Package sc.fiji.snt.tracing.auto

Class GWDTTracer<T extends net.imglib2.type.numeric.RealType<T>>

java.lang.Object

sc.fiji.snt.tracing.auto.AbstractAutoTracer

sc.fiji.snt.tracing.auto.AbstractGWDTTracer<T>

sc.fiji.snt.tracing.auto.GWDTTracer<T>

Type Parameters:

T - pixel type

All Implemented Interfaces:

AutoTracer

public class GWDTTracer<T extends net.imglib2.type.numeric.RealType<T>>
extends AbstractGWDTTracer<T>

In-memory GWDT tracer using array storage.

Fast but memory-intensive. Best for images < 1GB. Uses APP2-style algorithm: Gray-Weighted Distance Transform, Fast Marching, and hierarchical pruning.

Author:

Tiago Ferreira

See Also:

• AbstractGWDTTracer
• PMID: 23603332

Nested Class Summary

Nested classes/interfaces inherited from class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

AbstractGWDTTracer.HierarchySegment, AbstractGWDTTracer.WaypointBiasSource

Nested classes/interfaces inherited from interface sc.fiji.snt.tracing.auto.AutoTracer

AutoTracer.SeedRole

Field Summary

Fields inherited from class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

ALIVE, backgroundThreshold, branchTuneMaxAngle, cnnType, dims, FAR, jointLeafPruneEnabled, leafPruneEnabled, leafPruneOverlap, maxBounds, maxIntensity, minBounds, minBranchIntensityLength, minIntensity, overshootRemovalEnabled, parallelBranchPruneEnabled, resampleEnabled, resampleStep, scoreMap, scoreMapEnabled, scoreMapFilterType, scoreMapPruneThreshold, scoreMapScales, seedVoxel, smoothEnabled, smoothWindowSize, source, spacing, sphereOverlapThreshold, srRatio, storage, TRIAL, zigzagRemovalEnabled

Fields inherited from class sc.fiji.snt.tracing.auto.AbstractAutoTracer

logger, rootStrategy, somaRoi, somaRoiZPosition, verbose

Fields inherited from interface sc.fiji.snt.tracing.auto.AutoTracer

ROI_CENTROID, ROI_CENTROID_WEIGHTED, ROI_CONTAINED, ROI_EDGE, ROI_UNSET

Constructor Summary

Constructors

Constructor	Description
GWDTTracer(ij.ImagePlus source)	Creates a new GWDTTracer from an ImagePlus.
GWDTTracer(net.imagej.ImgPlus<T> source)	Creates a new GWDTTracer from an ImgPlus.
GWDTTracer(net.imglib2.RandomAccessibleInterval<T> source)	Creates a new GWDTTracer with isotropic spacing (1.0 for each dimension).
GWDTTracer(net.imglib2.RandomAccessibleInterval<T> source, double[] spacing)	Creates a new GWDTTracer.

Method Summary

Modifier and Type	Method	Description
static GWDTTracer<?>	create(ij.ImagePlus source)
static GWDTTracer<?>	create(net.imagej.ImgPlus<?> source)
protected StorageBackend	createStorageBackend()	Create the storage backend for this tracer.
static void	main(String[] args)

Methods inherited from class sc.fiji.snt.tracing.auto.AbstractGWDTTracer

addNeighborsToHeap, computeAndApplyScoreMap, computeAverageSpacing, computeIntensityRange, computeIntensityWeightedJointCoverage, createIsotropicSpacing, darkNodeAndSegmentPruning, getCaliperFraction, getDimensions, getEffectiveThreshold, getMaxGapVoxels, getMinSomaDistance, getNSomas, getScoreMap, getSpacing, getSpacing, getTipExtensionDistance, getTracedRegionBuffer, hierarchicalPrune, honoredSeedRoles, indexToPos, isAllowVoxelGap, isAutoFilter, isInBounds, isParallelBranchPruneEnabled, isPathFittingEnabled, iterateNeighbors, nodeToVoxelPos, posToIndex, posToIndex, pruneParallelBranches, recalculateRadiiFromImage, removeOvershoots, removeZigzags, resampleCurve, runFastMarching, setAllowVoxelGap, setAutoFilter, setBackgroundThreshold, setBranchTuneMaxAngle, setCaliperFraction, setConnectivityType, setJointLeafPruneEnabled, setLeafPruneOverlap, setMaxGapVoxels, setMinBranchIntensityLength, setMinSegmentLength, setMinSegmentLengthVoxels, setMinSomaDistance, setNSomas, setOvershootRemovalEnabled, setParallelBranchPruneEnabled, setPathFittingEnabled, setResampleStep, setRoots, setScoreMap, setScoreMapEnabled, setScoreMapFilterType, setScoreMapPruneThreshold, setScoreMapScales, setSeed, setSeedPhysical, setSmoothWindowSize, setSphereOverlapThreshold, setSrRatio, setTipExtensionDistance, setTips, setTracedRegionBuffer, setWaypointBiasFixedFactor, setWaypointBiasRadiusVoxels, setWaypointBiasSource, setWaypointBiasStrength, setWaypoints, setZigzagRemovalEnabled, smoothCurve, trace, traceMultiSoma, traceToGraph, traceTrees, tuneBranches

Methods inherited from class sc.fiji.snt.tracing.auto.AbstractAutoTracer

collapseSomaNodes, collapseSomaToRoiCentroid, collapseSomaToWeightedCentroid, computeAverageRadius, estimateBackgroundThreshold, findGraphRoot, findRoot, findRoot, findRootPhysical, findRootPhysical, findThickestPoint, findThickestPointPhysical, getRootStrategy, getSomaRoi, isInsideSomaRoi, isVerbose, log, removeDisconnectedComponents, setSomaRoi, setSomaRoi, setSomaRoiZPosition, setStatusListener, setVerbose, splitAtSomaBoundary, status

Methods inherited from class java.lang.Object

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

Constructor Details

GWDTTracer

public GWDTTracer(net.imglib2.RandomAccessibleInterval<T> source,
 double[] spacing)

Creates a new GWDTTracer.

Parameters:

source - the grayscale image to trace

spacing - voxel dimensions [x, y, z] in physical units

GWDTTracer

public GWDTTracer(net.imagej.ImgPlus<T> source)

Creates a new GWDTTracer from an ImgPlus.

Parameters:

source - the grayscale image to trace

GWDTTracer

public GWDTTracer(net.imglib2.RandomAccessibleInterval<T> source)

Creates a new GWDTTracer with isotropic spacing (1.0 for each dimension).

GWDTTracer

public GWDTTracer(ij.ImagePlus source)

Creates a new GWDTTracer from an ImagePlus.

Parameters:

source - the grayscale image to trace

Method Details

createStorageBackend

protected StorageBackend createStorageBackend()

Description copied from class: AbstractGWDTTracer

Create the storage backend for this tracer. Subclasses override to specify array, sparse, or disk-backed storage.

Specified by:

createStorageBackend in class AbstractGWDTTracer<T extends net.imglib2.type.numeric.RealType<T>>

create

public static GWDTTracer<?> create(net.imagej.ImgPlus<?> source)

create

public static GWDTTracer<?> create(ij.ImagePlus source)

main

public static void main(String[] args)