Package org.anchoranalysis.plugin.image.feature.bean.object.combine

Class PairNeighbors

Object

AnchorBean<CombineObjectsForFeatures<FeatureInputPairObjects>>

CombineObjectsForFeatures<FeatureInputPairObjects>

PairNeighbors

public class PairNeighbors
extends CombineObjectsForFeatures<FeatureInputPairObjects>

Creates a set of features, that creates pairs of neighboring-objects and applies a mixture of single-object features and pair features.

Specifically:

• Creates a graph of neighboring-objects.
• Passes each pair of immediately-neighboring objects, together with their merged object, as an input.

Features are formed by duplicating the input-feature list (inputfeatures, single-object features only):

   a) First.inputfeatures     applies the features to the first-object in the pair
   b) Second.inputfeatures    applies the features to the second-object in the pair
   c) Merged.inputfeatures    applies the features to the merged-object
 

Features (that are not duplicated) are also possible:

   d) Image.                                    additional single-object features that don't depend on any individual-object, only the image
   e) Pair.                                     additional pair-features (FeatureInputPairObjects)
 

The column order output is: Image, First, Second, Pair, Merged

For First and Second, we use a cache, to avoid repeated calculations.

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
PairNeighbors()

Method Summary

Modifier and Type	Method	Description
protected BoundingBox	boundingBoxThatSpansInput(FeatureInputPairObjects input)	Creates a bounding-box that tightly fits the input to a particular table row (could be for one or more objects).
FeatureTableCalculator<FeatureInputPairObjects>	createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>> list, NamedFeatureStoreFactory storeFactory, boolean suppressErrors)	Creates features that will be applied on the objects.
List<NamedBean<FeatureListProvider<FeatureInputStack>>>	getFeaturesImage()	Additional features that only depend on the image, so do not need to be replicated for every object.
List<NamedBean<FeatureListProvider<FeatureInputPairObjects>>>	getFeaturesPair()	Additional features that are processed on the pair of images (i.e.
boolean	isAvoidOverlappingObjects()	If true, no overlapping objects are treated as pairs
boolean	isDo3D()
boolean	isIncludeFirst()	Include features for the First-object of the pair
boolean	isIncludeMerged()	Include features for the Merged-object of the pair
boolean	isIncludeSecond()	Include features for the Second-object of the pair
ObjectCollection	objectsForThumbnail(FeatureInputPairObjects input)	Selects objects from an input that will be used for thumbnail generation.
void	setAvoidOverlappingObjects(boolean avoidOverlappingObjects)	If true, no overlapping objects are treated as pairs
void	setDo3D(boolean do3D)
void	setFeaturesImage(List<NamedBean<FeatureListProvider<FeatureInputStack>>> featuresImage)	Additional features that only depend on the image, so do not need to be replicated for every object.
void	setFeaturesPair(List<NamedBean<FeatureListProvider<FeatureInputPairObjects>>> featuresPair)	Additional features that are processed on the pair of images (i.e.
void	setIncludeFirst(boolean includeFirst)	Include features for the First-object of the pair
void	setIncludeMerged(boolean includeMerged)	Include features for the Merged-object of the pair
void	setIncludeSecond(boolean includeSecond)	Include features for the Second-object of the pair
List<FeatureInputPairObjects>	startBatchDeriveInputs(ObjectCollection objects, EnergyStack energyStack, Logger logger)	Derives a list of inputs from an object-collection.
String	uniqueIdentifierFor(FeatureInputPairObjects input)	Generates a unique identifier for a particular input.

Methods inherited from class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures

checkMisconfigured, deriveInputsStartBatch, getInterpolator, getThumbnail, setInterpolator, setThumbnail

Methods inherited from class org.anchoranalysis.bean.AnchorBean

describeBean, describeChildren, duplicateBean, fields, findFieldsOfClass, getBeanName, getLocalPath, localise, toString

Methods inherited from class java.lang.Object

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

Constructor Details

PairNeighbors

public PairNeighbors()

Method Details

createFeatures

public FeatureTableCalculator<FeatureInputPairObjects> createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>> list,
 NamedFeatureStoreFactory storeFactory,
 boolean suppressErrors)
                                                               throws CreateException

Description copied from class: CombineObjectsForFeatures

Creates features that will be applied on the objects. Features should always be duplicated from the input list.

