Chemical Data Processing Library Python API - Version 1.1.1
Public Member Functions | Static Public Attributes | Properties | List of all members
CDPL.Shape.GaussianShapeAlignment Class Reference
+ Inheritance diagram for CDPL.Shape.GaussianShapeAlignment:

Public Member Functions

None __init__ ()
 Initializes the GaussianShapeAlignment instance.
 
None __init__ (GaussianShape ref_shape)
 Initializes the GaussianShapeAlignment instance. More...
 
None __init__ (GaussianShapeSet ref_shapes)
 Initializes the GaussianShapeAlignment instance. More...
 
int getObjectID ()
 Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
 
None setOverlapFunction (GaussianShapeOverlapFunction func)
 
GaussianShapeOverlapFunction getOverlapFunction ()
 
FastGaussianShapeOverlapFunction getDefaultOverlapFunction ()
 
None setStartGenerator (GaussianShapeAlignmentStartGenerator gen)
 
GaussianShapeAlignmentStartGenerator getStartGenerator ()
 
PrincipalAxesAlignmentStartGenerator getDefaultStartGenerator ()
 
None setColorMatchFunction (Pharm.BoolSizeType2Functor func)
 
Pharm.BoolSizeType2Functor getColorMatchFunction ()
 
None setColorFilterFunction (BoolSizeTypeFunctor func)
 
BoolSizeTypeFunctor getColorFilterFunction ()
 
None setResultCompareFunction (BoolAlignmentResult2Functor func)
 
BoolAlignmentResult2Functor getResultCompareFunction ()
 
None setScoringFunction (DoubleAlignmentResultFunctor func)
 
DoubleAlignmentResultFunctor getScoringFunction ()
 
None setResultSelectionMode (int mode)
 
int getResultSelectionMode ()
 
None setMaxNumOptimizationIterations (int max_iter)
 
int getMaxNumOptimizationIterations ()
 
None setOptimizationStopGradient (float grad_norm)
 
float getOptimizationStopGradient ()
 
None performAlignment (bool perf_align)
 
bool performAlignment ()
 
None optimizeOverlap (bool optimize)
 
bool optimizeOverlap ()
 
None greedyOptimization (bool greedy)
 
bool greedyOptimization ()
 
None calcColorOverlaps (bool calc)
 
bool calcColorOverlaps ()
 
None calcSelfOverlaps (bool calc)
 
bool calcSelfOverlaps ()
 
None calcColorSelfOverlaps (bool calc)
 
bool calcColorSelfOverlaps ()
 
None setMaxOrder (int max_order)
 
int getMaxOrder ()
 
None setDistanceCutoff (float cutoff)
 
float getDistanceCutoff ()
 
None clearReferenceShapes ()
 
None addReferenceShape (GaussianShape shape, bool new_set=True)
 
None addReferenceShapes (GaussianShapeSet shapes, bool new_set=True)
 
int getNumReferenceShapes ()
 
GaussianShape getReferenceShape (int idx)
 
bool align (GaussianShape shape)
 
bool align (GaussianShapeSet shapes)
 
int getNumResults ()
 
AlignmentResult getResult (int idx)
 
int __len__ ()
 
AlignmentResult __getitem__ (int idx)
 

Static Public Attributes

float DEF_OPTIMIZATION_STOP_GRADIENT = 1.0
 
int DEF_MAX_OPTIMIZATION_ITERATIONS = 20
 
int DEF_MAX_PRODUCT_ORDER = 1
 
float DEF_DISTANCE_CUTOFF = 0.0
 
int DEF_RESULT_SELECTION_MODE = 3
 

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)
 

Constructor & Destructor Documentation

◆ __init__() [1/2]

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

Initializes the GaussianShapeAlignment instance.

Parameters
ref_shape

◆ __init__() [2/2]

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

Initializes the GaussianShapeAlignment instance.

Parameters
ref_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)
Parameters
func

◆ getOverlapFunction()

GaussianShapeOverlapFunction CDPL.Shape.GaussianShapeAlignment.getOverlapFunction ( )
Returns

◆ getDefaultOverlapFunction()

FastGaussianShapeOverlapFunction CDPL.Shape.GaussianShapeAlignment.getDefaultOverlapFunction ( )
Returns

◆ setStartGenerator()

None CDPL.Shape.GaussianShapeAlignment.setStartGenerator ( GaussianShapeAlignmentStartGenerator  gen)
Parameters
gen

◆ getStartGenerator()

GaussianShapeAlignmentStartGenerator CDPL.Shape.GaussianShapeAlignment.getStartGenerator ( )
Returns

◆ getDefaultStartGenerator()

PrincipalAxesAlignmentStartGenerator CDPL.Shape.GaussianShapeAlignment.getDefaultStartGenerator ( )
Returns

