Index
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
ImageServerfor 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
TMAGridand 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.PathObjectPredicatethrough 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
UriResourceobjects. - 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.Subdivisionwith 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 an
ImageServerMetadata. - build() - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel.Builder
-
Build a list of ImageResolutionLevels, which can be used with an
ImageServerMetadataobject. - build() - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
-
Build the
ImageServerwith the requested parameters. - build() - Method in class qupath.lib.images.servers.PixelCalibration.Builder
-
Build
PixelCalibrationobject. - 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
ImageServerthat 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.ImageResolutionLevelobjects 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
LabeledImageServerfor the specifiedImageData. - 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
ImageServerfor 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
ImageServerfor 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
TransformingImageServerthat 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
-
TypeAdapterto support serializing aColorTransforms.ColorTransform. - 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
SimpleProgressMonitorthat 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
PathClassor 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
Mapto a one-line JSON representation, omitting hidden parameters. - convertToJson(ParameterList) - Static method in class qupath.lib.plugins.parameters.ParameterList
-
Convert a
ParameterLista 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
-
Convert an
AffineTransformto anAffineTransformation. - convertTransform(AffineTransformation) - Static method in class qupath.lib.roi.GeometryTools
-
Convert an
AffineTransformationto anAffineTransform. - 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
UriResourceobjects. - 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
PathAnnotationObjecttiles 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.DisplayBandto 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.DisplayBandto 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
ImageChannelif 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.ColorModelBuilderwith 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
STRtreeto 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
SimpleImagebacked by an existing float array of pixels. - createFloatImage(int, int) - Static method in class qupath.lib.analysis.images.SimpleImages
-
Create a
SimpleImagebacked 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.Subdivisionusing the centroid coordinates of ROIs. - createFromGeometryCoordinates(Collection<PathObject>, boolean, double) - Static method in class qupath.lib.analysis.DelaunayTools
-
Create a
DelaunayTools.Subdivisionusing 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
Geometrytiles 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
TaskRunnerinstance, using the default number of threads fromThreadTools.getParallelism(). - createHeadlessTaskRunner(int) - Method in class qupath.lib.plugins.TaskRunnerUtils
-
Create a new headless
TaskRunnerinstance 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
IndexColorModelrepresenting 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
IndexColorModelfrom aColorMaps.ColorMap. - createIndexedColorModel8bit(ColorMaps.ColorMap, int) - Static method in class qupath.lib.color.ColorModelFactory
-
Create an 8-bit
IndexColorModelfrom aColorMaps.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.UriImageSupportfor (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.UriImageSupportfor 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.ServerBuilderthat 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.ServerBuilderthat 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 defaultObjectInputFilterfor 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
PathObjecttiles 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
ROItiles 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
TypeAdapterFactorythat is suitable for handling class hierarchies. - createTaskRunner() - Method in class qupath.lib.plugins.TaskRunnerUtils
-
Create a new
TaskRunnerinstance, using the default number of threads fromThreadTools.getParallelism(). - createTaskRunner(int) - Method in class qupath.lib.plugins.TaskRunnerUtils
-
Create a new
TaskRunnerinstance 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
PathTileObjecttiles 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.Subdivisionbased 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
Imageto aBufferedImageif necessary, or return the original image unchanged if it is already aBufferedImage. - 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
Envelopeto anImageRegion. - 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
Geometryobjects. - 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
PathObjecthas at least one of the specifiedPathClasses. - 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.ServerBuilderfrom 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
ImageServerBuildercan 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
PathObjectFilteras aPathObjectPredicates.PathObjectPredicateso 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
ROIobjects and Java Topology SuiteGeometryobjects. - GeometryTools() - Constructor for class qupath.lib.roi.GeometryTools
- GeometryTools.GeometryConverter - Class in qupath.lib.roi
- 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.UriImageSupportthat 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
TileRequestobjects 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
Areaobject 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
-
Get an average of
PixelCalibration.getPixelWidth()andPixelCalibration.getPixelHeight(). - 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
Rectanglecorresponding to the x,y,width,height of anImageRegion. - getBounds(ImageRegion, Rectangle) - Static method in class qupath.lib.awt.common.AwtTools
-
Set the bounds of an existing
