Module org.bonej.bonej_utilities

Package org.bonej.utilities

Class RoiManagerUtil

java.lang.Object

org.bonej.utilities.RoiManagerUtil

public final class RoiManagerUtil
extends Object

A class containing utility methods for the ImageJ RoiManager

Author:

Michael Doube, Richard Domander

Method Summary

Modifier and Type	Method	Description
static boolean	isActiveOnAllSlices(int sliceNumber)	Checks if a ROI is active on all slices.
static List<org.joml.Vector3d>	pointROICoordinates(ij.plugin.frame.RoiManager manager)	Gets the coordinates of all point ROIs in the manager.
static boolean	roiManagerIsEmpty()	Determine whether the ROI Manager is not active or has no entries
static net.imglib2.RandomAccessibleInterval<net.imglib2.type.logic.BitType>	unionMaskFromRoiManager(net.imglib2.RandomAccessibleInterval<?> xyView, int z1, int t1, int c1)	Build a 2D union mask (BitType) for the given XY view and (z,t,c) plane using ROIs from the (visible) IJ1 RoiManager.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Details

isActiveOnAllSlices

public static boolean isActiveOnAllSlices(int sliceNumber)

Checks if a ROI is active on all slices.

Parameters:

sliceNumber - the slice number or z-position of the ROI.

Returns:

true if the ROI is not associated with a particular slide.

pointROICoordinates

public static List<org.joml.Vector3d> pointROICoordinates(ij.plugin.frame.RoiManager manager)

Gets the coordinates of all point ROIs in the manager.

NB z-coordinates start from 1. If a ROI is not associated with a slice, it's z = 0.

Parameters:

manager - an instance of RoiManager.

Returns:

point ROI coordinates.

roiManagerIsEmpty

public static boolean roiManagerIsEmpty()

Determine whether the ROI Manager is not active or has no entries

Returns:

true if there are no ROIs to process

unionMaskFromRoiManager

public static net.imglib2.RandomAccessibleInterval<net.imglib2.type.logic.BitType> unionMaskFromRoiManager(net.imglib2.RandomAccessibleInterval<?> xyView,
 int z1,
 int t1,
 int c1)

Build a 2D union mask (BitType) for the given XY view and (z,t,c) plane using ROIs from the (visible) IJ1 RoiManager. The returned mask is aligned to the view's interval.

Parameters:

xyView - 2D view (may have non-zero min).

z1 - 1-based Z position (IJ1 convention)

t1 - 1-based T position (IJ1 convention)

c1 - 1-based C position (IJ1 convention)

Returns:

a BitType mask that represents all the ROIs active on this XY slice or null if the ROI Manager is null or empty, or if there are no ROIs active on this XY slice.