Package sc.fiji.snt.tracing

Class FillerThread

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	Description
FillerThread(net.imagej.Dataset dataset, double initialThreshold, int timeoutSeconds, long reportEveryMilliseconds, Cost costFunction)
FillerThread(net.imagej.Dataset dataset, double initialThreshold, int timeoutSeconds, long reportEveryMilliseconds, Cost costFunction, SNT.SearchImageType searchImageType)
FillerThread(net.imagej.Dataset dataset, double initialThreshold, Cost costFunction)
FillerThread(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> image, ij.measure.Calibration calibration, double initialThreshold, int timeoutSeconds, long reportEveryMilliseconds, Cost costFunction)
FillerThread(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> image, ij.measure.Calibration calibration, double initialThreshold, int timeoutSeconds, long reportEveryMilliseconds, Cost costFunction, SNT.SearchImageType searchImageType)
FillerThread(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> image, ij.measure.Calibration calibration, double initialThreshold, long reportEveryMilliseconds, Cost costFunction)
FillerThread(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> image, ij.measure.Calibration calibration, double initialThreshold, Cost costFunction)

Method Summary

Modifier and Type	Method	Description
static FillerThread	fromFill(ij.ImagePlus imagePlus, ij.process.ImageStatistics stats, Fill fill)
static FillerThread	fromFill(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.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()
protected void	precomputeNeighborDistances()	Precompute distances to all 27 neighbors (including self at 0,0,0).
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 Details

FillerThread

public FillerThread(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> image,
 ij.measure.Calibration calibration,
 double initialThreshold,
 Cost costFunction)

FillerThread

public FillerThread(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> image,
 ij.measure.Calibration calibration,
 double initialThreshold,
 long reportEveryMilliseconds,
 Cost costFunction)

FillerThread

public FillerThread(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> image,
 ij.measure.Calibration calibration,
 double initialThreshold,
 int timeoutSeconds,
 long reportEveryMilliseconds,
 Cost costFunction)

FillerThread

public FillerThread(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> image,
 ij.measure.Calibration calibration,
 double initialThreshold,
 int timeoutSeconds,
 long reportEveryMilliseconds,
 Cost costFunction,
 SNT.SearchImageType searchImageType)

FillerThread

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

FillerThread

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

FillerThread

public FillerThread(net.imagej.Dataset dataset,
 double initialThreshold,
 Cost costFunction)

Method Details

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(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.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)

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.

Overrides:

precomputeNeighborDistances in class AbstractSearch

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