Package sc.fiji.snt.plugin

Class GWDTMultiSomaCommonCmd

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

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:

GWDTMultiSomaCmd, GWDTMultiSomaFileCmd

public abstract class GWDTMultiSomaCommonCmd
extends GWDTTracerCommonCmd

Abstract base for multi-soma GWDT autotracing commands. Provides shared parameters (soma detection, territory control, multi-cell options) and the core runMultiSoma() workflow. Subclassed by GWDTMultiSomaCmd (interactive) and GWDTMultiSomaFileCmd (batch/file-based).

Author:

Tiago Ferreira

See Also:

• GWDTMultiSomaCmd
• GWDTMultiSomaFileCmd

Field Summary

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

abortRun, backgroundThreshold, branchTuneMaxAngle, chosenImp, debugMode, imgChoice, imgFileChoice, lengthThreshold, prefService, scoreMapFilter, SOMA_AUTO, SOMA_BOOKMARK, SOMA_ROI_AUTO_EDGE, somaStrategyChoice

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
GWDTMultiSomaCommonCmd()

Method Summary

Modifier and Type	Method	Description
protected void	applyDefaults()
protected void	initMultiSoma()	Initializes multi-soma commands: hides roiPlaneOnly (no Roi concept applies to either strategy here) and narrows somaStrategyChoice (inherited from the parent, whose 5 Roi-based choices don't apply to multi-soma tracing) down to just {SOMA_AUTO, SOMA_BOOKMARK}.
protected void	readPreferences()
protected void	runMultiSoma()
protected void	savePreferences()

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

applyWorldOriginOffsetIfAny, cancel, configureSecondaryScoreMap, createAndConfigureTracer, error, getImgFromImgChoice, handleTracedTrees, initForFile, initForImage, isFileMode, noValidImgError, runCommand, scoreMapFilterCallback

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

cancel, getConfirmationEdtSafe, getPixelPositionsOfBookmarks, getPromptWithCloseHandler, getPromptWithCloseHandler, init, isCanceled, msg, notifyExternalDataLoaded, notifyLoadingEnd, notifyLoadingStart, resetUI, resetUI, resetUI, run, setStatus, status, warnIfMaterializedCropActive

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

GWDTMultiSomaCommonCmd

public GWDTMultiSomaCommonCmd()

Method Details

initMultiSoma

protected void initMultiSoma()

Initializes multi-soma commands: hides roiPlaneOnly (no Roi concept applies to either strategy here) and narrows somaStrategyChoice (inherited from the parent, whose 5 Roi-based choices don't apply to multi-soma tracing) down to just {SOMA_AUTO, SOMA_BOOKMARK}.

Unlike the single-cell command, this is not Stream-mode-only

readPreferences

protected void readPreferences()

Overrides:

readPreferences in class GWDTTracerCommonCmd

savePreferences

protected void savePreferences()

Overrides:

savePreferences in class GWDTTracerCommonCmd

applyDefaults

protected void applyDefaults()

Overrides:

applyDefaults in class GWDTTracerCommonCmd

runMultiSoma

protected void runMultiSoma()