Uses of Class
org.anchoranalysis.bean.AnchorBean
Packages that use AnchorBean
Package
Description
Beans related to reading / writing / specifying annotations.
What to compare an annotation (ground truth) against?
Defining, loading, initializing Anchor Beans.
Define and related-classes.DefineAdder and related-classes.Initializing beans with particular parameters, including recursively.
Applying permutations to a bean's fields.
Imposes a permutation value on one or more properties of a bean.
Applying permutations to the properties of a bean.
Beans that implement collections of primitive element types, as well as
String.Utility beans which have a generally broader use than a specific module.
Beans that specify colors.
Beans that create lists or indices of colors according to particular schemes.
Setting, referencing and initializing key-value parameters.
Defines a root path directory on the filesystem whre files are read / written.
Specifies a particular type of random-number generator.
Specifies regular-expressions.
Specifies a binary relation of some kind between scalars.
Specifies a unary relation to a threshold value.
Custom factories for loading beans in custom ways from XML.
Beans related to executing an experiment by calling jobs on inputs.
Assigning unique names to experiments.
Generic experiments that handle input and output in structured ways.
Different approaches to where messages on the progress/status of an experiment are logged to.
How a task is executed on multiple inputs.
A test whether certain conditions on arguments to experiments are fulfilled.
Defines a task,
which is a set of operations run on an input, that may or may not generate an output.
Beans pertaining to feature-calculation.
A feature-list (custom list type for features) and associated providers.
Features that are sufficiently generic to work on any input-type.
Provider of a single feature.
Defines base class
FeatureResults together with
some implementations.Core (bean) classes for image processing.
Base classes for performing operations on
Channels.Beans for specifying image interpolators.
Classes that aren't AnchorBeans that pertain to the initialization of image-related beans.
Beans pertaining to
ObjectMask and their
collections.Base classes for providers of different core data entities related to images.
A provider of
Stacks.Base classes to perform image segmentation, transforming an image into another meaningful entity
or entities.
Base classes to perform binary-segmentation.
Base classes to segment a channel into objects.
Beans to define entities or operate that consider Euclidian space.
Beans to specify how to form a single-image by spatially combining other images.
Aligning a
BoundingBox to fit inside another BoundingBox.Montages images together to completely fill the available space, while preserving aspect ratio.
Combining other images through overlaying.
Combining other images through tiling.
Beans to specify a direction.
Base classes for thresholding and calculating levels for thresholding.
Reusable relations to a threshold.
Converting quantities of distance between units.
Converting quantities of extent (area or volume) between units.
Converting quantities of area between units.
Converting quantities of volume between units.
Beans pertaining to feature definition and calculation.
Beans that define context (which feature, which energy-stack) for evaluating feature-inputs.
Features that operate on a
Histogram.Features that operate on a
ObjectCollection.Features that operate on a pair of
ObjectMasks.Features that operate on a single
ObjectMask.Features that convert to/from physical spatial units (e.g. meters) as opposed to pixels/voxels.
Beans to reduce the number of results that are returned from inference, by removing overlaping
entities etc.
Instance-segmentation of a
Stack.Non-bean classes to reduce the number of results that are returned from inference, by removing
overlapping entities etc.
Beans pertaining to reading
Channels as input.How to represent an object-mask in a raster that is being drawn.
Beans to specify the outputting of features into CSV from a
ObjectCollection.Beans to combine multiple stacks into a single stack before outputting.
Bean classes for reading
ImageMetadata from the
file-system.Bean classes for reading raster-files from the filesystem.
Bean classes for writing raster-files to the filesystem.
Beans for filesystem I/O using Bioformats.
User-specified options that can modify metadata or other attributes of a loaded Bioformats image.
Writing stacks to the file system using the Bioformats library.
Performing interpolation with ImageJ.
Raster-writers that use ImageJ to write images to the filesystem.
Beans related to collecting inputs from the file-system for an experiment.
Methods to provide a
Dictionary.Methods to provide a collection of
Files.Determines how inputs are aggregated into groups, if at all.
Beans to derive names (compact unique identifiers) from files.
Beans pertaining to manipulating and matching against file-paths.
Beans to find a subset of files that match a particular conditions on their paths.
Methods to provide a single file-path.
Beans for the framework around writing files to the file-system.
Beans indicating whether a particular output is enabled or not.
Beans for generating paths for outputting files by adding a prefix, suffix etc.
Rules for determining if a particular output is enabled or not in a context of a hierarchy.
Loading and displaying pre-defined tasks.
Beans pertaining to marked-point-processes.
Lower and upper limits set around variables.
Bounds on how to rotate an entity in Euclidean space.
Beans generally related to
Marks.Beans related to creating
Marks.Operations based on sets of points.
Fitting structures to sets of points.
Proposing
Marks or other data-structures with particular
attributes.Voxel subregions of
Marks.Criteria for adding edges during optimization of marked-point-processes.
Implementations and helper classes for calculating energy during an energy-minimization
optimization scheme.
Creating
EnergySchemes.Features calculated on a
Mark.Non-bean classes for calculating feature-values related to
Marks.Beans for reading data structures related to marked point processes from the file system.
Pairs of
Marks.Beans relating to drawing an
Overlay on an image.Beans to combine two or more annotations.
Comparing the similarity of annotations from two images to each other.
Task to compare a set of annotations to a segmentation or another set of annotations.
Pairs annotations from two different sets, creating an assignment of some type.
FilesProviders for providing annotations.A label as used for annotating.
Strategies for how to annotate an image, such label per image etc.
Morphological grayscale-reconstruction algorithm.
Implementations of
ChannelProvider that use FIJI.Euclidean Distance Transform
implementations via FIJI.
Implementations of
MaskProvider that use FIJI.Implementations of
Thresholder that use FIJI.Filters that perform blurring.
Implementations of
ConvertChannelTo and ConvertChannelToWithHistogram.Implementations of
ConvertChannelTo and ConvertChannelToWithHistogram.Implementations of
ChannelProvider that are
generic base-classes or otherwise abstract or general.Implementations of
ChannelProvider that perform
arithmetic on voxels in one or more Channels.Implementations of
ChannelProvider that sets the
values of the voxels in a Channel.Implementations of
ChannelProvider that converts a
Channel from one voxel-type to another.Implementations of
ChannelProvider that calculate
the gradient of a Channel's voxels in one or more
dimensions.Implementations of
ChannelProvider that manipulate
the intensity-values of the voxels of a Channel's
voxels.Implementations of
ChannelProvider that involve
conversion from or application of Masks.Implementations of
ChannelProvider that involve
conversion from or application of ObjectMasks.Implementations of
ChannelProvider that assign a
score to particular subregions of a channel.Implementations of
ChannelProvider that process 3D
channels slice-by-slice.Implementations of
ColorProvider.Beans pertaining to
Dictionary.Implementations of
DimensionsProvider.Implementations of
HistogramProvider.Thresholding of intensity values represented in at
Histogram.Implementations of
MaskProvider.Implementations of
MaskProvider that combine
existing providers.Implementations of
MaskProvider that convert
providers of other types to ObjectMasks.Implementations of
MaskProvider that implement
morphological operations.Provides if-else conditions to a
MaskProvider.Implementations of
MaskProvider that process 3D
masks slice-by-slice.Implementations of
ObjectFilter.Implementations of
ObjectFilter that assess each
element in a collection collectively.Implementations of
ObjectFilter that combine two or
more other ObjectFilters.Implementations of
ObjectFilter that
independently assess each element in a collection.Implementations of
ObjectMatcher.Implementations of
ObjectCollectionProvider.Implementations of
ObjectCollectionProvider
involving connected-components.Implementations of
ObjectCollectionProvider
involving feature calculation.Implementations of
ObjectCollectionProvider that
filter objects.Implementations of
ObjectCollectionProvider
involving a Mask.Implementations of
ObjectCollectionProvider
involving merging objects together.Implementations of
ObjectCollectionProvider
involving morphological operations.Implementations of
ObjectCollectionProvider
involving segmentation.Implementations of
ObjectCollectionProvider
involving z-slice processing.Implementations of
ObjectCollectionProvider
involving splitting objects into smaller objects.Implementations of
SegmentChannelIntoObjects.Minima imposition for a Watershed transformation.
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction
Grayscale reconstruction to support the Watershed transformation.
Implementation of a Watershed transformation
based on Yeong et al. 2009.
Strategies for reducing the number of elements with a list by merging/removing lower-confidence
elements that overlap.
Implementations of
ScaleCalculator for calculating
a scaling-factor from dimensions.Implementations of
BinarySegmentation.Implementations of
StackProvider.Implementations of
StackProvider that color
portions of an image.Implementations of
ThumbnailFromObjects.Implementations of
ThumbnailFromStack.Features that are calculated from
Dimensions.Implementations of
FeatureHistogram that calculate
statistics.Implementations of
FeatureHistogram that perform
thresholding.Implementations of
FeatureListProvider.Implementations of
FeatureListProvider with
input-type FeatureInputPairObjects.Implementations of
FeatureListProvider that derive
new features with permuted property-values.Implementations of
FeatureImageMetadata.Beans that affects how morphological operations occur.
Implementations of
FeatureObjectCollection.Features from combinations of
ObjectMasks.Features from pairs of
ObjectMasks.Features that calculate the degree of overlap between two
ObjectMasks.Features that calculate how many other objects an
ObjectMask directly neighbors.Implementations of
FeatureSingleObject.Implementations of
FeatureSingleObject that determine if an
object lies at the border of an image.Implementations of
FeatureSingleObject that consider an
object's bounding-box.Implementations of
FeatureSingleObject that reference a
particular Channel in the associated EnergyStack.Implementations of
FeatureSingleObject that measure an object's
intensity on a corresponding Channel.Implementations of
FeatureSingleObject that measure an object's
gradient from corresponding Channels storing the
gradient.Implementations of
FeatureSingleObject based on calculating image moments, with or without image
intensity.Implementations of
FeatureSingleObject that implement
morphological operations.Implementations of
FeatureSingleObject that measure the shape
of the ObjectMask.Implementations of
FeatureSingleObject that use SharedObjects for calculations.Implementations of
FeatureSingleObject that use SharedObjects for calculations, and measure
the degree of intersection between objects.Implementations of
FeatureSingleObject that processes an object
slice-by-slice in the z-dimension.Implementations of
FeatureSingleObject that measures aspects of
the surface of an ObjectMask.Beans involving physical units for measurement.
Implementations of
VoxelScore.Beans involving
SharedObjects.Beans involving
SharedObjects and
ObjectCollection.Implementations of
FeatureStack or other features
that involve processing a Stack.Implementations of
FeatureStack that process an
ObjectCollection.A parent package for many different kinds of tasks.
Combining multiple images together into a single image.
Tasks pertaining to
Features.Source of rows in feature-tables with
FeatureSource and derived classes.Tasks for converting image-formats.
Different approaches for converting sets of channels (RGB, independently etc.) to another image
format.
Tasks that involved stacks (usually each channel from an image) that are somehow
grouped-together.
Task(s) to export histograms of intensity values.
Selecting a subset of a set of channels.
Associating labels with images.
Tasks to scale an image.
Tasks to segment an image.
Tasks that process on one or more slices from a z-stack.
Implementations of
ChannelProvider that call ImageJ.Non-linear filters using ImageJ that use the statistical moments of the
intensity values in the kernel.
Non-linear filters using ImageJ that use the statistical rank of the intensity values in the
kernel.
Implementations of
DefineAdderBean that call ImageJ.Implementations of
MaskProvider that call ImageJ.Implementations of
ObjectCollectionProvider that
call ImageJ.Implementations of
StackProvider that call
ImageJ.Implementations of
Thresholder that call ImageJ.Implementations of
ChannelMapCreator.Methods for copying files on the file-system.
Rules for preserving or changing the naming of files when copying on the file-system.
Implementations of
CopyFilesNaming
that perform clustering of files.Grouping files together so that they collectively represent a single entity.
Tests that are applied when grouping files in
org.anchoranalysis.plugin.io.bean.file.groupParsing file-paths to determine file-grouping in
org.anchoranalysis.plugin.io.bean.file.groupImplementations of
FileNamer.Implementations of
FileNamer that look for a
pattern across many files.Beans to specify a file-path.
Implementations of
PathPrefixer.Extracting a pattern from a file-path.
Implementations of
FilesProvider.Implementations of
Grouper.Implementations of
InputManager.InputManagers that accept a set of
named-channels.InputManagers that accept a set of named-files.Implementations of
FilesProvider.Implementations of
InputManager that filter inputs.Implementations of
InputManager that process Stacks.Different types of image-file-formats whose headers can provide
ImageMetadata.Implementations of
ImageMetadataReader.Implementations of
DerivePath.Implementations of
StackReader.Implementations of
StackWriter.Summarizing a set of elements into a descriptive-string.
Implementations of
Summarizer that summarize
images.Implementations of
Summarizer that summarize
generically InputFromManagers.Implementations of
Summarizer that summarize
generically Paths.Implementations of
Task related to file-system
I/O.Converting from
NamedChannelsInput to the
input-type expected by a Task.Implementations of
ObjectCollectionProvider.Implementation of
MarkCollectionProvider.Implementations of
StackProvider involving
Mark or related classes.Decodes the outputted tensors from a Mask
R-CNN implementation.
Decodes the outputted tensors from text-segmentation models.
Segmenting a
Stack using the ONNX Runtime to produce
an ObjectCollection.Operations involving color-spaces and OpenCV.
Extracting features using OpenCV.
Interpolation beans that use OpenCV.
Segmentation of a
Stack using OpenCV.Features that combine or convert other features in a generic way.
Arithmetic involving features.
Conditional operations involving features.
Operations that extract a single value from a list of features.
Features that compare against a range of values.
Replaces particular values if they are returned from a feature.
Converts feature values based upon a statistical measure of distribution.
Converting to/from physical units.
Beans that fit or otherwise manipulate sets of points.
Convex hull operations.
Features related to points and fitting points to conics.
Fitting geometric structures to points.
Testing utilities and fixtures with no greater downstream dependency than
anchor-experiment or anchor-mpp or anchor-mpp-io.
A mocked feature internally using a feature-calculation.
Utilities for testing-related reading and writing to the filesystem.
