- calculate(Ellipsoid, Vector3dc) - Method in class org.bonej.ops.ellipsoid.DistanceFromEllipsoidSurfaceOp
-
Calculates the shortest distance between a point and the surface of an
ellipsoid
- 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(byte[][], Vector3d) - Method in class org.bonej.ops.ellipsoid.EllipsoidOptimisationStrategy
-
- calculate(double[], Long) - Method in class org.bonej.ops.ellipsoid.EllipsoidPoints
-
Creates random points on an ellipsoid surface.
- calculate(Matrix4dc) - Method in class org.bonej.ops.ellipsoid.QuadricToEllipsoid
-
- calculate(RandomAccessibleInterval<B>, ParallelLineGenerator) - Method in class org.bonej.ops.mil.ParallelLineMIL
-
Calculates the MIL vector of the interval.
- calculate(RandomAccessibleInterval<BitType>) - Method in class org.bonej.ops.skeletonize.FindRidgePoints
-
- calibratedSpatialElementSize(T, UnitService) - Static method in class org.bonej.utilities.ElementUtil
-
Returns the calibrated size of a single spatial element in the given space,
e.g.
- cancelMacroSafe(ContextCommand, String) - Static method in class org.bonej.wrapperPlugins.wrapperUtils.Common
-
Cancels a command so that it won't show a dialog if a macro is running
- Centroid - Class in org.bonej.geometry
-
- cleanDuplicate(ImagePlus) - Static method in class org.bonej.utilities.ImagePlusUtil
-
Duplicates the image without changing the title of the copy, or cropping it
to the ROI.
- close() - Method in class org.bonej.plugins.Orienteer
-
- Common - Class in org.bonej.wrapperPlugins.wrapperUtils
-
Miscellaneous utility methods.
- Common() - Constructor for class org.bonej.wrapperPlugins.wrapperUtils.Common
-
- CommonMessages - Class in org.bonej.wrapperPlugins
-
Common messages displayed for the user
- conforms() - Method in class org.bonej.ops.ellipsoid.EllipsoidPoints
-
- conforms() - Method in class org.bonej.ops.mil.ParallelLineMIL
-
- ConnectedComponents - Class in org.bonej.plugins
-
Performs connected components labelling (sequential region labelling) in two-passes.
- ConnectedComponents() - Constructor for class org.bonej.plugins.ConnectedComponents
-
Constructor
- Connectivity - Class in org.bonej.plugins
-
Connectivity_
- Connectivity() - Constructor for class org.bonej.plugins.Connectivity
-
- ConnectivityWrapper<T extends RealType<T> & NativeType<T>> - Class in org.bonej.wrapperPlugins
-
A wrapper UI class for the Connectivity Ops
- ConnectivityWrapper() - Constructor for class org.bonej.wrapperPlugins.ConnectivityWrapper
-
- contactSensitivity - Variable in class org.bonej.ops.ellipsoid.OptimisationParameters
-
- contains(double, double, double) - Method in class org.bonej.geometry.Ellipsoid
-
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
- contains(double, double, double) - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
-
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.geometry.Ellipsoid
-
Constrict all three axes by a fractional increment
- contract(double) - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
-
Constrict all three axes by a fractional increment
- copy() - Method in class org.bonej.geometry.Ellipsoid
-
Perform a deep copy of this Ellipsoid
- copy() - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
-
Perform a deep copy of this QuickEllipsoid
- countSpatialDimensions(S) - Static method in class org.bonej.utilities.AxisUtils
-
Counts the number of spatial dimensions in the given space.
- ElementFractionWrapper<T extends RealType<T> & NativeType<T>> - Class in org.bonej.wrapperPlugins
-
This command estimates the size of the given sample by counting its
foreground elements, and the whole stack by counting all the elements (bone)
and the whole image stack.
- ElementFractionWrapper() - Constructor for class org.bonej.wrapperPlugins.ElementFractionWrapper
-
- ElementUtil - Class in org.bonej.utilities
-
Various utility methods for inspecting image element properties
- Ellipsoid - Class in org.bonej.geometry
-
Represents an ellipsoid defined by its centroid, eigenvalues and 3x3
eigenvector matrix.
