Index (anchor-mpp 0.2.1 API)

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

A

add(String) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNode: Adds an error message to this node.
add(String) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull
add(IndexByRegion<T>) - Method in class org.anchoranalysis.mpp.index.IndexByChannel: Adds an IndexByRegion to the channel index.
add(Mark) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Adds a mark to the collection.
add(Mark, Color) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks: Adds a mark with an associated color.
add(Mark, RGBColor) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks: Adds a mark with an associated RGBColor.
add(MemoForIndex, VoxelizedMarkMemo) - Method in interface org.anchoranalysis.mpp.mark.UpdatableMarks: Adds a new mark to the existing set of marks.
addAll(ColoredMarks) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks: Adds all marks and colors from another ColoredMarks instance.
addAll(MarkCollection) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Adds all marks from another collection to this collection.
addAll(MarkCollection, RGBColor) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks: Adds all marks from a MarkCollection with the same color.
addChangeID(Mark, Color) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks: Adds a mark, changes its ID, and associates it with a color.
addChangeID(Mark, RGBColor) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks: Adds a mark, changes its ID, and associates it with an RGBColor.
addErrorLevel(String) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext: Creates a new ProposerContext with an additional error level.
addForSlice(int, int) - Method in interface org.anchoranalysis.mpp.index.VoxelPartition: Adds a value to the voxel partition for a specific slice.
addForSlice(int, int) - Method in class org.anchoranalysis.mpp.index.VoxelPartitionHistogram
addToErrorNode(ErrorNode) - Method in exception org.anchoranalysis.mpp.proposer.error.ErrorNodeException: Adds the error message associated with this exception to an ErrorNode.
addToVoxelList(int, int, int) - Method in class org.anchoranalysis.mpp.index.IndexByRegion: Adds a value to the voxel list for a specific region and slice.
addUnused(Histogram) - Method in class org.anchoranalysis.mpp.index.factory.VoxelPartitonFactoryHistogram: Adds an unused histogram to the factory.
addUnused(T) - Method in interface org.anchoranalysis.mpp.index.factory.VoxelPartitionFactory: Adds an unused part to the factory.
assignFrom(Mark) - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo: Assigns a new mark to replace the existing mark.

B

Bound - Class in org.anchoranalysis.mpp.bean.bound: An abstract class representing an upper and lower bound.
Bound() - Constructor for class org.anchoranalysis.mpp.bean.bound.Bound
BoundDegrees - Class in org.anchoranalysis.mpp.bean.bound: Represents an upper and lower bound in degrees which is converted to radians when resolved.
BoundDegrees() - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundDegrees: Creates a new instance with default bounds of 0 to 360 degrees.
BoundDegrees(BoundDegrees) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundDegrees: Creates a new instance by copying an existing BoundDegrees.
boundingBox() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark: Gets the bounding-box enclosing the voxelized representation of the mark.
BoundingBoxCalculator - Class in org.anchoranalysis.mpp.mark.conic: Functions to calculate a bounding-box for a point surrounded by some form of radius.
boundingBoxFlattened() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark: Gets the bounding-box flattened in z dimension.
BoundMinMax - Class in org.anchoranalysis.mpp.bean.bound: An abstract class representing a bound with minimum and maximum values.
BoundMinMax() - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundMinMax: Creates a new instance with default minimum and maximum values.
BoundMinMax(double, double) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundMinMax: Creates a new instance with specified minimum and maximum values.
BoundMinMax(BoundMinMax) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundMinMax: Creates a new instance by copying another BoundMinMax.
BoundPhysicalExtent - Class in org.anchoranalysis.mpp.bean.bound: A bound representing physical extents, which can be resolved based on image resolution.
BoundPhysicalExtent() - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent
BoundPhysicalExtent(double, double) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent: Creates a new instance with specified minimum and maximum values.
BoundPhysicalExtent(BoundPhysicalExtent) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent: Creates a new instance by copying another BoundPhysicalExtent.
BoundRotation - Class in org.anchoranalysis.mpp.bean.bound.rotation: Abstract base class for defining bounds on rotations.
BoundRotation() - Constructor for class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation
BoundRotation2D - Class in org.anchoranalysis.mpp.bean.bound.rotation: Creates a randomly-generated orientation in 2D by uniformally sampling a scalar rotation angle
BoundRotation2D() - Constructor for class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation2D
BoundRotation3D - Class in org.anchoranalysis.mpp.bean.bound.rotation: Creates a randomly-generated orientation in 3D based upon Euler Angles
BoundRotation3D() - Constructor for class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation3D
BoundUnitless - Class in org.anchoranalysis.mpp.bean.bound: A bound representing unitless values, where the minimum and maximum are not affected by resolution.
BoundUnitless() - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundUnitless: Creates a new instance with default minimum and maximum values.
BoundUnitless(double, double) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundUnitless: Creates a new instance with specified minimum and maximum values.
BoundUnitless(BoundUnitless) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundUnitless: Creates a new instance by copying another BoundUnitless.
box() - Method in class org.anchoranalysis.mpp.mark.points.PointListBase: Creates a bounding box from the min and max points.
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.Mark: Calculates the bounding box for a specific region of the mark.
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
box(DrawOverlay, Dimensions) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.Mark: Calculates the bounding box for all regions of the mark.
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.points.PointList
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.points.Polygon
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
boxFromBounds(Point3d, double, boolean, Dimensions) - Static method in class org.anchoranalysis.mpp.mark.conic.BoundingBoxCalculator: Calculates a bounding box for a point with a scalar radius in all dimensions.
boxFromBounds(Point3d, DoubleMatrix1D, boolean, Dimensions) - Static method in class org.anchoranalysis.mpp.mark.conic.BoundingBoxCalculator: Calculates a bounding box for a point with varying radii in each dimension (that have already been resolved into a matrix)
boxList(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Creates a list of bounding boxes for all marks in the collection.

