Deprecated API

Contents

• Interfaces
• Classes
• Fields
• Methods
• Constructors

Deprecated Interfaces

Interface	Description
qupath.lib.objects.MetadataStore	v0.6.0. Use MinimalMetadataStore instead.
qupath.lib.objects.PathObjectConnectionGroup	v0.6.0, to be replaced by DelaunayTools.Subdivision

Deprecated Classes

Class	Description
qupath.imagej.gui.ImageJMacroRunner	since v0.6.0; use ImageJScriptRunner and ImageJScriptRunnerControllerinstead.
qupath.lib.gui.dialogs.Dialogs	since v0.5.0.
qupath.lib.gui.dialogs.Dialogs.Builder
qupath.lib.gui.tma.TMASummaryViewer	since v0.4.0
qupath.lib.gui.tools.PaneTools	since v0.5.0; GridPaneUtils contains many of the features.
qupath.lib.objects.classes.PathClassFactory	since v0.4.0 in favor of methods added to PathClass directly.
qupath.lib.objects.DefaultPathObjectConnectionGroup	v0.6.0, to be replaced by DelaunayTools.Subdivision
qupath.lib.roi.AreaROI	since v0.6.0 (but really not used in recent versions)
qupath.opencv.features.DelaunayClusteringPlugin	v0.6.0 to be replaced by DelaunayTools. See https://github.com/qupath/qupath/issues/1590 for discussion of the problems with this command.
qupath.opencv.features.DelaunayTriangulation	v0.6.0, to be replaced by DelaunayTools.Subdivision

Deprecated Fields

Field	Description
qupath.imagej.gui.IJExtension.IJExtensionCommands.actionCellMembraneDetection
qupath.imagej.gui.IJExtension.IJExtensionCommands.actionLegacyMacroRunner
qupath.imagej.gui.IJExtension.IJExtensionCommands.actionPixelCount
qupath.imagej.gui.IJExtension.IJExtensionCommands.actionSimpleTissueDetection
qupath.imagej.gui.IJExtension.IJExtensionCommands.actionSubcellularDetection
qupath.lib.objects.TMACoreObject.LEGACY_KEY_UNIQUE_ID
qupath.process.gui.ProcessingExtension.OpenCVCommands.actionDelaunay
qupath.process.gui.ProcessingExtension.OpenCVCommands.actionFastCellCounts

