Package sc.fiji.snt.analysis.curation

Class PlausibilityCheck.UncertainTerminal

java.lang.Object

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

sc.fiji.snt.analysis.curation.PlausibilityCheck.UncertainTerminal

Enclosing class:

PlausibilityCheck

public static class PlausibilityCheck.UncertainTerminal
extends PlausibilityCheck.DeepCheck

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. Distinct from PlausibilityCheck.SignalQuality (whole-path contrast) and PlausibilityCheck.BoundaryProximity (FOV truncation) -- this check is tip-specific and image-based.

The check reuses the same contrast machinery as SignalQuality via PlausibilityCheck.contrastOverNodeRange(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>>, sc.fiji.snt.Path, int, int), restricted to the last tailNodes of each terminal. A naturally tapering ending with bright signal scores high contrast; a tip that fades into noise scores low.

Field Summary

Fields

Modifier and Type	Field	Description
static final double	AUTO_THRESHOLD	Sentinel value indicating the threshold should be auto-resolved.

Constructor Summary

Constructors

Constructor	Description
UncertainTerminal()

Method Summary

Modifier and Type	Method	Description
double	getMinTipContrast()
String	getName()
double	getResolvedThreshold()
int	getTailNodes()
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.
void	prepareImage(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> rai)	Sets the image and, if no peer can supply equivalent stats, scans the full volume to populate min/max.
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 intensities define signal vs background.
void	setImageStats(double min, double max)	Sets image-level statistics used to auto-compute the contrast threshold when getMinTipContrast() == AUTO_THRESHOLD and the peer cannot supply a value.
void	setMinTipContrast(double v)
void	setSignalQualityPeer(PlausibilityCheck.SignalQuality peer)	Wires a peer PlausibilityCheck.SignalQuality.
void	setTailNodes(int n)

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

Field Details

AUTO_THRESHOLD

public static final double AUTO_THRESHOLD

Sentinel value indicating the threshold should be auto-resolved.

See Also:

• Constant Field Values

Constructor Details

UncertainTerminal

public UncertainTerminal()

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

setMinTipContrast

public void setMinTipContrast(double v)

getMinTipContrast

public double getMinTipContrast()

setTailNodes

public void setTailNodes(int n)

getTailNodes

public int getTailNodes()

setImage

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

Sets the image whose intensities define signal vs background.

hasImage

public boolean hasImage()

setSignalQualityPeer

public void setSignalQualityPeer(PlausibilityCheck.SignalQuality peer)

Wires a peer PlausibilityCheck.SignalQuality. When set, resolveThreshold() prefers the peer's resolved threshold (provided the peer is enabled and has run PlausibilityCheck.SignalQuality.prepareImage(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>>)). This avoids a duplicate full-volume scan and keeps the two checks numerically in sync. Pass null to disable peer borrowing.

setImageStats

public void setImageStats(double min,
 double max)

Sets image-level statistics used to auto-compute the contrast threshold when getMinTipContrast() == AUTO_THRESHOLD and the peer cannot supply a value.

prepareImage

public void prepareImage(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> rai)

Sets the image and, if no peer can supply equivalent stats, scans the full volume to populate min/max. Mirrors PlausibilityCheck.SignalQuality.prepareImage(net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>>). Skips the scan when a wired, enabled peer already has valid stats: in that case the peer's resolved threshold is reused, so rescanning would be wasted work.

Should always be called from a worker thread.

getResolvedThreshold

public double getResolvedThreshold()

Returns:

the resolved threshold (adopted from peer or derived from own stats).

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.