Rectangleto the x,y,width,height of anImageRegion. - getBounds(ROI) - Static method in class qupath.lib.awt.common.AwtTools
- getBounds2D(BufferedImage) - Method in interface qupath.lib.images.servers.transforms.BufferedImageNormalizer
- getBounds2D(ROI) - Static method in class qupath.lib.awt.common.AwtTools
-
Create a
Rectangle2Dcorresponding to bounding box of aROI. - getBounds2D(ROI, Rectangle2D) - Static method in class qupath.lib.awt.common.AwtTools
-
Set the bounds of an existing
Rectangle2Dto the x,y,width,height of aROI. - 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
Polylinehere 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
Polylinehere 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
ImageChannelusing 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
PathClassas 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
ImageDatathat 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
TaskRunnerinstances. - 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
-
Deprecated.since v0.4.0, use
PathClass.getInstance(PathClass, String, Integer) - 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
ProjectImageEntryassociated with anImageData - 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
ImagePlanefor 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
ImageRegioncorresponding to a specifiedRectanglebounding box. - getImageRegion(Shape, int, int) - Static method in class qupath.lib.awt.common.AwtTools
-
Create an
ImageRegioncorresponding to a the bounding box of aShape. - 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.UriImageSupportthat 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.UriImageSupportassociated with anImageServerBuilder, 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
IndexColorModelrepresenting 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
ImageServerBuilderssupporting 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 theMap.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 theMap.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 theMap.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.since v0.4.0, use
PathClass.getNegative(PathClass) - 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
-
Deprecated.use
PathIO.getObjectFileExtensions(boolean)instead - 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.v0.6.0, use
PathObjectHierarchy.getAllObjectsForRegion(ImageRegion, Collection)or its related methods instead. - 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.since v0.4.0, use
PathClass.getOnePlus(PathClass) - 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.use
ParameterList.convertToJson(Map)instead. - getParameterListJSON(ParameterList, String) - Static method in class qupath.lib.plugins.parameters.ParameterList
-
Deprecated.use
ParameterList.convertToJson(ParameterList)instead. - 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
Pathcorresponding 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
-
Deprecated.since v0.4.0 in favor of
PathClass.getInstance(String, Integer)orPathClass.fromString(String, Integer) - 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.since v0.4.0 in favor of
PathClass.fromCollection(java.util.Collection) - getPathClass(PathClassFactory.StandardPathClasses) - Static method in class qupath.lib.objects.classes.PathClassFactory
-
Deprecated.since v0.4.0, use
PathClass.StandardPathClasses - 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.v0.6.0 use
DelaunayTools.Subdivision.getObjects()instead. - 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
PixelCalibrationobject 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.since v0.4.0, use
PathClass.getPositive(PathClass) - 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.UriImageSupportfor 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.ServerBuilderthat 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
Shapeobject 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
ROIfrom an Shape. - getShapeROI(Shape, ImagePlane, double) - Static method in class qupath.lib.roi.RoiTools
-
Create a
ROIfrom 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.since v0.4.0, use
PathClass.getThreePlus(PathClass) - 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
TileRequestcontaining 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
TileRequestobjects necessary to fulfil a specificRegionRequest. - getTileRequestsForLevel(int) - Method in interface qupath.lib.images.servers.TileRequestManager
-
Get
TileRequestobjects 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.since v0.4.0, use
PathClass.getTwoPlus(PathClass) - getTypeAdapterFactory() - Static method in class qupath.lib.classifiers.object.ObjectClassifiers
-
Get a
TypeAdapterFactoryto handleObjectClassifierinstances. - 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
Geometryobjects. - getVoronoiROIs(Geometry) - Method in class qupath.lib.analysis.DelaunayTools.Subdivision
-
Get a map of Voronoi faces, converted to
ROIobjects. - 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
TypeAdapterFactorythat 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
ImageDataalready 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.ServerBuilderthat requires a URI and (optional) array of String arguments to create anImageServerwith the help of aImageServerBuilder. - 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
ImageServerBuilderfor 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
ImageServerMetadataobject. - 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.ImageResolutionLevelto 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
ImageServerobjects. - 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
ImageWriterobjects 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
ROIand anImageRegionintersect. - 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
trueif 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
trueif#getParentClass() != null. - isDerivedFrom(PathClass) - Method in class qupath.lib.objects.classes.PathClass
-
Returns
trueif 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() == 1return - 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 toImageData.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
trueif 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
PathObjectHierarchywhere 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
-
Deprecated.
