Index (BoneJ2 utilities 7.2.2 API)

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A

add(String, String, double) - Static method in class org.bonej.utilities.SharedTable: Adds new value as a Double to the shared table
add(String, String, long) - Static method in class org.bonej.utilities.SharedTable: Adds new value as a Double to the shared table.
add(String, String, Double) - Static method in class org.bonej.utilities.SharedTable: Adds new data to the shared table according to the shared table policy.
anisotropy(ImagePlus) - Static method in class org.bonej.utilities.ImagePlusUtil: Calculates the degree of spatial calibration anisotropy.
axisStream(S) - Static method in class org.bonej.utilities.Streamers: Generates a Stream from the axes in the given space.
AxisUtils - Class in org.bonej.utilities: Various utils for inspecting image axis properties

C

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. the volume of an element in a 3D space, or area in 2D.
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.
countSpatialDimensions(S) - Static method in class org.bonej.utilities.AxisUtils: Counts the number of spatial dimensions in the given space.

D

DatasetUtil - Class in org.bonej.utilities: Utility class for loading raw binary 3D image data into ImageJ2 Datasets.
display3DPoints(Collection<Vector3dc>, String) - Static method in class org.bonej.utilities.Visualiser: Plot a set of 3D coordinates in Benjamin Schmidt's ImageJ 3D Viewer

E

ElementUtil - Class in org.bonej.utilities: Various utility methods for inspecting image element properties
EMPTY_CELL - Static variable in class org.bonej.utilities.SharedTable: Sentinel value indicating an empty cell in the table.

G

getAnisotropy(S, UnitService) - Static method in class org.bonej.utilities.AxisUtils: Calculates the worst-case anisotropy deviation between spatial axes in the given space.
getScale(Dataset, AxisType) - Static method in class org.bonej.utilities.AxisUtils: Get the interval spacing in real units along an axis
getSpatialUnit(S, UnitService) - Static method in class org.bonej.utilities.AxisUtils: Returns the common unit of the spatial calibrations of the given space.
getTable() - Static method in class org.bonej.utilities.SharedTable: Gets a copy of the singleton Table.

H

has2SpatialDimensions(Dataset) - Static method in class org.bonej.utilities.AxisUtils: Check whether the dataset has exactly 2 spatial dimensions.
has3SpatialDimensions(Dataset) - Static method in class org.bonej.utilities.AxisUtils: Check whether the dataset has exactly 3 spatial dimensions.
hasChannelDimensions(S) - Static method in class org.bonej.utilities.AxisUtils: Checks if the given space has a channel dimension.
hasData() - Static method in class org.bonej.utilities.SharedTable: Checks whether the table contains any non-null data values.
hasNonXYZCTDimension(S) - Static method in class org.bonej.utilities.AxisUtils: Checks whether the given annotated space contains any dimension (axis) that is not one of the standard X, Y, Z, Channel, or Time axes.
hasNSpatialDimensions(Dataset, int) - Static method in class org.bonej.utilities.AxisUtils: Check whether the dataset has exactly N spatial dimensions.
hasSpatialDimensions(S) - Static method in class org.bonej.utilities.AxisUtils: Checks if the given space has any spatial dimensions.
hasTimeDimensions(S) - Static method in class org.bonej.utilities.AxisUtils: Checks if the given space has a time dimension.
hasXYDimensions(S) - Static method in class org.bonej.utilities.AxisUtils: Checks if the given annotated space contains both X and Y axes.