- Ellipsoid(Object[]) - Constructor for class org.bonej.geometry.Ellipsoid
-
Instantiate an ellipsoid from the result of FitEllipsoid
- Ellipsoid(double, double, double, double, double, double, double[][]) - Constructor for class org.bonej.geometry.Ellipsoid
-
Construct an Ellipsoid from the radii (a,b,c), centroid (cx, cy, cz) and
Eigenvectors.
- Ellipsoid - Class in org.bonej.ops.ellipsoid
-
A class that stores the properties of an ellipsoid.
- Ellipsoid(double, double, double) - Constructor for class org.bonej.ops.ellipsoid.Ellipsoid
-
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
-
- EllipsoidFactorWrapper - Class in org.bonej.wrapperPlugins
-
ImageJ plugin to describe the local geometry of a binary image in an
oblate/prolate spheroid space.
- EllipsoidFactorWrapper() - Constructor for class org.bonej.wrapperPlugins.EllipsoidFactorWrapper
-
- EllipsoidOptimisationStrategy - Class in org.bonej.ops.ellipsoid
-
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
-
Generates isotropically located random points on an ellipsoid surface.
- EllipsoidPoints() - Constructor for class org.bonej.ops.ellipsoid.EllipsoidPoints
-
- EMPTY_CELL - Static variable in class org.bonej.utilities.SharedTable
-
- get() - Static method in class org.bonej.util.BoneList
-
Return the array of bone names
- getA() - Method in class org.bonej.ops.ellipsoid.Ellipsoid
-
Gets the smallest radius of the ellipsoid.
- getAxisAlignedBoundingBox() - Method in class org.bonej.geometry.Ellipsoid
-
Calculate the minimal axis-aligned bounding box of this ellipsoid Thanks to
Tavian Barnes for the simplification of the maths
https://tavianator.com/2014/06/exact-bounding-boxes-for-spheres-ellipsoids
- getAxisAlignRandomlyDistributedSurfacePoints(int) - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
-
- getAxisTypes() - Method in class org.bonej.wrapperPlugins.wrapperUtils.HyperstackUtils.Subspace
-
Types of the additional hyperspace dimensions
- getB() - Method in class org.bonej.ops.ellipsoid.Ellipsoid
-
Gets the second radius of the ellipsoid.
- getC() - Method in class org.bonej.ops.ellipsoid.Ellipsoid
-
Gets the largest radius of the ellipsoid.
- getCentre() - Method in class org.bonej.geometry.Ellipsoid
-
- getCentre() - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
-
- getCentroid() - Method in class org.bonej.ops.ellipsoid.Ellipsoid
-
Gets a copy of center point of the ellipsoid.
- getConnDensity(ImagePlus, double) - Method in class org.bonej.plugins.Connectivity
-
Calculate connectivity density
- getConnectivity(double) - Method in class org.bonej.plugins.Connectivity
-
Return the connectivity of the image, which is 1 - deltaChi.
- getDeltaChi(ImagePlus, double) - Method in class org.bonej.plugins.Connectivity
-
Get the contribution of the stack's foreground particles to the Euler
characteristic of the universe the stack was cut from.
- getDirection() - Method in interface org.bonej.ops.mil.ParallelLineGenerator
-
- getDirection() - Method in class org.bonej.ops.mil.PlaneParallelLineGenerator
-
Returns the direction of the lines this generator creates
- getExponent(S) - Static method in class org.bonej.wrapperPlugins.wrapperUtils.ResultUtils
-
Returns the exponent character of the elements in this space, e.g.
- getInstance() - Static method in class org.bonej.util.ResultInserter
-
- getInstance(PrefService, PluginService, CommandService, Logger) - Static method in class org.bonej.wrapperPlugins.wrapperUtils.UsageReporter
-
- getLocalThickness(ImagePlus, boolean, boolean) - Static method in class org.bonej.menuWrappers.ThicknessHelper
-
Deprecated.
Get a local thickness map from an ImagePlus with optional masking
correction
A convenience method for legacy code
- getLocalThickness(ImagePlus, boolean) - Static method in class org.bonej.menuWrappers.ThicknessHelper
-
Deprecated.
Get a local thickness map from an ImagePlus, without masking correction
A convenience method for legacy code
- getNParticles() - Method in class org.bonej.plugins.ConnectedComponents
-
- getOrientation() - Method in class org.bonej.ops.ellipsoid.Ellipsoid
-
Gets a copy of the orientation unit vectors of the ellipsoid.
