Uses of Class
sc.fiji.snt.Path

Packages that use Path

Package	Description
sc.fiji.snt	SNT core classes
sc.fiji.snt.analysis	Analysis of Trees.
sc.fiji.snt.analysis.curation	Classes for curation of reconstructions, as implemented by the "Curation Assistant".
sc.fiji.snt.analysis.detection	Feature detectors for traced paths.
sc.fiji.snt.analysis.graph	Classes for handling neuronal reconstructions as graphs
sc.fiji.snt.analysis.growth	Classes for growth analysis of neurites across time
sc.fiji.snt.filter	Filters for detection of tube-like structures
sc.fiji.snt.gui	Customizations and commands for SNT's GUI.
sc.fiji.snt.tracing	Path-finding algorithms for interactive neuron tracing.
sc.fiji.snt.tracing.auto	Automatic neuron tracing algorithms that reconstruct complete neuronal morphologies from images without user interaction.
sc.fiji.snt.util	Miscellaneous SNT utilities, including classes defining reconstruction nodes.

Uses of Path in sc.fiji.snt

Fields in sc.fiji.snt declared as Path

Modifier and Type	Field	Description
protected Path	SNT.currentPath
protected Path	Path.fitted
protected Path	Path.fittedVersionOf
protected Path	Path.parentPath
protected Path	SNT.temporaryPath

Fields in sc.fiji.snt with type parameters of type Path

Modifier and Type	Field	Description
protected ArrayList<Path>	Path.children
protected ArrayList<Path>	Path.connectedPaths

Methods in sc.fiji.snt that return Path

Modifier and Type	Method	Description
Path	SNT.autoTrace(List<SNTPoint> pointList, PointInImage forkPoint)	Automatically traces a path from a list of points and adds it to the active PathAndFillManager instance.
Path	SNT.autoTrace(List<SNTPoint> pointList, PointInImage forkPoint, boolean headless)	Automatically traces a path from a point A to a point B.
Path	SNT.autoTrace(SNTPoint start, SNTPoint end, PointInImage forkPoint)	Automatically traces a path from a point A to a point B.
Path	SNT.autoTrace(SNTPoint start, SNTPoint end, PointInImage forkPoint, boolean headless)	Automatically traces a path from a point A to a point B.
Path	PathFitter.call()	Takes the signal from the image specified in the constructor to fit cross-section circles around the nodes of input path.
Path	Path.clone()	Creates a deep copy of this Path.
Path	Path.clone(boolean includeImmediateChildren)	Creates a copy of this Path with optional inclusion of immediate children.
Path	Path.createPath()	Returns a new Path with this Path's attributes (e.g. spatial scale), but no nodes.
Path	Tree.get(int index)	Returns the Path at the specified position.
Path	SNT.getCurrentPath()
protected Path	SNT.getEditingPath()
Path	Path.getFitted()	Gets the fitted version ('flavor') of this Path.
Path	Path.getInterpolatedPath(double maxDistance)	Returns a new Path in which nodes have been interpolated to ensure that the distance between consecutive nodes does not exceed the specified threshold.
Path	Path.getParentPath()	Gets the parent path that this path branches from.
Path	NearPoint.getPath()
Path	PathAndFillManager.getPath(int i)	Returns the Path at the specified position in the PathAndFillManager list.
Path	PathFitter.getPath()
protected Path	PathAndFillManager.getPathFrom3DViewerName(String name)
Path	PathAndFillManager.getPathFromID(int id)	Returns the Path with the specified id.
Path	PathAndFillManager.getPathFromName(String name, boolean caseSensitive)	Returns the Path with the specified name.
Path[]	PathAndFillManager.getPathsStructured()
Path[]	PathAndFillManager.getPathsStructured(Collection<Path> paths)
protected Path	SNT.getPreviousEditingPath()
Path	Path.getResampledPath(double targetSpacing)	Returns a new Path in which nodes have been resampled to ensure uniform spacing along the path.
Path	Path.getSection(int startIndex, int endIndex)	Gets a section between two nodes of this Path.
protected Path	SNT.getSingleSelectedPath()
Path	Path.getSmoothedPath(int windowSize)	Returns a smoothed version of this path using a simple moving average filter.
Path	Path.getStartJoins()	Deprecated. use getParentPath() instead
Path	Path.getUnfitted()	Gets the original (unfitted) path that this path is a fitted version of.
Path	MultiPathTracerCanvas.Entry.path()	Returns the value of the path record component.
Path	Path.reversed()
Path	Path.transform(PathTransformer transformation, ij.ImagePlus template, ij.ImagePlus model)

Methods in sc.fiji.snt that return types with arguments of type Path

Modifier and Type	Method	Description
List<Path>	Path.getChildren()	Gets the list of child paths that branch from this path.
List<Path>	PathAndFillManager.getPaths()	Returns the "main" paths managed by this PathAndFillManager.
List<Path>	SNTService.getPaths()	Gets the paths currently listed in the Path Manager
List<Path>	PathAndFillManager.getPathsFiltered()	Returns the 'de facto' Paths (excluding null or fitted versions).
Collection<Path>	PathAndFillManager.getPathsInROI(ij.gui.Roi roi)
Set<Path>	PathAndFillManager.getSelectedPaths()	Gets all paths selected in the GUI
List<Path>	PathManagerUI.getSelectedPaths(boolean ifNoneSelectedGetAll)	Gets the paths currently selected in the Manager's JTree list.
Collection<Path>	SNT.getSelectedPaths()
Collection<Path>	SNTService.getSelectedPaths()	Gets the paths currently selected in the Path Manager list.
Set<Path>	Fill.getSourcePaths()	Returns the set of source paths for the filled structure.
protected List<Path>	PathAndFillManager.getUnSelectedPathsRenderedInViewPort(TracerCanvas canvas)
List<Path>	Tree.list()	Gets all the paths from this tree.
static List<Path>	SNTUtils.randomPaths()	Generates a list of random paths.

Methods in sc.fiji.snt with parameters of type Path

Modifier and Type	Method	Description
void	BookmarkManager.add(Path path, int nodeIndex)
void	Path.add(Path other)
boolean	Tree.add(Path p)	Adds a new Path to this Tree.
void	MultiPathTracerCanvas.addEntry(Path path, Color color, boolean highlighted)	Appends a single entry without repainting
void	PathAndFillManager.addPath(Path p)	Adds a new path.
void	PathAndFillManager.addPath(Path p, boolean forceNewName, boolean forceNewId)
protected void	PathAndFillManager.addPath(Path p, boolean forceNewName, boolean forceNewId, boolean assumeMaxUsedTreeID)
void	PathAndFillManager.addPath(Path p, int id, int treeID)
int	Path.compareTo(Path o)
boolean	PathAndFillManager.deletePath(Path p)	Deletes a path.
protected boolean	SNT.editModeAllowed(boolean warnUserIfNot, Path pathToEdit)	Checks if edit mode can be enabled, optionally using a specific path.
protected boolean	PathAndFillManager.exportAllPathsAsSWC(Path[] primaryPaths, String baseFilename, String commonFileHeader)
protected boolean	PathAndFillManager.exportConnectedStructureAsSWC(Path primaryPath, File swcFile, String commonFileHeader)
static String	PathManagerUI.extractTagsFromPath(Path p)
protected String	PathAndFillManager.getDefaultName(Path p)
int	Tree.indexOf(Path path)	Returns the index of the specified Path in this Tree.
boolean	Path.isConnectedTo(Path other)
boolean	PathAndFillManager.isSelected(Path path)	Checks if a Path is currently selected in the GUI.
void	BookmarkManager.remove(Path path, int nodeIndex)
boolean	Tree.remove(Path p)	Removes a path from this tree.
protected void	SNT.replaceCurrentPath(Path path)
void	Path.replaceNodes(Path replacementPath)	Replaces all nodes of this path with those from the replacement path, preserving hierarchical relationships (parent, children, connections).
void	PathAndFillManager.resetListeners(Path justAdded)
protected void	PathAndFillManager.resetListeners(Path justAdded, boolean expandAll)
void	PathManagerUI.select(Path path)	Selects a specific path in the Path Manager.
void	SNT.selectPath(Path p, boolean addToExistingSelection)
void	Path.setBranchFrom(Path parentPath, PointInImage branchPoint)	Establishes this path as a child path originating from the specified parent path.
void	SNT.setCurrentPath(Path path)
protected void	SNT.setEditingPath(Path path)
protected void	Path.setFitted(Path p)
void	FillManagerUI.setPathList(List<Path> pathList, Path justAdded, boolean expandAll)
void	PathManagerUI.setPathList(List<Path> pathList, Path justAdded, boolean expandAll)
void	SNT.setPathList(List<Path> pathList, Path justAdded, boolean expandAll)
void	Fill.setSourcePaths(Path[] newSourcePaths)	Sets the source paths for the filled structure using an array of paths.
void	Path.setStartJoin(Path parentPath, PointInImage branchPoint)	Deprecated. use setBranchFrom(Path, PointInImage) instead
void	SNT.setTemporaryPath(Path path)