-
Uses of AnchorBean in org.anchoranalysis.annotation.io.bean
Subclasses of AnchorBean in org.anchoranalysis.annotation.io.beanModifier and TypeClassDescriptionclassHow to display one or moreStacks as background during an annotation process.classAnnotationInputManager<T extends ProvidesStackInput,S extends AnnotatorStrategy> AnInputManagerthat provides annotations corresponding to images.classHow an input is associated with annotations on the file-system, and how this is presented visually. -
Uses of AnchorBean in org.anchoranalysis.annotation.io.bean.comparer
Subclasses of AnchorBean in org.anchoranalysis.annotation.io.bean.comparerModifier and TypeClassDescriptionclassA set of elements, loaded from the file-system, to be compared to another set.classAllows comparison of an annotation with multiple other entities. -
Uses of AnchorBean in org.anchoranalysis.bean
Classes in org.anchoranalysis.bean with type parameters of type AnchorBeanModifier and TypeClassDescriptionclassNamedBean<T extends AnchorBean<?>>A bean with an associated textual name.Subclasses of AnchorBean in org.anchoranalysis.beanModifier and TypeClassDescriptionclassNamedBean<T extends AnchorBean<?>>A bean with an associated textual name.classA base class for beans that require initialization but the initializations needs no parameters.Methods in org.anchoranalysis.bean with type parameters of type AnchorBeanModifier and TypeMethodDescription<T extends AnchorBean<?>>
List<T> AnchorBean.findFieldsOfClass(Class<?> match) Finds all bean-fields that are instances of a certain class.Methods in org.anchoranalysis.bean with parameters of type AnchorBeanModifier and TypeMethodDescriptionFieldAccessor.fieldFromBean(AnchorBean<?> bean, Field field) Retrieves the value of aFieldfrom aAnchorBean. -
Uses of AnchorBean in org.anchoranalysis.bean.define
Subclasses of AnchorBean in org.anchoranalysis.bean.defineModifier and TypeClassDescriptionclassA bean where the definitions of many differentNamedBeans can be specified.Methods in org.anchoranalysis.bean.define with type parameters of type AnchorBeanModifier and TypeMethodDescription<T extends AnchorBean<?>>
voidAdds all the named-beans from source to the current map.<T extends AnchorBean<?>>
List<NamedBean<T>> Retrieves the list of elements associated with a grouping-root. -
Uses of AnchorBean in org.anchoranalysis.bean.define.adder
Subclasses of AnchorBean in org.anchoranalysis.bean.define.adderModifier and TypeClassDescriptionclassConcatenates a list of adders.classBase class forAnchorBeans that can add items to aDefine.classLikeDefineAdderBeanbut adds a prefix to the name of beans when adding.classAdds a list of Named-Items define in a XML file in the current directory.Methods in org.anchoranalysis.bean.define.adder with parameters of type AnchorBeanModifier and TypeMethodDescriptionprotected voidDefineAdderWithPrefixBean.addWithName(Define define, String name, AnchorBean<?> item) Add an item todefinewith a name being added. -
Uses of AnchorBean in org.anchoranalysis.bean.initializable
Subclasses of AnchorBean in org.anchoranalysis.bean.initializableModifier and TypeClassDescriptionclassInitializableBean<B,P extends BeanInitialization> A bean that must be initialized with some parameters before being used. -
Uses of AnchorBean in org.anchoranalysis.bean.permute
Classes in org.anchoranalysis.bean.permute with type parameters of type AnchorBeanModifier and TypeClassDescriptionclassPermutedCopyCreator<T extends AnchorBean<T>>Applies aPermutePropertyto a bean to create new duplicated beans each with different permuted values. -
Uses of AnchorBean in org.anchoranalysis.bean.permute.assign
Methods in org.anchoranalysis.bean.permute.assign with parameters of type AnchorBeanModifier and TypeMethodDescriptionvoidPermutationAssigner.assignValue(AnchorBean<?> bean, Object value) Assignsvalueto one or more properties inbean.static PermutationAssignerPermutationAssignerFactory.createForSingle(AnchorBean<?> bean, String propertyPath) Creates an assigner for one or more properties, as identified bypropertyPath. -
Uses of AnchorBean in org.anchoranalysis.bean.permute.property
Subclasses of AnchorBean in org.anchoranalysis.bean.permute.propertyModifier and TypeClassDescriptionclassChanges properties of anAnchorBeanto one of a range of possible values.classAssigns each element from a set of doubles to a particular property of a bean.classBase class for assigning a sequence of numbers to a particular property of a bean.classAssigns an arithmetic sequence of doubles, derived by diving an integer sequence by a divider.classAn arithmetic sequence of integers, each directly assigned to a property during permutation.classAssigns each element from a set of strings to a particular property of a bean.classA sequence of integers.Methods in org.anchoranalysis.bean.permute.property with parameters of type AnchorBeanModifier and TypeMethodDescriptionPermuteProperty.createSetter(AnchorBean<?> bean) Creates aPermutationAssignerwhich allows the particular property to be changed. -
Uses of AnchorBean in org.anchoranalysis.bean.primitive
Subclasses of AnchorBean in org.anchoranalysis.bean.primitive -
Uses of AnchorBean in org.anchoranalysis.bean.xml.factory
Classes in org.anchoranalysis.bean.xml.factory with type parameters of type AnchorBeanModifier and TypeClassDescriptionclassReplacePropertyBeanFactory<T extends AnchorBean<T>>Replaces a property (an XML element of attribute) on a bean before loading it.Methods in org.anchoranalysis.bean.xml.factory with parameters of type AnchorBeanModifier and TypeMethodDescriptionBeanPathCalculator.pathFromBean(AnchorBean<?> bean, String relativePath) Calculates a path from the current bean. -
Uses of AnchorBean in org.anchoranalysis.experiment.bean
Subclasses of AnchorBean in org.anchoranalysis.experiment.beanModifier and TypeClassDescriptionclassA base class for a type of task that produces some kind of result of interest. -
Uses of AnchorBean in org.anchoranalysis.experiment.bean.identifier
Subclasses of AnchorBean in org.anchoranalysis.experiment.bean.identifierModifier and TypeClassDescriptionclassA method to produce an identifier for an experiment.classAutomatically populates a experiment-name and version numberclassDefines constants for name and version of an experiment -
Uses of AnchorBean in org.anchoranalysis.experiment.bean.io
Subclasses of AnchorBean in org.anchoranalysis.experiment.bean.ioModifier and TypeClassDescriptionclassInputOutputExperiment<T extends InputFromManager,S> An experiment that uses both anInputManagerto specify inputs and aOutputManagerto specify outputting.classAnExperimentthat produces output files, as defined by aOutputManager. -
Uses of AnchorBean in org.anchoranalysis.experiment.bean.log
Subclasses of AnchorBean in org.anchoranalysis.experiment.bean.logModifier and TypeClassDescriptionclassThe destination(s) to which log-messages are sent.classLogs messages to a particular location ONLY if debug-mode is enabled.classSwitches between two log-reporters depending on whether detailed logging is switched on or notclassLogs messages to the console.classRather than logging to one location, logs to multiple locations (from a list).classLogs to a text-file created in the output-directory under a particular name.classLogs messages to a text-file create in the output-directory.classLogs to a text file like withToTextFilebut the log is ONLY written if a failure occurs in the experiment. -
Uses of AnchorBean in org.anchoranalysis.experiment.bean.processor
Subclasses of AnchorBean in org.anchoranalysis.experiment.bean.processorModifier and TypeClassDescriptionclassDebugDependentProcessor<T extends InputFromManager,S> Executes different processors depending on whether we are in debug mode or not.classJobProcessor<T extends InputFromManager,S> Base class for a method to apply a task on inputs.classParallelProcessor<T extends InputFromManager,S> Executes jobs in parallel across cores on the system.classSequentialProcessor<T extends InputFromManager,S> Executes jobs sequentially, without any parallelism. -
Uses of AnchorBean in org.anchoranalysis.experiment.bean.require
Subclasses of AnchorBean in org.anchoranalysis.experiment.bean.requireModifier and TypeClassDescriptionclassA predicate on whether all necessary arguments exist for some purpose.classRequire that debug-mode has been enabled. -
Uses of AnchorBean in org.anchoranalysis.experiment.bean.task
Subclasses of AnchorBean in org.anchoranalysis.experiment.bean.taskModifier and TypeClassDescriptionclassTask<T extends InputFromManager,S> Encapsulates some kind of processing to be performed on a set of inputs.classTaskWithoutSharedState<T extends InputFromManager>A particular type of task that doesn't share-state between running jobs -
Uses of AnchorBean in org.anchoranalysis.feature.bean
Subclasses of AnchorBean in org.anchoranalysis.feature.beanModifier and TypeClassDescriptionclassFeature<T extends FeatureInput>Base class for a measurement that calculates a result (double) given input parameters.classBeans-related toFeatures, and which require initialization withFeatureRelatedInitialization. -
Uses of AnchorBean in org.anchoranalysis.feature.bean.list
Subclasses of AnchorBean in org.anchoranalysis.feature.bean.listModifier and TypeClassDescriptionclassDefine<T extends FeatureInput>Specifies a list of features directly without assigning any custom-naming.classDefinedNamed<T extends FeatureInput>Specifies features via a list of names and associated with features.classDefineSingle<T extends FeatureInput>Specifies a single feature directly without assigning any custom-naming.classFeatureList<T extends FeatureInput>A list of features with the same input-type.classFeatureListProvider<T extends FeatureInput>Provides a list ofFeatures with identical input-type.classPrepends a string to the custom-name of each feature in a list.classReferencingFeatureListProvider<T extends FeatureInput>A base class for implementations ofFeatureListProviderthat may reference features created elsewhere. -
Uses of AnchorBean in org.anchoranalysis.feature.bean.operator
Subclasses of AnchorBean in org.anchoranalysis.feature.bean.operatorModifier and TypeClassDescriptionclassConstant<T extends FeatureInput>A constant value that is entirely invariant to the feature-input.classFeatureBinary<T extends FeatureInput>A base class for aFeaturethat is a binary-function of the results from two other features.classFeatureFromList<T extends FeatureInput>A base class for aFeaturethat is a function of the results from a list of other features.classFeatureGeneric<T extends FeatureInput>Base class for features that broadly accept any type of feature-input.classFeatureUnary<T extends FeatureInput,S extends FeatureInput> A feature that contains another feature as a bean-parameter.classFeatureUnaryGeneric<T extends FeatureInput>AFeatureUnarythat accepts anyFeatureInputirrespective of type.classReference<T extends FeatureInput>Uses another feature to calculate the value.classSum<T extends FeatureInput>Sums the results after calculating a list ofFeatures. -
Uses of AnchorBean in org.anchoranalysis.feature.bean.provider
Subclasses of AnchorBean in org.anchoranalysis.feature.bean.providerModifier and TypeClassDescriptionclassFeatureProvider<T extends FeatureInput>Provides a singleFeature.classFeatureProviderBean<B,P> classFeatureProviderDefine<T extends FeatureInput>Defines a singleFeatureto provide via a bean property.classProvides an existingFeatureidentified by its name and optionally a feature-list in which is resides. -
Uses of AnchorBean in org.anchoranalysis.feature.bean.results
Subclasses of AnchorBean in org.anchoranalysis.feature.bean.resultsModifier and TypeClassDescriptionclassThe sum of the results from a particular feature.classFeatures that processResultsVectorList.classBase class for an instance ofFeatureResultsthat calculating a statistic across all results in theResultsVectorListfor a particular feature-value.classThe maximum of the results from a particular feature.classThe mean of the results from a particular feature.classThe minimum of the results from a particular feature.classA quantile of the results from a particular feature.classThe standard-deviation of the results from a particular feature.classThe sum of the results from a particular feature. -
Uses of AnchorBean in org.anchoranalysis.image.bean
Subclasses of AnchorBean in org.anchoranalysis.image.beanModifier and TypeClassDescriptionclassImageBean<T>A bean that must be initialized withImageInitializationbefore usage. -
Uses of AnchorBean in org.anchoranalysis.image.bean.channel
Subclasses of AnchorBean in org.anchoranalysis.image.bean.channelModifier and TypeClassDescriptionclassA method of aggregating the voxels from many identically-sizedChannels into one.classCreates aChannelConverterfor converting a channel to a particular type.classCreates aChannelConverterAttached<Histogram, T>for converting a channel to a particular type, making use of aHistogram. -
Uses of AnchorBean in org.anchoranalysis.image.bean.displayer
Subclasses of AnchorBean in org.anchoranalysis.image.bean.displayerModifier and TypeClassDescriptionclassImplementation ofStackDisplayerthat converts to unsigned-8bit by taking the upper and lower quantiles of the intensity range.class -
Uses of AnchorBean in org.anchoranalysis.image.bean.interpolator
Subclasses of AnchorBean in org.anchoranalysis.image.bean.interpolatorModifier and TypeClassDescriptionclassResizes with an interpolator that uses Lanczos resampling as implemented in Imglib2.classResizes with an interpolator that uses linear interpolation as implemented in Imglib2.classDefines a particular type of interpolation method that can be used for resizing images.classAn implementation ofInterpolatorthat performs no interpolation. -
Uses of AnchorBean in org.anchoranalysis.image.bean.nonbean.init
Methods in org.anchoranalysis.image.bean.nonbean.init with type parameters of type AnchorBeanModifier and TypeMethodDescription<S extends AnchorBean<S>>
voidPopulateStoreFromDefine.copyWithoutInitialize(Class<?> defineClass, NamedProviderStore<S> destination) Copies objects of a particular class from the define without performing any initialization. -
Uses of AnchorBean in org.anchoranalysis.image.bean.object
Subclasses of AnchorBean in org.anchoranalysis.image.bean.objectModifier and TypeClassDescriptionclassBase class for filtering anObjectCollectionto remove objects according to a criteria.classMatches an object with other objects. -
Uses of AnchorBean in org.anchoranalysis.image.bean.provider
Subclasses of AnchorBean in org.anchoranalysis.image.bean.providerModifier and TypeClassDescriptionclassA provider base-class that as well as providing typeS, also provides aStack.classclassImplementation ofChannelProviderthat calls twoChannelProviders that must provideChannels of the same dimensions.classImplementation ofChannelProviderthat calls threeChannelProviders that must provideChannels of the same dimensions.classImplementation ofChannelProviderthat calls a single delegateChannelProvider.classclassBase class for beans that implementProviderto provideDimensions.classclassImplementation ofHistogramProviderthat calls a single delegateHistogramProvider.classclassImplementation ofMaskProviderthat calls a single delegateMaskProvider.classBase class for beans that implementProviderto provide anObjectCollection.classImplementation ofObjectCollectionProviderthat calls a single delegateProvider<ObjectCollection>. -
Uses of AnchorBean in org.anchoranalysis.image.bean.provider.stack
Subclasses of AnchorBean in org.anchoranalysis.image.bean.provider.stackModifier and TypeClassDescriptionclassCreates a stack that combines other stacks.classclassImplementation ofStackProviderthat calls a single delegateProvider<Stack>. -
Uses of AnchorBean in org.anchoranalysis.image.bean.segment
Subclasses of AnchorBean in org.anchoranalysis.image.bean.segmentModifier and TypeClassDescriptionclassPerforms some kind of segmentation on an image. -
Uses of AnchorBean in org.anchoranalysis.image.bean.segment.binary
Subclasses of AnchorBean in org.anchoranalysis.image.bean.segment.binaryModifier and TypeClassDescriptionclassPerforms a segmentation on voxels so that each voxel has an on or off state after the operation.classUses an existingBinarySegmentationthat is located by a unique identifier.classImplementation ofBinarySegmentationthat performs global thresholding.classAn implementation ofBinarySegmentationthat delegates to one otherBinarySegmentation. -
Uses of AnchorBean in org.anchoranalysis.image.bean.segment.object
Subclasses of AnchorBean in org.anchoranalysis.image.bean.segment.objectModifier and TypeClassDescriptionclassA base class for algorithms to segment a channel into one or more objects.classImplementation ofSegmentChannelIntoObjectsthat calls a single delegateSegmentChannelIntoObjects. -
Uses of AnchorBean in org.anchoranalysis.image.bean.spatial
Subclasses of AnchorBean in org.anchoranalysis.image.bean.spatialModifier and TypeClassDescriptionclassPadding (whitespace of certain extent) placed around an object in XY direction and in Z direction.classCalculating a scaling-factor from dimensions.classThe size of an entity in the X and Y dimensions. -
Uses of AnchorBean in org.anchoranalysis.image.bean.spatial.arrange
