Index

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All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

above(String) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder
Set the classification (by name) for objects for which the specified measurement has a value above the threshold.
above(PathClass) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder
Set the classification for objects for which the specified measurement has a value above the threshold.
aboveEquals(String) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder
Set the classification (by name) for objects for which the specified measurement has a value above or equal to the threshold.
aboveEquals(PathClass) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder
Set the classification for objects for which the specified measurement has a value above or equal to the threshold.
AbstractDetectionPlugin<T> - Class in qupath.lib.plugins
Abstract plugin aimed towards cases where new objects will be detected inside existing objects (normally TMA cores or annotations).
AbstractDetectionPlugin() - Constructor for class qupath.lib.plugins.AbstractDetectionPlugin
 
AbstractImageServer<T> - Class in qupath.lib.images.servers
Abstract implementation of ImageServer providing some common functionality.
AbstractImageServer(Class<T>) - Constructor for class qupath.lib.images.servers.AbstractImageServer
 
AbstractInteractivePlugin<T> - Class in qupath.lib.plugins
Abstract class to help with implementing an interactive plugin.
AbstractInteractivePlugin() - Constructor for class qupath.lib.plugins.AbstractInteractivePlugin
 
AbstractObjectClassifier<T> - Class in qupath.lib.classifiers.object
Abstract class to help with the creation of object classifiers.
AbstractObjectClassifier(PathObjectFilter) - Constructor for class qupath.lib.classifiers.object.AbstractObjectClassifier
 
AbstractPlugin<T> - Class in qupath.lib.plugins
General abstract plugin implementation, which defines some methods to facilitate creating plugins that do parallel processing.
AbstractPlugin() - Constructor for class qupath.lib.plugins.AbstractPlugin
 
AbstractTaskRunner - Class in qupath.lib.plugins
Abstract PluginRunner to help with the creation of plugin runners for specific circumstances, e.g.
AbstractTaskRunner() - Constructor for class qupath.lib.plugins.AbstractTaskRunner
Constructor for a PluginRunner that uses the default number of threads, read from ThreadTools.getParallelism().
AbstractTaskRunner(int) - Constructor for class qupath.lib.plugins.AbstractTaskRunner
Constructor for a PluginRunner that optionally uses a fixed number of threads.
AbstractTileableDetectionPlugin<T> - Class in qupath.lib.plugins
Abstract plugin used for detection tasks that support breaking large regions into smaller ones, and analyzing these in parallel - optionally with overlaps.
AbstractTileableDetectionPlugin() - Constructor for class qupath.lib.plugins.AbstractTileableDetectionPlugin
 
AbstractTileableImageServer - Class in qupath.lib.images.servers
Abstract ImageServer for BufferedImages that internally breaks up requests into constituent tiles.
AbstractTileableImageServer() - Constructor for class qupath.lib.images.servers.AbstractTileableImageServer
 
add(Padding) - Method in class qupath.lib.regions.Padding
Add this padding to another.
ADD - Enum constant in enum class qupath.lib.roi.RoiTools.CombineOp
Add ROIs (union).
addBooleanParameter(String, String, boolean) - Method in class qupath.lib.plugins.parameters.ParameterList
Add a boolean parameter.
addBooleanParameter(String, String, boolean, String) - Method in class qupath.lib.plugins.parameters.ParameterList
Add a boolean parameter, with help text.
addChildObject(PathObject) - Method in class qupath.lib.objects.PathObject
Add an object to the child list of this object.
addChildObjects(Collection<? extends PathObject>) - Method in class qupath.lib.objects.PathObject
Add a collection of objects to the child list of this object.
addChoiceParameter(String, String, S, List<S>) - Method in class qupath.lib.plugins.parameters.ParameterList
Add a choice parameter, with an list of choices.
addChoiceParameter(String, String, S, List<S>, String) - Method in class qupath.lib.plugins.parameters.ParameterList
Add a choice parameter, with an list of choices and help text.
addDoubleParameter(String, String, double) - Method in class qupath.lib.plugins.parameters.ParameterList
Add a double parameter to this list.
addDoubleParameter(String, String, double, String, double, double, String) - Method in class qupath.lib.plugins.parameters.ParameterList
Add a bounded double parameter to this list.
addDoubleParameter(String, String, double, String, String) - Method in class qupath.lib.plugins.parameters.ParameterList
Add a double parameter to this list, optionally including a unit and help text.
addDuplicate(ProjectImageEntry<T>, boolean) - Method in interface qupath.lib.projects.Project
Add an image by duplicating an existing entry.
ADDED - Enum constant in enum class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent.HierarchyEventType
An object has been added
addEmptyParameter(String) - Method in class qupath.lib.plugins.parameters.ParameterList
Add an 'empty' parameter, that is one that does not take any values.
addEvent(double, boolean) - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData
Insert a new event.
addEvents(Collection<KaplanMeierData.KaplanMeierEvent>) - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData
Add a collection of events.
addFullResolutionLevel() - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel.Builder
Add the full-resolution image as a level of the pyramid.
addGroup(PathObjectConnectionGroup) - Method in class qupath.lib.objects.PathObjectConnections
Add a new connections group.
addImage(ImageServerBuilder.ServerBuilder<T>) - Method in interface qupath.lib.projects.Project
Add an image for a particular ImageServer.
addIntParameter(String, String, int) - Method in class qupath.lib.plugins.parameters.ParameterList
Add an int parameter.
addIntParameter(String, String, int, String, double, double, String) - Method in class qupath.lib.plugins.parameters.ParameterList
Add a bounded int parameter, with optional unit and help text.
addIntParameter(String, String, int, String, String) - Method in class qupath.lib.plugins.parameters.ParameterList
Add an int parameter, with optional unit and help text.
addLabel(String, int) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Add a single label by classname, where the label represents the integer label used for annotations with the given classname.
addLabel(String, int, Integer) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Add a single label by classname, where the label represents the integer label used for annotations with the given classname.
addLabel(PathClass, int) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Add a single label by PathClass, where the label represents the integer label used for annotations with the given classification.
addLabel(PathClass, int, Integer) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Add a single label by PathClass, where the label represents the integer label used for annotations with the given classification.
addLabels(Map<PathClass, Integer>) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Add multiple labels by PathClass, where the key represents a PathClass and the value represents the integer label that should be used for annotations of the given class.
addLabelsByName(Map<String, Integer>) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Add multiple labels by classname, where the key represents a classname and the value represents the integer label that should be used for annotations of the given class.
addLevel(double, int, int) - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel.Builder
Add a new level by providing a downsample value, width and height.
addLevel(int, int) - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel.Builder
Add a new level based on level dimensions, estimating the corresponding downsample value as required.
addLevel(ImageServerMetadata.ImageResolutionLevel) - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel.Builder
Add a new level directly.
addLevelByDownsample(double) - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel.Builder
Add a new level, calculating dimensions using a downsample factor applied to the full-resolution image.
addListener(PathObjectHierarchyListener) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Add a hierarchy change listener.
addObject(PathObject) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Add an object to the hierarchy, firing an event.
addObject(PathObject, boolean) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Add an object to the hierarchy, optionally firing an event.
addObjectBelowParent(PathObject, PathObject, boolean) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Add path object as descendant of the requested parent.
addObjects(Collection<? extends PathObject>) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Add multiple objects to the hierarchy.
addPathObjectSelectionListener(PathObjectSelectionListener) - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel
Add listener for selection changes.
addPropertyChangeListener(PropertyChangeListener) - Method in class qupath.lib.images.ImageData
Add a new property change listener.
addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.AbstractPlugin
For a specified parent object, generate a task to run.
addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.AbstractTileableDetectionPlugin
Intercepts the 'standard' addRunnableTasks to (if necessary) insert ParallelTileObjects along the way, thereby breaking an excessively-large parentObject into more manageable pieces.
addStep(WorkflowStep) - Method in class qupath.lib.plugins.workflow.Workflow
Append a new step to the end of the workflow, firing an update event.
addSteps(Collection<WorkflowStep>) - Method in class qupath.lib.plugins.workflow.Workflow
Append multiple steps to the end of the workflow, firing a single update event.
addStringParameter(String, String, String) - Method in class qupath.lib.plugins.parameters.ParameterList
Add a String parameter.
addStringParameter(String, String, String, String) - Method in class qupath.lib.plugins.parameters.ParameterList
Add a String parameter, with help text.
addTitleParameter(String) - Method in class qupath.lib.plugins.parameters.ParameterList
Add a title parameter.
addTMAGrid(ImageData<?>, String, String, boolean, double) - Static method in class qupath.lib.objects.PathObjectTools
Create a new regular TMAGrid and set it as active on the hierarchy for an image.
addUnclassifiedLabel(int) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Add a single label for objects that are unclassified, where the label represents the integer label used for annotations that have no classification set.
addUnclassifiedLabel(int, Integer) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Add a single label for objects that are unclassified, where the label represents the integer label used for annotations that have no classification set.
addValue(double) - Method in class qupath.lib.analysis.stats.RunningStatistics
Add another value; NaN values are counted but do not contribute to the statistics.
addWorkflowListener(WorkflowListener) - Method in class qupath.lib.plugins.workflow.Workflow
Add a listener for changes to the workflow.
addWorkflowStep(ImageData<T>, String) - Method in class qupath.lib.plugins.AbstractPlugin
Add a workflow step to the ImageData indicating the argument that this plugin was run with.
AffineTransformImageServer - Class in qupath.lib.images.servers
ImageServer that dynamically applies an AffineTransform to an existing ImageServer.
AffineTransformImageServer(ImageServer<BufferedImage>, AffineTransform) - Constructor for class qupath.lib.images.servers.AffineTransformImageServer
 
AffineTransforms - Class in qupath.lib.awt.common
Helper class for working with affine transforms.
AffineTransforms() - Constructor for class qupath.lib.awt.common.AffineTransforms
 
alignBottomCenter() - Method in class qupath.lib.objects.utils.Tiler.Builder
Start tiles at the bottom center of the ROI bounding box.
alignBottomLeft() - Method in class qupath.lib.objects.utils.Tiler.Builder
Match tiles to the bottom left of the ROI bounding box.
alignBottomRight() - Method in class qupath.lib.objects.utils.Tiler.Builder
Match tiles to the bottom right of the ROI bounding box.
alignCenter() - Method in class qupath.lib.objects.utils.Tiler.Builder
Center tiles within the ROI bounding box.
alignCenterLeft() - Method in class qupath.lib.objects.utils.Tiler.Builder
Match tiles to the center left of the ROI bounding box.
alignCenterRight() - Method in class qupath.lib.objects.utils.Tiler.Builder
Match tiles to the center left of the ROI bounding box.
alignment(Tiler.TileAlignment) - Method in class qupath.lib.objects.utils.Tiler.Builder
Set the tile alignment.
alignTopCenter() - Method in class qupath.lib.objects.utils.Tiler.Builder
Start tiles at the top center of the ROI bounding box.
alignTopLeft() - Method in class qupath.lib.objects.utils.Tiler.Builder
Start tiles at the top left of the ROI bounding box.
alignTopRight() - Method in class qupath.lib.objects.utils.Tiler.Builder
Match tiles to the top right of the ROI bounding box.
allowSmoothInterpolation() - Method in class qupath.lib.images.servers.AbstractTileableImageServer
Returns true if this server is permitted to use smooth interpolation when resizing.
almostTheSame(double, double, double) - Static method in class qupath.lib.common.GeneralTools
Test if two doubles are approximately equal, within a specified tolerance.
alpha(int) - Static method in class qupath.lib.common.ColorTools
Extract the 8-bit alpha value from a packed ARGB value.
alwaysPromptForObjects() - Method in class qupath.lib.plugins.AbstractInteractivePlugin
 
alwaysPromptForObjects() - Method in interface qupath.lib.plugins.PathInteractivePlugin
If this returns true, then a prompt is requested every time the command is run - even if there are valid parent objects already selected.
and(PathObjectPredicates.PathObjectPredicate) - Method in interface qupath.lib.objects.PathObjectPredicates.PathObjectPredicate
Combine with another PathObjectPredicates.PathObjectPredicate through AND.
andThen(ObjectProcessor) - Method in interface qupath.lib.objects.utils.ObjectProcessor
Create a new ObjectProcessor that applies (at least) two processors sequentially.
annotatedCentroidTilesOnly(boolean) - Method in class qupath.lib.images.writers.TileExporter
Specify whether tiles without any annotations over the tile centroid should be included.
annotatedTilesOnly(boolean) - Method in class qupath.lib.images.writers.TileExporter
Specify whether tiles that do not overlap with any annotations should be included.
ANNOTATIONS - Enum constant in enum class qupath.lib.objects.PathObjectFilter
Accept annotation objects
apply() - Method in class qupath.lib.objects.classes.Reclassifier
Apply the stored classification.
applyClassification(ImageData<BufferedImage>, RegionRequest) - Method in interface qupath.lib.classifiers.pixel.PixelClassifier
Apply pixel classifier to a specified region of an image.
applyColorTransforms(Collection<? extends ColorTransforms.ColorTransform>) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Apply color transforms to the image.
applyColorTransforms(ColorTransforms.ColorTransform...) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Apply color transforms to the image.
applyReplacements() - Method in class qupath.lib.io.UriUpdater
Apply all current replacements, updating the UriResource objects.
AREA - Enum constant in enum class qupath.lib.roi.interfaces.ROI.RoiType
ROI represents a closed area (possibly with holes).
areaContains(ROI, double, double) - Static method in class qupath.lib.roi.RoiTools
Returns true if pathROI is an area that contains x & y somewhere within it.
AreaROI - Class in qupath.lib.roi
Deprecated.
since v0.6.0 (but really not used in recent versions)
arrayAsString(Locale) - Method in class qupath.lib.color.StainVector
Get a String representation of the stain vector array, formatting according to the specified Locale.
arrayToString(Object[], String) - Static method in class qupath.lib.common.GeneralTools
Convert a String array to a single string, with a specified delimiter string.
arrayToString(Locale, double[], int) - Static method in class qupath.lib.common.GeneralTools
Convert a double array to a String using a space as a delimiter.
arrayToString(Locale, double[], String, int) - Static method in class qupath.lib.common.GeneralTools
Convert a double array to string, with a specified number of decimal places.
ArrayWrappers - Class in qupath.lib.analysis.stats
Simple wrappers for primitive arrays that returns values as doubles.
ArrayWrappers() - Constructor for class qupath.lib.analysis.stats.ArrayWrappers
 
ArrayWrappers.ArrayWrapper - Interface in qupath.lib.analysis.stats
Simple wrapper for an array or list, enabling values to be returned as doubles.
asMap() - Method in interface qupath.lib.measurements.MeasurementList
Get a map view of this measurements list.
attemptOperation(Geometry, Function<Geometry, Geometry>) - Static method in class qupath.lib.roi.GeometryTools
Attempt to apply a function to a geometry, returning the input unchanged if there was an exception.
autoUnits() - Method in class qupath.lib.common.Timeit
 
averageChannelProject() - Method in class qupath.lib.images.servers.TransformedServerBuilder
Perform an average (mean) projection of the channels.
awaitCompletion() - Method in class qupath.lib.plugins.AbstractTaskRunner
Await the completion of currently-running tasks, notifying any listener if necessary.
AwtTools - Class in qupath.lib.awt.common
A collection of static methods useful when working with AWT shapes and ImageRegions.

B

BACKGROUND_KEY - Static variable in class qupath.lib.color.ColorDeconvolutionStains
 
backgroundLabel(int) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Specify the background label (0 by default).
backgroundLabel(int, Integer) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Specify the background label (0 by default) and color.
baseClassification(PathClass...) - Static method in class qupath.lib.objects.PathObjectPredicates
Predicate that returns true if an object has any of the specified base classifications, regardless of any subclassification.
below(String) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder
Set the classification (by name) for objects for which the specified measurement has a value below the threshold.
below(PathClass) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder
Set the classification for objects for which the specified measurement has a value below the threshold.
belowEquals(String) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder
Set the classification (by name) for objects for which the specified measurement has a value below or equal to the threshold.
belowEquals(PathClass) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder
Set the classification for objects for which the specified measurement has a value below or equal to the threshold.
Black - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
All pixels black
BLACK - Static variable in class qupath.lib.common.ColorTools
Packed int representing black.
blankString(String, boolean) - Static method in class qupath.lib.common.GeneralTools
Check if a string is blank, i.e.
blue(int) - Static method in class qupath.lib.common.ColorTools
Extract the 8-bit blue value from a packed RGB value.
Blue - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
Blue channel only
BLUE - Static variable in class qupath.lib.common.ColorTools
Packed int representing blue.
BLUE - Static variable in class qupath.lib.images.servers.ImageChannel
Default blue channel for RGB images.
Blue_chromaticity - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
Blue chromaticity value, blue / max(1, red + green + blue)
Blue_OD - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
Blue channel optical densities
blueChromaticity(int) - Static method in class qupath.lib.color.ColorTransformer
Extract blue chromaticity value from a packed RGB pixel, blue / max(1, red + green + blue)
BooleanParameter - Class in qupath.lib.plugins.parameters
Parameter that can take on true of false value - or null.
BOTTOM_CENTER - Enum constant in enum class qupath.lib.objects.utils.Tiler.TileAlignment
 
BOTTOM_LEFT - Enum constant in enum class qupath.lib.objects.utils.Tiler.TileAlignment
 
BOTTOM_RIGHT - Enum constant in enum class qupath.lib.objects.utils.Tiler.TileAlignment
 
boundaryDistancePredicate(double, boolean) - Static method in class qupath.lib.analysis.DelaunayTools
BiPredicate that returns true for objects with ROI boundaries within a specified distance.
BRIGHTFIELD_H_DAB - Enum constant in enum class qupath.lib.images.ImageData.ImageType
Brightfield image with hematoxylin and DAB stains.
BRIGHTFIELD_H_E - Enum constant in enum class qupath.lib.images.ImageData.ImageType
Brightfield image with hematoxylin and eosin stains.
BRIGHTFIELD_OTHER - Enum constant in enum class qupath.lib.images.ImageData.ImageType
Brightfield image with any stains.
brightness(int) - Static method in class qupath.lib.color.ColorTransformer
Extract brightness value from RGB-to-HSB transform.
Brightness - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
Brightness value (from RGB-HSB transform)
brown(int) - Static method in class qupath.lib.color.ColorTransformer
Extract brown value, (blue - (red + green)*0.3f)
Brown - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
Brown value, (blue - (red + green)*0.3f)
buffer(ROI, double) - Static method in class qupath.lib.roi.RoiTools
Buffer the specified ROI, dilating (or eroding) by the specified distance.
BufferedImageNormalizer - Interface in qupath.lib.images.servers.transforms
Interface for normalizing a BufferedImage.
BufferedImageTools - Class in qupath.lib.awt.common
Static methods for working with BufferedImages and QuPath objects.
build() - Method in class qupath.lib.analysis.DelaunayTools.Builder
Build the DelaunayTools.Subdivision with the current parameters.
build() - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder
Build the classifier defined by the parameters of this builder.
build() - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata.Builder
Build a new PixelClassifierMetadata object.
build() - Method in interface qupath.lib.color.ColorModels.ColorModelBuilder
Build a ColorModel.
build() - Method in class qupath.lib.images.servers.ImageServerBuilder.AbstractServerBuilder
 
build() - Method in interface qupath.lib.images.servers.ImageServerBuilder.ServerBuilder
Build a new ImageServer instance.
build() - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder
build() - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel.Builder
Build a list of ImageResolutionLevels, which can be used with an ImageServerMetadata object.
build() - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Build the ImageServer with the requested parameters.
build() - Method in class qupath.lib.images.servers.PixelCalibration.Builder
Build PixelCalibration object.
build() - Method in class qupath.lib.images.servers.SparseImageServer.Builder
Build a new SparseImageServer.
build() - Method in class qupath.lib.images.servers.TransformedServerBuilder
Get the ImageServer that applies the requested transforms sequentially.
build() - Method in class qupath.lib.objects.utils.OverlapFixer.Builder
Build the overlap fixer.
build() - Method in class qupath.lib.objects.utils.Tiler.Builder
Build a tiler object with the current settings.
build() - Method in class qupath.lib.roi.GeometryTools.GeometryConverter.Builder
Build a new converter with the specified parameters.
builder() - Static method in class qupath.lib.objects.utils.OverlapFixer
Create a new builder for the OverlapFixer.
builder(int) - Static method in class qupath.lib.objects.utils.Tiler
Create a new builder to generate square tiles.
builder(int, int) - Static method in class qupath.lib.objects.utils.Tiler
Create a new builder to generate rectangular tiles.
builder(Tiler) - Static method in class qupath.lib.objects.utils.Tiler
Create a new builder initialized with the settings from an existing Tiler.
Builder() - Constructor for class qupath.lib.classifiers.pixel.PixelClassifierMetadata.Builder
 
Builder() - Constructor for class qupath.lib.images.servers.ImageServerMetadata.Builder
Minimal builder for a new ImageServerMetadata; further properties must be set.
Builder() - Constructor for class qupath.lib.images.servers.PixelCalibration.Builder
Create a new builder with default (uncalibrated) values.
Builder() - Constructor for class qupath.lib.images.servers.SparseImageServer.Builder
 
Builder() - Constructor for class qupath.lib.roi.GeometryTools.GeometryConverter.Builder
Default constructor for a builder with flatness 0.5 and pixel width/height of 1.0.
Builder(int, int) - Constructor for class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel.Builder
Constructor to help build a list of ImageServerMetadata.ImageResolutionLevel objects to represent pyramidal resolutions.
Builder(Class<? extends ImageServer<?>>, String, int, int) - Constructor for class qupath.lib.images.servers.ImageServerMetadata.Builder
Builder for a new ImageServerMetadata; further properties must be set.
Builder(ImageData<BufferedImage>) - Constructor for class qupath.lib.images.servers.LabeledImageServer.Builder
Create a Builder for a LabeledImageServer for the specified ImageData.
Builder(ImageServerMetadata) - Constructor for class qupath.lib.images.servers.ImageServerMetadata.Builder
Builder for a new ImageServerMetadata object that takes an existing metadata object as a starting point, but allows individual properties to be overridden.
Builder(PixelCalibration) - Constructor for class qupath.lib.images.servers.PixelCalibration.Builder
Create a new builder, initialized values of an existing PixelCalibration.
buildOriginal() - Method in class qupath.lib.images.servers.ImageServerBuilder.AbstractServerBuilder
 
buildOriginal() - Method in class qupath.lib.images.servers.ImageServerBuilder.DefaultImageServerBuilder
 
buildServer(String, Class<T>, String...) - Static method in class qupath.lib.images.servers.ImageServerProvider
Attempt to create ImageServer<T> from the specified path and arguments.
buildServer(String, String...) - Static method in class qupath.lib.images.servers.ImageServers
Build a ImageServer for the specified URI path and optional args.
buildServer(URI, String...) - Method in interface qupath.lib.images.servers.ImageServerBuilder
Attempt to create ImageServer<T> from the specified path.
buildServer(URI, String...) - Static method in class qupath.lib.images.servers.ImageServers
Build a ImageServer for the specified URI and optional args.
buildServer(URI, String...) - Method in class qupath.lib.images.servers.JsonImageServerBuilder
 

C

calibration(PixelCalibration) - Method in class qupath.lib.analysis.DelaunayTools.Builder
Specify pixel calibration, which is used to calibrate the x and y coordinates.
cancelled() - Method in class qupath.lib.plugins.CommandLineTaskRunner.CommandLineProgressMonitor
 
cancelled() - Method in interface qupath.lib.plugins.SimpleProgressMonitor
Returns true if cancel has been requested, for example by the user pressing a 'cancel' button.
cells() - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder
Set the filter to accept cell objects only.
CELLS - Enum constant in enum class qupath.lib.objects.PathObjectFilter
Accept cells
CellTools - Class in qupath.lib.objects
Helper class for working with PathObjects that represent cells.
CellTools() - Constructor for class qupath.lib.objects.CellTools
 
CENTER - Enum constant in enum class qupath.lib.objects.utils.Tiler.TileAlignment
 
CENTER_LEFT - Enum constant in enum class qupath.lib.objects.utils.Tiler.TileAlignment
 
CENTER_RIGHT - Enum constant in enum class qupath.lib.objects.utils.Tiler.TileAlignment
 
centroidDistancePredicate(double, boolean) - Static method in class qupath.lib.analysis.DelaunayTools
BiPredicate that returns true for objects with ROI centroids within a specified distance.
centroids() - Method in class qupath.lib.analysis.DelaunayTools.Builder
Specify that the triangulation should be based on ROI centroids.
centroidToBoundsDistance2D(Collection<PathObject>, Collection<PathObject>, double, double, String) - Static method in class qupath.lib.analysis.DistanceTools
Calculate the distance between source object centroids and the boundary of specified target objects, adding the result to the measurement list of the source objects.
centroidToBoundsDistance2D(Collection<PathObject>, Collection<PathObject>, double, double, String, boolean) - Static method in class qupath.lib.analysis.DistanceTools
Calculate the (optionally signed) distance between source object centroids and the boundary of specified target objects, adding the result to the measurement list of the source objects.
centroidToCentroidDistance2D(Collection<PathObject>, Collection<PathObject>, double, double, String) - Static method in class qupath.lib.analysis.DistanceTools
Calculate the distance between source object centroids and the centroid of specified target objects, adding the result to the measurement list of the source objects.
CHANGE_CLASSIFICATION - Enum constant in enum class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent.HierarchyEventType
A change was made to one or more object classifications
CHANGE_MEASUREMENTS - Enum constant in enum class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent.HierarchyEventType
A change was made to one or more object measurements
CHANGE_OTHER - Enum constant in enum class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent.HierarchyEventType
A change was made to one or more objects that is more complex than the other changes allow for
changeMaxValues(double, double, double) - Method in class qupath.lib.color.ColorDeconvolutionStains
Create a new stains object with the same StainVectors but new max (background) values.
changeName(String) - Method in class qupath.lib.color.ColorDeconvolutionStains
Create a new stains object with the same StainVectors but a new name.
changeStain(StainVector, int) - Method in class qupath.lib.color.ColorDeconvolutionStains
Create a new stains object, identical to this one but for one StainVector having been changed.
channels(int...) - Method in class qupath.lib.images.writers.TileExporter
Export only specified channels.
channels(String...) - Method in class qupath.lib.images.writers.TileExporter
Export only specified channels, identified by name.
channels(Collection<ImageChannel>) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder
Specify the image channels.
ChannelTransformFeatureServer - Class in qupath.lib.images.servers
A TransformingImageServer that applies color transforms to generate channels.
channelType(ImageServerMetadata.ChannelType) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder
Specify the interpretation of channels.
checkExtensions(String, String...) - Static method in class qupath.lib.common.GeneralTools
Check whether a path ends with one of a number of specified extensions (case insensitive).
checkImageSupport(URI, String...) - Method in interface qupath.lib.images.servers.ImageServerBuilder
Check whether a URI is supported by this builder.
checkImageSupport(URI, String...) - Method in class qupath.lib.images.servers.JsonImageServerBuilder
 
checkpoint() - Method in class qupath.lib.common.Timeit
Create a new checkpoint with a default name.
checkpoint(String) - Method in class qupath.lib.common.Timeit
Create a new checkpoint with the specified name.
checkpointAndRun(Runnable) - Method in class qupath.lib.common.Timeit
Create a checkpoint with the default name and immediately run the provided runnable.
checkpointAndRun(String, Runnable) - Method in class qupath.lib.common.Timeit
Create a checkpoint and immediately run the provided Runnable.
checkpointAndRun(String, Runnable, int) - Method in class qupath.lib.common.Timeit
Create a checkpoint and immediately run the provided Runnable nIterations times.
checkType(URI) - Static method in class qupath.lib.images.servers.FileFormatInfo
Check the type of an image for a specified URI.
ChoiceParameter<S> - Class in qupath.lib.plugins.parameters
Parameter that supports a list of choices.
choices - Variable in class qupath.lib.plugins.parameters.ChoiceParameter
 
CLASSIFICATION - Enum constant in enum class qupath.lib.images.servers.ImageServerMetadata.ChannelType
Each channel represents a classification, such as in a labelled image.
classificationLabels(Map<Integer, PathClass>) - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata.Builder
Specify classification labels.
classificationLabels(Map<Integer, PathClass>) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder
Specify the interpretation of classification labels.
classificationLabelsToChannels(Map<Integer, PathClass>, boolean) - Static method in class qupath.lib.images.servers.ServerTools
Create a list of channels from classification labels.
CLASSIFIED - Enum constant in enum class qupath.lib.objects.PathObjectFilter
Accept any object that has a classification set (no matter what it is)
ClassifyByMeasurementBuilder(String) - Constructor for class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder
Constructor.
classifyObjects(ImageData<T>, boolean) - Method in class qupath.lib.classifiers.object.AbstractObjectClassifier
 
classifyObjects(ImageData<T>, boolean) - Method in interface qupath.lib.classifiers.object.ObjectClassifier
Classify all compatible objects from an ImageData.
classifyObjects(ImageData<T>, Collection<? extends PathObject>, boolean) - Method in interface qupath.lib.classifiers.object.ObjectClassifier
Classify the objects in the specified collection.
classifyObjectsByCluster(Collection<Collection<? extends PathObject>>) - Static method in class qupath.lib.analysis.DelaunayTools
Assign object classifications based upon pre-computed clusters.
classifyObjectsByCluster(Collection<Collection<? extends PathObject>>, Function<Integer, PathClass>) - Static method in class qupath.lib.analysis.DelaunayTools
Assign object classifications based upon pre-computed clusters.
clear() - Method in interface qupath.lib.measurements.MeasurementList
Remove all the measurements from the list.
clear() - Method in class qupath.lib.objects.PathObjectConnections
Clear all existing connections.
clear() - Method in class qupath.lib.plugins.workflow.Workflow
Remove all steps, firing an update event if the workflow was not previously empty.
clearAll() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Remove all objects from the hierarchy.
clearChildObjects() - Method in class qupath.lib.objects.PathObject
Remove all child objects.
clearMetadata() - Method in class qupath.lib.objects.TMACoreObject
Deprecated.
v0.6.0. Use PathObject.getMetadata() to directly access metadata instead.
clearMetadata() - Method in interface qupath.lib.projects.ProjectImageEntry
Deprecated.
v0.6.0, use MinimalMetadataStore.getMetadata() instead to directly access the metadata.
clearMetadataMap() - Method in class qupath.lib.objects.PathObject
Deprecated.
v0.6.0, use PathObject.getMetadata() to directly access the metadata instead.
clearSelection() - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel
Clear selection so that no objects are selected.
CLIP_OVERLAPS - Enum constant in enum class qupath.lib.objects.utils.OverlapFixer.Strategy
 
clip255(double) - Static method in class qupath.lib.common.ColorTools
Convert a double value to an int, flooring and clipping to the range 0-255.
clipOverlaps() - Method in class qupath.lib.objects.utils.OverlapFixer.Builder
Clip overlapping objects, excluding the parts that overlap with a 'higher priority' object according to the comparator.
clipToROI(ROI, Collection<? extends ROI>) - Static method in class qupath.lib.roi.RoiTools
Intersect a collection of ROIs with a single parent ROI, returning all results that are valid.
clipValue(double, double, double) - Static method in class qupath.lib.common.GeneralTools
Clip a value to be within a specific range.
clipValue(int, int, int) - Static method in class qupath.lib.common.GeneralTools
Clip a value to be within a specific range.
close() - Method in class qupath.lib.images.ImageData
Close the server if it has been loaded.
close() - Method in class qupath.lib.images.servers.AbstractImageServer
 
close() - Method in class qupath.lib.images.servers.SparseImageServer
 
close() - Method in class qupath.lib.images.servers.SparseImageServer.SparseImageServerManager
 
close() - Method in interface qupath.lib.measurements.MeasurementList
Close the list.
ColorDeconvMatrix3x3 - Class in qupath.lib.color
Simple class for representing - and inverting a 3x3 matrix.
ColorDeconvMatrix3x3(double[][]) - Constructor for class qupath.lib.color.ColorDeconvMatrix3x3
Constructor for a 3x3 matrix.
ColorDeconvolutionHelper - Class in qupath.lib.color
Static methods to assist with color deconvolution.
ColorDeconvolutionHelper() - Constructor for class qupath.lib.color.ColorDeconvolutionHelper
 
ColorDeconvolutionNormalizer - Class in qupath.lib.images.servers.transforms
Normalizes an image by applying color deconvolution to RGB input, rescaling intensities, and using color 'reconvolution' to generate a new RGB image.
ColorDeconvolutionStains - Class in qupath.lib.color
Helper class for storing stain vectors and maximum channel values to be used for color deconvolution.
ColorDeconvolutionStains() - Constructor for class qupath.lib.color.ColorDeconvolutionStains
Default constructor, for Externalizable.
ColorDeconvolutionStains(String, StainVector, StainVector, double, double, double) - Constructor for class qupath.lib.color.ColorDeconvolutionStains
Constructor for ColorDeconvolutionStains with two stain vectors.
ColorDeconvolutionStains(String, StainVector, StainVector, StainVector, double, double, double) - Constructor for class qupath.lib.color.ColorDeconvolutionStains
Constructor for ColorDeconvolutionStains with three stain vectors.
ColorDeconvolutionStains.DefaultColorDeconvolutionStains - Enum Class in qupath.lib.color
Enum for common stain defaults.
colorDeconvolve(float[], float[], float[], ColorDeconvolutionStains) - Static method in class qupath.lib.color.ColorDeconvolutionHelper
Apply color deconvolution in-place for RGB channels.
colorDeconvolve(BufferedImage, ColorDeconvolutionStains, int, float[]) - Static method in class qupath.lib.color.ColorDeconvolutionHelper
Apply color deconvolution to an input image, extracting a single channel as output and returning as a float array.
colorDeconvolveReconvolveRGBArray(int[], ColorDeconvolutionStains, ColorDeconvolutionStains, boolean, int[]) - Static method in class qupath.lib.color.ColorTransformer
Deconvolve RGB array with one set of stain vectors, and reconvolve with another.
colorDeconvolveReconvolveRGBArray(int[], ColorDeconvolutionStains, ColorDeconvolutionStains, int[], double[]) - Static method in class qupath.lib.color.ColorTransformer
Deconvolve RGB array with one set of stain vectors, and reconvolve with another - with optional scaling.
colorDeconvolveRGBPixel(int, ColorDeconvolutionStains, int) - Static method in class qupath.lib.color.ColorTransformer
Calculate the color deconvolved value for a single pixel, stored as a packed (A)RGB int.
ColorMaps - Class in qupath.lib.color
Helper class to manage colormaps, which are rather like lookup tables but easily support interpolation.
ColorMaps() - Constructor for class qupath.lib.color.ColorMaps
 
ColorMaps.ColorMap - Interface in qupath.lib.color
colormap, which acts as an interpolating lookup table with an arbitrary range.
ColorModelFactory - Class in qupath.lib.color
Factory methods to help create ColorModels for use with BufferedImages.
ColorModels - Class in qupath.lib.color
Helper class for creating a JSON-serializable way to generate a ColorModel.
ColorModels() - Constructor for class qupath.lib.color.ColorModels
 
ColorModels.ColorModelBuilder - Interface in qupath.lib.color
Simple builder to create a ColorModel.
ColorModels.DisplayBand - Class in qupath.lib.color
Helper class to the display of a single channel (band) in a ColorModel.
ColorTools - Class in qupath.lib.common
Static functions to help work with RGB(A) colors using packed ints.
ColorToolsAwt - Class in qupath.lib.color
Helper class for converting between packed RGB colors and Java's AWT representation, as well as creating some ColorModels for BufferedImages.
ColorToolsAwt() - Constructor for class qupath.lib.color.ColorToolsAwt
 
ColorTransformer - Class in qupath.lib.color
Static methods for computing a range of color transforms for packed RGB values.
ColorTransformer() - Constructor for class qupath.lib.color.ColorTransformer
 
ColorTransformer.ColorTransformMethod - Enum Class in qupath.lib.color
Enum consisting of color transforms that may be applied to RGB images.
ColorTransforms - Class in qupath.lib.images.servers
Color transforms that may be used to extract single-channel images from BufferedImages.
ColorTransforms.ColorTransform - Interface in qupath.lib.images.servers
Interface defining a color transform that can extract a float value from a BufferedImage.
ColorTransforms.ColorTransformTypeAdapter - Class in qupath.lib.images.servers
ColorTransformTypeAdapter() - Constructor for class qupath.lib.images.servers.ColorTransforms.ColorTransformTypeAdapter
 
combineROIs(ROI, ROI, RoiTools.CombineOp) - Static method in class qupath.lib.roi.RoiTools
Combine two shape ROIs together.
CommandLineProgressMonitor() - Constructor for class qupath.lib.plugins.CommandLineTaskRunner.CommandLineProgressMonitor
 
CommandLineTaskRunner - Class in qupath.lib.plugins
A PluginRunner that simply logs progress and output.
CommandLineTaskRunner() - Constructor for class qupath.lib.plugins.CommandLineTaskRunner
Constructor for a PluginRunner that send progress to a log, and runs tasks using the default number of threads
CommandLineTaskRunner(int) - Constructor for class qupath.lib.plugins.CommandLineTaskRunner
Constructor for a PluginRunner that send progress to a log.
CommandLineTaskRunner.CommandLineProgressMonitor - Class in qupath.lib.plugins
A SimpleProgressMonitor that sends progress to a log.
COMPARATOR_FULL - Static variable in class qupath.lib.common.Version
Compare full version, including any suffixes.
COMPARATOR_MAJOR - Static variable in class qupath.lib.common.Version
Compare major versions only.
COMPARATOR_MAJOR_MINOR - Static variable in class qupath.lib.common.Version
Compare major then minor versions.
COMPARATOR_MAJOR_MINOR_PATCH - Static variable in class qupath.lib.common.Version
Compare major then minor then patch versions (ignoring suffixes).
compare(PathObject, PathObject) - Method in class qupath.lib.objects.DefaultPathObjectComparator
 
compare(ROI, ROI) - Method in class qupath.lib.roi.DefaultROIComparator
 
compareTo(KaplanMeierData.KaplanMeierEvent) - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData.KaplanMeierEvent
 
compareTo(Version) - Method in class qupath.lib.common.Version
 
compareTo(Point2) - Method in class qupath.lib.geom.Point2
 
compareTo(PathClass) - Method in class qupath.lib.objects.classes.PathClass
This is now equivalent to this.toString().compareTo(o.toString()).
compareTo(ImagePlane) - Method in class qupath.lib.regions.ImagePlane
Compare with another ImagePlane, in the order t, z, c.
computeAboveThresholdCounts(WritableRaster, int, double, WritableRaster) - Static method in class qupath.lib.awt.common.BufferedImageTools
Count the number of above-threshold pixels in a specified band of a raster, with optional mask.
computeAboveThresholdCounts(WritableRaster, int, double, WritableRaster, Rectangle) - Static method in class qupath.lib.awt.common.BufferedImageTools
Count the number of above-threshold pixels in a specified band of a raster, with optional mask and/or bounding rectangle.
computeAngle(StainVector, StainVector) - Static method in class qupath.lib.color.StainVector
Calculate the angle between two stain vectors, in degrees.
computeArgMaxHistogram(WritableRaster, long[], WritableRaster) - Static method in class qupath.lib.awt.common.BufferedImageTools
Create a histogram that identifies the channels (bands) of an image with the maximum values according to the argmax criterion.
computeArgMaxHistogram(WritableRaster, long[], WritableRaster, Rectangle) - Static method in class qupath.lib.awt.common.BufferedImageTools
Create a histogram that identifies the channels (bands) of an image with the maximum values according to the argmax criterion, with an optional bounding rectangle.
computeCoordinateDistance(Coordinate, Collection<Coordinate>) - Static method in class qupath.lib.analysis.DistanceTools
Compute the shortest distance from a coordinate to one of a collection of target coordinates.
computeCoordinateDistance(Coordinate, STRtree) - Static method in class qupath.lib.analysis.DistanceTools
Compute the distance to the nearest coordinate stored within an STRtree.
computeDistance(Coordinate, Geometry, PointOnGeometryLocator) - Static method in class qupath.lib.analysis.DistanceTools
Compute the (unsigned) shortest distance from a coordinate to a target geometry, or zero if the coordinate occurs within
computeDistance(Coordinate, Geometry, PointOnGeometryLocator, boolean) - Static method in class qupath.lib.analysis.DistanceTools
Compute the shortest distance from a coordinate to a target geometry.
computeLogRankTest(KaplanMeierData, KaplanMeierData) - Static method in class qupath.lib.analysis.stats.survival.LogRankTest
Compare KaplanMeier objects using log-rank test.
computeRunningStatistics(double[]) - Static method in class qupath.lib.analysis.stats.StatisticsHelper
Create a RunningStatistics object using all the values from a specified array.
computeRunningStatistics(SimpleImage) - Static method in class qupath.lib.analysis.stats.StatisticsHelper
Compute running statistics using all pixels from a SimpleImage.
computeRunningStatistics(SimpleImage, SimpleImage, List<RunningStatistics>) - Static method in class qupath.lib.analysis.stats.StatisticsHelper
Calculate RunningStatistics for each label > 0 in an image, up to a maximum of statsList.size().
computeTiledROIs(ROI, ImmutableDimension, ImmutableDimension, boolean, int) - Static method in class qupath.lib.roi.RoiTools
Create a collection of tiled ROIs corresponding to a specified parentROI if it is larger than sizeMax, with optional overlaps.
computeUnsignedIntHistogram(WritableRaster, long[], WritableRaster) - Static method in class qupath.lib.awt.common.BufferedImageTools
Compute the full histogram for a raster containing 8-bit or 16-bit unsigned integer values.
computeUnsignedIntHistogram(WritableRaster, long[], WritableRaster, Rectangle) - Static method in class qupath.lib.awt.common.BufferedImageTools
Compute the full histogram for a raster containing 8-bit or 16-bit unsigned integer values, optionally restricted to a bounding rectangle.
concatChannels(Collection<ImageServer<BufferedImage>>) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Concatenate a collection of additional servers along the 'channels' dimension (iteration order is used).
concatChannels(ImageServer<BufferedImage>...) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Concatenate additional servers along the 'channels' dimension.
concatenate(Collection<? extends ArrayWrappers.ArrayWrapper>) - Static method in class qupath.lib.analysis.stats.ArrayWrappers
Concatenate a collection of array wrappers, to act as one long wrapper.
concatenate(ArrayWrappers.ArrayWrapper...) - Static method in class qupath.lib.analysis.stats.ArrayWrappers
Concatenate an array containing multiple array wrappers, to act as one long wrapper.
concatToZStack(List<ImageServer<BufferedImage>>) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Concatenate a list of additional servers along the 'z' dimension (iteration order is used).
concatToZStack(List<ImageServer<BufferedImage>>, Number) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Concatenate a list of additional servers along the 'z' dimension (iteration order is used).
constrainCellByNucleusDistance(PathCellObject, double, boolean) - Static method in class qupath.lib.objects.CellTools
Constrain a cell boundary to fall within a maximum region, determined by buffering the convex hull of the nucleus ROI by a fixed distance.
constrainCellByScaledNucleus(PathCellObject, double, boolean) - Static method in class qupath.lib.objects.CellTools
Constrain a cell boundary to fall within a maximum region, determined by scaling the nucleus ROI by a fixed scale factor about its centroid.
constrainCellOverlaps(Collection<? extends PathObject>) - Static method in class qupath.lib.objects.CellTools
Adjust cell boundary ROIs to be non-overlapping, by assigning overlaps to the cell with the closest nucleus.
constrainToBounds(Geometry, double, double, double, double) - Static method in class qupath.lib.roi.GeometryTools
Compute the intersection of a Geometry and a specified bounding box.
contains(double, double) - Method in class qupath.lib.roi.AreaROI
Deprecated.
 
contains(double, double) - Method in class qupath.lib.roi.EllipseROI
 
contains(double, double) - Method in class qupath.lib.roi.GeometryROI
 
contains(double, double) - Method in interface qupath.lib.roi.interfaces.ROI
Test is the ROI contains specified x, y coordinates.
contains(double, double) - Method in class qupath.lib.roi.LineROI
 
contains(double, double) - Method in class qupath.lib.roi.PointsROI
 
contains(double, double) - Method in class qupath.lib.roi.PolygonROI
 
contains(double, double) - Method in class qupath.lib.roi.PolylineROI
 
contains(double, double) - Method in class qupath.lib.roi.RectangleROI
 
contains(int, int, int, int) - Method in class qupath.lib.regions.ImageRegion
Check if this region contains a specified coordinate.
contains(String) - Method in interface qupath.lib.projects.ResourceManager.Manager
Returns true if the manager knows a resource with the specified name exists.
containsClassification(String...) - Static method in class qupath.lib.objects.PathObjectPredicates
Predicate that returns true if any component of its classification has any of the specified names.
containsKey(Object) - Method in class qupath.lib.plugins.parameters.ParameterList
Returns true if a parameter exists in this list with a specified key.
containsKey(String) - Method in interface qupath.lib.measurements.MeasurementList
Returns true if this list contains a measurement with the specified name.
containsMetadata(String) - Method in interface qupath.lib.projects.ProjectImageEntry
Deprecated.
v0.6.0, use MinimalMetadataStore.getMetadata() instead to directly access the metadata.
containsName(PathClass, String) - Static method in class qupath.lib.objects.classes.PathClassTools
Query whether a PathClass or any of its ancestor classes contains a specified name.
containsObject(PathObject) - Method in class qupath.lib.objects.DefaultPathObjectConnectionGroup
Deprecated.
 
containsObject(PathObject) - Method in interface qupath.lib.objects.PathObjectConnectionGroup
Deprecated.
Returns true if the specified PathObject is contained within this group.
ContourTracing - Class in qupath.lib.analysis.images
Class to convert labelled images to Geometry objects, ROIs and PathObjects.
ContourTracing() - Constructor for class qupath.lib.analysis.images.ContourTracing
 
