Package sc.fiji.snt.analysis.curation

Class PlausibilityCheck

java.lang.Object

sc.fiji.snt.analysis.curation.PlausibilityCheck

public final class PlausibilityCheck
extends Object

Framework for evaluating the morphological plausibility of path operations and reconstructions. Checks come in two tiers:

• PlausibilityCheck.LiveCheck: lightweight checks that run inline during interactive tracing (at fork, segment, and edit hook points).
• PlausibilityCheck.DeepCheck: heavier checks that scan an entire reconstruction on demand (e.g., overlap detection, global radius analysis).

Both tiers share the same PlausibilityCheck.Warning type and severity model.

Author:

Tiago Ferreira

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	PlausibilityCheck.BoundaryProximity	Flags terminal branches whose endpoint lies suspiciously close to the image's field-of-view boundary.
static class	PlausibilityCheck.BranchAngle	Warns when the bifurcation angle at a fork is outside a plausible range.
static class	PlausibilityCheck.BundledPaths	Detects regions where two unconnected paths run parallel to each other for an extended distance.
static class	PlausibilityCheck.ConstantRadii	Warns when a path has radii assigned, but they are all identical (likely unfitted defaults).
static class	PlausibilityCheck.Crossovers	Detects suspicious crossings between paths via CrossoverFinder: X-shape near-coincidences where two paths almost touch.
static class	PlausibilityCheck.DeepCheck	A heavier check that scans an entire collection of paths for issues.
static class	PlausibilityCheck.DirectionContinuity	Warns when the child path's initial direction deviates sharply from the parent's tangent at the branch point (potential U-turn).
static enum	PlausibilityCheck.ImpactKind	Classifies how an error propagates through the reconstruction.
static class	PlausibilityCheck.IntensityValley	Flags localized intensity valleys along a path's intensity profile: discrete dips of one or a few nodes whose intensity is markedly below the surrounding peaks.
static class	PlausibilityCheck.InterForkDistance	Warns when two consecutive forks on the same parent path are implausibly close together.
static class	PlausibilityCheck.InvalidRadius	Flags nodes whose radius is zero, negative, or NaN.
static class	PlausibilityCheck.LiveCheck	A lightweight check that evaluates the plausibility of a single fork operation (parent + child + branch index).
static final record	PlausibilityCheck.Measurements	Full distribution of a check's raw measurements across a reconstruction, collected without applying the warning threshold.
static class	PlausibilityCheck.RadiusContinuity	Warns when the child neurite's radius at the fork point exceeds the parent's radius at the branch point.
static class	PlausibilityCheck.RadiusJumps	Detects abrupt radius jumps between adjacent nodes within a path.
static class	PlausibilityCheck.RadiusMonotonicity	Detects sustained radius increases along a path (neurites should generally taper distally).
static enum	PlausibilityCheck.Severity	Severity levels for plausibility warnings.
static class	PlausibilityCheck.SignalQuality	Assesses local image signal quality around traced paths and flags those in regions with poor contrast.
static class	PlausibilityCheck.SomaDistance	Warns when a primary path starts far from any soma node.
static class	PlausibilityCheck.TerminalBranchLength	Warns when a terminal path is suspiciously short.
static class	PlausibilityCheck.TerminalNearAncestor	Flags terminal branches whose endpoint sits suspiciously close to a node on a non-ancestor path.
static class	PlausibilityCheck.TortuosityConsistency	Warns when child and parent have very different tortuosity (contraction).
static class	PlausibilityCheck.UncertainTerminal	Flags terminal branches whose final few nodes have low signal/background contrast: the tip's spatial location is poorly determined because the neurite faded into the background before the trace stopped.
static final record	PlausibilityCheck.Warning	A plausibility warning produced by a check.
static class	PlausibilityCheck.ZExtentRatio	Flags paths whose Z-extent is implausibly small relative to their length.

Method Summary

Modifier and Type	Method	Description
protected static double	mag(double[] v)

Methods inherited from class java.lang.Object

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

Method Details

mag

protected static double mag(double[] v)