Package sc.fiji.snt.analysis.curation

Class PlausibilityCheck.ZExtentRatio

java.lang.Object

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

sc.fiji.snt.analysis.curation.PlausibilityCheck.ZExtentRatio

Enclosing class:

PlausibilityCheck

public static class PlausibilityCheck.ZExtentRatio
extends PlausibilityCheck.DeepCheck

Flags paths whose Z-extent is implausibly small relative to their length. Pattern: the user traced in a single image slice instead of following the neurite through the stack. Caveat: legitimate flat arbors exist (RGC dendrites, some interneurons), so this check is disabled by default and is best enabled via a cell-type-specific preset. Also: if every path in the collection has zero Z-extent the dataset is treated as 2D and the check returns empty silently rather than flagging every path.

Constructor Summary

Constructors

Constructor	Description
ZExtentRatio()

Method Summary

Modifier and Type	Method	Description
double	getMinRatio()
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	setMinRatio(double r)

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

ZExtentRatio

public ZExtentRatio()

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

setMinRatio

public void setMinRatio(double r)

getMinRatio

public double getMinRatio()

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.