Uses of Class
sc.fiji.snt.seed.SeedPoint

Packages that use SeedPoint

Package	Description
sc.fiji.snt	SNT core classes
sc.fiji.snt.seed
sc.fiji.snt.tracing.auto	Automatic neuron tracing algorithms that reconstruct complete neuronal morphologies from images without user interaction.

Uses of SeedPoint in sc.fiji.snt

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

Modifier and Type	Method	Description
static Color	SeedOverlayRenderer.colorForSeed(net.imglib2.display.ColorTable table, SeedOverlay.ColorMode mode, SeedPoint s, double low, double high, double depthFalloff, Map<SeedPoint,Integer> seedIndexMap, Map<String,Integer> categoryOrdinals)	Dispatches to the per-mode color computation.

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

Modifier and Type	Method	Description
static Color	SeedOverlayRenderer.colorForSeed(net.imglib2.display.ColorTable table, SeedOverlay.ColorMode mode, SeedPoint s, double low, double high, double depthFalloff, Map<SeedPoint,Integer> seedIndexMap, Map<String,Integer> categoryOrdinals)	Dispatches to the per-mode color computation.

Uses of SeedPoint in sc.fiji.snt.seed

Methods in sc.fiji.snt.seed that return SeedPoint

Modifier and Type	Method	Description
SeedPoint	SeedOverlay.get(int index)
SeedPoint	SeedOverlay.nearest(double x, double y, double z, double maxDistance)	Returns the seed closest to (x, y, z) in physical units, or null if the overlay is empty or no seed lies within maxDistance.
SeedPoint	SeedOverlay.removeAt(int index)	Removes the seed at the given (data-list) index.

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

Modifier and Type	Method	Description
static List<SeedPoint>	LabelsToSeeds.compute(ij.ImagePlus imp, double minConfidence, String type, String source)	Computes one SeedPoint per non-zero label in imp.
List<SeedPoint>	SeedOverlay.filtered()	Returns a new list of seeds whose confidence falls in [lowConfidence, highConfidence].
Set<SeedPoint>	SeedOverlay.getSelectedSeeds()
List<SeedPoint>	SeedOverlay.list()	Returns a defensive snapshot of all held seeds (a fresh ArrayList, safe to iterate while the overlay continues to mutate on another thread).
List<SeedPoint>	SeedOverlay.topKByConfidence(int k)	Returns up to k seeds from the visible range ([lowConfidence, highConfidence]) with the highest confidence.
static List<SeedPoint>	SeedRois.toSeeds(ij.gui.Roi[] rois, ij.ImagePlus imp, double confidence, String type, String source)	Converts the given ROIs to seeds.

Methods in sc.fiji.snt.seed with parameters of type SeedPoint

Modifier and Type	Method	Description
void	SeedOverlay.add(SeedPoint seed)	Adds a single seed.
double	SeedPoint.distanceSqTo(SeedPoint other)	Squared 3D Euclidean distance to another seed (physical units).
int	SeedOverlay.indexOf(SeedPoint seed)	Returns the index of seed in the data list, or -1 if absent.
boolean	SeedOverlay.isSelected(SeedPoint seed)
boolean	SeedOverlay.remove(SeedPoint seed)	Removes a single seed by reference equality.
boolean	SeedOverlay.replaceAt(int index, SeedPoint replacement)	Replaces the seed at the given index.

Method parameters in sc.fiji.snt.seed with type arguments of type SeedPoint

Modifier and Type	Method	Description
void	SeedOverlay.addAll(Collection<? extends SeedPoint> batch)	Bulk-adds seeds.
int	SeedOverlay.removeAll(Collection<? extends SeedPoint> batch)	Bulk-removes seeds by reference equality.
void	SeedOverlay.replaceAll(Collection<? extends SeedPoint> replacement)	Replaces the current contents with the given seeds.
int	SeedOverlay.replaceAllAt(Map<Integer,SeedPoint> replacements)	Bulk-replaces seeds at multiple positions, firing listeners and invalidating the spatial index once at the end.
void	SeedOverlay.setSelectedSeeds(Collection<? extends SeedPoint> selection)	Replaces the selection set.
static List<ij.gui.Roi>	SeedRois.toRois(Collection<SeedPoint> seeds, ij.ImagePlus imp)	Converts the given seeds to ROIs.

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

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

Modifier and Type	Method	Description
void	AbstractGWDTTracer.setRoots(Collection<SeedPoint> seeds)	Sets the run's root from a collection of seeds.
default void	AutoTracer.setRoots(Collection<SeedPoint> seeds)	Hands the tracer a collection of seeds to use as roots in this run.
void	BinaryTracer.setRoots(Collection<SeedPoint> seeds)	Sets the run's root from a collection of seeds. v1 takes the first seed and bridges to the existing BinaryTracer.setRootRoi(Roi, int) API by synthesizing an oval ROI around the seed (diameter derived from radius, with a minimum of one voxel when radius is unset) and using AutoTracer.ROI_CENTROID placement.
void	AbstractGWDTTracer.setTips(Collection<SeedPoint> seeds)	Configures the run's tips.
default void	AutoTracer.setTips(Collection<SeedPoint> seeds)	Hands the tracer a collection of seeds to use as tips / targets in this run.
void	AbstractGWDTTracer.setWaypoints(Collection<SeedPoint> seeds)	Configures the run's waypoints.
default void	AutoTracer.setWaypoints(Collection<SeedPoint> seeds)	Hands the tracer a collection of seeds to use as waypoints (path constraints) in this run.