Uses of Class
org.anchoranalysis.io.input.InputReadFailedException

Packages that use InputReadFailedException

Package	Description
org.anchoranalysis.annotation.io	Reading and writing annotations to the filesystem.
org.anchoranalysis.annotation.io.bean	Beans related to reading / writing / specifying annotations.
org.anchoranalysis.annotation.io.bean.comparer	What to compare an annotation (ground truth) against?
org.anchoranalysis.annotation.io.image	Reading and writing whole-image label annotations.
org.anchoranalysis.io.input	Classes relating to creating inputs for an experiment / task.
org.anchoranalysis.io.input.bean	Beans related to collecting inputs from the file-system for an experiment.
org.anchoranalysis.io.input.bean.namer	Beans to derive names (compact unique identifiers) from files.
org.anchoranalysis.io.input.bean.path.matcher	Beans to find a subset of files that match a particular conditions on their paths.
org.anchoranalysis.mpp.io.bean.input	Beans for reading data structures related to marked point processes from the file system.
org.anchoranalysis.plugin.annotation.bean.comparer	Comparing the similarity of annotations from two images to each other.
org.anchoranalysis.plugin.annotation.bean.comparison	Task to compare a set of annotations to a segmentation or another set of annotations.
org.anchoranalysis.plugin.annotation.bean.strategy	Strategies for how to annotate an image, such label per image etc.
org.anchoranalysis.plugin.image.task.slice	Non-bean classes pertaining to combining stacks into a single stack.
org.anchoranalysis.plugin.io.bean.file.group	Grouping files together so that they collectively represent a single entity.
org.anchoranalysis.plugin.io.bean.file.path	Beans to specify a file-path.
org.anchoranalysis.plugin.io.bean.input	Implementations of InputManager.
org.anchoranalysis.plugin.io.bean.input.channel	InputManagers that accept a set of named-channels.
org.anchoranalysis.plugin.io.bean.input.files	InputManagers that accept a set of named-files.
org.anchoranalysis.plugin.io.bean.input.filter	Implementations of InputManager that filter inputs.
org.anchoranalysis.plugin.io.bean.input.stack	Implementations of InputManager that process Stacks.

Uses of InputReadFailedException in org.anchoranalysis.annotation.io

Methods in org.anchoranalysis.annotation.io that throw InputReadFailedException

Modifier and Type	Method	Description
Optional<T>	AnnotationReader.read(Path path, OperationContext context)	Reads an annotation, if possible, from the file-system.

Uses of InputReadFailedException in org.anchoranalysis.annotation.io.bean

Methods in org.anchoranalysis.annotation.io.bean that throw InputReadFailedException

Modifier and Type	Method	Description
InputsWithDirectory<AnnotationWithStrategy<S>>	AnnotationInputManager.inputs(InputManagerParameters parameters)

Uses of InputReadFailedException in org.anchoranalysis.annotation.io.bean.comparer

Methods in org.anchoranalysis.annotation.io.bean.comparer that throw InputReadFailedException

Modifier and Type	Method	Description
abstract Findable<ObjectCollection>	ComparableSource.loadAsObjects(Path reference, Dimensions dimensions, boolean debugMode, OperationContext context)	Loads the source of elements from the file-system and converts to a ObjectCollection.

Uses of InputReadFailedException in org.anchoranalysis.annotation.io.image

Methods in org.anchoranalysis.annotation.io.image that throw InputReadFailedException

Modifier and Type	Method	Description
Optional<ImageLabelAnnotation>	ImageLabelAnnotationReader.read(Path path, OperationContext context)

Uses of InputReadFailedException in org.anchoranalysis.io.input

Methods in org.anchoranalysis.io.input that throw InputReadFailedException

Modifier and Type	Method	Description
default NamedFile	InputFromManager.asFile()	Expresses the input as a file with a name (the unique identifier).
default Path	InputFromManager.pathForBindingRequired()	Like InputFromManager.pathForBinding() but throws an exception if a path isn't present.

Uses of InputReadFailedException in org.anchoranalysis.io.input.bean

Methods in org.anchoranalysis.io.input.bean that throw InputReadFailedException

Modifier and Type	Method	Description
abstract InputsWithDirectory<T>	InputManager.inputs(InputManagerParameters parameters)	Creates a list of inputs given particular parameters.
InputsWithDirectory<T>	InputManagerUnary.inputs(InputManagerParameters parameters)
protected abstract InputsWithDirectory<T>	InputManagerUnary.inputsFromDelegate(InputsWithDirectory<T> fromDelegate, InputManagerParameters parameters)	Calculates the inputs to return given the inputs from the delegate.

