Uses of Class
org.anchoranalysis.image.bean.provider.ObjectCollectionProvider
Packages that use ObjectCollectionProvider
Package
Description
Base classes for providers of different core data entities related to images.
Beans to specify the outputting of features into CSV from a
ObjectCollection.Euclidean Distance Transform
implementations via FIJI.
Implementations of
ChannelProvider that are
generic base-classes or otherwise abstract or general.Implementations of
ChannelProvider that sets the
values of the voxels in a Channel.Implementations of
ChannelProvider that involve
conversion from or application of ObjectMasks.Implementations of
ColorProvider.Implementations of
MaskProvider that convert
providers of other types to ObjectMasks.Implementations of
ObjectFilter that
independently assess each element in a collection.Implementations of
ObjectMatcher.Implementations of
ObjectCollectionProvider.Implementations of
ObjectCollectionProvider
involving connected-components.Implementations of
ObjectCollectionProvider
involving feature calculation.Implementations of
ObjectCollectionProvider that
filter objects.Implementations of
ObjectCollectionProvider
involving a Mask.Implementations of
ObjectCollectionProvider
involving merging objects together.Implementations of
ObjectCollectionProvider
involving morphological operations.Implementations of
ObjectCollectionProvider
involving segmentation.Implementations of
ObjectCollectionProvider
involving z-slice processing.Implementations of
ObjectCollectionProvider
involving splitting objects into smaller objects.Implementations of
StackProvider that color
portions of an image.Beans involving
SharedObjects and
ObjectCollection.Non-beans pertaining to
ObjectMasks.Non-beans for calculating
Features.Implementations of
ObjectCollectionProvider that
call ImageJ.Implementations of
ObjectCollectionProvider.Implementation of
MarkCollectionProvider.Beans that fit or otherwise manipulate sets of points.
Fitting geometric structures to points.
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Uses of ObjectCollectionProvider in org.anchoranalysis.image.bean.provider
Subclasses of ObjectCollectionProvider in org.anchoranalysis.image.bean.providerModifier and TypeClassDescriptionclassImplementation ofObjectCollectionProviderthat calls a single delegateProvider<ObjectCollection>. -
Uses of ObjectCollectionProvider in org.anchoranalysis.image.io.bean.object.feature
Methods in org.anchoranalysis.image.io.bean.object.feature that return ObjectCollectionProviderModifier and TypeMethodDescriptionOutputFeatureTable.getObjects()The objects for which features are calculated.Methods in org.anchoranalysis.image.io.bean.object.feature with parameters of type ObjectCollectionProviderModifier and TypeMethodDescriptionvoidOutputFeatureTable.setObjects(ObjectCollectionProvider objects) The objects for which features are calculated. -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance
Methods in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance that return ObjectCollectionProviderMethods in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance with parameters of type ObjectCollectionProviderModifier and TypeMethodDescriptionvoidDistanceTransformForEachObject3D.setObjects(ObjectCollectionProvider objects) -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.bean.channel.provider
Methods in org.anchoranalysis.plugin.image.bean.channel.provider that return ObjectCollectionProviderModifier and TypeMethodDescriptionUnaryWithObjectsBase.getObjects()The provider for the collection of objects to be used in channel creation.Methods in org.anchoranalysis.plugin.image.bean.channel.provider with parameters of type ObjectCollectionProviderModifier and TypeMethodDescriptionvoidUnaryWithObjectsBase.setObjects(ObjectCollectionProvider objects) The provider for the collection of objects to be used in channel creation. -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.bean.channel.provider.assign
Methods in org.anchoranalysis.plugin.image.bean.channel.provider.assign that return ObjectCollectionProviderModifier and TypeMethodDescriptionAssignFromIntersectingObjects.getObjectsSource()AssignFromIntersectingObjects.getObjectsTarget()Methods in org.anchoranalysis.plugin.image.bean.channel.provider.assign with parameters of type ObjectCollectionProviderModifier and TypeMethodDescriptionvoidAssignFromIntersectingObjects.setObjectsSource(ObjectCollectionProvider objectsSource) voidAssignFromIntersectingObjects.setObjectsTarget(ObjectCollectionProvider objectsTarget) -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.bean.channel.provider.object
Methods in org.anchoranalysis.plugin.image.bean.channel.provider.object that return ObjectCollectionProviderModifier and TypeMethodDescriptionLevelPerObjectBase.getObjects()The objects for whom a level is calculated.Methods in org.anchoranalysis.plugin.image.bean.channel.provider.object with parameters of type ObjectCollectionProviderModifier and TypeMethodDescriptionvoidLevelPerObjectBase.setObjects(ObjectCollectionProvider objects) The objects for whom a level is calculated. -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.bean.color.provider
Methods in org.anchoranalysis.plugin.image.bean.color.provider that return ObjectCollectionProviderMethods in org.anchoranalysis.plugin.image.bean.color.provider with parameters of type ObjectCollectionProviderModifier and TypeMethodDescriptionvoidGenerateToMatchObjects.setObjects(ObjectCollectionProvider objects) -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.bean.mask.provider.convert
Methods in org.anchoranalysis.plugin.image.bean.mask.provider.convert that return ObjectCollectionProviderMethods in org.anchoranalysis.plugin.image.bean.mask.provider.convert with parameters of type ObjectCollectionProvider -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.bean.object.filter.independent
Methods in org.anchoranalysis.plugin.image.bean.object.filter.independent that return ObjectCollectionProviderModifier and TypeMethodDescriptionIntersectsWith.getObjects()GreaterIntersectionWith.getObjectsGreater()GreaterIntersectionWith.getObjectsLesser()Methods in org.anchoranalysis.plugin.image.bean.object.filter.independent with parameters of type ObjectCollectionProviderModifier and TypeMethodDescriptionvoidIntersectsWith.setObjects(ObjectCollectionProvider objects) voidGreaterIntersectionWith.setObjectsGreater(ObjectCollectionProvider objectsGreater) voidGreaterIntersectionWith.setObjectsLesser(ObjectCollectionProvider objectsLesser) -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.bean.object.match
Methods in org.anchoranalysis.plugin.image.bean.object.match that return ObjectCollectionProviderModifier and TypeMethodDescriptionAlways.getObjects()Intersection.getObjects()Provider for the objects to intersect with the source objects.Methods in org.anchoranalysis.plugin.image.bean.object.match with parameters of type ObjectCollectionProviderModifier and TypeMethodDescriptionvoidAlways.setObjects(ObjectCollectionProvider objects) voidIntersection.setObjects(ObjectCollectionProvider objects) Provider for the objects to intersect with the source objects. -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.bean.object.provider
Modifier and TypeClassDescriptionclassExtract a singleObjectMaskinto a new collection.classAnObjectCollectionProviderthat concatenates multipleObjectCollections from a list of providers.classDuplicates (deep copy) an object-collection.classCreates an empty object-collection.classMultiplexes between two object-collection-providers depending on whether a parameter value equals a particular stringclassPermutes some changes over anObjectCollectionProviderand collects all the results in anObjectCollectionclassAnObjectCollectionProviderthat references an existingObjectCollectionby its identifier.classReturns a object-collection by name if it exists, or else callsobjectsElseif it doesn't exist.classScales all the objects in the collection by a particular scale-factor.classBase class forObjectCollectionProviderUnarythat also requires aChannel.classBase class forObjectCollectionProviders that create objects from aChannel.classBase class forObjectCollectionProviderUnarythat take an optionalobjectsContainerbean-field.classBase class forObjectCollectionProviderUnaryclasses that require dimensions to be specified.classBase class forObjectCollectionProviderUnaryclasses that offer an optional means to specify dimensions.Methods in org.anchoranalysis.plugin.image.bean.object.provider that return ObjectCollectionProviderModifier and TypeMethodDescriptionPermute.getObjects()WithContainerBase.getObjectsContainer()Optional provider for a container of objects.ReferenceOrElse.getObjectsElse()IfParamEqual.getWhenEqual()IfParamEqual.getWhenNotEqual()Methods in org.anchoranalysis.plugin.image.bean.object.provider that return types with arguments of type ObjectCollectionProviderModifier and TypeMethodDescriptionConcatenate.getList()List ofObjectCollectionProviders whoseObjectCollections will be concatenated.Methods in org.anchoranalysis.plugin.image.bean.object.provider with parameters of type ObjectCollectionProviderModifier and TypeMethodDescriptionvoidPermute.setObjects(ObjectCollectionProvider objects) voidWithContainerBase.setObjectsContainer(ObjectCollectionProvider objectsContainer) Optional provider for a container of objects.voidReferenceOrElse.setObjectsElse(ObjectCollectionProvider objectsElse) voidIfParamEqual.setWhenEqual(ObjectCollectionProvider whenEqual) voidIfParamEqual.setWhenNotEqual(ObjectCollectionProvider whenNotEqual) Method parameters in org.anchoranalysis.plugin.image.bean.object.provider with type arguments of type ObjectCollectionProviderModifier and TypeMethodDescriptionvoidConcatenate.setList(List<ObjectCollectionProvider> list) List ofObjectCollectionProviders whoseObjectCollections will be concatenated. -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.bean.object.provider.connected
Subclasses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.bean.object.provider.connectedModifier and TypeClassDescriptionclassConverts a binary-mask into its connected componentsclassEnsures each object in a collection is a connected-component, decomposing it if necessary into multiple objects.classRejects a set of objects, if any object is not fully connected (pixels form two or more separate connected components) -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.bean.object.provider.feature
