Index (anchor-plugin-image-task 1.0.2 API)

A B C D E F G H I L M N O P R S T W
All Classes and Interfaces|All Packages|Constant Field Values

A

add(String, Channel) - Method in class org.anchoranalysis.plugin.image.task.channel.aggregator.NamedChannels: Adds a Channel with a name.
add(Optional<String>, List<Pair<String, S>>) - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupMapByName: Adds an item with a non-group identifier, and also optionally a group identifier.
add(CheckedSupplier<LabelledResultsVector, OperationFailedException>, CheckedSupplier<Optional<DisplayStack>, OperationFailedException>) - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureResultsAndThumbnails: Adds results, together with a thumbnail.
add(S, T) - Method in interface org.anchoranalysis.plugin.image.task.grouped.AddToAggregateItem: Adds an individual item to an aggregate item.
add(T, String) - Method in class org.anchoranalysis.plugin.image.task.labeller.FileLabelMap: Adds a new file identifier and label pair to the map.
additionalLabelsFor(ImageMetadataInput) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImageMetadata
additionalLabelsFor(ProvidesStackInput) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
additionalLabelsFor(FileInput) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram
additionalLabelsFor(T) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput: Additional labels for an input to include (after the identifier, and before any group labels).
AddToAggregateItem<S,T> - Interface in org.anchoranalysis.plugin.image.task.grouped: Adds an individual-item to an aggregate-item.
afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
afterAllJobsAreExecuted(FeatureExporter<S>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
afterAllJobsAreExecuted(GroupedSharedState<S, T>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
afterAllJobsAreExecuted(SharedStateFilteredImageOutput<T>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
afterAllJobsAreExecuted(SharedStateSegmentInstance<T>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
afterAllJobsAreExecuted(MontageSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage
afterAllJobsAreExecuted(SharedStateSelectedSlice, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
afterAllJobsAreExecuted(S, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
AggregateChannelTask - Class in org.anchoranalysis.plugin.image.task.bean.combine: Creates a an aggregated-image for each group, where each voxel-value is aggregated across each channel in each image in the group.
AggregateChannelTask() - Constructor for class org.anchoranalysis.plugin.image.task.bean.combine.AggregateChannelTask
All - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels: Selects all possible channels from all possible stacks
All() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.All
allLabels(NoSharedState) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryOutcomeImageLabeller
allLabels(ImageCSVLabellerInitialization) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller
allLabels(ImageLabellerStringMapInitialization<T>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
allLabels(T) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabeller: Returns a set of identifiers for all groups that can be outputted by the labeller.
assignExtent(Extent) - Method in class org.anchoranalysis.plugin.image.task.size.SizeMapping: Replace the existing Extent with a new value.

B

beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<NamedChannelsInput>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<NamedChannelsInput>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<ProvidesStackInput>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<ProvidesStackInput>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<StackSequenceInput>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<StackSequenceInput>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageCommonSize
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<StackSequenceInput>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageIndependently
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<StackSequenceInput>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
binary - Variable in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage: Iff true the image to be scaled is treated as a binary-mask, and interpolation during scaling ensures only two binary-values are outputted.
BinaryClassifierImageLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller: Labels images using a binary classifier.
BinaryClassifierImageLabeller() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller
BinaryOutcomeImageLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller: Abstract base class for image labellers that produce binary outcomes (positive or negative).
BinaryOutcomeImageLabeller() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryOutcomeImageLabeller

C

calculateAndOutput(T, FeatureCalculationContext<FeatureList<S>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput
calculateAndOutput(T, FeatureCalculationContext<S>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource: Processes one input to calculate feature-results and output them to the file-system.
CalculateFeaturesForObjects<T> - Class in org.anchoranalysis.plugin.image.task.feature.calculator: Calculates features for objects and stores the results.
CalculateFeaturesForObjects(CombineObjectsForFeatures<T>, InitializationWithEnergyStack, boolean, FeatureCalculationContext<FeatureTableCalculator<T>>) - Constructor for class org.anchoranalysis.plugin.image.task.feature.calculator.CalculateFeaturesForObjects: Creates a new CalculateFeaturesForObjects.
calculateForObjects(ObjectCollectionProvider, LabelsForInput) - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.CalculateFeaturesForObjects: Calculates features for objects provided by a ObjectCollectionProvider.
calculateForObjects(ObjectCollection, EnergyStack, LabelsForInput) - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.CalculateFeaturesForObjects: Calculates the feature-results for objects, and stores the results.
calculateResultsForInput(ImageMetadataInput, FeatureCalculationContext<FeatureList<FeatureInputImageMetadata>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImageMetadata
calculateResultsForInput(ProvidesStackInput, FeatureCalculationContext<FeatureList<FeatureInputStack>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
calculateResultsForInput(FileInput, FeatureCalculationContext<FeatureList<FeatureInputHistogram>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram
calculateResultsForInput(T, FeatureCalculationContext<FeatureList<S>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput: Calculates feature-results for a particular input.
calculatorForAll(FeatureList<T>) - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.FeatureCalculatorFromProvider: Calculates all image-features in the feature-store.
calculatorSingleFromProvider(FeatureListProvider<T>, String) - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.FeatureCalculatorFromProvider: Calculates a single-feature that comes from a provider (but can reference the other features from the store).
canEqual(Object) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
ChangeableOutputSequence<T,S> - Class in org.anchoranalysis.plugin.image.task.bean.format: A wrapper class that allows changing the output sequence for a given type.
ChangeableOutputSequence() - Constructor for class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
ChannelConvertStyle - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle: Converts a channel(s) at a particular timepoint into a stack(s).
ChannelConvertStyle() - Constructor for class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.ChannelConvertStyle
ChannelGetterForTimepoint - Class in org.anchoranalysis.plugin.image.task.stack: A wrapper around ChannelGetter that retrieves channels for a specific timepoint.
ChannelGetterForTimepoint(ChannelGetter, int) - Constructor for class org.anchoranalysis.plugin.image.task.stack.ChannelGetterForTimepoint: Creates a new ChannelGetterForTimepoint instance.
ChannelSource - Class in org.anchoranalysis.plugin.image.task.grouped: Extracts a set of Channels from a NamedStacks, optionally resizing.
ChannelSource(NamedStacks, ConsistentChannelChecker, Optional<SizeXY>, VoxelsResizer) - Constructor for class org.anchoranalysis.plugin.image.task.grouped.ChannelSource: Creates a new ChannelSource instance.
checkChannelNames(Set<String>, boolean) - Method in class org.anchoranalysis.plugin.image.task.grouped.ConsistentChannelNamesChecker: Checks that the channel-names are consistent.
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
classificationString(boolean) - Static method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryOutcomeImageLabeller: Converts a boolean classification result to its string representation.
close() - Method in class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput: Closes the CSV writer.
close() - Method in class org.anchoranalysis.plugin.image.task.stack.SharedStateSelectedSlice: Closes the CSV writer if it exists.
closeAndWriteOutputs(Optional<NamedFeatureStore<FeatureInputResults>>, boolean, Function<InputOutputContext, FeatureCSVWriterFactory>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporter: Writes all the results that have been collected as a CSV file, and closes open I/O handles and memory structures.
closeAndWriteOutputs(ExportFeaturesStyle) - Method in class org.anchoranalysis.plugin.image.task.segment.SharedStateSegmentInstance: Writes all the results that have been collected as a CSV file, and closes open I/O handles and memory structures.
closeAnyOpenIO() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureResultsAndThumbnails: Closes any open IO and removes redundant structures stored in memory.
CommonSize - Class in org.anchoranalysis.plugin.image.task.size: Shared-state that exposes a common-size to all images.
CommonSize(Extent) - Constructor for class org.anchoranalysis.plugin.image.task.size.CommonSize: Creates a new CommonSize instance.
ConsistentChannelNamesChecker - Class in org.anchoranalysis.plugin.image.task.grouped: Checks that each image has an identical set of Channel-names, and RGB-state.
ConsistentChannelNamesChecker() - Constructor for class org.anchoranalysis.plugin.image.task.grouped.ConsistentChannelNamesChecker
convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.ChannelConvertStyle: Converts a particular set of channels.
convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.ExtractToRGB
convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.IndependentChannels
convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.RGBIfNamesMatch
ConvertImageFormat - Class in org.anchoranalysis.plugin.image.task.bean.format: Converts each input-image to an output format, optionally changing the bit depth.
ConvertImageFormat() - Constructor for class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
copyStackInto(CheckedSupplier<RGBStack, InputReadFailedException>, String, Path, Optional<String>) - Method in class org.anchoranalysis.plugin.image.task.slice.MontageSharedState: Copies a Stack into a BoundingBox in the combined image, resizing if necessary.
create(List<NamedBean<FeatureListProvider<T>>>, LabelHeaders, FeatureOutputNames, Optional<InputGrouper>, FeatureExporterContext) - Static method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporter: Alternative static constructor that creates a shared-state from a list of named FeatureListProviders.
create(FeatureOutputNames, FeatureTableCalculator<T>, LabelHeaders, Optional<InputGrouper>, FeatureExporterContext) - Static method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporter: Alternative static constructor that creates a shared-state from a NamedFeatureStore.
create(NamedFeatureStore<T>, LabelHeaders, FeatureOutputNames, Optional<InputGrouper>, FeatureExporterContext) - Static method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporter: Alternative static constructor that creates a shared-state from a NamedFeatureStore.
createCalculationContext(Optional<String>, ExecutionTimeRecorder, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporter: Creates a FeatureCalculationContext for calculating features to later use this exporter.
createCalculationContext(ExecutionTimeRecorder, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.segment.SharedStateSegmentInstance: Creates a FeatureCalculationContext for calculating features to later use this exporter.
createChannelDeriver(ChannelSource) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.AggregateChannelTask
createChannelDeriver(ChannelSource) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: A function to derive the individual type used for aggregation from a Channel.
createChannelDeriver(ChannelSource) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
createExporter(LabelHeaders, List<NamedBean<FeatureListProvider<S>>>, FeatureOutputNames, Optional<InputGrouper>, FeatureExporterContext) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput
createExporter(LabelHeaders, List<NamedBean<FeatureListProvider<U>>>, FeatureOutputNames, Optional<InputGrouper>, FeatureExporterContext) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource: Creates the FeatureExporter to be used for calculating and exporting feature-results.
createGroupMap(ConsistentChannelChecker, Optional<Stream<String>>, Optional<InputOutputContext>, OperationContext) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.AggregateChannelTask
createGroupMap(ConsistentChannelChecker, Optional<Stream<String>>, Optional<InputOutputContext>, OperationContext) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: Creates a map for the storing an aggregate-data-object for each group.
createGroupMap(ConsistentChannelChecker, Optional<Stream<String>>, Optional<InputOutputContext>, OperationContext) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
createHeaders(String[], Optional<String>, boolean) - Static method in class org.anchoranalysis.plugin.image.task.feature.LabelHeadersForCSV: Creates the label-headers (the headers for columns not associated with features).
createSharedStateJob(InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat: Sets a new output-sequence for the series.
createSharedStateJob(InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.RasterTask: Creates a shared-state for the duration of a particular input-job.
createWithoutStacks(InitializationContext) - Static method in class org.anchoranalysis.plugin.image.task.stack.InitializationFactory: Creates an ImageInitialization without adding any stacks.
createWithStacks(ProvidesStackInput, InitializationContext) - Static method in class org.anchoranalysis.plugin.image.task.stack.InitializationFactory: Creates an ImageInitialization with stacks added from the input.
csvWriter(FeatureCSVMetadata) - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporterContext: Creates a FeatureCSVWriter for the non-aggregated results.

D

defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.AggregateChannelTask
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
deriveContext(InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeaturesStyle: Derives a FeatureExporterContext from the current style and given context.
deriveLabels(String, Optional<String>, int) - Method in interface org.anchoranalysis.plugin.image.task.feature.calculator.LabelsForInput: Calculates labels for a given input (and index).
DescriptiveNameContainsImageLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller: Labels images based on whether their descriptive name contains a specific string.
DescriptiveNameContainsImageLabeller() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.DescriptiveNameContainsImageLabeller
doJobOnInput(InputBound<NamedChannelsInput, SharedStateSelectedSlice>) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
doJobOnInput(InputBound<NamedChannelsInput, S>) - Method in class org.anchoranalysis.plugin.image.task.bean.RasterTask
doJobOnInput(InputBound<ProvidesStackInput, GroupedSharedState<S, T>>) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
doJobOnInput(InputBound<ProvidesStackInput, SharedStateFilteredImageOutput<T>>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
doJobOnInput(InputBound<StackSequenceInput, SharedStateSegmentInstance<T>>) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
doJobOnInput(InputBound<StackSequenceInput, MontageSharedState>) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage
doJobOnInput(InputBound<StackSequenceInput, S>) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
doJobOnInput(InputBound<T, FeatureExporter<S>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
doStack(InputBound<NamedChannelsInput, NoSharedState>, OutputSequenceIndexed<Stack, String>, int, int, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
doStack(InputBound<NamedChannelsInput, S>, U, int, int, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.RasterTask: Processes one stack from a series.
drawAllLabels(double, BoxAligner) - Method in class org.anchoranalysis.plugin.image.task.slice.MontageSharedState: Draw all labels that have been queued during calls to MontageSharedState.copyStackInto(org.anchoranalysis.core.functional.checked.CheckedSupplier<org.anchoranalysis.image.core.stack.RGBStack, org.anchoranalysis.io.input.InputReadFailedException>, java.lang.String, java.nio.file.Path, java.util.Optional<java.lang.String>).

