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Anchor - merged Javadoc across key repositories. This documentation is a work-in-progress. 0.0.1-SNAPSHOT API

Packages 
Package Description
org.anchoranalysis.annotation
Ground truth for an image in diverse forms.
org.anchoranalysis.annotation.image
Annotations that apply to an image as a whole.
org.anchoranalysis.annotation.io
Reading and writing annotations to the filesystem.
org.anchoranalysis.annotation.io.assignment
A pairing of objects from two collections (bipartite matching).
org.anchoranalysis.annotation.io.assignment.generator
Generates output images to illustrate a Assignment between annotations.
org.anchoranalysis.annotation.io.bean
Beans related to reading / writing / specifying annotations.
org.anchoranalysis.annotation.io.bean.comparer
What to compare an annotation (ground truth) against?
org.anchoranalysis.annotation.io.image
Reading and writing whole-image label annotations.
org.anchoranalysis.annotation.io.image.findable
The outcome of searching for annotations or images on the file-system.
org.anchoranalysis.annotation.io.mark
Reading and writing Mark-related annotations from/to the file-system.
org.anchoranalysis.annotation.mark
Annotations that use one or more marks to describe entities in an image.
org.anchoranalysis.bean
Defining, loading, initializing Anchor Beans.
org.anchoranalysis.bean.annotation
Annotations that decorate fields in an Anchor Bean.
org.anchoranalysis.bean.define
Define and related-classes.
org.anchoranalysis.bean.define.adder
DefineAdder and related-classes.
org.anchoranalysis.bean.exception
Exceptions that can occur executing generic operations on Anchor Beans.
org.anchoranalysis.bean.initializable
Initializing beans with particular parameters, including recursively.
org.anchoranalysis.bean.initializable.params
Some kinds of parameters used when initializing beans.
org.anchoranalysis.bean.initializable.property
Performing initializion on particular properties in a bean.
org.anchoranalysis.bean.permute
Applying permutations to a bean's fields.
org.anchoranalysis.bean.permute.property
Applying permutations to the properties of a bean.
org.anchoranalysis.bean.permute.setter
Setter used to impose a permutation on bean properties.
org.anchoranalysis.bean.provider
A means of creating / loading / referencing a bean from another bean or class.
org.anchoranalysis.bean.shared
Utility beans which have a generally broader use than a specific module.
org.anchoranalysis.bean.shared.color
Beans that specify colors.
org.anchoranalysis.bean.shared.color.scheme
Beans that create lists or indices of colors according to particular schemes.
org.anchoranalysis.bean.shared.dictionary
Setting, referencing and initializing key-value parameters.
org.anchoranalysis.bean.shared.path
Defines a root path directory on the filesystem whre files are read / written.
org.anchoranalysis.bean.shared.random
Specifies a particular type of random-number generator.
org.anchoranalysis.bean.shared.regex
Specifies regular-expressions.
org.anchoranalysis.bean.shared.relation
Specifies a binary relation of some kind between scalars.
org.anchoranalysis.bean.shared.relation.threshold
Specifies a unary relation to a *threshold* value.
org.anchoranalysis.bean.xml
Reading Beans from XML files.
org.anchoranalysis.bean.xml.exception
Exceptions that can thrown when loading beans from XML.
org.anchoranalysis.bean.xml.factory
Custom factories for loading beans in custom ways from XML.
org.anchoranalysis.browser.launcher
Launching the anchor GUI interactive application from command-line.
org.anchoranalysis.core.cache
Caching (memozing) calls to a method so an operation does not need to be repeated.
org.anchoranalysis.core.color
Specifying particular colors and groups of colors.
org.anchoranalysis.core.concurrency
Specifying how many CPUs and GPUs can be allocated for some purpose.
org.anchoranalysis.core.exception
Very general exceptions and base classes for exceptions with wide applicability.
org.anchoranalysis.core.exception.combinable
Nested exceptions of similar type that can be combined together in a summary.
org.anchoranalysis.core.exception.friendly
Particular types of exceptions that are guaranteed to have a text/form that gives user-friendly error descriptions.
org.anchoranalysis.core.format
File formats and associated extensions.
org.anchoranalysis.core.functional
Utilities and interfaces for applying functional-programming.
org.anchoranalysis.core.functional.checked
Versions of many functional-interfaces in java.util.function that throw checked-exceptions.
org.anchoranalysis.core.graph
Data-structures for directed and undirected graphs, with or without an edge payload.
org.anchoranalysis.core.identifier.getter
Data structures for adding a unique name (a String or integer identifier) to other entities.
org.anchoranalysis.core.identifier.name
Data structures for name (String) and value associations.
org.anchoranalysis.core.identifier.provider
A collection of named-elements, a NamedProvider, and related operations.
org.anchoranalysis.core.identifier.provider.store
Data structures like NamedProvider with supporting for adding new elements.
org.anchoranalysis.core.index
Classes to support getting/setting/specifying unique-integers (indices) for elements.
org.anchoranalysis.core.index.bounded
A range of elements with indiced, bounded to lie between particular a minimum and maximum.
org.anchoranalysis.core.index.bounded.bridge
Exposes one type as a BoundedIndexContainer of another type.
org.anchoranalysis.core.log
Interfaces to log messages, both information and error messages.
org.anchoranalysis.core.log.error
Mechanism for reporting errors (exceptions/throwables) to the user.
org.anchoranalysis.core.progress
Classes to allow for tracking the progress of a task that can be broken into smaller units, for reporting to the user.
org.anchoranalysis.core.random
Generating random numbers.
org.anchoranalysis.core.serialize
Utilities for serializing and deserializing objects.
org.anchoranalysis.core.system
Utilities for interacting with the operating system or computer system generally
org.anchoranalysis.core.system.path
Utilities for converting/manipulating file-paths.
org.anchoranalysis.core.value
Encapsulating values or sets of named-values.
org.anchoranalysis.experiment
Classes related to executing an experiment by calling jobs on inputs.
org.anchoranalysis.experiment.arguments
Arguments that can further specify an experiment in addition to its bean specification.
org.anchoranalysis.experiment.bean
Beans related to executing an experiment by calling jobs on inputs.
org.anchoranalysis.experiment.bean.identifier
Assigning unique names to experiments.
org.anchoranalysis.experiment.bean.io
Generic experiments that handle input and output in structured ways.
org.anchoranalysis.experiment.bean.log
Different approaches to where messages on the progress/status of an experiment are logged to.
org.anchoranalysis.experiment.bean.processor
How a task is executed on multiple inputs.
org.anchoranalysis.experiment.bean.require
A test whether certain conditions on arguments to experiments are fulfilled.
org.anchoranalysis.experiment.bean.task
Defines a task, which is a set of operations run on an input, that may or may not generate an output.
org.anchoranalysis.experiment.io
Interfaces for replacing attributes of an experiment: input, output, task etc.
org.anchoranalysis.experiment.log
Helpful classes for logging.
