Package qupath.lib.gui.viewer.overlays

Class PixelClassificationOverlay

java.lang.Object

qupath.lib.gui.viewer.overlays.AbstractOverlay

qupath.lib.gui.viewer.overlays.AbstractImageOverlay

qupath.lib.gui.viewer.overlays.PixelClassificationOverlay

All Implemented Interfaces:

PathOverlay

public class PixelClassificationOverlay
extends AbstractImageOverlay

PathOverlay that gives the results of pixel classification.

Author:

Pete Bankhead

Property Summary

Properties

Type	Property	Description
ObjectProperty<ImageRenderer>	renderer	Get the ImageRenderer property used with this overlay.

Properties inherited from class qupath.lib.gui.viewer.overlays.AbstractImageOverlay

interpolation

Nested Class Summary

Nested classes/interfaces inherited from class qupath.lib.gui.viewer.overlays.AbstractOverlay

AbstractOverlay.LocationStringFunction

Method Summary

Modifier and Type	Method	Description
void	clearCache()	Clear any cached tiles.
static PixelClassificationOverlay	create(OverlayOptions options, Function<ImageData<BufferedImage>,ImageServer<BufferedImage>> fun, ImageRenderer renderer)	Create an overlay to display a live image that can be created from an existing ImageData.
static PixelClassificationOverlay	create(OverlayOptions options, Map<ImageData<BufferedImage>,ImageServer<BufferedImage>> map, ImageRenderer renderer)	Create an overlay to display a live image that can be created from an existing ImageData.
static PixelClassificationOverlay	create(OverlayOptions options, PixelClassifier classifier)	Create an overlay to display the live application of a PixelClassifier to an image, using the default number of parallel threads for classification.
static PixelClassificationOverlay	create(OverlayOptions options, PixelClassifier classifier, int nThreads)	Create an overlay to display the live application of a PixelClassifier to an image.
static PixelClassificationOverlay	createFeatureDisplayOverlay(OverlayOptions options, Function<ImageData<BufferedImage>,ImageServer<BufferedImage>> fun, ImageRenderer renderer)	Deprecated. Use create(OverlayOptions, Function, ImageRenderer) instead.
static String	getDefaultLocationString(ImageServer<BufferedImage> server, double x, double y, int z, int t)	Default method for getting a location string from an ImageServer using cached tiles.
boolean	getLivePrediction()	Query whether live prediction is turned on.
String	getLocationString(ImageData<BufferedImage> imageData, double x, double y, int z, int t)	Get a location string to display when showing a specified image.
int	getMaxThreads()	Get the maximum number of threads that may be used during live prediction.
ImageServer<BufferedImage>	getPixelClassificationServer(ImageData<BufferedImage> imageData)	Get the ImageServer that would be used by this overlay for the specified ImageData.
ImageRenderer	getRenderer()	Get the ImageRenderer used with this overlay, which may be null.
void	paintOverlay(Graphics2D g2d, ImageRegion imageRegion, double downsampleFactor, ImageData<BufferedImage> imageData, boolean paintCompletely)	Paint the overlay to a graphics object.
ObjectProperty<ImageRenderer>	rendererProperty()	Get the ImageRenderer property used with this overlay.
void	setLivePrediction(boolean livePrediction)	Turn on or off live prediction.
void	setMaxThreads(int nThreads)	Set the maximum number of threads that may be used during live prediction.
void	setRenderer(ImageRenderer renderer)	Set the ImageRenderer to be used with this overlay.
void	stop()	Stop the overlap, halting any pending tile requests.

Methods inherited from class qupath.lib.gui.viewer.overlays.AbstractImageOverlay

getInterpolation, interpolationProperty, setInterpolation, setInterpolation

Methods inherited from class qupath.lib.gui.viewer.overlays.AbstractOverlay

getAlphaComposite, getLocationStringFunction, getOpacity, getOverlayOptions, getPreferredOverlayColor, isVisible, setAlphaComposite, setLocationStringFunction, setOpacity, setPreferredOverlayColor

Methods inherited from class java.lang.Object

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

Property Details

renderer

public ObjectProperty<ImageRenderer> rendererProperty

Get the ImageRenderer property used with this overlay.

See Also:

• getRenderer()
• setRenderer(ImageRenderer)
• rendererProperty()

Method Details

create

public static PixelClassificationOverlay create(OverlayOptions options,
 PixelClassifier classifier)

Create an overlay to display the live application of a PixelClassifier to an image, using the default number of parallel threads for classification.

Parameters:

options - the options controlling the overlay display

classifier - the classifier

Returns:

create

public static PixelClassificationOverlay create(OverlayOptions options,
 PixelClassifier classifier,
 int nThreads)

Create an overlay to display the live application of a PixelClassifier to an image.

Parameters:

options - the options controlling the overlay display

classifier - the classifier

nThreads - number of parallel threads to use for classification (will be clipped to 1 or greater)

Returns:

create

public static PixelClassificationOverlay create(OverlayOptions options,
 Function<ImageData<BufferedImage>,ImageServer<BufferedImage>> fun,
 ImageRenderer renderer)

Create an overlay to display a live image that can be created from an existing ImageData.

