Index
All Classes and Interfaces|All Packages
A
- AnchorEllipsoidConstrain - Class in org.bonej.ops.ellipsoid.constrain
- AnchorEllipsoidConstrain() - Constructor for class org.bonej.ops.ellipsoid.constrain.AnchorEllipsoidConstrain
C
- calculate(byte[][], Vector3d) - Method in class org.bonej.ops.ellipsoid.EllipsoidOptimisationStrategy
- calculate(double[], Long) - Method in class org.bonej.ops.ellipsoid.EllipsoidPoints
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Creates random points on an ellipsoid surface.
- calculate(Img<FloatType>) - Method in class org.bonej.ops.ellipsoid.EllipsoidFactorErrorTracking
- calculate(IterableInterval<IntType>, List<QuickEllipsoid>) - Method in class org.bonej.ops.ellipsoid.EllipsoidFactorOutputGenerator
- calculate(RandomAccessibleInterval<B>, ParallelLineGenerator) - Method in class org.bonej.ops.mil.ParallelLineMIL
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Calculates the MIL vector of the interval.
- calculate(RandomAccessibleInterval<BitType>) - Method in class org.bonej.ops.skeletonize.FindRidgePoints
- calculate(Ellipsoid, Vector3dc) - Method in class org.bonej.ops.ellipsoid.DistanceFromEllipsoidSurfaceOp
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Calculates the shortest distance between a point and the surface of an ellipsoid
- calculate(Matrix4dc) - Method in class org.bonej.ops.ellipsoid.QuadricToEllipsoid
- conforms() - Method in class org.bonej.ops.ellipsoid.EllipsoidPoints
- conforms() - Method in class org.bonej.ops.mil.ParallelLineMIL
- contactSensitivity - Variable in class org.bonej.ops.ellipsoid.OptimisationParameters
- contains(double, double, double) - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
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Method based on the inequality (X-X0)^T H (X-X0) ≤ 1 Where X is the test point, X0 is the centroid, H is the ellipsoid's 3x3 matrix
- contract(double) - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
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Constrict all three axes by a fractional increment
- copy() - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
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Perform a deep copy of this QuickEllipsoid
D
- dilate(double, double, double) - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
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Dilate the ellipsoid semiaxes by independent absolute amounts
- DistanceFromEllipsoidSurfaceOp - Class in org.bonej.ops.ellipsoid
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An Op that calculates the distance between a point and an ellipsoid surface
- DistanceFromEllipsoidSurfaceOp() - Constructor for class org.bonej.ops.ellipsoid.DistanceFromEllipsoidSurfaceOp
E
- Ellipsoid - Class in org.bonej.ops.ellipsoid
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A class that stores the properties of an ellipsoid.
- Ellipsoid(double, double, double) - Constructor for class org.bonej.ops.ellipsoid.Ellipsoid
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Constructs an Ellipsoid.
- Ellipsoid(Vector3dc, Vector3dc, Vector3dc) - Constructor for class org.bonej.ops.ellipsoid.Ellipsoid
-
Constructs an Ellipsoid from semi-axes.
- EllipsoidConstrainStrategy - Interface in org.bonej.ops.ellipsoid.constrain
- EllipsoidFactorErrorTracking - Class in org.bonej.ops.ellipsoid
-
Class for tracking descriptive statistics of the change in EF from iteration to iteration
- EllipsoidFactorErrorTracking(OpService) - Constructor for class org.bonej.ops.ellipsoid.EllipsoidFactorErrorTracking
- EllipsoidFactorOutputGenerator - Class in org.bonej.ops.ellipsoid
- EllipsoidFactorOutputGenerator() - Constructor for class org.bonej.ops.ellipsoid.EllipsoidFactorOutputGenerator
- EllipsoidOptimisationStrategy - Class in org.bonej.ops.ellipsoid
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An Op that handles the stochastic optimisation of local ellipsoids for the Ellipsoid Factor algorithm
- EllipsoidOptimisationStrategy() - Constructor for class org.bonej.ops.ellipsoid.EllipsoidOptimisationStrategy
- EllipsoidPoints - Class in org.bonej.ops.ellipsoid
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Generates isotropically located random points on an ellipsoid surface.