Subclasses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.bean.object.provider.featureModifier and TypeClassDescriptionclassAn abstract base class for object collection providers that use a feature evaluator.classFinds the object with the maximum feature-value from a collection.classFinds the object with the maximum feature among a group of matches for each object.classCreates a new object-collection with objects sorted by a derived feature-value (in ascending order) -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.bean.object.provider.filter
Subclasses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.bean.object.provider.filterModifier and TypeClassDescriptionclassFilters anObjectCollectionusing the specifiedObjectFilter.classFilters anObjectCollectionby grouping objects and then applying a filter to each group.classReturns only the objects that intersect with at least one object in the containerclassProvides anObjectCollectionby matching objects using a specifiedObjectMatcher.classFilters objects to keep only those which are NOT in the container.classBase class for object collection providers that apply a filter to the objects.classConsiders all possible pairs of objects in a provider, and removes those that touch the border.Methods in org.anchoranalysis.plugin.image.bean.object.provider.filter that return ObjectCollectionProviderModifier and TypeMethodDescriptionFilterByGroup.getObjectsGrouped()Provides theObjectCollectionused for grouping the objects to be filtered.Methods in org.anchoranalysis.plugin.image.bean.object.provider.filter with parameters of type ObjectCollectionProviderModifier and TypeMethodDescriptionvoidFilterByGroup.setObjectsGrouped(ObjectCollectionProvider objectsGrouped) Provides theObjectCollectionused for grouping the objects to be filtered. -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.bean.object.provider.mask
Modifier and TypeClassDescriptionclassReduce the size of individual objects (if neccessary, and minimally) to fit within a binary-mask.classConverts a binary-mask to an object-collection (containing a single object) -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.bean.object.provider.merge
Subclasses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.bean.object.provider.mergeModifier and TypeClassDescriptionclassA base class for algorithms that merge object-masks.classNaive greedy merge strategy when any two neighboring objects are merged if it increases a feature.classMerges objects if a pair feature value satisfies a condition.classMerges neighboring objects if it results in an increase in the average feature-value calculated on each single object.classMerges itemwise objects from two collections.classBase class for object-merging strategies that involve calculating a feature.classExpandsMergeBaseby optionally imposing a maximum-distance requirement between objects that are possibly merged.Methods in org.anchoranalysis.plugin.image.bean.object.provider.merge that return ObjectCollectionProviderModifier and TypeMethodDescriptionMergeTwoCollectionsItemwise.getObjects1()First collection with items to be mergedMergeTwoCollectionsItemwise.getObjects2()Second collection with items to be mergedMethods in org.anchoranalysis.plugin.image.bean.object.provider.merge with parameters of type ObjectCollectionProviderModifier and TypeMethodDescriptionvoidMergeTwoCollectionsItemwise.setObjects1(ObjectCollectionProvider objects1) First collection with items to be mergedvoidMergeTwoCollectionsItemwise.setObjects2(ObjectCollectionProvider objects2) Second collection with items to be merged -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.bean.object.provider.morphological
Subclasses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.bean.object.provider.morphologicalModifier and TypeClassDescriptionclassDilates each object in the collection, growing bounding-boxes as necessary in relevant dimensions.classErodes each object in the collection, growing bounding-boxes as necessary in relevant dimensions.classBase class for providers that apply morphological operations to anObjectCollection. -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.bean.object.provider.segment
Subclasses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.bean.object.provider.segmentModifier and TypeClassDescriptionclassPerforms a binary-segmentation using the upstream objects as masks.classSegments a channel into objects using a specified segmentation algorithm.classPerforms segmentation of a channel using each object in the upstream collection as a mask.classSegmentStack<T extends InferenceModel>Segments a stack into objects.classTakes each object one-by-one fromobjectsSource, and finds matching seeds fromobjectsSeedsMethods in org.anchoranalysis.plugin.image.bean.object.provider.segment that return ObjectCollectionProviderModifier and TypeMethodDescriptionSegmentChannel.getObjectsSeeds()Optional provider for seed objects to guide the segmentation.SegmentWithSeeds.getObjectsSeeds()SegmentWithSeeds.getObjectsSource()Methods in org.anchoranalysis.plugin.image.bean.object.provider.segment with parameters of type ObjectCollectionProviderModifier and TypeMethodDescriptionvoidSegmentChannel.setObjectsSeeds(ObjectCollectionProvider objectsSeeds) Optional provider for seed objects to guide the segmentation.voidSegmentWithSeeds.setObjectsSeeds(ObjectCollectionProvider objectsSeeds) voidSegmentWithSeeds.setObjectsSource(ObjectCollectionProvider objectsSource) -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.bean.object.provider.slice
