Uses of Class
sc.fiji.snt.util.PointInImage

Packages that use PointInImage

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.sholl.parsers	Parsers to retrieve Sholl profiles from multiple sources (2D/3D images, reconstructions, and tables)
sc.fiji.snt.filter	Filters for detection of tube-like structures
sc.fiji.snt.util	Miscellaneous SNT utilities, including classes defining reconstruction nodes.

Uses of PointInImage in sc.fiji.snt

Subclasses of PointInImage in sc.fiji.snt

Modifier and Type	Class	Description
static class	Path.PathNode	Enhanced PointInImage that stores all node-specific properties.

Fields in sc.fiji.snt declared as PointInImage

Modifier and Type	Field	Description
protected PointInImage	NearPoint.near

Methods in sc.fiji.snt that return PointInImage

Modifier and Type	Method	Description
PointInImage	Path.firstNode()	Returns the first node of this path.
PointInImage	Path.getBranchPoint()	Gets the branch point (junction) where this path starts, i.e., connects to its parent path.
PointInImage	NearPoint.getNode()
PointInImage	Tree.getRoot()	Gets the first node of the main primary path of this tree
PointInImage	Path.getStartJoinsPoint()	Deprecated. Use Path.getBranchPoint() instead.
PointInImage	Path.lastNode()	Returns the last node of this path.
PointInImage	Path.nearestNodeTo(PointInImage node, double within)	Gets the closest node associated with the specified node.
PointInImage	PathAndFillManager.AllPointsIterator.next()

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

Modifier and Type	Method	Description
Iterator<PointInImage>	PathAndFillManager.allPointsIterator()
List<PointInImage>	Path.findJunctions()	Returns the nodes which are indicated to be a join (junction/branch point), either in this Path object, or any other that starts or ends on it.
Set<PointInImage>	Path.getBranchPoints()	This is a version of Path.findJunctions() ensuring that a junction node is only retrieved once even if multiple child paths are associated with it.
Set<PointInImage>	Path.getJunctionNodes()	Deprecated. use Path.getBranchPoints() instead
List<PointInImage>	Path.getNodes()	Gets all nodes as a list.
List<PointInImage>	Tree.getNodes()	Gets all the nodes (path points) forming this tree.
List<PointInImage>	Tree.getSomaNodes()	Gets the list of all nodes tagged as Path.SWC_SOMA.

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

Modifier and Type	Method	Description
void	Path.addNode(PointInImage point)	Appends a node to this Path.
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.
boolean	Path.contains(PointInImage pim)	Check whether this Path contains the specified point
boolean	Path.contains(PointInImage point, double tolerance)	Checks if this path contains the specified point within the given tolerance.
int	Path.getNodeIndex(PointInImage pim)	Gets the first node index associated with the specified image coordinates.
void	Path.insertNode(int index, PointInImage point)	Inserts a node at a specified position.
void	Path.moveNode(int index, PointInImage destination)	Assigns a new location to the specified node.
PointInImage	Path.nearestNodeTo(PointInImage node, double within)	Gets the closest node associated with the specified node.
protected NearPoint	PathAndFillManager.nearestPointOnAnyPath(Collection<Path> paths, PointInImage pim, double distanceLimitSquared, boolean unScaledPositions)
void	Path.setBranchFrom(Path parentPath, PointInImage branchPoint)	Establishes this path as a child path originating from the specified parent path.
void	Path.setStartJoin(Path parentPath, PointInImage branchPoint)	Deprecated. use Path.setBranchFrom(Path, PointInImage) instead
protected void	SNT.startSholl(PointInImage centerScaled)

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

Modifier	Constructor	Description
	NearPoint(PointInImage nearPoint, Path path, int indexInPath)
protected	NearPoint(PointInImage nearPoint, Path path, int indexInPath, boolean unScaledPositions)
	PathNodeCanvas(PointInImage pim, int index, TracerCanvas canvas)	Creates a path node from a PointInImage.

Uses of PointInImage in sc.fiji.snt.analysis

Classes in sc.fiji.snt.analysis with type parameters of type PointInImage

Modifier and Type	Class	Description
class	NodeStatistics<T extends PointInImage>	Computes summary and descriptive statistics from a Collection of nodes, including convenience methods to plot distributions of such data.

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

Modifier and Type	Field	Description
protected Set<PointInImage>	TreeStatistics.tips

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

Modifier and Type	Method	Description
static <T extends PointInImage> void	NodeStatistics.computeNearestNeighborDistances(List<T> points)	Computes nearest neighbor distances.

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

Modifier and Type	Method	Description
PointInImage	ConvexHullAnalyzer.getCentroid()
PointInImage	PeripathDetector.Detection.toSNTPoint()	Returns this detection as an SNTPoint.

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

Modifier and Type	Method	Description
Set<PointInImage>	MultiTreeStatistics.getBranchPoints()
Set<PointInImage>	TreeStatistics.getBranchPoints()	Gets the position of all the branch points in the analyzed tree.
Set<PointInImage>	TreeStatistics.getBranchPoints(BrainAnnotation annot)	Gets the position of all the branch points in the analyzed tree associated with the specified annotation.
Set<PointInImage>	TreeStatistics.getBranchPoints(BrainAnnotation annot, boolean includeChildren)	Gets the position of all the branch points in the analyzed tree associated with the specified annotation.
Set<PointInImage>	MultiTreeStatistics.getTips()
Set<PointInImage>	TreeStatistics.getTips()	Gets the position of all the tips in the analyzed tree.
Set<PointInImage>	TreeStatistics.getTips(double minDistance)	Gets the position of all tips in the analyzed tree that are further distant than the specified distance from the root.
Set<PointInImage>	TreeStatistics.getTips(double minDistance, double maxDistance)	Gets the position of all tips in the analyzed tree that are within the specified distance range from the root.
Set<PointInImage>	TreeStatistics.getTips(BrainAnnotation annot)	Gets the position of all the tips in the analyzed tree associated with the specified annotation.
Set<PointInImage>	TreeStatistics.getTips(BrainAnnotation annot, boolean includeChildren)	Gets the position of all the tips in the analyzed tree associated with the specified annotation.

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

Modifier and Type	Method	Description
void	TreeColorMapper.map(Collection<? extends PointInImage> points, String measurement, String lut)	Colorizes a collection of points after the specified measurement.

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

Methods in sc.fiji.snt.analysis.curation that return PointInImage

Modifier and Type	Method	Description
PointInImage	PlausibilityCheck.Warning.location()	Returns the value of the location record component.

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

Modifier and Type	Method	Description
List<PlausibilityCheck.Warning>	PlausibilityCheck.SomaDistance.checkDistance(PointInImage start, List<PointInImage> somaNodes)	Evaluates distance from a point to the nearest soma location.

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

Modifier and Type	Method	Description
List<PlausibilityCheck.Warning>	PlausibilityCheck.SomaDistance.checkDistance(PointInImage start, List<PointInImage> somaNodes)	Evaluates distance from a point to the nearest soma location.

Constructors in sc.fiji.snt.analysis.curation with parameters of type PointInImage

Modifier	Constructor	Description
	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 PointInImage in sc.fiji.snt.analysis.sholl.parsers

Methods in sc.fiji.snt.analysis.sholl.parsers that return PointInImage

Modifier and Type	Method	Description
PointInImage	TreeParser.getCenter()	Returns the center coordinates

Methods in sc.fiji.snt.analysis.sholl.parsers with parameters of type PointInImage

Modifier and Type	Method	Description
void	TreeParser.setCenter(PointInImage center)	Sets the center of the profile.

Uses of PointInImage in sc.fiji.snt.filter

Methods in sc.fiji.snt.filter with parameters of type PointInImage

Modifier and Type	Method	Description
static int[]	SpectralSimilarity.nodeToPixelCoords(PointInImage node, double xSpacing, double ySpacing, double zSpacing)	Converts a path node from calibrated (real-world) coordinates to pixel coordinates by dividing by the voxel spacing and rounding.

Uses of PointInImage in sc.fiji.snt.util

Subclasses of PointInImage in sc.fiji.snt.util

Modifier and Type	Class	Description
class	PointInCanvas	Defines a Point in a tracing canvas in pixel coordinates.
class	ShollPoint	Convenience flavor of PointInImage defining 2D/3D points for Sholl Analysis.
class	SWCPoint	Defines a node in an SWC reconstruction.

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

Modifier and Type	Field	Description
protected PointInImage	BoundingBox.origin	The bounding box origin (SE, lower corner)
protected PointInImage	BoundingBox.originOpposite	The origin opposite (NW, upper corner)

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

Modifier and Type	Method	Description
static PointInImage	SNTPoint.average(Collection<? extends SNTPoint> points)	Computes the average position of a collection of SNTPoints.
PointInImage	PointInImage.clone()	Creates a copy of this PointInImage.
PointInImage	TreeUtils.EndpointClusterAnalysis.clusterCentroid()	Returns the value of the clusterCentroid record component.
PointInImage	PointInCanvas.getScaledPoint()	Converts the pixels coordinates of this point into a physical location if this point is associated with a Path.
static PointInImage	SNTPoint.of(Number[] coords)
static PointInImage	SNTPoint.of(Number x, Number y, Number z)	Script friendly method for instantiating a new point.
PointInImage	BoundingBox.origin()	Retrieves the origin of this box.
PointInImage	BoundingBox.originOpposite()	Retrieves the origin opposite of this box.
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
PointInImage	PointInImage.transform(PathTransformer transformer)
PointInImage	BoundingBox.unscaledOrigin()	Retrieves the origin of this box in unscaled ("pixel" units)
PointInImage	BoundingBox.unscaledOriginOpposite()	Retrieves the origin opposite of this box in unscaled ("pixel" units)

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

Modifier and Type	Method	Description
double	PointInImage.chebyshevDxTo(PointInImage point)
double	PointInImage.chebyshevXYdxTo(PointInImage point)
double	PointInImage.chebyshevZdxTo(PointInImage point)
double	PointInImage.distanceSquaredTo(PointInImage o)
double	PointInImage.distanceTo(PointInImage o)
double	PointInImage.euclideanDxTo(PointInImage point)
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.
boolean	PointInImage.isSameLocation(PointInImage pim)
static int	TreeUtils.orientPathsTowardRoot(Collection<Path> paths, PointInImage rootLocation)	Orients paths so their start nodes point toward a given root location.
void	BoundingBox.setOrigin(PointInImage origin)	Sets the origin for this box, i.e., its (xMin, yMin, zMin) vertex.
void	BoundingBox.setOriginOpposite(PointInImage originOpposite)	Sets the origin opposite for this box, i.e., its (xMax, yMax, zMax) vertex.
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 zoomMagnification, PointInImage location, Path path)	Zooms the image canvas to a specific location on a path, correctly accounting for the path's canvas offset.

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

Modifier	Constructor	Description
	EndpointClusterAnalysis(boolean useStartNodes, PointInImage clusterCentroid, double variance)	Creates an instance of a EndpointClusterAnalysis record class.
	ShollPoint(PointInImage pim)