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 ObjectMask
s.Implementations of
ColorProvider
.Implementations of
MaskProvider
that convert
providers of other types to ObjectMask
s.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
ObjectMask
s.Non-beans for calculating
Feature
s.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.
-
Uses of ObjectCollectionProvider in org.anchoranalysis.image.bean.provider
Subclasses of ObjectCollectionProvider in org.anchoranalysis.image.bean.providerModifier and TypeClassDescriptionclass
Implementation ofObjectCollectionProvider
that 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 TypeMethodDescriptionvoid
OutputFeatureTable.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 TypeMethodDescriptionvoid
DistanceTransformForEachObject3D.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 TypeMethodDescriptionvoid
UnaryWithObjectsBase.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 TypeMethodDescriptionvoid
AssignFromIntersectingObjects.setObjectsSource
(ObjectCollectionProvider objectsSource) void
AssignFromIntersectingObjects.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 TypeMethodDescriptionvoid
LevelPerObjectBase.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 TypeMethodDescriptionvoid
GenerateToMatchObjects.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 TypeMethodDescriptionvoid
IntersectsWith.setObjects
(ObjectCollectionProvider objects) void
GreaterIntersectionWith.setObjectsGreater
(ObjectCollectionProvider objectsGreater) void
GreaterIntersectionWith.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 TypeMethodDescriptionvoid
Always.setObjects
(ObjectCollectionProvider objects) void
Intersection.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 TypeClassDescriptionclass
Extract a singleObjectMask
into a new collection.class
AnObjectCollectionProvider
that concatenates multipleObjectCollection
s from a list of providers.class
Duplicates (deep copy) an object-collection.class
Creates an empty object-collection.class
Multiplexes between two object-collection-providers depending on whether a parameter value equals a particular stringclass
Permutes some changes over anObjectCollectionProvider
and collects all the results in anObjectCollection
class
AnObjectCollectionProvider
that references an existingObjectCollection
by its identifier.class
Returns a object-collection by name if it exists, or else callsobjectsElse
if it doesn't exist.class
Scales all the objects in the collection by a particular scale-factor.class
Base class forObjectCollectionProviderUnary
that also requires aChannel
.class
Base class forObjectCollectionProvider
s that create objects from aChannel
.class
Base class forObjectCollectionProviderUnary
that take an optionalobjectsContainer
bean-field.class
Base class forObjectCollectionProviderUnary
classes that require dimensions to be specified.class
Base class forObjectCollectionProviderUnary
classes 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 ofObjectCollectionProvider
s whoseObjectCollection
s will be concatenated.Methods in org.anchoranalysis.plugin.image.bean.object.provider with parameters of type ObjectCollectionProviderModifier and TypeMethodDescriptionvoid
Permute.setObjects
(ObjectCollectionProvider objects) void
WithContainerBase.setObjectsContainer
(ObjectCollectionProvider objectsContainer) Optional provider for a container of objects.void
ReferenceOrElse.setObjectsElse
(ObjectCollectionProvider objectsElse) void
IfParamEqual.setWhenEqual
(ObjectCollectionProvider whenEqual) void
IfParamEqual.setWhenNotEqual
(ObjectCollectionProvider whenNotEqual) Method parameters in org.anchoranalysis.plugin.image.bean.object.provider with type arguments of type ObjectCollectionProviderModifier and TypeMethodDescriptionvoid
Concatenate.setList
(List<ObjectCollectionProvider> list) List ofObjectCollectionProvider
s whoseObjectCollection
s 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 TypeClassDescriptionclass
Converts a binary-mask into its connected componentsclass
Ensures each object in a collection is a connected-component, decomposing it if necessary into multiple objects.class
Rejects 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 TypeClassDescriptionclass
An abstract base class for object collection providers that use a feature evaluator.class
Finds the object with the maximum feature-value from a collection.class
Finds the object with the maximum feature among a group of matches for each object.class
Creates 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 TypeClassDescriptionclass
Filters anObjectCollection
using the specifiedObjectFilter
.class
Filters anObjectCollection
by grouping objects and then applying a filter to each group.class
Returns only the objects that intersect with at least one object in the containerclass
Provides anObjectCollection
by matching objects using a specifiedObjectMatcher
.class
Filters objects to keep only those which are NOT in the container.class