C

calculateMinMax(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.MarkBounds: Calculates the resolved minimum and maximum values as a ResolvedBound.
canEqual(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
canEqual(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
canEqual(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
canEqual(Object) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
centerPoint() - Method in class org.anchoranalysis.mpp.mark.Mark: Returns the center point of the mark.
centerPoint() - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
centerPoint() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
centerPoint() - Method in class org.anchoranalysis.mpp.mark.points.PointList
centerPoint() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
centerPoint() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
Circle - Class in org.anchoranalysis.mpp.mark.conic: Represents a 2D circle mark.
Circle() - Constructor for class org.anchoranalysis.mpp.mark.conic.Circle
Circle(Bound) - Constructor for class org.anchoranalysis.mpp.mark.conic.Circle: Creates a circle with a radius within particular bounds.
Circle(Circle) - Constructor for class org.anchoranalysis.mpp.mark.conic.Circle: Copy constructor.
circumference(int) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse: Calculates the circumference of the ellipse for a given region.
clamp(Point3d, Dimensions) - Static method in class org.anchoranalysis.mpp.mark.PointClamper: Clamps a double-precision point to be within the given dimensions.
clamp(Point3i, Dimensions) - Static method in class org.anchoranalysis.mpp.mark.PointClamper: Clamps an integer point to be within the given dimensions.
cleanUp() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark: Cleans up any resources associated with this voxelized mark.
cleanUp(VoxelPartitionFactory<Histogram>) - Method in class org.anchoranalysis.mpp.index.VoxelPartitionHistogram
cleanUp(VoxelPartitionFactory<T>) - Method in class org.anchoranalysis.mpp.index.IndexByChannel: Cleans up the voxel partitions for all channels using the provided factory.
cleanUp(VoxelPartitionFactory<T>) - Method in class org.anchoranalysis.mpp.index.IndexByRegion: Cleans up the voxel partitions using the provided factory.
cleanUp(VoxelPartitionFactory<T>) - Method in interface org.anchoranalysis.mpp.index.VoxelPartition: Cleans up the voxel partition using the provided factory.
ColoredMarks - Class in org.anchoranalysis.mpp.mark: A collection of marks, each associated with a color.
ColoredMarks() - Constructor for class org.anchoranalysis.mpp.mark.ColoredMarks: Creates an empty ColoredMarks instance.
ColoredMarks(MarkCollection, ColorIndex, IdentifierGetter<Mark>) - Constructor for class org.anchoranalysis.mpp.mark.ColoredMarks: Creates a ColoredMarks instance from a MarkCollection and assigns colors based on a ColorIndex.
ColoredMarks(MarkCollection, ColorList) - Constructor for class org.anchoranalysis.mpp.mark.ColoredMarks
ColoredMarks(Mark, RGBColor) - Constructor for class org.anchoranalysis.mpp.mark.ColoredMarks: Creates a ColoredMarks instance with a single mark and color.
CompatibleWithMark - Interface in org.anchoranalysis.mpp.mark: An interface for objects that can determine compatibility with a Mark.
ConicBase - Class in org.anchoranalysis.mpp.mark.conic: Abstract base class for conic marks (e.g., ellipsoids, spheres).
ConicBase() - Constructor for class org.anchoranalysis.mpp.mark.conic.ConicBase: Default constructor.
ConicBase(MarkWithPosition) - Constructor for class org.anchoranalysis.mpp.mark.conic.ConicBase: Constructor that copies from another MarkWithPosition.
contains(double) - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound: Checks if a value is contained within the bound.
contains(Object) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Checks if the collection contains a specific object.
convert(Mark) - Method in class org.anchoranalysis.mpp.mark.MarkToObjectConverter: Converts a Mark to an equivalent ObjectMask.
count(BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.mpp.overlap.CountIntersectingVoxels: Counts the number of intersecting voxels between two bounded voxel sets.
CountIntersectingVoxels - Class in org.anchoranalysis.mpp.overlap: Counts the number of intersecting voxels where bytes are encoded as region memberships.
CountIntersectingVoxels(byte) - Constructor for class org.anchoranalysis.mpp.overlap.CountIntersectingVoxels: Creates a new instance with a specific region membership flag.
CountIntersectingVoxels(PredicateRegionMembership) - Constructor for class org.anchoranalysis.mpp.overlap.CountIntersectingVoxels
countMasked(BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, byte) - Method in class org.anchoranalysis.mpp.overlap.CountIntersectingVoxels: Counts the number of intersecting voxels between two bounded voxel sets, considering a global mask.
create() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipseFactory
create() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipsoidFactory
create() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkFactory: Creates a new Mark object.
create() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkPointListFactory
create(int) - Method in interface org.anchoranalysis.mpp.index.factory.VoxelPartitionFactory: Creates a new VoxelPartition with the specified number of slices.
create(int) - Method in class org.anchoranalysis.mpp.index.factory.VoxelPartitonFactoryHistogram: Creates a new VoxelPartitionHistogram with the specified number of slices.
create(List<Point3d>) - Static method in class org.anchoranalysis.mpp.mark.points.PointListFactory: Creates a PointList from a list of Point3d objects.
create(List<Point3d>, int) - Static method in class org.anchoranalysis.mpp.mark.points.PointListFactory: Creates a PointList from a list of Point3d objects with a specified ID.
create(IntToFloatFunction, Point2i) - Static method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBoxFactory: Builds a bounding-box from the 5-element floating-point vector returned from the EAST algorithm.
create(ImageInitialization, SharedObjects) - Static method in class org.anchoranalysis.mpp.init.PointsInitialization: Creates a new PointsInitialization instance.
create(Mark) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext: Creates a VoxelizedMarkMemo for the given mark.
create(Mark, EnergyStackWithoutParameters, RegionMap) - Static method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemoFactory: Creates a new VoxelizedMarkMemo instance.
create(Mark, EnergyStackWithoutParameters, RegionMap) - Static method in class org.anchoranalysis.mpp.mark.voxelized.VoxelizedMarkFactory: Creates a new VoxelizedMarkHistogram instance.
createColor(ColoredMarks, RegionMembershipWithFlags) - Static method in class org.anchoranalysis.mpp.overlay.OverlayCollectionMarkFactory: Creates a ColoredOverlayCollection from ColoredMarks.
createHashMapToId() - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Creates a map of marks to their indices in the collection.
createIdArr() - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Creates an array of mark IDs.
createIdHashMap() - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Creates a map of marks indexed by their IDs.
createListMembershipWithFlags() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap: Creates a list of all region memberships with their corresponding flags.
createMarkFromPoint(Point3d, int, boolean) - Static method in class org.anchoranalysis.mpp.mark.conic.MarkConicFactory: Creates a mark from a double-precision 3D point.
createMarkFromPoint(Point3i, int, boolean) - Static method in class org.anchoranalysis.mpp.mark.conic.MarkConicFactory: Creates a mark from an integer 3D point.
CreateMarkFromPoints - Class in org.anchoranalysis.mpp.bean.points: Creates a mark by fitting it to a set of points extracted from other marks.
CreateMarkFromPoints() - Constructor for class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
createMarkFromPoints3f(List<Point3f>) - Static method in class org.anchoranalysis.mpp.mark.points.PointListFactory: Creates a PointList from a list of Point3f objects.
createMarkFromPoints3i(List<Point3i>) - Static method in class org.anchoranalysis.mpp.mark.points.PointListFactory: Creates a PointList from a list of Point3i objects.
createMerged(ColoredMarks) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks: Merges this ColoredMarks with another, avoiding duplicates.
createMerged(MarkCollection) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Creates a new collection by merging this collection with another.
createObject(Dimensions, BinaryValuesByte) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
createRadiiArray() - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase: Creates an array of radii in their original units.
createRadiiArray() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
createRadiiArray() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
createRadiiArrayResolved(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase: Creates an array of radii resolved to the given resolution.
createRadiiArrayResolved(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
createRadiiArrayResolved(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
createSet() - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Creates a set of all marks in the collection.
createStatisticsFor(VoxelizedMarkMemo, Dimensions) - Method in class org.anchoranalysis.mpp.bean.mark.MarkRegion: Creates voxel statistics for the mark region based on the given memo and dimensions.
createWithoutColor(MarkCollection, RegionMembershipWithFlags) - Static method in class org.anchoranalysis.mpp.overlay.OverlayCollectionMarkFactory: Creates an OverlayCollection from a MarkCollection without color information.

D

deepCopy() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks: Creates a deep copy of this ColoredMarks instance.
deepCopy() - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Creates a deep copy of the collection.
deriveObject(Dimensions, RegionMembershipWithFlags, BinaryValuesByte) - Method in class org.anchoranalysis.mpp.mark.Mark: Creates an ObjectMask representation of the mark.
deriveObjects(Dimensions, RegionMembershipWithFlags) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Derives objects from the marks in the collection.
describeBean() - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
describeBean() - Method in class org.anchoranalysis.mpp.bean.bound.BoundUnitless
describeBean() - Method in class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation2D
describeBean() - Method in class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation3D
describeBean() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkWithIdentifierFactory
dictionary() - Method in class org.anchoranalysis.mpp.init.MarksInitialization: Gets the DictionaryInitialization associated with this MarksInitialization.
dimensions() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext: Gets the dimensions of the energy stack.
doDuplicate(PointListBase) - Method in class org.anchoranalysis.mpp.mark.points.PointListBase: Duplicates this PointListBase into a new instance.
duplicate() - Method in class org.anchoranalysis.mpp.bean.bound.Bound: Creates a duplicate of this bound.
duplicate() - Method in class org.anchoranalysis.mpp.bean.bound.BoundDegrees
duplicate() - Method in class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent
duplicate() - Method in class org.anchoranalysis.mpp.bean.bound.BoundUnitless
duplicate() - Method in class org.anchoranalysis.mpp.mark.conic.Circle
duplicate() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
duplicate() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
duplicate() - Method in class org.anchoranalysis.mpp.mark.conic.Sphere
duplicate() - Method in class org.anchoranalysis.mpp.mark.Mark: Creates a duplicate of this mark.
duplicate() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
duplicate() - Method in class org.anchoranalysis.mpp.mark.points.PointList
duplicate() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
duplicate() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
duplicate() - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
duplicate() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark: Creates a duplicate of this voxelized mark.
duplicateFresh() - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo: Duplicates the current mark memo, resetting the calculation state.

