FillerThread (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- sc.fiji.snt.tracing.AbstractSearch
- - sc.fiji.snt.tracing.SearchThread
  - - sc.fiji.snt.tracing.FillerThread

All Implemented Interfaces:

Runnable, SearchInterface
```
public class FillerThread
extends SearchThread
```
Seeded-volume segmentation via single-source shortest paths. Path nodes are used as seed points in an open-ended variant of Dijkstra's algorithm. The threshold sets the maximum allowable distance for a node to be included in the Fill. This distance is represented in the g-score of a node, which is the length of the shortest path from a seed point to that node. The magnitudes of these distances are heavily dependent on the supplied cost function Cost, so the threshold should be set with a particular cost function in mind. It often helps to adjust the threshold interactively.

Author:

Cameron Arshadi, Tiago Ferreira, Mark Longair

Field Summary
- Fields inherited from class sc.fiji.snt.tracing.SearchThread
  CANCELLED, CLOSED_FROM_GOAL, closed_from_goal_count, CLOSED_FROM_START, closed_from_start_count, costFunction, EXIT_REASONS_STRINGS, exitReason, FREE, lastReportMilliseconds, loops, loops_at_last_report, nodes_as_image_from_goal, nodes_as_image_from_start, OPEN_FROM_GOAL, open_from_start, OPEN_FROM_START, OUT_OF_MEMORY, POINTS_EXHAUSTED, started_at, SUCCESS, TIMED_OUT, verbose
- Fields inherited from class sc.fiji.snt.tracing.AbstractSearch
  img, imgAccess, imgDepth, imgHeight, imgWidth, progressListeners, reportEveryMilliseconds, spacing_units, timeoutSeconds, xMax, xMin, xSep, yMax, yMin, ySep, zMax, zMin, zSep

Constructor Summary

Constructors
Constructor and Description
`FillerThread(Dataset dataset, double initialThreshold, Cost costFunction)`
`FillerThread(Dataset dataset, double initialThreshold, int timeoutSeconds, long reportEveryMilliseconds, Cost costFunction)`
`FillerThread(Dataset dataset, double initialThreshold, int timeoutSeconds, long reportEveryMilliseconds, Cost costFunction, SNT.SearchImageType searchImageType)`
`FillerThread(RandomAccessibleInterval<? extends RealType<?>> image, ij.measure.Calibration calibration, double initialThreshold, Cost costFunction)`
`FillerThread(RandomAccessibleInterval<? extends RealType<?>> image, ij.measure.Calibration calibration, double initialThreshold, int timeoutSeconds, long reportEveryMilliseconds, Cost costFunction)`
`FillerThread(RandomAccessibleInterval<? extends RealType<?>> image, ij.measure.Calibration calibration, double initialThreshold, int timeoutSeconds, long reportEveryMilliseconds, Cost costFunction, SNT.SearchImageType searchImageType)`
`FillerThread(RandomAccessibleInterval<? extends RealType<?>> image, ij.measure.Calibration calibration, double initialThreshold, long reportEveryMilliseconds, Cost costFunction)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static FillerThread`	`fromFill(ij.ImagePlus imagePlus, ij.process.ImageStatistics stats, Fill fill)`
`static FillerThread`	`fromFill(RandomAccessibleInterval<? extends RealType<?>> image, ij.measure.Calibration calibration, ij.process.ImageStatistics stats, Fill fill)`
`double`	`getDistanceAtPoint(double xd, double yd, double zd)`
`Fill`	`getFill()`
`SearchImageStack<DefaultSearchNode>`	`getNodesAsImage()`
`Path`	`getResult()`
`double`	`getThreshold()`
`void`	`reportFinished(boolean success)`
`protected void`	`reportPointsInSearch()`
`void`	`run()`
`void`	`setSourcePaths(Collection<Path> newSourcePaths)`
`void`	`setStopAtThreshold(boolean stopAtThreshold)` Whether to terminate the fill operation once all nodes less than or equal to the distance threshold have been explored.
`void`	`setStoreExtraNodes(boolean storeExtraNodes)` Whether to store above-threshold nodes in the `Fill` object.
`void`	`setThreshold(double threshold)`