Method parameters in sc.fiji.snt with type arguments of type Path

Modifier and Type	Method	Description
void	BookmarkManager.add(Map<Path,Set<Integer>> map, String commonLabel)	Adds multiple bookmarks from selected path nodes
boolean	PathAndFillManager.deletePaths(Collection<Path> paths)	Deletes a collection of paths.
static Set<String>	PathManagerUI.extractTagsFromPaths(Collection<Path> paths)
Path[]	PathAndFillManager.getPathsStructured(Collection<Path> paths)
List<SWCPoint>	PathAndFillManager.getSWCFor(Collection<Path> paths)	Converts a collection of connected Path objects into SWC points for export.
void	SNT.initPathsToFill(Set<Path> fromPaths, boolean splitFillerThreads)
ij.ImagePlus	SNT.makePathVolume(Collection<Path> paths, boolean labelsImage)	Rasterizes centerline of paths into an ImagePlus
NearPoint	PathAndFillManager.nearestPointOnAnyPath(Collection<Path> paths, PointInCanvas pic, double distanceLimit)
protected NearPoint	PathAndFillManager.nearestPointOnAnyPath(Collection<Path> paths, PointInImage pim, double distanceLimitSquared, boolean unScaledPositions)
protected static String	Path.pathsToIDListString(ArrayList<Path> a)
void	PathManagerUI.refreshForPaths(Collection<Path> paths)	Repaints the Path Manager view for the given paths.
void	Tree.replaceAll(List<Path> paths)	Replaces all Paths in this Tree.
protected void	Path.setChildren(Set<Path> pathsLeft)
void	FillManagerUI.setPathList(List<Path> pathList, Path justAdded, boolean expandAll)
void	PathManagerUI.setPathList(List<Path> pathList, Path justAdded, boolean expandAll)
void	SNT.setPathList(List<Path> pathList, Path justAdded, boolean expandAll)
protected void	PathAndFillManager.setSelected(Collection<Path> selectedPaths, Object sourceOfMessage)
void	FillManagerUI.setSelectedPaths(Collection<Path> selectedPathSet, Object source)
void	PathManagerUI.setSelectedPaths(Collection<Path> selectedPaths, Object source)
void	SNT.setSelectedPaths(Collection<Path> selectedPathsSet, Object source)
void	Fill.setSourcePaths(Set<Path> newSourcePaths)	Sets the source paths for the filled structure using a set of paths.

Constructors in sc.fiji.snt with parameters of type Path

Modifier	Constructor	Description
	Entry(Path path, Color color, boolean highlighted)	Creates an instance of a Entry record class.
	NearPoint(PointInImage nearPoint, Path path, int indexInPath)
protected	NearPoint(PointInImage nearPoint, Path path, int indexInPath, boolean unScaledPositions)
	PathFitter(ij.ImagePlus imp, Path path)	Instantiates a new PathFitter.
	PathFitter(net.imagej.ImgPlus<? extends net.imglib2.type.numeric.RealType<?>> img, Path path)	Instantiates a new PathFitter.
	PathFitter(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> img, Path path, double xSpacing, double ySpacing, double zSpacing, String unit)	Instantiates a new PathFitter directly from pixel data.
	PathFitter(SNT plugin, Path path)	Instantiates a new PathFitter.
	PathNodeCanvas(Path path, int index, TracerCanvas canvas)	Creates a node from a Path position.

Constructor parameters in sc.fiji.snt with type arguments of type Path

Modifier	Constructor	Description
	Tree(Collection<Path> paths)	Instantiates a new Tree from a set of paths.

Uses of Path in sc.fiji.snt.analysis

Fields in sc.fiji.snt.analysis with type parameters of type Path

Modifier and Type	Field	Description
protected List<Path>	TreeStatistics.innerBranches
protected List<Path>	TreeColorMapper.paths
protected List<Path>	TreeStatistics.primaryBranches
protected List<Path>	TreeStatistics.terminalBranches

Methods in sc.fiji.snt.analysis that return Path

Modifier and Type	Method	Description
Path	MultiSpectralRefiner.call()	Runs the multispectral refinement on this path.

Methods in sc.fiji.snt.analysis that return types with arguments of type Path

Modifier and Type	Method	Description
List<Path>	MultiTreeStatistics.getBranches()
List<Path>	PathStatistics.getBranches()	Gets all the paths being analyzed as branches.
Map<Integer,List<Path>>	StrahlerAnalyzer.getBranches()
List<Path>	StrahlerAnalyzer.getBranches(int order)
List<Path>	TreeStatistics.getBranches()	Gets all the branches in the analyzed tree.
List<Path>	MultiTreeStatistics.getInnerBranches()
List<Path>	PathStatistics.getInnerBranches()	Gets the inner branches from the analyzed paths.
List<Path>	TreeStatistics.getInnerBranches()	Retrieves the branches of highest Strahler order in the Tree.
List<Path>	MultiTreeStatistics.getPrimaryBranches()
List<Path>	PathStatistics.getPrimaryBranches()	Gets the primary branches from the analyzed paths.
List<Path>	TreeStatistics.getPrimaryBranches()	Retrieves the primary branches of the analyzed Tree.
List<Path>	TreeStatistics.getPrimaryPaths()	Retrieves all the Paths in the analyzed Tree tagged as primary.
List<Path>	StrahlerAnalyzer.getRootAssociatedBranches()
List<Path>	MultiTreeStatistics.getTerminalBranches()
List<Path>	PathStatistics.getTerminalBranches()	Gets the terminal branches from the analyzed paths.
List<Path>	TreeStatistics.getTerminalBranches()	Retrieves the terminal branches of the analyzed Tree.

