Package qupath.lib.gui.viewer

Class OverlayOptions

java.lang.Object

qupath.lib.gui.viewer.OverlayOptions

public class OverlayOptions
extends Object

Default class for storing overlay display options.

Author:

Pete Bankhead

Property Summary

Properties

Type	Property	Description
ObjectProperty<OverlayOptions.DetectionDisplayMode>	detectionDisplayMode	Property representing the current OverlayOptions.DetectionDisplayMode.
BooleanProperty	fillAnnotations
BooleanProperty	fillDetections
FloatProperty	fontSize
ObjectProperty<GridLines>	gridLines
ObservableSet<PathClass>	hiddenClasses
ObjectProperty<MeasurementMapper>	measurementMapper
FloatProperty	opacity	Property representing the global opacity for overlay drawing.
ObjectProperty<RegionFilter>	pixelClassificationFilterRegion
BooleanProperty	showAnnotations
BooleanProperty	showConnections
BooleanProperty	showDetections
BooleanProperty	showGrid
BooleanProperty	showNames
BooleanProperty	showPixelClassification
BooleanProperty	showTMACoreLabels
BooleanProperty	showTMAGrid

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	OverlayOptions.DetectionDisplayMode	Display modes for cells and other detections.

Constructor Summary

Constructors

Constructor	Description
OverlayOptions()	Constructor, using default values.
OverlayOptions(OverlayOptions options)	Constructor, initializing values based on an existing OverlayOptions object.

Method Summary

Modifier and Type	Method	Description
ObjectProperty<OverlayOptions.DetectionDisplayMode>	detectionDisplayModeProperty()	Property representing the current OverlayOptions.DetectionDisplayMode.
BooleanProperty	fillAnnotationsProperty()
BooleanProperty	fillDetectionsProperty()
FloatProperty	fontSizeProperty()
boolean	getAllPathClassesVisible()
OverlayOptions.DetectionDisplayMode	getDetectionDisplayMode()	Get the current OverlayOptions.DetectionDisplayMode.
boolean	getFillAnnotations()
boolean	getFillDetections()
float	getFontSize()
GridLines	getGridLines()
MeasurementMapper	getMeasurementMapper()
float	getOpacity()	Get the global opacity for overlay drawing.
RegionFilter	getPixelClassificationRegionFilter()
boolean	getShowAnnotations()
boolean	getShowCellBoundaries()	Query the current OverlayOptions.DetectionDisplayMode to see if cell boundary ROIs should be drawn.
boolean	getShowCellNuclei()	Query the current OverlayOptions.DetectionDisplayMode to see if nuclei ROIs should be drawn.
boolean	getShowConnections()
boolean	getShowDetections()
boolean	getShowGrid()
boolean	getShowNames()
boolean	getShowPixelClassification()
boolean	getShowTMACoreLabels()
boolean	getShowTMAGrid()
float	getThickStrokeWidth(double downsample)	Get the requested stroke thickness to use when drawing ROIs that should be represented with 'thick' lines (annotations, TMA cores).
ObjectProperty<GridLines>	gridLinesProperty()
ObservableSet<PathClass>	hiddenClassesProperty()
boolean	isPathClassHidden(PathClass pathClass)	Query whether objects with a specified classification should be displayed or hidden.
ReadOnlyLongProperty	lastChangeTimestamp()	Get a property representing the timestamp of the last recorded change for any property.
ObjectProperty<MeasurementMapper>	measurementMapperProperty()
FloatProperty	opacityProperty()	Property representing the global opacity for overlay drawing.
ObjectProperty<RegionFilter>	pixelClassificationFilterRegionProperty()
void	resetMeasurementMapper()	Reset any MeasurementMapper, so that measurements are not used to determine object colors.
void	setDetectionDisplayMode(OverlayOptions.DetectionDisplayMode mode)	Set the current OverlayOptions.DetectionDisplayMode.
void	setFillAnnotations(boolean fill)	Show annotation objects 'filled' in viewers.
void	setFillDetections(boolean fill)	Show detection objects 'filled' in viewers.
void	setFontSize(float size)	Set the requested font size for the 'Show names' option
void	setGridLines(GridLines gridLines)	Set the GridLines object that defines how a counting grid may be show in viewers
void	setMeasurementMapper(MeasurementMapper mapper)	Set the MeasurementMapper that defines how detections should be color coded according to their measurement values in viewers
void	setOpacity(float opacity)	Set global opacity for overlay drawing.
void	setPathClassHidden(PathClass pathClass, boolean hidden)	Request that objects with a particular PathClass not be displayed.
void	setPixelClassificationRegionFilter(RegionFilter region)	Control where pixel classifications should be calculated during live prediction
void	setShowAnnotations(boolean show)	Show the annotations on the image.
void	setShowConnections(boolean show)	Show connections between objects, if available.
void	setShowDetections(boolean show)	Show the objects as an overlay on the image.
void	setShowGrid(boolean showGrid)	Set whether a counting grid should be shown in viewers
void	setShowNames(boolean show)	Show the object names on the image.
void	setShowPixelClassification(boolean show)	Show pixel classification overlays.
void	setShowTMACoreLabels(boolean showTMALabels)	Show TMA core names on top of the image.
void	setShowTMAGrid(boolean show)	Show the TMA grid on the image, if present.
BooleanProperty	showAnnotationsProperty()
BooleanProperty	showConnectionsProperty()
BooleanProperty	showDetectionsProperty()
BooleanProperty	showGridProperty()
BooleanProperty	showNamesProperty()
BooleanProperty	showPixelClassificationProperty()
BooleanProperty	showTMACoreLabelsProperty()
BooleanProperty	showTMAGridProperty()