org.anchoranalysis.experiment.task
Non-bean classes related to a Task.
org.anchoranalysis.experiment.task.processor
Non-bean classes related to JobProcessor.
org.anchoranalysis.feature.bean
Beans pertaining to feature-calculation.
org.anchoranalysis.feature.bean.list
A feature-list (custom list type for features) and associated providers.
org.anchoranalysis.feature.bean.operator
Features that are sufficiently generic to work on any input-type.
org.anchoranalysis.feature.bean.provider
Provider of a single feature.
org.anchoranalysis.feature.bean.results
Defines base class FeatureResults together with some implementations.
org.anchoranalysis.feature.calculate
Sub-feature units of calculation that can be cached.
org.anchoranalysis.feature.calculate.cache
Classes to cache feature-results or parts of feature-results that occur repeatedly among features or across calculations of the same feature.
org.anchoranalysis.feature.energy
A particular stack used in feature-calculations called a EnergyStack together with related classes.
org.anchoranalysis.feature.input
Base classes providing inputs to feature calculations.
org.anchoranalysis.feature.io.csv
Writing feature calculation-results in CSV format.
org.anchoranalysis.feature.io.name
Naming items in a weay that breaks down into multiple elements.
org.anchoranalysis.feature.io.results
Writes feature-calculation results in different formats, also grouped results.
org.anchoranalysis.feature.io.results.group
Various different outputs that can be written for the a grouped version of the results in ResultsWriter.
org.anchoranalysis.feature.name
Data objects for the names of features.
org.anchoranalysis.feature.results
Results from one or more feature calculations.
org.anchoranalysis.feature.session
A defined context in which one or more features are provided inputs and produce results.
org.anchoranalysis.feature.session.cache
Creates a FeatureSessionCache to use during feature-calculations.
org.anchoranalysis.feature.session.cache.finder
Strategies to determine which child-cache (among hierarchy) to employ for a particular feature calculation.
org.anchoranalysis.feature.session.calculator.multi
Calculates results for one or more features for a given input.
org.anchoranalysis.feature.session.calculator.single
Calculates results for a single feature for a given input.
org.anchoranalysis.feature.session.replace
Strategies on whether to reuse or invalidate a feature-input's cache.
org.anchoranalysis.feature.shared
Features shared for referencing among calculations.
org.anchoranalysis.feature.store
A collection of named-Features.
org.anchoranalysis.image.bean
Core (bean) classes for image processing.
org.anchoranalysis.image.bean.channel.converter
Base classes for comparing a channel to another type.
org.anchoranalysis.image.bean.interpolator
Beans for specifying image interpolators.
org.anchoranalysis.image.bean.nonbean.error
Specific exception types that can be thrown in this module.
org.anchoranalysis.image.bean.nonbean.init
Initialization of image-related beans.
org.anchoranalysis.image.bean.nonbean.segment
Non-bean classes relating to image-segmentation.
org.anchoranalysis.image.bean.nonbean.spatial.arrange
Non-beans to specify how to form a single-image by spatially combining other images.
org.anchoranalysis.image.bean.object
Beans pertaining to ObjectMask and their collections.
org.anchoranalysis.image.bean.provider
Base classes for providers of different core data entities related to images.
org.anchoranalysis.image.bean.provider.stack
A provider of Stacks.
org.anchoranalysis.image.bean.segment
Base classes to perform image segmentation, transforming an image into another meaningful entity or entities.
org.anchoranalysis.image.bean.segment.binary
Base classes to perform binary-segmentation.
org.anchoranalysis.image.bean.segment.object
Base classes to segment a channel into objects.
org.anchoranalysis.image.bean.spatial
Beans to define entities or operate that consider Euclidian space.
org.anchoranalysis.image.bean.spatial.arrange
Beans to specify how to form a single-image by spatially combining other images.
org.anchoranalysis.image.bean.spatial.direction
Beans to specify a direction.
org.anchoranalysis.image.bean.threshold
Base classes for thresholding and calculating levels for thresholding.
org.anchoranalysis.image.bean.threshold.relation
Reusable relations to a threshold.
org.anchoranalysis.image.bean.unitvalue.distance
Converting quantities of distance between units.
org.anchoranalysis.image.bean.unitvalue.extent
Converting quantities of extent (area or volume) between units.
org.anchoranalysis.image.bean.unitvalue.extent.area
Converting quantities of area between units.
org.anchoranalysis.image.bean.unitvalue.extent.volume
Converting quantities of volume between units.
org.anchoranalysis.image.core.bufferedimage
Conversions and operations involving Java AWT's BufferedImage.
org.anchoranalysis.image.core.channel
The Channel core data-class and related operations and converters.
org.anchoranalysis.image.core.channel.convert
Converts a channel to other data-types.
org.anchoranalysis.image.core.channel.convert.attached
Converts a channel to another data-type based upon another object to which it is attached.
org.anchoranalysis.image.core.channel.convert.attached.channel
Converts a channel to another data-type based upon a Channel to which it is attached.
org.anchoranalysis.image.core.channel.convert.attached.histogram
Converts a channel to another data-type based upon a Histogram to which it is attached.
org.anchoranalysis.image.core.channel.factory
Factory classes for creating Channel for various voxel data-types.
org.anchoranalysis.image.core.dimensions
Classes to describe the size of images or components of images both in voxels and physically.
org.anchoranalysis.image.core.dimensions.size
Determining or changing the size of an image.
org.anchoranalysis.image.core.dimensions.size.suggestion
Suggestions on a size for an image.
org.anchoranalysis.image.core.mask
An image with only two permissible states.
org.anchoranalysis.image.core.mask.combine
Binary operations involving voxelwise combination of Mask.
org.anchoranalysis.image.core.merge
Merges two or more entities.
org.anchoranalysis.image.core.object
The key data entity org.anchoranalysis.image.voxel.object and related-classes and operations.
org.anchoranalysis.image.core.object.factory
Utilities to create ObjectMask and ObjectCollection.
org.anchoranalysis.image.core.object.label
Labelling elements (object-masks or similar) with unique successive integers in a channel.
org.anchoranalysis.image.core.object.properties
An ObjectCollection with associated key-value pairs.
org.anchoranalysis.image.core.object.scale
Scaling object-collections, or lists of elements with object-representations.
org.anchoranalysis.image.core.object.seed
Starting points for segmentation that are guaranteed to lie on one distinct object.
org.anchoranalysis.image.core.orientation
Various methods to specify the orientation (general direction) of an entity.
org.anchoranalysis.image.core.outline
Finds outline voxels, the pixels on the contour/edge of the object.
org.anchoranalysis.image.core.outline.traverser
Performs a walk on every voxel on the outline of an object-mask.
org.anchoranalysis.image.core.outline.traverser.distance
A list of visited pixels which forms one contiguous path where each voxel neighbors each other.
org.anchoranalysis.image.core.outline.traverser.path
A set of contiguously neighboring points along the outline of an object.