Subclasses of AnchorBean in org.anchoranalysis.image.bean.spatial.arrange -
Uses of AnchorBean in org.anchoranalysis.image.bean.spatial.arrange.align
Subclasses of AnchorBean in org.anchoranalysis.image.bean.spatial.arrange.alignModifier and TypeClassDescriptionclassAlign the bounding-box to thelargerwithout resizing.classAligns a smallerBoundingBoxto fit inside a largerBoundingBox.classGrow the bounding-box to filllargeras much as possible. -
Uses of AnchorBean in org.anchoranalysis.image.bean.spatial.arrange.fill
Subclasses of AnchorBean in org.anchoranalysis.image.bean.spatial.arrange.fill -
Uses of AnchorBean in org.anchoranalysis.image.bean.spatial.arrange.overlay
Subclasses of AnchorBean in org.anchoranalysis.image.bean.spatial.arrange.overlay -
Uses of AnchorBean in org.anchoranalysis.image.bean.spatial.arrange.tile
Subclasses of AnchorBean in org.anchoranalysis.image.bean.spatial.arrange.tileModifier and TypeClassDescriptionclassIndicates how to arrange one or moreRGBStacks in a cell in a table.classA higher-level aggregate structure that arranges otherStackArrangers in a tabular pattern. -
Uses of AnchorBean in org.anchoranalysis.image.bean.spatial.direction
Subclasses of AnchorBean in org.anchoranalysis.image.bean.spatial.directionModifier and TypeClassDescriptionclassCreates aDirectionVectorthat is a unit-vector along a particular image-axis.classA bean that creates aDirectionVector.classSpecifies each axis-component of a vector in a particular direction. -
Uses of AnchorBean in org.anchoranalysis.image.bean.threshold
Subclasses of AnchorBean in org.anchoranalysis.image.bean.thresholdModifier and TypeClassDescriptionclassCalculates a threshold-level from a histogram.classImplementation ofCalculateLevelthat calls a single delegateCalculateLevel.classThresholds voxels to create a binary-voxels using global thresholding.classPerforms global thresholding. -
Uses of AnchorBean in org.anchoranalysis.image.bean.threshold.relation
Subclasses of AnchorBean in org.anchoranalysis.image.bean.threshold.relationModifier and TypeClassDescriptionclassSelects voxels that are not off voxels.classSelects voxels that are not on voxels.classSelects only the off voxels.classSelects only the on pixels.classA base class for implementations ofRelationToThresholdwhere the threshold is derived from aBinaryValuesInt. -
Uses of AnchorBean in org.anchoranalysis.image.bean.unitvalue.distance
Subclasses of AnchorBean in org.anchoranalysis.image.bean.unitvalue.distanceModifier and TypeClassDescriptionclassImplementation ofUnitValueDistancethat specifies a value in physical units, as described by particular recognized strings.classImplementation ofUnitValueDistancethat specifies a value in voxels, ignoring any physical image resolution.classBase class for methods to specify a distance along a vector in an image. -
Uses of AnchorBean in org.anchoranalysis.image.bean.unitvalue.extent
Subclasses of AnchorBean in org.anchoranalysis.image.bean.unitvalue.extentModifier and TypeClassDescriptionclassA base class for a value that describes an area or volume measurement, which can then be resolved to a number of voxels. -
Uses of AnchorBean in org.anchoranalysis.image.bean.unitvalue.extent.area
Subclasses of AnchorBean in org.anchoranalysis.image.bean.unitvalue.extent.areaModifier and TypeClassDescriptionclassArea expressed in square meters, or units thereof.classArea expressed in pixels.classA base class for a value that describes an area measurement on the image. -
Uses of AnchorBean in org.anchoranalysis.image.bean.unitvalue.extent.volume
Subclasses of AnchorBean in org.anchoranalysis.image.bean.unitvalue.extent.volumeModifier and TypeClassDescriptionclassA base class for a value that describes a volume measurement on the image.classVolume expressed in cubic meters, or units thereof.classVolume expressed in voxels. -
Uses of AnchorBean in org.anchoranalysis.image.feature.bean
Subclasses of AnchorBean in org.anchoranalysis.image.feature.beanModifier and TypeClassDescriptionclassFeatureEnergy<T extends FeatureInputEnergy>A base class for features that only require an input that extends fromFeatureInputEnergyclassA base class for features that accept a histogram as input.classA base class for a feature that accepts aFeatureInputImageMetadataas input.classAn abstract base class for features that operate on image stacks.classCalculates a per-voxel score. -
Uses of AnchorBean in org.anchoranalysis.image.feature.bean.evaluator
Subclasses of AnchorBean in org.anchoranalysis.image.feature.bean.evaluatorModifier and TypeClassDescriptionclassFeatureEvaluator<T extends FeatureInput>Defines a feature and provides a means to calculate inputs for it, a session.classFeatureListEvaluator<T extends FeatureInput>Defines a list of features and provides a means to calculate inputs for it, a session. -
Uses of AnchorBean in org.anchoranalysis.image.feature.bean.histogram
Subclasses of AnchorBean in org.anchoranalysis.image.feature.bean.histogramModifier and TypeClassDescriptionclassBase class forFeatureHistogramimplementations that calculate a statistic from theHistogram.classCalculates the mean value of a histogram. -
Uses of AnchorBean in org.anchoranalysis.image.feature.bean.object.collection
Subclasses of AnchorBean in org.anchoranalysis.image.feature.bean.object.collectionModifier and TypeClassDescriptionclassA base class for a feature that accepts aObjectCollectionas input. -
Uses of AnchorBean in org.anchoranalysis.image.feature.bean.object.pair
Subclasses of AnchorBean in org.anchoranalysis.image.feature.bean.object.pairModifier and TypeClassDescriptionclassBase class for evaluatingFeaturePairObjectsin terms of another feature that operates on elements (first, second, merged etc.).classAn abstract base class for features that operate on pairs of objects.classEvaluates a feature on the first object in a pair of objects.classEvaluates a feature on the merged object created from a pair of objects.classCalculates the minimum value of a feature applied to both objects in a pair.classRatio of first-object to second-object in a pair.classEvaluates a feature on the second object in a pair of objects.classSubtract second-object from first-object in a pair. -
Uses of AnchorBean in org.anchoranalysis.image.feature.bean.object.single
Subclasses of AnchorBean in org.anchoranalysis.image.feature.bean.object.singleModifier and TypeClassDescriptionclassCalculates the center of gravity of a single object along a specified axis.classAn abstract base class for features that operate on a single object.classCalculates the number of voxels in a single object. -
Uses of AnchorBean in org.anchoranalysis.image.feature.bean.physical
Subclasses of AnchorBean in org.anchoranalysis.image.feature.bean.physicalModifier and TypeClassDescriptionclassConverts a feature from physical volume units to voxel units.classConverts a feature value representing area in pixel units to physical area units in an isometric XY plane.classConverts a distance feature to physical units along a specified direction.classConverts a feature value representing volume in voxel units to physical volume units.classFeatureConvertUnits<T extends FeatureInputWithResolution>An abstract base class for features that convert units between physical and voxel space.classWithResolutionBase<T extends FeatureInputWithResolution>Base class for a feature that requires input resolution to be calculated. -
Uses of AnchorBean in org.anchoranalysis.image.inference.bean.reduce
Subclasses of AnchorBean in org.anchoranalysis.image.inference.bean.reduceModifier and TypeClassDescriptionclassReduces the number or spatial-extent of elements by favouring higher-confidence elements over lower-confidence elements.classIntersecting objects are removed if they have sufficient overlap. -
Uses of AnchorBean in org.anchoranalysis.image.inference.bean.segment.instance
Subclasses of AnchorBean in org.anchoranalysis.image.inference.bean.segment.instanceModifier and TypeClassDescriptionclassDecodes inference output into segmented-objects.classSegmentStackIntoObjectsPooled<T extends InferenceModel>A base class for algorithms to segment a stack into one or more objects - using a pool of modelsclassSegmentStackIntoObjectsScaleDecode<T,S extends ImageInferenceModel<T>> ASegmentStackIntoObjectsScaleDecodethat scales the input image, before performing inference, and then decodes the output.classSuppressNonMaximum<T extends InferenceModel>Applies a segmentation procedure followed by non-maximum suppression. -
Uses of AnchorBean in org.anchoranalysis.image.inference.bean.segment.reduce
Subclasses of AnchorBean in org.anchoranalysis.image.inference.bean.segment.reduceModifier and TypeClassDescriptionclassReduces the number or spatial-extent of elements by favoring higher-confidence elements over lower-confidence elements. -
Uses of AnchorBean in org.anchoranalysis.image.io.bean.channel
Subclasses of AnchorBean in org.anchoranalysis.image.io.bean.channelModifier and TypeClassDescriptionclassCreates aChannelMapfor a particularOpenedImageFile.classA particularChannelto be read from a file, identified by its position (index) in the file. -
Uses of AnchorBean in org.anchoranalysis.image.io.bean.object.draw
Subclasses of AnchorBean in org.anchoranalysis.image.io.bean.object.drawModifier and TypeClassDescriptionclassDraws a filled-in shape for each object.classPerforms a flattening (maximum intensity projection in each channel) of the output of another writerclassBranches to two differentDrawObjectdepending on a predicate.classDraws the outline of each object-mask. -
Uses of AnchorBean in org.anchoranalysis.image.io.bean.object.feature
Subclasses of AnchorBean in org.anchoranalysis.image.io.bean.object.featureModifier and TypeClassDescriptionclassSpecifies a table of feature-calculations on objects. -
Uses of AnchorBean in org.anchoranalysis.image.io.bean.stack.combine
Subclasses of AnchorBean in org.anchoranalysis.image.io.bean.stack.combineModifier and TypeClassDescriptionclassCombines aProvider<Stack>with a label.classThe size and style of text as it should appear in an image.classTiles a number ofStackProviderWithLabels as a singleStackProvider.classCreates an image that contains text only. -
Uses of AnchorBean in org.anchoranalysis.image.io.bean.stack.metadata.reader
Subclasses of AnchorBean in org.anchoranalysis.image.io.bean.stack.metadata.readerModifier and TypeClassDescriptionclassUses aStackReaderto read the image-metadata.classReads anImageMetadatafrom the file-system. -
Uses of AnchorBean in org.anchoranalysis.image.io.bean.stack.reader
Subclasses of AnchorBean in org.anchoranalysis.image.io.bean.stack.readerModifier and TypeClassDescriptionclassInputManagerWithStackReader<T extends InputFromManager>Extends anInputManagerto add aStackReaderbean property.classReads an image-Stackfrom the file-system.classAStackReaderthat supports the correction of orientation as images are read from the file-system. -
Uses of AnchorBean in org.anchoranalysis.image.io.bean.stack.writer
Subclasses of AnchorBean in org.anchoranalysis.image.io.bean.stack.writerModifier and TypeClassDescriptionclassA base-class for aStackWriterthat writes an image that has either one or three channels.classWrites a stack (i.e. raster) to the filesystem. -
Uses of AnchorBean in org.anchoranalysis.io.bioformats.bean
Subclasses of AnchorBean in org.anchoranalysis.io.bioformats.bean -
Uses of AnchorBean in org.anchoranalysis.io.bioformats.bean.options
Subclasses of AnchorBean in org.anchoranalysis.io.bioformats.bean.optionsModifier and TypeClassDescriptionclassA default set ofReadOptionswithout special behavior.classForces the bits per pixel to be a specific-value, irrespective of what bioformats infers.classForces the number of channels to be a specific-value, irrespective of what bioformats infers.classForces the number of frames to be a specific-value, irrespective of what bioformats infers.classTreats a time-series as if it was a z-stackclassOptions that influence how stack is read inBioformatsReader.classForces a particular settings, but otherwise uses settings from a delegateclassTreats the channel index as if it's time, and vice versa -
Uses of AnchorBean in org.anchoranalysis.io.bioformats.bean.writer
Subclasses of AnchorBean in org.anchoranalysis.io.bioformats.bean.writerModifier and TypeClassDescriptionclassBase class for writing a stack to the filesystem using the Bioformats library.classWrites a stack to the filesystem as an OME-TIFF using the Bioformats library.classWrites a stack to the filesystem as an OME-XML using the Bioformats library.classWrites a stack to the filesystem as a TIFF using the Bioformats library. -
Uses of AnchorBean in org.anchoranalysis.io.imagej.bean.interpolator
Subclasses of AnchorBean in org.anchoranalysis.io.imagej.bean.interpolatorModifier and TypeClassDescriptionclassResizes with linear interpolation as implemented in ImageJ. -
Uses of AnchorBean in org.anchoranalysis.io.imagej.bean.stack.writer
Subclasses of AnchorBean in org.anchoranalysis.io.imagej.bean.stack.writerModifier and TypeClassDescriptionclassBase class for writing a raster using ImageJ.classWrites a PNG image using ImageJ.classWrites a TIFF image using ImageJ. -
Uses of AnchorBean in org.anchoranalysis.io.input.bean
Subclasses of AnchorBean in org.anchoranalysis.io.input.beanModifier and TypeClassDescriptionclassInputManager<T extends InputFromManager>Base class for describing the inputs.classInputManagerUnary<T extends InputFromManager>Base class for anInputManagerthat delegates to anotherInputManagerwith the same input-type. -
Uses of AnchorBean in org.anchoranalysis.io.input.bean.dictionary
Subclasses of AnchorBean in org.anchoranalysis.io.input.bean.dictionary -
Uses of AnchorBean in org.anchoranalysis.io.input.bean.files
Subclasses of AnchorBean in org.anchoranalysis.io.input.bean.filesModifier and TypeClassDescriptionclassBase class for providing a list ofFiles.classLikeFilesProviderbut employs a unary operator on a call to an existingFilesProvider.classBase class for implementations ofFilesProviderwhich do have an associated directory.classAFilesProviderWithDirectorywhere the directory is optionally specified as a string constantclassLikeFilesProviderWithDirectorybut employs a unary operator on a call to an existingFilesProviderWithDirectory.classBase class for implementations ofFilesProviderwhich do not have an associated directory.classSearches a directory for files whose paths match a particular predicate.classProvides a single file only.classA specific list of paths which form the input. -
Uses of AnchorBean in org.anchoranalysis.io.input.bean.grouper
Subclasses of AnchorBean in org.anchoranalysis.io.input.bean.grouperModifier and TypeClassDescriptionclassDerives the grouping-key via a call toDerivePath.classDetermines how partition inputs into groups.classAvoids grouping of inputs, effectively processing all inputs as one large group. -
Uses of AnchorBean in org.anchoranalysis.io.input.bean.namer
Subclasses of AnchorBean in org.anchoranalysis.io.input.bean.namerModifier and TypeClassDescriptionclassAssociates a name (a compact unique identifier) with a file.classBase class for methods that derive the name independently for each file. -
Uses of AnchorBean in org.anchoranalysis.io.input.bean.path
Subclasses of AnchorBean in org.anchoranalysis.io.input.bean.pathModifier and TypeClassDescriptionclassDerives a path from an existing path.classReturns the samePathas the argument passed in.class -
Uses of AnchorBean in org.anchoranalysis.io.input.bean.path.matcher
Subclasses of AnchorBean in org.anchoranalysis.io.input.bean.path.matcherModifier and TypeClassDescriptionclassMatches file-paths against some kind of pattern.classMaybe imposes a file-extension condition, optionally on top of an existing matcher.classMatches paths using a Java-style glob.classPredicates that matches a file-path against a regular expression. -
Uses of AnchorBean in org.anchoranalysis.io.input.bean.path.provider
Subclasses of AnchorBean in org.anchoranalysis.io.input.bean.path.providerModifier and TypeClassDescriptionclassclassCalls an existingFilePathProviderindirectly to provide an identical result.classExtracts a path from aFilesProvider. -
Uses of AnchorBean in org.anchoranalysis.io.output.bean
Subclasses of AnchorBean in org.anchoranalysis.io.output.beanModifier and TypeClassDescriptionclassResponsible for making decisions on where output goes and what form it takes.classSettings for how to write output, including default writers. -
Uses of AnchorBean in org.anchoranalysis.io.output.bean.enabled
Subclasses of AnchorBean in org.anchoranalysis.io.output.bean.enabledModifier and TypeClassDescriptionclassAll outputs are allowed irrespective ofoutputName.classAll outputs are allowed unless the name's first character is an underscore.classNo outputs are enabled.classWhether a particular output, identified by a textual name, is enabled or not.classOnly specific outputs, identified by a textual name, are disabled, and all others are enabled.classOnly specific outputs, identified by a textual name, are enabled. -
Uses of AnchorBean in org.anchoranalysis.io.output.bean.path.prefixer
