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.gui	Customizations and commands for SNT's GUI.
sc.fiji.snt.util	Miscellaneous SNT utilities, including classes defining reconstruction nodes.

Uses of Path in sc.fiji.snt

Methods in sc.fiji.snt that return Path

Modifier and Type	Method and Description
Path	SearchNode.asPath(double x_spacing, double y_spacing, double z_spacing, java.lang.String spacing_units)
Path	SearchNode.asPathReversed(double x_spacing, double y_spacing, double z_spacing, java.lang.String spacing_units)
Path	SNT.autoTrace(java.util.List<PointInImage> pointList, PointInImage forkPoint) Automatically traces a path from a list of points and adds it to the active PathAndFillManager instance.
Path	SNT.autoTrace(PointInImage start, PointInImage end, PointInImage forkPoint) 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()
Path	Tree.get(int index) Returns the Path at the specified position.
Path	SNT.getCurrentPath()
Path	Path.getEndJoins()
Path	Path.getFitted() Gets the fitted version ('flavor') of this Path.
Path	NearPoint.getPath()
Path	PathAndFillManager.getPath(int i) Returns the Path at the specified position in the PathAndFillManager list.
Path	PathAndFillManager.getPathFromID(int id) Returns the Path with the specified id.
Path	PathAndFillManager.getPathFromName(java.lang.String name, boolean caseSensitive) Returns the Path with the specified name.
Path[]	PathAndFillManager.getPathsStructured()
Path[]	PathAndFillManager.getPathsStructured(java.util.Collection<Path> paths)
Path	TubularGeodesicsTracer.getResult()
Path	FillerThread.getResult()
Path	ManualTracerThread.getResult()
Path	SearchInterface.getResult()
Path	TracerThread.getResult()
Path	Path.getSection(int startIndex, int endIndex) Gets a section between two nodes of this Path.
Path	Path.getStartJoins()
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 and Description
java.util.List<Path>	SNTService.getPaths() Gets the paths currently listed in the Path Manager
java.util.ArrayList<Path>	PathAndFillManager.getPaths() Returns all the paths.
java.util.ArrayList<Path>	PathAndFillManager.getPathsFiltered()
java.util.Collection<Path>	SNT.getSelectedPaths()
java.util.Collection<Path>	SNTService.getSelectedPaths() Gets the paths currently selected in the Path Manager list.
java.util.Set<Path>	PathAndFillManager.getSelectedPaths() Gets all paths selected in the GUI
java.util.Collection<Path>	PathManagerUI.getSelectedPaths(boolean ifNoneSelectedGetAll) Gets the paths currently selected in the Manager's JTree list.
java.util.ArrayList<Path>	Tree.list() Gets all the paths from this tree.
static java.util.List<Path>	SNTUtils.randomPaths() Generates a list of random paths.

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

Modifier and Type	Method and Description
boolean	Tree.add(Path p) Adds a new Path to this Tree.
void	PathAndFillManager.addPath(Path p) Adds a new path.
int	Path.compareTo(Path o)
boolean	PathAndFillManager.deletePath(Path p) Deletes a path.
static java.lang.String	PathManagerUI.extractTagsFromPath(Path p)
int	PathAndFillManager.getPathIndex(Path p) Gets the index of a Path
int	Tree.indexOf(Path path) Returns the index of the specified Path in this Tree.
boolean	PathAndFillManager.isSelected(Path path) Checks if a Path is currently selected in the GUI.
boolean	Tree.remove(Path p) Removes a path from this tree.
void	PathAndFillManager.resetListeners(Path justAdded)
void	SNT.selectPath(Path p, boolean addToExistingSelection)
void	SNT.setCurrentPath(Path path)
void	Path.setEndJoin(Path other, PointInImage joinPoint)
void	PathManagerUI.setPathList(java.lang.String[] pathList, Path justAdded, boolean expandAll)
void	SNT.setPathList(java.lang.String[] newList, Path justAdded, boolean expandAll)
void	FillManagerUI.setPathList(java.lang.String[] pathList, Path justAdded, boolean expandAll)
void	Fill.setSourcePaths(Path[] newSourcePaths)
void	Path.setStartJoin(Path other, PointInImage joinPoint)
void	SNT.setTemporaryPath(Path path)

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

Modifier and Type	Method and Description
Path[]	PathAndFillManager.getPathsStructured(java.util.Collection<Path> paths)
java.util.List<SWCPoint>	PathAndFillManager.getSWCFor(java.util.Collection<Path> paths) Gets the list of SWCPoints associated with a collection of Paths.
ij.ImagePlus	SNT.makePathVolume(java.util.Collection<Path> paths)
void	Tree.replaceAll(java.util.List<Path> paths) Replaces all Paths in this Tree.
void	PathManagerUI.setSelectedPaths(java.util.HashSet<Path> selectedPaths, java.lang.Object source)
void	SNT.setSelectedPaths(java.util.HashSet<Path> selectedPathsSet, java.lang.Object source)
void	FillManagerUI.setSelectedPaths(java.util.HashSet<Path> selectedPathSet, java.lang.Object source)
void	FillerThread.setSourcePaths(java.util.Collection<Path> newSourcePaths)
void	Fill.setSourcePaths(java.util.Set<Path> newSourcePaths)
void	SNT.startFillingPaths(java.util.Set<Path> fromPaths)

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

Constructor and Description
NearPoint(PointInImage nearPoint, Path path, int indexInPath)
PathFitter(ij.ImagePlus imp, Path path) Instantiates a new PathFitter.
PathFitter(SNT plugin, Path path) Instantiates a new PathFitter.

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

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

Uses of Path in sc.fiji.snt.analysis

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

Modifier and Type	Method and Description
java.util.Set<Path>	TreeAnalyzer.getPrimaryBranches() Retrieves the primary branches of the analyzed Tree.
java.util.Set<Path>	TreeAnalyzer.getPrimaryPaths() Retrieves all the Paths in the analyzed Tree tagged as primary.
java.util.Set<Path>	TreeAnalyzer.getTerminalBranches() Retrieves the terminal branches of the analyzed Tree.

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

Modifier and Type	Method and Description
void	PathProfiler.assignValues(Path p) Retrieves pixel intensities at each node of the Path storing them as Path values
java.util.Map<java.lang.String,java.util.List<java.lang.Double>>	PathProfiler.getValues(Path p) Gets the profile for the specified path as a map of lists, with distances stored under PathProfiler.X_VALUES ("x-values") and intensities under PathProfiler.Y_VALUES ("y-values").

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

Constructor and Description
PathProfiler(Path path, ij.ImagePlus imp) Instantiates a new Profiler from a single path

Uses of Path in sc.fiji.snt.gui

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

Modifier and Type	Method and Description
static void	ShollAnalysisDialog.addPathPointsToShollList(Path p, double x_start, double y_start, double z_start, java.util.List<ShollAnalysisDialog.ShollPoint> shollPointsList) Deprecated.

Uses of Path in sc.fiji.snt.util

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

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

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

Modifier and Type	Method and Description
Path	PointInImage.getPath() Returns the Path associated with this node (if any)

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

Modifier and Type	Method and Description
void	PointInImage.setPath(Path onPath) Associates a Path with this node