org.anchoranalysis.image.core.outline.traverser.path.merge
Merging multiple ContiguousVoxelPath together.
org.anchoranalysis.image.core.outline.traverser.path.merge.strategy
Strategies on which ContiguousVoxelPath should be prioritized for merging.
org.anchoranalysis.image.core.points
Operations that extract points from image data entities or vice versa.
org.anchoranalysis.image.core.stack
Defines the key data object, Stack, and related classes.
org.anchoranalysis.image.core.stack.named
A collection of Stacks, each with a unique identifier as a name.
org.anchoranalysis.image.core.stack.time
Wrapping a Stack as a TimeSequence and vice versa.
org.anchoranalysis.image.feature.bean
Beans pertaining to feature definition and calculation.
org.anchoranalysis.image.feature.bean.evaluator
Beans that define context (which feature, which energy-stack) for evaluating feature-inputs.
org.anchoranalysis.image.feature.bean.histogram
Features that operate on a Histogram.
org.anchoranalysis.image.feature.bean.object.collection
Features that operate on a ObjectCollection.
org.anchoranalysis.image.feature.bean.object.pair
Features that operate on a pair of ObjectMasks.
org.anchoranalysis.image.feature.bean.object.single
Features that operate on a single ObjectMask.
org.anchoranalysis.image.feature.bean.physical
Features that convert to/from physical spatial units (e.g.
org.anchoranalysis.image.feature.calculation
Reusable implementations of FeatureCalculation related to images.
org.anchoranalysis.image.feature.calculator
Implementations of FeatureCalculatorMulti related to images, especially to create tables of feature-calculations.
org.anchoranalysis.image.feature.calculator.merged
A particular implementation of FeatureCalculatorMulti for feature-calculations based upon pairs of image-objects.
org.anchoranalysis.image.feature.input
Image-related implementations of FeatureInput.
org.anchoranalysis.image.io
Reading and writing of image-related data objects to and from the filesystem.
org.anchoranalysis.image.io.bean.channel
Beans pertaining to reading Channels as input.
org.anchoranalysis.image.io.bean.object.draw
How to represent an object-mask in a raster that is being drawn.
org.anchoranalysis.image.io.bean.object.feature
Beans to specify the outputting of features into CSV from a ObjectCollection.
org.anchoranalysis.image.io.bean.stack.combine
Beans to combine multiple stacks into a single stack before outputting.
org.anchoranalysis.image.io.bean.stack.reader
Bean classes for reading raster-files from the filesystem.
org.anchoranalysis.image.io.bean.stack.writer
Bean classes for writing raster-files to the filesystem.
org.anchoranalysis.image.io.channel.input
Non-bean classes for reading a Channel from the filesystem.
org.anchoranalysis.image.io.channel.input.series
Non-bean classes for reading a series of Channels from the filesystem.
org.anchoranalysis.image.io.channel.output
Non-bean classes for writing a Channel to the filesystem.
org.anchoranalysis.image.io.histogram.input
Non-bean classes for reading a Histogram from the filesystem.
org.anchoranalysis.image.io.histogram.output
Non-bean classes for writing a Histogram to the filesystem.
org.anchoranalysis.image.io.object
Non-bean classes for reading / writing an ObjectCollection from and to the filesystem.
org.anchoranalysis.image.io.object.input
Non-bean classes for reading an ObjectCollection from the filesystem.
org.anchoranalysis.image.io.object.output.grayscale
Writing an ObjectCollection to the filesystem as a single-channeled stack.
org.anchoranalysis.image.io.object.output.hdf5
Writing an ObjectCollection to the filesystem in HDF5 format.
org.anchoranalysis.image.io.object.output.mask
Writing an ObjectCollection to the filesystem as multiple binary singled-channeled images.
org.anchoranalysis.image.io.object.output.rgb
Writing an ObjectCollection to the filesystem as RGB raster-images.
org.anchoranalysis.image.io.stack
Non-bean classes for reading / writing a Stack from and to the filesystem.
org.anchoranalysis.image.io.stack.input
Non-bean classes for reading a Stack from the filesystem.
org.anchoranalysis.image.io.stack.output
Non-bean classes for writing a Stack to the filesystem.
org.anchoranalysis.image.io.stack.output.box
Base classes for generators that ultimately write only a bounding-box portion of a Stack to the filesystem.
org.anchoranalysis.image.io.stack.output.generator
Base classes for generators that ultimately write a Stack to the filesystem.
org.anchoranalysis.image.voxel
Data-structures to store and manipulate image raster-data or voxels.
org.anchoranalysis.image.voxel.arithmetic
Arithmetic operations for Voxels.
org.anchoranalysis.image.voxel.assigner
Assigns values to some or all voxels.
org.anchoranalysis.image.voxel.binary
The BinaryVoxels class and related operations.
org.anchoranalysis.image.voxel.binary.connected
org.anchoranalysis.image.voxel.binary.values
Defining on and off intensity-values to interpret an image in a binary way.
org.anchoranalysis.image.voxel.buffer
A buffer of voxel-values, usually corresponding to a single z-slice in Voxels.
org.anchoranalysis.image.voxel.buffer.max
Buffer for performing a Maximum Intensity Projection.
org.anchoranalysis.image.voxel.buffer.mean
Buffer for performing a mean intensity projection.
org.anchoranalysis.image.voxel.buffer.primitive
Conversion of both primitive data types and image structures between Anchor's data-structures and other representations.
org.anchoranalysis.image.voxel.buffer.slice
A container with voxel-buffers for each z-slice.
org.anchoranalysis.image.voxel.convert
Converting Voxels to different data-types.
org.anchoranalysis.image.voxel.convert.imglib2
Converts anchor data-structures to those used by ImgLib2.
org.anchoranalysis.image.voxel.datatype
The different data-types that can be used to represent voxels.
org.anchoranalysis.image.voxel.extracter
Methods to read/copy/duplicate portions of voxels.
org.anchoranalysis.image.voxel.extracter.predicate
Methods to find or count voxels that satisfy a predicate.
org.anchoranalysis.image.voxel.factory
Creates new instances of Voxels and VoxelsWrapper with specific data-types.
org.anchoranalysis.image.voxel.interpolator
Different interpolator methods to use when scaling voxels.
org.anchoranalysis.image.voxel.iterator
Utilities to iterate over voxel-locations in images and sub-regions of images.
org.anchoranalysis.image.voxel.iterator.intersecting
Like org.anchoranalysis.image.voxel.iterator but refers to iterators that operation over the intersecting regions of two entities.
org.anchoranalysis.image.voxel.iterator.neighbor
Iterating over a point's neighboring voxels.
org.anchoranalysis.image.voxel.iterator.neighbor.kernel
Routines for moving a KernelPointCursor around the neighboring voxels of the point.
org.anchoranalysis.image.voxel.iterator.predicate
Functional-interfaces for processing different combinations of points and buffers that return a boolean.
org.anchoranalysis.image.voxel.iterator.process
Functional-interfaces for processing different combinations of points and buffers that do not return a value.
