Package sc.fiji.snt.plugin

Class GWDTMultiSomaFileCmd

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.GWDTMultiSomaCommonCmd

sc.fiji.snt.plugin.GWDTMultiSomaFileCmd

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 GWDTMultiSomaFileCmd
extends GWDTMultiSomaCommonCmd

Non-interactive command for file-based multi-soma GWDT autotracing with support for single images or batch processing of a directory. Traced trees are exported to disk as SWC files.

Author:

Tiago Ferreira

See Also:

• GWDTMultiSomaCommonCmd
• GWDTMultiSomaCmd
• GWDTTracerFileCmd

Field Summary

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
GWDTMultiSomaFileCmd()

Method Summary

Modifier and Type	Method	Description
protected void	error(String msg)
protected void	handleTracedTrees(List<Tree> trees)	Called after tracing completes with valid trees.
protected boolean	isFileMode()
void	run()

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

initMultiSoma, runMultiSoma

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

cancel, configureSecondaryScoreMap, createAndConfigureTracer, getImgFromImgChoice, initForFile, initForImage, noValidImgError, runCommand, 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

Constructor Details

GWDTMultiSomaFileCmd

public GWDTMultiSomaFileCmd()

Method Details

isFileMode

protected boolean isFileMode()

Specified by:

isFileMode in class GWDTTracerCommonCmd

run

public void run()

Specified by:

run in interface org.scijava.module.MutableModule

Specified by:

run in interface Runnable

Overrides:

run in class CommonDynamicCmd

error

protected void error(String msg)

Overrides:

error in class GWDTTracerCommonCmd

handleTracedTrees

protected void handleTracedTrees(List<Tree> trees)

Description copied from class: GWDTTracerCommonCmd

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.

Overrides:

handleTracedTrees in class GWDTTracerCommonCmd

Parameters:

trees - the traced trees (guaranteed non-empty)