussian-product expansion used by the overlap function. More...

std::size_t	getMaxOrder () const
	Returns the currently configured maximum order of the Gaussian-product expansion. More...

void	setDistanceCutoff (double cutoff)
	Sets the distance cutoff for pruning negligible overlap contributions. More...

double	getDistanceCutoff () const
	Returns the currently configured distance cutoff. More...

void	clearReferenceShapes ()
	Removes all reference shapes and reference shape sets. More...

void	addReferenceShape (const GaussianShape &shape, bool new_set=true)
	Adds shape to the reference shapes. More...

void	addReferenceShapes (const GaussianShapeSet &shapes, bool new_set=true)
	Adds the shapes in shapes to the reference shapes. More...

std::size_t	getNumReferenceShapes () const
	Returns the total number of reference shapes. More...

const GaussianShape &	getReferenceShape (std::size_t idx) const
	Returns the reference shape at index idx. More...

ConstShapeIterator	getReferenceShapesBegin () const
	Returns a constant iterator pointing to the first reference shape. More...

ConstShapeIterator	getReferenceShapesEnd () const
	Returns a constant iterator pointing one past the last reference shape. More...

bool	align (const GaussianShape &shape)
	Aligns shape against all reference shapes. More...

bool	align (const GaussianShapeSet &shapes)
	Aligns each shape in shapes against all reference shapes. More...

std::size_t	getNumResults () const
	Returns the number of stored alignment results. More...

const AlignmentResult &	getResult (std::size_t idx) const
	Returns the alignment result at index idx. More...

AlignmentResult &	getResult (std::size_t idx)
	Returns the alignment result at index idx. More...

ConstResultIterator	getResultsBegin () const
	Returns a constant iterator pointing to the first alignment result. More...

ConstResultIterator	getResultsEnd () const
	Returns a constant iterator pointing one past the last alignment result. More...

ResultIterator	getResultsBegin ()
	Returns a mutable iterator pointing to the first alignment result. More...

ResultIterator	getResultsEnd ()
	Returns a mutable iterator pointing one past the last alignment result. More...

Static Public Attributes
static constexpr double	DEF_OPTIMIZATION_STOP_GRADIENT = 1.0
	Default gradient norm at which the overlap optimization is stopped. More...

static constexpr std::size_t	DEF_MAX_OPTIMIZATION_ITERATIONS = 20
	Default maximum number of overlap-optimization iterations. More...

static constexpr std::size_t	DEF_MAX_PRODUCT_ORDER = 1
	Default maximum order of the Gaussian-product expansion. More...

static constexpr unsigned int	DEF_RESULT_SELECTION_MODE = AlignmentResultSelectionMode::BEST_PER_REFERENCE_SET
	Default alignment-result selection mode. More...

static constexpr double	DEF_DISTANCE_CUTOFF = 0.0
	Default distance cutoff for pruning negligible overlap contributions. More...

Detailed Description

High-level driver for the alignment of Gaussian shapes against a set of reference shapes.

The class manages a list of reference Gaussian shapes (organised into reference sets), runs the underlying Shape::GaussianShapeFunctionAlignment for each (reference, aligned) pair, and collects the Shape::AlignmentResult instances filtered according to the configured selection mode and comparator/scoring functions.

Member Typedef Documentation

◆ SharedPointer

typedef std::shared_ptr<GaussianShapeAlignment> CDPL::Shape::GaussianShapeAlignment::SharedPointer

A reference-counted smart pointer [SHPTR] for dynamically allocated GaussianShapeAlignment instances.

◆ ConstResultIterator

typedef ResultList::const_iterator CDPL::Shape::GaussianShapeAlignment::ConstResultIterator

A constant iterator over the alignment results.

◆ ResultIterator

typedef ResultList::iterator CDPL::Shape::GaussianShapeAlignment::ResultIterator

A mutable iterator over the alignment results.

◆ ConstShapeIterator

typedef boost::transform_iterator<GetShapeFunction, ShapeFunctionList::const_iterator> CDPL::Shape::GaussianShapeAlignment::ConstShapeIterator

A constant iterator over the reference shapes.