org.anchoranalysis.image.voxel.iterator.process.buffer
Functional-interfaces for processing different combinations of points and raw buffers, but not VoxelBuffer.
org.anchoranalysis.image.voxel.iterator.process.voxelbuffer
Functional-interfaces for processing different combinations of points and VoxelBuffer but not raw buffers.
org.anchoranalysis.image.voxel.kernel
Applying a kernel via convolution to voxels.
org.anchoranalysis.image.voxel.kernel.count
Kernels to count the number of voxels that are equal to a particular value.
org.anchoranalysis.image.voxel.kernel.morphological
Kernels that apply morphological operations.
org.anchoranalysis.image.voxel.kernel.outline
Kernel to find outline voxels on an object.
org.anchoranalysis.image.voxel.neighborhood
A region in proximity to a voxel, encompassing this voxel as well as others.
org.anchoranalysis.image.voxel.object
The fundamental data class that is an ObjectMask and related structures.
org.anchoranalysis.image.voxel.object.morphological
org.anchoranalysis.image.voxel.object.morphological.predicate
Predicates to match certain voxels as used in org.anchoranalysis.image.voxel.object.morphological.
org.anchoranalysis.image.voxel.statistics
Statistics about aggregated voxel intensities.
org.anchoranalysis.image.voxel.thresholder
Thresholding operations on voxels.
org.anchoranalysis.io.bioformats
Non-bean classes for filesystem I/O using Bioformats.
org.anchoranalysis.io.bioformats.bean
Beans for filesystem I/O using Bioformats.
org.anchoranalysis.io.bioformats.bean.options
User-specified options that can modify metadata or other attributes of a loaded Bioformats image.
org.anchoranalysis.io.bioformats.bean.writer
Writing stacks to the file system using the Bioformats library.
org.anchoranalysis.io.bioformats.copyconvert
Converts the byte stream opened by Bioformats into channels of particular data-type.
org.anchoranalysis.io.bioformats.copyconvert.tobyte
Converts the byte stream opened by Bioformats into channels of ByteBuffer.
org.anchoranalysis.io.bioformats.copyconvert.tofloat
Converts the byte stream opened by Bioformats into channels of FloatBuffer.
org.anchoranalysis.io.bioformats.copyconvert.toint
Converts the byte stream opened by Bioformats into channels of IntBuffer.
org.anchoranalysis.io.bioformats.copyconvert.toshort
Converts the byte stream opened by Bioformats into channels of ShortBuffer.
org.anchoranalysis.io.generator
Base-classes and utilities for generators, which write different types of objects to the file system.
org.anchoranalysis.io.generator.collection
Outputting more than one element collectively using a generator.
org.anchoranalysis.io.generator.combined
Combining multiple generators into one.
org.anchoranalysis.io.generator.sequence
Writing a sequence of elements using a generator.
org.anchoranalysis.io.generator.sequence.pattern
A particular naming pattern files follow when outputted.
org.anchoranalysis.io.generator.serialized
Generators for writing serialized objects.
org.anchoranalysis.io.generator.tabular
Generators for writing tabular data, including CSV.
org.anchoranalysis.io.generator.text
Generators for writing textual data, including strings.
org.anchoranalysis.io.generator.xml
Generators for writing XML data.
org.anchoranalysis.io.imagej.bean.stack.writer
Raster-writers that use ImageJ to write images to the filesystem.
org.anchoranalysis.io.imagej.convert
Converts to and from ImageJ data-structures for images.
org.anchoranalysis.io.input
Classes relating to creating inputs for an experiment / task.
org.anchoranalysis.io.input.bean
Beans related to collecting inputs from the file-system for an experiment.
org.anchoranalysis.io.input.bean.descriptivename
Beans to derive names (compact unique identifiers) from files.
org.anchoranalysis.io.input.bean.dictionary
Methods to provide a Dictionary.
org.anchoranalysis.io.input.bean.files
Methods to provide a collection of Files.
org.anchoranalysis.io.input.bean.path
Beans pertaining to manipulating and matching against file-paths.
org.anchoranalysis.io.input.bean.path.matcher
Beans to find a subset of files that match a particular conditions on their paths.
org.anchoranalysis.io.input.bean.path.provider
Methods to provide a single file-path.
org.anchoranalysis.io.input.csv
Classes for reading comma-separated-values (CSV) files.
org.anchoranalysis.io.input.files
Non-bean classes that relate to using files during inputting.
org.anchoranalysis.io.input.path
Non-bean classes pertaining to getting/extracting/manipulating paths as used in inputting.
org.anchoranalysis.io.input.path.matcher
Non-bean classes to help with org.anchoranalysis.io.input.bean.path.matcher.
org.anchoranalysis.io.manifest
A manifest that records what outputs occur and where they occur.
org.anchoranalysis.io.manifest.deserializer
Classes to read manifests from the file-system.
org.anchoranalysis.io.manifest.directory
Entities to indicate a directory in the manifest.
org.anchoranalysis.io.manifest.directory.sequenced
Classes related to a directory that has a particular sequence of outputted filenames.
org.anchoranalysis.io.manifest.file
Entities to indicate a file and its role in the manifest.
org.anchoranalysis.io.manifest.finder
Methods to search through a manifest-file to find outputs matching certain conditions.
org.anchoranalysis.io.manifest.finder.match
Predicates that are useful for matching against particular type of objects in finders.
org.anchoranalysis.io.manifest.operationrecorder
Makes a record of each file/subdirectory written as output.
org.anchoranalysis.io.manifest.sequencetype
Predictable patterns of indexes as used in sets of outputted files.
org.anchoranalysis.io.output.bean
Beans for the framework around writing files to the file-system.
org.anchoranalysis.io.output.bean.enabled
Beans indicating whether a particular output is enabled or not.
org.anchoranalysis.io.output.bean.path.prefixer
Beans for generating paths for outputting files by adding a prefix, suffix etc.
org.anchoranalysis.io.output.bean.rules
Rules for determining if a particular output is enabled or not in a context of a hierarchy.
org.anchoranalysis.io.output.enabled
Non-beans pertaining to whether a particular output is enabled or not.
org.anchoranalysis.io.output.enabled.multi
Non-beans that pertain to whether multiple-levels have outputs that are enabled or not.
org.anchoranalysis.io.output.enabled.single
Non-beans that pertain to whether a single level has outputs that are enabled or not.
org.anchoranalysis.io.output.error
Exceptions that may be thrown when writing files to the file-system.
org.anchoranalysis.io.output.namestyle
Methods of naming a file with an index in the file-name.
org.anchoranalysis.io.output.outputter
Classes for outputting to particular directories.
org.anchoranalysis.io.output.outputter.directory
BoundDirectory and related classes.
org.anchoranalysis.io.output.path.prefixer
Non-beans for generating paths for outputting files by adding a prefix, suffix etc.
org.anchoranalysis.io.output.recorded
Classes for recording the output-names used as they are written / queried.
org.anchoranalysis.io.output.writer
Allows a generators to write element(s) to the filesystem.
org.anchoranalysis.io.output.xml
Outputting XML to the file-system.
org.anchoranalysis.launcher
Parent package and entry-point classes for the Anchor command-line launcher application.
org.anchoranalysis.launcher.config
Specifies a configuration of the launcher for a particular application.
org.anchoranalysis.launcher.executor
Runs a particular experiment after identifying necessary paths and input files.
org.anchoranalysis.launcher.executor.selectparam
Different methods of selecting a object T that is used as a parameter for an experiment.
org.anchoranalysis.launcher.executor.selectparam.experiment
SelectParams for loading a Experiment.
org.anchoranalysis.launcher.executor.selectparam.path
SelectParams for loading a Optional<Path> for inputs, outputs or tasks.
org.anchoranalysis.launcher.executor.selectparam.path.convert
Converting paths to/from different formats as needed by org.anchoranalysis.launcher.executor.selectparam.path.
org.anchoranalysis.launcher.options
A centralized location for all command-line options used by the launcher.
org.anchoranalysis.launcher.options.outputs
Adding/removing/changing the output(s) from the experiment via command-line-options.
org.anchoranalysis.launcher.resources
Reading and integrating resources for the launcher.
org.anchoranalysis.launcher.run
Parses command-line arguments and runs an experiment.
org.anchoranalysis.launcher.run.tasks
Loading and displaying pre-defined tasks.
org.anchoranalysis.math.arithmetic
Performing primitive type conversion, counting and summing.
org.anchoranalysis.math.equation
Solving or manipulating equations.
org.anchoranalysis.math.histogram
The Histogram data class and related operations.
org.anchoranalysis.math.optimization
org.anchoranalysis.math.relation
Different kinds of binary-relations.
org.anchoranalysis.math.statistics
Data structures and algorithms to calculate statistics.
org.anchoranalysis.math.statistics.moment
Calculates first and second image moments from a covariance matrix of points.
org.anchoranalysis.mpp.bean  
org.anchoranalysis.mpp.bean.anneal  
org.anchoranalysis.mpp.bean.bound  
org.anchoranalysis.mpp.bean.init  
org.anchoranalysis.mpp.bean.mark  
org.anchoranalysis.mpp.bean.mark.bounds  
org.anchoranalysis.mpp.bean.mark.factory  
org.anchoranalysis.mpp.bean.points  
org.anchoranalysis.mpp.bean.points.fitter  
org.anchoranalysis.mpp.bean.points.updatable  
org.anchoranalysis.mpp.bean.proposer  
org.anchoranalysis.mpp.bean.proposer.radii  
org.anchoranalysis.mpp.bean.provider  
org.anchoranalysis.mpp.bean.regionmap  
org.anchoranalysis.mpp.bound  
org.anchoranalysis.mpp.feature.addcriteria  
org.anchoranalysis.mpp.feature.bean.energy.element  
org.anchoranalysis.mpp.feature.bean.energy.scheme  
org.anchoranalysis.mpp.feature.bean.mark  
org.anchoranalysis.mpp.feature.bean.mark.collection  
org.anchoranalysis.mpp.feature.energy  
org.anchoranalysis.mpp.feature.energy.marks  
org.anchoranalysis.mpp.feature.energy.saved  
org.anchoranalysis.mpp.feature.energy.scheme  
org.anchoranalysis.mpp.feature.error  
org.anchoranalysis.mpp.feature.input.memo  
org.anchoranalysis.mpp.feature.mark  
org.anchoranalysis.mpp.io.bean.input  
org.anchoranalysis.mpp.io.bean.report.feature  
org.anchoranalysis.mpp.io.input  
org.anchoranalysis.mpp.io.marks  
org.anchoranalysis.mpp.io.marks.generator  
org.anchoranalysis.mpp.io.output  
org.anchoranalysis.mpp.mark  
org.anchoranalysis.mpp.mark.conic  
org.anchoranalysis.mpp.mark.points  
org.anchoranalysis.mpp.mark.set  
org.anchoranalysis.mpp.mark.voxelized  
org.anchoranalysis.mpp.mark.voxelized.memo  
org.anchoranalysis.mpp.overlap  
org.anchoranalysis.mpp.overlay  
org.anchoranalysis.mpp.pair  
org.anchoranalysis.mpp.points  
org.anchoranalysis.mpp.probmap  
org.anchoranalysis.mpp.proposer  
org.anchoranalysis.mpp.proposer.error  
org.anchoranalysis.mpp.proposer.visualization  
org.anchoranalysis.mpp.segment.bean
Beans for segmentation algorithms related to marked-point-processes.
org.anchoranalysis.mpp.segment.bean.define
DefineOutputter and its sub-classes.
org.anchoranalysis.mpp.segment.bean.kernel
Base classes for kernels that transition a configuration of marks (a MarkCollection) into an altered version.
org.anchoranalysis.mpp.segment.bean.kernel.proposer  
org.anchoranalysis.mpp.segment.bean.optimization  
org.anchoranalysis.mpp.segment.bean.optimization.feedback  
org.anchoranalysis.mpp.segment.bean.optimization.termination  
org.anchoranalysis.mpp.segment.define  
org.anchoranalysis.mpp.segment.kernel  
org.anchoranalysis.mpp.segment.kernel.proposer  
org.anchoranalysis.mpp.segment.optimization  
org.anchoranalysis.mpp.segment.optimization.feedback  
org.anchoranalysis.mpp.segment.optimization.feedback.aggregate  
org.anchoranalysis.mpp.segment.optimization.feedback.period  
org.anchoranalysis.mpp.segment.optimization.step  
org.anchoranalysis.mpp.segment.transformer  
org.anchoranalysis.mpp.voxel.partition  
org.anchoranalysis.mpp.voxel.partition.factory  
org.anchoranalysis.overlay
Overlays and related classes involving drawing entities on top of an image.
org.anchoranalysis.overlay.bean
Beans relating to drawing an Overlay on an image.
org.anchoranalysis.overlay.collection
Collections of Overlays.
org.anchoranalysis.overlay.identifier
Uniquely identifying an Overlay.
org.anchoranalysis.overlay.object
An implementation of an Overlay that draws an ObjectMask on an image.
org.anchoranalysis.overlay.object.scaled
Creates a scaled version of ObjectMask to use as an overlay.
org.anchoranalysis.overlay.writer
Drawing an overlay on an image.
org.anchoranalysis.plot
Plotting data on charts.
org.anchoranalysis.plot.bean
Beans for plotting.
org.anchoranalysis.plot.bean.colorscheme
Color schemes associated with plots.
org.anchoranalysis.plot.index
Non-bean plot definitions.
org.anchoranalysis.plugin.annotation.bean.aggregate
Beans to combine two or more annotations.
org.anchoranalysis.plugin.annotation.bean.comparer
Comparing the similarity of annotations from two images to each other.
