Package qupath.imagej.detect.tissue

Class PositivePixelCounterIJ

java.lang.Object

qupath.lib.plugins.AbstractPlugin<BufferedImage>

qupath.lib.plugins.AbstractInteractivePlugin<BufferedImage>

qupath.lib.plugins.AbstractDetectionPlugin<BufferedImage>

qupath.imagej.detect.tissue.PositivePixelCounterIJ

All Implemented Interfaces:

PathInteractivePlugin<BufferedImage>, PathPlugin<BufferedImage>

public class PositivePixelCounterIJ
extends AbstractDetectionPlugin<BufferedImage>

Simple command to detect regions with positive staining.

For versions <= v0.1.2 this gave simple measurements that were influenced by the downsample values used. Later versions make calibrated measurements and give more flexibility in terms of output.

Author:

Pete Bankhead

Field Summary

Fields inherited from class qupath.lib.plugins.AbstractInteractivePlugin

params

Constructor Summary

Constructors

Constructor	Description
PositivePixelCounterIJ()

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.

Methods inherited from class qupath.lib.plugins.AbstractDetectionPlugin

getParentObjects, getSupportedParentObjectClasses

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

PositivePixelCounterIJ

public PositivePixelCounterIJ()

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:

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:

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:

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 -