Subclasses of AnchorBean in org.anchoranalysis.io.output.bean.path.prefixerModifier and TypeClassDescriptionclassOutputs an incrementing number for each output that occurs.classBase classes for methods to determine an output directory and associated file prefix.classA file-path-resolver that adds additional methods that perform the same function but output a relative-path rather than an absolute path after fully resolving paths -
Uses of AnchorBean in org.anchoranalysis.io.output.bean.rules
Subclasses of AnchorBean in org.anchoranalysis.io.output.bean.rulesModifier and TypeClassDescriptionclassAdds additional outputs-names to be enabled to the defaults.classLikeIgnoreUnderscorePrefixfor all first and level-outputs unless a particular outputs are explicitly specified.classAll outputs are disabled except particular ones.classBean that specifies an implementation ofMultiLevelOutputEnabled.classBase class for anOutputEnabledRulesthat specifies particular output-names for first and second levels.classAllows all output-names to be outputted in both first and second level.classAll outputs are enabled except particular ones. -
Uses of AnchorBean in org.anchoranalysis.launcher.run.tasks
Subclasses of AnchorBean in org.anchoranalysis.launcher.run.tasksModifier and TypeClassDescriptionclassHelloWorld<S extends InputFromManager>A dummy task that simply writes a message to all log files, specifically: 1. log file for experiment 2. log file for each input-object -
Uses of AnchorBean in org.anchoranalysis.mpp.bean
Subclasses of AnchorBean in org.anchoranalysis.mpp.beanModifier and TypeClassDescriptionclassMarksBean<T>An abstract base class for beans related to marks in MPP (Marked Point Process). -
Uses of AnchorBean in org.anchoranalysis.mpp.bean.bound
Subclasses of AnchorBean in org.anchoranalysis.mpp.bean.boundModifier and TypeClassDescriptionclassAn abstract class representing an upper and lower bound.classRepresents an upper and lower bound in degrees which is converted to radians when resolved.classAn abstract class representing a bound with minimum and maximum values.classA bound representing physical extents, which can be resolved based on image resolution.classA bound representing unitless values, where the minimum and maximum are not affected by resolution.classAbstract base class for defining bounds on marks in a marked point process.classA bound resolved into pixel units. -
Uses of AnchorBean in org.anchoranalysis.mpp.bean.bound.rotation
Subclasses of AnchorBean in org.anchoranalysis.mpp.bean.bound.rotationModifier and TypeClassDescriptionclassAbstract base class for defining bounds on rotations.classCreates a randomly-generated orientation in 2D by uniformally sampling a scalar rotation angleclassCreates a randomly-generated orientation in 3D based upon Euler Angles -
Uses of AnchorBean in org.anchoranalysis.mpp.bean.mark
Subclasses of AnchorBean in org.anchoranalysis.mpp.bean.markModifier and TypeClassDescriptionclassAn abstract base class for defining regions associated with marks. -
Uses of AnchorBean in org.anchoranalysis.mpp.bean.mark.factory
Subclasses of AnchorBean in org.anchoranalysis.mpp.bean.mark.factoryModifier and TypeClassDescriptionclassA factory for creating Ellipse marks.classA factory for creating Ellipsoid marks.classAn abstract base class for factories that create Mark objects.classA factory for creating PointList marks.classA factory for creating marks with unique identifiers. -
Uses of AnchorBean in org.anchoranalysis.mpp.bean.points
Subclasses of AnchorBean in org.anchoranalysis.mpp.bean.pointsModifier and TypeClassDescriptionclassCreates a mark by fitting it to a set of points extracted from other marks.classPointsBean<T>An abstract base class for beans that work with points and require initialization. -
Uses of AnchorBean in org.anchoranalysis.mpp.bean.points.fitter
Subclasses of AnchorBean in org.anchoranalysis.mpp.bean.points.fitterModifier and TypeClassDescriptionclassAbstract base class for fitting a mark (e.g., an ellipsoid) to a set of points. -
Uses of AnchorBean in org.anchoranalysis.mpp.bean.proposer
Subclasses of AnchorBean in org.anchoranalysis.mpp.bean.proposerModifier and TypeClassDescriptionclassAn abstract base class for proposing an entire collection (configuration) of marks.classAn abstract base class for proposing a selection of a single mark from a collection of marks.classAn abstract base class for proposing merges between marks.classAn abstract base class for proposing changes to a mark.classAn abstract base class for proposing splits of a mark into two new marks.classAn abstract base class for proposing orientations for marks.classAn abstract base class for proposing a list of points based on a given point and mark.classAn abstract base class for proposing positions.classProposerBean<T>An abstract base class for proposer beans in the MPP (Marked Point Process) framework.classAn abstract base class for proposing radii in a 3D space.classAn abstract base class for proposing scalar values. -
Uses of AnchorBean in org.anchoranalysis.mpp.bean.provider
Subclasses of AnchorBean in org.anchoranalysis.mpp.bean.providerModifier and TypeClassDescriptionclassAn abstract provider forMarkBounds.classProvides a collection of marksclassMarksBaseProvider<T,S> classProvides (maybe) a single mark -
Uses of AnchorBean in org.anchoranalysis.mpp.bean.regionmap
Subclasses of AnchorBean in org.anchoranalysis.mpp.bean.regionmapModifier and TypeClassDescriptionclassMaps integer IDs to sub-regions in the map.classAbstract class representing membership of regions using a bit-flag system.classA RegionMembership implementation that uses an AND operation to check membership.classARegionMembershipimplementation that uses an OR operation to check membership. -
Uses of AnchorBean in org.anchoranalysis.mpp.feature.addcriteria
Subclasses of AnchorBean in org.anchoranalysis.mpp.feature.addcriteriaModifier and TypeClassDescriptionclassAnAddCriteriaPairthat combines multiple criteria using a logical OR operation.classAbstract base class for criteria used to determine if a pair of marks should be included.classIf one arbitrarily point overlaps between two MarkPointList then true, otherwise falseclassAnAddCriteriaPairthat includes marks if their bounding boxes intersect.classAn implementation of aRandomCollectionthat usesAddCriteriato determine which marks to add. -
Uses of AnchorBean in org.anchoranalysis.mpp.feature.bean.energy.element
Subclasses of AnchorBean in org.anchoranalysis.mpp.feature.bean.energy.elementModifier and TypeClassDescriptionclassExtracts one of the memos from the pair, and processes as aFeatureSingleMemoclassAn abstract base class for features that operate onFeatureInputAllMemo.classAn abstract base class for features that operate on pairs of memoized objects.classAn abstract base class for features that operate on a single memoized object. -
Uses of AnchorBean in org.anchoranalysis.mpp.feature.bean.energy.scheme
Subclasses of AnchorBean in org.anchoranalysis.mpp.feature.bean.energy.schemeModifier and TypeClassDescriptionclassAn abstract class for creatingEnergySchemeinstances.classCreates anEnergySchemeby combining individual elements and their interactions. -
Uses of AnchorBean in org.anchoranalysis.mpp.feature.bean.mark
Subclasses of AnchorBean in org.anchoranalysis.mpp.feature.bean.markModifier and TypeClassDescriptionclassA bean for evaluating marks using features and energy schemes. -
Uses of AnchorBean in org.anchoranalysis.mpp.feature.mark
Subclasses of AnchorBean in org.anchoranalysis.mpp.feature.markModifier and TypeClassDescriptionclass -
Uses of AnchorBean in org.anchoranalysis.mpp.io.bean.input
Subclasses of AnchorBean in org.anchoranalysis.mpp.io.bean.inputModifier and TypeClassDescriptionclassManages input forMultiInputobjects, combining various input sources. -
Uses of AnchorBean in org.anchoranalysis.mpp.pair
Subclasses of AnchorBean in org.anchoranalysis.mpp.pairModifier and TypeClassDescriptionclassAn abstract collection of items from which one can randomly sample. -
Uses of AnchorBean in org.anchoranalysis.overlay.bean
Subclasses of AnchorBean in org.anchoranalysis.overlay.bean -
Uses of AnchorBean in org.anchoranalysis.plugin.annotation.bean.aggregate
Subclasses of AnchorBean in org.anchoranalysis.plugin.annotation.bean.aggregateModifier and TypeClassDescriptionclassAggregateAnnotations<S extends AnnotatorStrategy>Aggregates many per-image annotations together in form of a CSV file. -
Uses of AnchorBean in org.anchoranalysis.plugin.annotation.bean.comparer
Subclasses of AnchorBean in org.anchoranalysis.plugin.annotation.bean.comparerModifier and TypeClassDescriptionclassLoadsMaskto compared, converting it into anObjectMask.classAnObjectCollectionto be compared against something else. -
Uses of AnchorBean in org.anchoranalysis.plugin.annotation.bean.comparison
Subclasses of AnchorBean in org.anchoranalysis.plugin.annotation.bean.comparisonModifier and TypeClassDescriptionclassAnnotationComparisonInputManager<T extends InputFromManager>An input manager for annotation comparison that extendsInputManagerWithStackReader.classCompareAnnotations<T extends Assignment<ObjectMask>>Task to compare a set of annotations to a segmentation or another set of annotations. -
Uses of AnchorBean in org.anchoranalysis.plugin.annotation.bean.comparison.assigner
Subclasses of AnchorBean in org.anchoranalysis.plugin.annotation.bean.comparison.assignerModifier and TypeClassDescriptionclassAnnotationComparisonAssigner<T extends Assignment<ObjectMask>>Compares similar object-sets produced from two different sources.classAssigns an objects from one set of objects to another based upon a cost (degree of overlap).classNo outputs are produced. -
Uses of AnchorBean in org.anchoranalysis.plugin.annotation.bean.file
Subclasses of AnchorBean in org.anchoranalysis.plugin.annotation.bean.fileModifier and TypeClassDescriptionclassFromAnnotations<T extends AnnotatorStrategy>Provides files associated with annotations. -
Uses of AnchorBean in org.anchoranalysis.plugin.annotation.bean.label
Subclasses of AnchorBean in org.anchoranalysis.plugin.annotation.bean.labelModifier and TypeClassDescriptionclassRepresents a label used for annotation, with associated metadata. -
Uses of AnchorBean in org.anchoranalysis.plugin.annotation.bean.strategy
Subclasses of AnchorBean in org.anchoranalysis.plugin.annotation.bean.strategyModifier and TypeClassDescriptionclassAssigns a single label per image, as a whole.classAnnotates each image with a mark using a mark proposer and points fitter.classA base class for implementations ofAnnotatorStrategywhere a single unique path exists for every annotation. -
Uses of AnchorBean in org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction
Modifier and TypeClassDescriptionclassPerforms 2D grayscale reconstruction using ImageJ's implementation. -
Uses of AnchorBean in org.anchoranalysis.plugin.fiji.bean.channel.provider
Subclasses of AnchorBean in org.anchoranalysis.plugin.fiji.bean.channel.providerModifier and TypeClassDescriptionclassPerforms Perona-Malik Anisotropic Diffusion.classApplies a minimum filter to a channel using ImageJ's MinMaxMedian plugin. -
Uses of AnchorBean in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance
Subclasses of AnchorBean in org.anchoranalysis.plugin.fiji.bean.channel.provider.distanceModifier and TypeClassDescriptionclassEuclidian Distance Transform from ImageJ that works on 2D as well as 3D z-stacks.classLikeDistanceTransform3Dbut applies the distance transform separately for each object in a collection. -
Uses of AnchorBean in org.anchoranalysis.plugin.fiji.bean.mask.provider
Subclasses of AnchorBean in org.anchoranalysis.plugin.fiji.bean.mask.providerModifier and TypeClassDescriptionclassApplies local thresholding algorithm using Fiji's {link Auto_Local_Threshold} plugin -
Uses of AnchorBean in org.anchoranalysis.plugin.fiji.bean.threshold
Subclasses of AnchorBean in org.anchoranalysis.plugin.fiji.bean.thresholdModifier and TypeClassDescriptionclassApplies automatic thresholding using ImageJ's Auto_Threshold plugin. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.blur
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.blurModifier and TypeClassDescriptionclassPerforms a Gaussian Blur in 3DclassPerforms a Gaussian-blur in 2D on each slice independentlyclassA method for applying blurring to an image. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.channel.aggregator
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.channel.aggregatorModifier and TypeClassDescriptionclassMaximum-intensity-projection acrossChannels.classMean-intensity-projection acrossChannels.classMinimum-intensity-projection acrossChannels.classAn aggregator that calculates the aggregation of every voxel across successive channels via aProjectableBuffer.classProjection of the standard-deviation of voxels values across all inputs. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.channel.convert
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.channel.convertModifier and TypeClassDescriptionclassScales by compressing a certain range of values into the 8-bit signal.classScales by compressing a certain range of values into the 8-bit signalclassConverts a channel to unsigned byte format, scaling the values based on the original voxel type.classConverts a channel to unsigned byte format without any scaling.classConverts a channel to unsigned byte format using upper and lower quantile intensities from a histogram. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.channel.provider
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.channel.providerModifier and TypeClassDescriptionclassCreates a new channel with all values initialized to a constant (by default zero)classCreates a duplicate of the input channel.classAn abstract base class for creating a channel from specified dimensions.classFinds the input-stack using a conventional name ofinput_image- and extracts the first channelclassExtracts a channel from a provider of a stack.classProvides a channel based on a condition from a dictionary.classProvides a channel by referencing it from a a set of named-channels.classTakes the two channels and creates a NEW third channel whose pixels are a function of the two channelsclassAn abstract base class for creating a channel from an existing channel and a collection of objects.classAChannelProviderUnarywhich has a scalar value field. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
Modifier and TypeClassDescriptionfinal classAdds a constant value to each voxel in a channel.classBase-class for operations that perform a binary arithmetic operation with each voxel-value and a constant.classBase class for arithmetic operations that conditionally overwrite voxel values with a constant.classInverts the intensity values of aChannelby subtracting each voxel from the maximum value for the channel's data type.classCreates a new channel by taking the maximum value of corresponding voxels from two input channels.classReplaces voxel values with a constant value if the constant is greater than the original voxel value.classCreates a new channel that is the mean of three input channels.classCreates a new channel by taking the minimum value of corresponding voxels from two input channels.classReplaces voxel values with a constant value if the constant is less than the original voxel value.classMultiplies each voxel value in a channel by a constant value.classCreates a new channel by multiplying corresponding voxels from two input channels.classSubtracts each voxel value in a channel from a constant value.classSubtracts the mean intensity (of the entire channel or a masked portion thereof) from every voxel.classCreates a new channel by subtracting corresponding voxels of the second channel from the first channel. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.channel.provider.assign
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.channel.provider.assignModifier and TypeClassDescriptionclassCopies the pixels fromchannelAssignFromtochannel(possibly masking).classAssigns a value from a dictionary to all voxels in a channel.classMatches source-objects to target objects, based upon intersection, and assigns the value in the respective source object to the target objectclassAssigns a constant (scalar) value to the portion of the image covered by a mask -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.channel.provider.convert
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.channel.provider.convertModifier and TypeClassDescriptionclassConvert<T>Converts a channel by applying a converter (no histogram is involved in the conversion).classBase class for channel providers that perform conversions on a single input channel.classConverts a channel to a different voxel data-type by applying a converter with an associated histogram. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.channel.provider.gradientModifier and TypeClassDescriptionclassBase class to calculate the gradient of the voxels in aChannel.classLikeGradientBasebut allows an arbitrary constant to be added to voxels storing the gradient.classExtracts the gradient in the direction of a particular axis (identified by an index)classCalculates aChannel's gradient along the x and y axes.class3x3 Sobel Filter -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.channel.provider.intensity