org.anchoranalysis.plugin.annotation.bean.comparison
Task to compare a set of annotations to a segmentation or another set of annotations.
org.anchoranalysis.plugin.annotation.bean.comparison.assigner
Pairs annotations from two different sets, creating an assignment of some type.
org.anchoranalysis.plugin.annotation.bean.file
FilesProviders for providing annotations.
org.anchoranalysis.plugin.annotation.bean.label
A label as used for annotating.
org.anchoranalysis.plugin.annotation.bean.strategy
Strategies for how to annotate an image, such label per image etc.
org.anchoranalysis.plugin.annotation.comparison
Non-bean classes for comparing two sets of annotations.
org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction
Morphological grayscale-reconstruction algorithm.
org.anchoranalysis.plugin.fiji.bean.channel.provider
Implementations of ChannelProvider that use FIJI.
org.anchoranalysis.plugin.fiji.bean.channel.provider.distance
Euclidean Distance Transform implementations via FIJI.
org.anchoranalysis.plugin.fiji.bean.define
Implementations of DefineAdderBean that use FIJI.
org.anchoranalysis.plugin.fiji.bean.mask.provider
Implementations of MaskProvider that use FIJI.
org.anchoranalysis.plugin.fiji.bean.threshold
Implementations of Thresholder that use FIJI.
org.anchoranalysis.plugin.image.bean.blur
Filters that perform blurring.
org.anchoranalysis.plugin.image.bean.box
Bounding box manipulation.
org.anchoranalysis.plugin.image.bean.channel.convert  
org.anchoranalysis.plugin.image.bean.channel.convert.histogram  
org.anchoranalysis.plugin.image.bean.channel.provider  
org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic  
org.anchoranalysis.plugin.image.bean.channel.provider.assign  
org.anchoranalysis.plugin.image.bean.channel.provider.convert  
org.anchoranalysis.plugin.image.bean.channel.provider.gradient  
org.anchoranalysis.plugin.image.bean.channel.provider.intensity  
org.anchoranalysis.plugin.image.bean.channel.provider.mask  
org.anchoranalysis.plugin.image.bean.channel.provider.object  
org.anchoranalysis.plugin.image.bean.channel.provider.score  
org.anchoranalysis.plugin.image.bean.channel.provider.slice  
org.anchoranalysis.plugin.image.bean.color.provider  
org.anchoranalysis.plugin.image.bean.dimensions.provider  
org.anchoranalysis.plugin.image.bean.histogram.provider  
org.anchoranalysis.plugin.image.bean.histogram.threshold  
org.anchoranalysis.plugin.image.bean.mask.provider  
org.anchoranalysis.plugin.image.bean.mask.provider.combine  
org.anchoranalysis.plugin.image.bean.mask.provider.convert  
org.anchoranalysis.plugin.image.bean.mask.provider.dimensions  
org.anchoranalysis.plugin.image.bean.mask.provider.morphological  
org.anchoranalysis.plugin.image.bean.mask.provider.predicate  
org.anchoranalysis.plugin.image.bean.mask.provider.resize  
org.anchoranalysis.plugin.image.bean.mask.provider.segment  
org.anchoranalysis.plugin.image.bean.mask.provider.slice  
org.anchoranalysis.plugin.image.bean.object.filter  
org.anchoranalysis.plugin.image.bean.object.filter.combine  
org.anchoranalysis.plugin.image.bean.object.filter.dependent  
org.anchoranalysis.plugin.image.bean.object.filter.independent  
org.anchoranalysis.plugin.image.bean.object.match  
org.anchoranalysis.plugin.image.bean.object.provider  
org.anchoranalysis.plugin.image.bean.object.provider.connected  
org.anchoranalysis.plugin.image.bean.object.provider.feature  
org.anchoranalysis.plugin.image.bean.object.provider.filter  
org.anchoranalysis.plugin.image.bean.object.provider.mask  
org.anchoranalysis.plugin.image.bean.object.provider.merge  
org.anchoranalysis.plugin.image.bean.object.provider.morphological  
org.anchoranalysis.plugin.image.bean.object.provider.segment  
org.anchoranalysis.plugin.image.bean.object.provider.slice  
org.anchoranalysis.plugin.image.bean.object.provider.split  
org.anchoranalysis.plugin.image.bean.object.segment.channel  
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima  
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction  
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong  
org.anchoranalysis.plugin.image.bean.object.segment.reduce
Strategies for reducing the number of elements with a list by merging/removing lower-confidence elements that overlap.
org.anchoranalysis.plugin.image.bean.object.segment.stack
Instance-segmentation of a Stack.
org.anchoranalysis.plugin.image.bean.params  
org.anchoranalysis.plugin.image.bean.scale
Implementations of ScaleCalculator for calculating a scaling-factor from dimensions.
org.anchoranalysis.plugin.image.bean.segment.binary  
org.anchoranalysis.plugin.image.bean.stack.provider  
org.anchoranalysis.plugin.image.bean.stack.provider.color  
org.anchoranalysis.plugin.image.bean.stack.provider.plot  
org.anchoranalysis.plugin.image.bean.thumbnail.object  
org.anchoranalysis.plugin.image.bean.thumbnail.stack  
org.anchoranalysis.plugin.image.box
Non-beans pertaining to bounding-boxes.
org.anchoranalysis.plugin.image.channel  
org.anchoranalysis.plugin.image.feature.bean.dimensions  
org.anchoranalysis.plugin.image.feature.bean.histogram.statistic  
org.anchoranalysis.plugin.image.feature.bean.histogram.threshold  
org.anchoranalysis.plugin.image.feature.bean.list.pair  
org.anchoranalysis.plugin.image.feature.bean.list.permute  
org.anchoranalysis.plugin.image.feature.bean.morphological  
org.anchoranalysis.plugin.image.feature.bean.object.collection  
org.anchoranalysis.plugin.image.feature.bean.object.combine  
org.anchoranalysis.plugin.image.feature.bean.object.pair  
org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap  
org.anchoranalysis.plugin.image.feature.bean.object.pair.touching  
org.anchoranalysis.plugin.image.feature.bean.object.single  
org.anchoranalysis.plugin.image.feature.bean.object.single.border  
org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox  
org.anchoranalysis.plugin.image.feature.bean.object.single.energy  
org.anchoranalysis.plugin.image.feature.bean.object.single.intensity  
org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient  
org.anchoranalysis.plugin.image.feature.bean.object.single.moments  
org.anchoranalysis.plugin.image.feature.bean.object.single.morphological  
org.anchoranalysis.plugin.image.feature.bean.object.single.shape  
org.anchoranalysis.plugin.image.feature.bean.object.single.shared  
org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting  
org.anchoranalysis.plugin.image.feature.bean.object.single.slice  
org.anchoranalysis.plugin.image.feature.bean.object.single.surface  
org.anchoranalysis.plugin.image.feature.bean.physical  
org.anchoranalysis.plugin.image.feature.bean.score  
org.anchoranalysis.plugin.image.feature.bean.shared  
org.anchoranalysis.plugin.image.feature.bean.shared.object  
org.anchoranalysis.plugin.image.feature.bean.stack.intensity  
org.anchoranalysis.plugin.image.feature.bean.stack.object  
org.anchoranalysis.plugin.image.feature.object  
org.anchoranalysis.plugin.image.feature.object.calculation.delegate  
org.anchoranalysis.plugin.image.feature.object.calculation.single  
org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological  
org.anchoranalysis.plugin.image.feature.stack.calculation  
org.anchoranalysis.plugin.image.intensity  
org.anchoranalysis.plugin.image.intensity.level  
org.anchoranalysis.plugin.image.object  
org.anchoranalysis.plugin.image.object.merge  
org.anchoranalysis.plugin.image.object.merge.condition  
org.anchoranalysis.plugin.image.object.merge.priority  
org.anchoranalysis.plugin.image.provider  
org.anchoranalysis.plugin.image.segment  
org.anchoranalysis.plugin.image.segment.thresholder.slice  
org.anchoranalysis.plugin.image.segment.watershed.encoding  
org.anchoranalysis.plugin.image.task.bean
A parent package for many different kinds of tasks.
org.anchoranalysis.plugin.image.task.bean.feature
Tasks pertaining to Features.
org.anchoranalysis.plugin.image.task.bean.feature.source
Source of rows in feature-tables with FeatureSource and derived classes.
org.anchoranalysis.plugin.image.task.bean.format
Tasks for converting image-formats.
org.anchoranalysis.plugin.image.task.bean.format.convertstyle
Different approaches for converting sets of channels (RGB, independently etc.) to another image format.
org.anchoranalysis.plugin.image.task.bean.grouped
Tasks that involved stacks (usually each channel from an image) that are somehow grouped-together.
org.anchoranalysis.plugin.image.task.bean.grouped.histogram
Task(s) to export histograms of intensity values.
org.anchoranalysis.plugin.image.task.bean.grouped.raster
Task(s) to calculate the mean of channels grouped together.
org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels
Selecting a subset of a set of channels.
org.anchoranalysis.plugin.image.task.bean.labeller
Associating labels with images.
org.anchoranalysis.plugin.image.task.bean.scale
Tasks to scale an image.
org.anchoranalysis.plugin.image.task.bean.segment
Tasks to segment an image.
org.anchoranalysis.plugin.image.task.bean.slice
Tasks that process on one or more slices from a z-stack.
org.anchoranalysis.plugin.image.task.feature
Non-bean classes pertaining to Features as used in tasks.
org.anchoranalysis.plugin.image.task.feature.calculator
Non-beans for calculating Features.
org.anchoranalysis.plugin.image.task.grouped
Non-bean classes about grouping channels or other inputs.
org.anchoranalysis.plugin.image.task.labeller
Non-bean classes about labelling images.
org.anchoranalysis.plugin.image.task.segment
Non-bean classes for image-segmentation.
org.anchoranalysis.plugin.image.task.stack
Non-bean classes pertaining to stacks and channels as used in tasks.
org.anchoranalysis.plugin.image.thumbnail
Non-bean classes for thumbnail creation.
org.anchoranalysis.plugin.imagej.bean.channel.provider  
org.anchoranalysis.plugin.imagej.bean.channel.provider.filter  
org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments  
org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank  
org.anchoranalysis.plugin.imagej.bean.define  
org.anchoranalysis.plugin.imagej.bean.interpolator  
org.anchoranalysis.plugin.imagej.bean.mask.provider  
org.anchoranalysis.plugin.imagej.bean.object.provider  
org.anchoranalysis.plugin.imagej.bean.object.segment  
org.anchoranalysis.plugin.imagej.bean.stack.provider  
org.anchoranalysis.plugin.imagej.bean.threshold  
org.anchoranalysis.plugin.imagej.channel.provider  
org.anchoranalysis.plugin.imagej.mask  
org.anchoranalysis.plugin.io.bean.channel.map  
org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod  
org.anchoranalysis.plugin.io.bean.copyfilesmode.naming  
org.anchoranalysis.plugin.io.bean.descriptivename  
org.anchoranalysis.plugin.io.bean.descriptivename.patternspan  
org.anchoranalysis.plugin.io.bean.filepath  
org.anchoranalysis.plugin.io.bean.filepath.prefixer  
org.anchoranalysis.plugin.io.bean.groupfiles  
org.anchoranalysis.plugin.io.bean.groupfiles.check  
org.anchoranalysis.plugin.io.bean.groupfiles.parser  
org.anchoranalysis.plugin.io.bean.input  
org.anchoranalysis.plugin.io.bean.input.channel  
org.anchoranalysis.plugin.io.bean.input.files  
org.anchoranalysis.plugin.io.bean.input.files.provider  
org.anchoranalysis.plugin.io.bean.input.filter  
org.anchoranalysis.plugin.io.bean.input.manifest  
org.anchoranalysis.plugin.io.bean.input.stack  
org.anchoranalysis.plugin.io.bean.path.derive  
org.anchoranalysis.plugin.io.bean.provider.file  
org.anchoranalysis.plugin.io.bean.stack.reader  
org.anchoranalysis.plugin.io.bean.stack.writer  
org.anchoranalysis.plugin.io.bean.summarizer  
org.anchoranalysis.plugin.io.bean.summarizer.image  
org.anchoranalysis.plugin.io.bean.summarizer.input  
org.anchoranalysis.plugin.io.bean.summarizer.path  
org.anchoranalysis.plugin.io.bean.task  
org.anchoranalysis.plugin.io.input.filter  
org.anchoranalysis.plugin.io.input.path  
org.anchoranalysis.plugin.io.manifest  
org.anchoranalysis.plugin.io.multifile  
org.anchoranalysis.plugin.io.multifile.buffer  
org.anchoranalysis.plugin.io.shared
Objects used in shared-state in tasks.
org.anchoranalysis.plugin.io.xml
Reading and writing metadata XML.
org.anchoranalysis.plugin.ml.bean.classifier
Beans that perform classification in some way.
org.anchoranalysis.plugin.ml.bean.cluster
Beans that perform clustering in some way.