Base class for object collection providers that apply a filter to the objects.class
Considers 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 theObjectCollection
used for grouping the objects to be filtered.Methods in org.anchoranalysis.plugin.image.bean.object.provider.filter with parameters of type ObjectCollectionProviderModifier and TypeMethodDescriptionvoid
FilterByGroup.setObjectsGrouped
(ObjectCollectionProvider objectsGrouped) Provides theObjectCollection
used for grouping the objects to be filtered. -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.image.bean.object.provider.mask
Modifier and TypeClassDescriptionclass
Reduce the size of individual objects (if neccessary, and minimally) to fit within a binary-mask.class
Converts 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 TypeClassDescriptionclass
A base class for algorithms that merge object-masks.class
Naive greedy merge strategy when any two neighboring objects are merged if it increases a feature.class
Merges objects if a pair feature value satisfies a condition.class
Merges neighboring objects if it results in an increase in the average feature-value calculated on each single object.class
Merges itemwise objects from two collections.class
Base class for object-merging strategies that involve calculating a feature.class
ExpandsMergeBase
by 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 TypeMethodDescriptionvoid
MergeTwoCollectionsItemwise.setObjects1
(ObjectCollectionProvider objects1) First collection with items to be mergedvoid
MergeTwoCollectionsItemwise.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 TypeClassDescriptionclass
Dilates each object in the collection, growing bounding-boxes as necessary in relevant dimensions.class
Erodes each object in the collection, growing bounding-boxes as necessary in relevant dimensions.class
Base 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 TypeClassDescriptionclass
Performs a binary-segmentation using the upstream objects as masks.class
Segments a channel into objects using a specified segmentation algorithm.class
Performs segmentation of a channel using each object in the upstream collection as a mask.class
SegmentStack<T extends InferenceModel>
Segments a stack into objects.class
Takes each object one-by-one fromobjectsSource
, and finds matching seeds fromobjectsSeeds
Methods 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 TypeMethodDescriptionvoid
SegmentChannel.setObjectsSeeds
(ObjectCollectionProvider objectsSeeds) Optional provider for seed objects to guide the segmentation.void
SegmentWithSeeds.setObjectsSeeds
(ObjectCollectionProvider objectsSeeds) void
SegmentWithSeeds.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 TypeClassDescriptionclass
Creates a 3D version of an object by replicating each input-object across the z-dimension to meet (3D) dimensions.class
Extends an object (2D/3D) as much as it can within the z-slices of a containing objectclass
Flattens all object-masks in the z-dimension, so it is 2D instead of 3D (like a maximum intensity projection).class
Extracts 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 TypeClassDescriptionclass
Considers all possible pairs of objects in a provider, and removes any intersecting pixelsclass
Splits objects in a collection based on intersections with another set of objects.class
Splits 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 TypeMethodDescriptionvoid
SplitByObjects.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 TypeMethodDescriptionvoid
ColoredObjects.setObjects
(ObjectCollectionProvider objects) Objects to draw on a backgroundvoid
ThreeColoredObjects.setObjectsBlue
(ObjectCollectionProvider objectsBlue) void
ThreeColoredObjects.setObjectsGreen
(ObjectCollectionProvider objectsGreen) void
ThreeColoredObjects.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 TypeMethodDescriptionvoid
ColoredObjectCollection.addObjectsWithColor
(ObjectCollectionProvider provider, RGBColor color) Adds objects from aObjectCollectionProvider
all 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 TypeMethodDescriptionvoid
CalculateFeaturesForObjects.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 TypeClassDescriptionclass
Draws a lines between successive points on the convex-hull of an object.class
Fills holes in an object. -
Uses of ObjectCollectionProvider in org.anchoranalysis.plugin.mpp.bean.object.provider
Modifier and TypeClassDescriptionclass
Creates object-masks from aMarkCollection
where (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 TypeMethodDescriptionvoid
PointsFromObjects.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 TypeClassDescriptionclass
Splits 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 theObjectCollection
to be used in the fitting process.Methods in org.anchoranalysis.plugin.points.bean.fitter with parameters of type ObjectCollectionProviderModifier and TypeMethodDescriptionvoid
PointsFitterToMark.setObjects
(ObjectCollectionProvider objects) Provides theObjectCollection
to be used in the fitting process.