- 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
ColorModelto 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.Use
ObjectMerger.process(Collection)instead - 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
PathClassandImagePlane, 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
PathClasssharing the sameImagePlane, 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
PathClassandImagePlaneas 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
MinimalMetadataStoreinstead. - 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.Builderto 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
ObjectClassifierthat 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
-
TypeAdapterFactoryto 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.PathObjectPredicatethrough 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
Versionobject 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
RegionRequestcorresponding 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
PathClassdirectly. - 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
PathClassobjects. - 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
ImageDataobjects. - 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 forPathObjects. - PathObjectPredicates() - Constructor for class qupath.lib.objects.PathObjectPredicates
- PathObjectPredicates.PathObjectPredicate - Interface in qupath.lib.objects
-
A JSON-serializable
Predicatefor use withPathObjects. - 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
PixelCalibrationobjects. - 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
PixelClassifierMetadataobjects. - 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 theMap.put(Object, Object)method instead - putMetadataValue(String, String) - Method in class qupath.lib.objects.TMACoreObject
-
Deprecated.v0.6.0. Use
TMACoreObject.putMetadataValue(String, String)instead. - 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
ImageDataclass 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
ImageServershould overrideImageServer.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
PathObjectHierarchyfor 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
PathObjectHierarchyfrom 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
ImageDataassociated 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
ImageDatafrom 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
ImageDatafrom 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
ImageDatafrom 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
ImageDatafrom 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
PathObjectfrom a file. - readObjects(Path) - Static method in class qupath.lib.io.PathIO
-
Read a list of
PathObjectfrom a file. - readObjectsFromGeoJSON(InputStream) - Static method in class qupath.lib.io.PathIO
-
Read a list of
PathObjectfrom 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
ImageRegionto anEnvelope. - 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
ObjectClassifiersubtype 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.v0.6.0 use
MeasurementList.removeAll(String...)instead - 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
PathClasswith 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
PathClasswith 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
- 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
ImageDatafor 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
-
Set
ImageData.isChanged()status. - 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
PathClassfrom 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
TaskRunnerinstances. - setCreateHeadlessFunction(IntFunction<TaskRunner>) - Method in class qupath.lib.plugins.TaskRunnerUtils
-
Set the function used to generate new
TaskRunnerinstances. - 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
SimpleImageinstances 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
PathClasswith name elements sorted alphabetically. - sortNames(PathClass, Comparator<String>) - Static method in class qupath.lib.objects.classes.PathClassTools
-
Create a
PathClasswith name elements sorted using an arbitraryComparator. - 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
SparseImageServerinto 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
Externalizableinterface. - 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
PathClassof 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
TaskRunnerinstances. - 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
- 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
AffineTransformto the server. - TransformedServerBuilder - Class in qupath.lib.images.servers
-
Helper class for creating an
ImageServerthat 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
PathObjectwith 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
PathObjectand all its descendants, recursively. - transformObjectRecursive(PathObject, AffineTransform, boolean, boolean) - Static method in class qupath.lib.objects.PathObjectTools
-
Create (optionally) transformed versions of the
PathObjectand 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
RegionRequestequivalent 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
RegionRequestequivalent 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
RegionRequestequivalent 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
RegionRequestequivalent 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
RegionRequestequivalent 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
Pathif 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
-
Deprecated.in favor of
LabeledImageServer.Builder.useInstanceLabels()
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
UriResourceso 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
UriResourceso they can be updated together. - WrappedBufferedImageServer - Class in qupath.lib.images.servers
-
Implementation of an
ImageServerthat simply wraps an existingBufferedImage. - 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
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Write a full image to a specified path.
