JaqamanSegmentCostMatrixCreator (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- fiji.plugin.trackmate.tracking.sparselap.costmatrix.JaqamanSegmentCostMatrixCreator

All Implemented Interfaces:

CostMatrixCreator<Spot,Spot>, Algorithm, Benchmark, MultiThreaded, OutputAlgorithm<SparseCostMatrix>
```
public class JaqamanSegmentCostMatrixCreator
extends Object
implements CostMatrixCreator<Spot,Spot>, MultiThreaded
```
This class generates the top-left quadrant of the LAP segment linking cost matrix, following Jaqaman et al., 2008 Nature Methods. It can also computes the alternative cost value, to use to complete this quadrant with the 3 others in the final LAP cost matrix.
Warning: we changed and simplified some things compared to the original paper and the MATLAB implementation by Khulud Jaqaman:
- There is only one alternative cost for all segment linking, and it calculated as alternativeCostFactor x 90% percentile of all the non-infinite costs.
- Costs are based on square distance +/- feature penalties.
Author:

Jean-Yves Tinevez - 2014

Constructor Summary

Constructors
Constructor and Description
`JaqamanSegmentCostMatrixCreator(org.jgrapht.Graph<Spot,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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`checkInput()`
`double`	`getAlternativeCostForSource(Spot source)` Returns the value of the no-linking alternative cost for the specified source.
`double`	`getAlternativeCostForTarget(Spot target)` Returns the value of the no-linking alternative cost for the specified target.
`protected CostFunction<Spot,Spot>`	`getCostFunctionFor(Map<String,Double> featurePenalties)`
`String`	`getErrorMessage()`
`int`	`getNumThreads()`
`long`	`getProcessingTime()`
`SparseCostMatrix`	`getResult()`
`List<Spot>`	`getSourceList()` Returns the list of sources in the generated cost matrix.
`List<Spot>`	`getTargetList()` Returns the list of targets in the generated cost matrix.
`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
  - JaqamanSegmentCostMatrixCreator
```
public JaqamanSegmentCostMatrixCreator(org.jgrapht.Graph<Spot,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 Algorithm
  - getErrorMessage
```
public String getErrorMessage()
```
    Specified by:
    
    getErrorMessage in interface Algorithm
  - process
```
public boolean process()
```
    Specified by:
    
    process in interface Algorithm
  - getCostFunctionFor
```
protected CostFunction<Spot,Spot> getCostFunctionFor(Map<String,Double> featurePenalties)
```
  - getResult
```
public SparseCostMatrix getResult()
```
    Specified by:
    
    getResult in interface OutputAlgorithm<SparseCostMatrix>
  - getSourceList
```
public List<Spot> getSourceList()
```
    Description copied from interface: CostMatrixCreator
    
    Returns the list of sources in the generated cost matrix.
    
    Specified by:
    
    getSourceList in interface CostMatrixCreator<Spot,Spot>
    
    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<Spot> getTargetList()
```
    Description copied from interface: CostMatrixCreator
    
    Returns the list of targets in the generated cost matrix.
    
    Specified by:
    
    getTargetList in interface CostMatrixCreator<Spot,Spot>
    
    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()
  - getAlternativeCostForSource
```
public double getAlternativeCostForSource(Spot 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<Spot,Spot>
    
    Parameters:
    
    source - the source object.
    
    Returns:
    
    the alternative cost. Belongs to the list returned by CostMatrixCreator.getSourceList().
  - getAlternativeCostForTarget
```
public double getAlternativeCostForTarget(Spot 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<Spot,Spot>
    
    Parameters:
    
    target - the target object. Belongs to the list returned by CostMatrixCreator.getTargetList().
    
    Returns:
    
    the alternative cost.
  - getProcessingTime
```
public long getProcessingTime()
```
    Specified by:
    
    getProcessingTime in interface Benchmark
  - setNumThreads
```
public void setNumThreads()
```
    Specified by:
    
    setNumThreads in interface MultiThreaded
  - setNumThreads
```
public void setNumThreads(int numThreads)
```
    Specified by:
    
    setNumThreads in interface MultiThreaded
  - getNumThreads
```
public int getNumThreads()
```
    Specified by:
    
    getNumThreads in interface MultiThreaded

Class JaqamanSegmentCostMatrixCreator

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

JaqamanSegmentCostMatrixCreator

Method Detail

checkInput

getErrorMessage

process

getCostFunctionFor

getResult

getSourceList

getTargetList

getAlternativeCostForSource

getAlternativeCostForTarget

getProcessingTime

setNumThreads

setNumThreads

getNumThreads