E

Ellipse - Class in org.anchoranalysis.mpp.mark.conic: Represents a 2D ellipse mark.
Ellipse() - Constructor for class org.anchoranalysis.mpp.mark.conic.Ellipse: Creates a new Ellipse with default values.
Ellipse(Ellipse) - Constructor for class org.anchoranalysis.mpp.mark.conic.Ellipse: Creates a new Ellipse by copying an existing one.
Ellipsoid - Class in org.anchoranalysis.mpp.mark.conic: Represents a 3D ellipsoid mark with multiple sub-regions.
Ellipsoid() - Constructor for class org.anchoranalysis.mpp.mark.conic.Ellipsoid: Creates a new Ellipsoid with default values.
Ellipsoid(Ellipsoid) - Constructor for class org.anchoranalysis.mpp.mark.conic.Ellipsoid: Creates a new Ellipsoid by copying an existing one.
EllipsoidUtilities - Class in org.anchoranalysis.mpp.mark.conic: Utility class for operations related to Ellipsoid marks.
equals(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
equals(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
equals(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
equals(Object) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
equals(Object) - Method in class org.anchoranalysis.mpp.pair.MarkPair
equals(Object) - Method in class org.anchoranalysis.mpp.pair.PairVoxelizedMarkMemo
equals(Object) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.Mark: Checks if this mark is deeply equal to another mark.
equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition: Checks if this mark is equal to another mark by comparing all attributes.
equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
equalsDeep(MarkCollection) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Checks if this collection is deeply equal to another.
equalsID(Object) - Method in class org.anchoranalysis.mpp.mark.Mark: Checks if this mark has the same ID as another object.
ErrorNode - Class in org.anchoranalysis.mpp.proposer.error: An abstract class representing a node in an error tree structure.
ErrorNode() - Constructor for class org.anchoranalysis.mpp.proposer.error.ErrorNode
ErrorNodeException - Exception in org.anchoranalysis.mpp.proposer.error: An exception that adds a string to the current error node.
ErrorNodeException(Exception) - Constructor for exception org.anchoranalysis.mpp.proposer.error.ErrorNodeException: Constructs a new ErrorNodeException from another exception.
ErrorNodeException(String) - Constructor for exception org.anchoranalysis.mpp.proposer.error.ErrorNodeException: Constructs a new ErrorNodeException with the specified error message.
ErrorNodeNull - Class in org.anchoranalysis.mpp.proposer.error: A singleton implementation of ErrorNode that does nothing with errors.
exchange(int, Mark) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Replaces the mark at a specific index.
exchange(MemoForIndex, VoxelizedMarkMemo, int, VoxelizedMarkMemo) - Method in interface org.anchoranalysis.mpp.mark.UpdatableMarks: Exchanges an existing mark with a new one.

F

feature() - Method in class org.anchoranalysis.mpp.init.MarksInitialization: Gets the FeatureRelatedInitialization associated with this MarksInitialization.
fit(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.mpp.bean.points.fitter.PointsFitter: Fits a mark to a set of points within given dimensions.
fitMarkToPointsFromMarks(MarkCollection, Dimensions) - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints: Extracts points from marks, creates a new mark, and fits this mark to the extracted points.
flagForNoRegion() - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities: Gets the flag representing no region membership.
flagForRegion(int) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities: Gets the flag for a specific region index.
flagForRegion(int, int) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities: Combines flags for two regions.
flagForRegion(int, int, int) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities: Combines flags for three regions.
flags() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Calculates the flags as a byte based on the current region memberships.

G

get(int) - Method in class org.anchoranalysis.mpp.index.IndexByChannel: Gets the IndexByRegion for a specific channel.
get(int) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Gets a mark at a specific index.
getBoundRadius() - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
getColorList() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
getCombined() - Method in interface org.anchoranalysis.mpp.index.VoxelPartition: Gets the combined voxel partition for all slices.
getCombined() - Method in class org.anchoranalysis.mpp.index.VoxelPartitionHistogram
getDelegate() - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
getDestination() - Method in class org.anchoranalysis.mpp.pair.MarkPair: Gets the destination mark of the pair (the one with the higher identifier).
getDestination() - Method in class org.anchoranalysis.mpp.pair.PairVoxelizedMarkMemo: Gets the destination VoxelizedMarkMemo.
getDirectionVector() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment: Gets the direction vector of the line segment.
getDscr() - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound: Gets a description of the bound.
getEllipsoidCalculator() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid: Calculator for ellipsoid-related matrices.
getEllipsoidSum(double, double, double, DoubleMatrix2D) - Static method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid: Calculates the sum of squared coordinates relative to the ellipsoid's matrix.
getEndPoint() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment: Gets the end point of the line segment.
getEnergyStack() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext: Energy stack for the current context.
getErrorNode() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext: Error node for tracking and managing errors.
getForAllSlices(int) - Method in class org.anchoranalysis.mpp.index.IndexByRegion: Gets the combined voxel partition for all slices in a region.
getForSlice(int, int) - Method in class org.anchoranalysis.mpp.index.IndexByRegion: Gets the voxel partition for a specific slice in a region.
getIdentifier() - Method in class org.anchoranalysis.mpp.mark.Mark: Gets the identifier of the mark.
getIdentifier() - Method in class org.anchoranalysis.mpp.overlay.OverlayMark: Gets the identifier of the mark.
getImage() - Method in class org.anchoranalysis.mpp.init.PointsInitialization: The image initialization associated with this points initialization.
getInnerCoreDistance() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid: The distance to the inner core, expressed as a ratio of the radii.
getLastPoints1() - Method in class org.anchoranalysis.mpp.bean.proposer.MarkMergeProposer: Gets the points associated with the first mark from the last proposal.
getLastPoints2() - Method in class org.anchoranalysis.mpp.bean.proposer.MarkMergeProposer: Gets the points associated with the second mark from the last proposal.
getList() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap: List of region memberships.
getMark() - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo: The associated mark.
getMark() - Method in class org.anchoranalysis.mpp.overlay.OverlayMark: The Mark to overlay.
getMarkProvider() - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints: Provides the mark to be fitted.
getMarks() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
getMarks() - Method in class org.anchoranalysis.mpp.mark.MarkCollection: The underlying List that stores the Marks in the collection.
getMax() - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax: Gets the maximum value of the bound.
getMax() - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
getMax() - Method in class org.anchoranalysis.mpp.mark.points.PointListBase: The maximum x, y, z coordinates of all the points in the list.
getMaxResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundDegrees
getMaxResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent
getMaxResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundUnitless
getMaxResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.MarkBounds: Gets the resolved maximum value of the bound, considering resolution and dimensionality.
getMemoForIndex(int) - Method in interface org.anchoranalysis.mpp.mark.voxelized.memo.MemoForIndex: Retrieves the VoxelizedMarkMemo for the specified index.
getMin() - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax: Gets the minimum value of the bound.
getMin() - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
getMin() - Method in class org.anchoranalysis.mpp.mark.points.PointListBase: The minimum x, y, z coordinates of all the points in the list.
getMinNumPoints() - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints: Minimum number of points required to create a mark.
getMinResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundDegrees
getMinResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent
getMinResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundUnitless
getMinResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.MarkBounds: Gets the resolved minimum value of the bound, considering resolution and dimensionality.
getName() - Method in class org.anchoranalysis.mpp.mark.conic.Circle
getName() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
getName() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
getName() - Method in class org.anchoranalysis.mpp.mark.conic.Sphere
getName() - Method in class org.anchoranalysis.mpp.mark.Mark: Returns the name of this mark type.
getName() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
getName() - Method in class org.anchoranalysis.mpp.mark.points.PointList
getName() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
getName() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
getName() - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
getOperationContext() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext: Operation context for the current operation.
getOrientation() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
getOrientation() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid: The orientation of the ellipsoid.
getPointFitters() - Method in class org.anchoranalysis.mpp.init.PointsInitialization: Store for point fitters.
getPoints() - Method in class org.anchoranalysis.mpp.mark.points.PointListBase: The list of 3D points that make up this mark.
getPointsFitter() - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints: Fits the provided mark to the extracted points.
getPosition() - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition: The position of the mark in 3D space.
getRadii() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
getRadii() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid: The radii of the ellipsoid in 3D.
getRadius() - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
getRandomNumberGenerator() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext: Random number generator for sampling operations.
getReferencePoissonIntensity() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkWithIdentifierFactory: The reference Poisson intensity for mark creation.
getRegionID() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags: Gets the ID of the region.
getRegionMap() - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo: The region map.
getRegionMap() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext: Region map for the current context.
getRegionMembership() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags: Gets the underlying region membership.
getRotationAngle() - Method in class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation2D
getRotationX() - Method in class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation3D
getRotationY() - Method in class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation3D
getRotationZ() - Method in class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation3D
getShell() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipseFactory: The shell thickness of the ellipse.
getShell() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipsoidFactory: The shell thickness of the ellipsoid.
getShell() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse: The size of the shell, expressed as a ratio of the radius.
getShell() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid: The size of the shell, expressed as a ratio of the radii.
getSlice(int) - Method in interface org.anchoranalysis.mpp.index.VoxelPartition: Gets the voxel partition for a specific slice.
getSlice(int) - Method in class org.anchoranalysis.mpp.index.VoxelPartitionHistogram
getSource() - Method in class org.anchoranalysis.mpp.pair.MarkPair: Gets the source mark of the pair (the one with the lower identifier).
getSource() - Method in class org.anchoranalysis.mpp.pair.PairVoxelizedMarkMemo: Gets the source VoxelizedMarkMemo.
getStartPoint() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment: Gets the start point of the line segment.
getTemplateMark() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkWithIdentifierFactory: A template mark factory from which all new marks are created.
GlobalRegionIdentifiers - Class in org.anchoranalysis.mpp.mark: Defines global identifiers for different regions of a mark.

H

hashCode() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
hashCode() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
hashCode() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
hashCode() - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
hashCode() - Method in class org.anchoranalysis.mpp.pair.MarkPair
hashCode() - Method in class org.anchoranalysis.mpp.pair.PairVoxelizedMarkMemo
hashCode() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext

I

idAndIncrement() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkWithIdentifierFactory: Generates a new unique identifier and increments the counter.
identifier() - Method in class org.anchoranalysis.mpp.mark.Mark: Returns a string identifier for the mark.
image() - Method in class org.anchoranalysis.mpp.init.MarksInitialization: The image initialization associated with this marks initialization.
IndexByChannel<T> - Class in org.anchoranalysis.mpp.index: An index structure that organizes voxel partitions by channel.
IndexByChannel() - Constructor for class org.anchoranalysis.mpp.index.IndexByChannel
IndexByRegion<T> - Class in org.anchoranalysis.mpp.index: An index structure that organizes voxel partitions by region and slice.
IndexByRegion(VoxelPartitionFactory<T>, int, int) - Constructor for class org.anchoranalysis.mpp.index.IndexByRegion: Constructs an IndexByRegion with a specified number of regions and slices.
indexOf(Mark) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Finds the index of a specific mark in the collection.
initialize(VoxelPartitionFactory<T>, int, int, int) - Method in class org.anchoranalysis.mpp.index.IndexByChannel: Initializes the channel index with a specified number of channels, regions, and slices.
initializerForMarksBeans() - Static method in class org.anchoranalysis.mpp.bean.MarksBean: Creates a property-initializer for MPP-Beans.
initUpdatableMarks(MemoForIndex, EnergyStack, Logger, SharedFeatures) - Method in interface org.anchoranalysis.mpp.mark.UpdatableMarks: Initializes the updatable marks with necessary context.
instance() - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMapSingleton: Gets the singleton instance of RegionMap.
instance() - Static method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull: Gets the singleton instance of ErrorNodeNull.
InsufficientPointsException - Exception in org.anchoranalysis.mpp.bean.points.fitter: Exception thrown when there are not enough points to perform a fitting operation.
InsufficientPointsException() - Constructor for exception org.anchoranalysis.mpp.bean.points.fitter.InsufficientPointsException: Constructs an InsufficientPointsException with a default error message.
InsufficientPointsException(String) - Constructor for exception org.anchoranalysis.mpp.bean.points.fitter.InsufficientPointsException: Constructs an InsufficientPointsException with a specified error message.
InsufficientPointsException(String, Throwable) - Constructor for exception org.anchoranalysis.mpp.bean.points.fitter.InsufficientPointsException: Constructs an InsufficientPointsException with a specified error message and cause.
InsufficientPointsException(Throwable) - Constructor for exception org.anchoranalysis.mpp.bean.points.fitter.InsufficientPointsException: Constructs an InsufficientPointsException with a specified cause.
isBit0() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 0.
isBit1() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 1.
isBit2() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 2.
isBit3() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 3.
isBit4() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 4.
isBit5() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 5.
isBit6() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 6.
isBit7() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 7.
isCompatibleWith(Mark) - Method in interface org.anchoranalysis.mpp.mark.CompatibleWithMark: Tests if the implementing object is compatible with a mark of a particular type.
isEmpty() - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Checks if the collection is empty.
isMemberFlag(byte) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags: Checks if the given membership flag is set for this region.
isMemberFlag(byte, byte) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Checks if a given membership flag is set for a specific region.
isMemberFlag(byte, byte) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipAnd
isMemberFlag(byte, byte) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipOr
isMemberFlagAnd(byte, byte) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities: Checks if a membership flag is set using an AND operation.
isMemberFlagOr(byte, byte) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities: Checks if a membership flag is set using an OR operation.
isPointInside(Point3i) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
isPointInside(Point3i) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
isPointInside(Point3i) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
isPointInside(Point3i) - Method in class org.anchoranalysis.mpp.mark.Mark: Determines if a point is inside the mark.
isPointInside(Point3i) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
isPointInside(Point3i) - Method in class org.anchoranalysis.mpp.mark.points.PointList
isPointInside(Point3i) - Method in class org.anchoranalysis.mpp.mark.points.Polygon
isPointInside(Point3i) - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
isPointInside(Point3i) - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
isThrowExceptionForInsufficientPoints() - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints: Whether to throw an exception when there are insufficient points.
iterator() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
iterator() - Method in class org.anchoranalysis.mpp.mark.MarkCollection

L

LineSegment - Class in org.anchoranalysis.mpp.mark.points: Represents a line segment in 3D space as a Mark.
LineSegment() - Constructor for class org.anchoranalysis.mpp.mark.points.LineSegment
LineSegment(Point3i, Point3i) - Constructor for class org.anchoranalysis.mpp.mark.points.LineSegment: Constructs a LineSegment with given start and end points.