◆ ColorFilterFunction

typedef GaussianShapeFunctionAlignment::ColorFilterFunction CDPL::Shape::GaussianShapeAlignment::ColorFilterFunction

Type of the function used to filter color (pharmacophore) features by type.

◆ ColorMatchFunction

typedef GaussianShapeFunctionAlignment::ColorMatchFunction CDPL::Shape::GaussianShapeAlignment::ColorMatchFunction

Type of the function used to decide whether two color features match.

◆ ScoringFunction

typedef std::function<double(const AlignmentResult&)> CDPL::Shape::GaussianShapeAlignment::ScoringFunction

Type of the function used to score an alignment result.

◆ ResultCompareFunction

typedef std::function<bool(const AlignmentResult&, const AlignmentResult&)> CDPL::Shape::GaussianShapeAlignment::ResultCompareFunction

Type of the function used to compare two alignment results.

Constructor & Destructor Documentation

◆ GaussianShapeAlignment() [1/4]

CDPL::Shape::GaussianShapeAlignment::GaussianShapeAlignment ( )

Constructs the GaussianShapeAlignment instance.

◆ GaussianShapeAlignment() [2/4]

CDPL::Shape::GaussianShapeAlignment::GaussianShapeAlignment ( const GaussianShape & ref_shape )

Constructs the GaussianShapeAlignment instance with ref_shape as the single reference shape.

Parameters

ref_shape The reference shape.

◆ GaussianShapeAlignment() [3/4]

CDPL::Shape::GaussianShapeAlignment::GaussianShapeAlignment ( const GaussianShapeSet & ref_shapes )

Constructs the GaussianShapeAlignment instance with the shapes in ref_shapes as the reference set.

Parameters

ref_shapes The reference shapes.

◆ GaussianShapeAlignment() [4/4]

CDPL::Shape::GaussianShapeAlignment::GaussianShapeAlignment ( const GaussianShapeAlignment & alignment )

delete

◆ ~GaussianShapeAlignment()

CDPL::Shape::GaussianShapeAlignment::~GaussianShapeAlignment ( )

Destructor.

Member Function Documentation

◆ operator=()

GaussianShapeAlignment& CDPL::Shape::GaussianShapeAlignment::operator= ( const GaussianShapeAlignment & alignment )

delete

◆ setOverlapFunction()

void CDPL::Shape::GaussianShapeAlignment::setOverlapFunction ( GaussianShapeOverlapFunction & func )

Specifies the Gaussian-shape overlap function used during alignment.

Parameters

func	The overlap function.

◆ getOverlapFunction()

GaussianShapeOverlapFunction& CDPL::Shape::GaussianShapeAlignment::getOverlapFunction ( ) const

Returns the currently configured overlap function.

Returns: A reference to the overlap function.

◆ getDefaultOverlapFunction() [1/2]

const FastGaussianShapeOverlapFunction& CDPL::Shape::GaussianShapeAlignment::getDefaultOverlapFunction ( ) const

Returns the built-in default overlap function.

Returns: A const reference to the default overlap function.

◆ getDefaultOverlapFunction() [2/2]

FastGaussianShapeOverlapFunction& CDPL::Shape::GaussianShapeAlignment::getDefaultOverlapFunction ( )

Returns the built-in default overlap function.

Returns: A reference to the default overlap function.

◆ setStartGenerator()

void CDPL::Shape::GaussianShapeAlignment::setStartGenerator ( GaussianShapeAlignmentStartGenerator & gen )

Specifies the alignment-start generator used to seed the overlap optimization.

Parameters

gen	The alignment-start generator.

◆ getStartGenerator()

GaussianShapeAlignmentStartGenerator& CDPL::Shape::GaussianShapeAlignment::getStartGenerator ( ) const

Returns the currently configured alignment-start generator.

Returns: A reference to the alignment-start generator.

◆ getDefaultStartGenerator() [1/2]

const PrincipalAxesAlignmentStartGenerator& CDPL::Shape::GaussianShapeAlignment::getDefaultStartGenerator ( ) const

Returns the built-in principal-axes alignment-start generator.

Returns: A const reference to the default alignment-start generator.

◆ getDefaultStartGenerator() [2/2]

PrincipalAxesAlignmentStartGenerator& CDPL::Shape::GaussianShapeAlignment::getDefaultStartGenerator ( )

Returns the built-in principal-axes alignment-start generator.