Modifier and TypeClassDescriptionclassBlurs an image using a particular strategy (defaults to a gaussian blur in each slice)classCreates a new channel which is a merged version of two input channels according to rules.classApplies a median-filter with square kernelclassCorrects a channel in the following wayclassRewrites the intensity for each object-mask (assume no overlap) so that its mean is 128classChanges the voxel values to map the range of 0th quantile to xth quantile across the entire voxel data rangeclassScales the channel in the X and Y dimensions. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.channel.provider.mask
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.channel.provider.maskModifier and TypeClassDescriptionclassclassA base class for aChannelProviderwhich also uses a binary-mask, but which doesn't use any otherChannelProvideras an input.classA base class for aChannelProviderUnarywhich also uses a binary mask.classSet pixels NOT IN the mask to 0, but keep pixels IN the mask identical. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.channel.provider.object
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.channel.provider.objectModifier and TypeClassDescriptionclassCreates a channel with a level calculated for each object using various methods.classCreates a channel with different threshold-levels for each object, calculating the level only from the histogram of the particular object.classCalculates a threshold-level for each object collectively based on other objects -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.channel.provider.score
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.channel.provider.scoreModifier and TypeClassDescriptionclassAssigns a unique id number to each object.classCreates a channel by scoring objects based on a feature calculation.classAssigns a score (a value indicating how probable something is) to each voxel -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.channel.provider.slice
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.channel.provider.sliceModifier and TypeClassDescriptionclassExtracts the slice at the center (rounding down) of the range of z-stacks.classExtracts slices fromsliceStart(inclusive) tosliceEnd(inclusive).classCreates a maximum intensity projection of a 3DChannel.classCreates a mean intensity projection of a 3DChannel.classCreates a new channel with specific dimensions that repeatedly duplicates a slice from an existing channel -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.color.provider
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.color.providerModifier and TypeClassDescriptionclassCombines one or moreColorProviders into a unitaryColorProvider.classGenerates colors to match the size of an object-collection. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.dictionary
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.dictionaryModifier and TypeClassDescriptionclassChecks if a value in aDictionaryis equal to an expected value. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.dimensions.provider
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.dimensions.providerModifier and TypeClassDescriptionclassCreates image-dimensions by referencing them from aChannelProvider.classGuesses dimensions from an input-image if it exists.classSpecifies dimensions explicitly via bean properties. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.histogram.provider
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.histogram.providerModifier and TypeClassDescriptionclassThis cuts a Histogram below a threshold BUT TRANSFERS ALL THE COUNT greater than equal to the threshold into the bin just below the threshold valueclassclassThresholds a histogram using a CalculateLevel keeping only the values greater equal than the thresholdclassA provider that references an existingHistogramby its identifier. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.histogram.threshold
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.histogram.thresholdModifier and TypeClassDescriptionclassBase class forCalculateLevelimplementations that operate on a list of otherCalculateLevelobjects.classACalculateLevelUnarythat calculates a level relative to a threshold, with an alternative calculation method.classClamps the input-histogram to a certain maximum value, and then delegates the calculate-level.classA constant value for thresholding.classSpecifies a constant if a histogram is empty, otherwise delegates to another {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}classCalculates a level from the first delegate and if greater than a threshold, recalculates from a second delegate.classCalculates a level from the first delegate and if less than a threshold, recalculates from a second delegate.classThe maximum value of one or more {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}classThe minimum value of one or more {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}classPerforms auto-thresholding using Otsu's method.classSimilar to Otsu, but weighs the variances differently of background and foreground.classCalculates the threshold value from a quantile of a histogram. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.mask.provider
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.mask.providerModifier and TypeClassDescriptionclassCreates a new mask of particular dimensionality where all values are off.classCreates a new mask of particular dimensionality where all values are on.classA provider that creates a duplicate of a givenMask.classBase-class forMaskProviders that accept aChannelas input.classBase class forMaskProviders that create a mask based on given dimensions.classSwitches on voxels to off and vice-versa.classA provider that references an existingMaskby its identifier.classScales the mask in XY dimensions, but not in Z dimension. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.mask.provider.combine
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.mask.provider.combineModifier and TypeClassDescriptionclassOutputs the logical operation and voxelwise on both masks, modifying {mask} with the result.classBase class for combining two masks.classOutputs the logical operationiff first==HIGH and second==LOW then LOWvoxelwise on both masks, modifying {mask} with the result.classOutputs the logical operation or voxelwise on both masks, modifying {mask} with the result.classOutputs the logical operation xor (exclusive or) voxelwise on both masks, modifying {mask} with the result. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.mask.provider.convert
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.mask.provider.convert -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.mask.provider.morphological
Modifier and TypeClassDescriptionclassCreates aMaskwhere all pixels are on within a box region.classPerforms a dilation morphological operation onBinaryVoxels.classPerforms an erosion morphological operation onBinaryVoxels.classFinds the exterior outer contour for aMaskthat forms its outline.classFits a box around the on voxels.classBase class for performing morphological operations onBinaryVoxels. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.mask.provider.predicate
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.mask.provider.predicateModifier and TypeClassDescriptionclassThe currentmaskis returned if a condition on key-values is satisfied otherwisemaskElseis returned.classThe currentmaskis returned if it's non-empty (at least one on voxel) otherwisemaskElseis returned.classThe currentmaskis returned if the mask (treated as an object) passed an object-filter, otherwisemaskElseis returned.classBase class which multiplexes between the current mask and an alternative depending if a condition is met.classThe currentmaskis a particular stack exists (at least one on voxel) otherwisemaskElseis returned. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.mask.provider.segment
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.mask.provider.segmentModifier and TypeClassDescriptionclassApplies aBinarySegmentationalgorithm to derive a mask from a channelclassThresholds a channel to produce a mask, reusing (and modifying) the input-buffers of the channel if possible. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.mask.provider.slice
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.mask.provider.sliceModifier and TypeClassDescriptionclassFlattens a mask in the z-dimension, so it is 2D instead of 3D (like a maximum intensity projection).classCreates a new mask with specific dimensions that repeatedly duplicates a slice from an existing mask -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.filter
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.filterModifier and TypeClassDescriptionclassUses a predicate to make a decision whether to keep objects or not.classAn independent object-filter that uses a relation in its predicate. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.filter.collective
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.filter.collectiveModifier and TypeClassDescriptionclassCalculates features values for all objects, and discards any object less thanquantile - (minRatio * stdDev)classMatches each object with others, and keeps only those where a relation holds true for all matches (in terms of features) -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.filter.combine
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.filter.combineModifier and TypeClassDescriptionclassApplies multiples filter with logical AND i.e. an object must pass all objects in the list to remain.classA filter that combines other filters (in a list)classApplies multiples filter with logical OR i.e. an object must pass any one of the filter steps to remain. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.filter.independent
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.filter.independentModifier and TypeClassDescriptionclassOnly accepts an object if it has greater (or EQUAL) intersection withobjectsGreaterthanobjectsLesserclassOnly keep objects where at least one voxel (on a particular channel) has intensity greater or equal to a threshold.classKeeps objects which intersects with ANY ONE of a collection of other objects.classKeeps only objects that are not adjacent to the scene-border (i.e. have a bounding-box on the very edge of the image)classOnly keeps objects whose feature-value satisfies a condition relative to a threshold.classOnly keeps objects whose feature-value satisfies a condition relative to a threshold. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.match
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.matchModifier and TypeClassDescriptionclassSpecifies a single object that will always be the "match" for whatever source object.classMatches to another object, and then uses that object to bridge to anotherclassAnObjectMatcherthat matches objects based on their intersection with a provided set of objects. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.provider
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.providerModifier and TypeClassDescriptionclassExtract a singleObjectMaskinto a new collection.classAnObjectCollectionProviderthat concatenates multipleObjectCollections from a list of providers.classDuplicates (deep copy) an object-collection.classCreates an empty object-collection.classMultiplexes between two object-collection-providers depending on whether a parameter value equals a particular stringclassPermutes some changes over anObjectCollectionProviderand collects all the results in anObjectCollectionclassAnObjectCollectionProviderthat references an existingObjectCollectionby its identifier.classReturns a object-collection by name if it exists, or else callsobjectsElseif it doesn't exist.classScales all the objects in the collection by a particular scale-factor.classBase class forObjectCollectionProviderUnarythat also requires aChannel.classBase class forObjectCollectionProviders that create objects from aChannel.classBase class forObjectCollectionProviderUnarythat take an optionalobjectsContainerbean-field.classBase class forObjectCollectionProviderUnaryclasses that require dimensions to be specified.classBase class forObjectCollectionProviderUnaryclasses that offer an optional means to specify dimensions. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.provider.connected
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.provider.connectedModifier and TypeClassDescriptionclassConverts a binary-mask into its connected componentsclassEnsures each object in a collection is a connected-component, decomposing it if necessary into multiple objects.classRejects a set of objects, if any object is not fully connected (pixels form two or more separate connected components) -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.provider.feature
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.provider.featureModifier and TypeClassDescriptionclassAn abstract base class for object collection providers that use a feature evaluator.classFinds the object with the maximum feature-value from a collection.classFinds the object with the maximum feature among a group of matches for each object.classCreates a new object-collection with objects sorted by a derived feature-value (in ascending order) -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.provider.filter
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.provider.filterModifier and TypeClassDescriptionclassFilters anObjectCollectionusing the specifiedObjectFilter.classFilters anObjectCollectionby grouping objects and then applying a filter to each group.classReturns only the objects that intersect with at least one object in the containerclassProvides anObjectCollectionby matching objects using a specifiedObjectMatcher.classFilters objects to keep only those which are NOT in the container.classBase class for object collection providers that apply a filter to the objects.classConsiders all possible pairs of objects in a provider, and removes those that touch the border. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.provider.mask
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.provider.maskModifier and TypeClassDescriptionclassReduce the size of individual objects (if neccessary, and minimally) to fit within a binary-mask.classConverts a binary-mask to an object-collection (containing a single object) -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.provider.merge
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.provider.mergeModifier and TypeClassDescriptionclassA base class for algorithms that merge object-masks.classNaive greedy merge strategy when any two neighboring objects are merged if it increases a feature.classMerges objects if a pair feature value satisfies a condition.classMerges neighboring objects if it results in an increase in the average feature-value calculated on each single object.classMerges itemwise objects from two collections.classBase class for object-merging strategies that involve calculating a feature.classExpandsMergeBaseby optionally imposing a maximum-distance requirement between objects that are possibly merged. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.provider.morphological
Modifier and TypeClassDescriptionclassDilates each object in the collection, growing bounding-boxes as necessary in relevant dimensions.classErodes each object in the collection, growing bounding-boxes as necessary in relevant dimensions.classBase class for providers that apply morphological operations to anObjectCollection. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.provider.segment
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.provider.segmentModifier and TypeClassDescriptionclassPerforms a binary-segmentation using the upstream objects as masks.classSegments a channel into objects using a specified segmentation algorithm.classPerforms segmentation of a channel using each object in the upstream collection as a mask.classSegmentStack<T extends InferenceModel>Segments a stack into objects.classTakes each object one-by-one fromobjectsSource, and finds matching seeds fromobjectsSeeds -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.provider.slice
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.provider.sliceModifier and TypeClassDescriptionclassCreates a 3D version of an object by replicating each input-object across the z-dimension to meet (3D) dimensions.classExtends an object (2D/3D) as much as it can within the z-slices of a containing objectclassFlattens all object-masks in the z-dimension, so it is 2D instead of 3D (like a maximum intensity projection).classExtracts a specific slice from a collection of 3D objects. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.provider.split
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.provider.splitModifier and TypeClassDescriptionclassConsiders all possible pairs of objects in a provider, and removes any intersecting pixelsclassSplits objects in a collection based on intersections with another set of objects.classSplits objects into sub-objects by cutting by an orthogonal square lattice (like a chessboard). -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.segment.channel