M

Mark - Class in org.anchoranalysis.mpp.mark: Abstract base class representing a mark in 3D space.
Mark() - Constructor for class org.anchoranalysis.mpp.mark.Mark
Mark(Mark) - Constructor for class org.anchoranalysis.mpp.mark.Mark: Copy constructor.
markBounds() - Method in class org.anchoranalysis.mpp.init.MarksInitialization: Store for mark bounds.
MarkBounds - Class in org.anchoranalysis.mpp.bean.bound: Abstract base class for defining bounds on marks in a marked point process.
MarkBounds() - Constructor for class org.anchoranalysis.mpp.bean.bound.MarkBounds
MarkBoundsProvider - Class in org.anchoranalysis.mpp.bean.provider: An abstract provider for MarkBounds.
MarkBoundsProvider() - Constructor for class org.anchoranalysis.mpp.bean.provider.MarkBoundsProvider
MarkCollection - Class in org.anchoranalysis.mpp.mark: An ordered collection of Marks.
MarkCollection() - Constructor for class org.anchoranalysis.mpp.mark.MarkCollection: Creates with no elements in the collection.
MarkCollection(List<Mark>) - Constructor for class org.anchoranalysis.mpp.mark.MarkCollection
MarkCollection(Stream<Mark>) - Constructor for class org.anchoranalysis.mpp.mark.MarkCollection: Creates from a stream of Marks.
MarkCollection(Mark) - Constructor for class org.anchoranalysis.mpp.mark.MarkCollection: Creates from a single Mark.
MarkCollectionProposer - Class in org.anchoranalysis.mpp.bean.proposer: An abstract base class for proposing an entire collection (configuration) of marks.
MarkCollectionProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.MarkCollectionProposer
markCollectionProposers() - Method in class org.anchoranalysis.mpp.init.MarksInitialization: Store for mark collection proposers.
MarkCollectionProvider - Class in org.anchoranalysis.mpp.bean.provider: Provides a collection of marks
MarkCollectionProvider() - Constructor for class org.anchoranalysis.mpp.bean.provider.MarkCollectionProvider
MarkConicFactory - Class in org.anchoranalysis.mpp.mark.conic: Factory class for creating conic marks (ellipses and ellipsoids) from points.
MarkEllipseFactory - Class in org.anchoranalysis.mpp.bean.mark.factory: A factory for creating Ellipse marks.
MarkEllipseFactory() - Constructor for class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipseFactory
MarkEllipsoidFactory - Class in org.anchoranalysis.mpp.bean.mark.factory: A factory for creating Ellipsoid marks.
MarkEllipsoidFactory() - Constructor for class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipsoidFactory
MarkFactory - Class in org.anchoranalysis.mpp.bean.mark.factory: An abstract base class for factories that create Mark objects.
MarkFactory() - Constructor for class org.anchoranalysis.mpp.bean.mark.factory.MarkFactory
MarkFromCollectionProposer - Class in org.anchoranalysis.mpp.bean.proposer: An abstract base class for proposing a selection of a single mark from a collection of marks.
MarkFromCollectionProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.MarkFromCollectionProposer
MarkMergeProposer - Class in org.anchoranalysis.mpp.bean.proposer: An abstract base class for proposing merges between marks.
MarkMergeProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.MarkMergeProposer
markMergeProposers() - Method in class org.anchoranalysis.mpp.init.MarksInitialization: Store for mark merge proposers.
MarkPair<T extends Mark> - Class in org.anchoranalysis.mpp.pair: Represents a pair of marks, with a source and destination.
MarkPair(T, T) - Constructor for class org.anchoranalysis.mpp.pair.MarkPair: Constructs a new MarkPair.
markPairs() - Method in class org.anchoranalysis.mpp.init.MarksInitialization: Store for random collections of mark pairs.
MarkPointListFactory - Class in org.anchoranalysis.mpp.bean.mark.factory: A factory for creating PointList marks.
MarkPointListFactory() - Constructor for class org.anchoranalysis.mpp.bean.mark.factory.MarkPointListFactory
MarkProposer - Class in org.anchoranalysis.mpp.bean.proposer: An abstract base class for proposing changes to a mark.
MarkProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.MarkProposer
markProposers() - Method in class org.anchoranalysis.mpp.init.MarksInitialization: Store for mark proposers.
MarkRegion - Class in org.anchoranalysis.mpp.bean.mark: An abstract base class for defining regions associated with marks.
MarkRegion() - Constructor for class org.anchoranalysis.mpp.bean.mark.MarkRegion
marks() - Method in class org.anchoranalysis.mpp.init.MarksInitialization: Store for mark collections.
marksAt(Point3i, RegionMap, int) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Finds marks at a specific point that belong to a specific region.
MarksBaseProvider<T,S> - Class in org.anchoranalysis.mpp.bean.provider: Base class for MarksBean that implements Provider to provide an object of type S.
MarksBaseProvider() - Constructor for class org.anchoranalysis.mpp.bean.provider.MarksBaseProvider
MarksBean<T> - Class in org.anchoranalysis.mpp.bean: An abstract base class for beans related to marks in MPP (Marked Point Process).
MarksBean() - Constructor for class org.anchoranalysis.mpp.bean.MarksBean: Creates a new instance of MarksBean.
marksFromOverlays(ColoredOverlayCollection) - Static method in class org.anchoranalysis.mpp.overlay.OverlayCollectionMarkFactory: Creates ColoredMarks from a ColoredOverlayCollection.
marksFromOverlays(OverlayCollection) - Static method in class org.anchoranalysis.mpp.overlay.OverlayCollectionMarkFactory: Creates a MarkCollection from an OverlayCollection.
MarksInitialization - Class in org.anchoranalysis.mpp.init: Initialization class for marks-related components in the MPP framework.
MarksInitialization(ImageInitialization) - Constructor for class org.anchoranalysis.mpp.init.MarksInitialization: Constructs a MarksInitialization with the given ImageInitialization.
MarkSplitProposer - Class in org.anchoranalysis.mpp.bean.proposer: An abstract base class for proposing splits of a mark into two new marks.
MarkSplitProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.MarkSplitProposer
markSplitProposers() - Method in class org.anchoranalysis.mpp.init.MarksInitialization: Store for mark split proposers.
MarkToObjectConverter - Class in org.anchoranalysis.mpp.mark: Converts a confidence-associated Mark to an equivalent ObjectMask.
MarkToObjectConverter(Optional<ScaleFactor>, Dimensions) - Constructor for class org.anchoranalysis.mpp.mark.MarkToObjectConverter: Create for particular Dimensions with a scaling-factor.
MarkToObjectConverter(Optional<ScaleFactor>, Dimensions, RegionMembershipWithFlags, BinaryValuesByte) - Constructor for class org.anchoranalysis.mpp.mark.MarkToObjectConverter
MarkToObjectConverter(Dimensions) - Constructor for class org.anchoranalysis.mpp.mark.MarkToObjectConverter: Create for particular Dimensions without a scaling-factor.
MarkWithIdentifierFactory - Class in org.anchoranalysis.mpp.bean.mark.factory: A factory for creating marks with unique identifiers.
MarkWithIdentifierFactory() - Constructor for class org.anchoranalysis.mpp.bean.mark.factory.MarkWithIdentifierFactory
MarkWithIdentifierFactory(MarkFactory) - Constructor for class org.anchoranalysis.mpp.bean.mark.factory.MarkWithIdentifierFactory: Constructs a MarkWithIdentifierFactory with a specified template mark factory.
MarkWithPosition - Class in org.anchoranalysis.mpp.mark: An abstract base class for marks that have a position in 3D space.
MarkWithPosition() - Constructor for class org.anchoranalysis.mpp.mark.MarkWithPosition: Constructs a new MarkWithPosition with a default position at the origin.
MarkWithPosition(MarkWithPosition) - Constructor for class org.anchoranalysis.mpp.mark.MarkWithPosition: Copy constructor for MarkWithPosition.
MarkWithPositionAndSingleRadius - Class in org.anchoranalysis.mpp.mark.conic: Base-class for a conic that has a single radius (circle, sphere etc.)
MarkWithPositionAndSingleRadius() - Constructor for class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
MarkWithPositionAndSingleRadius(Bound) - Constructor for class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius: Constructor with a bound on the radius.
MarkWithPositionAndSingleRadius(MarkWithPositionAndSingleRadius) - Constructor for class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius: Copy constructor.
membershipForIndex(int) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap: Gets the region membership for a specific index.
membershipWithFlagsForIndex(int) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap: Gets the region membership with flags for a specific index.
MemoForIndex - Interface in org.anchoranalysis.mpp.mark.voxelized.memo: An interface for accessing voxelized mark memos by index.

N

newTemplateMark() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkWithIdentifierFactory: Creates a new mark based on the template and assigns it a unique identifier.
noOverlapWith(Mark, int) - Method in interface org.anchoranalysis.mpp.mark.QuickOverlapCalculation: A quick (computationally-efficient) test to see if we can reject the possibility of overlap
normalisedRadii(Ellipsoid, Optional<Resolution>) - Static method in class org.anchoranalysis.mpp.mark.conic.EllipsoidUtilities: Calculates the normalized radii of an Ellipsoid mark, taking into account rotation and optional resolution.
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.conic.Circle
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.conic.Sphere
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.Mark: Returns the number of dimensions of this mark.
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.points.PointList
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
numberDimensions() - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
numberRegions() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
numberRegions() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
numberRegions() - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
numberRegions() - Method in class org.anchoranalysis.mpp.mark.Mark: Returns the number of regions in this mark.
numberRegions() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
numberRegions() - Method in class org.anchoranalysis.mpp.mark.points.PointList
numberRegions() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
numberRegions() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
numberRegions() - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
numberSlices() - Method in interface org.anchoranalysis.mpp.index.VoxelPartition: Gets the number of slices in the partition.
numberSlices() - Method in class org.anchoranalysis.mpp.index.VoxelPartitionHistogram
numRegions() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap: Gets the number of regions in the map.
numSlices() - Method in class org.anchoranalysis.mpp.index.IndexByRegion: Gets the number of slices in each region.