Returns: A reference to the default alignment-start generator.

◆ setColorMatchFunction()

void CDPL::Shape::GaussianShapeAlignment::setColorMatchFunction ( const ColorMatchFunction & func )

Specifies the function used to decide whether two color features match.

Parameters

func	The color-match function.

◆ getColorMatchFunction()

const ColorMatchFunction& CDPL::Shape::GaussianShapeAlignment::getColorMatchFunction ( ) const

Returns the currently configured color-match function.

Returns: A const reference to the color-match function.

◆ setColorFilterFunction()

void CDPL::Shape::GaussianShapeAlignment::setColorFilterFunction ( const ColorFilterFunction & func )

Specifies the function used to filter color features by type.

Parameters

func	The color-filter function.

◆ getColorFilterFunction()

const ColorFilterFunction& CDPL::Shape::GaussianShapeAlignment::getColorFilterFunction ( ) const

Returns the currently configured color-filter function.

Returns: A const reference to the color-filter function.

◆ setResultCompareFunction()

void CDPL::Shape::GaussianShapeAlignment::setResultCompareFunction ( const ResultCompareFunction & func )

Specifies the function used to compare two alignment results for sorting and filtering.

Parameters

func	The result-compare function.

◆ getResultCompareFunction()

const ResultCompareFunction& CDPL::Shape::GaussianShapeAlignment::getResultCompareFunction ( ) const

Returns the currently configured result-compare function.

Returns: A const reference to the result-compare function.

◆ setScoringFunction()

void CDPL::Shape::GaussianShapeAlignment::setScoringFunction ( const ScoringFunction & func )

Specifies the function used to score an alignment result.

Parameters

func	The scoring function.

◆ getScoringFunction()

const ScoringFunction& CDPL::Shape::GaussianShapeAlignment::getScoringFunction ( ) const

Returns the currently configured scoring function.

Returns: A const reference to the scoring function.

◆ setResultSelectionMode()

void CDPL::Shape::GaussianShapeAlignment::setResultSelectionMode ( unsigned int mode )

Sets the alignment-result selection mode (see namespace Shape::AlignmentResultSelectionMode).

Parameters

mode	The new result-selection mode.

◆ getResultSelectionMode()

unsigned int CDPL::Shape::GaussianShapeAlignment::getResultSelectionMode ( ) const

Returns the currently configured alignment-result selection mode.

Returns: The result-selection mode (see namespace Shape::AlignmentResultSelectionMode).

◆ calcSelfOverlaps() [1/2]

void CDPL::Shape::GaussianShapeAlignment::calcSelfOverlaps ( bool calc )

Specifies whether shape self-overlaps shall be computed for the involved shapes.

Parameters

calc	`true` to compute shape self-overlaps, and `false` to skip them.

◆ calcSelfOverlaps() [2/2]

bool CDPL::Shape::GaussianShapeAlignment::calcSelfOverlaps ( ) const

Tells whether shape self-overlaps are computed for the involved shapes.

Returns: true if shape self-overlaps are computed, and false otherwise.

◆ calcColorSelfOverlaps() [1/2]

void CDPL::Shape::GaussianShapeAlignment::calcColorSelfOverlaps ( bool calc )

Specifies whether color self-overlaps shall be computed for the involved shapes.

Parameters

calc	`true` to compute color self-overlaps, and `false` to skip them.

◆ calcColorSelfOverlaps() [2/2]

bool CDPL::Shape::GaussianShapeAlignment::calcColorSelfOverlaps ( ) const

Tells whether color self-overlaps are computed for the involved shapes.

Returns: true if color self-overlaps are computed, and false otherwise.

◆ calcColorOverlaps() [1/2]

void CDPL::Shape::GaussianShapeAlignment::calcColorOverlaps ( bool calc )

Specifies whether color overlaps shall be computed in addition to shape overlaps.

Parameters

calc	`true` to compute color overlaps, and `false` to skip them.

◆ calcColorOverlaps() [2/2]

bool CDPL::Shape::GaussianShapeAlignment::calcColorOverlaps ( ) const

Tells whether color overlaps are computed in addition to shape overlaps.

Returns: true if color overlaps are computed, and false otherwise.