- getParticleSizes() - Method in class org.bonej.plugins.ParticleAnalysis
-
- getParticleSizes(int[][], int) - Method in class org.bonej.plugins.ParticleAnalysis
-
Run the particle size analysis.
- getPosition() - Method in class org.bonej.wrapperPlugins.wrapperUtils.HyperstackUtils.Subspace
-
Position of the subspace in each additional dimension of the hyperspace.
- getRadii() - Method in class org.bonej.geometry.Ellipsoid
-
Gets a copy of the radii.
- getRadii() - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
-
Gets a copy of the radii.
- getRotation() - Method in class org.bonej.geometry.Ellipsoid
-
Return a copy of the ellipsoid's eigenvector matrix
- getRotation() - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
-
Return a copy of the ellipsoid's eigenvector matrix
- getSemiAxes() - Method in class org.bonej.ops.ellipsoid.Ellipsoid
-
Returns a copy of the semi-axes of the ellipsoid.
- getSizeDescription(S) - Static method in class org.bonej.wrapperPlugins.wrapperUtils.ResultUtils
-
Returns a verbal description of the size of the elements in the given
space, e.g.
- getSkeleton(ImagePlus) - Static method in class org.bonej.util.SkeletonUtils
-
Gets a medial axis skeleton from a binary imp using a topology-preserving
iterative algorithm
- getSortedRadii() - Method in class org.bonej.geometry.Ellipsoid
-
Get the radii sorted in ascending order.
- getSortedRadii() - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
-
Get the radii sorted in ascending order.
- getSpatialUnit(S, UnitService) - Static method in class org.bonej.utilities.AxisUtils
-
Returns the common unit of the spatial calibrations of the given space.
- getSubScripts() - Method in class org.bonej.wrapperPlugins.wrapperUtils.HyperstackUtils.Subspace
-
Subscripts of the additional hyperspace dimensions
- getSumEuler(ImagePlus) - Method in class org.bonej.plugins.Connectivity
-
Calculate the Euler characteristic of the foreground in a binary stack
- getSurfacePoints(int) - Method in class org.bonej.geometry.Ellipsoid
-
- getSurfacePoints(double[][]) - Method in class org.bonej.geometry.Ellipsoid
-
- getSurfacePoints(double[][]) - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
-
- getTable() - Static method in class org.bonej.utilities.SharedTable
-
Gets a copy of the singleton
Table.
- getUnitHeader(S, UnitService, String) - Static method in class org.bonej.wrapperPlugins.wrapperUtils.ResultUtils
-
Returns the common unit string, e.g.
- getUnitHeader(ImagePlus) - Static method in class org.bonej.wrapperPlugins.wrapperUtils.ResultUtils
-
Gets the unit of the image calibration, which can be displayed to the user.
- getVolume() - Method in class org.bonej.geometry.Ellipsoid
-
Gets the volume of this ellipsoid, calculated as PI * a * b * c * 4 / 3
- getVolume() - Method in class org.bonej.ops.ellipsoid.Ellipsoid
-
Gets the volume of the ellipsoid.
- getVolume() - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
-
Gets the volume of this ellipsoid, calculated as PI * a * b * c * 4 / 3
- getWorkArray() - Method in class org.bonej.plugins.ConnectedComponents
-
- getYMinAndMax() - Method in class org.bonej.geometry.Ellipsoid
-
Calculate the minimal and maximal y values bounding this ellipsoid
- getZMinAndMax() - Method in class org.bonej.geometry.Ellipsoid
-
Calculate the minimal and maximal z values bounding this ellipsoid
- guessBone(CharSequence) - Static method in class org.bonej.util.BoneList
-
Return the boneID of a bone in boneList that matches the input string
- randomVector() - Static method in class org.bonej.geometry.Vectors
-
Generate a single randomly-oriented vector on the unit sphere
- randomVectors(int) - Static method in class org.bonej.geometry.Vectors
-
Generate an array of randomly-oriented 3D unit vectors
- registerMacroValues(GenericDialog, Component[]) - Static method in class org.bonej.util.DialogModifier
-
Go through all values in a GenericDialog's Components and call the
appropriate get method.
- regularVectors(int) - Static method in class org.bonej.geometry.Vectors
-
Generate an array of regularly-spaced 3D unit vectors.
