Package sc.fiji.snt.plugin

Class BinaryTracerFileCmd

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.BinaryTracerFileCmd

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 BinaryTracerFileCmd
extends BinaryTracerCommonCmd

Non-interactive command for batch BinaryTracer autotracing of all images in a directory. Each image is processed independently and traced trees are exported to disk as SWC files.

Failures on individual images are logged but do not abort the batch. ROI-based root detection is supported when images contain embedded ROIs (e.g., from TIFF headers).

Author:

Tiago Ferreira

See Also:

• BinaryTracerCommonCmd
• BinaryTracerCmd

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
BinaryTracerFileCmd()

Method Summary

Modifier and Type	Method	Description
protected void	error(String msg)
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()
protected boolean	validateBeforeTracing(ij.gui.Roi roi, boolean inferRootFromRoi, boolean isSame, boolean isSegmented, boolean isValidOrigImg, boolean isSameDim, boolean isCompatible, boolean isValidConnectDist, boolean isValidRoi)	Validates configuration before tracing begins.

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

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

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

BinaryTracerFileCmd

public BinaryTracerFileCmd()

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

error

protected void error(String msg)

Overrides:

error in class BinaryTracerCommonCmd

validateBeforeTracing

protected boolean validateBeforeTracing(ij.gui.Roi roi,
 boolean inferRootFromRoi,
 boolean isSame,
 boolean isSegmented,
 boolean isValidOrigImg,
 boolean isSameDim,
 boolean isCompatible,
 boolean isValidConnectDist,
 boolean isValidRoi)

Description copied from class: BinaryTracerCommonCmd

Validates configuration before tracing begins. The default (non-interactive) implementation logs warnings and adjusts flags as needed without prompting the user. Interactive subclasses may override this to display a confirmation dialog.

This method may modify BinaryTracerCommonCmd.connectComponents and BinaryTracerCommonCmd.ensureMaskImgVisibleOnAbort directly.

Overrides:

validateBeforeTracing in class BinaryTracerCommonCmd

Parameters:

roi - the active ROI (may be null)

inferRootFromRoi - whether root inference from ROI is requested

isSame - whether mask and original image are the same

isSegmented - whether the mask image is binary/thresholded

isValidOrigImg - whether the original image path is valid

isSameDim - whether mask and original share dimensions

isCompatible - whether images share spatial calibration

isValidConnectDist - whether the max connection distance is valid

isValidRoi - whether the ROI is a valid area ROI

Returns:

true to proceed with tracing, false to abort

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)