Index
All Classes and Interfaces|All Packages|Constant Field Values
A
- AbstractImageOverlay - Class in qupath.lib.gui.viewer.overlays
-
Abstract
PathOverlaywith additional properties relevant when drawingBufferedImages. - AbstractImageOverlay(OverlayOptions) - Constructor for class qupath.lib.gui.viewer.overlays.AbstractImageOverlay
- AbstractImageRenderer - Class in qupath.lib.gui.images.stores
-
Abstract
ImageRenderer, which adds a timestamp variable. - AbstractImageRenderer() - Constructor for class qupath.lib.gui.images.stores.AbstractImageRenderer
- AbstractOverlay - Class in qupath.lib.gui.viewer.overlays
-
Abstract class to help with implementing PathOverlays.
- AbstractOverlay(OverlayOptions) - Constructor for class qupath.lib.gui.viewer.overlays.AbstractOverlay
- AbstractOverlay.LocationStringFunction - Interface in qupath.lib.gui.viewer.overlays
-
Define a function to perform the task of
PathOverlay.getLocationString(ImageData, double, double, int, int) - accelerator(ObservableValue<KeyCombination>) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
-
Bind the accelerator property of the action to an
ObservableValue, bidirectionally if possible. - accelerator(KeyCombination) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
-
Set the accelerator property of the action.
- acceleratorTextProperty() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry
-
Property corresponding to
CommandFinderTools.CommandEntry.getAcceleratorText() - ActionAccelerator - Annotation Interface in qupath.lib.gui.actions.annotations
-
Annotation used to specify a preferred accelerator for an an action.
- actionBuilder() - Static method in class qupath.lib.gui.actions.ActionTools
-
Create an
ActionTools.ActionBuilderwith no properties set. - actionBuilder(String, Consumer<ActionEvent>) - Static method in class qupath.lib.gui.actions.ActionTools
-
Create an
ActionTools.ActionBuilderwith the specified text and event handler. - actionBuilder(Consumer<ActionEvent>) - Static method in class qupath.lib.gui.actions.ActionTools
-
Create an
ActionTools.ActionBuilderwith the specified event handler. - ActionConfig - Annotation Interface in qupath.lib.gui.actions.annotations
-
Annotation indicating the a key in the external resources file containing the menu, text and (optional) description.
- ActionIcon - Annotation Interface in qupath.lib.gui.actions.annotations
-
Default icon for an action.
- ActionMenu - Annotation Interface in qupath.lib.gui.actions.annotations
-
Annotation indicating the menu path where an action should be installed.
- ActionMethod - Annotation Interface in qupath.lib.gui.actions.annotations
-
Annotation indicating that a method should be converted to an
Actionif possible. - Actions() - Constructor for class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
- Actions() - Constructor for class qupath.lib.gui.actions.menus.AutomateMenuActions.Actions
- Actions() - Constructor for class qupath.lib.gui.actions.menus.ClassifyMenuActions.Actions
- Actions() - Constructor for class qupath.lib.gui.actions.menus.ExtensionsMenuActions.Actions
- Actions() - Constructor for class qupath.lib.gui.actions.menus.FileMenuActions.Actions
- Actions() - Constructor for class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
- Actions() - Constructor for class qupath.lib.gui.actions.menus.ObjectsMenuActions.Actions
- Actions() - Constructor for class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
- Actions() - Constructor for class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- Actions() - Constructor for class qupath.lib.gui.actions.menus.WindowMenuActions.Actions
- ActionTools - Class in qupath.lib.gui.actions
-
Helper methods for generating and configuring Actions and UI elements.
- ActionTools() - Constructor for class qupath.lib.gui.actions.ActionTools
- ActionTools.ActionBuilder - Class in qupath.lib.gui.actions
-
Builder class for custom
Actionobjects. - ACTIVE_SERVER - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- activeToolProperty() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return the activeTool property of this tracker.
- activeViewerProperty() - Method in class qupath.lib.gui.viewer.ViewerManager
-
Get a read-only property representing the currently active viewer.
- ADD_COLUMN_AFTER - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions.AddActions
- ADD_COLUMN_BEFORE - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions.AddActions
- ADD_ROW_AFTER - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions.AddActions
- ADD_ROW_BEFORE - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions.AddActions
- addActions - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
- AddActions() - Constructor for class qupath.lib.gui.actions.menus.TMAMenuActions.Actions.AddActions
- addAllRegions(ImageServer<BufferedImage>, int) - Method in class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
-
Add all regions for a specific level of an
ImageServer. - addChartExportMenu(XYChart<Number, Number>, ContextMenu) - Static method in class qupath.lib.gui.charts.ChartTools
-
Add a menu item to a context menu for displaying a chart for export.
- addChoicePropertyPreference(Property<T>, ObservableList<T>, Class<? extends T>, String, String, String) - Method in class qupath.lib.gui.panes.PreferencePane
-
Deprecated.
- addChoicePropertyPreference(Property<T>, ObservableList<T>, Class<? extends T>, String, String, String, boolean) - Method in class qupath.lib.gui.panes.PreferencePane
-
Deprecated.use
PropertyItemBuilderinstead - addColorPropertyPreference(IntegerProperty, String, String, String) - Method in class qupath.lib.gui.panes.PreferencePane
-
Deprecated.use
PropertyItemBuilderinstead - addColumn(QuPathViewer) - Method in class qupath.lib.gui.viewer.ViewerManager
- addCompletion(AutoCompletions.Completion) - Method in class qupath.lib.gui.scripting.completors.DefaultAutoCompletor
- addCompletions(Collection<? extends AutoCompletions.Completion>) - Method in class qupath.lib.gui.scripting.completors.DefaultAutoCompletor
- addCompletions(AutoCompletions.Completion...) - Method in class qupath.lib.gui.scripting.completors.DefaultAutoCompletor
- addDirectoryPropertyPreference(Property<String>, String, String, String) - Method in class qupath.lib.gui.panes.PreferencePane
-
Deprecated.use
PropertyItemBuilderinstead - addFileDropHandler(DragDropImportListener.DropHandler<File>) - Method in class qupath.lib.gui.viewer.DragDropImportListener
-
Add a new File DropHandler.
- addGridRow(GridPane, int, int, String, Node...) - Static method in class qupath.lib.gui.tools.PaneTools
-
Deprecated.Add a row of nodes.
- AdditiveChannelInfo - Class in qupath.lib.display
-
Class for combining channels additively, then providing controls on the resulting RGB image.
- AdditiveChannelInfo(ImageData<BufferedImage>, List<DirectServerChannelInfo>) - Constructor for class qupath.lib.display.AdditiveChannelInfo
- addJsonDropHandler(DragDropImportListener.DropHandler<JsonElement>) - Method in class qupath.lib.gui.viewer.DragDropImportListener
-
Add a new DropHandler specifically for JSON elements.
- addMenuItems(List<MenuItem>, Object...) - Static method in class qupath.lib.gui.tools.MenuTools
-
Add menu items to the specified list.
- addMenuItems(Menu, Object...) - Static method in class qupath.lib.gui.tools.MenuTools
-
Add menu items to an existing menu.
- addNewScript(String, ScriptLanguage, boolean) - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
-
Create a new script in the specified language.
- addParameterChangeListener(ParameterChangeListener) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX
-
Add a
ParameterChangeListenerto be notified as the user modifies parameters. - addPropertyPreference(Property<T>, Class<? extends T>, String, String, String) - Method in class qupath.lib.gui.panes.PreferencePane
-
Deprecated.use
PropertyItemBuilderinstead - addRow(QuPathViewer) - Method in class qupath.lib.gui.viewer.ViewerManager
- addSeries(String, double[], double[]) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Create and add a scatterplot using arrays of numeric values.
- addSeries(String, double[], double[], List<T>) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Create and add a scatterplot series using collections of numeric values, with an associated custom object.
- addSeries(String, double[], double[], T[]) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Create and add a scatterplot using collections of numeric values, with an associated custom object.
- addSeries(String, Collection<? extends Number>, Collection<? extends Number>) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Create and add a scatterplot using collections of numeric values.
- addSeries(String, Collection<? extends T>, Function<T, Number>, Function<T, Number>) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Add values extracted from objects within a specified collection.
- addSeries(String, Collection<XYChart.Data<Number, Number>>) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Create and add a scatterplot series from existing data.
- addSeries(XYChart.Series<Number, Number>) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Create a scatterplot series from existing data.
- addSingleImageToProject(Project<BufferedImage>, ImageServer<BufferedImage>, ImageData.ImageType) - Static method in class qupath.lib.gui.commands.ProjectCommands
-
Add a single image to a project.
- addSlice(Object, Number) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
-
Add a slice to the pie.
- addTextAppendableFX(TextAppendable) - Static method in class qupath.lib.gui.logging.LogManager
-
Register a
TextAppendablethat will be accept logging events and be updated on the JavaFX Application thread. - addThreshold(double) - Method in class qupath.lib.gui.charts.ChartThresholdPane
-
Add a threshold value.
- addThreshold(double, Color) - Method in class qupath.lib.gui.charts.ChartThresholdPane
-
Add a threshold value with its display color.
- addThreshold(ObservableNumberValue) - Method in class qupath.lib.gui.charts.ChartThresholdPane
-
Add a threshold value.
- addTileListener(TileListener<BufferedImage>) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
- addViewerListener(QuPathViewerListener) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Add a viewer listener.
- alertType(Alert.AlertType) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Deprecated.Create a dialog styled as a specified alert type.
- ALL - Enum constant in enum class qupath.lib.gui.logging.LogManager.LogLevel
-
All log messages
- ALL_WINDOWS - Enum constant in enum class qupath.lib.gui.prefs.SystemMenuBar.SystemMenuBarOption
-
Use the system menubar for all windows.
- allDetections() - Method in class qupath.lib.gui.tools.MeasurementExporter
-
Specify that detection measurements (only) should be export.
- allredMinPercentagePositiveProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
The minimum positive percentage of cells for Allred proportion score to be non-zero.
- ALWAYS - Enum constant in enum class qupath.lib.gui.tools.CommandFinderTools.CommandBarDisplay
-
Always display
- alwaysPaintSelected - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
- alwaysPaintSelectedObjectsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Always paint selected objects in the viewer, even if the opacity setting is 0.
- AnalyzeMenuActions - Class in qupath.lib.gui.actions.menus
- AnalyzeMenuActions.Actions - Class in qupath.lib.gui.actions.menus
- ANNOTATION_COPY_TO_PLANE - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
- ANNOTATION_DUPLICATE - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
- annotationActions - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.Actions
- AnnotationActions() - Constructor for class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
- AnnotationPane - Class in qupath.lib.gui.panes
-
Component for displaying annotations within the active image.
- AnnotationPane(QuPathGUI) - Constructor for class qupath.lib.gui.panes.AnnotationPane
-
Constructor.
- AnnotationPane(QuPathGUI, ObservableValue<ImageData<BufferedImage>>) - Constructor for class qupath.lib.gui.panes.AnnotationPane
-
Constructor.
- annotations() - Method in class qupath.lib.gui.tools.MeasurementExporter
-
Specify that annotation measurements (only) should be export.
- ANNOTATIONS - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
- ANNOTATIONS_FILL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- annotationStrokeThickness - Variable in class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
- annotationStrokeThicknessProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Preferred stroke thickness to use when drawing annotation ROIs.
- ANY_ANNOTATIONS - Enum constant in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters
-
Regions overlapping the ROIs of any annotations
- ANY_ANNOTATIONS_BOUNDS - Enum constant in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters
-
Regions overlapping the bounding box of any annotations
- ANY_OBJECTS - Enum constant in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters
-
Regions overlapping the ROIs of any objects
- ANY_OBJECTS_BOUNDS - Enum constant in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters
-
Regions overlapping the bounding box of any objects
- AppearancePreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.AppearancePreferences
- append(Collection<? extends PathObjectValueFactory>) - Method in class qupath.lib.gui.measure.DefaultPathObjectValueFactoryBuilder
- append(PathObjectValueFactory...) - Method in class qupath.lib.gui.measure.DefaultPathObjectValueFactoryBuilder
- appendFrame(ViewRecordingFrame) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Append frame to the collection of frames.
- appendText(String) - Method in interface qupath.lib.gui.logging.TextAppendable
-
Append the specified text to the appendable.
- appendText(String) - Method in interface qupath.lib.gui.scripting.EditableText
-
Append the specified text.
- appendText(String) - Method in class qupath.lib.gui.scripting.TextAreaControl
- applyDisplaySettings(String) - Static method in class qupath.lib.gui.scripting.QPEx
-
Apply the display settings with the specified name or file path to the current version.
- applyDisplaySettings(ImageDisplaySettings) - Static method in class qupath.lib.gui.scripting.QPEx
-
Apply the display settings to the current viewer.
- applyDisplaySettings(QuPathViewer, ImageDisplaySettings) - Static method in class qupath.lib.gui.scripting.QPEx
-
Apply the display settings to the specified viewer.
- applyLastAnnotationToActiveViewer() - Method in class qupath.lib.gui.viewer.ViewerManager
- applySettingsToDisplay(ImageDisplay, ImageDisplaySettings) - Static method in class qupath.lib.display.settings.DisplaySettingUtils
-
Apply the settings to the display, if they are compatible.
- applyTransforms(BufferedImage, BufferedImage) - Method in class qupath.lib.display.ImageDisplay
-
Apply the required transforms to a BufferedImage to get the appropriate display.
- applyTransforms(BufferedImage, BufferedImage) - Method in class qupath.lib.gui.images.stores.ColorModelRenderer
- applyTransforms(BufferedImage, BufferedImage) - Method in interface qupath.lib.gui.images.stores.ImageRenderer
-
Apply the required transforms to a BufferedImage to get the appropriate display.
- applyTransforms(BufferedImage, BufferedImage, List<? extends ChannelDisplayInfo>, ChannelDisplayMode) - Static method in class qupath.lib.display.ImageDisplay
-
Convert an image to RGB by applying the specified ChannelDisplayInfos and
ChannelDisplayMode. - AREA - Enum constant in enum class qupath.lib.gui.charts.HistogramChart.DisplayMode
-
Show as areas.
- ARROW_DOUBLE - Static variable in class qupath.lib.gui.viewer.tools.PathTools
-
Arrow drawing tool, with arrowhead at both ends
- ARROW_DOUBLE_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- ARROW_END - Static variable in class qupath.lib.gui.viewer.tools.PathTools
-
Arrow drawing tool, with arrowhead at the end
- ARROW_END_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- ARROW_START - Static variable in class qupath.lib.gui.viewer.tools.PathTools
-
Arrow drawing tool, with arrowhead at the start
- ARROW_START_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- ATTACH_VIEWER - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
- ATTACH_VIEWER - Variable in class qupath.lib.gui.actions.ViewerActions
- attachActiveViewerToGrid() - Method in class qupath.lib.gui.viewer.ViewerManager
-
Insert the currently active viewer back into the viewer grid.
- attachViewerToGrid(QuPathViewer) - Method in class qupath.lib.gui.viewer.ViewerManager
-
Attach the specified viewer to the viewer grid, if possible.
- AUTO_ESTIMATE - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.ImageTypeSetting
-
Automatically estimate the image type
- autoBrightnessContrastSaturationPercentProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Controls percentage of saturated pixels to apply when automatically setting brightness/contrast.
- AutomateActions - Class in qupath.lib.gui.actions
-
Default actions associated with QuPath's 'Automate' (scripting) menu.
- AutomateActions(QuPathGUI) - Constructor for class qupath.lib.gui.actions.AutomateActions
- AutomateMenuActions - Class in qupath.lib.gui.actions.menus
- AutomateMenuActions.Actions - Class in qupath.lib.gui.actions.menus
- autorangeToFullDataProperty() - Method in class qupath.lib.gui.charts.PathObjectScatterChart
-
Get a property representing whether to use the entire dataset when calculating axis limits automatically.
- autoSaturationPercent - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
- autoSetAnnotationClassProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Classification that should automatically be applied to all new annotations.
- autoSetDisplayRange(ChannelDisplayInfo) - Method in class qupath.lib.display.ImageDisplay
-
Automatically set the display range for a channel, using the default saturation defined in
PathPrefs.autoBrightnessContrastSaturationPercentProperty(). - autoSetDisplayRange(ChannelDisplayInfo, double) - Method in class qupath.lib.display.ImageDisplay
-
Automatically set the display range for a channel.
- autoUpdate - Variable in class qupath.lib.gui.panes.PreferencePane.AppearancePreferences
- autoUpdate - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
- autoUpdateCheckProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Check for updates when launching QuPath, if possible.
- availableChannels() - Method in class qupath.lib.display.ImageDisplay
-
Read-only observable list containing the channels currently available for display.
- availableFontsProperty() - Static method in class qupath.lib.gui.prefs.QuPathStyleManager
-
Get a list of available fonts.
- availableStylesProperty() - Static method in class qupath.lib.gui.prefs.QuPathStyleManager
-
Get the current available styles as an observable list.
B
- backgroundColor - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
- backgroundColor(int, boolean) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder
-
Specify a base color.
- backgroundColor(Color) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder
-
Specify a base color.
- badges - Variable in class qupath.lib.gui.panes.PreferencePane.AppearancePreferences
- BAR - Enum constant in enum class qupath.lib.gui.charts.HistogramChart.DisplayMode
-
Show as bars.
- barChart() - Static method in class qupath.lib.gui.charts.Charts
-
Create a
Charts.ScatterChartBuilderfor generating a custom scatter plot. - beautify(String) - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
-
Beautifies the specified text, according to the syntax.
- beautifySourceAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- BILINEAR - Enum constant in enum class qupath.lib.gui.viewer.ImageInterpolation
-
Bilinear interpolation.
- bindLocale() - Element in annotation interface qupath.lib.gui.actions.annotations.ActionConfig
- bindUserStylesheetToStyle(WebEngine) - Static method in class qupath.lib.gui.tools.WebViews
-
Bind the
WebEngine.userStyleSheetLocationProperty()to a stylesheet determined based on QuPath's current style (e.g. - BOUNDARIES_ONLY - Enum constant in enum class qupath.lib.gui.viewer.OverlayOptions.DetectionDisplayMode
-
Show only cell boundaries.
- BRIGHTNESS_CONTRAST - Variable in class qupath.lib.gui.actions.CommonActions
- BRIGHTNESS_CONTRAST - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- BrightnessContrastChannelPane - Class in qupath.lib.gui.commands.display
-
A pane responsible for the display and selection of channels from an image display.
- BrightnessContrastChannelPane() - Constructor for class qupath.lib.gui.commands.display.BrightnessContrastChannelPane
- BrightnessContrastCommand - Class in qupath.lib.gui.commands
-
Command to show a Brightness/Contrast dialog to adjust the image display.
- BrightnessContrastCommand(QuPathGUI) - Constructor for class qupath.lib.gui.commands.BrightnessContrastCommand
-
Constructor.
- BrightnessContrastHistogramPane - Class in qupath.lib.gui.commands.display
-
A pane to display a histogram for brightness/contrast adjustment, allowing the user to select min/max values.
- BrightnessContrastHistogramPane() - Constructor for class qupath.lib.gui.commands.display.BrightnessContrastHistogramPane
- BrightnessContrastSettingsPane - Class in qupath.lib.gui.commands.display
-
A pane to save and load display settings, using a
ResourceManager. - BrightnessContrastSettingsPane() - Constructor for class qupath.lib.gui.commands.display.BrightnessContrastSettingsPane
- BrightnessContrastSliderPane - Class in qupath.lib.gui.commands.display
-
A pane containing sliders for adjusting the min/max display range and gamma value associated with an
ImageDisplay. - BrightnessContrastSliderPane() - Constructor for class qupath.lib.gui.commands.display.BrightnessContrastSliderPane
- browseDirectory(File) - Static method in class qupath.lib.gui.tools.GuiTools
-
Open the directory containing a file for browsing.
- browseURI(URI) - Static method in class qupath.lib.gui.tools.GuiTools
-
Try to open a URI in a web browser.
- BRUSH - Static variable in class qupath.lib.gui.viewer.tools.PathTools
-
Brush drawing tool
- BRUSH_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- BRUSH_TOOL - Variable in class qupath.lib.gui.ToolManager
- brushCreateNewObjectsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Create new objects by default when drawing with the Brush tool.
- brushDiameter - Variable in class qupath.lib.gui.panes.PreferencePane.DrawingPreferences
- brushDiameterProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Default brush tool diameter, in pixels.
- brushScaleByMag - Variable in class qupath.lib.gui.panes.PreferencePane.DrawingPreferences
- brushScaleByMagProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Optionally scale the default brush tool diameter by the viewer magnification (downsample value).
- BrushToolEventHandler - Class in qupath.lib.gui.viewer.tools.handlers
-
Tool for drawing (and subtract from) freehand regions, optionally adapting brush size to magnification.
- BrushToolEventHandler() - Constructor for class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
- BufferedImageOverlay - Class in qupath.lib.gui.viewer.overlays
-
An overlay used to display one or more
BufferedImageobjects on top of a primary image shown in a viewer. - BufferedImageOverlay(OverlayOptions) - Constructor for class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
-
Create an empty overlay without any images to display.
- BufferedImageOverlay(OverlayOptions, Map<? extends ImageRegion, BufferedImage>) - Constructor for class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
-
Create an overlay to display multiple image regions.
- BufferedImageOverlay(OverlayOptions, ImageRegion, BufferedImage) - Constructor for class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
-
Create an overlay to display one specified image region.
- BufferedImageOverlay(QuPathViewer, BufferedImage) - Constructor for class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
-
Create an overlay to show an image rescaled to overlay the entire current image in the specified viewer.
- BufferedImageOverlay(QuPathViewer, Map<ImageRegion, BufferedImage>) - Constructor for class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
-
Create an overlay to show an image rescaled to overlay the entire current image in the specified viewer.
- BufferedImageOverlay(QuPathViewer, OverlayOptions, Map<? extends ImageRegion, BufferedImage>) - Constructor for class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
-
Create an overlay to display multiple image regions.
- bufferedImageProperty() - Method in class qupath.lib.gui.panes.SimpleImageViewer
-
Get a read-only property representing the buffered image.
- BUGS - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
- build() - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
-
Create an
Actionwith this builder. - build() - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Build a chart according to the specified parameters.
- build() - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
-
Build a chart according to the specified parameters.
- build() - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
- build() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Deprecated.Build the dialog.
- build() - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder
-
Create the rendered image server.
- build() - Method in class qupath.lib.gui.measure.DefaultPathObjectValueFactoryBuilder
- builder() - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Create a new builder to generate a custom dialog.
- Builder() - Constructor for class qupath.lib.gui.dialogs.Dialogs.Builder
-
Deprecated.
- Builder(QuPathViewer) - Constructor for class qupath.lib.gui.images.servers.RenderedImageServer.Builder
-
Create a rendered image server build using viewer defaults.
- Builder(ImageData<BufferedImage>) - Constructor for class qupath.lib.gui.images.servers.RenderedImageServer.Builder
-
Create a rendered image server for the specified
ImageData; - BuildInfo - Class in qupath.lib.gui
-
Basic version information about the current QuPath build.
- bundle() - Element in annotation interface qupath.lib.gui.actions.annotations.ActionConfig
- buttons(String...) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Deprecated.Specify the buttons to display in the dialog.
- buttons(ButtonType...) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Deprecated.Specify the buttons to display in the dialog.
C
- cache - Variable in class qupath.lib.gui.images.stores.DefaultImageRegionStore
- calibratedLocationString - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
- canBeautify() - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
- CANCEL - Enum constant in enum class qupath.lib.gui.dialogs.Dialogs.DialogButton
-
Deprecated."Cancel" option
- cancelDirection(boolean) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler.ViewerMover
-
Cancel either the x- or y-axis direction of the movement.
- canCompress() - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
- canRedo() - Method in class qupath.lib.gui.UndoRedoManager
-
True if it's possible to call redoOnce for the currently-active viewer in QuPath, false otherwise.
- canUndo() - Method in class qupath.lib.gui.UndoRedoManager
-
True if it's possible to call undoOnce for the currently-active viewer in QuPath, false otherwise.
- caretPositionProperty() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
-
Property for the current caret position.
- caretPositionProperty() - Method in class qupath.lib.gui.scripting.TextAreaControl
- CELL_NUCLEI_BOTH - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- CELL_ONLY - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- cellDisplayActions - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- CellDisplayActions() - Constructor for class qupath.lib.gui.actions.menus.ViewMenuActions.CellDisplayActions
- cells() - Method in class qupath.lib.gui.tools.MeasurementExporter
-
Specify that cell measurements (only) should be export.
- CENTER_ALL - Variable in class qupath.lib.gui.actions.menus.WindowMenuActions.Actions
- CENTER_OFFSCREEN - Variable in class qupath.lib.gui.actions.menus.WindowMenuActions.Actions
- centerImage() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Center the current image in the viewer, while keeping the same downsample factor.
- centerROI(ROI) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Center the specified ROI in the viewer
- centroids(Collection<? extends PathObject>) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Plot centroids for the specified objects in pixel units.
- centroids(Collection<? extends PathObject>, PixelCalibration) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Plot centroids for the specified objects using a fixed pixel calibration.
- CENTROIDS - Enum constant in enum class qupath.lib.gui.viewer.OverlayOptions.DetectionDisplayMode
-
Show only detection centroids, not boundaries.
- CENTROIDS_ONLY - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- changed(ObservableValue<? extends QuPathViewer>, QuPathViewer, QuPathViewer) - Method in class qupath.lib.gui.UndoRedoManager
- changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.commands.CountingDialogCommand
- changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.commands.PathObjectGridView
- changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.panes.AnnotationPane
- changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.panes.ImageDetailsPane
- changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.panes.PathObjectHierarchyView
- changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.panes.ProjectBrowser
- changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.panes.SelectedMeasurementTableView
- changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.panes.SlideLabelView
- changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.panes.WorkflowCommandLogView
- changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
- CHANNEL_VIEWER - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- ChannelColor - Class in qupath.lib.display.settings
-
A simple class to store the color of an image channel.
- ChannelColor() - Constructor for class qupath.lib.display.settings.ChannelColor
- ChannelDisplayInfo - Interface in qupath.lib.display
-
Interface used to control the display of single channels of image data, where 'single channel' means one value per pixel (in Java's parlance, one band for the SampleModel).
- ChannelDisplayInfo.ModifiableChannelDisplayInfo - Interface in qupath.lib.display
-
Helper interface to indicate that the display ranges can be modified.
- ChannelDisplayMode - Enum Class in qupath.lib.display
-
Display mode for an image channel, used in combination with
ImageDisplayandChannelDisplayInfo. - ChannelDisplayTransformServer - Class in qupath.lib.gui.images.servers
-
ImageServer that applies a color transform to an image.
- ChannelSettings - Class in qupath.lib.display.settings
-
A simple class to store the main information needed by QuPath to display an image channel with a requested color and brightness/contrast setting.
- ChannelSettings() - Constructor for class qupath.lib.display.settings.ChannelSettings
- Charts - Class in qupath.lib.gui.charts
-
Helper class for generating interactive charts.
- Charts() - Constructor for class qupath.lib.gui.charts.Charts
- Charts.BarChartBuilder - Class in qupath.lib.gui.charts
-
Builder for creating scatter charts.
- Charts.PieChartBuilder - Class in qupath.lib.gui.charts
-
Builder for creating pie charts.
- Charts.ScatterChartBuilder - Class in qupath.lib.gui.charts
-
Builder for creating scatter charts.
- ChartThresholdPane - Class in qupath.lib.gui.charts
-
Pane that can be used to contain an XYChart, adding adjustable thresholds to be displayed.
- ChartThresholdPane(XYChart<Number, Number>) - Constructor for class qupath.lib.gui.charts.ChartThresholdPane
-
Note: xAxis and yAxis must be instances of NumberAxis.
- ChartTools - Class in qupath.lib.gui.charts
-
Collection of static methods to help when working with JavaFX charts, and adapting these for QuPath's purposes.
- ChartTools() - Constructor for class qupath.lib.gui.charts.ChartTools
- CHECK_URIS - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
- checkForUpdate() - Static method in class qupath.lib.gui.extensions.UpdateChecker
-
Query the most recent QuPath release on GitHub.
- checkForUpdate(GitHubProject.GitHubRepo) - Static method in class qupath.lib.gui.extensions.UpdateChecker
-
Query the latest release from a GitHub repo.
- CITE - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
- classifications(Collection<? extends PathObject>) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Plot two measurements against one another for the specified objects.
- ClassifyMenuActions - Class in qupath.lib.gui.actions.menus
- ClassifyMenuActions.Actions - Class in qupath.lib.gui.actions.menus
- clear() - Method in interface qupath.lib.gui.scripting.EditableText
-
Request clear the contents of the control.
- clear() - Method in class qupath.lib.gui.scripting.TextAreaControl
- clear() - Method in class qupath.lib.gui.UndoRedoManager
-
Clear all undo/redo stacks (useful when memory is low).
- CLEAR_CORES - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
- clearCache() - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
-
Clear the cache, including thumbnails, and cancel any pending requests.
- clearCache() - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
-
Clear any cached tiles.
- clearCache(boolean) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
-
Clear the cache, optionally including thumbnails and stopping any pending requests.
- clearCachedOverlay() - Method in class qupath.lib.gui.viewer.overlays.HierarchyOverlay
-
Clear previously-cached tiles for this overlay.
- clearCachedOverlayForRegion(ImageRegion) - Method in class qupath.lib.gui.viewer.overlays.HierarchyOverlay
-
Clear previously-cached tiles for a specified region of this overlay.
- clearCacheForRequestOverlap(RegionRequest) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
- clearCacheForServer(ImageServer<BufferedImage>) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
- clearThresholds() - Method in class qupath.lib.gui.charts.ChartThresholdPane
-
Clear all thresholds.
- clipROIsForHierarchy - Variable in class qupath.lib.gui.panes.PreferencePane.DrawingPreferences
- clipROIsForHierarchyProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Request ROIs to be clipped and inserted as the right place in the hierarchy when drawing (to prevent overlapping ROIs being created accidentally).
- clipToAllowed - Variable in class qupath.lib.display.AdditiveChannelInfo
- clipToAllowed - Variable in class qupath.lib.display.DirectServerChannelInfo
- close() - Method in class qupath.lib.gui.images.servers.RenderedImageServer
- close() - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
- close() - Method in class qupath.lib.gui.SharedThreadPoolManager
-
Shutdown any threadpools created by this manager.
- closeProject(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
-
Close the current project open in the
QuPathGUI. - closeViewer() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Request that this viewer is closed.
- closeViewer() - Method in class qupath.lib.gui.viewer.QuPathViewerPlus
- closeViewer(QuPathViewer) - Method in class qupath.lib.gui.QuPathGUI
-
Close the image within a viewer, prompting to save changes if necessary.
- CM_GRAYSCALE - Static variable in class qupath.lib.display.DirectServerChannelInfo
- CM_GRAYSCALE_INVERTED - Static variable in class qupath.lib.display.DirectServerChannelInfo
- COG - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- COLOR - Enum constant in enum class qupath.lib.display.ChannelDisplayMode
-
Show using default color LUT (may be composite)
- COLOR_DECONVOLUTION_REFINE - Variable in class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
- colorDefaultObjectsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
The default color used to display objects of any type, where a default has not otherwise been specified.
- ColorMapCanvas - Class in qupath.lib.gui
-
Canvas to show the range of a ColorMap (i.e.
- ColorMapCanvas(double, ColorMaps.ColorMap) - Constructor for class qupath.lib.gui.ColorMapCanvas
- ColorMapCanvas(double, ColorMaps.ColorMap, Function<Double, String>) - Constructor for class qupath.lib.gui.ColorMapCanvas
-
Create a canvas that displays the range of the specified
ColorMaps.ColorMapwith key tooltips. - colorMapProperty() - Method in class qupath.lib.gui.ColorMapCanvas
-
Return the ColorMap property of this canvas.
- colormapsDirectoryProperty() - Method in class qupath.lib.gui.UserDirectoryManager
-
Read only property representing the custom colormaps directory.
- ColorModelRenderer - Class in qupath.lib.gui.images.stores
-
An
ImageRendererthat uses aColorModel. - ColorModelRenderer(ColorModel) - Constructor for class qupath.lib.gui.images.stores.ColorModelRenderer
-
Constructor.
- colorSelectedObjectProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
The default color used to display selected objects.
- colorTileProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
The default color used to display tile objects.
- colorTMAProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
The default color used to display TMA core objects.
- ColorToolsFX - Class in qupath.lib.gui.tools
-
Helper class for converting between packed RGB colors and Java's AWT representation, as well as creating some ColorModels for BufferedImages.
- ColorToolsFX() - Constructor for class qupath.lib.gui.tools.ColorToolsFX
- combineSelectedAnnotations(ImageData<?>, RoiTools.CombineOp) - Static method in class qupath.lib.gui.commands.Commands
-
Combine the selected annotations for the specified hierarchy.
- comboPasteEscape - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- COMMAND_LIST - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- COMMAND_LIST - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- commandBarDisplay - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
- commandBarDisplayProperty() - Static method in class qupath.lib.gui.tools.CommandFinderTools
-
Property specifying where the command bar should be displayed relative to the main viewer window.
- CommandFinderTools - Class in qupath.lib.gui.tools
-
Helper tools for creating components that enable fast access to menu commands via a filtered list.
- CommandFinderTools() - Constructor for class qupath.lib.gui.tools.CommandFinderTools
- CommandFinderTools.CommandBarDisplay - Enum Class in qupath.lib.gui.tools
-
Available modes for displaying the command bar.
- CommandFinderTools.CommandEntry - Class in qupath.lib.gui.tools
-
Helper class to wrap summary data for a command to display in the list.
- Commands - Class in qupath.lib.gui.commands
-
Helper class implementing simple 'single-method' commands for easy inclusion in the GUI.
- Commands() - Constructor for class qupath.lib.gui.commands.Commands
- CommonActions - Class in qupath.lib.gui.actions
-
Default actions associated with a specific QuPath instance.
- CommonActions(QuPathGUI) - Constructor for class qupath.lib.gui.actions.CommonActions
- completionCodeCombination - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- componentContains(double, double) - Method in class qupath.lib.gui.viewer.QuPathViewer
- componentPointToImagePoint(double, double, Point2D, boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Convert x and y coordinates from the component space to the image space.
- componentPointToImagePoint(Point2D, Point2D, boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Convert a coordinate from the viewer into the corresponding pixel coordinate in the full-resolution image - optionally constraining it to any server bounds.
- compress(String) - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
-
Compresses the specified text by removing extra space, according to the syntax.
- compressSourceAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- configureRecentItemsMenu(Menu, ObservableList<URI>, Consumer<URI>) - Static method in class qupath.lib.gui.tools.GuiTools
-
Configure a menu to displays recent items, stored in the form of URIs.
- confirmation() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Deprecated.Create an confirmation alert dialog.
- content(Node) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Deprecated.Specify a
Nodeto display within the dialog. - contentText(String) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Deprecated.Specify the dialog content text.
- ContextHelpViewer - Class in qupath.lib.gui.commands
-
Help window providing context-dependent help.
- CONTRAST - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- convertDetectionsToPoints(ImageData<?>, boolean) - Static method in class qupath.lib.gui.commands.Commands
-
Convert detection objects to point annotations based upon their ROI centroids.
- convertToPercentages(boolean) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
-
Request that pie chart values are converted to percentages for tooltips.
- CONVEX_HULL - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
- CONVEX_POINTS - Variable in class qupath.lib.gui.actions.CommonActions
- copy() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
-
Request copy the current selection.
- copy() - Method in class qupath.lib.gui.scripting.TextAreaControl
- COPY_ANNOTATION_OBJECTS - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.CopyActions
- COPY_FULL_SCREENSHOT - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.CopyActions
- COPY_SELECTED_OBJECTS - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.CopyActions
- COPY_VIEW - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.CopyActions
- COPY_WINDOW - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.CopyActions
- COPY_WINDOW_SCREENSHOT - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.CopyActions
- copyAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- copyActions - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.Actions
- CopyActions() - Constructor for class qupath.lib.gui.actions.menus.EditMenuActions.CopyActions
- copyAnnotationsToClipboard(ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands
-
Attempt to annotation objects to the system clipboard, if available
- copySelectedAnnotationsToCurrentPlane(QuPathViewer) - Static method in class qupath.lib.gui.commands.Commands
-
Copy the selected objects and add them to the plane currently active in the viewer.
- copySelectedObjectsToClipboard(ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands
-
Attempt to copy selected objects to the system clipboard, if available
- copyTableContentsToClipboard(PathTableData<?>, Collection<String>) - Static method in class qupath.lib.gui.measure.ui.SummaryMeasurementTable
-
Get a single String representing the data in a table and copy it to the clipboard.
- copyToClipboard(Object) - Static method in class qupath.lib.gui.scripting.QPEx
-
Try to copy an object to the clipboard.
- CountingDialogCommand - Class in qupath.lib.gui.commands
-
Command to open up a counting panel to aid with creating Point annotations.
- CountingDialogCommand(QuPathGUI) - Constructor for class qupath.lib.gui.commands.CountingDialogCommand
-
Constructor.
- countProperty() - Method in class qupath.lib.gui.actions.InfoMessage
-
Read only property containing any count associated with the text (may be null).
- countsTransformProperty() - Method in class qupath.lib.gui.charts.HistogramChart
-
Property to control how counts should be transformed before being shown in the histogram
- create() - Static method in class qupath.lib.gui.SharedThreadPoolManager
-
Create a new instance
- create() - Static method in class qupath.lib.gui.ToolManager
-
Create a new instance
- create(boolean) - Static method in class qupath.lib.gui.tools.WebViews
-
Create a new
WebView. - create(String, double, boolean, List<ChannelSettings>) - Static method in class qupath.lib.display.settings.ImageDisplaySettings
-
Create a new image display settings object.
- create(String, float, float, ChannelColor, boolean) - Static method in class qupath.lib.display.settings.ChannelSettings
-
Create a new channel settings object.
- create(String, String, String) - Static method in class qupath.lib.gui.extensions.GitHubProject.GitHubRepo
-
Create a new
GitHubProject. - create(String, Version, URI) - Static method in class qupath.lib.gui.extensions.UpdateChecker.ReleaseVersion
-
Create a new
UpdateChecker.ReleaseVersion. - create(Collection<? extends ImageServer<BufferedImage>>) - Static method in class qupath.lib.gui.panes.ServerSelector
- create(QuPathGUI) - Static method in class qupath.lib.gui.viewer.ViewerManager
-
Create a new instance
- create(OverlayOptions, Function<ImageData<BufferedImage>, ImageServer<BufferedImage>>, ImageRenderer) - Static method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
-
Create an overlay to display a live image that can be created from an existing
ImageData. - create(OverlayOptions, Map<ImageData<BufferedImage>, ImageServer<BufferedImage>>, ImageRenderer) - Static method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
-
Create an overlay to display a live image that can be created from an existing
ImageData. - create(OverlayOptions, PixelClassifier) - Static method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
-
Create an overlay to display the live application of a
PixelClassifierto an image, using the default number of parallel threads for classification. - create(OverlayOptions, PixelClassifier, int) - Static method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
-
Create an overlay to display the live application of a
PixelClassifierto an image. - create(QuPathViewer) - Static method in class qupath.lib.gui.viewer.overlays.ZProjectOverlay
- create(ImageData<?>, Collection<? extends PathObject>) - Static method in class qupath.lib.gui.measure.PathObjectListWrapper
-
Create a warpper containing the specified objects.
- create(ImageData<?>, Predicate<PathObject>) - Static method in class qupath.lib.gui.measure.PathObjectListWrapper
-
Create a wrapper that includes all objects selected by the specified predicate.
- create(ImageData<BufferedImage>) - Static method in class qupath.lib.display.ImageDisplay
-
Create a new image display, and set the specified image data.
- CREATE_MANUAL - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
- CREATE_TILES - Variable in class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
- createAction(Runnable) - Static method in class qupath.lib.gui.actions.ActionTools
-
Create an action whose event handler calls a runnable.
- createAction(Runnable, String) - Static method in class qupath.lib.gui.actions.ActionTools
-
Create an action whose event handler calls a runnable, with a specified name.
- createAllMenuActions(QuPathGUI) - Static method in class qupath.lib.gui.actions.menus.Menus
-
Create a collection of all the actions that should be installed in QuPath's main menubar.
- createAnnotationView(QuPathGUI) - Static method in class qupath.lib.gui.commands.PathObjectGridView
-
Create a grid view for annotations.
- createArrowEndEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
- createArrowStartEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
- createBrushEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
- createButton(Action) - Static method in class qupath.lib.gui.actions.ActionTools
-
Create a button from an action, showing both the text and graphic if available.
- createButtonWithGraphicOnly(Action) - Static method in class qupath.lib.gui.actions.ActionTools
-
Create a button from an action, showing only the graphic and not any text.
