Package sc.fiji.snt.plugin

Class AutotraceFromSeedsCmd

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.AutotraceFromSeedsCmd

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 AutotraceFromSeedsCmd
extends GWDTTracerCommonCmd

Batch autotracing wrapper that iterates over the seeds currently held by SNT's SeedOverlay and runs the GWDT tracer once per seed (each seed acts as the root of a new Tree). Trees are accumulated and loaded into the active PathAndFillManager at the end.

Inherits all GWDT tracing knobs from GWDTTracerCommonCmd; adds three seed-source filter parameters (source, type, channel override). Failures on individual seeds are logged and reported but do not abort the whole run.

Author:

Tiago Ferreira

See Also:

• GWDTTracerCommonCmd
• SeedOverlay

Field Summary

Fields

Modifier and Type	Field	Description
static final String	SOURCE_SELECTION

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
AutotraceFromSeedsCmd()

Method Summary

Modifier and Type	Method	Description
protected void	init()	Initializer.
protected boolean	isFileMode()
void	run()
protected void	runCommand()

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

cancel, configureSecondaryScoreMap, createAndConfigureTracer, error, getImgFromImgChoice, handleTracedTrees, initForFile, initForImage, noValidImgError, 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

Field Details

SOURCE_SELECTION

public static final String SOURCE_SELECTION

See Also:

• Constant Field Values

Constructor Details

AutotraceFromSeedsCmd

public AutotraceFromSeedsCmd()

Method Details

init

protected void init()

Initializer. Inherits image-related setup from GWDTTracerCommonCmd.initForImage(), hides ROI-strategy parameters that don't apply (seeds drive root placement), and populates the type-filter choices from the distinct types currently on the overlay.

run

public void run()

Specified by:

run in interface org.scijava.module.MutableModule

Specified by:

run in interface Runnable

Overrides:

run in class CommonDynamicCmd

runCommand

protected void runCommand()

Overrides:

runCommand in class GWDTTracerCommonCmd

isFileMode

protected boolean isFileMode()

Specified by:

isFileMode in class GWDTTracerCommonCmd