Index (anchor-annotation-io 0.2.1 API)

A C D E F G H I L M N O P R S T U W
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A

addAssignedPair(ObjectMask, ObjectMask, double) - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: Adds an assigned pair of objects with a particular overlap-ratio.
addDouble(String, double) - Method in class org.anchoranalysis.annotation.io.comparer.StatisticsToExport: Adds a statistic that is a double.
addInt(String, int) - Method in class org.anchoranalysis.annotation.io.comparer.StatisticsToExport: Adds a statistic that is an int.
addMeanExtrema(String, double, double, double) - Method in class org.anchoranalysis.annotation.io.comparer.StatisticsToExport: Adds three statistics a mean, min and max.
addMeanExtrema(String, RunningSumExtrema) - Method in class org.anchoranalysis.annotation.io.comparer.StatisticsToExport: Like StatisticsToExport.addMeanExtrema(String, double, double, double) but determines the statistics from a RunningSumExtrema.
addString(String, String) - Method in class org.anchoranalysis.annotation.io.comparer.StatisticsToExport: Adds a statistic that is a String.
addUnassignedLeft(ObjectCollection) - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: Add unassigned objects to the left set.
addUnassignedLeft(ObjectMask) - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: Add an unassigned object to the left set.
addUnassignedRight(ObjectCollection) - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: Add unassigned objects to the right set.
addUnassignedRight(ObjectMask) - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: Add an unassigned object to the right set.
AnnotationBackground - Class in org.anchoranalysis.annotation.io.bean: How to display one or more Stacks as background during an annotation process.
AnnotationBackground() - Constructor for class org.anchoranalysis.annotation.io.bean.AnnotationBackground
AnnotationDeleter - Interface in org.anchoranalysis.annotation.io: Allows an annotation to be deleted from the file-system.
AnnotationInputManager<T extends ProvidesStackInput,S extends AnnotatorStrategy> - Class in org.anchoranalysis.annotation.io.bean: An InputManager that provides annotations corresponding to images.
AnnotationInputManager() - Constructor for class org.anchoranalysis.annotation.io.bean.AnnotationInputManager
annotationLabelFor(ProvidesStackInput, OperationContext) - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy: A human-friendly textual description of the annotation, or Optional.empty() if no label is available.
AnnotationReader<T extends Annotation> - Interface in org.anchoranalysis.annotation.io: Allows an annotation to be read from the file-system.
AnnotationWithStrategy<T extends AnnotatorStrategy> - Class in org.anchoranalysis.annotation.io: One particular annotation, associated with its strategy.
AnnotationWithStrategy(ProvidesStackInput, T) - Constructor for class org.anchoranalysis.annotation.io.AnnotationWithStrategy: Creates for a particular input and associated annotation strategy.
AnnotationWriter<T extends Annotation> - Interface in org.anchoranalysis.annotation.io: Allows an annotation to be written to the file-system.
AnnotatorStrategy - Class in org.anchoranalysis.annotation.io.bean: How an input is associated with annotations on the file-system, and how this is presented visually.
AnnotatorStrategy() - Constructor for class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy
append(StatisticsToExport) - Method in class org.anchoranalysis.annotation.io.comparer.StatisticsToExport: Appends the names and values from another AnnotationComparison to the existing.
Assignment<T> - Interface in org.anchoranalysis.annotation.io.assignment: A one-to-one pairing between items in two respective sets.
AssignmentColorPool - Class in org.anchoranalysis.annotation.io.assignment.generator: Different ColorSchemes that can be used to select colors for paired and unpaired objects.
AssignmentColorPool(int, ColorScheme) - Constructor for class org.anchoranalysis.annotation.io.assignment.generator.AssignmentColorPool: Creates with a number and colors for the paired objects, and defaults colors for unpaired.
AssignmentColorPool(int, ColorScheme, ColorScheme, boolean) - Constructor for class org.anchoranalysis.annotation.io.assignment.generator.AssignmentColorPool
AssignmentGenerator - Class in org.anchoranalysis.annotation.io.assignment.generator: Outputs a raster showing an Assignment on a background.
AssignmentGenerator(DrawColoredObjects, IntFunction<AssignmentColorPool>, Tuple2<String, String>, boolean) - Constructor for class org.anchoranalysis.annotation.io.assignment.generator.AssignmentGenerator
AssignOverlappingObjects - Class in org.anchoranalysis.annotation.io.assignment: Creates a one-to-one assignment between two sets of ObjectMasks.
AssignOverlappingObjects(FeatureEvaluator<FeatureInputPairObjects>, boolean) - Constructor for class org.anchoranalysis.annotation.io.assignment.AssignOverlappingObjects
associatedFile() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy: The file associated with the annotation, if such a file exists.

C

ComparableSource - Class in org.anchoranalysis.annotation.io.bean.comparer: A set of elements, loaded from the file-system, to be compared to another set.
ComparableSource() - Constructor for class org.anchoranalysis.annotation.io.bean.comparer.ComparableSource
CostMatrix<T> - Class in org.anchoranalysis.annotation.io.assignment: Stores costs between all possible pairings between elements from two lists.
create(List<T>, List<T>, boolean, CheckedToDoubleBiFunction<T, T, CreateException>) - Static method in class org.anchoranalysis.annotation.io.assignment.CostMatrix: Creates by calculating the cost between elements.
createAssignment(ObjectCollection, ObjectCollection, double, Dimensions) - Method in class org.anchoranalysis.annotation.io.assignment.AssignOverlappingObjects: Creates an assignment from the objects in left to those in right.
createColors(int) - Method in class org.anchoranalysis.annotation.io.assignment.generator.AssignmentColorPool: Creates a list of colors to describe the assignment.
createComparisonStacks(AnnotationWithMarks, DisplayStack, Path, ColorScheme, Path, OperationContext, boolean) - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer: Creates a Stack illustrating the comparison between annotation and each source in sources.
createObjectsImage(Assignment<ObjectMask>, boolean, AssignmentColorPool) - Method in class org.anchoranalysis.annotation.io.assignment.generator.DrawColoredObjects: Creates an image with the objects colored, as indicated in the class description.
createWithLeftUnassigned(ObjectCollection) - Static method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: Creates with only left unassigned objects.
createWithRight(ObjectCollection) - Static method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: Creates with only right unassigned objects.

D

delete(Path) - Method in interface org.anchoranalysis.annotation.io.AnnotationDeleter: Deletes all files at this path (or any other paths derived from this one.
delete(Path) - Method in class org.anchoranalysis.annotation.io.mark.DualMarksAnnotationDeleter
delete(Path) - Method in class org.anchoranalysis.annotation.io.SimpleAnnotationDeleter
DrawColoredObjects - Class in org.anchoranalysis.annotation.io.assignment.generator: Outlines or completely fills in each ObjectMask with a color.
DrawColoredObjects(DisplayStack, boolean, int) - Constructor for class org.anchoranalysis.annotation.io.assignment.generator.DrawColoredObjects
DualMarksAnnotationDeleter - Class in org.anchoranalysis.annotation.io.mark: Deletes DualMarksAnnotations from the file-system.
DualMarksAnnotationDeleter() - Constructor for class org.anchoranalysis.annotation.io.mark.DualMarksAnnotationDeleter
DualMarksAnnotationWriter<T> - Class in org.anchoranalysis.annotation.io.mark: Writes DualMarksAnnotations to the file-system.
DualMarksAnnotationWriter() - Constructor for class org.anchoranalysis.annotation.io.mark.DualMarksAnnotationWriter
DualMarksAnnotationWriter(boolean) - Constructor for class org.anchoranalysis.annotation.io.mark.DualMarksAnnotationWriter

E

equals(Object) - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
equals(Object) - Method in class org.anchoranalysis.annotation.io.image.findable.Found
equals(Object) - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound

F

Findable<T> - Interface in org.anchoranalysis.annotation.io.image.findable: Parent class for an element that exists in one of two-states, either Found or NotFound.
Found<T> - Class in org.anchoranalysis.annotation.io.image.findable: A positive-result when an object is found at a particular location.
Found(T) - Constructor for class org.anchoranalysis.annotation.io.image.findable.Found

