fiji.plugin.trackmate.tracking.jaqaman.costmatrix

Class JaqamanLinkingCostMatrixCreator<K extends Comparable<K>,J extends Comparable<J>>

java.lang.Object

fiji.plugin.trackmate.tracking.jaqaman.costmatrix.JaqamanLinkingCostMatrixCreator<K,J>

Type Parameters:

K -

J -

All Implemented Interfaces:

CostMatrixCreator<K,J>, Algorithm, Benchmark, OutputAlgorithm<SparseCostMatrix>

public class JaqamanLinkingCostMatrixCreator<K extends Comparable<K>,J extends Comparable<J>>
extends Object
implements CostMatrixCreator<K,J>

A CostMatrixCreator that can generate a cost matrix from a list of sources, a list of targets and a CostFunction that can generate a cost for any combination.

Author:

Jean-Yves Tinevez - 2014

Constructor Summary

Constructors

Constructor and Description
JaqamanLinkingCostMatrixCreator(Iterable<K> sources, Iterable<J> targets, CostFunction<K,J> costFunction, double costThreshold, double alternativeCostFactor, double percentile)

Method Summary

Modifier and Type	Method and Description
boolean	checkInput()
double	getAlternativeCostForSource(K source) Returns the value of the no-linking alternative cost for the specified source.
double	getAlternativeCostForTarget(J target) Returns the value of the no-linking alternative cost for the specified target.
String	getErrorMessage()
long	getProcessingTime()
SparseCostMatrix	getResult() Returns the cost matrix generated.
List<K>	getSourceList() Returns the list of sources in the generated cost matrix.
List<J>	getTargetList() Returns the list of targets in the generated cost matrix.
boolean	process()

Methods inherited from class java.lang.Object

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

Constructor Detail

JaqamanLinkingCostMatrixCreator

public JaqamanLinkingCostMatrixCreator(Iterable<K> sources,
                                       Iterable<J> targets,
                                       CostFunction<K,J> costFunction,
                                       double costThreshold,
                                       double alternativeCostFactor,
                                       double percentile)

Method Detail

checkInput

public boolean checkInput()

Specified by:

checkInput in interface Algorithm

process

public boolean process()

Specified by:

process in interface Algorithm

getErrorMessage

public String getErrorMessage()

Specified by:

getErrorMessage in interface Algorithm

getResult

public SparseCostMatrix getResult()

Returns the cost matrix generated.

Careful, it can be null if not acceptable costs have been found for the specified configuration. In that case, the lists returned by getSourceList() and getTargetList() are empty.

Specified by:

getResult in interface OutputAlgorithm<SparseCostMatrix>

Returns:

a new SparseCostMatrix or null.

getSourceList

public List<K> getSourceList()

Description copied from interface: CostMatrixCreator

Returns the list of sources in the generated cost matrix.

Specified by:

getSourceList in interface CostMatrixCreator<K extends Comparable<K>,J extends Comparable<J>>

Returns:

the list of object, such that sourceList.get( i ) is the source corresponding to the row i in the generated cost matrix.

See Also:

CostMatrixCreator.getTargetList(), OutputAlgorithm.getResult()

getTargetList

public List<J> getTargetList()

Description copied from interface: CostMatrixCreator

Returns the list of targets in the generated cost matrix.

Specified by:

getTargetList in interface CostMatrixCreator<K extends Comparable<K>,J extends Comparable<J>>

Returns:

the list of objects, such that targetList.get( j ) is the target corresponding to the column j in the generated cost matrix.

See Also:

CostMatrixCreator.getSourceList(), OutputAlgorithm.getResult()

getProcessingTime

public long getProcessingTime()

Specified by:

getProcessingTime in interface Benchmark

getAlternativeCostForSource

public double getAlternativeCostForSource(K source)

Description copied from interface: CostMatrixCreator

Returns the value of the no-linking alternative cost for the specified source.

Specified by:

getAlternativeCostForSource in interface CostMatrixCreator<K extends Comparable<K>,J extends Comparable<J>>

Parameters:

source - the source object.

Returns:

the alternative cost. Belongs to the list returned by CostMatrixCreator.getSourceList().

getAlternativeCostForTarget

public double getAlternativeCostForTarget(J target)

Description copied from interface: CostMatrixCreator

Returns the value of the no-linking alternative cost for the specified target.

Specified by:

getAlternativeCostForTarget in interface CostMatrixCreator<K extends Comparable<K>,J extends Comparable<J>>

Parameters:

target - the target object. Belongs to the list returned by CostMatrixCreator.getTargetList().

Returns:

the alternative cost.