ContourTracing.ChannelThreshold - Class in qupath.lib.analysis.images
Helper class defining global thresholds to apply to a single image channel.
convertImageType(BufferedImage, PixelType, List<? extends ImageChannel>) - Static method in class qupath.lib.awt.common.BufferedImageTools
Convert a raster to have a specified pixel type.
convertPixelsToOpticalDensities(float[], double, boolean) - Static method in class qupath.lib.color.ColorDeconvolutionHelper
For originally-8-bit images, optical densities can usually be computed faster by preallocating a LUT with the 0-255 required values.
convertRasterType(Raster, PixelType) - Static method in class qupath.lib.awt.common.BufferedImageTools
Convert a raster to have a specified pixel type.
convertToJson(Map<String, ?>) - Static method in class qupath.lib.plugins.parameters.ParameterList
Convert a Map to a one-line JSON representation, omitting hidden parameters.
convertToJson(ParameterList) - Static method in class qupath.lib.plugins.parameters.ParameterList
Convert a ParameterList a one-line JSON representation, omitting hidden parameters.
convertToOpticalDensity(float[], double) - Static method in class qupath.lib.color.ColorDeconvolutionHelper
Convert an array of pixel values to optical densities in-place, normalizing using the specified maximum.
convertToPoints(Collection<? extends PathObject>, boolean) - Static method in class qupath.lib.objects.PathObjectTools
Convert a collection of PathObjects to Point annotations, based on ROI centroids.
convertToPoints(PathObjectHierarchy, Collection<? extends PathObject>, boolean, boolean) - Static method in class qupath.lib.objects.PathObjectTools
Convert a collection of PathObjects to Point annotations, based on ROI centroids, and add the points to the hierarchy.
convertTransform(AffineTransform) - Static method in class qupath.lib.roi.GeometryTools
convertTransform(AffineTransformation) - Static method in class qupath.lib.roi.GeometryTools
convertType(PixelType) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Convert to the specified pixel type.
ConvexHull - Class in qupath.lib.roi
Helper method for calculating the convex hull from a list of points.
ConvexHull() - Constructor for class qupath.lib.roi.ConvexHull
 
coordinateExtractor(Function<PathObject, Collection<Coordinate>>) - Method in class qupath.lib.analysis.DelaunayTools.Builder
Specify a default method of extracting coordinates for triangulation from an object, rather than centroids or the ROI boundary.
countDescendants(PathObject) - Static method in class qupath.lib.objects.PathObjectTools
Count the descendants of a PathObject recursively.
countMissing() - Method in class qupath.lib.io.UriUpdater
Get a count of the items flagged as missing.
countObjectsWithClass(Collection<? extends PathObject>, PathClass, boolean) - Static method in class qupath.lib.objects.PathObjectTools
Count the number of PathObjects in a collection with a specified class or base class.
countReplacements() - Method in class qupath.lib.io.UriUpdater
Get a count of the number of replacements for missing items.
create(double[], double[]) - Static method in class qupath.lib.images.servers.transforms.SubtractOffsetAndScaleNormalizer
Create a normalizer that subtracts a constant from each channel, then multiples the result by a scale factor.
create(int) - Static method in class qupath.lib.analysis.images.ContourTracing.ChannelThreshold
Create a simple channel threshold.
create(int, double, double) - Static method in class qupath.lib.analysis.images.ContourTracing.ChannelThreshold
Create a threshold to select values between a minimum and maximum (inclusive).
create(Gson, TypeToken<R>) - Method in class qupath.lib.io.GsonTools.SubTypeAdapterFactory
 
create(Gson, TypeToken<T>) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ObjectClassifierTypeAdapterFactory
 
create(Collection<T>) - Static method in class qupath.lib.io.UriUpdater
Create a new UriUpdater to support updating URIs for one or more UriResource objects.
create(Collection<T>, Collection<UriUpdater.SingleUriItem>, Map<UriUpdater.SingleUriItem, UriUpdater.SingleUriItem>) - Static method in class qupath.lib.io.UriUpdater
Create a new UriUpdater using the specified collections.
create(List<TMACoreObject>, int) - Static method in class qupath.lib.objects.hierarchy.DefaultTMAGrid
Create a new TMAGrid based on a list of cores and grid width.
create(ColorDeconvolutionStains, ColorDeconvolutionStains, double...) - Static method in class qupath.lib.images.servers.transforms.ColorDeconvolutionNormalizer
Create a normalizer using color deconvolution and reconvolution.
create(T) - Static method in class qupath.lib.io.UriUpdater
Create a new UriUpdater to support updating URIs for a single UriResource.
createAbove(int, double) - Static method in class qupath.lib.analysis.images.ContourTracing.ChannelThreshold
Create a threshold to select values greater than or equal to a specified threshold.
createAllRequests(ImageServer<?>, double) - Static method in class qupath.lib.regions.RegionRequest
Create requests for the full width and height of an ImageServer, for all planes (z-slices and time points).
createAnnotationObject(ROI) - Static method in class qupath.lib.objects.PathObjects
Create an unclassified annotation object.
createAnnotationObject(ROI, PathClass) - Static method in class qupath.lib.objects.PathObjects
Create a classified annotation object.
createAnnotationObject(ROI, PathClass, MeasurementList) - Static method in class qupath.lib.objects.PathObjects
Create a classified annotation object with a specified measurement list.
createAnnotations(SimpleImage, RegionRequest, int, int) - Static method in class qupath.lib.analysis.images.ContourTracing
Create annotation objects from a labelled image.
createAnnotations(ROI) - Method in class qupath.lib.objects.utils.Tiler
Create a list of PathAnnotationObject tiles from the input.
createAnnotationsFromSubdivision(DelaunayTools.Subdivision, ROI) - Static method in class qupath.lib.analysis.DelaunayTools
Create annotations surrounding objects within a specified subdivision based on Voronoi faces.
createAreaROI(Shape, ImagePlane) - Static method in class qupath.lib.roi.ROIs
Deprecated.
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.
createBand(String, int, double, double) - Static method in class qupath.lib.color.ColorModels
Create a ColorModels.DisplayBand to define the colormap associated with an image band (channel).
createBand(String, int, double, double, double) - Static method in class qupath.lib.color.ColorModels
Create a ColorModels.DisplayBand to define the colormap associated with an image band (channel).
createBelow(int, double) - Static method in class qupath.lib.analysis.images.ContourTracing.ChannelThreshold
Create a threshold to select values less than or equal to a specified threshold.
createCellObject(ROI, ROI) - Static method in class qupath.lib.objects.PathObjects
Create a cell object.
createCellObject(ROI, ROI, PathClass) - Static method in class qupath.lib.objects.PathObjects
Create a cell object with an optional classification.
createCellObject(ROI, ROI, PathClass, MeasurementList) - Static method in class qupath.lib.objects.PathObjects
Create a cell object with an optional classification and measurements list.
createCells(Raster, int, int, RegionRequest, int, int) - Static method in class qupath.lib.analysis.images.ContourTracing
Create cell objects from two bands of a raster representing a labelled image.
createCells(SimpleImage, SimpleImage, RegionRequest, int, int) - Static method in class qupath.lib.analysis.images.ContourTracing
Create cell objects from a pair of labelled images.
createChannelClassifier(PathObjectFilter, ImageChannel, String, double) - Static method in class qupath.lib.classifiers.object.ObjectClassifiers
Create a classifier that thresholds a single measurement, assigning a class based on an ImageChannel if the value is ≥ threshold.
createChannelExtractor(int) - Static method in class qupath.lib.images.servers.ColorTransforms
Create a ColorTransform that extracts a channel based on its index.
createChannelExtractor(String) - Static method in class qupath.lib.images.servers.ColorTransforms
Create a ColorTransform that extracts a channel based on its name.
createClassificationMap(Collection<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools
Create a mapping between PathObjects and their current PathClasses.
createColorDeconvolvedChannel(ColorDeconvolutionStains, int) - Static method in class qupath.lib.images.servers.ColorTransforms
Create a ColorTransform that applies color deconvolution.
createColorMap(String, double[], double[], double[]) - Static method in class qupath.lib.color.ColorMaps
Create a colormap using floating point values for red, green and blue.
createColorMap(String, int[], int[], int[]) - Static method in class qupath.lib.color.ColorMaps
Create a colormap using integer values for red, green and blue.
createColorMap(String, int, int, int) - Static method in class qupath.lib.color.ColorMaps
Create a colormap using int values for red, green and blue corresponding to the maximum value; the minimum color will be black.
createColorModel(PixelType, int, boolean, int...) - Static method in class qupath.lib.color.ColorModelFactory
Create a new ColorModel that can be used to display an image where pixels per channel reflect probabilities, either as float or byte.
createColorModel(PixelType, List<? extends ImageChannel>) - Static method in class qupath.lib.color.ColorModelFactory
Create a ColorModel for displaying an image with the specified channel colors.
createColorModel(PixelType, ColorMaps.ColorMap, int) - Static method in class qupath.lib.color.ColorModelFactory
Create a color model from a ColorMaps.ColorMap.
createColorModel(PixelType, ColorMaps.ColorMap, int, double, double, int, DoubleToIntFunction) - Static method in class qupath.lib.color.ColorModelFactory
Create a color model from a ColorMaps.ColorMap, scaled within a defined range and with an optional additional alpha channel used to determine opacity.
createColorModelBuilder(ColorModels.DisplayBand, ColorModels.DisplayBand) - Static method in class qupath.lib.color.ColorModels
Create a ColorModels.ColorModelBuilder with a main channel and an optional alpha channel.
createCompatibleDestImage(BufferedImage, ColorModel) - Method in interface qupath.lib.images.servers.transforms.BufferedImageNormalizer
 
createCompositeClassifier(Collection<ObjectClassifier<T>>) - Static method in class qupath.lib.classifiers.object.ObjectClassifiers
Create a composite ObjectClassifier, which sequentially applies multiple (usually single-class) classifiers.
createCompositeClassifier(ObjectClassifier<T>...) - Static method in class qupath.lib.classifiers.object.ObjectClassifiers
Create a composite ObjectClassifier, which sequentially applies multiple (usually single-class) classifiers.
createCoordinateCache(Collection<Coordinate>) - Static method in class qupath.lib.analysis.DistanceTools
Create an STRtree to enable nearest neighbor searching for a collection of coordinates.
createDefaultRGBImage(int, int) - Method in class qupath.lib.images.servers.AbstractTileableImageServer
Create the default (blank) RGB image for this server.
createDefaultRGBImage(int, int) - Method in class qupath.lib.images.servers.LabeledImageServer
 
createDetectionObject(ROI) - Static method in class qupath.lib.objects.PathObjects
Create an unclassified detection object.
createDetectionObject(ROI, PathClass) - Static method in class qupath.lib.objects.PathObjects
Create a classified detection object.
createDetectionObject(ROI, PathClass, MeasurementList) - Static method in class qupath.lib.objects.PathObjects
Create a classified detection object with a specified measurement list.
createDetections(SimpleImage, RegionRequest, int, int) - Static method in class qupath.lib.analysis.images.ContourTracing
Create detection objects from a labelled image.
createDetector(ImageData<T>, ParameterList) - Method in class qupath.lib.plugins.AbstractTileableDetectionPlugin
Create a new ObjectDetector, compatible with the specified ImageData and ParameterList.
createEllipse(double, double, double, double, int) - Static method in class qupath.lib.roi.GeometryTools
Create a polygonal geometry that approximates an ellipse.
createEllipseROI(double, double, double, double) - Static method in class qupath.lib.roi.ROIs
Create an ellipse ROI defined by its bounding box on the default image plane.
createEllipseROI(double, double, double, double, ImagePlane) - Static method in class qupath.lib.roi.ROIs
Create an ellipse ROI defined by its bounding box.
createEllipseROI(ImageRegion) - Static method in class qupath.lib.roi.ROIs
Create an ellipse ROI defined by its bounding box.
createEmptyMeasurementList() - Method in class qupath.lib.objects.PathDetectionObject
Default to a simple, float measurement list.
createEmptyMeasurementList() - Method in class qupath.lib.objects.PathObject
Create a new MeasurementList of the preferred type for this object.
createEmptyROI() - Static method in class qupath.lib.roi.ROIs
Create an 'empty' ROI with no length or area on the default image plane.
createExactly(int, double) - Static method in class qupath.lib.analysis.images.ContourTracing.ChannelThreshold
Create a threshold to select values that are exactly equal to a specified threshold.
createFloatImage(float[], int, int) - Static method in class qupath.lib.analysis.images.SimpleImages
Create a SimpleImage backed by an existing float array of pixels.
createFloatImage(int, int) - Static method in class qupath.lib.analysis.images.SimpleImages
Create a SimpleImage backed by a float array of pixels.
createFormatter(int) - Static method in class qupath.lib.common.GeneralTools
Create a new DecimalFormat that may be used to convert a number to have a maximum of nDecimalPlaces (trailing zeros are not shown).
createFromCentroids(Collection<PathObject>, boolean) - Static method in class qupath.lib.analysis.DelaunayTools
Create a DelaunayTools.Subdivision using the centroid coordinates of ROIs.
createFromGeometryCoordinates(Collection<PathObject>, boolean, double) - Static method in class qupath.lib.analysis.DelaunayTools
Create a DelaunayTools.Subdivision using the boundary coordinates of ROIs.
createGammaFunction(double, double, double) - Static method in class qupath.lib.color.ColorModelFactory
Create a gamma function between a given range, which can be used to determine a suitable alpha value for an image that should have opacity based upon pixel values.
createGammaFunction(double, PixelType) - Static method in class qupath.lib.color.ColorModelFactory
Create a gamma function for a specific pixel type, which can be used to determine a suitable alpha value for an image that should have opacity based upon pixel values.
createGeometries(Geometry) - Method in class qupath.lib.objects.utils.Tiler
Create a list of Geometry tiles from the input.
createGeometries(SimpleImage, RegionRequest, int, int) - Static method in class qupath.lib.analysis.images.ContourTracing
Create Geometries from a labelled image containing integer labels.
createHeadlessTaskRunner() - Method in class qupath.lib.plugins.TaskRunnerUtils
Create a new headless TaskRunner instance, using the default number of threads from ThreadTools.getParallelism().
createHeadlessTaskRunner(int) - Method in class qupath.lib.plugins.TaskRunnerUtils
Create a new headless TaskRunner instance with the specified number of threads.
createID() - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer
Returns a random UUID.
createID() - Method in class qupath.lib.images.servers.AbstractImageServer
Create a unique ID for the server, which can be returned as the default value of AbstractImageServer.getPath().
createID() - Method in class qupath.lib.images.servers.AffineTransformImageServer
 
createID() - Method in class qupath.lib.images.servers.ChannelTransformFeatureServer
Returns a UUID.
createID() - Method in class qupath.lib.images.servers.CroppedImageServer
 
createID() - Method in class qupath.lib.images.servers.LabeledImageServer
Returns a UUID.
createID() - Method in class qupath.lib.images.servers.NormalizedImageServer
 
createID() - Method in class qupath.lib.images.servers.RearrangeRGBImageServer
 
createID() - Method in class qupath.lib.images.servers.RotatedImageServer
 
createID() - Method in class qupath.lib.images.servers.SlicedImageServer
 
createID() - Method in class qupath.lib.images.servers.SparseImageServer
Returns a UUID.
createID() - Method in class qupath.lib.images.servers.TypeConvertImageServer
 
createID() - Method in class qupath.lib.images.servers.WrappedBufferedImageServer
Returns a UUID.
createID() - Method in class qupath.lib.images.servers.ZConcatenatedImageServer
 
createID() - Method in class qupath.lib.images.servers.ZProjectedImageServer
 
createImage(int, int, PixelType, int) - Static method in class qupath.lib.awt.common.BufferedImageTools
Create a new image with the specified width, height, pixel type, and number of channels.
createImage(int, int, PixelType, List<? extends ImageChannel>) - Static method in class qupath.lib.awt.common.BufferedImageTools
Create a new image with the specified width, height, pixel type, and channels.
createImageRegionPredicate(ImageRegion) - Static method in class qupath.lib.objects.PathObjectTools
Create a predicate that only accepts PathObjects if they have ROIs that fall within a specified ImageRegion.
createIndexColorModel(int, int, int, boolean) - Static method in class qupath.lib.color.ColorToolsAwt
Get an IndexColorModel representing a linear LUT based on a RGB color.
createIndexedColorModel(Map<Integer, Integer>, boolean) - Static method in class qupath.lib.color.ColorModelFactory
Create an indexed colormap for a labelled (indexed color) image.
createIndexedColorModel8bit(ColorMaps.ColorMap) - Static method in class qupath.lib.color.ColorModelFactory
Create an 8-bit IndexColorModel from a ColorMaps.ColorMap.
createIndexedColorModel8bit(ColorMaps.ColorMap, int) - Static method in class qupath.lib.color.ColorModelFactory
Create an 8-bit IndexColorModel from a ColorMaps.ColorMap, allowing for a transparent pixel to be set (e.g.
createInstance() - Static method in class qupath.lib.roi.RoiEditor
Create a new RoiEditor.
createInstance(int, int, int, int, int, int) - Static method in class qupath.lib.regions.ImageRegion
Create a region based on its bounding box coordinates, z-slice index and time point index.
createInstance(Class<? extends ImageServerBuilder<T>>, float, Collection<ImageServerBuilder.ServerBuilder<T>>) - Static method in class qupath.lib.images.servers.ImageServerBuilder.UriImageSupport
Create a ImageServerBuilder.UriImageSupport for (possibly multiple) images that can be read from a single URI.
createInstance(Class<? extends ImageServerBuilder<T>>, float, ImageServerBuilder.ServerBuilder<T>) - Static method in class qupath.lib.images.servers.ImageServerBuilder.UriImageSupport
Create a ImageServerBuilder.UriImageSupport for a single image that can be read from a single URI.
createInstance(Class<? extends ImageServerBuilder<T>>, URI, String...) - Static method in class qupath.lib.images.servers.ImageServerBuilder.DefaultImageServerBuilder
Create a ImageServerBuilder.ServerBuilder that reads an image from a URI and args, using the default server metadata.
createInstance(Class<? extends ImageServerBuilder<T>>, ImageServerMetadata, URI, String...) - Static method in class qupath.lib.images.servers.ImageServerBuilder.DefaultImageServerBuilder
Create a ImageServerBuilder.ServerBuilder that reads an image from a URI and args, and uses the specified metadata (possibly replacing the default metadata).
createInstance(String, double, int, int, int, int) - Static method in class qupath.lib.regions.RegionRequest
Create a request for a region specified in terms of its bounding box, using the first z-slice and time point.
createInstance(String, double, int, int, int, int, int, int) - Static method in class qupath.lib.regions.RegionRequest
Create a request for a region specified in terms of its bounding box, z-slice and time point.
createInstance(String, double, int, int, int, int, ImagePlane) - Static method in class qupath.lib.regions.RegionRequest
Create a request for a region specified in terms of its bounding box and ImagePlane.
createInstance(String, double, Collection<? extends ROI>) - Static method in class qupath.lib.regions.RegionRequest
Create a request that contains the pixels of the specified ROIs.
createInstance(String, double, ImageRegion) - Static method in class qupath.lib.regions.RegionRequest
Create a request corresponding to a specified ImageRegion.
createInstance(String, double, ROI) - Static method in class qupath.lib.regions.RegionRequest
Create a request that contains the pixels of the specified ROI.
createInstance(String, int, double, ImageRegion) - Static method in class qupath.lib.images.servers.TileRequest
Create a new tile request for a specified region, downsample and resolution level.
createInstance(String, RegionRequest) - Static method in class qupath.lib.regions.RegionRequest
Create a request that matches another request but with a different path.
createInstance(Collection<? extends ROI>) - Static method in class qupath.lib.regions.ImageRegion
Create the smallest region that completely contains the specified ROIs.
createInstance(ImageServer<?>) - Static method in class qupath.lib.regions.RegionRequest
Create a request for the full width and height of an ImageServer, for the default plane (first z-slice, time point) and first resolution level downsample (usually 1, but not always).
createInstance(ImageServer<?>, double) - Static method in class qupath.lib.regions.RegionRequest
Create a request for the full width and height of an ImageServer, for the default plane (first z-slice, time point).
createInstance(ImageServer<?>, int, ImageRegion) - Static method in class qupath.lib.images.servers.TileRequest
Create a new tile request for a specified region and resolution level of an image.
createInstance(ROI) - Static method in class qupath.lib.regions.ImageRegion
Create the smallest region that completely contains a specified ROI.
createIoMinMerger(double) - Static method in class qupath.lib.objects.utils.ObjectMerger
 
createIoMinMerger(double, MeasurementStrategy) - Static method in class qupath.lib.objects.utils.ObjectMerger
Create an object merger that can merge together any objects with sufficiently large intersection over minimum area (IoMin).
createIoUMerger(double) - Static method in class qupath.lib.objects.utils.ObjectMerger
 
createIoUMerger(double, MeasurementStrategy) - Static method in class qupath.lib.objects.utils.ObjectMerger
Create an object merger that can merge together any objects with sufficiently large intersection over union.
createLike(PathObject, ROI) - Static method in class qupath.lib.objects.PathObjectTools
Create a new object with the same type and classification as the input object, but a new ROI and ID.
createLike(PathObject, ROI, ROI) - Static method in class qupath.lib.objects.PathObjectTools
Create a new object with the same type, classification, name and color as the input object, but a new ROI and ID.
createLinearCombinationChannelTransform(double...) - Static method in class qupath.lib.images.servers.ColorTransforms
Create a ColorTransform that apply a linear combination to the channels.
createLinearCombinationChannelTransform(List<? extends Number>) - Static method in class qupath.lib.images.servers.ColorTransforms
Create a ColorTransform that apply a linear combination to the channels.
createLinearCombinationChannelTransform(Map<String, ? extends Number>) - Static method in class qupath.lib.images.servers.ColorTransforms
Create a ColorTransform that apply a linear combination to the channels.
createLinearFunction(double, double) - Static method in class qupath.lib.color.ColorModelFactory
Create a linear function between a given range, which can be used to determine a suitable alpha value for an image that should have opacity based upon pixel values.
createLinearFunction(PixelType) - Static method in class qupath.lib.color.ColorModelFactory
Create a linear function for a specific pixel type, which can be used to determine a suitable alpha value for an image that should have opacity based upon pixel values.
createLineROI(double, double, double, double) - Static method in class qupath.lib.roi.ROIs
Create a line ROI with start and end coordinates on the default image plane.
createLineROI(double, double, double, double, ImagePlane) - Static method in class qupath.lib.roi.ROIs
Create a line ROI with start and end coordinates.
createLineROI(double, double, ImagePlane) - Static method in class qupath.lib.roi.ROIs
Create a ROI representing a line with zero length.
createLineString(double, double, double, double) - Static method in class qupath.lib.roi.GeometryTools
Create a line Geometry for the specified end points.
createLineString(Point2...) - Static method in class qupath.lib.roi.GeometryTools
Create a line Geometry for the specified array of points.
createMaximumChannelTransform() - Static method in class qupath.lib.images.servers.ColorTransforms
Create a ColorTransform that calculates the maximum of all channels.
createMeanChannelTransform() - Static method in class qupath.lib.images.servers.ColorTransforms
Create a ColorTransform that calculates the mean of all channels.
createMeasurementList(int, MeasurementList.MeasurementListType) - Static method in class qupath.lib.measurements.MeasurementListFactory
Create a measurement list.
createMinimumChannelTransform() - Static method in class qupath.lib.images.servers.ColorTransforms
Create a ColorTransform that calculates the minimum of all channels.
createNumberedObjectFunction(Function<ROI, PathObject>) - Static method in class qupath.lib.analysis.images.ContourTracing
Create a (bi)function to generate an object from a ROI and a number, setting the name of the object to match the number.
createObjectAddedEvent(Object, PathObjectHierarchy, PathObject, PathObject) - Static method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent
Create a hierarchy event indicated objects were added.
createObjectFunction(Function<ROI, PathObject>, BiConsumer<PathObject, Number>) - Static method in class qupath.lib.analysis.images.ContourTracing
Create a (bi)function to generate an object from a ROI and a number.
createObjectInputStream(InputStream) - Static method in class qupath.lib.io.PathIO
Create a new ObjectInputStream, setting the default ObjectInputFilter for core QuPath-related and Java classes only.
createObjectRemovedEvent(Object, PathObjectHierarchy, PathObject, PathObject) - Static method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent
Create a hierarchy event indicating objects were removed.
createObjects(Raster, int, RegionRequest, int, int, BiFunction<ROI, Number, PathObject>) - Static method in class qupath.lib.analysis.images.ContourTracing
Create objects from one band of a raster containing integer labels.
createObjects(SimpleImage, RegionRequest, int, int, BiFunction<ROI, Number, PathObject>) - Static method in class qupath.lib.analysis.images.ContourTracing
Create objects from a labelled image.
createObjects(ROI, Function<ROI, PathObject>) - Method in class qupath.lib.objects.utils.Tiler
Create a list of PathObject tiles from the input.
createObjectsChangedEvent(Object, PathObjectHierarchy, PathObjectHierarchyEvent.HierarchyEventType, Collection<? extends PathObject>, boolean) - Static method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent
Create a hierarchy event indicating objects have changed in a way consistent with the specified event type.
createPointsROI() - Static method in class qupath.lib.roi.ROIs
Create an empty points ROI on the default image plane.
createPointsROI(double[], double[]) - Static method in class qupath.lib.roi.ROIs
Create a points ROI from an array of x and y coordinates on the default image plane.
createPointsROI(double[], double[], ImagePlane) - Static method in class qupath.lib.roi.ROIs
Create a points ROI from an array of x and y coordinates.
createPointsROI(double, double) - Static method in class qupath.lib.roi.ROIs
Create a points ROI containing a single point on the default image plane.
createPointsROI(double, double, ImagePlane) - Static method in class qupath.lib.roi.ROIs
Create a points ROI containing a single point.
createPointsROI(List<? extends Point2>) - Static method in class qupath.lib.roi.ROIs
Create a points ROI from a list of points on the default image plane.
createPointsROI(List<? extends Point2>, ImagePlane) - Static method in class qupath.lib.roi.ROIs
Create a points ROI from a list of points.
createPointsROI(ImagePlane) - Static method in class qupath.lib.roi.ROIs
Create an empty points ROI.
createPolygonROI(double[], double[]) - Static method in class qupath.lib.roi.ROIs
Create a polygon ROI from an array of x and y coordinates on the default image plane
createPolygonROI(double[], double[], ImagePlane) - Static method in class qupath.lib.roi.ROIs
Create a polygon ROI from an array of x and y coordinates.
createPolygonROI(double, double) - Static method in class qupath.lib.roi.ROIs
Create an empty, closed polygon ROI consisting of a single point on the default image plane.
createPolygonROI(double, double, ImagePlane) - Static method in class qupath.lib.roi.ROIs
Create an empty, closed polygon ROI consisting of a single point.
createPolygonROI(List<? extends Point2>) - Static method in class qupath.lib.roi.ROIs
Create a closed polygon ROI from a list of points on the default image plane.
createPolygonROI(List<? extends Point2>, ImagePlane) - Static method in class qupath.lib.roi.ROIs
Create a closed polygon ROI from a list of points.
createPolylineROI(double[], double[]) - Static method in class qupath.lib.roi.ROIs
Create a polyline ROI from an array of x and y coordinates on the default image plane.
createPolylineROI(double[], double[], ImagePlane) - Static method in class qupath.lib.roi.ROIs
Create a polyline ROI from an array of x and y coordinates.
createPolylineROI(double, double) - Static method in class qupath.lib.roi.ROIs
Create an empty polyline ROI consisting of a single point on the default iamge plane.
createPolylineROI(double, double, ImagePlane) - Static method in class qupath.lib.roi.ROIs
Create an empty polyline ROI consisting of a single point.
createPolylineROI(List<? extends Point2>) - Static method in class qupath.lib.roi.ROIs
Create a polyline ROI from a list of points on the default image plane.
createPolylineROI(List<? extends Point2>, ImagePlane) - Static method in class qupath.lib.roi.ROIs
Create a polyline ROI from a list of points.
createProject(File, Class<T>) - Static method in class qupath.lib.projects.Projects
Create a new project using the local file system.
createRandomRectangle(ImageRegion, double, double) - Static method in class qupath.lib.roi.RoiTools
Create a randomly-located rectangle ROI with the specified width and height, constrained to fall within the provided mask region.
createRandomRectangle(ImageRegion, double, double, Random) - Static method in class qupath.lib.roi.RoiTools
Create a randomly-located rectangle ROI with the specified width and height, constrained to fall within the provided mask region.
createRandomRectangle(ROI, double, double) - Static method in class qupath.lib.roi.RoiTools
Create a randomly-located rectangle ROI with the specified width and height, constrained to fall within the provided mask ROI.
createRandomRectangle(ROI, double, double, int, boolean, Random) - Static method in class qupath.lib.roi.RoiTools
Create a randomly-located rectangle ROI with the specified width and height, constrained to fall within the provided mask ROI, using a specified maximum number of attempts.
createRectangle(double, double, double, double) - Static method in class qupath.lib.roi.GeometryTools
Create a rectangular Geometry for the specified bounding box.
createRectangleROI(double, double, double, double) - Static method in class qupath.lib.roi.ROIs
Create a rectangle ROI defined by its bounding box on the default image plane.
createRectangleROI(double, double, double, double, ImagePlane) - Static method in class qupath.lib.roi.ROIs
Create a rectangle ROI defined by its bounding box.
createRectangleROI(ImageRegion) - Static method in class qupath.lib.roi.ROIs
Create a rectangle ROI that matches an ImageRegion.
createROIMask(int, int, ROI, double, double, double) - Static method in class qupath.lib.awt.common.BufferedImageTools
Create a grayscale BufferedImage representing a mask for a specified ROI.
createROIMask(int, int, ROI, RegionRequest) - Static method in class qupath.lib.awt.common.BufferedImageTools
Create a grayscale BufferedImage representing a mask for a specified ROI.
createROIMask(Shape, double) - Static method in class qupath.lib.awt.common.BufferedImageTools
Create a Shape mask using the minimal bounding box for the Shape.
createROIMask(ROI, double) - Static method in class qupath.lib.awt.common.BufferedImageTools
Create a ROI mask using the minimal bounding box for the ROI.
createROIs(Raster, int, RegionRequest, int, int) - Static method in class qupath.lib.analysis.images.ContourTracing
Create ROIs from one band of a raster containing integer label values.
createROIs(SimpleImage, RegionRequest, int, int) - Static method in class qupath.lib.analysis.images.ContourTracing
Create ROIs from a labelled image containing integer labels.
createROIs(ROI) - Method in class qupath.lib.objects.utils.Tiler
Create a list of ROI tiles from the input.
createRunnableTask(ObjectDetector<T>, ParameterList, ImageData<T>, PathObject) - Static method in class qupath.lib.plugins.DetectionPluginTools
Create a task that applies an object detector to a parent object.
createRunningStatisticsList(int) - Static method in class qupath.lib.analysis.stats.StatisticsHelper
Create a list of n (empty) RunningStatistics objects.
createScaled(double...) - Static method in class qupath.lib.images.servers.transforms.SubtractOffsetAndScaleNormalizer
Create a normalizer that scales each channel by a constant.
createScaledInstance(double, double) - Method in class qupath.lib.images.servers.PixelCalibration
Get a scaled instance of this PixelCalibration, multiplying pixel sizes for x and y by the specified scale values.
createScaledInstance(double, double, double) - Method in class qupath.lib.images.servers.PixelCalibration
Get a scaled instance of this PixelCalibration, multiplying pixel sizes for x, y and z by the specified scale values.
createScript() - Method in class qupath.lib.plugins.workflow.Workflow
Generate a script from the current workflow steps.
createServerBuilder() - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer
Returns null (does not support ServerBuilders).
createServerBuilder() - Method in class qupath.lib.images.servers.AbstractImageServer
Create a ServerBuilder, which can be used to construct an identical ImageServer.
createServerBuilder() - Method in class qupath.lib.images.servers.AffineTransformImageServer
 
createServerBuilder() - Method in class qupath.lib.images.servers.ChannelTransformFeatureServer
Returns null (does not support ServerBuilders).
createServerBuilder() - Method in class qupath.lib.images.servers.CroppedImageServer
 
createServerBuilder() - Method in class qupath.lib.images.servers.LabeledImageServer
Returns null (does not support ServerBuilders).
createServerBuilder() - Method in class qupath.lib.images.servers.NormalizedImageServer
 
createServerBuilder() - Method in class qupath.lib.images.servers.RearrangeRGBImageServer
 
createServerBuilder() - Method in class qupath.lib.images.servers.RotatedImageServer
 
createServerBuilder() - Method in class qupath.lib.images.servers.SlicedImageServer
 
createServerBuilder() - Method in class qupath.lib.images.servers.SparseImageServer
 
createServerBuilder() - Method in class qupath.lib.images.servers.TypeConvertImageServer
 
createServerBuilder() - Method in class qupath.lib.images.servers.WrappedBufferedImageServer
Returns null (does not support ServerBuilders).
createServerBuilder() - Method in class qupath.lib.images.servers.ZConcatenatedImageServer
 
createServerBuilder() - Method in class qupath.lib.images.servers.ZProjectedImageServer
 
createShape() - Method in class qupath.lib.roi.AreaROI
Deprecated.
 
createShape() - Method in class qupath.lib.roi.EllipseROI
 
createShape() - Method in class qupath.lib.roi.GeometryROI
 
createShape() - Method in class qupath.lib.roi.LineROI
 
createShape() - Method in class qupath.lib.roi.PointsROI
 
createShape() - Method in class qupath.lib.roi.PolygonROI
 
createShape() - Method in class qupath.lib.roi.PolylineROI
 
createShape() - Method in class qupath.lib.roi.RectangleROI
 
createShapeMask(int, int, Shape, double, double, double) - Static method in class qupath.lib.awt.common.BufferedImageTools
Create a grayscale BufferedImage representing a mask for a specified ROI.
createSharedClassificationMerger() - Static method in class qupath.lib.objects.utils.ObjectMerger
 
createSharedClassificationMerger(MeasurementStrategy) - Static method in class qupath.lib.objects.utils.ObjectMerger
Create an object merger that can merge together any objects with similar ROIs (e.g.
createSharedTileBoundaryMerger(double) - Static method in class qupath.lib.objects.utils.ObjectMerger
 
createSharedTileBoundaryMerger(double, double) - Static method in class qupath.lib.objects.utils.ObjectMerger
 
createSharedTileBoundaryMerger(double, double, MeasurementStrategy) - Static method in class qupath.lib.objects.utils.ObjectMerger
Create an object merger that uses a shared boundary IoU criterion and overlap tolerance.
createSharedTileBoundaryMerger(double, MeasurementStrategy) - Static method in class qupath.lib.objects.utils.ObjectMerger
Create an object merger that uses a shared boundary IoU criterion and default overlap tolerance.
createStainVector(String, double, double, double) - Static method in class qupath.lib.color.StainVector
Create a stain vector.
createStructureChangeEvent(Object, PathObjectHierarchy, PathObject) - Static method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent
Create a hierarchy event indicating that the hierarchy structure has been changed.
createSubProject(String, Collection<ProjectImageEntry<T>>) - Method in interface qupath.lib.projects.Project
Create a sub-project that provides a view on the specified entries.
createSubtractOffset(double...) - Static method in class qupath.lib.images.servers.transforms.SubtractOffsetAndScaleNormalizer
Create a normalizer that subtracts a constant from each channel, without clipping.
createSubtractOffsetAndClipZero(double...) - Static method in class qupath.lib.images.servers.transforms.SubtractOffsetAndScaleNormalizer
Create a normalizer that subtracts a constant from each channel, clipping the lower bound to 0.
createSubTypeAdapterFactory(Class<T>, String) - Static method in class qupath.lib.io.GsonTools
Create a TypeAdapterFactory that is suitable for handling class hierarchies.
createTaskRunner() - Method in class qupath.lib.plugins.TaskRunnerUtils
Create a new TaskRunner instance, using the default number of threads from ThreadTools.getParallelism().
createTaskRunner(int) - Method in class qupath.lib.plugins.TaskRunnerUtils
Create a new TaskRunner instance with the specified number of threads.
createThreadFactory(String, boolean) - Static method in class qupath.lib.common.ThreadTools
Create a named thread factory with Thread.NORM_PRIORITY.
createThreadFactory(String, boolean, int) - Static method in class qupath.lib.common.ThreadTools
Create a named thread factory with a specified priority.
createTileObject(ROI) - Static method in class qupath.lib.objects.PathObjects
Create an unclassified tile object.
createTileObject(ROI, PathClass) - Static method in class qupath.lib.objects.PathObjects
Create a tile object.
createTileObject(ROI, PathClass, MeasurementList) - Static method in class qupath.lib.objects.PathObjects
Create a tile object, with a classification and measurements list.
createTiles(ROI) - Method in class qupath.lib.objects.utils.Tiler
Create a list of PathTileObject tiles from the input.
createTMACoreObject(double, double, double, boolean) - Static method in class qupath.lib.objects.PathObjects
Create a TMA core object with an circular ROI.
createTMACoreObject(double, double, double, boolean, ImagePlane) - Static method in class qupath.lib.objects.PathObjects
Create a TMA core object with an circular ROI.
createTMACoreObject(double, double, double, double, boolean) - Static method in class qupath.lib.objects.PathObjects
Create a TMA core object with an ellipse ROI.
createTMACoreObject(double, double, double, double, boolean, ImagePlane) - Static method in class qupath.lib.objects.PathObjects
Create a TMA core object with an ellipse ROI.
createTMAGrid(String, String, boolean, double, ImageRegion) - Static method in class qupath.lib.objects.PathObjectTools
Create a new regular TMAGrid, fit within a specified region.
createTouchingMerger() - Static method in class qupath.lib.objects.utils.ObjectMerger
 
createTouchingMerger(MeasurementStrategy) - Static method in class qupath.lib.objects.utils.ObjectMerger
Create an object merger that can merge together any objects with similar ROIs (e.g.
createTracedGeometry(Raster, double, double, int, RegionRequest) - Static method in class qupath.lib.analysis.images.ContourTracing
Create a traced geometry from a raster.
createTracedGeometry(SimpleImage, double, double, RegionRequest) - Static method in class qupath.lib.analysis.images.ContourTracing
Create a traced geometry from a SimpleImage.
createTracedROI(Raster, double, double, int, RegionRequest) - Static method in class qupath.lib.analysis.images.ContourTracing
Create a traced ROI from a raster.
createTracedROI(SimpleImage, double, double, RegionRequest) - Static method in class qupath.lib.analysis.images.ContourTracing
Create a traced ROI from a SimpleImage.
createWithClipRange(double[], double[], double, double) - Static method in class qupath.lib.images.servers.transforms.SubtractOffsetAndScaleNormalizer
Create a normalizer that subtracts a constant from each channel, then multiples the result by a scale factor - clipping the result to a defined range.
crop(BufferedImage, int, int, int, int) - Static method in class qupath.lib.awt.common.BufferedImageTools
Create a crop of the image using the specified bounding box.
crop(ImageRegion) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Crop a specified region based on a bounding box.
CroppedImageServer - Class in qupath.lib.images.servers
ImageServer that treats a particular sub-region of another ImageServer as a full image, i.e.
CroppedImageServer(ImageServer<BufferedImage>, ImageRegion) - Constructor for class qupath.lib.images.servers.CroppedImageServer
Create an ImageServer that represents a cropped region of another (larger) server.
cropTiles(boolean) - Method in class qupath.lib.objects.utils.Tiler.Builder
Set whether the tiler is set to crop the output to the input parent.
cross3(double[], double[]) - Static method in class qupath.lib.color.StainVector
Compute the cross product of two vectors.
CYAN - Static variable in class qupath.lib.common.ColorTools
Packed int representing cyan.

D

DAB - Enum constant in enum class qupath.lib.color.StainVector.DefaultStains
DAB
DAB - Static variable in class qupath.lib.color.ColorDeconvolutionStains
Default name for DAB stain
DAB_H_DAB - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
DAB after color deconvolution with default H-DAB stains
DAB_H_DAB_8_bit - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
DAB after color deconvolution with default H-DAB stains and conversion to 8-bit
darkenColor(Color) - Static method in class qupath.lib.color.ColorToolsAwt
Get a (slightly) darker version of the specified color.
deconvolveStains(ColorDeconvolutionStains, int...) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Apply color deconvolution to the brightfield image, so that deconvolved stains behave as separate channels.
DEFAULT - Enum constant in enum class qupath.lib.images.servers.ImageServerMetadata.ChannelType
Default channel interpretation.
DEFAULT_CLASSIFICATION_LABELS_CHANNEL - Static variable in class qupath.lib.images.servers.ImageServerMetadata
Default channel to use with images where the channel type is ImageServerMetadata.ChannelType.CLASSIFICATION.
DEFAULT_PROJECT_EXTENSION - Static variable in class qupath.lib.projects.ProjectIO
Default file extension for a QuPath project.
DEFAULT_PROJECT_NAME - Static variable in class qupath.lib.projects.ProjectIO
Default file name for a QuPath project.
DefaultPathObjectComparator - Class in qupath.lib.objects
Default comparator to enable objects to be sorted in a more predictable manner.
DefaultPathObjectComparator() - Constructor for class qupath.lib.objects.DefaultPathObjectComparator
 
DefaultPathObjectConnectionGroup - Class in qupath.lib.objects
Deprecated.
v0.6.0, to be replaced by DelaunayTools.Subdivision
DefaultPathObjectConnectionGroup() - Constructor for class qupath.lib.objects.DefaultPathObjectConnectionGroup
Deprecated.
Default constructor.
DefaultPathObjectConnectionGroup(PathObjectConnectionGroup) - Constructor for class qupath.lib.objects.DefaultPathObjectConnectionGroup
Deprecated.
Create a connections group, copying the connections from an existing group.
DefaultROIComparator - Class in qupath.lib.roi
Default comparator to enable ROIs to be sorted in a more predictable manner.
DefaultROIComparator() - Constructor for class qupath.lib.roi.DefaultROIComparator
 
DefaultScriptableWorkflowStep - Class in qupath.lib.plugins.workflow
A scriptable workflow step where the script is provided directly as an argument.
DefaultScriptableWorkflowStep(String, String) - Constructor for class qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep
Create a workflow step using a provided script string that will be called as-is.
DefaultScriptableWorkflowStep(String, Map<String, ?>, String) - Constructor for class qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep
Constructor that takes a parameter map for display.
DefaultTMAGrid - Class in qupath.lib.objects.hierarchy
Default implementation of a TMAGrid.
DelaunayTools - Class in qupath.lib.analysis
Tools for creating and querying Delaunay triangulations and Voronoi diagrams.
DelaunayTools() - Constructor for class qupath.lib.analysis.DelaunayTools
 
DelaunayTools.Builder - Class in qupath.lib.analysis
Builder class to create a DelaunayTools.Subdivision based on Delaunay triangulation.
DelaunayTools.Subdivision - Class in qupath.lib.analysis
Helper class for extracting information from a Delaunay triangulation computed from PathObjects.
deleteFile(File, boolean) - Static method in class qupath.lib.common.GeneralTools
Delete a file, optionally requesting that it be moved to the trash rather than permanently deleted.
DELIMITER - Static variable in class qupath.lib.objects.classes.PathClass
Get the delimiter to use between names of the PathClass when converting to a string.
DENSITY - Enum constant in enum class qupath.lib.images.servers.ImageServerMetadata.ChannelType
Each channel represents a density value, such as in a density map (e.g.
deselectObject(PathObject) - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel
Ensure that the specified object is removed from the selection.
deselectObjects(Collection<? extends PathObject>) - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel
Ensure the specified objects are deselected.
detectionCentroidDistances(ImageData<?>, boolean) - Static method in class qupath.lib.analysis.DistanceTools
Compute the distance for all detection object centroids to the closest annotation with each valid, not-ignored classification and add the result to the detection measurement list.
DetectionPluginTools - Class in qupath.lib.plugins
Helper methods to convert ObjectDetectors into runnable tasks, which take care of resolving overlaps when using ParallelTileObjects after the detection is complete and firing notification events in a PathObjectHierarchy.
DetectionPluginTools() - Constructor for class qupath.lib.plugins.DetectionPluginTools
 
detections() - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder
Set the filter to accept all detection objects only.
DETECTIONS - Enum constant in enum class qupath.lib.objects.PathObjectFilter
Accept detection objects (no subtypes, e.g.
DETECTIONS_ALL - Enum constant in enum class qupath.lib.objects.PathObjectFilter
Accept detection objects (all subtypes)
detectionsToCells(Collection<? extends PathObject>, double, double) - Static method in class qupath.lib.objects.CellTools
Create cell objects by expanding the (nucleus) ROIs from existing detections to approximate the full cell boundary.
detectionToAnnotationDistances(ImageData<?>, boolean) - Static method in class qupath.lib.analysis.DistanceTools
Compute the distance for all detection object centroids to the closest annotation with each valid, not-ignored classification and add the result to the detection measurement list.
detectionToAnnotationDistances(ImageData<?>, boolean, boolean) - Static method in class qupath.lib.analysis.DistanceTools
Compute the distance for all detection object centroids to the closest annotation with each valid, not-ignored classification and add the result to the detection measurement list.
detectionToAnnotationDistancesSigned(ImageData<?>, boolean) - Static method in class qupath.lib.analysis.DistanceTools
Compute the signed distance for all detection object centroids to the closest annotation with each valid, not-ignored classification and add the result to the detection measurement list.
determinant() - Method in class qupath.lib.color.ColorDeconvMatrix3x3
Calculate the determinant of the matrix.
difference(ROI, ROI) - Static method in class qupath.lib.roi.RoiTools
Compute the difference between two ROIs.
dim() - Method in interface qupath.lib.geom.Point
Number of values used to represent this point.
dim() - Method in class qupath.lib.geom.Point2
 
discardFragments() - Method in class qupath.lib.objects.utils.OverlapFixer.Builder
Equivalent to keepFragments(false).
distance(double, double) - Method in class qupath.lib.geom.Point2
Calculate the distance between this point and a specified x and y location.
distance(Point) - Method in class qupath.lib.geom.Point2
 
distance(Point) - Method in interface qupath.lib.geom.Point
Calculate the distance to another point, with the same Point.dim().
distance(Point2) - Method in class qupath.lib.geom.Point2
Calculate the distance between this point and another point.
distanceSq(double, double) - Method in class qupath.lib.geom.Point2
Calculate the squared distance between this point and a specified x and y location.
distanceSq(Point) - Method in class qupath.lib.geom.Point2
 
distanceSq(Point) - Method in interface qupath.lib.geom.Point
Calculate the squared distance to another point, with the same Point.dim().
DistanceTools - Class in qupath.lib.analysis
Static methods for calculating distances between objects.
DistanceTools() - Constructor for class qupath.lib.analysis.DistanceTools
 
do8BitRangeCheck(double) - Static method in class qupath.lib.common.ColorTools
Clip an input value to be an integer in the range 0-255 (with rounding down).
do8BitRangeCheck(float) - Static method in class qupath.lib.common.ColorTools
Clip an input value to be an integer in the range 0-255 (with rounding down).
do8BitRangeCheck(int) - Static method in class qupath.lib.common.ColorTools
Clip an input value to be an integer in the range 0-255.
DONE - Enum constant in enum class qupath.lib.plugins.ParallelTileObject.Status
Tile processing complete
DOUBLE - Enum constant in enum class qupath.lib.measurements.MeasurementList.MeasurementListType
A list backed by an array of doubles.
DoubleParameter - Class in qupath.lib.plugins.parameters
Parameter to represent a floating point numeric value.
downsample(double) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Specify downsample factor.
downsample(double) - Method in class qupath.lib.images.writers.TileExporter
Define resolution as a downsample value.
DownsampleCalculator - Interface in qupath.lib.images.servers.downsamples
Interface for classes that can calculate a downsample value to use when requesting pixels from an image.
DownsampleCalculators - Class in qupath.lib.images.servers.downsamples
Helper class to create downsample calculators, which can figure out how much to downsample a specified image region.
DownsampleCalculators() - Constructor for class qupath.lib.images.servers.downsamples.DownsampleCalculators
 
DROP_OVERLAPS - Enum constant in enum class qupath.lib.objects.utils.OverlapFixer.Strategy
 
dropOverlaps() - Method in class qupath.lib.objects.utils.OverlapFixer.Builder
Retain only the 'highest priority' objects when overlaps occur, and drop the others.
duplicate() - Method in class qupath.lib.images.servers.ImageServerMetadata
Duplicate this metatadata.
duplicate() - Method in class qupath.lib.plugins.parameters.BooleanParameter
 
duplicate() - Method in class qupath.lib.plugins.parameters.ChoiceParameter
 
duplicate() - Method in class qupath.lib.plugins.parameters.DoubleParameter
 
duplicate() - Method in class qupath.lib.plugins.parameters.EmptyParameter
 
duplicate() - Method in class qupath.lib.plugins.parameters.IntParameter
 
duplicate() - Method in interface qupath.lib.plugins.parameters.Parameter
Create a new Parameter with the same text and value.
duplicate() - Method in class qupath.lib.plugins.parameters.ParameterList
Create a deep copy of this parameter list.
duplicate() - Method in class qupath.lib.plugins.parameters.StringParameter
 
duplicate() - Method in class qupath.lib.roi.AreaROI
Deprecated.
duplicate() - Method in class qupath.lib.roi.EllipseROI
Deprecated.
duplicate() - Method in class qupath.lib.roi.GeometryROI
 
duplicate() - Method in interface qupath.lib.roi.interfaces.ROI
Deprecated.
duplicate() - Method in class qupath.lib.roi.LineROI
Deprecated.
duplicate() - Method in class qupath.lib.roi.PointsROI
Deprecated.
duplicate() - Method in class qupath.lib.roi.PolygonROI
Deprecated.
duplicate() - Method in class qupath.lib.roi.PolylineROI
Deprecated.
duplicate() - Method in class qupath.lib.roi.RectangleROI
Deprecated.
duplicate(BufferedImage) - Static method in class qupath.lib.awt.common.BufferedImageTools
Duplicate a BufferedImage.
duplicateAllSelectedObjects(PathObjectHierarchy) - Static method in class qupath.lib.objects.PathObjectTools
Duplicate all the selected objects in a hierarchy.
duplicateObjects(PathObjectHierarchy, Collection<PathObject>) - Static method in class qupath.lib.objects.PathObjectTools
Duplicate the specified objects, assigning new IDs for each object.
duplicateObjects(PathObjectHierarchy, Collection<PathObject>, boolean) - Static method in class qupath.lib.objects.PathObjectTools
Duplicate the specified objects, optionally creating new IDs.
duplicateSelectedAnnotations(PathObjectHierarchy) - Static method in class qupath.lib.objects.PathObjectTools
Duplicate the selected annotation objects.
duplicateSelectedObjects(PathObjectHierarchy, Predicate<PathObject>) - Static method in class qupath.lib.objects.PathObjectTools
Duplicate the selected objects

E

EllipseROI - Class in qupath.lib.roi
ROI implementing a circle, or (unrotated) ellipse.
empty() - Static method in class qupath.lib.regions.Padding
Get an empty padding object (0 on all sides).
EmptyParameter - Class in qupath.lib.plugins.parameters
Parameter that doesn't actually store any value, but might contain some useful text (or a title) that may need to be displayed.
ensureBufferedImage(Image) - Static method in class qupath.lib.awt.common.BufferedImageTools
Convert an Image to a BufferedImage if necessary, or return the original image unchanged if it is already a BufferedImage.
ensureBufferedImageType(BufferedImage, int) - Static method in class qupath.lib.awt.common.BufferedImageTools
Convert a BufferedImage to have a specified type.
ensureHandlesUpdated() - Method in class qupath.lib.roi.RoiEditor
In the event that the current ROI has been modified elsewhere (which generally it shouldn't be) request the handles to be recomputed to avoid inconsistency.
ensurePolygonal(Geometry) - Static method in class qupath.lib.roi.GeometryTools
Strip non-polygonal parts from a GeometryCollection (non-recursive).
ensurePrecision(Geometry) - Static method in class qupath.lib.roi.GeometryTools
Update a geometry to have the precision model of the default factory.
ensurePrecision(Geometry, PrecisionModel) - Static method in class qupath.lib.roi.GeometryTools
Update a geometry to have the specified precision model.
envelopToRegion(Envelope, int, int) - Static method in class qupath.lib.roi.GeometryTools
Convert an Envelope to an ImageRegion.
EOSIN - Enum constant in enum class qupath.lib.color.StainVector.DefaultStains
Eosin
EOSIN - Static variable in class qupath.lib.color.ColorDeconvolutionStains
Default name for eosin stain
Eosin_H_E - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
Eosin after color deconvolution with default H&E stains
Eosin_H_E_8_bit - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
Eosin after color deconvolution with default H&E stains and conversion to 8-bit
equalParameters(ParameterList, ParameterList) - Static method in class qupath.lib.plugins.parameters.ParameterList
Check whether two parameter lists contain the same parameters with the same values (or defaults, if no values are set).
equals(Object) - Method in class qupath.lib.color.ColorDeconvolutionStains
 
equals(Object) - Method in class qupath.lib.color.StainVector
 
equals(Object) - Method in class qupath.lib.common.Version
 
equals(Object) - Method in class qupath.lib.geom.Point2
 
equals(Object) - Method in class qupath.lib.images.servers.ImageChannel
 
equals(Object) - Method in class qupath.lib.images.servers.ImageServerBuilder.DefaultImageServerBuilder
 
equals(Object) - Method in class qupath.lib.images.servers.ImageServerMetadata
 
equals(Object) - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel
 
equals(Object) - Method in class qupath.lib.images.servers.PixelCalibration
 
equals(Object) - Method in class qupath.lib.images.servers.TileRequest
 
equals(Object) - Method in class qupath.lib.io.UriUpdater.SingleUriItem
 
equals(Object) - Method in class qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep
 
equals(Object) - Method in class qupath.lib.regions.ImagePlane
 
equals(Object) - Method in class qupath.lib.regions.ImageRegion
 
equals(Object) - Method in class qupath.lib.regions.RegionRequest
 
equals(Object) - Method in class qupath.lib.roi.EllipseROI
 
equals(Object) - Method in class qupath.lib.roi.RectangleROI
 
equals(Object) - Method in class qupath.lib.roi.AreaROI
Deprecated.
 
equals(Object) - Method in class qupath.lib.roi.GeometryROI
 
equals(Object) - Method in class qupath.lib.roi.LineROI
 
equals(Object) - Method in class qupath.lib.roi.PointsROI
Test if this ROI is equal to another.
equals(Object) - Method in class qupath.lib.roi.PolygonROI
 
equals(Object) - Method in class qupath.lib.roi.PolylineROI
 
equalTo(String) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder
Set the classification (by name) for objects for which the specified measurement has a value exactly equal to the threshold.
equalTo(PathClass) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder
Set the classification for objects for which the specified measurement has a value exactly equal to the threshold.
escapeFilePath(String) - Static method in class qupath.lib.common.GeneralTools
Escape backslashes in an absolute file path - useful when scripting.
estimateAvailableMemory() - Static method in class qupath.lib.common.GeneralTools
Estimate the current available memory in bytes, based upon the JVM max and the memory currently used.
estimateCellBoundary(Geometry, double, double) - Static method in class qupath.lib.objects.CellTools
Estimate a cell boundary using Geometry objects.
estimateUsedMemory() - Static method in class qupath.lib.common.GeneralTools
Estimate the current used memory.
estimateWhiteValues(int[]) - Static method in class qupath.lib.color.ColorDeconvolutionHelper
Estimate white (background) values for a brightfield image.
exactClassification(PathClass...) - Static method in class qupath.lib.objects.PathObjectPredicates
Predicate that returns true if a PathObject has at least one of the specified PathClasses.
EXCLUDE_MEASUREMENTS - Enum constant in enum class qupath.lib.io.PathIO.GeoJsonExportOptions
Optionally exclude measurements from objects.
EXISTS - Enum constant in enum class qupath.lib.io.UriUpdater.UriStatus
URI refers to a file that is known to exist.
exportJson(boolean) - Method in class qupath.lib.images.writers.TileExporter
Optionally export a JSON file that includes label information and image/label pairs, where available.
exportObjectsAsGeoJSON(File, Collection<? extends PathObject>, PathIO.GeoJsonExportOptions...) - Static method in class qupath.lib.io.PathIO
Export a collection of objects as a GeoJSON "FeatureCollection" to a file.
exportObjectsAsGeoJSON(OutputStream, Collection<? extends PathObject>, PathIO.GeoJsonExportOptions...) - Static method in class qupath.lib.io.PathIO
Export a collection of objects as a GeoJSON "FeatureCollection" to an output stream.
exportObjectsAsGeoJSON(Path, Collection<? extends PathObject>, PathIO.GeoJsonExportOptions...) - Static method in class qupath.lib.io.PathIO
Export a collection of objects as a GeoJSON "FeatureCollection" to a file specified by its path.
extractBand(Raster, int) - Static method in class qupath.lib.analysis.images.ContourTracing
Extract a band from a a raster as a SimpleImage.
extractChannel(ImageServer<BufferedImage>, BufferedImage, float[]) - Method in interface qupath.lib.images.servers.ColorTransforms.ColorTransform
Extract a (row-wise) array containing the pixels extracted from a BufferedImage.
extractChannels(int...) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Extract specified channels for an image.
extractChannels(String...) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Extract specified channels for an image.
extractServerBuilder(Path) - Static method in class qupath.lib.io.PathIO
Extract a ImageServerBuilder.ServerBuilder from a serialized .qpdata file.

F

factory(GeometryFactory) - Method in class qupath.lib.roi.GeometryTools.GeometryConverter.Builder
Specify the GeometryFactory, which can define a precision model in JTS.
FastPolygonUnion - Class in qupath.lib.roi
Compute a faster union of large numbers of polygons.
FastPolygonUnion() - Constructor for class qupath.lib.roi.FastPolygonUnion
 
FEATURE - Enum constant in enum class qupath.lib.images.servers.ImageServerMetadata.ChannelType
Each channel represents a feature for a pixel classifier.
FEATURE_COLLECTION - Enum constant in enum class qupath.lib.io.PathIO.GeoJsonExportOptions
Request that objects are export as a FeatureCollection.
FeatureCollection - Class in qupath.lib.io
Class to wrap a collection of objects to indicate they should be export as a GeoJSON "FeatureCollection".
FileFormatInfo - Class in qupath.lib.images.servers
Helper class that, given a path, determines some basic file format information without enlisting the help of an external library or performing extensive parsing of the data.
FileFormatInfo() - Constructor for class qupath.lib.images.servers.FileFormatInfo
 
FileFormatInfo.ImageCheckType - Interface in qupath.lib.images.servers
Interface defining some basic image metadata that may be extracted from an image file to help ascertain whether an ImageServerBuilder can handle it.
fillHoles(Geometry) - Static method in class qupath.lib.roi.GeometryTools
Fill all interior rings for the specified geometry.
fillHoles(ROI) - Static method in class qupath.lib.roi.RoiTools
Fill the holes of an Area ROI, or return the ROI unchanged if it contains no holes.
filter(BufferedImage, BufferedImage) - Method in class qupath.lib.images.servers.transforms.ColorDeconvolutionNormalizer
 
filter(BufferedImage, BufferedImage) - Method in class qupath.lib.images.servers.transforms.SubtractOffsetAndScaleNormalizer
 
filter(PathObjectFilter) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder
Define the filter used to identify objects compatible with this classifier.
filter(PathObjectFilter) - Static method in class qupath.lib.objects.PathObjectPredicates
Wrap a PathObjectFilter as a PathObjectPredicates.PathObjectPredicate so that it can remain JSON-serializable when used in combination with other predicates.
filterByCentroid(boolean) - Method in class qupath.lib.objects.utils.Tiler.Builder
Set if the tiler will filter the output based on whether the centroid of tiles lies within the parent
filterByROIContainsCentroid(ROI, Collection<T>) - Static method in class qupath.lib.objects.PathObjectTools
Filter a collection of PathObjects to identify those with centroids that fall within specified ROI.
filterByROIContainsNucleusCentroid(ROI, Collection<T>) - Static method in class qupath.lib.objects.PathObjectTools
Filter a collection of PathObjects to identify those with centroids that fall within specified ROI.
filterByROICovers(ROI, Collection<T>) - Static method in class qupath.lib.objects.PathObjectTools
Filter a collection of PathObjects to identify those that have ROIs that are covered by a specified ROI.
filterByROICoversNucleus(ROI, Collection<T>) - Static method in class qupath.lib.objects.PathObjectTools
Filter a collection of PathObjects to identify those that have ROIs that are covered by a specified ROI, using the object's nucleus ROI where available.
filterByROIIntersects(ROI, Collection<T>) - Static method in class qupath.lib.objects.PathObjectTools
Filter a collection of PathObjects to identify those that intersect with a specified ROI.
filterByROIIntersectsNucleus(ROI, Collection<T>) - Static method in class qupath.lib.objects.PathObjectTools
Filter a collection of PathObjects to identify those that intersect with a specified ROI, using the object's nucleus ROI where available.
findAllNeighbors(PathObject) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Find all neighbors of a PathObject, having the same class as the object (e.g.
findByStringID(Collection<String>, Collection<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools
Find objects based on a String representation of their IDs.
findByUUID(Collection<UUID>, Collection<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools
Find objects based on their IDs.
findLargestPolygon(Geometry) - Static method in class qupath.lib.roi.GeometryTools
Find the polygon with the largest area in a Geometry.
findNearestNeighbor(PathObject) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Find the nearest neighbor of a PathObject, having the same class as the object (e.g.
findObjectsOutsideImage(Collection<? extends PathObject>, ImageServer<?>, boolean) - Static method in class qupath.lib.objects.PathObjectTools
Get all the objects with ROIs that are outside the bounds of an image.
findObjectsOutsideRegion(Collection<? extends PathObject>, ImageRegion, boolean) - Static method in class qupath.lib.objects.PathObjectTools
Get all the objects in a collection that are outside a defined region.
findObjectsOutsideRegion(Collection<? extends PathObject>, ImageRegion, int, int, int, int, boolean) - Static method in class qupath.lib.objects.PathObjectTools
Get all the objects in a collection that are outside a defined region, expanded for multiple z-slices and timepoints.
findTouchingBounds(ROI, Collection<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools
Find all objects with ROIs that touch (or cross) a parent ROI's boundary.
findTouchingImageBounds(ImageServer<?>, Collection<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools
Find all the objects that touch (or cross) a rectangle representing the image bounds.
finishTranslation() - Method in class qupath.lib.roi.RoiEditor
Notify the editor that translation should end.
fireHierarchyChangedEvent(Object) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Fire a hierarchy update indicating the hierarchy structure has changed.
fireHierarchyChangedEvent(Object, PathObject) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Fire a hierarchy update indicating the hierarchy structure has changed, impacting descendants of a specified object.
fireObjectClassificationsChangedEvent(Object, Collection<? extends PathObject>) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Fire a hierarchy update indicating object classifications have changed.
fireObjectMeasurementsChangedEvent(Object, Collection<? extends PathObject>) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Fire a hierarchy update indicating object measurements have changed.
fireObjectMeasurementsChangedEvent(Object, Collection<? extends PathObject>, boolean) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Fire a hierarchy update indicating object measurements have changed.
fireObjectsChangedEvent(Object, Collection<? extends PathObject>) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Fire a hierarchy update indicating objects have changed.
fireObjectsChangedEvent(Object, Collection<? extends PathObject>, boolean) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Fire a hierarchy update indicating objects have changed, and may still be changing.
fireWorkflowUpdatedEvent() - Method in class qupath.lib.plugins.workflow.Workflow
 
fixedDownsample(double) - Static method in class qupath.lib.images.servers.downsamples.DownsampleCalculators
Create a downsample calculator that simply returns a fixed value.
fixUris(UriResource, Project<?>) - Static method in class qupath.lib.io.UriUpdater
Attempt to fix any broken paths by updating URIs based upon the current project.
flatness(double) - Method in class qupath.lib.roi.GeometryTools.GeometryConverter.Builder
Specify the flatness for any operation where a PathIterator is required.
FLOAT - Enum constant in enum class qupath.lib.measurements.MeasurementList.MeasurementListType
A list backed by an array of floats.
FLOAT32 - Enum constant in enum class qupath.lib.images.servers.PixelType
32-bit floating point
FLOAT64 - Enum constant in enum class qupath.lib.images.servers.PixelType
64-bit floating point
FLUORESCENCE - Enum constant in enum class qupath.lib.images.ImageData.ImageType
Fluorescence image.
formatNumber(double, int) - Static method in class qupath.lib.common.GeneralTools
Format a value with a maximum number of decimal places, using the default Locale.
formatNumber(Locale, double, int) - Static method in class qupath.lib.common.GeneralTools
Format a value with a maximum number of decimal places, using a specified Locale.
from2D(double[][]) - Static method in class qupath.lib.awt.common.AffineTransforms
Create an affine transform from a 2x3 double array, or 3x3 if the last row has the values [0, 0, 1] only.
fromArray(String...) - Static method in class qupath.lib.objects.classes.PathClass
Get a PathClass from an array of individual names.
fromCollection(Collection<String>) - Static method in class qupath.lib.objects.classes.PathClass
Get a PathClass using all the name elements specified in the collection, without providing a default color.
fromCollection(Collection<String>, Integer) - Static method in class qupath.lib.objects.classes.PathClass
Get a PathClass instance using all the name elements specified in the collection, with optional default color if a new instance is created.
fromColumns(double...) - Static method in class qupath.lib.awt.common.AffineTransforms
Create an affine transform from a flat matrix with 6 elements, assumed to be in the order [[0, 2, 4], [1, 3, 5]].
fromJTS(AffineTransformation) - Static method in class qupath.lib.awt.common.AffineTransforms
Create a Java affine transform from a Java Topology Suite representation.
fromRows(double...) - Static method in class qupath.lib.awt.common.AffineTransforms
Create an affine transform from a flat matrix with 6 elements, assumed to be in the order [[0, 1, 2], [3, 4, 5]].
fromScale(double) - Static method in class qupath.lib.awt.common.AffineTransforms
Create an affine transform representing scaling, using the same scale for x and y.
fromScale(double, double) - Static method in class qupath.lib.awt.common.AffineTransforms
Create an affine transform representing scaling, optionally using a different scale for x and y.
fromString(String) - Static method in class qupath.lib.objects.classes.PathClass
Get a PathClass instance from a string representation, without specifying a default color.
fromString(String, Integer) - Static method in class qupath.lib.objects.classes.PathClass
Get a PathClass instance from a string representation, optionally providing a default color if a new instance needs to be created.
fullImageTile() - Method in class qupath.lib.images.writers.TileExporter
Specify that a single tile should be generated corresponding to the full image.

G

gammaColorMap(ColorMaps.ColorMap, double) - Static method in class qupath.lib.color.ColorMaps
Apply gamma to a colormap.
GENERAL - Enum constant in enum class qupath.lib.measurements.MeasurementList.MeasurementListType
A general list, which can contain any kind of measurement - at the expense of being rather memory-hungry.
GeneralTools - Class in qupath.lib.common
Collection of generally useful static methods.
generateDistinctName(String, Collection<String>) - Static method in class qupath.lib.common.GeneralTools
Generate a name that is distinct from the names in an existing collection, while being based on a provided name.
generateMedianStainVectorFromPixels(String, int[], double, double, double) - Static method in class qupath.lib.color.ColorDeconvolutionHelper
Determine median RGB optical densities for an array of pixels (packed RGB), and combine these into a StainVector with the specified name.
generateMedianStainVectorFromPixels(String, BufferedImage, double, double, double) - Static method in class qupath.lib.color.ColorDeconvolutionHelper
Generate a stain vector by taking the median optical densities from an input image.
GeneratingImageServer<T> - Interface in qupath.lib.images.servers
Marker interface to indicate that this ImageServer generates tiles on request.
GeometryROI - Class in qupath.lib.roi
ROI based on Java Topology Suite Geometry objects.
GeometryTools - Class in qupath.lib.roi
Convert between QuPath ROI objects and Java Topology Suite Geometry objects.
GeometryTools() - Constructor for class qupath.lib.roi.GeometryTools
 
GeometryTools.GeometryConverter - Class in qupath.lib.roi
Converter to help switch from a ROI to a Geometry.
GeometryTools.GeometryConverter.Builder - Class in qupath.lib.roi
Builder to help define how ROIs and Geometry objects should be converted.
geometryToROI(Geometry) - Static method in class qupath.lib.roi.GeometryTools
Convert a JTS Geometry to a QuPath ROI on the default image plane.
geometryToROI(Geometry, ImagePlane) - Static method in class qupath.lib.roi.GeometryTools
Convert a JTS Geometry to a QuPath ROI.
geometryToShape(Geometry) - Static method in class qupath.lib.roi.GeometryTools
Convert a JTS Geometry to a java.awt.Shape.
get(int) - Method in interface qupath.lib.geom.Point
Get the value of the ordinate for the specified dimension.
get(int) - Method in class qupath.lib.geom.Point2
 
get(String) - Method in interface qupath.lib.measurements.MeasurementList
Get value for the measurement with the specified name.
get(String) - Method in interface qupath.lib.projects.ResourceManager.Manager
Retrieve a resource by name.
getAlignment() - Method in class qupath.lib.objects.utils.Tiler
Get the tiling alignment.
getAllDetectionsForRegion(ImageRegion) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get all the detection objects overlapping or close to a specified region.
getAllDetectionsForRegion(ImageRegion, Collection<PathObject>) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get all the detection objects overlapping or close to a specified region, optionally adding to an existing collection.
getAllDetectionsForROI(ROI) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get all the detection objects with centroids falling within the specified ROI - including subclasses of detections, such as cells and tiles.
getAllImageSupports(URI, String...) - Static method in class qupath.lib.images.servers.ImageServers
Get all ImageServerBuilder.UriImageSupport that claim to be able to open the specified URI with optional args.
getAllNeighbors() - Method in class qupath.lib.analysis.DelaunayTools.Subdivision
Get a list of neighbors for all objects.
getAllObjects(boolean) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get all the objects in the hierarchy, optionally including the root object.
getAllObjectsForRegion(ImageRegion) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get all the objects overlapping or close to a specified region.
getAllObjectsForRegion(ImageRegion, Collection<PathObject>) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get all the objects overlapping or close to a specified region, optionally adding to an existing collection.
getAllObjectsForROI(ROI) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get all objects for a ROI.
getAllPointAnnotations() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get all annotation objects in the hierarchy that have a point (or multi-point) ROI.
getAllPointObjects() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get all objects in the hierarchy that have a point (or multi-point) ROI.
getAllPoints() - Method in class qupath.lib.roi.AreaROI
Deprecated.
Beware this method! This will return all polygon points (useful e.g.
getAllPoints() - Method in class qupath.lib.roi.EllipseROI
Since ellipses aren't represented internally with simple polygon points, this currently returns only 4 points (rather more diamond-like that would be ideal).
getAllPoints() - Method in class qupath.lib.roi.GeometryROI
 
getAllPoints() - Method in interface qupath.lib.roi.interfaces.ROI
Get a list of points representing the vertices of the ROI.
getAllPoints() - Method in class qupath.lib.roi.LineROI
 
getAllPoints() - Method in class qupath.lib.roi.PointsROI
 
getAllPoints() - Method in class qupath.lib.roi.PolygonROI
 
getAllPoints() - Method in class qupath.lib.roi.PolylineROI
 
getAllPoints() - Method in class qupath.lib.roi.RectangleROI
 
getAllTileRequests() - Method in interface qupath.lib.images.servers.TileRequestManager
Get TileRequest objects for all tiles that this server supports.
getAllTimes() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData
Retrieve a sorted array containing all times where 'something happened' (observed or censored).
getAncestorList(PathObject) - Static method in class qupath.lib.objects.PathObjectTools
Return a list of object ancestors, starting from the root object and ending with PathObject (assuming that the object is part of a hierarchy with a root).
getAncestorTMACore(PathObject) - Static method in class qupath.lib.objects.PathObjectTools
Get the TMA core object that contains a specified PathObject, or null if the object is not contained within a TMA core.
getAnnotationObjects() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get all annotation objects in the hierarchy.
getAnnotationsForRegion(ImageRegion) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get all the annotation objects overlapping or close to a specified region.
getAnnotationsForRegion(ImageRegion, Collection<PathObject>) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get all the annotation objects overlapping or close to a specified region, optionally adding to an existing collection.
getAnnotationsForROI(ROI) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get all the annotations covered by the specified ROI.
getAnnotationSubdivision(ImagePlane) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get a subdivision containing annotation objects.
getArea() - Method in class qupath.lib.roi.EllipseROI
 
getArea() - Method in class qupath.lib.roi.RectangleROI
 
getArea() - Method in class qupath.lib.roi.AreaROI
Deprecated.
 
getArea() - Method in class qupath.lib.roi.GeometryROI
 
getArea() - Method in interface qupath.lib.roi.interfaces.ROI
Get the area of this ROI.
getArea() - Method in class qupath.lib.roi.LineROI
 
getArea() - Method in class qupath.lib.roi.PointsROI
 
getArea() - Method in class qupath.lib.roi.PolygonROI
 
getArea() - Method in class qupath.lib.roi.PolylineROI
 
getArea(ROI) - Static method in class qupath.lib.roi.RoiTools
Get an Area object representing a ROI.
getAreaObjects(Collection<T>) - Static method in class qupath.lib.objects.PathObjectTools
Get a list of objects with area ROIs from a collection of objects.
getArgs() - Method in class qupath.lib.images.servers.ImageServerBuilder.DefaultImageServerBuilder
Get the args array.
getArray() - Method in class qupath.lib.color.StainVector
Get the stain vector as a 3 element array (red, green, blue).
getArray(boolean) - Method in interface qupath.lib.analysis.images.SimpleModifiableImage
Request the pixel array representing all the pixels in this image, returned row-wise.
getAssociatedImage(String) - Method in class qupath.lib.images.servers.AbstractImageServer
 
getAssociatedImage(String) - Method in interface qupath.lib.images.servers.ImageServer
Get the image for a given associated image name.
getAssociatedImageList() - Method in class qupath.lib.images.servers.AbstractImageServer
 
getAssociatedImageList() - Method in interface qupath.lib.images.servers.ImageServer
Get a list of 'associated images', e.g.
getAtRisk(double) - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData
Get the number at risk at a specified time.
getAvailableFeatures(Collection<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools
Get a set containing the names of all measurements found in the measurement lists of a specified object collection.
getAveragedPixelSize() - Method in class qupath.lib.images.servers.ImageServerMetadata
Get the averaged pixel size in microns, if available - or Double.NaN otherwise.
getAveragedPixelSize() - Method in class qupath.lib.images.servers.PixelCalibration
getAveragedPixelSizeMicrons() - Method in class qupath.lib.images.servers.PixelCalibration
Get the average of the pixel width and height in microns if possible, or Double.NaN if the pixel size is not available.
getBaseClass() - Method in class qupath.lib.objects.classes.PathClass
Get the 'base' class, i.e.
getBaseDirectory(Project<?>) - Static method in class qupath.lib.projects.Projects
Get the base directory of a project stored on the local file system.
getBinCenter(int) - Method in class qupath.lib.analysis.stats.Histogram
Get average of the left and right bin edges.
getBinIndexForValue(double, double) - Method in class qupath.lib.analysis.stats.Histogram
Get the index of the bin that should contain the specified value.
getBinLeftEdge(int) - Method in class qupath.lib.analysis.stats.Histogram
Get the lower edge for a specified bin.
getBinRightEdge(int) - Method in class qupath.lib.analysis.stats.Histogram
Get the upper edge for a specified bin.
getBinWidth(int) - Method in class qupath.lib.analysis.stats.Histogram
Get the width of a bin, which is the difference between its upper and lower edges.
getBitsPerPixel() - Method in enum class qupath.lib.images.servers.PixelType
Number of bits per pixel.
getBlue() - Method in class qupath.lib.color.StainVector
Get the blue component of the (normalized) stain vector.
getBlueOpticalDensities(int[], double, float[]) - Static method in class qupath.lib.color.ColorDeconvolutionHelper
Convert red channel of packed rgb pixel to optical density values, using a specified maximum value.
getBooleanParameterValue(String) - Method in class qupath.lib.plugins.parameters.ParameterList
Get a boolean parameter value (or its default) for the specified key.
getBoundaryDistance(ROI, ROI) - Static method in class qupath.lib.roi.RoiTools
Get the Euclidean distance between the boundaries of two ROIs.
getBoundaryDistance(ROI, ROI, double, double) - Static method in class qupath.lib.roi.RoiTools
Get the calibrated Euclidean distance between the boundaries of two ROIs using specified pixel sizes.
getBoundaryLabels() - Method in class qupath.lib.images.servers.LabeledImageServer
Get an unmodifiable map of classifications and their corresponding boundary labels, if available.
getBounds(ImageRegion) - Static method in class qupath.lib.awt.common.AwtTools
Create a Rectangle corresponding to the x,y,width,height of an ImageRegion.
getBounds(ImageRegion, Rectangle) - Static method in class qupath.lib.awt.common.AwtTools
Set the bounds of an existing Rectangle to the x,y,width,height of an ImageRegion.
getBounds(ROI) - Static method in class qupath.lib.awt.common.AwtTools
Create a Rectangle corresponding to bounding box of a ROI.
getBounds2D(BufferedImage) - Method in interface qupath.lib.images.servers.transforms.BufferedImageNormalizer
 
getBounds2D(ROI) - Static method in class qupath.lib.awt.common.AwtTools
Create a Rectangle2D corresponding to bounding box of a ROI.
getBounds2D(ROI, Rectangle2D) - Static method in class qupath.lib.awt.common.AwtTools
Set the bounds of an existing Rectangle2D to the x,y,width,height of a ROI.
getBoundsHeight() - Method in class qupath.lib.roi.EllipseROI
 
getBoundsHeight() - Method in class qupath.lib.roi.RectangleROI
 
getBoundsHeight() - Method in class qupath.lib.roi.AreaROI
Deprecated.
 
getBoundsHeight() - Method in class qupath.lib.roi.GeometryROI
 
getBoundsHeight() - Method in interface qupath.lib.roi.interfaces.ROI
Returns the height of the ROI bounding box.
getBoundsHeight() - Method in class qupath.lib.roi.LineROI
 
getBoundsHeight() - Method in class qupath.lib.roi.PointsROI
 
getBoundsHeight() - Method in class qupath.lib.roi.PolygonROI
 
getBoundsHeight() - Method in class qupath.lib.roi.PolylineROI
 
getBoundsWidth() - Method in class qupath.lib.roi.EllipseROI
 
getBoundsWidth() - Method in class qupath.lib.roi.RectangleROI
 
getBoundsWidth() - Method in class qupath.lib.roi.AreaROI
Deprecated.
 
getBoundsWidth() - Method in class qupath.lib.roi.GeometryROI
 
getBoundsWidth() - Method in interface qupath.lib.roi.interfaces.ROI
Returns the width of the ROI bounding box.
getBoundsWidth() - Method in class qupath.lib.roi.LineROI
 
getBoundsWidth() - Method in class qupath.lib.roi.PointsROI
 
getBoundsWidth() - Method in class qupath.lib.roi.PolygonROI
 
getBoundsWidth() - Method in class qupath.lib.roi.PolylineROI
 
getBoundsX() - Method in class qupath.lib.roi.EllipseROI
 
getBoundsX() - Method in class qupath.lib.roi.RectangleROI
 
getBoundsX() - Method in class qupath.lib.roi.AreaROI
Deprecated.
 
getBoundsX() - Method in class qupath.lib.roi.GeometryROI
 
getBoundsX() - Method in interface qupath.lib.roi.interfaces.ROI
Returns the x coordinate for the top left of the ROI bounding box.
getBoundsX() - Method in class qupath.lib.roi.LineROI
 
getBoundsX() - Method in class qupath.lib.roi.PointsROI
 
getBoundsX() - Method in class qupath.lib.roi.PolygonROI
 
getBoundsX() - Method in class qupath.lib.roi.PolylineROI
 
getBoundsY() - Method in class qupath.lib.roi.EllipseROI
 
getBoundsY() - Method in class qupath.lib.roi.RectangleROI
 
getBoundsY() - Method in class qupath.lib.roi.AreaROI
Deprecated.
 
getBoundsY() - Method in class qupath.lib.roi.GeometryROI
 
getBoundsY() - Method in interface qupath.lib.roi.interfaces.ROI
Returns the y coordinate for the top left of the ROI bounding box.
getBoundsY() - Method in class qupath.lib.roi.LineROI
 
getBoundsY() - Method in class qupath.lib.roi.PointsROI
 
getBoundsY() - Method in class qupath.lib.roi.PolygonROI
 
getBoundsY() - Method in class qupath.lib.roi.PolylineROI
 
getBuilder() - Method in class qupath.lib.images.servers.AbstractImageServer
 
getBuilder() - Method in interface qupath.lib.images.servers.ImageServer
Get a ServerBuilder capable of building a server the same as this one.
getBuilders() - Method in class qupath.lib.images.servers.ImageServerBuilder.UriImageSupport
Get a list of ServerBuilders, one for each image that can be read based on the specified URI.
getByIndex(int) - Method in interface qupath.lib.measurements.MeasurementList
Get an immutable representation of a single measurement.
getBytesPerPixel() - Method in enum class qupath.lib.images.servers.PixelType
Number of bytes per pixel.
getC() - Method in class qupath.lib.regions.ImagePlane
Get the channel index.
getC() - Method in class qupath.lib.roi.AreaROI
 
getC() - Method in class qupath.lib.roi.EllipseROI
 
getC() - Method in class qupath.lib.roi.GeometryROI
 
getC() - Method in class qupath.lib.roi.LineROI
 
getC() - Method in class qupath.lib.roi.PointsROI
 
getC() - Method in class qupath.lib.roi.PolygonROI
 
getC() - Method in class qupath.lib.roi.PolylineROI
 
getC() - Method in class qupath.lib.roi.RectangleROI
 
getC() - Method in interface qupath.lib.roi.interfaces.ROI
Get channel index, or -1 if the ROI relates to all available channels.
getCache() - Method in class qupath.lib.images.servers.AbstractImageServer
Get the internal cache.
getCache(Class<T>) - Static method in class qupath.lib.images.servers.ImageServerProvider
Get the cache in use for image tiles of a specific type.
getCachedColor(int, int, int) - Static method in class qupath.lib.color.ColorToolsAwt
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.color.ColorToolsAwt
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.color.ColorToolsAwt
Get cached color.
getCachedColor(Integer, boolean) - Static method in class qupath.lib.color.ColorToolsAwt
Get cached color, explicitly stating whether alpha should be included or not.
getCachedTile(TileRequest) - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer
 
getCachedTile(TileRequest) - Method in class qupath.lib.images.servers.AbstractImageServer
Get a cached tile, or null if the tile has not been cached.
getCachedTile(TileRequest) - Method in interface qupath.lib.images.servers.ImageServer
Get a cached tile, or null if the tile has not been cached.
getCaseID() - Method in class qupath.lib.objects.TMACoreObject
Get the case ID metadata value.
getCellObjects() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get all cell objects in the hierarchy.
getCellsForROI(ROI) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get all the cell objects with centroids falling within the specified ROI.
getCellSubdivision(ImagePlane) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get a subdivision containing cell objects.
getCentroidDistance(ROI, ROI) - Static method in class qupath.lib.roi.RoiTools
Get the Euclidean distance between the centroids of two ROIs.
getCentroidDistance(ROI, ROI, double, double) - Static method in class qupath.lib.roi.RoiTools
Get the calibrated Euclidean distance between the centroids of two ROIs using specified pixel sizes.
getCentroidX() - Method in class qupath.lib.roi.EllipseROI
 
getCentroidX() - Method in class qupath.lib.roi.RectangleROI
 
getCentroidX() - Method in class qupath.lib.roi.AreaROI
Deprecated.
Get the x coordinate of the ROI centroid;
getCentroidX() - Method in class qupath.lib.roi.GeometryROI
 
getCentroidX() - Method in interface qupath.lib.roi.interfaces.ROI
Returns the x coordinate for the ROI centroid.
getCentroidX() - Method in class qupath.lib.roi.LineROI
 
getCentroidX() - Method in class qupath.lib.roi.PointsROI
 
getCentroidX() - Method in class qupath.lib.roi.PolygonROI
 
getCentroidX() - Method in class qupath.lib.roi.PolylineROI
The centroid for a Polyline here is represented by the centroid of its bounding box.
getCentroidY() - Method in class qupath.lib.roi.EllipseROI
 
getCentroidY() - Method in class qupath.lib.roi.RectangleROI
 
getCentroidY() - Method in class qupath.lib.roi.AreaROI
Deprecated.
Get the y coordinate of the ROI centroid;
getCentroidY() - Method in class qupath.lib.roi.GeometryROI
 
getCentroidY() - Method in interface qupath.lib.roi.interfaces.ROI
Returns the y coordinate for the ROI centroid.
getCentroidY() - Method in class qupath.lib.roi.LineROI
 
getCentroidY() - Method in class qupath.lib.roi.PointsROI
 
getCentroidY() - Method in class qupath.lib.roi.PolygonROI
 
getCentroidY() - Method in class qupath.lib.roi.PolylineROI
The centroid for a Polyline here is represented by the centroid of its bounding box.
getChangedObjects() - Method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent
The objects that were affected by whichever changes were made.
getChannel() - Method in class qupath.lib.analysis.images.ContourTracing.ChannelThreshold
Get the channel to threshold.
getChannel(int) - Method in class qupath.lib.images.servers.AbstractImageServer
 
getChannel(int) - Method in interface qupath.lib.images.servers.ImageServer
Request information for one channel (0-based index).
getChannel(int) - Method in class qupath.lib.images.servers.ImageServerMetadata
Get the specified channel.
getChannelIndex(ImageServer<?>, String) - Static method in class qupath.lib.images.servers.ServerTools
Get the index of the first channel of a server with a specified channel name.
getChannelList(String...) - Static method in class qupath.lib.images.servers.ImageChannel
Convert an array of channel names into a list of ImageChannel using default colors.
getChannels() - Method in class qupath.lib.images.servers.ImageServerMetadata
Get an unmodifiable list of all channels.
getChannelType() - Method in class qupath.lib.images.servers.ImageServerMetadata
Get the channel type, which can be used to interpret the channels.
getCheckpoints() - Method in class qupath.lib.common.Timeit
Get an list of all the checkpoints.
getChildObjects() - Method in class qupath.lib.objects.PathObject
Get a collection of child objects.
getChildObjects(Collection<PathObject>) - Method in class qupath.lib.objects.PathObject
Get a collection containing all child objects.
getChildObjectsAsArray() - Method in class qupath.lib.objects.PathObject
Get a defensive copy of child objects as an array.
getChoiceParameterValue(String) - Method in class qupath.lib.plugins.parameters.ParameterList
Get a choice parameter value (or its default) for the specified key.
getChoices() - Method in class qupath.lib.plugins.parameters.ChoiceParameter
Get a list of available choices.
getCircularity(ROI) - Static method in class qupath.lib.roi.RoiTools
Get circularity measurement for Area ROIs, calculated as 4 * PI * (area / perimeter^2).
getCircularity(ROI, double, double) - Static method in class qupath.lib.roi.RoiTools
Get circularity measurement for area ROIs, with optional pixel calibration, calculated as 4 * PI * (area / perimeter^2).
getClassification() - Method in class qupath.lib.objects.PathObject
Convenience method to get a string representation of the classification (PathClass).
getClassificationLabels() - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata
Map between integer labels and classifications.
getClassificationLabels() - Method in class qupath.lib.images.servers.ImageServerMetadata
Get map between labels and classification names.
getClassifications() - Method in class qupath.lib.objects.PathObject
Get the components of the PathClass as an unmodifiable set.
getClassifier() - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer
Get the PixelClassifier performing the classification.
getClassProbability() - Method in class qupath.lib.objects.PathObject
Request the classification probability, or Double.NaN if no probability is available.
getClassProbability() - Method in class qupath.lib.objects.PathROIObject
 
getClassProbability() - Method in class qupath.lib.objects.PathRootObject
 
getClusters(BiPredicate<PathObject, PathObject>) - Method in class qupath.lib.analysis.DelaunayTools.Subdivision
Get clusters of connected objects, where connections are made between neighboring objects that meet the specified predicate.
getColor() - Method in class qupath.lib.color.StainVector
Get a Color that (roughly) corresponds to color represented by this stain vector.
getColor() - Method in class qupath.lib.images.servers.ImageChannel
Color used to display the output channel
getColor() - Method in class qupath.lib.objects.classes.PathClass
Get the color that should be used to display objects with this classification.
getColor() - Method in class qupath.lib.objects.PathObject
Return any stored color as a packed RGB value.
getColor(double, double, double) - Method in interface qupath.lib.color.ColorMaps.ColorMap
Get a packed ARGB representation of the (interpolated) color at the specified value,.
getColorDeconvolutionStains() - Method in class qupath.lib.images.ImageData
Get the stains defined for this image, or null if this is not a brightfield image suitable for color deconvolution.
getColorDeconvolutionStainsAsMap() - Method in class qupath.lib.color.ColorDeconvolutionStains
Create a map containing information on the stain vectors and maximum RGB values of this object.
getColorDeconvolutionStainsAsString(ColorDeconvolutionStains, int) - Static method in class qupath.lib.color.ColorDeconvolutionStains
Get a String representation of the stains and background.
getColorMaps() - Static method in class qupath.lib.color.ColorMaps
Get an unmodifiable map representing all the currently-available colormaps.
getColorModel() - Method in class qupath.lib.images.servers.ChannelTransformFeatureServer
 
getColors(ColorMaps.ColorMap, int, boolean) - Static method in class qupath.lib.color.ColorMaps
Get an array of packed RGB values for a specific colormap.
getColorWithOpacity(Color, double) - Static method in class qupath.lib.color.ColorToolsAwt
Get a color with a specified opacity, setting the alpha channel accordingly.
getColorWithOpacity(Integer, double) - Static method in class qupath.lib.color.ColorToolsAwt
Get a color with a specified opacity, based on the packed RGB values in an Integer.
getCompatibleObjects(ImageData<T>) - Method in class qupath.lib.classifiers.object.AbstractObjectClassifier
 
getCompatibleObjects(ImageData<T>) - Method in interface qupath.lib.classifiers.object.ObjectClassifier
Get the objects from an ImageData that are compatible with this classifier.
getCompatibleWriters(Class<T>, String) - Static method in class qupath.lib.images.writers.ImageWriterTools
Get a list of compatible ImageWriters for a specific image class.
getCompatibleWriters(ImageServer<T>, String) - Static method in class qupath.lib.images.writers.ImageWriterTools
Get a list of compatible ImageWriters compatible with a specific server.
getConnectedObjects(PathObject) - Method in class qupath.lib.objects.DefaultPathObjectConnectionGroup
Deprecated.
 
getConnectedObjects(PathObject) - Method in interface qupath.lib.objects.PathObjectConnectionGroup
Deprecated.
Get all the connections to a specified PathObject stored in this group.
getConnectionGroups() - Method in class qupath.lib.objects.PathObjectConnections
Get an unmodifiable list containing all connections groups.
getConnections(PathObject) - Method in class qupath.lib.objects.PathObjectConnections
Get all the connections to a specified PathObject.
getConvexHull() - Method in class qupath.lib.roi.AreaROI
Default implementation using JTS.
getConvexHull() - Method in class qupath.lib.roi.GeometryROI
Default implementation using JTS.
getConvexHull() - Method in class qupath.lib.roi.PolygonROI
Default implementation using JTS.
getConvexHull() - Method in class qupath.lib.roi.PolylineROI
Default implementation using JTS.
getConvexHull() - Method in class qupath.lib.roi.EllipseROI
 
getConvexHull() - Method in interface qupath.lib.roi.interfaces.ROI
Get a ROI representing the convex hull of this ROI.
getConvexHull() - Method in class qupath.lib.roi.LineROI
 
getConvexHull() - Method in class qupath.lib.roi.PointsROI
 
getConvexHull() - Method in class qupath.lib.roi.RectangleROI
 
getConvexHull(List<Point2>) - Static method in class qupath.lib.roi.ConvexHull
For implementation details, see http://en.wikipedia.org/wiki/Gift_wrapping_algorithm http://en.wikipedia.org/wiki/Graham_scan
getCountsForBin(int) - Method in class qupath.lib.analysis.stats.Histogram
Get the histogram counts for the specified bin.
getCountSum() - Method in class qupath.lib.analysis.stats.Histogram
Sum of all histogram counts.
getCreationTimestamp() - Method in interface qupath.lib.projects.Project
Request a timestamp from when the project was created.
getCropRegion() - Method in class qupath.lib.images.servers.CroppedImageServer
Get the region being cropped, in terms of the bounding box within the base ImageServer.
getCropToParent() - Method in class qupath.lib.objects.utils.Tiler
Check if the tiler is set to crop the output to the input parent.
getCurrentDataFileVersion() - Static method in class qupath.lib.io.PathIO
Get the current preferred data file version.
getDataBufferType(PixelType) - Static method in class qupath.lib.awt.common.BufferedImageTools
Get the appropriate DataBuffer type for a given PixelType.
getDefaultBuilder() - Static method in class qupath.lib.io.GsonTools
Access the builder used with GsonTools.getInstance().
getDefaultChannelColor(int) - Static method in class qupath.lib.images.servers.ImageChannel
Get the default color for a specified channel, for use when no channel colors are already known.
getDefaultChannelList(int) - Static method in class qupath.lib.images.servers.ImageChannel
Get default channel list for an image with a specified number of channels.
getDefaultColorMap() - Static method in class qupath.lib.color.ColorMaps
Get a default, general-purpose ColorMaps.ColorMap.
getDefaultColorModel() - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer
 
getDefaultColorModel() - Method in class qupath.lib.images.servers.AbstractTileableImageServer
Get an appropriate colormodel that may be used.
getDefaultColorModel() - Method in class qupath.lib.images.servers.SparseImageServer
 
getDefaultColorModel(ColorTransformer.ColorTransformMethod) - Static method in class qupath.lib.color.ColorTransformer
This does not guarantee a ColorModel will be returned! If it is not, then a default grayscale LUT should be used.
getDefaultCreateFunction() - Static method in class qupath.lib.plugins.TaskRunnerUtils
Get the default function used to create TaskRunner instances.
getDefaultExtension() - Method in interface qupath.lib.images.writers.ImageWriter
Get the default extension.
getDefaultFactory() - Static method in class qupath.lib.roi.GeometryTools
Get the default GeometryFactory to construct Geometries within QuPath.
getDefaultInstance() - Static method in class qupath.lib.images.servers.PixelCalibration
Get the default PixelCalibration.
getDefaultInstance() - Static method in class qupath.lib.plugins.TaskRunnerUtils
Get the default instance.
getDefaultParameterList(ImageData<T>) - Method in class qupath.lib.plugins.AbstractInteractivePlugin
This should return a default ParameterList containing any information that is needed to repeat the task exactly.
getDefaultParameterList(ImageData<T>) - Method in interface qupath.lib.plugins.PathInteractivePlugin
This should return a default ParameterList.
getDefaultPlane() - Static method in class qupath.lib.regions.ImagePlane
Returns an ImagePlane with channel -1, z of 0 and t of 0.
getDefaultRGBChannels() - Static method in class qupath.lib.images.servers.ImageChannel
Get default channel list for RGB images.
getDefaultShortServerName(URI) - Static method in class qupath.lib.images.servers.ServerTools
Get the default shortened server name given the server's path.
getDefaultThumbnail(int, int) - Method in class qupath.lib.images.servers.AbstractImageServer
 
getDefaultThumbnail(int, int) - Method in interface qupath.lib.images.servers.ImageServer
Get the default thumbnail for a specified z-slice and timepoint.
getDefaultTransformedMax(ColorTransformer.ColorTransformMethod) - Static method in class qupath.lib.color.ColorTransformer
Get default maximum value to use with a specific transform method.
getDefaultValue() - Method in class qupath.lib.plugins.parameters.BooleanParameter
 
getDefaultValue() - Method in class qupath.lib.plugins.parameters.ChoiceParameter
 
getDefaultValue() - Method in class qupath.lib.plugins.parameters.DoubleParameter
 
getDefaultValue() - Method in class qupath.lib.plugins.parameters.EmptyParameter
 
getDefaultValue() - Method in class qupath.lib.plugins.parameters.IntParameter
 
getDefaultValue() - Method in class qupath.lib.plugins.parameters.NumericParameter
 
getDefaultValue() - Method in class qupath.lib.plugins.parameters.StringParameter
 
getDefaultValue() - Method in interface qupath.lib.plugins.parameters.Parameter
Get a default value to use if the Parameter has not been otherwise set.
getDerivedPathClass(PathClass, String, Integer) - Static method in class qupath.lib.objects.classes.PathClassFactory
getDescendantObjects(Collection<PathObject>) - Method in class qupath.lib.objects.PathObject
Get a collection containing all descendant objects.
getDescendantObjects(PathObject, Collection<PathObject>, Class<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools
Get all descendant objects with a specified type.
getDescription() - Method in interface qupath.lib.images.servers.FileFormatInfo.ImageCheckType
Get the image description, as stored in a TIFF, or null if no description is available.
getDescription() - Method in interface qupath.lib.images.servers.ImageServerBuilder
Get a short, human-readable description for display in a GUI.
getDescription() - Method in class qupath.lib.images.servers.JsonImageServerBuilder
 
getDescription() - Method in class qupath.lib.objects.PathAnnotationObject
Get a free text description previously set for this annotation.
getDescription() - Method in interface qupath.lib.plugins.PathPlugin
Get a brief description of the plugin's purpose & operation.
getDescription() - Method in interface qupath.lib.projects.ProjectImageEntry
Get a description; this is free text describing the image.
getDetails() - Method in interface qupath.lib.images.writers.ImageWriter
Get further details of the writer, which may be displayed to a user.
getDetails() - Method in class qupath.lib.images.writers.JpegWriter
 
getDetails() - Method in class qupath.lib.images.writers.PngWriter
 
getDetectionObjects() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get all detection objects in the hierarchy (including sub-classes of detections).
getDetectionSubdivision(ImagePlane) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get a subdivision containing detections.
getDisplayableImageName(ImageServer<?>) - Static method in class qupath.lib.images.servers.ServerTools
Get an ImageServer name suitable for displaying.
getDisplayedName() - Method in class qupath.lib.objects.PathObject
Request an object name in a form suitable for displaying.
getDouble(int) - Method in interface qupath.lib.analysis.stats.ArrayWrappers.ArrayWrapper
Extract one entry from the array, converting to double as necessary.
getDoubleParameterValue(String) - Method in class qupath.lib.plugins.parameters.ParameterList
Get a double parameter value (or its default) for the specified key.
getDownsample() - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel
Get the downsample factor for this level.
getDownsample() - Method in class qupath.lib.images.servers.TileRequest
Get the downsample value for this tile.
getDownsample() - Method in class qupath.lib.regions.RegionRequest
Get the requested downsample factor, defining the resolution at which pixels should be returned.
getDownsample(ImageServer<?>, ImageRegion) - Method in interface qupath.lib.images.servers.downsamples.DownsampleCalculator
Calculate the downsample value to use when requesting a region from the server.
getDownsampleFactor() - Method in interface qupath.lib.images.PathImage
Get the downsample factor originally used when obtaining the image from an ImageServer; will be 1 if the image is full-resolution.
getDownsampleFactor(ImageServer<?>, double) - Static method in class qupath.lib.images.servers.ServerTools
Calculate a downsample factor for a server given a preferred pixel size.
getDownsampleForLevel(int) - Method in class qupath.lib.images.servers.ImageServerMetadata
Get the downsample factor for a specific resolution level.
getDownsampleForResolution(int) - Method in class qupath.lib.images.servers.AbstractImageServer
 
getDownsampleForResolution(int) - Method in interface qupath.lib.images.servers.ImageServer
Get the downsample factor for a specified resolution level, where level 0 is the full resolution image and nResolutions() - 1 is the lowest resolution available.
getDummyColorModel(int) - Static method in class qupath.lib.color.ColorModelFactory
Get a dummy ColorModel instance.
getEdgeMax() - Method in class qupath.lib.analysis.stats.Histogram
Get the maximum edge of the histogram.
getEdgeMin() - Method in class qupath.lib.analysis.stats.Histogram
Get the minimum edge of the histogram.
getEdgeRange() - Method in class qupath.lib.analysis.stats.Histogram
Get the histogram edge range, defined as the maximum edge - the minimum edge.
getEmptyTile(int, int) - Method in class qupath.lib.images.servers.AbstractTileableImageServer
 
getEmptyTile(int, int, boolean) - Method in class qupath.lib.images.servers.AbstractTileableImageServer
Create an empty tile for this server, using the default color model.
getEntry(ImageData<T>) - Method in interface qupath.lib.projects.Project
Request a ProjectImageEntry associated with an ImageData
getEntryPath() - Method in interface qupath.lib.projects.ProjectImageEntry
Get a path to the data for this image entry, or null if this entry is not stored on the local file system.
getEventCount() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get the number of events that were fired.
getEvents() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData
Get an unmodifiable list of all events.
getEventsAtTime(double) - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData
Get the number of events at a specified time (exactly).
getEventType() - Method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent
Get the hierarchy event type.
getExtension(File) - Static method in class qupath.lib.common.GeneralTools
Get filename extension.
getExtension(String) - Static method in class qupath.lib.common.GeneralTools
Get extension from a filename.
getExtensions() - Method in interface qupath.lib.images.writers.ImageWriter
Get the file extensions used by the image writer.
getExtensions() - Method in class qupath.lib.images.writers.JpegWriter
 
getExtensions() - Method in class qupath.lib.images.writers.PngWriter
 
getFile() - Method in interface qupath.lib.images.servers.FileFormatInfo.ImageCheckType
Get a File object representing the local image file - or null if no file could be found.
getFilterByCentroid() - Method in class qupath.lib.objects.utils.Tiler
Check if the tiler will filter the output based on whether the centroid of tiles lies within the parent
getFilteredNeighbors(BiPredicate<PathObject, PathObject>) - Method in class qupath.lib.analysis.DelaunayTools.Subdivision
Get a list of neighbors for all objects, filtering out objects that do not meet specified criteria.
getFilteredNeighbors(PathObject, BiPredicate<PathObject, PathObject>) - Method in class qupath.lib.analysis.DelaunayTools.Subdivision
Get a list of neighbors for a specified object, filtering out objects that do not meet specified criteria.
getFlattenedObjectList(List<PathObject>) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get a flattened list containing all PathObjects in the hierarchy (including from the root object).
getFlattenedObjectList(PathObject, List<PathObject>, boolean) - Static method in class qupath.lib.objects.PathObjectTools
Get all descendant objects as a flattened list.
getGeometry() - Method in class qupath.lib.roi.EllipseROI
 
getGeometry() - Method in class qupath.lib.roi.LineROI
 
getGeometry() - Method in class qupath.lib.roi.PointsROI
 
getGeometry() - Method in class qupath.lib.roi.PolylineROI
 
getGeometry() - Method in class qupath.lib.roi.RectangleROI
 
getGeometry() - Method in class qupath.lib.roi.AreaROI
Deprecated.
 