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.segment.channelModifier and TypeClassDescriptionclassPerform a segmentation at a different scale, and then fit the results back to the original scale.classPerforms a binary-segmentation of the channel and converts its connected-components into objectsclassApplies an object-filter to the results of an upstream segmentation.classImposes minima in seed locations on the input-channel before performing the segmentationclassApplies the MSER algorithm from imglib2classPerform a segmentation in a MIP instead of z-stacks, and fits the result back into a 3D segmentation. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minimaModifier and TypeClassDescriptionclassAbstract base class for imposing minima on a channel for watershed segmentation.classImposes minima on a channel using grayscale reconstruction by erosion. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstructionModifier and TypeClassDescriptionclassAbstract base class for performing grayscale reconstruction by erosion.classImplements grayscale reconstruction using Robinson's algorithm. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong
-
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.segment.reduce
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.object.segment.reduceModifier and TypeClassDescriptionclassCombines object-masks by projecting the maximum confidence-level for each voxel and thresholding. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.scale
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.scaleModifier and TypeClassDescriptionclassScale X and Y dimension by a constant floating-point number.classScales an image to approximately similar in size to aSizeXY.classInvert theScaleFactorcalculated by thescaleCalculatordelegate.classCalculates a scale factor to ensure a minimum XY resolution is achieved.classCalculates a scaling-factor to make the source image have identical dimensions asdimensionsTarget.classScales to the suggested-size if one is provided, otherwise callsfallback. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.segment.binary
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.segment.binaryModifier and TypeClassDescriptionclassPerforms a segmentation and inverts and on and off bytesclassRepeats a binary segmentation operation for a specified number of iterations.classPerforms a sequence of succesive segmentationsclassThresholds each voxels by comparing against another channel that has per-voxel thresholds -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.stack.provider
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.stack.providerModifier and TypeClassDescriptionclassCombines all the channels from one or more sources (stacks, channels etc.)classclassFinds the input-stack using a conventional name ofinput_imageclassRetrieves an existing stack. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.stack.provider.color
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.stack.provider.colorModifier and TypeClassDescriptionclassBase class for providers that draw entities (an outline or filled) on a background.classLikeColoredBasebut uses a generator to determine the colors for the objects.classDraws a colored representation (outline or filled) of aObjectMaskon a backgroundclassDraws a colored representation (outline or filled) of anObjectCollectionon a backgroundclassProvides aStackby combining up to three channels (red, green, blue) into an RGB image.classColors three collections of objects in RED, GREEN, BLUE channels on top of a background. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.thumbnail.object
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.thumbnail.objectModifier and TypeClassDescriptionclassCreate a thumbnail by drawing an outline of an object at a particular-scale, and placing it centered in a window of a certain size.classCreates a thumbnail of one or more objects on a stack by drawing the outline of the objects. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.bean.thumbnail.stack
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.bean.thumbnail.stackModifier and TypeClassDescriptionclassCreate a thumbnail by scales an image to a particular size.classCreates a thumbnail from a stack. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.dimensions
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.dimensionsModifier and TypeClassDescriptionclassArea<T extends FeatureInputEnergy>Area of the stack (XY dimensions only, Z dimension is not considered).classExtent<T extends FeatureInputEnergy>Width/height/depth of energy-stack in pixels depending on axis.classForSpecificAxis<T extends FeatureInputEnergy>Dimensions-calculation for one specific axis only.classFromDimensionsBase<T extends FeatureInputDimensions>Base class for features that are calculated fromDimensions.classVolume<T extends FeatureInputEnergy>Calculates the volume (x, y and z dimensions) of the scene from the dimensionsclassVoxelPhysicalSize<T extends FeatureInputEnergy>The physical size of a pixel in a specific dimension. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
Modifier and TypeClassDescriptionclassCalculates the coefficient of variation of all the values in the histogram.classCounts the number of items in a histogram (posssibly in relation to a threshold: above, below etc.)classCalculates the kurtosis of all the values in the histogram.classCalculates the maximum value in a histogram.classCalculates the mean value in aHistogram, and raises it to a power.classCalculates the median value in aHistogram.classCalculates the minimum value in aHistogram.classCalculates the skewness of all the values in the histogram.classNumber of unique values in histogram.classCalculates a specified quantile value from aHistogram.classThe range (difference in values) between two quantilesclassCalculates the ratio of non-mode pixels to total pixels in aHistogram.classCalculates the skewness of all the values in the histogram.classCalculates the standard deviation of values in aHistogram.classCalculates the sum of all values in aHistogram.classCalculates the total count of all entries in aHistogram.classCalculates the variance of all the values in the histogram. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.histogram.threshold
Modifier and TypeClassDescriptionclassCalculates a level (a threshold-value) from a histogram.classCalculates the ratio of values in aHistogramthat satisfy a specified threshold condition.classThresholds the histogram (using a weightedOtsu) and then applies a feature to the thresholded version. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.list
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.listModifier and TypeClassDescriptionclassCalculate various moment-related statistics about the intensity of each channel of an image. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.list.pair
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.list.pairModifier and TypeClassDescriptionclassEmbeds each feature in aFeatureDeriveFromPairfeature (first, second or merge) and prepends with a string.classCalculates features on each part of a pair (first, second, merged etc.) and then reduces the calculation to a single number.classCalculates the aggregate of a feature applied to both the first and second objects in aFeatureInputPairObjects.classCalculates the aggregate of the ratio offirst:secondandsecond:firstfor aFeatureInputPairObjectsclassCalculatesmerged - reduce(first,second)for aFeatureInputPairObjects -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.list.permute
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.list.permuteModifier and TypeClassDescriptionclassPermuteDivideByParam<T extends FeatureInputDictionary>Similar to FeatureListProviderPermute but embeds the feature in a GaussianScoreclassPermuteFeature<S,T extends FeatureInput> Permutes one or more properties of a Feature, so as to create a set of FeaturesclassPermuteFeatureBase<T extends FeatureInput>Creates permutations of a feature by modifying a particular property of it in different ways.classPermutes a property on a feature with a sequence of integers.classPermuteFirstSecondOrder<T extends FeatureInputDictionary>Permutes a feature by applying first and second order statistical operations.classPermuteGaussianScore<T extends FeatureInputDictionary>Permutes a feature by embedding it in aGaussianCumulativescore.classPermuteZScore<T extends FeatureInputDictionary>Permutes a feature by embedding it in aZScore. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.metadata
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.metadataModifier and TypeClassDescriptionclassThe bit-depth of the image per channel.classThe number of channels in an image.classThe number of frames in an image.classThe number of resolution-levels in an image in a file.classThe number of series in an image-file. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.morphological
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.morphologicalModifier and TypeClassDescriptionclassSpecifies a certain number of iterations of the morphological operations of dilation and erosion. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.object.collection
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.object.collectionModifier and TypeClassDescriptionclassCalculates the number of objects in aFeatureInputObjectCollection. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.object.combine
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.object.combineModifier and TypeClassDescriptionclassCombineObjectsForFeatures<T extends FeatureInput>A way to combine (or not combine) objects so that they provide a feature-table.classSelects features and objects directly from the input list, treating each object independently.classCreates a set of features, that creates pairs of neighboring-objects and applies a mixture of single-object features and pair features. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.object.pair
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.object.pairModifier and TypeClassDescriptionclassFinds the intersection of two objects and calculates a feature on it -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
Modifier and TypeClassDescriptionclassTODO the center-of-gravity calculation can be turned into a FeatureCalculation which is cacheableclassExpresses the number of intersecting pixels between two objects as a ratio to a denominator.classCalculates the overlap ratio between two objects relative to the size of the first object.classOverlap ratio to the maximum number of pixelsclassCalculates the overlap ratio between two objects relative to the size of the merged object.classCalculates the overlap ratio between two objects relative to the size of the second object. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching
Modifier and TypeClassDescriptionclassA simple scheme for counting the touching voxels.classA scheme for counting the touching voxels by intersection of object-masksclassA scheme for counting touching voxels.classBase class for features that calculate touching with a dilated bounding box intersection. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.object.single
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.object.singleModifier and TypeClassDescriptionclassCalculates deterministically a point that is definitely inside the object-mask and outputs a selected axis value.classBase class for features that apply a kernel to the outline of an object. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.object.single.border
Modifier and TypeClassDescriptionclassBase class for features that check if an object is at the border of an image.classChecks if an object's bounding box is at the border of the image in the XY plane.classChecks if an object's bounding box is at the border of the image in the Z dimension.classCalculates the number of voxels at the border of an object. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
Modifier and TypeClassDescriptionclassBase class for features that calculate a value along a specific axis of an object's bounding box.classCalculates the extent of an object's bounding box along a specified axis.classCalculates the maximum coordinate of an object's bounding box along a specified axis.classCalculates the minimum coordinate of an object's bounding box along a specified axis.classCalculates the number of voxels in the bounding box of an object. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.object.single.energy
Modifier and TypeClassDescriptionclassCounts the number of voxels in an object that have a specific intensity value in a channel.classCalculates the number of voxels on the object that have a neighbor.classA base class for features that operate on a specific channel from the energy stack. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
Modifier and TypeClassDescriptionclassA feature that uses a channel from the energy-stack as identified by an index.classCalculates a statistic from the intensity values covered by a single object-mask in a channel.classCalculates the maximum mean intensity across all slices of an object in a channel.classConstructs a 'shell' around an object by a number of dilation/erosion operations (not including the original object-mask) and measures the mean intensity of this shellclassConstructs a shell around an object-mask using a standard dilation and erosion process.classConstructs a 'shell' around an object by a number of dilation/erosion operations (not including the original object-mask) and measures the mean intensity of this shellclassFrom Page 727 from Lin et al (A Multi-Model Approach to Simultaneous Segmentation and Classification of Heterogeneous Populations of Cell Nuclei -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradientModifier and TypeClassDescriptionclassCalculates the mean of the intensity-gradient defined by multiple Energy channels in a particular directionclassCalculates the mean of the intensity-gradient defined by multiple Energy channels in a particular directionclassBase class for features that calculate intensity gradients from multiple channels. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.object.single.moments
Modifier and TypeClassDescriptionclassA base class for features that are calculated using image-moments.classCalculates the eccentricity of the Principal Axes (as defined by Image Moments).classThe length of a principal-axis (as defined by Image Moments).classAn element from orientation of a principal-axis (as defined by Image Moments).classCalculates the ratio of prinicpal-axis length using Image Moments.classA feature based on one specific principal-axis as identified by image moments. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.object.single.morphologicalModifier and TypeClassDescriptionclassA base class for features that operate on a derived object mask and calculate a feature on it.classA feature that erodes an object mask and then calculates another feature on the eroded object.classHow many pixels are removed after a morphological closing operation on the object-mask.classCreates a shell around anObjectMaskby applying morphological operations. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.object.single.shape
Modifier and TypeClassDescriptionclassCalculates the standard deviation of distances from surface voxels to the centroid of anObjectMask.classCalculates the shape regularity of the center slice of anObjectMask.classCalculates the shape regularity of the maximum intensity projection of anObjectMask. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.object.single.slice
Modifier and TypeClassDescriptionclassMaximum number of voxels on any slice's contour (edge voxels) across all slices.classMaximum number of voxels in the object-mask across all slices. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.object.single.surface
Modifier and TypeClassDescriptionclassThe number of voxel-faces along the surface (the faces of each voxel that touch outside)classThe number of voxels on the surface (all voxels on the exterior of the object)classA base class for features that calculate the number of voxels on the surface of an object. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.physical
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.physicalModifier and TypeClassDescriptionclassUnitsWithinRange<T extends FeatureInputWithResolution>Checks if a value lies within a range defined by units (a minimum and maximum boundary) -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.score
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.scoreModifier and TypeClassDescriptionclassCalculates a level score based on voxel intensity and a given threshold.classBase class for calculating a score based on a threshold level derived from a histogram.classclassSimilar toDifferencebut calculates the width as the standard-deviation of the histogramclassAn abstract base class for features that require aDictionaryfor initialization.classA voxel score that can optionally normalize and adjust the intensity values.classA voxel score that imposes a value relation to a histogram.classNormalizes the voxel intensity by dividing it by a constant value.classThis assumes the histograms correspond to the energy channels exactly (in terms of indexing)classCalculates a voxel score based on whether the voxel intensity is outside a specified range.classRejects voxels with intensity less than a specified minimum, otherwise calculates a score using anotherVoxelScore.classA score that is calculated on a single channel only. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.stack.intensity
