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

Inheritance diagram for CDPL.Shape.GaussianShapeAlignment:

Public Member Functions
None	__init__ ()
	Constructs the `GaussianShapeAlignment` instance.

None	__init__ (GaussianShape ref_shape)
	Constructs the `GaussianShapeAlignment` instance with ref_shape as the single reference shape. More...

None	__init__ (GaussianShapeSet ref_shapes)
	Constructs the `GaussianShapeAlignment` instance with the shapes in ref_shapes as the reference set. More...

int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...

None	setOverlapFunction (GaussianShapeOverlapFunction func)
	Specifies the Gaussian-shape overlap function used during alignment. More...

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

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

None	setStartGenerator (GaussianShapeAlignmentStartGenerator gen)
	Specifies the alignment-start generator used to seed the overlap optimization. More...

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

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

None	setColorMatchFunction (Pharm.BoolSizeType2Functor func)
	Specifies the function used to decide whether two color features match. More...

Pharm.BoolSizeType2Functor	getColorMatchFunction ()
	Returns the currently configured color-match function. More...

None	setColorFilterFunction (BoolSizeTypeFunctor func)
	Specifies the function used to filter color features by type. More...

BoolSizeTypeFunctor	getColorFilterFunction ()
	Returns the currently configured color-filter function. More...

None	setResultCompareFunction (BoolAlignmentResult2Functor func)
	Specifies the function used to compare two alignment results for sorting and filtering. More...

BoolAlignmentResult2Functor	getResultCompareFunction ()
	Returns the currently configured result-compare function. More...

None	setScoringFunction (DoubleAlignmentResultFunctor func)
	Specifies the function used to score an alignment result. More...

DoubleAlignmentResultFunctor	getScoringFunction ()
	Returns the currently configured scoring function. More...

None	setResultSelectionMode (int mode)
	Sets the alignment-result selection mode (see namespace Shape.AlignmentResultSelectionMode). More...

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

None	setMaxNumOptimizationIterations (int max_iter)
	Sets the maximum number of overlap-optimization iterations. More...

int	getMaxNumOptimizationIterations ()
	Returns the currently configured maximum number of overlap-optimization iterations. More...

None	setOptimizationStopGradient (float grad_norm)
	Sets the gradient norm at which the overlap optimization is stopped. More...

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

None	performAlignment (bool perf_align)
	Specifies whether the actual alignment shall be performed (vs. More...

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

None	optimizeOverlap (bool optimize)
	Specifies whether the overlap shall be optimized iteratively after the initial alignment. More...

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

None	greedyOptimization (bool greedy)
	Specifies whether the overlap optimization shall use a greedy strategy that stops at the first local maximum. More...

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

None	calcColorOverlaps (bool calc)
	Specifies whether color overlaps shall be computed in addition to shape overlaps. More...

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

None	calcSelfOverlaps (bool calc)
	Specifies whether shape self-overlaps shall be computed for the involved shapes. More...

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

None	calcColorSelfOverlaps (bool calc)
	Specifies whether color self-overlaps shall be computed for the involved shapes. More...

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

None	setMaxOrder (int max_order)
	Sets the maximum order of the Gaussian-product expansion used by the overlap function. More...

int	getMaxOrder ()
	Returns the currently configured maximum order of the Gaussian-product expansion. More...

None	setDistanceCutoff (float cutoff)
	Sets the distance cutoff for pruning negligible overlap contributions. More...

float	getDistanceCutoff ()
	Returns the currently configured distance cutoff. More...

None	clearReferenceShapes ()
	Removes all reference shapes and reference shape sets.

None	addReferenceShape (GaussianShape shape, bool new_set=True)
	Adds shape to the reference shapes. More...

None	addReferenceShapes (GaussianShapeSet shapes, bool new_set=True)
	Adds the shapes in shapes to the reference shapes. More...

int	getNumReferenceShapes ()
	Returns the total number of reference shapes. More...

GaussianShape	getReferenceShape (int idx)
	Returns the reference shape at index idx. More...

