Package sc.fiji.snt.tracing.auto

Class DiskBackedGWDTTracer<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.DiskBackedGWDTTracer<T>

Type Parameters:

T - pixel type

All Implemented Interfaces:

AutoTracer

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

Disk-backed GWDT tracer for very large images.

Uses disk-based caching to process images of arbitrary size with bounded memory usage (~500MB-1GB). Temporary files are automatically created in the system temp directory and deleted after tracing.

Trade-offs:

• Memory: Constant (~500MB-1GB) regardless of image size
• Speed: 2-5× slower than GWDTTracer due to disk I/O
• Disk: Requires ~25 bytes per voxel temporary storage
• Best for: Images > 2GB or systems with limited RAM

Example use cases:

• Whole-brain light-sheet images (4096×4096×1000)
• High-resolution tile scans
• Processing on laptops with limited RAM

Author:

Tiago Ferreira

See Also:

• AbstractGWDTTracer
• GWDTTracer

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

Method Summary

Modifier and Type	Method	Description
static DiskBackedGWDTTracer<?>	create(ij.ImagePlus source)
static DiskBackedGWDTTracer<?>	create(net.imagej.ImgPlus<?> source)
protected StorageBackend	createStorageBackend()	Create the storage backend for this tracer.

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

DiskBackedGWDTTracer

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

Creates a new DiskBackedGWDTTracer.

Parameters:

source - the grayscale image to trace

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

DiskBackedGWDTTracer

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

Creates a new DiskBackedGWDTTracer from an ImgPlus.

Parameters:

source - the grayscale image to trace

DiskBackedGWDTTracer

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

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

DiskBackedGWDTTracer

public DiskBackedGWDTTracer(ij.ImagePlus source)

Creates a new DiskBackedGWDTTracer 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 DiskBackedGWDTTracer<?> create(net.imagej.ImgPlus<?> source)

create

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