Package sc.fiji.snt.tracing.auto

Class AutoTraceConfig

java.lang.Object

sc.fiji.snt.tracing.auto.AutoTraceConfig

public class AutoTraceConfig
extends Object

Derives AbstractGWDTTracer configuration parameters from one or more example paths. This is the "learn from example" mechanism: the user traces or selects a representative neurite, and this class extracts morphometric and signal properties to autofill tracer settings.

Usage:

   AutoTraceConfig config = AutoTraceConfig.fromPaths(paths, sourceImage, spacing);
   config.applyTo(tracer);
 

If input paths lack fitted radii, a non-destructive fit is attempted automatically (PathFitter.setReplaceNodes(boolean) = false).

Author:

Tiago Ferreira

Method Summary

Modifier and Type	Method	Description
<T extends net.imglib2.type.numeric.RealType<T>> void	applyTo(AbstractGWDTTracer<T> tracer)	Applies this configuration to a tracer, setting all derived parameters.
static AutoTraceConfig	fromPaths(List<Path> paths, net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> source, double[] spacing)	Derives auto-trace configuration from one or more example paths.
double	getBackgroundThreshold()
double	getBranchTuneMaxAngle()
double	getMeanContraction()
double	getMeanIntensity()
double	getMeanRadius()
double	getMinBranchIntensityLength()
int	getNodeCount()
int	getPathCount()
double	getReconnectMaxAngleDeg()
double	getReconnectMaxBridgeDist()
double	getReconnectMinContraction()
double[]	getScoreMapScales()
String	getSummary()	Returns a human-readable summary of the derived configuration, suitable for display in a dialog or log.

Methods inherited from class java.lang.Object

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

Method Details

fromPaths

public static AutoTraceConfig fromPaths(List<Path> paths,
 net.imglib2.RandomAccessibleInterval<? extends net.imglib2.type.numeric.RealType<?>> source,
 double[] spacing)

Derives auto-trace configuration from one or more example paths.

Parameters:

paths - representative paths (at least one required)

source - the grayscale image being traced

spacing - voxel dimensions [x, y, z] in physical units

Returns:

a new configuration with derived parameters

Throws:

IllegalArgumentException - if paths is null or empty

applyTo

public <T extends net.imglib2.type.numeric.RealType<T>>
void applyTo(AbstractGWDTTracer<T> tracer)

Applies this configuration to a tracer, setting all derived parameters. Parameters that could not be derived (NaN) are left at the tracer's current defaults.

Type Parameters:

T - pixel type

Parameters:

tracer - the tracer to configure

getSummary

public String getSummary()

Returns a human-readable summary of the derived configuration, suitable for display in a dialog or log.

Returns:

multi-line summary string

getScoreMapScales

public double[] getScoreMapScales()

getBackgroundThreshold

public double getBackgroundThreshold()

getMinBranchIntensityLength

public double getMinBranchIntensityLength()

getBranchTuneMaxAngle

public double getBranchTuneMaxAngle()

getReconnectMinContraction

public double getReconnectMinContraction()

getReconnectMaxAngleDeg

public double getReconnectMaxAngleDeg()

getReconnectMaxBridgeDist

public double getReconnectMaxBridgeDist()

getMeanRadius

public double getMeanRadius()

getMeanIntensity

public double getMeanIntensity()

getMeanContraction

public double getMeanContraction()

getPathCount

public int getPathCount()

getNodeCount

public int getNodeCount()