E

endSeries(NoSharedState, OutputSequenceIndexed<Stack, String>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
endSeries(S, U, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.RasterTask: Ends processing of a series.
entrySet() - Method in class org.anchoranalysis.plugin.image.task.labeller.FileLabelMap: Gets the entry set of the internal map.
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporterContext
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.feature.InitializationWithEnergyStack
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.feature.LabelledResultsVectorWithThumbnail
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.grouped.NamedChannel
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageCSVLabellerInitialization
equals(Object) - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitialization
ExportFeatures<T,S,U> - Class in org.anchoranalysis.plugin.image.task.bean.feature: Calculates features and exports them as a CSV file.
ExportFeatures() - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
ExportFeaturesStyle - Class in org.anchoranalysis.plugin.image.task.bean.feature: Visual style for how features are exported.
ExportFeaturesStyle() - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeaturesStyle
ExportFeaturesStyle(boolean, boolean, boolean) - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeaturesStyle: Creates a new ExportFeaturesStyle instance.
ExportImageHistograms - Class in org.anchoranalysis.plugin.image.task.bean.grouped.histogram: Exports a histogram of voxel intensities as a CSV file for each channel of an image.
ExportImageHistograms() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
extent() - Method in class org.anchoranalysis.plugin.image.task.size.CommonSize: The common-size of all images.
extractChannel(String, boolean) - Method in class org.anchoranalysis.plugin.image.task.grouped.ChannelSource: Extracts a Channel from a particular Stack in stackStore.
extractChannel(String, boolean, int) - Method in class org.anchoranalysis.plugin.image.task.grouped.ChannelSource: Extracts a Channel from a particular Stack in stackStore.
extractChannel(Stack, boolean, int) - Method in class org.anchoranalysis.plugin.image.task.grouped.ChannelSource: Extracts a Channel from a given Stack.
ExtractSlice - Class in org.anchoranalysis.plugin.image.task.bean.slice: Reduces a z-stack to a single-slice by taking the optima of a feature calculated for each slice.
ExtractSlice() - Constructor for class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
extractStack(ProvidesStackInput, StackProvider, InputOutputContext) - Static method in class org.anchoranalysis.plugin.image.task.feature.calculator.FeatureCalculatorRepeated: Extracts an EnergyStack from the given input and stack provider.
ExtractToRGB - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle: Extracts three channels to make an RGB image.
ExtractToRGB() - Constructor for class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.ExtractToRGB

F

FeatureCalculationContext<S> - Class in org.anchoranalysis.plugin.image.task.feature: The context in which features are calculated, so as to be later exported as a CSV.
FeatureCalculationContext(FeatureResultsAndThumbnails, S, FeatureNameList, Optional<String>, ExecutionTimeRecorder, boolean, InputOutputContext) - Constructor for class org.anchoranalysis.plugin.image.task.feature.FeatureCalculationContext: Creates a new FeatureCalculationContext.
FeatureCalculatorFromProvider<T> - Class in org.anchoranalysis.plugin.image.task.feature.calculator: Calculates feature or feature values.
FeatureCalculatorFromProvider(ProvidesStackInput, Optional<StackProvider>, InputOutputContext) - Constructor for class org.anchoranalysis.plugin.image.task.feature.calculator.FeatureCalculatorFromProvider: Creates a new FeatureCalculatorFromProvider.
FeatureCalculatorRepeated - Class in org.anchoranalysis.plugin.image.task.feature.calculator: Utility class for extracting an EnergyStack from a StackProvider.
FeatureExporter<S> - Class in org.anchoranalysis.plugin.image.task.feature: Shared-state for an ExportFeatures task.
FeatureExporter(FeatureOutputMetadata, Supplier<S>, Optional<InputGrouper>, FeatureExporterContext) - Constructor for class org.anchoranalysis.plugin.image.task.feature.FeatureExporter: Creates the shared state.
FeatureExporterContext - Class in org.anchoranalysis.plugin.image.task.feature: Context for exporting features, containing configuration and output settings.
FeatureExporterContext(InputOutputContext, boolean, boolean, boolean) - Constructor for class org.anchoranalysis.plugin.image.task.feature.FeatureExporterContext: Creates a new FeatureExporterContext instance.
FeatureResultsAndThumbnails - Class in org.anchoranalysis.plugin.image.task.feature: A collection of results from feature calculation, and associated thumbnails.
FeatureResultsAndThumbnails(FeatureOutputMetadata, FeatureExporterContext) - Constructor for class org.anchoranalysis.plugin.image.task.feature.FeatureResultsAndThumbnails: Creates a new FeatureResultsAndThumbnails.
FeatureSource<T,S,U> - Class in org.anchoranalysis.plugin.image.task.bean.feature.source: Extracts features from some kind of inputs to produce one or more rows in a feature-table.
FeatureSource() - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource
FileLabelMap<T> - Class in org.anchoranalysis.plugin.image.task.labeller: A map that associates file identifiers with labels, typically loaded from a CSV file.
FromHistogram - Class in org.anchoranalysis.plugin.image.task.bean.feature.source: Each input-file describes a histogram that produces one row of features.
FromHistogram() - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram: Creates a new FromHistogram instance.
FromImage - Class in org.anchoranalysis.plugin.image.task.bean.feature.source: Calculates features from a single image.
FromImage() - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage: Creates a new FromImage instance.
FromImageMetadata - Class in org.anchoranalysis.plugin.image.task.bean.feature.source: Calculates features from the metadata from single image.
FromImageMetadata() - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImageMetadata: Creates a new FromImageMetadata instance.
FromStacks - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels: Selects a subset of channels from a set of stacks.
FromStacks() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.FromStacks

G

get(T) - Method in class org.anchoranalysis.plugin.image.task.labeller.FileLabelMap: Gets the label associated with a file identifier.
getAggregator() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.AggregateChannelTask: How to aggregate the Channels.
getAlign() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageCommonSize: How a smaller image (after scaling) is aligned to the larger image (with the common size).
getAligner() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: When varyImageSize==false and varyImageLocation==false, how to align a smaller image inside a larger cell.
getAlignerLabel() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: When label==false and varyImageLocation==false, how to align the label with its associated image.
getBackgroundIntensity() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageCommonSize: The background intensity to use in each channel when the scaled image does not cover the entire canvas.
getChannel() - Method in class org.anchoranalysis.plugin.image.task.grouped.NamedChannel: The Channel instance.
getChannel(String, Logger) - Method in class org.anchoranalysis.plugin.image.task.stack.ChannelGetterForTimepoint: Retrieves a channel with the given name for the specified timepoint.
getChannelChecker() - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupedSharedState: Checks that Channels have a consistent voxel-data type.
getChannelConversionStyle() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat: To convert as RGB or independently or in another way.
getChannelConverter() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat: Optionally, how to convert from one bit-depth to another (scaling, clamping etc.)
getChannelIndex() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One: The index of the channel to retrieve from stackName.
getChannelMask() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms: If defined, this is the name of channel used as a mask over the values which are fed into the histogram
getChannelNames() - Method in class org.anchoranalysis.plugin.image.task.grouped.ConsistentChannelNamesChecker: The names of Channels that are consistent across all images.
getChannelNamesChecker() - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupedSharedState: Checks that each image provides a consistent set of channels, and that they have the same RGB-state.
getClassifierProvider() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller: Provider for the classifier feature list.
getContains() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.DescriptiveNameContainsImageLabeller: The string to search for in the image's descriptive name.
getContext() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureCalculationContext: The input-output context for the operation.
getContext() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporterContext: Context for reading from or writing outputs to the file-system.
getDisplayer() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: How to convert an image to be displayed to the user.
getEnergyStack() - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.FeatureCalculatorFromProvider: The energy stack used for feature calculations.
getEnergyStack() - Method in class org.anchoranalysis.plugin.image.task.feature.InitializationWithEnergyStack: The energy stack.
getExecutionTimeRecorder() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureCalculationContext: Records the execution-time of particular operations.
getExtent() - Method in class org.anchoranalysis.plugin.image.task.size.SizeMapping: The size.
getFallback() - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.ExtractToRGB: If a channel doesn't match an RGB pattern, this conversion-style can be used instead.
getFallback() - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.RGBIfNamesMatch: If a channel doesn't match an RGB pattern, this conversion-style can be used instead.
getFeatureNames() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureCalculationContext: The name of each feature being calculated, in identical order, as that is placed in the exported CSV.
getFeatureNames() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporter: The names of the features to be exported.
getFeatures() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: The features to be exported (after possibly some manipulation or augmentation).
getFeatures() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: Features to calculate for objects in the features output.
getFeaturesAggregate() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Features applied to each group to aggregate values (accepting FeatureInputResults).
getFeatureSource() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureCalculationContext: The features that are calculated, encapsulated in some object.
getFilter() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
getFilterInitialization(Path) - Method in class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput: Gets the filter initialization, initializing it if necessary.
getFixedSizeScaler() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: How to calculate the size of each image, when varyImageSize==false.
getGroup() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Includes an additional group column in CSVs, and creates group-specific feature files.
getGroup() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: How to partition the inputs into groups.
getGrouper() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporter: When defined, assigns each input to a group.
getGrouper() - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupedSharedState: How to group the inputs.
getGroupGeneratorName() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureCalculationContext: The optional name of the group generator.
getGroupMap() - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupedSharedState: Gets the group map, creating it if it doesn't exist yet.
getHistogram() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram: If non-null, a histogram is extracted from this provider rather than the histogram from the inputted CSV.
getId() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Translates an input file name to a unique ID.
getImage() - Method in class org.anchoranalysis.plugin.image.task.feature.InitializationWithEnergyStack: The image initialization.
getImageLabeller() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel: Maps a label to an image
getImageMetadataReader() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: How to read the ImageMetadata from the file-system.
getImageMetadataReader() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageCommonSize: How to read the ImageMetadata from the file-system.
getInitialization() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitialization
getInterpolator() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: How to resize images.
getInterpolator() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: The interpolator to use for scaling images.
getInterpolator() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage: The interpolator to use for scaling images.
getInterpolator() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: The interpolator to use for scaling images.
getLabelMap() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageCSVLabellerInitialization: The map associating file identifiers with labels.
getLabels() - Method in class org.anchoranalysis.plugin.image.task.feature.LabelledResultsVectorWithThumbnail: The labels describing the results.
getList() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.SpecificAndRename
getListFeatures() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller: List of named feature list providers for additional features.
getLogger() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureCalculationContext: Gets the logger for the context.
getMap() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
getMap() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitialization
getMaskValue() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms: What voxel value to read as "On" in the mask above.
getModelDirectory() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureCalculationContext: Gets the model directory path.
getModelPool() - Method in class org.anchoranalysis.plugin.image.task.segment.SharedStateSegmentInstance: The concurrent model pool for inference.
getName() - Method in class org.anchoranalysis.plugin.image.task.grouped.NamedChannel: The name associated with the channel.
getOperationContext() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureCalculationContext: Gets the operation context.
getOutlineColor() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: The color of the outline.
getOutlineWidth() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: The width of the outline.
getOutputName() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.AggregateChannelTask: How to name the aggregated channel in the output.
getOutputStackProvider() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel: If it's set, a stack is generated that is outputted into subdirectory corresponding to the groupIdentifier.
getOutputterFor(String) - Method in class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput: Gets the outputter for a specific group identifier.
getPath() - Method in class org.anchoranalysis.plugin.image.task.size.SizeMapping: The path.
getPathLabel() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller: Path to a CSV label file (comma-separated, with header, no quotes).
getRatioHeightForLabel() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: When label==true, this determines the height of the label.
getRatioRowsToColumns() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: An ideal approximate ratio of the number of rows to the number of columns.
getResizeTo() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: If set, each channel is scaled to a specific size before aggregation (useful for combining different sized images).
getResults() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureCalculationContext: The stored results and thumbnail writer.
getResults() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporter: Saved store feature calculation results, and writes associated thumbnails.
getResults() - Method in class org.anchoranalysis.plugin.image.task.feature.LabelledResultsVectorWithThumbnail: The results vector with an optional thumbnail.
getResultsVector() - Method in class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail: Supplier for the ResultsVector.
getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage: Calculates what scale-factor to apply on the image.
getScoreProvider() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
getSegment() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: The segmentation algorithm.
getSelectChannels() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: Selects which channels are included, optionally renaming.
getSequence() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence: The current output sequence.
getSource() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Source of feature-values to be exported.
getStack() - Method in class org.anchoranalysis.plugin.image.task.slice.MontageSharedState: The stack into which individual images are written.
getStackEnergy() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage: Optionally defines an energy-stack for feature calculation (if not set, the energy-stack is considered to be the input stacks).
getStackEnergy() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller: Provider for the energy stack.
getStackEnergy() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
getStackName() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One: If defined, processing only occurs the stack with this specific name and index.
getStackReader() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: Fallback for imageMetadataReader to read image files without a directy metadata reader.
getStackReader() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageCommonSize: Fallback for imageMetadataReader to read image files without a direct metadata reader.
getStackStore() - Method in class org.anchoranalysis.plugin.image.task.grouped.ChannelSource: A named set of Stacks from which Channels may be extracted.
getStyle() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Visual style for how feature export occurs.
getStyle() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: Visual style for how feature export occurs.
getThumbnail() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage: Method to generate a thumbnail for images.
getThumbnail() - Method in class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail: Supplier for the optional thumbnail DisplayStack.
getVaryingSizeWidth() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: If no specific width or scaling-factor is suggested, this determines the default width that the combined-montage should have, when varyImageSize==true.
getVaryingSizeWidthRatio() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: If no specific width or scaling-factor is suggested, this determines the default percentage of the existing size, the combined-montage should have, when varyImageSize==true.
GroupedSharedState<S,T> - Class in org.anchoranalysis.plugin.image.task.grouped: Commonality between shared state for grouped export tasks.
GroupedSharedState(Optional<InputGrouper>, Function<ConsistentChannelChecker, GroupMapByName<S, T>>) - Constructor for class org.anchoranalysis.plugin.image.task.grouped.GroupedSharedState: Creates a new GroupedSharedState instance.
GroupedStackBase<S,T> - Class in org.anchoranalysis.plugin.image.task.bean.grouped: Base class for stacks (usually each channel from an image) that are somehow grouped-together.
GroupedStackBase() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
GroupMapByName<S,T> - Class in org.anchoranalysis.plugin.image.task.grouped: Adds items to aggregate structures identified uniquely by a name, and allows these items to be later outputted.
GroupMapByName(String, Optional<Stream<String>>, Optional<InputOutputContext>, Supplier<T>, CheckedBiConsumer<S, T, OperationFailedException>) - Constructor for class org.anchoranalysis.plugin.image.task.grouped.GroupMapByName: Creates a group-map.

H

hasChannel(String) - Method in class org.anchoranalysis.plugin.image.task.stack.ChannelGetterForTimepoint: Checks if a channel with the given name exists.
hashCode() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
hashCode() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporterContext
hashCode() - Method in class org.anchoranalysis.plugin.image.task.feature.InitializationWithEnergyStack
hashCode() - Method in class org.anchoranalysis.plugin.image.task.feature.LabelledResultsVectorWithThumbnail
hashCode() - Method in class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail
hashCode() - Method in class org.anchoranalysis.plugin.image.task.grouped.NamedChannel
hashCode() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageCSVLabellerInitialization
hashCode() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitialization
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
headers(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource: Generates label-headers for the non-feature-result columns in the CSV.
headers(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput

I

ImageAssignLabel<T> - Class in org.anchoranalysis.plugin.image.task.bean.labeller: Assigns a label to each image and copies into subdirectories for each label, and creates a labelling CSV.
ImageAssignLabel() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
ImageCSVLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller: Labels images based on a CSV file containing image identifiers and corresponding labels.
ImageCSVLabeller() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller
ImageCSVLabellerInitialization - Class in org.anchoranalysis.plugin.image.task.labeller: Initialization data for an image CSV labeller.
ImageCSVLabellerInitialization(FileLabelMap<String>) - Constructor for class org.anchoranalysis.plugin.image.task.labeller.ImageCSVLabellerInitialization: Creates a new ImageCSVLabellerInitialization instance.
ImageLabeller<T> - Class in org.anchoranalysis.plugin.image.task.bean.labeller: Associates a label with an image.
ImageLabeller() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabeller
ImageLabellerStringMap<T> - Class in org.anchoranalysis.plugin.image.task.bean.labeller: Maps one set of labels to another
ImageLabellerStringMap() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
ImageLabellerStringMapInitialization<T> - Class in org.anchoranalysis.plugin.image.task.labeller
ImageLabellerStringMapInitialization(Map<String, String>, T) - Constructor for class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitialization
ImageSizePrereader - Class in org.anchoranalysis.plugin.image.task.stack: Reads the size of each image initially, before normal (parallel) task execution.
ImageSizePrereader(ImageMetadataReader, StackReader, OperationContext) - Constructor for class org.anchoranalysis.plugin.image.task.stack.ImageSizePrereader: Creates a new ImageSizePrereader instance.
imageSizesFor(List<StackSequenceInput>) - Method in class org.anchoranalysis.plugin.image.task.stack.ImageSizePrereader: Extract the image-size for each StackSequenceInput.
includeGroupInExperiment(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource: Determines if group columns should be added to the CSV exports and other group exports may occur in sub-directories.
includeGroupInExperiment(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram
includeGroupInExperiment(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
includeGroupInExperiment(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImageMetadata
IndependentChannels - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle: Converts each channel independently and creates a single-channeled stack from the conversion.
IndependentChannels() - Constructor for class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.IndependentChannels
InitializationFactory - Class in org.anchoranalysis.plugin.image.task.stack: Factory for creating ImageInitialization instances.
InitializationWithEnergyStack - Class in org.anchoranalysis.plugin.image.task.feature: Combines ImageInitialization with an EnergyStack.
InitializationWithEnergyStack(EnergyStack, InitializationContext) - Constructor for class org.anchoranalysis.plugin.image.task.feature.InitializationWithEnergyStack: Creates a new instance with a given energy stack and initialization context.
InitializationWithEnergyStack(ImageInitialization, EnergyStack) - Constructor for class org.anchoranalysis.plugin.image.task.feature.InitializationWithEnergyStack: Creates a new InitializationWithEnergyStack instance.
initialize(Path) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryOutcomeImageLabeller
initialize(Path) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller
initialize(Path) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabeller: Initializes the labeller.
initialize(Path) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource: Specifies the highest class(es) that will function as a valid input.
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImageMetadata
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.RasterTask
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
isBinary() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage: Iff true the image to be scaled is treated as a binary-mask, and interpolation during scaling ensures only two binary-values are outputted.
isCsvIgnoreZeros() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms: Iff true, bins with zero-counts are not written as a row in the CSV file.
isFindMaxima() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice: If true, the maxima of the score is searched for.
isIgnoreMissingChannel() - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.IndependentChannels: Iff true and we cannot find a channel in the file, we ignore it and carry on
isIgnoreNoObjects() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: When true, then the outputs (outline, mask, image etc.) are not written for images that produce no objects.
isRemoveNaNColumns() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeaturesStyle: When true, columns containing all Double.NaN values are removed before outputting.
isRemoveNaNColumns() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporterContext: When true, columns containing all Double.NaN values are removed before outputting.
isRgb() - Method in class org.anchoranalysis.plugin.image.task.channel.aggregator.NamedChannels: Whether the channels originate from a Stack that is RGB, or not.
isSlicewise() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.AggregateChannelTask: When true, a 3D image is added slice-by-slice to the aggregation, treating each slice as a separate image.
isSuppressErrors() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeaturesStyle: When false, an image is reported as errored, if any exception is thrown during calculation.
isSuppressErrors() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureCalculationContext: When false, an image is reported as errored, if any exception is thrown during calculation.
isSuppressErrors() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporterContext: If false, an image is reported as errored, if any exception is thrown during calculation.
isSuppressSeries() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat: If true, the series index is not included in the outputted file-names.
isThumbnailsEnabled() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureCalculationContext: Whether thumbnails are enabled for output.
isVaryColors() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: When true, the colors change for different objects in the image (using a default color set).
isVaryImageLocation() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: When true, the location of an image in the grid, as well as the number of images in each row are both allowed to vary to fill space.
isVaryImageSize() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: When true, the images may vary in width/height in their respective rows to fill space, while preserving the aspect-ratio of each image.
isVisuallyShortenDecimals() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeaturesStyle: When true, feature-values are shown as visually compressed as possible, including suppressing decimal places.
isVisuallyShortenDecimals() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporterContext: When true double values are printed to be as short as possible without losing precision.
iterator() - Method in class org.anchoranalysis.plugin.image.task.channel.aggregator.NamedChannels

L

labelFor(NoSharedState, ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller: Determines the label for a given input image.
labelFor(NoSharedState, ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.DescriptiveNameContainsImageLabeller
labelFor(ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput: Determines a particular group-identifier for an input.
labelFor(ImageCSVLabellerInitialization, ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller
labelFor(ImageLabellerStringMapInitialization<T>, ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
labelFor(T, ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabeller: Determines a particular group-identifier (label) for an input.
LabelHeadersForCSV - Class in org.anchoranalysis.plugin.image.task.feature: Generates a list of header-names for columns unrelated to features (identifiers and groups)
LabelledResultsVectorWithThumbnail - Class in org.anchoranalysis.plugin.image.task.feature: Like a ResultsVectorWithThumbnail but additionally contains labels to describe the calculated results.
LabelledResultsVectorWithThumbnail(RowLabels, ResultsVectorWithThumbnail) - Constructor for class org.anchoranalysis.plugin.image.task.feature.LabelledResultsVectorWithThumbnail: Creates a new LabelledResultsVectorWithThumbnail instance.
labels() - Method in class org.anchoranalysis.plugin.image.task.labeller.FileLabelMap: Gets a set of all unique labels in the map.
LabelsForInput - Interface in org.anchoranalysis.plugin.image.task.feature.calculator: Calculates labels for a given input (and index).

M

Montage - Class in org.anchoranalysis.plugin.image.task.bean.combine: Creates a montage of images, by tiling them side-by-side.
Montage() - Constructor for class org.anchoranalysis.plugin.image.task.bean.combine.Montage
MontageSharedState - Class in org.anchoranalysis.plugin.image.task.slice: A Stack into which individual images are written, together with the necessary information on where to write each image.
MontageSharedState(Map<Path, BoundingBoxEnclosed>, Extent, VoxelsResizer, ExecutionTimeRecorder) - Constructor for class org.anchoranalysis.plugin.image.task.slice.MontageSharedState: Create with a mapping from Paths to boxes.

N

NamedChannel - Class in org.anchoranalysis.plugin.image.task.grouped: Associates a name with a Channel.
NamedChannel(String, Channel) - Constructor for class org.anchoranalysis.plugin.image.task.grouped.NamedChannel: Creates a new NamedChannel instance.
NamedChannels - Class in org.anchoranalysis.plugin.image.task.channel.aggregator: A collection of Channels each with an associated unique-name.
NamedChannels(boolean) - Constructor for class org.anchoranalysis.plugin.image.task.channel.aggregator.NamedChannels: Creates a new NamedChannels instance.
NamedChannels(Stream<NamedChannels>) - Constructor for class org.anchoranalysis.plugin.image.task.channel.aggregator.NamedChannels: Creates by combining multiple existing NamedChannels.
names() - Method in class org.anchoranalysis.plugin.image.task.channel.aggregator.NamedChannels: The names of the Channels.

O

One - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels: Selects one specific channel from a set of stacks
One() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One
org.anchoranalysis.plugin.image.task.bean - package org.anchoranalysis.plugin.image.task.bean: A parent package for many different kinds of tasks.
org.anchoranalysis.plugin.image.task.bean.combine - package org.anchoranalysis.plugin.image.task.bean.combine: Combining multiple images together into a single image.
org.anchoranalysis.plugin.image.task.bean.feature - package org.anchoranalysis.plugin.image.task.bean.feature: Tasks pertaining to Features.
org.anchoranalysis.plugin.image.task.bean.feature.source - package 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 - package org.anchoranalysis.plugin.image.task.bean.format: Tasks for converting image-formats.
org.anchoranalysis.plugin.image.task.bean.format.convertstyle - package 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 - package 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 - package org.anchoranalysis.plugin.image.task.bean.grouped.histogram: Task(s) to export histograms of intensity values.
org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels - package org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels: Selecting a subset of a set of channels.
org.anchoranalysis.plugin.image.task.bean.labeller - package org.anchoranalysis.plugin.image.task.bean.labeller: Associating labels with images.
org.anchoranalysis.plugin.image.task.bean.scale - package org.anchoranalysis.plugin.image.task.bean.scale: Tasks to scale an image.
org.anchoranalysis.plugin.image.task.bean.segment - package org.anchoranalysis.plugin.image.task.bean.segment: Tasks to segment an image.
org.anchoranalysis.plugin.image.task.bean.slice - package 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 - package org.anchoranalysis.plugin.image.task.channel.aggregator: Combines multiple Channels voxel-wise to form a single aggregated Channel.
org.anchoranalysis.plugin.image.task.feature - package org.anchoranalysis.plugin.image.task.feature: Non-bean classes pertaining to Features as used in tasks.
org.anchoranalysis.plugin.image.task.feature.calculator - package org.anchoranalysis.plugin.image.task.feature.calculator: Non-beans for calculating Features.
org.anchoranalysis.plugin.image.task.grouped - package org.anchoranalysis.plugin.image.task.grouped: Non-bean classes about grouping channels or other inputs.
org.anchoranalysis.plugin.image.task.labeller - package org.anchoranalysis.plugin.image.task.labeller: Non-bean classes about labelling images.
org.anchoranalysis.plugin.image.task.segment - package org.anchoranalysis.plugin.image.task.segment: Non-bean classes for image-segmentation.
org.anchoranalysis.plugin.image.task.size - package org.anchoranalysis.plugin.image.task.size: Non-bean classes pertaining to determining the size of an image.
org.anchoranalysis.plugin.image.task.slice - package org.anchoranalysis.plugin.image.task.slice: Non-bean classes pertaining to combining stacks into a single stack.
org.anchoranalysis.plugin.image.task.stack - package org.anchoranalysis.plugin.image.task.stack: Non-bean classes pertaining to stacks and channels as used in tasks.
OUTPUT_NAMES - Static variable in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Default names for various outputs from the task.
OUTPUT_THUMBNAILS - Static variable in class org.anchoranalysis.plugin.image.task.feature.FeatureExporter: The output-name for writing thumbnails.
outputAnyRemainingGroups() - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupMapByName: Outputs any groups that have not already been outputted.
outputGroupIntoSubdirectory(Collection<Map.Entry<String, T>>, Function<Boolean, InputOutputContext>, Optional<String>) - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupMapByName: Output a particular group into a subdirectory.
outputNameForGroups() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.AggregateChannelTask
outputNameForGroups() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: The first-level output-name used for determining if groups are written.
outputNameForGroups() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms

P

processIndividual(String, Channel, boolean, CheckedBiConsumer<String, Channel, OperationFailedException>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.AggregateChannelTask
processIndividual(String, Histogram, boolean, CheckedBiConsumer<String, Histogram, OperationFailedException>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
processIndividual(String, S, boolean, CheckedBiConsumer<String, S, OperationFailedException>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: Processes each derived individual element from a Channel, calling consumeIndividual one or more times.

R

RasterTask<S,U> - Class in org.anchoranalysis.plugin.image.task.bean: An experiment that takes (primarily) a series of raster images as an input.
RasterTask() - Constructor for class org.anchoranalysis.plugin.image.task.bean.RasterTask
readFromCSV(Path, boolean) - Static method in class org.anchoranalysis.plugin.image.task.labeller.FileLabelMap: Reads a FileLabelMap from a CSV file.
ResultsVectorWithThumbnail - Class in org.anchoranalysis.plugin.image.task.feature: A results-vector with an optional thumbnail associated with it.
ResultsVectorWithThumbnail(CheckedSupplier<ResultsVector, OperationFailedException>) - Constructor for class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail: Creates a new instance with a results vector and no thumbnail.
ResultsVectorWithThumbnail(CheckedSupplier<ResultsVector, OperationFailedException>, CheckedSupplier<Optional<DisplayStack>, OperationFailedException>) - Constructor for class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail: Creates a new ResultsVectorWithThumbnail instance.
RGBIfNamesMatch - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle: Converts a set of channels to a single RGB-stack if the channel-names match, otherwise uses fallback.
RGBIfNamesMatch() - Constructor for class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.RGBIfNamesMatch

S

scaleCalculator - Variable in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage: Calculates what scale-factor to apply on the image.
ScaleImage<S> - Class in org.anchoranalysis.plugin.image.task.bean.scale: Base class for tasks whose primary aim is to scale (resize) an image.
ScaleImage() - Constructor for class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
ScaleImageCommonSize - Class in org.anchoranalysis.plugin.image.task.bean.scale: Creates a scaled copy of images, ensuring all images have identical output size.
ScaleImageCommonSize() - Constructor for class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageCommonSize
ScaleImageIndependently - Class in org.anchoranalysis.plugin.image.task.bean.scale: Creates a scaled copy of images, treating each image independently, and without any padding or alignment.
ScaleImageIndependently() - Constructor for class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageIndependently
scaleStack(Stack, Optional<ImageSizeSuggestion>, VoxelsResizer, NoSharedState) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageIndependently
scaleStack(Stack, Optional<ImageSizeSuggestion>, VoxelsResizer, CommonSize) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageCommonSize
scaleStack(Stack, Optional<ImageSizeSuggestion>, VoxelsResizer, S) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage: Produce a scaled version of a Stack, mapping each channel to a scaled version of itself.
scaleXYBy(ScaleFactor) - Method in class org.anchoranalysis.plugin.image.task.size.SizeMapping: Scales the XY dimensions the factor.
SegmentInstanceWithModel<T> - Class in org.anchoranalysis.plugin.image.task.bean.segment: Using a model-pool, performs instance segmentation on an image producing zero, one or more objects per image.
SegmentInstanceWithModel() - Constructor for class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
selectChannels(ChannelSource, boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.All
selectChannels(ChannelSource, boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.FromStacks: Takes a stack-collection and extracts a set of references to particular channels (each with a name).
selectChannels(ChannelSource, boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One
selectChannels(ChannelSource, boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.SpecificAndRename
setAggregator(ChannelAggregator) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.AggregateChannelTask: How to aggregate the Channels.
setAlign(Align) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageCommonSize: How a smaller image (after scaling) is aligned to the larger image (with the common size).
setAligner(BoxAligner) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: When varyImageSize==false and varyImageLocation==false, how to align a smaller image inside a larger cell.
setAlignerLabel(BoxAligner) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: When label==false and varyImageLocation==false, how to align the label with its associated image.
setBackgroundIntensity(int) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageCommonSize: The background intensity to use in each channel when the scaled image does not cover the entire canvas.
setBinary(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage: Iff true the image to be scaled is treated as a binary-mask, and interpolation during scaling ensures only two binary-values are outputted.
setChannelConversionStyle(ChannelConvertStyle) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat: To convert as RGB or independently or in another way.
setChannelConverter(ConvertChannelTo<?>) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat: Optionally, how to convert from one bit-depth to another (scaling, clamping etc.)
setChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One: The index of the channel to retrieve from stackName.
setChannelMask(String) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms: If defined, this is the name of channel used as a mask over the values which are fed into the histogram
setClassifierProvider(FeatureListProvider<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller: Provider for the classifier feature list.
setContains(String) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.DescriptiveNameContainsImageLabeller: The string to search for in the image's descriptive name.
setCsvIgnoreZeros(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms: Iff true, bins with zero-counts are not written as a row in the CSV file.
setDisplayer(StackDisplayer) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: How to convert an image to be displayed to the user.
setFallback(ChannelConvertStyle) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.ExtractToRGB: If a channel doesn't match an RGB pattern, this conversion-style can be used instead.
setFallback(ChannelConvertStyle) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.RGBIfNamesMatch: If a channel doesn't match an RGB pattern, this conversion-style can be used instead.
setFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: Features to calculate for objects in the features output.
setFeatures(List<NamedBean<FeatureListProvider<U>>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: The features to be exported (after possibly some manipulation or augmentation).
setFeaturesAggregate(List<NamedBean<FeatureListProvider<FeatureInputResults>>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Features applied to each group to aggregate values (accepting FeatureInputResults).
setFilter(ImageLabeller<T>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
setFindMaxima(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice: If true, the maxima of the score is searched for.
setFixedSizeScaler(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: How to calculate the size of each image, when varyImageSize==false.
setGroup(Grouper) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Includes an additional group column in CSVs, and creates group-specific feature files.
setGroup(Grouper) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: How to partition the inputs into groups.
setHistogram(HistogramProvider) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram: If non-null, a histogram is extracted from this provider rather than the histogram from the inputted CSV.
setId(DerivePath) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Translates an input file name to a unique ID.
setIgnoreMissingChannel(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.IndependentChannels: Iff true and we cannot find a channel in the file, we ignore it and carry on
setIgnoreNoObjects(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: When true, then the outputs (outline, mask, image etc.) are not written for images that produce no objects.
setImageLabeller(ImageLabeller<T>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel: Maps a label to an image
setImageMetadataReader(ImageMetadataReader) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: How to read the ImageMetadata from the file-system.
setImageMetadataReader(ImageMetadataReader) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageCommonSize: How to read the ImageMetadata from the file-system.
setInterpolator(Interpolator) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: How to resize images.
setInterpolator(Interpolator) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: The interpolator to use for scaling images.
setInterpolator(Interpolator) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage: The interpolator to use for scaling images.
setInterpolator(Interpolator) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: The interpolator to use for scaling images.
setList(List<NamedBean<FromStack>>) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.SpecificAndRename
setListFeatures(List<NamedBean<FeatureListProvider<FeatureInputStack>>>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller: List of named feature list providers for additional features.
setMap(StringMap) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
