Uses of Class
org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo

Packages that use VoxelizedMarkMemo

Package	Description
org.anchoranalysis.mpp.bean.mark	Beans generally related to Marks.
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.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.energy.scheme	Factorized form of storing the energy during an energy-minimization optimization scheme.
org.anchoranalysis.mpp.feature.input	Inputs to mark-point-processes related Features.
org.anchoranalysis.mpp.feature.mark	Non-bean classes for calculating feature-values related to Marks.
org.anchoranalysis.mpp.mark	Non-bean classes related to Marks.
org.anchoranalysis.mpp.mark.voxelized.memo	Memoization of VoxelizedMarks.
org.anchoranalysis.mpp.overlap	Calculating overlaps between two Marks.
org.anchoranalysis.mpp.pair	Pairs of Marks.
org.anchoranalysis.mpp.proposer	Non-bean classes for proposing Marks or other data-structures with particular attributes.
org.anchoranalysis.plugin.points.bean	Beans that fit or otherwise manipulate sets of points.

Uses of VoxelizedMarkMemo in org.anchoranalysis.mpp.bean.mark

Methods in org.anchoranalysis.mpp.bean.mark with parameters of type VoxelizedMarkMemo

Modifier and Type	Method	Description
abstract VoxelStatistics	MarkRegion.createStatisticsFor(VoxelizedMarkMemo memo, Dimensions dimensions)	Creates voxel statistics for the mark region based on the given memo and dimensions.

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

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

Modifier and Type	Method	Description
abstract Optional<Mark>	MarkMergeProposer.propose(VoxelizedMarkMemo mark1, VoxelizedMarkMemo mark2, ProposerContext context)	Proposes a merge between two marks.
abstract boolean	MarkProposer.propose(VoxelizedMarkMemo inputMark, ProposerContext context)	Proposes changes to the input mark according to the internal rules of the proposer.
abstract Optional<PairVoxelizedMarkMemo>	MarkSplitProposer.propose(VoxelizedMarkMemo mark, ProposerContext context, MarkWithIdentifierFactory markFactory)	Proposes a split of the input mark into two new marks.

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

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

Modifier and Type	Method	Description
void	RandomCollectionWithAddCriteria.add(MemoForIndex marksExisting, VoxelizedMarkMemo newMark)
void	RandomCollectionWithAddCriteria.exchange(MemoForIndex memo, VoxelizedMarkMemo oldMark, int indexOldMark, VoxelizedMarkMemo newMark)
Optional<T>	AddCriteria.generateEdge(VoxelizedMarkMemo mark1, VoxelizedMarkMemo mark2, EnergyStack energyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>> session, boolean do3D)	Generates an edge between two marks based on the defined criteria.
Optional<EnergyPair>	AddCriteriaEnergyPair.generateEdge(VoxelizedMarkMemo mark1, VoxelizedMarkMemo mark2, EnergyStack energyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>> session, boolean do3D)
Optional<T>	AddCriteriaNever.generateEdge(VoxelizedMarkMemo mark1, VoxelizedMarkMemo mark2, EnergyStack energyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>> session, boolean do3D)
Optional<MarkPair<Mark>>	AddCriteriaPair.generateEdge(VoxelizedMarkMemo mark1, VoxelizedMarkMemo mark2, EnergyStack energyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>> session, boolean do3D)
boolean	AddCriteriaOr.includeMarks(VoxelizedMarkMemo mark1, VoxelizedMarkMemo mark2, Dimensions dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>> session, boolean do3D)
abstract boolean	AddCriteriaPair.includeMarks(VoxelizedMarkMemo mark1, VoxelizedMarkMemo mark2, Dimensions dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>> session, boolean do3D)	Determines whether to include a pair of marks based on specific criteria.
boolean	ArbitraryPointCommon.includeMarks(VoxelizedMarkMemo mark1, VoxelizedMarkMemo mark2, Dimensions dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>> session, boolean do3D)
boolean	BoundingBoxIntersection.includeMarks(VoxelizedMarkMemo mark1, VoxelizedMarkMemo mark2, Dimensions dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>> session, boolean do3D)
void	RandomCollectionWithAddCriteria.remove(MemoForIndex marksExisting, VoxelizedMarkMemo mark)

