Package sc.fiji.snt.plugin

Class BinaryTracerCmd

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.BinaryTracerCommonCmd

sc.fiji.snt.plugin.BinaryTracerCmd

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 BinaryTracerCmd
extends BinaryTracerCommonCmd

Interactive command providing a GUI for BinaryTracer-based autotracing when an image is already loaded in SNT. Uses choice widgets to select from open images.

Author:

Cameron Arshadi, Tiago Ferreira

See Also:

• BinaryTracerCommonCmd
• BinaryTracerFileCmd

Field Summary

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

abortRun, afterTracingChoice, chosenMaskImp, connectComponents, cullSingleNodePaths, debugMode, ensureMaskImgVisibleOnAbort, headless, impMap, inputDir, lengthThreshold, loopSolvingChoice, maskImgFileBeingProcessed, maxConnectDist, originalImgChoice, pruneByLength, ROI_AUTO_DETECT, ROI_CENTROID, ROI_CENTROID_WEIGHTED, ROI_CONTAINED, ROI_EDGE, ROI_UNSET, roiPlane, rootChoice

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
BinaryTracerCmd()

Method Summary

Modifier and Type	Method	Description
protected void	handleTracedTrees(List<Tree> trees)	Called after tracing completes with valid trees.
protected boolean	isFileMode()	Returns whether this command operates in file mode (loading images from file paths) or in image-choice mode (selecting from open images).
void	run()

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

assignRoiZPosition, cancel, cancel, confirmIfNotSegmented, createAndConfigureConverter, error, getRoi, getRootStrategy, info, initForFile, initForImage, isSegmented, noImgError, pruneModeToString, runCommand, setPruneMode, validateBeforeTracing

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

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

BinaryTracerCmd

public BinaryTracerCmd()

Method Details

isFileMode

protected boolean isFileMode()

Description copied from class: BinaryTracerCommonCmd

Returns whether this command operates in file mode (loading images from file paths) or in image-choice mode (selecting from open images).

Specified by:

isFileMode in class BinaryTracerCommonCmd

Returns:

true for file-based operation, false for choice-widget operation

run

public void run()

Specified by:

run in interface org.scijava.module.MutableModule

Specified by:

run in interface Runnable

Overrides:

run in class CommonDynamicCmd

handleTracedTrees

protected void handleTracedTrees(List<Tree> trees)

Description copied from class: BinaryTracerCommonCmd

Called after tracing completes with valid trees. The default implementation honors BinaryTracerCommonCmd.afterTracingChoice: optionally replaces existing paths, assigns colors (per-tree "dim" palette when proofreading, inter-tree otherwise), adds trees via PathAndFillManager, and optionally calibrates the Curation Manager for proofreading. Subclasses may override to export trees to disk or adopt the mask image as tracing canvas.

Overrides:

handleTracedTrees in class BinaryTracerCommonCmd

Parameters:

trees - the traced trees (guaranteed non-null and non-empty)