◆ performAlignment() [1/2]

void CDPL::Shape::GaussianShapeAlignment::performAlignment ( bool perf_align )

Specifies whether the actual alignment shall be performed (vs. only computing overlaps in the initial pose).

Parameters

perf_align true to perform the alignment, and false to only evaluate the initial pose.

◆ performAlignment() [2/2]

bool CDPL::Shape::GaussianShapeAlignment::performAlignment ( ) const

Tells whether the actual alignment is performed.

Returns: true if the alignment is performed, and false otherwise.

◆ optimizeOverlap() [1/2]

void CDPL::Shape::GaussianShapeAlignment::optimizeOverlap ( bool optimize )

Specifies whether the overlap shall be optimized iteratively after the initial alignment.

Parameters

optimize true to optimize the overlap, and false to skip optimization.

◆ optimizeOverlap() [2/2]

bool CDPL::Shape::GaussianShapeAlignment::optimizeOverlap ( ) const

Tells whether the overlap is optimized iteratively.

Returns: true if the overlap is optimized, and false otherwise.

◆ greedyOptimization() [1/2]

void CDPL::Shape::GaussianShapeAlignment::greedyOptimization ( bool greedy )

Specifies whether the overlap optimization shall use a greedy strategy that stops at the first local maximum.

Parameters

greedy true to use the greedy strategy, and false to use the full optimization.

◆ greedyOptimization() [2/2]

bool CDPL::Shape::GaussianShapeAlignment::greedyOptimization ( ) const

Tells whether the overlap optimization uses a greedy strategy.

Returns: true if the greedy strategy is used, and false otherwise.

◆ setMaxNumOptimizationIterations()

void CDPL::Shape::GaussianShapeAlignment::setMaxNumOptimizationIterations ( std::size_t max_iter )

Sets the maximum number of overlap-optimization iterations.

Parameters

max_iter The new maximum number of iterations.

◆ getMaxNumOptimizationIterations()

std::size_t CDPL::Shape::GaussianShapeAlignment::getMaxNumOptimizationIterations ( ) const

Returns the currently configured maximum number of overlap-optimization iterations.

Returns: The maximum number of iterations.

◆ setOptimizationStopGradient()

void CDPL::Shape::GaussianShapeAlignment::setOptimizationStopGradient ( double grad_norm )

Sets the gradient norm at which the overlap optimization is stopped.

Parameters

grad_norm The new stop gradient norm.

◆ getOptimizationStopGradient()

double CDPL::Shape::GaussianShapeAlignment::getOptimizationStopGradient ( ) const

Returns the currently configured overlap-optimization stop gradient.

Returns: The stop gradient norm.

◆ setMaxOrder()

void CDPL::Shape::GaussianShapeAlignment::setMaxOrder ( std::size_t max_order )

Sets the maximum order of the Gaussian-product expansion used by the overlap function.

Parameters

max_order The new maximum product order.

◆ getMaxOrder()

std::size_t CDPL::Shape::GaussianShapeAlignment::getMaxOrder ( ) const

Returns the currently configured maximum order of the Gaussian-product expansion.

Returns: The maximum product order.

◆ setDistanceCutoff()

void CDPL::Shape::GaussianShapeAlignment::setDistanceCutoff ( double cutoff )

Sets the distance cutoff for pruning negligible overlap contributions.

Parameters

cutoff The new distance cutoff.

◆ getDistanceCutoff()

double CDPL::Shape::GaussianShapeAlignment::getDistanceCutoff ( ) const

Returns the currently configured distance cutoff.

Returns: The distance cutoff.

◆ clearReferenceShapes()

void CDPL::Shape::GaussianShapeAlignment::clearReferenceShapes ( )

Removes all reference shapes and reference shape sets.

◆ addReferenceShape()

void CDPL::Shape::GaussianShapeAlignment::addReferenceShape	(	const GaussianShape &	shape,
		bool	new_set = `true`
	)

Adds shape to the reference shapes.

Parameters

shape	The reference shape.
new_set	If `true`, shape is added to a new reference set; otherwise it is appended to the most recent reference set.

◆ addReferenceShapes()

void CDPL::Shape::GaussianShapeAlignment::addReferenceShapes	(	const GaussianShapeSet &	shapes,
		bool	new_set = `true`
	)

Adds the shapes in shapes to the reference shapes.

