Uses of Package
org.anchoranalysis.bean

Packages that use org.anchoranalysis.bean
Package
Description
Beans related to reading / writing / specifying annotations.
What to compare an annotation (ground truth) against?
Defining, loading, initializing Anchor Beans.
Define and related-classes.
DefineAdder and related-classes.
Initializing beans with particular parameters, including recursively.
Applying permutations to a bean's fields.
Imposes a permutation value on one or more properties of a bean.
Applying permutations to the properties of a bean.
Beans that implement collections of primitive element types, as well as String.
Utility beans which have a generally broader use than a specific module.
Beans that specify colors.
Beans that create lists or indices of colors according to particular schemes.
Setting, referencing and initializing key-value parameters.
Defines a root path directory on the filesystem whre files are read / written.
Specifies a particular type of random-number generator.
Specifies regular-expressions.
Specifies a binary relation of some kind between scalars.
Specifies a unary relation to a threshold value.
Reading Beans from XML files.
Custom factories for loading beans in custom ways from XML.
Beans related to executing an experiment by calling jobs on inputs.
Assigning unique names to experiments.
Generic experiments that handle input and output in structured ways.
Different approaches to where messages on the progress/status of an experiment are logged to.
How a task is executed on multiple inputs.
A test whether certain conditions on arguments to experiments are fulfilled.
Defines a task, which is a set of operations run on an input, that may or may not generate an output.
Beans pertaining to feature-calculation.
A feature-list (custom list type for features) and associated providers.
Features that are sufficiently generic to work on any input-type.
Provider of a single feature.
Defines base class FeatureResults together with some implementations.
Initialization parameters used for beans in org.anchoranalysis.feature.bean.
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 aren't AnchorBeans that pertain to the initialization of image-related beans.
Beans pertaining to ObjectMask and their collections.
Base classes for providers of different core data entities related to images.
A provider of Stacks.
Base classes to perform image segmentation, transforming an image into another meaningful entity or entities.
Base classes to perform binary-segmentation.
Base classes to segment a channel into objects.
Beans to define entities or operate that consider Euclidian space.
Beans to specify how to form a single-image by spatially combining other images.
Aligning a BoundingBox to fit inside another BoundingBox.
Montages images together to completely fill the available space, while preserving aspect ratio.
Combining other images through overlaying.
Combining other images through tiling.
Beans to specify a direction.
Base classes for thresholding and calculating levels for thresholding.
Reusable relations to a threshold.
Converting quantities of distance between units.
Converting quantities of extent (area or volume) between units.
Converting quantities of area between units.
Converting quantities of volume between units.
Beans pertaining to feature definition and calculation.
Beans that define context (which feature, which energy-stack) for evaluating feature-inputs.
Features that operate on a Histogram.
Features that operate on a ObjectCollection.
Features that operate on a pair of ObjectMasks.
Features that operate on a single ObjectMask.
Features that convert to/from physical spatial units (e.g. meters) as opposed to pixels/voxels.
Beans to reduce the number of results that are returned from inference, by removing overlaping entities etc.
Non-bean classes to reduce the number of results that are returned from inference, by removing overlapping entities etc.
Beans pertaining to reading Channels as input.
How to represent an object-mask in a raster that is being drawn.
Beans to specify the outputting of features into CSV from a ObjectCollection.
Beans to combine multiple stacks into a single stack before outputting.
Bean classes for reading ImageMetadata from the file-system.
Bean classes for reading raster-files from the filesystem.
Bean classes for writing raster-files to the filesystem.
Beans for filesystem I/O using Bioformats.
User-specified options that can modify metadata or other attributes of a loaded Bioformats image.
Writing stacks to the file system using the Bioformats library.
Performing interpolation with ImageJ.
Raster-writers that use ImageJ to write images to the filesystem.
Beans related to collecting inputs from the file-system for an experiment.
Methods to provide a Dictionary.
Methods to provide a collection of Files.
