Index (BoneJ2 wrapper plugins 7.2.2 API)

A B C E F G H I M N O R S T W
All Classes and Interfaces|All Packages|Constant Field Values

A

AnalyseSkeletonWrapper - Class in org.bonej.wrapperPlugins: A wrapper plugin to bundle AnalyzeSkeleton into BoneJ2
AnalyseSkeletonWrapper() - Constructor for class org.bonej.wrapperPlugins.AnalyseSkeletonWrapper
AnisotropyWrapper<T> - Class in org.bonej.wrapperPlugins: A command that analyses the degree of anisotropy in an image.
AnisotropyWrapper() - Constructor for class org.bonej.wrapperPlugins.AnisotropyWrapper

B

BoneJCommand - Class in org.bonej.wrapperPlugins: Abstract base class for BoneJ command plugins.
BoneJCommand() - Constructor for class org.bonej.wrapperPlugins.BoneJCommand: Default constructor for BoneJ command plugin instantiation by SciJava framework.
BoneJMain - Class in org.bonej.wrapperPlugins: A main class for quickly testing the wrapper plugins
BoneJMain() - Constructor for class org.bonej.wrapperPlugins.BoneJMain

C

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
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

E

ElementFractionWrapper<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
EllipsoidFactorWrapper<T> - 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

F

find3DSubspaces(ImgPlus<C>) - Method in class org.bonej.wrapperPlugins.BoneJCommand
FitEllipsoidWrapper - Class in org.bonej.wrapperPlugins: A command that takes point ROIs from the ROI manager, and tries to fit an ellipsoid on them.
FitEllipsoidWrapper() - Constructor for class org.bonej.wrapperPlugins.FitEllipsoidWrapper
FractalDimensionWrapper<T> - Class in org.bonej.wrapperPlugins: This command estimates the fractal dimension of a binary image with the box-counting algorithm.
FractalDimensionWrapper() - Constructor for class org.bonej.wrapperPlugins.FractalDimensionWrapper

G

get2DSlice(ImgPlus<T>, int, int, int) - Static method in class org.bonej.wrapperPlugins.ElementFractionWrapper
getAxisTypes() - Method in class org.bonej.wrapperPlugins.wrapperUtils.HyperstackUtils.Subspace: Types of the additional hyperspace dimensions
getExponent(S) - Static method in class org.bonej.wrapperPlugins.wrapperUtils.ResultUtils: Returns the exponent character of the elements in this space, e.g. '³' for a spatial 3D space.
getPosition() - Method in class org.bonej.wrapperPlugins.wrapperUtils.HyperstackUtils.Subspace: Position of the subspace in each additional dimension of the hyperspace.
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.
getSubScripts() - Method in class org.bonej.wrapperPlugins.wrapperUtils.HyperstackUtils.Subspace: Subscripts of the additional hyperspace dimensions
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.
getUnitHeader(Dataset) - Static method in class org.bonej.wrapperPlugins.wrapperUtils.ResultUtils: Get a formatted unit string for use in the result table header.
getUnitHeader(S, UnitService, String) - Static method in class org.bonej.wrapperPlugins.wrapperUtils.ResultUtils: Returns the common unit string, e.g.

H

HAS_ANISOTROPIC_AXES - Static variable in class org.bonej.wrapperPlugins.CommonMessages
HAS_CHANNEL_DIMENSIONS - Static variable in class org.bonej.wrapperPlugins.CommonMessages
HAS_NONSTANDARD_DIMENSIONS - Static variable in class org.bonej.wrapperPlugins.CommonMessages
HAS_TIME_DIMENSIONS - Static variable in class org.bonej.wrapperPlugins.CommonMessages
HyperstackUtils - Class in org.bonej.wrapperPlugins.wrapperUtils: A static class containing utilities for splitting an n-dimensional hyperstack into arbitrary subspaces
HyperstackUtils.Subspace<T> - Class in org.bonej.wrapperPlugins.wrapperUtils: A class which stores a subspace interval of an n-dimensional hyperspace, and metadata
HyperstackUtils.Subspace.HyperAxisMeta - Class in org.bonej.wrapperPlugins.wrapperUtils: Describes the metadata of the subspace in relation to one of the axes in the hyperspace

I

IntertrabecularAngleWrapper - Class in org.bonej.wrapperPlugins: A wrapper UI class to calculate the inter-trabecular angles based on the study by Reznikov et al (2016): (https://doi.org/10.1016/j.actbio.2016.08.040 ).
IntertrabecularAngleWrapper() - Constructor for class org.bonej.wrapperPlugins.IntertrabecularAngleWrapper
interval - Variable in class org.bonej.wrapperPlugins.wrapperUtils.HyperstackUtils.Subspace

M

main(String...) - Static method in class org.bonej.wrapperPlugins.BoneJMain
make332RGB() - Static method in class org.bonej.wrapperPlugins.wrapperUtils.Common: Generates the '3-3-2 RGB' look-up table (LUT) and returns it as an IJ1 LUT object
makeFire() - Static method in class org.bonej.wrapperPlugins.wrapperUtils.Common: Generates the 'fire' look-up table (LUT) and returns it as an IJ1 LUT object

N

NO_IMAGE_OPEN - Static variable in class org.bonej.wrapperPlugins.CommonMessages
NO_RESULTS_MSG - Static variable in class org.bonej.wrapperPlugins.IntertrabecularAngleWrapper
NO_SKELETONS - Static variable in class org.bonej.wrapperPlugins.CommonMessages
NOT_3D_IMAGE - Static variable in class org.bonej.wrapperPlugins.CommonMessages
NOT_BINARY - Static variable in class org.bonej.wrapperPlugins.CommonMessages

O

org.bonej.bonej_plugins - module org.bonej.bonej_plugins
org.bonej.wrapperPlugins - package org.bonej.wrapperPlugins
org.bonej.wrapperPlugins.tableTools - package org.bonej.wrapperPlugins.tableTools
org.bonej.wrapperPlugins.wrapperUtils - package org.bonej.wrapperPlugins.wrapperUtils

R

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
run() - Method in class org.bonej.wrapperPlugins.AnalyseSkeletonWrapper
run() - Method in class org.bonej.wrapperPlugins.AnisotropyWrapper
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.TestLoadRawCommand
run() - Method in class org.bonej.wrapperPlugins.TestSaveRawCommand
run() - Method in class org.bonej.wrapperPlugins.ThicknessWrapper

S

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
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.
subspaces - Variable in class org.bonej.wrapperPlugins.BoneJCommand
SurfaceAreaWrapper<T> - Class in org.bonej.wrapperPlugins: A wrapper command to calculate mesh surface area
SurfaceAreaWrapper() - Constructor for class org.bonej.wrapperPlugins.SurfaceAreaWrapper
SurfaceFractionWrapper<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

T

TestLoadRawCommand - Class in org.bonej.wrapperPlugins: Test command to load raw data using DatasetUtil and display it.
TestLoadRawCommand() - Constructor for class org.bonej.wrapperPlugins.TestLoadRawCommand
TestSaveRawCommand - Class in org.bonej.wrapperPlugins: Test command to save the current active Dataset as a raw file using DatasetUtil.
TestSaveRawCommand() - Constructor for class org.bonej.wrapperPlugins.TestSaveRawCommand
ThicknessWrapper - Class in org.bonej.wrapperPlugins: An ImageJ2 command that wraps the sc.fiji.localThickness plugin
ThicknessWrapper() - Constructor for class org.bonej.wrapperPlugins.ThicknessWrapper
toBitTypeImgPlus(OpEnvironment, ImgPlus<C>) - Static method in class org.bonej.wrapperPlugins.wrapperUtils.Common: Converts the ImgPlus to a new ImgPlus with BitType elements.
toConventionalIndex(AxisType, long) - Static method in class org.bonej.wrapperPlugins.wrapperUtils.ResultUtils: If needed, converts the given index to the ImageJ1 convention where Z, Channel and Time axes start from 1.
toString() - Method in class org.bonej.wrapperPlugins.wrapperUtils.HyperstackUtils.Subspace.HyperAxisMeta
toString() - Method in class org.bonej.wrapperPlugins.wrapperUtils.HyperstackUtils.Subspace

W

warnAnisotropy(double, UIService, LogService) - Static method in class org.bonej.wrapperPlugins.wrapperUtils.Common: Shows a warning dialog about image anisotropy, and asks if the user wants to continue.
warnAnisotropy(ImagePlus, UIService, LogService) - Static method in class org.bonej.wrapperPlugins.wrapperUtils.Common: Deprecated.
Phase out this method because of the shift towards Datasets for IO and IO validation.
WEIRD_SPATIAL - Static variable in class org.bonej.wrapperPlugins.CommonMessages

A B C E F G H I M N O R S T W
All Classes and Interfaces|All Packages|Constant Field Values