Parameters

shapes	The reference shapes.
new_set	If `true`, the shapes are added to a new reference set; otherwise they are appended to the most recent reference set.

◆ getNumReferenceShapes()

std::size_t CDPL::Shape::GaussianShapeAlignment::getNumReferenceShapes ( ) const

Returns the total number of reference shapes.

Returns: The number of reference shapes.

◆ getReferenceShape()

const GaussianShape& CDPL::Shape::GaussianShapeAlignment::getReferenceShape ( std::size_t idx ) const

Returns the reference shape at index idx.

Parameters

idx	The zero-based index of the reference shape.

Returns: A const reference to the reference shape.

Exceptions

Base::IndexError if the number of reference shapes is zero or idx is not in the range [0, getNumReferenceShapes() - 1].

◆ getReferenceShapesBegin()

ConstShapeIterator CDPL::Shape::GaussianShapeAlignment::getReferenceShapesBegin ( ) const

Returns a constant iterator pointing to the first reference shape.

Returns: A constant iterator pointing to the first reference shape.

◆ getReferenceShapesEnd()

ConstShapeIterator CDPL::Shape::GaussianShapeAlignment::getReferenceShapesEnd ( ) const

Returns a constant iterator pointing one past the last reference shape.

Returns: A constant iterator pointing one past the last reference shape.

◆ align() [1/2]

bool CDPL::Shape::GaussianShapeAlignment::align ( const GaussianShape & shape )

Aligns shape against all reference shapes.

Parameters

shape The shape to align.

Returns: true if at least one alignment result was produced, and false otherwise.

◆ align() [2/2]

bool CDPL::Shape::GaussianShapeAlignment::align ( const GaussianShapeSet & shapes )

Aligns each shape in shapes against all reference shapes.

Parameters

shapes The shapes to align.

Returns: true if at least one alignment result was produced, and false otherwise.

◆ getNumResults()

std::size_t CDPL::Shape::GaussianShapeAlignment::getNumResults ( ) const

Returns the number of stored alignment results.

Returns: The number of alignment results.

◆ getResult() [1/2]

const AlignmentResult& CDPL::Shape::GaussianShapeAlignment::getResult ( std::size_t idx ) const

Returns the alignment result at index idx.

Parameters

idx	The zero-based result index.

Returns: A const reference to the result.

Exceptions

Base::IndexError if the number of results is zero or idx is not in the range [0, getNumResults() - 1].

◆ getResult() [2/2]

AlignmentResult& CDPL::Shape::GaussianShapeAlignment::getResult ( std::size_t idx )

Returns the alignment result at index idx.

Parameters

idx	The zero-based result index.

Returns: A reference to the result.

Exceptions

Base::IndexError if the number of results is zero or idx is not in the range [0, getNumResults() - 1].

◆ getResultsBegin() [1/2]

ConstResultIterator CDPL::Shape::GaussianShapeAlignment::getResultsBegin ( ) const

Returns a constant iterator pointing to the first alignment result.

Returns: A constant iterator pointing to the first alignment result.

◆ getResultsEnd() [1/2]

ConstResultIterator CDPL::Shape::GaussianShapeAlignment::getResultsEnd ( ) const

Returns a constant iterator pointing one past the last alignment result.

Returns: A constant iterator pointing one past the last alignment result.

◆ getResultsBegin() [2/2]

ResultIterator CDPL::Shape::GaussianShapeAlignment::getResultsBegin ( )

Returns a mutable iterator pointing to the first alignment result.

Returns: A mutable iterator pointing to the first alignment result.

◆ getResultsEnd() [2/2]

ResultIterator CDPL::Shape::GaussianShapeAlignment::getResultsEnd ( )

Returns a mutable iterator pointing one past the last alignment result.

Returns: A mutable iterator pointing one past the last alignment result.

Member Data Documentation

◆ DEF_OPTIMIZATION_STOP_GRADIENT

constexpr double CDPL::Shape::GaussianShapeAlignment::DEF_OPTIMIZATION_STOP_GRADIENT = 1.0

staticconstexpr

Default gradient norm at which the overlap optimization is stopped.