O

onInitialization() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkWithIdentifierFactory
OptionalPointProposer - Interface in org.anchoranalysis.mpp.proposer: An interface for proposing a position in 3D space.
org.anchoranalysis.mpp.bean - package org.anchoranalysis.mpp.bean: Beans pertaining to marked-point-processes.
org.anchoranalysis.mpp.bean.bound - package org.anchoranalysis.mpp.bean.bound: Lower and upper limits set around variables.
org.anchoranalysis.mpp.bean.bound.rotation - package org.anchoranalysis.mpp.bean.bound.rotation: Bounds on how to rotate an entity in Euclidean space.
org.anchoranalysis.mpp.bean.mark - package org.anchoranalysis.mpp.bean.mark: Beans generally related to Marks.
org.anchoranalysis.mpp.bean.mark.factory - package org.anchoranalysis.mpp.bean.mark.factory: Beans related to creating Marks.
org.anchoranalysis.mpp.bean.points - package org.anchoranalysis.mpp.bean.points: Operations based on sets of points.
org.anchoranalysis.mpp.bean.points.fitter - package org.anchoranalysis.mpp.bean.points.fitter: Fitting structures to sets of points.
org.anchoranalysis.mpp.bean.proposer - package org.anchoranalysis.mpp.bean.proposer: Proposing Marks or other data-structures with particular attributes.
org.anchoranalysis.mpp.bean.provider - package org.anchoranalysis.mpp.bean.provider: Implementations of Provider involving Marks.
org.anchoranalysis.mpp.bean.regionmap - package org.anchoranalysis.mpp.bean.regionmap: Voxel subregions of Marks.
org.anchoranalysis.mpp.index - package org.anchoranalysis.mpp.index: Indexing voxel-values in different ways.
org.anchoranalysis.mpp.index.factory - package org.anchoranalysis.mpp.index.factory: Factories for classes in org.anchoranalysis.mpp.index.
org.anchoranalysis.mpp.init - package org.anchoranalysis.mpp.init: Parameters used to initialize certain types of beans.
org.anchoranalysis.mpp.mark - package org.anchoranalysis.mpp.mark: Non-bean classes related to Marks.
org.anchoranalysis.mpp.mark.conic - package org.anchoranalysis.mpp.mark.conic: Marks implementing conic sections.
org.anchoranalysis.mpp.mark.points - package org.anchoranalysis.mpp.mark.points: Marks implementing structures based on points.
org.anchoranalysis.mpp.mark.voxelized - package org.anchoranalysis.mpp.mark.voxelized: A mark after a voxel-representation has been inferred.
org.anchoranalysis.mpp.mark.voxelized.memo - package org.anchoranalysis.mpp.mark.voxelized.memo: Memoization of VoxelizedMarks.
org.anchoranalysis.mpp.overlap - package org.anchoranalysis.mpp.overlap: Calculating overlaps between two Marks.
org.anchoranalysis.mpp.overlay - package org.anchoranalysis.mpp.overlay: Any Overlay related to a Mark.
org.anchoranalysis.mpp.pair - package org.anchoranalysis.mpp.pair: Pairs of Marks.
org.anchoranalysis.mpp.proposer - package org.anchoranalysis.mpp.proposer: Non-bean classes for proposing Marks or other data-structures with particular attributes.
org.anchoranalysis.mpp.proposer.error - package org.anchoranalysis.mpp.proposer.error: Recording errors related to proposing Marks or other data-structures with particular attributes.
OrientationProposer - Class in org.anchoranalysis.mpp.bean.proposer: An abstract base class for proposing orientations for marks.
OrientationProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.OrientationProposer
OverlapUtilities - Class in org.anchoranalysis.mpp.overlap: Utility class for calculating overlap between voxelized marks.
overlapWith(VoxelizedMarkMemo, VoxelizedMarkMemo, int) - Static method in class org.anchoranalysis.mpp.overlap.OverlapUtilities: Calculates the overlap between two voxelized marks for a specific region.
overlapWithMaskGlobal(VoxelizedMarkMemo, VoxelizedMarkMemo, int, Voxels<UnsignedByteBuffer>, byte) - Static method in class org.anchoranalysis.mpp.overlap.OverlapUtilities: Counts the number of overlapping voxels between two VoxelizedMarkMemo objects, considering a global mask.
OverlayCollectionMarkFactory - Class in org.anchoranalysis.mpp.overlay: Factory for creating OverlayCollections from marks and retrieving marks from OverlayCollections.
OverlayMark - Class in org.anchoranalysis.mpp.overlay: An implementation of Overlay that draws a Mark on an image.
OverlayMark(Mark, RegionMembershipWithFlags) - Constructor for class org.anchoranalysis.mpp.overlay.OverlayMark

P

PairVoxelizedMarkMemo - Class in org.anchoranalysis.mpp.pair: Represents a pair of VoxelizedMarkMemo objects, with a defined source and destination.
PairVoxelizedMarkMemo(VoxelizedMarkMemo, VoxelizedMarkMemo) - Constructor for class org.anchoranalysis.mpp.pair.PairVoxelizedMarkMemo: Constructs a new PairVoxelizedMarkMemo.
PointClamper - Class in org.anchoranalysis.mpp.mark: Utility class to ensure a point has values contained inside image-dimensions.
PointList - Class in org.anchoranalysis.mpp.mark.points: A a list of 3D points.
PointList() - Constructor for class org.anchoranalysis.mpp.mark.points.PointList: Constructs an empty PointList.
PointList(Stream<Point3d>) - Constructor for class org.anchoranalysis.mpp.mark.points.PointList: Constructs a PointList from a stream of Point3d objects.
PointListBase - Class in org.anchoranalysis.mpp.mark.points: A base class for marks that consist of a list of 3D points.
PointListBase() - Constructor for class org.anchoranalysis.mpp.mark.points.PointListBase: Constructs an empty PointListBase.
PointListBase(Stream<Point3d>) - Constructor for class org.anchoranalysis.mpp.mark.points.PointListBase: Constructs a PointListBase from a stream of Point3d objects.
PointListFactory - Class in org.anchoranalysis.mpp.mark.points: A factory for creating PointList objects from various types of point collections.
points() - Method in class org.anchoranalysis.mpp.init.MarksInitialization: The points initialization associated with this marks initialization.
PointsBean<T> - Class in org.anchoranalysis.mpp.bean.points: An abstract base class for beans that work with points and require initialization.
PointsBean() - Constructor for class org.anchoranalysis.mpp.bean.points.PointsBean: Constructs a new PointsBean.
PointsFitter - Class in org.anchoranalysis.mpp.bean.points.fitter: Abstract base class for fitting a mark (e.g., an ellipsoid) to a set of points.
PointsFitter() - Constructor for class org.anchoranalysis.mpp.bean.points.fitter.PointsFitter
PointsFitterException - Exception in org.anchoranalysis.mpp.bean.points.fitter: Exception thrown when an error occurs during the point fitting process.
PointsFitterException(Exception) - Constructor for exception org.anchoranalysis.mpp.bean.points.fitter.PointsFitterException: Constructs a new PointsFitterException with the specified cause.
PointsFitterException(String) - Constructor for exception org.anchoranalysis.mpp.bean.points.fitter.PointsFitterException: Constructs a new PointsFitterException with the specified detail message.
PointsInitialization - Class in org.anchoranalysis.mpp.init: Initialization class for points-related components in the MPP framework.
PointsProposer - Class in org.anchoranalysis.mpp.bean.proposer: An abstract base class for proposing a list of points based on a given point and mark.
PointsProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.PointsProposer
Polygon - Class in org.anchoranalysis.mpp.mark.points: Represents a polygon in 2D space as a Mark.
Polygon() - Constructor for class org.anchoranalysis.mpp.mark.points.Polygon
PolygonCurve - Class in org.anchoranalysis.mpp.mark.points: Represents a polygon curve in 3D space as a Mark.
PolygonCurve() - Constructor for class org.anchoranalysis.mpp.mark.points.PolygonCurve
populate(BeanInitializer<?>, Define, Logger) - Method in class org.anchoranalysis.mpp.init.MarksInitialization: Populates the stores with beans from the given Define.
populate(BeanInitializer<?>, Define, Logger) - Method in class org.anchoranalysis.mpp.init.PointsInitialization: Populates the stores with beans from the given Define.
PositionProposer - Class in org.anchoranalysis.mpp.bean.proposer: An abstract base class for proposing positions.
PositionProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.PositionProposer
positionString() - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition: Describes the position of the mark as a string.
ProposalAbnormalFailureException - Exception in org.anchoranalysis.mpp.proposer: An exception thrown when a proposal could not be made for an abnormal reason.
ProposalAbnormalFailureException(String) - Constructor for exception org.anchoranalysis.mpp.proposer.ProposalAbnormalFailureException: Constructs a new exception with the specified detail message.
ProposalAbnormalFailureException(String, Throwable) - Constructor for exception org.anchoranalysis.mpp.proposer.ProposalAbnormalFailureException: Constructs a new exception with the specified detail message and cause.
ProposalAbnormalFailureException(Throwable) - Constructor for exception org.anchoranalysis.mpp.proposer.ProposalAbnormalFailureException: Constructs a new exception with the specified cause.
propose(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.mpp.bean.proposer.ScalarProposer: Proposes a scalar value based on the given parameters.
propose(MarkWithIdentifierFactory, ProposerContext) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkCollectionProposer: Proposes a collection of marks.
propose(Mark, Dimensions, RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.bean.proposer.OrientationProposer: Proposes an orientation for a given mark.
propose(VoxelizedMarkMemo, VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkMergeProposer: Proposes a merge between two marks.
propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkProposer: Proposes changes to the input mark according to the internal rules of the proposer.
propose(VoxelizedMarkMemo, ProposerContext, MarkWithIdentifierFactory) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkSplitProposer: Proposes a split of the input mark into two new marks.
propose(ProposerContext) - Method in interface org.anchoranalysis.mpp.proposer.OptionalPointProposer: Proposes a position in 3D space.
propose(Point3d, RandomNumberGenerator, Dimensions, Orientation) - Method in class org.anchoranalysis.mpp.bean.proposer.RadiiProposer: Proposes a new point representing radii based on the given parameters.
propose(Point3d, Mark, Dimensions, RandomNumberGenerator, ErrorNode) - Method in class org.anchoranalysis.mpp.bean.proposer.PointsProposer: Proposes a list of points based on the given parameters.
ProposerBean<T> - Class in org.anchoranalysis.mpp.bean.proposer: An abstract base class for proposer beans in the MPP (Marked Point Process) framework.
ProposerBean() - Constructor for class org.anchoranalysis.mpp.bean.proposer.ProposerBean
ProposerContext - Class in org.anchoranalysis.mpp.proposer: Context for proposing operations in the MPP framework.
ProposerContext(RandomNumberGenerator, EnergyStack, RegionMap, OperationContext, ErrorNode) - Constructor for class org.anchoranalysis.mpp.proposer.ProposerContext
ProposerException - Exception in org.anchoranalysis.mpp.proposer: An exception thrown when something goes wrong in a Proposer.
ProposerException(String) - Constructor for exception org.anchoranalysis.mpp.proposer.ProposerException: Constructs a new exception with the specified detail message.
ProposerException(Throwable) - Constructor for exception org.anchoranalysis.mpp.proposer.ProposerException: Constructs a new exception with the specified cause.

