Index

A B C D E F G H I K L M N O P R S T W
All Classes All Packages

A

add(ImageCounter<T>) - Method in class org.anchoranalysis.plugin.annotation.counter.ImageCounterList

Adds an ImageCounter to the list.

addAll(Collection<S>) - Method in class org.anchoranalysis.plugin.annotation.counter.ImageCounterList

Adds a collection of ImageCounters to the list.

addAnnotatedImage(T) - Method in interface org.anchoranalysis.plugin.annotation.counter.ImageCounter

Add an image that had an associated annotation.

addAnnotatedImage(T) - Method in class org.anchoranalysis.plugin.annotation.counter.ImageCounterList

addDefaultOutputs(OutputEnabledMutable) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.AnnotationComparisonAssigner

Adds any default outputs that should occur from the assigner.

addDefaultOutputs(OutputEnabledMutable) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner

addDefaultOutputs(OutputEnabledMutable) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.MaskIntersectionAssigner

addUnannotatedImage() - Method in interface org.anchoranalysis.plugin.annotation.counter.ImageCounter

Add an image that did not have an associated annotation.

addUnannotatedImage() - Method in class org.anchoranalysis.plugin.annotation.counter.ImageCounterList

afterAllJobsAreExecuted(AggregateSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations

afterAllJobsAreExecuted(ComparisonSharedState<T>, InputOutputContext) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

AggregateAnnotations<S extends org.anchoranalysis.annotation.io.bean.AnnotatorStrategy> - Class in org.anchoranalysis.plugin.annotation.bean.aggregate

Aggregates many per-image annotations together in form of a CSV file.

AggregateAnnotations() - Constructor for class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations

AnnotationAggregateCSVGenerator - Class in org.anchoranalysis.plugin.annotation.bean.aggregate

Generates a CSV file containing aggregated annotation data.

AnnotationAggregateCSVGenerator() - Constructor for class org.anchoranalysis.plugin.annotation.bean.aggregate.AnnotationAggregateCSVGenerator

Constructs an AnnotationAggregateCSVGenerator with predefined column headers.

AnnotationComparisonAssigner<T extends org.anchoranalysis.annotation.io.assignment.Assignment<org.anchoranalysis.image.voxel.object.ObjectMask>> - Class in org.anchoranalysis.plugin.annotation.bean.comparison.assigner

Compares similar object-sets produced from two different sources.

AnnotationComparisonAssigner() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.AnnotationComparisonAssigner

AnnotationComparisonInput<T extends org.anchoranalysis.io.input.InputFromManager> - Class in org.anchoranalysis.plugin.annotation.comparison

Input for annotation comparison, containing sources to compare and associated metadata.

AnnotationComparisonInput(T, Tuple2<ComparableSource, ComparableSource>, Tuple2<String, String>, StackReader) - Constructor for class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput

Creates an annotation comparison input.

AnnotationComparisonInputManager<T extends org.anchoranalysis.io.input.InputFromManager> - Class in org.anchoranalysis.plugin.annotation.bean.comparison

An input manager for annotation comparison that extends InputManagerWithStackReader.

AnnotationComparisonInputManager() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager

AnnotationLabel - Class in org.anchoranalysis.plugin.annotation.bean.label

Represents a label used for annotation, with associated metadata.

AnnotationLabel() - Constructor for class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel

annotationLabelFor(ProvidesStackInput, OperationContext) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.ImageLabelStrategy

annotationLabelFor(ProvidesStackInput, OperationContext) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy

B

beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<AnnotationWithStrategy<S>>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations

beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<AnnotationComparisonInput<ProvidesStackInput>>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

C

CompareAnnotations<T extends org.anchoranalysis.annotation.io.assignment.Assignment<org.anchoranalysis.image.voxel.object.ObjectMask>> - Class in org.anchoranalysis.plugin.annotation.bean.comparison

Task to compare a set of annotations to a segmentation or another set of annotations.