org.anchoranalysis.plugin.mpp.bean.addcriteria  
org.anchoranalysis.plugin.mpp.bean.bound  
org.anchoranalysis.plugin.mpp.bean.check  
org.anchoranalysis.plugin.mpp.bean.define  
org.anchoranalysis.plugin.mpp.bean.distance  
org.anchoranalysis.plugin.mpp.bean.object.provider  
org.anchoranalysis.plugin.mpp.bean.outline  
org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler  
org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection  
org.anchoranalysis.plugin.mpp.bean.proposer.mark.single  
org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection  
org.anchoranalysis.plugin.mpp.bean.proposer.merge  
org.anchoranalysis.plugin.mpp.bean.proposer.orientation  
org.anchoranalysis.plugin.mpp.bean.proposer.points  
org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation  
org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline  
org.anchoranalysis.plugin.mpp.bean.proposer.position  
org.anchoranalysis.plugin.mpp.bean.proposer.radii  
org.anchoranalysis.plugin.mpp.bean.proposer.scalar  
org.anchoranalysis.plugin.mpp.bean.proposer.split  
org.anchoranalysis.plugin.mpp.bean.provider.collection  
org.anchoranalysis.plugin.mpp.bean.provider.single  
org.anchoranalysis.plugin.mpp.bean.region  
org.anchoranalysis.plugin.mpp.bean.segment.binary  
org.anchoranalysis.plugin.mpp.bean.stack.provider  
org.anchoranalysis.plugin.mpp.experiment  
org.anchoranalysis.plugin.mpp.experiment.bean  
org.anchoranalysis.plugin.mpp.experiment.bean.define  
org.anchoranalysis.plugin.mpp.experiment.bean.feature  
org.anchoranalysis.plugin.mpp.experiment.bean.feature.report  
org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task  
org.anchoranalysis.plugin.mpp.experiment.bean.feature.source  
org.anchoranalysis.plugin.mpp.experiment.bean.objects  
org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition  
org.anchoranalysis.plugin.mpp.experiment.bean.segment  
org.anchoranalysis.plugin.mpp.experiment.objects  
org.anchoranalysis.plugin.mpp.experiment.objects.csv  
org.anchoranalysis.plugin.mpp.feature.bean.mark.collection  
org.anchoranalysis.plugin.mpp.feature.bean.mark.direction  
org.anchoranalysis.plugin.mpp.feature.bean.mark.radii  
org.anchoranalysis.plugin.mpp.feature.bean.mark.region  
org.anchoranalysis.plugin.mpp.feature.bean.memo.all  
org.anchoranalysis.plugin.mpp.feature.bean.memo.ind  
org.anchoranalysis.plugin.mpp.feature.bean.memo.pair  
org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance  
org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap  
org.anchoranalysis.plugin.mpp.feature.bean.unit  
org.anchoranalysis.plugin.mpp.feature.overlap  
org.anchoranalysis.plugin.mpp.segment  
org.anchoranalysis.plugin.mpp.segment.bean.annealing  
org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark  
org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent  
org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized  
org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer  
org.anchoranalysis.plugin.mpp.segment.bean.marks  
org.anchoranalysis.plugin.mpp.segment.bean.marks.dual  
org.anchoranalysis.plugin.mpp.segment.bean.marks.partition  
org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized  
org.anchoranalysis.plugin.mpp.segment.bean.marks.weight  
org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract  
org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge  
org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode  
org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter  
org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme  
org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter  
org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination  
org.anchoranalysis.plugin.mpp.segment.kernel.assigner  
org.anchoranalysis.plugin.mpp.segment.kernel.updater  
org.anchoranalysis.plugin.mpp.segment.optimization  
org.anchoranalysis.plugin.opencv  
org.anchoranalysis.plugin.opencv.bean.color  
org.anchoranalysis.plugin.opencv.bean.feature  
org.anchoranalysis.plugin.opencv.bean.object.segment.stack  
org.anchoranalysis.plugin.opencv.bean.stack
Implementations of StackWriter and StackReader that involve OpenCV.
org.anchoranalysis.plugin.opencv.convert  
org.anchoranalysis.plugin.operator.feature.bean  
org.anchoranalysis.plugin.operator.feature.bean.arithmetic  
org.anchoranalysis.plugin.operator.feature.bean.conditional  
org.anchoranalysis.plugin.operator.feature.bean.list  
org.anchoranalysis.plugin.operator.feature.bean.range  
org.anchoranalysis.plugin.operator.feature.bean.range.feature  
org.anchoranalysis.plugin.operator.feature.bean.replace  
org.anchoranalysis.plugin.operator.feature.bean.score  
org.anchoranalysis.plugin.operator.feature.physical  
org.anchoranalysis.plugin.operator.feature.score  
org.anchoranalysis.plugin.points.bean.contour  
org.anchoranalysis.plugin.points.bean.feature.object.conic  
org.anchoranalysis.plugin.points.bean.fitter  
org.anchoranalysis.plugin.points.bean.mark.proposer.single  
org.anchoranalysis.plugin.points.bean.mark.provider.collection  
org.anchoranalysis.plugin.points.bean.mark.provider.single  
org.anchoranalysis.plugin.points.bean.mask.provider  
org.anchoranalysis.plugin.points.bean.provider.object  
org.anchoranalysis.plugin.points.calculate  
org.anchoranalysis.plugin.points.calculate.ellipse  
org.anchoranalysis.plugin.points.calculate.ellipsoid  
org.anchoranalysis.plugin.points.contour  
org.anchoranalysis.plugin.points.convexhull  
org.anchoranalysis.plugin.quick.bean.experiment  
org.anchoranalysis.plugin.quick.bean.file.path.derive  
org.anchoranalysis.plugin.quick.bean.input  
org.anchoranalysis.plugin.quick.bean.input.filepathappend  
org.anchoranalysis.plugin.quick.bean.structure  
org.anchoranalysis.spatial
Classes for geometry or other mathematical operations in Euclidian space.
org.anchoranalysis.spatial.axis
Identifying the three standard axes in 3D cartesian coordinates.
org.anchoranalysis.spatial.box
Axis-aligned bounding-boxes and related operations.
org.anchoranalysis.spatial.point
A cartesian-coordinate, across varying primitive types, in 2D and 3D space.
org.anchoranalysis.spatial.point.consumer
Functional interfaces that accept cartesian coordinate points specified in different ways.
org.anchoranalysis.spatial.rotation
A matrix to apply a rotation to a point.
org.anchoranalysis.spatial.rotation.factory
Creates RotationMatrix in varying ways.
org.anchoranalysis.spatial.rtree
R-Tree data structure and related operations.
org.anchoranalysis.spatial.scale
How to much to scale an entity in Cartesian space by.
org.anchoranalysis.test
Testing utilities and fixtures with no greater downstream dependency than anchor-core.
org.anchoranalysis.test.experiment
Testing utilities and fixtures with no greater downstream dependency than anchor-experiment or anchor-mpp or anchor-mpp-io.
org.anchoranalysis.test.experiment.launcher
Launches an anchor binary from a shell and runs an experiment.
org.anchoranalysis.test.feature
Testing utilities and fixtures with no greater downstream dependency than anchor-feature.
org.anchoranalysis.test.feature.plugins
Testing utilities and fixtures with no greater downstream dependency than anchor-image-feature or anchor-mpp.
org.anchoranalysis.test.feature.plugins.mockfeature
A mocked feature internally using a feature-calculation.
org.anchoranalysis.test.feature.plugins.objects
Fixtures for creating object-masks and related feature-inputs.
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Copyright © 2010–2021 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.