getGeometry() - Method in class qupath.lib.roi.GeometryROI
 
getGeometry() - Method in interface qupath.lib.roi.interfaces.ROI
Returns a org.locationtech.jts.geom.Geometry object.
getGeometry() - Method in class qupath.lib.roi.PolygonROI
 
getGreen() - Method in class qupath.lib.color.StainVector
Get the green component of the (normalized) stain vector.
getGreenOpticalDensities(int[], double, float[]) - Static method in class qupath.lib.color.ColorDeconvolutionHelper
Convert red channel of packed rgb pixel to optical density values, using a specified maximum value.
getGridHeight() - Method in class qupath.lib.objects.hierarchy.DefaultTMAGrid
 
getGridHeight() - Method in interface qupath.lib.objects.hierarchy.TMAGrid
Number of cores along the vertical axis of the grid.
getGridWidth() - Method in class qupath.lib.objects.hierarchy.DefaultTMAGrid
 
getGridWidth() - Method in interface qupath.lib.objects.hierarchy.TMAGrid
Number of cores along the horizontal axis of the grid.
getHandles() - Method in class qupath.lib.roi.RoiEditor
Get all the handles for the current ROI being edited, or an empty list if no handles are available.
getHazardRatio() - Method in class qupath.lib.analysis.stats.survival.LogRankTest.LogRankResult
Get the calculated hazard ratio.
getHazardRatioLowerConfidence() - Method in class qupath.lib.analysis.stats.survival.LogRankTest.LogRankResult
Get the lower bound of the hazard ratio confidence interval.
getHazardRatioUpperConfidence() - Method in class qupath.lib.analysis.stats.survival.LogRankTest.LogRankResult
Get the upper bound of the hazard ratio confidence interval.
getHeight() - Method in interface qupath.lib.analysis.images.SimpleImage
Get the image height.
getHeight() - Method in class qupath.lib.geom.ImmutableDimension
Get the ImmutableDimension height.
getHeight() - Method in class qupath.lib.images.servers.AbstractImageServer
 
getHeight() - Method in interface qupath.lib.images.servers.ImageServer
Height of the full-resolution image in pixels.
getHeight() - Method in class qupath.lib.images.servers.ImageServerMetadata
Get the full-resolution image height.
getHeight() - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel
Get the image height at this level.
getHeight() - Method in class qupath.lib.regions.ImageRegion
Get the height of the region bounding box.
getHelpText() - Method in class qupath.lib.plugins.parameters.BooleanParameter
 
getHelpText() - Method in class qupath.lib.plugins.parameters.ChoiceParameter
 
getHelpText() - Method in class qupath.lib.plugins.parameters.DoubleParameter
 
getHelpText() - Method in class qupath.lib.plugins.parameters.EmptyParameter
 
getHelpText() - Method in class qupath.lib.plugins.parameters.IntParameter
 
getHelpText() - Method in class qupath.lib.plugins.parameters.NumericParameter
 
getHelpText() - Method in class qupath.lib.plugins.parameters.StringParameter
 
getHelpText() - Method in interface qupath.lib.plugins.parameters.Parameter
Get a description of the meaning of the Parameter; may be displayed e.g.
getHierarchy() - Method in class qupath.lib.images.ImageData
Get the object hierarchy.
getHierarchy() - Method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent
The hierarchy to which this event refers.
getHistoryWorkflow() - Method in class qupath.lib.images.ImageData
Get a workflow representing a history of the processing steps applied to the ImageData.
getID() - Method in class qupath.lib.objects.PathObject
Get the ID for this object.
getID() - Method in interface qupath.lib.projects.ProjectImageEntry
Get a unique ID to represent this entry.
getImage() - Method in interface qupath.lib.images.PathImage
Get the pixel data (image).
getImageClass() - Method in class qupath.lib.images.servers.AbstractImageServer
 
getImageClass() - Method in interface qupath.lib.images.servers.ImageServer
Get the class of the image representation returned by this ImageServer.
getImageClass() - Method in class qupath.lib.images.writers.JpegWriter
 
getImageClass() - Method in class qupath.lib.images.writers.PngWriter
 
getImageClass() - Method in interface qupath.lib.images.writers.ImageWriter
Get the class of supported images.
getImageData() - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer
Get the underlying ImageData used for classification.
getImageHeight() - Method in class qupath.lib.images.servers.TileRequest
Get the height of the bounding box for this tile in the full resolution image.
getImageList() - Method in interface qupath.lib.projects.Project
Get a list of image entries for the project.
getImageName() - Method in interface qupath.lib.projects.ProjectImageEntry
Get a name that may be used for this entry.
getImagePlane() - Method in class qupath.lib.analysis.DelaunayTools.Subdivision
Get the ImagePlane for this subdivision.
getImagePlane() - Method in class qupath.lib.images.servers.TileRequest
Get the ImagePlane for this request.
getImagePlane() - Method in class qupath.lib.regions.ImageRegion
Get the z-slice and time point for this region as an ImagePlane.
getImagePlane() - Method in class qupath.lib.roi.AreaROI
 
getImagePlane() - Method in class qupath.lib.roi.EllipseROI
 
getImagePlane() - Method in class qupath.lib.roi.GeometryROI
 
getImagePlane() - Method in class qupath.lib.roi.LineROI
 
getImagePlane() - Method in class qupath.lib.roi.PointsROI
 
getImagePlane() - Method in class qupath.lib.roi.PolygonROI
 
getImagePlane() - Method in class qupath.lib.roi.PolylineROI
 
getImagePlane() - Method in class qupath.lib.roi.RectangleROI
 
getImagePlane() - Method in interface qupath.lib.roi.interfaces.ROI
Get the ImagePlane, which contains the values for c, z and t in a single object.
getImageRegion() - Method in interface qupath.lib.images.PathImage
The region within the (original, possibly larger) image that this particular image corresponds to.
getImageRegion(Rectangle, int, int) - Static method in class qupath.lib.awt.common.AwtTools
Create an ImageRegion corresponding to a specified Rectangle bounding box.
getImageRegion(Shape, int, int) - Static method in class qupath.lib.awt.common.AwtTools
Create an ImageRegion corresponding to a the bounding box of a Shape.
getImages() - Method in interface qupath.lib.projects.ProjectImageEntry
Access additional images associated with the project entry, e.g.
getImageServerTypeAdapterFactory(boolean) - Static method in class qupath.lib.images.servers.ImageServers
Get a TypeAdapterFactory for ImageServers, optionally including metadata in the serialized form of the server.
getImageSupport(URI, String...) - Static method in class qupath.lib.images.servers.ImageServers
Get the ImageServerBuilder.UriImageSupport that is best able to open the specified image with optional args.
getImageSupport(ImageServerBuilder<BufferedImage>, URI, String...) - Static method in class qupath.lib.images.servers.ImageServers
Get the ImageServerBuilder.UriImageSupport associated with an ImageServerBuilder, or null if the builder does not support the image.
getImageType() - Method in class qupath.lib.images.ImageData
Get the image type
getImageType() - Method in interface qupath.lib.images.servers.ImageServerBuilder
Returns the base class for the images supported by this server.
getImageType() - Method in class qupath.lib.images.servers.JsonImageServerBuilder
 
getImageWidth() - Method in class qupath.lib.images.servers.TileRequest
Get the width of the bounding box for this tile in the full resolution image.
getImageX() - Method in class qupath.lib.images.servers.TileRequest
Get the x-coordinate of the bounding box for this tile in the full resolution image.
getImageY() - Method in class qupath.lib.images.servers.TileRequest
Get the y-coordinate of the bounding box for this tile in the full resolution image.
getIncludeChildren() - Method in class qupath.lib.io.FeatureCollection
If true, include child objects nested within the output.
getIndexColorModel(StainVector) - Static method in class qupath.lib.color.ColorToolsAwt
Create an IndexColorModel, ranging from white (low values) to a stain vector color (high values).
getIndexColorModel(StainVector, boolean) - Static method in class qupath.lib.color.ColorToolsAwt
Get an IndexColorModel representing a color deconvolution stain.
getIndexedClassificationColorModel(Map<Integer, PathClass>) - Static method in class qupath.lib.color.ColorModelFactory
Get a ColorModel suitable for showing output pixel classifications, using an 8-bit or 16-bit labeled image.
getInputHeight() - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata
Requested height of input image, or -1 if the classifier is not fussy
getInputNumChannels() - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata
Requested number of channels in input image; default is 3 (consistent with assuming RGB)
getInputPadding() - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata
Requested input padding (above, below, left and right).
getInputResolution() - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata
Requested pixel size for input.
getInputWidth() - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata
Requested width of input image, or -1 if the classifier is not fussy
getInstalledImageServerBuilders() - Static method in class qupath.lib.images.servers.ImageServerProvider
Request all available ImageServerBuilders.
getInstalledImageServerBuilders(Class<T>) - Static method in class qupath.lib.images.servers.ImageServerProvider
Request all available ImageServerBuilders supporting a given image class.
getInstance() - Static method in class qupath.lib.io.GsonTools
Get default Gson instance, capable of serializing/deserializing some key QuPath classes.
getInstance() - Static method in class qupath.lib.objects.DefaultPathObjectComparator
Get shared comparator instance to sort PathObjects repeatably.
getInstance() - Static method in class qupath.lib.roi.DefaultROIComparator
Get a static instance of this comparator, to avoid needing to construct it.
getInstance(boolean) - Static method in class qupath.lib.io.GsonTools
Get default Gson, optionally with pretty printing enabled.
getInstance(int, int) - Static method in class qupath.lib.geom.ImmutableDimension
Get an ImmutableDimension representing the specified width and height.
getInstance(String) - Static method in class qupath.lib.objects.classes.PathClass
 
getInstance(String, Integer) - Static method in class qupath.lib.images.servers.ImageChannel
Get a channel instance with the specified name and color.
getInstance(String, Integer) - Static method in class qupath.lib.objects.classes.PathClass
Get a base PathClass instance, without any parent PathClass.
getInstance(PathClass, String, Integer) - Static method in class qupath.lib.objects.classes.PathClass
Get a derived PathClass instance with the specified parent.
getInstanceLabels() - Method in class qupath.lib.images.servers.LabeledImageServer
Get a mapping between objects and instance labels.
getIntParameterValue(String) - Method in class qupath.lib.plugins.parameters.ParameterList
Get a integer parameter value (or its default) for the specified key.
getItems(UriUpdater.UriStatus) - Method in class qupath.lib.io.UriUpdater
Get all items with the specified status, or all items is status is null.
getKeyValueParameters(boolean) - Method in class qupath.lib.plugins.parameters.ParameterList
Returns a map of keys and their corresponding parameter values
getLabels() - Method in class qupath.lib.images.servers.LabeledImageServer
Get an unmodifiable map of classifications and their corresponding labels.
getLargestImageHeight() - Method in interface qupath.lib.images.servers.FileFormatInfo.ImageCheckType
Get the height of the largest image, if known.
getLargestImageWidth() - Method in interface qupath.lib.images.servers.FileFormatInfo.ImageCheckType
Get the width of the largest image, if known.
getLastResultsDescription() - Method in interface qupath.lib.plugins.ObjectDetector
Get a String summarizing the result, which may be displayed to a user or logged.
getLastResultsDescription() - Method in interface qupath.lib.plugins.PathPlugin
(Optional) short one-line description of the results, e.g.
getLastResultsDescription() - Method in interface qupath.lib.plugins.PathTask
Get a description of the results from running this task, which may be used e.g.
getLastSavedPath() - Method in class qupath.lib.images.ImageData
Get the last path used to save this object;
getLastStep() - Method in class qupath.lib.plugins.workflow.Workflow
Get the last WorkflowStep in the workflow, or null if no steps are available.
getLength() - Method in class qupath.lib.roi.EllipseROI
 
getLength() - Method in class qupath.lib.roi.RectangleROI
 
getLength() - Method in class qupath.lib.roi.AreaROI
Deprecated.
 
getLength() - Method in class qupath.lib.roi.GeometryROI
 
getLength() - Method in interface qupath.lib.roi.interfaces.ROI
Get ROI length.
getLength() - Method in class qupath.lib.roi.LineROI
 
getLength() - Method in class qupath.lib.roi.PointsROI
 
getLength() - Method in class qupath.lib.roi.PolygonROI
 
getLength() - Method in class qupath.lib.roi.PolylineROI
 
getLevel() - Method in class qupath.lib.images.servers.TileRequest
Get the resolution level.
getLevel() - Method in class qupath.lib.objects.PathObject
The level of the object in a hierarchy.
getLevel(int) - Method in class qupath.lib.images.servers.ImageServerMetadata
Get resolution information for a specified pyramidal level.
getLevels() - Method in class qupath.lib.images.servers.ImageServerMetadata
Get an unmodifiable list containing the resolution levels
getLineObjects(Collection<T>) - Static method in class qupath.lib.objects.PathObjectTools
Get a list of objects with line ROIs from a collection of objects.
getLoggableParameters(ImageData<T>) - Method in class qupath.lib.plugins.AbstractInteractivePlugin
Get a copy of the current parameter list (with empty parameters removed) suitable for logging.
getLowerBound() - Method in enum class qupath.lib.images.servers.PixelType
Get a number representing the minimum value permitted by this type (may be negative).
getLowerBound() - Method in class qupath.lib.plugins.parameters.NumericParameter
Retrieve the lower bound.
getMagnification() - Method in class qupath.lib.images.servers.ImageServerMetadata
Get the magnification value, or Double.NaN if this is unavailable.
getMajor() - Method in class qupath.lib.common.Version
Get the major version number (X.0.0).
getManager() - Method in class qupath.lib.images.servers.SparseImageServer
Get the manager, which defines from whence the regions originate.
getMaskImageNames() - Method in interface qupath.lib.projects.Project
Query whether 'true' or masked image names are being returned.
getMatrixInverse() - Method in class qupath.lib.color.ColorDeconvolutionStains
Get matrix inverse, as useful for color deconvolution.
getMax() - Method in class qupath.lib.analysis.stats.RunningStatistics
Get the maximum non-NaN value added.
getMaxBlue() - Method in class qupath.lib.color.ColorDeconvolutionStains
Get the maximum value for the blue channel (default = 255).
getMaxCount() - Method in class qupath.lib.analysis.stats.Histogram
Get the highest count found for any bin.
getMaxDecimalPlaces() - Method in class qupath.lib.common.Timeit
Get the maximum number of decimal places when reporting timings.
getMaxGreen() - Method in class qupath.lib.color.ColorDeconvolutionStains
Get the maximum value for the green channel (default = 255).
getMaxNormalizedCount() - Method in class qupath.lib.analysis.stats.Histogram
Get the highest count found for any bin, divided by the total counts across the entire histogram.
getMaxRed() - Method in class qupath.lib.color.ColorDeconvolutionStains
Get the maximum value for the red channel (default = 255).
getMaxThreshold() - Method in class qupath.lib.analysis.images.ContourTracing.ChannelThreshold
Get the maximum threshold value.
getMaxTime() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData
Get the time of the last event, or -1 if there are no events.
getMaxValue() - Method in class qupath.lib.analysis.stats.Histogram
Get the maximum of all the values being histogrammed.
getMaxValue() - Method in class qupath.lib.images.servers.ImageServerMetadata
Get the minimum value supported by this image.
getMaxX() - Method in class qupath.lib.regions.ImageRegion
Get the x coordinate of the bottom right of the region bounding box.
getMaxY() - Method in class qupath.lib.regions.ImageRegion
Get the y coordinate of the bottom right of the region bounding box.
getMean() - Method in class qupath.lib.analysis.stats.RunningStatistics
Get the mean of all non-NaN values that were added.
getMeanValue() - Method in class qupath.lib.analysis.stats.Histogram
Get the mean of all the values being histogrammed.
getMeasurementList() - Method in class qupath.lib.objects.PathObject
Retrieve the list stored measurements for the object.
getMeasurementNames() - Method in interface qupath.lib.measurements.MeasurementList
Deprecated.
v0.6.0 use MeasurementList.getNames() instead
getMeasurements() - Method in interface qupath.lib.measurements.MeasurementList
Get an unmodifiable list of all measurements.
getMeasurements() - Method in class qupath.lib.objects.PathObject
Get a map-based view on PathObject.getMeasurementList().
getMeasurementValues(Collection<PathObject>, String) - Static method in class qupath.lib.analysis.stats.Histogram
Extract a specific measurement for each PathObject in a collection, storing the result in an array.
getMedian(float[]) - Static method in class qupath.lib.color.ColorDeconvolutionHelper
Get the median value from a float array.
getMedianRGB(int[]) - Static method in class qupath.lib.color.ColorDeconvolutionHelper
Determine median of RGB values.
getMetadata() - Method in interface qupath.lib.classifiers.pixel.PixelClassifier
Get metadata that describes how the classifier should be called, and the kind of output it provides.
getMetadata() - Method in class qupath.lib.images.servers.AbstractImageServer
 
getMetadata() - Method in interface qupath.lib.images.servers.ImageServer
Get essential metadata associated with the ImageServer as a distinct object.
getMetadata() - Method in class qupath.lib.images.servers.ImageServerBuilder.AbstractServerBuilder
 
getMetadata() - Method in interface qupath.lib.images.servers.ImageServerBuilder.ServerBuilder
Optional method to get metadata associated with the image.
getMetadata() - Method in interface qupath.lib.interfaces.MinimalMetadataStore
Returns a modifiable map containing the metadata.
getMetadata() - Method in class qupath.lib.objects.PathObject
Get a key/value pair map for object metadata.
getMetadataKeys() - Method in interface qupath.lib.objects.MetadataStore
Deprecated.
as of v0.6.0. Use MinimalMetadataStore.getMetadata() with the Map.keySet() method instead
getMetadataKeys() - Method in class qupath.lib.objects.TMACoreObject
Deprecated.
v0.6.0. Use PathObject.getMetadata() to directly access metadata instead.
getMetadataKeys() - Method in interface qupath.lib.projects.ProjectImageEntry
Deprecated.
v0.6.0, use MinimalMetadataStore.getMetadata() instead to directly access the metadata.
getMetadataMap() - Method in interface qupath.lib.objects.MetadataStore
Deprecated.
getMetadataMap() - Method in interface qupath.lib.projects.ProjectImageEntry
Deprecated.
v0.6.0, use MinimalMetadataStore.getMetadata() instead to directly access the metadata.
getMetadataString(String) - Method in interface qupath.lib.objects.MetadataStore
Deprecated.
as of v0.6.0. Use MinimalMetadataStore.getMetadata() with the Map.get(Object) method instead
getMetadataString(String) - Method in class qupath.lib.objects.TMACoreObject
Deprecated.
v0.6.0. Use PathObject.getMetadata() to directly access metadata instead.
getMetadataSummaryString() - Method in interface qupath.lib.projects.ProjectImageEntry
Get a formatted string representation of the metadata map's contents.
getMetadataValue(String) - Method in interface qupath.lib.objects.MetadataStore
Deprecated.
as of v0.6.0. Use MinimalMetadataStore.getMetadata() with the Map.get(Object) method instead
getMetadataValue(String) - Method in class qupath.lib.objects.TMACoreObject
Deprecated.
v0.6.0. Use PathObject.getMetadata() to directly access metadata instead.
getMetadataValue(String) - Method in interface qupath.lib.projects.ProjectImageEntry
Deprecated.
v0.6.0, use MinimalMetadataStore.getMetadata() instead to directly access the metadata.
getMin() - Method in class qupath.lib.analysis.stats.RunningStatistics
Get the minimum non-NaN value added.
getMinor() - Method in class qupath.lib.common.Version
Get the minor version number (0.X.0).
getMinThreshold() - Method in class qupath.lib.analysis.images.ContourTracing.ChannelThreshold
Get the minimum threshold value.
getMinValue() - Method in class qupath.lib.analysis.stats.Histogram
Get the minimum of all the values being histogrammed.
getMinValue() - Method in class qupath.lib.images.servers.ImageServerMetadata
Get the minimum value supported by this image.
getMinX() - Method in class qupath.lib.regions.ImageRegion
Get the x coordinate of the top left of the region bounding box.
getMinY() - Method in class qupath.lib.regions.ImageRegion
Get the y coordinate of the top left of the region bounding box.
getMissingFeatures(ImageData<T>, Collection<? extends PathObject>) - Method in interface qupath.lib.classifiers.object.ObjectClassifier
Check for missing features, returning the names and number of input objects missing the specified features.
getMissingItems() - Method in class qupath.lib.io.UriUpdater
Get all missing items.
getModificationTimestamp() - Method in interface qupath.lib.projects.Project
Request a timestamp from when the project was last synchronized.
getMoreTranslucentColor(Color) - Static method in class qupath.lib.color.ColorToolsAwt
Get a (slightly more) translucent version of the specified color.
getName() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData
Get the name of this data, generally used for display.
getName() - Method in class qupath.lib.color.ColorDeconvolutionStains
Get the stains name.
getName() - Method in interface qupath.lib.color.ColorMaps.ColorMap
Get the name of the colormap.
getName() - Method in class qupath.lib.color.StainVector
Returns the name of the stain vector.
getName() - Method in class qupath.lib.common.Timeit.Checkpoint
Get the checkpoint name.
getName() - Method in interface qupath.lib.images.servers.ColorTransforms.ColorTransform
Get a displayable name for the transform.
getName() - Method in class qupath.lib.images.servers.ImageChannel
Name of the output channel.
getName() - Method in interface qupath.lib.images.servers.ImageServerBuilder
Get a human-readable name for the kind of ImageServer this builds.
getName() - Method in class qupath.lib.images.servers.ImageServerMetadata
Get the image name.
getName() - Method in class qupath.lib.images.servers.JsonImageServerBuilder
 
getName() - Method in interface qupath.lib.images.writers.ImageWriter
Get the name of the image writer.
getName() - Method in class qupath.lib.images.writers.JpegWriter
 
getName() - Method in class qupath.lib.images.writers.PngWriter
 
getName() - Method in interface qupath.lib.measurements.Measurement
Get the name of the measurement.
getName() - Method in class qupath.lib.objects.classes.PathClass
Get the name of this classification.
getName() - Method in class qupath.lib.objects.PathObject
Request the stored object name.
getName() - Method in interface qupath.lib.plugins.PathPlugin
Get the name of the plugin for display.
getName() - Method in class qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep
 
getName() - Method in class qupath.lib.plugins.workflow.RunSavedClassifierWorkflowStep
 
getName() - Method in class qupath.lib.plugins.workflow.SimplePluginWorkflowStep
 
getName() - Method in interface qupath.lib.plugins.workflow.WorkflowStep
Get the name of the workflow step.
getName() - Method in interface qupath.lib.projects.Project
Get the name of the project.
getNameFromURI(URI) - Static method in interface qupath.lib.projects.Project
Extract a usable project name from a URI.
getNames() - Method in interface qupath.lib.measurements.MeasurementList
Get the names of all measurements currently in the list.
getNames() - Method in interface qupath.lib.projects.ResourceManager.Manager
Get a list of the available resources.
getNameWithoutExtension(File) - Static method in class qupath.lib.common.GeneralTools
Get the file name with extension removed.
getNameWithoutExtension(String) - Static method in class qupath.lib.common.GeneralTools
Deprecated.
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.
getNanoseconds() - Method in class qupath.lib.common.Timeit.Checkpoint
Get the checkpoint timestamp in nanoseconds.
getNearest(double, double, double) - Method in class qupath.lib.roi.PointsROI
Identify the closest point within a specified distance to coordinates x,y - or null if no points are found.
getNearestNeighbor(PathObject) - Method in class qupath.lib.analysis.DelaunayTools.Subdivision
Get the nearest neighbor for the specified object.
getNearestNeighbor(PathObject, BiPredicate<PathObject, PathObject>) - Method in class qupath.lib.analysis.DelaunayTools.Subdivision
Get the nearest neighbor for the specified object, filtered by a predicate.
getNegative(PathClass) - Static method in class qupath.lib.objects.classes.PathClass
Get a standalone or derived Negative classification
getNegative(PathClass) - Static method in class qupath.lib.objects.classes.PathClassFactory
Deprecated.
getNeighbors(PathObject) - Method in class qupath.lib.analysis.DelaunayTools.Subdivision
Get all neighbors for a specified object.
getNonIntensityAncestorClass(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools
Get the first ancestor class that is not an intensity class (i.e.
getNormalizedCountsForBin(int) - Method in class qupath.lib.analysis.stats.Histogram
Get the normalized histogram count for the specified bin.
getNormalizerFactory() - Static method in class qupath.lib.images.servers.ImageServers
Get a TypeAdapterFactory to handle BufferedImageNormalizers.
getNucleusOrMainROI(PathObject) - Static method in class qupath.lib.objects.PathObjectTools
Get the nucleus ROI for a cell, or the main ROI if no nucleus is found.
getNucleusROI() - Method in class qupath.lib.objects.PathCellObject
Get the nucleus ROI for this cell.
getNucleusROI(PathObject) - Static method in class qupath.lib.objects.PathObjectTools
Get the nucleus ROI for a cell, or null if the input is not a cell or no nucleus is found.
getNullClass() - Static method in class qupath.lib.objects.classes.PathClass
Get the value of PathClass.NULL_CLASS, used to represent no classification.
getNumNaNs() - Method in class qupath.lib.analysis.stats.RunningStatistics
Get count of the number of NaN values added.
getNumPoints() - Method in class qupath.lib.roi.AreaROI
Default implementation, calls ROI.getAllPoints() and then caches the result.
getNumPoints() - Method in class qupath.lib.roi.GeometryROI
Default implementation, calls ROI.getAllPoints() and then caches the result.
getNumPoints() - Method in class qupath.lib.roi.PolygonROI
Default implementation, calls ROI.getAllPoints() and then caches the result.
getNumPoints() - Method in class qupath.lib.roi.PolylineROI
Default implementation, calls ROI.getAllPoints() and then caches the result.
getNumPoints() - Method in class qupath.lib.roi.EllipseROI
Returns 4 (since the ellipse is defined by its bounding box).
getNumPoints() - Method in interface qupath.lib.roi.interfaces.ROI
Get the number of points, as would be returned by ROI.getAllPoints().
getNumPoints() - Method in class qupath.lib.roi.LineROI
Returns 2 (since the line is defined by its end points).
getNumPoints() - Method in class qupath.lib.roi.PointsROI
 
getNumPoints() - Method in class qupath.lib.roi.RectangleROI
Returns 4 (since the rectangle is defined by its bounding box).
getNumThreads() - Static method in class qupath.lib.common.Prefs
Get the requested number of threads to use for parallelization.
getObjectClassifiers() - Method in interface qupath.lib.projects.Project
Get a manager for object classifiers saved within this project.
getObjectFileExtensions() - Static method in class qupath.lib.io.PathIO
getObjectFileExtensions(boolean) - Static method in class qupath.lib.io.PathIO
Get a list of known file extensions that may contain objects, optionally including compressed files.
getObjects() - Method in class qupath.lib.analysis.DelaunayTools.Subdivision
Get all the objects associated with this subdivision.
getObjects(Collection<PathObject>, Class<? extends PathObject>) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get all objects in the hierarchy, optionally filtering to return only objects that are instances of a specific class.
getObjectsForLocation(PathObjectHierarchy, double, double, int, int, double) - Static method in class qupath.lib.objects.PathObjectTools
Get a collection of objects that overlap a specified pixel location.
getObjectsForRegion(Class<? extends PathObject>, ImageRegion, Collection<PathObject>) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Deprecated.
getObjectsForRegion(ImageRegion) - Method in class qupath.lib.analysis.DelaunayTools.Subdivision
Get objects with edges that may intersect a specific region.
getObjectsForRegion(ImageRegion) - Method in class qupath.lib.images.servers.LabeledImageServer
Get the objects to be painted that fall within a specified region.
getObjectsForROI(Class<? extends PathObject>, ROI) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get the objects within a specified ROI, as defined by the general rules for resolving the hierarchy.
getObjectsOfClass(Collection<? extends PathObject>, Class<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools
Get the PathObjects in a collection that are instances of a specified class.
getODNormalizedColor(int, double, float, float) - Static method in class qupath.lib.color.ColorTransformer
Create a 'normalized' color for visualization.
getOnePlus(PathClass) - Static method in class qupath.lib.objects.classes.PathClass
Get a standalone or derived 1+ classification, indicating weak positivity
getOnePlus(PathClass) - Static method in class qupath.lib.objects.classes.PathClassFactory
Deprecated.
getOpticalDensities(Raster, int, double, float[]) - Static method in class qupath.lib.color.ColorDeconvolutionHelper
Extract a band from a raster and convert the pixel values to optical densities, using the specified maximum value.
getOrDefault(String, double) - Method in interface qupath.lib.measurements.MeasurementList
Get the specified measurement, or the provided default value if it is not contained in the list.
getOriginalImageName() - Method in interface qupath.lib.projects.ProjectImageEntry
Get the original image name, without any randomization.
getOriginalMetadata() - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer
 
getOriginalMetadata() - Method in class qupath.lib.images.servers.AffineTransformImageServer
 
getOriginalMetadata() - Method in class qupath.lib.images.servers.ChannelTransformFeatureServer
 
getOriginalMetadata() - Method in class qupath.lib.images.servers.CroppedImageServer
 
getOriginalMetadata() - Method in interface qupath.lib.images.servers.ImageServer
Get the original metadata read during creation of the server.
getOriginalMetadata() - Method in class qupath.lib.images.servers.LabeledImageServer
 
getOriginalMetadata() - Method in class qupath.lib.images.servers.NormalizedImageServer
 
getOriginalMetadata() - Method in class qupath.lib.images.servers.RotatedImageServer
 
getOriginalMetadata() - Method in class qupath.lib.images.servers.SlicedImageServer
 
getOriginalMetadata() - Method in class qupath.lib.images.servers.SparseImageServer
 
getOriginalMetadata() - Method in class qupath.lib.images.servers.TiledTransformingImageServer
 
getOriginalMetadata() - Method in class qupath.lib.images.servers.TransformingImageServer
 
getOriginalMetadata() - Method in class qupath.lib.images.servers.TypeConvertImageServer
 
getOriginalMetadata() - Method in class qupath.lib.images.servers.WrappedBufferedImageServer
 
getOriginalMetadata() - Method in class qupath.lib.images.servers.ZConcatenatedImageServer
 
getOriginalMetadata() - Method in class qupath.lib.images.servers.ZProjectedImageServer
 
getOutputChannels() - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata
List representing the names & display colors for each output channel, or for the output classifications if outputType == OutputType.Classification
getOutputPixelType() - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata
Pixel type of output; default is null indicating the pixel type is unknown.
getOutputType() - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata
Channel type of output; default is ImageServerMetadata.ChannelType.CLASSIFICATION
getPackageVersion(Class<?>) - Static method in class qupath.lib.common.GeneralTools
Try to determine the version of a jar containing a specified class.
getPaddedRequest(ImageServer<BufferedImage>, RegionRequest, Padding) - Static method in class qupath.lib.images.servers.ServerTools
Get a raster, padded by the specified amount, to the left, right, above and below.
getPadding(int, int) - Static method in class qupath.lib.regions.Padding
Get an padding object 'x' pixels to the left and right, and 'y' pixels above and below.
getPadding(int, int, int, int) - Static method in class qupath.lib.regions.Padding
Get a padding object that may have different padding on each side.
getParallelism() - Static method in class qupath.lib.common.ThreadTools
Get the requested level of parallelism.
getParameterList() - Method in interface qupath.lib.plugins.parameters.Parameterizable
Get the parameter list associated with the class.
getParameterList(ImageData<T>) - Method in class qupath.lib.plugins.AbstractInteractivePlugin
Get a reference to a ParameterList stored internally, and which will be used for analysis.
getParameterListJSON(Map<String, ?>, String) - Static method in class qupath.lib.plugins.parameters.ParameterList
Deprecated.
getParameterListJSON(ParameterList, String) - Static method in class qupath.lib.plugins.parameters.ParameterList
getParameterMap() - Method in class qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep
 
getParameterMap() - Method in class qupath.lib.plugins.workflow.RunSavedClassifierWorkflowStep
 
getParameterMap() - Method in class qupath.lib.plugins.workflow.SimplePluginWorkflowStep
 
getParameterMap() - Method in interface qupath.lib.plugins.workflow.WorkflowStep
Get a map of parameters required for this step.
getParameters() - Method in class qupath.lib.plugins.parameters.ParameterList
Returns a map of keys and their corresponding parameters
getParent() - Method in class qupath.lib.objects.PathObject
Request the parent object.
getParentClass() - Method in class qupath.lib.objects.classes.PathClass
Get the parent classification, or null if this classification has no parent.
getParentObjects(ImageData<T>) - Method in class qupath.lib.plugins.AbstractDetectionPlugin
Get all selected objects that are instances of a supported class.
getParentObjects(ImageData<T>) - Method in class qupath.lib.plugins.AbstractPlugin
Get a collection of objects to process, based on the contents of the PluginRunner.
getPatch() - Method in class qupath.lib.common.Version
Get the patch version number (0.0.X).
getPath() - Method in class qupath.lib.images.servers.AbstractImageServer
Default implementation lazily calls AbstractImageServer.createID() on demand.
getPath() - Method in interface qupath.lib.images.servers.ImageServer
Get a String path that can uniquely identify this image.
getPath() - Method in class qupath.lib.io.UriUpdater.SingleUriItem
Get the Path corresponding to the URI, or none if the URI does not refer to a file.
getPath() - Method in interface qupath.lib.projects.Project
Get a path to this project, or null if this project is not on a local file system.
getPath() - Method in class qupath.lib.regions.RegionRequest
Get the requested ImageServer path, used as an identifier.
getPathClass() - Method in class qupath.lib.objects.PathObject
Get the classification of the object.
getPathClass() - Method in class qupath.lib.objects.PathROIObject
 
getPathClass() - Method in class qupath.lib.objects.PathRootObject
 
getPathClass(String) - Static method in class qupath.lib.objects.classes.PathClassFactory
Deprecated.
Get a PathClass, without specifying any color.
getPathClass(String, Integer) - Static method in class qupath.lib.objects.classes.PathClassFactory
getPathClass(String, String...) - Static method in class qupath.lib.objects.classes.PathClassFactory
Deprecated.
since v0.4.0 in favor of PathClass.fromArray(String...)
getPathClass(List<String>) - Static method in class qupath.lib.objects.classes.PathClassFactory
Deprecated.
getPathClass(PathClassFactory.StandardPathClasses) - Static method in class qupath.lib.objects.classes.PathClassFactory
Deprecated.
getPathClasses() - Method in interface qupath.lib.classifiers.object.ObjectClassifier
Get the classifications set by this classifier.
getPathClasses() - Method in interface qupath.lib.projects.Project
Get an unmodifiable list representing the PathClasses associated with this project.
getPathClassUnclassified() - Static method in class qupath.lib.objects.classes.PathClassFactory
Deprecated.
since v0.4.0, use instead PathClass.NULL_CLASS
getPathObject() - Method in class qupath.lib.objects.classes.Reclassifier
Get the stored PathObject for which the PathClass may be set.
getPathObjects() - Method in class qupath.lib.analysis.DelaunayTools.Subdivision
Deprecated.
getPathObjects() - Method in class qupath.lib.io.FeatureCollection
Get the objects being wrapped.
getPathObjects() - Method in class qupath.lib.objects.DefaultPathObjectConnectionGroup
Deprecated.
 
getPathObjects() - Method in interface qupath.lib.objects.PathObjectConnectionGroup
Deprecated.
Get an unmodifiable collection containing all the PathObjects contained within this group.
getPathObjectsForRegion(ImageRegion) - Method in class qupath.lib.objects.DefaultPathObjectConnectionGroup
Deprecated.
 
getPathObjectsForRegion(ImageRegion) - Method in interface qupath.lib.objects.PathObjectConnectionGroup
Deprecated.
Get all the objects with connections that may intersect the specified region.
getPixelCalibration() - Method in interface qupath.lib.images.PathImage
Get the PixelCalibration representing actual pixel sizes in this image, with downsampling applied if necessary.
getPixelCalibration() - Method in interface qupath.lib.images.servers.ImageServer
Get the PixelCalibration object from the current metadata.
getPixelCalibration() - Method in class qupath.lib.images.servers.ImageServerMetadata
Get a PixelCalibration object representing the pixel size information for this metadata object.
getPixelClassifiers() - Method in interface qupath.lib.projects.Project
Get a manager for pixel classifiers saved within this project.
getPixelHeight() - Method in class qupath.lib.images.servers.PixelCalibration
Get the numeric value representing the pixel height, in the stored units.
getPixelHeightMicrons() - Method in class qupath.lib.images.servers.ImageServerMetadata
Get the pixel height in microns, if available - or Double.NaN otherwise.
getPixelHeightMicrons() - Method in class qupath.lib.images.servers.PixelCalibration
Get the pixel height in microns, or Double.NaN if this is unknown.
getPixelHeightUnit() - Method in class qupath.lib.images.servers.PixelCalibration
Get a String representation of the preferred pixel height unit.
getPixels(Raster, int) - Static method in class qupath.lib.color.ColorDeconvolutionHelper
Extract a band from a raster and return the values in a float array.
getPixels(Raster, int, float[]) - Static method in class qupath.lib.color.ColorDeconvolutionHelper
Extract a band from a raster and return the values in a float array.
getPixels(SimpleImage, boolean) - Static method in class qupath.lib.analysis.images.SimpleImages
Get the pixel values for the image.
getPixelType() - Method in class qupath.lib.images.servers.AbstractImageServer
 
getPixelType() - Method in interface qupath.lib.images.servers.ImageServer
The bit-depth and type of the image.
getPixelType() - Method in class qupath.lib.images.servers.ImageServerMetadata
Returns the bit-depth for individual pixels in the image.
getPixelValue(int, ColorTransformer.ColorTransformMethod) - Static method in class qupath.lib.color.ColorTransformer
Get the value of a single packed RGB pixel after applying a specified color transform method.
getPixelValue(int, ColorTransformer.ColorTransformMethod, ColorDeconvolutionStains) - Static method in class qupath.lib.color.ColorTransformer
Get the value of a single packed RGB pixel after applying a specified color transform method, with color deconvolution stains provided.
getPixelWidth() - Method in class qupath.lib.images.servers.PixelCalibration
Get the numeric value representing the pixel width, in the stored units.
getPixelWidthMicrons() - Method in class qupath.lib.images.servers.ImageServerMetadata
Get the pixel width in microns, if available - or Double.NaN otherwise.
getPixelWidthMicrons() - Method in class qupath.lib.images.servers.PixelCalibration
Get the pixel width in microns, or Double.NaN if this is unknown.
getPixelWidthUnit() - Method in class qupath.lib.images.servers.PixelCalibration
Get a String representation of the preferred pixel width unit.
getPlane() - Method in class qupath.lib.images.servers.TileRequest
Deprecated.
v0.4.0 use TileRequest.getImagePlane() instead (changed for better consistency with other classes)
getPlane() - Method in class qupath.lib.regions.ImageRegion
Deprecated.
v0.4.0 use ImageRegion.getImagePlane() instead (changed for better consistency with other classes)
getPlane(int, int) - Static method in class qupath.lib.regions.ImagePlane
Returns an ImagePlus, where the z-slice and time point can be specified and channel is ignored (i.e.
getPlane(ImageRegion) - Static method in class qupath.lib.regions.ImagePlane
Returns an ImagePlane with channel -1 and z and t set from an existing ImageRegion.
getPlane(ROI) - Static method in class qupath.lib.regions.ImagePlane
Returns an ImagePlane with channel -1, and z and t set from an existing ROI.
getPlaneWithChannel(int, int, int) - Static method in class qupath.lib.regions.ImagePlane
Returns an ImagePlane, where the channel, z-slice and time point can be specified.
getPlaneWithChannel(ROI) - Static method in class qupath.lib.regions.ImagePlane
Returns an ImagePlane with channel, z and t set from an existing ROI.
getPluginClass() - Method in class qupath.lib.plugins.workflow.SimplePluginWorkflowStep
Get the full name of the plugin class.
getPoint2D(Point2D, Point2D) - Method in interface qupath.lib.images.servers.transforms.BufferedImageNormalizer
 
getPointObjects(Class<? extends PathObject>) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Deprecated.
v0.6.0; use PathObjectHierarchy.getAllPointObjects() instead, and filter by object type if required.
getPointObjects(Collection<T>) - Static method in class qupath.lib.objects.PathObjectTools
Get a list of objects with point ROIs from a collection of objects.
getPositive(PathClass) - Static method in class qupath.lib.objects.classes.PathClass
Get a standalone or derived Positive classification
getPositive(PathClass) - Static method in class qupath.lib.objects.classes.PathClassFactory
Deprecated.
getPreferredDownsampleFactor(ImageServer<?>, double) - Static method in class qupath.lib.images.servers.ServerTools
Get the downsample factor supported by the server that is the best match for the requested downsample.
getPreferredDownsamples() - Method in class qupath.lib.images.servers.AbstractImageServer
Request the preferred downsamples from the image metadata.
getPreferredDownsamples() - Method in interface qupath.lib.images.servers.ImageServer
Get an array of downsample factors supported by the server
getPreferredDownsamplesArray() - Method in class qupath.lib.images.servers.ImageServerMetadata
Request the preferred downsamples from the image metadata.
getPreferredPixelSizeMicrons(ImageData<T>, ParameterList) - Method in class qupath.lib.plugins.AbstractTileableDetectionPlugin
Get the preferred pixel size that would be used for the specified ImageData and ParameterList.
getPreferredResolutionLevel(ImageServer<?>, double) - Static method in class qupath.lib.images.servers.ServerTools
Get the preferred resolution level to request regions from an ImageServer at a specified downsample level.
getPreferredTileHeight() - Method in class qupath.lib.images.servers.ImageServerMetadata
Get the preferred tile height, which can be used to optimize pixel requests for large images.
getPreferredTileWidth() - Method in class qupath.lib.images.servers.ImageServerMetadata
Get the preferred tile width, which can be used to optimize pixel requests for large images.
getPreferredUriImageSupport(Class<T>, String, String...) - Static method in class qupath.lib.images.servers.ImageServerProvider
Get the preferred ImageServerBuilder.UriImageSupport for a specified image path.
getPrettyPrintInstance() - Static method in class qupath.lib.io.GsonTools
Get Gson instance capable of serializing/deserializing some key QuPath classes, and configured for pretty printing.
getPreviousURI() - Method in interface qupath.lib.projects.Project
Sometimes projects move (unfortunately).
getProbabilityColorModel32Bit(List<ImageChannel>) - Static method in class qupath.lib.color.ColorModelFactory
Get a ColorModel suitable for showing 32-bit (pseudo-)probabilities for multiple channels.
getProbabilityColorModel8Bit(List<ImageChannel>) - Static method in class qupath.lib.color.ColorModelFactory
Get a ColorModel suitable for showing 8-bit pseudo-probabilities for multiple channels.
getProjectExtension() - Static method in class qupath.lib.projects.ProjectIO
Get the default extension for a QuPath project file, without the 'dot'.
getProjectExtension(boolean) - Static method in class qupath.lib.projects.ProjectIO
Get the default extension for a QuPath project file.
getPrompt() - Method in class qupath.lib.plugins.parameters.BooleanParameter
 
getPrompt() - Method in class qupath.lib.plugins.parameters.ChoiceParameter
 
getPrompt() - Method in class qupath.lib.plugins.parameters.DoubleParameter
 
getPrompt() - Method in class qupath.lib.plugins.parameters.EmptyParameter
 
getPrompt() - Method in class qupath.lib.plugins.parameters.IntParameter
 
getPrompt() - Method in class qupath.lib.plugins.parameters.NumericParameter
 
getPrompt() - Method in class qupath.lib.plugins.parameters.StringParameter
 
getPrompt() - Method in interface qupath.lib.plugins.parameters.Parameter
Get some prompt text that may be displayed to a user.
getProperties() - Method in class qupath.lib.images.ImageData
Get an unmodifiable map representing all known properties for this ImageData.
getProperty(String) - Method in class qupath.lib.images.ImageData
Get a specified property.
getProviderClass() - Method in class qupath.lib.images.servers.ImageServerBuilder.UriImageSupport
Get the class of the associated ImageServerBuilder.
getPValue() - Method in class qupath.lib.analysis.stats.survival.LogRankTest.LogRankResult
Get the calculated p-value.
getQuartiles(double[]) - Static method in class qupath.lib.analysis.stats.StatisticsHelper
Determine thresholds for dividing an array of double values into quartiles.
getRange() - Method in class qupath.lib.analysis.stats.RunningStatistics
Get the range, i.e.
getRed() - Method in class qupath.lib.color.StainVector
Get the red component of the (normalized) stain vector.
getRedOpticalDensities(int[], double, float[]) - Static method in class qupath.lib.color.ColorDeconvolutionHelper
Convert red channel of packed rgb pixel to optical density values, using a specified maximum value.
getRegionRequest() - Method in class qupath.lib.images.servers.TileRequest
Get the RegionRequest that this tile represents.
getRegions() - Method in class qupath.lib.images.servers.SparseImageServer.SparseImageServerManager
Get an unmodifiable collection for all available regions.
getRenderingHints() - Method in interface qupath.lib.images.servers.transforms.BufferedImageNormalizer
 
getReplacements() - Method in class qupath.lib.io.UriUpdater
Get a map of all replacements.
getRepresentedPathClasses(PathObjectHierarchy, Class<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools
Get a set of the represented path classes, i.e.
getRequestedDataFileVersion() - Static method in class qupath.lib.io.PathIO
Get the requested version for .qpdata files.
getResources(String, Class<S>, String) - Method in interface qupath.lib.projects.Project
Get a manager for objects of a specified class within this project.
getResultString() - Method in class qupath.lib.analysis.stats.survival.LogRankTest.LogRankResult
Returns a presentable representation of the log-rank test result, including hazard ratio and confidence interval.
getROI() - Method in class qupath.lib.objects.PathObject
Get the region of interest (ROI) for the object.
getROI() - Method in class qupath.lib.objects.PathROIObject
 
getROI() - Method in class qupath.lib.objects.PathRootObject
 
getROI() - Method in class qupath.lib.roi.RoiEditor
Retrieve the ROI currently being edited (may be null).
getROI(PathObject, boolean) - Static method in class qupath.lib.objects.PathObjectTools
Get the ROI for a PathObject, with a preference for the nucleus ROI of a cell.
getRoiName() - Method in class qupath.lib.roi.AreaROI
Deprecated.
 
getRoiName() - Method in class qupath.lib.roi.EllipseROI
 
getRoiName() - Method in class qupath.lib.roi.GeometryROI
 
getRoiName() - Method in interface qupath.lib.roi.interfaces.ROI
Get a String representation of the kind of ROI we have, e.g.
getRoiName() - Method in class qupath.lib.roi.LineROI
 
getRoiName() - Method in class qupath.lib.roi.PointsROI
 
getRoiName() - Method in class qupath.lib.roi.PolygonROI
 
getRoiName() - Method in class qupath.lib.roi.PolylineROI
 
getRoiName() - Method in class qupath.lib.roi.RectangleROI
 
getRoiType() - Method in class qupath.lib.roi.AreaROI
Deprecated.
 
getRoiType() - Method in class qupath.lib.roi.EllipseROI
 
getRoiType() - Method in class qupath.lib.roi.GeometryROI
 
getRoiType() - Method in interface qupath.lib.roi.interfaces.ROI
Get the RoiType, used to distinguish between points, lines and areas.
getRoiType() - Method in class qupath.lib.roi.LineROI
 
getRoiType() - Method in class qupath.lib.roi.PointsROI
 
getRoiType() - Method in class qupath.lib.roi.PolygonROI
 
getRoiType() - Method in class qupath.lib.roi.PolylineROI
 
getRoiType() - Method in class qupath.lib.roi.RectangleROI
 
getRootObject() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get the root object.
getRotatedBuilder(ImageServerBuilder.ServerBuilder<BufferedImage>, RotatedImageServer.Rotation) - Static method in class qupath.lib.images.servers.RotatedImageServer
Get a ServerBuilder that applies a rotation to another server.
getRotation() - Method in class qupath.lib.images.servers.RotatedImageServer
Get the rotation applied by this server.
getScaledArea(double, double) - Method in class qupath.lib.roi.AreaROI
Deprecated.
 
getScaledArea(double, double) - Method in class qupath.lib.roi.EllipseROI
 
getScaledArea(double, double) - Method in class qupath.lib.roi.GeometryROI
 
getScaledArea(double, double) - Method in interface qupath.lib.roi.interfaces.ROI
Get scaled area of the ROI, for use with calibrated pixel sizes.
getScaledArea(double, double) - Method in class qupath.lib.roi.LineROI
 
getScaledArea(double, double) - Method in class qupath.lib.roi.PointsROI
 
getScaledArea(double, double) - Method in class qupath.lib.roi.PolygonROI
 
getScaledArea(double, double) - Method in class qupath.lib.roi.PolylineROI
 
getScaledArea(double, double) - Method in class qupath.lib.roi.RectangleROI
 
getScaledArea(PixelCalibration) - Method in interface qupath.lib.roi.interfaces.ROI
Get the scaled area, using the pixel width and height from a calibration object.
getScaledLength(double, double) - Method in class qupath.lib.roi.AreaROI
Deprecated.
 
