Package sc.fiji.snt.tracing

Class SearchThread

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	Description
static final int	CANCELLED
static final byte	CLOSED_FROM_GOAL
protected long	closed_from_goal_count
static final byte	CLOSED_FROM_START
protected long	closed_from_start_count
protected final Cost	costFunction
static final String[]	EXIT_REASONS_STRINGS
protected int	exitReason
static final 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 final byte	OPEN_FROM_GOAL
protected org.jheaps.AddressableHeap<DefaultSearchNode,Void>	open_from_start
static final byte	OPEN_FROM_START
static final int	OUT_OF_MEMORY
static final int	POINTS_EXHAUSTED
protected long	started_at
static final int	SUCCESS
static final int	TIMED_OUT
protected final boolean	verbose

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

img, imgAccess, imgDepth, imgHeight, imgWidth, neighborDistances, progressListeners, reportEveryMilliseconds, spacing_units, timeoutSeconds, xMax, xMin, xSep, yMax, yMin, ySep, zMax, zMin, zSep

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	SearchThread(net.imagej.Dataset dataset, boolean bidirectional, boolean definedGoal, int timeoutSeconds, long reportEveryMilliseconds, SNT.SearchImageType searchImageType, Cost costFunction)
protected	SearchThread(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> image, ij.measure.Calibration calibration, boolean bidirectional, boolean definedGoal, int timeoutSeconds, long reportEveryMilliseconds, SNT.SearchImageType searchImageType, Cost costFunction)
protected	SearchThread(SNT snt, net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> image, Cost costFunction)

Method Summary

Modifier and Type	Method	Description
void	addNode(DefaultSearchNode n, boolean fromStart)
void	addProgressListener(SearchProgressCallback callback)	Registers a callback to receive progress updates during the search.
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()	Returns the total number of points evaluated so far during the search.
void	printStatus()	Prints the current search status to the log.
void	reportFinished(boolean success)
protected void	reportPointsInSearch()
void	run()

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

precomputeNeighborDistances

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 Details

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 Details

SearchThread

protected SearchThread(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> image,
 ij.measure.Calibration calibration,
 boolean bidirectional,
 boolean definedGoal,
 int timeoutSeconds,
 long reportEveryMilliseconds,
 SNT.SearchImageType searchImageType,
 Cost costFunction)

SearchThread

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

SearchThread

protected SearchThread(SNT snt,
 net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> image,
 Cost costFunction)

Method Details

reportPointsInSearch

protected void reportPointsInSearch()

Specified by:

reportPointsInSearch in class AbstractSearch

pointsConsideredInSearch

public long pointsConsideredInSearch()

Description copied from class: AbstractSearch

Returns the total number of points evaluated so far during the search.

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)

Description copied from class: AbstractSearch

Registers a callback to receive progress updates during the search.

Specified by:

addProgressListener in class AbstractSearch

reportFinished

public void reportFinished(boolean success)

printStatus

public void printStatus()

Description copied from class: AbstractSearch

Prints the current search status to the log.

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()