- createCanvasViewer(QuPathViewer, ImageServer<BufferedImage>, boolean) - Static method in class qupath.lib.gui.tools.PathObjectImageViewers
-
Create an item viewer to display a
PathObjectusing a canvas. - createCheckBox(Action) - Static method in class qupath.lib.gui.actions.ActionTools
-
Create a checkbox from an action.
- createCheckMenuItem(Action) - Static method in class qupath.lib.gui.actions.ActionTools
-
Create a menu item from an action that makes use of a selected property.
- createCheckMenuItem(Action, ToggleGroup) - Static method in class qupath.lib.gui.actions.ActionTools
-
Create a menu item from an action that makes use of a selected property.
- createColorTransformServer(ImageServer<BufferedImage>, List<ChannelDisplayInfo>) - Static method in class qupath.lib.gui.images.servers.ChannelDisplayTransformServer
-
Create an
ImageServerfor which the channels are created dynamically from a list of ChannelDisplayInfos. - createColumnGrid(int) - Static method in class qupath.lib.gui.tools.PaneTools
-
Deprecated.Create a GridPane containing columns that resize similarly to Swing's GridLayout().
- createColumnGrid(Node...) - Static method in class qupath.lib.gui.tools.PaneTools
-
Deprecated.Create a GridPane containing columns that resize similarly to Swing's GridLayout().
- createColumnGridControls(Node...) - Static method in class qupath.lib.gui.tools.PaneTools
-
Deprecated.Create a GridPane containing columns that resize similarly to Swing's GridLayout(), where controls have their widths bound to their parent.
- createCommandFinderDialog(QuPathGUI) - Static method in class qupath.lib.gui.tools.CommandFinderTools
-
Create a dialog showing a filtered list of menu commands, for fast selection.
- createCommandFinderPane(QuPathGUI, Node, ObjectProperty<CommandFinderTools.CommandBarDisplay>) - Static method in class qupath.lib.gui.tools.CommandFinderTools
-
Create a component that contains a
TextFieldfor entering menu commands to run quickly. - createContext(ScriptParameters) - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
-
Create a
ScriptContextcontaining information from theScriptParameters. - createDefaultRGBImage(int, int) - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer
- createDefaultRGBImage(int, int) - Method in class qupath.lib.gui.images.servers.RenderedImageServer
- createDoubleArrowEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
- createEllipseEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
- createExtendedTool(PathTool...) - Static method in class qupath.lib.gui.viewer.tools.PathTools
- createFeatureDisplayOverlay(OverlayOptions, Function<ImageData<BufferedImage>, ImageServer<BufferedImage>>, ImageRenderer) - Static method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
-
Deprecated.
- createFontAwesome(char) - Static method in class qupath.lib.gui.tools.IconFactory
-
Create a node from a FontAwesome Glyph with the default size for toolbars.
- createFontAwesome(char, int) - Static method in class qupath.lib.gui.tools.IconFactory
-
Create a node from a FontAwesome Glyph with the default size for toolbars.
- createForObservableViewer(ObservableValue<? extends QuPathViewer>) - Static method in class qupath.lib.gui.UndoRedoManager
- createFromBuilders(Collection<? extends ImageServerBuilder.ServerBuilder<BufferedImage>>) - Static method in class qupath.lib.gui.panes.ServerSelector
- createFullImageAnnotation(QuPathViewer) - Static method in class qupath.lib.gui.commands.Commands
-
Create a full image annotation for the image in the specified viewer.
- createGridView(QuPathGUI, Function<PathObjectHierarchy, Collection<? extends PathObject>>) - Static method in class qupath.lib.gui.commands.PathObjectGridView
-
Create a grid view for a custom object extractor.
- createHiddenInstance() - Static method in class qupath.lib.gui.QuPathGUI
-
Create a new QuPath instance that is not visible (i.e.
- createHistogramData(Histogram, Integer) - Static method in class qupath.lib.gui.charts.HistogramChart
-
Create a HistogramData object to wrap a histogram & some info about its display.
- createHistogramData(Histogram, Color) - Static method in class qupath.lib.gui.charts.HistogramChart
-
Create a HistogramData object to wrap a histogram & some info about its display.
- createIconImage(IconFactory.PathIcons, int) - Static method in class qupath.lib.gui.tools.IconFactory
-
Create an image from a default icon glyph.
- createID() - Method in class qupath.lib.gui.images.servers.ChannelDisplayTransformServer
- createID() - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer
-
Returns a UUID.
- createID() - Method in class qupath.lib.gui.images.servers.RenderedImageServer
- createImageChoicePane(QuPathGUI, List<ProjectImageEntry<BufferedImage>>, List<ProjectImageEntry<BufferedImage>>, String) - Static method in class qupath.lib.gui.dialogs.ProjectDialogs
-
Populates a given
ListSelectionViewwith all the project entries. - createImageDataAction(Consumer<ImageData<BufferedImage>>) - Method in class qupath.lib.gui.QuPathGUI
-
Create an
Actionthat depends upon anImageData. - createImageDataAction(Consumer<ImageData<BufferedImage>>, String) - Method in class qupath.lib.gui.QuPathGUI
-
Create an
Actionthat depends upon anImageData. - createImageRegionStore() - Static method in class qupath.lib.gui.images.stores.ImageRegionStoreFactory
-
Create an
ImageRegionStoreusing a default tile cache size, based upon the available memory and user preferences. - createImageRegionStore(long) - Static method in class qupath.lib.gui.images.stores.ImageRegionStoreFactory
-
Create an
ImageRegionStorewith a specified tile cache size, in bytes. - createImageViewer(QuPathViewer, ImageServer<BufferedImage>, boolean) - Static method in class qupath.lib.gui.tools.PathObjectImageViewers
-
Create an item viewer to display a
PathObjectusing anImageView. - createInstance(Stage) - Static method in class qupath.lib.gui.QuPathGUI
-
Static method to launch QuPath on the JavaFX Application thread.
- createInstance(Stage, HostServices) - Static method in class qupath.lib.gui.QuPathGUI
-
Static method to launch QuPath from a JavaFX application.
- createJsonTreeBrowser(String, Object) - Static method in class qupath.lib.gui.panes.ObjectTreeBrowser
-
Create a
TreeTableViewshowing the names and values of fields within aJsonElement. - createLeftRightTitledPane(String, Node...) - Static method in class qupath.lib.gui.tools.GuiTools
-
Create a
TitledPanewith a text heading aligned to the left, and additional content (usually one or more buttons) aligned to the right. - createLeftRightTitledPane(Node, Node) - Static method in class qupath.lib.gui.tools.GuiTools
-
Create a
TitledPanewith content aligned to the left and right of the title. - createLicensesWindow(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
-
Create a window summarizing license information for QuPath and its third party dependencies.
- createLineEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
- createListCell() - Static method in class qupath.lib.gui.tools.PathObjectLabels
- createListCell(Function<PathObject, String>) - Static method in class qupath.lib.gui.tools.PathObjectLabels
-
Create a
ListCellfor displaying aPathObjectusing a custom method to create a string representation of the object. - createListSelectionView() - Static method in class qupath.lib.gui.tools.GuiTools
-
Create a new
ListSelectionView. - createLogFiles - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
- createManager(QuPathViewer) - Static method in class qupath.lib.gui.commands.MiniViewers
-
Create a
MiniViewers.MiniViewerManagerassociated with a specified viewer. - createManager(QuPathViewer, Collection<? extends ChannelDisplayInfo>) - Static method in class qupath.lib.gui.commands.MiniViewers
-
Create a
MiniViewers.MiniViewerManagerdisplaying multiple channels and associated with a specified viewer. - createMeasurementMapDialog(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
-
Create a dialog for displaying measurement maps.
- createMemoryMonitorDialog(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
-
Create a dialog to monitor memory usage.
- createMenu(String, Object...) - Static method in class qupath.lib.gui.tools.MenuTools
-
Create a menu, optionally add new menu items with
MenuTools.addMenuItems(List, Object...). - createMenuItem(Action) - Static method in class qupath.lib.gui.actions.ActionTools
-
Create a menu item from an action.
- createMoreButton(ContextMenu, Side) - Static method in class qupath.lib.gui.tools.GuiTools
-
Create a
Buttonwith a standardized icon and tooltip text to indicate 'More', which triggers aContextMenuwhen clicked. - createMoveEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
- createNewAnnotation(MouseEvent, double, double) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
-
Create a new annotation and set it in the current viewer.
- createNewChart() - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
- createNewChart() - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
- createNewChart() - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
- createNewChart(Axis<Number>, Axis<Number>) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
- createNewChart(Axis<String>, Axis<Number>) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
- createNewEditor() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
- createNewROI(MouseEvent, double, double, ImagePlane) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
- createNode(int, int, IconFactory.PathIcons) - Static method in class qupath.lib.gui.tools.IconFactory
-
Create a node from a default icon glyph.
- createNode(FontAwesome.Glyph) - Static method in class qupath.lib.gui.tools.IconFactory
-
Create a node from a FontAwesome Glyph with the default size for toolbars.
- createNode(FontAwesome.Glyph, int) - Static method in class qupath.lib.gui.tools.IconFactory
-
Create a node from a FontAwesome Glyph.
- createObjectDescriptionsDialog(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
-
Create a stage to display object descriptions.
- createObjectTreeBrowser(String, Object) - Static method in class qupath.lib.gui.panes.ObjectTreeBrowser
-
Create a
TreeTableViewshowing the names and values of object fields, accessed via reflection. - createPane() - Method in class qupath.lib.gui.panes.WorkflowCommandLogView
- createPane() - Static method in class qupath.lib.gui.tools.PathObjectLabels
-
Create a
PathObjectLabels.PathObjectMiniPaneusing the defaultPathObject.toString()method. - createPane(Function<PathObject, String>) - Static method in class qupath.lib.gui.tools.PathObjectLabels
-
Create a
PathObjectLabels.PathObjectMiniPaneusing a custom method to create a string representation of the object. - createPane(ObservableValue<ImageData<T>>) - Static method in class qupath.lib.gui.panes.ObjectDescriptionPane
- createPane(ObservableValue<ImageData<T>>, boolean) - Static method in class qupath.lib.gui.panes.ObjectDescriptionPane
- createPathObjectIcon(PathObject, int, int) - Static method in class qupath.lib.gui.tools.IconFactory
-
Create an icon depicting a PathObject.
- createPersistentPreference(String, boolean) - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Create a persistent property, which is one that will be saved to/reloaded from the user preferences.
- createPersistentPreference(String, double) - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Create a persistent property, which is one that will be saved to/reloaded from the user preferences.
- createPersistentPreference(String, int) - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Create a persistent property, which is one that will be saved to/reloaded from the user preferences.
- createPersistentPreference(String, long) - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Create a persistent property, which is one that will be saved to/reloaded from the user preferences.
- createPersistentPreference(String, String) - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Create a persistent property, which is one that will be saved to/reloaded from the user preferences.
- createPersistentPreference(String, T, Class<T>) - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Create a persistent property, which is one that will be saved to/reloaded from the user preferences.
- createPersistentPreference(String, T, Function<T, String>, Function<String, T>) - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Create a persistent property representing any object serializable as a String, which will be saved to/reloaded from the user preferences.
- createPersistentUriList(String, int, String...) - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Create an observable list backed by preferences to store URIs.
- createPlaceholderText(String) - Static method in class qupath.lib.gui.tools.GuiTools
-
Create a
Textobject for use as a placeholder in a list or table. - createPlugin(Class<? extends PathPlugin>) - Method in class qupath.lib.gui.QuPathGUI
-
Create a plugin from a specified class.
- createPluginAction(String, Class<? extends PathPlugin>, String) - Method in class qupath.lib.gui.QuPathGUI
-
Create an action for a plugin to be run through this QuPath instance.
- createPluginAction(String, PathPlugin<BufferedImage>, String) - Method in class qupath.lib.gui.QuPathGUI
-
Create an Action to call the specified plugin for the current image.
- createPointsEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
- createPolygonEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
- createPolylineEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
- createPreferencesDialog(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
-
Show a dialog to adjust QuPath preferences.
- createProjectAction(Consumer<Project<BufferedImage>>) - Method in class qupath.lib.gui.QuPathGUI
-
Create an
Actionthat depends upon aProject. - createPropertySheetItem(Property<T>, Class<? extends T>) - Static method in class qupath.lib.gui.panes.PreferencePane
-
Deprecated.use
PropertyItemBuilderinstead - createRecentCommandsDialog(QuPathGUI) - Static method in class qupath.lib.gui.tools.CommandFinderTools
-
Create a dialog showing a filtered list of recently-used commands, for fast selection.
- createRecentItemsMenu(String, ObservableList<URI>, Consumer<URI>) - Static method in class qupath.lib.gui.tools.GuiTools
-
Create a menu that displays recent items, stored in the form of URIs.
- createRectangleEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
- createRelativePathProperty(String) - Method in class qupath.lib.gui.UserDirectoryManager
-
Create a read only property for a relative path of the user subdirectory.
- createRenderedServer(QuPathViewer) - Static method in class qupath.lib.gui.images.servers.RenderedImageServer
-
Create an
ImageServerthat returns tiles based on how approximately they would appear within the viewer. - createRenderedServer(ImageServer<BufferedImage>, ImageRenderer) - Static method in class qupath.lib.gui.images.servers.RenderedImageServer
-
Create an
ImageServerthat converts the image to RGB using the specifiedImageRenderer. - createROIIcon(ROI, int, int, Color) - Static method in class qupath.lib.gui.tools.IconFactory
-
Create an icon depicting a ROI.
- createRotateImageDialog(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
-
Create a dialog for rotating the image in the current viewer (for display only).
- createRowGrid(Node...) - Static method in class qupath.lib.gui.tools.PaneTools
-
Deprecated.Create a GridPane containing rows that resize similarly to Swing's GridLayout().
- createRowGridControls(Node...) - Static method in class qupath.lib.gui.tools.PaneTools
-
Deprecated.Create a GridPane containing columns that resize similarly to Swing's GridLayout(), while also resizing contained objects to have the corresponding widths.
- createSelectableAction(ObservableValue<Boolean>) - Static method in class qupath.lib.gui.actions.ActionTools
-
Create an unnamed action with its
Action.selectedProperty()bound to a specified property. - createSelectableAction(ObservableValue<Boolean>, String) - Static method in class qupath.lib.gui.actions.ActionTools
-
Create an action with its
Action.selectedProperty()bound to a specified property. - createSelectableAction(ObservableValue<Boolean>, String, Node, KeyCombination) - Static method in class qupath.lib.gui.actions.ActionTools
-
Create an action with its
Action.selectedProperty()bound to a specified property, with optional graphic and accelerator. - createSelectableCommandAction(ObservableBooleanValue) - Static method in class qupath.lib.gui.actions.ActionTools
- createSelectableCommandAction(SelectableItem<T>) - Static method in class qupath.lib.gui.actions.ActionTools
- createSelectableCommandAction(SelectableItem<T>, String) - Static method in class qupath.lib.gui.actions.ActionTools
-
Create an action from a selectable icon.
- createSelectableCommandAction(SelectableItem<T>, String, Node, KeyCombination) - Static method in class qupath.lib.gui.actions.ActionTools
- createSelectableCommandAction(SelectableItem<T>, ObservableValue<String>, ObservableValue<Node>, KeyCombination) - Static method in class qupath.lib.gui.actions.ActionTools
- createSeparator() - Static method in class qupath.lib.gui.actions.ActionTools
-
Create an action indicating that a separator should be added (e.g.
- createSeries(String, double[], double[]) - Static method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Create a scatterplot using arrays of numeric values.
- createSeries(String, double[], double[], List<T>) - Static method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Create a scatterplot using collections of numeric values, with an associated custom object.
- createSeries(String, double[], double[], T[]) - Static method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Create a series of data using collections of numeric values, with an associated custom object.
- createSeries(String, Collection<? extends Number>, Collection<? extends Number>) - Static method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Create a series using collections of numeric values.
- createSeries(String, Collection<? extends T>, Function<T, Number>, Function<T, Number>) - Static method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Create a data series extracted from objects within a specified collection.
- createSeriesFromMeasurements(Collection<? extends PathObject>, String, String) - Static method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Create a data series from two measurements for the specified objects.
- createServerBuilder() - Method in class qupath.lib.gui.images.servers.ChannelDisplayTransformServer
-
Returns null (does not support ServerBuilders).
- createServerBuilder() - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer
-
Returns null (does not support ServerBuilders).
- createServerBuilder() - Method in class qupath.lib.gui.images.servers.RenderedImageServer
- createShape(MouseEvent, double, double, boolean, Geometry) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
-
Create a new Geometry using the specified tool, assuming a user click/drag at the provided x & y coordinates.
- createSharedPoolCompletionService(Class<V>) - Method in class qupath.lib.gui.QuPathGUI
-
Deprecated.since v0.5.0; use
QuPathGUI.getThreadPoolManager() - createSharedPoolCompletionService(Class<V>) - Method in class qupath.lib.gui.SharedThreadPoolManager
-
Create a completion service that uses a shared threadpool for the application.
- createShowSystemInfoDialog(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
-
Create a window summarizing key system information relevant for QuPath.
- createSingleStageAction(Supplier<Stage>) - Static method in class qupath.lib.gui.commands.Commands
-
Create a command that generates a persistent single dialog on demand.
- createSingleStageAction(Supplier<Stage>, String) - Static method in class qupath.lib.gui.commands.Commands
-
Create a named command that generates a persistent single dialog on demand.
- createSingleThreadExecutor(Object) - Method in class qupath.lib.gui.QuPathGUI
-
Deprecated.since v0.5.0; use
QuPathGUI.getThreadPoolManager() - createSpecifyAnnotationDialog(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
-
Create a stage to prompt the user to specify an annotation to add.
- createTableCell(QuPathViewer, ImageServer<BufferedImage>, boolean, double) - Static method in class qupath.lib.gui.tools.PathObjectImageViewers
-
Create a table cell to show an object.
- createTaskRunner() - Static method in class qupath.lib.gui.scripting.QPEx
-
Create a task runner with the default number of threads defined by
ThreadTools.getParallelism(). - createTaskRunner(int) - Static method in class qupath.lib.gui.scripting.QPEx
-
Create a task runner with the specified number of threads.
- createTileWorker(ImageServer<BufferedImage>, RegionRequest, Map<RegionRequest, BufferedImage>, boolean) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
- createTmaCoreView(QuPathGUI) - Static method in class qupath.lib.gui.commands.PathObjectGridView
-
Create a grid view for TMA core objects.
- createToggleButton(Action) - Static method in class qupath.lib.gui.actions.ActionTools
-
Create a toggle button from an action, showing both the text and graphic if available.
- createToggleButtonWithGraphicOnly(Action) - Static method in class qupath.lib.gui.actions.ActionTools
-
Create a toggle button from an action, showing only the graphic and not any text.
- createTool(EventHandler<MouseEvent>, String, Node) - Static method in class qupath.lib.gui.viewer.tools.PathTools
-
Create a tool from the specified
MouseEventhandler. - createTool(EventType<T>, EventHandler<T>, String, Node) - Static method in class qupath.lib.gui.viewer.tools.PathTools
-
Create a tool from the specified event handler.
- createTreeCell() - Static method in class qupath.lib.gui.tools.PathObjectLabels
- createTreeCell(Function<PathObject, String>) - Static method in class qupath.lib.gui.tools.PathObjectLabels
-
Create a
TreeCellfor displaying aPathObjectusing a custom method to create a string representation of the object. - createValues(PathObjectListWrapper) - Method in class qupath.lib.gui.measure.MeasurementListValueFactory
- createValues(PathObjectListWrapper) - Method in class qupath.lib.gui.measure.MetadataValueFactory
- createValues(PathObjectListWrapper) - Method in interface qupath.lib.gui.measure.PathObjectValueFactory
-
Create the lazy values for the objects contained in the wrapper.
- createViewer() - Method in class qupath.lib.gui.viewer.ViewerManager
-
Create a viewer, adding it to the stored array but not adding it to any component (which is left up to the calling code to handle)
- createViewerAction(Consumer<QuPathViewer>) - Method in class qupath.lib.gui.QuPathGUI
-
Create an
Actionthat depends upon anQuPathViewer. - createWindow(QuPathGUI) - Static method in class qupath.lib.gui.panes.ObjectDescriptionPane
- createWorkflowDisplayDialog(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
-
Create a dialog to show the workflow history for the current image data.
- createZoomCommand(QuPathGUI, int) - Static method in class qupath.lib.gui.commands.Commands
-
Create a zoom in/out command action.
- cssDirectoryProperty() - Method in class qupath.lib.gui.UserDirectoryManager
-
Read only property representing the css directory.
- CssLanguage - Class in qupath.lib.gui.scripting.languages
-
Class for representing CSS in QuPath.
- currentChannelProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane
-
Get the currently-selected channel.
- currentChannelVisible() - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane
-
Read-only property indicating whether the currently-selected channel is visible, i.e.
- currentLanguageProperty() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
- currentSyntaxProperty() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
- cursorTrackingProperty() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return the cursorTracking property of this tracker.
- cut() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
-
Request cut the current selection.
- cut() - Method in class qupath.lib.gui.scripting.TextAreaControl
- cutAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
D
- data(Map<?, ? extends Number>) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
-
Specify data for the pie chart as a map.
- dataItemAdded(XYChart.Series<Number, Number>, int, XYChart.Data<Number, Number>) - Method in class qupath.lib.gui.charts.PathObjectScatterChart
- dataItemRemoved(XYChart.Data<Number, Number>, XYChart.Series<Number, Number>) - Method in class qupath.lib.gui.charts.PathObjectScatterChart
- DEBUG - Enum constant in enum class qupath.lib.gui.logging.LogManager.LogLevel
-
Debug logging (a lot of messages)
- decelerate() - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler.ViewerMover
-
Stop moving, by smoothly decelerating.
- DECIMAL_PLACES_DEFAULT - Static variable in class qupath.lib.gui.tools.MeasurementExporter
-
Constant representing that the number of decimal places to use when exporting measurements can be chosen automatically.
- decimalPlaces(int) - Method in class qupath.lib.gui.tools.MeasurementExporter
-
Specify how many decimal places to use for numeric output.
- DEFAULT - Enum constant in enum class qupath.lib.gui.prefs.QuPathStyleManager.Fonts
-
JavaFX default.
- DEFAULT_DECIMAL_PLACES - Static variable in interface qupath.lib.gui.measure.PathTableData
-
The default number of decimal places when converting floating point values to strings.
- DEFAULT_DELIMITER - Static variable in interface qupath.lib.gui.measure.PathTableData
-
The default delimiter to use.
- DEFAULT_PREFIX - Static variable in class qupath.lib.gui.images.servers.PathHierarchyImageServer
-
Prefix used for the path of all instances of this class.
- DefaultAutoCompletor - Class in qupath.lib.gui.scripting.completors
-
Default auto-completor for JVM-based languages, optionally including QuPath default imports.
- DefaultAutoCompletor() - Constructor for class qupath.lib.gui.scripting.completors.DefaultAutoCompletor
-
Constructor, using the default Java code completions for QuPath.
- DefaultAutoCompletor(Collection<? extends AutoCompletions.Completion>) - Constructor for class qupath.lib.gui.scripting.completors.DefaultAutoCompletor
-
Constructor.
- defaultColor - Variable in class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
- DefaultImageRegionStore - Class in qupath.lib.gui.images.stores
-
An ImageRegionStore suitable for either Swing or JavaFX applications.
- defaultLocaleDisplayProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Get a property for setting the default
LocaleforLocale.Category.DISPLAY. - defaultLocaleFormatProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Get a property for setting the default
LocaleforLocale.Category.FORMAT. - defaultLocaleProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Get a property for setting the default
Locale. - DefaultPathObjectValueFactoryBuilder - Class in qupath.lib.gui.measure
- DefaultPathObjectValueFactoryBuilder() - Constructor for class qupath.lib.gui.measure.DefaultPathObjectValueFactoryBuilder
- DefaultScriptEditor - Class in qupath.lib.gui.scripting
-
Default multilingual script editor.
- DefaultScriptEditor(QuPathGUI) - Constructor for class qupath.lib.gui.scripting.DefaultScriptEditor
-
Constructor.
- DefaultScriptLanguage - Class in qupath.lib.gui.scripting.languages
-
Default implementation for a
ScriptLanguage, based on aScriptEngine. - DefaultScriptLanguage(String, Collection<String>, ScriptAutoCompletor) - Constructor for class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
-
Constructor for a
ExecutableLanguage. - DefaultScriptLanguage(ScriptEngineFactory) - Constructor for class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
-
Constructor for a
ExecutableLanguagebased on aScriptEngineFactory. - DefaultScriptLanguage.ImportStatementGenerator - Interface in qupath.lib.gui.scripting.languages
-
Interface defining how the import statements should be generated for the language.
- defaultStringFunction(PathClass) - Static method in class qupath.lib.gui.tools.PathClassListCell
-
Default function to convert a PathClass to a string.
- DELETE_ALL - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.DeleteActions
- DELETE_ANNOTATION - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.DeleteActions
- DELETE_DETECTIONS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.DeleteActions
- DELETE_IMAGE_BOUNDARY - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.DeleteActions
- DELETE_SELECTED_BOUNDARY - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.DeleteActions
- DELETE_SELECTED_OBJECTS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.DeleteActions
- deleteActions - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.Actions
- DeleteActions() - Constructor for class qupath.lib.gui.actions.menus.ObjectsMenuActions.DeleteActions
- DeleteObjectsOnBoundsCommand - Class in qupath.lib.gui.commands
-
Interactive command to remove objects with ROIs that touch or overlap the boundary of other objects.
- DeleteObjectsOnBoundsCommand(QuPathGUI) - Constructor for class qupath.lib.gui.commands.DeleteObjectsOnBoundsCommand
- deleteText(int, int) - Method in interface qupath.lib.gui.scripting.EditableText
-
Request deleting the text within the specified range.
- deleteText(int, int) - Method in class qupath.lib.gui.scripting.TextAreaControl
- DEMOS - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
- deregisterTool(QuPathViewer) - Method in class qupath.lib.gui.viewer.tools.ExtendedPathTool
- deregisterTool(QuPathViewer) - Method in interface qupath.lib.gui.viewer.tools.PathTool
-
Deregister the tool from the viewer.
- deselect() - Method in interface qupath.lib.gui.scripting.EditableText
-
Deselect any currently-selected text.
- deselect() - Method in class qupath.lib.gui.scripting.TextAreaControl
- DETACH_VIEWER - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
- DETACH_VIEWER - Variable in class qupath.lib.gui.actions.ViewerActions
- detachActiveViewerFromGrid() - Method in class qupath.lib.gui.viewer.ViewerManager
-
Detach the currently active viewer from the viewer grid, if possible.
- detachViewerFromGrid(QuPathViewer) - Method in class qupath.lib.gui.viewer.ViewerManager
-
Detach the specified viewer from the viewer grid, if possible.
- detectionCentroidDistances2D(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands
-
Compute the distance between the centroids of all detections, for all available classifications.
- detectionDisplayModeProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Property representing the current
OverlayOptions.DetectionDisplayMode. - DETECTIONS - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- DETECTIONS - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
- DETECTIONS_FILL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- detectionStrokeThicknessProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Preferred stroke thickness to use when drawing detections ROIs.
- detectionTreeDisplayModeProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Define how detections should be displayed in lists and tree views.
- detectonStrokeThickness - Variable in class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
- df - Static variable in class qupath.lib.display.DirectServerChannelInfo
- df - Static variable in class qupath.lib.gui.viewer.recording.ViewTracker
- Dialogs - Class in qupath.lib.gui.dialogs
-
Deprecated.since v0.5.0.
- Dialogs() - Constructor for class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.
- Dialogs.Builder - Class in qupath.lib.gui.dialogs
-
Deprecated.
- Dialogs.DialogButton - Enum Class in qupath.lib.gui.dialogs
-
Deprecated.Possible buttons pressed in a yes/no/cancel dialog.
- DIR_COLORMAPS - Static variable in class qupath.lib.gui.UserDirectoryManager
-
Name of subdirectory containing colormaps.
- DIR_CSS - Static variable in class qupath.lib.gui.UserDirectoryManager
-
Name of subdirectory containing css files for styling.
- DIR_EXTENSIONS - Static variable in class qupath.lib.gui.UserDirectoryManager
-
Name of subdirectory containing extensions.
- DIR_LOCALIZATION - Static variable in class qupath.lib.gui.UserDirectoryManager
-
Name of subdirectory containing properties files for localization.
- DIR_LOGS - Static variable in class qupath.lib.gui.UserDirectoryManager
-
Name of subdirectory containing log files.
- DIR_SCRIPTS - Static variable in class qupath.lib.gui.UserDirectoryManager
-
Name of subdirectory containing shared scripts.
- DirectServerChannelInfo - Class in qupath.lib.display
-
ChannelInfo intended for use with a single or multichannel image (possibly fluorescence) where the pixel's value is used to scale a single color according to a specified display range according to the following rules: If the pixel's value is >= maxDisplay, the pure color is used. If the pixel's value is <= minDisplay, the black is used. Otherwise, a scaled version of the color is used The end result is like having a lookup table (LUT) that stretches from black to the 'pure' color specified, but without actually generating the LUT.
- DirectServerChannelInfo(ImageData<BufferedImage>, int) - Constructor for class qupath.lib.display.DirectServerChannelInfo
-
Constructor.
- disabled(boolean) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
-
Set the disabled property of the action.
- disabled(ObservableValue<Boolean>) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
-
Bind the disabled property of the action to an
ObservableValue, bidirectionally if possible. - disableGammaAdjustmentProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSliderPane
-
Prevent gamma from being adjusted.
- disableMinMaxAdjustmentProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSliderPane
-
Prevent the min and max sliders from being adjusted.
- disableToggleMenuItemsProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane
-
Property to disable options to toggle the visibility of channels.
- disableUpdatesProperty() - Method in class qupath.lib.gui.panes.AnnotationPane
-
Property that may be used to prevent updates on every hierarchy or selection change event.
- disableUpdatesProperty() - Method in class qupath.lib.gui.panes.PathObjectHierarchyView
-
Property that may be used to prevent updates on every hierarchy or selection change event.
- display(ImageDisplay) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder
-
Deprecated.use
RenderedImageServer.Builder.renderer(ImageRenderer)instead (since anImageDisplayis also anImageRenderer. - displayMode() - Method in class qupath.lib.display.ImageDisplay
-
Get the value of
ImageDisplay.useInvertedBackgroundProperty() - displayModeProperty() - Method in class qupath.lib.gui.charts.HistogramChart
-
Property to control how the histogram is displayed, either using areas or bars.
- DisplaySettingUtils - Class in qupath.lib.display.settings
-
Utility class for working with image display and image display settings objects.
- DisplaySettingUtils() - Constructor for class qupath.lib.display.settings.DisplaySettingUtils
- displayToSettings(ImageDisplay, String) - Static method in class qupath.lib.display.settings.DisplaySettingUtils
-
Create a new image display settings object from the image display.
- DISTANCE_CENTROIDS - Variable in class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
- DISTANCE_TO_ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
- distanceToAnnotations2D(ImageData<?>, boolean) - Static method in class qupath.lib.gui.commands.Commands
-
Compute the distance between all detections and the closest annotation, for all annotation classifications.
- DocGenerator - Class in qupath.lib.gui.tools
-
Command line tool to export icons and markdown documentation for QuPath commands.
- DocGenerator() - Constructor for class qupath.lib.gui.tools.DocGenerator
- doCopy() - Method in class qupath.lib.gui.FileCopier
-
Perform the copying.
- doCreateLogFilesProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Request a log file to be generated.
- DOCS - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
- doesSomething() - Method in class qupath.lib.display.AdditiveChannelInfo
- doesSomething() - Method in interface qupath.lib.display.ChannelDisplayInfo
-
Returns true if this does something - anything - and false otherwise.
- doesSomething() - Method in class qupath.lib.display.DirectServerChannelInfo
- doLogCountsProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastHistogramPane
-
Property to control whether the histogram shows pixel counts, or the natural logarithm of the counts.
- doubleClickToZoom - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
- doubleClickToZoomProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Request that double-clicking the viewer can be used to zoom in.
- DOWNLOAD - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- DownsampledShapeCache - Class in qupath.lib.gui.viewer
-
Helper class for managing simplified versions of a shape for rendering shapes at lower resolutions.
- downsamples(double...) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder
-
Specify downsamples; this is especially important for 'thick' objects (annotations, TMA cores) because the downsamples define the resolutions at which these will be rendered.
- DragDropImportListener - Class in qupath.lib.gui.viewer
-
Drag and drop support for main QuPath application, which can support a range of different object types (Files, URLs, Strings,..)
- DragDropImportListener(QuPathGUI) - Constructor for class qupath.lib.gui.viewer.DragDropImportListener
-
Constructor.
- DragDropImportListener.DropHandler<T> - Interface in qupath.lib.gui.viewer
-
Interface to define a new drop handler.
- DrawingPreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.DrawingPreferences
- duplicateSelectedAnnotations(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands
-
Duplicate the selected annotations.
E
- EditableText - Interface in qupath.lib.gui.scripting
-
Interface for objects that manage editable text, including a caret position and selection.
- EditMenuActions - Class in qupath.lib.gui.actions.menus
- EditMenuActions.Actions - Class in qupath.lib.gui.actions.menus
- EditMenuActions.CopyActions - Class in qupath.lib.gui.actions.menus
- editSelectedAnnotation(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
-
Prompt to edit the selected annotation by translation and rotation.
- ELLIPSE - Static variable in class qupath.lib.gui.viewer.tools.PathTools
-
Ellipse drawing tool
- ELLIPSE_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- ELLIPSE_TOOL - Variable in class qupath.lib.gui.ToolManager
- enableFreehand - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
- enableFreehandToolsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Enable polygon/polyline tools to support 'freehand' mode; this means that if the ROI is started by dragging, then it will end by lifting the mouse (rather than requiring a double-click).
- ensureCursorType(Cursor) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
-
Ensure that the specified cursor is set in the current viewer.
- ensureCursorType(Cursor) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
-
Ensure that the specified cursor is set in the current viewer.
- ensureDuplicatableGlyph(Glyph) - Static method in class qupath.lib.gui.tools.GuiTools
-
Ensure that a
Glyphis 'duplicatable', without losing its key properties. - ensureDuplicatableGlyph(Glyph, boolean) - Static method in class qupath.lib.gui.tools.GuiTools
-
Ensure that a
Glyphis 'duplicatable', optionally retaining any fill. - equals(Object) - Method in class qupath.lib.gui.extensions.GitHubProject.GitHubRepo
- error() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Deprecated.Create an error alert dialog.
- error(String) - Static method in class qupath.lib.gui.actions.InfoMessage
-
Create an error message with static text.
- error(String, int) - Static method in class qupath.lib.gui.actions.InfoMessage
-
Create an error message with static text and a count.
- error(ObservableNumberValue) - Static method in class qupath.lib.gui.actions.InfoMessage
-
Create a error message to show a count of errors.
- error(ObservableValue<String>) - Static method in class qupath.lib.gui.actions.InfoMessage
-
Create an error message.
- error(ObservableValue<String>, ObservableNumberValue) - Static method in class qupath.lib.gui.actions.InfoMessage
-
Create an error message with a count.
- ERROR - Enum constant in enum class qupath.lib.gui.actions.InfoMessage.MessageType
-
Error or exception.
- ERROR - Enum constant in enum class qupath.lib.gui.logging.LogManager.LogLevel
-
Error logging (only if something goes recognizably wrong)
- estimateImageType(ImageServer<BufferedImage>, BufferedImage) - Static method in class qupath.lib.gui.tools.GuiTools
-
Make a semi-educated guess at the image type of a PathImageServer.
- eventCountProperty() - Method in class qupath.lib.display.ImageDisplay
-
Counter for the number of display changes that have been made.
- EVERYWHERE - Enum constant in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters
-
Accept all requests
- excludeColumns(String...) - Method in class qupath.lib.gui.tools.MeasurementExporter
-
Specify the columns that will be excluded during the export.
- execute(ScriptParameters) - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
- execute(ScriptParameters) - Method in class qupath.lib.gui.scripting.languages.MarkdownLanguage
- EXPAND_ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
- expandableContent(Node) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Deprecated.Specify a
Nodeto display within the dialog as expandable content, not initially visible. - expandChartClip(Chart, double) - Static method in class qupath.lib.gui.charts.ChartTools
-
Expand the clip region for a chart.
- expandToWindowProperty() - Method in class qupath.lib.gui.panes.SimpleImageViewer
-
Get the property indicating whether the image should grow to fill the window (while maintaining its aspect ratio).
- EXPORT - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
- EXPORT_GEOJSON - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
- EXPORT_IMAGE_LIST - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
- EXPORT_ORIGINAL - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ExportImageActions
- EXPORT_RENDERED - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ExportImageActions
- exportImageActions - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
- ExportImageActions() - Constructor for class qupath.lib.gui.actions.menus.FileMenuActions.ExportImageActions
- exportMeasurements(File) - Method in class qupath.lib.gui.tools.MeasurementExporter
-
Exports the measurements of one or more entries in the project.
- exportMeasurements(OutputStream) - Method in class qupath.lib.gui.tools.MeasurementExporter
-
Exports the measurements of one or more entries in the project.
- ExportObjectsCommand - Class in qupath.lib.gui.commands
-
Command to export object(s) in GeoJSON format to an output file.
- exportPreferences(OutputStream) - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Export preferences to a stream.
- exportSnapshotActions - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
- ExportSnapshotActions() - Constructor for class qupath.lib.gui.actions.menus.FileMenuActions.ExportSnapshotActions
- exportTMAData(String, double) - Static method in class qupath.lib.gui.scripting.QPEx
-
Export TMA summary data for the current image.
- exportTMAData(ImageData<BufferedImage>, String, double) - Static method in class qupath.lib.gui.scripting.QPEx
-
Export TMA summary data for the specified image.
- exportType(Class<? extends PathObject>) - Method in class qupath.lib.gui.tools.MeasurementExporter
-
Specify what type of object should be exported.
- ExtendedPathTool - Class in qupath.lib.gui.viewer.tools
- ExtensionPreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.ExtensionPreferences
- EXTENSIONS - Variable in class qupath.lib.gui.actions.menus.ExtensionsMenuActions.Actions
- EXTENSIONS_ONLY - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.AutoUpdateType
-
Check for extensions on GitHub only (not new QuPath releases)
- extensionsDirectoryProperty() - Method in class qupath.lib.gui.UserDirectoryManager
-
Read only property representing the extensions directory.
- ExtensionsMenuActions - Class in qupath.lib.gui.actions.menus
- ExtensionsMenuActions.Actions - Class in qupath.lib.gui.actions.menus
- EXTRACT_REGION - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- eyeTrackingProperty() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return the eyeTracking property of this tracker.
F
- FileCopier - Class in qupath.lib.gui
-
Copy files to an output directory, prompting the user if necessary.
- FileCopier() - Constructor for class qupath.lib.gui.FileCopier
- FileMenuActions - Class in qupath.lib.gui.actions.menus
- FileMenuActions(QuPathGUI) - Constructor for class qupath.lib.gui.actions.menus.FileMenuActions
- FileMenuActions.Actions - Class in qupath.lib.gui.actions.menus
- FileMenuActions.ExportImageActions - Class in qupath.lib.gui.actions.menus
- FileMenuActions.ExportSnapshotActions - Class in qupath.lib.gui.actions.menus
- FileMenuActions.ProjectActions - Class in qupath.lib.gui.actions.menus
- FileMenuActions.TmaActions - Class in qupath.lib.gui.actions.menus
- FILL_ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- FILL_ANNOTATIONS - Variable in class qupath.lib.gui.actions.OverlayActions
- FILL_DETECTIONS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- FILL_DETECTIONS - Variable in class qupath.lib.gui.actions.OverlayActions
- FILL_HOLES - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
- fillAnnotationsProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
- fillDetectionsProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
- filter(Predicate<PathObject>) - Method in class qupath.lib.gui.tools.MeasurementExporter
-
Filter the
PathObjects before export (objects returningtruefor the predicate will be included). - findAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- fireImageDataChanged(ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.viewer.QuPathViewer
- fireVisibleRegionChangedEvent(Shape) - Method in class qupath.lib.gui.viewer.QuPathViewer
- fontProperty() - Static method in class qupath.lib.gui.prefs.QuPathStyleManager
-
Get the current selected font.
- fontSizeProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
- forAnnotations(ImageData<?>) - Static method in class qupath.lib.gui.measure.PathObjectListWrapper
-
Create a wrapper including all annotations.
- forCells(ImageData<?>) - Static method in class qupath.lib.gui.measure.PathObjectListWrapper
-
Create a wrapper containing all cells.
- forceOverlayUpdate() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Force the overlay displaying detections and annotations to be repainted.
- forDetections(ImageData<?>) - Static method in class qupath.lib.gui.measure.PathObjectListWrapper
-
Create a wrapper including all detections.
- forRoot(ImageData<?>) - Static method in class qupath.lib.gui.measure.PathObjectListWrapper
-
Create a wrapper including only the root object.
- forTiles(ImageData<?>) - Static method in class qupath.lib.gui.measure.PathObjectListWrapper
-
Create a wrapper containing all tile objects.
- forTmaCores(ImageData<?>) - Static method in class qupath.lib.gui.measure.PathObjectListWrapper
-
Create a wrapper containing all TMA cores.
- FORUM - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
- fromPackedARGB(int) - Static method in class qupath.lib.display.settings.ChannelColor
-
Create a channel color from a packed ARGB value.
- fromRGB(int, int, int) - Static method in class qupath.lib.display.settings.ChannelColor
-
Create a channel color from 8-bit RGB values.
- fromString(String) - Static method in class qupath.lib.gui.scripting.languages.ScriptLanguageProvider
-
Get the
ScriptLanguageobject corresponding to the specified String. - FULL_SCREENSHOT - Enum constant in enum class qupath.lib.gui.tools.GuiTools.SnapshotType
-
Full screenshot, including items outside of QuPath.
G
- gammaProperty() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the gamma property for this viewer.
- gammaValueProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSliderPane
-
Value of the gamma slider.
- GeneralPreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
- GESTURES_ALL - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultitouchActions
- GESTURES_NONE - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultitouchActions
- GESTURES_ROTATE - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultitouchActions
- GESTURES_SCROLL - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultitouchActions
- GESTURES_ZOOM - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultitouchActions
- getAcceleratorText() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry
-
Get a String representation of any accelerator for the command
- getActionProperty(MenuItem) - Static method in class qupath.lib.gui.actions.ActionTools
-
Retrieve an Action stored within the properties of a menu item, or null if no action is found.
- getActionProperty(Node) - Static method in class qupath.lib.gui.actions.ActionTools
-
Retrieve an Action stored within the properties of a node, or null if no action is found.
- getActions() - Method in class qupath.lib.gui.actions.menus.AnalyzeMenuActions
- getActions() - Method in class qupath.lib.gui.actions.menus.AutomateMenuActions
- getActions() - Method in class qupath.lib.gui.actions.menus.ClassifyMenuActions
- getActions() - Method in class qupath.lib.gui.actions.menus.EditMenuActions
- getActions() - Method in class qupath.lib.gui.actions.menus.ExtensionsMenuActions
- getActions() - Method in class qupath.lib.gui.actions.menus.FileMenuActions
- getActions() - Method in class qupath.lib.gui.actions.menus.HelpMenuActions
- getActions() - Method in class qupath.lib.gui.actions.menus.MeasureMenuActions
- getActions() - Method in interface qupath.lib.gui.actions.menus.MenuActions
-
Get all the actions to include in the menu, in order.
- getActions() - Method in class qupath.lib.gui.actions.menus.ObjectsMenuActions
- getActions() - Method in class qupath.lib.gui.actions.menus.TMAMenuActions
- getActions() - Method in class qupath.lib.gui.actions.menus.ViewMenuActions
- getActions() - Method in class qupath.lib.gui.actions.menus.WindowMenuActions
- getActiveTool() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the active
PathToolfor this viewer. - getActiveToolIfRequired() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
- getActiveViewer() - Method in class qupath.lib.gui.viewer.ViewerManager
-
Get the value of
ViewerManager.activeViewerProperty(). - getAllFrames() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return the collection of recorded frames.
- getAllNames() - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
- getAllNames() - Method in interface qupath.lib.gui.measure.PathTableData
-
Return an ordered list of all names, including both numeric measurements and
Stringvalues. - getAllPathClassesVisible() - Method in class qupath.lib.gui.viewer.OverlayOptions
- getAllSelectedObjects() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get all currently-selected objects from the hierarchy.
- getAllThumbnails() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get thumbnails for all z-slices & time points
- getAllViewers() - Method in class qupath.lib.gui.QuPathGUI
-
Get an unmodifiable observable list of all viewers.
- getAllViewers() - Method in class qupath.lib.gui.viewer.ViewerManager
-
Get an observable list of viewers.
- getAlphaComposite() - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay
- getAnalysisTabPane() - Method in class qupath.lib.gui.QuPathGUI
-
Access the main tab pane shown in the QuPath window.
- getAnnotatedActions(Object) - Static method in class qupath.lib.gui.actions.ActionTools
-
Actions can be parsed from the accessible (usually public) fields of any object, as well as methods annotated with
ActionMethod. - getARGB(Color) - Static method in class qupath.lib.gui.tools.ColorToolsFX
-
Get a packed int (ARGB) representation of a Color object.
- getAutoCompletor() - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
- getAutoCompletor() - Method in class qupath.lib.gui.scripting.languages.ImageJMacroLanguage
- getAutoCompletor() - Method in class qupath.lib.gui.scripting.languages.XmlLanguage
- getAutomateActions() - Method in class qupath.lib.gui.QuPathGUI
-
Get the automated actions associated with this QuPath instance.
- getAutorangeToFullData() - Method in class qupath.lib.gui.charts.PathObjectScatterChart
-
Get the value of
PathObjectScatterChart.autorangeToFullDataProperty() - getAvailableLanguages() - Static method in class qupath.lib.gui.scripting.languages.ScriptLanguageProvider
-
Get the available script languages.
- getAvailablePathClasses() - Method in class qupath.lib.gui.QuPathGUI
-
Get an observable list of available PathClasses.
- getAvailableSyntaxes() - Static method in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
-
Get the available script syntaxes.
- getAvailableTools() - Method in class qupath.lib.gui.viewer.tools.ExtendedPathTool
- getBackingList() - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
-
Access all the objects used to generate the table.
- getBackingListEntries() - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
-
Deprecated.v0.6.0 use instead
ObservableMeasurementTableData.getBackingList() - getBlue() - Method in class qupath.lib.display.settings.ChannelColor
-
Get the blue value.
- getBorderColor() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the border color set for this viewer.
- getBrushDiameter() - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
- getBufferedImage() - Method in class qupath.lib.gui.panes.SimpleImageViewer
-
Get the buffered image.
- getBuildString() - Method in class qupath.lib.gui.BuildInfo
-
Get the build String, or null if no build String is available.
- getBuildString() - Static method in class qupath.lib.gui.QuPathGUI
-
Get a String representing the QuPath version & build time.
- getCache() - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
- getCachedColor(int, int, int) - Static method in class qupath.lib.gui.tools.ColorToolsFX
-
Get a Color object, possibly from a shared map (used to avoid creating too many objects unnecessarily).
- getCachedColor(int, int, int, int) - Static method in class qupath.lib.gui.tools.ColorToolsFX
-
Get a Color object, possibly from a shared map (used to avoid creating too many objects unnecessarily).
- getCachedColor(Integer) - Static method in class qupath.lib.gui.tools.ColorToolsFX
-
Get cached color.
- getCachedColor(Integer, boolean) - Static method in class qupath.lib.gui.tools.ColorToolsFX
-
Get cached color, explicitly stating whether alpha should be included or not.
- getCachedRegion(ImageServer<BufferedImage>, RegionRequest) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
- getCachedStroke(double) - Static method in class qupath.lib.gui.viewer.PathObjectPainter
-
Get a
BasicStrokewith the specified thickness. - getCachedThumbnail(ImageServer<BufferedImage>, int, int) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
- getCachedTile(ImageServer<BufferedImage>, RegionRequest) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
- getCachedTilesForServer(ImageServer<BufferedImage>) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
-
Get a map of all cached tiles pertaining to a specific ImageServer.
- getCaretPosition() - Method in interface qupath.lib.gui.scripting.EditableText
-
Get the current caret position.
- getCaretPosition() - Method in class qupath.lib.gui.scripting.TextAreaControl
-
Gets the value of the
caretPositionproperty. - getCenterPixelX() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the x-coordinate of the pixel currently centered in the viewer, in the full size image space.
- getCenterPixelY() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the y-coordinate of the pixel currently centered in the viewer, in the full size image space.
- getChannel() - Method in class qupath.lib.display.DirectServerChannelInfo
-
Get the channel number.
- getChannels() - Method in class qupath.lib.display.AdditiveChannelInfo
-
Get an unmodifiable list of the channels that are merged here for display.
- getChannels() - Method in class qupath.lib.display.settings.ImageDisplaySettings
-
Get all the available channels.
- getChartDataAsString(XYChart<Number, Number>) - Static method in class qupath.lib.gui.charts.ChartTools
-
Get a string representation of chart data, in such a way that it could be pasted into a spreadsheet.
- getChooser(Window) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Get a
QuPathChooserinstance linked to a specific window. - getCitationUrl() - Static method in class qupath.lib.gui.Urls
-
Get a URL pointing to a page that explains how to cite this version of QuPath in a publication.
- getClipboardText(boolean) - Static method in class qupath.lib.gui.scripting.DefaultScriptEditor
-
Get the text from the system clipboard, optionally escaping characters.
- getColor() - Method in class qupath.lib.display.AdditiveChannelInfo
- getColor() - Method in interface qupath.lib.display.ChannelDisplayInfo
-
Predominate color used when this ChannelDisplayInfo uses a Color LUT (e.g.
- getColor() - Method in class qupath.lib.display.DirectServerChannelInfo
- getColor() - Method in class qupath.lib.display.settings.ChannelSettings
-
Get the color used to display the channel, or null if a color is not relevant.
- getColorForObject(PathObject) - Method in class qupath.lib.gui.tools.MeasurementMapper
-
Get the display color for a specified object, according to the settings of this mapper.
- getColorMap() - Method in class qupath.lib.gui.ColorMapCanvas
-
Return the currently displayed
ColorMaps.ColorMap. - getColorMapper() - Method in class qupath.lib.gui.tools.MeasurementMapper
-
Get the color mapper, which is effectively a lookup table.
- getColormapsDirectoryPath() - Method in class qupath.lib.gui.UserDirectoryManager
-
Get the path to where colormaps should be written.
- getColorModel() - Method in class qupath.lib.gui.images.stores.ColorModelRenderer
-
Get the
ColorModelfor this renderer (may be null). - getColorModel() - Method in class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
- getColorModel(ChannelDisplayMode) - Method in class qupath.lib.display.DirectServerChannelInfo
- getColorScheme() - Method in interface qupath.lib.gui.prefs.QuPathStyleManager.StyleOption
-
Get the color scheme.
- getColorWithOpacity(Color, double) - Static method in class qupath.lib.gui.tools.ColorToolsFX
-
Derived a Color from an existing one, setting the alpha component to match the desired opacity.
- getColorWithOpacityFX(Integer, double) - Static method in class qupath.lib.gui.tools.ColorToolsFX
-
Get a Color from a packed RGB value, setting the alpha component to match the desired opacity.
- getCommandPath() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry
-
Get a string representation of the menu path for this command, including the menu path and the text.
- getCommonActions() - Method in class qupath.lib.gui.QuPathGUI
-
Get the common actions associated with this QuPath instance.
- getCompletions(String, int) - Method in class qupath.lib.gui.scripting.completors.DefaultAutoCompletor
- getConfigPath() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Try to get the path to the config file.
- getContents(Parent, Collection<Node>, boolean) - Static method in class qupath.lib.gui.tools.PaneTools
-
Deprecated.Get the nodes that are included within a
Parent, optionally adding other nodes recursively. - getContentsOfType(Parent, Class<T>, boolean) - Static method in class qupath.lib.gui.tools.PaneTools
-
Deprecated.Get the nodes of type T that are contained within a
Parent, optionally adding other nodes recursively. - getContextMenu() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
-
Get the context menu for the control.
- getContextMenu() - Method in class qupath.lib.gui.scripting.TextAreaControl
- getCoreClasses() - Static method in class qupath.lib.gui.scripting.QPEx
-
Get a list of core classes that are likely to be useful for scripting.
- getCount() - Method in class qupath.lib.gui.actions.InfoMessage
-
Counts associated with the message, or -1 if the count is null.
- getCountsTransform() - Method in class qupath.lib.gui.charts.HistogramChart
-
Get the current counts transform.
- getCssStylesPath() - Method in class qupath.lib.gui.UserDirectoryManager
-
Get the path to where user directory for storing CSS styles.
- getCurrentConsoleControl() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
- getCurrentEditorControl() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
- getCurrentImages(QuPathGUI) - Static method in class qupath.lib.gui.dialogs.ProjectDialogs
-
Get the
ProjectImageEntryfor each of the current images open in QuPath, if available. - getCurrentLanguage() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
-
Gets the value of the
currentLanguageproperty. - getCurrentParent() - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
- getCurrentParent() - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
- getCurrentROI() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the current ROI, i.e.
- getCurrentScriptTab() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
- getCurrentSyntax() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
-
Gets the value of the
currentSyntaxproperty. - getCurrentText() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
- getCurrentViewer() - Static method in class qupath.lib.gui.scripting.QPEx
-
Get the active viewer in the current QuPath instance.
- getCursor() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the current cursor for this viewer
- getCustomOverlayLayers() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get direct access to the custom overlay list.
- getCustomPixelLayerOverlay() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the custom pixel layer overlay, or null if it has not be set.
- getDataMaxValue() - Method in class qupath.lib.gui.tools.MeasurementMapper
-
Get the maximum measurement value from the objects passed to the constructor of this mapper.
- getDataMinValue() - Method in class qupath.lib.gui.tools.MeasurementMapper
-
Get the minimum measurement value from the objects passed to the constructor of this mapper.
- getDefaultAutoCompletor(String) - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
-
Default method to get a suitable auto completor for the given language name.
- getDefaultDragDropListener() - Method in class qupath.lib.gui.QuPathGUI
-
Get a reference to the default drag & drop listener, so this may be added to additional windows if needed.
- getDefaultLocationString(ImageServer<BufferedImage>, double, double, int, int) - Static method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
-
Default method for getting a location string from an
ImageServerusing cached tiles. - getDefaultQuPathUserDirectory() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Get the default location for extensions.
- getDefaultScriptName() - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
- getDefaultWindowTitle() - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
- getDefaultWindowTitle() - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
- getDefaultWindowTitle() - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
- getDefaultZoomFactor() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
The amount by which the downsample factor is scaled for one increment of
QuPathViewer.zoomIn()orQuPathViewer.zoomOut(). - getDescription() - Method in interface qupath.lib.gui.extensions.QuPathExtension
-
A short description of the extension for displaying in the main GUI.
- getDescription() - Method in interface qupath.lib.gui.prefs.QuPathStyleManager.StyleOption
-
Get a user-friendly description of the style.
- getDetectionDisplayMode() - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Get the current
OverlayOptions.DetectionDisplayMode. - getDisplayedClipShape(Shape) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Transform a clip shape into image coordinates for this viewer.
- getDisplayedColor(PathObject) - Static method in class qupath.lib.gui.tools.ColorToolsFX
-
Get a Color appropriate for displaying an object.
- getDisplayedColorARGB(PathObject) - Static method in class qupath.lib.gui.tools.ColorToolsFX
-
Get the color with which an object should be displayed, as a packaged ARGB integer.
- getDisplayedImageName(ImageData<BufferedImage>) - Method in class qupath.lib.gui.QuPathGUI
-
Get the image name to display for a specified image.
- getDisplayedRegionShape() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get a shape corresponding to the region of the image currently visible in this viewer.
- getDisplayMaxValue() - Method in class qupath.lib.gui.tools.MeasurementMapper
-
Get the measurement value that maps to the last color in the color mapper.
- getDisplayMinValue() - Method in class qupath.lib.gui.tools.MeasurementMapper
-
Get the measurement value that maps to the first color in the color mapper.
- getDisplayMode() - Method in class qupath.lib.gui.charts.HistogramChart
-
Get the histogram display mode.
- getDocsUrl() - Static method in class qupath.lib.gui.Urls
-
Get the base URL for the QuPath documentation (independent of version).
- getDoubleValues(String) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
- getDoubleValues(String) - Method in interface qupath.lib.gui.measure.PathTableData
-
Get all double values for all items.
- getDownsample() - Method in class qupath.lib.gui.commands.MiniViewers.MiniViewerManager
-
Get the downsample used within the mini viewers.
- getDownsampleFactor() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the current downsample factor.
- getEngineByName(String) - Static method in class qupath.lib.gui.scripting.languages.ScriptLanguageProvider
-
Get the
ScriptEnginebased on its name. - getExcludeColumns() - Method in class qupath.lib.gui.tools.MeasurementExporter
-
Returns the list of columns to exclude from export.
- getExcludeOutsideRange() - Method in class qupath.lib.gui.tools.MeasurementMapper
-
Returns true if objects with values outside the specified min/max range have the min/max colors returned, false if null should be returned instead.
- getExpandToWindow() - Method in class qupath.lib.gui.panes.SimpleImageViewer
-
Query whether the image is allowed to expand beyond its preferred width and height to fill the window.
- getExtensionCatalogManager() - Static method in class qupath.lib.gui.QuPathGUI
- getExtensionsDocsUrl() - Static method in class qupath.lib.gui.Urls
-
Get a URL pointing to a page that explains how to install QuPath extensions.
- getExtensionsPath() - Method in class qupath.lib.gui.UserDirectoryManager
-
Get the path to where extensions should be stored.
- getEyeFixatedIfRequired() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
- getEyePointIfRequired() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
- getFile() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return the file associated with this
ViewTracker. - getFill() - Method in class qupath.lib.gui.charts.HistogramChart.HistogramData
-
Get the histogram fill color.
- getFillAnnotations() - Method in class qupath.lib.gui.viewer.OverlayOptions
- getFillDetections() - Method in class qupath.lib.gui.viewer.OverlayOptions
- getFlattenedMenuItems(boolean, MenuItem...) - Static method in class qupath.lib.gui.tools.MenuTools
-
Get a flattened list of all menu items recursively.
- getFlattenedMenuItems(List<? extends MenuItem>, boolean) - Static method in class qupath.lib.gui.tools.MenuTools
-
Get a flattened list of all menu items recursively.
- getFontSize() - Method in enum class qupath.lib.gui.prefs.PathPrefs.FontSize
-
Get the font size as a CSS-compatible string.
- getFontSize() - Method in class qupath.lib.gui.viewer.OverlayOptions
- getFrame(int) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return the frame at the specified
index. - getFrameForTime(long) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return the frame visible at the specified
timestamp(in ms). - getFrameIndexForTime(long) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return the index of the frame visible at the specified
timestamp(in ms). - getFrames() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return an unmodifiable list of all the frames stored by this view tracker.
- getFullLocationString(boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get a string to summarize the pixel found below the most recent known mouse location, or "" if the mouse is outside this viewer.
- getFullMagnification() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the full magnification for the image.
- getGamma() - Method in class qupath.lib.display.settings.ImageDisplaySettings
-
Get the requested vamma value for the viewer.
- getGamma() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the gamma value used for this viewer.
- getGammaOp() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get a
LookupOpthat can perform any requested gamma correction in this viewer. - getGeoJsonDataFormat() - Static method in class qupath.lib.gui.commands.InteractiveObjectImporter
-
Get a
DataFormatsuitable for storing GeoJSON data on a clipboard. - getGeometryFactory() - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
- getGitHubIssuesUrl() - Static method in class qupath.lib.gui.Urls
-
Get a URL pointing to the main GitHub issues page.
- getGitHubRepoUrl() - Static method in class qupath.lib.gui.Urls
-
Get a URL pointing to the main QuPath GitHub repo.
- getGreen() - Method in class qupath.lib.display.settings.ChannelColor
-
Get the green value.
- getGridLines() - Method in class qupath.lib.gui.viewer.OverlayOptions
- getHelpText(String) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
-
Get help text for a measurement if available, or null if no help text is found.
- getHideIfEmpty() - Method in class qupath.lib.gui.charts.HistogramChart
-
Query whether the chart is automatically hidden (visibility set to false) when there is no data.
- getHierarchy() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the object hierarchy for the current image data, or null if no image data is available.
- getHistogram() - Method in class qupath.lib.gui.charts.HistogramChart.HistogramData
-
Get the histogram.
- getHistogram(ChannelDisplayInfo) - Method in class qupath.lib.display.ImageDisplay
-
Returns a histogram for a channel of the current image.
- getHistogramData() - Method in class qupath.lib.gui.charts.HistogramChart
-
Get all histogram data objects.
- getIcon() - Method in interface qupath.lib.gui.viewer.tools.PathTool
-
Get the icon of the tool.
- getImage() - Method in class qupath.lib.gui.panes.SimpleImageViewer
-
Get the JavaFX image.
- getImageData() - Method in class qupath.lib.display.AdditiveChannelInfo
- getImageData() - Method in class qupath.lib.display.DirectServerChannelInfo
- getImageData() - Method in class qupath.lib.display.ImageDisplay
-
Get the current image data
- getImageData() - Method in class qupath.lib.gui.QuPathGUI
-
Get the value of
QuPathGUI.imageDataProperty(). - getImageData() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the image data currently being displayed within thie viewer.
- getImageDisplay() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the
ImageDisplayobject used to determine how the image is converted to RGB for display. - getImageList() - Method in class qupath.lib.gui.tools.MeasurementExporter
-
Returns the list of images (
ProjectImageEntry). - getImageObjectClassificationString(double, double) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get a string representing the object classification x & y location in the viewer component, or an empty String if no object is found.
- getImagePlane() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the
ImagePlanecurrently being displayed, including z and t positions. - getImageRegionStore() - Method in class qupath.lib.gui.QuPathGUI
-
Return the global
DefaultImageRegionStoreinstance, used to cache and paint image tiles. - getImageRegionStore() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the region store used by this viewer for tile caching and painting.
- getImageServer() - Method in class qupath.lib.display.AdditiveChannelInfo
- getImageServer() - Method in class qupath.lib.display.DirectServerChannelInfo
- getImportStatementGenerator() - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
- getImportStatementGenerator() - Method in class qupath.lib.gui.scripting.languages.GroovyLanguage
- getImportStatements(Collection<Class<?>>) - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
-
Get the import statements as a String, to add at the beginning of the executed script.
- getImportStatments(Collection<Class<?>>) - Method in interface qupath.lib.gui.scripting.languages.DefaultScriptLanguage.ImportStatementGenerator
- getIncludeColumns() - Method in class qupath.lib.gui.tools.MeasurementExporter
-
Returns the list of columns to include in the export.
- getInfoMessage() - Method in class qupath.lib.gui.commands.ContextHelpViewer
-
Get a message that may be used to create a badge indicating that info or warning messages are available.
- getInfoMessage() - Method in class qupath.lib.gui.commands.LogViewerCommand
-
Get a string expression to draw attention to error messages.
- getInstallationUrl() - Static method in class qupath.lib.gui.Urls
-
Get a URL pointing to a page that explains how to install this version of QuPath.
- getInstance() - Static method in class qupath.lib.gui.BuildInfo
-
Get the shared
BuildInfoinstance. - getInstance() - Static method in class qupath.lib.gui.QuPathGUI
-
Get the static instance of the current QuPath GUI.
- getInstance() - Static method in class qupath.lib.gui.scripting.languages.CssLanguage
-
Get the static instance of this class.
- getInstance() - Static method in class qupath.lib.gui.scripting.languages.GroovyLanguage
-
Get the static instance of this class, using the default code completions.
- getInstance() - Static method in class qupath.lib.gui.scripting.languages.ImageJMacroLanguage
-
Get the static instance of this class.
- getInstance() - Static method in class qupath.lib.gui.scripting.languages.JsonLanguage
-
Get the static instance of this class.
- getInstance() - Static method in class qupath.lib.gui.scripting.languages.MarkdownLanguage
-
Get the static instance of this class.
- getInstance() - Static method in class qupath.lib.gui.scripting.languages.PlainLanguage
-
Get the static instance of this class.
- getInstance() - Static method in class qupath.lib.gui.scripting.languages.PropertiesLanguage
-
Get the static instance of this class.
- getInstance() - Static method in class qupath.lib.gui.scripting.languages.XmlLanguage
-
Get the static instance of this class.
- getInstance() - Static method in class qupath.lib.gui.scripting.languages.YamlLanguage
-
Get the static instance of this class.
- getInstance() - Static method in class qupath.lib.gui.UserDirectoryManager
-
Get the singleton instance of the UserDirectoryManager.
- getInstance(QuPathGUI) - Static method in class qupath.lib.gui.commands.ContextHelpViewer
-
Get the single
ContextHelpViewerinstance associated with a specific QuPath instance. - getInstance(QuPathGUI) - Static method in class qupath.lib.gui.WelcomeStage
- getInstanceWithCompletions(Collection<? extends AutoCompletions.Completion>) - Static method in class qupath.lib.gui.scripting.languages.GroovyLanguage
-
Get an instead of this class that uses the specified code completions, rather than the defaults.
- getInterpolation() - Method in class qupath.lib.gui.viewer.overlays.AbstractImageOverlay
-
Get the preferred method of interpolation to use for display.
- getItem() - Method in class qupath.lib.gui.SelectableItem
-
Get the current item.
- getItems() - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
- getItems() - Method in interface qupath.lib.gui.measure.PathTableData
-
Get internal list of the items used to provide measurements.
- getJavadocViewer() - Method in class qupath.lib.gui.JavadocViewerRunner
-
Get a reference to the viewer launched by the
JavadocViewerCommand. - getLanguage() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
-
Get any language stored for text to be displayed by this control.
- getLanguageFromExtension(String) - Static method in class qupath.lib.gui.scripting.languages.ScriptLanguageProvider
-
Return the first
ScriptLanguagecompatible with the specified extension (can be runnable or not). - getLanguageFromName(String) - Static method in class qupath.lib.gui.scripting.languages.ScriptLanguageProvider
-
Given a file name, determine the associated language - or null if no suitable (supported) language can be found.
- getLanguageNames() - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
-
Get a set of the scripting languages supported by this syntax.
- getLastChangeTimestamp() - Method in class qupath.lib.display.ImageDisplay
-
Get the event count, which is here used as an alternative to a timestamp.
- getLastChangeTimestamp() - Method in class qupath.lib.gui.images.stores.ColorModelRenderer
- getLastChangeTimestamp() - Method in interface qupath.lib.gui.images.stores.ImageRenderer
-
Timestamp of the last change.
- getLastTime() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return the time associated with the last recorded frame.
- getLatestCommit() - Method in class qupath.lib.gui.BuildInfo
-
Get reference to the latest git commit, if known, or null if this has not be preserved.
- getLineCommentString() - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
-
Get the String that represents the start of a comment line.
- getLineWidth() - Method in class qupath.lib.gui.charts.ChartThresholdPane
-
Get the threshold line width.
- getLivePrediction() - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
-
Query whether live prediction is turned on.
- getLocalizationDirectoryPath() - Method in class qupath.lib.gui.UserDirectoryManager
-
Get the path to where localization property files should be written.
- getLocalizedResourceManager() - Static method in class qupath.lib.gui.localization.QuPathResources
-
Get a localized resource manager, which can be used to manage localized strings, and update these whenever the locale preferences are updated.
- getLocationString(ImageData<BufferedImage>, double, double, int, int) - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay
- getLocationString(ImageData<BufferedImage>, double, double, int, int) - Method in interface qupath.lib.gui.viewer.overlays.AbstractOverlay.LocationStringFunction
- getLocationString(ImageData<BufferedImage>, double, double, int, int) - Method in interface qupath.lib.gui.viewer.overlays.PathOverlay
-
Get a location string to display when showing a specified image.
- getLocationString(ImageData<BufferedImage>, double, double, int, int) - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
- getLocationStringFunction() - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay
- getLogDirectoryPath() - Method in class qupath.lib.gui.UserDirectoryManager
-
Get the path to where log files should be written.
- getLogMessageCounts() - Method in class qupath.lib.gui.commands.LogViewerCommand
-
Get the counts of all messages logged by the log viewer.
- getLogViewerCommand() - Method in class qupath.lib.gui.QuPathGUI
-
Get the log viewer associated with this QuPath instance.
- getLongText() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry
-
Get the long text (description) for the command, if available.
- getMagnification() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the magnification for the image within this viewer, or Double.NaN if no image is present.
- getMagnificationString(QuPathViewer) - Static method in class qupath.lib.gui.tools.GuiTools
-
Get an appropriate String to represent the magnification of the image currently in the viewer.
- getMaxAllowed() - Method in class qupath.lib.display.AdditiveChannelInfo
- getMaxAllowed() - Method in class qupath.lib.display.DirectServerChannelInfo
- getMaxAllowed() - Method in interface qupath.lib.display.ChannelDisplayInfo
-
Get the max allowed display value.
- getMaxDisplay() - Method in class qupath.lib.display.AdditiveChannelInfo
- getMaxDisplay() - Method in class qupath.lib.display.DirectServerChannelInfo
- getMaxDisplay() - Method in interface qupath.lib.display.ChannelDisplayInfo
-
Get the max display value.
- getMaxDisplay() - Method in class qupath.lib.display.settings.ChannelSettings
-
Get the requested maximum display value for the channel, This should be used with the last entry in any lookup table.
- getMaxDownsample() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the maximum downsample value supported by this viewer.
- getMaxPoints() - Method in class qupath.lib.gui.charts.PathObjectScatterChart
-
Get the value of
PathObjectScatterChart.maxPointsProperty() - getMaxROIHandleSize() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the maximum size for which ROI handles may be drawn.
- getMaxThreads() - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
-
Get the maximum number of threads that may be used during live prediction.
- getMeasurementMapper() - Method in class qupath.lib.gui.viewer.OverlayOptions
- getMeasurementNames() - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
- getMeasurementNames() - Method in interface qupath.lib.gui.measure.PathTableData
-
Get the names of all numeric measurements.
- getMenu(String, boolean) - Method in class qupath.lib.gui.QuPathGUI
-
Get a reference to an existing menu from the main QuPath menubar, optionally creating a new menu if it is not present.
- getMenu(List<Menu>, String, boolean) - Static method in class qupath.lib.gui.tools.MenuTools
-
Get a reference to an existing menu, optionally creating a new menu if it is not present.
- getMenuBar() - Method in class qupath.lib.gui.QuPathGUI
-
Get the menubar for the main QuPath application.
- getMenuItem() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry
-
Get the menu item corresponding to this command.
- getMenuPath() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry
-
Get a String representation of the menu containing this command.
- getMessageType() - Method in class qupath.lib.gui.actions.InfoMessage
-
Type of the message.
- getMetadataNames() - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
-
Get the names of all columns corresponding to metadata (String) values.
- getMethod() - Method in interface qupath.lib.display.ChannelDisplayInfo
-
Get the
ColorTransformer.ColorTransformMethodassociated with this channel, or null if no method is relevant. - getMinAllowed() - Method in class qupath.lib.display.AdditiveChannelInfo
- getMinAllowed() - Method in class qupath.lib.display.DirectServerChannelInfo
- getMinAllowed() - Method in interface qupath.lib.display.ChannelDisplayInfo
-
Get the min allowed display value.
- getMinDisplay() - Method in class qupath.lib.display.AdditiveChannelInfo
- getMinDisplay() - Method in class qupath.lib.display.DirectServerChannelInfo
- getMinDisplay() - Method in interface qupath.lib.display.ChannelDisplayInfo
-
Get the min display value.
- getMinDisplay() - Method in class qupath.lib.display.settings.ChannelSettings
-
Get the requested minimum display value for the channel.
- getMinDownsample() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the minimum downsample value supported by this viewer.
- getModel() - Method in class qupath.lib.gui.charts.ScatterPlotDisplay
-
Get the value of
ScatterPlotDisplay.modelProperty(). - getMousePointIfRequired() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
- getMousePosition() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the current cursor position within this viewer, or null if the cursor is outside the viewer.
- getName() - Method in class qupath.lib.display.AdditiveChannelInfo
- getName() - Method in interface qupath.lib.display.ChannelDisplayInfo
-
Get the channel name.
- getName() - Method in class qupath.lib.display.DirectServerChannelInfo
- getName() - Method in class qupath.lib.display.settings.ChannelSettings
-
Get the name of the channel.
- getName() - Method in class qupath.lib.display.settings.ImageDisplaySettings
-
Get the name of the settings.
- getName() - Method in class qupath.lib.gui.actions.menus.AnalyzeMenuActions
- getName() - Method in class qupath.lib.gui.actions.menus.AutomateMenuActions
- getName() - Method in class qupath.lib.gui.actions.menus.ClassifyMenuActions
- getName() - Method in class qupath.lib.gui.actions.menus.EditMenuActions
- getName() - Method in class qupath.lib.gui.actions.menus.ExtensionsMenuActions
- getName() - Method in class qupath.lib.gui.actions.menus.FileMenuActions
- getName() - Method in class qupath.lib.gui.actions.menus.HelpMenuActions
- getName() - Method in class qupath.lib.gui.actions.menus.MeasureMenuActions
- getName() - Method in interface qupath.lib.gui.actions.menus.MenuActions
-
Get the name of the menu.
- getName() - Method in class qupath.lib.gui.actions.menus.ObjectsMenuActions
- getName() - Method in class qupath.lib.gui.actions.menus.TMAMenuActions
- getName() - Method in class qupath.lib.gui.actions.menus.ViewMenuActions
- getName() - Method in class qupath.lib.gui.actions.menus.WindowMenuActions
- getName() - Method in class qupath.lib.gui.extensions.GitHubProject.GitHubRepo
-
Get the name.
- getName() - Method in interface qupath.lib.gui.extensions.QuPathExtension
-
A readable name for the extension.
- getName() - Method in class qupath.lib.gui.extensions.UpdateChecker.ReleaseVersion
-
Get the release name (any text).
- getName() - Method in class qupath.lib.gui.panes.SimpleImageViewer
-
Get the name of the image.
- getName() - Method in interface qupath.lib.gui.prefs.QuPathStyleManager.StyleOption
-
Get a user-friendly name for the style.
- getName() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return the name of this
ViewTracker. - getName() - Method in interface qupath.lib.gui.viewer.tools.PathTool
-
Get the name of the tool
- getNavigationAccelerationProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Get whether to apply the navigation acceleration (& deceleration) effects or not.
- getNewConsole() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
- getNewEditor() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
- getNode() - Method in interface qupath.lib.gui.tools.PathObjectImageViewers.ItemViewer
-
Get the node to display
- getNode() - Method in class qupath.lib.gui.tools.PathObjectLabels.PathObjectMiniPane
-
Get the node to display.
- getNumBins() - Method in class qupath.lib.gui.charts.HistogramDisplay
-
Get the requested number of bins used for the histogram.
- getNumericValue(PathObject, String) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
- getNumericValue(T, String) - Method in interface qupath.lib.gui.measure.PathTableData
-
Get the numeric value from an item for the specific measurement.
- getObjectClassificationString(double, double) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get a string representing the object classification x & y location in the viewer component, or an empty String if no object is found.
- getOpacity() - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Get the global opacity for overlay drawing.
- getOpacity() - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay
-
Get opacity, between 0 (completely transparent) and 1 (completely opaque).
- getOriginalChannelName() - Method in class qupath.lib.display.DirectServerChannelInfo
-
Get the original channel name, extracted for the current ImageData if available.
- getOriginalMetadata() - Method in class qupath.lib.gui.images.servers.ChannelDisplayTransformServer
- getOriginalMetadata() - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer
- getOriginalMetadata() - Method in class qupath.lib.gui.images.servers.RenderedImageServer
- getOverlayActions() - Method in class qupath.lib.gui.QuPathGUI
-
Get the actions associated with the viewer overlay options.
- getOverlayLayers() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get an unmodifiable list containing the overlay layers, in order.
- getOverlayOptions() - Method in class qupath.lib.gui.actions.OverlayActions
-
Get the overlay options controlled by these actions.
- getOverlayOptions() - Method in class qupath.lib.gui.QuPathGUI
-
Return the global
OverlayOptionsinstance, used to control display within viewers by default. - getOverlayOptions() - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay
-
Get the overlay options, which may influence the display of this overlay.
- getOverlayOptions() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the overlay options that control the viewer display.
- getOverlayOptions() - Method in class qupath.lib.gui.viewer.ViewerManager
-
Get the overlay options shared by all viewers created by this manager.
- getOverrideSystemMenuBar() - Static method in class qupath.lib.gui.prefs.SystemMenuBar
-
Get the current value of the override property, which specifies whether the system menubar should not be used by any window - no matter what the value of
SystemMenuBar.systemMenubarProperty(). - getOwner() - Method in class qupath.lib.gui.extensions.GitHubProject.GitHubRepo
-
Get the owner.
- getPane() - Method in class qupath.lib.gui.charts.HistogramDisplay
-
Get the pane containing the histogram and associated UI components, for addition to a scene.
- getPane() - Method in class qupath.lib.gui.charts.ScatterPlotDisplay
-
Get the pane containing the scatter plot and associated UI components, for addition to a scene.
- getPane() - Method in class qupath.lib.gui.commands.MiniViewers.MiniViewerManager
-
Get the pane containing all mini viewers, which can be added to a scene for display.
- getPane() - Method in class qupath.lib.gui.dialogs.ParameterPanelFX
-
Get the
Panethat can be displayed. - getPane() - Method in class qupath.lib.gui.measure.ui.SummaryMeasurementTable
- getPane() - Method in class qupath.lib.gui.panes.AnnotationPane
-
Get the pane for display.
- getPane() - Method in class qupath.lib.gui.panes.ImageDetailsPane
-
Get the
Panecomponent for addition to a scene. - getPane() - Method in class qupath.lib.gui.panes.MeasurementMapPane
-
Get the pane, which can be added to a scene for display.
- getPane() - Method in class qupath.lib.gui.panes.PathObjectHierarchyView
-
Get the pane for display.
- getPane() - Method in class qupath.lib.gui.panes.PreferencePane
-
Get a pane to display.
- getPane() - Method in class qupath.lib.gui.panes.ProjectBrowser
-
Get the
Panecomponent for addition to a scene. - getPane() - Method in class qupath.lib.gui.panes.SelectedMeasurementTableView
-
Get the
Panecontaining the table and a filter field. - getPane() - Method in class qupath.lib.gui.panes.WorkflowCommandLogView
-
Get the pane to add to a scene.
- getParameterEnabled(String) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX
-
Returns true if a parameter exists with the given key and is enabled (and is therefore editable).
- getParameterEnabled(Parameter<?>) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX
-
Returns true if a parameter is enabled (and is therefore editable).
- getParameters() - Method in class qupath.lib.gui.dialogs.ParameterPanelFX
-
Get the
ParameterListdisplayed in this panel. - getPathClassColor(PathClass) - Static method in class qupath.lib.gui.tools.ColorToolsFX
-
Get a Color appropriate for displaying a
PathClass. - getPenManager() - Static method in class qupath.lib.gui.viewer.tools.QuPathPenManager
-
Get the current PenInputManager.
- getPixelClassificationRegionFilter() - Method in class qupath.lib.gui.viewer.OverlayOptions
- getPixelClassificationServer(ImageData<BufferedImage>) - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
-
Get the
ImageServerthat would be used by this overlay for the specifiedImageData. - getPixelLayer(ImageData<?>) - Static method in class qupath.lib.gui.measure.ObservableMeasurementTableData
-
Request the pixel layer from an
ImageData. - getPlaceholderText() - Method in class qupath.lib.gui.panes.SimpleImageViewer
-
Get the placeholder text to show if no image is available.
- getPointOpacity() - Method in class qupath.lib.gui.charts.PathObjectScatterChart
-
Get the value o
PathObjectScatterChart.pointOpacityProperty() - getPointRadius() - Method in class qupath.lib.gui.charts.PathObjectScatterChart
-
Get the value of
PathObjectScatterChart.pointOpacityProperty() - getPredicateTextField() - Method in class qupath.lib.gui.panes.SelectedMeasurementTableView
-
Get the predict text field that is used to filter measurements.
- getPreferencePane() - Method in class qupath.lib.gui.QuPathGUI
-
Get a reference to the
PreferencePane. - getPreferredOverlayColor() - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay
-
Return the preferred overlay color.
- getPressure() - Method in interface qupath.lib.gui.viewer.tools.QuPathPenManager.PenInputManager
-
Returns a pressure value, between 0 and 1.
- getPreviousSelectedTool() - Method in class qupath.lib.gui.ToolManager
-
Get the value of
ToolManager.selectedToolProperty(). - getProject() - Method in class qupath.lib.gui.QuPathGUI
-
Get the value of
QuPathGUI.projectProperty(). - getProjection() - Method in class qupath.lib.gui.viewer.overlays.ZProjectOverlay
-
Gets the value of the
projectionproperty. - getPropertySheet() - Method in class qupath.lib.gui.panes.PreferencePane
-
Get the property sheet for this
PreferencePane. - getQuPath() - Method in class qupath.lib.gui.actions.CommonActions
-
Get the QuPath instance associated with these actions.
- getQuPath() - Static method in class qupath.lib.gui.scripting.QPEx
-
Get the current QuPath instance.
- getQuPathVersion() - Method in interface qupath.lib.gui.extensions.QuPathExtension
-
Get a QuPath version for which this extension was written.
- getRecentProjectList() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Get a list of the most recent projects that were opened.