getScaledLength(double, double) - Method in class qupath.lib.roi.EllipseROI
 
getScaledLength(double, double) - Method in class qupath.lib.roi.GeometryROI
 
getScaledLength(double, double) - Method in interface qupath.lib.roi.interfaces.ROI
Get the scaled length, for use with calibrated pixel sizes.
getScaledLength(double, double) - Method in class qupath.lib.roi.LineROI
 
getScaledLength(double, double) - Method in class qupath.lib.roi.PointsROI
 
getScaledLength(double, double) - Method in class qupath.lib.roi.PolygonROI
 
getScaledLength(double, double) - Method in class qupath.lib.roi.PolylineROI
 
getScaledLength(double, double) - Method in class qupath.lib.roi.RectangleROI
 
getScaledLength(PixelCalibration) - Method in interface qupath.lib.roi.interfaces.ROI
Get the scaled length, using the pixel width and height from a calibration object.
getScript() - Method in class qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep
 
getScript() - Method in class qupath.lib.plugins.workflow.RunSavedClassifierWorkflowStep
 
getScript() - Method in interface qupath.lib.plugins.workflow.ScriptableWorkflowStep
Get one or more script lines that may be used to apply the step.
getScript() - Method in class qupath.lib.plugins.workflow.SimplePluginWorkflowStep
 
getScripts() - Method in interface qupath.lib.projects.Project
Get a manager for scripts saved within this project.
getSelectedObject() - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel
Get the current primary selected object.
getSelectedObjects() - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel
Get an unmodifiable set containing all the currently-selected objects.
getSelectedROI() - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel
Get the ROI of the selected object, if available, or null
getSelectionModel() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get the selection model, which handles the selection status of objects.
getSemanticVersion() - Static method in class qupath.lib.common.GeneralTools
Get a representation of QuPath's version, parsed according to the rules of semantic versioning if possible.
getServer() - Method in class qupath.lib.images.ImageData
Get the ImageServer, loading it if necessary.
getServer(ImageRegion, double) - Method in class qupath.lib.images.servers.SparseImageServer.SparseImageServerManager
Request the server for a specific downsample.
getServerBuilder() - Method in class qupath.lib.images.ImageData
Get the ServerBuilde corresponding to the ImageServer associated with this ImageData.
getServerBuilder() - Method in interface qupath.lib.projects.ProjectImageEntry
Get a ImageServerBuilder.ServerBuilder that can be used to open this image.
getServerBuilderFactory() - Static method in class qupath.lib.images.servers.ImageServers
Get a TypeAdapterFactory to handle ServerBuilders.
getServerMetadata() - Method in class qupath.lib.images.ImageData
Get the metadata for the server.
getServerPath() - Method in class qupath.lib.images.ImageData
Get the path of the ImageServer.
getServerType() - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer
 
getServerType() - Method in class qupath.lib.images.servers.AffineTransformImageServer
 
getServerType() - Method in class qupath.lib.images.servers.ChannelTransformFeatureServer
 
getServerType() - Method in class qupath.lib.images.servers.CroppedImageServer
 
getServerType() - Method in interface qupath.lib.images.servers.ImageServer
A string describing the type of server, for example the name of the library used (Openslide, Bioformats...)
getServerType() - Method in class qupath.lib.images.servers.LabeledImageServer
 
getServerType() - Method in class qupath.lib.images.servers.NormalizedImageServer
 
getServerType() - Method in class qupath.lib.images.servers.RearrangeRGBImageServer
 
getServerType() - Method in class qupath.lib.images.servers.RotatedImageServer
 
getServerType() - Method in class qupath.lib.images.servers.SlicedImageServer
 
getServerType() - Method in class qupath.lib.images.servers.SparseImageServer
 
getServerType() - Method in class qupath.lib.images.servers.TypeConvertImageServer
 
getServerType() - Method in class qupath.lib.images.servers.WrappedBufferedImageServer
 
getServerType() - Method in class qupath.lib.images.servers.ZConcatenatedImageServer
 
getServerType() - Method in class qupath.lib.images.servers.ZProjectedImageServer
 
getShape() - Method in class qupath.lib.roi.AreaROI
Deprecated.
 
getShape() - Method in class qupath.lib.roi.EllipseROI
 
getShape() - Method in class qupath.lib.roi.GeometryROI
 
getShape() - Method in interface qupath.lib.roi.interfaces.ROI
Returns a java.awt.Shape representing this ROI, if possible.
getShape() - Method in class qupath.lib.roi.LineROI
 
getShape() - Method in class qupath.lib.roi.PointsROI
It is not possible to convert a PointROI to a java.awt.Shape.
getShape() - Method in class qupath.lib.roi.PolygonROI
 
getShape() - Method in class qupath.lib.roi.PolylineROI
 
getShape() - Method in class qupath.lib.roi.RectangleROI
 
getShape(ROI) - Static method in class qupath.lib.roi.RoiTools
Get a Shape object representing a ROI.
getShapeInternal() - Method in class qupath.lib.roi.AreaROI
Get a (possibly cached) shape representation of the ROI.
getShapeInternal() - Method in class qupath.lib.roi.EllipseROI
Get a (possibly cached) shape representation of the ROI.
getShapeInternal() - Method in class qupath.lib.roi.GeometryROI
Get a (possibly cached) shape representation of the ROI.
getShapeInternal() - Method in class qupath.lib.roi.LineROI
Get a (possibly cached) shape representation of the ROI.
getShapeInternal() - Method in class qupath.lib.roi.PointsROI
Get a (possibly cached) shape representation of the ROI.
getShapeInternal() - Method in class qupath.lib.roi.PolygonROI
Get a (possibly cached) shape representation of the ROI.
getShapeInternal() - Method in class qupath.lib.roi.PolylineROI
Get a (possibly cached) shape representation of the ROI.
getShapeInternal() - Method in class qupath.lib.roi.RectangleROI
Get a (possibly cached) shape representation of the ROI.
getShapeROI(Area, ImagePlane) - Static method in class qupath.lib.roi.RoiTools
Create a ROI from an Shape.
getShapeROI(Shape, ImagePlane, double) - Static method in class qupath.lib.roi.RoiTools
Create a ROI from an Shape with a specified 'flatness'.
getSimpleTransformedPixels(int[], ColorTransformer.ColorTransformMethod, float[]) - Static method in class qupath.lib.color.ColorTransformer
Apply a color transform to all pixels in a packed (A)RGB array.
getSingleton(PathClass) - Static method in class qupath.lib.objects.classes.PathClass
Get the singleton PathClass that is equivalent to the PathClass provided.
getSingletonPathClass(PathClass) - Static method in class qupath.lib.objects.classes.PathClassFactory
Deprecated.
since v0.4.0 in favor of PathClass.getSingleton(PathClass)
getSizeC() - Method in class qupath.lib.images.servers.ImageServerMetadata
Get the number of image channels.
getSizeT() - Method in class qupath.lib.images.servers.ImageServerMetadata
Get the number of time points.
getSizeZ() - Method in class qupath.lib.images.servers.ImageServerMetadata
Get the number of z-slices.
getSolidity() - Method in class qupath.lib.roi.AreaROI
 
getSolidity() - Method in class qupath.lib.roi.EllipseROI
 
getSolidity() - Method in class qupath.lib.roi.GeometryROI
 
getSolidity() - Method in class qupath.lib.roi.LineROI
 
getSolidity() - Method in class qupath.lib.roi.PointsROI
 
getSolidity() - Method in class qupath.lib.roi.PolygonROI
 
getSolidity() - Method in class qupath.lib.roi.PolylineROI
 
getSolidity() - Method in class qupath.lib.roi.RectangleROI
 
getSolidity() - Method in interface qupath.lib.roi.interfaces.ROI
Calculate the solidity, defined as ROI area / convex hull area.
getSource() - Method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent
Get the source that triggered the event.
getStain(int) - Method in class qupath.lib.color.ColorDeconvolutionStains
Get a specified color deconvolution stain vector, where n should be 1, 2 or 3 (because color deconvolution on a 3-channel image can recover [to some extent] up to 3 stains).
getStainNumber(StainVector) - Method in class qupath.lib.color.ColorDeconvolutionStains
Get the number for a specific stain (1, 2 or 3).
getStainProjection(int, double, double, double, double[], double[], double[]) - Static method in class qupath.lib.color.ColorTransformer
Calculate magnitude of projection of pixel OD onto stain OD.
getStainRejection(int, double, double, double, double[], double[], double[]) - Static method in class qupath.lib.color.ColorTransformer
Calculate magnitude of rejection of pixel OD onto stain OD.
getStains() - Method in class qupath.lib.color.ColorDeconvolutionStains
Get an unmodifiable list containing the 3 stains.
getStains(boolean) - Method in class qupath.lib.color.ColorDeconvolutionStains
Get a collection of all the stains.
getStatistic() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData
Retrieve a sorted array containing the value corresponding to a time from KaplanMeierData.getAllTimes().
getStatus() - Method in class qupath.lib.io.UriUpdater.SingleUriItem
Get the URI status.
getStatus() - Method in class qupath.lib.plugins.ParallelTileObject
Get the current status (pending, processing or done).
getStdDev() - Method in class qupath.lib.analysis.stats.Histogram
Get the standard deviation of all the values being histogrammed.
getStdDev() - Method in class qupath.lib.analysis.stats.RunningStatistics
Get the standard deviation of all non-NaN values that were added.
getSteps() - Method in class qupath.lib.plugins.workflow.Workflow
Get an unmodifiable list of the steps.
getStringParameterValue(String) - Method in class qupath.lib.plugins.parameters.ParameterList
Get a String parameter value (or its default) for the specified key.
getStructureChangeBase() - Method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent
If this is a structure change event, return the base object, i.e.
getSubdivision(PathObject) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get the subdivision containing a specific PathObject.
getSuffix() - Method in class qupath.lib.common.Version
Get the (optional) suffix, which may be appended at the end of the version number to indicate a pre-release (0.0.0-X).
getSuitableName(Class<? extends PathObject>, boolean) - Static method in class qupath.lib.objects.PathObjectTools
Get a user-friendly name for a specific type of PathObject, based on its Java class.
getSum() - Method in class qupath.lib.analysis.stats.Histogram
Get the sum of all the values being histogrammed.
getSum() - Method in class qupath.lib.analysis.stats.RunningStatistics
Get the sum of all non-NaN values that were added.
getSummary() - Method in interface qupath.lib.projects.ProjectImageEntry
Get a summary string representing this image entry.
getSupportedObjects(Collection<? extends PathObject>, Collection<Class<? extends PathObject>>) - Static method in class qupath.lib.objects.PathObjectTools
From a collection of available objects, extract those that are instances of specified supported classes.
getSupportedParentObjectClasses() - Method in class qupath.lib.plugins.AbstractDetectionPlugin
 
getSupportedParentObjectClasses() - Method in interface qupath.lib.plugins.PathInteractivePlugin
Get a collection of possible parent objects that the plugin could have.
getSupportLevel() - Method in class qupath.lib.images.servers.ImageServerBuilder.UriImageSupport
Estimated 'support level' for a given file path, where support level is a summary of the likelihood that pixel values and metadata will be returned correctly and in a way that achieves good performance.
getSwapRedBlueBuilder(ImageServerBuilder.ServerBuilder<BufferedImage>, String) - Static method in class qupath.lib.images.servers.RearrangeRGBImageServer
Get a ServerBuilder that swaps red and blue channels for another (RGB) server.
getT() - Method in class qupath.lib.images.servers.TileRequest
Get the time point index for this request.
getT() - Method in class qupath.lib.regions.ImagePlane
Get the time point index.
getT() - Method in class qupath.lib.regions.ImageRegion
Get the time point index for the region.
getT() - Method in class qupath.lib.roi.AreaROI
 
getT() - Method in class qupath.lib.roi.EllipseROI
 
getT() - Method in class qupath.lib.roi.GeometryROI
 
getT() - Method in class qupath.lib.roi.LineROI
 
getT() - Method in class qupath.lib.roi.PointsROI
 
getT() - Method in class qupath.lib.roi.PolygonROI
 
getT() - Method in class qupath.lib.roi.PolylineROI
 
getT() - Method in class qupath.lib.roi.RectangleROI
 
getT() - Method in interface qupath.lib.roi.interfaces.ROI
Get time point index.
getTags() - Method in interface qupath.lib.projects.ProjectImageEntry
Returns a modifiable set containing tag values.
getTasks(ImageData<T>) - Method in class qupath.lib.plugins.AbstractPlugin
Get a collection of tasks to perform.
getTertiles(double[]) - Static method in class qupath.lib.analysis.stats.StatisticsHelper
Determine thresholds for dividing an array of double values into tertiles.
getThreePlus(PathClass) - Static method in class qupath.lib.objects.classes.PathClass
Get a standalone or derived 3+ classification, indicating strong positivity
getThreePlus(PathClass) - Static method in class qupath.lib.objects.classes.PathClassFactory
Deprecated.
getThumbnail() - Method in interface qupath.lib.projects.ProjectImageEntry
Request a thumbnail for the image.
getThumbnailDownsampleFactor(int, int) - Method in class qupath.lib.images.servers.AbstractImageServer
 
getTile(TileRequest) - Method in class qupath.lib.images.servers.AbstractTileableImageServer
Get a tile for the request - ideally from the cache, but otherwise read it and then add it to the cache.
getTileHeight() - Method in class qupath.lib.images.servers.TileRequest
Get the height of the bounding box for this tile at the tile resolution.
getTileHeight() - Method in class qupath.lib.objects.utils.Tiler
Get the height of output tiles
getTileObjects() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get all tile objects in the hierarchy.
getTileOverlap(ImageData<T>, ParameterList) - Method in class qupath.lib.plugins.AbstractTileableDetectionPlugin
Get an appropriate overlap, in pixels, if analysis of the specified ImageData will be tiled.
getTileRequest(int, int, int, int, int) - Method in interface qupath.lib.images.servers.TileRequestManager
Get the single TileRequest containing a specified pixel, or null if no such request exists.
getTileRequestManager() - Method in class qupath.lib.images.servers.AbstractImageServer
 
getTileRequestManager() - Method in interface qupath.lib.images.servers.ImageServer
Get a TileRequestManager that can be used to identify image tiles that may be efficiently requested from this ImageServer.
getTileRequests(RegionRequest) - Method in interface qupath.lib.images.servers.TileRequestManager
Get a collection of TileRequest objects necessary to fulfil a specific RegionRequest.
getTileRequestsForLevel(int) - Method in interface qupath.lib.images.servers.TileRequestManager
Get TileRequest objects for all tiles that this server supports at the specified resolution level.
getTilesForROI(ROI) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get all the tile objects with centroids falling within the specified ROI.
getTileWidth() - Method in class qupath.lib.images.servers.TileRequest
Get the width of the bounding box for this tile at the tile resolution.
getTileWidth() - Method in class qupath.lib.objects.utils.Tiler
Get the width of output tiles
getTileX() - Method in class qupath.lib.images.servers.TileRequest
Get the x-coordinate of the bounding box for this tile at the tile resolution.
getTileY() - Method in class qupath.lib.images.servers.TileRequest
Get the y-coordinate of the bounding box for this tile at the tile resolution.
getTimepoint(int) - Method in class qupath.lib.images.servers.ImageServerMetadata
Get the time point, defined in ImageServerMetadata.getTimeUnit(), or Double.NaN if this is unknown.
getTimepoint(int) - Method in class qupath.lib.images.servers.PixelCalibration
Get the time for the specified time point, or Double.NaN if this is unknown.
getTimeToEvent() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData.KaplanMeierEvent
Get the stored time to event (units are unspecified).
getTimeUnit() - Method in class qupath.lib.images.servers.ImageServerMetadata
Get the time unit for a time series.
getTimeUnit() - Method in class qupath.lib.images.servers.PixelCalibration
Get the time unit for a time series.
getTMACore(int, int) - Method in class qupath.lib.objects.hierarchy.DefaultTMAGrid
 
getTMACore(int, int) - Method in interface qupath.lib.objects.hierarchy.TMAGrid
Get the TMACoreObject for a specified grid location.
getTMACore(String) - Method in class qupath.lib.objects.hierarchy.DefaultTMAGrid
 
getTMACore(String) - Method in interface qupath.lib.objects.hierarchy.TMAGrid
Retrieve a TMA core based upon its name.
getTMACoreForPixel(TMAGrid, double, double) - Static method in class qupath.lib.objects.PathObjectTools
Get the TMA core that contains the specified x & y coordinate, or null if no core is available for the coordinates give.
getTMACoreList() - Method in class qupath.lib.objects.hierarchy.DefaultTMAGrid
 
getTMACoreList() - Method in interface qupath.lib.objects.hierarchy.TMAGrid
Get an unmodifiable list of all TMA core objects.
getTMACoreObjects(PathObjectHierarchy, boolean) - Static method in class qupath.lib.objects.PathObjectTools
Extract a list of TMA cores from an object hierarchy.
getTMAGrid() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Get the TMAGrid, or null if there is no TMA grid associated with this hierarchy.
getTransform() - Method in class qupath.lib.images.servers.AffineTransformImageServer
Get the affine transform for this server.
getTransformedPixels(int[], ColorTransformer.ColorTransformMethod, float[], ColorDeconvolutionStains) - Static method in class qupath.lib.color.ColorTransformer
Apply a color transform to all pixels in a packed (A)RGB array.
getTranslucentColor(Color) - Static method in class qupath.lib.color.ColorToolsAwt
Get a (slightly) translucent version of the specified color.
getTwoPlus(PathClass) - Static method in class qupath.lib.objects.classes.PathClass
Get a standalone or derived 2+ classification, indicating moderate positivity
getTwoPlus(PathClass) - Static method in class qupath.lib.objects.classes.PathClassFactory
Deprecated.
getTypeAdapterFactory() - Static method in class qupath.lib.classifiers.object.ObjectClassifiers
Get a TypeAdapterFactory to handle ObjectClassifier instances.
getUnit() - Method in class qupath.lib.plugins.parameters.NumericParameter
Get the unit to display for this parameter (may be null if no unit is available).
getUnmodifiableMetadataMap() - Method in class qupath.lib.objects.PathObject
Deprecated.
v0.6.0, use PathObject.getMetadata() to directly access the metadata instead.
getUpperBound() - Method in enum class qupath.lib.images.servers.PixelType
Get a number representing the maximum value permitted by this type.
getUpperBound() - Method in class qupath.lib.plugins.parameters.NumericParameter
Retrieve the upper bound.
getURI() - Method in class qupath.lib.images.servers.ImageServerBuilder.DefaultImageServerBuilder
Get the URI used by this builder.
getURI() - Method in class qupath.lib.io.UriUpdater.SingleUriItem
Get the URI.
getURI() - Method in interface qupath.lib.projects.Project
Get a URI that can be used when saving/reloading this project.
getUris() - Method in interface qupath.lib.io.UriResource
 
getURIs() - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer
 
getURIs() - Method in interface qupath.lib.images.servers.ImageServer
Get the URIs for images required for this server.
getURIs() - Method in class qupath.lib.images.servers.ImageServerBuilder.DefaultImageServerBuilder
 
getURIs() - Method in interface qupath.lib.images.servers.ImageServerBuilder.ServerBuilder
Get a list of URIs required by this builder.
getURIs() - Method in class qupath.lib.images.servers.LabeledImageServer
 
getURIs() - Method in class qupath.lib.images.servers.NormalizedImageServer
 
getURIs() - Method in class qupath.lib.images.servers.SparseImageServer
 
getURIs() - Method in class qupath.lib.images.servers.TiledTransformingImageServer
 
getURIs() - Method in class qupath.lib.images.servers.TransformingImageServer
 
getURIs() - Method in class qupath.lib.images.servers.TypeConvertImageServer
 
getURIs() - Method in class qupath.lib.images.servers.WrappedBufferedImageServer
 
getURIs() - Method in class qupath.lib.images.servers.ZConcatenatedImageServer
 
getURIs() - Method in class qupath.lib.images.servers.ZProjectedImageServer
 
getURIs() - Method in interface qupath.lib.io.UriResource
Get all the URIs required for this resource.
getValue() - Method in interface qupath.lib.measurements.Measurement
Get the numeric value of the measurement.
getValue() - Method in class qupath.lib.plugins.parameters.BooleanParameter
 
getValue() - Method in class qupath.lib.plugins.parameters.ChoiceParameter
 
getValue() - Method in class qupath.lib.plugins.parameters.DoubleParameter
 
getValue() - Method in class qupath.lib.plugins.parameters.EmptyParameter
 
getValue() - Method in class qupath.lib.plugins.parameters.IntParameter
 
getValue() - Method in class qupath.lib.plugins.parameters.NumericParameter
 
getValue() - Method in class qupath.lib.plugins.parameters.StringParameter
 
getValue() - Method in interface qupath.lib.plugins.parameters.Parameter
Get the current set value (may be null).
getValue(int, int) - Method in interface qupath.lib.analysis.images.SimpleImage
Get the value of a single pixel as a float.
getValueOrDefault() - Method in class qupath.lib.plugins.parameters.BooleanParameter
 
getValueOrDefault() - Method in class qupath.lib.plugins.parameters.ChoiceParameter
 
getValueOrDefault() - Method in class qupath.lib.plugins.parameters.DoubleParameter
 
getValueOrDefault() - Method in class qupath.lib.plugins.parameters.EmptyParameter
 
getValueOrDefault() - Method in class qupath.lib.plugins.parameters.IntParameter
 
getValueOrDefault() - Method in class qupath.lib.plugins.parameters.NumericParameter
 
getValueOrDefault() - Method in class qupath.lib.plugins.parameters.StringParameter
 
getValueOrDefault() - Method in interface qupath.lib.plugins.parameters.Parameter
Get the current set value, or any default if no value has been set.
getVariance() - Method in class qupath.lib.analysis.stats.Histogram
Get the variance of all the values being histogrammed.
getVariance() - Method in class qupath.lib.analysis.stats.RunningStatistics
Get the variance of all non-NaN values that were added.
getVersion() - Static method in class qupath.lib.common.GeneralTools
Get a String representation of QuPath's version, if known.
getVersion() - Method in interface qupath.lib.projects.Project
The version string for this project, which can be used to distinguish new and older project (which may contain different information).
getVoronoiFaces() - Method in class qupath.lib.analysis.DelaunayTools.Subdivision
Get a map of Voronoi faces as JTS Geometry objects.
getVoronoiROIs(Geometry) - Method in class qupath.lib.analysis.DelaunayTools.Subdivision
Get a map of Voronoi faces, converted to ROI objects.
getWidth() - Method in interface qupath.lib.analysis.images.SimpleImage
Get the image width.
getWidth() - Method in class qupath.lib.geom.ImmutableDimension
Get the ImmutableDimension width.
getWidth() - Method in class qupath.lib.images.servers.AbstractImageServer
 
getWidth() - Method in interface qupath.lib.images.servers.ImageServer
Width of the full-resolution image in pixels.
getWidth() - Method in class qupath.lib.images.servers.ImageServerMetadata
Get the full-resolution image width.
getWidth() - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel
Get the image width at this level.
getWidth() - Method in class qupath.lib.regions.ImageRegion
Get the width of the region bounding box.
getWrappedServer() - Method in class qupath.lib.images.servers.NormalizedImageServer
Get underlying ImageServer, i.e.
getWrappedServer() - Method in class qupath.lib.images.servers.TiledTransformingImageServer
Get underlying ImageServer, i.e.
getWrappedServer() - Method in class qupath.lib.images.servers.TransformingImageServer
Get underlying ImageServer, i.e.
getWrappedServer() - Method in class qupath.lib.images.servers.TypeConvertImageServer
Get underlying ImageServer, i.e.
getX() - Method in class qupath.lib.geom.Point2
Get the x coordinate of this point.
getX() - Method in class qupath.lib.regions.ImageRegion
Get the x coordinate of the region bounding box (top left).
getX1() - Method in class qupath.lib.regions.Padding
Get the first horizontal padding (left of the image), in pixels.
getX1() - Method in class qupath.lib.roi.LineROI
Get the first x co-ordinate (start of the line).
getX2() - Method in class qupath.lib.regions.Padding
Get the second horizontal padding (right of the image), in pixels.
getX2() - Method in class qupath.lib.roi.LineROI
Get the second x co-ordinate (end of the line).
getXSum() - Method in class qupath.lib.regions.Padding
Get the total horizontal padding (sum of x1 and x2).
getY() - Method in class qupath.lib.geom.Point2
Get the y coordinate of this point.
getY() - Method in class qupath.lib.regions.ImageRegion
Get the y coordinate of the region bounding box (top left).
getY1() - Method in class qupath.lib.regions.Padding
Get the first vertical padding (top of the image), in pixels.
getY1() - Method in class qupath.lib.roi.LineROI
Get the first y co-ordinate (start of the line).
getY2() - Method in class qupath.lib.regions.Padding
Get the second vertical padding (bottom of the image), in pixels.
getY2() - Method in class qupath.lib.roi.LineROI
Get the second y co-ordinate (end of the line).
getYSum() - Method in class qupath.lib.regions.Padding
Get the total vertical padding (sum of x1 and x2).
getZ() - Method in class qupath.lib.images.servers.TileRequest
Get the z-slice index for this request.
getZ() - Method in class qupath.lib.regions.ImagePlane
Get the z-slice index.
getZ() - Method in class qupath.lib.regions.ImageRegion
Get the z-slice index for the region.
getZ() - Method in class qupath.lib.roi.AreaROI
 
getZ() - Method in class qupath.lib.roi.EllipseROI
 
getZ() - Method in class qupath.lib.roi.GeometryROI
 
getZ() - Method in class qupath.lib.roi.LineROI
 
getZ() - Method in class qupath.lib.roi.PointsROI
 
getZ() - Method in class qupath.lib.roi.PolygonROI
 
getZ() - Method in class qupath.lib.roi.PolylineROI
 
getZ() - Method in class qupath.lib.roi.RectangleROI
 
getZ() - Method in interface qupath.lib.roi.interfaces.ROI
Get z-stack slice index.
getZSpacing() - Method in class qupath.lib.images.servers.PixelCalibration
Get the numeric value representing the z-spacing, in the stored units.
getZSpacingMicrons() - Method in class qupath.lib.images.servers.ImageServerMetadata
Get the z-spacing in microns, if available - or Double.NaN otherwise.
getZSpacingMicrons() - Method in class qupath.lib.images.servers.PixelCalibration
Get the z-spacing in microns, or Double.NaN if this is unknown.
getZSpacingUnit() - Method in class qupath.lib.images.servers.PixelCalibration
Get a String representation of the preferred z-spacing unit.
grabHandle(double, double, double, boolean) - Method in class qupath.lib.roi.RoiEditor
Try to grab a ROI handle.
grayscale() - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Use grayscale LUT, rather than deriving colors from classifications.
grayscale(boolean) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Optionally use grayscale LUT, rather than deriving colors from classifications.
green(int) - Static method in class qupath.lib.common.ColorTools
Extract the 8-bit green value from a packed RGB value.
Green - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
Green channel only
GREEN - Static variable in class qupath.lib.common.ColorTools
Packed int representing green.
GREEN - Static variable in class qupath.lib.images.servers.ImageChannel
Default green channel for RGB images.
Green_chromaticity - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
Green chromaticity value, green / max(1, red + green + blue)
Green_divided_by_blue - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
Green value divided by blue value
Green_OD - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
Green channel optical densities
greenChromaticity(int) - Static method in class qupath.lib.color.ColorTransformer
Extract green chromaticity value from a packed RGB pixel, green / max(1, red + green + blue)
greenOverBlue(int) - Static method in class qupath.lib.color.ColorTransformer
Extract green over blue value from a packed RGB pixel, green / max(1, blue)
GsonTools - Class in qupath.lib.io
Helper class providing Gson instances with type adapters registered to serialize several key classes.
GsonTools() - Constructor for class qupath.lib.io.GsonTools
 
GsonTools.SubTypeAdapterFactory<T> - Class in qupath.lib.io
A TypeAdapterFactory that is suitable for handling class hierarchies.

H

H_DAB - Enum constant in enum class qupath.lib.color.ColorDeconvolutionStains.DefaultColorDeconvolutionStains
Hematoxylin and DAB
H_E - Enum constant in enum class qupath.lib.color.ColorDeconvolutionStains.DefaultColorDeconvolutionStains
Hematoxylin and eosin
hasActiveHandle() - Method in class qupath.lib.roi.RoiEditor
Returns true if a handle is currently active, for example being reposition.
hasAnnotationsForRegion(ImageRegion) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Returns true if the hierarchy contains any annotation objects intersecting a specific region.
hasChildObjects() - Method in class qupath.lib.objects.PathObject
Check if this object has children, or if its child object list is empty.
hasDetectionsForRegion(ImageRegion) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Returns true if the hierarchy contains any detection objects (including subclasses) intersecting a specific region.
hashCode() - Method in class qupath.lib.color.ColorDeconvolutionStains
 
hashCode() - Method in class qupath.lib.color.StainVector
 
hashCode() - Method in class qupath.lib.common.Version
 
hashCode() - Method in class qupath.lib.geom.Point2
 
hashCode() - Method in class qupath.lib.images.servers.ImageChannel
 
hashCode() - Method in class qupath.lib.images.servers.ImageServerBuilder.DefaultImageServerBuilder
 
hashCode() - Method in class qupath.lib.images.servers.ImageServerMetadata
 
hashCode() - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel
 
hashCode() - Method in class qupath.lib.images.servers.PixelCalibration
 
hashCode() - Method in class qupath.lib.images.servers.TileRequest
 
hashCode() - Method in class qupath.lib.io.UriUpdater.SingleUriItem
 
hashCode() - Method in class qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep
 
hashCode() - Method in class qupath.lib.regions.ImagePlane
 
hashCode() - Method in class qupath.lib.regions.ImageRegion
 
hashCode() - Method in class qupath.lib.regions.RegionRequest
 
hashCode() - Method in class qupath.lib.roi.EllipseROI
 
hashCode() - Method in class qupath.lib.roi.RectangleROI
 
hashCode() - Method in class qupath.lib.roi.AreaROI
Deprecated.
 
hashCode() - Method in class qupath.lib.roi.GeometryROI
 
hashCode() - Method in class qupath.lib.roi.LineROI
 
hashCode() - Method in class qupath.lib.roi.PointsROI
 
hashCode() - Method in class qupath.lib.roi.PolygonROI
 
hashCode() - Method in class qupath.lib.roi.PolylineROI
 
hasHelpText() - Method in class qupath.lib.plugins.parameters.BooleanParameter
 
hasHelpText() - Method in class qupath.lib.plugins.parameters.ChoiceParameter
 
hasHelpText() - Method in class qupath.lib.plugins.parameters.DoubleParameter
 
hasHelpText() - Method in class qupath.lib.plugins.parameters.EmptyParameter
 
hasHelpText() - Method in class qupath.lib.plugins.parameters.IntParameter
 
hasHelpText() - Method in class qupath.lib.plugins.parameters.NumericParameter
 
hasHelpText() - Method in class qupath.lib.plugins.parameters.StringParameter
 
hasHelpText() - Method in interface qupath.lib.plugins.parameters.Parameter
Query whether getHelpText() returns a meaningful String (as opposed to null).
hasImageData() - Method in interface qupath.lib.projects.ProjectImageEntry
Check if this entry has saved ImageData already available.
hasLowerAndUpperBounds() - Method in class qupath.lib.plugins.parameters.NumericParameter
Returns true if this parameter has both lower and upper bounds constraining valid values.
hasLowerBound() - Method in class qupath.lib.plugins.parameters.NumericParameter
Returns true if the parameter has a valid lower bound.
hasMeasurements() - Method in class qupath.lib.objects.PathObject
Returns true if the measurement list for this object is not empty.
hasMetadata() - Method in class qupath.lib.objects.PathObject
Query whether the object has any metadata associated with it.
hasNucleus() - Method in class qupath.lib.objects.PathCellObject
Returns true if a nucleus ROI is stored for this cell.
hasObjectsForRegion(Class<? extends PathObject>, ImageRegion) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Returns true if the hierarchy contains objects overlapping a specific region, optionally filtering to identify only objects of a specific class.
hasObjectsForRegion(ImageRegion) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Returns true if the hierarchy contains any objects intersecting a specific region.
hasPixelSizeMicrons() - Method in class qupath.lib.images.servers.PixelCalibration
Returns true if the pixel width and height information in microns is known.
hasPointROI(PathObject) - Static method in class qupath.lib.objects.PathObjectTools
Returns true if a PathObject has a Point ROI.
hasROI() - Method in class qupath.lib.objects.PathObject
Returns true if this object has a ROI.
hasROI() - Method in class qupath.lib.roi.RoiEditor
Returns true if this editor currently has a ROI.
hasSuffix() - Method in class qupath.lib.common.Version
Returns true if the version has a suffix, which typically indicates that it does not refer to a final stable version.
hasUpperBound() - Method in class qupath.lib.plugins.parameters.NumericParameter
Returns true if the parameter has a valid upper bound.
hasZSpacingMicrons() - Method in class qupath.lib.images.servers.PixelCalibration
Returns true if the z-spacing is known in microns.
height - Variable in class qupath.lib.geom.ImmutableDimension
Height of the ImmutableDimension.
height(int) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder
Specify the full-resolution image height.
HEMATOXYLIN - Enum constant in enum class qupath.lib.color.StainVector.DefaultStains
Hematoxylin
HEMATOXYLIN - Static variable in class qupath.lib.color.ColorDeconvolutionStains
Default name (and spelling) for hematoxylin stain
Hematoxylin_H_DAB - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
Hematoxylin after color deconvolution with default H-DAB stains
Hematoxylin_H_DAB_8_bit - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
Hematoxylin after color deconvolution with default H-DAB stains and conversion to 8-bit
Hematoxylin_H_E - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
Hematoxylin after color deconvolution with default H&E stains
Hematoxylin_H_E_8_bit - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
Hematoxylin after color deconvolution with default H&E stains and conversion to 8-bit
HIERARCHY_COMPARATOR - Static variable in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Comparator to use when looking for a parent annotation in the hierarchy.
hierarchyChanged(PathObjectHierarchyEvent) - Method in class qupath.lib.images.ImageData
 
hierarchyChanged(PathObjectHierarchyEvent) - Method in interface qupath.lib.objects.hierarchy.events.PathObjectHierarchyListener
Notify listeners of a change in the hierarchy or its objects.
hierarchyContainsObject(PathObjectHierarchy, PathObject) - Static method in class qupath.lib.objects.PathObjectTools
Check if a hierarchy contains a specified PathObject.
Histogram - Class in qupath.lib.analysis.stats
Class for storing histogram data & basic statistics.
Histogram(double[], int) - Constructor for class qupath.lib.analysis.stats.Histogram
Create histogram from a double array, using a specified number of bins and the data min/max as the min/max edges.
Histogram(double[], int, double, double) - Constructor for class qupath.lib.analysis.stats.Histogram
Create a histogram from an array of values, optionally specifying the minimum & maximum values to include.
Histogram(float[], int) - Constructor for class qupath.lib.analysis.stats.Histogram
Create histogram from a float array, using a specified number of bins and the data min/max as the min/max edges.
Histogram(float[], int, double, double) - Constructor for class qupath.lib.analysis.stats.Histogram
Create a histogram from an array of values, optionally specifying the minimum & maximum values to include.
Histogram(int[], int, double, double) - Constructor for class qupath.lib.analysis.stats.Histogram
Create a histogram from an array of values, optionally specifying the minimum & maximum values to include.
Histogram(ArrayWrappers.ArrayWrapper, int, double, double) - Constructor for class qupath.lib.analysis.stats.Histogram
Create histogram from an array wrapper, using a specified number of bins and the data min/max as the min/max edges.
homogenizeGeometryCollection(Geometry) - Static method in class qupath.lib.roi.GeometryTools
Ensure a GeometryCollection contains only Geometries of the same type (Polygonal, Lineal or Puntal).
hue(int) - Static method in class qupath.lib.color.ColorTransformer
Extract hue value from RGB-to-HSB transform.
Hue - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
Hue value (from RGB-HSB transform)

I

identity() - Static method in class qupath.lib.awt.common.AffineTransforms
Create an affine transform representing the identity transform.
IGNORE - Enum constant in enum class qupath.lib.objects.classes.PathClassFactory.StandardPathClasses
Deprecated.
Ignore classification, indicating what should not be further measured (e.g.
IGNORE - Static variable in class qupath.lib.objects.classes.PathClass.StandardPathClasses
Ignore classification, indicating what should not be further measured (e.g.
IGNORE - Static variable in interface qupath.lib.objects.utils.MeasurementStrategy
The default and previous strategy: ignore and discard.
IMAGE_ROOT - Enum constant in enum class qupath.lib.objects.classes.PathClassFactory.StandardPathClasses
Deprecated.
Root object classification
IMAGE_ROOT - Static variable in class qupath.lib.objects.classes.PathClass.StandardPathClasses
Root object classification
ImageChannel - Class in qupath.lib.images.servers
The name and display color for a single image channel.
ImageData<T> - Class in qupath.lib.images
Class that brings together the main data in connection with the analysis of a single image.
ImageData(ImageServer<T>) - Constructor for class qupath.lib.images.ImageData
Create a new ImageData with ImageType.UNKNOWN and a new PathObjectHierarchy.
ImageData(ImageServer<T>, ImageData.ImageType) - Constructor for class qupath.lib.images.ImageData
Create a new ImageData with a specified type and creating a new object hierarchy.
ImageData(ImageServer<T>, PathObjectHierarchy) - Constructor for class qupath.lib.images.ImageData
Create a new ImageData with ImageType.UNKNOWN.
ImageData(ImageServer<T>, PathObjectHierarchy, ImageData.ImageType) - Constructor for class qupath.lib.images.ImageData
Create a new ImageData with a specified server, hierarchy and type.
ImageData(ImageServerBuilder.ServerBuilder<T>, PathObjectHierarchy, ImageData.ImageType) - Constructor for class qupath.lib.images.ImageData
Create a new ImageData with a lazily-loaded server, hierarchy and type.
ImageData.ImageType - Enum Class in qupath.lib.images
Enum representing possible image types.
imageExtension(String) - Method in class qupath.lib.images.writers.TileExporter
Specify a file extension for the original pixels, which determines the export file format.
ImagePlane - Class in qupath.lib.regions
Helper class to store z-slice and time point indices, optionally along with a channel index as well.
ImageRegion - Class in qupath.lib.regions
Class for defining an image region.
ImageServer<T> - Interface in qupath.lib.images.servers
Generic ImageServer, able to return pixels and metadata.
ImageServerBuilder<T> - Interface in qupath.lib.images.servers
Helper class for creating ImageServers from a given URI and optional argument list.
ImageServerBuilder.AbstractServerBuilder<T> - Class in qupath.lib.images.servers
Abstract ServerBuilder implementation that handles metadata.
ImageServerBuilder.DefaultImageServerBuilder<T> - Class in qupath.lib.images.servers
Default ImageServerBuilder.ServerBuilder that requires a URI and (optional) array of String arguments to create an ImageServer with the help of a ImageServerBuilder.
ImageServerBuilder.ServerBuilder<T> - Interface in qupath.lib.images.servers
Interface that defines a class encapsulating all that is required to build an ImageServer.
ImageServerBuilder.UriImageSupport<T> - Class in qupath.lib.images.servers
Helper class to summarize which ImageServers can be build by a particular ImageServerBuilder for a given URI, and a level of confidence.
ImageServerMetadata - Class in qupath.lib.images.servers
Class for storing primary ImageServer metadata fields.
ImageServerMetadata.Builder - Class in qupath.lib.images.servers
Builder to create a new ImageServerMetadata object.
ImageServerMetadata.ChannelType - Enum Class in qupath.lib.images.servers
Enum representing possible channel (band) types for an image.
ImageServerMetadata.ImageResolutionLevel - Class in qupath.lib.images.servers
Width and height of each resolution in a multi-level image pyramid.
ImageServerMetadata.ImageResolutionLevel.Builder - Class in qupath.lib.images.servers
Builder to create a list of ImageServerMetadata.ImageResolutionLevel to represent pyramidal resolutions.
ImageServerProvider - Class in qupath.lib.images.servers
Service provider for creating ImageServers from a given path - which may be a file path or URL.
ImageServerProvider() - Constructor for class qupath.lib.images.servers.ImageServerProvider
 
ImageServers - Class in qupath.lib.images.servers
Helper class for working with ImageServer objects.
ImageServers() - Constructor for class qupath.lib.images.servers.ImageServers
 
imageSubDir(String) - Method in class qupath.lib.images.writers.TileExporter
Specify a subdirectory within which image tiles should be saved.
ImageWriter<T> - Interface in qupath.lib.images.writers
Interface for defining class that can write images.
ImageWriterTools - Class in qupath.lib.images.writers
Static methods to access ImageWriter objects and write images.
ImageWriterTools() - Constructor for class qupath.lib.images.writers.ImageWriterTools
 
IMMUNE_CELLS - Enum constant in enum class qupath.lib.objects.classes.PathClassFactory.StandardPathClasses
Deprecated.
Immune cell classification
IMMUNE_CELLS - Static variable in class qupath.lib.objects.classes.PathClass.StandardPathClasses
Immune cell classification
ImmutableDimension - Class in qupath.lib.geom
An immutable alternative to Java's AWT Dimension.
importFromCSV(File, PathObjectHierarchy) - Static method in class qupath.lib.io.TMAScoreImporter
Import TMA scores from a file into the TMAGrid of an object hierarchy.
importFromCSV(String, PathObjectHierarchy) - Static method in class qupath.lib.io.TMAScoreImporter
Import TMA scores from a String into the TMAGrid of an object hierarchy.
includePartialTiles(boolean) - Method in class qupath.lib.images.writers.TileExporter
Specify whether incomplete tiles at image boundaries should be included.
inputPadding(int) - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata.Builder
Amount of padding requested for the left, right, top and bottom of the image tile being classified.
inputResolution(PixelCalibration) - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata.Builder
Pixel size defining the resolution at which the classifier should operate.
inputShape(int, int) - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata.Builder
Preferred input image width and height.
insertPathObject(PathObject, boolean) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Insert an object into the hierarchy.
insertPathObjects(Collection<? extends PathObject>) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Insert a collection of objects into the hierarchy, firing a change event on completion.
installColorMaps(Path...) - Static method in class qupath.lib.color.ColorMaps
Install colormaps from the specified paths.
installColorMaps(ColorMaps.ColorMap...) - Static method in class qupath.lib.color.ColorMaps
Install colormaps.
INT16 - Enum constant in enum class qupath.lib.images.servers.PixelType
16-bit signed integer
INT32 - Enum constant in enum class qupath.lib.images.servers.PixelType
32-bit signed integer
INT8 - Enum constant in enum class qupath.lib.images.servers.PixelType
8-bit signed integer
INTERSECT - Enum constant in enum class qupath.lib.roi.RoiTools.CombineOp
Calculate intersection (overlap) between ROIs.
intersect2D(int, int, int, int) - Method in class qupath.lib.regions.RegionRequest
Intersect to the specified 2D region.
intersect2D(ImageRegion) - Method in class qupath.lib.regions.RegionRequest
Intersect to the specified 2D region, ignoring z and t.
intersection(Collection<? extends ROI>) - Static method in class qupath.lib.roi.RoiTools
Create intersection of multiple ROIs from a collection.
intersection(ROI...) - Static method in class qupath.lib.roi.RoiTools
Create intersection of multiple ROIs.
intersectionArea(Geometry, Geometry) - Static method in class qupath.lib.roi.GeometryTools
Calculate the intersection area between two polygonal geometries.
intersectionArea(ROI, ROI) - Static method in class qupath.lib.roi.RoiTools
Create area of intersection between two area ROIs.
intersects(double, double, double, double) - Method in class qupath.lib.regions.ImageRegion
Query if this region intersects with a specified bounding box, ignoring z-slice and time point information.
intersects(double, double, double, double) - Method in class qupath.lib.roi.AreaROI
Deprecated.
 