Subclasses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.bean.object.provider.sliceModifier and TypeClassDescriptionclassCreates a 3D version of an object by replicating each input-object across the z-dimension to meet (3D) dimensions.classExtends an object (2D/3D) as much as it can within the z-slices of a containing objectclassFlattens all object-masks in the z-dimension, so it is 2D instead of 3D (like a maximum intensity projection).classExtracts a specific slice from a collection of 3D objects. -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.bean.object.provider.split
Subclasses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.bean.object.provider.splitModifier and TypeClassDescriptionclassConsiders all possible pairs of objects in a provider, and removes any intersecting pixelsclassSplits objects in a collection based on intersections with another set of objects.classSplits objects into sub-objects by cutting by an orthogonal square lattice (like a chessboard).Methods in org.anchoranalysis.plugin.image.bean.object.provider.split that return ObjectCollectionProviderModifier and TypeMethodDescriptionSplitByObjects.getObjectsSplitBy()Provider for the collection of objects used to split the input objects.Methods in org.anchoranalysis.plugin.image.bean.object.provider.split with parameters of type ObjectCollectionProviderModifier and TypeMethodDescriptionvoidSplitByObjects.setObjectsSplitBy(ObjectCollectionProvider objectsSplitBy) Provider for the collection of objects used to split the input objects. -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.bean.stack.provider.color
Methods in org.anchoranalysis.plugin.image.bean.stack.provider.color that return ObjectCollectionProviderModifier and TypeMethodDescriptionColoredObjects.getObjects()Objects to draw on a backgroundThreeColoredObjects.getObjectsBlue()ThreeColoredObjects.getObjectsGreen()ThreeColoredObjects.getObjectsRed()Methods in org.anchoranalysis.plugin.image.bean.stack.provider.color with parameters of type ObjectCollectionProviderModifier and TypeMethodDescriptionvoidColoredObjects.setObjects(ObjectCollectionProvider objects) Objects to draw on a backgroundvoidThreeColoredObjects.setObjectsBlue(ObjectCollectionProvider objectsBlue) voidThreeColoredObjects.setObjectsGreen(ObjectCollectionProvider objectsGreen) voidThreeColoredObjects.setObjectsRed(ObjectCollectionProvider objectsRed) -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.object
Methods in org.anchoranalysis.plugin.image.object with parameters of type ObjectCollectionProviderModifier and TypeMethodDescriptionvoidColoredObjectCollection.addObjectsWithColor(ObjectCollectionProvider provider, RGBColor color) Adds objects from aObjectCollectionProviderall with one specific color -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.task.feature.calculator
Methods in org.anchoranalysis.plugin.image.task.feature.calculator with parameters of type ObjectCollectionProviderModifier and TypeMethodDescriptionvoidCalculateFeaturesForObjects.calculateForObjects(ObjectCollectionProvider provider, LabelsForInput labelsForInput) Calculates features for objects provided by aObjectCollectionProvider. -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.imagej.bean.object.provider
Modifier and TypeClassDescriptionclassDraws a lines between successive points on the convex-hull of an object.classFills holes in an object. -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.mpp.bean.object.provider
Modifier and TypeClassDescriptionclassCreates object-masks from aMarkCollectionwhere (a particular region of) each mark creates an object. -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.mpp.bean.provider.collection
Methods in org.anchoranalysis.plugin.mpp.bean.provider.collection that return ObjectCollectionProviderModifier and TypeMethodDescriptionPointsFromObjects.getObjects()Provider for the object collection from which to create point marks.Methods in org.anchoranalysis.plugin.mpp.bean.provider.collection with parameters of type ObjectCollectionProviderModifier and TypeMethodDescriptionvoidPointsFromObjects.setObjects(ObjectCollectionProvider objects) Provider for the object collection from which to create point marks. -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.points.bean
Subclasses of ObjectCollectionProvider in org.anchoranalysis.plugin.points.beanModifier and TypeClassDescriptionclassSplits a 2D contour represented by an object-mask into several contours, splitting at "turn" points. -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.points.bean.fitter
Methods in org.anchoranalysis.plugin.points.bean.fitter that return ObjectCollectionProviderModifier and TypeMethodDescriptionPointsFitterToMark.getObjects()Provides theObjectCollectionto be used in the fitting process.Methods in org.anchoranalysis.plugin.points.bean.fitter with parameters of type ObjectCollectionProviderModifier and TypeMethodDescriptionvoidPointsFitterToMark.setObjects(ObjectCollectionProvider objects) Provides theObjectCollectionto be used in the fitting process.