Package qupath.imagej.gui.scripts

Class ImageJScriptRunner

java.lang.Object

qupath.imagej.gui.scripts.ImageJScriptRunner

public class ImageJScriptRunner
extends Object

Class to run ImageJ macros and scripts.

Since:

v0.6.0

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	ImageJScriptRunner.ApplyToObjects	Enum representing the objects that the script should be applied to.
static class	ImageJScriptRunner.Builder
static class	ImageJScriptRunner.ImageJScriptParameters	Class to store parameters used to run ImageJ macros or scripts from QuPath.
static enum	ImageJScriptRunner.PathObjectType

Constructor Summary

Constructors

Constructor	Description
ImageJScriptRunner(ImageJScriptRunner.ImageJScriptParameters params)

Method Summary

Modifier and Type	Method	Description
static ImageJScriptRunner.Builder	builder()	Create a new builder for an instance of ImageJScriptRunner.
static ImageJScriptRunner.Builder	builder(ImageJScriptRunner.ImageJScriptParameters params)	Create a new builder for an instance of ImageJScriptRunner, initializing using the provided parameters.
static PathObject	createDetectionOrPointAnnotation(ROI roi)	Function to create an annotation object from any PointsROI, and detection object from any other ROI.
static ImageJScriptRunner	fromJson(String json)	Create a script runner from a JSON representation of ImageJScriptRunner.ImageJScriptParameters.
static ImageJScriptRunner	fromMap(Map<String,?> paramMap)	Create a script runner from a map representation of ImageJScriptRunner.ImageJScriptParameters.
static ImageJScriptRunner	fromParams(ImageJScriptRunner.ImageJScriptParameters params)	Create a script runner from the specified parameters.
static List<PathObject>	getObjectsToProcess(PathObjectHierarchy hierarchy, ImageJScriptRunner.ApplyToObjects applyTo)	Query which objects in a hierarchy would be used with the specified ImageJScriptRunner.ApplyToObjects value.
static void	main(String[] args)	Example program to log a script.
void	run()	Run the script for the 'current' image data, as requested from QP.
void	run(ImageData<BufferedImage> imageData)	Run the script for the specified image data.
void	test()	Test the script for the 'current' image data, as requested from QP.
void	test(ImageData<BufferedImage> imageData)	Test the script for the specified image data.

Methods inherited from class java.lang.Object

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

Constructor Details

ImageJScriptRunner

public ImageJScriptRunner(ImageJScriptRunner.ImageJScriptParameters params)

Method Details

fromParams

public static ImageJScriptRunner fromParams(ImageJScriptRunner.ImageJScriptParameters params)

Create a script runner from the specified parameters.

Parameters:

params -

Returns:

fromJson

public static ImageJScriptRunner fromJson(String json)

Create a script runner from a JSON representation of ImageJScriptRunner.ImageJScriptParameters.

Parameters:

json -

Returns:

fromMap

public static ImageJScriptRunner fromMap(Map<String,?> paramMap)

Create a script runner from a map representation of ImageJScriptRunner.ImageJScriptParameters.

This method is mostly available for convenience when writing a Groovy script.

Parameters:

paramMap -

Returns:

run

public void run()

Run the script for the 'current' image data, as requested from QP.

See Also:

• run()

run

public void run(ImageData<BufferedImage> imageData)

Run the script for the specified image data.

See Also:

• run(ImageData)

test

public void test()

Test the script for the 'current' image data, as requested from QP.

See Also:

• run()
• test(ImageData)

test

public void test(ImageData<BufferedImage> imageData)

Test the script for the specified image data.

Testing will run the script for no more than one parent object, and show the images within ImageJ. This is different from calling run(ImageData), which can process multiple parent objects and does not show images by default.

See Also:

• test()
• run(ImageData)

getObjectsToProcess

public static List<PathObject> getObjectsToProcess(PathObjectHierarchy hierarchy,
 ImageJScriptRunner.ApplyToObjects applyTo)

Query which objects in a hierarchy would be used with the specified ImageJScriptRunner.ApplyToObjects value.

Parameters:

hierarchy -

applyTo -

Returns:

a list of all objects that are compatible with the type

main

public static void main(String[] args)

Example program to log a script.

Parameters:

args -

createDetectionOrPointAnnotation

public static PathObject createDetectionOrPointAnnotation(ROI roi)

Function to create an annotation object from any PointsROI, and detection object from any other ROI.

Parameters:

roi - the input ROI (must not be null)

Returns:

a new object with the specified ROI

builder

public static ImageJScriptRunner.Builder builder()

Create a new builder for an instance of ImageJScriptRunner.

Returns:

builder

public static ImageJScriptRunner.Builder builder(ImageJScriptRunner.ImageJScriptParameters params)

Create a new builder for an instance of ImageJScriptRunner, initializing using the provided parameters.

Returns: