Package qupath.lib.gui.charts

Class PathObjectScatterChart

java.lang.Object

javafx.scene.Node

javafx.scene.Parent

javafx.scene.layout.Region

javafx.scene.chart.Chart

javafx.scene.chart.XYChart<Number,Number>

javafx.scene.chart.ScatterChart<Number,Number>

qupath.lib.gui.charts.PathObjectScatterChart

All Implemented Interfaces:

Styleable, EventTarget

public class PathObjectScatterChart
extends ScatterChart<Number,Number>

An interactive ScatterChart implementation for showing large(ish) numbers of PathObject, optionally linked to a QuPathViewer.

A goal of this class is to reduce expensive chart manipulations, such as adding and removing data points. Instead, data points are reused and updated where possible.

Additionally, the maximum number of data points can be specified, so that the chart can automatically randomly subsample points to show only some.

Since:

v0.6.0

Property Summary

Properties

Type	Property	Description
BooleanProperty	autorangeToFullData	Get a property representing whether to use the entire dataset when calculating axis limits automatically.
IntegerProperty	maxPoints	Get a property representing the maximum number of points that the plot will display.
DoubleProperty	pointOpacity	Get a property representing the opacity of all data points.
DoubleProperty	pointRadius	Get a property representing the radius of all data points.
IntegerProperty	rngSeed	Get a property representing the random number generator's seed for subsampling.

Properties inherited from class javafx.scene.chart.XYChart

alternativeColumnFillVisible, alternativeRowFillVisible, data, horizontalGridLinesVisible, horizontalZeroLineVisible, verticalGridLinesVisible, verticalZeroLineVisible

Properties inherited from class javafx.scene.chart.Chart

animated, legend, legendSide, legendVisible, title, titleSide

Properties inherited from class javafx.scene.layout.Region

background, border, cacheShape, centerShape, height, insets, maxHeight, maxWidth, minHeight, minWidth, opaqueInsets, padding, prefHeight, prefWidth, scaleShape, shape, snapToPixel, width

Properties inherited from class javafx.scene.Parent

needsLayout

Properties inherited from class javafx.scene.Node

accessibleHelp, accessibleRoleDescription, accessibleRole, accessibleText, blendMode, boundsInLocal, boundsInParent, cacheHint, cache, clip, cursor, depthTest, disabled, disable, effectiveNodeOrientation, effect, eventDispatcher, focused, focusTraversable, focusVisible, focusWithin, hover, id, inputMethodRequests, layoutBounds, layoutX, layoutY, localToParentTransform, localToSceneTransform, managed, mouseTransparent, nodeOrientation, onContextMenuRequested, onDragDetected, onDragDone, onDragDropped, onDragEntered, onDragExited, onDragOver, onInputMethodTextChanged, onKeyPressed, onKeyReleased, onKeyTyped, onMouseClicked, onMouseDragEntered, onMouseDragExited, onMouseDragged, onMouseDragOver, onMouseDragReleased, onMouseEntered, onMouseExited, onMouseMoved, onMousePressed, onMouseReleased, onRotate, onRotationFinished, onRotationStarted, onScrollFinished, onScroll, onScrollStarted, onSwipeDown, onSwipeLeft, onSwipeRight, onSwipeUp, onTouchMoved, onTouchPressed, onTouchReleased, onTouchStationary, onZoomFinished, onZoom, onZoomStarted, opacity, parent, pickOnBounds, pressed, rotate, rotationAxis, scaleX, scaleY, scaleZ, scene, style, translateX, translateY, translateZ, viewOrder, visible

Nested Class Summary

Nested classes/interfaces inherited from class javafx.scene.chart.XYChart

XYChart.Data<X,Y>, XYChart.Series<X,Y>

Field Summary

Fields

Modifier and Type	Field	Description
static final int	NO_SHUFFLE_SEED	Seed value to use to specify that no shuffling should be applied before displaying the objects.

Fields inherited from class javafx.scene.layout.Region

USE_COMPUTED_SIZE, USE_PREF_SIZE

Fields inherited from class javafx.scene.Node

BASELINE_OFFSET_SAME_AS_HEIGHT

Constructor Summary

Constructors

Constructor	Description
PathObjectScatterChart(QuPathViewer viewer)	Create an interactive scatter plot using the current viewer

Method Summary

Modifier and Type	Method	Description
BooleanProperty	autorangeToFullDataProperty()	Get a property representing whether to use the entire dataset when calculating axis limits automatically.
protected void	dataItemAdded(XYChart.Series<Number,Number> series, int itemIndex, XYChart.Data<Number,Number> item)
protected void	dataItemRemoved(XYChart.Data<Number,Number> item, XYChart.Series<Number,Number> series)
boolean	getAutorangeToFullData()	Get the value of autorangeToFullDataProperty()
int	getMaxPoints()	Get the value of maxPointsProperty()
double	getPointOpacity()	Get the value o pointOpacityProperty()
double	getPointRadius()	Get the value of pointOpacityProperty()
int	getRngSeed()	Get the value of rngSeedProperty().
IntegerProperty	maxPointsProperty()	Get a property representing the maximum number of points that the plot will display.
DoubleProperty	pointOpacityProperty()	Get a property representing the opacity of all data points.
DoubleProperty	pointRadiusProperty()	Get a property representing the radius of all data points.
void	refreshData()	Recalculate the values of all data points.
IntegerProperty	rngSeedProperty()	Get a property representing the random number generator's seed for subsampling.
void	setAutorangeToFullData(boolean useFullData)	Set the value of autorangeToFullDataProperty().
void	setData(Collection<? extends PathObject> pathObjects, Function<PathObject,Number> xFun, Function<PathObject,Number> yFun)	Set the data to display in the plot.
void	setDataFromTable(Collection<? extends PathObject> pathObjects, PathTableData<PathObject> model, String xMeasurement, String yMeasurement)	Set the data to display in the plot from a table model.
void	setMaxPoints(int maxPoints)	Set the value of maxPointsProperty().
void	setPointOpacity(double pointOpacity)	Set the value of pointOpacityProperty().
void	setPointRadius(double radius)	Set the value of pointOpacityProperty()
void	setRngSeed(int rngSeed)	Set the value of rngSeedProperty().
protected void	updateAxisRange()
protected void	updateLegend()

Methods inherited from class javafx.scene.chart.ScatterChart

dataItemChanged, layoutPlotChildren, seriesAdded, seriesRemoved

Methods inherited from class javafx.scene.chart.XYChart

alternativeColumnFillVisibleProperty, alternativeRowFillVisibleProperty, currentDisplayedExtraValueProperty, currentDisplayedXValueProperty, currentDisplayedYValueProperty, dataProperty, getClassCssMetaData, getCssMetaData, getCurrentDisplayedExtraValue, getCurrentDisplayedXValue, getCurrentDisplayedYValue, getData, getDisplayedDataIterator, getDisplayedSeriesIterator, getPlotChildren, getVerticalGridLinesVisible, getXAxis, getYAxis, horizontalGridLinesVisibleProperty, horizontalZeroLineVisibleProperty, isAlternativeColumnFillVisible, isAlternativeRowFillVisible, isHorizontalGridLinesVisible, isHorizontalZeroLineVisible, isVerticalZeroLineVisible, layoutChartChildren, removeDataItemFromDisplay, removeSeriesFromDisplay, seriesChanged, setAlternativeColumnFillVisible, setAlternativeRowFillVisible, setCurrentDisplayedExtraValue, setCurrentDisplayedXValue, setCurrentDisplayedYValue, setData, setHorizontalGridLinesVisible, setHorizontalZeroLineVisible, setVerticalGridLinesVisible, setVerticalZeroLineVisible, verticalGridLinesVisibleProperty, verticalZeroLineVisibleProperty

Methods inherited from class javafx.scene.chart.Chart

animate, animatedProperty, computeMinHeight, computeMinWidth, computePrefHeight, computePrefWidth, getAnimated, getChartChildren, getLegend, getLegendSide, getTitle, getTitleSide, isLegendVisible, layoutChildren, legendProperty, legendSideProperty, legendVisibleProperty, requestChartLayout, setAnimated, setLegend, setLegendSide, setLegendVisible, setTitle, setTitleSide, shouldAnimate, titleProperty, titleSideProperty

Methods inherited from class javafx.scene.layout.Region

backgroundProperty, borderProperty, cacheShapeProperty, centerShapeProperty, computeMaxHeight, computeMaxWidth, getBackground, getBorder, getHeight, getInsets, getMaxHeight, getMaxWidth, getMinHeight, getMinWidth, getOpaqueInsets, getPadding, getPrefHeight, getPrefWidth, getShape, getUserAgentStylesheet, getWidth, heightProperty, insetsProperty, isCacheShape, isCenterShape, isResizable, isScaleShape, isSnapToPixel, layoutInArea, layoutInArea, layoutInArea, layoutInArea, maxHeight, maxHeightProperty, maxWidth, maxWidthProperty, minHeight, minHeightProperty, minWidth, minWidthProperty, opaqueInsetsProperty, paddingProperty, positionInArea, positionInArea, prefHeight, prefHeightProperty, prefWidth, prefWidthProperty, resize, scaleShapeProperty, setBackground, setBorder, setCacheShape, setCenterShape, setHeight, setMaxHeight, setMaxSize, setMaxWidth, setMinHeight, setMinSize, setMinWidth, setOpaqueInsets, setPadding, setPrefHeight, setPrefSize, setPrefWidth, setScaleShape, setShape, setSnapToPixel, setWidth, shapeProperty, snappedBottomInset, snappedLeftInset, snappedRightInset, snappedTopInset, snapPosition, snapPositionX, snapPositionY, snapSize, snapSizeX, snapSizeY, snapSpace, snapSpaceX, snapSpaceY, snapToPixelProperty, widthProperty

Methods inherited from class javafx.scene.Parent

getBaselineOffset, getChildren, getChildrenUnmodifiable, getManagedChildren, getStylesheets, isNeedsLayout, layout, lookup, needsLayoutProperty, queryAccessibleAttribute, requestLayout, requestParentLayout, setNeedsLayout, updateBounds

Methods inherited from class javafx.scene.Node

accessibleHelpProperty, accessibleRoleDescriptionProperty, accessibleRoleProperty, accessibleTextProperty, addEventFilter, addEventHandler, applyCss, autosize, blendModeProperty, boundsInLocalProperty, boundsInParentProperty, buildEventDispatchChain, cacheHintProperty, cacheProperty, clipProperty, computeAreaInScreen, contains, contains, cursorProperty, depthTestProperty, disabledProperty, disableProperty, effectiveNodeOrientationProperty, effectProperty, eventDispatcherProperty, executeAccessibleAction, fireEvent, focusedProperty, focusTraversableProperty, focusVisibleProperty, focusWithinProperty, getAccessibleHelp, getAccessibleRole, getAccessibleRoleDescription, getAccessibleText, getBlendMode, getBoundsInLocal, getBoundsInParent, getCacheHint, getClip, getContentBias, getCursor, getDepthTest, getEffect, getEffectiveNodeOrientation, getEventDispatcher, getId, getInitialCursor, getInitialFocusTraversable, getInputMethodRequests, getLayoutBounds, getLayoutX, getLayoutY, getLocalToParentTransform, getLocalToSceneTransform, getNodeOrientation, getOnContextMenuRequested, getOnDragDetected, getOnDragDone, getOnDragDropped, getOnDragEntered, getOnDragExited, getOnDragOver, getOnInputMethodTextChanged, getOnKeyPressed, getOnKeyReleased, getOnKeyTyped, getOnMouseClicked, getOnMouseDragEntered, getOnMouseDragExited, getOnMouseDragged, getOnMouseDragOver, getOnMouseDragReleased, getOnMouseEntered, getOnMouseExited, getOnMouseMoved, getOnMousePressed, getOnMouseReleased, getOnRotate, getOnRotationFinished, getOnRotationStarted, getOnScroll, getOnScrollFinished, getOnScrollStarted, getOnSwipeDown, getOnSwipeLeft, getOnSwipeRight, getOnSwipeUp, getOnTouchMoved, getOnTouchPressed, getOnTouchReleased, getOnTouchStationary, getOnZoom, getOnZoomFinished, getOnZoomStarted, getOpacity, getParent, getProperties, getPseudoClassStates, getRotate, getRotationAxis, getScaleX, getScaleY, getScaleZ, getScene, getStyle, getStyleableParent, getStyleClass, getTransforms, getTranslateX, getTranslateY, getTranslateZ, getTypeSelector, getUserData, getViewOrder, hasProperties, hoverProperty, idProperty, inputMethodRequestsProperty, intersects, intersects, isCache, isDisable, isDisabled, isFocused, isFocusTraversable, isFocusVisible, isFocusWithin, isHover, isManaged, isMouseTransparent, isPickOnBounds, isPressed, isVisible, layoutBoundsProperty, layoutXProperty, layoutYProperty, localToParent, localToParent, localToParent, localToParent, localToParent, localToParentTransformProperty, localToScene, localToScene, localToScene, localToScene, localToScene, localToScene, localToScene, localToScene, localToScene, localToScene, localToSceneTransformProperty, localToScreen, localToScreen, localToScreen, localToScreen, localToScreen, lookupAll, managedProperty, mouseTransparentProperty, nodeOrientationProperty, notifyAccessibleAttributeChanged, onContextMenuRequestedProperty, onDragDetectedProperty, onDragDoneProperty, onDragDroppedProperty, onDragEnteredProperty, onDragExitedProperty, onDragOverProperty, onInputMethodTextChangedProperty, onKeyPressedProperty, onKeyReleasedProperty, onKeyTypedProperty, onMouseClickedProperty, onMouseDragEnteredProperty, onMouseDragExitedProperty, onMouseDraggedProperty, onMouseDragOverProperty, onMouseDragReleasedProperty, onMouseEnteredProperty, onMouseExitedProperty, onMouseMovedProperty, onMousePressedProperty, onMouseReleasedProperty, onRotateProperty, onRotationFinishedProperty, onRotationStartedProperty, onScrollFinishedProperty, onScrollProperty, onScrollStartedProperty, onSwipeDownProperty, onSwipeLeftProperty, onSwipeRightProperty, onSwipeUpProperty, onTouchMovedProperty, onTouchPressedProperty, onTouchReleasedProperty, onTouchStationaryProperty, onZoomFinishedProperty, onZoomProperty, onZoomStartedProperty, opacityProperty, parentProperty, parentToLocal, parentToLocal, parentToLocal, parentToLocal, parentToLocal, pickOnBoundsProperty, pressedProperty, pseudoClassStateChanged, relocate, removeEventFilter, removeEventHandler, requestFocus, resizeRelocate, rotateProperty, rotationAxisProperty, scaleXProperty, scaleYProperty, scaleZProperty, sceneProperty, sceneToLocal, sceneToLocal, sceneToLocal, sceneToLocal, sceneToLocal, sceneToLocal, sceneToLocal, sceneToLocal, screenToLocal, screenToLocal, screenToLocal, setAccessibleHelp, setAccessibleRole, setAccessibleRoleDescription, setAccessibleText, setBlendMode, setCache, setCacheHint, setClip, setCursor, setDepthTest, setDisable, setDisabled, setEffect, setEventDispatcher, setEventHandler, setFocused, setFocusTraversable, setHover, setId, setInputMethodRequests, setLayoutX, setLayoutY, setManaged, setMouseTransparent, setNodeOrientation, setOnContextMenuRequested, setOnDragDetected, setOnDragDone, setOnDragDropped, setOnDragEntered, setOnDragExited, setOnDragOver, setOnInputMethodTextChanged, setOnKeyPressed, setOnKeyReleased, setOnKeyTyped, setOnMouseClicked, setOnMouseDragEntered, setOnMouseDragExited, setOnMouseDragged, setOnMouseDragOver, setOnMouseDragReleased, setOnMouseEntered, setOnMouseExited, setOnMouseMoved, setOnMousePressed, setOnMouseReleased, setOnRotate, setOnRotationFinished, setOnRotationStarted, setOnScroll, setOnScrollFinished, setOnScrollStarted, setOnSwipeDown, setOnSwipeLeft, setOnSwipeRight, setOnSwipeUp, setOnTouchMoved, setOnTouchPressed, setOnTouchReleased, setOnTouchStationary, setOnZoom, setOnZoomFinished, setOnZoomStarted, setOpacity, setPickOnBounds, setPressed, setRotate, setRotationAxis, setScaleX, setScaleY, setScaleZ, setStyle, setTranslateX, setTranslateY, setTranslateZ, setUserData, setViewOrder, setVisible, snapshot, snapshot, startDragAndDrop, startFullDrag, styleProperty, toBack, toFront, toString, translateXProperty, translateYProperty, translateZProperty, usesMirroring, viewOrderProperty, visibleProperty

Methods inherited from class java.lang.Object

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

Methods inherited from interface javafx.css.Styleable

getStyleableNode

Property Details

autorangeToFullData

public BooleanProperty autorangeToFullDataProperty

Get a property representing whether to use the entire dataset when calculating axis limits automatically. This is useful whenever we are subsampling data points.

See Also:

• getAutorangeToFullData()
• setAutorangeToFullData(boolean)
• autorangeToFullDataProperty()

maxPoints

public IntegerProperty maxPointsProperty

Get a property representing the maximum number of points that the plot will display. Subsampling will be used to ensure only this number of points or fewer are displayed.

See Also:

• getMaxPoints()
• setMaxPoints(int)
• maxPointsProperty()

rngSeed

public IntegerProperty rngSeedProperty

Get a property representing the random number generator's seed for subsampling. The default value is #NO_SHUFFLE_SEED which indicates no shuffling should be performed.

See Also:

• getRngSeed()
• setRngSeed(int)
• rngSeedProperty()

pointOpacity

public DoubleProperty pointOpacityProperty

Get a property representing the opacity of all data points. Making points translucent can be helpful when there are a lot of them.

See Also:

• getPointOpacity()
• setPointOpacity(double)
• pointOpacityProperty()

pointRadius

public DoubleProperty pointRadiusProperty

Get a property representing the radius of all data points.

See Also:

• getPointRadius()
• setPointRadius(double)
• pointRadiusProperty()

Field Details

NO_SHUFFLE_SEED

public static final int NO_SHUFFLE_SEED

Seed value to use to specify that no shuffling should be applied before displaying the objects.

See Also:

• Constant Field Values

Constructor Details

PathObjectScatterChart

public PathObjectScatterChart(QuPathViewer viewer)

Create an interactive scatter plot using the current viewer

Parameters:

viewer - The QuPath viewer.

Method Details

setAutorangeToFullData

public void setAutorangeToFullData(boolean useFullData)

Set the value of autorangeToFullDataProperty().

Parameters:

useFullData - whether to use the full data when setting the axis autorange

autorangeToFullDataProperty

public BooleanProperty autorangeToFullDataProperty()

Get a property representing whether to use the entire dataset when calculating axis limits automatically. This is useful whenever we are subsampling data points.

Returns:

whether to use the full data when setting the axis autorange

See Also:

• getAutorangeToFullData()
• setAutorangeToFullData(boolean)

getAutorangeToFullData

public boolean getAutorangeToFullData()

Get the value of autorangeToFullDataProperty()

Returns:

whether to use the full data when setting the axis autorange

setMaxPoints

public void setMaxPoints(int maxPoints)

Set the value of maxPointsProperty().

Parameters:

maxPoints - the maximum number of elements

maxPointsProperty

public IntegerProperty maxPointsProperty()

Get a property representing the maximum number of points that the plot will display. Subsampling will be used to ensure only this number of points or fewer are displayed.

Returns:

the maximum number of points to show

See Also:

• getMaxPoints()
• setMaxPoints(int)

getMaxPoints

public int getMaxPoints()

Get the value of maxPointsProperty()

Returns:

the maximum number of points to show

setRngSeed

public void setRngSeed(int rngSeed)

Set the value of rngSeedProperty().

Parameters:

rngSeed - the random number generator seed to use

rngSeedProperty

public IntegerProperty rngSeedProperty()

Get a property representing the random number generator's seed for subsampling. The default value is #NO_SHUFFLE_SEED which indicates no shuffling should be performed.

Returns:

the rng seed property

See Also:

• getRngSeed()
• setRngSeed(int)

getRngSeed

public int getRngSeed()

Get the value of rngSeedProperty().

Returns:

the random number generator

setPointOpacity

public void setPointOpacity(double pointOpacity)

Set the value of pointOpacityProperty().

Parameters:

pointOpacity - the new point opacity

pointOpacityProperty

public DoubleProperty pointOpacityProperty()

Get a property representing the opacity of all data points. Making points translucent can be helpful when there are a lot of them.

Returns:

the point opacity property

See Also:

• getPointOpacity()
• setPointOpacity(double)

getPointOpacity

public double getPointOpacity()

Get the value o pointOpacityProperty()

Returns:

the point opacity property

setPointRadius

public void setPointRadius(double radius)

Set the value of pointOpacityProperty()

Parameters:

radius - the point radius

pointRadiusProperty

public DoubleProperty pointRadiusProperty()

Get a property representing the radius of all data points.

Returns:

the point radius property

See Also:

• getPointRadius()
• setPointRadius(double)

getPointRadius

public double getPointRadius()

Get the value of pointOpacityProperty()

Returns:

the point radius

updateLegend

protected void updateLegend()

Overrides:

updateLegend in class XYChart<Number,Number>

refreshData

public void refreshData()

Recalculate the values of all data points. This may be useful when measurements or classifications may have changed.

setData

public void setData(Collection<? extends PathObject> pathObjects,
 Function<PathObject,Number> xFun,
 Function<PathObject,Number> yFun)

Set the data to display in the plot.

Parameters:

pathObjects - the objects to display

xFun - a function to extract the x value to plot

yFun - a function to extract the y value to plot

setDataFromTable

public void setDataFromTable(Collection<? extends PathObject> pathObjects,
 PathTableData<PathObject> model,
 String xMeasurement,
 String yMeasurement)

Set the data to display in the plot from a table model.

This calls setData(Collection, Function, Function) in addition to setting the x and y labels.

Parameters:

pathObjects - the objects to display

model - the table model containing the measurements

xMeasurement - the column to use for x values

yMeasurement - the column to use for y values

dataItemAdded

protected void dataItemAdded(XYChart.Series<Number,Number> series,
 int itemIndex,
 XYChart.Data<Number,Number> item)

Overrides:

dataItemAdded in class ScatterChart<Number,Number>

dataItemRemoved

protected void dataItemRemoved(XYChart.Data<Number,Number> item,
 XYChart.Series<Number,Number> series)

Overrides:

dataItemRemoved in class ScatterChart<Number,Number>

updateAxisRange

protected void updateAxisRange()

Overrides:

updateAxisRange in class XYChart<Number,Number>