Q

quickOverlap() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
quickOverlap() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
quickOverlap() - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
quickOverlap() - Method in class org.anchoranalysis.mpp.mark.Mark: Provides an optional quick overlap calculation method.
QuickOverlapCalculation - Interface in org.anchoranalysis.mpp.mark: A method to quickly calculate overlap approximately

R

radiiOrdered() - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase: Returns an ordered array of radii in their original units.
radiiOrderedResolved(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase: Returns an ordered array of radii resolved to the given resolution.
RadiiProposer - Class in org.anchoranalysis.mpp.bean.proposer: An abstract base class for proposing radii in a 3D space.
RadiiProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.RadiiProposer
RadiiRandomizer - Class in org.anchoranalysis.mpp.mark.conic: Utility functions for generating random radii for ConicBase.
radiusForRegion(int) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius: Calculates the radius for a specific region.
radiusForRegionSquared(int) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius: Calculates the squared radius for a specific region.
RandomCollection<T> - Class in org.anchoranalysis.mpp.pair: An abstract collection of items from which one can randomly sample.
RandomCollection() - Constructor for class org.anchoranalysis.mpp.pair.RandomCollection
randomIndex(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Generates a random index within the collection.
randomizeRadii(Bound, RandomNumberGenerator, Optional<Resolution>, boolean) - Static method in class org.anchoranalysis.mpp.mark.conic.RadiiRandomizer: Generates random radii for a conic shape.
randomMark(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Gets a random mark from the collection.
randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation: Generates a random orientation within the defined bounds.
randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation2D
randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation3D
randOpen(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound: Generates a random value between the bounds (open interval).
RegionMap - Class in org.anchoranalysis.mpp.bean.regionmap: Maps integer IDs to sub-regions in the map.
RegionMap() - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMap
RegionMap(int) - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMap: Creates a region map with a single entry mapping to a particular region.
RegionMapSingleton - Class in org.anchoranalysis.mpp.bean.regionmap: A singleton class providing a default RegionMap.
RegionMembership - Class in org.anchoranalysis.mpp.bean.regionmap: Abstract class representing membership of regions using a bit-flag system.
RegionMembership() - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
RegionMembership(int) - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Constructs a RegionMembership with a single region set.
RegionMembershipAnd - Class in org.anchoranalysis.mpp.bean.regionmap: A RegionMembership implementation that uses an AND operation to check membership.
RegionMembershipAnd() - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipAnd: Constructs a RegionMembershipAnd with no regions set.
RegionMembershipAnd(int) - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipAnd: Constructs a RegionMembershipAnd with a single region set.
RegionMembershipOr - Class in org.anchoranalysis.mpp.bean.regionmap: A RegionMembership implementation that uses an OR operation to check membership.
RegionMembershipOr() - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipOr: Constructs a RegionMembershipOr with no regions set.
RegionMembershipOr(int) - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipOr: Constructs a RegionMembershipOr with a single region set.
RegionMembershipUtilities - Class in org.anchoranalysis.mpp.bean.regionmap: Utility class for managing 8-bit region membership.
RegionMembershipWithFlags - Class in org.anchoranalysis.mpp.bean.regionmap: A wrapper for RegionMembership that includes pre-calculated flags and a region ID.
RegionMembershipWithFlags(RegionMembership, int) - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags: Creates a new instance with the given region membership and region ID.
remove(int) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks: Removes a mark and its associated color at the specified index.
remove(int) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Removes a mark at a specific index.
remove(MemoForIndex, VoxelizedMarkMemo) - Method in interface org.anchoranalysis.mpp.mark.UpdatableMarks: Removes a mark from the existing set of marks.
removeTwo(int, int) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Removes two marks at specified indices.
replaceError(ErrorNode) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext: Creates a new ProposerContext with a replaced error node.
reset() - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo: Resets the cached voxelized mark.
resolve(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.Bound: Resolves the bound based on the given resolution and dimensionality.
ResolvedBound - Class in org.anchoranalysis.mpp.bean.bound: A bound resolved into pixel units.
ResolvedBound() - Constructor for class org.anchoranalysis.mpp.bean.bound.ResolvedBound
ResolvedBound(double, double) - Constructor for class org.anchoranalysis.mpp.bean.bound.ResolvedBound
ResolvedBound(ResolvedBound) - Constructor for class org.anchoranalysis.mpp.bean.bound.ResolvedBound: Creates a new instance by copying another ResolvedBound.
RotatableBoundingBox - Class in org.anchoranalysis.mpp.mark.points: A two-dimensional bounding-box rotated at arbitrary angle in XY plane around a point.
RotatableBoundingBox() - Constructor for class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox: Creates a new RotatableBoundingBox with default values.
RotatableBoundingBoxFactory - Class in org.anchoranalysis.mpp.mark.points: Creates instances of RotatableBoundingBox.