◆ DEF_MAX_OPTIMIZATION_ITERATIONS

constexpr std::size_t CDPL::Shape::GaussianShapeAlignment::DEF_MAX_OPTIMIZATION_ITERATIONS = 20

staticconstexpr

Default maximum number of overlap-optimization iterations.

◆ DEF_MAX_PRODUCT_ORDER

constexpr std::size_t CDPL::Shape::GaussianShapeAlignment::DEF_MAX_PRODUCT_ORDER = 1

staticconstexpr

Default maximum order of the Gaussian-product expansion.

◆ DEF_RESULT_SELECTION_MODE

constexpr unsigned int CDPL::Shape::GaussianShapeAlignment::DEF_RESULT_SELECTION_MODE = AlignmentResultSelectionMode::BEST_PER_REFERENCE_SET

staticconstexpr

Default alignment-result selection mode.

◆ DEF_DISTANCE_CUTOFF

constexpr double CDPL::Shape::GaussianShapeAlignment::DEF_DISTANCE_CUTOFF = 0.0

staticconstexpr

Default distance cutoff for pruning negligible overlap contributions.

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

GaussianShapeAlignment.hpp

Public Types

Public Member Functions

Static Public Attributes

Detailed Description

Member Typedef Documentation

◆ SharedPointer

◆ ConstResultIterator

◆ ResultIterator

◆ ConstShapeIterator

◆ ColorFilterFunction

◆ ColorMatchFunction

◆ ScoringFunction

◆ ResultCompareFunction

Constructor & Destructor Documentation

◆ GaussianShapeAlignment() [1/4]

◆ GaussianShapeAlignment() [2/4]

◆ GaussianShapeAlignment() [3/4]

◆ GaussianShapeAlignment() [4/4]

◆ ~GaussianShapeAlignment()

Member Function Documentation

◆ operator=()

◆ setOverlapFunction()

◆ getOverlapFunction()

◆ getDefaultOverlapFunction() [1/2]

◆ getDefaultOverlapFunction() [2/2]

◆ setStartGenerator()

◆ getStartGenerator()

◆ getDefaultStartGenerator() [1/2]

◆ getDefaultStartGenerator() [2/2]

◆ setColorMatchFunction()

◆ getColorMatchFunction()

◆ setColorFilterFunction()

◆ getColorFilterFunction()

◆ setResultCompareFunction()

◆ getResultCompareFunction()

◆ setScoringFunction()

◆ getScoringFunction()

◆ setResultSelectionMode()

◆ getResultSelectionMode()

◆ calcSelfOverlaps() [1/2]

◆ calcSelfOverlaps() [2/2]

◆ calcColorSelfOverlaps() [1/2]

◆ calcColorSelfOverlaps() [2/2]

◆ calcColorOverlaps() [1/2]

◆ calcColorOverlaps() [2/2]

◆ performAlignment() [1/2]

◆ performAlignment() [2/2]

◆ optimizeOverlap() [1/2]

◆ optimizeOverlap() [2/2]

◆ greedyOptimization() [1/2]

◆ greedyOptimization() [2/2]

◆ setMaxNumOptimizationIterations()

◆ getMaxNumOptimizationIterations()

◆ setOptimizationStopGradient()

◆ getOptimizationStopGradient()

◆ setMaxOrder()

◆ getMaxOrder()

◆ setDistanceCutoff()

◆ getDistanceCutoff()

◆ clearReferenceShapes()

◆ addReferenceShape()

◆ addReferenceShapes()

◆ getNumReferenceShapes()

◆ getReferenceShape()

◆ getReferenceShapesBegin()

◆ getReferenceShapesEnd()

◆ align() [1/2]

◆ align() [2/2]

◆ getNumResults()

◆ getResult() [1/2]

◆ getResult() [2/2]

◆ getResultsBegin() [1/2]

◆ getResultsEnd() [1/2]

◆ getResultsBegin() [2/2]

◆ getResultsEnd() [2/2]

Member Data Documentation

◆ DEF_OPTIMIZATION_STOP_GRADIENT

◆ DEF_MAX_OPTIMIZATION_ITERATIONS

◆ DEF_MAX_PRODUCT_ORDER

◆ DEF_RESULT_SELECTION_MODE