Package sc.fiji.snt.plugin

Class GWDTTracerCommonCmd

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

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

Direct Known Subclasses:

AutotraceFromSeedsCmd, AutotraceFromTipsCmd, AutotraceFromWaypointsCmd, GWDTMultiSomaCommonCmd, GWDTTracerCmd, GWDTTracerFileCmd

public abstract class GWDTTracerCommonCmd
extends CommonDynamicCmd

Base command providing shared parameters and logic for GWDT autotracing. Subclassed by GWDTTracerCmd (interactive, image already loaded) and GWDTTracerFileCmd (non-interactive, file-based).

Author:

Tiago Ferreira

See Also:

• GWDTTracerCmd
• GWDTTracerFileCmd

Field Summary

Fields

Modifier and Type	Field	Description
protected boolean	abortRun
protected double	backgroundThreshold
protected double	branchTuneMaxAngle
protected net.imagej.ImgPlus<?>	chosenImp
protected boolean	debugMode
protected String	imgChoice
protected File	imgFileChoice
protected double	lengthThreshold
protected String	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
GWDTTracerCommonCmd()

Method Summary

Modifier and Type	Method	Description
void	cancel(String reason)
protected boolean	configureSecondaryScoreMap(AbstractGWDTTracer<?> tracer)	Hook for configuring the tracer's score map from a user-supplied secondary image.
protected AbstractGWDTTracer<?>	createAndConfigureTracer(net.imagej.ImgPlus<?> img)	Creates and configures a tracer from the shared GUI parameters.
protected void	error(String msg)
protected net.imagej.ImgPlus<?>	getImgFromImgChoice()
protected void	handleTracedTrees(List<Tree> trees)	Called after tracing completes with valid trees.
protected void	initForFile()
protected void	initForImage()
protected abstract boolean	isFileMode()
protected void	noValidImgError()
protected void	runCommand()
protected void	scoreMapFilterCallback()	Toggles visibility of secondary-image inputs that are only relevant when scoreMapFilter == SCORE_MAP_OTHER.

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

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

imgChoice

protected String imgChoice

imgFileChoice

protected File imgFileChoice

backgroundThreshold

protected double backgroundThreshold

scoreMapFilter

protected String scoreMapFilter

lengthThreshold

protected double lengthThreshold

branchTuneMaxAngle

protected double branchTuneMaxAngle

debugMode

protected boolean debugMode

abortRun

protected boolean abortRun

chosenImp

protected net.imagej.ImgPlus<?> chosenImp

Constructor Details

GWDTTracerCommonCmd

public GWDTTracerCommonCmd()

Method Details

scoreMapFilterCallback

protected void scoreMapFilterCallback()

Toggles visibility of secondary-image inputs that are only relevant when scoreMapFilter == SCORE_MAP_OTHER. The base implementation handles any secondaryImageSuffix input declared by subclasses; subclasses may override to control additional related inputs. Safe to call when the input is not declared (no-op in that case).

initForImage

protected void initForImage()

initForFile

protected void initForFile()

createAndConfigureTracer

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

Creates and configures a tracer from the shared GUI parameters. Returns null if configuration failed (e.g., missing secondary image for score map).

Parameters:

img - the image to trace

Returns:

configured tracer, or null on error

configureSecondaryScoreMap

protected boolean configureSecondaryScoreMap(AbstractGWDTTracer<?> tracer)

Hook for configuring the tracer's score map from a user-supplied secondary image. Invoked only when scoreMapFilter == SCORE_MAP_OTHER.

Default implementation pulls from SNT.getSecondaryData() (the secondary layer currently loaded in the GUI) and aborts the command via error(String) if none is available.

Subclasses may override to source the secondary from disk (or elsewhere) and may choose to handle missing/incompatible inputs gracefully by disabling score mapping (tracer.setScoreMapEnabled(false)) and returning true so tracing proceeds without it.

Parameters:

tracer - the tracer being configured

Returns:

true to continue (score map configured, or gracefully disabled); false to abort the command

runCommand

protected void runCommand()

handleTracedTrees

protected void handleTracedTrees(List<Tree> trees)

Called after tracing completes with valid trees. The default implementation loads trees into PathAndFillManager and optionally triggers proofreading. Subclasses (e.g., GWDTTracerFileCmd) may override to export trees to disk instead.

Parameters:

trees - the traced trees (guaranteed non-empty)

isFileMode

protected abstract boolean isFileMode()

getImgFromImgChoice

protected net.imagej.ImgPlus<?> getImgFromImgChoice()

noValidImgError

protected void noValidImgError()

cancel

public void cancel(String reason)

Specified by:

cancel in interface org.scijava.Cancelable

Overrides:

cancel in class CommonDynamicCmd

error

protected void error(String msg)

Overrides:

error in class CommonDynamicCmd