Package sc.fiji.snt.analysis.curation

Class PlausibilityCheck.Crossovers

java.lang.Object

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

sc.fiji.snt.analysis.curation.PlausibilityCheck.Crossovers

Enclosing class:

PlausibilityCheck

public static class PlausibilityCheck.Crossovers
extends PlausibilityCheck.DeepCheck

Detects suspicious crossings between paths via CrossoverFinder: X-shape near-coincidences where two paths almost touch. Complementary to PlausibilityCheck.BundledPaths (||-shape parallel runs).

By default ignores self-crossovers (a path crossing itself) and direct parent/child overlap at fork points. Enable setIncludeSelfCrossovers(boolean) to also catch paths that loop back through themselves.

Constructor Summary

Constructors

Constructor	Description
Crossovers()

Method Summary

Modifier and Type	Method	Description
boolean	getIncludeSelfCrossovers()
String	getName()
double	getProximityUm()
PlausibilityCheck.ImpactKind	impactKind()	Declares how this check's errors propagate.
PlausibilityCheck.Measurements	measure(Collection<Path> paths)	Sweeps CrossoverFinder at 5x the current proximity threshold so the histogram shows context around the cutoff, not just flagged events.
List<PlausibilityCheck.Warning>	scan(Collection<Path> paths)	Scans a collection of paths for plausibility issues.
void	setIncludeSelfCrossovers(boolean b)	If true, paths that cross themselves (loops back through their own trajectory) are also flagged.
void	setProximityUm(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

Crossovers

public Crossovers()

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

setProximityUm

public void setProximityUm(double um)

getProximityUm

public double getProximityUm()

setIncludeSelfCrossovers

public void setIncludeSelfCrossovers(boolean b)

If true, paths that cross themselves (loops back through their own trajectory) are also flagged. Default false: only between-path crossings are reported.

getIncludeSelfCrossovers

public boolean getIncludeSelfCrossovers()

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)

Sweeps CrossoverFinder at 5x the current proximity threshold so the histogram shows context around the cutoff, not just flagged events. The threshold marker indicates where the user's current cutoff lies; events at distance > proximityUm appear unflagged.

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.