Deprecated Methods

Method	Description
qupath.imagej.processing.RoiLabeling.labelsToConnectedROIs(ImageProcessor, int)	since v0.6.0; use IJProcessing.labelsToRoisArray(ImageProcessor) or IJProcessing.labelsToRois(ImageProcessor) instead.
qupath.imagej.processing.RoiLabeling.wandToRoi(Wand)	since v0.6.0; use IJProcessing.wandToRoi(Wand) instead.
qupath.imagej.tools.IJTools.convertToAnnotation(ImagePlus, ImageServer<?>, Roi, double, ImagePlane)	use instead IJTools.convertToAnnotation(Roi, double, double, double, ImagePlane)
qupath.imagej.tools.IJTools.convertToDetection(ImagePlus, ImageServer<?>, Roi, double, ImagePlane)	use instead IJTools.convertToDetection(Roi, double, double, double, ImagePlane)
qupath.imagej.tools.IJTools.convertToPathObject(ImagePlus, ImageServer<?>, Roi, double, Function<ROI, PathObject>, ImagePlane)	use instead IJTools.convertToPathObject(Roi, double, double, double, Function, ImagePlane)
qupath.lib.analysis.DelaunayTools.Subdivision.getPathObjects()	v0.6.0 use DelaunayTools.Subdivision.getObjects() instead.
qupath.lib.common.ColorTools.makeRGB(int, int, int)	Use ColorTools.packRGB(int, int, int) or ColorTools.packClippedRGB(int, int, int) instead.
qupath.lib.common.ColorTools.makeRGBA(int, int, int, int)	The naming and order of arguments is misleading. The output is a packed ARGB value, but arguments are provided in the order red, green, blue, alpha.
qupath.lib.common.GeneralTools.getNameWithoutExtension(String)	v0.5.0 in favor of GeneralTools.stripExtension(String), which does the same thing but has a more descriptive name. See https://github.com/qupath/qupath/pull/1275 for details.
qupath.lib.experimental.pixels.PixelProcessor.Builder.merger(ObjectMerger)	v0.6.0, use PixelProcessor.Builder.postProcess(ObjectProcessor) instead
qupath.lib.gui.images.servers.RenderedImageServer.Builder.display(ImageDisplay)	use RenderedImageServer.Builder.renderer(ImageRenderer) instead (since an ImageDisplay is also an ImageRenderer.
qupath.lib.gui.measure.ObservableMeasurementTableData.getBackingListEntries()	v0.6.0 use instead ObservableMeasurementTableData.getBackingList()
qupath.lib.gui.panes.PreferencePane.addChoicePropertyPreference(Property<T>, ObservableList<T>, Class<? extends T>, String, String, String)	use PropertyItemBuilder instead
qupath.lib.gui.panes.PreferencePane.addChoicePropertyPreference(Property<T>, ObservableList<T>, Class<? extends T>, String, String, String, boolean)	use PropertyItemBuilder instead
qupath.lib.gui.panes.PreferencePane.addColorPropertyPreference(IntegerProperty, String, String, String)	use PropertyItemBuilder instead
qupath.lib.gui.panes.PreferencePane.addDirectoryPropertyPreference(Property<String>, String, String, String)	use PropertyItemBuilder instead
qupath.lib.gui.panes.PreferencePane.addPropertyPreference(Property<T>, Class<? extends T>, String, String, String)	use PropertyItemBuilder instead
qupath.lib.gui.panes.PreferencePane.createPropertySheetItem(Property<T>, Class<? extends T>)	use PropertyItemBuilder instead
qupath.lib.gui.prefs.PathPrefs.getUserPreferences()	since v0.5.0 - avoid direct use of the Preferences object, since this may be invalidated by a call to PathPrefs.resetPreferences()
qupath.lib.gui.prefs.PathPrefs.useSystemMenubarProperty()
qupath.lib.gui.QuPathGUI.createSharedPoolCompletionService(Class<V>)	since v0.5.0; use QuPathGUI.getThreadPoolManager()
qupath.lib.gui.QuPathGUI.createSingleThreadExecutor(Object)	since v0.5.0; use QuPathGUI.getThreadPoolManager()
qupath.lib.gui.QuPathGUI.submitShortTask(Runnable)	since v0.5.0; use QuPathGUI.getThreadPoolManager()
qupath.lib.gui.viewer.overlays.PixelClassificationOverlay.createFeatureDisplayOverlay(OverlayOptions, Function<ImageData<BufferedImage>, ImageServer<BufferedImage>>, ImageRenderer)	Use PixelClassificationOverlay.create(OverlayOptions, Function, ImageRenderer) instead.
qupath.lib.gui.viewer.PathObjectPainter.paintConnections(PathObjectConnections, PathObjectHierarchy, Graphics2D, Color, double, ImagePlane)	v0.6.0 as #paintConnections(DelaunayTools.Subdivision, PathObjectHierarchy, Graphics2D, Color, double, ImagePlane) is preferred
qupath.lib.images.servers.ImageServer.readBufferedImage(RegionRequest)	since v0.4.0. Implementations of ImageServer should override ImageServer.readRegion(RegionRequest) instead. This method will be removed in a future release; it exists now only to maintain compatibility with QuPath extensions that have not yet been updated to use the newer method.
qupath.lib.images.servers.LabeledImageServer.Builder.useUniqueLabels()	in favor of LabeledImageServer.Builder.useInstanceLabels()
qupath.lib.images.servers.TileRequest.getPlane()	v0.4.0 use TileRequest.getImagePlane() instead (changed for better consistency with other classes)
qupath.lib.images.writers.ome.OMEPyramidWriter.OMEPyramidSeries.writePyramid(String)	use OMEPyramidWriter.OMEPyramidSeries.writeSeries(String) instead
qupath.lib.images.writers.ome.OMEPyramidWriter.OMEPyramidSeries.writePyramid(PyramidOMETiffWriter, IMetadata, int)	use OMEPyramidWriter.OMEPyramidSeries.writeSeries(IFormatWriter, IMetadata, int) instead
qupath.lib.io.PathIO.getObjectFileExtensions()	use PathIO.getObjectFileExtensions(boolean) instead
qupath.lib.io.PathIO.readImageData(File, ImageData<T>, ImageServer<T>, Class<T>)	since v0.6.0
qupath.lib.io.PathIO.readImageData(InputStream, ImageData<T>, ImageServer<T>, Class<T>)	since v0.6.0
qupath.lib.io.PathIO.readImageData(Path, ImageData<T>, ImageServer<T>, Class<T>)	since v0.6.0
qupath.lib.io.PathIO.readSerializedServerPath(File)	This was useful in QuPath v0.1.2 and earlier, since all information to construct a server was stored within its path. In v0.2 and later, the server path is in general not sufficient to construct a server, and this method lingers only for backwards compatibility. It will be removed in a later version.
qupath.lib.io.PointIO.readPointsObjectList(File)
qupath.lib.measurements.MeasurementList.getMeasurementNames()	v0.6.0 use MeasurementList.getNames() instead
qupath.lib.measurements.MeasurementList.removeMeasurements(String...)	v0.6.0 use MeasurementList.removeAll(String...) instead
qupath.lib.objects.classes.PathClassFactory.getDerivedPathClass(PathClass, String, Integer)	since v0.4.0, use PathClass.getInstance(PathClass, String, Integer)
qupath.lib.objects.classes.PathClassFactory.getNegative(PathClass)	since v0.4.0, use PathClass.getNegative(PathClass)
qupath.lib.objects.classes.PathClassFactory.getOnePlus(PathClass)	since v0.4.0, use PathClass.getOnePlus(PathClass)
qupath.lib.objects.classes.PathClassFactory.getPathClass(String, Integer)	since v0.4.0 in favor of PathClass.getInstance(String, Integer) or PathClass.fromString(String, Integer)
qupath.lib.objects.classes.PathClassFactory.getPathClass(String, String...)	since v0.4.0 in favor of PathClass.fromArray(String...)
qupath.lib.objects.classes.PathClassFactory.getPathClass(List<String>)	since v0.4.0 in favor of PathClass.fromCollection(java.util.Collection)
qupath.lib.objects.classes.PathClassFactory.getPathClass(PathClassFactory.StandardPathClasses)	since v0.4.0, use PathClass.StandardPathClasses
qupath.lib.objects.classes.PathClassFactory.getPathClassUnclassified()	since v0.4.0, use instead PathClass.NULL_CLASS
qupath.lib.objects.classes.PathClassFactory.getPositive(PathClass)	since v0.4.0, use PathClass.getPositive(PathClass)
qupath.lib.objects.classes.PathClassFactory.getSingletonPathClass(PathClass)	since v0.4.0 in favor of PathClass.getSingleton(PathClass)
qupath.lib.objects.classes.PathClassFactory.getThreePlus(PathClass)	since v0.4.0, use PathClass.getThreePlus(PathClass)
qupath.lib.objects.classes.PathClassFactory.getTwoPlus(PathClass)	since v0.4.0, use PathClass.getTwoPlus(PathClass)
qupath.lib.objects.hierarchy.PathObjectHierarchy.getObjectsForRegion(Class<? extends PathObject>, ImageRegion, Collection<PathObject>)	v0.6.0, use PathObjectHierarchy.getAllObjectsForRegion(ImageRegion, Collection) or its related methods instead.
qupath.lib.objects.hierarchy.PathObjectHierarchy.getPointObjects(Class<? extends PathObject>)	v0.6.0; use PathObjectHierarchy.getAllPointObjects() instead, and filter by object type if required.
qupath.lib.objects.MetadataStore.getMetadataKeys()	as of v0.6.0. Use MinimalMetadataStore.getMetadata() with the Map.keySet() method instead
qupath.lib.objects.MetadataStore.getMetadataMap()
qupath.lib.objects.MetadataStore.getMetadataString(String)	as of v0.6.0. Use MinimalMetadataStore.getMetadata() with the Map.get(Object) method instead
qupath.lib.objects.MetadataStore.getMetadataValue(String)	as of v0.6.0. Use MinimalMetadataStore.getMetadata() with the Map.get(Object) method instead
qupath.lib.objects.MetadataStore.putMetadataValue(String, String)	as of v0.6.0. Use MinimalMetadataStore.getMetadata() with the Map.put(Object, Object) method instead
qupath.lib.objects.PathObject.clearMetadataMap()	v0.6.0, use PathObject.getMetadata() to directly access the metadata instead.
qupath.lib.objects.PathObject.getUnmodifiableMetadataMap()	v0.6.0, use PathObject.getMetadata() to directly access the metadata instead.
qupath.lib.objects.PathObject.retrieveMetadataKeys()	v0.6.0, use PathObject.getMetadata() to directly access the metadata instead.
qupath.lib.objects.PathObject.retrieveMetadataValue(String)	v0.6.0, use PathObject.getMetadata() to directly access the metadata instead.
qupath.lib.objects.PathObject.storeMetadataValue(String, String)	v0.6.0, use PathObject.getMetadata() to directly access the metadata instead.
qupath.lib.objects.PathROIObject.isEditable()	since v0.4.0
qupath.lib.objects.TMACoreObject.clearMetadata()	v0.6.0. Use PathObject.getMetadata() to directly access metadata instead.
qupath.lib.objects.TMACoreObject.getMetadataKeys()	v0.6.0. Use PathObject.getMetadata() to directly access metadata instead.
qupath.lib.objects.TMACoreObject.getMetadataString(String)	v0.6.0. Use PathObject.getMetadata() to directly access metadata instead.
qupath.lib.objects.TMACoreObject.getMetadataValue(String)	v0.6.0. Use PathObject.getMetadata() to directly access metadata instead.
qupath.lib.objects.TMACoreObject.putMetadataValue(String, String)	v0.6.0. Use TMACoreObject.putMetadataValue(String, String) instead.
qupath.lib.objects.utils.ObjectMerger.merge(Collection<? extends PathObject>)	Use ObjectMerger.process(Collection) instead
qupath.lib.plugins.parameters.ParameterList.getParameterListJSON(Map<String, ?>, String)	use ParameterList.convertToJson(Map) instead.
qupath.lib.plugins.parameters.ParameterList.getParameterListJSON(ParameterList, String)	use ParameterList.convertToJson(ParameterList) instead.
qupath.lib.projects.ProjectImageEntry.clearMetadata()	v0.6.0, use MinimalMetadataStore.getMetadata() instead to directly access the metadata.
