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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.comparer
Non-bean classes involving comparing results and annotations.
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.parameters
Some parameterization used when initializing beans.
org.anchoranalysis.bean.initializable.property
Initializating a bean with parameters.
org.anchoranalysis.bean.permute
Applying permutations to a bean's fields.
org.anchoranalysis.bean.permute.assign
Imposes a permutation value on one or more properties of a bean.
org.anchoranalysis.bean.permute.property
Applying permutations to the properties of a bean.
org.anchoranalysis.bean.primitive
Beans that implement collections of primitive element types, as well as String.
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.creator
Creates beans from XML.
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.bean.xml.factory.primitive
Factories to create beans in org.anchoranalysis.bean.primitive.
org.anchoranalysis.core.cache
Caching (memozing) calls to a method so an operation does not need to be repeated.
org.anchoranalysis.core.collection
Collection-related classes with general applicability that don't belong elsewhere.
org.anchoranalysis.core.color
Specifying particular colors and groups of colors.
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.functional.unchecked
Adds additional functional-interfaces, that are unavailable in java.util.function, and do not 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.range
A range of indices from minimum to maximum.
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.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.time
Recording the execution-time of operations for profiling.
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.experiment.time
How long particular operations take to execute.
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.bound
Interfaces like FeatureCalculator but bound to particular features.
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.calculate.cache.part
Equivalent classes to org.anchoranalysis.feature.calculate.part after having been resolved against a cache.
org.anchoranalysis.feature.calculate.part
A sub-part of the calculation of a feature, that can be cached, and reused by other features.
org.anchoranalysis.feature.energy
A particular stack used in feature-calculations called a EnergyStack together with related classes.
org.anchoranalysis.feature.initialization
Initialization parameters used for beans in org.anchoranalysis.feature.bean.
org.anchoranalysis.feature.input
Base classes providing inputs to feature calculations.
org.anchoranalysis.feature.io.csv
Metadata for writing feature calculation-results in CSV format.
org.anchoranalysis.feature.io.csv.metadata
Writing the results of feature calculations to the file-system.
org.anchoranalysis.feature.io.csv.results
Writing the results from feature-calculation to a CSV file.
org.anchoranalysis.feature.io.csv.table
A Generator for writing a table of feature values as a CSV.
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 LabelledResultsCollector.
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 FeatureCalculationCache 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
Base classes for methods to calculate results from features.
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
Base classes for performing operations on Channels.
org.anchoranalysis.image.bean.displayer  
org.anchoranalysis.image.bean.interpolator
Beans for specifying image interpolators.
org.anchoranalysis.image.bean.nonbean
Classes that are used elsewhere in this package but which aren't themselves AnchorBeans.
org.anchoranalysis.image.bean.nonbean.init
Classes that aren't AnchorBeans that pertain to the initialization of image-related beans.
org.anchoranalysis.image.bean.nonbean.segment
Non-bean classes relating to image-segmentation.
org.anchoranalysis.image.bean.nonbean.spatial.align
Non-bean classes to help specify the position of one entity relative to the others.
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.arrange.align
Aligning a BoundingBox to fit inside another BoundingBox.
org.anchoranalysis.image.bean.spatial.arrange.fill
Montages images together to completely fill the available space, while preserving aspect ratio.
org.anchoranalysis.image.bean.spatial.arrange.overlay
Combining other images through overlaying.
org.anchoranalysis.image.bean.spatial.arrange.tile
Combining other images through tiling.
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.contour
Finds outline voxels, the pixels on the contour/edge of the object.
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.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.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.scale.method
Scaling elements with an associated ObjectMask either collectively or independently.
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.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 CalculationPart 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.inference
Inference of machine learning models on images.
org.anchoranalysis.image.inference.bean.reduce
Beans to reduce the number of results that are returned from inference, by removing overlaping entities etc.
org.anchoranalysis.image.inference.bean.segment.instance
org.anchoranalysis.image.inference.bean.segment.reduce
Non-bean classes to reduce the number of results that are returned from inference, by removing overlapping entities etc.
org.anchoranalysis.image.inference.segment
Non-beans pertaining to segmentation of images via model inference.
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.metadata.reader
Bean classes for reading ImageMetadata from the file-system.
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.map
Non-bean classes for a mapping of names to Channels.
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.io.stack.time
A time-sequence of Stacks.
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.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.bufferedimage
Converts anchor data-structures to the BufferedImage used by Java's AWT.
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 VoxelsUntyped with specific data-types.
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.projection
Classes for calculating differnet kind of projections of voxel values across multiple buffers.
org.anchoranalysis.image.voxel.projection.extrema
Classes for performing both a Maximum Intensity Projection and a minimum projection.
org.anchoranalysis.image.voxel.resizer
Different interpolator methods to use when scaling voxels.
org.anchoranalysis.image.voxel.statistics
Statistics about aggregated voxel intensities.
org.anchoranalysis.image.voxel.thresholder
Thresholding operations on voxels.
org.anchoranalysis.inference
High-level classes for performing machine learning model inference.
org.anchoranalysis.inference.concurrency
Specifying how many CPUs and GPUs can be allocated for some purpose.
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.bioformats.metadata
Reading metadata information from files using EXIF and/or other metadata headers.
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.interpolator
Performing interpolation with ImageJ.
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.imagej.resizer
Image interpolation when scaling using ImageJ.
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.dictionary
Methods to provide a Dictionary.
org.anchoranalysis.io.input.bean.files
Methods to provide a collection of Files.
org.anchoranalysis.io.input.bean.grouper
Determines how inputs are aggregated into groups, if at all.
org.anchoranalysis.io.input.bean.namer
Beans to derive names (compact unique identifiers) from 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.file
Non-bean classes that relate to using files during inputting.
org.anchoranalysis.io.input.grouper
Non-bean classes pertaining grouping inputs.
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.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.process
Adding/removing/changing the arguments (input and output) 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
Beans pertaining to marked-point-processes.
org.anchoranalysis.mpp.bean.bound
Lower and upper limits set around variables.
org.anchoranalysis.mpp.bean.bound.rotation
Bounds on how to rotate an entity in Euclidean space.
org.anchoranalysis.mpp.bean.mark
Beans generally related to Marks.
org.anchoranalysis.mpp.bean.mark.factory
Beans related to creating Marks.
org.anchoranalysis.mpp.bean.points
Operations based on sets of points.
org.anchoranalysis.mpp.bean.points.fitter
Fitting structures to sets of points.
org.anchoranalysis.mpp.bean.proposer
Proposing Marks or other data-structures with particular attributes.
org.anchoranalysis.mpp.bean.provider
Implementations of Provider involving Marks.
org.anchoranalysis.mpp.bean.regionmap
Voxel subregions of Marks.
org.anchoranalysis.mpp.feature.addcriteria
Criteria for adding edges during optimization of marked-point-processes.
org.anchoranalysis.mpp.feature.bean.energy.element
Implementations and helper classes for calculating energy during an energy-minimization optimization scheme.
org.anchoranalysis.mpp.feature.bean.energy.scheme
Creating EnergySchemes.
org.anchoranalysis.mpp.feature.bean.mark
Features calculated on a Mark.
org.anchoranalysis.mpp.feature.bean.mark.collection
Features calculated on a org.anchoranalysis.mpp.feature.bean.mark.collection.
org.anchoranalysis.mpp.feature.energy
Non-bean classes pertaining to calculating energy during an energy-minimization optimization scheme.
org.anchoranalysis.mpp.feature.energy.marks
Non-bean classes pertaining to calculating energy of {org.anchoranalysis.mpp.mark.Mark}s.
org.anchoranalysis.mpp.feature.energy.saved
Saved snapshots of energy-calculations.
org.anchoranalysis.mpp.feature.energy.scheme
Factorized form of storing the energy during an energy-minimization optimization scheme.
org.anchoranalysis.mpp.feature.error
Exceptions relating to Features involving classes from anchor-mpp.
org.anchoranalysis.mpp.feature.input
Inputs to mark-point-processes related Features.
org.anchoranalysis.mpp.feature.mark
Non-bean classes for calculating feature-values related to Marks.
org.anchoranalysis.mpp.index
Indexing voxel-values in different ways.
org.anchoranalysis.mpp.index.factory
Factories for classes in org.anchoranalysis.mpp.index.
org.anchoranalysis.mpp.init
Parameters used to initialize certain types of beans.
org.anchoranalysis.mpp.io.bean.input
Beans for reading data structures related to marked point processes from the file system.
org.anchoranalysis.mpp.io.bean.report.feature
Beans for communicating feature-values from data-structures in human-readable manner.
org.anchoranalysis.mpp.io.input
Non-beans for reading data structures related to marked point processes from the file system.
org.anchoranalysis.mpp.io.marks
Non-beans to help write visualization of Marks to the filesystem.
org.anchoranalysis.mpp.io.marks.generator
Generator base classes to help write visualization of Marks to the filesystem.
org.anchoranalysis.mpp.io.output
Non-beans for writing data structures related to marked point processes from the file system.
org.anchoranalysis.mpp.mark
Non-bean classes related to Marks.
org.anchoranalysis.mpp.mark.conic
Marks implementing conic sections.
org.anchoranalysis.mpp.mark.points
Marks implementing structures based on points.
org.anchoranalysis.mpp.mark.voxelized
A mark after a voxel-representation has been inferred.
org.anchoranalysis.mpp.mark.voxelized.memo
Memoization of VoxelizedMarks.
org.anchoranalysis.mpp.overlap
Calculating overlaps between two Marks.
org.anchoranalysis.mpp.overlay
Any Overlay related to a Mark.
org.anchoranalysis.mpp.pair
Pairs of Marks.
org.anchoranalysis.mpp.proposer
Non-bean classes for proposing Marks or other data-structures with particular attributes.
org.anchoranalysis.mpp.proposer.error
Recording errors related to proposing Marks or other data-structures with particular attributes.
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.optimization
Schemes for finding optima (minima or maxima) via optimization.
org.anchoranalysis.mpp.segment.bean.optimization.feedback
Providing feedback on the progress of a OptimizationScheme.
org.anchoranalysis.mpp.segment.bean.optimization.kernel
Base classes for kernels that transition a configuration of marks (a MarkCollection) into an altered version.
org.anchoranalysis.mpp.segment.bean.optimization.termination
In which circumstances to terminate an OptimizationScheme that is underway.
org.anchoranalysis.mpp.segment.define
Non-bean classes used in org.anchoranalysis.mpp.segment.bean.define
org.anchoranalysis.mpp.segment.optimization
Non-bean classes used in org.anchoranalysis.mpp.segment.bean.optimization
org.anchoranalysis.mpp.segment.optimization.feedback
Non-bean classes used in org.anchoranalysis.mpp.segment.bean.optimization.feedback
org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
Aggregating optimization feedback over time.
org.anchoranalysis.mpp.segment.optimization.feedback.period
Collecting optimization feedback periodically.
org.anchoranalysis.mpp.segment.optimization.kernel
Non-bean classes used in org.anchoranalysis.mpp.segment.bean.optimization.kernel
org.anchoranalysis.mpp.segment.optimization.step
Describes an individual step in the optimization.
org.anchoranalysis.mpp.segment.transformer
Mapping one type of optimization state to another.
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.object
An implementation of an Overlay that draws an ObjectMask on an image.
org.anchoranalysis.overlay.writer
Drawing an overlay on an image.
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.annotation.counter
Utility classes for counting images incrementally.
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.channel.aggregator
org.anchoranalysis.plugin.image.bean.channel.convert
org.anchoranalysis.plugin.image.bean.channel.provider
Implementations of ChannelProvider that are generic base-classes or otherwise abstract or general.
org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
Implementations of ChannelProvider that perform arithmetic on voxels in one or more Channels.
org.anchoranalysis.plugin.image.bean.channel.provider.assign
Implementations of ChannelProvider that sets the values of the voxels in a Channel.
org.anchoranalysis.plugin.image.bean.channel.provider.convert
Implementations of ChannelProvider that converts a Channel from one voxel-type to another.
org.anchoranalysis.plugin.image.bean.channel.provider.gradient
Implementations of ChannelProvider that calculate the gradient of a Channel's voxels in one or more dimensions.
org.anchoranalysis.plugin.image.bean.channel.provider.intensity
Implementations of ChannelProvider that manipulate the intensity-values of the voxels of a Channel's voxels.
org.anchoranalysis.plugin.image.bean.channel.provider.mask
Implementations of ChannelProvider that involve conversion from or application of Masks.
org.anchoranalysis.plugin.image.bean.channel.provider.object
Implementations of ChannelProvider that involve conversion from or application of ObjectMasks.
org.anchoranalysis.plugin.image.bean.channel.provider.score
Implementations of ChannelProvider that assign a score to particular subregions of a channel.
org.anchoranalysis.plugin.image.bean.channel.provider.slice
Implementations of ChannelProvider that process 3D channels slice-by-slice.
org.anchoranalysis.plugin.image.bean.color.provider
Implementations of ColorProvider.
org.anchoranalysis.plugin.image.bean.dictionary
Beans pertaining to Dictionary.
org.anchoranalysis.plugin.image.bean.dimensions.provider
Implementations of DimensionsProvider.
org.anchoranalysis.plugin.image.bean.histogram.provider
Implementations of HistogramProvider.
org.anchoranalysis.plugin.image.bean.histogram.threshold
Thresholding of intensity values represented in at Histogram.
org.anchoranalysis.plugin.image.bean.mask.provider
Implementations of MaskProvider.
org.anchoranalysis.plugin.image.bean.mask.provider.combine
Implementations of MaskProvider that combine existing providers.
org.anchoranalysis.plugin.image.bean.mask.provider.convert
Implementations of MaskProvider that convert providers of other types to ObjectMasks.
org.anchoranalysis.plugin.image.bean.mask.provider.morphological
Implementations of MaskProvider that implement morphological operations.
org.anchoranalysis.plugin.image.bean.mask.provider.predicate
Provides if-else conditions to a MaskProvider.
org.anchoranalysis.plugin.image.bean.mask.provider.segment
Implementations of MaskProvider where an ObjectCollection is created by segmenting a Channel.
org.anchoranalysis.plugin.image.bean.mask.provider.slice
Implementations of MaskProvider that process 3D masks slice-by-slice.
org.anchoranalysis.plugin.image.bean.object.filter
Implementations of ObjectFilter.
org.anchoranalysis.plugin.image.bean.object.filter.collective
Implementations of ObjectFilter that assess each element in a collection collectively.
org.anchoranalysis.plugin.image.bean.object.filter.combine
Implementations of ObjectFilter that combine two or more other ObjectFilters.
org.anchoranalysis.plugin.image.bean.object.filter.independent
Implementations of ObjectFilter that independently assess each element in a collection.
org.anchoranalysis.plugin.image.bean.object.match
Implementations of ObjectMatcher.
org.anchoranalysis.plugin.image.bean.object.provider
Implementations of ObjectCollectionProvider.
org.anchoranalysis.plugin.image.bean.object.provider.connected
Implementations of ObjectCollectionProvider involving connected-components.
org.anchoranalysis.plugin.image.bean.object.provider.feature
Implementations of ObjectCollectionProvider involving feature calculation.
org.anchoranalysis.plugin.image.bean.object.provider.filter
Implementations of ObjectCollectionProvider that filter objects.
org.anchoranalysis.plugin.image.bean.object.provider.mask
Implementations of ObjectCollectionProvider involving a Mask.
org.anchoranalysis.plugin.image.bean.object.provider.merge
Implementations of ObjectCollectionProvider involving merging objects together.
org.anchoranalysis.plugin.image.bean.object.provider.morphological
Implementations of ObjectCollectionProvider involving morphological operations.
org.anchoranalysis.plugin.image.bean.object.provider.segment
Implementations of ObjectCollectionProvider involving segmentation.
org.anchoranalysis.plugin.image.bean.object.provider.slice
Implementations of ObjectCollectionProvider involving z-slice processing.
org.anchoranalysis.plugin.image.bean.object.provider.split
Implementations of ObjectCollectionProvider involving splitting objects into smaller objects.
org.anchoranalysis.plugin.image.bean.object.segment.channel
Implementations of SegmentChannelIntoObjects.
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima
Minima imposition for a Watershed transformation.
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction
Grayscale reconstruction to support the Watershed transformation.
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong
Implementation of a Watershed transformation based on Yeong et al.
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.scale
Implementations of ScaleCalculator for calculating a scaling-factor from dimensions.
org.anchoranalysis.plugin.image.bean.segment.binary
Implementations of BinarySegmentation.
org.anchoranalysis.plugin.image.bean.stack.provider
Implementations of StackProvider.
org.anchoranalysis.plugin.image.bean.stack.provider.color
Implementations of StackProvider that color portions of an image.
org.anchoranalysis.plugin.image.bean.thumbnail.object
Implementations of ThumbnailFromObjects.
org.anchoranalysis.plugin.image.bean.thumbnail.stack
Implementations of ThumbnailFromStack.
org.anchoranalysis.plugin.image.channel
Non-beans for operations or calculations relating to Channels.
org.anchoranalysis.plugin.image.feature.bean.dimensions
Features that are calculated from Dimensions.
org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
Implementations of FeatureHistogram that calculate statistics.
org.anchoranalysis.plugin.image.feature.bean.histogram.threshold
Implementations of FeatureHistogram that perform thresholding.
org.anchoranalysis.plugin.image.feature.bean.list
Implementations of FeatureListProvider.
org.anchoranalysis.plugin.image.feature.bean.list.pair
Implementations of FeatureListProvider with input-type FeatureInputPairObjects.
org.anchoranalysis.plugin.image.feature.bean.list.permute
Implementations of FeatureListProvider that derive new features with permuted property-values.
org.anchoranalysis.plugin.image.feature.bean.metadata
Implementations of FeatureImageMetadata.
org.anchoranalysis.plugin.image.feature.bean.morphological
Beans that affects how morphological operations occur.
org.anchoranalysis.plugin.image.feature.bean.object.collection
Implementations of FeatureObjectCollection.
org.anchoranalysis.plugin.image.feature.bean.object.combine
Features from combinations of ObjectMasks.
org.anchoranalysis.plugin.image.feature.bean.object.pair
Features from pairs of ObjectMasks.
org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
Features that calculate the degree of overlap between two ObjectMasks.
org.anchoranalysis.plugin.image.feature.bean.object.pair.touching
Features that calculate how many other objects an ObjectMask directly neighbors.
org.anchoranalysis.plugin.image.feature.bean.object.single
Implementations of FeatureSingleObject.
org.anchoranalysis.plugin.image.feature.bean.object.single.border
Implementations of FeatureSingleObject that determine if an object lies at the border of an image.
org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
Implementations of FeatureSingleObject that consider an object's bounding-box.
org.anchoranalysis.plugin.image.feature.bean.object.single.energy
Implementations of FeatureSingleObject that reference a particular Channel in the associated EnergyStack.
org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
Implementations of FeatureSingleObject that measure an object's intensity on a corresponding Channel.
org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient
Implementations of FeatureSingleObject that measure an object's gradient from corresponding Channels storing the gradient.
org.anchoranalysis.plugin.image.feature.bean.object.single.moments
Implementations of FeatureSingleObject based on calculating image moments, with or without image intensity.
org.anchoranalysis.plugin.image.feature.bean.object.single.morphological
Implementations of FeatureSingleObject that implement morphological operations.
org.anchoranalysis.plugin.image.feature.bean.object.single.shape
Implementations of FeatureSingleObject that measure the shape of the ObjectMask.
org.anchoranalysis.plugin.image.feature.bean.object.single.shared
Implementations of FeatureSingleObject that use SharedObjects for calculations.
org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
Implementations of FeatureSingleObject that use SharedObjects for calculations, and measure the degree of intersection between objects.
org.anchoranalysis.plugin.image.feature.bean.object.single.slice
Implementations of FeatureSingleObject that processes an object slice-by-slice in the z-dimension.
org.anchoranalysis.plugin.image.feature.bean.object.single.surface
Implementations of FeatureSingleObject that measures aspects of the surface of an ObjectMask.
org.anchoranalysis.plugin.image.feature.bean.physical
Beans involving physical units for measurement.
org.anchoranalysis.plugin.image.feature.bean.score
Implementations of VoxelScore.
org.anchoranalysis.plugin.image.feature.bean.shared
Beans involving SharedObjects.
org.anchoranalysis.plugin.image.feature.bean.shared.object
Beans involving SharedObjects and ObjectCollection.
org.anchoranalysis.plugin.image.feature.bean.stack.intensity
Implementations of FeatureStack or other features that involve processing a Stack.
org.anchoranalysis.plugin.image.feature.bean.stack.object
Implementations of FeatureStack that process an ObjectCollection.
org.anchoranalysis.plugin.image.feature.object
Non-bean classes that help calculate features from ObjectMasks.
org.anchoranalysis.plugin.image.feature.object.calculation.delegate
Implementations of CalculationPart as used by features elsewhere in this package.
org.anchoranalysis.plugin.image.feature.object.calculation.single
Implementations of CalculationPart that that process a single ObjectMask.
org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
Implementations of CalculationPart that that process a single ObjectMask - with morphological operations.
org.anchoranalysis.plugin.image.feature.stack.calculation
Implementations of CalculationPart that process Stacks as used by features elsewhere in this package.
org.anchoranalysis.plugin.image.intensity
Non-bean for operations or calculations relating to intensity.
org.anchoranalysis.plugin.image.intensity.level
Non-beans for calculating a thresholding level from itensity values.
org.anchoranalysis.plugin.image.object
Non-beans pertaining to ObjectMasks.
org.anchoranalysis.plugin.image.object.merge
Merging ObjectMasks.
org.anchoranalysis.plugin.image.object.merge.condition
Conditions for merging ObjectMasks.
org.anchoranalysis.plugin.image.object.merge.priority
Assigning priority when merging ObjectMasks.
org.anchoranalysis.plugin.image.provider
Non-bean classes pertaining to Providers.
org.anchoranalysis.plugin.image.segment.thresholder.slice
Non-beans pertaining to segmenting a z-stack slice-by-slice.
org.anchoranalysis.plugin.image.segment.watershed.encoding
Encoding voxels in a watershed-transformation implementation.
org.anchoranalysis.plugin.image.task.bean
A parent package for many different kinds of tasks.
org.anchoranalysis.plugin.image.task.bean.combine
Combining multiple images together into a single image.
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.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.channel.aggregator
Combines multiple Channels voxel-wise to form a single aggregated Channel.
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.size
Non-bean classes pertaining to determining the size of an image.
org.anchoranalysis.plugin.image.task.slice
Non-bean classes pertaining to combining stacks into a single stack.
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
Implementations of ChannelProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.bean.channel.provider.filter
org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments
Non-linear filters using ImageJ that use the statistical moments of the intensity values in the kernel.
org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank
Non-linear filters using ImageJ that use the statistical rank of the intensity values in the kernel.
org.anchoranalysis.plugin.imagej.bean.define
Implementations of DefineAdderBean that call ImageJ.
org.anchoranalysis.plugin.imagej.bean.mask.provider
Implementations of MaskProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.bean.object.provider
Implementations of ObjectCollectionProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.bean.object.segment
Implementations of ObjectCollectionProvider that call ImageJ to perform segmentation.
org.anchoranalysis.plugin.imagej.bean.stack.provider
Implementations of StackProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.bean.threshold
Implementations of Thresholder that call ImageJ.
org.anchoranalysis.plugin.imagej.channel.provider
Implementations of ChannelProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.mask
Non-bean classes involving ObjectMask that call ImageJ.
org.anchoranalysis.plugin.io.bean.channel.map
Implementations of ChannelMapCreator.
org.anchoranalysis.plugin.io.bean.file.copy.method
Methods for copying files on the file-system.
org.anchoranalysis.plugin.io.bean.file.copy.naming
Rules for preserving or changing the naming of files when copying on the file-system.
org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster
Implementations of CopyFilesNaming that perform clustering of files.
org.anchoranalysis.plugin.io.bean.file.group
Grouping files together so that they collectively represent a single entity.
org.anchoranalysis.plugin.io.bean.file.group.check
Tests that are applied when grouping files in org.anchoranalysis.plugin.io.bean.file.group
org.anchoranalysis.plugin.io.bean.file.group.parser
Parsing file-paths to determine file-grouping in org.anchoranalysis.plugin.io.bean.file.group
org.anchoranalysis.plugin.io.bean.file.namer
Implementations of FileNamer.
org.anchoranalysis.plugin.io.bean.file.namer.patternspan
Implementations of FileNamer that look for a pattern across many files.
org.anchoranalysis.plugin.io.bean.file.path
Beans to specify a file-path.
org.anchoranalysis.plugin.io.bean.file.path.prefixer
Implementations of PathPrefixer.
org.anchoranalysis.plugin.io.bean.file.pattern
Extracting a pattern from a file-path.
org.anchoranalysis.plugin.io.bean.file.provider
Implementations of FilesProvider.
org.anchoranalysis.plugin.io.bean.grouper
Implementations of Grouper.
org.anchoranalysis.plugin.io.bean.input
Implementations of InputManager.
org.anchoranalysis.plugin.io.bean.input.channel
InputManagers that accept a set of named-channels.
org.anchoranalysis.plugin.io.bean.input.files
InputManagers that accept a set of named-files.
org.anchoranalysis.plugin.io.bean.input.files.provider
Implementations of FilesProvider.
org.anchoranalysis.plugin.io.bean.input.filter
Implementations of InputManager that filter inputs.
org.anchoranalysis.plugin.io.bean.input.stack
Implementations of InputManager that process Stacks.
org.anchoranalysis.plugin.io.bean.metadata.header
Different types of image-file-formats whose headers can provide ImageMetadata.
org.anchoranalysis.plugin.io.bean.metadata.reader
Implementations of ImageMetadataReader.
org.anchoranalysis.plugin.io.bean.path.derive
Implementations of DerivePath.
org.anchoranalysis.plugin.io.bean.stack.reader
Implementations of StackReader.
org.anchoranalysis.plugin.io.bean.stack.writer
Implementations of StackWriter.
org.anchoranalysis.plugin.io.bean.summarizer
Summarizing a set of elements into a descriptive-string.
org.anchoranalysis.plugin.io.bean.summarizer.image
Implementations of Summarizer that summarize images.
org.anchoranalysis.plugin.io.bean.summarizer.input
Implementations of Summarizer that summarize generically InputFromManagers.
org.anchoranalysis.plugin.io.bean.summarizer.path
Implementations of Summarizer that summarize generically Paths.
org.anchoranalysis.plugin.io.bean.task
Implementations of Task related to file-system I/O.
org.anchoranalysis.plugin.io.file.copy
Non-bean classes to help tasks in org.anchoranalysis.plugin.io.bean.file.copy.
org.anchoranalysis.plugin.io.input.filter
Non-bean classes to help tasks in org.anchoranalysis.plugin.io.bean.input.filter.
org.anchoranalysis.plugin.io.input.path
Non-bean classes to help in processing paths.
org.anchoranalysis.plugin.io.multifile
Non-bean classes to help use multiple files to represent a single Stack.
org.anchoranalysis.plugin.io.multifile.buffer
Buffers used in org.anchoranalysis.plugin.io.multifile.
org.anchoranalysis.plugin.io.naming.interval
How to write parts of a time-interval in a file-name.
org.anchoranalysis.plugin.io.shared
Objects used in shared-state in Tasks in this plugin.
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
Implementations of AddCriteriaPair involving Mark or related classes.
org.anchoranalysis.plugin.mpp.bean.bound
Implementations of MarkBoundsProvider.
org.anchoranalysis.plugin.mpp.bean.check
Implementations of CheckMark.
org.anchoranalysis.plugin.mpp.bean.contour
Retrieving the contour outline pixels along the exterior outer contour of an ObjectMask.
org.anchoranalysis.plugin.mpp.bean.contour.visitscheduler
The VisitScheduler and related classes, as used in TraverseOuterContourOnImage.
org.anchoranalysis.plugin.mpp.bean.define
Beans related to Define involving Mark or related classes.
org.anchoranalysis.plugin.mpp.bean.object.provider
Implementations of ObjectCollectionProvider.
org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
Implementations of MarkCollectionProposer.
org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
Implementations of MarkProposer.
org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
Implementations of MarkFromCollectionProposer.
org.anchoranalysis.plugin.mpp.bean.proposer.merge
Implementations of MarkMergeProposer.
org.anchoranalysis.plugin.mpp.bean.proposer.orientation
Implementations of OrientationProposer.
org.anchoranalysis.plugin.mpp.bean.proposer.points
Implementations of PointsProposer.
org.anchoranalysis.plugin.mpp.bean.proposer.points.contour
Finding a point on the external outer contour of an ObjectMask.
org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation
PointsFromOrientationProposer and implementations.
org.anchoranalysis.plugin.mpp.bean.proposer.position
Implementations of PositionProposer involving Mark or related classes.
org.anchoranalysis.plugin.mpp.bean.proposer.radii
Implementations of RadiiProposer involving Mark or related classes.
org.anchoranalysis.plugin.mpp.bean.proposer.scalar
Implementations of ScalarProposer involving Mark or related classes.
org.anchoranalysis.plugin.mpp.bean.proposer.split
Implementations of MarkSplitProposer.
org.anchoranalysis.plugin.mpp.bean.provider.collection
Implementation of MarkCollectionProvider.
org.anchoranalysis.plugin.mpp.bean.provider.single
Implementations of SingleMarkProvider.
org.anchoranalysis.plugin.mpp.bean.region
Implementations of MarkRegion.
org.anchoranalysis.plugin.mpp.bean.segment.binary
Implementations of BinarySegmentation involving Mark or related classes.
org.anchoranalysis.plugin.mpp.bean.stack.provider
Implementations of StackProvider involving Mark or related classes.
org.anchoranalysis.plugin.mpp.contour
Performs a walk on every voxel on the contour of an object-mask.
org.anchoranalysis.plugin.mpp.contour.distance
A list of visited pixels which forms one contiguous path where each voxel neighbors each other.
org.anchoranalysis.plugin.mpp.contour.path
A set of contiguously neighboring points along the outline of an object.
org.anchoranalysis.plugin.mpp.contour.path.merge
Merging multiple ContiguousVoxelPath together.
org.anchoranalysis.plugin.mpp.contour.path.merge.strategy
Strategies on which ContiguousVoxelPath should be prioritized for merging.
org.anchoranalysis.plugin.mpp.experiment.bean.convert
Converting from NamedChannelsInput to the input-type expected by a Task.
org.anchoranalysis.plugin.mpp.experiment.bean.define
Tasks that use a DefineOutputter or related classes.
org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task
Tasks that calculate and export ReportFeatures.
org.anchoranalysis.plugin.mpp.experiment.bean.feature.source
Implementations of FeatureSource.
org.anchoranalysis.plugin.mpp.experiment.bean.objects
Tasks involving ObjectMasks.
org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition
Defining columns used in ExportObjectsFromCSV.
org.anchoranalysis.plugin.mpp.experiment.bean.segment
Tasks that segment an image to produce a MarkCollection.
org.anchoranalysis.plugin.mpp.experiment.objects
Non-bean classes used in org.anchoranalysis.plugin.mpp.experiment.bean.objects.
org.anchoranalysis.plugin.mpp.experiment.objects.csv
Reading rows from a CSV file.
org.anchoranalysis.plugin.mpp.experiment.shared
Shared-state use across tasks in this JAR.
org.anchoranalysis.plugin.mpp.feature.bean.mark.collection
Implementations of FeatureMarkCollection.
org.anchoranalysis.plugin.mpp.feature.bean.mark.direction
Implementations of FeatureMark to measure direction.
org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
Implementations of FeatureMark to measure or calculate radii.
org.anchoranalysis.plugin.mpp.feature.bean.mark.region
Implementations of FeatureMark to measure regions of Marks.
org.anchoranalysis.plugin.mpp.feature.bean.memo.all
Implementations of FeatureAllMemo.
org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
Implementations of FeatureSingleMemo.
org.anchoranalysis.plugin.mpp.feature.bean.memo.pair
Implementations of FeaturePairMemo.
org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance
Implementations of FeaturePairMemo to measure distance between Marks.
org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
Implementations of FeaturePairMemo to measure overlap between Marks.
org.anchoranalysis.plugin.mpp.feature.bean.unit
Beans to convert between units.
org.anchoranalysis.plugin.mpp.feature.overlap
Implementations of CalculationPart to calculate overlap between two entities.
org.anchoranalysis.plugin.mpp.segment.bean.annealing
Implementations of AnnealScheme.
org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark
Implementations of KernelBirth that are dependent.
org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
Implementations of KernelBirth that are independent.
org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.voxelized
Implementations of KernelBirth that are independent but use the voxelized state of a Mark.
org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer
Implementations of KernelProposerOption.
org.anchoranalysis.plugin.mpp.segment.bean.marks
Beans to perform segmentation involving Marks and related classes.
org.anchoranalysis.plugin.mpp.segment.bean.marks.dual
Implementations of StateTransformerBean involving DualVoxelizedMarks.
org.anchoranalysis.plugin.mpp.segment.bean.marks.partition
Implementations of StateTransformerBean involving MarksFromPartition.
org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized
Implementations of StateTransformerBean involving VoxelizedMarksWithEnergy.
org.anchoranalysis.plugin.mpp.segment.bean.marks.weight
Deriving a weight for a Mark.
org.anchoranalysis.plugin.mpp.segment.bean.optimization
Beans related to performing optimization with marked-point-processes.
org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract
Implementations of ExtractScoreSize.
org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge
KernelStateBridge and implementations.
org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode
AssignMode and implementations.
org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
Implementations of FeedbackReceiverBean.
org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme
Implementations of OptimizationScheme.
org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter
Implementations of StateReporter.