Methods in sc.fiji.snt.analysis with parameters of type Path

Modifier and Type	Method	Description
void	PathProfiler.assignValues(Path p)	Retrieves pixel intensities at each node of the Path storing them as Path values
<T extends net.imglib2.type.numeric.RealType<T>> void	PathProfiler.assignValues(Path p, int channel)	Retrieves pixel intensities at each node of the Path storing them as Path values
static double[]	MultiSpectralRefiner.computeNodeCosts(ij.ImagePlus imp, Path path)	Computes the cost at each node of a path without modifying it.
static <T extends net.imglib2.type.numeric.NumericType<T>> double[]	MultiSpectralRefiner.computeNodeCosts(net.imagej.ImgPlus<T> img, Path path)	Computes the cost at each node of a path without modifying it.
int[]	PathProfiler.findMaxima(Path path, int channel)	Finds the maxima in the profile of the specified path.
int[]	PathProfiler.findMinima(Path path, int channel)	Finds the minima in the profile of the specified path.
Number	PathStatistics.getMetric(String metric, Path path)	Gets a specific metric value for an individual path.
ij.gui.Plot	NodeProfiler.getPlot(Path path)
ij.gui.Plot	NodeProfiler.getPlot(Path path, int channel)
ij.gui.Plot	PathProfiler.getPlot(Path path)	Gets the plot profile as an ImageJ plot (all channels included).
static PCAnalyzer.PrincipalAxis[]	PCAnalyzer.getPrincipalAxes(Path path)	Computes the principal axes for a Path structure.
double	StrahlerAnalyzer.getRelativeExtensionAngle(Path branch)	Computes the relative extension angle for a StrahlerAnalyzer branch by finding the parent direction from the graph structure.
List<ij.gui.PolygonRoi>	RoiConverter.getROIs(Path path)	Gets ROI representations of the specified path.
SNTTable	NodeProfiler.getTable(Path path)
SNTTable	NodeProfiler.getTable(Path path, int channel)
<T extends net.imglib2.type.numeric.RealType<T>> SortedMap<Integer,List<Double>>	NodeProfiler.getValues(Path p)	Gets the profile for the specified path as a map of lists of pixel intensities (profile indices as keys)
<T extends net.imglib2.type.numeric.RealType<T>> SortedMap<Integer,List<Double>>	NodeProfiler.getValues(Path p, int channel, int frame)	Gets the profile for the specified path as a map of lists of pixel intensities (profile indices as keys)
Map<String,List<Double>>	PathProfiler.getValues(Path p)	Gets the profile for the specified path as a map of lists, with distances (or indices) stored under PathProfiler.X_VALUES ("x-values") and intensities under PathProfiler.Y_VALUES ("y-values").
Map<String,List<Double>>	PathProfiler.getValues(Path p, int channel)	Gets the profile for the specified path as a map of lists, with distances (or indices) stored under PathProfiler.X_VALUES ("x-values") and intensities under PathProfiler.Y_VALUES ("y-values").
static <T extends net.imglib2.type.numeric.RealType<T>> double[]	ProfileProcessor.profilePathNodes(net.imglib2.RandomAccessible<T> rai, Path path, double[] values)	Get the intensities for the point coordinates of a Path

Method parameters in sc.fiji.snt.analysis with type arguments of type Path

Modifier and Type	Method	Description
static ij.gui.Roi	RoiConverter.convert(Collection<Path> paths, ij.ImagePlus imp)
ij.gui.Overlay	RoiConverter.convertPaths(ij.gui.Overlay overlay, Collection<Path> paths)	Converts an ad-hoc collection of paths into 2D polyline ROIs.
static void	PeripathDetector.createTorusMask(Collection<Path> paths, ij.ImagePlus output, PeripathDetector.Config cfg, double fillValue)	Deprecated. Use PeripathDetector.createTorusMask(java.util.Collection<sc.fiji.snt.Path>, net.imglib2.RandomAccessibleInterval<T>, sc.fiji.snt.analysis.detection.PeripathDetector.Config, double) instead.
static <T extends net.imglib2.type.numeric.RealType<T>> void	PeripathDetector.createTorusMask(Collection<Path> paths, net.imglib2.RandomAccessibleInterval<T> output, PeripathDetector.Config cfg, double fillValue)	Deprecated. Use PeripathDetector.createTorusMask(java.util.Collection<sc.fiji.snt.Path>, net.imglib2.RandomAccessibleInterval<T>, sc.fiji.snt.analysis.detection.PeripathDetector.Config, double) instead.
static <T extends net.imglib2.type.numeric.RealType<T>> List<Detection>	PeripathDetector.detect(Collection<Path> paths, net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> img, PeripathDetector.Config cfg)	Deprecated. Use PeripathDetector.detect(java.util.Collection<sc.fiji.snt.Path>, net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>>, sc.fiji.snt.analysis.detection.PeripathDetector.Config) instead.
static ij.gui.Roi	RoiConverter.get2DBoundingBox(Collection<Path> paths, int exportPlane)
static void	ColorMapper.unMap(Collection<Path> paths)	Removes color mapping from the specified collection of paths.