CompareAnnotations() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

comparison() - Method in interface org.anchoranalysis.plugin.annotation.counter.ImageCounterWithStatistics

Creates statistics from counted images and the payload T passed for annotated images.

ComparisonSharedState<T extends org.anchoranalysis.annotation.io.assignment.Assignment<org.anchoranalysis.image.voxel.object.ObjectMask>> - Class in org.anchoranalysis.plugin.annotation.bean.comparison

Shared state for comparison operations, including grouping and statistics.

ComparisonSharedState(CSVAssignment, int, Function<String, ImageCounterWithStatistics<T>>) - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparison.ComparisonSharedState

Creates a new ComparisonSharedState.

create(InputManagerParameters) - Method in class org.anchoranalysis.plugin.annotation.bean.file.FromAnnotations

createAssignment(ObjectsToCompare, Dimensions, boolean, InputOutputContext) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.AnnotationComparisonAssigner

Creates an assignment based on the objects to compare.

createAssignment(ObjectsToCompare, Dimensions, boolean, InputOutputContext) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner

createAssignment(ObjectsToCompare, Dimensions, boolean, InputOutputContext) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.MaskIntersectionAssigner

D

defaultOutputs() - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations

defaultOutputs() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

derivePath(DerivePath, Path) - Static method in class org.anchoranalysis.plugin.annotation.bean.strategy.PathFromGenerator

Derives a path using a DerivePath generator and a binding path.

dictionaryDeriver() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy

Gets the dictionary deriver path if set.

doJobOnInput(InputBound<AnnotationWithStrategy<S>, AggregateSharedState>) - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations

doJobOnInput(InputBound<AnnotationComparisonInput<ProvidesStackInput>, ComparisonSharedState<T>>) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

E

equals(Object) - Method in class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare

F

FeatureCostAssigner - Class in org.anchoranalysis.plugin.annotation.bean.comparison.assigner

Assigns an objects from one set of objects to another based upon a cost (degree of overlap).

FeatureCostAssigner() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner

FromAnnotations<T extends org.anchoranalysis.annotation.io.bean.AnnotatorStrategy> - Class in org.anchoranalysis.plugin.annotation.bean.file

Provides files associated with annotations.

FromAnnotations() - Constructor for class org.anchoranalysis.plugin.annotation.bean.file.FromAnnotations

G

get(String) - Method in class org.anchoranalysis.plugin.annotation.bean.label.GroupedAnnotationLabels

Gets the collection of AnnotationLabels for a specific group.

getAdditionalBackgrounds() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy

Additional background-stacks that are possible to use while annotating.

getAnnotations() - Method in class org.anchoranalysis.plugin.annotation.bean.file.FromAnnotations

The annotation input manager.

getAssigner() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

The assigner used for annotation comparison.

getAssignmentCSV() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.ComparisonSharedState

The CSV assignment for the comparison.

getBackground() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

The name of the stack to use as background to the annotations.

getColor() - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel

An optional color associated with the label when displayed via GUI.

getColorsUnpaired() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

The color scheme for unpaired objects.

getComparerLeft() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager

The comparable source for the left side of the comparison.

getComparerMultiplex(boolean) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput

Gets one of the two ComparableSources based on a boolean flag.

getComparerRight() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager

The comparable source for the right side of the comparison.

getComparers() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput

The two ComparableSources to compare.

getDerivePath() - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskAsObject

Where to find the Mask to compare, as a function of the source file-path.

getDerivePath() - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.Objects

Where to find the objects to compare, as a function of the source file-path.

getDisplayer() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

How to convert an image to be displayed to the user.

getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner

getGroup() - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel

Specifies a group for the label (similar labels that are displayed together).

getInput() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager

The input manager for the base input type T.

getInput() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput

Gets the input from manager.

getLabels() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.ImageLabelStrategy

List of AnnotationLabels available for annotation.

getLeft() - Method in class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare

Objects on left-side of the comparison.