Uses of InputReadFailedException in org.anchoranalysis.io.input.bean.namer

Methods in org.anchoranalysis.io.input.bean.namer that throw InputReadFailedException

Modifier and Type	Method	Description
List<NamedFile>	FileNamer.deriveNameUnique(List<File> files, FileNamerContext context)	Like FileNamer.deriveName(List, FileNamerContext) but checks that the final list of named-files all have unique names.

Uses of InputReadFailedException in org.anchoranalysis.io.input.bean.path.matcher

Methods in org.anchoranalysis.io.input.bean.path.matcher that throw InputReadFailedException

Modifier and Type	Method	Description
protected abstract CheckedPredicate<Path,IOException>	FilePathMatcher.createMatcherFile(Path directory, Optional<InputContextParameters> inputContext)	Create a predicate to be used for matching against path.
protected CheckedPredicate<Path,IOException>	MatchExtensions.createMatcherFile(Path directory, Optional<InputContextParameters> inputContext)
protected CheckedPredicate<Path,IOException>	MatchGlob.createMatcherFile(Path directory, Optional<InputContextParameters> inputContext)
List<File>	FilePathMatcher.matchingFiles(Path directory, boolean recursive)	Like FilePathMatcher.matchingFiles(Path, boolean, boolean, boolean, Optional, Optional) but uses sensible defaults.
List<File>	FilePathMatcher.matchingFiles(Path directory, boolean recursive, boolean ignoreHidden, boolean acceptDirectoryErrors, Optional<Integer> maxDirectoryDepth, Optional<InputManagerParameters> parameters)	Finds a collection of files that match particular conditions on their paths.

Uses of InputReadFailedException in org.anchoranalysis.mpp.io.bean.input

Methods in org.anchoranalysis.mpp.io.bean.input that throw InputReadFailedException

Modifier and Type	Method	Description
InputsWithDirectory<MultiInput>	MultiInputManager.inputs(InputManagerParameters parameters)

Uses of InputReadFailedException in org.anchoranalysis.plugin.annotation.bean.comparer

Methods in org.anchoranalysis.plugin.annotation.bean.comparer that throw InputReadFailedException

Modifier and Type	Method	Description
Findable<ObjectCollection>	MaskAsObject.loadAsObjects(Path reference, Dimensions dimensions, boolean debugMode, OperationContext context)
Findable<ObjectCollection>	Objects.loadAsObjects(Path filePathSource, Dimensions dimensions, boolean debugMode, OperationContext context)

Uses of InputReadFailedException in org.anchoranalysis.plugin.annotation.bean.comparison

Methods in org.anchoranalysis.plugin.annotation.bean.comparison that throw InputReadFailedException

Modifier and Type	Method	Description
InputsWithDirectory<AnnotationComparisonInput<T>>	AnnotationComparisonInputManager.inputs(InputManagerParameters parameters)

Uses of InputReadFailedException in org.anchoranalysis.plugin.annotation.bean.strategy

Methods in org.anchoranalysis.plugin.annotation.bean.strategy that throw InputReadFailedException

Modifier and Type	Method	Description
static Optional<ImageLabelAnnotation>	ReadAnnotationFromFile.readAssumeExists(Path path, OperationContext context)	Reads an ImageLabelAnnotation from a file, assuming the file exists.
static Optional<ImageLabelAnnotation>	ReadAnnotationFromFile.readCheckExists(Path path, OperationContext context)	Reads an ImageLabelAnnotation from a file if it exists.

Uses of InputReadFailedException in org.anchoranalysis.plugin.image.task.slice

Method parameters in org.anchoranalysis.plugin.image.task.slice with type arguments of type InputReadFailedException

Modifier and Type	Method	Description
void	MontageSharedState.copyStackInto(CheckedSupplier<RGBStack,InputReadFailedException> source, String identifier, Path path, Optional<String> label)	Copies a Stack into a BoundingBox in the combined image, resizing if necessary.

