Package sc.fiji.snt.plugin

Class AutotraceFromTipsCmd

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.AutotraceFromTipsCmd

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 AutotraceFromTipsCmd
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 tip targets. The tracer extracts the union of root-to-tip parent walks instead of running its usual full-tree pruning pipeline, producing one Tree that connects the soma to every reachable tip.

Inherits all GWDT tracing knobs and the soma-ROI strategy from GWDTTracerCommonCmd; adds the same source and type seed filters as AutotraceFromSeedsCmd.

Tips whose nearest voxel is not reached by Fast Marching (state ≠ ALIVE) are logged and skipped by the tracer; they do not abort the run.

Author:

Tiago Ferreira

See Also:

• GWDTTracerCommonCmd
• AutotraceFromSeedsCmd
• SeedOverlay

Field Summary

Fields

Modifier and Type	Field	Description
protected static final String	SOURCE_ALL
static final String	SOURCE_SELECTION
protected static final String	SOURCE_VISIBLE

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
AutotraceFromTipsCmd()

Method Summary

Modifier and Type	Method	Description
protected AbstractGWDTTracer<?>	createAndConfigureTracer(net.imagej.ImgPlus<?> img)	Extends the parent's tracer setup with a setTips 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_ALL

protected static final String SOURCE_ALL

See Also:

• Constant Field Values

SOURCE_VISIBLE

protected static final String SOURCE_VISIBLE

See Also:

• Constant Field Values

SOURCE_SELECTION

public static final String SOURCE_SELECTION

See Also:

• Constant Field Values

Constructor Details

AutotraceFromTipsCmd

public AutotraceFromTipsCmd()

Method Details

init

protected void init()

Initializer. Inherits image-related setup from GWDTTracerCommonCmd.initForImage() (and unlike AutotraceFromSeedsCmd ) keeps somaStrategyChoice and roiPlaneOnly visible: the soma ROI on the canvas (or auto-detected) is the root for the single-cell trace, and the user needs the strategy picker to choose how that ROI is interpreted.

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 a setTips call. By the time the parent's runCommand reaches this method, all the standard GWDT knobs have been applied; we just hand it the user's tips and verify the tracer honors the TIP 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