Package qupath.imagej.gui

Class ImageJMacroRunner

java.lang.Object

qupath.lib.plugins.AbstractPlugin<BufferedImage>

qupath.imagej.gui.ImageJMacroRunner

All Implemented Interfaces:

PathPlugin<BufferedImage>

public class ImageJMacroRunner
extends AbstractPlugin<BufferedImage>

QuPath plugin for running ImageJ macros & returning detected regions. TODO: Support script recording.

Author:

Pete Bankhead

Constructor Summary

Constructors

Constructor	Description
ImageJMacroRunner(QuPathGUI qupath)	Constructor.

Method Summary

Modifier and Type	Method	Description
protected void	addRunnableTasks(ImageData<BufferedImage> imageData, PathObject parentObject, List<Runnable> tasks)	For a specified parent object, generate a task to run.
String	getDescription()	Get a brief description of the plugin's purpose & operation.
String	getLastResultsDescription()	(Optional) short one-line description of the results, e.g.
String	getName()	Get the name of the plugin for display.
protected Collection<? extends PathObject>	getParentObjects(ImageData<BufferedImage> imageData)	Get a collection of objects to process, based on the contents of the PluginRunner.
protected Collection<Class<? extends PathObject>>	getSupportedParentObjectClasses()
protected boolean	parseArgument(ImageData<BufferedImage> imageData, String arg)	Parse the input argument, returning 'true' if the argument is valid and it's possible to run the plugin.
boolean	runPlugin(TaskRunner runner, ImageData<BufferedImage> imageData, String arg)	Run the plugin.

Methods inherited from class qupath.lib.plugins.AbstractPlugin

addWorkflowStep, getTasks, postprocess, preprocess, rearrangeByStride, requestHierarchyUpdate

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

ImageJMacroRunner

public ImageJMacroRunner(QuPathGUI qupath)

Constructor.

Parameters:

qupath - QuPath instance where the command should be installed.

Method Details

getName

public String getName()

Description copied from interface: PathPlugin

Get the name of the plugin for display.

This should be descriptive and, above all, short - as it may be used for menu item names & dialog box titles.

Returns:

getDescription

public String getDescription()

Description copied from interface: PathPlugin

Get a brief description of the plugin's purpose & operation.

If no description is provided, this may return null.

Returns:

runPlugin

public boolean runPlugin(TaskRunner runner,
 ImageData<BufferedImage> imageData,
 String arg)

Description copied from interface: PathPlugin

Run the plugin. A PluginRunner may be provided that this plugin can use to update the user on its progress.

Note: This command should block until it has completed processing.

Specified by:

runPlugin in interface PathPlugin<BufferedImage>

Overrides:

runPlugin in class AbstractPlugin<BufferedImage>

Parameters:

runner -

arg -

Returns:

parseArgument

protected boolean parseArgument(ImageData<BufferedImage> imageData,
 String arg)

Description copied from class: AbstractPlugin

Parse the input argument, returning 'true' if the argument is valid and it's possible to run the plugin.

This is called from within runPlugin. If it returns 'true', getTasks will be called and then runTasks will submit these to the plugin runner to run. If it returns 'false', runPlugin will immediately abort and return false as well. Since this could result in some internal variables changed (e.g. a ParameterList), implementing classes can't be assumed to be thread-safe; plugins should be created and called from a single thread, although they may use multiple threads (via a PluginRunner) to complete their tasks.

Specified by:

parseArgument in class AbstractPlugin<BufferedImage>

Parameters:

imageData -

arg -

Returns:

getLastResultsDescription

public String getLastResultsDescription()

Description copied from interface: PathPlugin

(Optional) short one-line description of the results, e.g. to say how many objects detected. GUIs may choose to display this on a label during interactive processing.

Returns:

getSupportedParentObjectClasses

protected Collection<Class<? extends PathObject>> getSupportedParentObjectClasses()

addRunnableTasks

protected void addRunnableTasks(ImageData<BufferedImage> imageData,
 PathObject parentObject,
 List<Runnable> tasks)

Description copied from class: AbstractPlugin

For a specified parent object, generate a task to run. In practice, this method can be overridden to return anything/nothing if getTasks is overridden instead.

Specified by:

addRunnableTasks in class AbstractPlugin<BufferedImage>

Parameters:

imageData -

parentObject -

tasks -

getParentObjects

protected Collection<? extends PathObject> getParentObjects(ImageData<BufferedImage> imageData)

Description copied from class: AbstractPlugin

Get a collection of objects to process, based on the contents of the PluginRunner. This could (for example) return the selected object, the root object, all detection objects... depending upon what the plugin does. Each object this returns will be passed to addRunnableTasks to create a task to run. In practice, this method can be overridden to return anything/nothing if getTasks is overridden instead.

Specified by:

getParentObjects in class AbstractPlugin<BufferedImage>

Parameters:

imageData -

Returns: