Deprecated API

Contents

• Classes
• Fields
• Methods
• Constructors

Deprecated Classes

Class	Description
qupath.lib.gui.tma.TMASummaryViewer	since v0.4.0
qupath.lib.measurements.MeasurementFactory
qupath.lib.objects.classes.PathClassFactory	since v0.4.0 in favor of methods added to PathClass directly.

Deprecated Fields

Field	Description
qupath.imagej.gui.IJExtension.IJExtensionCommands.actionCellMembraneDetection
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.actionFastCellCounts

Deprecated Methods

Method	Description
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.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.display.ImageDisplay.applyTransforms(BufferedImage, BufferedImage, List<? extends ChannelDisplayInfo>, boolean)	use instead ImageDisplay.applyTransforms(BufferedImage, BufferedImage, List, ChannelDisplayMode)
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.createNumericMeasurement(PathObject, String)
qupath.lib.gui.measure.ObservableMeasurementTableData.createStringMeasurement(PathObject, String)
qupath.lib.gui.QuPathGUI.launchQuPath(HostServices)	as of v0.2.3 in favor of QuPathGUI.launchQuPath(HostServices, boolean)
qupath.lib.gui.viewer.overlays.PixelClassificationOverlay.createFeatureDisplayOverlay(OverlayOptions, Function<ImageData<BufferedImage>, ImageServer<BufferedImage>>, ImageRenderer)	Use PixelClassificationOverlay.create(OverlayOptions, Function, ImageRenderer) instead.
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.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.Measurement.isDynamic()
qupath.lib.measurements.MeasurementList.addMeasurement(String, double)	v0.4.0 use MeasurementList.put(String, double) instead
qupath.lib.measurements.MeasurementList.containsNamedMeasurement(String)	since v0.4.0; replaced by MeasurementList.containsKey(String)
qupath.lib.measurements.MeasurementList.getMeasurementName(int)	since v0.4.0; using names is preferred over indexing but MeasurementList.getMeasurementNames() can still be used
qupath.lib.measurements.MeasurementList.getMeasurementValue(int)	since v0.4.0; using MeasurementList.get(String) is preferred over using an index
qupath.lib.measurements.MeasurementList.getMeasurementValue(String)	since v0.4.0; use MeasurementList.get(String) instead
qupath.lib.measurements.MeasurementList.putMeasurement(String, double)	since v0.4.0; replaced by MeasurementList.put(String, double)
qupath.lib.measurements.MeasurementList.putMeasurement(Measurement)	since v0.4.0, since there is no real need to create a Measurement object and we don't currently use dynamic measurements
qupath.lib.measurements.MeasurementList.supportsDynamicMeasurements()	since v0.4.0; the initial implementation of dynamic measurements was never used
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.addPathObject(PathObject)	since v0.4.0; use PathObjectHierarchy.addObject(PathObject) instead (for naming consistency)
qupath.lib.objects.hierarchy.PathObjectHierarchy.addPathObjectBelowParent(PathObject, PathObject, boolean)	since v0.4.0; use PathObjectHierarchy.addObjectBelowParent(PathObject, PathObject, boolean)
qupath.lib.objects.hierarchy.PathObjectHierarchy.addPathObjectListener(PathObjectHierarchyListener)	since v0.4.0 (the name was confusing because it wasn't intended primarily to listen to changes within individual PathObjects)
qupath.lib.objects.hierarchy.PathObjectHierarchy.addPathObjects(Collection<? extends PathObject>)	since v0.4.0; use PathObjectHierarchy.addObjects(Collection) instead
qupath.lib.objects.hierarchy.PathObjectHierarchy.addPathObjectWithoutUpdate(PathObject)	since v0.4.0, use PathObjectHierarchy.addObject(PathObject, boolean) instead (for naming consistency)
qupath.lib.objects.hierarchy.PathObjectHierarchy.removePathObjectListener(PathObjectHierarchyListener)	since v0.4.0 (the name was confusing because it wasn't intended primarily to listen to changes within individual PathObjects)
qupath.lib.objects.PathObject.addPathObject(PathObject)	since v0.4.0, replaced by PathObject.addChildObject(PathObject)
qupath.lib.objects.PathObject.addPathObjects(Collection<? extends PathObject>)	since v0.4.0, replaced by PathObject.addChildObjects(Collection)
qupath.lib.objects.PathObject.clearPathObjects()	since v0.4.0, replaced by PathObject.clearChildObjects()
qupath.lib.objects.PathObject.getColorRGB()	since v0.4.0, use PathObject.getColor() instead.
qupath.lib.objects.PathObject.hasChildren()	since v0.4.0, replaced by PathObject.hasChildObjects()
qupath.lib.objects.PathObject.removePathObject(PathObject)	since v0.4.0, replaced by PathObject.removeChildObject(PathObject)
qupath.lib.objects.PathObject.removePathObjects(Collection<PathObject>)	since v0.4.0, replaced by PathObject.removeChildObjects(Collection)
qupath.lib.objects.PathObject.setColorRGB(Integer)	since v0.4.0, use PathObject.setColor(Integer) instead.
qupath.lib.objects.PathObjectTools.containsObject(PathObject, PathObject)
qupath.lib.objects.PathObjectTools.containsROI(ROI, ROI)
qupath.lib.objects.PathROIObject.isEditable()	since v0.4.0
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.getServerURIs()	use instead UriResource.getURIs()
qupath.lib.projects.ProjectImageEntry.updateServerURIs(Map<URI, URI>)	use instead UriResource.updateURIs(Map)
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.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.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.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.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.
qupathj.QuPath_Send_Overlay_to_QuPath.createPathObjectsFromROIs(ImagePlus, Roi[], ImageServer<?>, double, boolean, boolean, ImagePlane)	use instead QuPath_Send_Overlay_to_QuPath.createObjectsFromROIs(ImagePlus, Collection, double, boolean, boolean, ImagePlane)

Deprecated Constructors

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