qupath.lib.projects.ProjectImageEntry.containsMetadata(String)	v0.6.0, use MinimalMetadataStore.getMetadata() instead to directly access the metadata.
qupath.lib.projects.ProjectImageEntry.getMetadataKeys()	v0.6.0, use MinimalMetadataStore.getMetadata() instead to directly access the metadata.
qupath.lib.projects.ProjectImageEntry.getMetadataMap()	v0.6.0, use MinimalMetadataStore.getMetadata() instead to directly access the metadata.
qupath.lib.projects.ProjectImageEntry.getMetadataValue(String)	v0.6.0, use MinimalMetadataStore.getMetadata() instead to directly access the metadata.
qupath.lib.projects.ProjectImageEntry.putMetadataValue(String, String)	v0.6.0, use MinimalMetadataStore.getMetadata() instead to directly access the metadata.
qupath.lib.projects.ProjectImageEntry.removeMetadataValue(String)	v0.6.0, use MinimalMetadataStore.getMetadata() instead to directly access the metadata.
qupath.lib.regions.ImageRegion.getPlane()	v0.4.0 use ImageRegion.getImagePlane() instead (changed for better consistency with other classes)
qupath.lib.roi.AreaROI.duplicate()
qupath.lib.roi.EllipseROI.duplicate()
qupath.lib.roi.interfaces.ROI.duplicate()
qupath.lib.roi.LineROI.duplicate()
qupath.lib.roi.PointsROI.duplicate()
qupath.lib.roi.PolygonROI.duplicate()
qupath.lib.roi.PolylineROI.duplicate()
qupath.lib.roi.RectangleROI.duplicate()
qupath.lib.roi.ROIs.createAreaROI(Shape, ImagePlane)	v0.6.0, use RoiTools.getShapeROI(Shape, ImagePlane, double) instead. This method does not necessarily give the expected results for shapes that do not represent an area.
qupath.lib.scripting.QP.buildServer(String, Class<T>, String...)	In the usual case where BufferedImage is the class, use QP.buildServer(String, String...) instead because it handles default args.
qupath.lib.scripting.QP.clearAllObjects()	For naming consistency; use #removeAllObjects instead.
qupath.lib.scripting.QP.clearAllObjects(Class<? extends PathObject>)	For naming consistency; use #removeAllObjects instead.
qupath.lib.scripting.QP.clearAnnotationMeasurements()	For consistency in naming; use #removeAnnotationMeasurements instead.
qupath.lib.scripting.QP.clearAnnotationMeasurements(PathObjectHierarchy)	For consistency in naming; use #removeMeasurements instead.
qupath.lib.scripting.QP.clearAnnotations()	For naming consistency; use #removeAnnotations instead.
qupath.lib.scripting.QP.clearCellMeasurements()	For consistency in naming; use #removeCellMeasurements instead.
qupath.lib.scripting.QP.clearCellMeasurements(PathObjectHierarchy)	For consistency in naming; use #removeCellMeasurements instead.
qupath.lib.scripting.QP.clearDetectionMeasurements()	For consistency in naming; use #removeDetectionMeasurements instead.
qupath.lib.scripting.QP.clearDetectionMeasurements(PathObjectHierarchy)	For consistency in naming; use #removeDetectionMeasurements instead.
qupath.lib.scripting.QP.clearDetections()	For naming consistency; use #removeDetections instead.
qupath.lib.scripting.QP.clearMeasurements()	For consistency in naming; use #removeMeasurements instead.
qupath.lib.scripting.QP.clearMeasurements(Class<? extends PathObject>)	For consistency in naming; use #removeMeasurements instead.
qupath.lib.scripting.QP.clearMeasurements(PathObjectHierarchy, Class<? extends PathObject>)	For consistency in naming; use #removeMeasurements instead.
qupath.lib.scripting.QP.clearMeasurements(PathObjectHierarchy, Collection<? extends PathObject>)	For consistency in naming; use #removeMeasurements instead.
qupath.lib.scripting.QP.clearMeasurements(PathObjectHierarchy, PathObject...)	For consistency in naming; use #removeMeasurements instead.