- EllipsoidPoints() - Constructor for class org.bonej.ops.ellipsoid.EllipsoidPoints
F
- FindRidgePoints<R> - Class in org.bonej.ops.skeletonize
- FindRidgePoints() - Constructor for class org.bonej.ops.skeletonize.FindRidgePoints
G
- getA() - Method in class org.bonej.ops.ellipsoid.Ellipsoid
-
Gets the smallest radius of the ellipsoid.
- getAxisAlignRandomlyDistributedSurfacePoints(int) - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
- getB() - Method in class org.bonej.ops.ellipsoid.Ellipsoid
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Gets the second radius of the ellipsoid.
- getC() - Method in class org.bonej.ops.ellipsoid.Ellipsoid
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Gets the largest radius of the ellipsoid.
- getCentre() - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
- getCentroid() - Method in class org.bonej.ops.ellipsoid.Ellipsoid
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Gets a copy of center point of the ellipsoid.
- getDirection() - Method in interface org.bonej.ops.mil.ParallelLineGenerator
- getDirection() - Method in class org.bonej.ops.mil.PlaneParallelLineGenerator
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Returns the direction of the lines this generator creates
- getEllipsoidTensor() - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
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Gets an up to date ellipsoid tensor (H)
- getOrientation() - Method in class org.bonej.ops.ellipsoid.Ellipsoid
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Gets a copy of the orientation unit vectors of the ellipsoid.
- getRadii() - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
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Gets a copy of the radii.
- getRotation() - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
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Return a copy of the ellipsoid's eigenvector matrix
- getSemiAxes() - Method in class org.bonej.ops.ellipsoid.Ellipsoid
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Returns a copy of the semi-axes of the ellipsoid.
- getSortedRadii() - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
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Get the radii sorted in ascending order.
- getSurfacePoints(double[][]) - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
- getVolume() - Method in class org.bonej.ops.ellipsoid.Ellipsoid
-
Gets the volume of the ellipsoid.
- getVolume() - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
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Gets the volume of this ellipsoid, calculated as PI * a * b * c * 4 / 3
I
- initSampling(OpEnvironment) - Method in class org.bonej.ops.ellipsoid.Ellipsoid
-
Initializes the ellipsoid point sampling function.
L
- Line(Vector3dc, Vector3dc) - Constructor for class org.bonej.ops.mil.ParallelLineGenerator.Line
M
- maxDrift - Variable in class org.bonej.ops.ellipsoid.OptimisationParameters
- maxIterations - Variable in class org.bonej.ops.ellipsoid.OptimisationParameters
N
- nextLine() - Method in interface org.bonej.ops.mil.ParallelLineGenerator
- nextLine() - Method in class org.bonej.ops.mil.PlaneParallelLineGenerator
-
Generates the next random line.
- NoEllipsoidConstrain - Class in org.bonej.ops.ellipsoid.constrain
- NoEllipsoidConstrain() - Constructor for class org.bonej.ops.ellipsoid.constrain.NoEllipsoidConstrain
- nVectors - Variable in class org.bonej.ops.ellipsoid.OptimisationParameters
O
- OptimisationParameters - Class in org.bonej.ops.ellipsoid
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A class wrapping the optimisation parameters for
EllipsoidOptimisationStrategy. - OptimisationParameters(double, int, int, int, double) - Constructor for class org.bonej.ops.ellipsoid.OptimisationParameters
- org.bonej.bonej_ops - module org.bonej.bonej_ops
- org.bonej.ops.ellipsoid - package org.bonej.ops.ellipsoid
- org.bonej.ops.ellipsoid.constrain - package org.bonej.ops.ellipsoid.constrain
- org.bonej.ops.mil - package org.bonej.ops.mil
- org.bonej.ops.skeletonize - package org.bonej.ops.skeletonize
P
- ParallelLineGenerator - Interface in org.bonej.ops.mil
-
An interface for random parallel line generators.
- ParallelLineGenerator.Line - Class in org.bonej.ops.mil
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A line defined as a direction and point it passes through.
- ParallelLineMIL<B> - Class in org.bonej.ops.mil
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An op that finds the mean intercept length (MIL) vector of an interval.