Constructors in sc.fiji.snt.analysis with parameters of type Path

Modifier	Constructor	Description
	Detection(double x, double y, double z, double intensity, Path path, int nodeIndex, double distanceFromSkeleton)	Deprecated.
	MultiSpectralRefiner(ij.ImagePlus imp, Path path)	Creates a refiner for a single path using an ImagePlus.
	MultiSpectralRefiner(net.imagej.ImgPlus<T> img, Path path)	Creates a refiner for a single path using an ImgPlus.
	PathProfiler(Path path, ij.ImagePlus imp)	Deprecated. Use PathProfiler(Path, Dataset)
	PathProfiler(Path path, net.imagej.Dataset dataset)	Instantiates a new Profiler from a single path.
	PathStatistics(Path path)	Instantiates PathStatistics from a single path.
	PathStraightener(Path path, ij.ImagePlus imp)	Instantiates a new PathStraightener
	PathStraightener(Path path, SNT snt)	Instantiates a new PathStraightener
	ProfileProcessor(net.imglib2.RandomAccessibleInterval<T> rai, Path path)
	RoiConverter(Path path, ij.ImagePlus imp)	Instantiates a new Converter.

Constructor parameters in sc.fiji.snt.analysis with type arguments of type Path

Modifier	Constructor	Description
	PathStatistics(Collection<Path> paths, String label)	Instantiates PathStatistics from a collection of paths.
	RoiConverter(Collection<Path> paths, ij.ImagePlus imp)	Instantiates a new Converter.
	TreeStatistics(Collection<Path> paths, String label)	Instantiates Tree statistics from a collection of paths.

Uses of Path in sc.fiji.snt.analysis.curation

Methods in sc.fiji.snt.analysis.curation that return types with arguments of type Path

Modifier and Type	Method	Description
List<Path>	PlausibilityCheck.Warning.affectedPaths()	Returns the value of the affectedPaths record component.
List<Path>	CurationTags.Partition.negative()	Returns the value of the negative record component.
List<Path>	CurationTags.Partition.positive()	Returns the value of the positive record component.
List<Path>	CurationTags.Partition.unreviewed()	Returns the value of the unreviewed record component.
List<Path>	CurationTags.Partition.unsure()	Returns the value of the unsure record component.

Methods in sc.fiji.snt.analysis.curation with parameters of type Path

Modifier and Type	Method	Description
List<PlausibilityCheck.Warning>	PlausibilityCheck.BranchAngle.check(Path parent, Path child, int branchIndex)
List<PlausibilityCheck.Warning>	PlausibilityCheck.ConstantRadii.check(Path parent, Path child, int branchIndex)
List<PlausibilityCheck.Warning>	PlausibilityCheck.DirectionContinuity.check(Path parent, Path child, int branchIndex)
abstract List<PlausibilityCheck.Warning>	PlausibilityCheck.LiveCheck.check(Path parent, Path child, int branchIndex)	Evaluates the plausibility of a child path forking from a parent.
List<PlausibilityCheck.Warning>	PlausibilityCheck.RadiusContinuity.check(Path parent, Path child, int branchIndex)
List<PlausibilityCheck.Warning>	PlausibilityCheck.SomaDistance.check(Path parent, Path child, int branchIndex)	For this check, parent is ignored: it evaluates whether the child's first node is within range of any soma path.
List<PlausibilityCheck.Warning>	PlausibilityCheck.TerminalBranchLength.check(Path parent, Path child, int branchIndex)
List<PlausibilityCheck.Warning>	PlausibilityCheck.TortuosityConsistency.check(Path parent, Path child, int branchIndex)
static void	CurationTags.clearReview(Path path)	Removes every cur:* suffix from path's name.
static boolean	CurationTags.isNegative(Path path)
static boolean	CurationTags.isPositive(Path path)
static boolean	CurationTags.isReviewed(Path path)
static boolean	CurationTags.isUnsure(Path path)
static void	CurationTags.markNegative(Path path)	Tags path as a negative (rejected) review example.
static void	CurationTags.markPositive(Path path)	Tags path as a positive (accepted) review example.
static void	CurationTags.markUnsure(Path path)	Tags path as needing follow-up review ("not sure").
void	PlausibilityMonitor.onForkInitiated(Path parent, int branchIndex)	Hook 1: Fork initiation. Called from SNT.startPath() when the user Alt-clicks to start a branch.
List<PlausibilityCheck.Warning>	PlausibilityMonitor.onNodeEdited(Path editedPath, int nodeIndex)	Hook 4: Node editing. Called after a node is moved, inserted, or deleted during edit mode.
List<PlausibilityCheck.Warning>	PlausibilityMonitor.onPathFinalized(Path completedChild)	Hook 3: Path finalization. Called when the user completes an entire path (SNT.finishPath()).
List<PlausibilityCheck.Warning>	PlausibilityMonitor.onSegmentCompleted(Path candidateChild)	Hook 2: Segment completion. Called from SNT.searchFinished() when A* returns a candidate segment, before the user sees the keep/junk dialog.

