Package sc.fiji.snt.analysis.curation

Class PlausibilityCheck.BoundaryProximity

java.lang.Object

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

sc.fiji.snt.analysis.curation.PlausibilityCheck.BoundaryProximity

Enclosing class:

PlausibilityCheck

public static class PlausibilityCheck.BoundaryProximity
extends PlausibilityCheck.DeepCheck

Flags terminal branches whose endpoint lies suspiciously close to the image's field-of-view boundary. Pattern: the trace was truncated by the imaging window, not by an actual neurite ending. The check requires image data so it knows the FOV dimensions.

Constructor Summary

Constructors

Constructor	Description
BoundaryProximity()

Method Summary

Modifier and Type	Method	Description
double	getMinVoxelsFromBoundary()
String	getName()
boolean	hasImage()
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	setImage(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> image)	Sets the image whose FOV dimensions are used as the reference.
void	setMinVoxelsFromBoundary(double v)

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

BoundaryProximity

public BoundaryProximity()

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

setMinVoxelsFromBoundary

public void setMinVoxelsFromBoundary(double v)

getMinVoxelsFromBoundary

public double getMinVoxelsFromBoundary()

setImage

public void setImage(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> image)

Sets the image whose FOV dimensions are used as the reference.

hasImage

public boolean hasImage()

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.