All Classes

Class	Description
CalculateOrientationChange	Calculates any needed orientation change.
ChannelGenerator	Writes a single channel to a file.
ChannelGetter	Retrieves a Channel by name from a particular time-point.
ChannelMap	A mapping of assigned channel-names to particular indices.
ChannelMapCreator	Creates a ChannelMap for a particular OpenedImageFile.
ConvertStackToRGB	Converts a Stack or DisplayStack to a RGBStack.
DisplayStackGenerator	Writes a display-stack to the filesystem.
DrawCroppedObjectsGenerator	Similar to DrawObjectsGenerator, but with the background stack cropped to focus only on the region containing objects.
DrawObjectOnStackGenerator	Creates images of object(s) drawn on a background only in a local region around their bounding box.
DrawObjectsGenerator	Generates stacks of RGB images using a DrawObject to draw objects on a background.
ExtractBoundingBoxAreaFromStackGenerator	An iterable-generator that outputs the portion of a stack corresponding to a bounding-box
ExtractFrameStore	Exposes a NamedProviderStore<TimeSeries> as a NamedProviderStore<Stack> by extracting a frame from each series.
ExtractMidpoint	Extracts a Point3i representing the mid-point of an ObjectWithProperties.
Filled	Draws a filled-in shape for each object.
Flatten	Performs a flattening (maximum intensity projection in each channel) of the output of another writer
FlattenStackGenerator	Like a StackGenerator but first applies a maximum-intensity-projection.
FromStackReader	Uses a StackReader to read the image-metadata.
GeneratorOutputter	Settings and methods for writing to the filesystem from a generator.
HDF5ObjectsGenerator	A generator that writes a ObjectCollection to a HDF5 file.
HDF5PathHelper	Paths to identify objects in the HDF5 for object-masks.
HistogramCSVGenerator	Writes a histogram to a CSV file.
HistogramCSVReader	Reads a CSV file from the file-system that describes a histogram of voxel values.
IfElse	Branches to two different DrawObject depending on a predicate.
IfElse.Predicate	Interface for the condition that is tested, to determine which DrawObject to use.
ImageInitializationFactory	Creates instances of ImageInitialization based upon an InputOutputContext.
ImageIOException	When an error occurs reading or writing an image to/from the file-system.
ImageMetadataInput	An input that provides a ImageMetadata but only lazily when first called.
ImageMetadataReader	Reads an ImageMetadata from the file-system.
ImageTimestampsAttributes	This combines ImageFileAttributes plus a timestamp for image-acqusition.
IndexedChannel	A particular Channel to be read from a file, identified by its position (index) in the file.
InputManagerWithStackReader<T extends InputFromManager>	Extends an InputManager to add a StackReader bean property.
MaskReader	Utility functions for reading a Mask from the file-system.
NamedChannelsConcatenate	Exposes one or more instances of a NamedChannelsMap as a single aggregated NamedChannelsMap.
NamedChannelsInput	Provides a set of channels as an input, with each channel having a name.
NamedChannelsInputPart	One part of a NamedChannelsInput that can be combined with others.
NamedChannelsMap	A collection of Channels, each identified by a unique name and a time-index.
NamedStacksOutputter	Outputs a named-set of stacks, performing appropriate checks on what is enabled or not.
ObjectAsMaskGenerator	Writes an object-mask as a mask (i.e.
ObjectCollectionReader	Reads an ObjectCollection from the filesystem
ObjectCollectionWriter	Centralized point to access a Generator which writes an ObjectCollection to the file-system.
ObjectsAsGrayscaleGenerator	Base class for generators that accept a set of objects as input.
ObjectsAsRGBGenerator	A base class for generators that draw an ObjectCollection upon a RGBStack.
ObjectsAsUniqueValueGenerator	Writes objects as an image with an incrementing unique integer id value for each object.
ObjectsMergedAsMaskGenerator	Writes objects merged together as a mask.
ObjectWithBoundingBoxGenerator	Like ObjectAsMaskGenerator but additionally outputs a serialized bounding box.
OneOrThreeChannelsWriter	A base-class for a StackWriter that writes an image that has either one or three channels.
OpenedImageFile	An image file that has been opened for reading containing one or more series of image-Stacks.
OpenedNamedChannels	A set of named Channels available from an OpenedImageFile.
Outline	Draws the outline of each object-mask.
OutputFeatureTable	Specifies a table of feature-calculations on objects.
OutputSequenceStackFactory	Creates output-sequences of different kinds for writing stacks to a directory.
ProvidesStackInput	Base class for inputs which somehow eventually send up providing stacks, with or without names.
RasterDirectoryObjectsGenerator	Writes each object as a binary Mask in a directory.
RasterGenerator<T>	Transforms an entity to a Stack and writes it to the file-system.
RasterGeneratorBridge<T,V>	Allows us to call an RasterGenerator<S> as if it was an RasterGenerator<T> using an function to connect the two.
RasterGeneratorDelegateToDisplayStack<T>	Delegates a RasterGeneratorSelectFormat to a SingleFileTypeGenerator<T, DisplayStack>.
RasterGeneratorDelegateToRaster<S,T>	Uses a delegate raster-generator and optionally applies a conversions before calling RasterGeneratorDelegateToRaster.transform(T).
RasterGeneratorSelectFormat<T>	A RasterGenerator that selects an appropriate output-format based upon each generated image.
ScaleableBackground	A stack that can be used as a background (and maybe scaled).
StackGenerator	Writes a stack to the filesystem.
StackIdentifiers	Common identifiers used for storing particular types of images.
StackProviderWithLabel	Combines a Provider<Stack> with a label.
StackReader	Reads an image-Stack from the file-system.
StackReaderOrientationCorrection	A StackReader that supports the correction of orientation as images are read from the file-system.
StackRGBState	Whether a stack is RGB or RGBA or neither.
StackSequenceInput	Provides a single stack (or a time series of such stacks) as an input
StackWriteAttributes	Attributes describing stack which may determine which writer is used.
StackWriteAttributesFactory	Creates StackWriteAttributes to describe certain attributes.
StackWriteOptions	A combination of attributions describing how to write a particular stack and any suggestions from the user.
StackWriter	Writes a stack (i.e.
TextStyle	The size and style of text as it should appear in an image.
TileStackProviders	Tile multiple StackProviders into a single StackProvider.
TileWithLabels	Tiles a number of StackProviderWithLabels as a single StackProvider.
TimeSeries	An ordered collection of Stacks, each representing a frame in a time-series.
WriterErrorMessageHelper	Helps create similar error messages among StackWriters.
WriteText	Creates an image that contains text only.