ROIService (ImageJ2 Javadocs 0-SNAPSHOT API)

All Superinterfaces:

Comparable<Prioritized>, Contextual, Disposable, HasPluginInfo, Identifiable, ImageJService, Initializable, Locatable, Logged, Prioritized, RichPlugin, SciJavaPlugin, Service, Versioned

All Known Implementing Classes:

DefaultROIService, LegacyOMEROROIService
```
public interface ROIService
extends ImageJService
```
Service for working with Regions of Interest (ROI).

Author:

Alison Walter

Field Summary

Fields
Modifier and Type Field and Description

static String ROI_PROPERTY

Fields
Modifier and Type	Field and Description
`static String`	`ROI_PROPERTY`

Method Summary

All Methods Instance Methods Abstract Methods Default Methods
Modifier and Type	Method and Description
`default void`	`add(Object roi, Object img)` Attaches the given ROI to the given image
`default void`	`clear(Dataset img)` Clears all `MaskPredicate`s associated with the given `Dataset`
`default WritableBox`	`closedBox(double[] min, double[] max)` Creates a `WritableBox` with `closed` boundary behavior.
`default WritableEllipsoid`	`closedEllipsoid(double[] center, double[] semiAxisLengths)` Creates an `WritableEllipsoid` with `closed` boundary behavior.
`default WritablePolygon2D`	`closedPolygon2D(double[] x, double[] y)` Creates a `WritablePolygon2D` with `closed` boundary behavior.
`default WritablePolygon2D`	`closedPolygon2D(List<? extends RealLocalizable> vertices)` Creates a `WritablePolygon2D` with `closed` boundary behavior.
`default WritableSphere`	`closedSphere(double[] center, double radius)` Creates a `WritableSphere` with `closed` boundary behavior.
`default WritableSuperEllipsoid`	`closedSuperEllipsoid(double[] center, double[] semiAxisLengths, double exponent)` Creates a `WritableSuperEllipsoid` with `closed` boundary behavior.
`default ROITree`	`getROIs(Dataset img)` Returns the `ROITree` of the given `Dataset`
`default boolean`	`hasROIs(Object o)` Check if the given `Object` is or has ROIs
`default <L extends RealLocalizable> RealPointCollection<L>`	`kDTreeRealPointCollection(Collection<L> points)` Creates a read-only `RealPointCollection` containing the given points.
`default <L extends RealLocalizable> RealPointCollection<L>`	`kDTreeRealPointCollection(KDTree<L> tree)` Creates a read-only `RealPointCollection` containing the given points.
`default WritableLine`	`line(double[] pointOne, double[] pointTwo, boolean copy)` Creates a `WritableLine` with the given endpoints.
`default WritableLine`	`line(RealLocalizable pointOne, RealLocalizable pointTwo)` Creates a `WritableLine` with the given endpoints.
`default WritableBox`	`openBox(double[] min, double[] max)` Creates a `WritableBox` with `open` boundary behavior.
`default WritableEllipsoid`	`openEllipsoid(double[] center, double[] semiAxisLengths)` Creates an `WritableEllipsoid` with `open` boundary behavior.
`default WritablePolygon2D`	`openPolygon2D(double[] x, double[] y)` Creates a `WritablePolygon2D` with `open` boundary behavior.
`default WritablePolygon2D`	`openPolygon2D(List<? extends RealLocalizable> vertices)` Creates a `WritablePolygon2D` with `open` boundary behavior.
`default WritableSphere`	`openSphere(double[] center, double radius)` Creates a `WritableSphere` with `open` boundary behavior.
`default WritableSuperEllipsoid`	`openSuperEllipsoid(double[] center, double[] semiAxisLengths, double exponent)` Creates a `WritableSuperEllipsoid` with `open` boundary behavior.
`default WritablePointMask`	`pointMask(double[] point)` Creates a `WritablePointMask` at the given location.
`default WritablePointMask`	`pointMask(RealLocalizable point)` Creates a `WritablePointMask` at the given location.
`default WritablePolygon2D`	`polygon2D(double[] x, double[] y)` Creates a `WritablePolygon2D` with `unspecified` boundary behavior.
`default WritablePolygon2D`	`polygon2D(List<? extends RealLocalizable> vertices)` Creates a `WritablePolygon2D` with `unspecified` boundary behavior.
`default WritablePolyline`	`polyline(List<? extends RealLocalizable> vertices)` Creates a `WritablePolyline` containing the given vertices, in the given order.
`default <L extends RealLocalizable> WritableRealPointCollection<L>`	`realPointCollection(Collection<L> points)` Creates a `WritableRealPointCollection` containing the given points.
`default <L extends RealLocalizable> WritableRealPointCollection<L>`	`realPointCollection(HashMap<gnu.trove.list.array.TDoubleArrayList,L> points)` Creates a mutable `WritableRealPointCollection` containing the given points.
`default <L extends RealLocalizable> WritableRealPointCollection<L>`	`realPointSampleListRealPointCollection(Collection<L> points)` Creates a `WritableRealPointCollection` containing the given points.
`default <L extends RealLocalizable> WritableRealPointCollection<L>`	`realPointSampleListRealPointCollection(RealPointSampleList<L> points)` Creates a `WritableRealPointCollection` containing the given points.
`Mask`	`toMask(Object o)` Attempts to convert the given `Object` to a `Mask`
`MaskInterval`	`toMaskInterval(Object o)` Attempts to convert the given `Object` to a `MaskInterval`
`MaskPredicate<?>`	`toMaskPredicate(Object o)` Attempts to convert the given `Object` to a `MaskPredicate`.
`RandomAccessibleInterval<BoolType>`	`toRandomAccessibleInterval(Object o)` Attempts to convert the given `Object` to a `RandomAccessibleInterval<BoolType>`; otherwise, an exception is thrown.
`RandomAccessible<BoolType>`	`toRandomAcessible(Object o)` Attempts to convert the given `Object` to a `RandomAccessible<BoolType>`; otherwise, an exception is thrown.
`RealMask`	`toRealMask(Object o)` Attempts to convert the given `Object` to a `RealMask`
`RealMaskRealInterval`	`toRealMaskRealInterval(Object o)` Attempts to convert the given `Object` to a `RealMaskRealInterval`
`RealRandomAccessible<BoolType>`	`toRealRandomAccessible(Object o)` Attempts to convert the given `Object` to a `RealRandomAccessible`.
`RealRandomAccessibleRealInterval<BoolType>`	`toRealRandomAccessibleRealInterval(Object o)` Attempts to convert the given `Object` to a `RealRandomAccessibleRealInterval`.

Methods inherited from interface org.scijava.service.Service
initialize, registerEventHandlers

Methods inherited from interface org.scijava.plugin.RichPlugin
getIdentifier, log

Methods inherited from interface org.scijava.Contextual
context, getContext, setContext

Methods inherited from interface org.scijava.Prioritized
compareTo, getPriority, setPriority

Methods inherited from interface org.scijava.plugin.HasPluginInfo
getInfo, setInfo

Methods inherited from interface org.scijava.Locatable
getLocation

Methods inherited from interface org.scijava.Versioned
getVersion

Methods inherited from interface org.scijava.Disposable
dispose

- Field Detail
  - ROI_PROPERTY
```
static final String ROI_PROPERTY
```
    See Also:
    
    Constant Field Values
- Method Detail
  - getROIs
```
default ROITree getROIs(Dataset img)
```
    Returns the ROITree of the given Dataset
    
    Parameters:
    
    img - Dataset whose associated ROIs will be returned
    
    Returns:
    
    ROITree whose children are the associated ROIs as TreeNodes
  - add
```
default void add(Object roi,
                 Object img)
```
    Attaches the given ROI to the given image
    
    Parameters:
    
    roi - ROI (most likely MaskPredicate) to be attached
    
    img - image to attach ROI to
  - hasROIs
```
default boolean hasROIs(Object o)
```
    Check if the given Object is or has ROIs
    
    Parameters:
    
    o - Object to check
    
    Returns:
    
    true if it has or is a ROI, false otherwise
  - clear
```
default void clear(Dataset img)
```
    Clears all MaskPredicates associated with the given Dataset
    
    Parameters:
    
    img - Dataset whose rois will be cleared
  - toMask
```
Mask toMask(Object o)
```
    Attempts to convert the given Object to a Mask
    
    Parameters:
    
    o - the Object to be converted. This object should be something like an ImageJ 1.x Roi, RandomAccessible, etc.
    
    Returns:
    
    a Mask representation of the given object, if possible
  - toMaskInterval
```
MaskInterval toMaskInterval(Object o)
```
    Attempts to convert the given Object to a MaskInterval
    
    Parameters:
    
    o - the Object to be converted. This object should be something like an ImageJ 1.x Roi, RandomAccessibleInterval, etc.
    