Determines how inputs are aggregated into groups, if at all.
Beans to derive names (compact unique identifiers) from files.
Beans pertaining to manipulating and matching against file-paths.
Beans to find a subset of files that match a particular conditions on their paths.
Methods to provide a single file-path.
Beans for the framework around writing files to the file-system.
Beans indicating whether a particular output is enabled or not.
Beans for generating paths for outputting files by adding a prefix, suffix etc.
Rules for determining if a particular output is enabled or not in a context of a hierarchy.
Loading and displaying pre-defined tasks.
Beans pertaining to marked-point-processes.
Lower and upper limits set around variables.
Bounds on how to rotate an entity in Euclidean space.
Beans generally related to Marks.
Beans related to creating Marks.
Operations based on sets of points.
Fitting structures to sets of points.
Proposing Marks or other data-structures with particular attributes.
Implementations of Provider involving Marks.
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.
Factorized form of storing the energy during an energy-minimization optimization scheme.
Non-bean classes for calculating feature-values related to Marks.
Beans for reading data structures related to marked point processes from the file system.
Pairs of Marks.
Beans relating to drawing an Overlay on an image.
Beans to combine two or more annotations.
Comparing the similarity of annotations from two images to each other.
Task to compare a set of annotations to a segmentation or another set of annotations.
Pairs annotations from two different sets, creating an assignment of some type.
FilesProviders for providing annotations.
A label as used for annotating.
Strategies for how to annotate an image, such label per image etc.
Morphological grayscale-reconstruction algorithm.
Implementations of ChannelProvider that use FIJI.
Euclidean Distance Transform implementations via FIJI.
Implementations of MaskProvider that use FIJI.
Implementations of Thresholder that use FIJI.
Filters that perform blurring.
Implementations of 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 where an ObjectCollection is created by segmenting a Channel.
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.
Grayscale reconstruction to support the Watershed transformation.
Implementation of a Watershed transformation based on Yeong et al. 2009.
Strategies for reducing the number of elements with a list by merging/removing lower-confidence elements that overlap.
Implementations of ScaleCalculator for calculating a scaling-factor from dimensions.
Implementations of BinarySegmentation.
Implementations of StackProvider.
Implementations of StackProvider that color portions of an image.
Implementations of ThumbnailFromObjects.
Implementations of ThumbnailFromStack.
Features that are calculated from Dimensions.
Implementations of FeatureHistogram that calculate statistics.
Implementations of FeatureHistogram that perform thresholding.
Implementations of FeatureListProvider.
Implementations of FeatureListProvider with input-type FeatureInputPairObjects.
Implementations of FeatureListProvider that derive new features with permuted property-values.
Implementations of FeatureImageMetadata.
Beans that affects how morphological operations occur.
Implementations of FeatureObjectCollection.
Features from combinations of ObjectMasks.
Features from pairs of ObjectMasks.
Features that calculate the degree of overlap between two ObjectMasks.
Features that calculate how many other objects an ObjectMask directly neighbors.
Implementations of FeatureSingleObject.
Implementations of FeatureSingleObject that determine if an object lies at the border of an image.
Implementations of FeatureSingleObject that consider an object's bounding-box.
Implementations of FeatureSingleObject that reference a particular Channel in the associated EnergyStack.
Implementations of FeatureSingleObject that measure an object's intensity on a corresponding Channel.
Implementations of FeatureSingleObject that measure an object's gradient from corresponding Channels storing the gradient.
Implementations of FeatureSingleObject based on calculating image moments, with or without image intensity.
Implementations of FeatureSingleObject that implement morphological operations.
Implementations of FeatureSingleObject that measure the shape of the ObjectMask.
Implementations of FeatureSingleObject that use SharedObjects for calculations.
Implementations of FeatureSingleObject that use SharedObjects for calculations, and measure the degree of intersection between objects.
Implementations of FeatureSingleObject that processes an object slice-by-slice in the z-dimension.
Implementations of FeatureSingleObject that measures aspects of the surface of an ObjectMask.
Beans involving physical units for measurement.
Implementations of VoxelScore.
Beans involving SharedObjects.
Beans involving SharedObjects and ObjectCollection.
Implementations of FeatureStack or other features that involve processing a Stack.
Implementations of FeatureStack that process an ObjectCollection.
A parent package for many different kinds of tasks.
Combining multiple images together into a single image.
Tasks pertaining to Features.
Source of rows in feature-tables with FeatureSource and derived classes.
Tasks for converting image-formats.
Different approaches for converting sets of channels (RGB, independently etc.) to another image format.
Tasks that involved stacks (usually each channel from an image) that are somehow grouped-together.
Task(s) to export histograms of intensity values.
Selecting a subset of a set of channels.
Associating labels with images.
Tasks to scale an image.
Tasks to segment an image.
Tasks that process on one or more slices from a z-stack.
Non-bean classes pertaining to Features as used in tasks.
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 ObjectCollectionProvider that call ImageJ to perform segmentation.
Implementations of StackProvider that call ImageJ.
Implementations of Thresholder that call ImageJ.
Implementations of ChannelMapCreator.
Methods for copying files on the file-system.
Rules for preserving or changing the naming of files when copying on the file-system.
Implementations of CopyFilesNaming that perform clustering of files.
Grouping files together so that they collectively represent a single entity.
Tests that are applied when grouping files in org.anchoranalysis.plugin.io.bean.file.group
Parsing file-paths to determine file-grouping in org.anchoranalysis.plugin.io.bean.file.group
Implementations of FileNamer.
Implementations of FileNamer that look for a pattern across many files.
Beans to specify a file-path.
Implementations of PathPrefixer.
Extracting a pattern from a file-path.
Implementations of FilesProvider.
Implementations of Grouper.
Implementations of InputManager.
InputManagers that accept a set of named-channels.
InputManagers that accept a set of named-files.
Implementations of FilesProvider.
Implementations of InputManager that filter inputs.
Implementations of InputManager that process Stacks.
Different types of image-file-formats whose headers can provide ImageMetadata.
Implementations of ImageMetadataReader.
Implementations of DerivePath.
Implementations of StackReader.
Implementations of StackWriter.
Summarizing a set of elements into a descriptive-string.
Implementations of Summarizer that summarize images.
Implementations of Summarizer that summarize generically InputFromManagers.
Implementations of Summarizer that summarize generically Paths.
Implementations of Task related to file-system I/O.
Converting from NamedChannelsInput to the input-type expected by a Task.
Beans related to Define involving Mark or related classes.
Implementations of ObjectCollectionProvider.
Implementation of MarkCollectionProvider.
Implementations of StackProvider involving Mark or related classes.
Decodes the outputted tensors from a Mask R-CNN implementation.
Decodes the outputted tensors from text-segmentation models.
Segmenting a Stack using the ONNX Runtime to produce an ObjectCollection.
Operations involving color-spaces and OpenCV.
Extracting features using OpenCV.
Interpolation beans that use OpenCV.
Segmentation of a Stack using OpenCV.
Implementations of StackWriter and StackReader that involve OpenCV.
Features that combine or convert other features in a generic way.
Arithmetic involving features.
Conditional operations involving features.
Operations that extract a single value from a list of features.
Features that compare against a range of values.
Replaces particular values if they are returned from a feature.
Converts feature values based upon a statistical measure of distribution.
Converting to/from physical units.
Beans that fit or otherwise manipulate sets of points.
Convex hull operations.
Features related to points and fitting points to conics.
Fitting geometric structures to points.
Testing utilities and fixtures with no greater downstream dependency than anchor-experiment or anchor-mpp or anchor-mpp-io.
Testing utilities and fixtures with no greater downstream dependency than anchor-image-feature or anchor-mpp.
A mocked feature internally using a feature-calculation.
Utilities for testing-related reading and writing to the filesystem.