getMarkEvaluator() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy

A mark-evaluator that is added to the GUI to support this annotation

getMarkProposer() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy

Name of the MarkProposer to use.

getMaxCost() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner

getMaxSplitGroups() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

The maximum number of groups to split the identifier into.

getMultipleComparer() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy

Multiple comparer for comparing annotations.

getNameLeft() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager

The name of the left side in the comparison.

getNameRight() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager

The name of the right side in the comparison.

getNames() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput

Names associated with the two sources being compared.

getNumberDecimalPlaces() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner

getNumberLevelsGrouping() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

The number of levels for grouping.

getOutlineWidth() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

How many pixels should the outline be around objects.

getPathAnnotation() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.SinglePathStrategy

Derives the path to the corresponding annotation files, given a path to the image to be annotated.

getPathDefaultMarks() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy

Path to derive default marks from.

getPathDictionary() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy

Path to derive dictionary from.

getPointsFitter() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy

Name of the PointsFitter to use.

getRight() - Method in class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare

Objects on right-side of the comparison.

getSplitIdentifierRegex() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

If non-empty, the string (a regular-expression) is used to split the file's identifier into groups.

getStackReader() - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskAsObject

How to read the Mask from the file-system.

getStackReader() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput

The StackReader to use for reading image stacks.

getUniqueLabel() - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel

Label that uniquely identifies the ID (for machine purposes).

getUserFriendlyLabel() - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel

Descriptive user-friendly label displayed via GUI.

getWeightWidthDescription() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.ImageLabelStrategy

The weight to use for the width of the description.

GroupedAnnotationLabels - Class in org.anchoranalysis.plugin.annotation.bean.label

A set of AnnotationLabels partitioned into their unique groups.

GroupedAnnotationLabels(Collection<AnnotationLabel>) - Constructor for class org.anchoranalysis.plugin.annotation.bean.label.GroupedAnnotationLabels

Creates a new instance of GroupedAnnotationLabels.

groupedLabels() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.ImageLabelStrategy

Creates a GroupedAnnotationLabels from the current labels.

groupForKey(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.AnnotationComparisonAssigner

Gets the ImageCounterWithStatistics for a specific key.

groupForKey(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner

groupForKey(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.MaskIntersectionAssigner

groupsForImage(SplitString) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.ComparisonSharedState

Retrieves the groups for a given image based on its descriptive split.

H

hashCode() - Method in class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare

hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations

hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

I

ImageCounter<T> - Interface in org.anchoranalysis.plugin.annotation.counter

Counts images on aggregate, some with associated annotations, others without.

ImageCounterList<T extends org.anchoranalysis.annotation.io.assignment.Assignment<org.anchoranalysis.image.voxel.object.ObjectMask>> - Class in org.anchoranalysis.plugin.annotation.counter

Allows operations to be applied to several ImageCounters collectively.

ImageCounterList() - Constructor for class org.anchoranalysis.plugin.annotation.counter.ImageCounterList

ImageCounterWithStatistics<T> - Interface in org.anchoranalysis.plugin.annotation.counter

Like ImageCounter but also exports statistics.

ImageLabelStrategy - Class in org.anchoranalysis.plugin.annotation.bean.strategy

Assigns a single label per image, as a whole.

ImageLabelStrategy() - Constructor for class org.anchoranalysis.plugin.annotation.bean.strategy.ImageLabelStrategy

inputs(InputManagerParameters) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager

inputTypesExpected() - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations

inputTypesExpected() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

isFlatten() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane, before comparison.

isInvert() - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskAsObject

If true the Mask is inverted before conversion into an ObjectCollection.

isRemoveTouchingBorderXY() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner

isReplaceMatchesWithSolids() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

If true, matched objects are replaced with solid colors.

iterator() - Method in class org.anchoranalysis.plugin.annotation.counter.ImageCounterList

K

keySet() - Method in class org.anchoranalysis.plugin.annotation.bean.label.GroupedAnnotationLabels

Gets the set of group keys.