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

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

Modifier and Type	Method	Description
void	MarksWithEnergyBreakdown.add(EnergyMemoList wrapperInd, VoxelizedMarkMemo newPxlMarkMemo, EnergyStackWithoutParameters stack)	Adds a new mark to the collection and updates energies.
void	MarksWithTotalEnergy.add(VoxelizedMarkMemo voxelizedMark)	Adds a voxelized mark to the collection.
void	MarksWithEnergyBreakdown.exchange(int index, VoxelizedMarkMemo newMark)	Exchanges a mark at a specific index with a new mark.
void	MarksWithEnergyBreakdown.exchange(EnergyMemoList wrapperInd, int index, VoxelizedMarkMemo newMark, EnergyStack energyStack)	Exchanges a mark at a specific index with a new mark and updates energies.
void	MarksWithTotalEnergy.exchange(int index, VoxelizedMarkMemo newMark)	Exchanges a mark at a particular index with a new mark.
void	MarksWithEnergyBreakdown.remove(EnergyMemoList wrapperInd, int index, VoxelizedMarkMemo markToRemove, EnergyStackWithoutParameters stack)	Removes a mark at a specific index from the collection and updates energies.
void	MarksWithEnergyBreakdown.remove(EnergyMemoList wrapperInd, VoxelizedMarkMemo markToRemove, EnergyStackWithoutParameters stack)	Removes a specific mark from the collection and updates energies.

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

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

Modifier and Type	Method	Description
void	EnergySavedPairs.add(MemoForIndex pxlMarkMemoList, VoxelizedMarkMemo newMark)
void	EnergySavedPairs.exchange(MemoForIndex memo, VoxelizedMarkMemo oldMark, int indexOldMark, VoxelizedMarkMemo newMark)
void	EnergySavedPairs.remove(MemoForIndex marksExisting, VoxelizedMarkMemo mark)

Uses of VoxelizedMarkMemo in org.anchoranalysis.mpp.feature.energy.scheme

Methods in org.anchoranalysis.mpp.feature.energy.scheme with parameters of type VoxelizedMarkMemo

Modifier and Type	Method	Description
EnergyTotal	EnergySchemeWithSharedFeatures.totalIndividual(VoxelizedMarkMemo pmm, EnergyStackWithoutParameters raster)	Calculates the total energy for an individual mark.

Uses of VoxelizedMarkMemo in org.anchoranalysis.mpp.feature.input

Methods in org.anchoranalysis.mpp.feature.input that return VoxelizedMarkMemo

Modifier and Type	Method	Description
VoxelizedMarkMemo	FeatureInputSingleMemo.getMemo()	The memoized voxelized mark.
VoxelizedMarkMemo	FeatureInputPairMemo.getObject1()	The first memoized voxelized mark.
VoxelizedMarkMemo	FeatureInputPairMemo.getObject2()	The second memoized voxelized mark.

Methods in org.anchoranalysis.mpp.feature.input with parameters of type VoxelizedMarkMemo

Modifier and Type	Method	Description
void	FeatureInputSingleMemo.setMemo(VoxelizedMarkMemo memo)	The memoized voxelized mark.

Constructors in org.anchoranalysis.mpp.feature.input with parameters of type VoxelizedMarkMemo

Modifier	Constructor	Description
	FeatureInputPairMemo(VoxelizedMarkMemo object1, VoxelizedMarkMemo object2, EnergyStack energyStack)	Creates a new instance with two memoized voxelized marks and an energy stack.
	FeatureInputSingleMemo(VoxelizedMarkMemo pxlPartMemo, Optional<EnergyStack> energyStack)	Creates a new instance with a memoized voxelized mark and an optional energy stack.
	FeatureInputSingleMemo(VoxelizedMarkMemo pxlPartMemo, EnergyStack energyStack)	Creates a new instance with a memoized voxelized mark and a non-optional energy stack.

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

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

Modifier and Type	Method	Description
VoxelizedMarkMemo	EnergyMemoList.add(EnergySavedIndividual energySavedInd, VoxelizedMarkMemo memo, EnergyStackWithoutParameters stack, EnergySchemeWithSharedFeatures energyScheme)	Adds a new mark to the list and calculates its energy.
VoxelizedMarkMemo	EnergyMemoList.exchange(EnergySavedIndividual energySavedInd, int index, VoxelizedMarkMemo newMark, EnergyStackWithoutParameters stack, EnergySchemeWithSharedFeatures energySchemeTotal)	Exchanges a mark at a specific index with a new mark and recalculates energies.
VoxelizedMarkMemo	MemoList.get(int index)	Returns the element at the specified position in this list.
VoxelizedMarkMemo	EnergyMemoList.getMemoForIndex(int index)	Gets the memo for a specific index.
VoxelizedMarkMemo	MemoList.getMemoForIndex(int index)
VoxelizedMarkMemo	EnergyMemoList.getMemoForMark(MarkCollection marks, Mark mark)	Gets the memo for a specific mark in the collection.
VoxelizedMarkMemo	MemoList.remove(int index)	Removes the element at the specified position in this list.
VoxelizedMarkMemo	MemoList.set(int index, VoxelizedMarkMemo element)	Replaces the element at the specified position in this list with the specified element.

