Package qupath.lib.experimental.pixels

Class ImageJProcessor

java.lang.Object

qupath.lib.experimental.pixels.ImageJProcessor

public class ImageJProcessor
extends Object

Class to generate a PixelProcessor when using ImageJ for the primary image representation.

Constructor Summary

Constructors

Constructor	Description
ImageJProcessor()

Method Summary

Modifier and Type	Method	Description
static PixelProcessor.Builder<ImagePlus,ImagePlus,Object>	builder(Processor<ImagePlus,ImagePlus,Object> processor)	Create a PixelProcessor.Builder for an ImageJ ImagePlus.
static OutputHandler.OutputToObjectConverter<ImagePlus,ImagePlus,Object>	createAnnotationConverter()	Create an OutputHandler.OutputToObjectConverter that attempts to convert the output into annotation objects.
static OutputHandler<ImagePlus,ImagePlus,Object>	createAnnotationOutputHandler()	Create an OutputHandler that attempts to convert the output into annotation objects.
static OutputHandler.OutputToObjectConverter<ImagePlus,ImagePlus,Object>	createDetectionConverter()	Create an OutputHandler.OutputToObjectConverter that attempts to convert the output into detection objects.
static OutputHandler<ImagePlus,ImagePlus,Object>	createDetectionOutputHandler()	Create an OutputHandler that attempts to convert the output into detection objects.
static ImageSupplier<ImagePlus>	createImagePlusImageSupplier()	Create an ImageSupplier that returns an ImageJ ImagePlus.
static MaskSupplier<ImagePlus,ImagePlus>	createImagePlusMaskSupplier()	Create a MaskSupplier that returns an ImageJ ByteProcessor.
static <U> OutputHandler.OutputToObjectConverter<ImagePlus,ImagePlus,U>	createObjectConverter(Class<U> cls, Function<ROI,PathObject> creator)	Create an OutputHandler.OutputToObjectConverter for one specify type.
static OutputHandler.OutputToObjectConverter<ImagePlus,ImagePlus,Object>	createObjectConverter(Function<ROI,PathObject> creator)	Create an OutputHandler.OutputToObjectConverter that attempts to convert a range of output types into objects.

Methods inherited from class java.lang.Object

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

Constructor Details

ImageJProcessor

public ImageJProcessor()

Method Details

createImagePlusImageSupplier

public static ImageSupplier<ImagePlus> createImagePlusImageSupplier()

Create an ImageSupplier that returns an ImageJ ImagePlus.

Returns:

createImagePlusMaskSupplier

public static MaskSupplier<ImagePlus,ImagePlus> createImagePlusMaskSupplier()

Create a MaskSupplier that returns an ImageJ ByteProcessor.

Returns:

createDetectionOutputHandler

public static OutputHandler<ImagePlus,ImagePlus,Object> createDetectionOutputHandler()

Create an OutputHandler that attempts to convert the output into detection objects.

Returns:

createAnnotationOutputHandler

public static OutputHandler<ImagePlus,ImagePlus,Object> createAnnotationOutputHandler()

Create an OutputHandler that attempts to convert the output into annotation objects.

Returns:

createAnnotationConverter

public static OutputHandler.OutputToObjectConverter<ImagePlus,ImagePlus,Object> createAnnotationConverter()

Create an OutputHandler.OutputToObjectConverter that attempts to convert the output into annotation objects.

Returns:

createDetectionConverter

public static OutputHandler.OutputToObjectConverter<ImagePlus,ImagePlus,Object> createDetectionConverter()

Create an OutputHandler.OutputToObjectConverter that attempts to convert the output into detection objects.

Returns:

createObjectConverter

public static OutputHandler.OutputToObjectConverter<ImagePlus,ImagePlus,Object> createObjectConverter(Function<ROI,PathObject> creator)

Create an OutputHandler.OutputToObjectConverter that attempts to convert a range of output types into objects.

The behavior depends upon whatever the Processor return. For example, the converter is able to generate one or more objects from

• an ImageJ Roi, or list or array of Roi objects
• an ImageJ Overlay
• a BinaryProcessor (creating a single object)
• a ByteProcessor or ShortProcessor (treated as a labeled image, to create 0 or more objects)
• another ImageProcessor with a threshold set (handled similar to a binary image)
• an ImagePlus, after extracting the ImageProcessor

Parameters:

creator - the creator function to determine the type of object (e.g. detection, annotation)

Returns:

the converter

createObjectConverter

public static <U>
OutputHandler.OutputToObjectConverter<ImagePlus,ImagePlus,U> createObjectConverter(Class<U> cls,
 Function<ROI,PathObject> creator)

Create an OutputHandler.OutputToObjectConverter for one specify type. See #createObjectConverter(Function) for more details; this method reduces ambiguity by handling only one possible kind of output.

Type Parameters:

U -

Parameters:

cls - the class to handle

creator - the creator function to determine the type of object (e.g. detection, annotation)

Returns:

the converter

builder

public static PixelProcessor.Builder<ImagePlus,ImagePlus,Object> builder(Processor<ImagePlus,ImagePlus,Object> processor)

Create a PixelProcessor.Builder for an ImageJ ImagePlus. By default, this will attempt to convert any output to detection objects - but the builder may be further customized to override this behavior before building the processor.

Parameters:

processor -

Returns: