All Classes

Class	Description
AddToAggregateItem<S,T>	Adds an individual-item to an aggregate-item.
AggregateChannelTask	Creates a an aggregated-image for each group, where each voxel-value is aggregated across each channel in each image in the group.
All	Selects all possible channels from all possible stacks
BinaryClassifierImageLabeller	Labels images using a binary classifier.
BinaryOutcomeImageLabeller	Abstract base class for image labellers that produce binary outcomes (positive or negative).
CalculateFeaturesForObjects<T extends org.anchoranalysis.feature.input.FeatureInput>	Calculates features for objects and stores the results.
ChangeableOutputSequence<T,S>	A wrapper class that allows changing the output sequence for a given type.
ChannelConvertStyle	Converts a channel(s) at a particular timepoint into a stack(s).
ChannelGetterForTimepoint	A wrapper around ChannelGetter that retrieves channels for a specific timepoint.
ChannelSource	Extracts a set of Channels from a NamedStacks, optionally resizing.
CommonSize	Shared-state that exposes a common-size to all images.
ConsistentChannelNamesChecker	Checks that each image has an identical set of Channel-names, and RGB-state.
ConvertImageFormat	Converts each input-image to an output format, optionally changing the bit depth.
DescriptiveNameContainsImageLabeller	Labels images based on whether their descriptive name contains a specific string.
ExportFeatures<T extends org.anchoranalysis.io.input.InputFromManager,S,U extends org.anchoranalysis.feature.input.FeatureInput>	Calculates features and exports them as a CSV file.
ExportFeaturesStyle	Visual style for how features are exported.
ExportImageHistograms	Exports a histogram of voxel intensities as a CSV file for each channel of an image.
ExtractSlice	Reduces a z-stack to a single-slice by taking the optima of a feature calculated for each slice.
ExtractToRGB	Extracts three channels to make an RGB image.
FeatureCalculationContext<S>	The context in which features are calculated, so as to be later exported as a CSV.
FeatureCalculatorFromProvider<T extends org.anchoranalysis.feature.input.FeatureInputEnergy>	Calculates feature or feature values.
FeatureCalculatorRepeated	Utility class for extracting an EnergyStack from a StackProvider.
FeatureExporter<S>	Shared-state for an ExportFeatures task.
FeatureExporterContext	Context for exporting features, containing configuration and output settings.
FeatureResultsAndThumbnails	A collection of results from feature calculation, and associated thumbnails.
FeatureSource<T extends org.anchoranalysis.io.input.InputFromManager,S,U extends org.anchoranalysis.feature.input.FeatureInput>	Extracts features from some kind of inputs to produce one or more rows in a feature-table.
FileLabelMap<T>	A map that associates file identifiers with labels, typically loaded from a CSV file.
FromHistogram	Each input-file describes a histogram that produces one row of features.
FromImage	Calculates features from a single image.
FromImageMetadata	Calculates features from the metadata from single image.
FromStacks	Selects a subset of channels from a set of stacks.
GroupedSharedState<S,T>	Commonality between shared state for grouped export tasks.
GroupedStackBase<S,T>	Base class for stacks (usually each channel from an image) that are somehow grouped-together.
GroupMapByName<S,T>	Adds items to aggregate structures identified uniquely by a name, and allows these items to be later outputted.
ImageAssignLabel<T>	Assigns a label to each image and copies into subdirectories for each label, and creates a labelling CSV.
ImageCSVLabeller	Labels images based on a CSV file containing image identifiers and corresponding labels.
ImageCSVLabellerInitialization	Initialization data for an image CSV labeller.
ImageLabeller<T>	Associates a label with an image.
ImageLabellerStringMap<T>	Maps one set of labels to another
ImageLabellerStringMapInitialization<T>
ImageSizePrereader	Reads the size of each image initially, before normal (parallel) task execution.
IndependentChannels	Converts each channel independently and creates a single-channeled stack from the conversion.
InitializationFactory	Factory for creating ImageInitialization instances.
InitializationWithEnergyStack	Combines ImageInitialization with an EnergyStack.
LabelHeadersForCSV	Generates a list of header-names for columns unrelated to features (identifiers and groups)
LabelledResultsVectorWithThumbnail	Like a ResultsVectorWithThumbnail but additionally contains labels to describe the calculated results.
LabelsForInput	Calculates labels for a given input (and index).
Montage	Creates a montage of images, by tiling them side-by-side.
MontageSharedState	A Stack into which individual images are written, together with the necessary information on where to write each image.
NamedChannel	Associates a name with a Channel.
NamedChannels	A collection of Channels each with an associated unique-name.
One	Selects one specific channel from a set of stacks
RasterTask<S,U>	An experiment that takes (primarily) a series of raster images as an input.
ResultsVectorWithThumbnail	A results-vector with an optional thumbnail associated with it.
RGBIfNamesMatch	Converts a set of channels to a single RGB-stack if the channel-names match, otherwise uses fallback.
ScaleImage<S>	Base class for tasks whose primary aim is to scale (resize) an image.
ScaleImageCommonSize	Creates a scaled copy of images, ensuring all images have identical output size.
ScaleImageIndependently	Creates a scaled copy of images, treating each image independently, and without any padding or alignment.
SegmentInstanceWithModel<T extends org.anchoranalysis.inference.InferenceModel>	Using a model-pool, performs instance segmentation on an image producing zero, one or more objects per image.
SharedStateFilteredImageOutput<T>	Manages filtered image output with shared state across multiple images.
SharedStateSegmentInstance<T extends org.anchoranalysis.inference.InferenceModel>	Shared-state for instance segmentation.
SharedStateSelectedSlice	Shared state for writing selected slice information to a CSV file.
SingleRowPerInput<T extends org.anchoranalysis.io.input.InputFromManager,S extends org.anchoranalysis.feature.input.FeatureInput>	Base class for exporting features, where features are calculated per-image using a NamedFeatureStore.
SizeMapping	Maps a Path to a particular image-size and orientation-change.
SpecificAndRename	Selects a specific set of channels from stacks, each identified by a stack-name and channel index