G

getAnnotatorStrategy() - Method in class org.anchoranalysis.annotation.io.bean.AnnotationInputManager: The strategy to be used for annotating.
getBackground() - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy: The visual background to use while annotating.
getBackgroundStackMap() - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground: If non-null, maps underlying stack-name to a background.
getCost(int, int) - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix: Gets the cost from an element from the first-list to an element from the second-list.
getCosts() - Method in class org.anchoranalysis.annotation.io.assignment.AssignOverlappingObjects: A matrix linking the overlap between each ObjectMask to each other, respectively as rows and columns.
getFeatureEvaluator() - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer: Calculates the cost used when making assignments.
getFirst() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix: The first set of elements.
getIgnoreContains() - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground: If non-empty, to not display any stacks in backgroundStackMap whose name contains this string.
getInput() - Method in class org.anchoranalysis.annotation.io.bean.AnnotationInputManager: The inputs to be annotated.
getLeftUnassigned() - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: The unassigned objects in the left set.
getMatrix() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix: A two-dimensional array mapping the costs from first to second.
getMaxCost() - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer: The maximum cost (as calculated by featureEvaluator) to accept when creating an assignment between objects.
getNames() - Method in class org.anchoranalysis.annotation.io.comparer.StatisticsToExport: The names of statistics describing the annotation-comparison, as produced by StatisticsToExport.getValues().
getObject() - Method in class org.anchoranalysis.annotation.io.image.findable.Found: The found object.
getOrLog(String, Logger) - Method in interface org.anchoranalysis.annotation.io.image.findable.Findable: Gets an object or otherwise logs a message describing what went wrong.
getOrLog(String, Logger) - Method in class org.anchoranalysis.annotation.io.image.findable.Found
getOrLog(String, Logger) - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound
getPath() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy: Path to annotation.
getPath() - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound: The path an object was not found at.
getReason() - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound: The reason an object could not be found.
getRightUnassigned() - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: The unassigned objects in the right set.
getSecond() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix: The second set of elements.
getSources() - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer: The other entities to compare with the annotation.
getStackNameDefault() - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground: The name of the default stack from backgroundStackMap to display as background when annotating.
getStackReader() - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy: How to read raster Stacks from the file-system.
getStrategy() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy: The strategy on how annotation occurs.
getValues() - Method in class org.anchoranalysis.annotation.io.comparer.StatisticsToExport: The values of statistics describing the annotation-comparison, corresponding exactly to the names in StatisticsToExport.getNames().
guaranteedImageAttributes() - Method in class org.anchoranalysis.annotation.io.assignment.generator.AssignmentGenerator

H

hashCode() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
hashCode() - Method in class org.anchoranalysis.annotation.io.image.findable.Found
hashCode() - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound

I

ImageLabelAnnotationReader - Class in org.anchoranalysis.annotation.io.image: Reads an ImageLabelAnnotation from the file-system.
ImageLabelAnnotationReader() - Constructor for class org.anchoranalysis.annotation.io.image.ImageLabelAnnotationReader
ImageLabelAnnotationWriter - Class in org.anchoranalysis.annotation.io.image: Writes an ImageLabelAnnotation to the file-system.
ImageLabelAnnotationWriter() - Constructor for class org.anchoranalysis.annotation.io.image.ImageLabelAnnotationWriter
inputs(InputManagerParameters) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationInputManager
isDifferentColorsForPairs() - Method in class org.anchoranalysis.annotation.io.assignment.generator.AssignmentColorPool: If true, different colors are used for paired objects, otherwise always the same color is used.
isFlatten() - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer: If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane, before comparison.

L

label(OperationContext) - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy: A human-friendly textual description of the annotation, or Optional.empty() if no label is available.
leftSize() - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: The total number of objects in the left set.
loadAsObjects(Path, Dimensions, boolean, OperationContext) - Method in class org.anchoranalysis.annotation.io.bean.comparer.ComparableSource: Loads the source of elements from the file-system and converts to a ObjectCollection.

M

MultipleComparer - Class in org.anchoranalysis.annotation.io.bean.comparer: Allows comparison of an annotation with multiple other entities.
MultipleComparer() - Constructor for class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer

N

NotFound<T> - Class in org.anchoranalysis.annotation.io.image.findable: A negative-result when an object is not found at a particular location.
NotFound(Path, String) - Constructor for class org.anchoranalysis.annotation.io.image.findable.NotFound
numberPaired() - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment: The number of items that are paired.
numberPaired() - Method in class org.anchoranalysis.annotation.io.assignment.ObjectVoxelIntersection
numberPaired() - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects
numberUnassigned(boolean) - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment: The number of items in a particular set that are not paired.
numberUnassigned(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.ObjectVoxelIntersection
numberUnassigned(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects
numberUnassignedLeft() - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: The number of unassigned objects in the left set.
numberUnassignedRight() - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: The number of unassigned objects in the right set.

O

ObjectVoxelIntersection - Class in org.anchoranalysis.annotation.io.assignment: Creates an assignment between intersecting voxels in two objects.
ObjectVoxelIntersection(ObjectMask, ObjectMask) - Constructor for class org.anchoranalysis.annotation.io.assignment.ObjectVoxelIntersection: Determines a voxel-assignment between two objects.
org.anchoranalysis.annotation.io - package org.anchoranalysis.annotation.io: Reading and writing annotations to the filesystem.
org.anchoranalysis.annotation.io.assignment - package org.anchoranalysis.annotation.io.assignment: A pairing of objects from two collections (bipartite matching).
org.anchoranalysis.annotation.io.assignment.generator - package org.anchoranalysis.annotation.io.assignment.generator: Generates output images to illustrate a Assignment between annotations.
org.anchoranalysis.annotation.io.bean - package org.anchoranalysis.annotation.io.bean: Beans related to reading / writing / specifying annotations.
org.anchoranalysis.annotation.io.bean.comparer - package org.anchoranalysis.annotation.io.bean.comparer: What to compare an annotation (ground truth) against?
org.anchoranalysis.annotation.io.comparer - package org.anchoranalysis.annotation.io.comparer: Non-bean classes involving comparing results and annotations.
org.anchoranalysis.annotation.io.image - package org.anchoranalysis.annotation.io.image: Reading and writing whole-image label annotations.
org.anchoranalysis.annotation.io.image.findable - package org.anchoranalysis.annotation.io.image.findable: The outcome of searching for annotations or images on the file-system.
org.anchoranalysis.annotation.io.mark - package org.anchoranalysis.annotation.io.mark: Reading and writing Mark-related annotations from/to the file-system.
OverlappingObjects - Class in org.anchoranalysis.annotation.io.assignment: Pairs an ObjectMask in one set with an ObjectMask in another, if deemed to overlap sufficiently.
OverlappingObjects() - Constructor for class org.anchoranalysis.annotation.io.assignment.OverlappingObjects