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

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

int	getNumResults ()
	Returns the number of stored alignment results. More...

AlignmentResult	getResult (int idx)
	Returns the alignment result at index idx. More...

int	__len__ ()

AlignmentResult	__getitem__ (int idx)

Static Public Attributes
float	DEF_OPTIMIZATION_STOP_GRADIENT = 1.0
	Default gradient norm at which the overlap optimization is stopped.

int	DEF_MAX_OPTIMIZATION_ITERATIONS = 20
	Default maximum number of overlap-optimization iterations.

int	DEF_MAX_PRODUCT_ORDER = 1
	Default maximum order of the Gaussian-product expansion.

float	DEF_DISTANCE_CUTOFF = 0.0
	Default distance cutoff for pruning negligible overlap contributions.

int	DEF_RESULT_SELECTION_MODE = 3
	Default alignment-result selection mode.

Properties
	objectID = property(getObjectID)

	numResults = property(getNumResults)

	overlapFunction = property(getOverlapFunction, setOverlapFunction)

	defaultOverlapFunction = property(getDefaultOverlapFunction)

	startGenerator = property(getStartGenerator, setStartGenerator)

	defaultStartGenerator = property(getDefaultStartGenerator)

	colorMatchFunction = property(getColorMatchFunction, setColorMatchFunction)

	colorFilterFunction = property(getColorFilterFunction, setColorFilterFunction)

	resultCompareFunction = property(getResultCompareFunction, setResultCompareFunction)

	scoringFunction = property(getScoringFunction, setScoringFunction)

	resultSelectionMode = property(getResultSelectionMode, setResultSelectionMode)

	maxNumOptIterations = property(getMaxNumOptimizationIterations, setMaxNumOptimizationIterations)

	optStopGradient = property(getOptimizationStopGradient, setOptimizationStopGradient)

	perfAlignment = property(performAlignment, performAlignment)

	optOverlap = property(optimizeOverlap, optimizeOverlap)

	greedyOpt = property(greedyOptimization, greedyOptimization)

	selfOverlaps = property(calcSelfOverlaps, calcSelfOverlaps)

	colorSelfOverlaps = property(calcColorSelfOverlaps, calcColorSelfOverlaps)

	colorOverlaps = property(calcColorOverlaps, calcColorOverlaps)

	maxOrder = property(getMaxOrder, setMaxOrder)

	distCutoff = property(getDistanceCutoff, setDistanceCutoff)

	numReferenceShapes = property(getNumReferenceShapes)

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.

Constructor & Destructor Documentation

◆ init() [1/2]

None CDPL.Shape.GaussianShapeAlignment.__init__ ( GaussianShape ref_shape )

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

Parameters

ref_shape The reference shape.

◆ init() [2/2]

None CDPL.Shape.GaussianShapeAlignment.__init__ ( GaussianShapeSet ref_shapes )

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

Parameters

ref_shapes The reference shapes.

Member Function Documentation

◆ getObjectID()

int CDPL.Shape.GaussianShapeAlignment.getObjectID ( )

Returns the numeric identifier (ID) of the wrapped C++ class instance.

Different Python GaussianShapeAlignment instances may reference the same underlying C++ class instance. The commonly used Python expression a is not b thus cannot tell reliably whether the two GaussianShapeAlignment instances a and b reference different C++ objects. The numeric identifier returned by this method allows to correctly implement such an identity test via the simple expression a.getObjectID() != b.getObjectID().

Returns: The numeric ID of the internally referenced C++ class instance.

◆ setOverlapFunction()

None 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 ( )

Returns the currently configured overlap function.

Returns: A reference to the overlap function.

◆ getDefaultOverlapFunction()

FastGaussianShapeOverlapFunction CDPL.Shape.GaussianShapeAlignment.getDefaultOverlapFunction ( )

Returns the built-in default overlap function.

Returns: A reference to the default overlap function.

◆ setStartGenerator()

None 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 ( )

Returns the currently configured alignment-start generator.

Returns: A reference to the alignment-start generator.

