Uses of Class
org.anchoranalysis.mpp.mark.MarkCollection

Packages that use MarkCollection

Package	Description
org.anchoranalysis.annotation.mark	Annotations that use one or more marks to describe entities in an image.
org.anchoranalysis.mpp.bean.points	Operations based on sets of points.
org.anchoranalysis.mpp.bean.proposer	Proposing Marks or other data-structures with particular attributes.
org.anchoranalysis.mpp.feature.addcriteria	Criteria for adding edges during optimization of marked-point-processes.
org.anchoranalysis.mpp.feature.bean.mark.collection	Features calculated on a org.anchoranalysis.mpp.feature.bean.mark.collection.
org.anchoranalysis.mpp.feature.energy.marks	Non-bean classes pertaining to calculating energy of {org.anchoranalysis.mpp.mark.Mark}s.
org.anchoranalysis.mpp.feature.energy.saved	Saved snapshots of energy-calculations.
org.anchoranalysis.mpp.feature.mark	Non-bean classes for calculating feature-values related to Marks.
org.anchoranalysis.mpp.init	Parameters used to initialize certain types of beans.
org.anchoranalysis.mpp.io.input	Non-beans for reading data structures related to marked point processes from the file system.
org.anchoranalysis.mpp.mark	Non-bean classes related to Marks.
org.anchoranalysis.mpp.overlay	Any Overlay related to a Mark.
org.anchoranalysis.plugin.mpp.bean.provider.collection	Implementation of MarkCollectionProvider.
org.anchoranalysis.plugin.points.bean	Beans that fit or otherwise manipulate sets of points.

Uses of MarkCollection in org.anchoranalysis.annotation.mark

Methods in org.anchoranalysis.annotation.mark that return MarkCollection

Modifier and Type	Method	Description
MarkCollection	DualMarks.accepted()	The accepted marks.
MarkCollection	DualMarksAnnotation.getMarksReject()	Marks covering area that should be rejected, can be null
MarkCollection	AnnotationWithMarks.marks()	The marks associated with the annotation
MarkCollection	DualMarksAnnotation.marks()
MarkCollection	DualMarks.rejected()	The rejected marks.

Uses of MarkCollection in org.anchoranalysis.mpp.bean.points

Methods in org.anchoranalysis.mpp.bean.points with parameters of type MarkCollection

Modifier and Type	Method	Description
Optional<Mark>	CreateMarkFromPoints.fitMarkToPointsFromMarks(MarkCollection marks, Dimensions dimensions)	Extracts points from marks, creates a new mark, and fits this mark to the extracted points.

Uses of MarkCollection in org.anchoranalysis.mpp.bean.proposer

Methods in org.anchoranalysis.mpp.bean.proposer that return types with arguments of type MarkCollection

Modifier and Type	Method	Description
abstract Optional<MarkCollection>	MarkCollectionProposer.propose(MarkWithIdentifierFactory markFactory, ProposerContext context)	Proposes a collection of marks.

Methods in org.anchoranalysis.mpp.bean.proposer with parameters of type MarkCollection

Modifier and Type	Method	Description
abstract Optional<Mark>	MarkFromCollectionProposer.selectMarkFrom(MarkCollection marks, ProposerContext context)	Selects a mark from a collection of marks.

Uses of MarkCollection in org.anchoranalysis.mpp.feature.addcriteria

Methods in org.anchoranalysis.mpp.feature.addcriteria with parameters of type MarkCollection

Modifier and Type	Method	Description
boolean	RandomCollectionWithAddCriteria.isMarksSpan(MarkCollection marks)	Checks if the given MarkCollection spans all marks in this collection.

Uses of MarkCollection in org.anchoranalysis.mpp.feature.bean.mark.collection

Methods in org.anchoranalysis.mpp.feature.bean.mark.collection that return MarkCollection

Modifier and Type	Method	Description
MarkCollection	FeatureInputMarkCollection.getMarks()	The collection of marks.

Constructors in org.anchoranalysis.mpp.feature.bean.mark.collection with parameters of type MarkCollection

Modifier	Constructor	Description
	FeatureInputMarkCollection(MarkCollection marks, Optional<Dimensions> dimensions)	Creates a new FeatureInputMarkCollection instance.

Uses of MarkCollection in org.anchoranalysis.mpp.feature.energy.marks

Methods in org.anchoranalysis.mpp.feature.energy.marks that return MarkCollection

Modifier and Type	Method	Description
MarkCollection	MarksWithEnergyBreakdown.getMarks()	Gets the collection of marks.
MarkCollection	MarksWithTotalEnergy.getMarks()	The marks in the collection.

Methods in org.anchoranalysis.mpp.feature.energy.marks with parameters of type MarkCollection

Modifier and Type	Method	Description
void	MarksWithTotalEnergy.setMarks(MarkCollection marks)	The marks in the collection.

Constructors in org.anchoranalysis.mpp.feature.energy.marks with parameters of type MarkCollection

Modifier	Constructor	Description
	MarksWithTotalEnergy(MarkCollection marks, EnergySchemeWithSharedFeatures energyScheme)	Creates a new instance with the given marks and energy scheme.