Methods inherited from class java.lang.Object

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

Property Details

opacity

public FloatProperty opacityProperty

Property representing the global opacity for overlay drawing.

See Also:

• getOpacity()
• setOpacity(float)
• opacityProperty()

detectionDisplayMode

public ObjectProperty<OverlayOptions.DetectionDisplayMode> detectionDisplayModeProperty

Property representing the current OverlayOptions.DetectionDisplayMode.

See Also:

• getDetectionDisplayMode()
• setDetectionDisplayMode(OverlayOptions.DetectionDisplayMode)
• detectionDisplayModeProperty()

showTMACoreLabels

public BooleanProperty showTMACoreLabelsProperty

See Also:

• getShowTMACoreLabels()
• setShowTMACoreLabels(boolean)
• showTMACoreLabelsProperty()

showConnections

public BooleanProperty showConnectionsProperty

See Also:

• getShowConnections()
• setShowConnections(boolean)
• showConnectionsProperty()

gridLines

public ObjectProperty<GridLines> gridLinesProperty

See Also:

• getGridLines()
• setGridLines(GridLines)
• gridLinesProperty()

measurementMapper

public ObjectProperty<MeasurementMapper> measurementMapperProperty

See Also:

• getMeasurementMapper()
• setMeasurementMapper(MeasurementMapper)
• measurementMapperProperty()

hiddenClasses

public ObservableSet<PathClass> hiddenClassesProperty

See Also:

• hiddenClassesProperty()

showAnnotations

public BooleanProperty showAnnotationsProperty

See Also:

• getShowAnnotations()
• setShowAnnotations(boolean)
• showAnnotationsProperty()

showNames

public BooleanProperty showNamesProperty

See Also:

• getShowNames()
• setShowNames(boolean)
• showNamesProperty()

fontSize

public FloatProperty fontSizeProperty

See Also:

• getFontSize()
• setFontSize(float)
• fontSizeProperty()

showTMAGrid

public BooleanProperty showTMAGridProperty

See Also:

• getShowTMAGrid()
• setShowTMAGrid(boolean)
• showTMAGridProperty()

showPixelClassification

public BooleanProperty showPixelClassificationProperty

See Also:

• getShowPixelClassification()
• setShowPixelClassification(boolean)
• showPixelClassificationProperty()

pixelClassificationFilterRegion

public ObjectProperty<RegionFilter> pixelClassificationFilterRegionProperty

See Also:

• pixelClassificationFilterRegionProperty()

showDetections

public BooleanProperty showDetectionsProperty

See Also:

• getShowDetections()
• setShowDetections(boolean)
• showDetectionsProperty()

fillDetections

public BooleanProperty fillDetectionsProperty

See Also:

• getFillDetections()
• setFillDetections(boolean)
• fillDetectionsProperty()

fillAnnotations

public BooleanProperty fillAnnotationsProperty

See Also:

• getFillAnnotations()
• setFillAnnotations(boolean)
• fillAnnotationsProperty()

showGrid

public BooleanProperty showGridProperty

See Also:

• getShowGrid()
• setShowGrid(boolean)
• showGridProperty()

Constructor Details

OverlayOptions

public OverlayOptions()

Constructor, using default values.

OverlayOptions

public OverlayOptions(OverlayOptions options)

Constructor, initializing values based on an existing OverlayOptions object.

Parameters:

options -

Method Details

lastChangeTimestamp

public ReadOnlyLongProperty lastChangeTimestamp()

Get a property representing the timestamp of the last recorded change for any property.

Returns:

setOpacity

public void setOpacity(float opacity)

Set global opacity for overlay drawing. Individual overlays may have their own opacity settings, but these should be concatenated with the global opacity.

Parameters:

opacity - opacity value between 0 (completely transparent) and 1 (completely opaque).

getOpacity

public float getOpacity()

Get the global opacity for overlay drawing.

Returns:

opacity value between 0 (completely transparent) and 1 (completely opaque).

opacityProperty

public FloatProperty opacityProperty()

Property representing the global opacity for overlay drawing.

Returns:

opacity property, which should accept values between 0 and 1.

See Also:

• getOpacity()
• setOpacity(float)

getDetectionDisplayMode

public OverlayOptions.DetectionDisplayMode getDetectionDisplayMode()

Get the current OverlayOptions.DetectionDisplayMode.

Returns:

the current display mode

getShowCellNuclei

public boolean getShowCellNuclei()

Query the current OverlayOptions.DetectionDisplayMode to see if nuclei ROIs should be drawn.

Returns:

true if nuclei should be drawn, false otherwise

getShowCellBoundaries

public boolean getShowCellBoundaries()

Query the current OverlayOptions.DetectionDisplayMode to see if cell boundary ROIs should be drawn.

Returns:

true if nuclei should be drawn, false otherwise

setDetectionDisplayMode

public void setDetectionDisplayMode(OverlayOptions.DetectionDisplayMode mode)

Set the current OverlayOptions.DetectionDisplayMode.

Parameters:

mode - the requested mode to set

detectionDisplayModeProperty

public ObjectProperty<OverlayOptions.DetectionDisplayMode> detectionDisplayModeProperty()

Property representing the current OverlayOptions.DetectionDisplayMode.

Returns:

See Also:

• getDetectionDisplayMode()
• setDetectionDisplayMode(OverlayOptions.DetectionDisplayMode)

getThickStrokeWidth

public float getThickStrokeWidth(double downsample)

Get the requested stroke thickness to use when drawing ROIs that should be represented with 'thick' lines (annotations, TMA cores).

Parameters:

downsample - downsample at which the annotations should be drawn

Returns:

preferred stroke thickness to use

setShowTMAGrid

public void setShowTMAGrid(boolean show)

Show the TMA grid on the image, if present.

Parameters:

show -

setShowAnnotations

public void setShowAnnotations(boolean show)

Show the annotations on the image.

Parameters:

show -

setShowNames

public void setShowNames(boolean show)

Show the object names on the image.

Parameters:

show -

setFontSize

public void setFontSize(float size)

Set the requested font size for the 'Show names' option

Parameters:

size -

setShowDetections

public void setShowDetections(boolean show)

Show the objects as an overlay on the image.

Parameters:

show -

setShowPixelClassification

public void setShowPixelClassification(boolean show)

Show pixel classification overlays.

Parameters:

show -

setFillDetections

public void setFillDetections(boolean fill)

Show detection objects 'filled' in viewers.

Parameters:

fill -

setFillAnnotations

public void setFillAnnotations(boolean fill)

Show annotation objects 'filled' in viewers.

Parameters:

fill -

setShowConnections

public void setShowConnections(boolean show)

Show connections between objects, if available.

Parameters:

show -

setShowTMACoreLabels

public void setShowTMACoreLabels(boolean showTMALabels)

Show TMA core names on top of the image.

Parameters:

showTMALabels -

getShowTMACoreLabels

public boolean getShowTMACoreLabels()

Returns:

true if TMA core labels should be shown in viewers, false otherwise

showTMACoreLabelsProperty

public BooleanProperty showTMACoreLabelsProperty()

Returns:

boolean property indicating whether TMA core labels should be shown in the viewer

See Also:

• getShowTMACoreLabels()
• setShowTMACoreLabels(boolean)

showConnectionsProperty

public BooleanProperty showConnectionsProperty()

Returns:

boolean property indicating whether collections between objects should be shown (e.g. after Delaunay triangulation)

See Also:

• getShowConnections()
• setShowConnections(boolean)

getShowPixelClassification

public boolean getShowPixelClassification()

Returns:

true if the current active pixel classification should be shown, false otherwise

getShowAnnotations

public boolean getShowAnnotations()

Returns:

true if annotations should be displayed in viewers, false otherwise

getShowNames

public boolean getShowNames()

Returns:

true if annotation names should be displayed in viewers, false otherwise

getFontSize

public float getFontSize()

Returns:

the requested font size for showing annotation names on the viewer

getShowTMAGrid

public boolean getShowTMAGrid()

Returns:

true if any TMA grids should be displayed in viewers, false otherwise

getShowDetections

public boolean getShowDetections()

Returns:

true if detections should be displayed in viewers, false otherwise

getShowConnections

public boolean getShowConnections()

Returns:

true if any calculated connections between objects should be displayed in viewers, false otherwise

getFillDetections

public boolean getFillDetections()

Returns:

true if detections should be displayed 'filled' in viewers, false otherwise

getFillAnnotations

public boolean getFillAnnotations()

Returns:

true if annotations should be displayed 'filled' in viewers, false otherwise

setShowGrid

public void setShowGrid(boolean showGrid)

Set whether a counting grid should be shown in viewers

Parameters:

showGrid -

See Also:

• setGridLines(GridLines)

getShowGrid

public boolean getShowGrid()

Returns:

true if a counting grid should be displayed in viewers, false otherwise

See Also:

• getGridLines()

getGridLines

public GridLines getGridLines()

Returns:

the GridLines object that defines how a counting grid may be show in viewers

See Also:

• getShowGrid()

setGridLines

public void setGridLines(GridLines gridLines)

Set the GridLines object that defines how a counting grid may be show in viewers

Parameters:

gridLines -

gridLinesProperty

public ObjectProperty<GridLines> gridLinesProperty()

Returns:

an object property containing a GridLines object that defines how a counting grid may be show in viewers

See Also:

• getGridLines()
• setGridLines(GridLines)

setMeasurementMapper

public void setMeasurementMapper(MeasurementMapper mapper)

Set the MeasurementMapper that defines how detections should be color coded according to their measurement values in viewers

Parameters:

mapper -

getMeasurementMapper

public MeasurementMapper getMeasurementMapper()

Returns:

the MeasurementMapper object that defines how detections should be color coded according to their measurement values in viewers

measurementMapperProperty

public ObjectProperty<MeasurementMapper> measurementMapperProperty()

Returns:

object property containing the current MeasurementMapper, if one has been set, or null otherwise

See Also:

• getMeasurementMapper()
• setMeasurementMapper(MeasurementMapper)

resetMeasurementMapper

public void resetMeasurementMapper()

Reset any MeasurementMapper, so that measurements are not used to determine object colors.

getAllPathClassesVisible

public boolean getAllPathClassesVisible()

Returns:

true if objects should be displayed regardless of classification (i.e. no classifications are 'hidden')

See Also:

• hiddenClassesProperty()

isPathClassHidden

public boolean isPathClassHidden(PathClass pathClass)

Query whether objects with a specified classification should be displayed or hidden.

Parameters:

pathClass - the classification to query

Returns:

true if objects with the classification should be displayed, false if they should be hidden

setPathClassHidden

public void setPathClassHidden(PathClass pathClass,
 boolean hidden)

Request that objects with a particular PathClass not be displayed. This may be null, indicating that all unclassified objects should be hidden.

Parameters:

pathClass -

hidden -

hiddenClassesProperty

public ObservableSet<PathClass> hiddenClassesProperty()

Returns:

an observable set containing classifications for which the corresponding objects should not be displayed

showAnnotationsProperty

public BooleanProperty showAnnotationsProperty()

Returns:

the boolean property indicating whether annotations should be displayed

See Also:

• getShowAnnotations()
• setShowAnnotations(boolean)

showNamesProperty

public BooleanProperty showNamesProperty()

Returns:

the boolean property indicating whether object labels should be displayed

See Also:

• getShowNames()
• setShowNames(boolean)

fontSizeProperty

public FloatProperty fontSizeProperty()

Returns:

the float property indicating the font size that should be used for displaying names

See Also:

• getFontSize()
• setFontSize(float)

showTMAGridProperty

public BooleanProperty showTMAGridProperty()

Returns:

the boolean property indicating whether any current TMA grid should be displayed

See Also:

• getShowTMAGrid()
• setShowTMAGrid(boolean)

showPixelClassificationProperty

public BooleanProperty showPixelClassificationProperty()

Returns:

the boolean property indicating whether any active pixel classification should be displayed

See Also:

• getShowPixelClassification()
• setShowPixelClassification(boolean)

pixelClassificationFilterRegionProperty

public ObjectProperty<RegionFilter> pixelClassificationFilterRegionProperty()

Returns:

the filter used to determine whether a pixel classification should be computed for a specified region

setPixelClassificationRegionFilter

public void setPixelClassificationRegionFilter(RegionFilter region)

Control where pixel classifications should be calculated during live prediction

Parameters:

region -

getPixelClassificationRegionFilter

public RegionFilter getPixelClassificationRegionFilter()

Returns:

a filter used to determine whether a pixel classification should be computed for a specified region

showDetectionsProperty

public BooleanProperty showDetectionsProperty()

Returns:

the boolean property indicating whether detections should be displayed

See Also:

• getShowDetections()
• setShowDetections(boolean)

fillDetectionsProperty

public BooleanProperty fillDetectionsProperty()

Returns:

the boolean property indicating whether detections should be displayed 'filled'

See Also:

• getFillDetections()
• setFillDetections(boolean)

fillAnnotationsProperty

public BooleanProperty fillAnnotationsProperty()

Returns:

the boolean property indicating whether annotations should be displayed 'filled'

See Also:

• getFillAnnotations()
• setFillAnnotations(boolean)

showGridProperty

public BooleanProperty showGridProperty()

Returns:

the boolean property indicating whether a counting grid should be shown over the viewer

See Also:

• getShowGrid()
• setShowGrid(boolean)