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SimplePairFinder Class Template Reference

#include <OpenMS/ANALYSIS/MAPMATCHING/SimplePairFinder.h>

Inheritance diagram for SimplePairFinder:

BasePairFinder FactoryProduct DefaultParamHandler

List of all members.


Detailed Description

template<typename MapT = FeatureMap< >>
class OpenMS::SimplePairFinder< MapT >

This class implements a simple point pair finding algorithm.

It offers a method to determine element pairs in two element maps, given two point maps and a transformation defined for the second element map (if no transformation is given, the pairs are found in the two original maps).

Note:
This pair finder does not offer a method to compute consensus elements given two element maps!
SimplePairFinder Parameters are explained on a separate page.

Public Types

enum  Maps { MODEL = 0, SCENE = 1 }
typedef BasePairFinder< MapT > Base
typedef Base::QualityType QualityType
 Quality.
typedef Base::PositionType PositionType
 Traits type.
typedef Base::IntensityType IntensityType
typedef Base::PointType PointType
 Type of elements considered here.
typedef Base::PointMapType PointMapType
 Container for input elements.
typedef Base::ElementPairType ElementPairType
 Type of element pairs.
typedef Base::ElementPairVectorType ElementPairVectorType
 Container for generated element pairs.
typedef Base::TransformationType TransformationType
 Type of estimated transformation.

Public Member Functions

 SimplePairFinder ()
 Constructor.
virtual ~SimplePairFinder ()
 Destructor.
double getDiffExponent (UInt dim)
 Get diff exponent.
void setDiffExponent (UInt dim, DoubleReal exponent)
 Set diff exponent.
double getDiffIntercept (UInt dim)
 Get diff intercept.
void setDiffIntercept (UInt dim, DoubleReal intercept)
 Set diff intercept.
double getPairMinQuality ()
 Get pair min quality.
void setPairMinQuality (DoubleReal quality)
 Set pair min quality.
virtual void findElementPairs ()
 Find pairs of elements in both maps.

Static Public Member Functions

static BasePairFinder
< PointMapType > * 
create ()
 returns an instance of this class
static const String getProductName ()
 returns the name of this module

Protected Member Functions

virtual void updateMembers_ ()
 This method is used to update extra member variables at the end of the setParam() method.
QualityType similarity_ (PointType const &left, PointType const &right, const PositionType &new_position) const
 Compute the similarity for a pair of elements; larger quality values are better.

Protected Attributes

QualityType diff_exponent_ [2]
 A parameter for similarity_().
QualityType diff_intercept_ [2]
 A parameter for similarity_().
QualityType pair_min_quality_
 A parameter for findElementPairs_().
std::vector< PositionTypetransformed_positions_second_map_
 The vector of transformed element positions of the second map.

Member Typedef Documentation

typedef BasePairFinder< MapT > Base

typedef Base::QualityType QualityType

Quality.

Reimplemented from BasePairFinder.

typedef Base::PositionType PositionType

Traits type.

Position

Reimplemented from BasePairFinder.

typedef Base::IntensityType IntensityType

Reimplemented from BasePairFinder.

typedef Base::PointType PointType

Type of elements considered here.

Reimplemented from BasePairFinder.

typedef Base::PointMapType PointMapType

Container for input elements.

Reimplemented from BasePairFinder.

typedef Base::ElementPairType ElementPairType

Type of element pairs.

Reimplemented from BasePairFinder.

typedef Base::ElementPairVectorType ElementPairVectorType

Container for generated element pairs.

Reimplemented from BasePairFinder.

typedef Base::TransformationType TransformationType

Type of estimated transformation.

Reimplemented from BasePairFinder.


Member Enumeration Documentation

enum Maps

Symbolic names for indices of element maps etc. This should make things more understandable and maintainable.

Enumerator:
MODEL 
SCENE 

Reimplemented from BasePairFinder.


Constructor & Destructor Documentation

SimplePairFinder (  )  [inline]

Constructor.

virtual ~SimplePairFinder (  )  [inline, virtual]

Destructor.


Member Function Documentation

static BasePairFinder<PointMapType>* create (  )  [inline, static]

returns an instance of this class

static const String getProductName (  )  [inline, static]

returns the name of this module

double getDiffExponent ( UInt  dim  )  [inline]

Get diff exponent.

See also:
similarity_()

void setDiffExponent ( UInt  dim,
DoubleReal  exponent 
) [inline]

Set diff exponent.

See also:
similarity_()

double getDiffIntercept ( UInt  dim  )  [inline]

Get diff intercept.

See also:
similarity_()

void setDiffIntercept ( UInt  dim,
DoubleReal  intercept 
) [inline]

Set diff intercept.

See also:
similarity_()

double getPairMinQuality (  )  [inline]

Get pair min quality.

void setPairMinQuality ( DoubleReal  quality  )  [inline]

Set pair min quality.

virtual void findElementPairs (  )  [inline, virtual]

Find pairs of elements in both maps.

For each feature, we find the nearest neighbor in the other map according to

See also:
similarity_(). If two features point at each other, they become a pair.

Implements BasePairFinder.

virtual void updateMembers_ (  )  [inline, protected, virtual]

This method is used to update extra member variables at the end of the setParam() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

QualityType similarity_ ( PointType const &  left,
PointType const &  right,
const PositionType new_position 
) const [inline, protected]

Compute the similarity for a pair of elements; larger quality values are better.

The returned value should express our confidence that one element might possibly be matched to the other.

The similarity is computed as follows.

The parameter diff_exponent_ controls the asymptotic decay rate for large differences. The parameter diff_intercept_ is important for small differences.


Member Data Documentation

QualityType diff_exponent_[2] [protected]

A parameter for similarity_().

QualityType diff_intercept_[2] [protected]

A parameter for similarity_().

QualityType pair_min_quality_ [protected]

A parameter for findElementPairs_().

std::vector<PositionType> transformed_positions_second_map_ [protected]

The vector of transformed element positions of the second map.


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:42 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1