org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination
Implementations of TerminationCondition.
org.anchoranalysis.plugin.mpp.segment.kernel.assigner
Implementations of KernelAssigner.
org.anchoranalysis.plugin.mpp.segment.kernel.updater
KernelUpdater and implementations.
org.anchoranalysis.plugin.mpp.segment.optimization
Non-bean classes to help with optimization in org.anchoranalysis.plugin.mpp.segment.bean.optimization and sub-packages.
org.anchoranalysis.plugin.mpp.segment.shared
Stared-state for segmentation tasks involving mark-point-processes.
org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnn
Decodes the outputted tensors from a Mask R-CNN implementation.
org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.text
Decodes the outputted tensors from text-segmentation models.
org.anchoranalysis.plugin.onnx.bean.object.segment.stack
Segmenting a Stack using the ONNX Runtime to produce an ObjectCollection.
org.anchoranalysis.plugin.onnx.model
Non-bean classes for running an inference model with the ONNX Runtime.
org.anchoranalysis.plugin.opencv
Plugins that call OpenCV.
org.anchoranalysis.plugin.opencv.bean.color
Operations involving color-spaces and OpenCV.
org.anchoranalysis.plugin.opencv.bean.feature
Extracting features using OpenCV.
org.anchoranalysis.plugin.opencv.bean.interpolate
Interpolation beans that use OpenCV.
org.anchoranalysis.plugin.opencv.bean.object.segment.stack
Segmentation of a Stack using OpenCV.
org.anchoranalysis.plugin.opencv.bean.stack
Implementations of StackWriter and StackReader that involve OpenCV.
org.anchoranalysis.plugin.opencv.convert
Conversion to/from OpenCV data-structures.
org.anchoranalysis.plugin.opencv.resizer
Interpolation non-beans that use OpenCV.
org.anchoranalysis.plugin.opencv.segment
Non-bean classes pertaining to segmentation.
org.anchoranalysis.plugin.operator.feature.bean
Features that combine or convert other features in a generic way.
org.anchoranalysis.plugin.operator.feature.bean.arithmetic
Arithmetic involving features.
org.anchoranalysis.plugin.operator.feature.bean.conditional
Conditional operations involving features.
org.anchoranalysis.plugin.operator.feature.bean.list
Operations that extract a single value from a list of features.
org.anchoranalysis.plugin.operator.feature.bean.range
Features that compare against a range of values.
org.anchoranalysis.plugin.operator.feature.bean.replace
Replaces particular values if they are returned from a feature.
org.anchoranalysis.plugin.operator.feature.bean.statistics
Converts feature values based upon a statistical measure of distribution.
org.anchoranalysis.plugin.operator.feature.physical
Converting to/from physical units.
org.anchoranalysis.plugin.operator.feature.statistics
Non-bean statistical operations.
org.anchoranalysis.plugin.points.bean
Beans that fit or otherwise manipulate sets of points.
org.anchoranalysis.plugin.points.bean.convexhull
Convex hull operations.
org.anchoranalysis.plugin.points.bean.feature
Features related to points and fitting points to conics.
org.anchoranalysis.plugin.points.bean.fitter
Fitting geometric structures to points.
org.anchoranalysis.plugin.points.calculate.ellipse
CalculationPart related to fitting ellipses to points by least-squares.
org.anchoranalysis.plugin.points.calculate.ellipsoid
CalculationPart related to fitting ellipsoids to points by least-squares.
org.anchoranalysis.plugin.points.convexhull
Non-bean convex hull operations.
org.anchoranalysis.plugin.quick.bean.experiment
Quickly defining experiments via several assumptions, including particular file-paths.
org.anchoranalysis.plugin.quick.bean.input
Specifying inputs when quickly defining an experiment.
org.anchoranalysis.plugin.quick.bean.input.filepathappend
Appending other entities to inputs when quickly defining experiments.
org.anchoranalysis.plugin.quick.bean.structure
Specifying a structure of subdirectories and filenames when quickly defining an experiment.
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.orientation
Various methods to specify the orientation (general direction) of an entity.
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.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.experiment.task
Helper classes to execute Tasks in tests.
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.
org.anchoranalysis.test.image
Testing utilities and fixtures with no greater downstream dependency than anchor-image-io or anchor-io-bioformats or anchor-imagej.
org.anchoranalysis.test.image.csv
Comparing two CSV files for equality (by a certain definition).
org.anchoranalysis.test.image.io
Utilities for testing-related reading and writing to the filesystem.
org.anchoranalysis.test.image.load
Load test image data.
org.anchoranalysis.test.image.object
Fixtures for creating object-masks.
org.anchoranalysis.test.image.rasterwriter.comparison
Different ways for comparing images.
org.anchoranalysis.test.image.segment
Fixtures or other helper classes for testing image segmentation algorithms.
org.anchoranalysis.test.image.stackwriter
Fixtures for testing StackWriter and related classes.
org.anchoranalysis.test.io.output
Fixtures for an OutputManager and related-classes.
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Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.