- writeImageData(File, ImageData<?>) - Static method in class qupath.lib.io.PathIO
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Write (binary) file containing
ImageDatafor later use. - writeImageData(OutputStream, ImageData<?>) - Static method in class qupath.lib.io.PathIO
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Serialize an ImageData object to an output stream.
- writeImageData(Path, ImageData<?>) - Static method in class qupath.lib.io.PathIO
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Write (binary) file containing
ImageDatafor later use. - writeImageRegion(ImageServer<BufferedImage>, RegionRequest, String) - Static method in class qupath.lib.images.writers.ImageWriterTools
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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
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Write a list of point annotations to a file.
- writePoints(OutputStream, Collection<? extends PathObject>) - Static method in class qupath.lib.io.PointIO
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Write a list of point annotations to a stream.
- writeTiles(String) - Method in class qupath.lib.images.writers.TileExporter
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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
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Packed int representing yellow.
Z
- Z_SLICE - Static variable in class qupath.lib.images.servers.PixelCalibration
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String to represent 'z-slice' units.
- zapGremlins(String) - Static method in class qupath.lib.common.GeneralTools
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Remove non-printable characters from a String.
- ZConcatenatedImageServer - Class in qupath.lib.images.servers
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An image server that combine similar images into a z-stack.
- zProject(ZProjectedImageServer.Projection) - Method in class qupath.lib.images.servers.TransformedServerBuilder
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Apply a Z-projection.
- zProject(ZProjectedImageServer.Projection, int) - Method in class qupath.lib.images.servers.TransformedServerBuilder
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Apply a Z-projection, either from all slices or using a running projection from adjacent slices.
- ZProjectedImageServer - Class in qupath.lib.images.servers
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An image server that converts a z-stack into a 2D image with a projection.
- ZProjectedImageServer.Projection - Enum Class in qupath.lib.images.servers
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A type of projection on the Z-axis.
- zProjectMax() - Method in class qupath.lib.images.servers.TransformedServerBuilder
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Apply a maximum Z-projection to the image.
- zProjectMax(int) - Method in class qupath.lib.images.servers.TransformedServerBuilder
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Apply a running maximum Z-projection to the image.
- zProjectMean() - Method in class qupath.lib.images.servers.TransformedServerBuilder
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Apply a mean Z-projection to the image.
- zProjectMean(int) - Method in class qupath.lib.images.servers.TransformedServerBuilder
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Apply a running mean Z-projection to the image.
- zProjectMedian() - Method in class qupath.lib.images.servers.TransformedServerBuilder
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Apply a median Z-projection to the image.
- zProjectMedian(int) - Method in class qupath.lib.images.servers.TransformedServerBuilder
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Apply a running median Z-projection to the image.
- zProjectMin() - Method in class qupath.lib.images.servers.TransformedServerBuilder
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Apply a minimum Z-projection to the image.
- zProjectMin(int) - Method in class qupath.lib.images.servers.TransformedServerBuilder
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Apply a running minimum Z-projection to the image.
- zProjectStandardDeviation() - Method in class qupath.lib.images.servers.TransformedServerBuilder
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Apply a standard deviation Z-projection to the image.
- zProjectStandardDeviation(int) - Method in class qupath.lib.images.servers.TransformedServerBuilder
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Apply a running standard deviation Z-projection to the image.
- zProjectSum() - Method in class qupath.lib.images.servers.TransformedServerBuilder
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Apply a sum Z-projection to the image.
- zRange(int, int) - Method in class qupath.lib.images.writers.TileExporter
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Define the range of Z-slices to process.
- zSpacingCalibrated() - Method in class qupath.lib.images.servers.ImageServerMetadata
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Returns true if z-spacing calibration information is available for the image.
- zSpacingMicrons(Number) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder
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Specify the spacing between z-slices, in microns.
- zSpacingMicrons(Number) - Method in class qupath.lib.images.servers.PixelCalibration.Builder
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Specify spacing between z-slices, in microns.
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