    Returns:
    
    a MaskInterval representation of the given object, if possible
  - toRealMask
```
RealMask toRealMask(Object o)
```
    Attempts to convert the given Object to a RealMask
    
    Parameters:
    
    o - the Object to be converted. This object should be something like an ImageJ 1.x Roi, RealRandomAccessible, etc.
    
    Returns:
    
    a RealMask representation of the given object, if possible
  - toRealMaskRealInterval
```
RealMaskRealInterval toRealMaskRealInterval(Object o)
```
    Attempts to convert the given Object to a RealMaskRealInterval
    
    Parameters:
    
    o - the Object to be converted. This object should be something like an ImageJ 1.x Roi, RealRandomAccessibleRealInterval, etc.
    
    Returns:
    
    a RealMaskRealInterval representation of the given object, if possible
  - toMaskPredicate
```
MaskPredicate<?> toMaskPredicate(Object o)
```
    Attempts to convert the given Object to a MaskPredicate.
    
    Parameters:
    
    o - the Object to be converted. This object should be something like an ImageJ 1.x Roi, (Real)RandomAccessible, etc.
    
    Returns:
    
    a MaskPredicate representation of the given Object, if possible
  - toRandomAcessible
```
RandomAccessible<BoolType> toRandomAcessible(Object o)
```
    Attempts to convert the given Object to a RandomAccessible<BoolType>; otherwise, an exception is thrown.
    
    Parameters:
    
    o - the Object to be converted. In general, this should be an ImageJ 1.x Roi or an Imglib2 MaskPredicate.
    
    Returns:
    
    a RandomAccessible representation of the given Object
  - toRandomAccessibleInterval
```
RandomAccessibleInterval<BoolType> toRandomAccessibleInterval(Object o)
```
    Attempts to convert the given Object to a RandomAccessibleInterval<BoolType>; otherwise, an exception is thrown.
    
    Parameters:
    
    o - the Object to be converted. In general, this should be an ImageJ 1.x Roi or an ImgLib2 MaskPredicate.
    
    Returns:
    
    a RandomAccessibleInterval representation of the given Object
  - toRealRandomAccessible
```
RealRandomAccessible<BoolType> toRealRandomAccessible(Object o)
```
    Attempts to convert the given Object to a RealRandomAccessible.
    
    Parameters:
    
    o - the Object to be converted. In general, this should be an ImageJ 1.x Roi or an ImgLib2 MaskPredicate.
    
    Returns:
    
    a RealRandomAccessible representation of the given Object
  - toRealRandomAccessibleRealInterval
```
RealRandomAccessibleRealInterval<BoolType> toRealRandomAccessibleRealInterval(Object o)
```
    Attempts to convert the given Object to a RealRandomAccessibleRealInterval.
    
    Parameters:
    
    o - the Object to be converted. In general, this should be an ImageJ 1.x Roi or an ImgLib2 MaskPredicate.
    
    Returns:
    
    a RealRandomAccessibleRealInterval representation of the given Object
  - closedBox
```
default WritableBox closedBox(double[] min,
                              double[] max)
```
    Creates a WritableBox with closed boundary behavior.
    
    Parameters:
    
    min - the minimum position of the Box in each dimension
    
    max - the maximum position of the Box in each dimension
    
    Returns:
    
    a WritableBox with the given min/max
  - openBox
```
default WritableBox openBox(double[] min,
                            double[] max)
```
    Creates a WritableBox with open boundary behavior.
    
    Parameters:
    
    min - the minimum position of the Box in each dimension
    
    max - the maximum position of the Box in each dimension
    
    Returns:
    
    a WritableBox with the given min/max
  - closedEllipsoid
```
default WritableEllipsoid closedEllipsoid(double[] center,
                                          double[] semiAxisLengths)
```
    Creates an WritableEllipsoid with closed boundary behavior.
    
    Parameters:
    
    center - the position of the ellipsoid's center
    
    semiAxisLengths - the extension of the ellipsoid in each dimension
    
    Returns:
    
    an ellipsoid positioned at the given center with corresponding semi axis lengths
  - openEllipsoid
```
default WritableEllipsoid openEllipsoid(double[] center,
                                        double[] semiAxisLengths)
```
    Creates an WritableEllipsoid with open boundary behavior.
    