qupath.lib.scripting.QP.clearRootMeasurements()	For consistency in naming; use #removeRootMeasurements instead.
qupath.lib.scripting.QP.clearRootMeasurements(PathObjectHierarchy)	For consistency in naming; use #removeRootMeasurements instead.
qupath.lib.scripting.QP.clearSelectedObjects()	For consistency in naming; use #removeSelectedObjects instead.
qupath.lib.scripting.QP.clearSelectedObjects(boolean)	For consistency in naming; use #removeSelectedObjects instead.
qupath.lib.scripting.QP.clearTileMeasurements()	For consistency in naming; use #removeTileMeasurements instead.
qupath.lib.scripting.QP.clearTileMeasurements(PathObjectHierarchy)	For consistency in naming; use #removeTileMeasurements instead.
qupath.lib.scripting.QP.clearTMACoreMeasurements()	For consistency in naming; use #removeTMACoreMeasurements instead.
qupath.lib.scripting.QP.clearTMACoreMeasurements(PathObjectHierarchy)	For consistency in naming; use #removeTMACoreMeasurements instead.
qupath.lib.scripting.QP.clearTMAGrid()	For naming consistency; use #removeTMAGrid instead.
qupath.lib.scripting.QP.createSelectAllObject(boolean)	v0.4.0 use QP.createFullImageAnnotation(boolean) instead
qupath.lib.scripting.QP.createSelectAllObject(boolean, int, int)	v0.4.0 use QP.createFullImageAnnotation(boolean, int, int) instead
qupath.lib.scripting.QP.detectionCentroidDistances()	retained only for compatibility of v0.2.0 milestone releases; use instead #detectionCentroidDistances(boolean)
qupath.lib.scripting.QP.detectionToAnnotationDistances()	retained only for compatibility of v0.2.0 milestone releases; use instead #detectionToAnnotationDistances(boolean)
qupath.lib.scripting.QP.getColorRGB(int...)	Use instead QP.makeRGB(int, int, int) or QP.makeARGB(int, int, int, int)
qupath.lib.scripting.QP.loadImageData(String, boolean)
qupath.lib.scripting.QP.makePathInProject(String...)	v0.6.0, use QP.createDirectoryInProject(String...) instead.
qupath.lib.scripting.QP.removeObject(PathObject, boolean)
qupath.lib.scripting.QP.removeObjects(Collection<? extends PathObject>, boolean)	Use QP.removeObjects(Collection) or QP.removeObjectsAndDescendants(Collection) instead.
qupath.lib.scripting.QP.removeObjects(PathObject[], boolean)	Use QP.removeObjects(PathObject[]) or QP.removeObjectsAndDescendants(PathObject[]) instead.
qupath.lib.scripting.QP.selectObjectsByMeasurement(ImageData<?>, String)
qupath.opencv.dnn.DnnTools.registerDnnModel(Class<T>, String)	since v0.4.0; use DnnModels.registerDnnModel(Class, String) instead.
qupath.opencv.features.DelaunayTriangulation.getConnectedNodes(Collection<PathObject>, Collection<double[]>)
qupath.opencv.ml.pixel.PixelClassificationMeasurementManager.getMeasurementValue(PathObject, String, boolean)	use PixelClassificationMeasurementManager.getMeasurementValue(PathObject, String) or PixelClassificationMeasurementManager.getCachedMeasurementValue(PathObject, String) instead
qupath.opencv.ml.pixel.PixelClassificationMeasurementManager.getMeasurementValue(ROI, String, boolean)	use PixelClassificationMeasurementManager.getMeasurementValue(ROI, String) or PixelClassificationMeasurementManager.getCachedMeasurementValue(ROI, String) instead
qupath.opencv.tools.OpenCVTools.getCircularStructuringElement(int)	OpenCVTools.createDisk(int, boolean) gives more reliable shapes.
qupath.opencv.tools.OpenCVTools.labelImage(Mat, Mat, int)	Use OpenCVTools.label(Mat, Mat, int) instead.

Deprecated Constructors

Constructor	Description
qupath.lib.gui.commands.MiniViewers.MiniViewerManager(QuPathViewer, Collection<? extends ChannelDisplayInfo>)	use MiniViewers.createManager(QuPathViewer, Collection) instead.