- getRecentScriptsList() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Get a list of the most recent scripts that were opened.
- getRed() - Method in class qupath.lib.display.settings.ChannelColor
-
Get the red value.
- getRegion() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
-
Get the region representing this control, so it may be added to a scene.
- getRegion() - Method in class qupath.lib.gui.scripting.TextAreaControl
- getRegion() - Method in class qupath.lib.gui.viewer.ViewerManager
-
Get the region node that can be added to a scene graph to display the viewers.
- getRegionMap() - Method in class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
-
Get an unmodifiable
Mapcontaining image regions to paint on this overlay. - getRelativePathOrNull(String) - Method in class qupath.lib.gui.UserDirectoryManager
- getRenderer() - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
-
Get the
ImageRendererused with this overlay, which may be null. - getRenderer() - Method in class qupath.lib.gui.viewer.overlays.ZProjectOverlay
-
Get the
ImageRendererused with this overlay, which may be null. - getRenderer() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Request a renderer that converts image tiles into RGB images.
- getRepo() - Method in class qupath.lib.gui.extensions.GitHubProject.GitHubRepo
-
Get the repo.
- getRepository() - Method in interface qupath.lib.gui.extensions.GitHubProject
-
Get the GitHub repository associated with the project.
- getRequestedCursor() - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
- getResourcesForProject(Project<?>) - Static method in class qupath.lib.display.settings.DisplaySettingUtils
-
Get the resource manager for image display settings from a project.
- getRGB(float, ChannelDisplayMode) - Method in class qupath.lib.display.DirectServerChannelInfo
-
Get a suitable RGB value for displaying a pixel with the specified value
- getRGB(BufferedImage, int[], ChannelDisplayMode) - Method in class qupath.lib.display.DirectServerChannelInfo
- getRGB(BufferedImage, int[], ChannelDisplayMode) - Method in class qupath.lib.display.AdditiveChannelInfo
- getRGB(BufferedImage, int[], ChannelDisplayMode) - Method in interface qupath.lib.display.ChannelDisplayInfo
-
Get the RGB values that would be used to display all the pixels of an image
- getRGB(BufferedImage, int, int, ChannelDisplayMode) - Method in class qupath.lib.display.DirectServerChannelInfo
- getRGB(BufferedImage, int, int, ChannelDisplayMode) - Method in class qupath.lib.display.AdditiveChannelInfo
- getRGB(BufferedImage, int, int, ChannelDisplayMode) - Method in interface qupath.lib.display.ChannelDisplayInfo
-
Get the RGB value that would be used to display a particular pixel
- getRGB(Color) - Static method in class qupath.lib.gui.tools.ColorToolsFX
-
Get a packed int (ARGB) representation of a Color object, omitting the alpha component.
- getRGBThumbnail() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get a thumbnail representing the image as displayed by this viewer.
- getRngSeed() - Method in class qupath.lib.gui.charts.PathObjectScatterChart
-
Get the value of
PathObjectScatterChart.rngSeedProperty(). - getROIEditor() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the
RoiEditorused by this viewer. - getRootLogLevel() - Static method in class qupath.lib.gui.logging.LogManager
-
Set the root log level, as set by this manager.
- getRotation() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the current rotation; angle in radians.
- getRowStrings() - Method in interface qupath.lib.gui.measure.PathTableData
-
Get a list of Strings representing table data for all items.
- getRowStrings(String, int, Predicate<String>) - Method in interface qupath.lib.gui.measure.PathTableData
-
Get a list of Strings representing table data for all items.
- getRowStrings(Collection<? extends T>, String, int, Predicate<String>) - Method in interface qupath.lib.gui.measure.PathTableData
-
Get a list of Strings representing table data for specific items.
- getSaturationPercent() - Method in class qupath.lib.gui.panes.SimpleImageViewer
-
Get the percentage of pixels to use when applying auto contrast settings to a non-8-bit image.
- getScaledNavigationSpeed() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Get navigation speed scaled as a proportion and forced to be in the range 0-1.
- getScaledRGBInstance(BufferedImage, int, int) - Static method in class qupath.lib.gui.tools.GuiTools
-
Get a scaled (RGB or ARGB) image, achieving reasonable quality even when scaling down by a considerably amount.
- getScaledScrollSpeed() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Get scroll speed scaled as a proportion and forced to be in the range 0-1.
- getScriptEditor() - Method in class qupath.lib.gui.QuPathGUI
-
Get a reference to the current
ScriptEditor(which may or may not be open at the moment). - getScriptsDirectoryPath() - Method in class qupath.lib.gui.UserDirectoryManager
-
Get the path to where shared script files should be written.
- getSelectedClassVisibilityMode() - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Get the value of
OverlayOptions.selectedClassVisibilityModeProperty(). - getSelectedObject() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the currently-selected object from the hierarchy.
- getSelectedText() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
- getSelectedText() - Method in interface qupath.lib.gui.scripting.EditableText
-
Get the selected text as a string.
- getSelectedText() - Method in class qupath.lib.gui.scripting.TextAreaControl
-
Gets the value of the
selectedTextproperty. - getSelectedTool() - Method in class qupath.lib.gui.ToolManager
-
Get the value of
ToolManager.selectedToolProperty(). - getSelection() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
-
Get the range of the currently-selected text.
- getSelection() - Method in class qupath.lib.gui.scripting.TextAreaControl
- getSelectionEnd() - Method in interface qupath.lib.gui.scripting.EditableText
-
Get the ending position for any selection (exclusive).
- getSelectionEnd() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
- getSelectionLength() - Method in interface qupath.lib.gui.scripting.EditableText
-
Get the selection length, or 0 if there is no selection.
- getSelectionModeAction() - Method in class qupath.lib.gui.ToolManager
-
Return the action associated with 'selection mode'.
- getSelectionModel() - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane
-
Get the selection model for the channels.
- getSelectionStart() - Method in interface qupath.lib.gui.scripting.EditableText
-
Get the starting position for any selection (inclusive).
- getSelectionStart() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
- getSeparator() - Method in class qupath.lib.gui.tools.MeasurementExporter
-
Returns the separator used in between measurements.
- getSerializationExtension() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
File extension used for serialization of ImageData (without the dot)
- getServer() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the
ImageServerfor the current image displayed within the viewer, or null if no image is displayed. - getServerBounds() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get an
ImageRegionrepresenting the full width and height of the current image. - getServerHeight() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the height in pixels of the full resolution of the current image, or 0 if no image is currently open.
- getServerType() - Method in class qupath.lib.gui.images.servers.ChannelDisplayTransformServer
- getServerType() - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer
- getServerType() - Method in class qupath.lib.gui.images.servers.RenderedImageServer
- getServerWidth() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the width in pixels of the full resolution of the current image, or 0 if no image is currently open.
- getShapeForDownsample(ROI, double) - Static method in class qupath.lib.gui.viewer.DownsampledShapeCache
-
Get the shape for a particular downsample.
- getSharedInstance() - Static method in class qupath.lib.gui.viewer.OverlayOptions
-
Get a shared OverlayOptions instance that makes some properties persistent.
- getSharedInstance() - Static method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
-
Get a shared instance with persistence properties.
- getShowAllRGBTransforms() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Request that all available color transforms are shown for RGB images.
- getShowAnnotations() - Method in class qupath.lib.gui.viewer.OverlayOptions
- getShowCellBoundaries() - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Query the current
OverlayOptions.DetectionDisplayModeto see if cell boundary ROIs should be drawn. - getShowCellNuclei() - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Query the current
OverlayOptions.DetectionDisplayModeto see if nuclei ROIs should be drawn. - getShowConnections() - Method in class qupath.lib.gui.viewer.OverlayOptions
- getShowDetections() - Method in class qupath.lib.gui.viewer.OverlayOptions
- getShowGrid() - Method in class qupath.lib.gui.viewer.OverlayOptions
- getShowLocation() - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
-
Get the value of
ViewerPlusDisplayOptions.showLocationProperty(). - getShowNames() - Method in class qupath.lib.gui.viewer.OverlayOptions
- getShowObjectPredicate() - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Get the value of
OverlayOptions.showObjectPredicateProperty(). - getShowOverview() - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
-
Get the value of
ViewerPlusDisplayOptions.showOverviewProperty(). - getShowPixelClassification() - Method in class qupath.lib.gui.viewer.OverlayOptions
- getShowScalebar() - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
-
Get the value of
ViewerPlusDisplayOptions.showScalebarProperty(). - getShowTMACoreLabels() - Method in class qupath.lib.gui.viewer.OverlayOptions
- getShowTMAGrid() - Method in class qupath.lib.gui.viewer.OverlayOptions
- getShowZProjectControls() - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
-
Get the value of
ViewerPlusDisplayOptions.showZProjectControlsProperty(). - getSingleThreadExecutor(Object) - Method in class qupath.lib.gui.SharedThreadPoolManager
-
Get a reusable executor using a single thread, creating a new executor if needed.
- getSize() - Method in enum class qupath.lib.gui.commands.PathObjectGridView.GridDisplaySize
- getSkipMissingCoresProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Return whether the viewer skips missing TMA cores when navigating TMA grids with arrow keys.
- getSpaceX() - Method in class qupath.lib.gui.viewer.GridLines
-
Horizontal spacing between lines for any counting grid.
- getSpaceY() - Method in class qupath.lib.gui.viewer.GridLines
-
Vertical spacing between lines for any counting grid.
- getStage() - Method in class qupath.lib.gui.commands.ContextHelpViewer
-
Get the help viewer stage.
- getStage() - Method in class qupath.lib.gui.commands.PathObjectGridView
-
Get the stage used to show the grid view.
- getStage() - Method in class qupath.lib.gui.panes.SimpleImageViewer
-
Get the stage used to display the image.
- getStage() - Method in class qupath.lib.gui.QuPathGUI
-
Get the main QuPath stage.
- getStage() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
-
Get the stage for this script editor.
- getStage() - Method in class qupath.lib.gui.tma.TMASummaryViewer
-
Deprecated.Get the stage for display.
- getStartTime() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return the time associated with the first recorded frame.
- getStartX() - Method in class qupath.lib.gui.viewer.GridLines
-
Starting x coordinate for any counting grid (usually 0).
- getStartY() - Method in class qupath.lib.gui.viewer.GridLines
-
Starting y coordinate for any counting grid (usually 0).
- getStaticImportStatements(Collection<Class<?>>) - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
-
Get the static import statements as a String, to add at the beginning of the executed script.
- getStaticImportStatments(Collection<Class<?>>) - Method in interface qupath.lib.gui.scripting.languages.DefaultScriptLanguage.ImportStatementGenerator
- getString(String) - Static method in class qupath.lib.gui.localization.QuPathResources
-
Get a string from the main
ResourceBundleused for the QuPath user interface. - getString(String, String) - Static method in class qupath.lib.gui.localization.QuPathResources
- getStringValue(PathObject, String) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
- getStringValue(PathObject, String, int) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
- getStringValue(T, String) - Method in interface qupath.lib.gui.measure.PathTableData
-
Get a string representation of the value.
- getStringValue(T, String, int) - Method in interface qupath.lib.gui.measure.PathTableData
-
Get a string value, converting to a fixed number of decimal places if the column is numeric.
- getStroke() - Method in class qupath.lib.gui.charts.HistogramChart.HistogramData
-
Get the histogram stroke color.
- getStyleColorScheme() - Static method in class qupath.lib.gui.prefs.QuPathStyleManager
-
Get the color scheme of the current style, or the system color scheme if no other is available.
- getStyles() - Method in class qupath.lib.gui.panes.PreferencePane.AppearancePreferences
- getStyleSheet() - Static method in class qupath.lib.gui.tools.WebViews
- getSwitchToGrayscaleChannel() - Method in class qupath.lib.display.ImageDisplay
-
Get the value of
ImageDisplay.switchToGrayscaleChannelProperty(). - getSynchronizeViewers() - Method in class qupath.lib.gui.viewer.ViewerManager
-
Gets the value of the
synchronizeViewersproperty. - getSyntaxFromName(String) - Static method in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
-
Get a script syntax from a specified language name.
- getTable() - Method in class qupath.lib.gui.panes.SelectedMeasurementTableView
-
Get the
TableView. - getTableModelString(PathTableData<T>, String, Collection<String>) - Static method in class qupath.lib.gui.measure.ui.SummaryMeasurementTable
-
Get a single String representing the data in a table.
- getTableModelStrings(PathTableData<T>, String, Collection<String>) - Static method in class qupath.lib.gui.measure.ui.SummaryMeasurementTable
-
Get a list of Strings representing table data.
- getTabString() - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
-
String to insert when tab key pressed
- getText() - Method in class qupath.lib.gui.actions.InfoMessage
-
Text of the message.
- getText() - Method in interface qupath.lib.gui.scripting.EditableText
-
Get all the text in the editor;
- getText() - Method in class qupath.lib.gui.scripting.TextAreaControl
-
Gets the value of the
textproperty. - getText() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry
-
Get the name of the command.
- getTextField(Parameter<?>, int, String) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX
- getThickStrokeWidth(double) - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Get the requested stroke thickness to use when drawing ROIs that should be represented with 'thick' lines (annotations, TMA cores).
- getThis() - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
- getThis() - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
- getThis() - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
- getThreadPoolManager() - Method in class qupath.lib.gui.QuPathGUI
-
Get a
SharedThreadPoolManagerto help with submitting tasks in other threads. - getThresholds() - Method in class qupath.lib.gui.charts.ChartThresholdPane
-
Get a list of all thresholds.
- getThumbnail() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get a thumbnail representing the image as displayed by this viewer.
- getThumbnail(ImageServer<BufferedImage>, int, int, boolean) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
- getThumbnailRGB(ImageServer<BufferedImage>) - Static method in class qupath.lib.gui.commands.ProjectCommands
-
Get an RGB thumbnail for an image server, suitable for showing as a project thumbnail.
- getTileCacheSize() - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
-
Get the tile cache size, in bytes.
- getTileRequest(ImageServer<BufferedImage>, double, double, double, int, int) - Static method in class qupath.lib.gui.images.stores.ImageRegionStoreHelpers
-
Given an
ImageServer, determine the boundaries of the image tile that contains specified x, y coordinates. - getTilesToRequest(ImageServer<?>, Shape, double, int, int, List<RegionRequest>) - Static method in class qupath.lib.gui.images.stores.ImageRegionStoreHelpers
-
Given ImageServer, determine the boundaries of the image tiles that would be needed to paint a specified shape (defined by coordinates in the full-resolution image space).
- getTool(String) - Static method in class qupath.lib.gui.viewer.tools.PathTools
-
Return the PathTool corresponding to the specified String.
- getToolAction(PathTool) - Method in class qupath.lib.gui.ToolManager
-
Get the action that corresponds to a specific
PathTool, creating a new action if one does not already exist. - getToolBar() - Method in class qupath.lib.gui.QuPathGUI
-
Get the main toolbar.
- getToolManager() - Method in class qupath.lib.gui.QuPathGUI
-
Get the ToolManager that handles available and selected tools.
- getTools() - Method in class qupath.lib.gui.ToolManager
-
Get a read-only list of all available tools.
- getTPosition() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the currently-visible time point.
- getTransformedValueAsString(BufferedImage, int, int) - Method in class qupath.lib.display.ImageDisplay
-
Get a string representation of a transformed pixel value, using the currently-selected channels.
- getType() - Method in class qupath.lib.gui.tools.MeasurementExporter
-
Returns the type of path objects used in the export.
- getUndoRedoManager() - Method in class qupath.lib.gui.QuPathGUI
-
Get the
UndoRedoManager, which can be useful if needing to clear it in cases where available memory is low. - getUniqueID() - Method in class qupath.lib.gui.images.stores.AbstractImageRenderer
- getUniqueID() - Method in class qupath.lib.gui.images.stores.ColorModelRenderer
- getUniqueID() - Method in interface qupath.lib.gui.images.stores.ImageRenderer
-
Get a unique key, which will be used for caching.
- getUri() - Method in class qupath.lib.gui.extensions.UpdateChecker.ReleaseVersion
-
Get a URI to download the release (may be null if no URI is available).
- getURIs() - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer
- getURIs() - Method in class qupath.lib.gui.images.servers.RenderedImageServer
- getUrlString() - Method in class qupath.lib.gui.extensions.GitHubProject.GitHubRepo
-
Get the URL for the main repo.
- getUseExactSelectedClasses() - Method in class qupath.lib.gui.viewer.OverlayOptions
- getUsefulValue(PathObject, double) - Method in class qupath.lib.gui.tools.MeasurementMapper
- getUserForumUrl() - Static method in class qupath.lib.gui.Urls
-
Get a URL pointing to the main QuPath user forum.
- getUserPath() - Method in class qupath.lib.gui.UserDirectoryManager
-
Get the user path where additional files may be stored.
- getUserPreferences() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Deprecated.since v0.5.0 - avoid direct use of the
Preferencesobject, since this may be invalidated by a call toPathPrefs.resetPreferences() - getValue(BufferedImage, int, int) - Method in class qupath.lib.display.DirectServerChannelInfo
- getValue(BufferedImage, int, int) - Method in interface qupath.lib.display.SingleChannelDisplayInfo
-
Extract the value for a single pixel of an image.
- getValueAsString(BufferedImage, int, int) - Method in class qupath.lib.display.DirectServerChannelInfo
- getValueAsString(BufferedImage, int, int) - Method in class qupath.lib.display.AdditiveChannelInfo
- getValueAsString(BufferedImage, int, int) - Method in interface qupath.lib.display.ChannelDisplayInfo
-
Get a string representation of a pixel's value.
- getValues(BufferedImage, int, int, int, int, float[]) - Method in class qupath.lib.display.DirectServerChannelInfo
- getValues(BufferedImage, int, int, int, int, float[]) - Method in interface qupath.lib.display.SingleChannelDisplayInfo
-
Extract values for a square of pixels from an image.
- getVersion() - Method in class qupath.lib.gui.BuildInfo
-
Get the version, or null if the version is unknown.
- getVersion() - Method in interface qupath.lib.gui.extensions.QuPathExtension
-
Get the version of the current extension.
- getVersion() - Method in class qupath.lib.gui.extensions.UpdateChecker.ReleaseVersion
-
Get the semantic version.
- getVersion() - Static method in class qupath.lib.gui.QuPathGUI
-
Get the current QuPath version.
- getVersionedDocsUrl() - Static method in class qupath.lib.gui.Urls
-
Get the base URL for the QuPath documentation, specifically for this software version.
- getVersionedDocsUrl(String) - Static method in class qupath.lib.gui.Urls
-
Get the base URL for the QuPath documentation for this software version, including a relative component to link to a specific page (without leading slash).
- getView() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the main JavaFX component representing this viewer.
- getViewer() - Method in class qupath.lib.gui.QuPathGUI
-
Get the currently active viewer.
- getViewer() - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
- getViewer() - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
- getViewerActions() - Method in class qupath.lib.gui.QuPathGUI
-
Get the associations associated with QuPath image viewers.
- getViewerManager() - Method in class qupath.lib.gui.actions.ViewerActions
- getViewerManager() - Method in class qupath.lib.gui.QuPathGUI
-
Get the viewer manager, which gives access to all the viewers available within this QuPath instance.
- getWindow(String) - Static method in class qupath.lib.gui.scripting.QPEx
-
Access a window currently open within QuPath by its title.
- getYouTubeUrl() - Static method in class qupath.lib.gui.Urls
-
Get a URL pointing to the QuPath YouTube channel.
- getZoomToFitDownsampleFactor() - Method in class qupath.lib.gui.viewer.QuPathViewer
- getZPosition() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the currently-visible z-slice.
- GITHUB - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- GitHubProject - Interface in qupath.lib.gui.extensions
-
Helper class to represent a project hosted on GitHub.
- GitHubProject.GitHubRepo - Class in qupath.lib.gui.extensions
-
Helper class to represent a GitHub repository.
- graphic(ObservableValue<Node>) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
-
Bind the graphic property of the action to an
ObservableValue, bidirectionally if possible. - graphic(Node) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
-
Set the graphic property of the action.
- GRAYSCALE - Enum constant in enum class qupath.lib.display.ChannelDisplayMode
-
Show using a grayscale LUT (black to white)
- GRID - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- GRID_ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
- GRID_SPACING - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- GRID_SPACING - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- GRID_SPACING - Variable in class qupath.lib.gui.actions.OverlayActions
- GRID_TMA - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
- GridLines - Class in qupath.lib.gui.viewer
-
Simple class used for storing information related to GridLines that may be painted over an image.
- GridLines() - Constructor for class qupath.lib.gui.viewer.GridLines
- gridLinesProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
- GridOverlay - Class in qupath.lib.gui.viewer.overlays
-
An overlay used to show a (counting) grid on top of an image.
- GridOverlay(OverlayOptions) - Constructor for class qupath.lib.gui.viewer.overlays.GridOverlay
-
Constructor.
- gridScaleMicrons - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
- gridScaleMicronsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Define counting grid optionally displayed on any viewer using microns rather than pixel coordinates.
- gridSpacingX - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
- gridSpacingXProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Horizontal spacing between lines for any counting grid.
- gridSpacingY - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
- gridSpacingYProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Vertical spacing between lines for any counting grid.
- gridStartXProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Starting x coordinate for any counting grid (usually 0).
- gridStartYProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Starting y coordinate for any counting grid (usually 0).
- GROOVY - Static variable in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
- GroovyAutoCompletor - Class in qupath.lib.gui.scripting.completors
-
Auto completion support for Groovy.
- GroovyAutoCompletor() - Constructor for class qupath.lib.gui.scripting.completors.GroovyAutoCompletor
-
Constructor using the default code completions for QuPath.
- GroovyAutoCompletor(Collection<? extends AutoCompletions.Completion>) - Constructor for class qupath.lib.gui.scripting.completors.GroovyAutoCompletor
-
Constructor that supports a custom set of completions.
- GroovyLanguage - Class in qupath.lib.gui.scripting.languages
-
Class for the representation of the Groovy programming language in QuPath.
- GuiTools - Class in qupath.lib.gui.tools
-
Assorted static methods to help with JavaFX and QuPath GUI-related tasks.
- GuiTools() - Constructor for class qupath.lib.gui.tools.GuiTools
- GuiTools.SnapshotType - Enum Class in qupath.lib.gui.tools
-
Kinds of snapshot image that can be created for QuPath.
H
- handle(DragEvent) - Method in class qupath.lib.gui.viewer.DragDropImportListener
- handle(MouseEvent) - Method in class qupath.lib.gui.commands.MiniViewers.MiniViewerManager
- handle(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
- handle(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
- handleBackspace(EditableText, boolean) - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
-
Handle a backspace.
- handleDrop(QuPathViewer, List<T>) - Method in interface qupath.lib.gui.viewer.DragDropImportListener.DropHandler
-
Handle drop onto a viewer.
- handleLeftParenthesis(EditableText, boolean) - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
-
Handle left parentheses
(. - handleLineComment(EditableText) - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
-
Handle line comments.
- handleNewLine(EditableText, boolean) - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
-
Handle a new line.
- handleQuotes(EditableText, boolean, boolean) - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
-
Handle single/double quotes.
- handleRightParenthesis(EditableText, boolean) - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
-
Handle right parentheses
). - handleTabPress(EditableText, boolean) - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
-
Handle tab key.
- hasActiveToolTrackingData() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return whether this
ViewTrackertracks the active tool. - hasAlpha() - Method in class qupath.lib.gui.images.servers.RenderedImageServer
- hasBundleForLocale(String, Locale) - Static method in class qupath.lib.gui.localization.QuPathResources
- hasCursorTrackingData() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return whether this
ViewTrackertracks the cursor. - hasDefaultBundleForLocale(Locale) - Static method in class qupath.lib.gui.localization.QuPathResources
- hasEyeTrackingData() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return whether this
ViewTrackertracks the eye. - hashCode() - Method in class qupath.lib.gui.extensions.GitHubProject.GitHubRepo
- hasJavaPreferences() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Attempt to load user JVM defaults - may fail if packager.jar (and any required native library) isn't found.
- hasServer() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Returns true if there is currently an ImageServer being displayed in this viewer.
- hasString(String) - Static method in class qupath.lib.gui.localization.QuPathResources
- hasString(String, String) - Static method in class qupath.lib.gui.localization.QuPathResources
- hasUnseenErrors() - Method in class qupath.lib.gui.commands.LogViewerCommand
-
Boolean binding indicating whether there are any unseen errors.
- hasZAndT() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return whether this
ViewTrackerhas Z and T information. - headerText(String) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Deprecated.Specify the dialog header text.
- height - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
- height - Variable in class qupath.lib.gui.charts.Charts.PieChartBuilder
- height - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
- height(double) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Set the preferred height of the chart.
- height(double) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
-
Set the preferred height of the chart.
- height(double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Set the preferred height of the chart.
- height(double) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Deprecated.Specify the dialog height.
- HELP - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- HELP_VIEWER - Variable in class qupath.lib.gui.actions.CommonActions
- HELP_VIEWER - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
- HelpMenuActions - Class in qupath.lib.gui.actions.menus
- HelpMenuActions.Actions - Class in qupath.lib.gui.actions.menus
- HIDE_SELECTED - Enum constant in enum class qupath.lib.gui.viewer.OverlayOptions.ClassVisibilityMode
-
Hide classes that are included in the selected class collection.
- hideIfEmptyProperty() - Method in class qupath.lib.gui.charts.HistogramChart
-
Property controlling whether the chart should be hidden if there is no data.
- hierarchyChanged(PathObjectHierarchyEvent) - Method in class qupath.lib.gui.commands.PathObjectGridView
- hierarchyChanged(PathObjectHierarchyEvent) - Method in class qupath.lib.gui.panes.AnnotationPane
- hierarchyChanged(PathObjectHierarchyEvent) - Method in class qupath.lib.gui.panes.PathObjectHierarchyView
- hierarchyChanged(PathObjectHierarchyEvent) - Method in class qupath.lib.gui.panes.SelectedMeasurementTableView
- hierarchyChanged(PathObjectHierarchyEvent) - Method in class qupath.lib.gui.UndoRedoManager
- hierarchyChanged(PathObjectHierarchyEvent) - Method in class qupath.lib.gui.viewer.QuPathViewer
- hierarchyDisplayMode - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
- HierarchyOverlay - Class in qupath.lib.gui.viewer.overlays
-
An overlay capable of painting a
PathObjectHierarchy, except for any TMA grid (which is handled byTMAGridOverlay). - HierarchyOverlay(DefaultImageRegionStore, OverlayOptions, ImageData<BufferedImage>) - Constructor for class qupath.lib.gui.viewer.overlays.HierarchyOverlay
-
Constructor.
- HistogramChart - Class in qupath.lib.gui.charts
-
JavaFX chart for displaying histograms.
- HistogramChart() - Constructor for class qupath.lib.gui.charts.HistogramChart
- HistogramChart.CountsTransformMode - Enum Class in qupath.lib.gui.charts
-
Enum to specify how the counts are displayed.
- HistogramChart.DisplayMode - Enum Class in qupath.lib.gui.charts
-
Display mode for the histogram.
- HistogramChart.HistogramData - Class in qupath.lib.gui.charts
-
Helper class for representing data that may be visualized with a
HistogramChart. - HistogramData(Histogram, Color) - Constructor for class qupath.lib.gui.charts.HistogramChart.HistogramData
-
Wrapper for histogram & data relevant to its display.
- HistogramDisplay - Class in qupath.lib.gui.charts
-
Wrapper close to enable the generation and display of histograms relating to a data table.
- HistogramDisplay(PathTableData<?>, boolean) - Constructor for class qupath.lib.gui.charts.HistogramDisplay
-
Constructor.
- HISTORY_SCRIPT - Variable in class qupath.lib.gui.actions.AutomateActions
- HISTORY_SCRIPT - Variable in class qupath.lib.gui.actions.menus.AutomateMenuActions.Actions
- HISTORY_SHOW - Variable in class qupath.lib.gui.actions.AutomateActions
- HISTORY_SHOW - Variable in class qupath.lib.gui.actions.menus.AutomateMenuActions.Actions
- HOVER - Enum constant in enum class qupath.lib.gui.tools.CommandFinderTools.CommandBarDisplay
-
Display only when the cursor hovers nearby
- HtmlRenderer - Interface in qupath.lib.gui.scripting.languages
-
Marker interface that indicates an executable language renders HTML.
- HUGE - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.FontSize
I
- IconFactory - Class in qupath.lib.gui.tools
-
Factory class for creating icons.
- IconFactory() - Constructor for class qupath.lib.gui.tools.IconFactory
- IconFactory.PathIcons - Enum Class in qupath.lib.gui.tools
-
Default icons for QuPath commands.
- iconProperty() - Method in class qupath.lib.gui.viewer.tools.ExtendedPathTool
- iconProperty() - Method in interface qupath.lib.gui.viewer.tools.PathTool
-
Property giving the icon that should be used for the tool
- image() - Method in class qupath.lib.gui.tools.MeasurementExporter
-
Specify that whole-image measurements (only) should be export.
- IMAGE - Enum constant in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters
-
Accept all requests for the image where the region is non-empty
- IMAGE_NAME - Variable in class qupath.lib.gui.actions.menus.WindowMenuActions.Actions
- imageData - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
- imageData - Variable in class qupath.lib.gui.charts.Charts.PieChartBuilder
- imageData - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
- imageData(ImageData<?>) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Specify an
ImageDataobject. - imageData(ImageData<?>) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
-
Specify an
ImageDataobject. - imageData(ImageData<?>) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Specify an
ImageDataobject. - imageDataChanged(QuPathViewer, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.UndoRedoManager
- imageDataChanged(QuPathViewer, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in interface qupath.lib.gui.viewer.QuPathViewerListener
-
Called with the image data within a viewer has changed.
- imageDataChanged(QuPathViewer, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
- imageDataChanged(QuPathViewer, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.viewer.ViewerManager
- imageDataProperty() - Method in class qupath.lib.gui.commands.PathObjectGridView
- imageDataProperty() - Method in class qupath.lib.gui.QuPathGUI
-
Read-only property containing the image open within the currently-active viewer.
- imageDataProperty() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Property for the image data currently being displayed within this viewer.
- imageDataProperty() - Method in class qupath.lib.gui.viewer.ViewerManager
-
Read-only property containing the image open within the currently-active viewer.
- ImageDetailsPane - Class in qupath.lib.gui.panes
-
A panel used for displaying basic info about an image, e.g.
- ImageDetailsPane(ObservableValue<ImageData<BufferedImage>>) - Constructor for class qupath.lib.gui.panes.ImageDetailsPane
-
Constructor.
- ImageDisplay - Class in qupath.lib.display
-
Class used to look after the color transforms that may be applied to an image, including brightness/contrast settings.
- ImageDisplay() - Constructor for class qupath.lib.display.ImageDisplay
-
Constructor.
- imageDisplayObjectProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSettingsPane
-
The current image display.
- imageDisplayProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane
-
Property for the image display that should be shown and managed by this pane.
- imageDisplayProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSliderPane
-
The image display to which the sliders are applied.
- ImageDisplaySettings - Class in qupath.lib.display.settings
-
A simple class to store the main information needed by QuPath to display an image, in a JSON-friendly form.
- ImageDisplaySettings() - Constructor for class qupath.lib.display.settings.ImageDisplaySettings
- ImageInterpolation - Enum Class in qupath.lib.gui.viewer
-
Supported interpolation methods when displaying images.
- IMAGEJ_MACRO - Static variable in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
- ImageJMacroCompletor - Class in qupath.lib.gui.scripting.completors
-
And autocompletor for the ImageJ macro language.
- ImageJMacroCompletor() - Constructor for class qupath.lib.gui.scripting.completors.ImageJMacroCompletor
-
Constructor.
- ImageJMacroLanguage - Class in qupath.lib.gui.scripting.languages
- imageList(List<ProjectImageEntry<BufferedImage>>) - Method in class qupath.lib.gui.tools.MeasurementExporter
-
Specify the list of images (
ProjectImageEntry) to export. - imageNameProperty() - Method in class qupath.lib.gui.panes.SimpleImageViewer
-
Get a read-only property indicating the name of the image.
- imagePointToComponentPoint(Point2D, Point2D, boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Convert a coordinate from the the full-resolution image into the corresponding pixel coordinate in the viewer - optionally constraining it to any viewer component bounds.
- imageProperty() - Method in class qupath.lib.gui.panes.SimpleImageViewer
-
Get a read-only property representing the JavaFX image.
- ImageRegionRenderer - Interface in qupath.lib.gui.images.stores
-
Interface for painting regions of an
ImageServeronto aGraphicsobject. - ImageRegionStoreFactory - Class in qupath.lib.gui.images.stores
-
Factory for creating an ImageRegionStore.
- ImageRegionStoreFactory() - Constructor for class qupath.lib.gui.images.stores.ImageRegionStoreFactory
- ImageRegionStoreHelpers - Class in qupath.lib.gui.images.stores
-
Helper methods related to image region storage.
- ImageRegionStoreHelpers() - Constructor for class qupath.lib.gui.images.stores.ImageRegionStoreHelpers
- ImageRenderer - Interface in qupath.lib.gui.images.stores
-
Interface for objects capable of converting a
BufferedImagefor rendering usingGraphics2D. - imageTypeSettingProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Specify how setting the image type should be handled for images when they are opened for the first time.
- imageUpdated - Variable in class qupath.lib.gui.viewer.QuPathViewer
-
Flag used to indicate that the image was updated for a repaint (otherwise it's assumed only the overlay may have changed)
- IMPORT_IMAGES - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
- IMPORT_IMAGES_LEGACY - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
- importDearrayedTMAData(File) - Static method in class qupath.lib.gui.tma.TMADataIO
-
Import a TMA grid from an exported TMA analysis file, i.e.
- importPreferences(InputStream) - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Import preferences from a stream.
- INACTIVE_SERVER - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- includeImage(boolean) - Method in class qupath.lib.gui.measure.DefaultPathObjectValueFactoryBuilder
- includeMeasurementList(boolean) - Method in class qupath.lib.gui.measure.DefaultPathObjectValueFactoryBuilder
- includeObjectCounts(boolean) - Method in class qupath.lib.gui.measure.DefaultPathObjectValueFactoryBuilder
- includeObjectMetadata(boolean) - Method in class qupath.lib.gui.measure.DefaultPathObjectValueFactoryBuilder
- includeObjectProperties(boolean) - Method in class qupath.lib.gui.measure.DefaultPathObjectValueFactoryBuilder
- includeOnlyColumns(String...) - Method in class qupath.lib.gui.tools.MeasurementExporter
-
Specify the columns that will be included in the export.
- includePixelClassification(boolean) - Method in class qupath.lib.gui.measure.DefaultPathObjectValueFactoryBuilder
- includeRoiProperties(boolean) - Method in class qupath.lib.gui.measure.DefaultPathObjectValueFactoryBuilder
- info(String) - Static method in class qupath.lib.gui.actions.InfoMessage
-
Create an information message with static text.
- info(String, int) - Static method in class qupath.lib.gui.actions.InfoMessage
-
Create an information message with static text and a count.
- info(ObservableNumberValue) - Static method in class qupath.lib.gui.actions.InfoMessage
-
Create a information message to show a count of messages.
- info(ObservableValue<String>) - Static method in class qupath.lib.gui.actions.InfoMessage
-
Create an information message.
- info(ObservableValue<String>, ObservableNumberValue) - Static method in class qupath.lib.gui.actions.InfoMessage
-
Create an information message with a count.
- INFO - Enum constant in enum class qupath.lib.gui.actions.InfoMessage.MessageType
-
Information only.
- INFO - Enum constant in enum class qupath.lib.gui.logging.LogManager.LogLevel
-
Info logging (default)
- INFO - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- INFO - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
- infoMessage() - Method in class qupath.lib.gui.commands.BrightnessContrastCommand
-
Get a string expression to draw attention to any warnings associated with the current display settings.
- InfoMessage - Class in qupath.lib.gui.actions
-
An informative message that should be shown to the user.
- InfoMessage.MessageType - Enum Class in qupath.lib.gui.actions
-
The type of message, which can be used for styling.
- information() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Deprecated.Create an information alert dialog.
- initializeForServer(ImageServer<BufferedImage>) - Method in class qupath.lib.gui.viewer.QuPathViewer
- initializeForServer(ImageServer<BufferedImage>) - Method in class qupath.lib.gui.viewer.QuPathViewerPlus
- INPUT_DISPLAY - Variable in class qupath.lib.gui.actions.CommonActions
- INPUT_DISPLAY - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- inputFiles(Collection<File>) - Method in class qupath.lib.gui.FileCopier
-
Collection of files to copy.
- InputOutputPreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.InputOutputPreferences
- inputPaths(Collection<Path>) - Method in class qupath.lib.gui.FileCopier
-
Collection of paths representing files to copy.
- INSERT_INTO_HIERARCHY - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
- insertAllDefaultImportAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- insertDetectionMeasurementsAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- insertMuAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- insertObjectClassifiersAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- insertPixelClassifiersAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- insertQPExImportAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- insertQPImportAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- insertSelectedObjectsInHierarchy(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands
-
Insert the selected objects in the hierarchy, resolving positions accordingly.
- insertText(int, String) - Method in interface qupath.lib.gui.scripting.EditableText
-
Request inserting the specified text.
- insertText(int, String) - Method in class qupath.lib.gui.scripting.TextAreaControl
- installActions(Collection<? extends Action>) - Method in class qupath.lib.gui.QuPathGUI
-
Install the specified actions.
- installCommand(String, Runnable) - Method in class qupath.lib.gui.QuPathGUI
-
Install a new command in QuPath.
- installDragAndDropHandler(QuPathGUI) - Static method in class qupath.lib.gui.commands.TMACommands
-
Command to install a drag and drop file handler for exported TMA data.
- installExtension(QuPathGUI) - Method in interface qupath.lib.gui.extensions.QuPathExtension
-
Install the extension for a QuPathGUI instance.
- installGroovyCommand(String, File) - Method in class qupath.lib.gui.QuPathGUI
-
Install a Groovy script as a new command in QuPath.
- installGroovyCommand(String, String) - Method in class qupath.lib.gui.QuPathGUI
-
Install a Groovy script as a new command in QuPath.
- installImageDataCommand(String, Consumer<ImageData<BufferedImage>>) - Method in class qupath.lib.gui.QuPathGUI
-
Install a new command in QuPath that takes the current
ImageDataas input. - installInfoMessage(Action, ObjectExpression<InfoMessage>) - Static method in class qupath.lib.gui.actions.ActionTools
-
Install an optional info message to the action.
- installLanguage(ScriptLanguage) - Static method in class qupath.lib.gui.scripting.languages.ScriptLanguageProvider
-
Install a new script language.
- installRangePrompt(Slider) - Static method in class qupath.lib.gui.tools.GuiTools
-
Install a mouse click listener to prompt the user to input min/max values for a slider.
- installStyles(Collection<File>) - Static method in class qupath.lib.gui.prefs.QuPathStyleManager
-
Handle installing CSS files (which can be used to style QuPath).
- installSyntax(ScriptSyntax) - Static method in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
-
Install a new
ScriptSyntaxprogrammatically. - installTool(PathTool, KeyCodeCombination) - Method in class qupath.lib.gui.ToolManager
-
Install a new tool for interacting with viewers.
- INTENSITY_FEATURES - Variable in class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
- InteractiveObjectImporter - Class in qupath.lib.gui.commands
-
Static methods to import object(s) from different sources.
- interpolateBilinear - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
- interpolationProperty() - Method in class qupath.lib.gui.viewer.overlays.AbstractImageOverlay
-
The preferred method of interpolation to use for display.
- invertBackground() - Method in class qupath.lib.display.settings.ImageDisplaySettings
-
Get whether the background should be shown 'inverted'.
- invertColors() - Method in enum class qupath.lib.display.ChannelDisplayMode
- INVERTED_COLOR - Enum constant in enum class qupath.lib.display.ChannelDisplayMode
-
Show using color LUT with an inverted background
- INVERTED_GRAYSCALE - Enum constant in enum class qupath.lib.display.ChannelDisplayMode
-
Show using an inverted grayscale LUT (white to black)
- invertScrolling - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
- invertScrollingProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Invert the scrolling direction of the mouse applied to the viewer.
- invertZSlider - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
- invertZSliderProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Invert the z-slider for the viewer.
- isAdditive() - Method in class qupath.lib.display.AdditiveChannelInfo
- isAdditive() - Method in interface qupath.lib.display.ChannelDisplayInfo
-
Returns true if this channel can be used additively to create a composite image display; returns false if this channel wants all the color information to itself, so can't be displayed with others.
- isAdditive() - Method in class qupath.lib.display.DirectServerChannelInfo
- isBrightnessContrastRescaled() - Method in class qupath.lib.display.AdditiveChannelInfo
- isBrightnessContrastRescaled() - Method in class qupath.lib.display.DirectServerChannelInfo
- isBrightnessContrastRescaled() - Method in interface qupath.lib.display.ChannelDisplayInfo
-
Returns true if rescaling according to min & max display levels is applied, false if the full display range is used.
- isCompatible(ImageDisplay) - Method in class qupath.lib.display.ImageDisplay
-
Check if an image display is 'compatible' with this one.
- isEmpty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane
-
Query if the table is empty, i.e.
- isEmpty() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return whether the collection of recorded frames is empty.
- isEmptyRegion(RegionRequest) - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer
-
Returns true if there are no objects to be painted within the requested region.
- isEraser() - Method in interface qupath.lib.gui.viewer.tools.QuPathPenManager.PenInputManager
-
Query if there is a pen currently being used as an eraser.
- iseScrollGestures - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
- isHidden(PathObject) - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Query whether an object should be hidden.
- isImageDataChanging() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Returns true between the time setImageData has been called, and before the first repaint has been completed.
- isInteractive() - Method in class qupath.lib.gui.charts.ChartThresholdPane
-
Returns the value of
ChartThresholdPane.isInteractiveProperty(). - isInteractiveProperty() - Method in class qupath.lib.gui.charts.ChartThresholdPane
-
Property indicating whether thresholds can be adjusted interactively.
- isLastFrame(ViewRecordingFrame) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return whether the specified
frameis the last one recorded. - isLocationVisible() - Method in class qupath.lib.gui.viewer.QuPathViewerPlus
-
Returns true if the cursor location is visible, false otherwise.
- isModified() - Method in class qupath.lib.gui.scripting.ScriptTab
-
Return
- isModifiedProperty() - Method in class qupath.lib.gui.scripting.ScriptTab
-
Return the
isModifiedPropertyof this script tab (true if the script is modified, i.e. - isMutable() - Method in class qupath.lib.display.DirectServerChannelInfo
- isMutable() - Method in interface qupath.lib.display.SingleChannelDisplayInfo
-
Check if
SingleChannelDisplayInfo.getValue(BufferedImage, int, int)returns fixed values, or if they are dependent on other properties of theImageData. - isNumericMeasurement(String) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
-
Query whether a named measurement returns a numeric value only.
- isOverviewVisible() - Method in class qupath.lib.gui.viewer.QuPathViewerPlus
-
Returns true if the image overview is visible, false otherwise.
- isPathClassHidden(PathClass) - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Query whether objects with a specified classification should be displayed or hidden.
- isReadOnly() - Method in class qupath.lib.gui.QuPathGUI
-
Query whether QuPath is in 'read-only' mode.
- isRecording() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return whether this
is currently recording. - isRedoable() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
-
Returns true if 'redo' can be applied to the control.
- isRedoable() - Method in class qupath.lib.gui.scripting.TextAreaControl
- isResizable() - Method in class qupath.lib.gui.ColorMapCanvas
- isRotated() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Returns true if
viewer.getRotation() != 0. - isScalebarVisible() - Method in class qupath.lib.gui.viewer.QuPathViewerPlus
-
Returns true if the scalebar is visible, false otherwise.
- isSelectable(Action) - Static method in class qupath.lib.gui.actions.ActionTools
-
Specify that an
Actionhas a meaningful 'selected' status. - isSelected() - Method in class qupath.lib.gui.SelectableItem
-
Returns true if the value of the selected property equals
SelectableItem.getItem(). - isShowing() - Method in class qupath.lib.display.settings.ChannelSettings
-
Get whether the channel should be displayed.
- isShowing() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Returns true if the viewer is visible, and attached to a scene.
- isSpaceDown() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Returns true if the spacebar was pressed when this component was focussed, and is still being held down.
- isStandalone() - Method in class qupath.lib.gui.QuPathGUI
-
Query whether this is a standalone QuPathGUI instance, as flagged during startup.
- isStringMeasurement(String) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
-
Query whether a named measurement returns a
Stringvalue only. - isSubtractMode(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
- isToolSwitchingEnabled() - Method in class qupath.lib.gui.ToolManager
-
Returns true if the user is able to activate another
PathTool, false otherwise. - isUndoable() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
-
Returns true if 'undo' can be applied to the control.
- isUndoable() - Method in class qupath.lib.gui.scripting.TextAreaControl
- isValid() - Method in class qupath.lib.gui.tools.MeasurementMapper
-
Query if the mapper is valid.
- isVisible() - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay
-
Check overlay visibility status.
- isVisible() - Method in class qupath.lib.gui.viewer.overlays.GridOverlay
- isVisible() - Method in class qupath.lib.gui.viewer.overlays.TMAGridOverlay
J
- JAVA_IMPORTER - Static variable in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
-
Java-like import statements
- JavadocViewerRunner - Class in qupath.lib.gui
-
A command to show a
JavadocViewerin a standalone window. - JavadocViewerRunner(Stage) - Constructor for class qupath.lib.gui.JavadocViewerRunner
-
Create the command.
- join(Collection<? extends PathObjectValueFactory>) - Static method in interface qupath.lib.gui.measure.PathObjectValueFactory
-
Join multiple factories for a collection to create all of their values.
- join(PathObjectValueFactory...) - Static method in interface qupath.lib.gui.measure.PathObjectValueFactory
-
Join multiple factories to create all of their values.
- JSON - Static variable in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
- JsonLanguage - Class in qupath.lib.gui.scripting.languages
-
Class for the representation of JSON syntax in QuPath.
K
- keepDisplaySettings - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
- keepDisplaySettingsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Retain display settings (channel colors, brightness/contrast) when opening new images that have the same properties (channels, channel names, bit-depths).
- KEYBOARD - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- killRunningScriptAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
L
- LARGE - Enum constant in enum class qupath.lib.gui.commands.PathObjectGridView.GridDisplaySize
- LARGE - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.FontSize
- lastChangeTimestamp() - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Get a property representing the timestamp of the last recorded change for any property.
- launchInstanceFromSwing() - Static method in class qupath.lib.gui.QuPathGUI
-
Static method to launch QuPath from within a Swing/AWT application.
- launchTMADataViewer(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
-
Open new window with the TMA data viewer.
- layers(Collection<PathOverlay>) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder
-
Specify one or more overlay layers as a collection.
- layers(PathOverlay...) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder
-
Specify one or more overlay layers.
- legend(boolean) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Specify whether the legend should be shown or not.
- legend(boolean) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
-
Specify whether the legend should be shown or not.
- legend(boolean) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Specify whether the legend should be shown or not.
- legend(String) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Specify the side of the chart where the legend should be shown.
- legend(String) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
-
Specify the side of the chart where the legend should be shown.
- legend(String) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Specify the side of the chart where the legend should be shown.
- legend(Side) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Specify the side of the chart where the legend should be shown.
- legend(Side) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
-
Specify the side of the chart where the legend should be shown.
- legend(Side) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Specify the side of the chart where the legend should be shown.
- legendSide - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
- legendSide - Variable in class qupath.lib.gui.charts.Charts.PieChartBuilder
- legendSide - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
- legendVisible - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
- legendVisible - Variable in class qupath.lib.gui.charts.Charts.PieChartBuilder
- legendVisible - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
- LICENSE - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
- licenseMessage - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
- limitDatapoints(int) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Choose the maximum number of supported datapoints per series.
- LINE - Static variable in class qupath.lib.gui.viewer.tools.PathTools
-
Line drawing tool
- LINE_OR_ARROW - Static variable in class qupath.lib.gui.viewer.tools.PathTools
-
Extended
PathToolthat can switch between drawing lines or arrows. - LINE_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- LINE_TOOL - Variable in class qupath.lib.gui.ToolManager
- lineWidthProperty() - Method in class qupath.lib.gui.charts.ChartThresholdPane
-
Line width property used for displaying threshold lines.
- loadDisplaySettings(String) - Static method in class qupath.lib.gui.scripting.QPEx
-
Load a display settings object from a file path or from the current project.
- localeDefault - Variable in class qupath.lib.gui.panes.PreferencePane.LocalePreferences
- localeDisplay - Variable in class qupath.lib.gui.panes.PreferencePane.LocalePreferences
- localeFormat - Variable in class qupath.lib.gui.panes.PreferencePane.LocalePreferences
- LocalePreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.LocalePreferences
- localizationDirectoryProperty() - Method in class qupath.lib.gui.UserDirectoryManager
-
Read only property representing the localization directory.
- locateFile(String) - Static method in class qupath.lib.gui.scripting.QPEx
-
Locate a specified file based upon its name or path, with a search depth of 4.
- locateFile(String, int) - Static method in class qupath.lib.gui.scripting.QPEx
-
Locate a specified file based upon its name or path.
- LOCATION - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- locationFontSize - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
- locationFontSizeProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Preferred font size for the location text in the viewer.
- locationUpdated - Variable in class qupath.lib.gui.viewer.QuPathViewer
-
Flag used to indicate that the visible region in the viewer has changed
- LOCK_SELECTED_OBJECTS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.LockActions
- lockActions - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.Actions
- LockActions() - Constructor for class qupath.lib.gui.actions.menus.ObjectsMenuActions.LockActions
- lockSelectedToolProperty() - Method in class qupath.lib.gui.ToolManager
-
Property to request that the selected tool be locked.
- LOG_DELIMITER - Static variable in class qupath.lib.gui.viewer.recording.ViewTracker
- LOG_VIEWER - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- LOGARITHM - Enum constant in enum class qupath.lib.gui.charts.HistogramChart.CountsTransformMode
-
Natural logarithm of raw bin counts.
- logDirectoryProperty() - Method in class qupath.lib.gui.UserDirectoryManager
-
Read only property representing the log file directory.
- logLevel - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
- LogManager - Class in qupath.lib.gui.logging
-
Manage logging levels.
- LogManager() - Constructor for class qupath.lib.gui.logging.LogManager
- LogManager.LogLevel - Enum Class in qupath.lib.gui.logging
-
Available log levels.
- logToFile(File) - Static method in class qupath.lib.gui.logging.LogManager
-
Request logging to the specified file.
- LogViewerCommand - Class in qupath.lib.gui.commands
-
A viewer for log messages.
- LogViewerCommand(Window) - Constructor for class qupath.lib.gui.commands.LogViewerCommand
-
Constructor.
- longText(String) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
-
Set the long text property of the action.
- longText(ObservableValue<String>) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
-
Bind the long text property of the action to an
ObservableValue, bidirectionally if possible. - longTextProperty() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry
-
Property corresponding to
CommandFinderTools.CommandEntry.getLongText() - lookupAccelerator(String) - Method in class qupath.lib.gui.QuPathGUI
-
Get the action or menu item associated with an accelerator.
- lookupAccelerator(KeyCombination) - Method in class qupath.lib.gui.QuPathGUI
-
Get the action or menu item associated with an key combination.
- lookupActionByText(String) - Method in class qupath.lib.gui.QuPathGUI
-
Search for an action based upon its text (name) property.
- lookupMenuItem(String, String...) - Method in class qupath.lib.gui.QuPathGUI
-
Search for a menu item based upon its path.
M
- main(String[]) - Static method in class qupath.lib.gui.tools.DocGenerator
- MAIN_SCENE - Enum constant in enum class qupath.lib.gui.tools.GuiTools.SnapshotType
-
Snapshot of the full Scene of the main QuPath Window.
- MAIN_WINDOW_SCREENSHOT - Enum constant in enum class qupath.lib.gui.tools.GuiTools.SnapshotType
-
Screenshot of the full QuPath window as it currently appears, including any overlapping windows.
- MAKE_INVERSE - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
- makeChartInteractive(Chart, NumberAxis, NumberAxis) - Static method in class qupath.lib.gui.charts.ChartTools
-
Make it possible to select chart regions to zoom in, and scroll to navigate around it.
- makeFullScreenshot() - Static method in class qupath.lib.gui.tools.GuiTools
-
Make a BufferedImage snapshot of the full screen.
- makeInverseAnnotation(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands
-
Make an inverse annotation for the selected objects, storing the command in the history workflow.
- makeProgressMonitor() - Method in class qupath.lib.gui.TaskRunnerFX
- makeSnapshot() - Static method in class qupath.lib.gui.tools.GuiTools
-
Make a BufferedImage snapshot of the current GUI.
- makeSnapshot(QuPathGUI, GuiTools.SnapshotType) - Static method in class qupath.lib.gui.tools.GuiTools
-
Make a snapshot (image) showing what is currently displayed in a QuPath window or the active viewer within QuPath, as determined by the SnapshotType.
- makeSnapshot(QuPathGUI, QuPathViewer, GuiTools.SnapshotType) - Static method in class qupath.lib.gui.tools.GuiTools
-
Make a snapshot (image) showing what is currently displayed in a QuPath window or the specified viewer, as determined by the SnapshotType.
- makeSnapshotFX(QuPathGUI, GuiTools.SnapshotType) - Static method in class qupath.lib.gui.tools.GuiTools
-
Make a snapshot as a JavaFX
Image, using the current viewer if a viewer is required. - makeSnapshotFX(QuPathGUI, QuPathViewer, GuiTools.SnapshotType) - Static method in class qupath.lib.gui.tools.GuiTools
-
Make a snapshot as a JavaFX
Image. - makeViewerSnapshot() - Static method in class qupath.lib.gui.tools.GuiTools
-
Make a BufferedImage snapshot of the current viewer.
- makeViewerSnapshot(QuPathViewer) - Static method in class qupath.lib.gui.tools.GuiTools
-
Make a BufferedImage snapshot of the specified viewer.
- manageChildMenuBar(MenuBar) - Static method in class qupath.lib.gui.prefs.SystemMenuBar
-
Request that a menubar is managed as a child menubar.
- manageMainMenuBar(MenuBar) - Static method in class qupath.lib.gui.prefs.SystemMenuBar
-
Request that a menubar is managed as a main menubar.
- MANAGER - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
- MAPS - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
- MarkdownLanguage - Class in qupath.lib.gui.scripting.languages
-
Class for the representation of JSON syntax in QuPath.
- markerOpacity - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
- markerOpacity - Variable in class qupath.lib.gui.charts.Charts.PieChartBuilder
- markerOpacity - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
- markerOpacity(double) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Specify the marker opacity.
- markerOpacity(double) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
-
Specify the marker opacity.
- markerOpacity(double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Specify the marker opacity.
- maskImageNames - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
- maskImageNamesProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Request that image names are hidden within the user interface.
- MATCH_VIEWER_RESOLUTIONS - Variable in class qupath.lib.gui.actions.ViewerActions
- matchResolutions() - Method in class qupath.lib.gui.viewer.ViewerManager
-
Match the display resolutions (downsamples) of all viewers to match the current viewer.
- maxAllowed - Variable in class qupath.lib.display.AdditiveChannelInfo
- maxAllowed - Variable in class qupath.lib.display.DirectServerChannelInfo
- maxClipboardObjects - Variable in class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
- maxDisplay - Variable in class qupath.lib.display.AdditiveChannelInfo
- maxDisplay - Variable in class qupath.lib.display.DirectServerChannelInfo
- maxHeight(double) - Method in class qupath.lib.gui.ColorMapCanvas
- maxMemoryGB - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
- maxMemoryMBProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Get property representing the maximum memory for the Java Virtual Machine, applied after restarting the application.
- maxObjectsToClipboardProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
The maximum number of objects that can be copied to the system clipboard.
- maxPointsProperty() - Method in class qupath.lib.gui.charts.PathObjectScatterChart
-
Get a property representing the maximum number of points that the plot will display.
- maxUndoHierarchySize - Variable in class qupath.lib.gui.panes.PreferencePane.UndoRedoPreferences
- maxUndoHierarchySizeProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
The requested maximum number of objects in a hierarchy for which QuPath should support undo/redo.
- maxUndoLevels - Variable in class qupath.lib.gui.panes.PreferencePane.UndoRedoPreferences
- maxUndoLevelsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
The requested maximum number of undo levels that QuPath should support.
- maxValueProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastHistogramPane
-
The maximum value displayed on the histogram.
- maxValueProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSliderPane
-
Value of the maximum slider.
- maxWidth(double) - Method in class qupath.lib.gui.ColorMapCanvas
- MEASURE - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- MEASURE_ANNOTATIONS - Variable in class qupath.lib.gui.actions.CommonActions
- MEASURE_DETECTIONS - Variable in class qupath.lib.gui.actions.CommonActions
- MEASURE_GRID_ANNOTATIONS - Variable in class qupath.lib.gui.actions.CommonActions
- MEASURE_GRID_TMA_CORES - Variable in class qupath.lib.gui.actions.CommonActions
- MEASURE_TMA - Variable in class qupath.lib.gui.actions.CommonActions
- MeasurementExportCommand - Class in qupath.lib.gui.commands
-
Dialog box to export measurements
- MeasurementExportCommand(QuPathGUI) - Constructor for class qupath.lib.gui.commands.MeasurementExportCommand
-
Creates a simple GUI for MeasurementExporter.
- MeasurementExporter - Class in qupath.lib.gui.tools
-
Helper class for exporting the measurements of one or more entries in a project.
- MeasurementExporter() - Constructor for class qupath.lib.gui.tools.MeasurementExporter
- MeasurementListValueFactory - Class in qupath.lib.gui.measure
-
Measurements that only extract metadata from objects.
- MeasurementListValueFactory() - Constructor for class qupath.lib.gui.measure.MeasurementListValueFactory
- MeasurementMapPane - Class in qupath.lib.gui.panes
-
Component used for displaying measurement maps, whereby detection objects are recolored according to measurement values.
- MeasurementMapPane(QuPathGUI) - Constructor for class qupath.lib.gui.panes.MeasurementMapPane
-
Constructor.
- MeasurementMapper - Class in qupath.lib.gui.tools
-
Helpers class that can be used to map an object's measurement to a color (packed RGB int).
- MeasurementMapper(ColorMaps.ColorMap, String, Collection<? extends PathObject>) - Constructor for class qupath.lib.gui.tools.MeasurementMapper
-
Constructor.
- measurementMapperProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
- MeasurementPreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.MeasurementPreferences
- measurements(Collection<? extends PathObject>, String, String) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Plot two measurements against one another for the specified objects.
- MeasureMenuActions - Class in qupath.lib.gui.actions.menus
- MeasureMenuActions.Actions - Class in qupath.lib.gui.actions.menus
- MEDIUM - Enum constant in enum class qupath.lib.gui.commands.PathObjectGridView.GridDisplaySize
- MEDIUM - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.FontSize
- MEMORY_MONITOR - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- MEMORY_MONITOR - Variable in class qupath.lib.gui.actions.CommonActions
- MEMORY_MONITOR - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- menu() - Element in annotation interface qupath.lib.gui.actions.annotations.ActionConfig
- MenuActions - Interface in qupath.lib.gui.actions.menus
-
Common interface to define the contents of a menu in terms of actions.
- menuPathProperty() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry
-
Property corresponding to
CommandFinderTools.CommandEntry.getMenuPath() - Menus - Class in qupath.lib.gui.actions.menus
-
Generate actions for installation in QuPath's main menubar.
- Menus() - Constructor for class qupath.lib.gui.actions.menus.Menus
- menusToMarkdown() - Static method in class qupath.lib.gui.tools.CommandFinderTools
-
Create a markdown representation of the menus for inclusion in the documentation, using the current QuPath instance.
- menusToMarkdown(QuPathGUI, Writer) - Static method in class qupath.lib.gui.tools.CommandFinderTools
-
Write a markdown representation of the menus for inclusion in the documentation.
- MenuTools - Class in qupath.lib.gui.tools
-
Static methods to help with creating and populating JavaFX menus.
- MenuTools() - Constructor for class qupath.lib.gui.tools.MenuTools
- MERGE_SELECTED - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
- mergeSelectedAnnotations(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands
-
Merge the currently-selected annotations for an image, replacing them with a single new annotation.
- METADATA - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
- MetadataValueFactory - Class in qupath.lib.gui.measure
-
Measurements that only extract metadata from objects.
- MetadataValueFactory() - Constructor for class qupath.lib.gui.measure.MetadataValueFactory
- MIME_TYPE_GEOJSON - Static variable in class qupath.lib.gui.commands.InteractiveObjectImporter
-
Mime type for GeoJson
- minAllowed - Variable in class qupath.lib.display.AdditiveChannelInfo
- minAllowed - Variable in class qupath.lib.display.DirectServerChannelInfo
- minDisplay - Variable in class qupath.lib.display.AdditiveChannelInfo
- minDisplay - Variable in class qupath.lib.display.DirectServerChannelInfo
- minHeight(double) - Method in class qupath.lib.gui.ColorMapCanvas
- MINI_VIEWER - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- minimumPyramidDimension - Variable in class qupath.lib.gui.panes.PreferencePane.InputOutputPreferences
- MiniViewerManager(QuPathViewer, Collection<? extends ChannelDisplayInfo>) - Constructor for class qupath.lib.gui.commands.MiniViewers.MiniViewerManager
-
Deprecated.use
MiniViewers.createManager(QuPathViewer, Collection)instead. - MiniViewers - Class in qupath.lib.gui.commands
-
Command to open a small viewer window, which displays a detail from the current image depending on where the cursor is over the image.
- MiniViewers() - Constructor for class qupath.lib.gui.commands.MiniViewers
- MiniViewers.MiniViewerManager - Class in qupath.lib.gui.commands
-
A manager for one or more mini-viewers, where the 'more' means a separate viewer per channel.
- minPyramidDimensionProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Minimum image width or height before pyramidalizing (if required).
- MINUS - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- minValueProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastHistogramPane
-
The minimum value displayed on the histogram.
- minValueProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSliderPane
-
Value of the minimum slider.
- minWidth(double) - Method in class qupath.lib.gui.ColorMapCanvas
- modality(Modality) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Deprecated.Specify the modality of the dialog.
- modelProperty() - Method in class qupath.lib.gui.charts.ScatterPlotDisplay
-
Get property representing the model used with this display.
- mouseClicked(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
- mouseClicked(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
- mouseDragged(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
- mouseDragged(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
- mouseEntered(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
- mouseEntered(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
- mouseExited(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
- mouseExited(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
- mouseLocationToImage(MouseEvent, boolean, boolean) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
- mouseLocationToImage(MouseEvent, boolean, boolean) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
- mouseMoved(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
- mouseMoved(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
- mousePressed(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
- mousePressed(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
- mouseReleased(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
- mouseReleased(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
- MOVE - Static variable in class qupath.lib.gui.viewer.tools.PathTools
-
Move tool
- MOVE_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- MOVE_TOOL - Variable in class qupath.lib.gui.ToolManager
- MoveToolEventHandler - Class in qupath.lib.gui.viewer.tools.handlers
-
The MoveTool is used for quite a lot of things, movement-related: movement around an image (panning), moving ROIs (translating) and moving individual 'handles' of ROIs (resizing/reshaping)
- MoveToolEventHandler() - Constructor for class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
- MoveToolEventHandler.ViewerMover - Class in qupath.lib.gui.viewer.tools.handlers
-
Helper class for panning a
QuPathViewer(reasonably) smoothly. - multipointToolProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Create multiple points within the same annotation when using the counting tool.
- multitouchActions - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- MultitouchActions() - Constructor for class qupath.lib.gui.actions.menus.ViewMenuActions.MultitouchActions
- MULTIVIEW_ADD_COLUMN - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
- MULTIVIEW_ADD_ROW - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
- MULTIVIEW_CLOSE_VIEWER - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
- MULTIVIEW_GRID_1x1 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
- MULTIVIEW_GRID_1x2 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
- MULTIVIEW_GRID_2x1 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
- MULTIVIEW_GRID_2x2 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
- MULTIVIEW_GRID_3x3 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
- MULTIVIEW_GRID_ACTIONS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
- MULTIVIEW_MATCH_RESOLUTIONS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
- MULTIVIEW_REMOVE_COLUMN - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
- MULTIVIEW_REMOVE_ROW - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
- MULTIVIEW_RESET_GRID - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
- MULTIVIEW_SYNCHRONIZE_VIEWERS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
- multiviewActions - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- MultiviewActions() - Constructor for class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
- MultiviewGridActions() - Constructor for class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
N
- NAME - Static variable in class qupath.lib.gui.scripting.languages.ImageJMacroLanguage
-
Constant representing the name of this language.
- NAME_OBJECT_ID - Static variable in class qupath.lib.gui.measure.ObservableMeasurementTableData
-
The name used for the Object ID column
- nameProperty() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return the String property of this
ViewTracker. - nameProperty() - Method in class qupath.lib.gui.viewer.tools.ExtendedPathTool
- nameProperty() - Method in interface qupath.lib.gui.viewer.tools.PathTool
-
Property giving the name of the tool
- navigationAcceleration - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
- navigationAccelerationProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Apply acceleration/deceleration effects when holding and releasing navigation key.
- navigationSpeed - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
- navigationSpeedProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Percentage to scale navigation speed.
- NEAREST - Enum constant in enum class qupath.lib.gui.viewer.ImageInterpolation
-
Nearest neighbor interpolation.
- NEVER - Enum constant in enum class qupath.lib.gui.prefs.SystemMenuBar.SystemMenuBarOption
-
Don't use the system menubar for any windows.
- NEVER - Enum constant in enum class qupath.lib.gui.tools.CommandFinderTools.CommandBarDisplay
-
Never display
- newDetectionRendering - Variable in class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
- newDetectionRenderingProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Flag to enable the new rendering strategy for detections.
- nFrames() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return the number of recorded frames.
- NO - Enum constant in enum class qupath.lib.gui.dialogs.Dialogs.DialogButton
-
Deprecated."No" option
- NO_SHUFFLE_SEED - Static variable in class qupath.lib.gui.charts.PathObjectScatterChart
-
Seed value to use to specify that no shuffling should be applied before displaying the objects.
- NONE - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.AutoUpdateType
-
Don't check for any updates automatically
- NONE - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.DetectionTreeDisplayModes
-
Do not show detections
- NONE - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.ImageTypeSetting
-
Do not set the image type
- nonModal() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Deprecated.Specify that the dialog should be non-modal.
- NORMALIZED - Enum constant in enum class qupath.lib.gui.charts.HistogramChart.CountsTransformMode
-
Normalized bin counts, so that the sum of all counts is 1.0.
- NUCLEI_AND_BOUNDARIES - Enum constant in enum class qupath.lib.gui.viewer.OverlayOptions.DetectionDisplayMode
-
Show both cell boundaries and cell nuclei, where available.
- NUCLEI_ONLY - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- NUCLEI_ONLY - Enum constant in enum class qupath.lib.gui.viewer.OverlayOptions.DetectionDisplayMode
-
Show only cell nuclei.
- numCommandThreadsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Property specifying the preferred number of threads QuPath should use for multithreaded commands.
- numThreads - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
O
- OBJECT_IMPORT - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
- ObjectDescriptionPane<T> - Class in qupath.lib.gui.panes
-
Wraps a pane used to display an object description, if one is available.
- ObjectPreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
- ObjectsMenuActions - Class in qupath.lib.gui.actions.menus
- ObjectsMenuActions.Actions - Class in qupath.lib.gui.actions.menus
- ObjectsMenuActions.AnnotationActions - Class in qupath.lib.gui.actions.menus
- ObjectsMenuActions.DeleteActions - Class in qupath.lib.gui.actions.menus
- ObjectsMenuActions.LockActions - Class in qupath.lib.gui.actions.menus
- ObjectsMenuActions.SelectActions - Class in qupath.lib.gui.actions.menus
- ObjectTreeBrowser - Class in qupath.lib.gui.panes
-
Simple browser for exploring fields (including private fields) within an object by reflection.
- ObjectTreeBrowser() - Constructor for class qupath.lib.gui.panes.ObjectTreeBrowser
- ObservableMeasurementTableData - Class in qupath.lib.gui.measure
-
A table data model to supply observable measurements of PathObjects.
- ObservableMeasurementTableData() - Constructor for class qupath.lib.gui.measure.ObservableMeasurementTableData
- OFF - Enum constant in enum class qupath.lib.gui.logging.LogManager.LogLevel
-
Turn off logging
- opacityProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Property representing the global opacity for overlay drawing.
- opacityTMAMissingProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
The default opacity to use when display TMA core objects, between 0 and 1.
- OPEN_IMAGE - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
- OPEN_IMAGE_OR_URL - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
- openFile(File) - Static method in class qupath.lib.gui.tools.GuiTools
-
Try to open a file in the native application.
- openImage(QuPathViewer, String) - Method in class qupath.lib.gui.QuPathGUI
- openImage(QuPathViewer, String, boolean, boolean) - Method in class qupath.lib.gui.QuPathGUI
-
Open a new whole slide image server, or ImageData.
- openImageEntry(ProjectImageEntry<BufferedImage>) - Method in class qupath.lib.gui.QuPathGUI
-
Open the image represented by the specified ProjectImageEntry.
- openInBrowser(String) - Static method in class qupath.lib.gui.QuPathGUI
-
Try to launch a browser window for a specified URL.
- openSavedData(QuPathViewer, File, boolean, boolean) - Method in class qupath.lib.gui.QuPathGUI
-
Open a saved data file within a particular viewer, optionally keeping the same ImageServer as is currently open.
- outputPath(String) - Method in class qupath.lib.gui.FileCopier
-
Name of the output directory.
- outputPath(Path) - Method in class qupath.lib.gui.FileCopier
-
Path representing the output directory.
- OverlayActions - Class in qupath.lib.gui.actions
-
Actions that interact with
OverlayOptions. - OverlayActions(OverlayOptions) - Constructor for class qupath.lib.gui.actions.OverlayActions
- overlayOpacity(double) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder
-
Specify the opacity for overlay layers.
- OverlayOptions - Class in qupath.lib.gui.viewer
-
Default class for storing overlay display options.
- OverlayOptions() - Constructor for class qupath.lib.gui.viewer.OverlayOptions
-
Constructor, using default values.
- OverlayOptions(OverlayOptions) - Constructor for class qupath.lib.gui.viewer.OverlayOptions
-
Constructor, initializing values based on an existing
OverlayOptionsobject. - OverlayOptions.ClassVisibilityMode - Enum Class in qupath.lib.gui.viewer
-
Visibility modes for classes.
- OverlayOptions.DetectionDisplayMode - Enum Class in qupath.lib.gui.viewer
-
Display modes for cells and other detections.
- overrideSystemMenuBarProperty() - Static method in class qupath.lib.gui.prefs.SystemMenuBar
-
Property requesting that the system menubar should never be used for managed menubars.
- OVERVIEW - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- owner(Window) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Deprecated.Specify the dialog owner.
P
- paintComponent(Graphics) - Method in class qupath.lib.gui.viewer.QuPathViewer
- paintConnections(DelaunayTools.Subdivision, PathObjectHierarchy, Graphics2D, Color, double, ImagePlane) - Static method in class qupath.lib.gui.viewer.PathObjectPainter
-
Paint connections between objects from a
DelaunayTools.Subdivision. - paintConnections(PathObjectConnections, PathObjectHierarchy, Graphics2D, Color, double, ImagePlane) - Static method in class qupath.lib.gui.viewer.PathObjectPainter
-
Deprecated.v0.6.0 as #paintConnections(DelaunayTools.Subdivision, PathObjectHierarchy, Graphics2D, Color, double, ImagePlane) is preferred
- paintHandles(List<Point2>, Graphics2D, double, double, Color, Color) - Static method in class qupath.lib.gui.viewer.PathObjectPainter
-
Paint the handles onto a Graphics object, if we have a suitable (non-point) ROI.
- paintHandles(RoiEditor, Graphics2D, double, double, Color, Color) - Static method in class qupath.lib.gui.viewer.PathObjectPainter
-
Paint the handles onto a Graphics object, if we have a suitable (non-point) ROI.
- paintImage(Canvas, Image) - Static method in class qupath.lib.gui.tools.GuiTools
-
Paint an image centered within a canvas, scaled to be as large as possible while maintaining its aspect ratio.
- paintImage(Canvas, Image, double) - Static method in class qupath.lib.gui.tools.GuiTools
-
Paint an image centered within a canvas, scaled by the specified scale factor.
- paintObject(PathObject, Graphics2D, OverlayOptions, PathObjectSelectionModel, double) - Static method in class qupath.lib.gui.viewer.PathObjectPainter
-
Paint an object (or, more precisely, its ROI).
- paintOverlay(Graphics2D, ImageRegion, double, ImageData<BufferedImage>, boolean) - Method in class qupath.lib.gui.viewer.overlays.AbstractImageOverlay
- paintOverlay(Graphics2D, ImageRegion, double, ImageData<BufferedImage>, boolean) - Method in class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
- paintOverlay(Graphics2D, ImageRegion, double, ImageData<BufferedImage>, boolean) - Method in class qupath.lib.gui.viewer.overlays.GridOverlay
- paintOverlay(Graphics2D, ImageRegion, double, ImageData<BufferedImage>, boolean) - Method in class qupath.lib.gui.viewer.overlays.HierarchyOverlay
- paintOverlay(Graphics2D, ImageRegion, double, ImageData<BufferedImage>, boolean) - Method in interface qupath.lib.gui.viewer.overlays.PathOverlay
-
Paint the overlay to a graphics object.
- paintOverlay(Graphics2D, ImageRegion, double, ImageData<BufferedImage>, boolean) - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
- paintOverlay(Graphics2D, ImageRegion, double, ImageData<BufferedImage>, boolean) - Method in class qupath.lib.gui.viewer.overlays.TMAGridOverlay
- paintOverlay(Graphics2D, ImageRegion, double, ImageData<BufferedImage>, boolean) - Method in class qupath.lib.gui.viewer.overlays.ZProjectOverlay
- paintRegion(ImageServer<BufferedImage>, Graphics, Shape, int, int, double, BufferedImage, ImageObserver, ImageRenderer) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
- paintRegion(ImageServer<BufferedImage>, Graphics, Shape, int, int, double, BufferedImage, ImageObserver, ImageRenderer) - Method in interface qupath.lib.gui.images.stores.ImageRegionRenderer
-
Paint an image region.
- paintRegionCompletely(ImageServer<BufferedImage>, Graphics, Shape, int, int, double, ImageObserver, ImageRenderer, long) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
-
Similar to paintRegion, but wait until all the tiles have arrived (or abort if it is taking too long)
- paintRegionCompletely(ImageServer<BufferedImage>, Graphics, Shape, int, int, double, ImageObserver, ImageRenderer, long) - Method in interface qupath.lib.gui.images.stores.ImageRegionRenderer
-
Similar to
ImageRegionRenderer.paintRegion(ImageServer, Graphics, Shape, int, int, double, BufferedImage, ImageObserver, ImageRenderer), but wait until all the tiles have arrived (or abort if it is taking too long). - paintSelectedBoundsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Specify whether the bounding box of selected objects should be painted.
- paintShape(Shape, Graphics2D, Color, Stroke, Color) - Static method in class qupath.lib.gui.viewer.PathObjectPainter
-
Paint the specified shape with specified stroke and fill colors.
- paintSpecifiedObjects(Graphics2D, Collection<? extends PathObject>, OverlayOptions, PathObjectSelectionModel, double) - Static method in class qupath.lib.gui.viewer.PathObjectPainter
-
Paint the specified objects.
- paintTMAGrid(Graphics2D, TMAGrid, OverlayOptions, PathObjectSelectionModel, double) - Static method in class qupath.lib.gui.viewer.PathObjectPainter
-
Paint the specified tissue microarray grid.
- paintViewer(Graphics, int, int) - Method in class qupath.lib.gui.viewer.QuPathViewer
- PaneTools - Class in qupath.lib.gui.tools
-
Deprecated.since v0.5.0;
GridPaneUtilscontains many of the features. - PaneTools() - Constructor for class qupath.lib.gui.tools.PaneTools
-
Deprecated.
- parameterChanged(ParameterList, String, boolean) - Method in class qupath.lib.gui.charts.HistogramDisplay
- ParameterPanelFX - Class in qupath.lib.gui.dialogs
-
A panel for displaying a list of parameters suitably to aid with creating JavaFX GUIs.
- ParameterPanelFX(ParameterList) - Constructor for class qupath.lib.gui.dialogs.ParameterPanelFX
-
Create a ParameterPanelFX.
- parent(Window) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Set the parent window.
- parent(Window) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
-
Set the parent window.
- parent(Window) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Set the parent window.
- parseAnnotations(Action, AnnotatedElement) - Static method in class qupath.lib.gui.actions.ActionTools
-
Parse annotations relating to an action, updating the properties of the action.
- parseAnnotations(Action, AnnotatedElement, String) - Static method in class qupath.lib.gui.actions.ActionTools
-
Parse annotations relating to an action, updating the properties of the action with an optional base menu.
- parseDisplaySettings(JsonElement) - Static method in class qupath.lib.display.settings.DisplaySettingUtils
-
Parse the JSON element into an image display settings object, if possible.
- parseDisplaySettings(Path) - Static method in class qupath.lib.display.settings.DisplaySettingUtils
-
Parse the JSON element into an image display settings object.
- paste() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
-
Request paste from the system clipboard.
- paste() - Method in class qupath.lib.gui.scripting.TextAreaControl
- PASTE - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.Actions
- PASTE_TO_PLANE - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.Actions
- pasteAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- pasteAndEscapeAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- pasteFromClipboard(QuPathGUI, boolean) - Static method in class qupath.lib.gui.commands.Commands
-
Attempt to paste objects from the system clipboard to the current image, if available; otherwise, check for text on the clipboard and paste it into a new script editor tab
- pasteFromClipboard(ScriptEditorControl<?>, boolean) - Static method in class qupath.lib.gui.scripting.DefaultScriptEditor
- PathClassListCell - Class in qupath.lib.gui.tools
-
A cell for displaying
PathClassobjects in a list view or combo box. - PathClassListCell() - Constructor for class qupath.lib.gui.tools.PathClassListCell
-
Create a list cell using the default string function.
- PathClassListCell(Function<PathClass, String>) - Constructor for class qupath.lib.gui.tools.PathClassListCell
-
Create a list cell using the specified string function.
- PathHierarchyImageServer - Class in qupath.lib.gui.images.servers
-
A special
ImageServerimplementation that doesn't have a backing image, but rather constructs tiles on request from aPathObjectHierarchyand its detection objects. - PathHierarchyImageServer(ImageData<BufferedImage>, OverlayOptions) - Constructor for class qupath.lib.gui.images.servers.PathHierarchyImageServer
-
Constructor.
- PathObjectGridView - Class in qupath.lib.gui.commands
-
Grid display of objects.
- PathObjectGridView.GridDisplaySize - Enum Class in qupath.lib.gui.commands
- PathObjectHierarchyView - Class in qupath.lib.gui.panes
-
Component for showing a tree-based view of the object hierarchy.
- PathObjectHierarchyView(QuPathGUI) - Constructor for class qupath.lib.gui.panes.PathObjectHierarchyView
-
Constructor.
- PathObjectHierarchyView(QuPathGUI, ObservableValue<ImageData<BufferedImage>>) - Constructor for class qupath.lib.gui.panes.PathObjectHierarchyView
-
Constructor.
- PathObjectImageViewers - Class in qupath.lib.gui.tools
-
Helper class for working with thumbnail images relating to path objects.
- PathObjectImageViewers() - Constructor for class qupath.lib.gui.tools.PathObjectImageViewers
- PathObjectImageViewers.ItemViewer<S,
T> - Interface in qupath.lib.gui.tools -
Interface for managing a node that can display an item.
- PathObjectLabels - Class in qupath.lib.gui.tools
- PathObjectLabels() - Constructor for class qupath.lib.gui.tools.PathObjectLabels
- PathObjectLabels.PathObjectMiniPane - Class in qupath.lib.gui.tools
-
Manage a small pane that can be used to display a
PathObject. - PathObjectListWrapper - Class in qupath.lib.gui.measure
-
Helper class to wrap a collection of PathObjects that should be measured.
- PathObjectMiniPane(Function<PathObject, String>) - Constructor for class qupath.lib.gui.tools.PathObjectLabels.PathObjectMiniPane
-
Constructor using a custom string extraction function.
- PathObjectPainter - Class in qupath.lib.gui.viewer
-
Static methods to assist with painting PathObjects.
- PathObjectScatterChart - Class in qupath.lib.gui.charts
-
An interactive
ScatterChartimplementation for showing large(ish) numbers ofPathObject, optionally linked to aQuPathViewer. - PathObjectScatterChart(QuPathViewer) - Constructor for class qupath.lib.gui.charts.PathObjectScatterChart
-
Create an interactive scatter plot using the current viewer
- PathObjectValueFactory - Interface in qupath.lib.gui.measure
-
Interface defining a way to create lazy values from an image and associated objects.
- PathOverlay - Interface in qupath.lib.gui.viewer.overlays
-
Interface defining an overlay to paint on top of a viewer.
- PathPrefs - Class in qupath.lib.gui.prefs
-
Central storage of QuPath preferences.
- PathPrefs() - Constructor for class qupath.lib.gui.prefs.PathPrefs
- PathPrefs.AutoUpdateType - Enum Class in qupath.lib.gui.prefs
-
Options for automatic updating checking of QuPath and/or extensions.
- PathPrefs.DetectionTreeDisplayModes - Enum Class in qupath.lib.gui.prefs
-
Enum for different ways that detections can be displayed in lists and trees.
- PathPrefs.FontSize - Enum Class in qupath.lib.gui.prefs
-
Enum to control font size.
- PathPrefs.ImageTypeSetting - Enum Class in qupath.lib.gui.prefs
-
Enum defining how setting the image type should be handled for new images.
- PathTableData<T> - Interface in qupath.lib.gui.measure
-
Interface defining a table model that enables measurement names to be mapped to string or numeric values (as appropriate).
- PathTool - Interface in qupath.lib.gui.viewer.tools
-
Interface defining how a toolbar tool interacts with a viewer.
- PathToolEventHandlers - Class in qupath.lib.gui.viewer.tools.handlers
- PathToolEventHandlers() - Constructor for class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
- PathTools - Class in qupath.lib.gui.viewer.tools
-
Default
PathToolimplementations. - PathTools() - Constructor for class qupath.lib.gui.viewer.tools.PathTools
- pieChart() - Static method in class qupath.lib.gui.charts.Charts
-
Create a
Charts.PieChartBuilderfor generating a custom pie chart. - PIXEL_CLASSIFICATION - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- pixelClassificationFilterRegionProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
- PixelClassificationOverlay - Class in qupath.lib.gui.viewer.overlays
-
PathOverlaythat gives the results of pixel classification. - pixelSnapping - Variable in class qupath.lib.gui.panes.PreferencePane.DrawingPreferences
- placeholderText - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
- placeholderTextProperty() - Method in class qupath.lib.gui.panes.SimpleImageViewer
-
Get the placeholder text to show if no image is available.
- placeholderTextProperty() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
String property to hold text that should be displayed whenever no image is open in the viewer.
- PLAIN - Static variable in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
- PlainLanguage - Class in qupath.lib.gui.scripting.languages
-
Class for the representation of plain text in QuPath.
- PLAYBACK_PLAY - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- pointOpacityProperty() - Method in class qupath.lib.gui.charts.PathObjectScatterChart
-
Get a property representing the opacity of all data points.
- pointRadius - Variable in class qupath.lib.gui.panes.PreferencePane.DrawingPreferences
- pointRadiusProperty() - Method in class qupath.lib.gui.charts.PathObjectScatterChart
-
Get a property representing the radius of all data points.
- pointRadiusProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Radius of the circle used to draw individual points in a point annotation (in pixels).
- POINTS - Static variable in class qupath.lib.gui.viewer.tools.PathTools
-
Points annotation and counting tool
- POINTS_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- POINTS_TOOL - Variable in class qupath.lib.gui.ToolManager
- POLYGON - Static variable in class qupath.lib.gui.viewer.tools.PathTools
-
Polygon drawing tool (closed)
- POLYGON_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- POLYGON_TOOL - Variable in class qupath.lib.gui.ToolManager
- POLYLINE - Static variable in class qupath.lib.gui.viewer.tools.PathTools
-
Polyline drawing tool (open)
- POLYLINE_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- POLYLINE_TOOL - Variable in class qupath.lib.gui.ToolManager
- populateAnnotationsMenu(QuPathGUI, ContextMenu) - Static method in class qupath.lib.gui.tools.GuiTools
-
Populate a
ContextMenuwith standard options to operate on selected annotation objects. - populateAnnotationsMenu(QuPathGUI, Menu) - Static method in class qupath.lib.gui.tools.GuiTools
-
Populate a
Menuwith standard options to operate on selected annotation objects. - positionCaret(int) - Method in interface qupath.lib.gui.scripting.EditableText
-
Set the caret position to the specified index
- positionCaret(int) - Method in class qupath.lib.gui.scripting.TextAreaControl
- postProcess(Collection<? extends PathTask>) - Method in class qupath.lib.gui.TaskRunnerFX
- PreferencePane - Class in qupath.lib.gui.panes
-
QuPath's preference pane, giving a means to modify many of the properties within PathPrefs.
- PreferencePane() - Constructor for class qupath.lib.gui.panes.PreferencePane
- PreferencePane.AppearancePreferences - Class in qupath.lib.gui.panes
- PreferencePane.DrawingPreferences - Class in qupath.lib.gui.panes
- PreferencePane.ExtensionPreferences - Class in qupath.lib.gui.panes
- PreferencePane.GeneralPreferences - Class in qupath.lib.gui.panes
- PreferencePane.InputOutputPreferences - Class in qupath.lib.gui.panes
- PreferencePane.LocalePreferences - Class in qupath.lib.gui.panes
- PreferencePane.MeasurementPreferences - Class in qupath.lib.gui.panes
- PreferencePane.ObjectPreferences - Class in qupath.lib.gui.panes
- PreferencePane.ScriptingPreferences - Class in qupath.lib.gui.panes
- PreferencePane.UndoRedoPreferences - Class in qupath.lib.gui.panes
- PreferencePane.ViewerPreferences - Class in qupath.lib.gui.panes
- PREFERENCES - Variable in class qupath.lib.gui.actions.CommonActions
- PREFERENCES - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.Actions
- preferReturnToMove() - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
-
Returns false.
- prefHeight(double) - Method in class qupath.lib.gui.ColorMapCanvas
- prefHeight(double) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Deprecated.Specify the preferred height of the dialog pane.
- prefWidth(double) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Deprecated.Specify the preferred width of the dialog pane.
- previousSelectedToolProperty() - Method in class qupath.lib.gui.ToolManager
-
Property storing the previous tool that was selected.
- progressMonitor(DoubleConsumer) - Method in class qupath.lib.gui.tools.MeasurementExporter
-
Set a progress monitor to be notified during export.
- PROJECT_ADD_IMAGES - Variable in class qupath.lib.gui.actions.CommonActions
- PROJECT_CLOSE - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
- PROJECT_NEW - Variable in class qupath.lib.gui.actions.CommonActions
- PROJECT_NEW - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
- PROJECT_OPEN - Variable in class qupath.lib.gui.actions.CommonActions
- PROJECT_OPEN - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
- projectActions - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
- ProjectActions() - Constructor for class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
- ProjectBrowser - Class in qupath.lib.gui.panes
-
Component for previewing and selecting images within a project.
- ProjectBrowser(QuPathGUI) - Constructor for class qupath.lib.gui.panes.ProjectBrowser
-
Constructor.
- ProjectCommands - Class in qupath.lib.gui.commands
-
Helper class implementing simple 'single-method' commands related to projects.
- ProjectCommands() - Constructor for class qupath.lib.gui.commands.ProjectCommands
- ProjectDialogs - Class in qupath.lib.gui.dialogs
-
Dialogs specifically related to managing projects.
- ProjectDialogs() - Constructor for class qupath.lib.gui.dialogs.ProjectDialogs
- projectionProperty() - Method in class qupath.lib.gui.viewer.overlays.ZProjectOverlay
- projectProperty() - Method in class qupath.lib.gui.QuPathGUI
-
Read-only property representing the currently-open project.
- PROMPT - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.ImageTypeSetting
-
Prompt the user to specified the image type
- promptForDirectory(File) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Prompt user to select a directory.
- promptForDirectory(String, File) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Prompt user to select a directory.
- promptForFile(File) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Prompt user to select a file.
- promptForFile(String...) - Static method in class qupath.lib.gui.scripting.QPEx
-
Prompt the user to select a file from a file chooser.
- promptForFile(String, File, String, String...) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Prompt the user for a file with some kind of file dialog.
- promptForFilePathOrURL(String, String, File, String, String...) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Prompt user to select a file or input a URL.
- promptForMultipleFiles(String, File, String, String...) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Prompt to open a list of files.
- promptForParentObjects(String, ImageData<?>, boolean, Collection<Class<? extends PathObject>>) - Static method in class qupath.lib.gui.tools.GuiTools
-
Get the parent objects to use when running the plugin, or null if no suitable parent objects are found.
- promptForSliderRange(Slider) - Static method in class qupath.lib.gui.tools.GuiTools
-
Prompt the user to input min/max values for a slider.
- promptToAddColumnAfterSelected(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands
-
Prompt to add a column to a TMA grid after the column containing the currently-selected object.
- promptToAddColumnBeforeSelected(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands
-
Prompt to add a column to a TMA grid before the column containing the currently-selected object.
- promptToAddNoteToSelectedCores(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands
-
Prompt to type a node to associate with the selected TMA cores.
- promptToAddRowAfterSelected(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands
-
Prompt to add a row to a TMA grid after the row containing the currently-selected object.
- promptToAddRowBeforeSelected(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands
-
Prompt to add a row to a TMA grid before the row containing the currently-selected object.
- promptToAddShapeFeatures(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
-
Prompt to add shape features for selected objects.
- promptToCheckURIs(Project<?>, boolean) - Static method in class qupath.lib.gui.commands.ProjectCommands
-
Check the URIs within a project, prompting the user to correct any broken links if required.
- promptToClearAllSelectedObjects(ImageData<?>) - Static method in class qupath.lib.gui.tools.GuiTools
-
Prompt user to select all currently-selected objects (except TMA core objects).
- promptToCreateProject(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
-
Prompt the user to select an empty directory, and use this to create a new project and set it as active.
- promptToCreateTMAGrid(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands
-
Prompt the user to manually create a new TMA grid.
- promptToDeleteObjects(ImageData<?>, Class<? extends PathObject>) - Static method in class qupath.lib.gui.commands.Commands
-
Prompt to delete objects of a specified type, or all objects.
- promptToDeleteTMAGridColumn(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands
-
Prompt to delete a column from a TMA grid.
- promptToDeleteTMAGridRow(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands
-
Prompt to delete a row from a TMA grid.
- promptToEditClass(PathClass) - Static method in class qupath.lib.gui.commands.Commands
-
Prompt to edit the name/color of a class.
- promptToEstimateStainVectors(ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands
-
Prompt to estimate stain vectors for the specified image, using any current region of interest.
- promptToExportImageList(Project<?>) - Static method in class qupath.lib.gui.commands.ProjectCommands
-
Prompt to export a text file containing a list of image paths for a project.
- promptToExportImageRegion(QuPathViewer, boolean) - Static method in class qupath.lib.gui.commands.Commands
-
Prompt to export the current image region selected in the viewer.
- promptToExportTMAData(QuPathGUI, ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.TMACommands
-
Prompt to export summary TMA data for a specific image to a directory.
- promptToImportImages(QuPathGUI, String...) - Static method in class qupath.lib.gui.commands.ProjectCommands
-
Show prompt for the user to select images to import into the current project in QuPath, choosing a suitable
ImageServerBuilder. - promptToImportImages(QuPathGUI, ImageServerBuilder<BufferedImage>, String...) - Static method in class qupath.lib.gui.commands.ProjectCommands
-
Show prompt for the user to select images to import into the current project in QuPath.
- promptToImportLegacyProject(QuPathGUI) - Static method in class qupath.lib.gui.commands.ProjectCommands
-
Prompt the user to select a legacy project file, and then import the images into the current project.
- promptToImportObjects(PathObjectHierarchy, Collection<? extends PathObject>) - Static method in class qupath.lib.gui.commands.InteractiveObjectImporter
-
Import a collection of objects to an object hierarchy, prompting to confirm and asking whether to update IDs.
- promptToImportObjectsFromFile(ImageData<BufferedImage>, File) - Static method in class qupath.lib.gui.commands.InteractiveObjectImporter
-
Prompt to import objects read from a file.
- promptToImportObjectsProjectEntry(ImageData<BufferedImage>, ProjectImageEntry<?>) - Static method in class qupath.lib.gui.commands.InteractiveObjectImporter
-
Prompt to import objects from a project entry.
- promptToImportTMAData(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands
-
Prompt to import TMA data for the specified image data.
- promptToOpenImageFile() - Method in class qupath.lib.gui.QuPathGUI
-
Show a file chooser to open a new image in the current viewer.
- promptToOpenImageFileOrUri() - Method in class qupath.lib.gui.QuPathGUI
-
Show a dialog to open a new image in the current viewer, with support for entering a URL (rather than requiring a local file only).
- promptToOpenProject(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
-
Prompt the user to open an existing project and set it as active.
- promptToPasteObjectsFromClipboard(ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.InteractiveObjectImporter
-
Prompt to paste objects from the system clipboard, if possible.
- promptToRelabelTMAGrid(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands
-
Prompt to relabel the core names within a TMA grid.
- promptToRemoveSelectedObject(PathObject, PathObjectHierarchy) - Static method in class qupath.lib.gui.tools.GuiTools
-
Prompt to remove a single, specified selected object.
- promptToResetPreferences() - Static method in class qupath.lib.gui.commands.Commands
-
Reset QuPath's preferences, after confirming with the user.
- promptToResolveHierarchy(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands
-
Resolve parent-child relationships within the object hierarchy.
- promptToSaveFile(String, File, String, String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Prompt user to select a file path to save.
- promptToSaveFile(String, File, String, Map<String, String>) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Prompt user to select a file path to save, providing zero or more file extensions as an option.
- promptToSaveImageData(QuPathGUI, ImageData<BufferedImage>, boolean) - Static method in class qupath.lib.gui.commands.Commands
-
Prompt to save the specified
ImageData. - promptToSelectImage(String, boolean) - Method in class qupath.lib.gui.panes.ServerSelector
-
Prompt to select a single
ImageServer. - promptToSelectImages(String) - Method in class qupath.lib.gui.panes.ServerSelector
-
Prompt to select multiple ImageServers.
- promptToSelectObjectsByClassification(QuPathGUI, ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands
-
Prompt to select objects according to their classifications.
- promptToSetActiveAnnotationProperties(PathObjectHierarchy) - Static method in class qupath.lib.gui.tools.GuiTools
-
Prompt the user to set properties for the currently-selected annotation(s).
- promptToSetFontSize() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
-
Update the font size for the script editor and console.
- promptToSetGridLineSpacing(OverlayOptions) - Static method in class qupath.lib.gui.commands.Commands
-
Prompt to input the spacing for the grid lines optionally displayed on viewers.
- promptToSetImageType(ImageData<BufferedImage>, ImageData.ImageType) - Static method in class qupath.lib.gui.panes.ImageDetailsPane
-
Prompt the user to set the
ImageData.ImageTypefor the image. - promptToSimplifySelectedAnnotations(ImageData<?>, double) - Static method in class qupath.lib.gui.commands.Commands
-
Show a prompt to selected annotations in a hierarchy.
- promptToUpdateUris(Collection<T>, URI, URI, boolean) - Static method in class qupath.lib.gui.commands.UpdateUrisCommand
-
Show dialog prompting the user to update URIs for missing files.
- PROPERTIES - Static variable in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
- PropertiesLanguage - Class in qupath.lib.gui.scripting.languages
-
Class for the representation of properties and config files in QuPath.
- propertyChange(PropertyChangeEvent) - Method in class qupath.lib.gui.panes.ImageDetailsPane
- propertyChange(PropertyChangeEvent) - Method in class qupath.lib.gui.panes.SelectedMeasurementTableView
- putActionProperty(MenuItem, Action) - Static method in class qupath.lib.gui.actions.ActionTools
-
Add an Action to the properties of a MenuItem, so that it may be retrieved later.
- putActionProperty(Node, Action) - Static method in class qupath.lib.gui.actions.ActionTools
-
Add an Action to the properties of a Node, so that it may be retrieved later.
- PYTHON - Static variable in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
- PYTHON_IMPORTER - Static variable in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
-
Pythonic import statements
- PythonAutoCompletor - Class in qupath.lib.gui.scripting.completors
-
Auto completion support for Python.
- PythonAutoCompletor() - Constructor for class qupath.lib.gui.scripting.completors.PythonAutoCompletor
-
Constructor.
Q
- QPEx - Class in qupath.lib.gui.scripting
-
Alternative to QP offering static methods of use for scripting, along with some extra methods that require access of GUI features.
- QPEx() - Constructor for class qupath.lib.gui.scripting.QPEx
- QUIT - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
- QUPATH_AND_EXTENSIONS - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.AutoUpdateType
-
Check for QuPath and extensions on GitHub
- QUPATH_ONLY - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.AutoUpdateType
-
Check for QuPath updates only
- QUPATH_STARTUP - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
- qupath.lib.display - package qupath.lib.display
-
Classes to control the display of images in a
QuPathViewer. - qupath.lib.display.settings - package qupath.lib.display.settings
-
Classes to support storing and retrieving image display settings.
- qupath.lib.gui - package qupath.lib.gui
-
The main QuPath user interface.
- qupath.lib.gui.actions - package qupath.lib.gui.actions
-
Classes to manage Actions.
- qupath.lib.gui.actions.annotations - package qupath.lib.gui.actions.annotations
-
Annotations that can be used to configure actions.
- qupath.lib.gui.actions.menus - package qupath.lib.gui.actions.menus
-
Classes to store actions that correspond to QuPath's main menus.
- qupath.lib.gui.charts - package qupath.lib.gui.charts
-
Classes for plotting and charting.
- qupath.lib.gui.commands - package qupath.lib.gui.commands
-
Commands shown within the main QuPath interface.
- qupath.lib.gui.commands.display - package qupath.lib.gui.commands.display
-
Extra package to organize the classes related to the Brightness/Contrast command.
- qupath.lib.gui.commands.objects - package qupath.lib.gui.commands.objects
- qupath.lib.gui.dialogs - package qupath.lib.gui.dialogs
-
Helper classes for creating dialogs, prompts and filt choosers within QuPath.
- qupath.lib.gui.extensions - package qupath.lib.gui.extensions
-
Interface to define QuPath extensions.
- qupath.lib.gui.images.servers - package qupath.lib.gui.images.servers
-
Custom ImageServers that depend upon the QuPath interface and image display settings.
- qupath.lib.gui.images.stores - package qupath.lib.gui.images.stores
-
Classes for requesting, caching and drawing image tiles.
- qupath.lib.gui.localization - package qupath.lib.gui.localization
- qupath.lib.gui.logging - package qupath.lib.gui.logging
-
Support for logging.
- qupath.lib.gui.measure - package qupath.lib.gui.measure
-
Classes related to extracting, calculating and displaying measurements.
- qupath.lib.gui.measure.ui - package qupath.lib.gui.measure.ui
- qupath.lib.gui.panes - package qupath.lib.gui.panes
-
Panes used to display information in the QuPath interface.
- qupath.lib.gui.prefs - package qupath.lib.gui.prefs
-
Custom preferences.
- qupath.lib.gui.scripting - package qupath.lib.gui.scripting
-
Scripting through the QuPath interface.
- qupath.lib.gui.scripting.completors - package qupath.lib.gui.scripting.completors
-
Classes for auto-completion in QuPath's script editor.
- qupath.lib.gui.scripting.languages - package qupath.lib.gui.scripting.languages
-
Language and syntax definitions for QuPath scripting.
- qupath.lib.gui.scripting.syntax - package qupath.lib.gui.scripting.syntax
-
Classes for syntax help in QuPath's script editor.
- qupath.lib.gui.tma - package qupath.lib.gui.tma
-
Display, summarize and query tissue microarray analysis results.
- qupath.lib.gui.tools - package qupath.lib.gui.tools
-
Assorted helper classes for the QuPath interface.
- qupath.lib.gui.viewer - package qupath.lib.gui.viewer
-
QuPath image viewing and display.
- qupath.lib.gui.viewer.overlays - package qupath.lib.gui.viewer.overlays
-
Support for overlays, which may be painted on top of
QuPathViewers. - qupath.lib.gui.viewer.recording - package qupath.lib.gui.viewer.recording
-
Record and display field of view changes made within a
QuPathViewer. - qupath.lib.gui.viewer.tools - package qupath.lib.gui.viewer.tools
-
Drawing and navigation tools for the QuPath toolbar.
- qupath.lib.gui.viewer.tools.handlers - package qupath.lib.gui.viewer.tools.handlers
- QuPathApp - Class in qupath.lib.gui
-
Launcher application to start QuPath.
- QuPathApp() - Constructor for class qupath.lib.gui.QuPathApp
- QuPathExtension - Interface in qupath.lib.gui.extensions
-
Simple interface for QuPath extensions.
- QuPathGUI - Class in qupath.lib.gui
-
Main GUI for QuPath, written using JavaFX.
- QuPathPenManager - Class in qupath.lib.gui.viewer.tools
-
Helper class for managing pressure-sensitive input.
- QuPathPenManager() - Constructor for class qupath.lib.gui.viewer.tools.QuPathPenManager
- QuPathPenManager.PenInputManager - Interface in qupath.lib.gui.viewer.tools
-
Interface defining minimal behavior for a pen input device.
- QuPathResources - Class in qupath.lib.gui.localization
-
Load strings from the default resource bundle.
- QuPathResources() - Constructor for class qupath.lib.gui.localization.QuPathResources
- QuPathStyleManager - Class in qupath.lib.gui.prefs
-
Class to facilitate the use of different styles within QuPath.
- QuPathStyleManager() - Constructor for class qupath.lib.gui.prefs.QuPathStyleManager
- QuPathStyleManager.Fonts - Enum Class in qupath.lib.gui.prefs
-
Available font families.
- QuPathStyleManager.StyleOption - Interface in qupath.lib.gui.prefs
-
Interface defining a style that may be applied to QuPath.
- QuPathTMAViewer - Class in qupath.lib.gui.tma
-
Standalone viewer for looking at TMA summary results.
- QuPathTMAViewer() - Constructor for class qupath.lib.gui.tma.QuPathTMAViewer
- QuPathViewer - Class in qupath.lib.gui.viewer
-
JavaFX component for viewing a (possibly large) image, along with overlays.
- QuPathViewer(DefaultImageRegionStore, OverlayOptions) - Constructor for class qupath.lib.gui.viewer.QuPathViewer
-
Create a new viewer.
- QuPathViewerListener - Interface in qupath.lib.gui.viewer
-
Interface for defining a listener that needs to know whenever the data related to a QuPathViewer has changed in some way - such as by changing the underlying ImageData, or by moving the field of view.
- QuPathViewerPlus - Class in qupath.lib.gui.viewer
-
A whole slide viewer with optional extras...
- QuPathViewerPlus(DefaultImageRegionStore, OverlayOptions, ViewerPlusDisplayOptions) - Constructor for class qupath.lib.gui.viewer.QuPathViewerPlus
-
Create a new viewer.
R
- random(Random) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Set the random number generator.
- RAW - Enum constant in enum class qupath.lib.gui.charts.HistogramChart.CountsTransformMode
-
Raw bin counts.
- readFile(File) - Method in class qupath.lib.gui.scripting.ScriptTab
-
Read the file, set the editor's text area with the content of the file and return the detected language (based on the file extension).
- readObjectsFromClipboard(ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.InteractiveObjectImporter
-
Try to read objects from the system clipboard.
- readOnlyProperty() - Method in class qupath.lib.gui.QuPathGUI
-
Property indicating whether QuPath is in 'read-only' mode.
- readPathObjects() - Method in class qupath.lib.gui.images.servers.ChannelDisplayTransformServer
- readRegion(RegionRequest) - Method in class qupath.lib.gui.images.servers.ChannelDisplayTransformServer
- readTile(TileRequest) - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer
- readTile(TileRequest) - Method in class qupath.lib.gui.images.servers.RenderedImageServer
- RECENT_COMMAND_LIST - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- RECENT_COMMANDS - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- recordingProperty() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return the recording property of this
ViewTracker. - RECTANGLE - Static variable in class qupath.lib.gui.viewer.tools.PathTools
-
Rectangle drawing tool
- RECTANGLE_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- RECTANGLE_TOOL - Variable in class qupath.lib.gui.ToolManager
- redo() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
-
Request redo.
- redo() - Method in class qupath.lib.gui.scripting.TextAreaControl
- REDO - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.Actions
- redoAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- redoOnce() - Method in class qupath.lib.gui.UndoRedoManager
-
Request to 'redo' the last 'undone' hierarchy change for the current active viewer.
- refineGeometryByParent(Geometry) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
- refineGeometryByParent(Geometry) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
- refineROIByParent(ROI) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
-
Apply clipping based on the current parent object.
- refineROIByParent(ROI) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
-
Apply clipping based on the current parent object.
- refresh() - Method in class qupath.lib.gui.commands.PathObjectGridView
-
Refresh the data in the grid view
- refresh() - Static method in class qupath.lib.gui.prefs.QuPathStyleManager
-
Refresh the current style.
- REFRESH - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- REFRESH_DUPLICATE_OBJECT_IDS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.Actions
- REFRESH_OBJECT_IDS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.Actions
- refreshAllEditors() - Method in class qupath.lib.gui.panes.PreferencePane
-
Request that all the property editors are regenerated.
- refreshChannelOptions() - Method in class qupath.lib.display.ImageDisplay
-
Refresh the channel options.
- refreshCombo() - Method in class qupath.lib.gui.charts.HistogramDisplay
-
Refresh the available measurements.
- refreshData() - Method in class qupath.lib.gui.charts.PathObjectScatterChart
-
Recalculate the values of all data points.
- refreshFileContents() - Method in class qupath.lib.gui.scripting.ScriptTab
- refreshHistogram() - Method in class qupath.lib.gui.charts.HistogramDisplay
-
Refresh the currently-displayed histogram (e.g.
- refreshList(ListView<T>) - Static method in class qupath.lib.gui.tools.GuiTools
-
Refresh a
ListViewin the Application thread. - refreshObjectIDs(ImageData<?>, boolean) - Static method in class qupath.lib.gui.commands.Commands
-
Refresh object IDs to ensure uniqueness.
- refreshProject() - Method in class qupath.lib.gui.panes.ProjectBrowser
-
Refresh the current project, updating the displayed entries.
- refreshProject() - Method in class qupath.lib.gui.QuPathGUI
-
Refresh the project, updating the display if required.
- refreshScatterPlot() - Method in class qupath.lib.gui.charts.ScatterPlotDisplay
-
Refresh the scatter plot, in case the underlying data has been updated.
- refreshSliders() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSliderPane
-
Refresh the sliders, to ensure they match with the current channel.
- refreshTitle() - Method in class qupath.lib.gui.QuPathGUI
-
Refresh the title bar in the main QuPath window.
- refreshTitles() - Method in class qupath.lib.gui.viewer.ViewerManager
-
Request that viewers refresh their titles.
- RegionFilter - Interface in qupath.lib.gui.viewer
-
Define the area of an image to which pixel classification should be applied.
- RegionFilter.StandardRegionFilters - Enum Class in qupath.lib.gui.viewer
-
Standard classification regions (hopefully all you will ever need).
- registerRequest(TileListener<BufferedImage>, ImageServer<BufferedImage>, Shape, double, int, int) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
-
Register a request so that the tile request queue will be populated, including potentially for nearby tiles (i.e.
- registerTool(QuPathViewer) - Method in class qupath.lib.gui.viewer.tools.ExtendedPathTool
- registerTool(QuPathViewer) - Method in interface qupath.lib.gui.viewer.tools.PathTool
-
Register the tool on the viewer.
- RELABEL - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
- relativeToUserDirectory() - Method in class qupath.lib.gui.FileCopier
-
Specify that the copying is relative to the QuPath user directory.
- RELOAD_DATA - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
- reloadImageData(QuPathGUI, ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands
-
Reload the specified image data from a previously saved version,if available.
- REMOVE_COLUMN - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions.RemoveActions
- REMOVE_FRAGMENTS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
- REMOVE_ROW - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions.RemoveActions
- removeActions - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
- RemoveActions() - Constructor for class qupath.lib.gui.actions.menus.TMAMenuActions.Actions.RemoveActions
- removeColumn(QuPathViewer) - Method in class qupath.lib.gui.viewer.ViewerManager
-
Try to remove the column containing the specified viewer, notifying the user if this isn't possible.
- removeFileDropHandler(DragDropImportListener.DropHandler<File>) - Method in class qupath.lib.gui.viewer.DragDropImportListener
-
Remove a File DropHandler.
- removeJsonDropHandler(DragDropImportListener.DropHandler<JsonElement>) - Method in class qupath.lib.gui.viewer.DragDropImportListener
-
Remove a JSON DropHandler.
- removeOnImageBounds(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands
-
Delete all objects touching the image boundary.
- removeParameterChangeListener(ParameterChangeListener) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX
-
Remove a
ParameterChangeListener. - removeRow(QuPathViewer) - Method in class qupath.lib.gui.viewer.ViewerManager
-
Try to remove the row containing the specified viewer, notifying the user if this isn't possible.
- removeTextAppendableFX(TextAppendable) - Static method in class qupath.lib.gui.logging.LogManager
-
Deregister a
TextAppendableso that it will no longer be informed of logging events. - removeTileListener(TileListener<BufferedImage>) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
- removeViewerListener(QuPathViewerListener) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Remove a viewer listener.
- RenderedImageServer - Class in qupath.lib.gui.images.servers
-
An ImageServer that can display a rendered image, with optional overlays.
- RenderedImageServer.Builder - Class in qupath.lib.gui.images.servers
-
Builder to create an ImageServer to display rendered images, with optional overlay layers.
- renderer(ImageRenderer) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder
-
Specify the
ImageRendererthat controls conversion to RGB. - rendererProperty() - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
-
Get the
ImageRendererproperty used with this overlay. - rendererProperty() - Method in class qupath.lib.gui.viewer.overlays.ZProjectOverlay
-
Get the
ImageRendererproperty used with this overlay. - repaint() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Request that the viewer is repainted.
- repaintAllViewers() - Method in class qupath.lib.gui.viewer.ViewerManager
-
Request that all viewers are repainted as soon as possible.
- repaintEntireImage() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Request that the entire image is repainted, including the thumbnail.
- repaintEntireImage() - Method in class qupath.lib.gui.viewer.QuPathViewerPlus
- repaintTimestamp() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the timestamp referring to the last time this viewer was repainted.
- replaceSelection(String) - Method in interface qupath.lib.gui.scripting.EditableText
-
Insert the specified text, replacing any existing selection.
- replaceSelection(String) - Method in class qupath.lib.gui.scripting.TextAreaControl
- requestAutomaticUpdateCheck() - Method in class qupath.lib.gui.QuPathGUI
-
Request an automated update check in a background thread.
- requestCancelDirection(boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Requests that the viewer cancels either the x- or y-axis direction.
- requestClose() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
- requestClose() - Method in interface qupath.lib.gui.scripting.ScriptEditor
-
Attempt to close the editor, saving changes if requested.
- requestDecelerate() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Request that a viewer decelerate any existing panning smoothly.
- requestFocus() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
-
Request that the control is focused.
- requestFocus() - Method in class qupath.lib.gui.scripting.TextAreaControl
- requestFollowCaret() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
-
Request that the X and Y scrolls are adjusted to ensure the caret is visible.
- requestFullUpdateCheck() - Method in class qupath.lib.gui.QuPathGUI
-
Request a manual update check in a background thread.
- requestImageTile(ImageServer<BufferedImage>, RegionRequest, Map<RegionRequest, BufferedImage>, boolean) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
-
Request an image tile.
- requestParentClipping(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
-
Query whether parent clipping should be applied.
- requestParentClipping(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
-
Query whether parent clipping should be applied.
- requestPixelSnapping() - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
-
Returns true if the tool requests that pixel coordinates be snapped to integer values.
- requestPixelSnapping() - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
-
Returns true if the tool requests that pixel coordinates be snapped to integer values.
- requestStartMoving(double, double) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Request that the viewer start panning with a velocity determined by dx and dy.
- requestStopMoving() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Request that the viewer stop any panning immediately.
- requestUserDirectory(boolean) - Static method in class qupath.lib.gui.commands.Commands
-
Request the current user directory, optionally prompting the user to request a directory if none is available.
- requiresTileRegion(String, ImageRegion) - Method in interface qupath.lib.gui.images.stores.TileListener
-
Check if the listener requires a particular tile.
- requiresTileRegion(String, ImageRegion) - Method in class qupath.lib.gui.viewer.QuPathViewer
- RESET_DETECTION_CLASSIFICATIONS - Variable in class qupath.lib.gui.actions.menus.ClassifyMenuActions.Actions
- RESET_METADATA - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
- RESET_PREFERENCES - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.Actions
- RESET_SELECTION - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
- resetAllSliders() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSliderPane
-
Reset all sliders to their default values.
- resetAvailablePathClasses() - Method in class qupath.lib.gui.QuPathGUI
-
Populate the availablePathClasses with a default list.
- resetClassifications(ImageData<?>, Class<? extends PathObject>) - Static method in class qupath.lib.gui.commands.Commands
-
Select objects that are instances of a specified class, logging an appropriate method in the workflow.
- resetConstrainingObjects() - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
-
Reset the constraining objects.
- resetConstrainingObjects() - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
-
Reset the constraining objects.
- resetCustomPixelLayerOverlay() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Reset the custom pixel layer overlay to null.
- resetGridSize() - Method in class qupath.lib.gui.viewer.ViewerManager
- resetImage() - Method in class qupath.lib.gui.panes.SimpleImageViewer
-
Remove the image.
- resetImageData() - Method in class qupath.lib.gui.viewer.overlays.HierarchyOverlay
-
Reset the last image data.
- resetImageData() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Reset the image data to null.
- resetMeasurementMapper() - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Reset any
MeasurementMapper, so that measurements are not used to determine object colors. - resetMinimumRepaintSpacingMillis() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Return to processing all repainting requests.
- resetPreferences() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Reset the preferences to their defaults.
- resetSelection(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands
-
Reset the selection for an image.
- resetShowObjectPredicate() - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Reset the value of
OverlayOptions.showObjectPredicateProperty(). - resetTMAMetadata(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands
-
Reset TMA metadata, if available.
- resizable() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Deprecated.Make the dialog resizable (but default it is not).
- resize(double, double) - Method in class qupath.lib.gui.ColorMapCanvas
- RESOLVE_HIERARCHY - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
- resourceManagerProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSettingsPane
-
The resource manager used to handle saving/loading.
- returnToMove - Variable in class qupath.lib.gui.panes.PreferencePane.DrawingPreferences
- returnToMoveModeProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Request that the GUI returns to using the PAN tool after a ROI is drawn.
- RIGID_OBJECT_EDITOR - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
- rngSeedProperty() - Method in class qupath.lib.gui.charts.PathObjectScatterChart
-
Get a property representing the random number generator's seed for subsampling.
- rootLogLevelProperty() - Static method in class qupath.lib.gui.logging.LogManager
-
Property representing the current requested root log level.
- ROTATE_IMAGE - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- rotationProperty() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Return the rotation property of this viewer.
- run() - Method in class qupath.lib.gui.commands.BrightnessContrastCommand
- run() - Method in class qupath.lib.gui.commands.CountingDialogCommand
- run() - Method in class qupath.lib.gui.commands.MeasurementExportCommand
- run() - Method in class qupath.lib.gui.JavadocViewerRunner
- run() - Method in class qupath.lib.gui.tma.TMAExplorer
- run() - Method in class qupath.lib.gui.tools.DocGenerator
- run() - Method in class qupath.lib.gui.viewer.recording.ViewTrackerControlPane
- run(ImageData<?>) - Method in class qupath.lib.gui.commands.objects.SplitAnnotationsByLineCommand
-
Run the command for the specified image data.
- runForImage(ImageData<?>) - Method in class qupath.lib.gui.commands.DeleteObjectsOnBoundsCommand
-
Run the command interactively for the specified image.
- runGeoJsonExport(QuPathGUI) - Static method in class qupath.lib.gui.commands.ExportObjectsCommand
-
Run the path object GeoJSON export command.
- runGeoJsonObjectExport(QuPathGUI, ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands
-
Show a dialog to export object(s) to a GeoJSON file.
- runObjectImport(QuPathGUI, ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands
-
Show a dialog to import object(s) from a file.
- runPlugin(String, String) - Static method in class qupath.lib.gui.scripting.QPEx
- runPlugin(String, ImageData<?>, String) - Static method in class qupath.lib.gui.scripting.QPEx
- runPlugin(PathPlugin<BufferedImage>, String, boolean) - Method in class qupath.lib.gui.QuPathGUI
-
Run a plugin, interactively (i.e.
- runProjectScriptAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- runProjectScriptNoSaveAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- runScript(File, String) - Method in class qupath.lib.gui.QuPathGUI
-
Convenience method to execute a script.
- runScriptAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- runSelectedAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- runTasks(String, Collection<? extends Runnable>) - Method in class qupath.lib.gui.TaskRunnerFX
S
- SANS_SERIF - Enum constant in enum class qupath.lib.gui.prefs.QuPathStyleManager.Fonts
-
Preferred sans-serif font.
- saturationPercentProperty() - Method in class qupath.lib.gui.panes.SimpleImageViewer
-
Get the percentage of any non-8-bit image that should be saturated when applying auto contrast settings.
- SAVE_DATA - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
- SAVE_DATA_AS - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
- saveAnnotationMeasurements(String, String...) - Static method in class qupath.lib.gui.scripting.QPEx
-
Save annotation measurements for the current image.
- saveAnnotationMeasurements(ImageData<?>, String, String...) - Static method in class qupath.lib.gui.scripting.QPEx
-
Save annotation measurements for the specified image.
- saveCellMeasurements(String, String...) - Static method in class qupath.lib.gui.scripting.QPEx
-
Save cell measurements for the current image.
- saveChannelColorProperties() - Method in class qupath.lib.display.ImageDisplay
-
Save color channels in the ImageData properties.
- saveDetectionMeasurements(String, String...) - Static method in class qupath.lib.gui.scripting.QPEx
-
Save detection measurements for the current image.
- saveDetectionMeasurements(ImageData<?>, String, String...) - Static method in class qupath.lib.gui.scripting.QPEx
-
Save detection measurements for the specified image.
- saveImageMeasurements(String, String...) - Static method in class qupath.lib.gui.scripting.QPEx
-
Save whole image measurements for the current image.
- saveImageMeasurements(ImageData<?>, String, String...) - Static method in class qupath.lib.gui.scripting.QPEx
-
Save whole image measurements for the specified image.
- saveMeasurements(Class<? extends PathObject>, String, String...) - Static method in class qupath.lib.gui.scripting.QPEx
-
Save measurements for the current image for objects of a fixed type.
- saveMeasurements(ImageData<?>, Class<? extends PathObject>, String, String...) - Static method in class qupath.lib.gui.scripting.QPEx
-
Save measurements for the specified image for objects of a fixed type.
- savePreferences() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Save the preferences.
- saveSnapshot(QuPathGUI, GuiTools.SnapshotType) - Static method in class qupath.lib.gui.commands.Commands
-
Save an image snapshot, prompting the user to select the output file.
- saveSnapshotWithDelay(QuPathGUI, GuiTools.SnapshotType, long) - Static method in class qupath.lib.gui.commands.Commands
-
Save an image snapshot after a specified delay, prompting the user to select the output file.
- saveTableModel(PathTableData<?>, File, Collection<String>) - Static method in class qupath.lib.gui.measure.ui.SummaryMeasurementTable
-
Save the data from a table to a text file, using the default delimiter from
PathPrefs. - saveTileMeasurements(String, String...) - Static method in class qupath.lib.gui.scripting.QPEx
-
Save tile measurements for the current image.
- saveTMAMeasurements(String, String...) - Static method in class qupath.lib.gui.scripting.QPEx
-
Save TMA measurements for the current image.
- saveTMAMeasurements(ImageData<?>, String, String...) - Static method in class qupath.lib.gui.scripting.QPEx
-
Save TMA measurements for the specified image.
- scalebarFontSize - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
- scalebarFontSizeProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Preferred font size for the scalebar in the viewer.
- scalebarFontWeight - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
- scalebarFontWeightProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Preferred font weight in the viewer.
- scalebarLineWidth - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
- scalebarLineWidthProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Preferred line width for the scalebar.
- scatterChart() - Static method in class qupath.lib.gui.charts.Charts
-
Create a
Charts.ScatterChartBuilderfor generating a custom scatter plot. - ScatterPlotDisplay - Class in qupath.lib.gui.charts
-
A wrapper around
PathObjectScatterChartfor displaying data about PathObject measurements. - ScatterPlotDisplay() - Constructor for class qupath.lib.gui.charts.ScatterPlotDisplay
-
Create a scatter plot from a table of PathObject measurements.
- SCREENSHOT - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- SCRIPT_EDITOR - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- SCRIPT_EDITOR - Variable in class qupath.lib.gui.actions.AutomateActions
- SCRIPT_EDITOR - Variable in class qupath.lib.gui.actions.menus.AutomateMenuActions.Actions
- SCRIPT_INTERPRETER - Variable in class qupath.lib.gui.actions.AutomateActions
- SCRIPT_INTERPRETER - Variable in class qupath.lib.gui.actions.menus.AutomateMenuActions.Actions
- ScriptEditor - Interface in qupath.lib.gui.scripting
-
Minimal interface for a script editor that the GUI can call.
- ScriptEditorControl<T> - Interface in qupath.lib.gui.scripting
-
Basic script editor control using JavaFX.
- ScriptingPreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.ScriptingPreferences
- ScriptLanguageProvider - Class in qupath.lib.gui.scripting.languages
-
Class with static methods to fetch all the available ScriptLanguages.
