Module sc.fiji.filamentdetector

Package sc.fiji.filamentdetector.tracking.lap

Class JaqamanFilamentSegmentCostMatrixCreator

java.lang.Object

sc.fiji.filamentdetector.tracking.lap.JaqamanFilamentSegmentCostMatrixCreator

All Implemented Interfaces:

fiji.plugin.trackmate.tracking.jaqaman.costmatrix.CostMatrixCreator<Filament,Filament>, net.imglib2.algorithm.Algorithm, net.imglib2.algorithm.Benchmark, net.imglib2.algorithm.MultiThreaded, net.imglib2.algorithm.OutputAlgorithm<fiji.plugin.trackmate.tracking.jaqaman.costmatrix.SparseCostMatrix>

public class JaqamanFilamentSegmentCostMatrixCreator
extends Object
implements fiji.plugin.trackmate.tracking.jaqaman.costmatrix.CostMatrixCreator<Filament,Filament>, net.imglib2.algorithm.MultiThreaded

Constructor Summary

Constructors

Constructor	Description
JaqamanFilamentSegmentCostMatrixCreator(org.jgrapht.Graph<Filament,org.jgrapht.graph.DefaultWeightedEdge> graph, Map<String,Object> settings)	Instantiates a cost matrix creator for the top-left quadrant of the segment linking cost matrix.

Method Summary

Modifier and Type	Method	Description
boolean	checkInput()
double	getAlternativeCostForSource(Filament source)
double	getAlternativeCostForTarget(Filament target)
protected fiji.plugin.trackmate.tracking.jaqaman.costfunction.CostFunction<Filament,Filament>	getCostFunctionFor(Map<String,Double> featurePenalties)
String	getErrorMessage()
int	getNumThreads()
long	getProcessingTime()
fiji.plugin.trackmate.tracking.jaqaman.costmatrix.SparseCostMatrix	getResult()
List<Filament>	getSourceList()
List<Filament>	getTargetList()
boolean	process()
void	setNumThreads()
void	setNumThreads(int numThreads)

Methods inherited from class java.lang.Object

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

Constructor Detail

JaqamanFilamentSegmentCostMatrixCreator

public JaqamanFilamentSegmentCostMatrixCreator(org.jgrapht.Graph<Filament,org.jgrapht.graph.DefaultWeightedEdge> graph,
                                               Map<String,Object> settings)

Instantiates a cost matrix creator for the top-left quadrant of the segment linking cost matrix.

Method Detail

checkInput

public boolean checkInput()

Specified by:

checkInput in interface net.imglib2.algorithm.Algorithm

getErrorMessage

public String getErrorMessage()

Specified by:

getErrorMessage in interface net.imglib2.algorithm.Algorithm

process

public boolean process()

Specified by:

process in interface net.imglib2.algorithm.Algorithm

getCostFunctionFor

protected fiji.plugin.trackmate.tracking.jaqaman.costfunction.CostFunction<Filament,Filament> getCostFunctionFor(Map<String,Double> featurePenalties)

getResult

public fiji.plugin.trackmate.tracking.jaqaman.costmatrix.SparseCostMatrix getResult()

Specified by:

getResult in interface net.imglib2.algorithm.OutputAlgorithm<fiji.plugin.trackmate.tracking.jaqaman.costmatrix.SparseCostMatrix>

getSourceList

public List<Filament> getSourceList()

Specified by:

getSourceList in interface fiji.plugin.trackmate.tracking.jaqaman.costmatrix.CostMatrixCreator<Filament,Filament>

getTargetList

public List<Filament> getTargetList()

Specified by:

getTargetList in interface fiji.plugin.trackmate.tracking.jaqaman.costmatrix.CostMatrixCreator<Filament,Filament>

getAlternativeCostForSource

public double getAlternativeCostForSource(Filament source)

Specified by:

getAlternativeCostForSource in interface fiji.plugin.trackmate.tracking.jaqaman.costmatrix.CostMatrixCreator<Filament,Filament>

getAlternativeCostForTarget

public double getAlternativeCostForTarget(Filament target)

Specified by:

getAlternativeCostForTarget in interface fiji.plugin.trackmate.tracking.jaqaman.costmatrix.CostMatrixCreator<Filament,Filament>

getProcessingTime

public long getProcessingTime()

Specified by:

getProcessingTime in interface net.imglib2.algorithm.Benchmark

setNumThreads

public void setNumThreads()

Specified by:

setNumThreads in interface net.imglib2.algorithm.MultiThreaded

setNumThreads

public void setNumThreads(int numThreads)

Specified by:

setNumThreads in interface net.imglib2.algorithm.MultiThreaded

getNumThreads

public int getNumThreads()

Specified by:

getNumThreads in interface net.imglib2.algorithm.MultiThreaded