Uses of InputReadFailedException in org.anchoranalysis.plugin.io.bean.file.group

Methods in org.anchoranalysis.plugin.io.bean.file.group that throw InputReadFailedException

Modifier and Type	Method	Description
InputsWithDirectory<NamedChannelsInput>	GroupFiles.inputs(InputManagerParameters parameters)

Uses of InputReadFailedException in org.anchoranalysis.plugin.io.bean.file.path

Methods in org.anchoranalysis.plugin.io.bean.file.path that throw InputReadFailedException

Modifier and Type	Method	Description
abstract Path	FilePath.path(boolean debugMode)
Path	RootedFilePath.path(boolean debugMode)
Path	StaticFilePath.path(boolean debugMode)

Uses of InputReadFailedException in org.anchoranalysis.plugin.io.bean.input

Methods in org.anchoranalysis.plugin.io.bean.input that throw InputReadFailedException

Modifier and Type	Method	Description
InputsWithDirectory<T>	Concatenate.inputs(InputManagerParameters parameters)
protected InputsWithDirectory<T>	BranchIfDebug.inputsFromDelegate(InputsWithDirectory<T> fromDelegate, InputManagerParameters parameters)
protected InputsWithDirectory<T>	Exclude.inputsFromDelegate(InputsWithDirectory<T> fromDelegate, InputManagerParameters parameters)
protected InputsWithDirectory<T>	Limit.inputsFromDelegate(InputsWithDirectory<T> fromDelegate, InputManagerParameters parameters)
protected InputsWithDirectory<T>	LimitIfRequested.inputsFromDelegate(InputsWithDirectory<T> fromDelegate, InputManagerParameters parameters)
protected InputsWithDirectory<T>	ShuffleIfRequested.inputsFromDelegate(InputsWithDirectory<T> fromDelegate, InputManagerParameters parameters)
protected InputsWithDirectory<T>	SortAlphabetically.inputsFromDelegate(InputsWithDirectory<T> fromDelegate, InputManagerParameters parameters)

Uses of InputReadFailedException in org.anchoranalysis.plugin.io.bean.input.channel

Methods in org.anchoranalysis.plugin.io.bean.input.channel that throw InputReadFailedException

Modifier and Type	Method	Description
InputsWithDirectory<NamedChannelsInputPart>	NamedChannels.inputs(InputManagerParameters parameters)
InputsWithDirectory<NamedChannelsInputPart>	NamedChannelsAppend.inputs(InputManagerParameters parameters)

Uses of InputReadFailedException in org.anchoranalysis.plugin.io.bean.input.files

Methods in org.anchoranalysis.plugin.io.bean.input.files that throw InputReadFailedException

Modifier and Type	Method	Description
protected InputsWithDirectory<T>	NamedFilesBase.createInputsFromFiles(FilesProvider files, InputManagerParameters parameters, Function<NamedFile,T> mapToInput)	Creates a list of inputs from a FilesProvider which together with the namer can create the inputs.
InputsWithDirectory<FileInput>	NamedFiles.inputs(InputManagerParameters parameters)
InputsWithDirectory<FileWithDirectoryInput>	NamedFilesWithDirectory.inputs(InputManagerParameters parameters)

Uses of InputReadFailedException in org.anchoranalysis.plugin.io.bean.input.filter

Methods in org.anchoranalysis.plugin.io.bean.input.filter that throw InputReadFailedException

Modifier and Type	Method	Description
protected InputsWithDirectory<T>	FilterCSVColumn.inputsFromDelegate(InputsWithDirectory<T> fromDelegate, InputManagerParameters parameters)
protected InputsWithDirectory<T>	FilterDescriptiveName.inputsFromDelegate(InputsWithDirectory<T> fromDelegate, InputManagerParameters parameters)
protected InputsWithDirectory<T>	FilterIfDebug.inputsFromDelegate(InputsWithDirectory<T> fromDelegate, InputManagerParameters parameters)

Uses of InputReadFailedException in org.anchoranalysis.plugin.io.bean.input.stack

Methods in org.anchoranalysis.plugin.io.bean.input.stack that throw InputReadFailedException

Modifier and Type	Method	Description
InputsWithDirectory<StackSequenceInput>	ConvertNamedChannelsToStack.inputs(InputManagerParameters parameters)
InputsWithDirectory<StackSequenceInput>	Stacks.inputs(InputManagerParameters parameters)