intersects(double, double, double, double) - Method in class qupath.lib.roi.EllipseROI
 
intersects(double, double, double, double) - Method in class qupath.lib.roi.GeometryROI
 
intersects(double, double, double, double) - Method in interface qupath.lib.roi.interfaces.ROI
Test if the ROI intersects a specified region.
intersects(double, double, double, double) - Method in class qupath.lib.roi.LineROI
 
intersects(double, double, double, double) - Method in class qupath.lib.roi.PointsROI
 
intersects(double, double, double, double) - Method in class qupath.lib.roi.PolygonROI
 
intersects(double, double, double, double) - Method in class qupath.lib.roi.PolylineROI
 
intersects(double, double, double, double) - Method in class qupath.lib.roi.RectangleROI
 
intersects(ImageRegion) - Method in class qupath.lib.regions.ImageRegion
Returns true if the region specified by this region overlaps with another.
intersects(ImageRegion) - Method in interface qupath.lib.roi.interfaces.ROI
Test if the ROI intersects a specified image region.
intersectsBounds(double, double, double, double) - Method in class qupath.lib.roi.AreaROI
Quick check whether the specified rectangle intersects with the bounds of this ROI.
intersectsBounds(double, double, double, double) - Method in class qupath.lib.roi.EllipseROI
Quick check whether the specified rectangle intersects with the bounds of this ROI.
intersectsBounds(double, double, double, double) - Method in class qupath.lib.roi.GeometryROI
Quick check whether the specified rectangle intersects with the bounds of this ROI.
intersectsBounds(double, double, double, double) - Method in class qupath.lib.roi.LineROI
Quick check whether the specified rectangle intersects with the bounds of this ROI.
intersectsBounds(double, double, double, double) - Method in class qupath.lib.roi.PointsROI
Quick check whether the specified rectangle intersects with the bounds of this ROI.
intersectsBounds(double, double, double, double) - Method in class qupath.lib.roi.PolygonROI
Quick check whether the specified rectangle intersects with the bounds of this ROI.
intersectsBounds(double, double, double, double) - Method in class qupath.lib.roi.PolylineROI
Quick check whether the specified rectangle intersects with the bounds of this ROI.
intersectsBounds(double, double, double, double) - Method in class qupath.lib.roi.RectangleROI
Quick check whether the specified rectangle intersects with the bounds of this ROI.
intersectsRegion(ROI, ImageRegion) - Static method in class qupath.lib.roi.RoiTools
Test whether a ROI and an ImageRegion intersect.
IntParameter - Class in qupath.lib.plugins.parameters
Parameter to represent an integer numeric value.
inverse() - Method in class qupath.lib.color.ColorDeconvMatrix3x3
Calculate the 3x3 matrix inverse.
iou(Geometry, Geometry) - Static method in class qupath.lib.roi.GeometryTools
Calculate the intersection over union, based on geometry areas.
iou(ROI, ROI) - Static method in class qupath.lib.roi.RoiTools
Create intersection over union for two area ROIs.
is8bitColorType(int) - Static method in class qupath.lib.awt.common.BufferedImageTools
Returns true if a BufferedImage type represents an 8-bit color image.
isAddedOrRemovedEvent() - Method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent
Returns true if objects have been added or removed from the hierarchy.
isAncestor(PathObject, PathObject) - Static method in class qupath.lib.objects.PathObjectTools
Query if one object is the ancestor of another.
isAncestorOf(PathClass) - Method in class qupath.lib.objects.classes.PathClass
Returns true if this class is equal to the specified child class, or an ancestor of that class.
isAnnotation() - Method in class qupath.lib.objects.PathObject
Returns true if the object is an annotation.
isAppleSilicon() - Static method in class qupath.lib.common.GeneralTools
Return true if running on macOS and Apple Silicon.
isArea() - Method in class qupath.lib.roi.AreaROI
 
isArea() - Method in class qupath.lib.roi.EllipseROI
 
isArea() - Method in class qupath.lib.roi.GeometryROI
 
isArea() - Method in class qupath.lib.roi.LineROI
 
isArea() - Method in class qupath.lib.roi.PointsROI
 
isArea() - Method in class qupath.lib.roi.PolygonROI
 
isArea() - Method in class qupath.lib.roi.PolylineROI
 
isArea() - Method in class qupath.lib.roi.RectangleROI
 
isArea() - Method in interface qupath.lib.roi.interfaces.ROI
Returns true if this ROI encloses an area.
isBigTiff() - Method in interface qupath.lib.images.servers.FileFormatInfo.ImageCheckType
Returns true if URI is for a local file known/expected to be a BigTIFF image.
isBrightfield() - Method in class qupath.lib.images.ImageData
Returns true if the image type is set to brightfield.
isCancelled() - Method in class qupath.lib.plugins.AbstractTaskRunner
 
isCancelled() - Method in interface qupath.lib.plugins.TaskRunner
Query if the plugin can be cancelled while running.
isCell() - Method in class qupath.lib.objects.PathObject
Returns true if the object is a cell object (a special type of detection, which can contain second ROI for the nucleus).
isCensored() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData.KaplanMeierEvent
Returns true if the event should be considered right-censored.
isChanged() - Method in class qupath.lib.images.ImageData
Returns true if changes have been recorded since the last time this object was notified that it was saved.
isChanging() - Method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent
Returns true if changes are still being made, so more events will be fired.
isCircle() - Method in class qupath.lib.roi.EllipseROI
Query if the width and height of the ellipse bounding box are the same, assuming 'square' pixels.
isCircle(double, double) - Method in class qupath.lib.roi.EllipseROI
Query if the width and height of the ellipse bounding box are the same, optionally using 'non-square' pixels.
isCompatibleMetadata(ImageServerMetadata) - Method in class qupath.lib.images.servers.ImageServerMetadata
Returns true if a specified ImageServerMetadata is compatible with this one, that is it has the same path and dimensions (but possibly different pixel sizes, magnifications etc.).
isComplete() - Method in class qupath.lib.plugins.ParallelTileObject
Returns true if setComplete() has been called.
isDAB(StainVector) - Static method in class qupath.lib.color.ColorDeconvolutionStains
Check if the name of a StainVector is "dab" or "d" (ignoring case)
isDerivedClass() - Method in class qupath.lib.objects.classes.PathClass
Returns true if #getParentClass() != null.
isDerivedFrom(PathClass) - Method in class qupath.lib.objects.classes.PathClass
Returns true if this class, or any ancestor class, is equal to the specified parent class.
isDetection() - Method in class qupath.lib.objects.PathObject
Returns true if the object is a detection.
isEditable() - Method in class qupath.lib.objects.PathDetectionObject
Always returns false - detection objects shouldn't be edited.
isEditable() - Method in class qupath.lib.objects.PathObject
Flag indicating that the object is editable.
isEditable() - Method in class qupath.lib.objects.PathROIObject
Deprecated.
since v0.4.0
isEditable() - Method in class qupath.lib.objects.PathRootObject
The root object is never locked.
isEmpty() - Method in class qupath.lib.analysis.DelaunayTools.Subdivision
Query if the subdivision is empty, i.e.
isEmpty() - Method in interface qupath.lib.analysis.stats.ArrayWrappers.ArrayWrapper
Query if size() == 1 return
isEmpty() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData
Returns true if there are no events included.
isEmpty() - Method in interface qupath.lib.measurements.MeasurementList
Returns true if the list does not contain any measurements.
isEmpty() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Check if the hierarchy is empty (i.e.
isEmpty() - Method in class qupath.lib.objects.PathObjectConnections
Returns true if the group is empty.
isEmpty() - Method in class qupath.lib.plugins.workflow.Workflow
Returns true if the workflow does not contain any steps.
isEmpty() - Method in interface qupath.lib.projects.Project
Test if the project contains any images.
isEmpty() - Method in class qupath.lib.regions.Padding
Returns true of the padding is zero.
isEmpty() - Method in class qupath.lib.roi.EllipseROI
 
isEmpty() - Method in class qupath.lib.roi.RectangleROI
 
isEmpty() - Method in class qupath.lib.roi.AreaROI
True if the bounding box has zero area
isEmpty() - Method in class qupath.lib.roi.GeometryROI
True if the bounding box has zero area
isEmpty() - Method in class qupath.lib.roi.PolygonROI
True if the bounding box has zero area
isEmpty() - Method in class qupath.lib.roi.PolylineROI
True if the bounding box has zero area
isEmpty() - Method in interface qupath.lib.roi.interfaces.ROI
Returns true if the ROI bounds have zero width and height.
isEmpty() - Method in class qupath.lib.roi.LineROI
 
isEmpty() - Method in class qupath.lib.roi.PointsROI
A Points ROI is empty if it contains no points (*not* if its bounds have no width or height...
isEmptyRegion(RegionRequest) - Method in class qupath.lib.images.servers.AbstractImageServer
Always returns false.
isEmptyRegion(RegionRequest) - Method in interface qupath.lib.images.servers.ImageServer
Test whether a region is empty, i.e.
isEmptyRegion(RegionRequest) - Method in class qupath.lib.images.servers.LabeledImageServer
Returns true if there are no objects to be painted within the requested region.
isEosin(StainVector) - Static method in class qupath.lib.color.ColorDeconvolutionStains
Check if the name of a StainVector is "eosin", "eos" or "e" (ignoring case)
isFloatingPoint() - Method in enum class qupath.lib.images.servers.PixelType
Returns true if the type is a floating point representation.
isFluorescence() - Method in class qupath.lib.images.ImageData
Returns true if the image type is set to fluorescence.
isGradedIntensityClass(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools
Return true if the PathClass represents a built-in intensity class.
isH_DAB() - Method in class qupath.lib.color.ColorDeconvolutionStains
Check if we have H-DAB staining, by checking the names of the first two stains and confirming that the third stain is a residual.
isH_E() - Method in class qupath.lib.color.ColorDeconvolutionStains
Check if we have H&E staining, by checking the names of the first two stains and confirming that the third stain is a residual.
isHematoxylin(StainVector) - Static method in class qupath.lib.color.ColorDeconvolutionStains
Check if the name of a StainVector is "haematoxylin", "hematoxylin", "haem" or "h" (ignoring case)
isHidden() - Method in class qupath.lib.plugins.parameters.BooleanParameter
 
isHidden() - Method in class qupath.lib.plugins.parameters.ChoiceParameter
 
isHidden() - Method in class qupath.lib.plugins.parameters.DoubleParameter
 
isHidden() - Method in class qupath.lib.plugins.parameters.EmptyParameter
 
isHidden() - Method in class qupath.lib.plugins.parameters.IntParameter
 
isHidden() - Method in class qupath.lib.plugins.parameters.NumericParameter
 
isHidden() - Method in class qupath.lib.plugins.parameters.StringParameter
 
isHidden() - Method in interface qupath.lib.plugins.parameters.Parameter
Test is the 'hidden' flag is set for the parameter.
isIgnoredClass(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools
Return true if the PathClass should be ignored from some operations, or is null.
isInteger() - Method in class qupath.lib.analysis.stats.Histogram
Check if the histogram has been generated from integer values only.
isIntegerWrapper() - Method in interface qupath.lib.analysis.stats.ArrayWrappers.ArrayWrapper
Returns true if the array wrapper only supports integer values.
isLine() - Method in class qupath.lib.roi.AreaROI
 
isLine() - Method in class qupath.lib.roi.EllipseROI
 
isLine() - Method in class qupath.lib.roi.GeometryROI
 
isLine() - Method in class qupath.lib.roi.LineROI
 
isLine() - Method in class qupath.lib.roi.PointsROI
 
isLine() - Method in class qupath.lib.roi.PolygonROI
 
isLine() - Method in class qupath.lib.roi.PolylineROI
 
isLine() - Method in class qupath.lib.roi.RectangleROI
 
isLine() - Method in interface qupath.lib.roi.interfaces.ROI
Returns true if this ROI consists of line segments and does not enclose an area.
isLinux() - Static method in class qupath.lib.common.GeneralTools
Return true if running on Linux.
isLoaded() - Method in class qupath.lib.images.ImageData
Query whether the corresponding ImageServer was lazy-loaded or not, If isLoaded() returns false, then calls to ImageData.getServer() will result in an attempt to load the server.
isLocked() - Method in class qupath.lib.objects.PathObject
Query the locked status.
isLocked() - Method in class qupath.lib.objects.PathROIObject
Query the locked status for the object, indicating whether it should be editable or not.
isMac() - Static method in class qupath.lib.common.GeneralTools
Return true if running on macOS.
isMissing() - Method in class qupath.lib.objects.TMACoreObject
Query the 'missing' flag for this core.
isMultipartExtension(String) - Static method in class qupath.lib.common.GeneralTools
Returns true for file extensions containing multiple parts (or 'dots').
isNegativeClass(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools
Return true if the PathClass has the name "Negative".
isNotRGB() - Method in interface qupath.lib.images.servers.FileFormatInfo.ImageCheckType
Returns true if we can say with reasonable confidence that the image is not RGB.
isNullClass(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools
Return true if the PathClass is null, its name is null or if it is equal to the special case of 'Unclassified' path object.
isObjectClassificationEvent() - Method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent
Returns true if the event indicates that object classifications have changed.
isObjectMeasurementEvent() - Method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent
Returns true if the event indicates that object measurements have changed.
isOnePlus(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools
Returns true if the name of the class is "1+", indicating a weakly-positive staining.
isPoint() - Method in class qupath.lib.roi.AreaROI
 
isPoint() - Method in class qupath.lib.roi.EllipseROI
 
isPoint() - Method in class qupath.lib.roi.GeometryROI
 
isPoint() - Method in class qupath.lib.roi.LineROI
 
isPoint() - Method in class qupath.lib.roi.PointsROI
 
isPoint() - Method in class qupath.lib.roi.PolygonROI
 
isPoint() - Method in class qupath.lib.roi.PolylineROI
 
isPoint() - Method in class qupath.lib.roi.RectangleROI
 
isPoint() - Method in interface qupath.lib.roi.interfaces.ROI
Returns true if this ROI represents distinct (unconnected) points.
isPositiveClass(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools
Return true if the PathClass has the name "Positive".
isPositiveOrGradedIntensityClass(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools
Return true if the name of the class is "Positive", "1+", "2+" or "3+", indicating positive staining.
isProcessing() - Method in class qupath.lib.plugins.ParallelTileObject
Returns true if setIsProcessing(true) has recently been called.
isResidual() - Method in class qupath.lib.color.StainVector
Returns true if this vector represents the residual (orthogonal) stain, used whenever color deconvolution is required with two stains only.
isRGB() - Method in class qupath.lib.images.servers.AbstractImageServer
 
isRGB() - Method in interface qupath.lib.images.servers.ImageServer
True if the image has 8-bit red, green & blue channels (and nothing else), false otherwise.
isRGB() - Method in class qupath.lib.images.servers.ImageServerMetadata
Returns true if the pixels are stored in (A)RGB form.
isRootObject() - Method in class qupath.lib.objects.PathObject
Returns true if the object is the 'root' of an object hierarchy.
isRootObject() - Method in class qupath.lib.objects.PathRootObject
 
isSelected(PathObject) - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel
Query whether a specific object is selected.
isShapeROI(ROI) - Static method in class qupath.lib.roi.RoiTools
Returns true if the ROI is not null and is not a point ROI.
isSignedInteger() - Method in enum class qupath.lib.images.servers.PixelType
Returns true if the type is a signed integer representation.
isStructureChangeEvent() - Method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent
Returns true if the hierarchy structure has changed, e.g.
isSymmetric() - Method in class qupath.lib.regions.Padding
Returns true of the padding is identical on all sides (x1 == x2 == y1 == y2).
isThreePlus(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools
Return true if the name of the class is "3+", indicating a weakly-positive staining.
isTiff() - Method in interface qupath.lib.images.servers.FileFormatInfo.ImageCheckType
Returns true if URI is for a local file known/expected to be a TIFF image.
isTile() - Method in class qupath.lib.objects.PathObject
Returns true if this object represents an image tile.
isTitle - Variable in class qupath.lib.plugins.parameters.EmptyParameter
 
isTitle() - Method in class qupath.lib.plugins.parameters.EmptyParameter
Returns true if the parameter should be considered a title.
isTMACore() - Method in class qupath.lib.objects.PathObject
Returns true if this object represents a TMA core.
isTranslating() - Method in class qupath.lib.roi.RoiEditor
Query if a ROI is currently being translated through this editor.
isTransparent() - Method in class qupath.lib.images.servers.ImageChannel
Check if the color is 'transparent'; this is used for background/ignored channels.
isTwoPlus(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools
Return true if the name of the class is "2+", indicating a moderately-positive staining.
isUnbounded() - Method in class qupath.lib.plugins.parameters.NumericParameter
Returns true if this neither a lower nor an upper bound constraining valid values.
isUnsignedInteger() - Method in enum class qupath.lib.images.servers.PixelType
Returns true if the type is an unsigned integer representation.
isURL() - Method in interface qupath.lib.images.servers.FileFormatInfo.ImageCheckType
Return true if URI has a scheme beginning with http.
isValid() - Method in class qupath.lib.analysis.stats.survival.LogRankTest.LogRankResult
Returns true if the p-value is not NaN.
isValid() - Method in class qupath.lib.objects.classes.PathClass
A PathClass is valid if its name is not null.
isValidClass(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools
Returns true if the PathClass represents a valid (non-null) classification.
isValidFilename(String) - Static method in class qupath.lib.common.GeneralTools
Returns true if the output of GeneralTools.stripInvalidFilenameChars(String) matches the provided name, and the name is not null or blank.
isValidInput(Boolean) - Method in class qupath.lib.plugins.parameters.BooleanParameter
 
isValidInput(String) - Method in class qupath.lib.plugins.parameters.EmptyParameter
Always returns false
isValidInput(String) - Method in class qupath.lib.plugins.parameters.StringParameter
 
isValidInput(S) - Method in class qupath.lib.plugins.parameters.ChoiceParameter
 
isValidInput(S) - Method in class qupath.lib.plugins.parameters.NumericParameter
Numbers are considered valid if they are not NaN
isValidInput(S) - Method in interface qupath.lib.plugins.parameters.Parameter
Query if a specified value would be valid for this parameter.
isWindows() - Static method in class qupath.lib.common.GeneralTools
Return true if running on Windows.

J

JpegWriter - Class in qupath.lib.images.writers
ImageWriter implementation to write JPEG images using ImageIO.
JpegWriter() - Constructor for class qupath.lib.images.writers.JpegWriter
 
JsonImageServerBuilder - Class in qupath.lib.images.servers
ImageServerBuilder that constructs an ImageServer from a JSON representation.
JsonImageServerBuilder() - Constructor for class qupath.lib.images.servers.JsonImageServerBuilder
 
jsonRegion(ImageRegion, double, ImageServerBuilder.ServerBuilder<BufferedImage>) - Method in class qupath.lib.images.servers.SparseImageServer.Builder
Add a region based on a JSON representation of an ImageServer.

K

KaplanMeierData - Class in qupath.lib.analysis.stats.survival
Structure used to store data related to generating Kaplan-Meier survival curves.
KaplanMeierData(String) - Constructor for class qupath.lib.analysis.stats.survival.KaplanMeierData
Create a new KaplanMeierData object with the specified display name.
KaplanMeierData(String, Collection<KaplanMeierData.KaplanMeierEvent>) - Constructor for class qupath.lib.analysis.stats.survival.KaplanMeierData
Create a new KaplanMeierData object with the specified display name and events.
KaplanMeierData.KaplanMeierEvent - Class in qupath.lib.analysis.stats.survival
Simple class to store event time and censored flag.
KEEP_OVERLAPS - Enum constant in enum class qupath.lib.objects.utils.OverlapFixer.Strategy
 
keepFragments() - Method in class qupath.lib.objects.utils.OverlapFixer.Builder
Equivalent to keepFragments(true).
keepFragments(boolean) - Method in class qupath.lib.objects.utils.OverlapFixer.Builder
Set whether to keep fragments when clipping objects.
KEY_CASE_ID - Static variable in class qupath.lib.objects.TMACoreObject
Metadata key to store a case identify for the TMA core.
KEY_OBJECT_CONNECTIONS - Static variable in class qupath.lib.objects.DefaultPathObjectConnectionGroup
Deprecated.
Key to use when storing object connections as a property of an ImageData object.
KEY_OS_CENSORED - Static variable in class qupath.lib.objects.TMACoreObject
Metadata key for an overall survival censored flag.
KEY_OVERALL_SURVIVAL - Static variable in class qupath.lib.objects.TMACoreObject
Metadata key for an overall survival (temporal) value.
KEY_RECURRENCE_FREE_SURVIVAL - Static variable in class qupath.lib.objects.TMACoreObject
Metadata key for an recurrence-free survival (temporal) value.
KEY_RFS_CENSORED - Static variable in class qupath.lib.objects.TMACoreObject
Metadata key for an recurrence-free survival censored flag.
keySet() - Method in interface qupath.lib.measurements.MeasurementList
Get all available names as a set.

L

labeledImageExtension(String) - Method in class qupath.lib.images.writers.TileExporter
Specify a file extension for the labelled image, which determines the export file format.
labeledImageId(String) - Method in class qupath.lib.images.writers.TileExporter
Specify an identifier appended to the filename for labeled images.
LabeledImageServer - Class in qupath.lib.images.servers
A special ImageServer implementation that doesn't have a backing image, but rather constructs tiles from a PathObjectHierarchy where pixel values are integer labels corresponding stored and classified annotations.
LabeledImageServer.Builder - Class in qupath.lib.images.servers
Helper class for building a LabeledImageServer.
labeledImageSubDir(String) - Method in class qupath.lib.images.writers.TileExporter
Specify a subdirectory within which labeled image tiles should be saved.
labeledServer(ImageServer<BufferedImage>) - Method in class qupath.lib.images.writers.TileExporter
Optional server providing image labels.
labelsToAnnotations(Path, RegionRequest) - Static method in class qupath.lib.analysis.images.ContourTracing
Convert a labeled image to annotation objects.
labelsToAnnotations(Collection<Path>, boolean) - Static method in class qupath.lib.analysis.images.ContourTracing
Convert labeled images to annotation objects, determining the region from the filename if possible.
labelsToCells(Path, RegionRequest) - Static method in class qupath.lib.analysis.images.ContourTracing
Convert a 2-channel labeled image to cell objects.
labelsToCells(Collection<Path>, boolean) - Static method in class qupath.lib.analysis.images.ContourTracing
Convert 2-channel labeled images to cell objects, determining the region from the filename if possible.
labelsToDetections(Path, RegionRequest) - Static method in class qupath.lib.analysis.images.ContourTracing
Convert a labeled image to detection objects.
labelsToDetections(Collection<Path>, boolean) - Static method in class qupath.lib.analysis.images.ContourTracing
Convert labeled images to detection objects, determining the region from the filename if possible.
labelsToObjects(Path, RegionRequest, BiFunction<ROI, Number, PathObject>) - Static method in class qupath.lib.analysis.images.ContourTracing
Convert a labeled image to objects.
lastValue - Variable in class qupath.lib.plugins.parameters.BooleanParameter
 
lastValue - Variable in class qupath.lib.plugins.parameters.ChoiceParameter
 
lastValue - Variable in class qupath.lib.plugins.parameters.DoubleParameter
 
lastValue - Variable in class qupath.lib.plugins.parameters.EmptyParameter
 
lastValue - Variable in class qupath.lib.plugins.parameters.IntParameter
 
lastValue - Variable in class qupath.lib.plugins.parameters.NumericParameter
 
lastValue - Variable in class qupath.lib.plugins.parameters.StringParameter
 
LEGACY_KEY_UNIQUE_ID - Static variable in class qupath.lib.objects.TMACoreObject
Deprecated.
legacyPathToURI(String) - Static method in class qupath.lib.images.servers.ImageServerProvider
Method to help with converting legacy image paths to URIs.
levels(Collection<ImageServerMetadata.ImageResolutionLevel>) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder
Specify resolution levels, where the largest image should come first.
levelsFromDownsamples(double...) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder
Specify downsample values for pyramidal levels.
LINE - Enum constant in enum class qupath.lib.roi.interfaces.ROI.RoiType
ROI represents a line or polyline.
LineROI - Class in qupath.lib.roi
ROI representing a straight line, defined by its end points.
lineThickness(float) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Thickness of boundary lines and line annotations, defined in terms of pixels at the resolution specified by the downsample value of the server.
loadProject(File, Class<T>) - Static method in class qupath.lib.projects.ProjectIO
Load a project from a local file.
loadProject(URI, Class<T>) - Static method in class qupath.lib.projects.ProjectIO
Read project from URI.
locateFile(String, int, Path...) - Static method in class qupath.lib.io.UriUpdater
Attempt to update a file using the specified search paths.
locateFile(URI, int, Path...) - Static method in class qupath.lib.io.UriUpdater
Attempt to update a URI to find an existing file using the specified search paths.
lockObjects(PathObjectHierarchy, Collection<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools
Set specified objects to be 'locked'.
lockSelectedObjects(PathObjectHierarchy) - Static method in class qupath.lib.objects.PathObjectTools
Set selected objects to be 'locked', firing an update event if the status of any object is changed.
logOnce(Logger, String) - Static method in class qupath.lib.common.LogTools
Log a message once at the INFO level.
logOnce(Logger, Level, String) - Static method in class qupath.lib.common.LogTools
Log a message once at the specified level.
LogRankTest - Class in qupath.lib.analysis.stats.survival
Helper class to apply a log-rank test.
LogRankTest() - Constructor for class qupath.lib.analysis.stats.survival.LogRankTest
 
LogRankTest.LogRankResult - Class in qupath.lib.analysis.stats.survival
Simple structure used to manage the result of a log rank test.
LogTools - Class in qupath.lib.common
Helper class for logging.
LogTools() - Constructor for class qupath.lib.common.LogTools
 

M

MAGENTA - Static variable in class qupath.lib.common.ColorTools
Packed int representing magenta.
magnification(double) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder
Specify a magnification value for the highest-resolution image.
main(String[]) - Static method in class qupath.lib.common.Timeit
 
makeDefaultColorDeconvolutionStains(ColorDeconvolutionStains.DefaultColorDeconvolutionStains) - Static method in class qupath.lib.color.ColorDeconvolutionStains
Create a ColorDeconvolutionStains for a default stain combination, and default max values (255 for all channels).
makeDefaultStainVector(StainVector.DefaultStains) - Static method in class qupath.lib.color.StainVector
Get a default stain vector.
makeDoubleArrayWrapper(double[]) - Static method in class qupath.lib.analysis.stats.ArrayWrappers
Create a wrapper for a double array, returning values (predictably) as doubles.
makeFloatArrayWrapper(float[]) - Static method in class qupath.lib.analysis.stats.ArrayWrappers
Create a wrapper for a float array, returning values as doubles.
makeIntArrayWrapper(int[]) - Static method in class qupath.lib.analysis.stats.ArrayWrappers
Create a wrapper for an int array, returning values as doubles.
makeMeasurementHistogram(Collection<PathObject>, String, int) - Static method in class qupath.lib.analysis.stats.Histogram
Create a histogram depicting values of a specific measurement extracted from a collection of PathObjects.
makeOD(double, double) - Static method in class qupath.lib.color.ColorDeconvolutionHelper
Convert a single pixel value to an optical density as max(0, -log10(val/max).
makeODByLUT(float, double[]) - Static method in class qupath.lib.color.ColorDeconvolutionHelper
Convert a float pixel to an optical density value using a pre-computed lookup table.
makeODByLUT(int, double[]) - Static method in class qupath.lib.color.ColorDeconvolutionHelper
Convert an int pixel to an optical density value using a pre-computed lookup table.
makeODLUT(double) - Static method in class qupath.lib.color.ColorDeconvolutionHelper
Create an optical density lookup table with 256 entries, normalizing to the specified background value.
makeODLUT(double, int) - Static method in class qupath.lib.color.ColorDeconvolutionHelper
Create an optical density lookup table, normalizing to the specified background value.
makeProgressMonitor() - Method in class qupath.lib.plugins.AbstractTaskRunner
Create a progress monitor to update the user on what is happening.
makeProgressMonitor() - Method in class qupath.lib.plugins.CommandLineTaskRunner
 
makeReplacement(URI, URI) - Method in class qupath.lib.io.UriUpdater
Add a single replacement to the replacement map.
makeRGB(int, int, int) - Static method in class qupath.lib.common.ColorTools
makeRGBA(int, int, int, int) - Static method in class qupath.lib.common.ColorTools
Deprecated.
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.
makeScaledRGB(int, double) - Static method in class qupath.lib.common.ColorTools
Scale the RGB channels for a color by a fixed amount.
makeScaledRGBwithRangeCheck(float, float, float, ColorModel) - Static method in class qupath.lib.color.ColorTransformer
Create a packed RGB pixel value by applying a ColorModel to a (possibly scaled and offset) floating point value.
makeTiles(ROI, int, int, boolean) - Static method in class qupath.lib.roi.RoiTools
Make fixed-size rectangular tile ROIs for a specified area.
makeUnsignedByteArrayWrapper(byte[]) - Static method in class qupath.lib.analysis.stats.ArrayWrappers
Create a wrapper for a byte array, returning values as doubles.
makeUnsignedShortArrayWrapper(short[]) - Static method in class qupath.lib.analysis.stats.ArrayWrappers
Create a wrapper for a short array, returning values as doubles.
MASK_ALPHA - Static variable in class qupath.lib.common.ColorTools
Mask for use when extracting the alpha component from a packed ARGB int value.
MASK_BLUE - Static variable in class qupath.lib.common.ColorTools
Mask for use when extracting the blue component from a packed (A)RGB int value.
MASK_GREEN - Static variable in class qupath.lib.common.ColorTools
Mask for use when extracting the green component from a packed (A)RGB int value.
MASK_RED - Static variable in class qupath.lib.common.ColorTools
Mask for use when extracting the red component from a packed (A)RGB int value.
matchByID(Collection<? extends PathObject>, Collection<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools
Match objects according to their IDs.
matchClassName(String...) - Method in interface qupath.lib.images.servers.ImageServerBuilder
Check if this provider matches one or more specified classnames.
max(Padding) - Method in class qupath.lib.regions.Padding
Compare two paddings, and take the larger padding value on all sides.
MAX - Enum constant in enum class qupath.lib.images.servers.ZProjectedImageServer.Projection
A maximum projection on the z-stacks.
MAX - Static variable in interface qupath.lib.objects.utils.MeasurementStrategy
Calculate the maximum of each measurement and pass these to the output object.
maxChannelProject() - Method in class qupath.lib.images.servers.TransformedServerBuilder
Perform a maximum projection of the channels.
maxDecimalPlaces(int) - Method in class qupath.lib.common.Timeit
Set the maximum number of decimal places when reporting timings using seconds or minutes.
maxDimension(int) - Static method in class qupath.lib.images.servers.downsamples.DownsampleCalculators
Create a downsample calculator that resizes an image to ensure that its width and height are ≤ a specified maximum length.
maxOutputChannelLimit(int) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Specify the maximum number of output channels allowed before QuPath will throw an exception.
maxValue(Number) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder
Specify the maximum value supported by this image.
maybeCellLabels(Raster, int, int, int) - Static method in class qupath.lib.analysis.images.ContourTracing
Check whether a raster could be used to generate cell objects, by providing a nucleus and corresponding cell labels.
maybeCellLabels(SimpleImage, SimpleImage, int) - Static method in class qupath.lib.analysis.images.ContourTracing
Check whether two images could be used to generate cell objects, by providing a nucleus and corresponding cell labels.
MEAN - Enum constant in enum class qupath.lib.images.servers.ZProjectedImageServer.Projection
A mean projection on the z-stacks.
MEAN - Static variable in interface qupath.lib.objects.utils.MeasurementStrategy
Calculate the mean of each measurement and pass these to the output object.
MEAN_VARIANCE - Enum constant in enum class qupath.lib.classifiers.Normalization
Normalize by subtracting the mean and dividing by the standard deviation
Measurement - Interface in qupath.lib.measurements
Basic interface to define a measurement.
MeasurementList - Interface in qupath.lib.measurements
Interface defining a feature measurement list, consisting of key value pairs.
MeasurementList.MeasurementListType - Enum Class in qupath.lib.measurements
Enum representing different types of measurement list, with different priorities regarding flexibility and efficiency.
MeasurementListFactory - Class in qupath.lib.measurements
Factory for creating new measurement lists.
MeasurementStrategy - Interface in qupath.lib.objects.utils
A strategy for handling measurements between objects being merged.
MEDIAN - Enum constant in enum class qupath.lib.images.servers.ZProjectedImageServer.Projection
A median projection on the z-stacks.
MEDIAN - Static variable in interface qupath.lib.objects.utils.MeasurementStrategy
Calculate the median of each measurement and pass these to the output object.
merge(Collection<? extends PathObject>) - Method in class qupath.lib.objects.utils.ObjectMerger
Deprecated.
mergeClasses(PathClass, PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools
Merge two classifications together.
mergeMeasurements(List<? extends PathObject>, MeasurementList) - Method in interface qupath.lib.objects.utils.MeasurementStrategy
Merge the measurements for a set of input objects to a single measurement list.
mergeObjects(Collection<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools
Merge objects by calculating the union of their ROIs.
mergeObjects(Collection<? extends PathObject>, Function<? super PathObject, ? extends K>) - Static method in class qupath.lib.objects.PathObjectTools
Merge objects that share a property in common.
mergePointsForAllClasses(PathObjectHierarchy) - Static method in class qupath.lib.objects.PathObjectTools
Merge point annotations sharing the same PathClass and ImagePlane, creating multi-point annotations for all matching points and removing the (previously-separated) annotations.
mergePointsForClass(PathObjectHierarchy, PathClass) - Static method in class qupath.lib.objects.PathObjectTools
Merge point annotations with the specified PathClass sharing the same ImagePlane, creating a single multi-point annotation for all matching points and removing the (previously-separated) annotations.
mergePointsForSelectedObjectClasses(PathObjectHierarchy) - Static method in class qupath.lib.objects.PathObjectTools
Merge point annotations sharing the same PathClass and ImagePlane as the selected annotations, creating multi-point annotations for all matching points and removing the (previously-separated) annotations.
MetadataStore - Interface in qupath.lib.objects
Deprecated.
v0.6.0. Use MinimalMetadataStore instead.
MICROMETER - Static variable in class qupath.lib.images.servers.PixelCalibration
String to represent 'micrometer' units.
micrometerSymbol() - Static method in class qupath.lib.common.GeneralTools
Get a string to represent um (but with the proper 'mu' symbol)
microseconds() - Method in class qupath.lib.common.Timeit
Report timings in microseconds.
milliseconds() - Method in class qupath.lib.common.Timeit
Report timings in milliseconds.
MIN - Enum constant in enum class qupath.lib.images.servers.ZProjectedImageServer.Projection
A minimum projection on the z-stacks.
MIN - Static variable in interface qupath.lib.objects.utils.MeasurementStrategy
Calculate the minimum of each measurement and pass these to the output object.
MIN_MAX - Enum constant in enum class qupath.lib.classifiers.Normalization
Normalize into the range 0-1 using min and max values
minChannelProject() - Method in class qupath.lib.images.servers.TransformedServerBuilder
Perform a minimum projection of the channels.
MinimalMetadataStore - Interface in qupath.lib.interfaces
Minimal interface to indicate that an object can provide a map of metadata key/value pairs.
minutes() - Method in class qupath.lib.common.Timeit
Report timings in minutes.
minValue(Number) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder
Specify the minimum value supported by this image.
MISSING - Enum constant in enum class qupath.lib.io.UriUpdater.UriStatus
URI refers to a file that does not appear to exist or is inaccessible.
multichannelOutput(boolean) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
If true, the output image consists of multiple binary images concatenated as different channels, so that the channel number relates to a classification.
MULTICLASS_PROBABILITY - Enum constant in enum class qupath.lib.images.servers.ImageServerMetadata.ChannelType
Each channel represents a probability value, where each pixel is potentially part of multiple classes.

N

name(String) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder
Specify the image name.
NAME_NEGATIVE - Static variable in class qupath.lib.objects.classes.PathClass
Default name for a class representing "Negative" staining intensity
NAME_ONE_PLUS - Static variable in class qupath.lib.objects.classes.PathClass
Default name for a class representing "1+" staining intensity (i.e.
NAME_POSITIVE - Static variable in class qupath.lib.objects.classes.PathClass
Default name for a class representing "Positive" staining intensity
NAME_THREE_PLUS - Static variable in class qupath.lib.objects.classes.PathClass
Default name for a class representing "3+" staining intensity (i.e.
NAME_TWO_PLUS - Static variable in class qupath.lib.objects.classes.PathClass
Default name for a class representing "2+" staining intensity (i.e.
nameObjectsByCluster(Collection<Collection<? extends PathObject>>) - Static method in class qupath.lib.analysis.DelaunayTools
Assign object names based upon pre-computed clusters.
nameObjectsByCluster(Collection<Collection<? extends PathObject>>, Function<Integer, PathClass>) - Static method in class qupath.lib.analysis.DelaunayTools
Assign object classifications based upon pre-computed clusters.
nanoseconds() - Method in class qupath.lib.common.Timeit
Report timings in nanoseconds.
nBins() - Method in class qupath.lib.analysis.stats.Histogram
Total number of histogram bins.
nCensored() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData
Get the number of censored events.
nChannels() - Method in class qupath.lib.images.servers.AbstractImageServer
 
nChannels() - Method in interface qupath.lib.images.servers.ImageServer
Number of channels (3 for RGB).
nChildObjects() - Method in class qupath.lib.objects.PathObject
Total number of child objects.
nCores() - Method in class qupath.lib.objects.hierarchy.DefaultTMAGrid
 
nCores() - Method in interface qupath.lib.objects.hierarchy.TMAGrid
Total number of cores in the TMA grid.
nDescendants() - Method in class qupath.lib.objects.PathObject
Total number of descendant objects.
NECROSIS - Enum constant in enum class qupath.lib.objects.classes.PathClassFactory.StandardPathClasses
Deprecated.
Necrosis classification
NECROSIS - Static variable in class qupath.lib.objects.classes.PathClass.StandardPathClasses
Necrosis classification
negate() - Method in interface qupath.lib.objects.PathObjectPredicates.PathObjectPredicate
 
NEGATIVE - Enum constant in enum class qupath.lib.objects.classes.PathClassFactory.StandardPathClasses
Deprecated.
General class to represent something 'negative'
NEGATIVE - Static variable in class qupath.lib.objects.classes.PathClass.StandardPathClasses
General class to represent something 'negative'
nEvents() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData
Get the number of events, either observed or censored.
newBuilder(Collection<PathObject>) - Static method in class qupath.lib.analysis.DelaunayTools
Create a new DelaunayTools.Builder to compute a triangulation using the specified objects.
newInstance() - Static method in class qupath.lib.plugins.TaskRunnerUtils
Create a new instance.
nImages() - Method in interface qupath.lib.images.servers.FileFormatInfo.ImageCheckType
Return an estimate of the number of images if known, or -1 if unknown.
nImagesLargest() - Method in interface qupath.lib.images.servers.FileFormatInfo.ImageCheckType
Return the number of images with the largest image size, if known, or -1 if unknown.
nLevels() - Method in class qupath.lib.images.servers.ImageServerMetadata
Get the number of resolution levels.
nMissingValues() - Method in class qupath.lib.analysis.stats.Histogram
Number of NaNs in the input array.
NO_RUNNING_OFFSET - Static variable in class qupath.lib.images.servers.ZProjectedImageServer
Constant indicating that a full z-projection should be made using all slices, rather than a running z-projection made across a group of adjacent slices.
nObjects() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Number of objects in the hierarchy, excluding the root.
nObserved() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData
Get the number of observed (not censored) events.
NONE - Enum constant in enum class qupath.lib.classifiers.Normalization
Do not normalize features.
Normalization - Enum Class in qupath.lib.classifiers
Methods for normalizing features.
normalize(BufferedImageNormalizer) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Normalize the image using the provided normalizer.
NormalizedImageServer - Class in qupath.lib.images.servers
An ImageServer implementation used for stain normalization.
NormalizedImageServer(ImageServer<BufferedImage>, BufferedImageNormalizer) - Constructor for class qupath.lib.images.servers.NormalizedImageServer
 
noSelection() - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel
Returns true if no objects are selected.
nResolutions() - Method in class qupath.lib.images.servers.AbstractImageServer
 
nResolutions() - Method in interface qupath.lib.images.servers.ImageServer
Number of resolutions for the image.
nTimepoints() - Method in class qupath.lib.images.servers.AbstractImageServer
 
nTimepoints() - Method in interface qupath.lib.images.servers.ImageServer
Number of time points in a time series.
nTimepoints() - Method in class qupath.lib.images.servers.PixelCalibration
Get the number of known time points.
NULL_CLASS - Static variable in class qupath.lib.objects.classes.PathClass
Default PathClass that represents no classification.
NumericParameter<S> - Class in qupath.lib.plugins.parameters
Abstract parameter to represent a numeric value.
numNaNs(double[]) - Static method in class qupath.lib.common.GeneralTools
Count the number of NaN values in an array.
nValues() - Method in class qupath.lib.analysis.stats.Histogram
Number of values represented in the histogram (i.e.
nVertices() - Method in class qupath.lib.roi.AreaROI
Deprecated.
Get the number of vertices used to represent this area.
nVertices() - Method in class qupath.lib.roi.PolygonROI
Get the total number of vertices in the polygon.
nZSlices() - Method in class qupath.lib.images.servers.AbstractImageServer
 
nZSlices() - Method in interface qupath.lib.images.servers.ImageServer
Number of slices in a z-stack.

O

ObjectClassifier<T> - Interface in qupath.lib.classifiers.object
Interface defining object classifiers, which assign PathClasses to PathObjects.
ObjectClassifiers - Class in qupath.lib.classifiers.object
Helper class for creating ObjectClassifiers.
ObjectClassifiers() - Constructor for class qupath.lib.classifiers.object.ObjectClassifiers
 
ObjectClassifiers.ClassifyByMeasurementBuilder<T> - Class in qupath.lib.classifiers.object
Builder to create a simple ObjectClassifier that assigns a classification based upon whether the measurement of an object is above, equal to or below a specified threshold.
ObjectClassifiers.ObjectClassifierTypeAdapterFactory - Class in qupath.lib.classifiers.object
TypeAdapterFactory to help with serializing ObjectClassifiers to and from JSON.
objectCountPostfix() - Method in class qupath.lib.objects.PathObject
 
ObjectDetector<T> - Interface in qupath.lib.plugins
Minimal interface that may be used to plugins that perform detection within a specified ROI and using a specified ImageData with set parameters.
ObjectMerger - Class in qupath.lib.objects.utils
Helper class for merging objects using different criteria.
ObjectProcessor - Interface in qupath.lib.objects.utils
Minimal interface for processing one or more objects.
OD_Normalized - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
RGB values normalized to OD vector (to reduce intensity information)
Optical_density_sum - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
Sum of red, green and blue optical densities
opticalDensitySum(int, double[]) - Static method in class qupath.lib.color.ColorTransformer
Extract optical density sum value from a packed RGB pixel.
opticalDensitySum(int, double[], double[], double[]) - Static method in class qupath.lib.color.ColorTransformer
Extract optical density sum value from a packed RGB pixel.
or(PathObjectPredicates.PathObjectPredicate) - Method in interface qupath.lib.objects.PathObjectPredicates.PathObjectPredicate
Combine with another PathObjectPredicates.PathObjectPredicate through OR.
Original - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
Original image
OTHER - Enum constant in enum class qupath.lib.images.ImageData.ImageType
Other image type, not covered by any of the alternatives above.
OTHER - Enum constant in enum class qupath.lib.objects.classes.PathClassFactory.StandardPathClasses
Deprecated.
Other classification
OTHER - Static variable in class qupath.lib.objects.classes.PathClass.StandardPathClasses
Other classification
OTHER_STRUCTURE_CHANGE - Enum constant in enum class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent.HierarchyEventType
A more complex structural change was made than simply either adding or removing objects
outputChannels(Collection<ImageChannel>) - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata.Builder
Specify channels for output.
outputChannels(ImageChannel...) - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata.Builder
Specify channels for output.
outputPixelType(PixelType) - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata.Builder
Output pixel type.
overlap(int) - Method in class qupath.lib.images.writers.TileExporter
Define tile overlap (both x and y) in pixel units at the export resolution.
overlap(int, int) - Method in class qupath.lib.images.writers.TileExporter
Define tile overlap (x and y separately) in pixel units at the export resolution.
OverlapFixer - Class in qupath.lib.objects.utils
 
OverlapFixer.Builder - Class in qupath.lib.objects.utils
Builder for the OverlapFixer.
OverlapFixer.Strategy - Enum Class in qupath.lib.objects.utils
 
overlapsRequest(RegionRequest) - Method in class qupath.lib.regions.RegionRequest
Returns true if the region specified by this request overlaps with that of another request.

P

packARGB(int, int, int, int) - Static method in class qupath.lib.common.ColorTools
Make a packed ARGB value from specified input values.
packClippedARGB(int, int, int, int) - Static method in class qupath.lib.common.ColorTools
Make a packed ARGB value from specified input values, clipping to the range 0-255.
packClippedRGB(int, int, int) - Static method in class qupath.lib.common.ColorTools
Make a packed RGB value from specified input values, clipping to the range 0-255.
packRGB(int, int, int) - Static method in class qupath.lib.common.ColorTools
Make a packed RGB value from specified input values.
pad2D(int, int) - Method in class qupath.lib.regions.RegionRequest
Add symmetric padding to the x and y dimensions of a request.
pad2D(Padding) - Method in class qupath.lib.regions.RegionRequest
Add symmetric padding to the x and y dimensions of a request.
Padding - Class in qupath.lib.regions
Requested padding for a 2D image.
ParallelTileObject - Class in qupath.lib.plugins
A temporary object, used during parallel processing to represent a tile currently being used for object detection.
ParallelTileObject.Status - Enum Class in qupath.lib.plugins
Current processing status for the tile.
Parameter<S> - Interface in qupath.lib.plugins.parameters
Interface defining algorithm parameters, which need to be displayed to users somehow.
parameterChanged(ParameterList, String, boolean) - Method in interface qupath.lib.plugins.parameters.ParameterChangeListener
Notify listener that a parameter value has changed.
ParameterChangeListener - Interface in qupath.lib.plugins.parameters
Interface for objects that need to be notified when parameters have their values changed.
Parameterizable - Interface in qupath.lib.plugins.parameters
Interface for indicating that the implementing class takes adjustable parameters.
ParameterList - Class in qupath.lib.plugins.parameters
A collection of Parameters, which can be used for analysis & queried to construct appropriate GUIs.
ParameterList() - Constructor for class qupath.lib.plugins.parameters.ParameterList
 
params - Variable in class qupath.lib.plugins.AbstractInteractivePlugin
 
parentObjects(Collection<? extends PathObject>) - Method in class qupath.lib.images.writers.TileExporter
Specify parent objects to define tiles.
parentObjects(Predicate<PathObject>) - Method in class qupath.lib.images.writers.TileExporter
Specify a filter to extract parent objects to define tiles.
parse(String) - Static method in class qupath.lib.common.Version
Parse a Version object representing a semantic version number from a String.
parseArgStringValues(String) - Static method in class qupath.lib.common.GeneralTools
Parse the contents of a JSON String.
parseArgument(ImageData<T>, String) - Method in class qupath.lib.plugins.AbstractInteractivePlugin
 
parseArgument(ImageData<T>, String) - Method in class qupath.lib.plugins.AbstractPlugin
Parse the input argument, returning 'true' if the argument is valid and it's possible to run the plugin.
parseColorDeconvolutionStains(String, Map<String, List<Number>>) - Static method in class qupath.lib.color.ColorDeconvolutionStains
Create color deconvolution stains from the provided name and map.
parseColorDeconvolutionStainsArg(String) - Static method in class qupath.lib.color.ColorDeconvolutionStains
Parse color deconvolution stains from a JSON String, with keys 'Stain 1', 'Stain 2', (optionally) 'Stain 3' and 'Background'.
parseNumeric(List<String>, boolean) - Static method in class qupath.lib.io.TMAScoreImporter
Parse numeric values from a list of strings.
parseObjectsFromGeoJSON(JsonElement) - Static method in class qupath.lib.io.GsonTools
Attempt to read PathObjects from a JsonElement, interpreting it as GeoJSON.
parseObjectsFromGeoJSON(String) - Static method in class qupath.lib.io.GsonTools
Attempt to read PathObjects from a JSON string, interpreting it as GeoJSON.
parseRegion(String, int, int) - Static method in class qupath.lib.analysis.images.ContourTracing
Attempt to parse a RegionRequest corresponding to an image region from the file name.
parseStainValues(Locale, String) - Static method in class qupath.lib.color.ColorDeconvolutionStains
Parses 3 values, suitable for use as a stain vector
parseTMALabelString(String) - Static method in class qupath.lib.objects.PathObjectTools
Parse a string input representing potential TMA core labels.
parseTransformMatrix(String) - Static method in class qupath.lib.roi.GeometryTools
Parse the matrix (String) to create and return an AffineTransformation.
PathAnnotationObject - Class in qupath.lib.objects
An annotation PathObject.
PathAnnotationObject() - Constructor for class qupath.lib.objects.PathAnnotationObject
Default constructor.
PathCellObject - Class in qupath.lib.objects
A subclass of a PathDetectionObject, which also supports storing an (optional) extra ROI to represent the cell nucleus.
PathCellObject() - Constructor for class qupath.lib.objects.PathCellObject
Default constructor.
PathClass - Class in qupath.lib.objects.classes
Representation of an object's classification - which can be defined using any unique string identifier (e.g.
PathClass.StandardPathClasses - Class in qupath.lib.objects.classes
Enum representing standard classifications.
PathClassFactory - Class in qupath.lib.objects.classes
Deprecated.
since v0.4.0 in favor of methods added to PathClass directly.
PathClassFactory.StandardPathClasses - Enum Class in qupath.lib.objects.classes
Deprecated.
Enum representing standard classifications.
PathClassTools - Class in qupath.lib.objects.classes
Static methods for use with PathClass objects.
PathDetectionObject - Class in qupath.lib.objects
A detection PathObject.
PathDetectionObject() - Constructor for class qupath.lib.objects.PathDetectionObject
Default constructor.
PathDetectionObject(ROI, PathClass) - Constructor for class qupath.lib.objects.PathDetectionObject
Create a new PathDetectionObject with a float measurement list.
PathImage<T> - Interface in qupath.lib.images
Interface used when needing to associate pixel data with information regarding the image from which it was obtained.
PathInteractivePlugin<T> - Interface in qupath.lib.plugins
Interface to define a PathPlugin that requires a list of (user-adjustable) parameters.
PathIO - Class in qupath.lib.io
Primary class for loading/saving ImageData objects.
PathIO.GeoJsonExportOptions - Enum Class in qupath.lib.io
Options to customize the export of PathObjects as GeoJSON.
PathObject - Class in qupath.lib.objects
Fundamental object of interest in QuPath.
PathObject() - Constructor for class qupath.lib.objects.PathObject
Default constructor.
PathObject(MeasurementList) - Constructor for class qupath.lib.objects.PathObject
Create a PathObject with a specific measurement list.
PathObjectConnectionGroup - Interface in qupath.lib.objects
Deprecated.
v0.6.0, to be replaced by DelaunayTools.Subdivision
PathObjectConnections - Class in qupath.lib.objects
Data structure for storing multiple PathObjectConnectionGroups.
PathObjectConnections() - Constructor for class qupath.lib.objects.PathObjectConnections
Default constructor.
PathObjectFilter - Enum Class in qupath.lib.objects
Enumeration of filters (predicates) that can be used to select objects based on their type.
PathObjectHierarchy - Class in qupath.lib.objects.hierarchy
A basic hierarchy in which to store PathObjects.
PathObjectHierarchy() - Constructor for class qupath.lib.objects.hierarchy.PathObjectHierarchy
Default constructor, creates an empty hierarchy.
PathObjectHierarchyEvent - Class in qupath.lib.objects.hierarchy.events
An event class for passing on information about modifications to a PathObjectHierarchy.
PathObjectHierarchyEvent.HierarchyEventType - Enum Class in qupath.lib.objects.hierarchy.events
Enum representing different ways in which the hierarchy may have been updated.
PathObjectHierarchyListener - Interface in qupath.lib.objects.hierarchy.events
A listener for modifications to a PathObjectHierarchy (i.e.
PathObjectPredicates - Class in qupath.lib.objects
Classes to define JSON-serializable Predicates for PathObjects.
PathObjectPredicates() - Constructor for class qupath.lib.objects.PathObjectPredicates
 
PathObjectPredicates.PathObjectPredicate - Interface in qupath.lib.objects
A JSON-serializable Predicate for use with PathObjects.
PathObjectReader - Interface in qupath.lib.objects
Interface for classes capable of reading PathObjects from some source.
PathObjects - Class in qupath.lib.objects
Helper class to create PathObject.
PathObjects() - Constructor for class qupath.lib.objects.PathObjects
 
PathObjectSelectionListener - Interface in qupath.lib.objects.hierarchy.events
A listener to selection changes within a PathObjectSelectionModel.
PathObjectSelectionModel - Class in qupath.lib.objects.hierarchy.events
Model for handling selection of single and multiple PathObjects.
PathObjectSelectionModel() - Constructor for class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel
 
PathObjectTools - Class in qupath.lib.objects
A collection of static methods to help work with PathObjects.
PathObjectTools() - Constructor for class qupath.lib.objects.PathObjectTools
 
PathPlugin<T> - Interface in qupath.lib.plugins
Primary interface for defining a 'plugin' command.
PathROIObject - Class in qupath.lib.objects
Abstract class used for PathObjects that have ROIs associated with them.
PathRootObject - Class in qupath.lib.objects
The root object used at the base of a PathObjectHierarchy.
PathRootObject() - Constructor for class qupath.lib.objects.PathRootObject
 
PathTask - Interface in qupath.lib.plugins
Helper interface to define plugin tasks that require post-processing on a specific thread (i.e.
PathTileObject - Class in qupath.lib.objects
A subclass of PathDetectionObject, generally used to represent an image region that doesn't (in itself) correspond to any particularly interesting structure.
PathTileObject() - Constructor for class qupath.lib.objects.PathTileObject
Default constructor.
PathTileObject(ROI) - Constructor for class qupath.lib.objects.PathTileObject
 
PENDING - Enum constant in enum class qupath.lib.plugins.ParallelTileObject.Status
Tile waiting to be processed
PIXEL - Static variable in class qupath.lib.images.servers.PixelCalibration
String to represent 'pixel' units.
PixelCalibration - Class in qupath.lib.images.servers
Class used to represent pixel sizes.
PixelCalibration.Builder - Class in qupath.lib.images.servers
Builder class for PixelCalibration objects.
PixelClassificationImageServer - Class in qupath.lib.classifiers.pixel
ImageServer that delivers pixels derived from applying a PixelClassifier to another ImageServer.
PixelClassificationImageServer(ImageData<BufferedImage>, PixelClassifier) - Constructor for class qupath.lib.classifiers.pixel.PixelClassificationImageServer
Constructor.
PixelClassificationImageServer(ImageData<BufferedImage>, PixelClassifier, String, ColorModel) - Constructor for class qupath.lib.classifiers.pixel.PixelClassificationImageServer
Constructor.
PixelClassifier - Interface in qupath.lib.classifiers.pixel
Interface defining a pixel classifier.
PixelClassifierMetadata - Class in qupath.lib.classifiers.pixel
Metadata to control the behavior of a pixel classifier.
PixelClassifierMetadata.Builder - Class in qupath.lib.classifiers.pixel
Builder to create PixelClassifierMetadata objects.
pixelSize(double, double) - Method in class qupath.lib.roi.GeometryTools.GeometryConverter.Builder
Specify the pixel width and height, used to scale x and y coordinates during conversion (default is 1.0 for both).
pixelSize(PixelCalibration) - Static method in class qupath.lib.images.servers.downsamples.DownsampleCalculators
Create a downsample calculator that aims to downsample an image to have a fixed pixel size.
pixelSizeCalibrated() - Method in class qupath.lib.images.servers.ImageServerMetadata
Returns true if pixel width and height calibration information is available for the image.
pixelSizeMicrons(double) - Static method in class qupath.lib.images.servers.downsamples.DownsampleCalculators
Create a downsample calculator that aims to downsample an image to have a fixed pixel size, defined in microns.
pixelSizeMicrons(Number, Number) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder
Specify the pixel sizes, in microns.
pixelSizeMicrons(Number, Number) - Method in class qupath.lib.images.servers.PixelCalibration.Builder
Specify the pixel width and height in microns (the most common calibration value).
pixelType(PixelType) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder
Specify the bit-depth of the image.
PixelType - Enum Class in qupath.lib.images.servers
Image bit-depths and types.
pluginCompleted(String) - Method in class qupath.lib.plugins.CommandLineTaskRunner.CommandLineProgressMonitor
 
pluginCompleted(String) - Method in interface qupath.lib.plugins.SimpleProgressMonitor
Notify the monitor that the plugin has completed its work.
PngWriter - Class in qupath.lib.images.writers
ImageWriter implementation to write PNG images using ImageIO.
PngWriter() - Constructor for class qupath.lib.images.writers.PngWriter
 
Point - Interface in qupath.lib.geom
Simple interface defining a point.
POINT - Enum constant in enum class qupath.lib.roi.interfaces.ROI.RoiType
ROI represents points.
Point2 - Class in qupath.lib.geom
A 2D point (x & y coordinates).
Point2() - Constructor for class qupath.lib.geom.Point2
Default constructor for a point at location (0,0).
Point2(double, double) - Constructor for class qupath.lib.geom.Point2
Point constructor.
PointIO - Class in qupath.lib.io
Helper class for reading/writing point objects in terms of their x,y coordinates.
PointIO() - Constructor for class qupath.lib.io.PointIO
 
PointsROI - Class in qupath.lib.roi
ROI representing a collection of 2D points (distinct x,y coordinates).
PolygonROI - Class in qupath.lib.roi
ROI representing an arbitrary closed polygon.
PolylineROI - Class in qupath.lib.roi
ROI representing an arbitrary open polyline.
POSITIVE - Enum constant in enum class qupath.lib.objects.classes.PathClassFactory.StandardPathClasses
Deprecated.
General class to represent something 'positive'
POSITIVE - Static variable in class qupath.lib.objects.classes.PathClass.StandardPathClasses
General class to represent something 'positive'
positiveClassification(boolean) - Static method in class qupath.lib.objects.PathObjectPredicates
Predicate that returns true of an object has a positive classification.
postprocess(TaskRunner, ImageData<T>) - Method in class qupath.lib.plugins.AbstractPlugin
Called immediately after running any generated tasks.
postProcess(Collection<? extends PathTask>) - Method in class qupath.lib.plugins.AbstractTaskRunner
Perform post-processing after a task has complete.
preferNucleus(boolean) - Method in class qupath.lib.analysis.DelaunayTools.Builder
Specify that the triangulation should be based on nucleus ROIs where possible (only affects cell objects).
preferredTileSize(int, int) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder
Specify the preferred tile height and width.
Prefs - Class in qupath.lib.common
Core QuPath preferences.
Prefs() - Constructor for class qupath.lib.common.Prefs
 
preprocess(TaskRunner, ImageData<T>) - Method in class qupath.lib.plugins.AbstractPlugin
Called after parsing the argument String, and immediately before creating & running any generated tasks.
PRETTY_JSON - Enum constant in enum class qupath.lib.io.PathIO.GeoJsonExportOptions
Request pretty-printing for the JSON.
PROBABILITY - Enum constant in enum class qupath.lib.images.servers.ImageServerMetadata.ChannelType
Each channel represents a probability value, where it is assumed that there is only one true class per pixel.
process(Collection<? extends PathObject>) - Method in class qupath.lib.objects.utils.ObjectMerger
Calculate the result of applying the merging strategy to the input objects.
process(Collection<? extends PathObject>) - Method in interface qupath.lib.objects.utils.ObjectProcessor
Process a collection of objects and return the result.
process(Collection<? extends PathObject>) - Method in class qupath.lib.objects.utils.OverlapFixer
Fix overlaps in a collection of PathObjects, by the criteria specified in the builder.
PROCESSING - Enum constant in enum class qupath.lib.plugins.ParallelTileObject.Status
Tile currently being processed
Project<T> - Interface in qupath.lib.projects
Data structure to manage images and associated data in QuPath.
PROJECT_LOCATION - Static variable in interface qupath.lib.classifiers.object.ObjectClassifier
Default location to use when storing object classifiers in a project.
PROJECT_LOCATION - Static variable in interface qupath.lib.classifiers.pixel.PixelClassifier
Default location to use when storing object classifiers in a project.
ProjectImageEntry<T> - Interface in qupath.lib.projects
Class to represent an image entry within a project.
ProjectIO - Class in qupath.lib.projects
Read QuPath projects.
ProjectIO() - Constructor for class qupath.lib.projects.ProjectIO
 
Projects - Class in qupath.lib.projects
Static methods to help when working with Projects.
Projects() - Constructor for class qupath.lib.projects.Projects
 
put(String, double) - Method in interface qupath.lib.measurements.MeasurementList
Put a measurement value into the list, replacing any previous measurement with the same name.
put(String, T) - Method in interface qupath.lib.projects.ResourceManager.Manager
Save a resource within the project.
putAll(Collection<? extends Measurement>) - Method in interface qupath.lib.measurements.MeasurementList
Put all the measurements from the specified list into this one
putAll(Map<String, ? extends Number>) - Method in interface qupath.lib.measurements.MeasurementList
Put all the values from the specified map into this list
putAll(MeasurementList) - Method in interface qupath.lib.measurements.MeasurementList
Put all the measurements from the specified list into this one
putMetadataValue(String, String) - Method in interface qupath.lib.objects.MetadataStore
Deprecated.
as of v0.6.0. Use MinimalMetadataStore.getMetadata() with the Map.put(Object, Object) method instead
putMetadataValue(String, String) - Method in class qupath.lib.objects.TMACoreObject
Deprecated.
putMetadataValue(String, String) - Method in interface qupath.lib.projects.ProjectImageEntry
Deprecated.
v0.6.0, use MinimalMetadataStore.getMetadata() instead to directly access the metadata.
pyramidalize(ImageServer<BufferedImage>, double...) - Static method in class qupath.lib.images.servers.ImageServers
Wrap an ImageServer to dynamically generate a pyramid.
pyramidalizeTiled(ImageServer<BufferedImage>, int, int, double...) - Static method in class qupath.lib.images.servers.ImageServers
Wrap an ImageServer to dynamically generate a pyramid, using specified tile sizes.