    Parameters:
    
    center - the position of the ellipsoid's center
    
    semiAxisLengths - the extension of the ellipsoid in each dimension
    
    Returns:
    
    an ellipsoid positioned at the given center with corresponding semi axis lengths
  - line
```
default WritableLine line(RealLocalizable pointOne,
                          RealLocalizable pointTwo)
```
    Creates a WritableLine with the given endpoints.
    
    Parameters:
    
    pointOne - position of the first endpoint of the line
    
    pointTwo - position of the second endpoint of the line
    
    Returns:
    
    a line with the given endpoints
  - line
```
default WritableLine line(double[] pointOne,
                          double[] pointTwo,
                          boolean copy)
```
    Creates a WritableLine with the given endpoints.
    
    Parameters:
    
    pointOne - position of the first endpoint of the line
    
    pointTwo - position of the second endpoint of the line
    
    copy - if true create copies are created and stored of the two arrays, if false arrays are just stored
    
    Returns:
    
    a line with the given endpoints
  - pointMask
```
default WritablePointMask pointMask(double[] point)
```
    Creates a WritablePointMask at the given location.
    
    Parameters:
    
    point - location of the point
    
    Returns:
    
    a point at the given location
  - pointMask
```
default WritablePointMask pointMask(RealLocalizable point)
```
    Creates a WritablePointMask at the given location.
    
    Parameters:
    
    point - location of the point
    
    Returns:
    
    a point at the given location
  - polygon2D
```
default WritablePolygon2D polygon2D(List<? extends RealLocalizable> vertices)
```
    Creates a WritablePolygon2D with unspecified boundary behavior.
    
    Parameters:
    
    vertices - a list containing the location of each vertex in 2D space
    
    Returns:
    
    a 2D polygon with the given vertices
  - polygon2D
```
default WritablePolygon2D polygon2D(double[] x,
                                    double[] y)
```
    Creates a WritablePolygon2D with unspecified boundary behavior.
    
    Parameters:
    
    x - the x-coordinates of the vertices
    
    y - the y-coordinates of the vertices
    
    Returns:
    
    a 2D polygon with the given vertices
  - closedPolygon2D
```
default WritablePolygon2D closedPolygon2D(List<? extends RealLocalizable> vertices)
```
    Creates a WritablePolygon2D with closed boundary behavior.
    
    Parameters:
    
    vertices - a list containing the location of each vertex in 2D space
    
    Returns:
    
    a 2D polygon with the given vertices
  - closedPolygon2D
```
default WritablePolygon2D closedPolygon2D(double[] x,
                                          double[] y)
```
    Creates a WritablePolygon2D with closed boundary behavior.
    
    Parameters:
    
    x - the x-coordinates of the vertices
    
    y - the y-coordinates of the vertices
    
    Returns:
    
    a 2D polygon with the given vertices
  - openPolygon2D
```
default WritablePolygon2D openPolygon2D(List<? extends RealLocalizable> vertices)
```
    Creates a WritablePolygon2D with open boundary behavior.
    
    Parameters:
    
    vertices - a list containing the location of each vertex in 2D space
    
    Returns:
    
    a 2D polygon with the given vertices
  - openPolygon2D
```
default WritablePolygon2D openPolygon2D(double[] x,
                                        double[] y)
```
    Creates a WritablePolygon2D with open boundary behavior.
    
    Parameters:
    
    x - the x-coordinates of the vertices
    
    y - the y-coordinates of the vertices
    
    Returns:
    
    a 2D polygon with the given vertices
  - polyline
```
default WritablePolyline polyline(List<? extends RealLocalizable> vertices)
```
    Creates a WritablePolyline containing the given vertices, in the given order.
    
    Parameters:
    
    vertices - contains the vertices of the polyline in order from start to end
    
    Returns:
    
    a polyline with the given vertices
  - realPointCollection
```
default <L extends RealLocalizable> WritableRealPointCollection<L> realPointCollection(HashMap<gnu.trove.list.array.TDoubleArrayList,L> points)
```
    Creates a mutable WritableRealPointCollection containing the given points.
    
    Parameters:
    
    points - contains the locations of the points in this collection
    
    Returns:
    
    a WritableRealPointCollection containing the given points
  - realPointCollection
```
default <L extends RealLocalizable> WritableRealPointCollection<L> realPointCollection(Collection<L> points)
```
    Creates a WritableRealPointCollection containing the given points.
    
    Parameters:
    
    points - contains the locations of the points in this collection
    
    Returns:
    
    a WritableRealPointCollection containing the given points
  - kDTreeRealPointCollection
```
default <L extends RealLocalizable> RealPointCollection<L> kDTreeRealPointCollection(KDTree<L> tree)
```
    Creates a read-only RealPointCollection containing the given points.
    