L

loadAsObjects(Path, Dimensions, boolean, OperationContext) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskAsObject

loadAsObjects(Path, Dimensions, boolean, OperationContext) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.Objects

M

MarkProposerStrategy - Class in org.anchoranalysis.plugin.annotation.bean.strategy

Annotates each image with a mark using a mark proposer and points fitter.

MarkProposerStrategy() - Constructor for class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy

marksDeriver() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy

Gets the marks deriver path if set.

MaskAsObject - Class in org.anchoranalysis.plugin.annotation.bean.comparer

Loads Mask to compared, converting it into an ObjectMask.

MaskAsObject() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparer.MaskAsObject

MaskIntersectionAssigner - Class in org.anchoranalysis.plugin.annotation.bean.comparison.assigner

No outputs are produced.

MaskIntersectionAssigner() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.MaskIntersectionAssigner

moreThanOneObject() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.AnnotationComparisonAssigner

Checks if more than one object can exist in the assignment.

moreThanOneObject() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner

moreThanOneObject() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.MaskIntersectionAssigner

N

numberGroups() - Method in class org.anchoranalysis.plugin.annotation.bean.label.GroupedAnnotationLabels

Gets the number of unique groups.

O

Objects - Class in org.anchoranalysis.plugin.annotation.bean.comparer

An ObjectCollection to be compared against something else.

Objects() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparer.Objects

ObjectsToCompare - Class in org.anchoranalysis.plugin.annotation.comparison

Holds two ObjectCollections for comparison purposes.

ObjectsToCompare(ObjectCollection, ObjectCollection) - Constructor for class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare

org.anchoranalysis.plugin.annotation.bean.aggregate - package org.anchoranalysis.plugin.annotation.bean.aggregate

Beans to combine two or more annotations.

org.anchoranalysis.plugin.annotation.bean.comparer - package org.anchoranalysis.plugin.annotation.bean.comparer

Comparing the similarity of annotations from two images to each other.

org.anchoranalysis.plugin.annotation.bean.comparison - package 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.comparison.assigner - package org.anchoranalysis.plugin.annotation.bean.comparison.assigner

Pairs annotations from two different sets, creating an assignment of some type.

org.anchoranalysis.plugin.annotation.bean.file - package org.anchoranalysis.plugin.annotation.bean.file

FilesProviders for providing annotations.

org.anchoranalysis.plugin.annotation.bean.label - package org.anchoranalysis.plugin.annotation.bean.label

A label as used for annotating.

org.anchoranalysis.plugin.annotation.bean.strategy - package org.anchoranalysis.plugin.annotation.bean.strategy

Strategies for how to annotate an image, such label per image etc.

org.anchoranalysis.plugin.annotation.comparison - package org.anchoranalysis.plugin.annotation.comparison

Non-bean classes for comparing two sets of annotations.

org.anchoranalysis.plugin.annotation.counter - package org.anchoranalysis.plugin.annotation.counter

Utility classes for counting images incrementally.

OUTPUT_BY_GROUP - Static variable in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

Output name for the CSV file containing summary statistics for all groups of images.

P

pathFor(ProvidesStackInput) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.SinglePathStrategy

PathFromGenerator - Class in org.anchoranalysis.plugin.annotation.bean.strategy

Utility class for deriving paths from a generator.

R

ReadAnnotationFromFile - Class in org.anchoranalysis.plugin.annotation.bean.strategy

Utility class for reading ImageLabelAnnotation from a file.

readAssumeExists(Path, OperationContext) - Static method in class org.anchoranalysis.plugin.annotation.bean.strategy.ReadAnnotationFromFile

Reads an ImageLabelAnnotation from a file, assuming the file exists.

readCheckExists(Path, OperationContext) - Static method in class org.anchoranalysis.plugin.annotation.bean.strategy.ReadAnnotationFromFile

Reads an ImageLabelAnnotation from a file if it exists.