Method parameters in sc.fiji.snt.analysis.curation with type arguments of type Path

Modifier and Type	Method	Description
static CurationTags.Partition	CurationTags.partitionByReviewStatus(Collection<Path> paths)	Sibling of CurationTags.partitionByReviewStatus(Tree) that accepts any iterable of paths.
List<PlausibilityCheck.Warning>	PlausibilityMonitor.runDeepScan(Collection<Path> paths)	Runs all enabled PlausibilityCheck.DeepChecks against the given paths.
List<PlausibilityCheck.Warning>	PlausibilityMonitor.runFullScan(Collection<Path> paths)	Runs all enabled checks (both live and deep) against the given paths.
abstract List<PlausibilityCheck.Warning>	PlausibilityCheck.DeepCheck.scan(Collection<Path> paths)	Scans a collection of paths for plausibility issues.
List<PlausibilityCheck.Warning>	PlausibilityCheck.PathOverlap.scan(Collection<Path> paths)
List<PlausibilityCheck.Warning>	PlausibilityCheck.RadiusJumps.scan(Collection<Path> paths)
List<PlausibilityCheck.Warning>	PlausibilityCheck.RadiusMonotonicity.scan(Collection<Path> paths)
List<PlausibilityCheck.Warning>	PlausibilityCheck.SignalQuality.scan(Collection<Path> paths)

Constructor parameters in sc.fiji.snt.analysis.curation with type arguments of type Path

Modifier	Constructor	Description
	Partition(List<Path> positive, List<Path> negative, List<Path> unsure, List<Path> unreviewed)	Creates an instance of a Partition record class.
	Warning(String checkName, PlausibilityCheck.Severity severity, String message, PointInImage location, List<Path> affectedPaths, double value, double threshold)	Compact constructor: guarantees affectedPaths is never null.

Uses of Path in sc.fiji.snt.analysis.detection

Fields in sc.fiji.snt.analysis.detection declared as Path

Modifier and Type	Field	Description
final Path	Detection.path	The path this detection is associated with

Methods in sc.fiji.snt.analysis.detection with parameters of type Path

Modifier and Type	Method	Description
static double[]	DetectorUtils.prepareRadii(Path path)	Prepares a sanitized radius array for the given path.
static List<double[]>	DetectorUtils.sampleDistancesWithIndices(Path path, net.imglib2.img.Img<net.imglib2.type.numeric.real.FloatType> edt)	Samples the EDT at each node of a single path, returning the distance value and node index for each in-bounds node.

Method parameters in sc.fiji.snt.analysis.detection with type arguments of type Path

Modifier and Type	Method	Description
static List<Detection>	DetectorUtils.assignToNearestPaths(List<Detection> detections, Collection<Path> allPaths)	Reassigns each detection to the nearest path (by minimum node distance).
static void	PeripathDetector.createTorusMask(Collection<Path> paths, ij.ImagePlus output, PeripathDetector.Config cfg, double fillValue)	Creates a binary torus mask around the given paths, writing into an ImagePlus.
static <T extends net.imglib2.type.numeric.RealType<T>> void	PeripathDetector.createTorusMask(Collection<Path> paths, net.imglib2.RandomAccessibleInterval<T> output, PeripathDetector.Config cfg, double fillValue)	Creates a binary torus mask around the given paths.
static <T extends net.imglib2.type.numeric.RealType<T>> List<Detection>	AlongPathDetector.detect(Collection<Path> paths, net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> img, AlongPathDetector.Config cfg)	Detects swellings (boutons/varicosities) along the given paths by analyzing the longitudinal radius profile and, optionally, on-skeleton image intensity.
static List<Detection>	AlongPathDetector.detect(Collection<Path> paths, AlongPathDetector.Config cfg)	Convenience overload that performs radius-only detection (no image).
static List<Detection>	LabelProximityDetector.detect(Collection<Path> paths, net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> labelImg, LabelProximityDetector.Config config)	Detects proximity contacts between paths and labeled surfaces.
static <T extends net.imglib2.type.numeric.RealType<T>> List<Detection>	PeripathDetector.detect(Collection<Path> paths, net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> img, PeripathDetector.Config cfg)	Detects intensity maxima along the given paths.
static double[]	DetectorUtils.sampleDistances(Collection<Path> paths, net.imglib2.img.Img<net.imglib2.type.numeric.real.FloatType> edt)	Samples the EDT at every node position of the given paths.

Constructors in sc.fiji.snt.analysis.detection with parameters of type Path

Modifier	Constructor	Description
	Detection(double x, double y, double z, double intensity, Path path, int nodeIndex, double distanceFromSkeleton)	Creates a new detection.
	Detection(double x, double y, double z, double intensity, Path path, int nodeIndex, double distanceFromSkeleton, int labelValue)	Creates a new detection with an associated label value.

Uses of Path in sc.fiji.snt.analysis.graph

Methods in sc.fiji.snt.analysis.graph that return Path

Modifier and Type	Method	Description
Path	DirectedWeightedGraph.getLongestPath(boolean useDirected)	Return the sequence of nodes representing the longest shortest-path in the graph, as a Path.
Path	DirectedWeightedGraph.getShortestPath(SWCPoint v1, SWCPoint v2)	Gets the shortest path between source and target vertex as a Path object.

Uses of Path in sc.fiji.snt.analysis.growth

Methods in sc.fiji.snt.analysis.growth that return Path

Modifier and Type	Method	Description
Path	GrowthAnalyzer.TimePoint.path()	Returns the value of the path record component.

Method parameters in sc.fiji.snt.analysis.growth with type arguments of type Path

Modifier and Type	Method	Description
GrowthAnalysisResults	GrowthAnalyzer.analyze(Collection<Path> paths, double frameInterval, String timeUnits)	Performs growth analysis on a collection of time-matched paths.