◆ setColorMatchFunction()

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

◆ getColorMatchFunction()

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

◆ setColorFilterFunction()

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

◆ getColorFilterFunction()

BoolSizeTypeFunctor CDPL.Shape.GaussianShapeAlignment.getColorFilterFunction ( )
Returns

◆ setResultCompareFunction()

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

◆ getResultCompareFunction()

BoolAlignmentResult2Functor CDPL.Shape.GaussianShapeAlignment.getResultCompareFunction ( )
Returns

◆ setScoringFunction()

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

◆ getScoringFunction()

DoubleAlignmentResultFunctor CDPL.Shape.GaussianShapeAlignment.getScoringFunction ( )
Returns

◆ setResultSelectionMode()

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

◆ getResultSelectionMode()

int CDPL.Shape.GaussianShapeAlignment.getResultSelectionMode ( )
Returns

◆ setMaxNumOptimizationIterations()

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

◆ getMaxNumOptimizationIterations()

int CDPL.Shape.GaussianShapeAlignment.getMaxNumOptimizationIterations ( )
Returns

◆ setOptimizationStopGradient()

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

◆ getOptimizationStopGradient()

float CDPL.Shape.GaussianShapeAlignment.getOptimizationStopGradient ( )
Returns

◆ performAlignment() [1/2]

None CDPL.Shape.GaussianShapeAlignment.performAlignment ( bool  perf_align)
Parameters
perf_align

◆ performAlignment() [2/2]

bool CDPL.Shape.GaussianShapeAlignment.performAlignment ( )
Returns

◆ optimizeOverlap() [1/2]

None CDPL.Shape.GaussianShapeAlignment.optimizeOverlap ( bool  optimize)
Parameters
optimize

◆ optimizeOverlap() [2/2]

bool CDPL.Shape.GaussianShapeAlignment.optimizeOverlap ( )
Returns

◆ greedyOptimization() [1/2]

None CDPL.Shape.GaussianShapeAlignment.greedyOptimization ( bool  greedy)
Parameters
greedy

◆ greedyOptimization() [2/2]

bool CDPL.Shape.GaussianShapeAlignment.greedyOptimization ( )
Returns

◆ calcColorOverlaps() [1/2]

None CDPL.Shape.GaussianShapeAlignment.calcColorOverlaps ( bool  calc)
Parameters
calc

◆ calcColorOverlaps() [2/2]

bool CDPL.Shape.GaussianShapeAlignment.calcColorOverlaps ( )
Returns

◆ calcSelfOverlaps() [1/2]

None CDPL.Shape.GaussianShapeAlignment.calcSelfOverlaps ( bool  calc)
Parameters
calc

◆ calcSelfOverlaps() [2/2]

bool CDPL.Shape.GaussianShapeAlignment.calcSelfOverlaps ( )
Returns

◆ calcColorSelfOverlaps() [1/2]

None CDPL.Shape.GaussianShapeAlignment.calcColorSelfOverlaps ( bool  calc)
Parameters
calc

◆ calcColorSelfOverlaps() [2/2]

bool CDPL.Shape.GaussianShapeAlignment.calcColorSelfOverlaps ( )
Returns

◆ setMaxOrder()

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

◆ getMaxOrder()

int CDPL.Shape.GaussianShapeAlignment.getMaxOrder ( )
Returns

◆ setDistanceCutoff()

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

◆ getDistanceCutoff()

float CDPL.Shape.GaussianShapeAlignment.getDistanceCutoff ( )
Returns

◆ addReferenceShape()

None CDPL.Shape.GaussianShapeAlignment.addReferenceShape ( GaussianShape  shape,
bool   new_set = True 
)
Parameters
shape
new_set

◆ addReferenceShapes()

None CDPL.Shape.GaussianShapeAlignment.addReferenceShapes ( GaussianShapeSet  shapes,
bool   new_set = True 
)
Parameters
shapes
new_set

◆ getNumReferenceShapes()

int CDPL.Shape.GaussianShapeAlignment.getNumReferenceShapes ( )
Returns

◆ getReferenceShape()

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

◆ align() [1/2]

bool CDPL.Shape.GaussianShapeAlignment.align ( GaussianShape  shape)
Parameters
shape
Returns

◆ align() [2/2]

bool CDPL.Shape.GaussianShapeAlignment.align ( GaussianShapeSet  shapes)
Parameters
shapes
Returns

◆ getNumResults()

int CDPL.Shape.GaussianShapeAlignment.getNumResults ( )
Returns

◆ getResult()

AlignmentResult CDPL.Shape.GaussianShapeAlignment.getResult ( int  idx)
Parameters
idx
Returns

◆ __len__()

int CDPL.Shape.GaussianShapeAlignment.__len__ ( )
Returns

◆ __getitem__()

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