- ScriptLanguageProvider() - Constructor for class qupath.lib.gui.scripting.languages.ScriptLanguageProvider
- scriptRunning() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
-
Observable value indicating whether a script is currently running or not.
- scriptsDirectoryProperty() - Method in class qupath.lib.gui.UserDirectoryManager
-
Read only property representing the shared scripts directory.
- scriptsPath - Variable in class qupath.lib.gui.panes.PreferencePane.ExtensionPreferences
- scriptsPath - Variable in class qupath.lib.gui.panes.PreferencePane.ScriptingPreferences
- scriptsPathProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Path to a directory containing scripts for quick-access through the user interface.
- ScriptSyntax - Interface in qupath.lib.gui.scripting.syntax
-
Interface for classes that apply some syntax formatting to an
EditableText. - ScriptSyntaxProvider - Class in qupath.lib.gui.scripting.syntax
-
Class with static methods to fetch all the available ScriptSyntaxes.
- ScriptSyntaxProvider() - Constructor for class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
- ScriptTab - Class in qupath.lib.gui.scripting
-
Class representing a script tab (e.g.
- scrollSpeed - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
- scrollSpeedProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Percentage to scale scroll speed for zooming etc.
- SELECT_ALL_ANNOTATION - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
- SELECT_ALL_DETECTIONS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
- SELECT_ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
- SELECT_BY_CLASSIFICATION - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
- SELECT_BY_PLANE - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
- SELECT_CELLS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
- SELECT_TILES - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
- SELECT_TMA_CORES - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
- selectable(boolean) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
-
Sets the selectable property of the action.
- SelectableItem<T> - Class in qupath.lib.gui
-
Helper class for managing items when only one of them may be selected.
- SelectableItem(ObjectProperty<T>, T) - Constructor for class qupath.lib.gui.SelectableItem
-
Constructor.
- selectActions - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.Actions
- SelectActions() - Constructor for class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
- selectAllObjects(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands
-
Select all objects (excluding the root object) in the imageData.
- selected(boolean) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
-
Set the selected property of the action.
- selected(ObservableValue<Boolean>) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
-
Bind the selected property of the action to an
ObservableValue, bidirectionally if possible. - selectedChannelProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSliderPane
-
The channel to which the sliders are applied.
- selectedChannels() - Method in class qupath.lib.display.ImageDisplay
-
Read-only observable list containing the channels currently selected for display.
- selectedClassesProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
- selectedClassVisibilityModeProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Request that only exact matches to classes in
OverlayOptions.selectedClassesProperty()should be hidden. - selectedColor - Variable in class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
- SelectedMeasurementTableView - Class in qupath.lib.gui.panes
-
Component to show measurements for a currently-selected object.
- SelectedMeasurementTableView(ObservableValue<ImageData<BufferedImage>>) - Constructor for class qupath.lib.gui.panes.SelectedMeasurementTableView
-
Constructor.
- selectedObjectChanged(QuPathViewer, PathObject) - Method in class qupath.lib.gui.UndoRedoManager
- selectedObjectChanged(QuPathViewer, PathObject) - Method in interface qupath.lib.gui.viewer.QuPathViewerListener
-
Called when the primary selected object has changed in a viewer.
- selectedObjectChanged(QuPathViewer, PathObject) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
- selectedObjectChanged(QuPathViewer, PathObject) - Method in class qupath.lib.gui.viewer.ViewerManager
- selectedPathObjectChanged(PathObject, PathObject, Collection<PathObject>) - Method in class qupath.lib.gui.panes.AnnotationPane
- selectedPathObjectChanged(PathObject, PathObject, Collection<PathObject>) - Method in class qupath.lib.gui.panes.PathObjectHierarchyView
- selectedPathObjectChanged(PathObject, PathObject, Collection<PathObject>) - Method in class qupath.lib.gui.panes.SelectedMeasurementTableView
- selectedPathObjectChanged(PathObject, PathObject, Collection<PathObject>) - Method in class qupath.lib.gui.viewer.QuPathViewer
- selectedProperty() - Method in class qupath.lib.gui.SelectableItem
-
Property representing the item that has been selected (which may or may not be the same as
SelectableItem.getItem()). - selectedScriptProperty() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
-
Get a property representing the current selected ScriptTab.
- selectedStyleProperty() - Static method in class qupath.lib.gui.prefs.QuPathStyleManager
-
Get the current selected style.
- selectedTextProperty() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
-
Text currently selected in the editor control.
- selectedTextProperty() - Method in class qupath.lib.gui.scripting.TextAreaControl
- selectedTool() - Method in class qupath.lib.gui.viewer.tools.ExtendedPathTool
- selectedToolProperty() - Method in class qupath.lib.gui.ToolManager
-
Property containing the currently-selected
PathTool. - SELECTION_MODE - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- SELECTION_MODE - Variable in class qupath.lib.gui.ToolManager
- selectionModeProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Convert drawing tools to select objects, rather than creating new objects.
- selectionModeStatus() - Static method in class qupath.lib.gui.prefs.PathPrefs
- selectObjectsByClass(ImageData<?>, Class<? extends PathObject>) - Static method in class qupath.lib.gui.commands.Commands
-
Select objects that are instances of a specified class, logging an appropriate method in the workflow.
- selectObjectsByClassification(ImageData<?>, PathClass...) - Static method in class qupath.lib.gui.commands.Commands
-
Select objects by classification, logging the step (if performed) in the history workflow.
- selectObjectsOnCurrentPlane(QuPathViewer) - Static method in class qupath.lib.gui.commands.Commands
-
Select all the objects on the current plane of the viewer.
- selectRange(int, int) - Method in interface qupath.lib.gui.scripting.EditableText
-
Set the range of the selected text.
- selectRange(int, int) - Method in class qupath.lib.gui.scripting.TextAreaControl
- sendLogToConsoleProperty() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
-
Boolean property indicating whether the console should display the log, rather than directly-printed information.
- sendQuitRequest() - Method in class qupath.lib.gui.QuPathGUI
-
Request to quit QuPath.
- SEP - Variable in class qupath.lib.gui.actions.menus.WindowMenuActions.Actions
- SEP_0 - Variable in class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
- SEP_0 - Variable in class qupath.lib.gui.actions.menus.AutomateMenuActions.Actions
- SEP_0 - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.Actions
- SEP_0 - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
- SEP_0 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- SEP_00 - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.CopyActions
- SEP_00 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
- SEP_00 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
- SEP_01 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
- SEP_01 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
- SEP_02 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
- SEP_02 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
- SEP_1 - Variable in class qupath.lib.gui.actions.menus.ClassifyMenuActions.Actions
- SEP_1 - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.Actions
- SEP_1 - Variable in class qupath.lib.gui.actions.menus.ExtensionsMenuActions.Actions
- SEP_1 - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
- SEP_1 - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
- SEP_1 - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
- SEP_1 - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.DeleteActions
- SEP_1 - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
- SEP_1 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- SEP_2 - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
- SEP_2 - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
- SEP_2 - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
- SEP_2 - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.DeleteActions
- SEP_2 - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
- SEP_2 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- SEP_22 - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
- SEP_3 - Variable in class qupath.lib.gui.actions.menus.ClassifyMenuActions.Actions
- SEP_3 - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
- SEP_3 - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
- SEP_3 - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
- SEP_3 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.ZoomActions
- SEP_4 - Variable in class qupath.lib.gui.actions.menus.ClassifyMenuActions.Actions
- SEP_4 - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
- SEP_4 - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.Actions
- SEP_4 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- SEP_5 - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
- SEP_5 - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
- SEP_5 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- SEP_6 - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
- SEP_6 - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
- SEP_6 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- SEP_7 - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
- SEP_7 - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
- SEP_7 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- SEP_8 - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
- SEP_8 - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
- SEP_8 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- SEP_9 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultitouchActions
- separator(String) - Method in class qupath.lib.gui.tools.MeasurementExporter
-
Specify the separator used between measurement values.
- series(String, String[], double[]) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Create a bar chart using arrays of String values and associated numeric values.
- series(String, String[], double[], List<T>) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Create a bar chart using collections of String values and associated numeric values, with an associated custom object.
- series(String, String[], double[], T[]) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Create a bar chart using collections String values and associated numeric values, with an associated custom object.
- series(String, Collection<? extends String>, Collection<T>) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Create a bar chart using collections of numeric values.
- series(String, Collection<? extends T>, Function<T, PathClass>) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Plot values extracted from objects within a specified collection.
- series(String, Collection<XYChart.Data<String, Number>>) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Create a bar chart from existing data plots.
- series(String, Map<String, T>) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Create a bar chart using a map of String values and associated numeric values.
- SERIF - Enum constant in enum class qupath.lib.gui.prefs.QuPathStyleManager.Fonts
-
Preferred serif font.
- ServerSelector - Class in qupath.lib.gui.panes
-
Helper class for selecting one image server out of a collection.
- setAccelerator(String, String) - Method in class qupath.lib.gui.QuPathGUI
-
Set an accelerator for the specified menu command.
- setAccelerator(MenuItem, KeyCombination) - Method in class qupath.lib.gui.QuPathGUI
-
Set the accelerator for the specified menu item.
- setAccelerator(Action, KeyCombination) - Method in class qupath.lib.gui.QuPathGUI
-
Set the accelerator for the specified action.
- setActiveTool(PathTool) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Set the active
PathToolfor input to this viewer. - setActiveViewer(QuPathViewer) - Method in class qupath.lib.gui.viewer.ViewerManager
-
Sets the value of the
activeViewerproperty. - setAll() - Static method in class qupath.lib.gui.logging.LogManager
-
Set the root log level to LogLevel.ALL.
- setAlphaComposite(Graphics2D) - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay
- setAutorangeToFullData(boolean) - Method in class qupath.lib.gui.charts.PathObjectScatterChart
-
Set the value of
PathObjectScatterChart.autorangeToFullDataProperty(). - setBorderColor(Color) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Set the border color for this viewer.
- setCenterPixelLocation(double, double) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Set the image pixel to display in the center of the viewer (using image pixel coordinates at the full-resolution)
- setChannelDisplayRange(int, double, double) - Static method in class qupath.lib.gui.scripting.QPEx
-
Set the minimum and maximum display range for the current
ImageDatafor a channel identified by number. - setChannelDisplayRange(String, double, double) - Static method in class qupath.lib.gui.scripting.QPEx
-
Set the minimum and maximum display range for the current
ImageDatafor a channel identified by name. - setChannelDisplayRange(ImageData<BufferedImage>, int, double, double) - Static method in class qupath.lib.gui.scripting.QPEx
-
Set the minimum and maximum display range for the specified
ImageDatafor a channel identified by number. - setChannelDisplayRange(ImageData<BufferedImage>, String, double, double) - Static method in class qupath.lib.gui.scripting.QPEx
-
Set the minimum and maximum display range for the specified
ImageDatafor a channel identified by name. - setChannelSelected(ChannelDisplayInfo, boolean) - Method in class qupath.lib.display.ImageDisplay
-
Set the selection of a channel on or off.
- setColorMap(ColorMaps.ColorMap) - Method in class qupath.lib.gui.ColorMapCanvas
-
Set the
ColorMaps.ColorMapto display to the one with the specified list index. - setColorMapper(ColorMaps.ColorMap) - Method in class qupath.lib.gui.tools.MeasurementMapper
-
Set a new color mapper.
- setColorModel(ColorModel) - Method in class qupath.lib.gui.images.stores.ColorModelRenderer
-
Set the color model to use.
- setColorModel(ColorModel) - Method in class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
-
Optionally set a custom
ColorModel. - setContextMenu(ContextMenu) - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
-
Set the context menu for the control.
- setContextMenu(ContextMenu) - Method in class qupath.lib.gui.scripting.TextAreaControl
- setCountsTransform(HistogramChart.CountsTransformMode) - Method in class qupath.lib.gui.charts.HistogramChart
-
Set the current counts transform.
- setCursor(Cursor) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Set the requested cursor to display in this viewer
- setCustomPixelLayerOverlay(PathOverlay) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Optionally set a custom overlay to use for the pixel layer.
- setData(Collection<? extends PathObject>, Function<PathObject, Number>, Function<PathObject, Number>) - Method in class qupath.lib.gui.charts.PathObjectScatterChart
-
Set the data to display in the plot.
- setDataFromTable(Collection<? extends PathObject>, PathTableData<PathObject>, String, String) - Method in class qupath.lib.gui.charts.PathObjectScatterChart
-
Set the data to display in the plot from a table model.
- setDebug() - Static method in class qupath.lib.gui.logging.LogManager
-
Set the root log level to DEBUG.
- setDetectionDisplayMode(OverlayOptions.DetectionDisplayMode) - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Set the current
OverlayOptions.DetectionDisplayMode. - setDisplayMaxValue(double) - Method in class qupath.lib.gui.tools.MeasurementMapper
-
Set the measurement value that maps to the last color in the color mapper.
- setDisplayMinValue(double) - Method in class qupath.lib.gui.tools.MeasurementMapper
-
Set the measurement value that maps to the first color in the color mapper.
- setDisplayMode(HistogramChart.DisplayMode) - Method in class qupath.lib.gui.charts.HistogramChart
-
Set the histogram display mode.
- setDoFasterRepaint(boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Set flag to indicate that repaints should prefer speed over accuracy.
- setDownsample(double) - Method in class qupath.lib.gui.commands.MiniViewers.MiniViewerManager
-
Set the downsample to use within the mini viewers.
- setDownsampleFactor(double) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Set the downsample factor for this viewer.
- setDownsampleFactor(double, double, double) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Set downsample factor, so that the specified coordinate in the image space is not shifted in the viewer afterwards.
- setDownsampleFactor(double, double, double, boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Set downsample factor, so that the specified coordinate in the image space is not shifted in the viewer afterwards.
- setError() - Static method in class qupath.lib.gui.logging.LogManager
-
Set the root log level to LogLevel.ERROR.
- setExcludeOutsideRange(boolean) - Method in class qupath.lib.gui.tools.MeasurementMapper
-
Specify whether out-of-range values should be excluded.
- setExpandToWindow(boolean) - Method in class qupath.lib.gui.panes.SimpleImageViewer
-
Control whether the image should be allowed to expand beyond its preferred width and height to fill the window.
- setFile(File) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Set the file for this
ViewTracker. - setFillAnnotations(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Show annotation objects 'filled' in viewers.
- setFillDetections(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Show detection objects 'filled' in viewers.
- setFillHeight(Boolean, Node...) - Static method in class qupath.lib.gui.tools.PaneTools
-
Deprecated.Set the
GridPane.setFillHeight(Node, Boolean)property for specified nodes. - setFillWidth(Boolean, Node...) - Static method in class qupath.lib.gui.tools.PaneTools
-
Deprecated.Set the
GridPane.setFillWidth(Node, Boolean)property for specified nodes. - setFontSize(float) - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Set the requested font size for the 'Show names' option
- setGamma(double) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Set the gamma value for this viewer.
- setGridLines(GridLines) - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Set the
GridLinesobject that defines how a counting grid may be show in viewers - setGridSize(int, int) - Method in class qupath.lib.gui.viewer.ViewerManager
-
Set the grid to have a specific number of rows and columns.
- setHGrowPriority(Priority, Node...) - Static method in class qupath.lib.gui.tools.PaneTools
-
Deprecated.Set the
GridPane.setHgrow(Node, Priority)property for specified nodes. - setHideChannel(ChannelDisplayInfo) - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane
-
Request that the specified channel is hidden.
- setHideIfEmpty(boolean) - Method in class qupath.lib.gui.charts.HistogramChart
-
Request that the chart is automatically hidden (visibility set to false) when there is no data.
- setImageData(ImageData<?>, Collection<? extends PathObject>) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
-
Set the
ImageDataand a collection of objects to measure. - setImageData(ImageData<BufferedImage>) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Set the current image for this viewer.
- setImageData(ImageData<BufferedImage>, boolean) - Method in class qupath.lib.display.ImageDisplay
-
Set the
ImageDatato a new value - setImageType - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
- setInfo() - Static method in class qupath.lib.gui.logging.LogManager
-
Set the root log level to DEBUG.
- setInputFile(File) - Method in class qupath.lib.gui.tma.TMASummaryViewer
-
Deprecated.Set the input file for the summary viewer.
- setInterpolation(Graphics2D) - Method in class qupath.lib.gui.viewer.overlays.AbstractImageOverlay
- setInterpolation(ImageInterpolation) - Method in class qupath.lib.gui.viewer.overlays.AbstractImageOverlay
-
Set the preferred method of interpolation to use for display.
- setIsInteractive(boolean) - Method in class qupath.lib.gui.charts.ChartThresholdPane
-
Sets the value of
ChartThresholdPane.isInteractiveProperty(). - setItem(S) - Method in interface qupath.lib.gui.tools.PathObjectImageViewers.ItemViewer
-
Set the item to display
- setLanguage(ScriptLanguage) - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
-
Set the language for text to be displayed by this control.
- setLineChartLegendLines(Chart, double) - Static method in class qupath.lib.gui.charts.ChartTools
-
Charts tend to show their legends with circular/square markers...
- setLineWidth(double) - Method in class qupath.lib.gui.charts.ChartThresholdPane
-
Set the threshold line width.
- setLivePrediction(boolean) - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
-
Turn on or off live prediction.
- setLocationStringFunction(AbstractOverlay.LocationStringFunction) - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay
-
Set a custom function to calculate a location string for the overlay.
- setLUTColor(int, int, int) - Method in class qupath.lib.display.DirectServerChannelInfo
-
Set the 'maximum' color, which defines the lookup table to use.
- setMagnification(double) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Set the downsample factor based upon magnification values.
- setMaxDisplay(float) - Method in class qupath.lib.display.AdditiveChannelInfo
- setMaxDisplay(float) - Method in class qupath.lib.display.DirectServerChannelInfo
- setMaxDisplay(float) - Method in interface qupath.lib.display.ChannelDisplayInfo.ModifiableChannelDisplayInfo
-
Set the max display value for this channel.
- setMaxHeight(double, Region...) - Static method in class qupath.lib.gui.tools.PaneTools
-
Deprecated.Set the max height property for the specified regions.
- setMaxPoints(int) - Method in class qupath.lib.gui.charts.PathObjectScatterChart
-
Set the value of
PathObjectScatterChart.maxPointsProperty(). - setMaxThreads(int) - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
-
Set the maximum number of threads that may be used during live prediction.
- setMaxWidth(double, Region...) - Static method in class qupath.lib.gui.tools.PaneTools
-
Deprecated.Set the max width property for the specified regions.
- setMeasurementMapper(MeasurementMapper) - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Set the
MeasurementMapperthat defines how detections should be color coded according to their measurement values in viewers - setMetadata(ImageServerMetadata) - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer
-
Throws an exception - metadata should not be set for a hierarchy image server directly.
- setMinDisplay(float) - Method in class qupath.lib.display.AdditiveChannelInfo
- setMinDisplay(float) - Method in class qupath.lib.display.DirectServerChannelInfo
- setMinDisplay(float) - Method in interface qupath.lib.display.ChannelDisplayInfo.ModifiableChannelDisplayInfo
-
Set the min display value for this channel.
- setMinHeight(double, Region...) - Static method in class qupath.lib.gui.tools.PaneTools
-
Deprecated.Set the min height property for the specified regions.
- setMinimumRepaintSpacingMillis(long) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Prevent frequent repaints (temporarily) by setting a minimum time that must have elapsed after the previous repaint for a new one to be triggered.
- setMinMaxAllowed(float, float) - Method in class qupath.lib.display.AdditiveChannelInfo
- setMinMaxAllowed(float, float) - Method in class qupath.lib.display.DirectServerChannelInfo
- setMinMaxAllowed(float, float) - Method in interface qupath.lib.display.ChannelDisplayInfo.ModifiableChannelDisplayInfo
-
Set the maximum permissible range for the image display.
- setMinMaxDisplay(ChannelDisplayInfo, float, float) - Method in class qupath.lib.display.ImageDisplay
-
Set the min/max display values for a specified ChannelDisplayInfo.
- setMinWidth(double, Region...) - Static method in class qupath.lib.gui.tools.PaneTools
-
Deprecated.Set the min width property for the specified regions.
- setModel(PathTableData<PathObject>) - Method in class qupath.lib.gui.charts.ScatterPlotDisplay
-
Set the value of
ScatterPlotDisplay.modelProperty(). - setName(String) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Set the name of this
ViewTracker. - setNumBins(int) - Method in class qupath.lib.gui.charts.HistogramDisplay
-
Set the number of bins for the histogram.
- setNumericParameterValue(String, Number) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX
-
Set a numeric parameter value (either int or double).
- setNumericParameterValueRange(String, double, double) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX
-
Set the minimum and maximum value for a numeric parameter.
- setOff() - Static method in class qupath.lib.gui.logging.LogManager
-
Set the root log level to LogLevel.OFF.
- setOpacity(double) - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay
-
Set opacity between 0 (completely transparent) and 1 (completely opaque).
- setOpacity(float) - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Set global opacity for overlay drawing.
- setOptionalParameters(boolean, boolean, boolean, boolean) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Set optional parameters for this
ViewTracker. - setOverrideSystemMenuBar(boolean) - Static method in class qupath.lib.gui.prefs.SystemMenuBar
-
Set the current value of the override property, which optionally specifies whether the system menubar should not be used by any window - no matter what the value of
SystemMenuBar.systemMenubarProperty(). - setParameterEnabled(String, boolean) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX
-
Set the enabled status of a parameter by key, to determine if it can be edited.
- setParameterEnabled(Parameter<?>, boolean) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX
-
Set the enabled status of a parameter, to determine if it can be edited.
- setPathClassHidden(PathClass, boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Request that objects with a particular PathClass not be displayed.
- setPathObject(PathObject) - Method in class qupath.lib.gui.tools.PathObjectLabels.PathObjectMiniPane
-
Set the
PathObjectto display (may be null). - setPenManager(QuPathPenManager.PenInputManager) - Static method in class qupath.lib.gui.viewer.tools.QuPathPenManager
-
Set the PenInputManager.
- setPieChartData(PieChart, Map<T, ? extends Number>, Function<T, String>, Function<T, Color>, boolean, boolean) - Static method in class qupath.lib.gui.charts.ChartTools
-
Set pie chart data from a count map.
- setPixelClassificationRegionFilter(RegionFilter) - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Control where pixel classifications should be calculated during live prediction
- setPixelLayer(ImageData<BufferedImage>, ImageServer<BufferedImage>) - Static method in class qupath.lib.gui.measure.ObservableMeasurementTableData
-
Set an
ImageServeras a property in theImageData. - setPlaceholderText(String) - Method in class qupath.lib.gui.panes.SimpleImageViewer
-
Set the placeholder text to show if no image is available.
- setPointOpacity(double) - Method in class qupath.lib.gui.charts.PathObjectScatterChart
-
Set the value of
PathObjectScatterChart.pointOpacityProperty(). - setPointRadius(double) - Method in class qupath.lib.gui.charts.PathObjectScatterChart
-
Set the value of
PathObjectScatterChart.pointOpacityProperty() - setPredicate(Predicate<? super PathObject>) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
-
Set a predicate used to filter the rows of the table.
- setPreferredOverlayColor(Color) - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay
-
Set a preferred overlay color, which the overlay may or may not make use of.
- setProject(Project<BufferedImage>) - Method in class qupath.lib.gui.panes.ProjectBrowser
-
Set the project.
- setProject(Project<BufferedImage>) - Method in class qupath.lib.gui.QuPathGUI
-
Set the active project, triggering any necessary GUI updates.
- setProjection(ZProjectedImageServer.Projection) - Method in class qupath.lib.gui.viewer.overlays.ZProjectOverlay
-
Sets the value of the
projectionproperty. - setReadOnly(boolean) - Method in class qupath.lib.gui.QuPathGUI
-
Specify whether QuPath should be in 'read-only' mode.
- setRecording(boolean) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Set the recording property of this
ViewTracker. - setRenderer(ImageRenderer) - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
-
Set the
ImageRendererto be used with this overlay. - setRenderer(ImageRenderer) - Method in class qupath.lib.gui.viewer.overlays.ZProjectOverlay
-
Set the
ImageRendererproperty used with this overlay. - setRngSeed(int) - Method in class qupath.lib.gui.charts.PathObjectScatterChart
-
Set the value of
PathObjectScatterChart.rngSeedProperty(). - setRootLogLevel(LogManager.LogLevel) - Static method in class qupath.lib.gui.logging.LogManager
-
Set the root log level.
- setRotation(double) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Set the rotation; angle in radians.
- setSaturationPercent(double) - Method in class qupath.lib.gui.panes.SimpleImageViewer
-
Set the percentage of pixels to use when applying auto contrast settings to a non-8-bit image.
- setScriptEditor(ScriptEditor) - Method in class qupath.lib.gui.QuPathGUI
-
Set a new ScriptEditor, which will be used from now on.
- setSelectable(Action, boolean) - Static method in class qupath.lib.gui.actions.ActionTools
-
Set the selectable property for an action.
- setSelected(boolean) - Method in class qupath.lib.gui.SelectableItem
-
Set the item to be selected.
- setSelectedClassVisibilityMode(OverlayOptions.ClassVisibilityMode) - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Set the value of
OverlayOptions.selectedClassVisibilityModeProperty(). - setSelectedObject(PathObject) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Set selected object in the current hierarchy, without centering the viewer.
- setSelectedObject(PathObject, boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Set selected object in the current hierarchy, without centering the viewer.
- setSelectedTool(PathTool) - Method in class qupath.lib.gui.ToolManager
-
Programmatically select the active
PathTool. - setShowAnnotations(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Show the annotations on the image.
- setShowChannel(ChannelDisplayInfo) - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane
-
Request that the specified channel is shown.
- setShowConnections(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Show connections between objects, if available.
- setShowDetections(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Show the objects as an overlay on the image.
- setShowGrid(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Set whether a counting grid should be shown in viewers
- setShowLocation(boolean) - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
-
Set the value of
ViewerPlusDisplayOptions.showLocationProperty(). - setShowNames(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Show the object names on the image.
- setShowObjectPredicate(Predicate<PathObject>) - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Set the value of
OverlayOptions.showObjectPredicateProperty(). - setShowOverview(boolean) - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
-
Set the value of
ViewerPlusDisplayOptions.showOverviewProperty(). - setShowPixelClassification(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Show pixel classification overlays.
- setShowScalebar(boolean) - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
-
Set the value of
ViewerPlusDisplayOptions.showScalebarProperty(). - setShowTickLabels(boolean) - Method in class qupath.lib.gui.charts.HistogramChart
-
Request that tick labels are visible or not for both x and y axis.
- setShowTMACoreLabels(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Show TMA core names on top of the image.
- setShowTMAGrid(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Show the TMA grid on the image, if present.
- setShowZProjectControls(boolean) - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
-
Set the value of
ViewerPlusDisplayOptions.showZProjectControlsProperty(). - setSpaceDown(boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Notify this viewer that the isSpaceDown status should be changed.
- setSpaceX(double) - Method in class qupath.lib.gui.viewer.GridLines
-
Set the horizontal spacing between lines for any counting grid.
- setSpaceY(double) - Method in class qupath.lib.gui.viewer.GridLines
-
Set the vertical spacing between lines for any counting grid.
- setSpinnersPosition(boolean) - Method in class qupath.lib.gui.viewer.QuPathViewerPlus
-
Sets the Z and T spinner' position to allow space for command bar
- setStyle() - Method in interface qupath.lib.gui.prefs.QuPathStyleManager.StyleOption
-
Set the style for the QuPath application.
- setSwitchToGrayscaleChannel(ChannelDisplayInfo) - Method in class qupath.lib.display.ImageDisplay
-
Set the value of
ImageDisplay.switchToGrayscaleChannelProperty(). - setSynchronizeViewers(boolean) - Method in class qupath.lib.gui.viewer.ViewerManager
-
Sets the value of the
synchronizeViewersproperty. - setText(String) - Method in interface qupath.lib.gui.scripting.EditableText
-
Set all the text in the editor.
- setText(String) - Method in class qupath.lib.gui.scripting.TextAreaControl
-
Sets the value of the
textproperty. - setTextFieldFromNumber(TextField, Number, String) - Static method in class qupath.lib.gui.dialogs.ParameterPanelFX
- setThresholdColor(ObservableNumberValue, Color) - Method in class qupath.lib.gui.charts.ChartThresholdPane
-
Set the color of a specified threshold line.
- setThresholds(Color, double...) - Method in class qupath.lib.gui.charts.ChartThresholdPane
-
Set thresholds, which are visualized as vertical lines.
- settings(ImageDisplaySettings) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder
-
Specify the
ImageDisplaySettingsthat control conversion to RGB. - settingsCompatibleWithDisplay(ImageDisplay, ImageDisplaySettings) - Static method in class qupath.lib.display.settings.DisplaySettingUtils
-
Check if the settings are compatible with the display.
- setTMAEntriesFromImageData(ImageData<BufferedImage>) - Method in class qupath.lib.gui.tma.TMASummaryViewer
-
Deprecated.Set the TMA entries from the TMACoreObjects of a specific ImageData.
- setToExpandGridPaneHeight(Node...) - Static method in class qupath.lib.gui.tools.PaneTools
-
Deprecated.Set constraints and max width values (where possible) so that the specified nodes fill all available vertical space in a
GridPane. - setToExpandGridPaneWidth(Node...) - Static method in class qupath.lib.gui.tools.PaneTools
-
Deprecated.Set constraints and max width values (where possible) so that the specified nodes fill all available horizontal space in a
GridPane. - setToolSwitchingEnabled(boolean) - Method in class qupath.lib.gui.ToolManager
-
Toggle whether the user is permitted to switch to a new active
PathTool. - setTooltipFunction(Function<Double, String>) - Method in class qupath.lib.gui.ColorMapCanvas
-
Set the function that will take a value between 0 and 255 (from the color map) and output a displayable string
- setTPosition(int) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Set the requested time point to be visible.
- setTrace() - Static method in class qupath.lib.gui.logging.LogManager
-
Set the root log level to LogLevel.TRACE.
- setupTarget(Node) - Method in class qupath.lib.gui.viewer.DragDropImportListener
-
Prepare a target node to accept drag and drop events.
- setupTarget(Scene) - Method in class qupath.lib.gui.viewer.DragDropImportListener
-
Prepare a target scene to accept drag and drop events.
- setUseExactSelectedClasses(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Set the value of
OverlayOptions.useExactSelectedClassesProperty() - setUseGrayscaleLuts(boolean) - Method in class qupath.lib.display.ImageDisplay
-
Set the value of
ImageDisplay.useGrayscaleLutProperty() - setUseInvertedBackground(boolean) - Method in class qupath.lib.display.ImageDisplay
-
Set the value of
ImageDisplay.useInvertedBackgroundProperty() - setUseMicrons(boolean) - Method in class qupath.lib.gui.viewer.GridLines
-
Specify whether to use calibrated units when calculating coordinates for any counting grid.
- setUserPath(Path) - Method in class qupath.lib.gui.UserDirectoryManager
-
Set the user path where additional files may be stored.
- setVGrowPriority(Priority, Node...) - Static method in class qupath.lib.gui.tools.PaneTools
-
Deprecated.Set the
GridPane.setVgrow(Node, Priority)property for specified nodes. - setViewerDownsample(QuPathViewer, double) - Static method in class qupath.lib.gui.commands.Commands
-
Set the downsample factor for the specified viewer.
- setWarn() - Static method in class qupath.lib.gui.logging.LogManager
-
Set the root log level to LogLevel.WARN.
- setZPosition(int) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Set the requested z-slice to be visible.
- SHAPE_FEATURES - Variable in class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
- SharedThreadPoolManager - Class in qupath.lib.gui
-
Manager to simplify submitting short tasks in background threads using a shared
ExecutorService. - show() - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Add the chart to a stage, and show it in the Application thread.
- show() - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
-
Add the chart to a stage, and show it in the Application thread.
- show() - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Add the chart to a stage, and show it in the Application thread.
- show() - Method in class qupath.lib.gui.commands.LogViewerCommand
- show() - Method in class qupath.lib.gui.commands.PathObjectGridView
-
Create the stage and show the grid view.
- show() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Deprecated.Show the dialog.
- SHOW_ANALYSIS_PANE - Variable in class qupath.lib.gui.actions.CommonActions
- SHOW_ANALYSIS_PANEL - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- SHOW_ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- SHOW_ANNOTATIONS - Variable in class qupath.lib.gui.actions.OverlayActions
- SHOW_CELL_BOUNDARIES - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.CellDisplayActions
- SHOW_CELL_BOUNDARIES - Variable in class qupath.lib.gui.actions.OverlayActions
- SHOW_CELL_BOUNDARIES_AND_NUCLEI - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.CellDisplayActions
- SHOW_CELL_BOUNDARIES_AND_NUCLEI - Variable in class qupath.lib.gui.actions.OverlayActions
- SHOW_CELL_CENTROIDS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.CellDisplayActions
- SHOW_CELL_CENTROIDS - Variable in class qupath.lib.gui.actions.OverlayActions
- SHOW_CELL_NUCLEI - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.CellDisplayActions
- SHOW_CELL_NUCLEI - Variable in class qupath.lib.gui.actions.OverlayActions
- SHOW_CONNECTIONS - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- SHOW_CONNECTIONS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- SHOW_CONNECTIONS - Variable in class qupath.lib.gui.actions.OverlayActions
- SHOW_DETECTIONS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- SHOW_DETECTIONS - Variable in class qupath.lib.gui.actions.OverlayActions
- SHOW_GRID - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- SHOW_GRID - Variable in class qupath.lib.gui.actions.OverlayActions
- SHOW_LICENSE - Variable in class qupath.lib.gui.actions.CommonActions
- SHOW_LOCATION - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- SHOW_LOCATION - Variable in class qupath.lib.gui.actions.ViewerActions
- SHOW_LOG - Variable in class qupath.lib.gui.actions.CommonActions
- SHOW_LOG - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- SHOW_NAMES - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- SHOW_NAMES - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- SHOW_NAMES - Variable in class qupath.lib.gui.actions.OverlayActions
- SHOW_OBJECT_DESCRIPTIONS - Variable in class qupath.lib.gui.actions.CommonActions
- SHOW_OBJECT_DESCRIPTIONS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.Actions
- SHOW_OVERVIEW - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- SHOW_OVERVIEW - Variable in class qupath.lib.gui.actions.ViewerActions
- SHOW_PIXEL_CLASSIFICATION - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- SHOW_PIXEL_CLASSIFICATION - Variable in class qupath.lib.gui.actions.OverlayActions
- SHOW_POINTS_DIALOG - Variable in class qupath.lib.gui.actions.CommonActions
- SHOW_SCALEBAR - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- SHOW_SCALEBAR - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- SHOW_SCALEBAR - Variable in class qupath.lib.gui.actions.ViewerActions
- SHOW_SELECTED - Enum constant in enum class qupath.lib.gui.viewer.OverlayOptions.ClassVisibilityMode
-
Show classes that are included in the selected class collection.
- SHOW_TMA_GRID - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- SHOW_TMA_GRID - Variable in class qupath.lib.gui.actions.OverlayActions
- SHOW_TMA_GRID_LABELS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- SHOW_TMA_GRID_LABELS - Variable in class qupath.lib.gui.actions.OverlayActions
- SHOW_Z_PROJECT - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- SHOW_Z_PROJECT - Variable in class qupath.lib.gui.actions.ViewerActions
- showAnalysisPaneProperty() - Method in class qupath.lib.gui.QuPathGUI
- showAndWait() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Deprecated.Show the dialog.
- showAnnotationGridView(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
-
Show a grid view for annotation objects.
- showAnnotationMeasurementTable() - Static method in class qupath.lib.gui.scripting.QPEx
-
Show a measurement table for annotation objects from the current image.
- showAnnotationMeasurementTable(QuPathGUI, ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands
-
Show a measurement table for all annotation objects.
- showAnnotationMeasurementTable(ImageData<BufferedImage>) - Static method in class qupath.lib.gui.scripting.QPEx
-
Show a measurement table for annotation objects from the specified image.
- showAnnotationsProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
- showCellMeasurementTable() - Static method in class qupath.lib.gui.scripting.QPEx
-
Show a measurement table for tile objects from the current image.
- showCellMeasurementTable(QuPathGUI, ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands
-
Show a measurement table for all cell objects.
- showCellMeasurementTable(ImageData<BufferedImage>) - Static method in class qupath.lib.gui.scripting.QPEx
-
Show a measurement table for cell objects from the specified image.
- showChannelViewer(QuPathViewer) - Static method in class qupath.lib.gui.commands.Commands
-
Show a channel viewer window associated with a specific viewer.
- showChoiceDialog(String, String, Collection<T>, T) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Show a choice dialog with a collection of choices (selection from ComboBox or similar).
- showChoiceDialog(String, String, T[], T) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Show a choice dialog with an array of choices (selection from ComboBox or similar).
- showConfirmDialog(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Show a confirm dialog (OK/Cancel).
- showConfirmDialog(String, Node) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Show a confirm dialog (OK/Cancel).
- showConnectionsProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
- showDeprecatedCommands - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
- showDetectionMeasurementManager(QuPathGUI, ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands
-
Show a simple dialog for viewing (and optionally removing) detection measurements.
- showDetectionMeasurementTable() - Static method in class qupath.lib.gui.scripting.QPEx
-
Show a measurement table for all detection objects from the current image.
- showDetectionMeasurementTable(QuPathGUI, ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands
-
Show a measurement table for all detection objects.
- showDetectionMeasurementTable(ImageData<BufferedImage>) - Static method in class qupath.lib.gui.scripting.QPEx
-
Show a measurement table for all detection objects from the specified image.
- showDetectionsProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
- showEditor() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
- showEditor() - Method in interface qupath.lib.gui.scripting.ScriptEditor
-
Show the script editor.
- showErrorMessage(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Show an error message.
- showErrorMessage(String, Throwable) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Show an error message, displaying the localized message of a
Throwable. - showErrorMessage(String, Node) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Show an error message, with the content defined within a
Node. - showErrorNotification(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Show an error notification.
- showErrorNotification(String, Throwable) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Show an error notification, displaying the localized message of a
Throwable. - showExperimentalCommands - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
- showExperimentalOptionsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Flag to indicate that menu items marked 'experimental' should be shown to the user.
- showGridProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
- showHistogram(String) - Method in class qupath.lib.gui.charts.HistogramDisplay
-
Show the histogram for a specified data column.
- showImageNameInTitle - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
- showImageNameInTitleProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Property specifying if QuPath should show the image title in the main window title.
- showInfoNotification(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Show an info notification.
- showingProperty() - Method in class qupath.lib.gui.panes.SlideLabelView
-
Property indicating whether the label is showing on screen or not.
- showInputDialog(String, String, Double) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Show an input dialog requesting a numeric value.
- showInputDialog(String, String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Show an input dialog requesting a String input.
- showInputDisplayProperty() - Method in class qupath.lib.gui.QuPathGUI
-
Property to indicate whether the input display is currently showing
- showInstalledExtensions(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
-
Show a dialog displaying the extensions installed for a specified QuPath instance.
- showLegacyOptionsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Flag to indicate that the legacy options should be shown to the user - normally not desirable.
- showLicenseMessageOnStartupProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Show a startup message about license when QuPath is launched.
- showLocationProperty() - Method in class qupath.lib.gui.viewer.ViewerManager
-
Show the cursor location.
- showLocationProperty() - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
-
Show the cursor location.
- showMeasurementTable(Predicate<PathObject>) - Static method in class qupath.lib.gui.scripting.QPEx
-
Show a measurement table for the current image.
- showMeasurementTable(ImageData<BufferedImage>, Predicate<PathObject>) - Static method in class qupath.lib.gui.scripting.QPEx
-
Show a measurement table for the specified image.
- showMeasurementTableObjectIDs - Variable in class qupath.lib.gui.panes.PreferencePane.MeasurementPreferences
- showMeasurementTableObjectIDsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Specify whether measurement tables should show object IDs by default or not.
- showMeasurementTableThumbnails - Variable in class qupath.lib.gui.panes.PreferencePane.MeasurementPreferences
- showMeasurementTableThumbnailsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Specify whether measurement tables should show thumbnail images by default or not.
- showMessageDialog(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Show a standard message dialog.
- showMessageDialog(String, Node) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Show a message dialog (OK button only), with the content contained within a Node.
- showMiniViewer(QuPathViewer) - Static method in class qupath.lib.gui.commands.Commands
-
Show a mini viewer window associated with a specific viewer.
- showNamesProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
- showNoImageError(String) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Show an error message that no image is available.
- showNoImageError(String) - Static method in class qupath.lib.gui.tools.GuiTools
-
Show an error message that no image is available.
- showNoProjectError(String) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Show an error message that no project is available.
- showNoProjectError(String) - Static method in class qupath.lib.gui.tools.GuiTools
-
Show an error message that no project is available.
- showObjectPredicateProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Get the predicate used to determine whether an object should be displayed or hidden.
- showOverviewProperty() - Method in class qupath.lib.gui.viewer.ViewerManager
-
Show the overview image.
- showOverviewProperty() - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
-
Show the overview image.
- showParameterDialog(String, ParameterList) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Show a (modal) dialog for a specified ParameterList.
- showParameterDialog(String, ParameterList) - Static method in class qupath.lib.gui.tools.GuiTools
-
Show a (modal) dialog for a specified ParameterList.
- showPixelClassificationProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
- showPlainMessage(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Show a plain message.
- showPlainNotification(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Show a plain notification.
- showPointHullsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Show the convex hull for point annotations within the viewer.
- showProjectMetadataEditor(Project<?>) - Static method in class qupath.lib.gui.commands.ProjectCommands
-
Show the metadata editor for the specified project.
- showScalebarProperty() - Method in class qupath.lib.gui.viewer.ViewerManager
-
Show the scalebar.
- showScalebarProperty() - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
-
Show the scalebar.
- showScript(File) - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
- showScript(File) - Method in interface qupath.lib.gui.scripting.ScriptEditor
-
Show the script editor, opening an existing script file.
- showScript(String, String) - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
- showScript(String, String) - Method in interface qupath.lib.gui.scripting.ScriptEditor
-
Show the script editor, including a new script with the specified name.
- showScript(ScriptEditor, Workflow) - Static method in class qupath.lib.gui.panes.WorkflowCommandLogView
-
Show a script in the script editor based on the specified workflow.
- showScriptEditor(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
-
Show the script editor, or bring the window to the front if it is already open.
- showScriptInterpreter(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
-
Show a script interpreter window for a Qupath instance.
- showStartupMessageProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Show a startup message when QuPath is launched.
- showTable(ImageData<BufferedImage>, Predicate<PathObject>) - Method in class qupath.lib.gui.commands.SummaryMeasurementTableCommand
-
Show a measurement table for the specified image data.
- showTextWindow(Window, String, String, Modality, boolean) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Show a window containing plain text, with the specified properties.
- showTileMeasurementTable() - Static method in class qupath.lib.gui.scripting.QPEx
-
Show a measurement table for tile objects from the current image.
- showTileMeasurementTable(ImageData<BufferedImage>) - Static method in class qupath.lib.gui.scripting.QPEx
-
Show a measurement table for tile objects from the specified image.
- showTMACommands - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
- showTMACoreGridView(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
-
Show a grid view for TMA core objects.
- showTMACoreLabelsProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
- showTmaCoreMeasurementTable() - Static method in class qupath.lib.gui.scripting.QPEx
-
Show a measurement table for TMA core objects from the current image.
- showTmaCoreMeasurementTable(ImageData<BufferedImage>) - Static method in class qupath.lib.gui.scripting.QPEx
-
Show a measurement table for TMA core objects from the specified image.
- showTMAGridProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
- showTMAMeasurementTable(QuPathGUI, ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands
-
Show a measurement table for all TMA core objects.
- showTMAOptionsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Flag to indicate that the TMA menu should be shown to the user - only relevant when working with Tissue Microarrays.
- showToolBarBadgesProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Show badges on the toolbar, e.g.
- showViewerPlaceholderTextProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Property to determine whether placeholder text should be shown when the viewer is empty.
- showViewTracker(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
-
Show a dialog to track the viewed region of an image.
- showWarningNotification(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Show a warning notification.
- showWithScreenSizeConstraints(Stage, double) - Static method in class qupath.lib.gui.tools.GuiTools
-
Show a stage, while ensuring that it cannot be larger than the screen size.
- showWithSizeConstraints(Stage, double, double) - Static method in class qupath.lib.gui.tools.GuiTools
-
Show a stage, while ensuring that it cannot be larger the maximum dimensions provided This effectively sets the maximum dimensions of the stage, shows it, and then restores the previous maximum dimensions.
- showWorkflowScript(QuPathGUI, ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands
-
Show the QuPath script editor with a script corresponding to the command history of a specified image.
- showYesNoCancelDialog(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Show a Yes/No/Cancel dialog.
- showYesNoDialog(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Deprecated.Show a Yes/No dialog.
- showZProjectControlsProperty() - Method in class qupath.lib.gui.viewer.ViewerManager
-
Show z-projection overlay options, where relevant
- showZProjectControlsProperty() - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
-
Show controls to view z-projection overlays, where available.
- SIGNED_DISTANCE_TO_ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
- SimpleImageViewer - Class in qupath.lib.gui.panes
-
A simple viewer for a single image, with options to save or copy.
- SimpleImageViewer() - Constructor for class qupath.lib.gui.panes.SimpleImageViewer
-
Create a new simple image viewer.
- SIMPLIFY_SHAPE - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
- simplifyTitledPane(TitledPane, boolean) - Static method in class qupath.lib.gui.tools.PaneTools
-
Deprecated.Simplify the appearance of a
TitledPaneusing CSS. - SingleChannelDisplayInfo - Interface in qupath.lib.display
-
ChannelDisplayInfothat determines colors based upon a single value for each pixel. - size(double, double) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Set the preferred size of the chart.
- size(double, double) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
-
Set the preferred size of the chart.
- size(double, double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Set the preferred size of the chart.
- size(double, double) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Deprecated.Specify the dialog height.
- skipMissingCores - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
- skipMissingCoresProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Skip ('jump over') missing cores when navigating through TMA grids.
- skipProjectUriChecks - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
- skipProjectUriChecksProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Property to suppress checking whether image files exists in the project browser.
- SLIDE_LABEL - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- SlideLabelView - Class in qupath.lib.gui.panes
-
A simple viewer for a slide label, tied to the current viewer.
- SlideLabelView(QuPathGUI) - Constructor for class qupath.lib.gui.panes.SlideLabelView
-
Constructor.
- SMALL - Enum constant in enum class qupath.lib.gui.commands.PathObjectGridView.GridDisplaySize
- SMALL - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.FontSize
- smartEditing - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- smartEditingAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- SMOOTHED_FEATURES - Variable in class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
- SNAPSHOT_VIEWER_CONTENT - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ExportSnapshotActions
- SNAPSHOT_WINDOW - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ExportSnapshotActions
- SNAPSHOT_WINDOW_CONTENT - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ExportSnapshotActions
- SOURCE - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
- SPECIFY_ANNOTATION - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
- SPLIT_ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
- SPLIT_ANNOTATIONS_BY_LINES - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
- SplitAnnotationsByLineCommand - Class in qupath.lib.gui.commands.objects
-
Command to split annotations using lines.
- SplitAnnotationsByLineCommand() - Constructor for class qupath.lib.gui.commands.objects.SplitAnnotationsByLineCommand
- splitViewer(QuPathViewer, boolean) - Method in class qupath.lib.gui.viewer.ViewerManager
- start(Stage) - Method in class qupath.lib.gui.QuPathApp
- start(Stage) - Method in class qupath.lib.gui.tma.QuPathTMAViewer
- startMoving(double, double, boolean) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler.ViewerMover
-
Start moving, with initial velocity given by dx and dy.
- startupMessage - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
- startupScriptPath - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
- startupScriptProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Path to a startup script that should be run immediately after QuPath's launch.
- stop() - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
-
Stop the overlap, halting any pending tile requests.
- stopMoving() - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler.ViewerMover
-
Stop moving immediately.
- stopWaiting(RegionRequest) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
- store(DefaultImageRegionStore) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder
-
Specify the region store used to paint the underlying image.
- STYLE_PLACEHOLDER_TEXT - Static variable in class qupath.lib.gui.tools.GuiTools
-
Style class to use with placeholder text.
- Subcommand - Interface in qupath.lib.gui.extensions
-
A subcommand for the command line interface.
- submitShortTask(Runnable) - Method in class qupath.lib.gui.QuPathGUI
-
Deprecated.since v0.5.0; use
QuPathGUI.getThreadPoolManager() - submitShortTask(Runnable) - Method in class qupath.lib.gui.SharedThreadPoolManager
-
Submit a short task to a shared thread pool
- SummaryMeasurementTable - Class in qupath.lib.gui.measure.ui
-
Control to show a table to view measurements and properties of
PathObject. - SummaryMeasurementTable(ImageData<BufferedImage>, Predicate<PathObject>) - Constructor for class qupath.lib.gui.measure.ui.SummaryMeasurementTable
-
Create a new measurement table.
- SummaryMeasurementTableCommand - Class in qupath.lib.gui.commands
-
Show a summary table for an object of a particular type (annotation, detection, TMA core...)
- SummaryMeasurementTableCommand(QuPathGUI) - Constructor for class qupath.lib.gui.commands.SummaryMeasurementTableCommand
-
Command to show a summary measurement table, for PathObjects of a specified type (e.g.
- supportsFile(File) - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
-
Query whether a file represents a supported script.
- supportsFile(File) - Method in interface qupath.lib.gui.scripting.ScriptEditor
-
Check if the script editor supports a particular file.
- supportsSystemMenubar() - Static method in class qupath.lib.gui.prefs.SystemMenuBar
-
Returns true if the platform supports (or maybe supports) the system menubar.
- switchToGrayscaleChannelProperty() - Method in class qupath.lib.display.ImageDisplay
-
Property indicating which channel should be used if
ImageDisplay.useGrayscaleLutProperty()is turned on. - synchronizeViewersProperty() - Method in class qupath.lib.gui.viewer.ViewerManager
- syncProject(Project<?>) - Static method in class qupath.lib.gui.panes.ProjectBrowser
-
Try to save a project, showing an error message if this fails.
- SYSTEM_MENUBAR - Variable in class qupath.lib.gui.actions.menus.WindowMenuActions.Actions
- systemMenubar - Variable in class qupath.lib.gui.panes.PreferencePane.AppearancePreferences
- SystemMenuBar - Class in qupath.lib.gui.prefs
-
Helper class for managing
MenuBar.useSystemMenuBarProperty()values based upon a property value. - SystemMenuBar() - Constructor for class qupath.lib.gui.prefs.SystemMenuBar
- SystemMenuBar.SystemMenuBarOption - Enum Class in qupath.lib.gui.prefs
-
Enum specifying when and where the system menubar should be used.
- systemMenubarProperty() - Static method in class qupath.lib.gui.prefs.SystemMenuBar
-
Property used to specify whether the system menubar should be used for the main QuPath stage.
T
- TABLE - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- tableDelimiterProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Delimiter to use when exporting tables.
- TaskRunnerFX - Class in qupath.lib.gui
-
Plugin runner that takes care of showing progress (in the appropriate thread) using JavaFX components.
- TaskRunnerFX(QuPathGUI) - Constructor for class qupath.lib.gui.TaskRunnerFX
-
Constructor.
- TaskRunnerFX(QuPathGUI, int) - Constructor for class qupath.lib.gui.TaskRunnerFX
-
Constructor specifying the number of threads.
- tempSelectionModeProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Temporarily request selection mode, without changing the value of #selectionModeProperty().
- test(ImageData<?>, RegionRequest) - Method in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters
- text(String) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
-
Set the text property of the action.
- text(ObservableValue<String>) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
-
Bind the text property of the action to an
ObservableValue, bidirectionally if possible. - TextAppendable - Interface in qupath.lib.gui.logging
-
Interface to indicate anything for which text can be appended.
- TextAreaControl - Class in qupath.lib.gui.scripting
-
Simple text area control (JavaFX) with basic operations and no styling support.
- TextAreaControl(boolean) - Constructor for class qupath.lib.gui.scripting.TextAreaControl
-
Constructor to create a new text area and wrap it in a
TextAreaControl. - TextAreaControl(TextArea, boolean) - Constructor for class qupath.lib.gui.scripting.TextAreaControl
-
Constructor to wrap an existing text area and wrap it in a
TextAreaControl. - textProperty() - Method in class qupath.lib.gui.actions.InfoMessage
-
Read only property containing the message text.
- textProperty() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
-
Text currently in the editor control.
- textProperty() - Method in class qupath.lib.gui.scripting.TextAreaControl
- textProperty() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry
-
Property corresponding to
CommandFinderTools.CommandEntry.getText() - theme - Variable in class qupath.lib.gui.panes.PreferencePane.AppearancePreferences
- tileAvailable(String, ImageRegion, BufferedImage) - Method in class qupath.lib.gui.viewer.QuPathViewer
- tileAvailable(String, ImageRegion, T) - Method in interface qupath.lib.gui.images.stores.TileListener
-
Notify a listener that an image tile has been received read & is available.
- tileBrush - Variable in class qupath.lib.gui.panes.PreferencePane.DrawingPreferences
- tileCache - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
- tileCachePercentageProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Requested percentage of available memory to use for tile caching.
- TileListener<T> - Interface in qupath.lib.gui.images.stores
-
Interface for anything that needs to know when image tiles become available.
- tileListeners - Variable in class qupath.lib.gui.images.stores.DefaultImageRegionStore
- tiles() - Method in class qupath.lib.gui.tools.MeasurementExporter
-
Specify that tile measurements (only) should be export.
- TINY - Enum constant in enum class qupath.lib.gui.commands.PathObjectGridView.GridDisplaySize
- TINY - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.FontSize
- title - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
- title - Variable in class qupath.lib.gui.charts.Charts.PieChartBuilder
- title - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
- title(String) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Specify the chart title.
- title(String) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
-
Specify the chart title.
- title(String) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Specify the chart title.
- title(String) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Deprecated.Specify the dialog title.
- title(String) - Method in class qupath.lib.gui.FileCopier
-
Title for any dialog.
- TMA - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
- TMA_ADD_NOTE - Variable in class qupath.lib.gui.actions.CommonActions
- TMA_DEARRAYING_DATA_EXTENSION - Static variable in class qupath.lib.gui.tma.TMADataIO
- TMA_EXPORT - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.TmaActions
- TMA_GRID - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- TMA_IMPORT - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.TmaActions
- TMA_VIEWER - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.TmaActions
- tmaActions - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
- TmaActions() - Constructor for class qupath.lib.gui.actions.menus.FileMenuActions.TmaActions
- tmaColor - Variable in class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
- TMACommands - Class in qupath.lib.gui.commands
-
Helper class implementing simple 'single-method' commands related to tissue microarrays for easy inclusion in the GUI.
- TMACommands() - Constructor for class qupath.lib.gui.commands.TMACommands
- tmaCores() - Method in class qupath.lib.gui.tools.MeasurementExporter
-
Specify that TMA core measurements (only) should be export.
- TMADataIO - Class in qupath.lib.gui.tma
-
Static methods for exporting TMA data, optionally with small images.
- TMADataIO() - Constructor for class qupath.lib.gui.tma.TMADataIO
- TMAExplorer - Class in qupath.lib.gui.tma
-
The aim of this is to enable the exploration of TMA data from multiple images in a project.
- TMAExplorer(QuPathGUI) - Constructor for class qupath.lib.gui.tma.TMAExplorer
-
Constructor.
- tmaExportDownsample - Variable in class qupath.lib.gui.panes.PreferencePane.InputOutputPreferences
- tmaExportDownsampleProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Default downsample factor to use when exporting TMA cores.
- TMAGridOverlay - Class in qupath.lib.gui.viewer.overlays
-
An overlay capable of painting a TMA Grid.
- TMAGridOverlay(OverlayOptions) - Constructor for class qupath.lib.gui.viewer.overlays.TMAGridOverlay
-
Constructor.
- TMAMenuActions - Class in qupath.lib.gui.actions.menus
- TMAMenuActions.Actions - Class in qupath.lib.gui.actions.menus
- TMAMenuActions.Actions.AddActions - Class in qupath.lib.gui.actions.menus
- TMAMenuActions.Actions.RemoveActions - Class in qupath.lib.gui.actions.menus
- tmaMissingOpacity - Variable in class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
- TMASummaryViewer - Class in qupath.lib.gui.tma
-
Deprecated.since v0.4.0
- TMASummaryViewer(Stage) - Constructor for class qupath.lib.gui.tma.TMASummaryViewer
-
Deprecated.Constructor.
- TOGGLE_SELECTED_OBJECTS_LOCKED - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.LockActions
- TOGGLE_SYNCHRONIZE_VIEWERS - Variable in class qupath.lib.gui.actions.ViewerActions
- toggleShowHideChannel(ChannelDisplayInfo) - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane
-
Toggle the visibility of the specified channel.
- toJSON(boolean) - Method in class qupath.lib.display.ImageDisplay
-
Create a JSON representation of the main components of the current display.
- TOOLBAR_ICON_SIZE - Static variable in class qupath.lib.gui.QuPathGUI
-
Icon size to use in the main QuPath toolbar
- ToolManager - Class in qupath.lib.gui
-
Manage (drawing) tool selection in a QuPath UI.
- tooltips(boolean) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
-
Request tooltips to be shown when the cursor hovers over the pie chart.
- toStage() - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Add the chart to a stage, but do not show it.
- toStage() - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
-
Add the chart to a stage, but do not show it.
- toStage() - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Add the chart to a stage, but do not show it.
- toString() - Method in class qupath.lib.display.AdditiveChannelInfo
- toString() - Method in class qupath.lib.display.DirectServerChannelInfo
- toString() - Method in class qupath.lib.gui.BuildInfo
- toString() - Method in enum class qupath.lib.gui.charts.HistogramChart.CountsTransformMode
- toString() - Method in enum class qupath.lib.gui.commands.PathObjectGridView.GridDisplaySize
- toString() - Method in class qupath.lib.gui.extensions.GitHubProject.GitHubRepo
- toString() - Method in class qupath.lib.gui.extensions.UpdateChecker.ReleaseVersion
- toString() - Method in enum class qupath.lib.gui.prefs.PathPrefs.AutoUpdateType
- toString() - Method in enum class qupath.lib.gui.prefs.PathPrefs.DetectionTreeDisplayModes
- toString() - Method in enum class qupath.lib.gui.prefs.PathPrefs.FontSize
- toString() - Method in enum class qupath.lib.gui.prefs.PathPrefs.ImageTypeSetting
- toString() - Method in enum class qupath.lib.gui.prefs.QuPathStyleManager.Fonts
- toString() - Method in enum class qupath.lib.gui.prefs.SystemMenuBar.SystemMenuBarOption
- toString() - Method in class qupath.lib.gui.scripting.ScriptTab
- toString() - Method in enum class qupath.lib.gui.tools.CommandFinderTools.CommandBarDisplay
- toString() - Method in enum class qupath.lib.gui.viewer.ImageInterpolation
- toString() - Method in class qupath.lib.gui.viewer.QuPathViewer
- toString() - Method in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters
- totalBytes() - Method in class qupath.lib.gui.UndoRedoManager
-
The total number of bytes used for all viewers.
- tPositionProperty() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Current t-position for the timepoint currently visible in the viewer.
- TRACE - Enum constant in enum class qupath.lib.gui.logging.LogManager.LogLevel
-
Trace logging (an awful lot of messages)
- TRACKING_RECORD - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- TRACKING_REWIND - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- TRACKING_STOP - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- TRANSFER_ANNOTATION - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
- TRANSLUCENT_BLACK_FX - Static variable in class qupath.lib.gui.tools.ColorToolsFX
-
Black with opacity at 50%.
- TRANSLUCENT_WHITE_FX - Static variable in class qupath.lib.gui.tools.ColorToolsFX
-
White with opacity at 50%.
- tryToInterpretMessage(Throwable, int, boolean) - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
- tryToSelect(PathObject, QuPathViewer, ImageData<?>, boolean, boolean) - Static method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Try to select an object if possible (e.g.
U
- uiBlocked() - Method in class qupath.lib.gui.QuPathGUI
-
Observable value indicating that the user interface is/should be blocked.
- undo() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
-
Request undo.
- undo() - Method in class qupath.lib.gui.scripting.TextAreaControl
- UNDO - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- UNDO - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.Actions
- undoAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- undoOnce() - Method in class qupath.lib.gui.UndoRedoManager
-
Request to 'undo' the last observed hierarchy change for the current active viewer.
- UndoRedoManager - Class in qupath.lib.gui
-
Helper class to add undo/redo support to QuPath.
- UndoRedoPreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.UndoRedoPreferences
- unlimitedDatapoints() - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Show all datapoints, without subsampling, even when this may cause performance issues.
- UNLOCK_SELECTED_OBJECTS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.LockActions
- unmanageMenuBar(MenuBar) - Static method in class qupath.lib.gui.prefs.SystemMenuBar
-
Do not manage the system menubar status for the given menubar.
- UPDATE - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
- updateAffineTransform() - Method in class qupath.lib.gui.viewer.QuPathViewer
- updateAffineTransform() - Method in class qupath.lib.gui.viewer.QuPathViewerPlus
- updateAvailableStyles() - Static method in class qupath.lib.gui.prefs.QuPathStyleManager
-
Request that the list of available styles is updated.
- updateAxisRange() - Method in class qupath.lib.gui.charts.PathObjectScatterChart
- updateChart(BarChart<String, Number>) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
- updateChart(PieChart) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
- updateChart(ScatterChart<Number, Number>) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
- UpdateChecker - Class in qupath.lib.gui.extensions
-
Helper class to query for updates using GitHub's web API.
- UpdateChecker() - Constructor for class qupath.lib.gui.extensions.UpdateChecker
- UpdateChecker.ReleaseVersion - Class in qupath.lib.gui.extensions
-
Class to represent a release version.
- updateCursor() - Method in class qupath.lib.gui.viewer.QuPathViewer
- updateFromDisplay(ImageDisplay) - Method in class qupath.lib.display.ImageDisplay
-
Update the current display based upon a different display.
- updateHistogram(ImageDisplay, ChannelDisplayInfo) - Method in class qupath.lib.gui.commands.display.BrightnessContrastHistogramPane
-
Update the histogram to show the data for the given channel.
- updateImage(String, BufferedImage) - Method in class qupath.lib.gui.panes.SimpleImageViewer
-
Update the image using a buffered image.
- updateImage(String, Image) - Method in class qupath.lib.gui.panes.SimpleImageViewer
-
Update the image using a JavaFX image.
- updateItem(PathClass, boolean) - Method in class qupath.lib.gui.tools.PathClassListCell
- updateLegend() - Method in class qupath.lib.gui.charts.PathObjectScatterChart
- updateMeasurementList() - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
-
Update the entire measurement list for the current objects.
- updateMeasurements() - Method in class qupath.lib.gui.panes.MeasurementMapPane
-
Update the measurements according to the current image
- updateRGBAdditive(BufferedImage, int[], ChannelDisplayMode) - Method in class qupath.lib.display.DirectServerChannelInfo
- updateRGBAdditive(BufferedImage, int[], ChannelDisplayMode) - Method in class qupath.lib.display.AdditiveChannelInfo
- updateRGBAdditive(BufferedImage, int[], ChannelDisplayMode) - Method in interface qupath.lib.display.ChannelDisplayInfo
-
Update an array of existing pixels (packed RGB) additively using the colors to display a specified image.
- updateRGBAdditive(BufferedImage, int, int, int, ChannelDisplayMode) - Method in class qupath.lib.display.AdditiveChannelInfo
- updateRGBAdditive(BufferedImage, int, int, int, ChannelDisplayMode) - Method in class qupath.lib.display.DirectServerChannelInfo
- updateRGBAdditive(BufferedImage, int, int, int, ChannelDisplayMode) - Method in interface qupath.lib.display.ChannelDisplayInfo
-
Update an existing pixel (packed RGB) additively using the color used to display a specified one
- updateTable() - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane
-
Ensure the table is up-to-date.
- UpdateUrisCommand<T> - Class in qupath.lib.gui.commands
-
Fix broken URIs by using relative paths or prompting the user to select files.
- updatingConstrainingObjects(QuPathViewer, double, double, Collection<PathObject>) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
-
New annotations can be constrained while they are being drawn, to avoid overlaps with existing annotations or to ensure they are drawn within a parent annotation.
- updatingConstrainingObjects(QuPathViewer, double, double, Collection<PathObject>) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
-
New annotations can be constrained while they are being drawn, to avoid overlaps with existing annotations or to ensure they are drawn within a parent annotation.
- Urls - Class in qupath.lib.gui
-
Class to return core QuPath URLs centrally.
- Urls() - Constructor for class qupath.lib.gui.Urls
- useCalibratedLocationStringProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Show the cursor location on a viewer in calibrated units, rather than pixels.
- useColorLUTs() - Method in class qupath.lib.display.ImageDisplay
-
The opposite of
ImageDisplay.useGrayscaleLuts() - useExactSelectedClassesProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Property to control whether entries in
OverlayOptions.selectedClassesProperty()should be used exactly, or should also include all related classes (i.e. - useGrayscaleLutProperty() - Method in class qupath.lib.display.ImageDisplay
-
Property that specifies whether grayscale lookup tables should be preferred to color lookup tables
- useGrayscaleLuts() - Method in class qupath.lib.display.ImageDisplay
-
Get the value of
ImageDisplay.useGrayscaleLutProperty() - useInvertedBackground() - Method in class qupath.lib.display.ImageDisplay
-
Get the value of
ImageDisplay.useInvertedBackgroundProperty() - useInvertedBackgroundProperty() - Method in class qupath.lib.display.ImageDisplay
-
Property that specifies whether the background should be inverted (i.e.
- useMicrons() - Method in class qupath.lib.gui.viewer.GridLines
-
Query whether to use calibrated units when calculating coordinates for any counting grid.
- useMultipoint - Variable in class qupath.lib.gui.panes.PreferencePane.DrawingPreferences
- usePixelSnappingProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
If true, pixels should be snapped to integer coordinates when using the drawing tools.
- UserDirectoryManager - Class in qupath.lib.gui
-
Helper class for managing a user directory, and associated subdirectories.
- userDirectoryProperty() - Method in class qupath.lib.gui.UserDirectoryManager
-
Property representing the user directory.
- useRotateGestures - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
- useRotateGesturesProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Support rotate gestures for touchscreens and trackpads.
- userPathProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
A path where additional files may be stored, such as extensions and log files.
- useScrollGesturesProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Support scroll gestures for touchscreens and trackpads.
- useSelectedColor - Variable in class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
- useSelectedColorProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Use a specified color for highlighting selected objects in the viewer.
- useSystemMenubarProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Deprecated.
- useTileBrushProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Request that the brush tool automatically uses any available tiles, rather than creating 'circles' as normal.
- useZoomGestures - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
- useZoomGesturesProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Support zoom gestures for touchscreens and trackpads.
V
- value() - Element in annotation interface qupath.lib.gui.actions.annotations.ActionAccelerator
-
String form of an accelerator, compatible with
KeyCombination.valueOf(String). - value() - Element in annotation interface qupath.lib.gui.actions.annotations.ActionConfig
-
Key to external properties file.
- value() - Element in annotation interface qupath.lib.gui.actions.annotations.ActionIcon
-
Icon to associate with the action's graphic property.
- value() - Element in annotation interface qupath.lib.gui.actions.annotations.ActionMenu
-
Menu path, in the form
"Menu>Submenu>Command name". - valueOf(String) - Static method in enum class qupath.lib.display.ChannelDisplayMode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class qupath.lib.gui.actions.InfoMessage.MessageType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class qupath.lib.gui.charts.HistogramChart.CountsTransformMode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class qupath.lib.gui.charts.HistogramChart.DisplayMode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class qupath.lib.gui.commands.PathObjectGridView.GridDisplaySize
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class qupath.lib.gui.dialogs.Dialogs.DialogButton
-
Deprecated.Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class qupath.lib.gui.logging.LogManager.LogLevel
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class qupath.lib.gui.prefs.PathPrefs.AutoUpdateType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class qupath.lib.gui.prefs.PathPrefs.DetectionTreeDisplayModes
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class qupath.lib.gui.prefs.PathPrefs.FontSize
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class qupath.lib.gui.prefs.PathPrefs.ImageTypeSetting
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class qupath.lib.gui.prefs.QuPathStyleManager.Fonts
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class qupath.lib.gui.prefs.SystemMenuBar.SystemMenuBarOption
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class qupath.lib.gui.tools.CommandFinderTools.CommandBarDisplay
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class qupath.lib.gui.tools.GuiTools.SnapshotType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class qupath.lib.gui.tools.IconFactory.PathIcons
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class qupath.lib.gui.viewer.ImageInterpolation
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class qupath.lib.gui.viewer.OverlayOptions.ClassVisibilityMode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class qupath.lib.gui.viewer.OverlayOptions.DetectionDisplayMode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters
-
Returns the enum constant of this class with the specified name.
- values() - Static method in enum class qupath.lib.display.ChannelDisplayMode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class qupath.lib.gui.actions.InfoMessage.MessageType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class qupath.lib.gui.charts.HistogramChart.CountsTransformMode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class qupath.lib.gui.charts.HistogramChart.DisplayMode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class qupath.lib.gui.commands.PathObjectGridView.GridDisplaySize
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class qupath.lib.gui.dialogs.Dialogs.DialogButton
-
Deprecated.Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class qupath.lib.gui.logging.LogManager.LogLevel
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class qupath.lib.gui.prefs.PathPrefs.AutoUpdateType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class qupath.lib.gui.prefs.PathPrefs.DetectionTreeDisplayModes
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class qupath.lib.gui.prefs.PathPrefs.FontSize
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class qupath.lib.gui.prefs.PathPrefs.ImageTypeSetting
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class qupath.lib.gui.prefs.QuPathStyleManager.Fonts
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class qupath.lib.gui.prefs.SystemMenuBar.SystemMenuBarOption
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class qupath.lib.gui.tools.CommandFinderTools.CommandBarDisplay
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class qupath.lib.gui.tools.GuiTools.SnapshotType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class qupath.lib.gui.tools.IconFactory.PathIcons
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class qupath.lib.gui.viewer.ImageInterpolation
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class qupath.lib.gui.viewer.OverlayOptions.ClassVisibilityMode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class qupath.lib.gui.viewer.OverlayOptions.DetectionDisplayMode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters
-
Returns an array containing the constants of this enum class, in the order they are declared.
- VIEW_TRACKER - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- viewer - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
- viewer - Variable in class qupath.lib.gui.charts.Charts.PieChartBuilder
- viewer - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
- viewer(QuPathViewer) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Specify a viewer.
- viewer(QuPathViewer) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
-
Specify a viewer.
- viewer(QuPathViewer) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Specify a viewer.
- VIEWER - Enum constant in enum class qupath.lib.gui.tools.GuiTools.SnapshotType
-
Snapshot of the current viewer content.
- VIEWER_GRID_1x1 - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- VIEWER_GRID_1x1 - Variable in class qupath.lib.gui.actions.ViewerActions
- VIEWER_GRID_1x2 - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- VIEWER_GRID_1x2 - Variable in class qupath.lib.gui.actions.ViewerActions
- VIEWER_GRID_2x1 - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- VIEWER_GRID_2x1 - Variable in class qupath.lib.gui.actions.ViewerActions
- VIEWER_GRID_2x2 - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- VIEWER_GRID_2x2 - Variable in class qupath.lib.gui.actions.ViewerActions
- VIEWER_GRID_3x3 - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- VIEWER_GRID_3x3 - Variable in class qupath.lib.gui.actions.ViewerActions
- ViewerActions - Class in qupath.lib.gui.actions
-
Actions that interact with one or more viewers.
- ViewerActions(ViewerManager) - Constructor for class qupath.lib.gui.actions.ViewerActions
- viewerBackgroundColorProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Color to paint behind any image.
- viewerClosed(QuPathViewer) - Method in class qupath.lib.gui.UndoRedoManager
- viewerClosed(QuPathViewer) - Method in interface qupath.lib.gui.viewer.QuPathViewerListener
-
Called when a viewer is closed.
- viewerClosed(QuPathViewer) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
- viewerClosed(QuPathViewer) - Method in class qupath.lib.gui.viewer.ViewerManager
- viewerGammaProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Requested gamma value applied to the image in each viewer (for display only).
- viewerInterpolateBilinearProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Request that images are displayed in viewers using bilinear interpolation.
- ViewerManager - Class in qupath.lib.gui.viewer
-
Class to manage multiple
QuPathViewerinstances in a UI region. - ViewerMover(QuPathViewer) - Constructor for class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler.ViewerMover
-
Constructor.
- ViewerPlusDisplayOptions - Class in qupath.lib.gui.viewer
-
A group of properties determining what should be displayed for each viewer.
- ViewerPlusDisplayOptions() - Constructor for class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
- ViewerPreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
- viewerProperty() - Method in class qupath.lib.gui.QuPathGUI
-
Property representing the viewer currently active.
- ViewMenuActions - Class in qupath.lib.gui.actions.menus
- ViewMenuActions.Actions - Class in qupath.lib.gui.actions.menus
- ViewMenuActions.CellDisplayActions - Class in qupath.lib.gui.actions.menus
- ViewMenuActions.MultitouchActions - Class in qupath.lib.gui.actions.menus
- ViewMenuActions.MultiviewActions - Class in qupath.lib.gui.actions.menus
- ViewMenuActions.MultiviewGridActions - Class in qupath.lib.gui.actions.menus
- ViewMenuActions.ZoomActions - Class in qupath.lib.gui.actions.menus
- ViewTracker - Class in qupath.lib.gui.viewer.recording
-
Default ViewTracker implementation.
- ViewTrackerControlPane - Class in qupath.lib.gui.viewer.recording
-
Panel for viewing ViewTracker controls.
- ViewTrackerControlPane(QuPathGUI) - Constructor for class qupath.lib.gui.viewer.recording.ViewTrackerControlPane
-
Create a ViewTrackerControlPane.
- ViewTrackerDataMap - Class in qupath.lib.gui.viewer.recording
-
Class for storing the values of a data map as well as generating a proper
BufferedImagewith the appropriate pixel type. - visibleRegionChanged(QuPathViewer, Shape) - Method in class qupath.lib.gui.UndoRedoManager
- visibleRegionChanged(QuPathViewer, Shape) - Method in interface qupath.lib.gui.viewer.QuPathViewerListener
-
Called when the visible region has changed in a viewer.
- visibleRegionChanged(QuPathViewer, Shape) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
- visibleRegionChanged(QuPathViewer, Shape) - Method in class qupath.lib.gui.viewer.ViewerManager
W
- WAND_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- WARN - Enum constant in enum class qupath.lib.gui.actions.InfoMessage.MessageType
-
Warning.
- WARN - Enum constant in enum class qupath.lib.gui.logging.LogManager.LogLevel
-
Warn logging (only if something is moderately important)
- warning() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Deprecated.Create a warning alert dialog.
- warning(String) - Static method in class qupath.lib.gui.actions.InfoMessage
-
Create a warning message with static text.
- warning(String, int) - Static method in class qupath.lib.gui.actions.InfoMessage
-
Create a warning message with static text and a count.
- warning(ObservableNumberValue) - Static method in class qupath.lib.gui.actions.InfoMessage
-
Create a warning message to show a count of warnings.
- warning(ObservableValue<String>) - Static method in class qupath.lib.gui.actions.InfoMessage
-
Create a warning message.
- warning(ObservableValue<String>, ObservableNumberValue) - Static method in class qupath.lib.gui.actions.InfoMessage
-
Create a warning message with a count.
- WARNING - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- WebViews - Class in qupath.lib.gui.tools
-
Helper class for creating a
WebViewin a standardized way. - WebViews() - Constructor for class qupath.lib.gui.tools.WebViews
- WelcomeStage - Class in qupath.lib.gui
-
Welcome page when launching QuPath.
- WelcomeStage() - Constructor for class qupath.lib.gui.WelcomeStage
- width - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
- width - Variable in class qupath.lib.gui.charts.Charts.PieChartBuilder
- width - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
- width(double) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Set the preferred width of the chart.
- width(double) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
-
Set the preferred width of the chart.
- width(double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Set the preferred width of the chart.
- width(double) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Deprecated.Specify the dialog width.
- WindowMenuActions - Class in qupath.lib.gui.actions.menus
-
Actions associated with showing/hiding/centering windows, or other window-related features.
- WindowMenuActions.Actions - Class in qupath.lib.gui.actions.menus
- windowTitle(String) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Title to use for the window, if the chart is shown.
- windowTitle(String) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
-
Title to use for the window, if the chart is shown.
- windowTitle(String) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Title to use for the window, if the chart is shown.
- WITH_ICONS - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.DetectionTreeDisplayModes
-
Show detections with ROI icons
- WITHOUT_ICONS - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.DetectionTreeDisplayModes
-
Show detections without ROI icons
- workerComplete(TileWorker<BufferedImage>) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
-
Every TileWorker should call this when the task is done!
- WorkflowCommandLogView - Class in qupath.lib.gui.panes
-
Show logged commands, and optionally generate a script.
- WorkflowCommandLogView(QuPathGUI) - Constructor for class qupath.lib.gui.panes.WorkflowCommandLogView
-
Construct a view to display the workflow for the currently-active ImageData within a running QuPath instance.
- WorkflowCommandLogView(QuPathGUI, Workflow) - Constructor for class qupath.lib.gui.panes.WorkflowCommandLogView
-
Construct a view displaying a static workflow (i.e.
- workflowUpdated(Workflow) - Method in class qupath.lib.gui.panes.WorkflowCommandLogView
- wrapTextProperty() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
-
Request wordwrap.
- wrapTextProperty() - Method in class qupath.lib.gui.scripting.TextAreaControl
- writeImage(Image, String) - Static method in class qupath.lib.gui.scripting.QPEx
-
Write a JavaFX image to the specified path.
- writeRenderedImage(QuPathViewer, String) - Static method in class qupath.lib.gui.scripting.QPEx
-
Write a rendered image for the current viewer to the specified path.
- writeRenderedImage(ImageData<BufferedImage>, String) - Static method in class qupath.lib.gui.scripting.QPEx
-
Write a rendered image to the specified path.
- writeRenderedImageRegion(QuPathViewer, RegionRequest, String) - Static method in class qupath.lib.gui.scripting.QPEx
-
Write a rendered image region for the current viewer to the specified path.
- writeRenderedImageRegion(ImageData<BufferedImage>, RegionRequest, String) - Static method in class qupath.lib.gui.scripting.QPEx
-
Write a rendered image region to the specified path.
- writeTMAData(File, ImageData<BufferedImage>) - Static method in class qupath.lib.gui.tma.TMADataIO
-
Write TMA summary data, without any image export.
- writeTMAData(File, ImageData<BufferedImage>, OverlayOptions, double) - Static method in class qupath.lib.gui.tma.TMADataIO
-
Write TMA data in a human-readable (and viewable) way, with JPEGs and TXT/CSV files.
X
- xAxisMax(double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Set the upper bound for the x-axis.
- xAxisMin(double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Set the lower bound for the x-axis.
- xAxisRange(double, double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Set the lower and upper bounds for the x-axis.
- xLabel - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
- xLabel - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
- xLabel(String) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Specify the x-axis label.
- xLabel(String) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Specify the x-axis label.
- XML - Static variable in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
- XmlLanguage - Class in qupath.lib.gui.scripting.languages
-
Class for representing XML in QuPath.
Y
- YAML - Static variable in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
- YamlLanguage - Class in qupath.lib.gui.scripting.languages
-
Class for the representation of YAML syntax in QuPath.
- yAxisMax(double) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Set the upper bound for the y-axis.
- yAxisMax(double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Set the upper bound for the y-axis.
- yAxisMin(double) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Set the lower bound for the y-axis.
- yAxisMin(double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Set the lower bound for the y-axis.
- yAxisRange(double, double) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Set the lower and upper bounds for the y-axis.
- yAxisRange(double, double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Set the lower and upper bounds for the y-axis.
- YES - Enum constant in enum class qupath.lib.gui.dialogs.Dialogs.DialogButton
-
Deprecated."Yes" option
- yLabel - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
- yLabel - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
- yLabel(String) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
-
Specify the y-axis label.
- yLabel(String) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
-
Specify the y-axis label.
Z
- Z_PROJECT - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- ZOOM_1 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.ZoomActions
- ZOOM_10 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.ZoomActions
- ZOOM_100 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.ZoomActions
- ZOOM_400 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.ZoomActions
- ZOOM_IN - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- ZOOM_IN - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.ZoomActions
- ZOOM_OUT - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- ZOOM_OUT - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.ZoomActions
- ZOOM_TO_FIT - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- ZOOM_TO_FIT - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.ZoomActions
- ZOOM_TO_FIT - Variable in class qupath.lib.gui.actions.ViewerActions
- zoomActions - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
- zoomIn() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Zoom in by one step.
- zoomIn(int) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Zoom in by a specified number of steps, where one 'step' indicates a minimal zoom increment.
- zoomOut() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Zoom out by one step.
- zoomOut(int) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Zoom out by a specified number of steps, where one 'step' indicates a minimal zoom increment.
- zoomToFit() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Request that the downsample is set to contain the entire image, and the image is centered in the viewer.
- zPositionProperty() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Current z-position for the z-slice currently visible in the viewer.
- ZProjectOverlay - Class in qupath.lib.gui.viewer.overlays
- ZProjectOverlay(OverlayOptions) - Constructor for class qupath.lib.gui.viewer.overlays.ZProjectOverlay
All Classes and Interfaces|All Packages|Constant Field Values
PropertyItemBuilderinstead