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.stack.intensityModifier and TypeClassDescriptionclassDataTypeMaxIntensity<T extends FeatureInputEnergy>The maximum-intensity allowed by the data-type of the stack.classThe intensity of a particular channel of the stack, by default the mean-intensity.classThe number of channels in an image-stack. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.stack.object
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.feature.bean.stack.objectModifier and TypeClassDescriptionclassTreats a channel as an object-mask, assuming binary values of 0 and 255 and calls an object-mask featureclassCalculates the median of a feature applied to each connected component -
Uses of AnchorBean in org.anchoranalysis.plugin.image.task.bean
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.task.beanModifier and TypeClassDescriptionclassRasterTask<S,U> An experiment that takes (primarily) a series of raster images as an input. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.task.bean.combine
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.task.bean.combineModifier and TypeClassDescriptionclassCreates a an aggregated-image for each group, where each voxel-value is aggregated across each channel in each image in the group.classCreates a montage of images, by tiling them side-by-side. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.task.bean.feature
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.task.bean.featureModifier and TypeClassDescriptionclassExportFeatures<T extends InputFromManager,S, U extends FeatureInput> Calculates features and exports them as a CSV file.classVisual style for how features are exported. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.task.bean.feature.source
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.task.bean.feature.sourceModifier and TypeClassDescriptionclassFeatureSource<T extends InputFromManager,S, U extends FeatureInput> Extracts features from some kind of inputs to produce one or more rows in a feature-table.classEach input-file describes a histogram that produces one row of features.classCalculates features from a single image.classCalculates features from the metadata from single image.classSingleRowPerInput<T extends InputFromManager,S extends FeatureInput> Base class for exporting features, where features are calculated per-image using aNamedFeatureStore. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.task.bean.format
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.task.bean.formatModifier and TypeClassDescriptionclassConverts each input-image to an output format, optionally changing the bit depth. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.task.bean.format.convertstyle
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.task.bean.format.convertstyleModifier and TypeClassDescriptionclassConverts a channel(s) at a particular timepoint into a stack(s).classExtracts three channels to make an RGB image.classConverts each channel independently and creates a single-channeled stack from the conversion.classConverts a set of channels to a single RGB-stack if the channel-names match, otherwise usesfallback. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.task.bean.grouped
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.task.bean.groupedModifier and TypeClassDescriptionclassGroupedStackBase<S,T> Base class for stacks (usually each channel from an image) that are somehow grouped-together. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.task.bean.grouped.histogram
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.task.bean.grouped.histogramModifier and TypeClassDescriptionclassExports a histogram of voxel intensities as a CSV file for each channel of an image. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels
Modifier and TypeClassDescriptionclassSelects all possible channels from all possible stacksclassSelects a subset of channels from a set of stacks.classSelects one specific channel from a set of stacksclassSelects a specific set of channels from stacks, each identified by a stack-name and channel index -
Uses of AnchorBean in org.anchoranalysis.plugin.image.task.bean.labeller
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.task.bean.labellerModifier and TypeClassDescriptionclassLabels images using a binary classifier.classAbstract base class for image labellers that produce binary outcomes (positive or negative).classLabels images based on whether their descriptive name contains a specific string.classAssigns a label to each image and copies into subdirectories for each label, and creates a labelling CSV.classLabels images based on a CSV file containing image identifiers and corresponding labels.classAssociates a label with an image.classMaps one set of labels to another -
Uses of AnchorBean in org.anchoranalysis.plugin.image.task.bean.scale
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.task.bean.scaleModifier and TypeClassDescriptionclassScaleImage<S>Base class for tasks whose primary aim is to scale (resize) an image.classCreates a scaled copy of images, ensuring all images have identical output size.classCreates a scaled copy of images, treating each image independently, and without any padding or alignment. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.task.bean.segment
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.task.bean.segmentModifier and TypeClassDescriptionclassSegmentInstanceWithModel<T extends InferenceModel>Using a model-pool, performs instance segmentation on an image producing zero, one or more objects per image. -
Uses of AnchorBean in org.anchoranalysis.plugin.image.task.bean.slice
Subclasses of AnchorBean in org.anchoranalysis.plugin.image.task.bean.sliceModifier and TypeClassDescriptionclassReduces a z-stack to a single-slice by taking the optima of a feature calculated for each slice. -
Uses of AnchorBean in org.anchoranalysis.plugin.imagej.bean.channel.provider
Subclasses of AnchorBean in org.anchoranalysis.plugin.imagej.bean.channel.providerModifier and TypeClassDescriptionclassSubtracts background from a channel using ImageJ'sBackgroundSubtracter.classA base class for applying ImageJ rank filters to channels.classAChannelProviderUnarywith a 'radius' parameter. -
Uses of AnchorBean in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter
Subclasses of AnchorBean in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter -
Uses of AnchorBean in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments
Modifier and TypeClassDescriptionclassApplies a 2D mean filter to a channel using ImageJ'sRankFilters.classApplies a 2D variance filter to a channel using ImageJ'sRankFilters. -
Uses of AnchorBean in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank
Modifier and TypeClassDescriptionclassApplies a 2D median filter to a channel using ImageJ'sRankFilters.classApplies a 3D median filter to a channel using a hybrid 3D median filter ImageJ plugin. -
Uses of AnchorBean in org.anchoranalysis.plugin.imagej.bean.define
Subclasses of AnchorBean in org.anchoranalysis.plugin.imagej.bean.define -
Uses of AnchorBean in org.anchoranalysis.plugin.imagej.bean.mask.provider
Subclasses of AnchorBean in org.anchoranalysis.plugin.imagej.bean.mask.providerModifier and TypeClassDescriptionclassFills holes in a mask, with options to skip holes touching the border or exceeding a maximum volume.classApplies an ImageJ (2D) morphological operation to each slice -
Uses of AnchorBean in org.anchoranalysis.plugin.imagej.bean.object.provider
Subclasses of AnchorBean in org.anchoranalysis.plugin.imagej.bean.object.providerModifier and TypeClassDescriptionclassDraws a lines between successive points on the convex-hull of an object.classFills holes in an object. -
Uses of AnchorBean in org.anchoranalysis.plugin.imagej.bean.object.segment
Subclasses of AnchorBean in org.anchoranalysis.plugin.imagej.bean.object.segmentModifier and TypeClassDescriptionclassCreates an object for each separate intensity-value (beginning atstartingColor) by flood-filling. -
Uses of AnchorBean in org.anchoranalysis.plugin.imagej.bean.stack.provider
Subclasses of AnchorBean in org.anchoranalysis.plugin.imagej.bean.stack.provider -
Uses of AnchorBean in org.anchoranalysis.plugin.imagej.bean.threshold
Subclasses of AnchorBean in org.anchoranalysis.plugin.imagej.bean.thresholdModifier and TypeClassDescriptionclassA thresholder that applies a simple intensity threshold and then fills holes in 2D. -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.channel.map
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.channel.mapModifier and TypeClassDescriptionclassNames of the channels from the metadata if it exists, or after RGB, or by index.classclassclassFor an image with a single channel -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.file.copy.method
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.file.copy.methodModifier and TypeClassDescriptionclassMakes a simple bytewise copy of a file, where no byte is changed.classCreate a voxelwise compressed copy of any TIFF file being copied, and otherwise do aBytewisecopy.classA method used for copying files (e.g. bytewise or activating compression etc.). -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.file.copy.naming
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.file.copy.namingModifier and TypeClassDescriptionclassCopies files to a number001, 002etc. in the same order they are inputted.classHow an output name (and path) is selected for an input file when copying.classclassBase class for implementations ofCopyFilesNamingwhere each file is copied independently of the others.classRejects files that fail to match a particular regular-expressionclassCopies files using whatever prefix is assigned to an input by theOutputManageras the file-name, adding the same extension as the source file.classCopies files to maintain the same relative-path from the destination file to the destination-directory, as existed from the source file to the source-directory.classA base class forCopyFilesNamingclasses that use a regular-expression.classRemoves any whitespace characters from the pathclassA regular expression substitution (replaceAll) is applied to the relative-path -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.file.copy.naming.clusterModifier and TypeClassDescriptionclassAssociates particular timestamp with each file, and clusters. -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.file.group
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.file.groupModifier and TypeClassDescriptionclassAnInputManagerWithStackReaderthat can unify separate images in separate files to form a singleStack. -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.file.group.check
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.file.group.check -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.file.group.parser
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.file.group.parser -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.file.namer
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.file.namerModifier and TypeClassDescriptionclassclassMultiplexes between two namers depending on if the relative-to-directory option is selected.classDerives a name by taking the filename together with optionally several subdirectories names.classUses the normalized path (always with forward slashes) of each file as it's descriptive-nameclassclassConstructs a name by finding the relative-path between the file and the input-directory.classRemoves extensions from the identifier (but not from the file) and only if the extension hasn't already been removed upstream.classIf specified in the context, the existing name if subsetted according to an index range. -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.file.namer.patternspan
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.file.namer.patternspanModifier and TypeClassDescriptionclassFinds a pattern in the file-path, and uses a portion of the file-path in that pattern to form the name. -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.file.path
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.file.path -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.file.path.prefixer
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.file.path.prefixerModifier and TypeClassDescriptionclassReuses the directories between a path and its root to form the output - and also the filename.classThe prefixer uses a combination of a out-path-prefix and the descriptive-name of inputs to create an output prefix.classclassMultiplexes between twoPathPrefixers depending on whether an incrementing number sequence was output was requested.classLooks for the last directory-name, and removes it in favour of using it as a prefix on a filenameclassMatches a regex against incoming file-paths to form a prefix for outputclassPrepend a 'root' before the file-path-prefix obtained from a delegate -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.file.pattern
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.file.patternModifier and TypeClassDescriptionclassExtracts a timestamp from a file-name if it exists. -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.file.provider
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.file.providerModifier and TypeClassDescriptionclassclassclassclassclassclassclassRepresents a set of files, with a different path-root depending on context.classclassclass -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.grouper
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.grouperModifier and TypeClassDescriptionclassWhen aIndexRangeNegativeis passed as an argument, anInputGrouperis constructed that extracts elements from aPath.classSplits an identifier into elements by the directory separator, and removes the final element. -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.input
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.inputModifier and TypeClassDescriptionclassBranchIfDebug<T extends InputFromManager>Uses one input-manager normally, but a different one if in debug mode.classConcatenate<T extends InputFromManager>Concatenates the inputs from multipleInputManagers that all provide the same input-type.classExclude<T extends InputFromManager>Excludes all inputs whose identifiers match a regular expression.classLimit<T extends InputFromManager>Limits the number of input-objects to a certain hard-maximumclassLimitIfRequested<T extends InputFromManager>LikeLimitif it is requested in theInputContextParameters, makes no change to the inputs.classShuffle<T extends InputFromManager>Randomly shuffles the order of the inputs.classShuffleIfRequested<T extends InputFromManager>LikeShuffleif requested in theInputContextParametersotherwise makes no change to the inputs.classSortAlphabetically<T extends InputFromManager>Sorts the input-items in alphabetical order of their input-name. -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.input.channel
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.input.channelModifier and TypeClassDescriptionclassAn image viewed as a set of channels, each with a unique name.classclassParent for all theNamedChannelsclasses -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.input.files
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.input.filesModifier and TypeClassDescriptionclassImplementation ofNamedFilesBasethat is anInputManagerthat acceptsFileInputas input and derives a name.classNamedFilesBase<T extends InputFromManager>Base class for anInputManagerthat produces inputs that are created from aNamedFile.class -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.input.files.provider
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.input.files.providerModifier and TypeClassDescriptionclassLists all directories to a certain depthclass -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.input.filter
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.input.filterModifier and TypeClassDescriptionclassFilterCSVColumn<T extends InputFromManager>Finds a CSV file with the names of an input as the first-column.classFilterDescriptiveName<T extends InputFromManager>Filters all the input objects for only those with certain types of descriptive-names.classFilterIfDebug<T extends InputFromManager>Filters a list of inputs when in debug-mode -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.input.stack
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.input.stackModifier and TypeClassDescriptionclassManager that converts (one channel)NamedChannelsInputtoStackSequenceInput.classAnInputManagerwhere each file provides one or moreStacks. -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.metadata.header
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.metadata.headerModifier and TypeClassDescriptionclassThe headers found in a BMP file.classPopulatesImageMetadatafrom the header of an image-file.classThe headers found in a JPEG file.classThe headers found in a PNG file. -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.metadata.reader