Specified by:

createFeatures in class CombineObjectsForFeatures<FeatureInputPairObjects>

Parameters:

list - beans defining features to be applied to single-objects.

storeFactory - creates a new NamedFeatureStore as needed.

suppressErrors - when true, exceptions aren't thrown when feature-calculations fail, but rather a log error message is written.

Returns:

a FeatureTableCalculator for feature tables that may apply various features derived from featuresSingleObject.

Throws:

CreateException - if there's an error creating the features.

startBatchDeriveInputs

public List<FeatureInputPairObjects> startBatchDeriveInputs(ObjectCollection objects,
 EnergyStack energyStack,
 Logger logger)
                                                     throws CreateException

Description copied from class: CombineObjectsForFeatures

Derives a list of inputs from an object-collection.

Specified by:

startBatchDeriveInputs in class CombineObjectsForFeatures<FeatureInputPairObjects>

Parameters:

objects - the object-collection

energyStack - energy-stack used during feature calculation

logger - the logger

Returns:

the list of inputs

Throws:

CreateException - if there's an error deriving the inputs

uniqueIdentifierFor

public String uniqueIdentifierFor(FeatureInputPairObjects input)

Description copied from class: CombineObjectsForFeatures

Generates a unique identifier for a particular input.

Specified by:

uniqueIdentifierFor in class CombineObjectsForFeatures<FeatureInputPairObjects>

Parameters:

input - the input to generate a unique identifier for

Returns:

a unique identifier string

objectsForThumbnail

public ObjectCollection objectsForThumbnail(FeatureInputPairObjects input)
                                     throws CreateException

Description copied from class: CombineObjectsForFeatures

Selects objects from an input that will be used for thumbnail generation.

Specified by:

objectsForThumbnail in class CombineObjectsForFeatures<FeatureInputPairObjects>

Parameters:

input - the input

Returns:

the ObjectCollection for thumbnail generation

Throws:

CreateException - if there's an error creating the object collection

boundingBoxThatSpansInput

protected BoundingBox boundingBoxThatSpansInput(FeatureInputPairObjects input)

Description copied from class: CombineObjectsForFeatures

Creates a bounding-box that tightly fits the input to a particular table row (could be for one or more objects).

Specified by:

boundingBoxThatSpansInput in class CombineObjectsForFeatures<FeatureInputPairObjects>

Parameters:

input - the input

Returns:

a BoundingBox that fully fits around all objects used in input

getFeaturesPair

public List<NamedBean<FeatureListProvider<FeatureInputPairObjects>>> getFeaturesPair()

Additional features that are processed on the pair of images (i.e. First+Second as a pair)

setFeaturesPair

public void setFeaturesPair(List<NamedBean<FeatureListProvider<FeatureInputPairObjects>>> featuresPair)

Additional features that are processed on the pair of images (i.e. First+Second as a pair)

getFeaturesImage

public List<NamedBean<FeatureListProvider<FeatureInputStack>>> getFeaturesImage()

Additional features that only depend on the image, so do not need to be replicated for every object.

setFeaturesImage

public void setFeaturesImage(List<NamedBean<FeatureListProvider<FeatureInputStack>>> featuresImage)

Additional features that only depend on the image, so do not need to be replicated for every object.

isIncludeFirst

public boolean isIncludeFirst()

Include features for the First-object of the pair

setIncludeFirst

public void setIncludeFirst(boolean includeFirst)

Include features for the First-object of the pair

isIncludeSecond

public boolean isIncludeSecond()

Include features for the Second-object of the pair

setIncludeSecond

public void setIncludeSecond(boolean includeSecond)

Include features for the Second-object of the pair

isIncludeMerged

public boolean isIncludeMerged()

Include features for the Merged-object of the pair

setIncludeMerged

public void setIncludeMerged(boolean includeMerged)

Include features for the Merged-object of the pair

isAvoidOverlappingObjects

public boolean isAvoidOverlappingObjects()

If true, no overlapping objects are treated as pairs

setAvoidOverlappingObjects

public void setAvoidOverlappingObjects(boolean avoidOverlappingObjects)

If true, no overlapping objects are treated as pairs

isDo3D

public boolean isDo3D()

setDo3D

public void setDo3D(boolean do3D)