Package sc.fiji.snt.plugin

Class GWDTTracerFileCmd

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.GWDTTracerFileCmd

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 GWDTTracerFileCmd
extends GWDTTracerCommonCmd

Non-interactive command for file-based GWDT autotracing with support for single images or batch processing of an entire directory. Traced trees can be exported to disk as SWC files.

When imgFileChoice points to a directory, each image is processed independently with automatic soma detection. Failures on individual images are logged but do not abort the batch operation.

Author:

Tiago Ferreira

See Also:

• GWDTTracerCommonCmd
• GWDTTracerCmd

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
GWDTTracerFileCmd()

Method Summary

Modifier and Type	Method	Description
protected boolean	configureSecondaryScoreMap(AbstractGWDTTracer<?> tracer)	Locates a paired secondary image on disk via secondaryImageSuffix.
protected void	error(String msg)
protected void	handleTracedTrees(List<Tree> trees)	Called after tracing completes with valid trees (already corrected for any world origin offset - see GWDTTracerCommonCmd.applyWorldOriginOffsetIfAny(java.util.List<sc.fiji.snt.Tree>)).
protected boolean	isFileMode()
void	run()

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

applyDefaults, applyWorldOriginOffsetIfAny, cancel, createAndConfigureTracer, getImgFromImgChoice, initForFile, initForImage, noValidImgError, readPreferences, runCommand, savePreferences, 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, 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

GWDTTracerFileCmd

public GWDTTracerFileCmd()

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 (already corrected for any world origin offset - see GWDTTracerCommonCmd.applyWorldOriginOffsetIfAny(java.util.List<sc.fiji.snt.Tree>)). 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)

configureSecondaryScoreMap

protected boolean configureSecondaryScoreMap(AbstractGWDTTracer<?> tracer)

Locates a paired secondary image on disk via secondaryImageSuffix. The expected file is <inputBase><suffix>.<any-ext> in the same directory as GWDTTracerCommonCmd.imgFileChoice.

Failures (missing file, unreadable image, dimension mismatch, exception) are logged and result in score mapping being disabled for the current input; the trace still proceeds. This keeps batch runs robust to partial coverage of secondary maps.

Overrides:

configureSecondaryScoreMap in class GWDTTracerCommonCmd

Parameters:

tracer - the tracer being configured

Returns:

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