S

setAdditionalBackgrounds(List<DerivePath>) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy

Additional background-stacks that are possible to use while annotating.

setAnnotations(AnnotationInputManager<NamedChannelsInputPart, T>) - Method in class org.anchoranalysis.plugin.annotation.bean.file.FromAnnotations

The annotation input manager.

setAssigner(AnnotationComparisonAssigner<T>) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

The assigner used for annotation comparison.

setBackground(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

The name of the stack to use as background to the annotations.

setColor(RGBColorBean) - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel

An optional color associated with the label when displayed via GUI.

setColorsUnpaired(ColorScheme) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

The color scheme for unpaired objects.

setComparerLeft(ComparableSource) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager

The comparable source for the left side of the comparison.

setComparerRight(ComparableSource) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager

The comparable source for the right side of the comparison.

setDerivePath(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskAsObject

Where to find the Mask to compare, as a function of the source file-path.

setDerivePath(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.Objects

Where to find the objects to compare, as a function of the source file-path.

setDisplayer(StackDisplayer) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

How to convert an image to be displayed to the user.

setFeatureEvaluator(FeatureEvaluator<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner

setFlatten(boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane, before comparison.

setGroup(String) - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel

Specifies a group for the label (similar labels that are displayed together).

setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager

The input manager for the base input type T.

setInvert(boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskAsObject

If true the Mask is inverted before conversion into an ObjectCollection.

setLabels(List<AnnotationLabel>) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.ImageLabelStrategy

List of AnnotationLabels available for annotation.

setMarkEvaluator(NamedBean<MarkEvaluator>) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy

A mark-evaluator that is added to the GUI to support this annotation

setMarkProposer(String) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy

Name of the MarkProposer to use.

setMaxCost(double) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner

setMaxSplitGroups(int) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

The maximum number of groups to split the identifier into.

setMultipleComparer(MultipleComparer) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy

Multiple comparer for comparing annotations.

setNameLeft(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager

The name of the left side in the comparison.

setNameRight(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager

The name of the right side in the comparison.

setNumberDecimalPlaces(int) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner

setNumberLevelsGrouping(int) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

The number of levels for grouping.

setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

How many pixels should the outline be around objects.

setPathAnnotation(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.SinglePathStrategy

Derives the path to the corresponding annotation files, given a path to the image to be annotated.

setPathDefaultMarks(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy

Path to derive default marks from.

setPathDictionary(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy

Path to derive dictionary from.

setPointsFitter(String) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy

Name of the PointsFitter to use.

setRemoveTouchingBorderXY(boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner

setReplaceMatchesWithSolids(boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

If true, matched objects are replaced with solid colors.

setSplitIdentifierRegex(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations

If non-empty, the string (a regular-expression) is used to split the file's identifier into groups.

setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskAsObject

How to read the Mask from the file-system.

setUniqueLabel(String) - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel

Label that uniquely identifies the ID (for machine purposes).

setUserFriendlyLabel(String) - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel

Descriptive user-friendly label displayed via GUI.

setWeightWidthDescription(int) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.ImageLabelStrategy

The weight to use for the width of the description.

SinglePathStrategy - Class in org.anchoranalysis.plugin.annotation.bean.strategy

A base class for implementations of AnnotatorStrategy where a single unique path exists for every annotation.

SinglePathStrategy() - Constructor for class org.anchoranalysis.plugin.annotation.bean.strategy.SinglePathStrategy

statisticsForAllGroups() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.ComparisonSharedState

Retrieves statistics for all groups.

stream() - Method in class org.anchoranalysis.plugin.annotation.counter.ImageCounterList

Returns a sequential Stream with this list as its source.

T

toString() - Method in class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare

W

weightWidthDescription() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.ImageLabelStrategy

weightWidthDescription() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy

writeFeaturesToCSV(CSVWriter, List<ImageAnnotation>, List<String>) - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AnnotationAggregateCSVGenerator

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