Package qupath.imagej.detect.tissue

Class SimpleTissueDetection2

java.lang.Object

qupath.lib.plugins.AbstractPlugin<BufferedImage>

qupath.lib.plugins.AbstractInteractivePlugin<BufferedImage>

qupath.lib.plugins.AbstractDetectionPlugin<BufferedImage>

qupath.imagej.detect.tissue.SimpleTissueDetection2

All Implemented Interfaces:

PathInteractivePlugin<BufferedImage>, PathPlugin<BufferedImage>

public class SimpleTissueDetection2
extends AbstractDetectionPlugin<BufferedImage>

Very basic global thresholding command to identify tissue regions. Uses fixed approach to downsampling images & global threshold applied to RGB images only. TODO: Provide choice of channels to threshold TODO: Support 16-bit data

Author:

Pete Bankhead

Constructor Summary

Constructors

Constructor	Description
SimpleTissueDetection2()	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<? extends PathObject>	getParentObjects(ImageData<BufferedImage> imageData)	Get all selected objects that are instances of a supported class.
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

SimpleTissueDetection2

public SimpleTissueDetection2()

Constructor.

Method Details

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:

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: AbstractDetectionPlugin

Get all selected objects that are instances of a supported class.

Overrides:

getParentObjects in class AbstractDetectionPlugin<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.

Specified by:

getSupportedParentObjectClasses in interface PathInteractivePlugin<BufferedImage>

Overrides:

getSupportedParentObjectClasses in class AbstractDetectionPlugin<BufferedImage>

Returns: