SparseLAPSegmentTracker (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- fiji.plugin.trackmate.tracking.sparselap.SparseLAPSegmentTracker

All Implemented Interfaces:

SpotTracker, Algorithm, Benchmark, MultiThreaded, OutputAlgorithm<org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge>>
```
public class SparseLAPSegmentTracker
extends Object
implements SpotTracker, Benchmark
```
This class tracks deals with the second step of tracking according to the LAP tracking framework formulated by Jaqaman, K. et al. "Robust single-particle tracking in live-cell time-lapse sequences." Nature Methods, 2008.
In this tracking framework, tracking is divided into two steps:
1. Identify individual track segments
2. Gap closing, merging and splitting
and this class does the second step.
It first extract track segment from a specified graph, and create a cost matrix corresponding to the following events: Track segments can be:
- Linked end-to-tail (gap closing)
- Split (the start of one track is linked to the middle of another track)
- Merged (the end of one track is linked to the middle of another track
- Terminated (track ends)
- Initiated (track starts)
The cost matrix for this step is illustrated in Figure 1c in the paper. However, there is some important deviations from the paper: The alternative costs that specify the cost for track termination or initiation are all equals to the same fixed value.
The class itself uses a sparse version of the cost matrix and a solver that can exploit it. Therefore it is optimized for memory usage rather than speed.

Constructor Summary

Constructors
Constructor and Description
`SparseLAPSegmentTracker(org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge> graph, Map<String,Object> settings)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`checkInput()`
`String`	`getErrorMessage()`
`int`	`getNumThreads()`
`long`	`getProcessingTime()`
`org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge>`	`getResult()`
`boolean`	`process()`
`void`	`setLogger(Logger logger)` Sets the `Logger` instance that will receive messages from this `SpotTracker`.
`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
  - SparseLAPSegmentTracker
```
public SparseLAPSegmentTracker(org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge> graph,
                               Map<String,Object> settings)
```
- Method Detail
  - getResult
```
public org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge> getResult()
```
    Specified by:
    
    getResult in interface OutputAlgorithm<org.jgrapht.graph.SimpleWeightedGraph<Spot,org.jgrapht.graph.DefaultWeightedEdge>>
  - 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
  - getProcessingTime
```
public long getProcessingTime()
```
    Specified by:
    
    getProcessingTime in interface Benchmark
  - setLogger
```
public void setLogger(Logger logger)
```
    Description copied from interface: SpotTracker
    
    Sets the Logger instance that will receive messages from this SpotTracker.
    
    Specified by:
    
    setLogger in interface SpotTracker
    
    Parameters:
    
    logger - the logger to echo messages to.
  - 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 SparseLAPSegmentTracker

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

SparseLAPSegmentTracker

Method Detail

getResult

checkInput

process

getErrorMessage

getProcessingTime

setLogger

setNumThreads

setNumThreads

getNumThreads