Q

qupath.lib.analysis - package qupath.lib.analysis
Classes to aid with analysis.
qupath.lib.analysis.images - package qupath.lib.analysis.images
Helper interfaces and methods to write pixel processing algorithms.
qupath.lib.analysis.stats - package qupath.lib.analysis.stats
Calculate simple statistics from arrays.
qupath.lib.analysis.stats.survival - package qupath.lib.analysis.stats.survival
Helper classes for survival analysis.
qupath.lib.awt.common - package qupath.lib.awt.common
Static classes and methods to help work with Java AWT.
qupath.lib.classifiers - package qupath.lib.classifiers
Classes and interfaces to support machine learning classifiers.
qupath.lib.classifiers.object - package qupath.lib.classifiers.object
Classes for object classification in QuPath.
qupath.lib.classifiers.pixel - package qupath.lib.classifiers.pixel
Core support for pixel classification.
qupath.lib.color - package qupath.lib.color
Classes to assist with color, including stain separation and color transforms.
qupath.lib.common - package qupath.lib.common
General-purpose helper classes.
qupath.lib.geom - package qupath.lib.geom
Simple, immutable classes to represent points and dimensions.
qupath.lib.images - package qupath.lib.images
Defines the ImageData class to represent the key data associated with an analyzed image.
qupath.lib.images.servers - package qupath.lib.images.servers
Supports accessing pixels and metadata in QuPath.
qupath.lib.images.servers.downsamples - package qupath.lib.images.servers.downsamples
Different ways to calculate a reasonable downsample value when extracting a region from an ImageServer.
qupath.lib.images.servers.transforms - package qupath.lib.images.servers.transforms
 
qupath.lib.images.writers - package qupath.lib.images.writers
Supports for writing images of various kinds in various ways.
qupath.lib.interfaces - package qupath.lib.interfaces
 
qupath.lib.io - package qupath.lib.io
Supports reading and writing some core QuPath data structures.
qupath.lib.measurements - package qupath.lib.measurements
Provides measurement lists for use with PathObjects.
qupath.lib.objects - package qupath.lib.objects
Provides PathObjects, used to represent annotations and other image structures within QuPath.
qupath.lib.objects.classes - package qupath.lib.objects.classes
Defines classes to represent classifications for PathObjects.
qupath.lib.objects.hierarchy - package qupath.lib.objects.hierarchy
Classes to represent the object hierarchy.
qupath.lib.objects.hierarchy.events - package qupath.lib.objects.hierarchy.events
Events triggered when the hierarchy changes, such as objects being added, removed or reclassified.
qupath.lib.objects.utils - package qupath.lib.objects.utils
Helper classes for working with PathObjects.
qupath.lib.plugins - package qupath.lib.plugins
Classes to support general analysis commands.
qupath.lib.plugins.parameters - package qupath.lib.plugins.parameters
Defines classes for handling parameters used in interactive dialogs or as method arguments.
qupath.lib.plugins.workflow - package qupath.lib.plugins.workflow
Classes and interfaces related to logging analysis steps to assist scripting and reproducibility.
qupath.lib.projects - package qupath.lib.projects
Classes and interfaces related to projects, which are used to manage multiple images.
qupath.lib.regions - package qupath.lib.regions
Defines immutable classes for representing image planes and regions.
qupath.lib.roi - package qupath.lib.roi
Classes that define regions of interest (ROIs).
qupath.lib.roi.interfaces - package qupath.lib.roi.interfaces
Interface that define regions of interest (ROIs).

R

RANDOM - Static variable in interface qupath.lib.objects.utils.MeasurementStrategy
Choose an object at random and use the measurements from this object.
read(JsonReader) - Method in class qupath.lib.images.servers.ColorTransforms.ColorTransformTypeAdapter
 
readAllTiles() - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer
Read all the tiles.
readBufferedImage(RegionRequest) - Method in interface qupath.lib.images.servers.ImageServer
Deprecated.
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.
readClassifier(Path) - Static method in class qupath.lib.classifiers.object.ObjectClassifiers
Read the classifier from a file.
readCSV(File) - Static method in class qupath.lib.io.TMAScoreImporter
Read CSV data from a file into a map connecting column headers (keys) to lists of Strings (entries).
readCSV(String) - Static method in class qupath.lib.io.TMAScoreImporter
Read CSV data from a String into a map connecting column headers (keys) to lists of Strings (entries).
readCSV(Scanner) - Static method in class qupath.lib.io.TMAScoreImporter
Read CSV data into a map connecting column headers (keys) to lists of Strings (entries).
readExternal(ObjectInput) - Method in class qupath.lib.color.ColorDeconvolutionStains
 
readExternal(ObjectInput) - Method in class qupath.lib.color.StainVector
 
readExternal(ObjectInput) - Method in class qupath.lib.geom.Point2
 
readExternal(ObjectInput) - Method in class qupath.lib.objects.DefaultPathObjectConnectionGroup
Deprecated.
 
readExternal(ObjectInput) - Method in class qupath.lib.objects.PathCellObject
 
readExternal(ObjectInput) - Method in class qupath.lib.objects.PathObject
 
readExternal(ObjectInput) - Method in class qupath.lib.objects.PathObjectConnections
 
readExternal(ObjectInput) - Method in class qupath.lib.objects.PathROIObject
 
readExternal(ObjectInput) - Method in class qupath.lib.objects.TMACoreObject
 
readExternal(ObjectInput) - Method in class qupath.lib.plugins.workflow.SimplePluginWorkflowStep
 
readExternal(ObjectInput) - Method in class qupath.lib.plugins.workflow.Workflow
 
readFileAsString(File) - Static method in class qupath.lib.common.GeneralTools
Read the entire contents of a file into a single String.
readFileAsString(String) - Static method in class qupath.lib.common.GeneralTools
Read the entire contents of a file given by the specified path into a single String.
readHierarchy() - Method in interface qupath.lib.projects.ProjectImageEntry
Read the PathObjectHierarchy for this entry, or return an empty hierarchy if none is available.
readHierarchy(File) - Static method in class qupath.lib.io.PathIO
Read a hierarchy from a .qpdata file.
readHierarchy(InputStream) - Static method in class qupath.lib.io.PathIO
Read a PathObjectHierarchy from a saved data file (omitting all other contents).
readHierarchy(Path) - Static method in class qupath.lib.io.PathIO
Read a hierarchy from a .qpdata file.
readImageData() - Method in interface qupath.lib.projects.ProjectImageEntry
Read the ImageData associated with this entry, or create a new ImageData if none is currently present.
readImageData(File) - Static method in class qupath.lib.io.PathIO
Read and initialize an ImageData from a data file.
readImageData(File, ImageData<T>, ImageServer<T>, Class<T>) - Static method in class qupath.lib.io.PathIO
Deprecated.
since v0.6.0
readImageData(File, ImageServer<T>) - Static method in class qupath.lib.io.PathIO
Read and initialize an ImageData from a data file.
readImageData(InputStream, ImageData<T>, ImageServer<T>, Class<T>) - Static method in class qupath.lib.io.PathIO
Deprecated.
since v0.6.0
readImageData(InputStream, ImageServerBuilder.ServerBuilder<T>) - Static method in class qupath.lib.io.PathIO
Read an ImageData, optionally providing a serverBuilder for lazy image loading.
readImageData(Path) - Static method in class qupath.lib.io.PathIO
Read and initialize an ImageData from a data file.
readImageData(Path, ImageData<T>, ImageServer<T>, Class<T>) - Static method in class qupath.lib.io.PathIO
Deprecated.
since v0.6.0
readImageData(Path, ImageServer<T>) - Static method in class qupath.lib.io.PathIO
Read and initialize an ImageData from a data file.
readImageData(Path, ImageServerBuilder.ServerBuilder<T>) - Static method in class qupath.lib.io.PathIO
Read an ImageData, optionally providing a serverBuilder for lazy image loading.
readInputStreamAsString(InputStream) - Static method in class qupath.lib.common.GeneralTools
Read the entire contents of an InputStream into a single String.
readObjects(File) - Static method in class qupath.lib.io.PathIO
Read a list of PathObject from a file.
readObjects(Path) - Static method in class qupath.lib.io.PathIO
Read a list of PathObject from a file.
readObjectsFromGeoJSON(InputStream) - Static method in class qupath.lib.io.PathIO
Read a list of PathObject from an input stream.
readPathObjects() - Method in interface qupath.lib.objects.PathObjectReader
Read a collection of objects from the source.
readPoints(File) - Static method in class qupath.lib.io.PointIO
Read a list of point annotations from a file.
readPoints(InputStream) - Static method in class qupath.lib.io.PointIO
Read a list of point annotations from a stream.
readPointsObjectList(File) - Static method in class qupath.lib.io.PointIO
Deprecated.
readRegion(double, int, int, int, int) - Method in interface qupath.lib.images.servers.ImageServer
Read a 2D(+C) image region from the default ImagePlane (i.e.
readRegion(double, int, int, int, int, int, int) - Method in interface qupath.lib.images.servers.ImageServer
Read a 2D(+C) image region for a specified z-plane and timepoint.
readRegion(RegionRequest) - Method in class qupath.lib.images.servers.AbstractTileableImageServer
 
readRegion(RegionRequest) - Method in class qupath.lib.images.servers.AffineTransformImageServer
 
readRegion(RegionRequest) - Method in class qupath.lib.images.servers.ChannelTransformFeatureServer
 
readRegion(RegionRequest) - Method in class qupath.lib.images.servers.CroppedImageServer
 
readRegion(RegionRequest) - Method in interface qupath.lib.images.servers.ImageServer
Read a 2D(+C) image region for a specified RegionRequest.
readRegion(RegionRequest) - Method in class qupath.lib.images.servers.RearrangeRGBImageServer
 
readRegion(RegionRequest) - Method in class qupath.lib.images.servers.RotatedImageServer
 
readRegion(RegionRequest) - Method in class qupath.lib.images.servers.SlicedImageServer
 
readRegion(RegionRequest) - Method in class qupath.lib.images.servers.TransformingImageServer
 
readResolve() - Method in class qupath.lib.objects.classes.PathClass
Called during deserialization to ensure that only a single instance of each PathClass exists.
readSerializedServerPath(File) - Static method in class qupath.lib.io.PathIO
Deprecated.
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.
readTile(TileRequest) - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer
 
readTile(TileRequest) - Method in class qupath.lib.images.servers.AbstractTileableImageServer
Read a single image tile.
readTile(TileRequest) - Method in class qupath.lib.images.servers.LabeledImageServer
 
readTile(TileRequest) - Method in class qupath.lib.images.servers.NormalizedImageServer
 
readTile(TileRequest) - Method in class qupath.lib.images.servers.SparseImageServer
 
readTile(TileRequest) - Method in class qupath.lib.images.servers.TypeConvertImageServer
 
readTile(TileRequest) - Method in class qupath.lib.images.servers.WrappedBufferedImageServer
 
readTile(TileRequest) - Method in class qupath.lib.images.servers.ZConcatenatedImageServer
 
readTile(TileRequest) - Method in class qupath.lib.images.servers.ZProjectedImageServer
 
readURLAsString(URL, int) - Static method in class qupath.lib.common.GeneralTools
Read URL as String, with specified timeout in milliseconds.
rearrangeByStride(Collection<T>, T[], int) - Static method in class qupath.lib.plugins.AbstractPlugin
Test method for rearranging a collection so that entries are interleaved with a regularity given by stride.
RearrangeRGBImageServer - Class in qupath.lib.images.servers
Simple image server to swap the red and blue channels of an RGB image.
RearrangeRGBImageServer(ImageServer<BufferedImage>, String) - Constructor for class qupath.lib.images.servers.RearrangeRGBImageServer
 
Reclassifier - Class in qupath.lib.objects.classes
Helper class when classifying PathObjects.
Reclassifier(PathObject, PathClass, boolean) - Constructor for class qupath.lib.objects.classes.Reclassifier
Helper class to store an object prior to reclassifying it.
Reclassifier(PathObject, PathClass, boolean, double) - Constructor for class qupath.lib.objects.classes.Reclassifier
Helper class to store an object prior to reclassifying it, including a classification probability.
recomputeBounds() - Method in class qupath.lib.roi.PointsROI
 
RectangleROI - Class in qupath.lib.roi
ROI representing a square or rectangle (unrotated).
red(int) - Static method in class qupath.lib.common.ColorTools
Extract the 8-bit red value from a packed RGB value.
Red - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
Red channel only
RED - Static variable in class qupath.lib.common.ColorTools
Packed int representing red.
RED - Static variable in class qupath.lib.images.servers.ImageChannel
Default red channel for RGB images.
Red_chromaticity - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
Red chromaticity value, red / max(1, red + green + blue)
Red_OD - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
Red channel optical densities
redChromaticity(int) - Static method in class qupath.lib.color.ColorTransformer
Extract red chromaticity value from a packed RGB pixel, red / max(1, red + green + blue)
refineAreas(Geometry, double, double) - Static method in class qupath.lib.roi.GeometryTools
Remove small fragments and fill small interior rings within a Geometry.
refineColorDeconvolutionStains(int[], ColorDeconvolutionStains, double, double) - Static method in class qupath.lib.color.ColorDeconvolutionHelper
Attempt to automatically refine color deconvolution stains based upon pixel values.
refreshID() - Method in class qupath.lib.objects.PathObject
Regenerate a new random ID.
region(ImageRegion) - Method in class qupath.lib.images.writers.TileExporter
Define the region to be processed.
region(RegionRequest) - Method in class qupath.lib.images.writers.TileExporter
Define the region to be processed, including downsample.
REGION - Enum constant in enum class qupath.lib.objects.classes.PathClassFactory.StandardPathClasses
Deprecated.
Region class.
REGION - Static variable in class qupath.lib.objects.classes.PathClass.StandardPathClasses
Region class.
RegionRequest - Class in qupath.lib.regions
Class for defining an image region that can also be used to request these region from an ImageServer.
regionToEnvelope(ImageRegion) - Static method in class qupath.lib.roi.GeometryTools
Convert an ImageRegion to an Envelope.
regionToGeometry(ImageRegion) - Static method in class qupath.lib.roi.GeometryTools
Convert an ImageRegion to a rectangular Geometry.
registerAlias(Class<? extends T>, String) - Method in class qupath.lib.io.GsonTools.SubTypeAdapterFactory
Register an alias label for a specified subtype.
registerSubtype(Class<? extends ObjectClassifier>) - Static method in class qupath.lib.classifiers.object.ObjectClassifiers.ObjectClassifierTypeAdapterFactory
Register a new ObjectClassifier subtype for compatibility with Gson serialization.
registerSubtype(Class<? extends T>) - Method in class qupath.lib.io.GsonTools.SubTypeAdapterFactory
Register a subtype using the default label (the simple name of the class).
registerSubtype(Class<? extends T>, String) - Method in class qupath.lib.io.GsonTools.SubTypeAdapterFactory
Register a subtype using a custom label.
relabelTMAGrid(TMAGrid, String, String, boolean) - Static method in class qupath.lib.objects.PathObjectTools
Relabel a TMA grid.
relative(URI, URI) - Method in class qupath.lib.io.UriUpdater
Identify replacements for missing URIs by relativizing the URI.
relative(Path, Path) - Method in class qupath.lib.io.UriUpdater
Identify replacements for missing URIs by relativizing paths.
remove(String) - Method in interface qupath.lib.measurements.MeasurementList
Remove a named measurement
remove(String) - Method in interface qupath.lib.projects.ResourceManager.Manager
Remove a resource within the project.
removeAll(String...) - Method in interface qupath.lib.measurements.MeasurementList
Remove all the measurements with the specified names.
removeAllImages(Collection<ProjectImageEntry<T>>, boolean) - Method in interface qupath.lib.projects.Project
Remove multiple images from the project, optionally including associated data.
removeChildObject(PathObject) - Method in class qupath.lib.objects.PathObject
Remove a single object from the child list of this object.
removeChildObjects(Collection<PathObject>) - Method in class qupath.lib.objects.PathObject
Remove multiple objects from the child list of this object.
REMOVED - Enum constant in enum class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent.HierarchyEventType
An object has been removed
removeEmptyParameters() - Method in class qupath.lib.plugins.parameters.ParameterList
Remove all empty parameters from this list.
removeFragments(Geometry, double) - Static method in class qupath.lib.roi.GeometryTools
Remove fragments smaller than the specified area from a Geometry, ignoring internal rings.
removeGroup(PathObjectConnectionGroup) - Method in class qupath.lib.objects.PathObjectConnections
Remove a connections group.
removeImage(ProjectImageEntry<?>, boolean) - Method in interface qupath.lib.projects.Project
Remove an image from the project, optionally including associated data.
removeInteriorRings(Geometry, double) - Static method in class qupath.lib.roi.GeometryTools
Fill all interior rings for the specified geometry that have an area < a specified threshold.
removeListener(PathObjectHierarchyListener) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Remove a hierarchy change listener.
removeMeasurements(String...) - Method in interface qupath.lib.measurements.MeasurementList
Deprecated.
removeMetadataValue(String) - Method in interface qupath.lib.projects.ProjectImageEntry
Deprecated.
v0.6.0, use MinimalMetadataStore.getMetadata() instead to directly access the metadata.
removeNames(PathClass, String...) - Static method in class qupath.lib.objects.classes.PathClassTools
Create a PathClass with specific name elements removed (if present) from an existing classification.
removeNames(PathClass, Collection<String>) - Static method in class qupath.lib.objects.classes.PathClassTools
Create a PathClass with specific name elements removed (if present) from an existing classification.
removeObject(PathObject, boolean) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Remove a single object from the hierarchy, firing a remove event.
removeObjects(Collection<? extends PathObject>, boolean) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Remove a collection of objects, firing a single 'hierarchy changed' event afterwards to notify listeners if anything happened (i.e.
removeObjectWithoutUpdate(PathObject, boolean) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Remove a single object from the hierarchy, without firing a remove event.
removeOverlaps(Collection<? extends PathObject>, Comparator<PathObject>, double) - Static method in class qupath.lib.objects.PathObjectTools
Resolve overlaps, discarding one and keeping the other.
removeOverlapsByLocation(Collection<? extends PathObject>, double) - Static method in class qupath.lib.objects.PathObjectTools
Resolve overlapping object by location, retaining the object closest to the image 'origin' and discarding the object further away.
removeOverlapsBySize(Collection<? extends PathObject>, double) - Static method in class qupath.lib.objects.PathObjectTools
Resolve overlapping objects by size, retaining the object with the larger ROI and discarding the object with the smaller ROI.
removeParameter(String) - Method in class qupath.lib.plugins.parameters.ParameterList
Remove a parameter from this list.
removePathObjectSelectionListener(PathObjectSelectionListener) - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel
Remove listener for selection changes.
removeProperty(String) - Method in class qupath.lib.images.ImageData
Remove a specified property.
removePropertyChangeListener(PropertyChangeListener) - Method in class qupath.lib.images.ImageData
Remove a property change listener.
removeSmallPieces(ROI, double, double) - Static method in class qupath.lib.roi.RoiTools
Remove small fragments and fill small holes of an area ROI.
removeStep(int) - Method in class qupath.lib.plugins.workflow.Workflow
Remove a single step, identified by its list index.
removeStep(WorkflowStep) - Method in class qupath.lib.plugins.workflow.Workflow
Remove a single step, firing an update event if the step was successfully removed.
removeSteps(Collection<WorkflowStep>) - Method in class qupath.lib.plugins.workflow.Workflow
Remove a collection of steps, firing an update event if the workflow was changed.
removeTouchingBounds(PathObjectHierarchy, PathObject) - Static method in class qupath.lib.objects.PathObjectTools
Remove all objects with ROIs that touch or overlap the ROI of the parent object.
removeTouchingBounds(PathObjectHierarchy, PathObject, Predicate<PathObject>) - Static method in class qupath.lib.objects.PathObjectTools
/** Remove all objects with ROIs that touch or overlap the ROI of the parent object, optionally filtering to consider only filtered objects for removal.
removeTouchingImageBounds(ImageData<?>) - Static method in class qupath.lib.objects.PathObjectTools
Find all the objects that touch (or cross) a rectangle representing the image bounds.
removeTouchingImageBounds(ImageData<?>, Predicate<PathObject>) - Static method in class qupath.lib.objects.PathObjectTools
Find all the objects that touch (or cross) a rectangle representing the image bounds.
removeWorkflowListener(WorkflowListener) - Method in class qupath.lib.plugins.workflow.Workflow
Remove a listener for changes to the workflow.
reorderRGB(String) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Rearrange the channel order of an RGB image.
replaceCurlyQuotes(String) - Static method in class qupath.lib.common.GeneralTools
Replace different kinds of 'curly quote' in a String with straight quotes.
replaceGremlins(String, CharSequence) - Static method in class qupath.lib.common.GeneralTools
Replace non-printable characters from a String with a specified replacement (may be null).
replaceLastStep(WorkflowStep) - Method in class qupath.lib.plugins.workflow.Workflow
Replace the most recently added step with this one.
requestedPixelSize(double) - Method in class qupath.lib.images.writers.TileExporter
Define resolution as a pixel size in calibrated units.
requestHierarchyUpdate() - Method in class qupath.lib.plugins.AbstractPlugin
Optionally request a hierarchy update after the tasks have run.
requestNewHandle(double, double) - Method in class qupath.lib.roi.RoiEditor
Request an updated ROI with a new handle inserted - useful e.g.
resetActiveHandle() - Method in class qupath.lib.roi.RoiEditor
Ensure that no handle is active.
resetColors(Collection<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools
Reset the color to null for the specified objects.
resetPathClass() - Method in class qupath.lib.objects.PathObject
Reset the classification (i.e.
resetValue() - Method in class qupath.lib.plugins.parameters.BooleanParameter
 
resetValue() - Method in class qupath.lib.plugins.parameters.ChoiceParameter
 
resetValue() - Method in class qupath.lib.plugins.parameters.DoubleParameter
 
resetValue() - Method in class qupath.lib.plugins.parameters.EmptyParameter
 
resetValue() - Method in class qupath.lib.plugins.parameters.IntParameter
 
resetValue() - Method in class qupath.lib.plugins.parameters.NumericParameter
 
resetValue() - Method in class qupath.lib.plugins.parameters.StringParameter
 
resetValue() - Method in interface qupath.lib.plugins.parameters.Parameter
Set last value to null (so default can be used).
RESIDUAL_KEY - Static variable in class qupath.lib.color.ColorDeconvolutionStains
 
resize(BufferedImage, int, int, boolean) - Static method in class qupath.lib.awt.common.BufferedImageTools
Resize the image to have the requested width/height, using area averaging and bilinear interpolation.
resolveHierarchy() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Attempt to resolve the parent-child relationships between all objects within the hierarchy.
resolveOverlaps() - Method in class qupath.lib.plugins.ParallelTileObject
Request that the tile object attempts to resolve overlaps with its neighboring tiles.
ResourceManager - Class in qupath.lib.projects
Manage the storage and retrieval of resources with a ResourceManager.
ResourceManager() - Constructor for class qupath.lib.projects.ResourceManager
 
ResourceManager.Manager<T> - Interface in qupath.lib.projects
Simple manager to handle saving and retrieving resources of different kinds, for example from projects or a user directory.
restoreClassificationsFromMap(Map<PathObject, PathClass>) - Static method in class qupath.lib.objects.PathObjectTools
Reassign classifications to objects, as were previously obtained using PathObjectTools.createClassificationMap(Collection).
retrieveMetadataKeys() - Method in class qupath.lib.objects.PathObject
Deprecated.
v0.6.0, use PathObject.getMetadata() to directly access the metadata instead.
retrieveMetadataValue(String) - Method in class qupath.lib.objects.PathObject
Deprecated.
v0.6.0, use PathObject.getMetadata() to directly access the metadata instead.
rgb(boolean) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder
Specify that the image stores pixels in (A)RGB form.
RGB_mean - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
Mean of red, green and blue channels
rgbMean(int) - Static method in class qupath.lib.color.ColorTransformer
Extract mean of RGB values from a packed RGB pixel.
ROI - Enum constant in enum class qupath.lib.objects.PathObjectFilter
Accept any object that has a ROI
ROI - Interface in qupath.lib.roi.interfaces
Base interface for defining regions of interest (ROIs) within QuPath.
ROI_AREA - Enum constant in enum class qupath.lib.objects.PathObjectFilter
Accept any object that has an area ROI
ROI_LINE - Enum constant in enum class qupath.lib.objects.PathObjectFilter
Accept any object that has a line ROI
ROI_POINT - Enum constant in enum class qupath.lib.objects.PathObjectFilter
Accept any object that has a points ROI
ROI.RoiType - Enum Class in qupath.lib.roi.interfaces
Enum representing the major different types of ROI.
roiBounds() - Method in class qupath.lib.analysis.DelaunayTools.Builder
Specify that the triangulation should be based on ROI boundary coordinates with the default densify factor.
roiBounds(double, double) - Method in class qupath.lib.analysis.DelaunayTools.Builder
Specify that the triangulation should be based on ROI boundary coordinates with a specified densify factor.
RoiEditor - Class in qupath.lib.roi
Helper class for interactively modifying existing ROIs.
ROIs - Class in qupath.lib.roi
This class consists exclusively of static methods that operate on or return regions of interest (ROIs).
ROIs() - Constructor for class qupath.lib.roi.ROIs
 
roiToEnvelope(ROI) - Static method in class qupath.lib.roi.GeometryTools
Convert the bounding box of a ROI to an Envelope.
roiToGeometry(ROI) - Method in class qupath.lib.roi.GeometryTools.GeometryConverter
Convert a QuPath ROI to a JTS Geometry.
roiToGeometry(ROI) - Static method in class qupath.lib.roi.GeometryTools
Convert to QuPath ROI to a JTS Geometry.
RoiTools - Class in qupath.lib.roi
A collection of static methods for working with ROIs.
RoiTools() - Constructor for class qupath.lib.roi.RoiTools
 
RoiTools.CombineOp - Enum Class in qupath.lib.roi
Methods of combining two ROIs.
rotate(RotatedImageServer.Rotation) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Rotate the image, using an increment of 90 degrees.
ROTATE_180 - Enum constant in enum class qupath.lib.images.servers.RotatedImageServer.Rotation
Rotate 180 degrees.
ROTATE_270 - Enum constant in enum class qupath.lib.images.servers.RotatedImageServer.Rotation
Rotate 270 degrees clockwise.
ROTATE_90 - Enum constant in enum class qupath.lib.images.servers.RotatedImageServer.Rotation
Rotate 90 degrees clockwise.
ROTATE_NONE - Enum constant in enum class qupath.lib.images.servers.RotatedImageServer.Rotation
No rotation.
RotatedImageServer - Class in qupath.lib.images.servers
ImageServer that wraps another ImageServer, but intercepts region requests to effectively rotate the image by 90, 180 or 270 degrees.
RotatedImageServer(ImageServer<BufferedImage>, RotatedImageServer.Rotation) - Constructor for class qupath.lib.images.servers.RotatedImageServer
Create an image server that rotates pixel requests for a second server by a specified increment of 90 degrees.
RotatedImageServer.Rotation - Enum Class in qupath.lib.images.servers
Enum for rotations in increments of 90 degrees.
roundCoordinates(Geometry) - Static method in class qupath.lib.roi.GeometryTools
Round coordinates in a Geometry to integer values.
runDetection(ImageData<T>, ParameterList, ROI) - Method in interface qupath.lib.plugins.ObjectDetector
Detect objects.
RunningStatistics - Class in qupath.lib.analysis.stats
Helper class for computing basic statistics from values as they are added.
RunningStatistics() - Constructor for class qupath.lib.analysis.stats.RunningStatistics
Default constructor.
runPlugin(TaskRunner, ImageData<T>, String) - Method in class qupath.lib.plugins.AbstractPlugin
 
runPlugin(TaskRunner, ImageData<T>, String) - Method in interface qupath.lib.plugins.PathPlugin
Run the plugin.
RunSavedClassifierWorkflowStep - Class in qupath.lib.plugins.workflow
WorkflowStep for running a saved PathObjectClassifier.
RunSavedClassifierWorkflowStep(String) - Constructor for class qupath.lib.plugins.workflow.RunSavedClassifierWorkflowStep
Constructor, taking the path to the serialized classifier.
RunSavedClassifierWorkflowStep(String, String) - Constructor for class qupath.lib.plugins.workflow.RunSavedClassifierWorkflowStep
Create a workflow step to run a classifier.
runTasks(String, Collection<? extends Runnable>) - Method in class qupath.lib.plugins.AbstractTaskRunner
 
runTasks(String, Collection<? extends Runnable>) - Method in interface qupath.lib.plugins.TaskRunner
Pass a collection of parallelizable tasks to run.
runTasks(Collection<? extends Runnable>) - Method in interface qupath.lib.plugins.TaskRunner
Pass a collection of parallelizable tasks to run.

S

sameClassificationPredicate() - Static method in class qupath.lib.analysis.DelaunayTools
BiPredicate that returns true for objects that share the same classification.
saturation(int) - Static method in class qupath.lib.color.ColorTransformer
Extract saturation value from RGB-to-HSB transform.
Saturation - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
Saturation value (from RGB-HSB transform)
saveImageData(ImageData<T>) - Method in interface qupath.lib.projects.ProjectImageEntry
Save the ImageData for this entry using the default storage location for the project.
scale(double, double) - Method in interface qupath.lib.roi.interfaces.ROI
Create a scaled version of this ROI.
scale(double, double, double, double) - Method in class qupath.lib.roi.AreaROI
Deprecated.
 
scale(double, double, double, double) - Method in class qupath.lib.roi.EllipseROI
 
scale(double, double, double, double) - Method in class qupath.lib.roi.GeometryROI
 
scale(double, double, double, double) - Method in interface qupath.lib.roi.interfaces.ROI
Create a scaled version of this ROI.
scale(double, double, double, double) - Method in class qupath.lib.roi.LineROI
 
scale(double, double, double, double) - Method in class qupath.lib.roi.PointsROI
 
scale(double, double, double, double) - Method in class qupath.lib.roi.PolygonROI
 
scale(double, double, double, double) - Method in class qupath.lib.roi.PolylineROI
 
scale(double, double, double, double) - Method in class qupath.lib.roi.RectangleROI
 
scaleChannels(double...) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Scale all channels by a constant factor.
scaleColor(Color, double) - Static method in class qupath.lib.color.ColorToolsAwt
Get a scaled version of the specified color, where the RGB values are independently scaled by a specified factor.
ScriptableWorkflowStep - Interface in qupath.lib.plugins.workflow
A WorkflowStep that can also return some Javascript that, if run, would perform the step.
searchDepth(int) - Method in class qupath.lib.io.UriUpdater
Maximum search depth when using UriUpdater.searchDepth(int) to match filenames in directories and subdirectories.
searchPath(Path) - Method in class qupath.lib.io.UriUpdater
Search for filenames that match missing URIs, recursively up to the depth specified by UriUpdater.searchDepth(int).
seconds() - Method in class qupath.lib.common.Timeit
Report timings in seconds.
selectedPathObjectChanged(PathObject, PathObject, Collection<PathObject>) - Method in interface qupath.lib.objects.hierarchy.events.PathObjectSelectionListener
Fired when the selected objects have changed.
selectObjects(Collection<? extends PathObject>) - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel
Ensure the specified objects are selected.
serverRegion(ImageRegion, double, ImageServer<BufferedImage>) - Method in class qupath.lib.images.servers.SparseImageServer.Builder
Add a region based on an existing ImageServer.
ServerTools - Class in qupath.lib.images.servers
Static methods helpful when dealing with ImageServers.
ServerTools() - Constructor for class qupath.lib.images.servers.ServerTools
 
setActiveHandlePosition(double, double, double, boolean) - Method in class qupath.lib.roi.RoiEditor
If a handle has been grabbed, update its displacement.
setBoundaryLabel(String, int) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Set the classification and label to use for boundaries for classified areas.
setBoundaryLabel(String, int, Integer) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Set the classification and label to use for boundaries for classified areas.
setBoundaryLabel(PathClass, int) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Set the classification and label to use for boundaries for classified areas.
setBoundaryLabel(PathClass, int, Integer) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Set the classification and label to use for boundaries for classified areas.
setCache(Map<RegionRequest, T>, Class<T>) - Static method in class qupath.lib.images.servers.ImageServerProvider
Set the cache to be used for image tiles of a specific type.
setCaseID(String) - Method in class qupath.lib.objects.TMACoreObject
Set the case ID metadata value.
setChanged(boolean) - Method in class qupath.lib.images.ImageData
setChannelType(ImageServerMetadata.ChannelType) - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata.Builder
Specify the output channel type.
setClassification(Object) - Method in class qupath.lib.objects.PathObject
Companion method for PathObject.setClassification(String) to reduce the risk of issues when using Groovy.
setClassification(String) - Method in class qupath.lib.objects.PathObject
Convenience method to set the classification of the object from a string representation.
setClassifications(Collection<String>) - Method in class qupath.lib.objects.PathObject
Set the PathClass from a collection of names according to the rules: If the collection is empty, reset the PathClass If the collection has one element, set it to be the name of the PathClass If the collection has multiple element, create and set a derived PathClass with each unique element the name of a PathClass component The uniqueness is equivalent to copying the elements into a set; if a set is provided as input then a defensive copy will be made..
setColor(int, int, int) - Method in class qupath.lib.objects.classes.PathClass
Set the color as 8-bit RGB values
setColor(int, int, int) - Method in class qupath.lib.objects.PathObject
Set the display color as 8-bit RGB values
setColor(Integer) - Method in class qupath.lib.objects.classes.PathClass
Set the color that should be used to display objects with this classification.
setColor(Integer) - Method in class qupath.lib.objects.PathObject
Set the display color as a packed (A)RGB integer (alpha may not be used by viewing code).
setColorDeconvolutionStains(ColorDeconvolutionStains) - Method in class qupath.lib.images.ImageData
Set the color deconvolution stain vectors for the current image type.
setComparator(Comparator<PathObject>) - Method in class qupath.lib.objects.utils.OverlapFixer.Builder
Set the comparator to use for sorting objects.
setComplete(boolean) - Method in class qupath.lib.plugins.ParallelTileObject
Notify the tile that its processing is done.
setCreateFunction(IntFunction<TaskRunner>) - Method in class qupath.lib.plugins.TaskRunnerUtils
Set the function used to generate new headless TaskRunner instances.
setCreateHeadlessFunction(IntFunction<TaskRunner>) - Method in class qupath.lib.plugins.TaskRunnerUtils
Set the function used to generate new TaskRunner instances.
setDefaultColorMap(ColorMaps.ColorMap) - Static method in class qupath.lib.color.ColorMaps
Set the default ColorMaps.ColorMap.
setDescription(String) - Method in class qupath.lib.objects.PathAnnotationObject
Set a free text description for this annotation.
setDescription(String) - Method in interface qupath.lib.projects.ProjectImageEntry
Set the description.
setDoubleLastValue(double) - Method in class qupath.lib.plugins.parameters.DoubleParameter
 
setDoubleLastValue(double) - Method in class qupath.lib.plugins.parameters.IntParameter
 
setDoubleLastValue(double) - Method in class qupath.lib.plugins.parameters.NumericParameter
A class for setting the numeric value as a double (subclasses should convert this as needed).
setHidden(boolean) - Method in class qupath.lib.plugins.parameters.BooleanParameter
 
setHidden(boolean) - Method in class qupath.lib.plugins.parameters.ChoiceParameter
 
setHidden(boolean) - Method in class qupath.lib.plugins.parameters.DoubleParameter
 
setHidden(boolean) - Method in class qupath.lib.plugins.parameters.EmptyParameter
 
setHidden(boolean) - Method in class qupath.lib.plugins.parameters.IntParameter
 
setHidden(boolean) - Method in class qupath.lib.plugins.parameters.NumericParameter
 
setHidden(boolean) - Method in class qupath.lib.plugins.parameters.StringParameter
 
setHidden(boolean) - Method in interface qupath.lib.plugins.parameters.Parameter
Mark that a parameter should not be displayed to a user.
setHiddenParameters(boolean, String...) - Method in class qupath.lib.plugins.parameters.ParameterList
Set the 'hidden' flag for parameters with the specified keys.
setHierarchy(PathObjectHierarchy) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Set the contents of this hierarchy to be the same as that of another hierarchy.
setID(UUID) - Method in class qupath.lib.objects.PathObject
Set the ID for this object.
setImageName(String) - Method in interface qupath.lib.projects.ProjectImageEntry
Set the image name for this project entry.
setImageName(ImageServer<?>, String) - Static method in class qupath.lib.images.servers.ServerTools
Set the name property of the metadata for an ImageServer.
setImageType(ImageData.ImageType) - Method in class qupath.lib.images.ImageData
Set the image type.
setIntensityClassification(PathObject, String, double...) - Static method in class qupath.lib.objects.PathObjectTools
Assign cell classifications as positive or negative based upon a specified measurement, using up to 3 intensity bins.
setIntensityClassifications(Collection<? extends PathObject>, String, double...) - Static method in class qupath.lib.objects.PathObjectTools
Set the intensity classifications for the specified objects.
setLastSavedPath(String, boolean) - Method in class qupath.lib.images.ImageData
Set the last path used to save this object;
setLocked(boolean) - Method in class qupath.lib.objects.PathObject
Set locked status, if possible.
setLocked(boolean) - Method in class qupath.lib.objects.PathROIObject
Set locked flag, indicating that the object ROI should not be modified.
setMaskImageNames(boolean) - Method in interface qupath.lib.projects.Project
Request that entries return masked image names, rather than the 'true' image names.
setMetadata(ImageServerMetadata) - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer
Not allowed - throws an UnsupportedOperationException.
setMetadata(ImageServerMetadata) - Method in class qupath.lib.images.servers.AbstractImageServer
 
setMetadata(ImageServerMetadata) - Method in interface qupath.lib.images.servers.ImageServer
Set the metadata to use, e.g.
setMetadata(ImageServerMetadata) - Method in class qupath.lib.images.servers.LabeledImageServer
Throws an exception - metadata should not be set for a hierarchy image server directly.
setMinArea(double) - Method in class qupath.lib.objects.utils.OverlapFixer.Builder
Set the minimum area for objects to be retained, in pixels.
setMissing(boolean) - Method in class qupath.lib.objects.TMACoreObject
Set the missing flag for this core, for example because insufficient tissue is present.
setName(String) - Method in class qupath.lib.objects.PathObject
Set the stored object name.
setNumThreads(int) - Static method in class qupath.lib.common.Prefs
Set the requested number of threads.
setParallelism(int) - Static method in class qupath.lib.common.ThreadTools
Set the requested level of parallelism.
setPathClass(PathClass) - Method in class qupath.lib.objects.PathObject
Set the classification of the object, without specifying any classification probability.
setPathClass(PathClass, double) - Method in class qupath.lib.objects.PathObject
Set the classification of the object, specifying a classification probability.
setPathClass(PathClass, double) - Method in class qupath.lib.objects.PathROIObject
 
setPathClass(PathClass, double) - Method in class qupath.lib.objects.PathRootObject
 
setPathClasses(Collection<? extends PathClass>) - Method in interface qupath.lib.projects.Project
Update the available PathClasses.
setProperty(String, Object) - Method in class qupath.lib.images.ImageData
Set a property.
setRandomColors(Collection<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools
Set each of the specified objects to have a random color.
setRandomColors(Collection<? extends PathObject>, Random) - Static method in class qupath.lib.objects.PathObjectTools
Set each of the specified objects to have a random color.
setRange(double, double) - Method in class qupath.lib.plugins.parameters.NumericParameter
Set the upper and lower bounds.
setRequestedDataFileVersion(int) - Static method in class qupath.lib.io.PathIO
Set the requested version for .qpdata files.
setROI(ROI) - Method in class qupath.lib.objects.PathROIObject
Set the ROI for this object.
setROI(ROI) - Method in class qupath.lib.roi.RoiEditor
Set the active ROI, stopping any ROI translation currently in progress.
setROI(ROI, boolean) - Method in class qupath.lib.roi.RoiEditor
Set the active ROI, optionally stopping any ROI translation currently in progress.
setSelectedObject(PathObject) - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel
Set the specified object to be selected, deselecting all others.
setSelectedObject(PathObject, boolean) - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel
Select the specified object to be the primary selected object, optionally retaining the existing selected objects.
setSelectedObjects(Collection<? extends PathObject>, PathObject) - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel
Specify a collection of objects to be selected, and which among them should be the primary.
setServiceLoader(ServiceLoader<ImageServerBuilder>) - Static method in class qupath.lib.images.servers.ImageServerProvider
Replace the default service loader with another.
setStrategy(OverlapFixer.Strategy) - Method in class qupath.lib.objects.utils.OverlapFixer.Builder
Set the strategy for handling overlaps.
setStringLastValue(Locale, String) - Method in class qupath.lib.plugins.parameters.BooleanParameter
 
setStringLastValue(Locale, String) - Method in class qupath.lib.plugins.parameters.ChoiceParameter
This will only work for string choices...
setStringLastValue(Locale, String) - Method in class qupath.lib.plugins.parameters.EmptyParameter
 
setStringLastValue(Locale, String) - Method in class qupath.lib.plugins.parameters.NumericParameter
 
setStringLastValue(Locale, String) - Method in interface qupath.lib.plugins.parameters.Parameter
Set last value using a string; implementing classes may need to parse this
setStringLastValue(Locale, String) - Method in class qupath.lib.plugins.parameters.StringParameter
 
setThumbnail(T) - Method in interface qupath.lib.projects.ProjectImageEntry
Set a thumbnail for the image.
setTMAGrid(TMAGrid) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Set the tma grid for this hierarchy.
setValue(int, int, float) - Method in interface qupath.lib.analysis.images.SimpleModifiableImage
Set the value of a single pixel.
setValue(Double) - Method in class qupath.lib.plugins.parameters.DoubleParameter
Set the last value; this will apply a range check using clipping.
setValue(Integer) - Method in class qupath.lib.plugins.parameters.IntParameter
Set the last value; this will apply a range check using clipping.
setValue(Boolean) - Method in class qupath.lib.plugins.parameters.BooleanParameter
 
setValue(S) - Method in class qupath.lib.plugins.parameters.ChoiceParameter
 
setValue(String) - Method in class qupath.lib.plugins.parameters.EmptyParameter
 
setValue(S) - Method in class qupath.lib.plugins.parameters.NumericParameter
 
setValue(String) - Method in class qupath.lib.plugins.parameters.StringParameter
 
setValue(S) - Method in interface qupath.lib.plugins.parameters.Parameter
Set the Parameter to have a specified value.
setValues(DataBuffer, double) - Static method in class qupath.lib.awt.common.BufferedImageTools
Set all values in a DataBuffer.
setValueWithBoundsCheck(Double) - Method in class qupath.lib.plugins.parameters.DoubleParameter
 
setValueWithBoundsCheck(Integer) - Method in class qupath.lib.plugins.parameters.IntParameter
 
setValueWithBoundsCheck(S) - Method in class qupath.lib.plugins.parameters.NumericParameter
Set the value of this parameter, constraining it to be within any lower and upper bounds if necessary.
ShapeSimplifier - Class in qupath.lib.roi
Helper methods for simplifying shapes, such removing polygon points while retaining a similar overall shape at a coarser level.
ShapeSimplifier() - Constructor for class qupath.lib.roi.ShapeSimplifier
 
shapeToGeometry(Shape) - Static method in class qupath.lib.roi.GeometryTools
Convert a java.awt.Shape to a JTS Geometry.
shuffleInstanceLabels(boolean) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Optionally request that instance labels are shuffled.
SimpleImage - Interface in qupath.lib.analysis.images
A minimal interface for accessing pixel values in a single-channel image.
SimpleImages - Class in qupath.lib.analysis.images
Create SimpleImage instances for basic pixel processing.
SimpleImages() - Constructor for class qupath.lib.analysis.images.SimpleImages
 
