Index

A B C D F G I M O P R S T V W
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

adjustmentValueChanged(AdjustmentEvent) - Method in class org.bonej.plugins.Orienteer

alignImage(ImagePlus, Matrix, int) - Method in class org.bonej.plugins.Moments

Deprecated.

only use from a deprecated class

B

BACK - Static variable in class org.bonej.plugins.ConnectedComponents

Background value

C

close() - Method in class org.bonej.plugins.Orienteer

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

D

DeleteSliceRange - Class in org.bonej.plugins

DeleteSliceRange() - Constructor for class org.bonej.plugins.DeleteSliceRange

DensityCalibrator - Class in org.bonej.plugins

DensityCalibrator() - Constructor for class org.bonej.plugins.DensityCalibrator

dialogItemChanged(GenericDialog, AWTEvent) - Method in class org.bonej.plugins.SphereFitter

F

filterParticles(ImagePlus, int[][], byte[][], int, int, boolean, double, double) - Method in class org.bonej.plugins.ParticleAnalysis

Remove edge-touching, too small and too big particles.

FORE - Static variable in class org.bonej.plugins.ConnectedComponents

Foreground value

G

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.

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

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

getNParticles() - Method in class org.bonej.plugins.ConnectedComponents

Returns the number of particles detected in the image.

getParticleSizes() - Method in class org.bonej.plugins.ParticleAnalysis

getParticleSizes(int[][], int) - Method in class org.bonej.plugins.ParticleAnalysis

Run the particle size analysis.

getSumEuler(ImagePlus) - Method in class org.bonej.plugins.Connectivity

Calculate the Euler characteristic of the foreground in a binary stack

getWorkArray() - Method in class org.bonej.plugins.ConnectedComponents

Returns the binary work array containing foreground and background pixels.

I

itemStateChanged(ItemEvent) - Method in class org.bonej.plugins.Orienteer

M

MAX_FINAL_LABEL - Static variable in class org.bonej.plugins.ConnectedComponents

2^23 - greatest integer that can be represented precisely by a float

Moments - Class in org.bonej.plugins

Calculate centroid and principal axes of a thresholded stack; originally designed for 16-bit CT scans of a bone in air so default thresholds are 0 and 4000 HU, but most greyscale images should be handled

Moments() - Constructor for class org.bonej.plugins.Moments

mouseWheelMoved(MouseWheelEvent) - Method in class org.bonej.plugins.Orienteer

O

org.bonej - package org.bonej

org.bonej.bonej_legacy_plugins_ - module org.bonej.bonej_legacy_plugins_

org.bonej.menuWrappers - package org.bonej.menuWrappers

org.bonej.plugins - package org.bonej.plugins

Orienteer - Class in org.bonej.plugins

Indicator to show directions such as medial, proximal, cranial, north, left

Orienteer() - Constructor for class org.bonej.plugins.Orienteer

P

ParticleAnalysis - Class in org.bonej.plugins

Perform analysis of particles

ParticleAnalysis() - Constructor for class org.bonej.plugins.ParticleAnalysis

Constructor

ParticleCounter - Class in org.bonej.plugins

This class implements mutithreaded linear O(n) 3D particle identification and shape analysis.

ParticleCounter() - Constructor for class org.bonej.plugins.ParticleCounter

ParticleDisplay - Class in org.bonej.plugins

Display stacks and 3D visualisation of particles and particle analysis

ParticleDisplay() - Constructor for class org.bonej.plugins.ParticleDisplay

Purify - Class in org.bonej.plugins

Purify_ plugin for ImageJ

Purify() - Constructor for class org.bonej.plugins.Purify

R

run() - Method in class org.bonej.plugins.Connectivity

Modern scijava Plugin entry point.

run() - Method in class org.bonej.plugins.Moments

Modern scijava Plugin entry point.

run() - Method in class org.bonej.plugins.ParticleCounter

Modern scijava Plugin entry point.

run() - Method in class org.bonej.plugins.Purify

Modern scijava Plugin entry point.

run() - Method in class org.bonej.plugins.SliceGeometry

Modern scijava Plugin entry point.

run() - Method in class org.bonej.plugins.SphereFitter

Modern scijava Plugin entry point.

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.DeleteSliceRange

run(String) - Method in class org.bonej.plugins.DensityCalibrator

run(String) - Method in class org.bonej.plugins.SphereFitter

run(String) - Method in class org.bonej.plugins.VoxelDepthChecker

S

SliceGeometry - Class in org.bonej.plugins

Calculate 2D geometrical parameters

SliceGeometry() - Constructor for class org.bonej.plugins.SliceGeometry

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

T

textValueChanged(TextEvent) - Method in class org.bonej.plugins.Orienteer

ThicknessHelper - Class in org.bonej.menuWrappers

Deprecated.

Replaced by ThicknessWrapper in BoneJ2

ThicknessHelper() - Constructor for class org.bonej.menuWrappers.ThicknessHelper

Deprecated.

V

VoxelDepthChecker - Class in org.bonej.plugins

VoxelDepthChecker() - Constructor for class org.bonej.plugins.VoxelDepthChecker

W

windowActivated(WindowEvent) - Method in class org.bonej.plugins.Orienteer

windowClosing(WindowEvent) - Method in class org.bonej.plugins.Orienteer

A B C D F G I M O P R S T V W
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form