- ParallelLineMIL() - Constructor for class org.bonej.ops.mil.ParallelLineMIL
- PlaneParallelLineGenerator - Class in org.bonej.ops.mil
-
A class that generates random lines that pass through a plane.
- PlaneParallelLineGenerator(I, Quaterniondc, BinaryHybridCFI1<Vector3d, Quaterniondc, Vector3d>, long) - Constructor for class org.bonej.ops.mil.PlaneParallelLineGenerator
-
Creates and initializes an instance for generating lines.
- postConstrain(QuickEllipsoid) - Method in class org.bonej.ops.ellipsoid.constrain.AnchorEllipsoidConstrain
- postConstrain(QuickEllipsoid) - Method in interface org.bonej.ops.ellipsoid.constrain.EllipsoidConstrainStrategy
- postConstrain(QuickEllipsoid) - Method in class org.bonej.ops.ellipsoid.constrain.NoEllipsoidConstrain
- preConstrain(QuickEllipsoid, Vector3d) - Method in class org.bonej.ops.ellipsoid.constrain.AnchorEllipsoidConstrain
- preConstrain(QuickEllipsoid, Vector3d) - Method in interface org.bonej.ops.ellipsoid.constrain.EllipsoidConstrainStrategy
- preConstrain(QuickEllipsoid, Vector3d) - Method in class org.bonej.ops.ellipsoid.constrain.NoEllipsoidConstrain
Q
- QuadricToEllipsoid - Class in org.bonej.ops.ellipsoid
-
Tries to create an
Ellipsoidfrom a general equation of a quadratic surface i.e. quadric. - QuadricToEllipsoid() - Constructor for class org.bonej.ops.ellipsoid.QuadricToEllipsoid
- QuickEllipsoid - Class in org.bonej.ops.ellipsoid
-
Represents an ellipsoid defined by its centroid, eigenvalues and 3x3 eigenvector matrix.
- QuickEllipsoid(double[], double[], double[][]) - Constructor for class org.bonej.ops.ellipsoid.QuickEllipsoid
-
Construct an QuickEllipsoid from the radii (a,b,c), centroid (cx, cy, cz) and Eigenvectors.
R
- reset() - Method in class org.bonej.ops.mil.PlaneParallelLineGenerator
-
Resets the cycle of the line generation
- rotate(double[][]) - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
-
Rotate the ellipsoid by the given 3x3 Matrix
S
- samplePoints(long) - Method in class org.bonej.ops.ellipsoid.Ellipsoid
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Return a random collection of points on the ellipsoid surface.
- setA(double) - Method in class org.bonej.ops.ellipsoid.Ellipsoid
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Sets the smallest radius of the ellipsoid.
- setB(double) - Method in class org.bonej.ops.ellipsoid.Ellipsoid
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Sets the second radius of the ellipsoid.
- setC(double) - Method in class org.bonej.ops.ellipsoid.Ellipsoid
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Sets the largest radius of the ellipsoid.
- setCentroid(double, double, double) - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
-
Translate the ellipsoid to a given new centroid
- setCentroid(Vector3dc) - Method in class org.bonej.ops.ellipsoid.Ellipsoid
-
Sets the coordinates of the centroid of the ellipsoid.
- setOrientation(Matrix3dc) - Method in class org.bonej.ops.ellipsoid.Ellipsoid
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Sets the values of the orientation vectors of the ellipsoid.
- setRotation(double[][]) - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
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Set rotation to the supplied rotation matrix.
- setSeed(long) - Static method in class org.bonej.ops.mil.ParallelLineMIL
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Sets the seed of the underlying random number generator
- setSeed(long) - Method in class org.bonej.ops.mil.PlaneParallelLineGenerator
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Sets the seed of the underlying random number generator
- setSemiAxes(Vector3dc, Vector3dc, Vector3dc) - Method in class org.bonej.ops.ellipsoid.Ellipsoid
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Sets the semi-axes of the ellipsoid.
T
- transpose(double[][]) - Static method in class org.bonej.ops.ellipsoid.QuickEllipsoid
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Transpose a 3x3 matrix in double[][] format.
V
- vectorIncrement - Variable in class org.bonej.ops.ellipsoid.OptimisationParameters
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