◆ getDefaultStartGenerator()

PrincipalAxesAlignmentStartGenerator CDPL.Shape.GaussianShapeAlignment.getDefaultStartGenerator ( )

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

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

◆ setColorMatchFunction()

None CDPL.Shape.GaussianShapeAlignment.setColorMatchFunction ( Pharm.BoolSizeType2Functor func )

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

Parameters

func	The color-match function.

◆ getColorMatchFunction()

Pharm.BoolSizeType2Functor CDPL.Shape.GaussianShapeAlignment.getColorMatchFunction ( )

Returns the currently configured color-match function.

Returns: A reference to the color-match function.

◆ setColorFilterFunction()

None CDPL.Shape.GaussianShapeAlignment.setColorFilterFunction ( BoolSizeTypeFunctor func )

Specifies the function used to filter color features by type.

Parameters

func	The color-filter function.

◆ getColorFilterFunction()

BoolSizeTypeFunctor CDPL.Shape.GaussianShapeAlignment.getColorFilterFunction ( )

Returns the currently configured color-filter function.

Returns: A reference to the color-filter function.

◆ setResultCompareFunction()

None CDPL.Shape.GaussianShapeAlignment.setResultCompareFunction ( BoolAlignmentResult2Functor func )

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

Parameters

func	The result-compare function.

◆ getResultCompareFunction()

BoolAlignmentResult2Functor CDPL.Shape.GaussianShapeAlignment.getResultCompareFunction ( )

Returns the currently configured result-compare function.

Returns: A reference to the result-compare function.

◆ setScoringFunction()

None CDPL.Shape.GaussianShapeAlignment.setScoringFunction ( DoubleAlignmentResultFunctor func )

Specifies the function used to score an alignment result.

Parameters

func	The scoring function.

◆ getScoringFunction()

DoubleAlignmentResultFunctor CDPL.Shape.GaussianShapeAlignment.getScoringFunction ( )

Returns the currently configured scoring function.

Returns: A reference to the scoring function.

◆ setResultSelectionMode()

None CDPL.Shape.GaussianShapeAlignment.setResultSelectionMode ( int mode )

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

Parameters

mode	The new result-selection mode.

◆ getResultSelectionMode()

int CDPL.Shape.GaussianShapeAlignment.getResultSelectionMode ( )

Returns the currently configured alignment-result selection mode.

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

◆ setMaxNumOptimizationIterations()

None CDPL.Shape.GaussianShapeAlignment.setMaxNumOptimizationIterations ( int max_iter )

Sets the maximum number of overlap-optimization iterations.

Parameters

max_iter The new maximum number of iterations.

◆ getMaxNumOptimizationIterations()

int CDPL.Shape.GaussianShapeAlignment.getMaxNumOptimizationIterations ( )

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

Returns: The maximum number of iterations.

◆ setOptimizationStopGradient()

None CDPL.Shape.GaussianShapeAlignment.setOptimizationStopGradient ( float grad_norm )

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

Parameters

grad_norm The new stop gradient norm.

◆ getOptimizationStopGradient()

float CDPL.Shape.GaussianShapeAlignment.getOptimizationStopGradient ( )

Returns the currently configured overlap-optimization stop gradient.

Returns: The stop gradient norm.

◆ performAlignment() [1/2]

None 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 ( )

Tells whether the actual alignment is performed.

Returns: True if the alignment is performed, and False otherwise.

◆ optimizeOverlap() [1/2]

None 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 ( )

Tells whether the overlap is optimized iteratively.

Returns: True if the overlap is optimized, and False otherwise.

◆ greedyOptimization() [1/2]

None 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 ( )

Tells whether the overlap optimization uses a greedy strategy.

Returns: True if the greedy strategy is used, and False otherwise.

◆ calcColorOverlaps() [1/2]

None 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 ( )

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

Returns: True if color overlaps are computed, and False otherwise.

◆ calcSelfOverlaps() [1/2]

None 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 ( )

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]

None 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 ( )

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

Returns: True if color self-overlaps are computed, and False otherwise.