setMaskValue(int) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms: What voxel value to read as "On" in the mask above.
setOutlineColor(RGBColorBean) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: The color of the outline.
setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: The width of the outline.
setOutputName(String) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.AggregateChannelTask: How to name the aggregated channel in the output.
setOutputStackProvider(StackProvider) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel: If it's set, a stack is generated that is outputted into subdirectory corresponding to the groupIdentifier.
setPathLabel(DerivePath) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller: Path to a CSV label file (comma-separated, with header, no quotes).
setRatioHeightForLabel(double) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: When label==true, this determines the height of the label.
setRatioRowsToColumns(double) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: An ideal approximate ratio of the number of rows to the number of columns.
setRemoveNaNColumns(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeaturesStyle: When true, columns containing all Double.NaN values are removed before outputting.
setResizeTo(SizeXY) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: If set, each channel is scaled to a specific size before aggregation (useful for combining different sized images).
setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage: Calculates what scale-factor to apply on the image.
setScoreProvider(FeatureListProvider<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
setSegment(SegmentStackIntoObjectsPooled<T>) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: The segmentation algorithm.
setSelectChannels(FromStacks) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: Selects which channels are included, optionally renaming.
setSequence(OutputSequenceIndexed<T, S>) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence: The current output sequence.
setSlicewise(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.AggregateChannelTask: When true, a 3D image is added slice-by-slice to the aggregation, treating each slice as a separate image.
setSource(FeatureSource<T, S, U>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Source of feature-values to be exported.
setStackEnergy(StackProvider) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage: Optionally defines an energy-stack for feature calculation (if not set, the energy-stack is considered to be the input stacks).
setStackEnergy(StackProvider) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller: Provider for the energy stack.
setStackEnergy(StackProvider) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
setStackName(String) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One: If defined, processing only occurs the stack with this specific name and index.
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: Fallback for imageMetadataReader to read image files without a directy metadata reader.
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImageCommonSize: Fallback for imageMetadataReader to read image files without a direct metadata reader.
setStyle(ExportFeaturesStyle) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures: Visual style for how feature export occurs.
setStyle(ExportFeaturesStyle) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: Visual style for how feature export occurs.
setSuppressErrors(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeaturesStyle: When false, an image is reported as errored, if any exception is thrown during calculation.
setSuppressSeries(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat: If true, the series index is not included in the outputted file-names.
setThumbnail(ThumbnailFromStack) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage: Method to generate a thumbnail for images.
setVaryColors(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel: When true, the colors change for different objects in the image (using a default color set).
setVaryImageLocation(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: When true, the location of an image in the grid, as well as the number of images in each row are both allowed to vary to fill space.
setVaryImageSize(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: When true, the images may vary in width/height in their respective rows to fill space, while preserving the aspect-ratio of each image.
setVaryingSizeWidth(int) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: If no specific width or scaling-factor is suggested, this determines the default width that the combined-montage should have, when varyImageSize==true.
setVaryingSizeWidthRatio(double) - Method in class org.anchoranalysis.plugin.image.task.bean.combine.Montage: If no specific width or scaling-factor is suggested, this determines the default percentage of the existing size, the combined-montage should have, when varyImageSize==true.
setVisuallyShortenDecimals(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeaturesStyle: When true, feature-values are shown as visually compressed as possible, including suppressing decimal places.
SharedStateFilteredImageOutput<T> - Class in org.anchoranalysis.plugin.image.task.labeller: Manages filtered image output with shared state across multiple images.
SharedStateFilteredImageOutput(Outputter, ImageLabeller<T>, String, String) - Constructor for class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput: Creates a new SharedStateFilteredImageOutput.
SharedStateSegmentInstance<T> - Class in org.anchoranalysis.plugin.image.task.segment: Shared-state for instance segmentation.
SharedStateSegmentInstance(ConcurrentModelPool<T>, FeatureTableCalculator<FeatureInputSingleObject>, LabelHeaders, String, FeatureExporterContext) - Constructor for class org.anchoranalysis.plugin.image.task.segment.SharedStateSegmentInstance: Creates a new instance of SharedStateSegmentInstance.
SharedStateSelectedSlice - Class in org.anchoranalysis.plugin.image.task.stack: Shared state for writing selected slice information to a CSV file.
SharedStateSelectedSlice(Outputter) - Constructor for class org.anchoranalysis.plugin.image.task.stack.SharedStateSelectedSlice: Creates a new instance of SharedStateSelectedSlice.
SingleRowPerInput<T,S> - Class in org.anchoranalysis.plugin.image.task.bean.feature.source: Base class for exporting features, where features are calculated per-image using a NamedFeatureStore.
SingleRowPerInput(String) - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput: Creates with a single non-group header that should be describe an identifier.
SingleRowPerInput(String[]) - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput: Creates a new SingleRowPerInput instance.
SizeMapping - Class in org.anchoranalysis.plugin.image.task.size: Maps a Path to a particular image-size and orientation-change.
SizeMapping(Path, Extent) - Constructor for class org.anchoranalysis.plugin.image.task.size.SizeMapping: Creates a new SizeMapping instance.
SpecificAndRename - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels: Selects a specific set of channels from stacks, each identified by a stack-name and channel index
SpecificAndRename() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.SpecificAndRename
startSeries(NoSharedState, OutputSequenceIndexed<Stack, String>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
startSeries(S, U, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.RasterTask: Starts processing of a series.
subdirectoryForGroupOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.combine.AggregateChannelTask
subdirectoryForGroupOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase: An optional subdirectory where the group outputs are placed.
subdirectoryForGroupOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms

T

toString() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
toString() - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureExporterContext
toString() - Method in class org.anchoranalysis.plugin.image.task.feature.InitializationWithEnergyStack
toString() - Method in class org.anchoranalysis.plugin.image.task.feature.LabelledResultsVectorWithThumbnail
toString() - Method in class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail
toString() - Method in class org.anchoranalysis.plugin.image.task.grouped.NamedChannel
toString() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageCSVLabellerInitialization
toString() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitialization

W

withoutThumbnail() - Method in class org.anchoranalysis.plugin.image.task.feature.LabelledResultsVectorWithThumbnail: Exposes as a LabelledResultsVector without a thumbnail.
writeGroupedResults(Optional<NamedFeatureStore<FeatureInputResults>>, boolean, Function<InputOutputContext, FeatureCSVWriterFactory>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.feature.FeatureResultsAndThumbnails: Writes all the results that have been collected as a CSV file.
writeRow(String, int, double) - Method in class org.anchoranalysis.plugin.image.task.stack.SharedStateSelectedSlice: Writes a row of selected slice information to the CSV file.
writeRow(String, String) - Method in class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput: Writes a row to the CSV file with image name and group identifier.

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