Package sc.fiji.snt.plugin

Class AutotraceFromBinarySeedsCmd

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.AutotraceFromBinarySeedsCmd

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 AutotraceFromBinarySeedsCmd
extends BinaryTracerCommonCmd

Batch autotracing wrapper that iterates over the seeds currently held by SNT's SeedOverlay and runs the BinaryTracer (skeleton-based autotracer) once per seed, each seed acting as the root of its own tree. Trees are accumulated and loaded into the active path manager at the end.

This is the binary/skeleton counterpart of AutotraceFromSeedsCmd. The typical workflow is to start from a labels image (e.g. cellpose / StarDist segmentations), generate one seed per labeled object via Generate Seeds from Labels Image, and then run this command to produce per-cell skeleton trees in a single batch.

Inherits every binary-tracer knob from BinaryTracerCommonCmd (segmented-image choice, optional intensity image, loop-resolution strategy, gap bridging, prune-by-length, etc.); adds the same seed ource/type filters used by AutotraceFromSeedsCmd. Failures on individual seeds are logged and reported but do not abort the whole run.

Author:

Tiago Ferreira

See Also:

• BinaryTracerCommonCmd
• AutotraceFromSeedsCmd
• SeedOverlay

Field Summary

Fields

Modifier and Type	Field	Description
static final String	SOURCE_SELECTION

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
AutotraceFromBinarySeedsCmd()

Method Summary

Modifier and Type	Method	Description
protected void	init()	Initializer.
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()
protected void	runCommand()	Executes the core tracing pipeline: loads images (from file or choice widgets based on BinaryTracerCommonCmd.isFileMode()), validates inputs, runs BinaryTracer, and post-processes the resulting trees.

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

assignRoiZPosition, cancel, cancel, confirmIfNotSegmented, createAndConfigureConverter, error, getRoi, getRootStrategy, handleTracedTrees, info, initForFile, initForImage, isSegmented, noImgError, pruneModeToString, 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

Field Details

SOURCE_SELECTION

public static final String SOURCE_SELECTION

See Also:

• Constant Field Values

Constructor Details

AutotraceFromBinarySeedsCmd

public AutotraceFromBinarySeedsCmd()

Method Details

init

protected void init()

Initializer. Inherits image-related setup from BinaryTracerCommonCmd.initForImage(), hides root-strategy and active-plane-only parameters (seeds drive root placement here, not an ROI), 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

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

runCommand

protected void runCommand()

Description copied from class: BinaryTracerCommonCmd

Executes the core tracing pipeline: loads images (from file or choice widgets based on BinaryTracerCommonCmd.isFileMode()), validates inputs, runs BinaryTracer, and post-processes the resulting trees.

Overrides:

runCommand in class BinaryTracerCommonCmd