Index

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B

BoneList - Class in org.bonej.util
Utility methods for making lists of bones and guessing which bone is in an image

C

Centroid - Class in org.bonej.geometry
 
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
contract(double) - Method in class org.bonej.geometry.Ellipsoid
Constrict all three axes by a fractional increment
copy() - Method in class org.bonej.geometry.Ellipsoid
Perform a deep copy of this Ellipsoid

D

diag(Matrix) - Static method in class org.bonej.util.MatrixUtils
Get the diagonal of the matrix as a column vector
DialogModifier - Class in org.bonej.util
 
dicomVoxelDepth(ImagePlus) - Static method in class org.bonej.util.ImageCheck
Check that the voxel thickness is correct in the DICOM image metadata.
dilate(double, double, double) - Method in class org.bonej.geometry.Ellipsoid
Dilate the ellipsoid semiaxes by independent absolute amounts
distance3D(double, double, double) - Static method in class org.bonej.geometry.Trig
Calculate the distance to the origin, (0,0,0).
distance3D(double, double, double, double, double, double) - Static method in class org.bonej.geometry.Trig
Calculate the distance between 2 3D points p(x, y, z) and q (x, y, z) using Pythagoras' theorem

E

Ellipsoid - Class in org.bonej.geometry
Represents an ellipsoid defined by its centroid, eigenvalues and 3x3 eigenvector matrix.
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(Object[]) - Constructor for class org.bonej.geometry.Ellipsoid
Instantiate an ellipsoid from the result of FitEllipsoid

F

FitEllipsoid - Class in org.bonej.geometry
Ellipsoid fitting methods.
fitSphere(double[][]) - Static method in class org.bonej.geometry.FitSphere
Fit a sphere to 3D coordinates
FitSphere - Class in org.bonej.geometry
Find the best fitting sphere Ported from Angelo Tardugno's C++

G

get() - Static method in class org.bonej.util.BoneList
Return the array of bone names
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
getBoneID(String) - Static method in class org.bonej.util.BoneList
Get the bone ID for a given bone name
getCentre() - Method in class org.bonej.geometry.Ellipsoid
 
getRadii() - Method in class org.bonej.geometry.Ellipsoid
Gets a copy of the radii.
getRotation() - Method in class org.bonej.geometry.Ellipsoid
Return a copy of the ellipsoid's eigenvector matrix
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.
getSurfacePoints(double[][]) - Method in class org.bonej.geometry.Ellipsoid
 
getSurfacePoints(int) - Method in class org.bonej.geometry.Ellipsoid
 
getVolume() - Method in class org.bonej.geometry.Ellipsoid
Gets the volume of this ellipsoid, calculated as PI * a * b * c * 4 / 3
getXMinAndMax() - Method in class org.bonej.geometry.Ellipsoid
Calculate the minimal and maximal x values bounding this ellipsoid
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

H

hasInvalidNumber(Iterable<?>) - Static method in class org.bonej.util.DialogModifier
Check all the numeric text fields in a dialog and return false if any of them cannot be parsed into a number.
huCalibrated(ImagePlus) - Static method in class org.bonej.util.ImageCheck
Guess whether an image is Hounsfield unit calibrated

I

id - Variable in class org.bonej.geometry.Ellipsoid
ID field for tracking this particular ellipsoid
ImageCheck - Class in org.bonej.util
Check if an image conforms to the type defined by each method.
isBinary(ImagePlus) - Static method in class org.bonej.util.ImageCheck
Check if image is binary
isSingleSlice(ImagePlus) - Static method in class org.bonej.util.ImageCheck
Checks if an image is a single slice image.
isVoxelIsotropic(ImagePlus, double) - Static method in class org.bonej.util.ImageCheck
Check if the image's voxels are isotropic in all 3 dimensions (i.e. are placed on a cubic grid)

M

MatrixUtils - Class in org.bonej.util
Utility methods for working with Matrixes
MatrixUtils() - Constructor for class org.bonej.util.MatrixUtils
 
Multithreader - Class in org.bonej.util
Multithreader utility class for convenient multithreading of ImageJ plugins

N

newThreads() - Static method in class org.bonej.util.Multithreader
 

O

org.bonej.bonej_legacy_util_ - module org.bonej.bonej_legacy_util_
 
org.bonej.geometry - package org.bonej.geometry
 
org.bonej.util - package org.bonej.util
 

P

printToIJ2Log(LogService, Matrix, String) - Method in class org.bonej.util.MatrixUtils
 
printToIJLgog(Matrix, String) - Static method in class org.bonej.util.MatrixUtils
Print the Matrix to the ImageJ log

R

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
rotate(double[][]) - Method in class org.bonej.geometry.Ellipsoid
Rotate the ellipsoid by the given 3x3 Matrix

S

setCentroid(double, double, double) - Method in class org.bonej.geometry.Ellipsoid
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.
setRotation(double[][]) - Method in class org.bonej.geometry.Ellipsoid
Set rotation to the supplied rotation matrix.
SkeletonUtils - Class in org.bonej.util
Utility methods for working with the Skeletonize3D_ plugin
startAndJoin(Thread[]) - Static method in class org.bonej.util.Multithreader
 

T

testEllipsoid(double, double, double, double, double, double, double, double, int, boolean) - Static method in class org.bonej.geometry.FitEllipsoid
Return points on an ellipsoid with optional noise.
ThresholdGuesser - Class in org.bonej.util
 
transpose(double[][]) - Static method in class org.bonej.geometry.Ellipsoid
Transpose a 3x3 matrix in double[][] format.
Trig - Class in org.bonej.geometry
Provides simple trigonometric calculations

V

Vectors - Class in org.bonej.geometry
 

Y

yuryPetrov(double[][]) - Static method in class org.bonej.geometry.FitEllipsoid
Ellipsoid fitting method by Yury Petrov.
B C D E F G H I M N O P R S T V Y 
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