Package qupath.lib.algorithms

Class HaralickFeaturesPlugin

java.lang.Object

qupath.lib.plugins.AbstractPlugin<BufferedImage>

qupath.lib.plugins.AbstractInteractivePlugin<BufferedImage>

qupath.lib.algorithms.HaralickFeaturesPlugin

All Implemented Interfaces:

PathInteractivePlugin<BufferedImage>, PathPlugin<BufferedImage>

public class HaralickFeaturesPlugin
extends AbstractInteractivePlugin<BufferedImage>

Plugin for calculating Haralick texture features, within or around detections or tiles.

The ROIs of the detections can be used directly as masks, or else the textures can alternatively be calculated within square or circular regions around the object centroids. This latter option makes it possible to calculate a high density of tiles (for example), and then to compute textures at different resolutions independently of the tile size.

Author:

Pete Bankhead

Constructor Summary

Constructors

Constructor	Description
HaralickFeaturesPlugin()	Default 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.
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.

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, runPlugin

Methods inherited from class java.lang.Object

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

Methods inherited from interface qupath.lib.plugins.PathPlugin

runPlugin

Constructor Details

HaralickFeaturesPlugin

public HaralickFeaturesPlugin()

Default constructor.

Method Details

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: