Package sc.fiji.snt.analysis.curation

Class PlausibilityCheck.SomaDistance

java.lang.Object

sc.fiji.snt.analysis.curation.PlausibilityCheck.LiveCheck

sc.fiji.snt.analysis.curation.PlausibilityCheck.SomaDistance

Enclosing class:

PlausibilityCheck

public static class PlausibilityCheck.SomaDistance
extends PlausibilityCheck.LiveCheck

Warns when a primary path starts far from any soma node.

Constructor Summary

Constructors

Constructor	Description
SomaDistance()

Method Summary

Modifier and Type	Method	Description
List<PlausibilityCheck.Warning>	check(Path parent, Path child, int branchIndex)	For this check, parent is ignored: it evaluates whether the child's first node is within range of any soma path.
List<PlausibilityCheck.Warning>	checkDistance(PointInImage start, List<PointInImage> somaNodes)	Evaluates distance from a point to the nearest soma location.
double	getMaxDistUm()
String	getName()
void	setMaxDistUm(double dist)

Methods inherited from class sc.fiji.snt.analysis.curation.PlausibilityCheck.LiveCheck

isEnabled, setEnabled

Methods inherited from class java.lang.Object

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

Constructor Details

SomaDistance

public SomaDistance()

Method Details

getName

public String getName()

Specified by:

getName in class PlausibilityCheck.LiveCheck

Returns:

a short human-readable name for this check

setMaxDistUm

public void setMaxDistUm(double dist)

getMaxDistUm

public double getMaxDistUm()

check

public List<PlausibilityCheck.Warning> check(Path parent,
 Path child,
 int branchIndex)

For this check, parent is ignored: it evaluates whether the child's first node is within range of any soma path. The soma paths must be supplied by the monitor via context.

Specified by:

check in class PlausibilityCheck.LiveCheck

Parameters:

parent - the parent path

child - the child (candidate) path

branchIndex - the node index in the parent where the fork occurs

Returns:

list of warnings (empty if the operation is plausible)

checkDistance

public List<PlausibilityCheck.Warning> checkDistance(PointInImage start,
 List<PointInImage> somaNodes)

Evaluates distance from a point to the nearest soma location.

Parameters:

start - the start point of the new path

somaNodes - the soma node locations (may be empty)

Returns:

list of warnings (empty if within range or no soma exists)