Constructors in sc.fiji.snt.analysis.growth with parameters of type Path

Modifier	Constructor	Description
	TimePoint(int frame, double length, Path path)	Creates an instance of a TimePoint record class.

Uses of Path in sc.fiji.snt.filter

Method parameters in sc.fiji.snt.filter with type arguments of type Path

Modifier and Type	Method	Description
static <T extends net.imglib2.type.numeric.RealType<T>> double[]	SpectralSimilarity.averageColorFromPaths(net.imglib2.RandomAccessibleInterval<T> input, List<Path> paths, double xSpacing, double ySpacing, double zSpacing)	Computes the average color vector from path node positions.

Uses of Path in sc.fiji.snt.gui

Methods in sc.fiji.snt.gui that return types with arguments of type Path

Modifier and Type	Method	Description
Collection<Path>	PathManagerUISearchableBar.getPaths()

Methods in sc.fiji.snt.gui with parameters of type Path

Modifier and Type	Method	Description
void	CostPalette.Listener.costFunctionPicked(SNT.CostType chosen, Path chosenPath)	User picked a CostType; chosenPath is the corresponding A* result.

Method parameters in sc.fiji.snt.gui with type arguments of type Path

Modifier and Type	Method	Description
void	PathManagerUISearchableBar.doMorphoFiltering(Collection<Path> paths, String property, Number min, Number max)

Uses of Path in sc.fiji.snt.tracing

Fields in sc.fiji.snt.tracing declared as Path

Modifier and Type	Field	Description
protected Path	BiSearch.result

Methods in sc.fiji.snt.tracing that return Path

Modifier and Type	Method	Description
Path	DefaultSearchNode.asPath(double x_spacing, double y_spacing, double z_spacing, String spacing_units)
Path	DefaultSearchNode.asPathReversed(double x_spacing, double y_spacing, double z_spacing, String spacing_units)
Path	BiSearch.getResult()
Path	FillerThread.getResult()
Path	ManualTracerThread.getResult()
Path	SearchInterface.getResult()
Path	TracerThread.getResult()
Path	TubularGeodesicsTracer.getResult()
protected Path	BiSearch.reconstructPath(double x_spacing, double y_spacing, double z_spacing, String spacing_units)

Methods in sc.fiji.snt.tracing with parameters of type Path

Modifier and Type	Method	Description
protected void	SearchThread.foundGoal(Path pathToGoal)
protected void	TracerThread.foundGoal(Path pathToGoal)

Method parameters in sc.fiji.snt.tracing with type arguments of type Path

Modifier and Type	Method	Description
void	FillerThread.setSourcePaths(Collection<Path> newSourcePaths)

Uses of Path in sc.fiji.snt.tracing.auto

Methods in sc.fiji.snt.tracing.auto that return Path

Modifier and Type	Method	Description
static Path	SomaUtils.roiToSomaPath(ij.gui.Roi roi, double[] spacing)	Creates a single-node soma Path from an ImageJ ROI.
static Path	SomaUtils.roiToSomaPath(ij.gui.Roi roi, Path referencePath)	Creates a single-node soma Path from an ImageJ ROI using calibration from a reference Path.
Path	SomaUtils.SomaResult.toPath(double[] spacing)	Creates a single-node Path representing the soma.

Methods in sc.fiji.snt.tracing.auto with parameters of type Path

Modifier and Type	Method	Description
static Path	SomaUtils.roiToSomaPath(ij.gui.Roi roi, Path referencePath)	Creates a single-node soma Path from an ImageJ ROI using calibration from a reference Path.

Method parameters in sc.fiji.snt.tracing.auto with type arguments of type Path

Modifier and Type	Method	Description
static AutoTraceConfig	AutoTraceConfig.fromPaths(List<Path> paths, net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> source, double[] spacing)	Derives auto-trace configuration from one or more example paths.

Uses of Path in sc.fiji.snt.util

Fields in sc.fiji.snt.util declared as Path

Modifier and Type	Field	Description
Path	PointInImage.onPath	The Path associated with this node, if any (optional field)

Fields in sc.fiji.snt.util with type parameters of type Path

Modifier and Type	Field	Description
final Map<Path,IntSummaryStatistics>	CrossoverFinder.CrossoverEvent.indexWindow	Min/max of node indices per path near the event
final Set<Path>	CrossoverFinder.CrossoverEvent.participants	Unique paths taking part in the crossover

Methods in sc.fiji.snt.util that return Path

Modifier and Type	Method	Description
Path	PointInImage.getPath()	Returns the Path associated with this node (if any)
static Path	TreeUtils.getRootPath(Path path)	Gets the root path of the tree containing the given path.
static Path	TreeUtils.mergePaths(List<Path> orderedPaths, boolean reparentChildren)	Merges a list of paths into a single path by appending nodes sequentially.

Methods in sc.fiji.snt.util that return types with arguments of type Path

Modifier and Type	Method	Description
static List<Path>	TreeUtils.findPathsNeedingReversal(Collection<Path> paths, PointInImage rootLocation)	Determines which paths need to be reversed so that their start nodes point toward a given root location.
static List<Path>	TreeUtils.orderByEndpointProximity(Collection<Path> paths)	Orders a collection of paths to form a spatially continuous chain based on endpoint proximity.