Uses of MarkCollection in org.anchoranalysis.mpp.feature.energy.saved

Methods in org.anchoranalysis.mpp.feature.energy.saved with parameters of type MarkCollection

Modifier and Type	Method	Description
String	EnergySavedIndividual.describeMarks(MarkCollection marks)	Generates a string description of the marks and their associated energies.
boolean	EnergySavedPairs.isMarksSpan(MarkCollection marks)	Checks if the pair collection only contains items from a particular mark configuration.

Uses of MarkCollection in org.anchoranalysis.mpp.feature.mark

Methods in org.anchoranalysis.mpp.feature.mark that return MarkCollection

Modifier and Type	Method	Description
MarkCollection	EnergyMemoList.asMarks()	Converts the energy memo list to a collection of marks.

Methods in org.anchoranalysis.mpp.feature.mark with parameters of type MarkCollection

Modifier and Type	Method	Description
VoxelizedMarkMemo	EnergyMemoList.getMemoForMark(MarkCollection marks, Mark mark)	Gets the memo for a specific mark in the collection.

Constructors in org.anchoranalysis.mpp.feature.mark with parameters of type MarkCollection

Modifier	Constructor	Description
	EnergyMemoList(EnergySavedIndividual savedInd, EnergyStackWithoutParameters energyStack, MarkCollection marks, EnergySchemeWithSharedFeatures energySchemeTotal)	Creates an energy memo list with the given parameters.

Uses of MarkCollection in org.anchoranalysis.mpp.init

Methods in org.anchoranalysis.mpp.init that return types with arguments of type MarkCollection

Modifier and Type	Method	Description
NamedProviderStore<MarkCollection>	MarksInitialization.marks()	Store for mark collections.

Uses of MarkCollection in org.anchoranalysis.mpp.io.input

Methods in org.anchoranalysis.mpp.io.input that return types with arguments of type MarkCollection

Modifier and Type	Method	Description
MultiInputSubMap<MarkCollection>	MultiInput.marks()	Gets the map of MarkCollections.

Uses of MarkCollection in org.anchoranalysis.mpp.mark

Methods in org.anchoranalysis.mpp.mark that return MarkCollection

Modifier and Type	Method	Description
MarkCollection	MarkCollection.createMerged(MarkCollection toMerge)	Creates a new collection by merging this collection with another.
MarkCollection	MarkCollection.deepCopy()	Creates a deep copy of the collection.
MarkCollection	ColoredMarks.getMarks()
MarkCollection	MarkCollection.marksAt(Point3i point, RegionMap regionMap, int regionID)	Finds marks at a specific point that belong to a specific region.
MarkCollection	MarkCollection.shallowCopy()	Creates a shallow copy of the collection.

Methods in org.anchoranalysis.mpp.mark with parameters of type MarkCollection

Modifier and Type	Method	Description
void	ColoredMarks.addAll(MarkCollection marks, RGBColor color)	Adds all marks from a MarkCollection with the same color.
void	MarkCollection.addAll(MarkCollection marks)	Adds all marks from another collection to this collection.
MarkCollection	MarkCollection.createMerged(MarkCollection toMerge)	Creates a new collection by merging this collection with another.
boolean	MarkCollection.equalsDeep(MarkCollection other)	Checks if this collection is deeply equal to another.

Constructors in org.anchoranalysis.mpp.mark with parameters of type MarkCollection

Modifier	Constructor	Description
	ColoredMarks(MarkCollection marks, ColorIndex colorIndex, IdentifierGetter<Mark> colorIDGetter)	Creates a ColoredMarks instance from a MarkCollection and assigns colors based on a ColorIndex.
	ColoredMarks(MarkCollection marks, ColorList colorList)

Uses of MarkCollection in org.anchoranalysis.mpp.overlay

Methods in org.anchoranalysis.mpp.overlay that return MarkCollection

Modifier and Type	Method	Description
static MarkCollection	OverlayCollectionMarkFactory.marksFromOverlays(OverlayCollection overlays)	Creates a MarkCollection from an OverlayCollection.

Methods in org.anchoranalysis.mpp.overlay with parameters of type MarkCollection

Modifier and Type	Method	Description
static OverlayCollection	OverlayCollectionMarkFactory.createWithoutColor(MarkCollection marks, RegionMembershipWithFlags regionMembership)	Creates an OverlayCollection from a MarkCollection without color information.

Uses of MarkCollection in org.anchoranalysis.plugin.mpp.bean.provider.collection

Methods in org.anchoranalysis.plugin.mpp.bean.provider.collection that return MarkCollection

Modifier and Type	Method	Description
MarkCollection	CreateNew.get()
MarkCollection	FromSingleMark.get()
MarkCollection	PointsFromObjects.get()
MarkCollection	Reference.get()
MarkCollection	ReferenceOrEmpty.get()
MarkCollection	ScaleXY.get()

Uses of MarkCollection in org.anchoranalysis.plugin.points.bean

Methods in org.anchoranalysis.plugin.points.bean that return MarkCollection

Modifier and Type	Method	Description
MarkCollection	FitPointsFromObjects.get()