Methods inherited from class sc.fiji.snt.tracing.SearchThread
addNode, addProgressListener, atGoal, checkStatus, createNewNode, foundGoal, getExitReason, getNodesAsImageFromGoal, getNodesAsImageFromStart, pointsConsideredInSearch, printStatus

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

FillerThread

public FillerThread(RandomAccessibleInterval<? extends RealType<?>> image,
                    ij.measure.Calibration calibration,
                    double initialThreshold,
                    Cost costFunction)

FillerThread

public FillerThread(RandomAccessibleInterval<? extends RealType<?>> image,
                    ij.measure.Calibration calibration,
                    double initialThreshold,
                    long reportEveryMilliseconds,
                    Cost costFunction)

FillerThread

public FillerThread(RandomAccessibleInterval<? extends RealType<?>> image,
                    ij.measure.Calibration calibration,
                    double initialThreshold,
                    int timeoutSeconds,
                    long reportEveryMilliseconds,
                    Cost costFunction)

FillerThread

public FillerThread(RandomAccessibleInterval<? extends RealType<?>> image,
                    ij.measure.Calibration calibration,
                    double initialThreshold,
                    int timeoutSeconds,
                    long reportEveryMilliseconds,
                    Cost costFunction,
                    SNT.SearchImageType searchImageType)

FillerThread

public FillerThread(Dataset dataset,
                    double initialThreshold,
                    int timeoutSeconds,
                    long reportEveryMilliseconds,
                    Cost costFunction,
                    SNT.SearchImageType searchImageType)

FillerThread

public FillerThread(Dataset dataset,
                    double initialThreshold,
                    int timeoutSeconds,
                    long reportEveryMilliseconds,
                    Cost costFunction)

FillerThread

public FillerThread(Dataset dataset,
                    double initialThreshold,
                    Cost costFunction)

Method Detail

setStopAtThreshold
```
public void setStopAtThreshold(boolean stopAtThreshold)
```
Whether to terminate the fill operation once all nodes less than or equal to the distance threshold have been explored. If false, the search will run until it has explored the entire image. The default is false.

Parameters:

stopAtThreshold -

setStoreExtraNodes
```
public void setStoreExtraNodes(boolean storeExtraNodes)
```
Whether to store above-threshold nodes in the Fill object. The default is true.

Parameters:

storeExtraNodes -

See Also:

getFill()

fromFill

public static FillerThread fromFill(RandomAccessibleInterval<? extends RealType<?>> image,
                                    ij.measure.Calibration calibration,
                                    ij.process.ImageStatistics stats,
                                    Fill fill)

fromFill

public static FillerThread fromFill(ij.ImagePlus imagePlus,
                                    ij.process.ImageStatistics stats,
                                    Fill fill)

getDistanceAtPoint

public double getDistanceAtPoint(double xd,
                                 double yd,
                                 double zd)

getFill
```
public Fill getFill()
```

getThreshold
```
public double getThreshold()
```

setThreshold

public void setThreshold(double threshold)

setSourcePaths

public void setSourcePaths(Collection<Path> newSourcePaths)

run
```
public void run()
```
Specified by:

run in interface Runnable

Overrides:

run in class SearchThread

getNodesAsImage

public SearchImageStack<DefaultSearchNode> getNodesAsImage()

reportPointsInSearch
```
protected void reportPointsInSearch()
```
Overrides:

reportPointsInSearch in class SearchThread

getResult
```
public Path getResult()
```

reportFinished
```
public void reportFinished(boolean success)
```
Overrides:

reportFinished in class SearchThread

Class FillerThread

Field Summary

Fields inherited from class sc.fiji.snt.tracing.SearchThread

Fields inherited from class sc.fiji.snt.tracing.AbstractSearch

Constructor Summary

Method Summary

Methods inherited from class sc.fiji.snt.tracing.SearchThread

Methods inherited from class java.lang.Object

Constructor Detail

FillerThread

FillerThread

FillerThread

FillerThread

FillerThread

FillerThread

FillerThread

Method Detail

setStopAtThreshold

setStoreExtraNodes

fromFill

fromFill

getDistanceAtPoint

getFill

getThreshold

setThreshold

setSourcePaths

run

getNodesAsImage

reportPointsInSearch

getResult

reportFinished