Package qupath.lib.gui.viewer.overlays

Class HierarchyOverlay

java.lang.Object

qupath.lib.gui.viewer.overlays.AbstractOverlay

qupath.lib.gui.viewer.overlays.HierarchyOverlay

All Implemented Interfaces:

PathOverlay

public class HierarchyOverlay
extends AbstractOverlay

An overlay capable of painting a PathObjectHierarchy, except for any TMA grid (which is handled by TMAGridOverlay).

Author:

Pete Bankhead

Nested Class Summary

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

AbstractOverlay.LocationStringFunction

Constructor Summary

Constructors

Constructor	Description
HierarchyOverlay(DefaultImageRegionStore regionStore, OverlayOptions overlayOptions, ImageData<BufferedImage> imageData)	Constructor.

Method Summary

Modifier and Type	Method	Description
void	clearCachedOverlay()	Clear previously-cached tiles for this overlay.
void	clearCachedOverlayForRegion(ImageRegion region)	Clear previously-cached tiles for a specified region of this overlay.
void	paintOverlay(Graphics2D g2d, ImageRegion imageRegion, double downsampleFactor, ImageData<BufferedImage> imageData, boolean paintCompletely)	Paint the overlay to a graphics object.
void	resetImageData()	Reset the last image data.

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

getAlphaComposite, getLocationString, 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

Constructor Details

HierarchyOverlay

public HierarchyOverlay(DefaultImageRegionStore regionStore,
 OverlayOptions overlayOptions,
 ImageData<BufferedImage> imageData)

Constructor. Note that a HierarchyOverlay cannot adapt very efficient to changes in ImageData, and therefore should not be reused across viewers.

Parameters:

regionStore - region store to cache image tiles

overlayOptions - overlay options to control display

imageData - current image data

Method Details

resetImageData

public void resetImageData()

Reset the last image data. The hierarchy overlay stores the last-seen image data internally to assist with caching, but retaining a reference too long could become a memory leak.

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.

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.

clearCachedOverlay

public void clearCachedOverlay()

Clear previously-cached tiles for this overlay.

clearCachedOverlayForRegion

public void clearCachedOverlayForRegion(ImageRegion region)

Clear previously-cached tiles for a specified region of this overlay.

Parameters:

region - the region for which tiles should be removed