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.annotation.io.mark |
Reading and writing
Mark -related annotations from/to the
file-system. |
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 |
InputManager s that accept a set of
named-channels. |
org.anchoranalysis.plugin.io.bean.input.files |
InputManager s 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 Stack s. |
org.anchoranalysis.plugin.mpp.experiment.bean.objects |
Tasks involving
ObjectMask s. |
org.anchoranalysis.plugin.quick.bean.input |
Specifying inputs when quickly defining an experiment.
|
Modifier and Type | Method and Description |
---|---|
Optional<T> |
AnnotationReader.read(Path path,
OperationContext context)
Reads an annotation, if possible, from the file-system.
|
Modifier and Type | Method and Description |
---|---|
InputsWithDirectory<AnnotationWithStrategy<S>> |
AnnotationInputManager.inputs(InputManagerParameters parameters) |
Modifier and Type | Method and 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 . |
Modifier and Type | Method and Description |
---|---|
Optional<ImageLabelAnnotation> |
ImageLabelAnnotationReader.read(Path path,
OperationContext context) |
Modifier and Type | Method and Description |
---|---|
Optional<DualMarksAnnotation<T>> |
DualMarksAnnotationReader.read(Path path,
OperationContext context) |
Modifier and Type | Method and 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. |
Modifier and Type | Method and Description |
---|---|
InputsWithDirectory<T> |
InputManagerUnary.inputs(InputManagerParameters parameters) |
abstract InputsWithDirectory<T> |
InputManager.inputs(InputManagerParameters parameters)
Creates a list of inputs given particular parameters.
|
protected abstract InputsWithDirectory<T> |
InputManagerUnary.inputsFromDelegate(InputsWithDirectory<T> fromDelegate,
InputManagerParameters parameters)
Calculates the inputs to return given the inputs from the delegate.
|
Modifier and Type | Method and 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. |
Modifier and Type | Method and Description |
---|---|
protected CheckedPredicate<Path,IOException> |
MatchGlob.createMatcherFile(Path directory,
Optional<InputContextParameters> inputContext) |
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) |
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.
|
Modifier and Type | Method and Description |
---|---|
InputsWithDirectory<MultiInput> |
MultiInputManager.inputs(InputManagerParameters parameters) |
Modifier and Type | Method and Description |
---|---|
Findable<ObjectCollection> |
Objects.loadAsObjects(Path filePathSource,
Dimensions dimensions,
boolean debugMode,
OperationContext context) |
Findable<ObjectCollection> |
DualMarksAnnotationAsObjects.loadAsObjects(Path reference,
Dimensions dimensions,
boolean debugMode,
OperationContext context) |
Findable<ObjectCollection> |
MarksAsObjects.loadAsObjects(Path reference,
Dimensions dimensions,
boolean debugMode,
OperationContext context) |
Findable<ObjectCollection> |
MaskAsObject.loadAsObjects(Path reference,
Dimensions dimensions,
boolean debugMode,
OperationContext context) |
Modifier and Type | Method and Description |
---|---|
InputsWithDirectory<AnnotationComparisonInput<T>> |
AnnotationComparisonInputManager.inputs(InputManagerParameters parameters) |
Modifier and Type | Method and Description |
---|---|
static Optional<ImageLabelAnnotation> |
ReadAnnotationFromFile.readAssumeExists(Path path,
OperationContext context) |
static Optional<ImageLabelAnnotation> |
ReadAnnotationFromFile.readCheckExists(Path path,
OperationContext context) |
Modifier and Type | Method and 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. |
Modifier and Type | Method and Description |
---|---|
InputsWithDirectory<NamedChannelsInput> |
GroupFiles.inputs(InputManagerParameters parameters) |
Modifier and Type | Method and Description |
---|---|
Path |
RootedFilePath.path(boolean debugMode) |
Path |
StaticFilePath.path(boolean debugMode) |
abstract Path |
FilePath.path(boolean debugMode) |
Modifier and Type | Method and Description |
---|---|
InputsWithDirectory<NamedChannelsInputPart> |
NamedChannelsAppend.inputs(InputManagerParameters parameters) |
InputsWithDirectory<NamedChannelsInputPart> |
NamedChannels.inputs(InputManagerParameters parameters) |
Modifier and Type | Method and Description |
---|---|
protected InputsWithDirectory<T> |
NamedFilesBase.createInputsFromFiles(FilesProvider files,
InputManagerParameters parameters,
java.util.function.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) |
Modifier and Type | Method and Description |
---|---|
protected InputsWithDirectory<T> |
FilterCSVColumn.inputsFromDelegate(InputsWithDirectory<T> fromDelegate,
InputManagerParameters parameters) |
protected InputsWithDirectory<T> |
FilterIfDebug.inputsFromDelegate(InputsWithDirectory<T> fromDelegate,
InputManagerParameters parameters) |
protected InputsWithDirectory<T> |
FilterDescriptiveName.inputsFromDelegate(InputsWithDirectory<T> fromDelegate,
InputManagerParameters parameters) |
Modifier and Type | Method and Description |
---|---|
InputsWithDirectory<StackSequenceInput> |
ConvertNamedChannelsToStack.inputs(InputManagerParameters parameters) |
InputsWithDirectory<StackSequenceInput> |
Stacks.inputs(InputManagerParameters parameters) |
Modifier and Type | Method and Description |
---|---|
InputsWithDirectory<FromCSVInput> |
FromCSVInputManager.inputs(InputManagerParameters parameters) |
Modifier and Type | Method and Description |
---|---|
InputsWithDirectory<MultiInput> |
MultiInputManagerQuick.inputs(InputManagerParameters parameters) |
InputsWithDirectory<NamedChannelsInputPart> |
NamedChannelsQuick.inputs(InputManagerParameters parameters) |
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.