Parameters:

options - options to control the overlay display

fun - function to create an ImageServer from the ImageData. Note that the server generated by the function call will be cached. If it is necessary to control the caching, this needs to be done externally and create(OverlayOptions, Map, ImageRenderer) should be used instead.

renderer - rendered used to create an RGB image

Returns:

the PixelClassificationOverlay

create

public static PixelClassificationOverlay create(OverlayOptions options,
 Map<ImageData<BufferedImage>,ImageServer<BufferedImage>> map,
 ImageRenderer renderer)

Create an overlay to display a live image that can be created from an existing ImageData. This differs from create(OverlayOptions, Function, ImageRenderer) in that a cached map of classifier servers is used directly.

Parameters:

options - options to control the overlay display

map - map to obtain an ImageServer from an ImageData

renderer - rendered used to create an RGB image

Returns:

the PixelClassificationOverlay

createFeatureDisplayOverlay

@Deprecated
public static PixelClassificationOverlay createFeatureDisplayOverlay(OverlayOptions options,
 Function<ImageData<BufferedImage>,ImageServer<BufferedImage>> fun,
 ImageRenderer renderer)

Deprecated.

Use create(OverlayOptions, Function, ImageRenderer) instead.

Create an overlay to display a live image that can be created from an existing ImageData.

Parameters:

options - options to control the overlay display

fun - function to create an ImageServer from the ImageData

renderer - rendered used to create an RGB image

Returns:

the PixelClassificationOverlay

rendererProperty

public ObjectProperty<ImageRenderer> rendererProperty()

Get the ImageRenderer property used with this overlay.

Returns:

See Also:

• getRenderer()
• setRenderer(ImageRenderer)

getRenderer

public ImageRenderer getRenderer()

Get the ImageRenderer used with this overlay, which may be null.

Returns:

setMaxThreads

public void setMaxThreads(int nThreads)

Set the maximum number of threads that may be used during live prediction.

Parameters:

nThreads -

getMaxThreads

public int getMaxThreads()

Get the maximum number of threads that may be used during live prediction.

Returns:

setRenderer

public void setRenderer(ImageRenderer renderer)

Set the ImageRenderer to be used with this overlay.

Parameters:

renderer -

getLivePrediction

public boolean getLivePrediction()

Query whether live prediction is turned on.

Returns:

setLivePrediction

public void setLivePrediction(boolean livePrediction)

Turn on or off live prediction. This requests tile classifications as the overlay is being viewed.

Parameters:

livePrediction -

getPixelClassificationServer

public ImageServer<BufferedImage> getPixelClassificationServer(ImageData<BufferedImage> imageData)

Get the ImageServer that would be used by this overlay for the specified ImageData. Note that the servers are cached internally.

Parameters:

imageData -

Returns:

paintOverlay

public void paintOverlay(Graphics2D g2d,
 ImageRegion imageRegion,
 double downsampleFactor,
 ImageData<BufferedImage> imageData,
 boolean paintCompletely)

Description copied from interface: PathOverlay

Paint the overlay to a graphics object. The graphics object will have a transform applied to it, so the painting should make use of coordinates in the original image space.

Specified by:

paintOverlay in interface PathOverlay

Overrides:

paintOverlay in class AbstractImageOverlay

Parameters:

g2d - Graphics2D object to which drawing should be performed. This should have any transform already applied to it.

imageRegion - The maximum image region that should be shown.

downsampleFactor - The downsample factor at which the overlay will be viewed. There is no need for rescaling according to this value since it has already been applied to the Graphics2D as part of its AffineTransform, however it may optionally be needed within the method e.g. to correct line thicknesses.

imageData - the ImageData associated with this overlay. If the overlay is being displayed on a viewer, this is the ImageData open within the viewer. Not all overlays require this, and it may be null.

paintCompletely - If true, the method is permitted to return without completely painting everything, for performance reasons.

clearCache

public void clearCache()

Clear any cached tiles.

stop

public void stop()

Stop the overlap, halting any pending tile requests.

getLocationString

public String getLocationString(ImageData<BufferedImage> imageData,
 double x,
 double y,
 int z,
 int t)

Description copied from interface: PathOverlay

Get a location string to display when showing a specified image.

The default implementation returns null. If subclasses override this method, they must return quickly, as it may be used to determine text to display as the mouse moves over an image.

Specified by:

getLocationString in interface PathOverlay

Overrides:

getLocationString in class AbstractOverlay

Parameters:

imageData -

x - x-coordinate, in the image space (not the viewer component space)

y - y-coordinate, in the image space (not the viewer component space)

z - z-index for the region currently being viewed

t - t-index for the region currently being viewed

Returns:

getDefaultLocationString

public static String getDefaultLocationString(ImageServer<BufferedImage> server,
 double x,
 double y,
 int z,
 int t)

Default method for getting a location string from an ImageServer using cached tiles. If tiles are not cached, no string is returned.

May be used by classes implementing PathOverlay.getLocationString(ImageData, double, double, int, int)

Parameters:

server -

x -

y -

z -

t -

Returns:

location String based upon pixel values and cached tiles, or null if no String is available