Package qupath.imagej.detect.cells

Class SubcellularDetection

java.lang.Object

qupath.lib.plugins.AbstractPlugin<BufferedImage>

qupath.lib.plugins.AbstractInteractivePlugin<BufferedImage>

qupath.imagej.detect.cells.SubcellularDetection

All Implemented Interfaces:

PathInteractivePlugin<BufferedImage>, PathPlugin<BufferedImage>

public class SubcellularDetection
extends AbstractInteractivePlugin<BufferedImage>

Experimental plugin to help with the quantification of subcellular structures.

Field Summary

Fields inherited from class qupath.lib.plugins.AbstractInteractivePlugin

params

Constructor Summary

Constructors

Constructor	Description
SubcellularDetection()

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.
ParameterList	getDefaultParameterList(ImageData<BufferedImage> imageData)	This should return a default ParameterList containing any information that is needed to repeat the task exactly.
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<PathObject>	getParentObjects(ImageData<BufferedImage> imageData)	Get a collection of objects to process, based on the contents of the PluginRunner.
Collection<Class<? extends PathObject>>	getSupportedParentObjectClasses()	Get a collection of possible parent objects that the plugin could have.
boolean	runPlugin(TaskRunner taskRunner, ImageData<BufferedImage> imageData, String arg)	Run the plugin.

Methods inherited from class qupath.lib.plugins.AbstractInteractivePlugin

alwaysPromptForObjects, getLoggableParameters, getParameterList, parseArgument

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

SubcellularDetection

public SubcellularDetection()

Method Details

runPlugin

public boolean runPlugin(TaskRunner taskRunner,
 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:

taskRunner -

arg -

Returns:

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 -

getDefaultParameterList

public ParameterList getDefaultParameterList(ImageData<BufferedImage> imageData)

Description copied from class: AbstractInteractivePlugin

This should return a default ParameterList containing any information that is needed to repeat the task exactly.

Specified by:

getDefaultParameterList in interface PathInteractivePlugin<BufferedImage>

Specified by:

getDefaultParameterList in class AbstractInteractivePlugin<BufferedImage>

Parameters:

imageData -

Returns:

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:

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:

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:

getParentObjects

protected Collection<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:

getSupportedParentObjectClasses

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

Description copied from interface: PathInteractivePlugin

Get a collection of possible parent objects that the plugin could have. This may be used, for example, to specified that analysis may be applied to any/all TMA cores or annotations. If no parent objects are required, PathRootObject.class should be returned in the list.

Returns: