Package org.anchoranalysis.image.io.object.output.rgb

Class ObjectsAsRGBGenerator

Object

RasterGenerator<ObjectCollectionWithProperties>

RasterGeneratorSelectFormat<ObjectCollectionWithProperties>

ObjectsAsRGBGenerator

All Implemented Interfaces:

Generator<ObjectCollectionWithProperties>, TransformingGenerator<ObjectCollectionWithProperties,Stack>, ElementWriter<ObjectCollectionWithProperties>

Direct Known Subclasses:

DrawCroppedObjectsGenerator, DrawObjectsGenerator

public abstract class ObjectsAsRGBGenerator
extends RasterGeneratorSelectFormat<ObjectCollectionWithProperties>

A base class for generators that draw an ObjectCollection upon a RGBStack.

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
ObjectsAsRGBGenerator(DrawObject drawObject, ObjectDrawAttributes attributes, io.vavr.control.Either<Dimensions,DisplayStack> background)	Creates a new ObjectsAsRGBGenerator instance.

Method Summary

Modifier and Type	Method	Description
protected static RGBStack	createEmptyStackFor(Dimensions dimensions)	Creates an empty RGBStack.
protected abstract RGBStack	generateBackgroundRegion(ObjectCollectionWithProperties objects, io.vavr.control.Either<Dimensions,DisplayStack> background)	Creates a RGBStack containing the background, without objects being drawn upon it.
protected abstract ObjectCollectionWithProperties	generateMasks(ObjectCollectionWithProperties objects)	Creates a ObjectCollectionWithProperties indicative of the masks that will be imposed on top of the background-region.
io.vavr.control.Either<Dimensions,DisplayStack>	getBackground()	A background image or dimensions to define an empty background.
StackWriteAttributes	guaranteedImageAttributes()	Guarantees on the attributes of all images created by the generator.
void	setBackground(io.vavr.control.Either<Dimensions,DisplayStack> background)	A background image or dimensions to define an empty background.
Stack	transform(ObjectCollectionWithProperties element)	Applies any necessary preprocessing to create an element suitable for writing to the filesystem.

Methods inherited from class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorSelectFormat

selectFileExtension, writeToFile

Methods inherited from class org.anchoranalysis.image.io.stack.output.generator.RasterGenerator

write, writeWithIndex

Methods inherited from class java.lang.Object

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

Constructor Details

ObjectsAsRGBGenerator

public ObjectsAsRGBGenerator(DrawObject drawObject,
 ObjectDrawAttributes attributes,
 io.vavr.control.Either<Dimensions,DisplayStack> background)

Creates a new ObjectsAsRGBGenerator instance.

Parameters:

drawObject - Determines how an object is drawn (on the background).

attributes - An association of color and/or other identifies with each object.

background - A background image or dimensions to define an empty background.

Method Details

transform

public Stack transform(ObjectCollectionWithProperties element)
                throws OutputWriteFailedException

Description copied from interface: TransformingGenerator

Applies any necessary preprocessing to create an element suitable for writing to the filesystem.

Parameters:

element - element to be assigned and then transformed.

Returns:

the transformed element after necessary preprocessing.

Throws:

OutputWriteFailedException - if anything goes wrong.

guaranteedImageAttributes

public StackWriteAttributes guaranteedImageAttributes()

Description copied from class: RasterGenerator

Guarantees on the attributes of all images created by the generator.

Specified by:

guaranteedImageAttributes in class RasterGenerator<ObjectCollectionWithProperties>

Returns:

options that are guaranteed to be true of all images by the generator.

generateBackgroundRegion

protected abstract RGBStack generateBackgroundRegion(ObjectCollectionWithProperties objects,
 io.vavr.control.Either<Dimensions,DisplayStack> background)
                                              throws CreateException

Creates a RGBStack containing the background, without objects being drawn upon it.

This background may be all or only a region of the entire background-stack.

Parameters:

objects - the current objects to be drawn.

background - the entire background.

Returns:

a newly created RGBStack, as above.

Throws:

CreateException - if the background cannot be successfully created.

generateMasks

protected abstract ObjectCollectionWithProperties generateMasks(ObjectCollectionWithProperties objects)
                                                         throws CreateException

Creates a ObjectCollectionWithProperties indicative of the masks that will be imposed on top of the background-region.

Parameters:

objects - the objects to draw.

Returns:

either objects or a derived-representation of objects, as will be drawn on the background-region.

Throws:

CreateException - if the background cannot be successfully created.

createEmptyStackFor

protected static RGBStack createEmptyStackFor(Dimensions dimensions)

Creates an empty RGBStack.

Empty implies all voxels are zero-valued i.e. have black color.

Parameters:

dimensions - the size of the stack to create.

Returns:

the newly created RGBStack.

getBackground

public io.vavr.control.Either<Dimensions,DisplayStack> getBackground()

A background image or dimensions to define an empty background.

setBackground

public void setBackground(io.vavr.control.Either<Dimensions,DisplayStack> background)

A background image or dimensions to define an empty background.