Package sc.fiji.snt.analysis.curation

Class PlausibilityCheck.TerminalNearAncestor

java.lang.Object

sc.fiji.snt.analysis.curation.PlausibilityCheck.DeepCheck

sc.fiji.snt.analysis.curation.PlausibilityCheck.TerminalNearAncestor

Enclosing class:

PlausibilityCheck

public static class PlausibilityCheck.TerminalNearAncestor
extends PlausibilityCheck.DeepCheck

Flags terminal branches whose endpoint sits suspiciously close to a node on a non-ancestor path. Pattern: the user traced two paths that should really have been one branching event off a shared ancestor; the terminal "ends" near the ancestor it should have forked off of. Direct parents and ancestors are excluded from the proximity check (it's normal for a terminal to be near its own parent right after the fork), so we only flag "stranger" proximity.

Constructor Summary

Constructors

Constructor	Description
TerminalNearAncestor()

Method Summary

Modifier and Type	Method	Description
double	getMaxProximityUm()
String	getName()
PlausibilityCheck.ImpactKind	impactKind()	Declares how this check's errors propagate.
PlausibilityCheck.Measurements	measure(Collection<Path> paths)	Computes the full distribution of this check's metric across paths, without applying the warning threshold.
List<PlausibilityCheck.Warning>	scan(Collection<Path> paths)	Scans a collection of paths for plausibility issues.
void	setMaxProximityUm(double um)

Methods inherited from class sc.fiji.snt.analysis.curation.PlausibilityCheck.DeepCheck

isEnabled, setEnabled

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

TerminalNearAncestor

public TerminalNearAncestor()

Method Details

getName

public String getName()

Specified by:

getName in class PlausibilityCheck.DeepCheck

Returns:

a short human-readable name for this check

impactKind

public PlausibilityCheck.ImpactKind impactKind()

Description copied from class: PlausibilityCheck.DeepCheck

Declares how this check's errors propagate. Default LOCAL for deep checks because most deep checks (radius jumps, monotonicity, signal quality) measure intrinsic per-path properties that don't propagate to descendants. Topology-class checks (e.g., Crossovers) override to PlausibilityCheck.ImpactKind.SUBTREE.

Overrides:

impactKind in class PlausibilityCheck.DeepCheck

setMaxProximityUm

public void setMaxProximityUm(double um)

getMaxProximityUm

public double getMaxProximityUm()

scan

public List<PlausibilityCheck.Warning> scan(Collection<Path> paths)

Description copied from class: PlausibilityCheck.DeepCheck

Scans a collection of paths for plausibility issues.

Specified by:

scan in class PlausibilityCheck.DeepCheck

Parameters:

paths - the paths to scan

Returns:

list of warnings (empty if no issues found)

measure

public PlausibilityCheck.Measurements measure(Collection<Path> paths)

Description copied from class: PlausibilityCheck.DeepCheck

Computes the full distribution of this check's metric across paths, without applying the warning threshold. Default implementation returns PlausibilityCheck.Measurements.EMPTY; subclasses override to enable per-check histogram popups in the Curation Assistant.

Overrides:

measure in class PlausibilityCheck.DeepCheck

Parameters:

paths - the paths to evaluate; null or empty yields PlausibilityCheck.Measurements.EMPTY.

Returns:

a PlausibilityCheck.Measurements record; never null.