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.metadata.readerModifier and TypeClassDescriptionclassA specialImageMetadataReaderthat will always throw an exception and reject a file.classTries to construct theImageMetadatafrom EXIF and other metadata, if available, or otherwise falls back to another reader. -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.path.derive
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.path.deriveModifier and TypeClassDescriptionclassRemoves the file-name from a path, but keeps the directories and preserves the file-extension.classAlways generates a constant path irrespective of the the inputclassGenerates an out string where $digit$ is replaced with the #digit group from a regexclassGenerates an outstring of the formclassclassGenerates a file-path by replacing all occurrences of a string-pattern with anotherclass -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.stack.reader
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.stack.readerModifier and TypeClassDescriptionclassIf the extension(s) of a path matches a particular value, then use a particular reader, otherwise a fallback.classCombines all series and frames returned by a reader by converting them into multiple channels in the same image.classAdds an explicitResolutionto an image after it has been read.classclassReadsResolutionfrom an XML file associated an image.classIf the XY resolution of an opened-image meets a certain condition then the resolution is scaled by a factor.classRotates an image to match any EXIF orientation information, if it exists. -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.stack.writer
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.stack.writerModifier and TypeClassDescriptionclassUses different raster-writers depending on the number/type of channels.classUses different raster-writers depending on whether it is always 2D (not a z-stack) or possibly 3D.classSelects particular writers based on if particular suggested image formats are present.classclassA base class for aStackWriterdelegates to anotherStackWriterbased on values of aStackWriteAttributes.classWhen writing a stack, an additional file is written to indicate the physical voxel sizes, if this information is known. -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.summarizer
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.summarizerModifier and TypeClassDescriptionclassSummarizer<T>Summarizes a set of elements by outputting a descriptive string.classCollects summary data about a set of input files that will eventually be outputted to the userclassA count of the number of inputs.classCreates a string where each line is an element.classMultiplexes between two summarizers depending on the total number of count. -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.summarizer.image
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.summarizer.imageModifier and TypeClassDescriptionclassclassSummarizes the size of images.classclassSummarizesImageMetadataInputin different ways.classA simple summarizer, where there's one summary-item per image. -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.summarizer.input
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.summarizer.inputModifier and TypeClassDescriptionclassExtractIdentifier<T extends InputFromManager>Extracts the identifier from anInputFromManagerto summarize further.classExtractIdentifierAndPath<T extends InputFromManager>Extracts the identifier and path from anInputFromManagerto summarize further.classExtractPath<T extends InputFromManager>Extracts aPathfrom an input to summarize further.classSummarizerInputFromManager<T extends InputFromManager,S> Extracts a particular item from anInputFromManagerfor further summarization downstream. -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.summarizer.path
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.summarizer.pathModifier and TypeClassDescriptionclassRemembers each unique extension, and associated countclassConverts a list of file-paths into a form that tries to find a pattern in the naming style using the path-pattern-finder library.classTracks the range of file-size.classBase class forSummarizers that operate on thePathassociated with inputs. -
Uses of AnchorBean in org.anchoranalysis.plugin.io.bean.task
Subclasses of AnchorBean in org.anchoranalysis.plugin.io.bean.taskModifier and TypeClassDescriptionclassCombines multiple CSV files into a single CSV file.classCopyFiles<T>Copy files to the output-directory, possibly changing the name or performing other operations like compression in the process.classSummarizeBase<T extends InputFromManager,S> classSummarizeInputs<T extends InputFromManager> -
Uses of AnchorBean in org.anchoranalysis.plugin.mpp.bean.convert
Subclasses of AnchorBean in org.anchoranalysis.plugin.mpp.bean.convertModifier and TypeClassDescriptionclassConvertNamedChannels<T extends NamedChannelsInput,S, U extends InputFromManager> ConvertsNamedChannelsInputto a variety of others to match a delegate task. -
Uses of AnchorBean in org.anchoranalysis.plugin.mpp.bean.define
Subclasses of AnchorBean in org.anchoranalysis.plugin.mpp.bean.defineModifier and TypeClassDescriptionclassApplies aDefineon inputs and outputs produced entities (images, histograms, objects etc.).classLike aDefinebut outputs also an energy-stack.classDerives various types of outputs (images, histograms etc.) fromMultiInputs.classAdds a visualization for all binary-masks and object-collections that are added using a particular background -
Uses of AnchorBean in org.anchoranalysis.plugin.mpp.bean.object.provider
Subclasses of AnchorBean in org.anchoranalysis.plugin.mpp.bean.object.providerModifier and TypeClassDescriptionclassCreates object-masks from aMarkCollectionwhere (a particular region of) each mark creates an object. -
Uses of AnchorBean in org.anchoranalysis.plugin.mpp.bean.provider.collection
Subclasses of AnchorBean in org.anchoranalysis.plugin.mpp.bean.provider.collectionModifier and TypeClassDescriptionclassCreates a new empty collection of marksclassCreates aMarkCollectionfrom a single mark provided by aSingleMarkProvider.classCreates aMarkCollectionof point marks from anObjectCollection.classProvides aMarkCollectionby referencing it from the initialization context using an ID.classReturns an existing marks-collection or an empty set if it doesn't existclassScales the X and Y coordinates of marks in aMarkCollectionusing aScaleCalculator. -
Uses of AnchorBean in org.anchoranalysis.plugin.mpp.bean.stack.provider
Subclasses of AnchorBean in org.anchoranalysis.plugin.mpp.bean.stack.providerModifier and TypeClassDescriptionclassDraws a colored representation (outline or filled) of anMarkCollectionon a background -
Uses of AnchorBean in org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnn
Subclasses of AnchorBean in org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnnModifier and TypeClassDescriptionclassDecodes the inference output from a Mask-RCNN implementation. -
Uses of AnchorBean in org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.text
Modifier and TypeClassDescriptionclassExtracts text from a RGB image by using the EAST deep neural network model and the ONNX Runtime. -
Uses of AnchorBean in org.anchoranalysis.plugin.onnx.bean.object.segment.stack
Subclasses of AnchorBean in org.anchoranalysis.plugin.onnx.bean.object.segment.stackModifier and TypeClassDescriptionclassPerforms instance-segmentation using the ONNX Runtime and an.onnxmodel file. -
Uses of AnchorBean in org.anchoranalysis.plugin.opencv.bean.color
Subclasses of AnchorBean in org.anchoranalysis.plugin.opencv.bean.colorModifier and TypeClassDescriptionclassConverts a RGB stack into another color space using OpenCV.classConverts a RGB image to the HSV color space.classConverts a RGB image to the Lab color space. -
Uses of AnchorBean in org.anchoranalysis.plugin.opencv.bean.feature
Subclasses of AnchorBean in org.anchoranalysis.plugin.opencv.bean.featureModifier and TypeClassDescriptionclassCreates the entire HOG descriptor for an image.classOne part of a Histogram of Oriented Gradients descriptor, as applied to an image stack.classParameters for calculating a HOG Descriptor covering window-size, block-size etc. -
Uses of AnchorBean in org.anchoranalysis.plugin.opencv.bean.interpolate
Subclasses of AnchorBean in org.anchoranalysis.plugin.opencv.bean.interpolate -
Uses of AnchorBean in org.anchoranalysis.plugin.opencv.bean.object.segment.stack
Subclasses of AnchorBean in org.anchoranalysis.plugin.opencv.bean.object.segment.stackModifier and TypeClassDescriptionclassPerforms instance-segmentation using OpenCV's DNN module and a TensorFlow.pbSavedModel file. -
Uses of AnchorBean in org.anchoranalysis.plugin.opencv.bean.stack
Subclasses of AnchorBean in org.anchoranalysis.plugin.opencv.bean.stackModifier and TypeClassDescriptionclassReads a stack from the file-system using OpenCV.classWrites a stack to the file-system using OpenCV and a specified extension. -
Uses of AnchorBean in org.anchoranalysis.plugin.operator.feature.bean
Subclasses of AnchorBean in org.anchoranalysis.plugin.operator.feature.beanModifier and TypeClassDescriptionclassFromDictionary<T extends FeatureInputDictionary>Extracts a key-value from aDictionaryas a double.classWithValueBase<T extends FeatureInput>A base class for operations that use a specified constant value in combination with a feature. -
Uses of AnchorBean in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
Subclasses of AnchorBean in org.anchoranalysis.plugin.operator.feature.bean.arithmeticModifier and TypeClassDescriptionclassAbsoluteValue<T extends FeatureInput>A feature that calculates the absolute value of another feature's result.classAddConstantTo<T extends FeatureInput>A feature that adds a constant value to the result of another feature.classConstantToThePowerOf<T extends FeatureInput>A feature that raises a constant value to the power of another feature's result.classDivide<T extends FeatureInput>A feature that divides the results of multiple features sequentially.classDivideByConstant<T extends FeatureInput>A feature that divides the result of another feature by a constant value.classInvertedMax<T extends FeatureInput>Finds the repciprocal (multiplicate inverse), but imposes a maximum ceiling via a constant.classMultiply<T extends FeatureInput>A feature that multiplies the results of multiple features together.classMultiplyByConstant<T extends FeatureInput>A feature that multiplies the result of another feature by a constant value.classSubtractFrom<T extends FeatureInput>A feature that subtracts the result of another feature from a constant value.classToThePowerOfConstant<T extends FeatureInput>A feature that raises the result of another feature to the power of a constant value. -
Uses of AnchorBean in org.anchoranalysis.plugin.operator.feature.bean.conditional
Subclasses of AnchorBean in org.anchoranalysis.plugin.operator.feature.bean.conditionalModifier and TypeClassDescriptionclassIfCondition<T extends FeatureInput>The result of featureCondition is compared to a threshold, and then either the underlying feature is calculated (positive case), or featureElse is (negative case) -
Uses of AnchorBean in org.anchoranalysis.plugin.operator.feature.bean.list
Subclasses of AnchorBean in org.anchoranalysis.plugin.operator.feature.bean.listModifier and TypeClassDescriptionclassMaximum<T extends FeatureInput>A feature that calculates the maximum value from a list of features.classMean<T extends FeatureInput>Arithmetic mean of a list of featuresclassMeanGeometric<T extends FeatureInput>A feature that calculates the geometric mean of a list of features.classMinimum<T extends FeatureInput>A feature that calculates the minimum value from a list of features. -
Uses of AnchorBean in org.anchoranalysis.plugin.operator.feature.bean.range
Subclasses of AnchorBean in org.anchoranalysis.plugin.operator.feature.bean.rangeModifier and TypeClassDescriptionclassCompareWithRange<T extends FeatureInput>Compares a value with a range, returning specified constants if its inside the range, below it or above itclassCompareWithRangeFeature<T extends FeatureInput>LikeCompareWithRangebut uses features to calculate boundary valuesclassIfConditionWithinRange<T extends FeatureInput>Calculates a value if a condition lies within a certain range, otherwise returns constantsclassIfOutsideRange<T extends FeatureInput>Clamps a feature value if it lies outside a specified range.classNormalizedRange<T extends FeatureInput>The range of two feature values (i.e. max - min), divided by their mean.classRange<T extends FeatureInput>Calculates the statistical range between two feature values, with optional weighting.classRangeCompareBase<T extends FeatureInput>A base class for features that compare a value against a range and return different results based on the comparison.classRangeCompareFromScalars<T extends FeatureInput>A base class for setting the boundaries of a range using constant scalar values. -
Uses of AnchorBean in org.anchoranalysis.plugin.operator.feature.bean.replace
Subclasses of AnchorBean in org.anchoranalysis.plugin.operator.feature.bean.replaceModifier and TypeClassDescriptionclassReplaceInfinity<T extends FeatureInput>Replaces infinite values in a feature's result with a specified replacement value.classReplaceNaN<T extends FeatureInput>Replaces NaN (Not a Number) values in a feature's result with a specified replacement value.classReplaceUnusualValue<T extends FeatureInput>Calculates the underlying feature, but replaces the result with a constant if it is an "unusual" value. -
Uses of AnchorBean in org.anchoranalysis.plugin.operator.feature.bean.statistics
Subclasses of AnchorBean in org.anchoranalysis.plugin.operator.feature.bean.statisticsModifier and TypeClassDescriptionclassGaussianCumulative<T extends FeatureInput>Calculates a score between 0 and 1 based on the Cumulative Distribution Function (CDF) of a Gaussian distribution.classStatisticalBase<T extends FeatureInput>Calculates a score based upon the statistical mean and standard deviation.classZScore<T extends FeatureInput>Calculates the Z-score of a value based on the mean and standard deviation. -
Uses of AnchorBean in org.anchoranalysis.plugin.operator.feature.physical
Subclasses of AnchorBean in org.anchoranalysis.plugin.operator.feature.physicalModifier and TypeClassDescriptionclassConvertUnits<T extends FeatureInput>Converts a feature value from one unit type to another. -
Uses of AnchorBean in org.anchoranalysis.plugin.points.bean
Subclasses of AnchorBean in org.anchoranalysis.plugin.points.beanModifier and TypeClassDescriptionclassclassAMarkCollectionProviderthat fits points from objects to create marks.classSplits a 2D contour represented by an object-mask into several contours, splitting at "turn" points. -
Uses of AnchorBean in org.anchoranalysis.plugin.points.bean.convexhull
Subclasses of AnchorBean in org.anchoranalysis.plugin.points.bean.convexhullModifier and TypeClassDescriptionclassSets particular voxels to high only if they exist on the convex-hull of the outline of a mask.classCalculates a 3D convex hull from a binary mask.classBase class for convex hull implementations. -
Uses of AnchorBean in org.anchoranalysis.plugin.points.bean.feature
Subclasses of AnchorBean in org.anchoranalysis.plugin.points.bean.featureModifier and TypeClassDescriptionclassCalculates the axis ratio of anEllipsoid.classBase class for features that calculate properties of anEllipsoidfitted to an object.classCalculates the ellipsoidicity of an object by fitting anEllipsoidto it.classCalculates the ellipticity of anObjectMask(on the center of gravity slice if it's a z-stack). -
Uses of AnchorBean in org.anchoranalysis.plugin.points.bean.fitter
Subclasses of AnchorBean in org.anchoranalysis.plugin.points.bean.fitterModifier and TypeClassDescriptionclassBase class for conic fitters, providing common properties and methods.classFits a set of points to an ellipse using a linear least squares method.classFits an ellipsoid to points using a linear least squares approachclassBase class for linear least squares fitting using the normal equation method.classA bean for fitting points to a mark using a specified points fitter.classAPointsFitterthat references anotherPointsFitterby its ID.classReflects points in each axes if all points are within a certain distance from it -
Uses of AnchorBean in org.anchoranalysis.test.experiment
Methods in org.anchoranalysis.test.experiment with type parameters of type AnchorBeanModifier and TypeMethodDescriptionstatic <T extends AnchorBean<?>>
TBeanTestChecker.check(T bean) Checks if a bean has all necessary items, throwing a run-time exception if it does not. -
Uses of AnchorBean in org.anchoranalysis.test.feature.plugins.mockfeature
Subclasses of AnchorBean in org.anchoranalysis.test.feature.plugins.mockfeatureModifier and TypeClassDescriptionclassA feature that returns the number-of-voxels in an object by using am internal mock-calculation. -
Uses of AnchorBean in org.anchoranalysis.test.image.io
Methods in org.anchoranalysis.test.image.io with type parameters of type AnchorBeanModifier and TypeMethodDescriptionstatic <T extends AnchorBean<?>>
TBeanInstanceMapFixture.check(T bean) Checks if a bean has all necessary items, throwing a run-time exception if it does not.