Package sc.fiji.snt.analysis.curation

Class PlausibilityCheck.BundledPaths

java.lang.Object

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

sc.fiji.snt.analysis.curation.PlausibilityCheck.BundledPaths

Enclosing class:

PlausibilityCheck

public static class PlausibilityCheck.BundledPaths
extends PlausibilityCheck.DeepCheck

Detects regions where two unconnected paths run parallel to each other for an extended distance. Complementary to PlausibilityCheck.Crossovers (which catches brief perpendicular near-crossings -- the X-shape): this check catches sustained parallel proximity (the ||-shape) that CrossoverFinder's default high-angle filter intentionally discards. Wraps BundleDetector, which is itself a thin reuse layer over CrossoverFinder with an inverted angle filter.

Off by default. The check serves the "is this a duplicate trace?" curation question rather than the "did I miss a fork?" question served by Crossovers. Bundled axons exist legitimately in many neuroanatomies (parallel fibers, callosal projections, optic tract), so the check will flag those as well -- it's an INFO prompt asking the user to verify, not an assertion of error.

Constructor Summary

Constructors

Constructor	Description
BundledPaths()

Method Summary

Modifier and Type	Method	Description
double	getMaxParallelAngleDeg()
int	getMinRunNodes()
String	getName()
double	getProximityUm()
PlausibilityCheck.ImpactKind	impactKind()	Declares how this check's errors propagate.
PlausibilityCheck.Measurements	measure(Collection<Path> paths)	The measurement is each detected proximity-run's median angle: the histogram lets the user see how their maxParallelAngleDeg sits in the angle distribution.
List<PlausibilityCheck.Warning>	scan(Collection<Path> paths)	Scans a collection of paths for plausibility issues.
void	setMaxParallelAngleDeg(double v)
void	setMinRunNodes(int n)
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

BundledPaths

public BundledPaths()

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

setMaxParallelAngleDeg

public void setMaxParallelAngleDeg(double v)

getMaxParallelAngleDeg

public double getMaxParallelAngleDeg()

setMinRunNodes

public void setMinRunNodes(int n)

getMinRunNodes

public int getMinRunNodes()

setProximityUm

public void setProximityUm(double um)

getProximityUm

public double getProximityUm()

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)

The measurement is each detected proximity-run's median angle: the histogram lets the user see how their maxParallelAngleDeg sits in the angle distribution. Sweep at the full 0-90° range so the histogram reflects the true distribution irrespective of the spinner value

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.