S

sampleInteger(int) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext: Samples an integer uniformly between [0..maxValExclusive).
sampleRandomPairNonUniform(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.pair.RandomCollection: Samples a random pair of items from the collection using a non-uniform distribution.
ScalarProposer - Class in org.anchoranalysis.mpp.bean.proposer: An abstract base class for proposing scalar values.
ScalarProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.ScalarProposer
scale(double) - Method in class org.anchoranalysis.mpp.bean.bound.Bound: Scales the bound by a multiplication factor.
scale(double) - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
scale(double) - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound: Scales the bound by a multiplication factor.
scale(ScaleFactor) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
scale(ScaleFactor) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
scale(ScaleFactor) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius: Objects are scaled in pre-rotated position.
scale(ScaleFactor) - Method in class org.anchoranalysis.mpp.mark.Mark: Scales the mark in X and Y dimensions.
scale(ScaleFactor) - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
scale(ScaleFactor) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
scale(ScaleFactor) - Method in class org.anchoranalysis.mpp.mark.points.PointList: Scales the points in the list by a given scale factor.
scale(ScaleFactor) - Method in class org.anchoranalysis.mpp.mark.points.Polygon
scale(ScaleFactor) - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
scale(ScaleFactor) - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
scaleRadii(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse: Scales the radii of the ellipse.
scaleXY(ScaleFactor) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Scales all marks in the collection in X and Y dimensions.
selectMarkFrom(MarkCollection, ProposerContext) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkFromCollectionProposer: Selects a mark from a collection of marks.
set(int, Mark) - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Replaces the mark at a specific index.
setAsMemberFlag(byte, byte) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities: Sets a membership flag.
setBit0(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 0.
setBit1(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 1.
setBit2(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 2.
setBit3(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 3.
setBit4(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 4.
setBit5(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 5.
setBit6(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 6.
setBit7(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership: Flag for region 7.
setDelegate(ResolvedBound) - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
setId(int) - Method in class org.anchoranalysis.mpp.mark.Mark: Sets the identifier of the mark.
setInnerCoreDistance(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid: The distance to the inner core, expressed as a ratio of the radii.
setList(List<RegionMembership>) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap: List of region memberships.
setMarkProvider(SingleMarkProvider) - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints: Provides the mark to be fitted.
setMarks(Point2d, Orientation) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse: Sets the marks with radii and orientation.
setMarksExplicit(Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase: Sets the mark's position explicitly.
setMarksExplicit(Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
setMarksExplicit(Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
setMarksExplicit(Point3d, Orientation) - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase: Sets the mark's position and orientation explicitly.
setMarksExplicit(Point3d, Orientation) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
setMarksExplicit(Point3d, Orientation) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
setMarksExplicit(Point3d, Orientation, Point2d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse: Sets the marks explicitly with position, orientation, and radii.
setMarksExplicit(Point3d, Orientation, Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase: Sets the mark's properties explicitly.
setMarksExplicit(Point3d, Orientation, Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
setMarksExplicit(Point3d, Orientation, Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
setMax(double) - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax: Sets the maximum value of the bound.
setMax(double) - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
setMin(double) - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax: Sets the minimum value of the bound.
setMin(double) - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
setMinNumPoints(int) - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints: Minimum number of points required to create a mark.
setPoints(Point3d, Point3d) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment: Sets the start and end points of the line segment.
setPoints(Point3i, Point3i) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment: Sets the start and end points of the line segment.
setPointsFitter(PointsFitter) - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints: Fits the provided mark to the extracted points.
setPosition(Point3d) - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition: The position of the mark in 3D space.
setRadius(double) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius: Sets the radius of the mark.
setReferencePoissonIntensity(double) - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkWithIdentifierFactory: The reference Poisson intensity for mark creation.
setRotationAngle(Bound) - Method in class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation2D
setRotationX(Bound) - Method in class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation3D
setRotationY(Bound) - Method in class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation3D
setRotationZ(Bound) - Method in class org.anchoranalysis.mpp.bean.bound.rotation.BoundRotation3D
setShell(double) - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipseFactory: The shell thickness of the ellipse.
setShell(double) - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipsoidFactory: The shell thickness of the ellipsoid.
setShell(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse: The size of the shell, expressed as a ratio of the radius.
setShell(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid: The size of the shell, expressed as a ratio of the radii.
setTemplateMark(MarkFactory) - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkWithIdentifierFactory: A template mark factory from which all new marks are created.
setThrowExceptionForInsufficientPoints(boolean) - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints: Whether to throw an exception when there are insufficient points.
shallowCopy() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks: Creates a shallow copy of this ColoredMarks instance.
shallowCopy() - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Creates a shallow copy of the collection.
SingleMarkProvider - Class in org.anchoranalysis.mpp.bean.provider: Provides (maybe) a single mark
SingleMarkProvider() - Constructor for class org.anchoranalysis.mpp.bean.provider.SingleMarkProvider
size() - Method in class org.anchoranalysis.mpp.bean.bound.BoundUnitless: Calculates the size of the bound range.
size() - Method in class org.anchoranalysis.mpp.index.IndexByChannel: Gets the number of channels in the index.
size() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks: Returns the number of marks in the collection.
size() - Method in class org.anchoranalysis.mpp.mark.MarkCollection: Returns the number of marks in the collection.
size() - Method in interface org.anchoranalysis.mpp.mark.voxelized.memo.MemoForIndex: Returns the total number of memos available.
Sphere - Class in org.anchoranalysis.mpp.mark.conic: Represents a 3D sphere mark.
Sphere() - Constructor for class org.anchoranalysis.mpp.mark.conic.Sphere
Sphere(Bound) - Constructor for class org.anchoranalysis.mpp.mark.conic.Sphere: Creates a sphere with a radius within particular bounds.
Sphere(Sphere) - Constructor for class org.anchoranalysis.mpp.mark.conic.Sphere: Copy constructor.
statisticsFor(int, int, int) - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark: Calculates statistics for a specific slice in a specific channel and region.
statisticsForAllSlices(int, int) - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark: Calculates statistics for all slices in a specific channel and region.
statisticsForAllSlicesMaskSlice(int, int, int) - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark: Calculates statistics for all slices in a specific channel and region, using a mask from another channel.
strMarks() - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius: Returns a string representation of the mark's attributes.
SUBMARK_CORE - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers: Identifier for the core region of a submark.
SUBMARK_CORE_INNER - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers: Identifier for the inner core region of a submark.
SUBMARK_INSIDE - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers: Identifier for the inside region of a submark.
SUBMARK_OUTSIDE - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers: Identifier for the outside region of a submark.
SUBMARK_SHELL - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers: Identifier for the shell region of a submark.
SUBMARK_SHELL_OUTSIDE - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers: Identifier for the outer shell region of a submark.
subsetWhereBBoxIntersects(Dimensions, int, List<BoundingBox>) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks: Creates a subset of marks whose bounding boxes intersect with given boxes.

T

toString() - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
toString() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
toString() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
toString() - Method in class org.anchoranalysis.mpp.mark.conic.Circle
toString() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
toString() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
toString() - Method in class org.anchoranalysis.mpp.mark.conic.Sphere
toString() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
toString() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
toString() - Method in class org.anchoranalysis.mpp.mark.points.PointList
toString() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
toString() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
toString() - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
toString() - Method in class org.anchoranalysis.mpp.pair.MarkPair
toString() - Method in class org.anchoranalysis.mpp.pair.PairVoxelizedMarkMemo
toString() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext

U

UnsupportedMarkTypeException - Exception in org.anchoranalysis.mpp.mark: Exception thrown when an unsupported mark type is encountered.
UnsupportedMarkTypeException(Exception) - Constructor for exception org.anchoranalysis.mpp.mark.UnsupportedMarkTypeException: Constructs a new UnsupportedMarkTypeException with the specified cause.
UnsupportedMarkTypeException(String) - Constructor for exception org.anchoranalysis.mpp.mark.UnsupportedMarkTypeException: Constructs a new UnsupportedMarkTypeException with the specified detail message.
UpdatableMarks - Interface in org.anchoranalysis.mpp.mark: An interface for managing a set of marks that can be updated.
update(Point2d, Point2d, Orientation) - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox: Updates the bounding box with new dimensions and orientation.
updateAfterMarkChange() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid: Updates internal calculations after a change in the mark's properties.
updateAfterPointsChange() - Method in class org.anchoranalysis.mpp.mark.points.PointList
updateAfterPointsChange() - Method in class org.anchoranalysis.mpp.mark.points.PointListBase: Updates the min and max points after the list of points has changed.
updateAfterPointsChange() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
UpdateMarkSetException - Exception in org.anchoranalysis.mpp.mark: Exception thrown when an error occurs while updating a mark set.
UpdateMarkSetException(Exception) - Constructor for exception org.anchoranalysis.mpp.mark.UpdateMarkSetException: Constructs a new UpdateMarkSetException with the specified cause.
UpdateMarkSetException(String) - Constructor for exception org.anchoranalysis.mpp.mark.UpdateMarkSetException: Constructs a new UpdateMarkSetException with the specified detail message.
updateshell(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse: Updates the shell size and recalculates internal values.

V

volume(int) - Method in class org.anchoranalysis.mpp.mark.conic.Circle
volume(int) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
volume(int) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
volume(int) - Method in class org.anchoranalysis.mpp.mark.conic.Sphere
volume(int) - Method in class org.anchoranalysis.mpp.mark.Mark: Calculates the volume of a specific region of the mark.
volume(int) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
volume(int) - Method in class org.anchoranalysis.mpp.mark.points.PointList
volume(int) - Method in class org.anchoranalysis.mpp.mark.points.Polygon
volume(int) - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
volume(int) - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
voxelized() - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo: Gets the voxelized representation of the mark.
VoxelizedMark - Interface in org.anchoranalysis.mpp.mark.voxelized: A voxelized representation of a Mark i.e.
VoxelizedMarkFactory - Class in org.anchoranalysis.mpp.mark.voxelized: Factory class for creating VoxelizedMarkHistogram instances.
VoxelizedMarkMemo - Class in org.anchoranalysis.mpp.mark.voxelized.memo: Memoization of retrieving a VoxelizedMark from a mark.
VoxelizedMarkMemo(Mark, EnergyStackWithoutParameters, RegionMap) - Constructor for class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo: Creates a new VoxelizedMarkMemo.
VoxelizedMarkMemoFactory - Class in org.anchoranalysis.mpp.mark.voxelized.memo: Factory class for creating VoxelizedMarkMemo instances.
VoxelPartition<T> - Interface in org.anchoranalysis.mpp.index: A partition of voxel values by slice.
VoxelPartitionFactory<T> - Interface in org.anchoranalysis.mpp.index.factory: A factory for creating VoxelPartition instances.
VoxelPartitionHistogram - Class in org.anchoranalysis.mpp.index: A voxel partition implementation using histograms to represent voxel value distributions.
VoxelPartitionHistogram(int, Supplier<Histogram>) - Constructor for class org.anchoranalysis.mpp.index.VoxelPartitionHistogram: Constructs a VoxelPartitionHistogram with a specified number of slices.
VoxelPartitonFactoryHistogram - Class in org.anchoranalysis.mpp.index.factory: A factory for creating VoxelPartition instances that use Histograms as parts.
VoxelPartitonFactoryHistogram() - Constructor for class org.anchoranalysis.mpp.index.factory.VoxelPartitonFactoryHistogram
voxels() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark: Gets the voxel representation of the mark.
voxelsMaximumIntensityProjection() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark: Gets the maximum intensity projection of the voxelized mark.

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