Methods in org.anchoranalysis.mpp.feature.mark that return types with arguments of type VoxelizedMarkMemo

Modifier and Type	Method	Description
Iterator<VoxelizedMarkMemo>	MemoList.iterator()

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

Modifier and Type	Method	Description
VoxelizedMarkMemo	EnergyMemoList.add(EnergySavedIndividual energySavedInd, VoxelizedMarkMemo memo, EnergyStackWithoutParameters stack, EnergySchemeWithSharedFeatures energyScheme)	Adds a new mark to the list and calculates its energy.
boolean	MemoList.add(VoxelizedMarkMemo e)	Appends the specified element to the end of this list.
VoxelizedMarkMemo	EnergyMemoList.exchange(EnergySavedIndividual energySavedInd, int index, VoxelizedMarkMemo newMark, EnergyStackWithoutParameters stack, EnergySchemeWithSharedFeatures energySchemeTotal)	Exchanges a mark at a specific index with a new mark and recalculates energies.
int	EnergyMemoList.getIndexForMemo(VoxelizedMarkMemo memo)	Gets the index for a specific memo.
boolean	MemoList.remove(VoxelizedMarkMemo memo)	Removes the first occurrence of the specified element from this list, if it is present.
VoxelizedMarkMemo	MemoList.set(int index, VoxelizedMarkMemo element)	Replaces the element at the specified position in this list with the specified element.

Uses of VoxelizedMarkMemo in org.anchoranalysis.mpp.mark

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

Modifier and Type	Method	Description
void	UpdatableMarks.add(MemoForIndex marksExisting, VoxelizedMarkMemo newMark)	Adds a new mark to the existing set of marks.
void	UpdatableMarks.exchange(MemoForIndex memo, VoxelizedMarkMemo oldMark, int indexOldMark, VoxelizedMarkMemo newMark)	Exchanges an existing mark with a new one.
void	UpdatableMarks.remove(MemoForIndex marksExisting, VoxelizedMarkMemo mark)	Removes a mark from the existing set of marks.

Uses of VoxelizedMarkMemo in org.anchoranalysis.mpp.mark.voxelized.memo

Methods in org.anchoranalysis.mpp.mark.voxelized.memo that return VoxelizedMarkMemo

Modifier and Type	Method	Description
static VoxelizedMarkMemo	VoxelizedMarkMemoFactory.create(Mark mark, EnergyStackWithoutParameters stack, RegionMap regionMap)	Creates a new VoxelizedMarkMemo instance.
VoxelizedMarkMemo	VoxelizedMarkMemo.duplicateFresh()	Duplicates the current mark memo, resetting the calculation state.
VoxelizedMarkMemo	MemoForIndex.getMemoForIndex(int index)	Retrieves the VoxelizedMarkMemo for the specified index.

Uses of VoxelizedMarkMemo in org.anchoranalysis.mpp.overlap

Methods in org.anchoranalysis.mpp.overlap with parameters of type VoxelizedMarkMemo

Modifier and Type	Method	Description
static double	OverlapUtilities.overlapWith(VoxelizedMarkMemo memo1, VoxelizedMarkMemo memo2, int regionID)	Calculates the overlap between two voxelized marks for a specific region.
static double	OverlapUtilities.overlapWithMaskGlobal(VoxelizedMarkMemo memo1, VoxelizedMarkMemo memo2, int regionID, Voxels<UnsignedByteBuffer> globalMask, byte onGlobalMask)	Counts the number of overlapping voxels between two VoxelizedMarkMemo objects, considering a global mask.

Uses of VoxelizedMarkMemo in org.anchoranalysis.mpp.pair

Methods in org.anchoranalysis.mpp.pair that return VoxelizedMarkMemo

Modifier and Type	Method	Description
VoxelizedMarkMemo	PairVoxelizedMarkMemo.getDestination()	Gets the destination VoxelizedMarkMemo.
VoxelizedMarkMemo	PairVoxelizedMarkMemo.getSource()	Gets the source VoxelizedMarkMemo.

Constructors in org.anchoranalysis.mpp.pair with parameters of type VoxelizedMarkMemo

Modifier	Constructor	Description
	PairVoxelizedMarkMemo(VoxelizedMarkMemo source, VoxelizedMarkMemo destination)	Constructs a new PairVoxelizedMarkMemo.

Uses of VoxelizedMarkMemo in org.anchoranalysis.mpp.proposer

Methods in org.anchoranalysis.mpp.proposer that return VoxelizedMarkMemo

Modifier and Type	Method	Description
VoxelizedMarkMemo	ProposerContext.create(Mark mark)	Creates a VoxelizedMarkMemo for the given mark.

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

Methods in org.anchoranalysis.plugin.points.bean with parameters of type VoxelizedMarkMemo

Modifier and Type	Method	Description
boolean	FitPoints.propose(VoxelizedMarkMemo inputMark, ProposerContext context)