    Parameters:
    
    tree - a KDTree containing the location of each point in the collection
    
    Returns:
    
    a RealPointCollection containing the given points
  - kDTreeRealPointCollection
```
default <L extends RealLocalizable> RealPointCollection<L> kDTreeRealPointCollection(Collection<L> points)
```
    Creates a read-only RealPointCollection containing the given points.
    
    Parameters:
    
    points - contains the location of each point in the collection
    
    Returns:
    
    a RealPointCollection containing the given points
  - realPointSampleListRealPointCollection
```
default <L extends RealLocalizable> WritableRealPointCollection<L> realPointSampleListRealPointCollection(RealPointSampleList<L> points)
```
    Creates a WritableRealPointCollection containing the given points.
    
    Parameters:
    
    points - contains the locations of the points in the collection
    
    Returns:
    
    a WritableRealPointCollection containing the given points
  - realPointSampleListRealPointCollection
```
default <L extends RealLocalizable> WritableRealPointCollection<L> realPointSampleListRealPointCollection(Collection<L> points)
```
    Creates a WritableRealPointCollection containing the given points.
    
    Parameters:
    
    points - contains the locations of the points in the collection
    
    Returns:
    
    a WritableRealPointCollection containing the given points
  - closedSphere
```
default WritableSphere closedSphere(double[] center,
                                    double radius)
```
    Creates a WritableSphere with closed boundary behavior.
    
    Parameters:
    
    center - location of the center of the sphere
    
    radius - radius of the sphere
    
    Returns:
    
    a sphere with the given radius positioned at the given center
  - openSphere
```
default WritableSphere openSphere(double[] center,
                                  double radius)
```
    Creates a WritableSphere with open boundary behavior.
    
    Parameters:
    
    center - location of the center of the sphere
    
    radius - radius of the sphere
    
    Returns:
    
    a sphere with the given radius positioned at the given center
  - closedSuperEllipsoid
```
default WritableSuperEllipsoid closedSuperEllipsoid(double[] center,
                                                    double[] semiAxisLengths,
                                                    double exponent)
```
    Creates a WritableSuperEllipsoid with closed boundary behavior.
    
    Parameters:
    
    center - location of the center of the super-ellipsoid
    
    semiAxisLengths - extension of the super-ellipsoid in each dimensions
    
    exponent - exponent of the super-ellipsoid
    
    Returns:
    
    a super-ellipsoid with the given semi-axis lengths and exponent positioned at the given center
  - openSuperEllipsoid
```
default WritableSuperEllipsoid openSuperEllipsoid(double[] center,
                                                  double[] semiAxisLengths,
                                                  double exponent)
```
    Creates a WritableSuperEllipsoid with open boundary behavior.
    
    Parameters:
    
    center - location of the center of the super-ellipsoid
    
    semiAxisLengths - extension of the super-ellipsoid in each dimensions
    
    exponent - exponent of the super-ellipsoid
    
    Returns:
    
    a super-ellipsoid with the given semi-axis lengths and exponent positioned at the given center

Interface ROIService

Field Summary

Method Summary

Methods inherited from interface org.scijava.service.Service

Methods inherited from interface org.scijava.plugin.RichPlugin

Methods inherited from interface org.scijava.Contextual

Methods inherited from interface org.scijava.Prioritized

Methods inherited from interface org.scijava.plugin.HasPluginInfo

Methods inherited from interface org.scijava.Locatable

Methods inherited from interface org.scijava.Versioned

Methods inherited from interface org.scijava.Disposable

Field Detail

ROI_PROPERTY

Method Detail

getROIs

add

hasROIs

clear

toMask

toMaskInterval

toRealMask

toRealMaskRealInterval

toMaskPredicate

toRandomAcessible

toRandomAccessibleInterval

toRealRandomAccessible

toRealRandomAccessibleRealInterval

closedBox

openBox

closedEllipsoid

openEllipsoid

line

line

pointMask

pointMask

polygon2D

polygon2D

closedPolygon2D

closedPolygon2D

openPolygon2D

openPolygon2D

polyline

realPointCollection

realPointCollection

kDTreeRealPointCollection

kDTreeRealPointCollection

realPointSampleListRealPointCollection

realPointSampleListRealPointCollection

closedSphere

openSphere

closedSuperEllipsoid

openSuperEllipsoid