Anchor - merged Javadoc across key repositories. This documentation is a work-in-progress. 1.0.0-SNAPSHOT API
Packages
Package
Description
Ground truth for an image in diverse forms.
Annotations that apply to an image as a whole.
Reading and writing annotations to the filesystem.
A pairing of objects from two collections (bipartite matching).
Generates output images to illustrate a
Assignment between annotations.Beans related to reading / writing / specifying annotations.
What to compare an annotation (ground truth) against?
Non-bean classes involving comparing results and annotations.
Reading and writing whole-image label annotations.
The outcome of searching for annotations or images on the file-system.
Reading and writing
Mark-related annotations from/to the
file-system.Annotations that use one or more marks to describe entities in an image.
Defining, loading, initializing Anchor Beans.
Annotations that decorate fields in an Anchor Bean.
Define and related-classes.DefineAdder and related-classes.Exceptions that can occur executing generic operations on Anchor Beans.
Initializing beans with particular parameters, including recursively.
Some parameterization used when initializing beans.
Initializating a bean with parameters.
Applying permutations to a bean's fields.
Imposes a permutation value on one or more properties of a bean.
Applying permutations to the properties of a bean.
Beans that implement collections of primitive element types, as well as
String.Utility beans which have a generally broader use than a specific module.
Beans that specify colors.
Beans that create lists or indices of colors according to particular schemes.
Setting, referencing and initializing key-value parameters.
Defines a root path directory on the filesystem whre files are read / written.
Specifies a particular type of random-number generator.
Specifies regular-expressions.
Specifies a binary relation of some kind between scalars.
Specifies a unary relation to a threshold value.
Reading Beans from XML files.
Creates beans from XML.
Exceptions that can thrown when loading beans from XML.
Custom factories for loading beans in custom ways from XML.
Factories to create beans in
org.anchoranalysis.bean.primitive.Caching (memozing) calls to a method so an operation does not need to be repeated.
Collection-related classes with general applicability that don't belong elsewhere.
Specifying particular colors and groups of colors.
Very general exceptions and base classes for exceptions with wide applicability.
Nested exceptions of similar type that can be combined together in a summary.
Particular types of exceptions that are guaranteed to have a text/form that gives user-friendly
error descriptions.
File formats and associated extensions.
Utilities and interfaces for applying functional-programming.
Versions of many functional-interfaces in
java.util.function that throw
checked-exceptions.Adds additional functional-interfaces, that are unavailable in
java.util.function, and do
not throw checked exceptions.Data-structures for directed and undirected graphs, with or without an edge payload.
Data structures for adding a unique name (a String or integer identifier) to other entities.
Data structures for name (String) and value associations.
A collection of named-elements, a
NamedProvider and related operations.Data structures like
NamedProvider with
supporting for adding new elements.Classes to support getting / setting / specifying unique-integers (indices) for elements.
A range of indices from minimum to maximum.
Interfaces to log messages, both information and error messages.
Mechanism for reporting errors (exceptions/throwables) to the user.
Generating random numbers.
Utilities for serializing and deserializing objects.
Utilities for interacting with the operating system or computer system generally
Utilities for converting/manipulating file-paths.
Recording the execution-time of operations for profiling.
Encapsulating values or sets of named-values.
Classes related to executing an experiment by calling jobs on inputs.
Arguments that can further specify an experiment in addition to its bean specification.
Beans related to executing an experiment by calling jobs on inputs.
Assigning unique names to experiments.
Generic experiments that handle input and output in structured ways.
Different approaches to where messages on the progress/status of an experiment are logged to.
How a task is executed on multiple inputs.
A test whether certain conditions on arguments to experiments are fulfilled.
Defines a task,
which is a set of operations run on an input, that may or may not generate an output.
Interfaces for replacing attributes of an experiment: input, output, task etc.
Helpful classes for logging.
Non-bean classes related to a
Task.Non-bean classes related to
JobProcessor.How long particular operations take to execute.
Beans pertaining to feature-calculation.
A feature-list (custom list type for features) and associated providers.
Features that are sufficiently generic to work on any input-type.
Provider of a single feature.
Defines base class
FeatureResults together with
some implementations.Sub-feature units of calculation that can be cached.
Interfaces like
FeatureCalculator but bound to
particular features.Classes to cache feature-results or parts of feature-results that occur repeatedly among features
or across calculations of the same feature.
Equivalent classes to
org.anchoranalysis.feature.calculate.part after having been
resolved against a cache.A sub-part of the calculation of a feature, that can be cached, and reused by other features.
A particular stack used in feature-calculations called a
EnergyStack together with related classes.Initialization parameters used for beans in
org.anchoranalysis.feature.bean.Base classes providing inputs to feature calculations.
Metadata for writing feature calculation-results in CSV format.
Writing the results of feature calculations to the file-system.
Writing the results from feature-calculation to a CSV file.
A
Generator for writing a table of feature values as a
CSV.Naming items in a weay that breaks down into multiple elements.
Writes feature-calculation results in different formats, also grouped results.
Various different outputs that can be written for the a grouped version of the results in
LabelledResultsCollector.Data objects for the names of features.
Results from one or more feature calculations.
A defined context in which one or more features are provided inputs and produce results.
Creates a
FeatureCalculationCache to use
during feature-calculations.Strategies to determine which child-cache (among hierarchy) to employ for a particular feature
calculation.
Base classes for methods to calculate results from features.
Strategies on whether to reuse or invalidate a feature-input's cache.
Features shared for referencing among calculations.
A collection of named-
Features.Core (bean) classes for image processing.
Base classes for performing operations on
Channels.Beans for specifying image interpolators.
Classes that are used elsewhere in this package but which aren't themselves AnchorBeans.
Classes that aren't AnchorBeans that pertain to the initialization of image-related beans.
Non-bean classes relating to image-segmentation.
Non-bean classes to help specify the position of one entity relative to the others.
Non-beans to specify how to form a single-image by spatially combining other images.
Beans pertaining to
ObjectMask and their
collections.Base classes for providers of different core data entities related to images.
A provider of
Stacks.Base classes to perform image segmentation, transforming an image into another meaningful entity
or entities.
Base classes to perform binary-segmentation.
Base classes to segment a channel into objects.
Beans to define entities or operate that consider Euclidian space.
Beans to specify how to form a single-image by spatially combining other images.
Aligning a
BoundingBox to fit inside another BoundingBox.Montages images together to completely fill the available space, while preserving aspect ratio.
Combining other images through overlaying.
Combining other images through tiling.
Beans to specify a direction.
Base classes for thresholding and calculating levels for thresholding.
Reusable relations to a threshold.
Converting quantities of distance between units.
Converting quantities of extent (area or volume) between units.
Converting quantities of area between units.
Converting quantities of volume between units.
Conversions and operations involving Java AWT's
BufferedImage.The
Channel core data-class and related operations
and converters.Converts a channel to other data-types.
Converts a channel to another data-type based upon another object to which it is attached.
Converts a channel to another data-type based upon a
Channel to which it is attached.Converts a channel to another data-type based upon a
Histogram to which it is attached.Factory classes for creating
Channel for various
voxel data-types.Finds outline voxels, the pixels on the contour/edge of the object.
Classes to describe the size of images or components of images both in voxels and physically.
Suggestions on a size for an image.
An image with only two permissible states.
Binary operations involving voxelwise combination of
Mask.Merges two or more entities.
The key data entity
org.anchoranalysis.image.voxel.object and related-classes and
operations.Labelling elements (object-masks or similar) with unique successive integers in a channel.
An
ObjectCollection with associated key-value
pairs.Scaling object-collections, or lists of elements with object-representations.
Scaling elements with an associated
ObjectMask
either collectively or independently.Operations that extract points from image data entities or vice versa.
Defines the key data object,
Stack, and related
classes.A collection of
Stacks, each with a unique identifier
as a name.Beans pertaining to feature definition and calculation.
Beans that define context (which feature, which energy-stack) for evaluating feature-inputs.
Features that operate on a
Histogram.Features that operate on a
ObjectCollection.Features that operate on a pair of
ObjectMasks.Features that operate on a single
ObjectMask.Features that convert to/from physical spatial units (e.g. meters) as opposed to pixels/voxels.
Reusable implementations of
CalculationPart
related to images.Implementations of
FeatureCalculatorMulti
related to images, especially to create tables of feature-calculations.A particular implementation of
FeatureCalculatorMulti for feature-calculations based
upon pairs of image-objects.Image-related implementations of
FeatureInput.Inference of machine learning models on images.
Beans to reduce the number of results that are returned from inference, by removing overlaping
entities etc.
Instance-segmentation of a
Stack.Non-bean classes to reduce the number of results that are returned from inference, by removing
overlapping entities etc.
Non-beans pertaining to segmentation of images via model inference.
Reading and writing of image-related data objects to and from the filesystem.
Beans pertaining to reading
Channels as input.How to represent an object-mask in a raster that is being drawn.
Beans to specify the outputting of features into CSV from a
ObjectCollection.Beans to combine multiple stacks into a single stack before outputting.
Bean classes for reading
ImageMetadata from the
file-system.Bean classes for reading raster-files from the filesystem.
Bean classes for writing raster-files to the filesystem.
Non-bean classes for reading a
Channel from the
filesystem.Non-bean classes for a mapping of names to
Channels.Non-bean classes for writing a
Channel to the
filesystem.Non-bean classes for reading a
Histogram from the
filesystem.Non-bean classes for writing a
Histogram to the
filesystem.Non-bean classes for reading / writing an
ObjectCollection from and to the filesystem.Non-bean classes for reading an
ObjectCollection
from the filesystem.Writing an
ObjectCollection to the filesystem as a
single-channeled stack.Writing an
ObjectCollection to the filesystem in
HDF5 format.Writing an
ObjectCollection to the filesystem as
multiple binary singled-channeled images.Writing an
ObjectCollection to the filesystem as
RGB raster-images.Non-bean classes for reading / writing a
Stack from
and to the filesystem.Non-bean classes for reading a
Stack from the
filesystem.Non-bean classes for writing a
Stack to the
filesystem.Base classes for generators that ultimately write only a bounding-box portion of a
Stack to the filesystem.Base classes for generators that ultimately write a
Stack to the filesystem.A time-sequence of
Stacks.Data-structures to store and manipulate image raster-data or voxels.
Arithmetic operations for
Voxels.Assigns values to some or all voxels.
The
BinaryVoxels class and related operations.Defining on and off intensity-values to interpret an image in a binary way.
A buffer of voxel-values, usually corresponding to a single z-slice in
Voxels.Conversion of both primitive data types and image structures between Anchor's data-structures and
other representations.
A container with voxel-buffers for each z-slice.
Converting
Voxels to different data-types.Converts anchor data-structures to the
BufferedImage used by Java's AWT.Converts anchor data-structures to those used by ImgLib2.
The different data-types that can be used to represent voxels.
Methods to read/copy/duplicate portions of voxels.
Methods to find or count voxels that satisfy a predicate.
Creates new instances of
Voxels and VoxelsUntyped with specific data-types.Utilities to iterate over voxel-locations in images and sub-regions of images.
Like
org.anchoranalysis.image.voxel.iterator but refers to iterators that operation over
the intersecting regions of two entities.Iterating over a point's neighboring voxels.
Routines for moving a
KernelPointCursor around the
neighboring voxels of the point.Functional-interfaces for processing different combinations of points and buffers that return a
boolean.
Functional-interfaces for processing different combinations of points and buffers that do not
return a value.
Functional-interfaces for processing different combinations of points and raw buffers, but not
VoxelBuffer.Functional-interfaces for processing different combinations of points and
VoxelBuffer but not raw buffers.Applying a kernel via
convolution to voxels.
Kernels to count the number of voxels that are equal to a particular value.
Kernels that apply morphological operations.
Kernel to find outline voxels on an object.
A region in proximity to a voxel, encompassing this voxel as well as others.
The fundamental data class that is an
ObjectMask
and related structures.Morphological operations
applied to
ObjectMasks.Predicates to match certain voxels as used in
org.anchoranalysis.image.voxel.object.morphological.Classes for calculating differnet kind of projections of voxel values across multiple buffers.
Classes for performing both a Maximum Intensity
Projection and a minimum projection.
Different interpolator methods to use when scaling voxels.
Statistics about aggregated voxel intensities.
Thresholding operations on voxels.
High-level classes for performing machine learning model inference.
Specifying how many CPUs and GPUs can be allocated for some purpose.
Non-bean classes for filesystem I/O using Bioformats.
Beans for filesystem I/O using Bioformats.
User-specified options that can modify metadata or other attributes of a loaded Bioformats image.
Writing stacks to the file system using the Bioformats library.
Converts the byte stream opened by Bioformats into channels of particular data-type.
Converts the byte stream opened by Bioformats into channels of
ByteBuffer.Converts the byte stream opened by Bioformats into channels of
FloatBuffer.Converts the byte stream opened by Bioformats into channels of
IntBuffer.Converts the byte stream opened by Bioformats into channels of
ShortBuffer.Reading metadata information from files using EXIF and/or other metadata headers.
Base-classes and utilities for generators, which write different types of objects to the file
system.
Outputting more than one element collectively using a generator.
Combining multiple generators into one.
Writing a sequence of elements using a generator.
A particular naming pattern files follow when outputted.
Generators for writing serialized objects.
Generators for writing tabular data, including CSV.
Generators for writing textual data, including strings.
Generators for writing XML data.
Performing interpolation with ImageJ.
Raster-writers that use ImageJ to write images to the filesystem.
Converts to and from ImageJ data-structures for images.
Image interpolation when scaling using ImageJ.
Classes relating to creating inputs for an experiment / task.
Beans related to collecting inputs from the file-system for an experiment.
Methods to provide a
Dictionary.Methods to provide a collection of
Files.Determines how inputs are aggregated into groups, if at all.
Beans to derive names (compact unique identifiers) from files.
Beans pertaining to manipulating and matching against file-paths.
Beans to find a subset of files that match a particular conditions on their paths.
Methods to provide a single file-path.
Classes for reading comma-separated-values (CSV) files.
Non-bean classes that relate to using files during inputting.
Non-bean classes pertaining grouping inputs.
Non-bean classes pertaining to getting/extracting/manipulating paths as used in inputting.
Non-bean classes to help with
org.anchoranalysis.io.input.bean.path.matcher.Beans for the framework around writing files to the file-system.
Beans indicating whether a particular output is enabled or not.
Beans for generating paths for outputting files by adding a prefix, suffix etc.
Rules for determining if a particular output is enabled or not in a context of a hierarchy.
Non-beans pertaining to whether a particular output is enabled or not.
Non-beans that pertain to whether multiple-levels have outputs that are enabled or not.
Non-beans that pertain to whether a single level has outputs that are enabled or not.
Exceptions that may be thrown when writing files to the file-system.
Methods of naming a file with an index in the file-name.
Classes for outputting to particular directories.
BoundDirectory and related classes.Non-beans for generating paths for outputting files by adding a prefix, suffix etc.
Classes for recording the output-names used as they are written / queried.
Allows a generators to write element(s) to the filesystem.
Outputting XML to the file-system.
Parent package and entry-point classes for the Anchor command-line launcher application.
Specifies a configuration of the launcher for a particular application.
Runs a particular experiment after identifying necessary paths and input files.
Different methods of selecting a object
T that is used as a parameter for an experiment.SelectParams for loading a Experiment.SelectParams for loading a
Optional<Path> for inputs, outputs or tasks.Converting paths to/from different formats as needed by
org.anchoranalysis.launcher.executor.selectparam.path.A centralized location for all command-line options used by the launcher.
Adding/removing/changing the arguments (input and output) from the experiment via
command-line-options.
Reading and integrating resources for the launcher.
Parses command-line arguments and runs an experiment.
Loading and displaying pre-defined tasks.
Performing primitive type conversion, counting and summing.
Solving or manipulating equations.
The
Histogram data class and related operations.Mathemathical optimization
algorithms.
Different kinds of binary-relations.
Data structures and algorithms to calculate statistics.
Calculates first and second image
moments from a covariance matrix of points.
Beans pertaining to marked-point-processes.
Lower and upper limits set around variables.
Bounds on how to rotate an entity in Euclidean space.
Beans generally related to
Marks.Beans related to creating
Marks.Operations based on sets of points.
Fitting structures to sets of points.
Proposing
Marks or other data-structures with particular
attributes.Voxel subregions of
Marks.Criteria for adding edges during optimization of marked-point-processes.
Implementations and helper classes for calculating energy during an energy-minimization
optimization scheme.
Creating
EnergySchemes.Features calculated on a
Mark.Features calculated on a
org.anchoranalysis.mpp.feature.bean.mark.collection.Non-bean classes pertaining to calculating energy during an energy-minimization optimization
scheme.
Non-bean classes pertaining to calculating energy of {org.anchoranalysis.mpp.mark.Mark}s.
Saved snapshots of energy-calculations.
Factorized form of storing the energy during an energy-minimization optimization scheme.
Inputs to mark-point-processes related
Features.Non-bean classes for calculating feature-values related to
Marks.Indexing voxel-values in different ways.
Factories for classes in
org.anchoranalysis.mpp.index.Parameters used to initialize certain types of beans.
Beans for reading data structures related to marked point processes from the file system.
Non-beans for reading data structures related to marked point processes from the file system.
Non-beans for writing data structures related to marked point processes from the file system.
Non-bean classes related to
Marks.Marks implementing conic sections.Marks implementing structures based on points.A mark after a voxel-representation has been inferred.
Memoization of
VoxelizedMarks.Calculating overlaps between two
Marks.Pairs of
Marks.Non-bean classes for proposing
Marks or other data-structures
with particular attributes.Recording errors related to proposing
Marks or other
data-structures with particular attributes.Overlays and related classes involving drawing entities on top
of an image.Beans relating to drawing an
Overlay on an image.Collections of
Overlays.An implementation of an
Overlay that draws an ObjectMask on an image.Drawing an overlay on an image.
Beans to combine two or more annotations.
Comparing the similarity of annotations from two images to each other.
Task to compare a set of annotations to a segmentation or another set of annotations.
Pairs annotations from two different sets, creating an assignment of some type.
FilesProviders for providing annotations.A label as used for annotating.
Strategies for how to annotate an image, such label per image etc.
Non-bean classes for comparing two sets of annotations.
Utility classes for counting images incrementally.
Morphological grayscale-reconstruction algorithm.
Implementations of
ChannelProvider that use FIJI.Euclidean Distance Transform
implementations via FIJI.
Implementations of
MaskProvider that use FIJI.Implementations of
Thresholder that use FIJI.Filters that perform blurring.
Implementations of
ConvertChannelTo and ConvertChannelToWithHistogram.Implementations of
ConvertChannelTo and ConvertChannelToWithHistogram.Implementations of
ChannelProvider that are
generic base-classes or otherwise abstract or general.Implementations of
ChannelProvider that perform
arithmetic on voxels in one or more Channels.Implementations of
ChannelProvider that sets the
values of the voxels in a Channel.Implementations of
ChannelProvider that converts a
Channel from one voxel-type to another.Implementations of
ChannelProvider that calculate
the gradient of a Channel's voxels in one or more
dimensions.Implementations of
ChannelProvider that manipulate
the intensity-values of the voxels of a Channel's
voxels.Implementations of
ChannelProvider that involve
conversion from or application of Masks.Implementations of
ChannelProvider that involve
conversion from or application of ObjectMasks.Implementations of
ChannelProvider that assign a
score to particular subregions of a channel.Implementations of
ChannelProvider that process 3D
channels slice-by-slice.Implementations of
ColorProvider.Beans pertaining to
Dictionary.Implementations of
DimensionsProvider.Implementations of
HistogramProvider.Thresholding of intensity values represented in at
Histogram.Implementations of
MaskProvider.Implementations of
MaskProvider that combine
existing providers.Implementations of
MaskProvider that convert
providers of other types to ObjectMasks.Implementations of
MaskProvider that implement
morphological operations.Provides if-else conditions to a
MaskProvider.Implementations of
MaskProvider that process 3D
masks slice-by-slice.Implementations of
ObjectFilter.Implementations of
ObjectFilter that assess each
element in a collection collectively.Implementations of
ObjectFilter that combine two or
more other ObjectFilters.Implementations of
ObjectFilter that
independently assess each element in a collection.Implementations of
ObjectMatcher.Implementations of
ObjectCollectionProvider.Implementations of
ObjectCollectionProvider
involving connected-components.Implementations of
ObjectCollectionProvider
involving feature calculation.Implementations of
ObjectCollectionProvider that
filter objects.Implementations of
ObjectCollectionProvider
involving a Mask.Implementations of
ObjectCollectionProvider
involving merging objects together.Implementations of
ObjectCollectionProvider
involving morphological operations.Implementations of
ObjectCollectionProvider
involving segmentation.Implementations of
ObjectCollectionProvider
involving z-slice processing.Implementations of
ObjectCollectionProvider
involving splitting objects into smaller objects.Implementations of
SegmentChannelIntoObjects.Minima imposition for a Watershed transformation.
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction
Grayscale reconstruction to support the Watershed transformation.
Implementation of a Watershed transformation
based on Yeong et al. 2009.
Strategies for reducing the number of elements with a list by merging/removing lower-confidence
elements that overlap.
Implementations of
ScaleCalculator for calculating
a scaling-factor from dimensions.Implementations of
BinarySegmentation.Implementations of
StackProvider.Implementations of
StackProvider that color
portions of an image.Implementations of
ThumbnailFromObjects.Implementations of
ThumbnailFromStack.Non-beans for operations or calculations relating to
Channels.Features that are calculated from
Dimensions.Implementations of
FeatureHistogram that calculate
statistics.Implementations of
FeatureHistogram that perform
thresholding.Implementations of
FeatureListProvider.Implementations of
FeatureListProvider with
input-type FeatureInputPairObjects.Implementations of
FeatureListProvider that derive
new features with permuted property-values.Implementations of
FeatureImageMetadata.Beans that affects how morphological operations occur.
Implementations of
FeatureObjectCollection.Features from combinations of
ObjectMasks.Features from pairs of
ObjectMasks.Features that calculate the degree of overlap between two
ObjectMasks.Features that calculate how many other objects an
ObjectMask directly neighbors.Implementations of
FeatureSingleObject.Implementations of
FeatureSingleObject that determine if an
object lies at the border of an image.Implementations of
FeatureSingleObject that consider an
object's bounding-box.Implementations of
FeatureSingleObject that reference a
particular Channel in the associated EnergyStack.Implementations of
FeatureSingleObject that measure an object's
intensity on a corresponding Channel.Implementations of
FeatureSingleObject that measure an object's
gradient from corresponding Channels storing the
gradient.Implementations of
FeatureSingleObject based on calculating image moments, with or without image
intensity.Implementations of
FeatureSingleObject that implement
morphological operations.Implementations of
FeatureSingleObject that measure the shape
of the ObjectMask.Implementations of
FeatureSingleObject that use SharedObjects for calculations.Implementations of
FeatureSingleObject that use SharedObjects for calculations, and measure
the degree of intersection between objects.Implementations of
FeatureSingleObject that processes an object
slice-by-slice in the z-dimension.Implementations of
FeatureSingleObject that measures aspects of
the surface of an ObjectMask.Beans involving physical units for measurement.
Implementations of
VoxelScore.Beans involving
SharedObjects.Beans involving
SharedObjects and
ObjectCollection.Implementations of
FeatureStack or other features
that involve processing a Stack.Implementations of
FeatureStack that process an
ObjectCollection.Non-bean classes that help calculate features from
ObjectMasks.Implementations of
CalculationPart as used by
features elsewhere in this package.Implementations of
CalculationPart that that
process a single ObjectMask.Implementations of
CalculationPart that that
process a single ObjectMask - with morphological operations.Implementations of
CalculationPart that process
Stacks as used by features elsewhere in this package.Non-bean for operations or calculations relating to intensity.
Non-beans for calculating a thresholding level from itensity values.
Non-beans pertaining to
ObjectMasks.Merging
ObjectMasks.Conditions for merging
ObjectMasks.Assigning priority when merging
ObjectMasks.Non-bean classes pertaining to
Providers.Non-beans pertaining to segmenting a z-stack slice-by-slice.
Encoding voxels in a watershed-transformation implementation.
A parent package for many different kinds of tasks.
Combining multiple images together into a single image.
Tasks pertaining to
Features.Source of rows in feature-tables with
FeatureSource and derived classes.Tasks for converting image-formats.
Different approaches for converting sets of channels (RGB, independently etc.) to another image
format.
Tasks that involved stacks (usually each channel from an image) that are somehow
grouped-together.
Task(s) to export histograms of intensity values.
Selecting a subset of a set of channels.
Associating labels with images.
Tasks to scale an image.
Tasks to segment an image.
Tasks that process on one or more slices from a z-stack.
Non-bean classes pertaining to
Features as used in tasks.Non-beans for calculating
Features.Non-bean classes about grouping channels or other inputs.
Non-bean classes about labelling images.
Non-bean classes for image-segmentation.
Non-bean classes pertaining to determining the size of an image.
Non-bean classes pertaining to combining stacks into a single stack.
Non-bean classes pertaining to stacks and channels as used in tasks.
Non-bean classes for thumbnail creation.
Implementations of
ChannelProvider that call ImageJ.Non-linear filters using ImageJ that use the statistical moments of the
intensity values in the kernel.
Non-linear filters using ImageJ that use the statistical rank of the intensity values in the
kernel.
Implementations of
DefineAdderBean that call ImageJ.Implementations of
MaskProvider that call ImageJ.Implementations of
ObjectCollectionProvider that
call ImageJ.Implementations of
StackProvider that call
ImageJ.Implementations of
Thresholder that call ImageJ.Implementations of
ChannelProvider that call ImageJ.Non-bean classes involving
ObjectMask that call ImageJ.Implementations of
ChannelMapCreator.Methods for copying files on the file-system.
Rules for preserving or changing the naming of files when copying on the file-system.
Implementations of
CopyFilesNaming
that perform clustering of files.Grouping files together so that they collectively represent a single entity.
Tests that are applied when grouping files in
org.anchoranalysis.plugin.io.bean.file.groupParsing file-paths to determine file-grouping in
org.anchoranalysis.plugin.io.bean.file.groupImplementations of
FileNamer.Implementations of
FileNamer that look for a
pattern across many files.Beans to specify a file-path.
Implementations of
PathPrefixer.Extracting a pattern from a file-path.
Implementations of
FilesProvider.Implementations of
Grouper.Implementations of
InputManager.InputManagers that accept a set of
named-channels.InputManagers that accept a set of named-files.Implementations of
FilesProvider.Implementations of
InputManager that filter inputs.Implementations of
InputManager that process Stacks.Different types of image-file-formats whose headers can provide
ImageMetadata.Implementations of
ImageMetadataReader.Implementations of
DerivePath.Implementations of
StackReader.Implementations of
StackWriter.Summarizing a set of elements into a descriptive-string.
Implementations of
Summarizer that summarize
images.Implementations of
Summarizer that summarize
generically InputFromManagers.Implementations of
Summarizer that summarize
generically Paths.Implementations of
Task related to file-system
I/O.Non-bean classes to help tasks in
org.anchoranalysis.plugin.io.bean.file.copy.Non-bean classes to help tasks in
org.anchoranalysis.plugin.io.bean.input.filter.Non-bean classes to help in processing paths.
Non-bean classes to help use multiple files to represent a single
Stack.Buffers used in
org.anchoranalysis.plugin.io.multifile.How to write parts of a time-interval in a file-name.
Objects used in shared-state in
Tasks in this
plugin.Reading and writing metadata XML.
Converting from
NamedChannelsInput to the
input-type expected by a Task.Implementations of
ObjectCollectionProvider.Implementation of
MarkCollectionProvider.Implementations of
StackProvider involving
Mark or related classes.Shared-state use across tasks in this JAR.
Decodes the outputted tensors from a Mask
R-CNN implementation.
Decodes the outputted tensors from text-segmentation models.
Segmenting a
Stack using the ONNX Runtime to produce
an ObjectCollection.Non-bean classes for running an inference model with the ONNX
Runtime.
Plugins that call OpenCV.
Operations involving color-spaces and OpenCV.
Extracting features using OpenCV.
Interpolation beans that use OpenCV.
Segmentation of a
Stack using OpenCV.Conversion to/from OpenCV data-structures.
Interpolation non-beans that use OpenCV.
Non-bean classes pertaining to segmentation.
Features that combine or convert other features in a generic way.
Arithmetic involving features.
Conditional operations involving features.
Operations that extract a single value from a list of features.
Features that compare against a range of values.
Replaces particular values if they are returned from a feature.
Converts feature values based upon a statistical measure of distribution.
Converting to/from physical units.
Non-bean statistical operations.
Beans that fit or otherwise manipulate sets of points.
Convex hull operations.
Features related to points and fitting points to conics.
Fitting geometric structures to points.
CalculationPart related to fitting
ellipses to points by least-squares.CalculationPart related to fitting
ellipsoids to points by least-squares.Non-bean convex hull operations.
Identifying the three standard axes in 3D cartesian coordinates.
Axis-aligned bounding-boxes and related operations.
Various methods to specify the orientation (general direction) of an entity.
A cartesian-coordinate, across varying primitive types, in 2D and 3D space.
Functional interfaces that accept cartesian coordinate points specified in different ways.
R-Tree data structure and related operations.
How to much to scale an entity in Cartesian space by.
Testing utilities and fixtures with no greater downstream dependency than anchor-core.
Testing utilities and fixtures with no greater downstream dependency than
anchor-experiment or anchor-mpp or anchor-mpp-io.
Launches an anchor binary from a shell and runs an experiment.
Helper classes to execute
Tasks in tests.Testing utilities and fixtures with no greater downstream dependency than anchor-feature.
Testing utilities and fixtures with no greater downstream dependency than
anchor-image-feature or anchor-mpp.
A mocked feature internally using a feature-calculation.
Fixtures for creating object-masks and related feature-inputs.
Testing utilities and fixtures with no greater downstream dependency than anchor-image-io
or anchor-io-bioformats or anchor-imagej.
Comparing two CSV files for equality (by a certain definition).
Utilities for testing-related reading and writing to the filesystem.
Load test image data.
Fixtures for creating object-masks.
Different ways for comparing images.
Fixtures or other helper classes for testing image segmentation algorithms.
Fixtures for testing
StackWriter and
related classes.Fixtures for an
OutputManager and related-classes.