◆ setMaxOrder()

None CDPL.Shape.GaussianShapeAlignment.setMaxOrder ( int 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()

int CDPL.Shape.GaussianShapeAlignment.getMaxOrder ( )

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

Returns: The maximum product order.

◆ setDistanceCutoff()

None CDPL.Shape.GaussianShapeAlignment.setDistanceCutoff ( float cutoff )

Sets the distance cutoff for pruning negligible overlap contributions.

Parameters

cutoff The new distance cutoff.

◆ getDistanceCutoff()

float CDPL.Shape.GaussianShapeAlignment.getDistanceCutoff ( )

Returns the currently configured distance cutoff.

Returns: The distance cutoff.

◆ addReferenceShape()

None CDPL.Shape.GaussianShapeAlignment.addReferenceShape	(	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()

None CDPL.Shape.GaussianShapeAlignment.addReferenceShapes	(	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()

int CDPL.Shape.GaussianShapeAlignment.getNumReferenceShapes ( )

Returns the total number of reference shapes.

Returns: The number of reference shapes.

◆ getReferenceShape()

GaussianShape CDPL.Shape.GaussianShapeAlignment.getReferenceShape ( int idx )

Returns the reference shape at index idx.

Parameters

idx	The zero-based index of the reference shape.

Returns: A 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].

◆ align() [1/2]

bool CDPL.Shape.GaussianShapeAlignment.align ( 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 ( 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()

int CDPL.Shape.GaussianShapeAlignment.getNumResults ( )

Returns the number of stored alignment results.

Returns: The number of alignment results.

◆ getResult()

AlignmentResult CDPL.Shape.GaussianShapeAlignment.getResult ( int 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].

◆ len()

int CDPL.Shape.GaussianShapeAlignment.__len__ ( )

Returns

◆ getitem()

AlignmentResult CDPL.Shape.GaussianShapeAlignment.__getitem__ ( int idx )

Parameters

idx

Returns

Public Member Functions

Static Public Attributes

Properties

Detailed Description

Constructor & Destructor Documentation

◆ __init__() [1/2]

◆ __init__() [2/2]

Member Function Documentation

◆ getObjectID()

◆ setOverlapFunction()

◆ getOverlapFunction()

◆ getDefaultOverlapFunction()

◆ setStartGenerator()

◆ getStartGenerator()

◆ getDefaultStartGenerator()

◆ setColorMatchFunction()

◆ getColorMatchFunction()

◆ setColorFilterFunction()

◆ getColorFilterFunction()

◆ setResultCompareFunction()

◆ getResultCompareFunction()

◆ setScoringFunction()

◆ getScoringFunction()

◆ setResultSelectionMode()

◆ getResultSelectionMode()

◆ setMaxNumOptimizationIterations()

◆ getMaxNumOptimizationIterations()

◆ setOptimizationStopGradient()

◆ getOptimizationStopGradient()

◆ performAlignment() [1/2]

◆ performAlignment() [2/2]

◆ optimizeOverlap() [1/2]

◆ optimizeOverlap() [2/2]

◆ greedyOptimization() [1/2]

◆ greedyOptimization() [2/2]

◆ calcColorOverlaps() [1/2]

◆ calcColorOverlaps() [2/2]

◆ calcSelfOverlaps() [1/2]

◆ calcSelfOverlaps() [2/2]

◆ calcColorSelfOverlaps() [1/2]

◆ calcColorSelfOverlaps() [2/2]

◆ setMaxOrder()

◆ getMaxOrder()

◆ setDistanceCutoff()

◆ getDistanceCutoff()

◆ addReferenceShape()

◆ addReferenceShapes()

◆ getNumReferenceShapes()

◆ getReferenceShape()

◆ align() [1/2]

◆ align() [2/2]

◆ getNumResults()

◆ getResult()

◆ __len__()

◆ __getitem__()

◆ init() [1/2]

◆ init() [2/2]

◆ len()

◆ getitem()