Package sc.fiji.snt.plugin

Class AutotraceFromWaypointsCmd

java.lang.Object

org.scijava.module.AbstractModule

org.scijava.module.DefaultMutableModule

org.scijava.command.DynamicCommand

sc.fiji.snt.gui.cmds.CommonDynamicCmd

sc.fiji.snt.plugin.GWDTTracerCommonCmd

sc.fiji.snt.plugin.AutotraceFromWaypointsCmd

All Implemented Interfaces:

Runnable, org.scijava.Cancelable, org.scijava.command.Command, org.scijava.Contextual, org.scijava.module.Module, org.scijava.module.MutableModule, org.scijava.plugin.SciJavaPlugin

public class AutotraceFromWaypointsCmd
extends GWDTTracerCommonCmd

Single-cell GWDT autotracing wrapper that uses the soma ROI on the canvas (or the auto-detected soma) as the root and the filtered seeds from SNT's SeedOverlay as soft path attractors. Seeds preferentially pull the trace through them by biasing the GWDT cost map before Fast Marching; the resulting root-to-waypoint paths are protected from the pruning passes that would otherwise remove them.

Inherits the soma-ROI strategy and all GWDT tracing options from GWDTTracerCommonCmd; adds the same source and type seed filters as AutotraceFromSeedsCmd plus three bias controls (source, strength, sphere radius).

Author:

Tiago Ferreira

See Also:

• GWDTTracerCommonCmd
• AutotraceFromSeedsCmd
• AutotraceFromTipsCmd
• SeedOverlay

Field Summary

Fields

Modifier and Type	Field	Description
static final String	SOURCE_SELECTION

Fields inherited from class sc.fiji.snt.plugin.GWDTTracerCommonCmd

abortRun, backgroundThreshold, branchTuneMaxAngle, chosenImp, debugMode, imgChoice, imgFileChoice, lengthThreshold, scoreMapFilter

Fields inherited from class sc.fiji.snt.gui.cmds.CommonDynamicCmd

EMPTY_LABEL, HEADER_HTML, snt, sntService, statusService, ui, uiService

Fields inherited from class org.scijava.command.DynamicCommand

moduleService, pluginService

Constructor Summary

Constructors

Constructor	Description
AutotraceFromWaypointsCmd()

Method Summary

Modifier and Type	Method	Description
protected AbstractGWDTTracer<?>	createAndConfigureTracer(net.imagej.ImgPlus<?> img)	Extends the parent's tracer setup with bias configuration and a setWaypoints call.
protected void	init()	Initializer.
protected boolean	isFileMode()
void	run()
protected void	runCommand()

Methods inherited from class sc.fiji.snt.plugin.GWDTTracerCommonCmd

cancel, configureSecondaryScoreMap, error, getImgFromImgChoice, handleTracedTrees, initForFile, initForImage, noValidImgError, scoreMapFilterCallback

Methods inherited from class sc.fiji.snt.gui.cmds.CommonDynamicCmd

cancel, getPromptWithCloseHandler, getPromptWithCloseHandler, init, isCanceled, msg, notifyExternalDataLoaded, notifyLoadingEnd, notifyLoadingStart, resetUI, resetUI, resetUI, status

Methods inherited from class org.scijava.command.DynamicCommand

context, getCancelReason, getContext, getInfo, getInput, getOutput, saveInputs, setContext, setInput, setOutput, uncancel

Methods inherited from class org.scijava.module.AbstractModule

getDelegateObject, getInputs, getOutputs, initialize, isInputResolved, isOutputResolved, preview, resolveInput, resolveOutput, setInputs, setOutputs, unresolveInput, unresolveOutput

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.scijava.module.Module

getDelegateObject, getInputs, getOutputs, initialize, isInputResolved, isOutputResolved, isResolved, preview, resolveInput, resolveOutput, setInputs, setOutputs, setResolved, unresolveInput, unresolveOutput

Methods inherited from interface org.scijava.module.MutableModule

addInput, addInput, addOutput, addOutput, removeInput, removeOutput

Field Details

SOURCE_SELECTION

public static final String SOURCE_SELECTION

See Also:

• Constant Field Values

Constructor Details

AutotraceFromWaypointsCmd

public AutotraceFromWaypointsCmd()

Method Details

init

protected void init()

Initializer. Inherits image-related setup from GWDTTracerCommonCmd.initForImage() and keeps the soma-ROI inputs visible: the soma ROI on the canvas (or its auto-detection) is the root for the single-cell trace.

run

public void run()

Specified by:

run in interface org.scijava.module.MutableModule

Specified by:

run in interface Runnable

Overrides:

run in class CommonDynamicCmd

runCommand

protected void runCommand()

Overrides:

runCommand in class GWDTTracerCommonCmd

createAndConfigureTracer

protected AbstractGWDTTracer<?> createAndConfigureTracer(net.imagej.ImgPlus<?> img)

Extends the parent's tracer setup with bias configuration and a setWaypoints call. By the time the parent's runCommand reaches this method, all the standard GWDT knobs have been applied; we just hand it the bias parameters, the waypoint list, and verify the tracer honors the WAYPOINT role.

Overrides:

createAndConfigureTracer in class GWDTTracerCommonCmd

Parameters:

img - the image to trace

Returns:

configured tracer, or null on error

isFileMode

protected boolean isFileMode()

Specified by:

isFileMode in class GWDTTracerCommonCmd