- replaceUnitString(GenericDialog, CharSequence, CharSequence) - Static method in class org.bonej.util.DialogModifier
-
Replace the unit string to the right of all numeric textboxes in a
GenericDialog
- ReporterOptions - Class in org.bonej.plugins
-
- ReporterOptions() - Constructor for class org.bonej.plugins.ReporterOptions
-
- reportEvent(Object) - Static method in class org.bonej.plugins.UsageReporter
-
- reportEvent(String) - Method in class org.bonej.wrapperPlugins.wrapperUtils.UsageReporter
-
Reports a the usage of a plug-in to bonej.org
- reportUsage() - Method in class org.bonej.wrapperPlugins.BoneJCommand
-
- reset() - Method in class org.bonej.ops.mil.PlaneParallelLineGenerator
-
Resets the cycle of the line generation
- reset() - Static method in class org.bonej.utilities.SharedTable
-
Initializes the table into a new empty table
- ResultInserter - Class in org.bonej.util
-
Receive results from analytic methods and insert them into the Results table
in a sensible way.
- resultsTable - Variable in class org.bonej.wrapperPlugins.BoneJCommand
-
The results of the command in a
Table.
- ResultUtils - Class in org.bonej.wrapperPlugins.wrapperUtils
-
Static utility methods that help display results to the user
- RoiManagerUtil - Class in org.bonej.utilities
-
A class containing utility methods for the ImageJ RoiManager
- rotate(double[][]) - Method in class org.bonej.geometry.Ellipsoid
-
Rotate the ellipsoid by the given 3x3 Matrix
- rotate(double[][]) - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
-
Rotate the ellipsoid by the given 3x3 Matrix
- run(ImagePlus, int) - Method in class org.bonej.plugins.ConnectedComponents
-
Run connected components filter on a binary image
- run(String) - Method in class org.bonej.plugins.Connectivity
-
- run(String) - Method in class org.bonej.plugins.DeleteSliceRange
-
- run(String) - Method in class org.bonej.plugins.DensityCalibrator
-
- run(String) - Method in class org.bonej.plugins.Moments
-
- run(String) - Method in class org.bonej.plugins.ParticleCounter
-
- run(String) - Method in class org.bonej.plugins.Purify
-
- run(String) - Method in class org.bonej.plugins.ReporterOptions
-
- run(String) - Method in class org.bonej.plugins.SliceGeometry
-
- run(String) - Method in class org.bonej.plugins.SphereFitter
-
- run(String) - Method in class org.bonej.plugins.VoxelDepthChecker
-
- run() - Method in class org.bonej.wrapperPlugins.AnalyseSkeletonWrapper
-
- run() - Method in class org.bonej.wrapperPlugins.AnisotropyWrapper
-
- run() - Method in class org.bonej.wrapperPlugins.ConnectivityWrapper
-
- run() - Method in class org.bonej.wrapperPlugins.ElementFractionWrapper
-
- run() - Method in class org.bonej.wrapperPlugins.EllipsoidFactorWrapper
-
- run() - Method in class org.bonej.wrapperPlugins.FitEllipsoidWrapper
-
- run() - Method in class org.bonej.wrapperPlugins.FractalDimensionWrapper
-
- run() - Method in class org.bonej.wrapperPlugins.IntertrabecularAngleWrapper
-
- run() - Method in class org.bonej.wrapperPlugins.SkeletoniseWrapper
-
- run() - Method in class org.bonej.wrapperPlugins.SurfaceAreaWrapper
-
- run() - Method in class org.bonej.wrapperPlugins.SurfaceFractionWrapper
-
- run() - Method in class org.bonej.wrapperPlugins.tableTools.SharedTableCleaner
-
- run() - Method in class org.bonej.wrapperPlugins.ThicknessWrapper
-
- run() - Method in class org.bonej.wrapperPlugins.wrapperUtils.UsageReporterOptions
-
- samplePoints(long) - Method in class org.bonej.ops.ellipsoid.Ellipsoid
-
Return a random collection of points on the ellipsoid surface.
- send() - Method in class org.bonej.plugins.UsageReporter
-
Send the report to Google Analytics in the form of an HTTP request for a
1-pixel GIF with lots of parameters set
- setA(double) - Method in class org.bonej.ops.ellipsoid.Ellipsoid
-
Sets the smallest radius of the ellipsoid.
- setB(double) - Method in class org.bonej.ops.ellipsoid.Ellipsoid
-
Sets the second radius of the ellipsoid.