P

paired(boolean) - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment: The items that are paired for a particular set.
paired(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.ObjectVoxelIntersection
paired(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects
pathFor(ProvidesStackInput) - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy: The path to where an annotation file for a particular input would be located.
percentLeftAssigned() - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: The percentage of objects in the left set that have been paired.
percentRightAssigned() - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: The percentage of objects in the right set that have been paired.

R

read(Path, OperationContext) - Method in interface org.anchoranalysis.annotation.io.AnnotationReader: Reads an annotation, if possible, from the file-system.
read(Path, OperationContext) - Method in class org.anchoranalysis.annotation.io.image.ImageLabelAnnotationReader
removeTouchingBorderXY(Extent) - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: Removes any objects from the assignment if they touch the X or Y scene border.
rightSize() - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: The total number of objects in the right set.

S

setAnnotatorStrategy(S) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationInputManager: The strategy to be used for annotating.
setBackground(AnnotationBackground) - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy: The visual background to use while annotating.
setBackgroundStackMap(StringMap) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground: If non-null, maps underlying stack-name to a background.
setFeatureEvaluator(FeatureEvaluator<FeatureInputPairObjects>) - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer: Calculates the cost used when making assignments.
setFlatten(boolean) - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer: If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane, before comparison.
setIgnoreContains(String) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground: If non-empty, to not display any stacks in backgroundStackMap whose name contains this string.
setInput(InputManager<T>) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationInputManager: The inputs to be annotated.
setMaxCost(double) - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer: The maximum cost (as calculated by featureEvaluator) to accept when creating an assignment between objects.
setSources(List<NamedBean<ComparableSource>>) - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer: The other entities to compare with the annotation.
setStackNameDefault(String) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground: The name of the default stack from backgroundStackMap to display as background when annotating.
setStackReader(StackReader) - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy: How to read raster Stacks from the file-system.
SimpleAnnotationDeleter - Class in org.anchoranalysis.annotation.io: Deletes any annotation when it is represented by a single file.
SimpleAnnotationDeleter() - Constructor for class org.anchoranalysis.annotation.io.SimpleAnnotationDeleter
sizeFirst() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix: The number of elements in the first list.
sizeSecond() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix: The number of elements in the second list.
stacks(Logger) - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy: All stacks associated with the input, lazily evaluated.
statistics() - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment: The statistics associated with the assignment.
statistics() - Method in class org.anchoranalysis.annotation.io.assignment.ObjectVoxelIntersection
statistics() - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects
StatisticsToExport - Class in org.anchoranalysis.annotation.io.comparer: Statistics to be exported, comprised of name-value pairs.
StatisticsToExport() - Constructor for class org.anchoranalysis.annotation.io.comparer.StatisticsToExport
sumOverlapFromPaired() - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects: Sums the overlap-ratio across all assigned pairs.

T

toString() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
toString() - Method in class org.anchoranalysis.annotation.io.image.findable.Found
toString() - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound
transform(Assignment<ObjectMask>) - Method in class org.anchoranalysis.annotation.io.assignment.generator.AssignmentGenerator

U

unassigned(boolean) - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment: The items that are not paired for a particular set.
unassigned(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.ObjectVoxelIntersection
unassigned(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.OverlappingObjects

W

weightWidthDescription() - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy: The degree as to how lengthy the labels from AnnotatorStrategy.annotationLabelFor(ProvidesStackInput, OperationContext) can be.
write(ImageLabelAnnotation, Path) - Method in class org.anchoranalysis.annotation.io.image.ImageLabelAnnotationWriter
write(DualMarksAnnotation<T>, Path) - Method in class org.anchoranalysis.annotation.io.mark.DualMarksAnnotationWriter
write(T, Path) - Method in interface org.anchoranalysis.annotation.io.AnnotationWriter: Saves the annotation to the filesystem.

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