SearchThread (Fiji Javadocs 0-SNAPSHOT API)

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

All Implemented Interfaces:

Runnable, SearchInterface

Direct Known Subclasses:

FillerThread, TracerThread
```
public abstract class SearchThread
extends AbstractSearch
```
Implements a common thread that explores the image using a variety of strategies, e.g., to trace tubular structures or surfaces.

Author:

Mark Longair, Tiago Ferreira, Cameron Arshadi

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`CANCELLED`
`static byte`	`CLOSED_FROM_GOAL`
`protected long`	`closed_from_goal_count`
`static byte`	`CLOSED_FROM_START`
`protected long`	`closed_from_start_count`
`protected Cost`	`costFunction`
`static String[]`	`EXIT_REASONS_STRINGS`
`protected int`	`exitReason`
`static byte`	`FREE`
`protected long`	`lastReportMilliseconds`
`protected long`	`loops`
`protected long`	`loops_at_last_report`
`protected SearchImageStack<DefaultSearchNode>`	`nodes_as_image_from_goal`
`protected SearchImageStack<DefaultSearchNode>`	`nodes_as_image_from_start`
`static byte`	`OPEN_FROM_GOAL`
`protected org.jheaps.AddressableHeap<DefaultSearchNode,Void>`	`open_from_start`
`static byte`	`OPEN_FROM_START`
`static int`	`OUT_OF_MEMORY`
`static int`	`POINTS_EXHAUSTED`
`protected long`	`started_at`
`static int`	`SUCCESS`
`static int`	`TIMED_OUT`
`protected boolean`	`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
Modifier	Constructor and Description
`protected`	`SearchThread(Dataset dataset, boolean bidirectional, boolean definedGoal, int timeoutSeconds, long reportEveryMilliseconds, SNT.SearchImageType searchImageType, Cost costFunction)`
`protected`	`SearchThread(RandomAccessibleInterval<? extends RealType<?>> image, ij.measure.Calibration calibration, boolean bidirectional, boolean definedGoal, int timeoutSeconds, long reportEveryMilliseconds, SNT.SearchImageType searchImageType, Cost costFunction)`
`protected`	`SearchThread(SNT snt, RandomAccessibleInterval<? extends RealType<?>> image, Cost costFunction)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addNode(DefaultSearchNode n, boolean fromStart)`
`void`	`addProgressListener(SearchProgressCallback callback)`
`protected boolean`	`atGoal(int x, int y, int z, boolean fromStart)`
`protected boolean`	`checkStatus()`
`DefaultSearchNode`	`createNewNode(int x, int y, int z, double g, double h, DefaultSearchNode predecessor, byte searchStatus)`
`protected void`	`foundGoal(Path pathToGoal)`
`int`	`getExitReason()`
`SearchImageStack<DefaultSearchNode>`	`getNodesAsImageFromGoal()`
`SearchImageStack<DefaultSearchNode>`	`getNodesAsImageFromStart()`
`long`	`pointsConsideredInSearch()`
`void`	`printStatus()`
`void`	`reportFinished(boolean success)`
`protected void`	`reportPointsInSearch()`
`void`	`run()`

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

Methods inherited from interface sc.fiji.snt.tracing.SearchInterface
getResult

Field Detail

OPEN_FROM_START
```
public static final byte OPEN_FROM_START
```
See Also:

Constant Field Values

CLOSED_FROM_START
```
public static final byte CLOSED_FROM_START
```
See Also:

Constant Field Values

OPEN_FROM_GOAL
```
public static final byte OPEN_FROM_GOAL
```
See Also:

Constant Field Values

CLOSED_FROM_GOAL
```
public static final byte CLOSED_FROM_GOAL
```
See Also:

Constant Field Values

FREE
```
public static final byte FREE
```
See Also:

Constant Field Values

SUCCESS
```
public static final int SUCCESS
```
See Also:

Constant Field Values

CANCELLED
```
public static final int CANCELLED
```
See Also:

Constant Field Values

TIMED_OUT
```
public static final int TIMED_OUT
```
See Also:

Constant Field Values

POINTS_EXHAUSTED
```
public static final int POINTS_EXHAUSTED
```
See Also:

Constant Field Values

OUT_OF_MEMORY
```
public static final int OUT_OF_MEMORY
```
See Also:

Constant Field Values

EXIT_REASONS_STRINGS

public static final String[] EXIT_REASONS_STRINGS

costFunction
```
protected final Cost costFunction
```

open_from_start

protected org.jheaps.AddressableHeap<DefaultSearchNode,Void> open_from_start

closed_from_start_count
```
protected long closed_from_start_count
```

closed_from_goal_count
```
protected long closed_from_goal_count
```

nodes_as_image_from_start

protected SearchImageStack<DefaultSearchNode> nodes_as_image_from_start

nodes_as_image_from_goal

protected SearchImageStack<DefaultSearchNode> nodes_as_image_from_goal

exitReason
```
protected int exitReason
```

verbose
```
protected final boolean verbose
```

started_at
```
protected long started_at
```

loops
```
protected long loops
```

loops_at_last_report
```
protected long loops_at_last_report
```

lastReportMilliseconds
```
protected long lastReportMilliseconds
```

Constructor Detail

SearchThread

protected SearchThread(RandomAccessibleInterval<? extends RealType<?>> image,
                       ij.measure.Calibration calibration,
                       boolean bidirectional,
                       boolean definedGoal,
                       int timeoutSeconds,
                       long reportEveryMilliseconds,
                       SNT.SearchImageType searchImageType,
                       Cost costFunction)

SearchThread

protected SearchThread(Dataset dataset,
                       boolean bidirectional,
                       boolean definedGoal,
                       int timeoutSeconds,
                       long reportEveryMilliseconds,
                       SNT.SearchImageType searchImageType,
                       Cost costFunction)

SearchThread

protected SearchThread(SNT snt,
                       RandomAccessibleInterval<? extends RealType<?>> image,
                       Cost costFunction)

Method Detail

reportPointsInSearch
```
protected void reportPointsInSearch()
```
Specified by:

reportPointsInSearch in class AbstractSearch

pointsConsideredInSearch
```
public long pointsConsideredInSearch()
```
Specified by:

pointsConsideredInSearch in class AbstractSearch

createNewNode

public DefaultSearchNode createNewNode(int x,
                                       int y,
                                       int z,
                                       double g,
                                       double h,
                                       DefaultSearchNode predecessor,
                                       byte searchStatus)

foundGoal

protected void foundGoal(Path pathToGoal)

atGoal

protected boolean atGoal(int x,
                         int y,
                         int z,
                         boolean fromStart)

addProgressListener
```
public void addProgressListener(SearchProgressCallback callback)
```
Specified by:

addProgressListener in class AbstractSearch

reportFinished

public void reportFinished(boolean success)

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

printStatus in class AbstractSearch

checkStatus
```
protected boolean checkStatus()
```

run
```
public void run()
```

getExitReason
```
public int getExitReason()
```

addNode

public void addNode(DefaultSearchNode n,
                    boolean fromStart)

getNodesAsImageFromStart

public SearchImageStack<DefaultSearchNode> getNodesAsImageFromStart()

getNodesAsImageFromGoal

public SearchImageStack<DefaultSearchNode> getNodesAsImageFromGoal()

Class SearchThread

Field Summary

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

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface sc.fiji.snt.tracing.SearchInterface

Field Detail

OPEN_FROM_START

CLOSED_FROM_START

OPEN_FROM_GOAL

CLOSED_FROM_GOAL

FREE

SUCCESS

CANCELLED

TIMED_OUT

POINTS_EXHAUSTED

OUT_OF_MEMORY

EXIT_REASONS_STRINGS

costFunction

open_from_start

closed_from_start_count

closed_from_goal_count

nodes_as_image_from_start

nodes_as_image_from_goal

exitReason

verbose

started_at

loops

loops_at_last_report

lastReportMilliseconds

Constructor Detail

SearchThread

SearchThread

SearchThread

Method Detail

reportPointsInSearch

pointsConsideredInSearch

createNewNode

foundGoal

atGoal

addProgressListener

reportFinished

printStatus

checkStatus

run

getExitReason

addNode

getNodesAsImageFromStart

getNodesAsImageFromGoal