Package sc.fiji.snt.viewer

Class Bvv.AnnotationOverlay

java.lang.Object

sc.fiji.snt.viewer.Bvv.AnnotationOverlay

All Implemented Interfaces:

AbstractBigViewer.AnnotationOverlay

Enclosing class:

Bvv

public static class Bvv.AnnotationOverlay
extends Object
implements AbstractBigViewer.AnnotationOverlay

Renders spherical annotations at SNTPoint world coordinates. Rendered with CPU (Java2D) but optimized with caching and batched rendering.

Method Summary

Modifier and Type	Method	Description
void	addAnnotation(Object owner, SNTPoint p, float radius, Color color)	Owner-scoped variant of AbstractBigViewer.AnnotationOverlay.addAnnotation(SNTPoint, float, Color).
void	addAnnotation(SNTPoint p, float radius, Color color)	Add a single annotation.
void	addAnnotations(Collection<SNTPoint> points, float radius, Color color)	Add annotations to the current list.
void	clear()	Remove all annotations, from every layer/owner.
void	clear(Object owner)	Owner-scoped variant of AbstractBigViewer.AnnotationOverlay.clear(): removes only owner's annotations, leaving every other owner's layer (and the legacy ownerless one) untouched, and triggers a repaint.
void	clearAll()	Removes every layer's annotations and triggers a repaint.
int	getCount()	Returns the number of annotations currently in the overlay, across all layers/owners.
int	hitTest(int screenX, int screenY)	Hit-tests the last-rendered screen circles against (screenX, screenY).
int	hitTest(Object owner, int screenX, int screenY)	Owner-scoped hit-test: same screen-circle test as hitTest(int, int), restricted to owner's own [start, end) range within the flattened, currently-rendered annotation list (see layerRanges), with the result translated back to an owner-local index.
boolean	isVisible()	Returns true if the overlay is currently rendered.
void	replaceAll(Object owner, List<SNTPoint> points, List<Float> sizes, List<Color> colors)	Owner-scoped variant: replaces only owner's layer with a single repaint, leaving every other owner's annotations (bookmarks, seeds, the legacy ownerless layer, ...)
void	replaceAll(List<SNTPoint> points, List<Float> sizes, List<Color> colors)	Replaces all annotations in one shot with a single repaint.
void	setAnnotations(Collection<SNTPoint> points, float radius, Color color)	Replace the current annotations with the provided list.
void	setSelectedIndex(int index)	Highlights the annotation at the given model index by rendering it in a contrasting color.
void	setSelectedIndex(Object owner, int index)	Owner-scoped variant of AbstractBigViewer.AnnotationOverlay.setSelectedIndex(int): index is local to owner's own layer (e.g. a row index into that owner's model), not a global index into the combined, all-layers annotation list.
void	setVisible(boolean visible)	Show/hide annotations
void	updateScene()	Ensure renderers/nodes reflect current annotation list.

Methods inherited from class java.lang.Object

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

Method Details

setAnnotations

public void setAnnotations(Collection<SNTPoint> points,
 float radius,
 Color color)

Replace the current annotations with the provided list.

addAnnotations

public void addAnnotations(Collection<SNTPoint> points,
 float radius,
 Color color)

Add annotations to the current list.

addAnnotation

public void addAnnotation(SNTPoint p,
 float radius,
 Color color)

Add a single annotation.

Specified by:

addAnnotation in interface AbstractBigViewer.AnnotationOverlay

Parameters:

p - the position (world coordinates)

radius - sphere radius in physical units

color - fill color

addAnnotation

public void addAnnotation(Object owner,
 SNTPoint p,
 float radius,
 Color color)

Description copied from interface: AbstractBigViewer.AnnotationOverlay

Owner-scoped variant of AbstractBigViewer.AnnotationOverlay.addAnnotation(SNTPoint, float, Color). Independent callers (e.g. BookmarkManager and SeedOverlayBigViewerHandler) pass a distinct, stable owner key (typically their own Class object) so their annotations are tracked as a separate layer: clearing/replacing one owner's layer never touches another owner's. All layers - including the legacy ownerless one used by AbstractBigViewer.AnnotationOverlay.addAnnotation(SNTPoint, float, Color) - are rendered together. Implementations that don't support per-owner layers may fall back to the shared/ownerless behavior.

Specified by:

addAnnotation in interface AbstractBigViewer.AnnotationOverlay

Parameters:

owner - identifies the layer this annotation belongs to

p - the position (world coordinates)

radius - sphere radius in physical units

color - fill color

clear

public void clear()

Remove all annotations, from every layer/owner.

Specified by:

clear in interface AbstractBigViewer.AnnotationOverlay

clearAll

public void clearAll()

Description copied from interface: AbstractBigViewer.AnnotationOverlay

Removes every layer's annotations and triggers a repaint. Equivalent to AbstractBigViewer.AnnotationOverlay.clear() for implementations without per-owner layers; named separately from the owner-scoped AbstractBigViewer.AnnotationOverlay.clear(Object) to make the "wipe everything" intent explicit at call sites.

Specified by:

clearAll in interface AbstractBigViewer.AnnotationOverlay

clear

public void clear(Object owner)

Description copied from interface: AbstractBigViewer.AnnotationOverlay

Owner-scoped variant of AbstractBigViewer.AnnotationOverlay.clear(): removes only owner's annotations, leaving every other owner's layer (and the legacy ownerless one) untouched, and triggers a repaint. Implementations that don't support per-owner layers may fall back to AbstractBigViewer.AnnotationOverlay.clear(), which - unlike this method - clears everything.

Specified by:

clear in interface AbstractBigViewer.AnnotationOverlay

Parameters:

owner - identifies the layer to clear

isVisible

public boolean isVisible()

Description copied from interface: AbstractBigViewer.AnnotationOverlay

Returns true if the overlay is currently rendered.

Specified by:

isVisible in interface AbstractBigViewer.AnnotationOverlay

getCount

public int getCount()

Returns the number of annotations currently in the overlay, across all layers/owners.

Specified by:

getCount in interface AbstractBigViewer.AnnotationOverlay

setVisible

public void setVisible(boolean visible)

Show/hide annotations

Specified by:

setVisible in interface AbstractBigViewer.AnnotationOverlay

Parameters:

visible - true to show, false to hide

updateScene

public void updateScene()

Ensure renderers/nodes reflect current annotation list.

Specified by:

updateScene in interface AbstractBigViewer.AnnotationOverlay

setSelectedIndex

public void setSelectedIndex(int index)

Description copied from interface: AbstractBigViewer.AnnotationOverlay

Highlights the annotation at the given model index by rendering it in a contrasting color. Pass -1 to clear any existing highlight.

Specified by:

setSelectedIndex in interface AbstractBigViewer.AnnotationOverlay

Parameters:

index - model index of the annotation to highlight, or -1 for none

setSelectedIndex

public void setSelectedIndex(Object owner,
 int index)

Description copied from interface: AbstractBigViewer.AnnotationOverlay

Owner-scoped variant of AbstractBigViewer.AnnotationOverlay.setSelectedIndex(int): index is local to owner's own layer (e.g. a row index into that owner's model), not a global index into the combined, all-layers annotation list. Implementations that don't support per-owner layers may fall back to AbstractBigViewer.AnnotationOverlay.setSelectedIndex(int).

Specified by:

setSelectedIndex in interface AbstractBigViewer.AnnotationOverlay

Parameters:

owner - identifies the layer index is relative to

index - layer-local index of the annotation to highlight, or -1 for none

hitTest

public int hitTest(int screenX,
 int screenY)

Hit-tests the last-rendered screen circles against (screenX, screenY). Uses a minimum hit radius of 4 px so tiny markers remain clickable.

Specified by:

hitTest in interface AbstractBigViewer.AnnotationOverlay

Parameters:

screenX - x coordinate in viewer-display pixels

screenY - y coordinate in viewer-display pixels

hitTest

public int hitTest(Object owner,
 int screenX,
 int screenY)

Owner-scoped hit-test: same screen-circle test as hitTest(int, int), restricted to owner's own [start, end) range within the flattened, currently-rendered annotation list (see layerRanges), with the result translated back to an owner-local index.

Specified by:

hitTest in interface AbstractBigViewer.AnnotationOverlay

Parameters:

owner - identifies the layer to hit-test against

screenX - x coordinate in viewer-display pixels

screenY - y coordinate in viewer-display pixels

replaceAll

public void replaceAll(List<SNTPoint> points,
 List<Float> sizes,
 List<Color> colors)

Replaces all annotations in one shot with a single repaint. Overrides the default to avoid the per-call repaints from clear() and addAnnotation(), which can produce visible flicker.

Specified by:

replaceAll in interface AbstractBigViewer.AnnotationOverlay

Parameters:

points - list of positions (world coordinates); null entries are skipped

sizes - sphere radii in physical units, parallel to points

colors - fill colors, parallel to points; null entries use Color.YELLOW

replaceAll

public void replaceAll(Object owner,
 List<SNTPoint> points,
 List<Float> sizes,
 List<Color> colors)

Owner-scoped variant: replaces only owner's layer with a single repaint, leaving every other owner's annotations (bookmarks, seeds, the legacy ownerless layer, ...) untouched. This is what BookmarkManager and SeedOverlayBigViewerHandler use, each with its own owner key, so neither wipes the other's markers.

Specified by:

replaceAll in interface AbstractBigViewer.AnnotationOverlay

Parameters:

owner - identifies the layer to replace

points - list of positions (world coordinates); null entries are skipped

sizes - sphere radii in physical units, parallel to points

colors - fill colors, parallel to points; null entries use Color.YELLOW