SimpleModifiableImage - Interface in qupath.lib.analysis.images
A minimal interface to define a means to provide access to pixel values from a 2D, 1-channel image.
SimplePluginWorkflowStep - Class in qupath.lib.plugins.workflow
Updated version of DefaultPluginWorkflowStep, adapted to use Externalizable and to avoid storing the plugin class as a class object (preferring a String instead).
SimplePluginWorkflowStep() - Constructor for class qupath.lib.plugins.workflow.SimplePluginWorkflowStep
Default public constructor, required for Externalizable.
SimplePluginWorkflowStep(String, Class<? extends PathPlugin<?>>, String) - Constructor for class qupath.lib.plugins.workflow.SimplePluginWorkflowStep
Constructor for a workflow step that calls a plugin.
SimplePluginWorkflowStep(String, Class<? extends PathPlugin<?>>, String, String, String) - Constructor for class qupath.lib.plugins.workflow.SimplePluginWorkflowStep
Constructor for a workflow step that calls a plugin, which optionally should include additional scripting lines before or afterwards.
SimpleProgressMonitor - Interface in qupath.lib.plugins
Class for monitoring the process of a plugin and displaying feedback to the user.
simplifyPath(Path2D, double) - Static method in class qupath.lib.roi.ShapeSimplifier
Create a simplified path (fewer coordinates) using method based on Visvalingam's Algorithm, processing all segments.
simplifyPath(Path2D, double, int, double) - Static method in class qupath.lib.roi.ShapeSimplifier
Create a simplified path (fewer coordinates) using method based on Visvalingam's Algorithm, optionally skipping segments with few points.
simplifyPolygon(PolygonROI, double) - Static method in class qupath.lib.roi.ShapeSimplifier
Create a simplified polygon (fewer coordinates) using method based on Visvalingam's Algorithm.
simplifyPolygonPoints(List<Point2>, double) - Static method in class qupath.lib.roi.ShapeSimplifier
Create a simplified polygon (fewer coordinates) using method based on Visvalingam's Algorithm.
simplifyROI(ROI, double) - Static method in class qupath.lib.roi.ShapeSimplifier
Simplify a ROI using either polygon or general shape methods.
simplifyShape(ROI, double) - Static method in class qupath.lib.roi.ShapeSimplifier
Create a simplified shape (fewer coordinates) using method based on Visvalingam's Algorithm.
singleSelection() - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel
Returns true if only one object has been selected, accessible by getSelectedObject();
size - Variable in class qupath.lib.analysis.stats.RunningStatistics
 
size() - Method in class qupath.lib.analysis.DelaunayTools.Subdivision
Get the number of objects in this subdivision.
size() - Method in interface qupath.lib.analysis.stats.ArrayWrappers.ArrayWrapper
Number of entries in the array.
size() - Method in class qupath.lib.analysis.stats.RunningStatistics
Get count of the number of non-NaN values added.
size() - Method in interface qupath.lib.measurements.MeasurementList
Returns the number of measurements in the list.
size() - Method in class qupath.lib.plugins.workflow.Workflow
Total number of steps in the workflow.
sizeT(int) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder
Specify the number of time points.
sizeZ(int) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder
Specify the number of z-slices.
slice(int, int, int, int) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Slice a specific region along the z or the t axis.
slice(int, int, int, int, int, int) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Slice a specific region along the z or the t axis with a step.
SlicedImageServer - Class in qupath.lib.images.servers
ImageServer that treats a particular set of z-slices and timepoints of another ImageServer as a full image.
smartStringComparator() - Static method in class qupath.lib.common.GeneralTools
Comparator for smart String sorting.
smartStringSort(Collection<T>) - Static method in class qupath.lib.common.GeneralTools
Smart-sort a collection using the Object.toString() method applied to each element.
smartStringSort(Collection<T>, Function<T, String>) - Static method in class qupath.lib.common.GeneralTools
Smart-sort a collection after extracting a String representation of each element.
smoothPoints(List<Point2>) - Static method in class qupath.lib.roi.ShapeSimplifier
Apply a simple 3-point moving average to a list of points.
sortByArea() - Method in class qupath.lib.objects.utils.OverlapFixer.Builder
Set the comparator to sort by area, with the largest objects given a higher priority.
sortBySolidity() - Method in class qupath.lib.objects.utils.OverlapFixer.Builder
Set the comparator to sort by solidity, with the most solid objects given a higher priority.
sortNames(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools
Create a PathClass with name elements sorted alphabetically.
sortNames(PathClass, Comparator<String>) - Static method in class qupath.lib.objects.classes.PathClassTools
Create a PathClass with name elements sorted using an arbitrary Comparator.
SparseImageServer - Class in qupath.lib.images.servers
An ImageServer that combines regions from multiple separate ImageServers, repositioning these as necessary to generate one larger field of view.
SparseImageServer.Builder - Class in qupath.lib.images.servers
Builder to create a new SparseImageServer.
SparseImageServer.SparseImageServerManager - Class in qupath.lib.images.servers
Helper class for SparseImageServers, capable of returning the appropriate ImageServer for different ImageRegions and different resolutions.
SparseImageServerManager() - Constructor for class qupath.lib.images.servers.SparseImageServer.SparseImageServerManager
 
splitAreasByBufferedLines(Collection<? extends PathObject>, double) - Static method in class qupath.lib.objects.PathObjectTools
Given a collection of objects, split the objects with area ROIs using dividing lines extracted from the objects with line ROIs, after 'buffering' the lines to increase their thickness.
splitAreasByBufferedLines(Collection<? extends PathObject>, Collection<? extends PathObject>, double) - Static method in class qupath.lib.objects.PathObjectTools
Split the objects with area ROIs using dividing lines extracted from the objects with line ROIs, after 'buffering' the lines to increase their thickness.
splitAreasByLines(Collection<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools
Given a collection of objects, split the objects with area ROIs using dividing lines extracted from the objects with line ROIs.
splitAreasByLines(Collection<? extends PathObject>, Collection<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools
Given a collection of objects with area ROIs, split these using dividing lines extracted from objects with line ROIs.
splitAreaToPolygons(Area, int, int, int) - Static method in class qupath.lib.roi.RoiTools
Split Area into PolygonROIs for the exterior and the holes.
splitConnectedRegions(SparseImageServer, double, boolean) - Static method in class qupath.lib.images.servers.SparseImageServer
Split a SparseImageServer into multiple servers, whereby each split server represents one connected region.
splitGeometryByLineStrings(Geometry, Collection<? extends Geometry>) - Static method in class qupath.lib.roi.GeometryTools
Split an input polygonal geometry using a collection of split lines.
splitLines(String) - Static method in class qupath.lib.common.GeneralTools
Split new lines (in a cross-platform way...
splitNames(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools
Get a list containing the names of all constituent parts of a PathClass.
splitROI(ROI) - Static method in class qupath.lib.roi.RoiTools
Split a multi-part ROI into separate pieces.
Stain_1 - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
First stain after color deconvolution
Stain_2 - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
Second stain after color deconvolution
Stain_3 - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
Third stain after color deconvolution
stainNormalize(ColorDeconvolutionStains, ColorDeconvolutionStains, double...) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Normalize stains using color deconvolution and reconvolution.
StainVector - Class in qupath.lib.color
Representation of a color deconvolution stain vector, defined in terms of RGB optical densities.
StainVector() - Constructor for class qupath.lib.color.StainVector
Default constructor, required for Externalizable interface.
StainVector.DefaultStains - Enum Class in qupath.lib.color
Enum representing default stains.
STANDARD_DEVIATION - Enum constant in enum class qupath.lib.images.servers.ZProjectedImageServer.Projection
A standard deviation projection on the z-stacks.
standardizeClassifications(Collection<PathObject>) - Static method in class qupath.lib.objects.PathObjectTools
Standardize the classifications for a collection of objects.
standardizeClassifications(Collection<PathObject>, Comparator<String>) - Static method in class qupath.lib.objects.PathObjectTools
Standardize the classifications for a collection of objects.
StandardPathClasses() - Constructor for class qupath.lib.objects.classes.PathClass.StandardPathClasses
 
start() - Method in class qupath.lib.common.Timeit
Start the Timeit and create a checkpoint with the default name.
start(String) - Method in class qupath.lib.common.Timeit
Start the Timeit and create a checkpoint with the specified name.
startMonitoring(String, int, boolean) - Method in class qupath.lib.plugins.CommandLineTaskRunner.CommandLineProgressMonitor
 
startMonitoring(String, int, boolean) - Method in interface qupath.lib.plugins.SimpleProgressMonitor
Set the plugin to monitor, and begin monitoring.
startTranslation(double, double, boolean) - Method in class qupath.lib.roi.RoiEditor
Returns true if the current ROI is translatable, and at the end of this call the translation has started.
StatisticsHelper - Class in qupath.lib.analysis.stats
Static methods for computing statistics from images, with or without a corresponding labeled image.
StatisticsHelper() - Constructor for class qupath.lib.analysis.stats.StatisticsHelper
 
stop() - Method in class qupath.lib.common.Timeit
Stop the Timeit.
storeMetadataValue(String, String) - Method in class qupath.lib.objects.PathObject
Deprecated.
v0.6.0, use PathObject.getMetadata() to directly access the metadata instead.
StringParameter - Class in qupath.lib.plugins.parameters
Parameter to represent a String value.
stripEmptyAlpha(BufferedImage) - Static method in class qupath.lib.awt.common.BufferedImageTools
Remove the alpha channel for an 8-bit color BufferedImage if it contains only 255 for all pixels.
stripExtension(String) - Static method in class qupath.lib.common.GeneralTools
Strip the extension from a file name or path, leaving the rest of the string unchanged.
stripInvalidFilenameChars(String) - Static method in class qupath.lib.common.GeneralTools
Strip characters that would make a String invalid as a filename.
STROMA - Enum constant in enum class qupath.lib.objects.classes.PathClassFactory.StandardPathClasses
Deprecated.
Stroma classification
STROMA - Static variable in class qupath.lib.objects.classes.PathClass.StandardPathClasses
Stroma classification
subtract(Padding) - Method in class qupath.lib.regions.Padding
Add another padding from this one.
subtract(ROI, Collection<? extends ROI>) - Static method in class qupath.lib.roi.RoiTools
Subtract a collection of ROIs from another ROI.
subtract(ROI, ROI...) - Static method in class qupath.lib.roi.RoiTools
Subtract one or more ROIs from another ROI.
SUBTRACT - Enum constant in enum class qupath.lib.roi.RoiTools.CombineOp
Subtract from first ROI.
subtractOffset(double...) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Subtract a constant offset from all channels, without clipping.
subtractOffsetAndClipZero(double...) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Subtract a constant offset from all channels, clipping the result to be ≥ 0.
subtractOffsetAndScale(double[], double[]) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Subtract a constant offset from all channels, then multiply the result by a scale factor.
SubtractOffsetAndScaleNormalizer - Class in qupath.lib.images.servers.transforms
Normalizes the pixel values of a BufferedImage by subtracting and offset and multiplying by a scale factor.
suggestNeighbor(ParallelTileObject) - Method in class qupath.lib.plugins.ParallelTileObject
Register a neighboring tile, if it intersects with the bounds of this one
sum(long[]) - Static method in class qupath.lib.common.GeneralTools
Compute the sum of elements in a long array (possibly representing a histogram).
SUM - Enum constant in enum class qupath.lib.images.servers.ZProjectedImageServer.Projection
A sum projection on the z-stacks.
summarizeCheckpoints() - Method in class qupath.lib.common.Timeit
Request that checkpoints are summarized in the Timeit.toString() method.
summarizeCheckpoints(boolean) - Method in class qupath.lib.common.Timeit
Optionally request that checkpoints are summarized in the Timeit.toString() method.
supportsImage(ImageData<BufferedImage>) - Method in interface qupath.lib.classifiers.pixel.PixelClassifier
Query whether the classifier supports a particular image.
supportsImage(ImageServer<BufferedImage>) - Method in interface qupath.lib.images.servers.ColorTransforms.ColorTransform
Query whether this transform can be applied to the specified image.
supportsImageType(ImageServer<BufferedImage>) - Method in class qupath.lib.images.writers.JpegWriter
 
supportsImageType(ImageServer<BufferedImage>) - Method in class qupath.lib.images.writers.PngWriter
 
supportsImageType(ImageServer<T>) - Method in interface qupath.lib.images.writers.ImageWriter
Test whether images provided by a specified ImageServer can be successfully written.
supportsPixelSize() - Method in class qupath.lib.images.writers.JpegWriter
 
supportsPixelSize() - Method in class qupath.lib.images.writers.PngWriter
 
supportsPixelSize() - Method in interface qupath.lib.images.writers.ImageWriter
Returns true if the writer is capable of storing pixel size information.
supportsPyramidal() - Method in class qupath.lib.images.writers.JpegWriter
 
supportsPyramidal() - Method in class qupath.lib.images.writers.PngWriter
 
supportsPyramidal() - Method in interface qupath.lib.images.writers.ImageWriter
Returns true if the writer is capable of writing pyramidal images.
supportsRGB() - Method in class qupath.lib.images.writers.JpegWriter
 
supportsRGB() - Method in class qupath.lib.images.writers.PngWriter
 
supportsRGB() - Method in interface qupath.lib.images.writers.ImageWriter
Check if writer can handle RGB (it probably can...).
supportsT() - Method in class qupath.lib.images.writers.JpegWriter
 
supportsT() - Method in class qupath.lib.images.writers.PngWriter
 
supportsT() - Method in interface qupath.lib.images.writers.ImageWriter
Check if writer can handle multiple timepoints.
supportsZ() - Method in class qupath.lib.images.writers.JpegWriter
 
supportsZ() - Method in class qupath.lib.images.writers.PngWriter
 
supportsZ() - Method in interface qupath.lib.images.writers.ImageWriter
Check if writer can handle multiple z-slices.
swapNameAndClass(PathObject, boolean) - Static method in class qupath.lib.objects.PathObjectTools
Swap the name and PathClass of an object.
swapRGBOrder(BufferedImage, String) - Static method in class qupath.lib.awt.common.BufferedImageTools
Swap the order of pixels in an RGB image.
SYMBOL_MICROMETER - Static variable in class qupath.lib.common.GeneralTools
String to represent um (but with the proper 'mu' symbol)
SYMBOL_MU - Static variable in class qupath.lib.common.GeneralTools
Small Greek mu (useful for micrometers)
SYMBOL_SIGMA - Static variable in class qupath.lib.common.GeneralTools
Small Greek sigma (useful for Gaussian filter sizes, standard deviations)
symDifference(ROI, ROI) - Static method in class qupath.lib.roi.RoiTools
Compute the symmetric difference between two ROIs (XOR).
symmetric(int) - Static method in class qupath.lib.regions.Padding
Get a padding object with 'pad' pixels on all sides.
syncChanges() - Method in interface qupath.lib.projects.Project
Save the project.

T

taskComplete(boolean) - Method in interface qupath.lib.plugins.PathTask
Perform optional post-processing after a task has completed.
TaskRunner - Interface in qupath.lib.plugins
A minimal interface for a class capable of running tasks in parallel, giving feedback to the user.
TaskRunnerUtils - Class in qupath.lib.plugins
A utility class to help with the creation of TaskRunner instances.
TemporaryObject - Interface in qupath.lib.objects
Marker interface used to indicate that child objects shouldn't be added to any cache for display.
test(PathObject) - Method in enum class qupath.lib.objects.PathObjectFilter
 
ThreadTools - Class in qupath.lib.common
Create a thread factory that supports adding a prefix to the name and setting daemon status.
ThreadTools() - Constructor for class qupath.lib.common.ThreadTools
 
threshold(double) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder
Set the threshold value used for the classification.
TiledTransformingImageServer - Class in qupath.lib.images.servers
An ImageServer implementation used to apply transforms to another ImageServer.
TiledTransformingImageServer(ImageServer<BufferedImage>) - Constructor for class qupath.lib.images.servers.TiledTransformingImageServer
 
TileExporter - Class in qupath.lib.images.writers
Helper class for exporting image tiles, typically for further analysis elsewhere or for training up an AI algorithm.
TileExporter(ImageData<BufferedImage>) - Constructor for class qupath.lib.images.writers.TileExporter
Create a builder to export tiles.
tileHeight(int) - Method in class qupath.lib.objects.utils.Tiler.Builder
Change the height of output tiles
Tiler - Class in qupath.lib.objects.utils
A class used to split ROI or Geometry objects into rectangular tiles.
Tiler.Builder - Class in qupath.lib.objects.utils
 
Tiler.TileAlignment - Enum Class in qupath.lib.objects.utils
Enum representing the possible alignments for tiles.
TileRequest - Class in qupath.lib.images.servers
A wrapper for a RegionRequest, useful to precisely specify image tiles at a particular resolution.
TileRequestManager - Interface in qupath.lib.images.servers
Helper class to manage tile requests from an ImageServer.
tiles() - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder
Set the filter to accept tile objects only.
TILES - Enum constant in enum class qupath.lib.objects.PathObjectFilter
Accept tiles
tileSize(int) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Set tile width and height (square tiles).
tileSize(int) - Method in class qupath.lib.images.writers.TileExporter
Define the tile size in pixel units at the export resolution.
tileSize(int, int) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Set tile width and height.
tileSize(int, int) - Method in class qupath.lib.images.writers.TileExporter
Define the horizontal and vertical tile size in pixel units at the export resolution.
tileWidth(int) - Method in class qupath.lib.objects.utils.Tiler.Builder
Change the width of output tiles
Timeit - Class in qupath.lib.common
Helper class to time code execution.
Timeit() - Constructor for class qupath.lib.common.Timeit
 
Timeit.Checkpoint - Class in qupath.lib.common
Class representing a named checkpoint with a timestamp in nanoseconds.
timepoints(TimeUnit, double...) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder
Specify the time unit and individual time points.
timepoints(TimeUnit, double...) - Method in class qupath.lib.images.servers.PixelCalibration.Builder
Specify timepoints and units.
TMA_CORES - Enum constant in enum class qupath.lib.objects.PathObjectFilter
Accept TMA cores
TMACoreObject - Class in qupath.lib.objects
A special PathObject used exclusively to represent TMA cores.
TMACoreObject() - Constructor for class qupath.lib.objects.TMACoreObject
Default constructor.
TMAGrid - Interface in qupath.lib.objects.hierarchy
Interface defining a (rectangular) TMA grid.
TMAScoreImporter - Class in qupath.lib.io
Helper class for importing data in connection with TMA slides.
TMAScoreImporter() - Constructor for class qupath.lib.io.TMAScoreImporter
 
toEncodedURI(String) - Static method in class qupath.lib.common.GeneralTools
Try to convert a path to an encoded URI.
toggleObjectsLocked(PathObjectHierarchy, Collection<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools
Toggle the 'locked' status of specified objects.
toggleSelectedObjectsLocked(PathObjectHierarchy) - Static method in class qupath.lib.objects.PathObjectTools
Toggle the 'locked' status of selected objects, firing an update event if the status of any object is changed.
toJTS(AffineTransform) - Static method in class qupath.lib.awt.common.AffineTransforms
Create a Java Topology Suite affine transformation from a Java affine transform.
TOP_CENTER - Enum constant in enum class qupath.lib.objects.utils.Tiler.TileAlignment
 
TOP_LEFT - Enum constant in enum class qupath.lib.objects.utils.Tiler.TileAlignment
 
TOP_RIGHT - Enum constant in enum class qupath.lib.objects.utils.Tiler.TileAlignment
 
toPath(URI) - Static method in class qupath.lib.common.GeneralTools
Try to identify a Path from a URI, dropping any query or fragment elements.
toSet() - Method in class qupath.lib.objects.classes.PathClass
Return a view of this path class as an unmodifiable set, with each element representing the name of a path class component names.
toString() - Method in class qupath.lib.analysis.images.ContourTracing.ChannelThreshold
 
toString() - Method in class qupath.lib.analysis.stats.Histogram
 
toString() - Method in class qupath.lib.analysis.stats.RunningStatistics
 
toString() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData.KaplanMeierEvent
 
toString() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData
 
toString() - Method in enum class qupath.lib.classifiers.Normalization
 
toString() - Method in class qupath.lib.color.ColorDeconvMatrix3x3
 
toString() - Method in enum class qupath.lib.color.ColorDeconvolutionStains.DefaultColorDeconvolutionStains
 
toString() - Method in class qupath.lib.color.ColorDeconvolutionStains
 
toString() - Method in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
 
toString() - Method in enum class qupath.lib.color.StainVector.DefaultStains
 
toString() - Method in class qupath.lib.color.StainVector
 
toString() - Method in class qupath.lib.common.Timeit.Checkpoint
 
toString() - Method in class qupath.lib.common.Timeit
Returns a snapshot string representation of the Timeit's status.
toString() - Method in class qupath.lib.common.Version
 
toString() - Method in class qupath.lib.geom.Point2
 
toString() - Method in enum class qupath.lib.images.ImageData.ImageType
 
toString() - Method in class qupath.lib.images.ImageData
 
toString() - Method in class qupath.lib.images.servers.AbstractImageServer
 
toString() - Method in class qupath.lib.images.servers.ImageChannel
 
toString() - Method in class qupath.lib.images.servers.ImageServerBuilder.DefaultImageServerBuilder
 
toString() - Method in class qupath.lib.images.servers.ImageServerBuilder.UriImageSupport
 
toString() - Method in enum class qupath.lib.images.servers.ImageServerMetadata.ChannelType
 
toString() - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel
 
toString() - Method in class qupath.lib.images.servers.ImageServerMetadata
 
toString() - Method in class qupath.lib.images.servers.PixelCalibration
 
toString() - Method in enum class qupath.lib.images.servers.RotatedImageServer.Rotation
 
toString() - Method in class qupath.lib.images.servers.TileRequest
 
toString() - Method in class qupath.lib.io.UriUpdater.SingleUriItem
 
toString() - Method in class qupath.lib.objects.classes.PathClass
 
toString() - Method in class qupath.lib.objects.hierarchy.DefaultTMAGrid
 
toString() - Method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent
 
toString() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
 
toString() - Method in class qupath.lib.objects.PathObject
 
toString() - Method in enum class qupath.lib.objects.PathObjectFilter
 
toString() - Method in class qupath.lib.objects.PathRootObject
 
toString() - Method in class qupath.lib.objects.TMACoreObject
 
toString() - Method in class qupath.lib.plugins.parameters.BooleanParameter
 
toString() - Method in class qupath.lib.plugins.parameters.ChoiceParameter
 
toString() - Method in class qupath.lib.plugins.parameters.DoubleParameter
 
toString() - Method in class qupath.lib.plugins.parameters.IntParameter
 
toString() - Method in class qupath.lib.plugins.parameters.NumericParameter
 
toString() - Method in class qupath.lib.plugins.parameters.StringParameter
 
toString() - Method in class qupath.lib.plugins.parameters.EmptyParameter
 
toString() - Method in class qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep
 
toString() - Method in class qupath.lib.plugins.workflow.RunSavedClassifierWorkflowStep
 
toString() - Method in class qupath.lib.plugins.workflow.SimplePluginWorkflowStep
 
toString() - Method in class qupath.lib.regions.ImagePlane
 
toString() - Method in class qupath.lib.regions.ImageRegion
 
toString() - Method in class qupath.lib.regions.Padding
 
toString() - Method in class qupath.lib.regions.RegionRequest
 
toString() - Method in class qupath.lib.roi.AreaROI
 
toString() - Method in class qupath.lib.roi.EllipseROI
 
toString() - Method in class qupath.lib.roi.GeometryROI
 
toString() - Method in class qupath.lib.roi.LineROI
 
toString() - Method in class qupath.lib.roi.PolygonROI
 
toString() - Method in class qupath.lib.roi.PolylineROI
 
toString() - Method in class qupath.lib.roi.RectangleROI
 
toString() - Method in class qupath.lib.roi.PointsROI
 
toString(String) - Method in class qupath.lib.objects.classes.PathClass
Create a string representation, using the specified delimiter between elements of derived PathClasses.
toURI(String) - Static method in class qupath.lib.common.GeneralTools
Try to convert a path to a URI.
traceGeometries(ImageServer<BufferedImage>, RegionRequest, Geometry, ContourTracing.ChannelThreshold...) - Static method in class qupath.lib.analysis.images.ContourTracing
Trace one or more geometries in an image.
traceGeometry(ImageServer<BufferedImage>, RegionRequest, Geometry, int, double, double) - Static method in class qupath.lib.analysis.images.ContourTracing
Trace a geometry from a single channel of a single image.
tRange(int, int) - Method in class qupath.lib.images.writers.TileExporter
Define the range of timepoints to process.
transform(AffineTransform) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Apply an AffineTransform to the server.
TransformedServerBuilder - Class in qupath.lib.images.servers
Helper class for creating an ImageServer that applies one or more transforms to another (wrapped) ImageServer.
TransformedServerBuilder(ImageServer<BufferedImage>) - Constructor for class qupath.lib.images.servers.TransformedServerBuilder
Create a transformed ImageServer.
TransformingImageServer<T> - Class in qupath.lib.images.servers
An ImageServer implementation used to apply transforms to another ImageServer.
TransformingImageServer(ImageServer<T>) - Constructor for class qupath.lib.images.servers.TransformingImageServer
 
transformObject(PathObject, AffineTransform, boolean) - Static method in class qupath.lib.objects.PathObjectTools
Create a transformed version of a PathObject with a new ID.
transformObject(PathObject, AffineTransform, boolean, boolean) - Static method in class qupath.lib.objects.PathObjectTools
Create a transformed version of a PathObject, optionally with a new ID.
transformObjectRecursive(PathObject, AffineTransform, boolean) - Static method in class qupath.lib.objects.PathObjectTools
Create (optionally) transformed versions of the PathObject and all its descendants, recursively.
transformObjectRecursive(PathObject, AffineTransform, boolean, boolean) - Static method in class qupath.lib.objects.PathObjectTools
Create (optionally) transformed versions of the PathObject and all its descendants, recursively, optionally assigning new IDs to the created objects.
transformRGB(int[], int[], ColorTransformer.ColorTransformMethod, float, float, boolean) - Static method in class qupath.lib.color.ColorTransformer
Apply a specified color transform to a packed (A)RGB array and output another (A)RGB array.
transformROI(ROI, AffineTransform) - Static method in class qupath.lib.roi.RoiTools
Apply an affine transform to a ROI, returning the result.
translate(double, double) - Method in class qupath.lib.roi.AreaROI
Deprecated.
 
translate(double, double) - Method in class qupath.lib.roi.EllipseROI
 
translate(double, double) - Method in class qupath.lib.roi.GeometryROI
 
translate(double, double) - Method in interface qupath.lib.roi.interfaces.ROI
Create a translated version of this ROI.
translate(double, double) - Method in class qupath.lib.roi.LineROI
 
translate(double, double) - Method in class qupath.lib.roi.PointsROI
 
translate(double, double) - Method in class qupath.lib.roi.PolygonROI
 
translate(double, double) - Method in class qupath.lib.roi.PolylineROI
 
translate(double, double) - Method in class qupath.lib.roi.RectangleROI
 
translate(int, int) - Method in class qupath.lib.regions.RegionRequest
Create a RegionRequest equivalent to this one with the x and y coordinates updated by translation.
TRANSLUCENT_BLACK - Static variable in class qupath.lib.color.ColorToolsAwt
Black, with 50% opacity.
TRANSLUCENT_WHITE - Static variable in class qupath.lib.color.ColorToolsAwt
White, with 50% opacity.
TRANSPARENT - Static variable in class qupath.lib.images.servers.ImageChannel
Special color indicating pixel values for a channel indicate levels of transparency.
tryToFixPolygon(Polygon) - Static method in class qupath.lib.roi.GeometryTools
Test a polygon for validity, attempting to fix TopologyValidationErrors if possible.
TUMOR - Enum constant in enum class qupath.lib.objects.classes.PathClassFactory.StandardPathClasses
Deprecated.
Tumor classification
TUMOR - Static variable in class qupath.lib.objects.classes.PathClass.StandardPathClasses
Tumor classification
TypeConvertImageServer - Class in qupath.lib.images.servers
An ImageServer implementation that converts the pixel type of an image.
TypeConvertImageServer(ImageServer<BufferedImage>, PixelType) - Constructor for class qupath.lib.images.servers.TypeConvertImageServer
 

U

UINT16 - Enum constant in enum class qupath.lib.images.servers.PixelType
16-bit unsigned integer
UINT32 - Enum constant in enum class qupath.lib.images.servers.PixelType
32-bit unsigned integer (not supported by BufferedImage)
UINT8 - Enum constant in enum class qupath.lib.images.servers.PixelType
8-bit unsigned integer
UNCLASSIFIED - Enum constant in enum class qupath.lib.objects.PathObjectFilter
Accept any object that does not have a classification set
union(Collection<? extends Geometry>) - Static method in class qupath.lib.roi.FastPolygonUnion
Compute a union of all polygons contained in a collection of geometries.
union(Collection<? extends Geometry>) - Static method in class qupath.lib.roi.GeometryTools
Calculate the union of multiple Geometry objects.
union(Collection<? extends ROI>) - Static method in class qupath.lib.roi.RoiTools
Create union of multiple ROIs from a collection.
union(Geometry...) - Static method in class qupath.lib.roi.FastPolygonUnion
Compute a union of all polygons contained in an array of geometries.
union(Geometry...) - Static method in class qupath.lib.roi.GeometryTools
Calculate the union of multiple Geometry objects.
union(ROI...) - Static method in class qupath.lib.roi.RoiTools
Create union of multiple ROIs.
uniqueNames(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools
Remove duplicate names from a derived PathClass.
unitsMatch2D() - Method in class qupath.lib.images.servers.PixelCalibration
Returns true if the units for pixel width and height are the same.
unitsMatch3D() - Method in class qupath.lib.images.servers.PixelCalibration
Returns true if the units for pixel width, height and z-spacing are the same.
UNKNOWN - Enum constant in enum class qupath.lib.io.UriUpdater.UriStatus
URI status is unclear, e.g.
UNKNOWN - Static variable in class qupath.lib.common.Version
Constant representing any unknown version.
UNLOCKED - Enum constant in enum class qupath.lib.objects.PathObjectFilter
Accept any object that is 'unlocked'
unlockObjects(PathObjectHierarchy, Collection<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools
Set specified objects to be 'unlocked'.
unlockSelectedObjects(PathObjectHierarchy) - Static method in class qupath.lib.objects.PathObjectTools
Set selected objects to be 'unlocked', firing an update event if the status of any object is changed.
unpackARGB(int) - Static method in class qupath.lib.common.ColorTools
Unpack a packed ARGB int into red, green and blue values, returning the result as a 4-element int array.
unpackARGB(int, int[]) - Static method in class qupath.lib.common.ColorTools
Unpack a packed ARGB int into red, green and blue values, into a 4-element int array.
unpackRGB(int) - Static method in class qupath.lib.common.ColorTools
Unpack a packed (A)RGB int into red, green and blue values, returning the result as a 3-element int array.
unpackRGB(int, int[]) - Static method in class qupath.lib.common.ColorTools
Unpack a packed (A)RGB int into red, green and blue values, into a 3-element int array.
UNSET - Enum constant in enum class qupath.lib.images.ImageData.ImageType
Image type has not been set.
unzippedExtensions(Path, String...) - Static method in class qupath.lib.io.PathIO
Get the extension of a file, or of all entries within a zip file.
updateBounds(double, double) - Method in class qupath.lib.roi.PointsROI
 
updateDownsample(double) - Method in class qupath.lib.regions.RegionRequest
Create a RegionRequest equivalent to this one with the updated downsample value.
updateObject(PathObject, boolean) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
Update an object that is already in the hierarchy (e.g.
updateParameterList(ParameterList, Map<String, String>, Locale) - Static method in class qupath.lib.plugins.parameters.ParameterList
Update a ParameterList with the values specified in a map.
updatePath(String) - Method in class qupath.lib.regions.RegionRequest
Create a RegionRequest equivalent to this one with the updated path.
updatePlane(PathObject, ImagePlane, boolean, boolean) - Static method in class qupath.lib.objects.PathObjectTools
Update the ROI plane for a single object.
updatePlane(ImagePlane) - Method in class qupath.lib.roi.AreaROI
Deprecated.
 
updatePlane(ImagePlane) - Method in class qupath.lib.roi.EllipseROI
 
updatePlane(ImagePlane) - Method in class qupath.lib.roi.GeometryROI
 
updatePlane(ImagePlane) - Method in interface qupath.lib.roi.interfaces.ROI
Create a new ROI defining the same region on a different ImagePlane.
updatePlane(ImagePlane) - Method in class qupath.lib.roi.LineROI
 
updatePlane(ImagePlane) - Method in class qupath.lib.roi.PointsROI
 
updatePlane(ImagePlane) - Method in class qupath.lib.roi.PolygonROI
 
updatePlane(ImagePlane) - Method in class qupath.lib.roi.PolylineROI
 
updatePlane(ImagePlane) - Method in class qupath.lib.roi.RectangleROI
 
updatePlaneRecursive(PathObject, ImagePlane) - Static method in class qupath.lib.objects.PathObjectTools
Update the ROI plane for a single object and any descendant objects, creating new object IDs and ignoring any additional measurements.
updatePlaneRecursive(PathObject, ImagePlane, boolean, boolean) - Static method in class qupath.lib.objects.PathObjectTools
Update the ROI plane for a single object, and any descendant objects.
updateProgress(int, String, ImageRegion) - Method in class qupath.lib.plugins.CommandLineTaskRunner.CommandLineProgressMonitor
 
updateProgress(int, String, ImageRegion) - Method in interface qupath.lib.plugins.SimpleProgressMonitor
Update the displayed progress, and optionally inform the PluginRunner that data related to a specified image region has been updated.
updateRunningStatistics(RunningStatistics, SimpleImage) - Static method in class qupath.lib.analysis.stats.StatisticsHelper
Add all pixels from a SimpleImage to an existing RunningStatistics object.
updateServerMetadata(ImageServerMetadata) - Method in class qupath.lib.images.ImageData
Update the ImageServer metadata.
updateStatus(ParallelTileObject.Status) - Method in class qupath.lib.plugins.ParallelTileObject
Notify the object if it is currently being processed.
updateT(int) - Method in class qupath.lib.regions.RegionRequest
Create a RegionRequest equivalent to this one with the updated t value.
updateTranslation(double, double, ImageRegion) - Method in class qupath.lib.roi.RoiEditor
Update a ROI by translation, optionally constraining its movement within a specified boundary.
updateUris(Map<URI, URI>) - Method in interface qupath.lib.io.UriResource
 
updateURIs(Map<URI, URI>) - Method in class qupath.lib.images.servers.ImageServerBuilder.DefaultImageServerBuilder
 
updateURIs(Map<URI, URI>) - Method in interface qupath.lib.images.servers.ImageServerBuilder.ServerBuilder
Update the URIs required by this builder.
updateURIs(Map<URI, URI>) - Method in interface qupath.lib.io.UriResource
Update the specified URIs.
updateZ(int) - Method in class qupath.lib.regions.RegionRequest
Create a RegionRequest equivalent to this one with the updated z value.
UriResource - Interface in qupath.lib.io
Interface for objects that depend upon URIs.
UriUpdater<T> - Class in qupath.lib.io
Helper class for updating URIs, for example whenever files have moved or projects have been transferred between computers.
UriUpdater.SingleUriItem - Class in qupath.lib.io
Wrapper for a URI, providing access to a Path if available.
UriUpdater.UriStatus - Enum Class in qupath.lib.io
Enum representing the status of a URI, i.e.
USE_BIGGEST - Static variable in interface qupath.lib.objects.utils.MeasurementStrategy
Use the measurements of the largest object by area, length or number of points.
USE_FIRST - Static variable in interface qupath.lib.objects.utils.MeasurementStrategy
Assign the measurements of the first object to the output object.
useAnnotations() - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Use annotations for labels.
useCellNuclei() - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Use cells rather than annotations for labels, requesting the nucleus ROI where available.
useCells() - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Use cells rather than annotations for labels.
useDetections() - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Use detections rather than annotations for labels.
useFilter(Predicate<PathObject>) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Use a custom method of selecting objects for inclusion.
useInstanceLabels() - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Request that unique labels are used for all objects, rather than classifications.
useInstanceLabels(boolean) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
Optionally request that unique labels are used for all objects, rather than classifications.
useROIBounds(boolean) - Method in class qupath.lib.images.writers.TileExporter
Optionally use the full ROI for parent objects, rather than TileExporter.tileSize(int, int).
useUniqueLabels() - Method in class qupath.lib.images.servers.LabeledImageServer.Builder

V

valueOf(String) - Static method in enum class qupath.lib.classifiers.Normalization
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.color.ColorDeconvolutionStains.DefaultColorDeconvolutionStains
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.color.StainVector.DefaultStains
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.images.ImageData.ImageType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.images.servers.ImageServerMetadata.ChannelType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.images.servers.PixelType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.images.servers.RotatedImageServer.Rotation
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.images.servers.ZProjectedImageServer.Projection
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.io.PathIO.GeoJsonExportOptions
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.io.UriUpdater.UriStatus
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.measurements.MeasurementList.MeasurementListType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.objects.classes.PathClassFactory.StandardPathClasses
Deprecated.
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent.HierarchyEventType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.objects.PathObjectFilter
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.objects.utils.OverlapFixer.Strategy
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.objects.utils.Tiler.TileAlignment
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.plugins.ParallelTileObject.Status
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.roi.interfaces.ROI.RoiType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.roi.RoiTools.CombineOp
Returns the enum constant of this class with the specified name.
values() - Static method in enum class qupath.lib.classifiers.Normalization
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.color.ColorDeconvolutionStains.DefaultColorDeconvolutionStains
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.color.StainVector.DefaultStains
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.images.ImageData.ImageType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.images.servers.ImageServerMetadata.ChannelType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.images.servers.PixelType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.images.servers.RotatedImageServer.Rotation
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.images.servers.ZProjectedImageServer.Projection
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.io.PathIO.GeoJsonExportOptions
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.io.UriUpdater.UriStatus
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.measurements.MeasurementList.MeasurementListType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Method in interface qupath.lib.measurements.MeasurementList
Get a snapshot of all measurement values as a double array.
values() - Static method in enum class qupath.lib.objects.classes.PathClassFactory.StandardPathClasses
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.objects.hierarchy.events.PathObjectHierarchyEvent.HierarchyEventType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.objects.PathObjectFilter
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.objects.utils.OverlapFixer.Strategy
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.objects.utils.Tiler.TileAlignment
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.plugins.ParallelTileObject.Status
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.roi.interfaces.ROI.RoiType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.roi.RoiTools.CombineOp
Returns an array containing the constants of this enum class, in the order they are declared.
Version - Class in qupath.lib.common
Helper class for working with semantic versioning.

W

warnOnce(Logger, String) - Static method in class qupath.lib.common.LogTools
Log a message once at the WARN level.
WEIGHTED_MEAN - Static variable in interface qupath.lib.objects.utils.MeasurementStrategy
Calculate a mean weighted by object area and pass this to the output object.
White - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
All pixels white
WHITE - Static variable in class qupath.lib.common.ColorTools
Packed int representing white.
width - Variable in class qupath.lib.geom.ImmutableDimension
Width of the ImmutableDimension.
width(int) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder
Specify the full-resolution image width.
Workflow - Class in qupath.lib.plugins.workflow
A collection of steps that relate to how an image has been - or should be - processed.
Workflow() - Constructor for class qupath.lib.plugins.workflow.Workflow
 
WorkflowListener - Interface in qupath.lib.plugins.workflow
Interface for listening to changes in Workflows, e.g.
WorkflowStep - Interface in qupath.lib.plugins.workflow
Basic interface for a loggable workflow step.
workflowUpdated(Workflow) - Method in class qupath.lib.images.ImageData
 
workflowUpdated(Workflow) - Method in interface qupath.lib.plugins.workflow.WorkflowListener
Called whenever a Workflow has been updated in some way, such as a new step added.
wrap(URI...) - Static method in class qupath.lib.io.UriUpdater
Wrap one or more URIs in a UriResource so they can be updated together.
wrap(Collection<? extends PathObject>) - Static method in class qupath.lib.io.FeatureCollection
Wrap a collection of PathObjects as a FeatureCollection, ignoring nested (child) objects.
wrap(Collection<? extends PathObject>, boolean) - Static method in class qupath.lib.io.FeatureCollection
Wrap a collection of PathObjects as a FeatureCollection.
wrap(Collection<URI>) - Static method in class qupath.lib.io.UriUpdater
Wrap one or more URIs in a UriResource so they can be updated together.
WrappedBufferedImageServer - Class in qupath.lib.images.servers
Implementation of an ImageServer that simply wraps an existing BufferedImage.
WrappedBufferedImageServer(String, BufferedImage) - Constructor for class qupath.lib.images.servers.WrappedBufferedImageServer
Create an ImageServer<BufferedImage> using an image that has been provided directly.
WrappedBufferedImageServer(String, BufferedImage, List<ImageChannel>) - Constructor for class qupath.lib.images.servers.WrappedBufferedImageServer
Create an ImageServer<BufferedImage> using an image that has been provided directly.
write(JsonWriter, ColorTransforms.ColorTransform) - Method in class qupath.lib.images.servers.ColorTransforms.ColorTransformTypeAdapter
 
writeClassifier(ObjectClassifier<T>, Path) - Static method in class qupath.lib.classifiers.object.ObjectClassifiers
Write the classifier to a file.
writeExternal(ObjectOutput) - Method in class qupath.lib.color.ColorDeconvolutionStains
 
writeExternal(ObjectOutput) - Method in class qupath.lib.color.StainVector
 
writeExternal(ObjectOutput) - Method in class qupath.lib.geom.Point2
 
writeExternal(ObjectOutput) - Method in class qupath.lib.objects.DefaultPathObjectConnectionGroup
Deprecated.
 
writeExternal(ObjectOutput) - Method in class qupath.lib.objects.PathCellObject
 
writeExternal(ObjectOutput) - Method in class qupath.lib.objects.PathObject
 
writeExternal(ObjectOutput) - Method in class qupath.lib.objects.PathObjectConnections
 
writeExternal(ObjectOutput) - Method in class qupath.lib.objects.PathROIObject
 
writeExternal(ObjectOutput) - Method in class qupath.lib.objects.TMACoreObject
 
writeExternal(ObjectOutput) - Method in class qupath.lib.plugins.workflow.SimplePluginWorkflowStep
 
writeExternal(ObjectOutput) - Method in class qupath.lib.plugins.workflow.Workflow
 
writeImage(BufferedImage, OutputStream) - Method in class qupath.lib.images.writers.JpegWriter
 
writeImage(BufferedImage, OutputStream) - Method in class qupath.lib.images.writers.PngWriter
 
writeImage(BufferedImage, String) - Static method in class qupath.lib.images.writers.ImageWriterTools
Write a 2D image using the default writer based on the file path.
writeImage(BufferedImage, String) - Method in class qupath.lib.images.writers.JpegWriter
 
writeImage(BufferedImage, String) - Method in class qupath.lib.images.writers.PngWriter
 
writeImage(ImageServer<BufferedImage>, OutputStream) - Method in class qupath.lib.images.writers.JpegWriter
 
writeImage(ImageServer<BufferedImage>, OutputStream) - Method in class qupath.lib.images.writers.PngWriter
 
writeImage(ImageServer<BufferedImage>, String) - Method in class qupath.lib.images.writers.JpegWriter
 
writeImage(ImageServer<BufferedImage>, String) - Method in class qupath.lib.images.writers.PngWriter
 
writeImage(ImageServer<BufferedImage>, String) - Static method in class qupath.lib.images.writers.ImageWriterTools
Write a (possibly multidimensional) image region using the default writer based on the file path.
writeImage(ImageServer<BufferedImage>, RegionRequest, OutputStream) - Method in class qupath.lib.images.writers.JpegWriter
 
writeImage(ImageServer<BufferedImage>, RegionRequest, OutputStream) - Method in class qupath.lib.images.writers.PngWriter
 
writeImage(ImageServer<BufferedImage>, RegionRequest, String) - Method in class qupath.lib.images.writers.JpegWriter
 
writeImage(ImageServer<BufferedImage>, RegionRequest, String) - Method in class qupath.lib.images.writers.PngWriter
 
writeImage(ImageServer<T>, OutputStream) - Method in interface qupath.lib.images.writers.ImageWriter
Write a full image to a specified output stream.
writeImage(ImageServer<T>, String) - Method in interface qupath.lib.images.writers.ImageWriter
Write a full image to a specified path.
writeImage(ImageServer<T>, RegionRequest, OutputStream) - Method in interface qupath.lib.images.writers.ImageWriter
Write an image region to a specified output stream.
writeImage(ImageServer<T>, RegionRequest, String) - Method in interface qupath.lib.images.writers.ImageWriter
Write an image region to a specified path.
writeImage(T, OutputStream) - Method in interface qupath.lib.images.writers.ImageWriter
Write a full image to a specified output stream.
writeImage(T, String) - Method in interface qupath.lib.images.writers.ImageWriter
Write a full image to a specified path.
writeImageData(File, ImageData<?>) - Static method in class qupath.lib.io.PathIO
Write (binary) file containing ImageData for later use.
writeImageData(OutputStream, ImageData<?>) - Static method in class qupath.lib.io.PathIO
Serialize an ImageData object to an output stream.
writeImageData(Path, ImageData<?>) - Static method in class qupath.lib.io.PathIO
Write (binary) file containing ImageData for later use.
writeImageRegion(ImageServer<BufferedImage>, RegionRequest, String) - Static method in class qupath.lib.images.writers.ImageWriterTools
Write a 2D image region using the default writer based on the file path.
writePoints(File, Collection<? extends PathObject>) - Static method in class qupath.lib.io.PointIO
Write a list of point annotations to a file.
writePoints(OutputStream, Collection<? extends PathObject>) - Static method in class qupath.lib.io.PointIO
Write a list of point annotations to a stream.
writeTiles(String) - Method in class qupath.lib.images.writers.TileExporter
Export the image tiles to the specified directory.

X

x - Variable in class qupath.lib.roi.EllipseROI
 
x - Variable in class qupath.lib.roi.RectangleROI
 
x2 - Variable in class qupath.lib.roi.EllipseROI
 
x2 - Variable in class qupath.lib.roi.RectangleROI
 

Y

y - Variable in class qupath.lib.roi.EllipseROI
 
y - Variable in class qupath.lib.roi.RectangleROI
 
y2 - Variable in class qupath.lib.roi.EllipseROI
 
y2 - Variable in class qupath.lib.roi.RectangleROI
 
YELLOW - Static variable in class qupath.lib.common.ColorTools
Packed int representing yellow.

Z

Z_SLICE - Static variable in class qupath.lib.images.servers.PixelCalibration
String to represent 'z-slice' units.
zapGremlins(String) - Static method in class qupath.lib.common.GeneralTools
Remove non-printable characters from a String.
ZConcatenatedImageServer - Class in qupath.lib.images.servers
An image server that combine similar images into a z-stack.
zProject(ZProjectedImageServer.Projection) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Apply a Z-projection.
zProject(ZProjectedImageServer.Projection, int) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Apply a Z-projection, either from all slices or using a running projection from adjacent slices.
ZProjectedImageServer - Class in qupath.lib.images.servers
An image server that converts a z-stack into a 2D image with a projection.
ZProjectedImageServer.Projection - Enum Class in qupath.lib.images.servers
A type of projection on the Z-axis.
zProjectMax() - Method in class qupath.lib.images.servers.TransformedServerBuilder
Apply a maximum Z-projection to the image.
zProjectMax(int) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Apply a running maximum Z-projection to the image.
zProjectMean() - Method in class qupath.lib.images.servers.TransformedServerBuilder
Apply a mean Z-projection to the image.
zProjectMean(int) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Apply a running mean Z-projection to the image.
zProjectMedian() - Method in class qupath.lib.images.servers.TransformedServerBuilder
Apply a median Z-projection to the image.
zProjectMedian(int) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Apply a running median Z-projection to the image.
zProjectMin() - Method in class qupath.lib.images.servers.TransformedServerBuilder
Apply a minimum Z-projection to the image.
zProjectMin(int) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Apply a running minimum Z-projection to the image.
zProjectStandardDeviation() - Method in class qupath.lib.images.servers.TransformedServerBuilder
Apply a standard deviation Z-projection to the image.
zProjectStandardDeviation(int) - Method in class qupath.lib.images.servers.TransformedServerBuilder
Apply a running standard deviation Z-projection to the image.
zProjectSum() - Method in class qupath.lib.images.servers.TransformedServerBuilder
Apply a sum Z-projection to the image.
zRange(int, int) - Method in class qupath.lib.images.writers.TileExporter
Define the range of Z-slices to process.
zSpacingCalibrated() - Method in class qupath.lib.images.servers.ImageServerMetadata
Returns true if z-spacing calibration information is available for the image.
zSpacingMicrons(Number) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder
Specify the spacing between z-slices, in microns.
zSpacingMicrons(Number) - Method in class qupath.lib.images.servers.PixelCalibration.Builder
Specify spacing between z-slices, in microns.
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