I

ImageBoundsUtil - Class in org.bonej.utilities: Utility methods for checking image bounds.
ImagePlusUtil - Class in org.bonej.utilities: Utility methods for checking ImagePlus properties
is3D(ImagePlus) - Static method in class org.bonej.utilities.ImagePlusUtil: Checks if the image is 3D.
isActiveOnAllSlices(int) - Static method in class org.bonej.utilities.RoiManagerUtil: Checks if a ROI is active on all slices.
isBinary(IterableInterval<T>) - Static method in class org.bonej.utilities.ElementUtil: Checks whether the interval contains only two distinct values.
isBinaryColour(ImagePlus) - Static method in class org.bonej.utilities.ImagePlusUtil: Checks if the image has only two different colours.
isIJ1Binary(Dataset, long) - Static method in class org.bonej.utilities.ElementUtil: Check whether a Dataset's pixels conform to the IJ1 binary definition, 8-bit and only 0,255.
isNativeStack(ImagePlus) - Static method in class org.bonej.utilities.ImagePlusUtil: Checks if the ImageStack contains native arrays that can be accessed directly from the heap.
isSpatialCalibrationsIsotropic(S, double, UnitService) - Static method in class org.bonej.utilities.AxisUtils: Checks if the spatial axes in the space have the same i.e. isotropic scaling.

L

loadRaw2D(File, long, int, int, String, boolean, String, double, double, DatasetService) - Static method in class org.bonej.utilities.DatasetUtil: Loads a raw file as a 2D Dataset with spatial calibration.
loadRaw3D(File, long, int, int, int, String, boolean, String, double, double, double, DatasetService) - Static method in class org.bonej.utilities.DatasetUtil: Loads a raw file as a 3D Dataset with spatial calibration.
loadRaw3D(File, long, int, int, int, String, String, double, double, double, DatasetService) - Static method in class org.bonej.utilities.DatasetUtil: Overloaded version of DatasetUtil.loadRaw3D(File, long, int, int, int, String, boolean, String, double, double, double, DatasetService) that does not perform (0,1) to (0,255) binary conversion.

O

org.bonej.bonej_utilities - module org.bonej.bonej_utilities
org.bonej.utilities - package org.bonej.utilities
outOfBounds(Dimensions, long[]) - Static method in class org.bonej.utilities.ImageBoundsUtil: Checks whether a pixel position falls outside the bounds of the given dimensions.

P

pointROICoordinates(RoiManager) - Static method in class org.bonej.utilities.RoiManagerUtil: Gets the coordinates of all point ROIs in the manager.

R

reset() - Static method in class org.bonej.utilities.SharedTable: Initializes the table into a new empty table
roiManagerIsEmpty() - Static method in class org.bonej.utilities.RoiManagerUtil: Determine whether the ROI Manager is not active or has no entries
RoiManagerUtil - Class in org.bonej.utilities: A class containing utility methods for the ImageJ RoiManager

S

saveAsRaw(Dataset, File) - Static method in class org.bonej.utilities.DatasetUtil: Convenience method to save a Dataset to a raw file with default little-endian byte order and no binary conversion.
saveAsRaw(Dataset, File, boolean) - Static method in class org.bonej.utilities.DatasetUtil: Convenience method to save a Dataset to a raw file with default little-endian byte order.
saveAsRaw(Dataset, File, boolean, boolean) - Static method in class org.bonej.utilities.DatasetUtil: Writes the pixel data of a 3D Dataset to a raw binary file.
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.
spatialAxisStream(S) - Static method in class org.bonej.utilities.Streamers: Generates a Stream from the spatial axes in the given space.
Streamers - Class in org.bonej.utilities: Utility functions to generate streams from various ImageJ2 collections

T

toImagePlus(Dataset, DatasetService) - Static method in class org.bonej.utilities.DatasetUtil: Converts a Dataset to a native ImagePlus using a DatasetService to retrieve the Context and ConvertService.
toImagePlus(Dataset, Context) - Static method in class org.bonej.utilities.DatasetUtil: Converts a Dataset to a native ImagePlus using a Context to retrieve the ConvertService.
toImagePlus(Dataset, ConvertService) - Static method in class org.bonej.utilities.DatasetUtil: Converts a Dataset to a native ImagePlus backed by in-memory primitive arrays.

U

unionMaskFromRoiManager(RandomAccessibleInterval<?>, int, int, int) - Static method in class org.bonej.utilities.RoiManagerUtil: Build a 2D union mask (BitType) for the given XY view and (z,t,c) plane using ROIs from the (visible) IJ1 RoiManager.

V

Visualiser - Class in org.bonej.utilities: Convenience methods for displaying data.

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