- setC(double) - Method in class org.bonej.ops.ellipsoid.Ellipsoid
-
Sets the largest radius of the ellipsoid.
- setCentroid(double, double, double) - Method in class org.bonej.geometry.Ellipsoid
-
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.
- setCentroid(double, double, double) - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
-
Translate the ellipsoid to a given new centroid
- setDefaultThreshold(ImagePlus) - Static method in class org.bonej.util.ThresholdGuesser
-
Set up default thresholds and report them to the user as HU values if the
image has HU calibration or plain values if not.
- setOrientation(Matrix3dc) - Method in class org.bonej.ops.ellipsoid.Ellipsoid
-
Sets the values of the orientation vectors of the ellipsoid.
- setResultInRow(ImagePlus, String, double) - Method in class org.bonej.util.ResultInserter
-
Finds the first available space for a result, avoiding lots of empty space
when measurements of different types are made on the same image
- setRotation(double[][]) - Method in class org.bonej.geometry.Ellipsoid
-
Set rotation to the supplied rotation matrix.
- setRotation(double[][]) - Method in class org.bonej.ops.ellipsoid.QuickEllipsoid
-
Set rotation to the supplied rotation matrix.
- setSeed(long) - Static method in class org.bonej.ops.mil.ParallelLineMIL
-
Sets the seed of the underlying random number generator
- setSeed(long) - Method in class org.bonej.ops.mil.PlaneParallelLineGenerator
-
Sets the seed of the underlying random number generator
- setSemiAxes(Vector3dc, Vector3dc, Vector3dc) - Method in class org.bonej.ops.ellipsoid.Ellipsoid
-
Sets the semi-axes of the ellipsoid.
- SharedTable - Class in org.bonej.utilities
-
Stores a
Table, which is ordered according to the following rules:
Each row has a header label, which tells you which image was measured,
e.g.
- SharedTableCleaner - Class in org.bonej.wrapperPlugins.tableTools
-
A command that allows the user to clear the
SharedTable
- SharedTableCleaner() - Constructor for class org.bonej.wrapperPlugins.tableTools.SharedTableCleaner
-
- SkeletoniseWrapper - Class in org.bonej.wrapperPlugins
-
A wrapper plugin to bundle Skeletonize3D into BoneJ2
- SkeletoniseWrapper() - Constructor for class org.bonej.wrapperPlugins.SkeletoniseWrapper
-
- SkeletonUtils - Class in org.bonej.util
-
- SliceGeometry - Class in org.bonej.plugins
-
Calculate 2D geometrical parameters
- SliceGeometry() - Constructor for class org.bonej.plugins.SliceGeometry
-
- spatialAxisStream(S) - Static method in class org.bonej.utilities.Streamers
-
Generates a
Stream from the spatial axes in the given space.
- SphereFitter - Class in org.bonej.plugins
-
Takes point selections from ROI manager and returns the centroid and radius
of a best fit sphere Ported from Angelo Tardugno's C++
- SphereFitter() - Constructor for class org.bonej.plugins.SphereFitter
-
- split3DSubspaces(ImgPlus<T>) - Static method in class org.bonej.wrapperPlugins.wrapperUtils.HyperstackUtils
-
Splits the hyperstack into {X, Y, Z} subspaces.
- splitSubspaces(ImgPlus<T>, Collection<AxisType>) - Static method in class org.bonej.wrapperPlugins.wrapperUtils.HyperstackUtils
-
Splits the hyperstack into subspaces defined by the given axes.
- startAndJoin(Thread[]) - Static method in class org.bonej.util.Multithreader
-
- Streamers - Class in org.bonej.utilities
-
Utility functions to generate streams from various ImageJ2 collections
- subspaces - Variable in class org.bonej.wrapperPlugins.BoneJCommand
-
- SurfaceAreaWrapper<T extends RealType<T> & NativeType<T>> - Class in org.bonej.wrapperPlugins
-
A wrapper command to calculate mesh surface area
- SurfaceAreaWrapper() - Constructor for class org.bonej.wrapperPlugins.SurfaceAreaWrapper
-
- SurfaceFractionWrapper<T extends RealType<T> & NativeType<T>> - Class in org.bonej.wrapperPlugins
-
First this command creates a surface mesh from both all foreground voxels
(bone) and the whole image stack.
- SurfaceFractionWrapper() - Constructor for class org.bonej.wrapperPlugins.SurfaceFractionWrapper
-