Package org.anchoranalysis.mpp.feature.energy.scheme

Class EnergyScheme

Object

org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme

public class EnergyScheme
extends Object

The energy for a feature-list as factorized into different cliques.

elemInd: individual terms of clique-size==1 f_1(x) elemPair: pairwise terms of clique-size==2 f_2(x,y) elemAll: terms that include every item in the set f_all(x_1,x_2,....x_n) for all n

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
EnergyScheme(FeatureList<FeatureInputSingleMemo> elemInd, FeatureList<FeatureInputPairMemo> elemPair, FeatureList<FeatureInputAllMemo> elemAll, RegionMap regionMap, AddCriteriaPair pairAddCriteria)	Creates an energy scheme with the specified features and region map.
EnergyScheme(FeatureList<FeatureInputSingleMemo> elemInd, FeatureList<FeatureInputPairMemo> elemPair, FeatureList<FeatureInputAllMemo> elemAll, RegionMap regionMap, AddCriteriaPair pairAddCriteria, Optional<org.anchoranalysis.bean.shared.dictionary.DictionaryProvider> dictionary, List<NamedBean<Feature<org.anchoranalysis.image.feature.input.FeatureInputStack>>> listImageFeatures)	Creates an energy scheme with the specified features, region map, and additional options.

Method Summary

Modifier and Type	Method	Description
Dictionary	createDictionary()	Creates and returns the associated Dictionary or an empty dictionary if none is associated.
FeatureList<FeatureInputAllMemo>	getElemAllAsFeatureList()	Gets the feature list for all elements together.
<T extends FeatureInput> FeatureList<T>	getElemByCliqueSize(int cliqueSize)	Gets the feature list for a specific clique size.
FeatureList<FeatureInputSingleMemo>	getElemIndAsFeatureList()	Gets the feature list for individual elements.
FeatureList<FeatureInputPairMemo>	getElemPairAsFeatureList()	Gets the feature list for pairs of elements.
List<NamedBean<Feature<org.anchoranalysis.image.feature.input.FeatureInputStack>>>	getListImageFeatures()	Gets the list of image features to be calculated first.
AddCriteriaPair	getPairAddCriteria()	Gets the criteria for adding pairs to the energy calculation.
RegionMap	getRegionMap()	Gets the region map used in the energy scheme.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

EnergyScheme

public EnergyScheme(FeatureList<FeatureInputSingleMemo> elemInd, FeatureList<FeatureInputPairMemo> elemPair, FeatureList<FeatureInputAllMemo> elemAll, RegionMap regionMap, AddCriteriaPair pairAddCriteria) throws CreateException

Creates an energy scheme with the specified features and region map.

Parameters:

elemInd - features for individual elements

elemPair - features for pairs of elements

elemAll - features for all elements together

regionMap - the region map to use

pairAddCriteria - criteria for adding pairs

Throws:

CreateException - if the energy scheme cannot be created

EnergyScheme

public EnergyScheme(FeatureList<FeatureInputSingleMemo> elemInd, FeatureList<FeatureInputPairMemo> elemPair, FeatureList<FeatureInputAllMemo> elemAll, RegionMap regionMap, AddCriteriaPair pairAddCriteria, Optional<org.anchoranalysis.bean.shared.dictionary.DictionaryProvider> dictionary, List<NamedBean<Feature<org.anchoranalysis.image.feature.input.FeatureInputStack>>> listImageFeatures) throws CreateException

Creates an energy scheme with the specified features, region map, and additional options.

Parameters:

elemInd - features for individual elements

elemPair - features for pairs of elements

elemAll - features for all elements together

regionMap - the region map to use

pairAddCriteria - criteria for adding pairs

dictionary - optional dictionary provider

listImageFeatures - list of image features to be calculated first

Throws:

CreateException - if the energy scheme cannot be created

Method Details

createDictionary

public Dictionary createDictionary() throws CreateException

Creates and returns the associated Dictionary or an empty dictionary if none is associated.

Returns:

the created Dictionary

Throws:

CreateException - if the dictionary cannot be created

getElemByCliqueSize

public <T extends FeatureInput> FeatureList<T> getElemByCliqueSize(int cliqueSize)

Gets the feature list for a specific clique size.

Type Parameters:

T - the type of FeatureInput

Parameters:

cliqueSize - 1 for pairwise, 0 for unary, -1 for all

Returns:

the FeatureList for the specified clique size

Throws:

AnchorImpossibleSituationException - if an invalid clique size is provided

getElemIndAsFeatureList

public FeatureList<FeatureInputSingleMemo> getElemIndAsFeatureList()

Gets the feature list for individual elements.

Returns:

the FeatureList for individual elements

getElemPairAsFeatureList

public FeatureList<FeatureInputPairMemo> getElemPairAsFeatureList()

Gets the feature list for pairs of elements.

Returns:

the FeatureList for pairs of elements

getElemAllAsFeatureList

public FeatureList<FeatureInputAllMemo> getElemAllAsFeatureList()

Gets the feature list for all elements together.

Returns:

the FeatureList for all elements

getPairAddCriteria

public AddCriteriaPair getPairAddCriteria()

Gets the criteria for adding pairs to the energy calculation.

Returns:

the AddCriteriaPair for pair addition

getListImageFeatures

public List<NamedBean<Feature<org.anchoranalysis.image.feature.input.FeatureInputStack>>> getListImageFeatures()

Gets the list of image features to be calculated first.

Returns:

the list of NamedBeans containing image features

getRegionMap

public RegionMap getRegionMap()

Gets the region map used in the energy scheme.

Returns:

the RegionMap for the energy scheme