Package sc.fiji.snt.tracing

Class AbstractSearch

java.lang.Object

sc.fiji.snt.tracing.AbstractSearch

All Implemented Interfaces:

Runnable, SearchInterface

Direct Known Subclasses:

BiSearch, SearchThread

public abstract class AbstractSearch
extends Object
implements SearchInterface, Runnable

Abstract class for path-finding over RandomAccessibleIntervals

Author:

Cameron Arshadi

Field Summary

Fields

Modifier and Type	Field	Description
protected final net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>>	img
protected final net.imglib2.RandomAccess<? extends net.imglib2.type.numeric.RealType<?>>	imgAccess
final int	imgDepth	The depth (number of slices) of the search image.
final int	imgHeight	The height of the search image in pixels.
final int	imgWidth	The width of the search image in pixels.
protected double[][][]	neighborDistances
protected ArrayList<SearchProgressCallback>	progressListeners
protected long	reportEveryMilliseconds
protected final String	spacing_units
protected int	timeoutSeconds
protected final boolean	verbose
protected final long	xMax
protected final long	xMin
protected final double	xSep
protected final long	yMax
protected final long	yMin
protected final double	ySep
protected final long	zMax
protected final long	zMin
protected final double	zSep

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	AbstractSearch(ij.ImagePlus imagePlus, int timeoutSeconds, long reportEveryMilliseconds)
protected	AbstractSearch(net.imagej.Dataset image, int timeoutSeconds, long reportEveryMilliseconds)
protected	AbstractSearch(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> image, ij.measure.Calibration calibration, int timeoutSeconds, long reportEveryMilliseconds)
protected	AbstractSearch(SNT snt, ij.ImagePlus imagePlus)
protected	AbstractSearch(SNT snt, net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> image)

Method Summary

Modifier and Type	Method	Description
abstract void	addProgressListener(SearchProgressCallback callback)	Registers a callback to receive progress updates during the search.
abstract long	pointsConsideredInSearch()	Returns the total number of points evaluated so far during the search.
protected void	precomputeNeighborDistances()	Precompute distances to all 27 neighbors (including self at 0,0,0).
abstract void	printStatus()	Prints the current search status to the log.
protected abstract void	reportPointsInSearch()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.lang.Runnable

run

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

getResult

Field Details

img

protected final net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> img

imgAccess

protected final net.imglib2.RandomAccess<? extends net.imglib2.type.numeric.RealType<?>> imgAccess

imgWidth

public final int imgWidth

The width of the search image in pixels.

imgHeight

public final int imgHeight

The height of the search image in pixels.

imgDepth

public final int imgDepth

The depth (number of slices) of the search image.

xMin

protected final long xMin

yMin

protected final long yMin

zMin

protected final long zMin

xMax

protected final long xMax

yMax

protected final long yMax

zMax

protected final long zMax

xSep

protected final double xSep

ySep

protected final double ySep

zSep

protected final double zSep

spacing_units

protected final String spacing_units

timeoutSeconds

protected int timeoutSeconds

reportEveryMilliseconds

protected long reportEveryMilliseconds

progressListeners

protected ArrayList<SearchProgressCallback> progressListeners

neighborDistances

protected double[][][] neighborDistances

verbose

protected final boolean verbose

Constructor Details

AbstractSearch

protected AbstractSearch(ij.ImagePlus imagePlus,
 int timeoutSeconds,
 long reportEveryMilliseconds)

AbstractSearch

protected AbstractSearch(net.imagej.Dataset image,
 int timeoutSeconds,
 long reportEveryMilliseconds)

AbstractSearch

protected AbstractSearch(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> image,
 ij.measure.Calibration calibration,
 int timeoutSeconds,
 long reportEveryMilliseconds)

AbstractSearch

protected AbstractSearch(SNT snt,
 ij.ImagePlus imagePlus)

AbstractSearch

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

Method Details

precomputeNeighborDistances

protected void precomputeNeighborDistances()

Precompute distances to all 27 neighbors (including self at 0,0,0). Since xdiff, ydiff, zdiff ∈ {-1, 0, 1} and spacing is fixed, we can compute these once instead of per-neighbor in the search loop. Call this method once before starting the search.

addProgressListener

public abstract void addProgressListener(SearchProgressCallback callback)

Registers a callback to receive progress updates during the search.

printStatus

public abstract void printStatus()

Prints the current search status to the log.

reportPointsInSearch

protected abstract void reportPointsInSearch()

pointsConsideredInSearch

public abstract long pointsConsideredInSearch()

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