Methods in sc.fiji.snt.util with parameters of type Path

Modifier and Type	Method	Description
static void	TreeUtils.collectChildren(Path path, Collection<Path> children)	Collects direct children of a path into the provided collection.
static void	TreeUtils.collectDescendants(Path path, Collection<Path> descendants)	Collects all descendants (children, grandchildren, etc.) of a path into the provided collection.
static int	TreeUtils.countDescendants(Path path)	Counts all descendants (children, grandchildren, etc.) of a path.
static TreeUtils.EndpointMatch	TreeUtils.findClosestEndpoints(Path p1, Path p2)	Finds the closest endpoint pairing between two paths.
static Tree	TreeUtils.getConnectedTree(Path path)	Gets the connected tree (component) containing the given path.
static int	TreeUtils.getMaxOrder(Path path)	Returns the maximum path order in the connected tree containing the given path.
static Path	TreeUtils.getRootPath(Path path)	Gets the root path of the tree containing the given path.
static boolean	TreeUtils.isAncestorOf(Path potentialAncestor, Path potentialDescendant)	Checks if 'potentialAncestor' is an ancestor of 'potentialDescendant'.
static boolean	TreeUtils.isDescendantOf(Path potentialDescendant, Path potentialAncestor)	Checks if 'potentialDescendant' is a descendant of 'potentialAncestor'.
static boolean	TreeUtils.isInSubtree(Path target, Path root)	Checks if 'target' is in the subtree rooted at 'root'.
void	PointInImage.setPath(Path onPath)	Associates a Path with this node
static void	TreeUtils.syncCanvasOffset(Path child, Path parent)	Applies the parent's canvas offset to the child path and all its descendants.
static void	ImpUtils.zoomTo(ij.ImagePlus imp, double zoomMagnification, PointInImage location, Path path)	Zooms the image canvas to a specific location on a path, correctly accounting for the path's canvas offset.

Method parameters in sc.fiji.snt.util with type arguments of type Path

Modifier and Type	Method	Description
static TreeUtils.EndpointClusterAnalysis	TreeUtils.analyzeEndpointClusters(Collection<Path> paths)	Analyzes a collection of paths to determine which endpoint cluster (starts or ends) is more tightly grouped, suggesting the root location.
static boolean	TreeUtils.canFormContinuousChain(Collection<Path> paths, double tolerance)	Checks if a collection of paths can form a spatially continuous chain within a given tolerance.
static void	TreeUtils.collectChildren(Path path, Collection<Path> children)	Collects direct children of a path into the provided collection.
static void	TreeUtils.collectDescendants(Path path, Collection<Path> descendants)	Collects all descendants (children, grandchildren, etc.) of a path into the provided collection.
static List<CrossoverFinder.CrossoverEvent>	CrossoverFinder.find(Collection<Path> paths, CrossoverFinder.Config cfg)	Entry point: detect crossover events for a collection of paths using the given config.
static List<Path>	TreeUtils.findPathsNeedingReversal(Collection<Path> paths, PointInImage rootLocation)	Determines which paths need to be reversed so that their start nodes point toward a given root location.
static Path	TreeUtils.mergePaths(List<Path> orderedPaths, boolean reparentChildren)	Merges a list of paths into a single path by appending nodes sequentially.
static List<Path>	TreeUtils.orderByEndpointProximity(Collection<Path> paths)	Orders a collection of paths to form a spatially continuous chain based on endpoint proximity.
static void	TreeUtils.orientPathsForMerging(List<Path> orderedPaths)	Orients paths in a chain so they can be merged end-to-start.
static int	TreeUtils.orientPathsTowardRoot(Collection<Path> paths, PointInImage rootLocation)	Orients paths so their start nodes point toward a given root location.
static PointInImage	TreeUtils.suggestRootLocation(Collection<Path> paths, PointInImage referencePoint)	Analyzes paths and suggests auto-orientation based on: If a reference point (e.g., ROI centroid) is provided, orient toward it For 3+ paths: find the tighter endpoint cluster as the root For 2 paths: find the closest endpoint pair as the root
static void	ImpUtils.zoomTo(ij.ImagePlus imp, double zoomLevel, Collection<Path> paths, int plane)	Zooms the image canvas to the specified magnification level, centered on the bounding box of the given paths.
static double	ImpUtils.zoomTo(ij.ImagePlus imp, Collection<Path> paths)	Zooms the image canvas to optimally display the specified paths in the XY plane.
static double	ImpUtils.zoomTo(ij.ImagePlus imp, Collection<Path> paths, int plane)	Zooms the image canvas to optimally display the specified paths in the given plane.

Constructors in sc.fiji.snt.util with parameters of type Path

Modifier	Constructor	Description
	PathCursor(net.imglib2.RandomAccessible<T> accessible, Path path)
protected	PointInCanvas(double x, double y, double z, Path onPath)
protected	PointInImage(double x, double y, double z, Path onPath)