net.imglib2.roi.labeling

Class LabelRegion<T>

java.lang.Object

net.imglib2.AbstractEuclideanSpace

net.imglib2.AbstractLocalizable

net.imglib2.roi.util.PositionableInterval

net.imglib2.roi.labeling.LabelRegion<T>

Type Parameters:

T - the label type

All Implemented Interfaces:

Iterable<BoolType>, Dimensions, EuclideanSpace, Interval, IterableInterval<BoolType>, IterableRealInterval<BoolType>, Localizable, Positionable, RandomAccessible<BoolType>, RandomAccessibleInterval<BoolType>, RealInterval, RealLocalizable, IterableRegion<BoolType>, PositionableIterableRegion<BoolType>, Typed<BoolType>

public class LabelRegion<T>
extends PositionableInterval
implements PositionableIterableRegion<BoolType>

Present pixels of a given label in a ImgLabeling as a PositionableIterableRegion. The interval bounds represent the bounding box of all pixels having the label. If a RandomAccess is requested for an interval not fully contained in the bounding box, an OutOfBounds access is created with the value false for pixels outside the bounding box.

Author:

Tobias Pietzsch

Field Summary

Fields inherited from class net.imglib2.roi.util.PositionableInterval

currentOffset, initialMax, initialMin

Fields inherited from class net.imglib2.AbstractLocalizable

position

Fields inherited from class net.imglib2.AbstractEuclideanSpace

n

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	LabelRegion(LabelRegion<T> other) Copy constructor.
	LabelRegion(LabelRegions<T> regions, net.imglib2.roi.labeling.LabelRegions.LabelRegionProperties regionProperties, T label)

Method Summary

Modifier and Type	Method and Description
LabelRegion<T>	copy() Create a copy of this LabelRegion.
long	dimension(int d)
void	dimensions(long[] dimensions)
RealLocalizable	getCenterOfMass()
T	getLabel()
BoolType	getType()
PositionableIterableInterval<Void>	inside() Get an PositionableIterableInterval view of only the pixels contained in the region (having value true).
long	max(int d)
void	max(long[] max)
void	max(Positionable max)
long	min(int d)
void	min(long[] min)
void	min(Positionable min)
PositionableLocalizable	origin() Get the Positionable, Localizable origin of this interval.
LabelRegionRandomAccess<T>	randomAccess()
RandomAccess<BoolType>	randomAccess(Interval interval)
void	realMax(double[] max)
double	realMax(int d)
void	realMax(RealPositionable max)
void	realMin(double[] min)
double	realMin(int d)
void	realMin(RealPositionable min)

Methods inherited from class net.imglib2.roi.util.PositionableInterval

bck, fwd, move, move, move, move, move, setPosition, setPosition, setPosition, setPosition, setPosition, toString

Methods inherited from class net.imglib2.AbstractLocalizable

getDoublePosition, getFloatPosition, getIntPosition, getLongPosition, localize, localize, localize, localize

Methods inherited from class net.imglib2.AbstractEuclideanSpace

numDimensions

Methods inherited from class java.lang.Object

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

Methods inherited from interface net.imglib2.RandomAccessibleInterval

cursor, iterationOrder, localizingCursor, size

Methods inherited from interface net.imglib2.RandomAccessible

getAt, getAt, getAt

Methods inherited from interface net.imglib2.IterableInterval

localizingSpliterator, spliterator

Methods inherited from interface net.imglib2.IterableRealInterval

firstElement, iterator, parallelStream, stream

Methods inherited from interface java.lang.Iterable

forEach

Methods inherited from interface net.imglib2.Interval

maxAsLongArray, maxAsPoint, minAsLongArray, minAsPoint

Methods inherited from interface net.imglib2.RealInterval

maxAsDoubleArray, maxAsRealPoint, minAsDoubleArray, minAsRealPoint

Methods inherited from interface net.imglib2.Dimensions

allPositive, allPositive, dimensions, dimensionsAsLongArray, dimensionsAsPoint, verify, verify, verifyAllPositive, verifyAllPositive

Methods inherited from interface net.imglib2.EuclideanSpace

numDimensions

Methods inherited from interface net.imglib2.Localizable

getDoublePosition, getFloatPosition, getIntPosition, getLongPosition, localize, localize, localize, localize, positionAsLongArray, positionAsPoint

Methods inherited from interface net.imglib2.RealLocalizable

localize, localize, positionAsDoubleArray, positionAsRealPoint

Methods inherited from interface net.imglib2.Positionable

bck, fwd, move, move, move, move, move, setPosition, setPosition, setPosition, setPosition, setPosition

Constructor Detail

LabelRegion

public LabelRegion(LabelRegions<T> regions,
                   net.imglib2.roi.labeling.LabelRegions.LabelRegionProperties regionProperties,
                   T label)

LabelRegion

protected LabelRegion(LabelRegion<T> other)

Copy constructor.

Method Detail

copy

public LabelRegion<T> copy()

Create a copy of this LabelRegion. The copy can be independently positioned and its origin can be independently changed. All copies are linked to the original Labeling and reflect all changes.

Specified by:

copy in interface PositionableIterableRegion<BoolType>

Returns:

an independent copy of this LabelRegion.

origin

public PositionableLocalizable origin()

Description copied from class: PositionableInterval

Get the Positionable, Localizable origin of this interval.

The origin is the relative offset of the position to the minimum. For example if a positionable (bitmask) region is made from a BitType image with a circular pattern, then it is more natural if the region position refers to the center of the pattern instead of the upper left corner of the BitType image. This can be achieved by positioning the origin.

Assume a region is created from a 9x9 bitmask. The region initially has min=(0,0), max=(8,8), position=(0,0). Because both position and min are (0,0), initially origin=(0,0). Now assume the origin is moved to the center of the bitmask using origin().setPosition(new int[]{4,4}). After this, min=(-4,-4), max=(4,4), position=(0,0), and origin=(4,4).

Specified by:

origin in interface PositionableIterableRegion<BoolType>

Overrides:

origin in class PositionableInterval

Returns:

the origin to which the interval is relative.

getLabel

public T getLabel()

getCenterOfMass

public RealLocalizable getCenterOfMass()

randomAccess

public LabelRegionRandomAccess<T> randomAccess()

Specified by:

randomAccess in interface RandomAccessible<BoolType>

randomAccess

public RandomAccess<BoolType> randomAccess(Interval interval)

Specified by:

randomAccess in interface RandomAccessible<BoolType>

getType

public BoolType getType()

Specified by:

getType in interface IterableRealInterval<BoolType>

Specified by:

getType in interface Typed<BoolType>

inside

public PositionableIterableInterval<Void> inside()

Description copied from interface: PositionableIterableRegion

Get an PositionableIterableInterval view of only the pixels contained in the region (having value true).

The position of the PositionableIterableRegion.inside() view is the same as the position of this PositionableIterableRegion. Moving one will also move the other.

Specified by:

inside in interface IterableRegion<BoolType>

Specified by:

inside in interface PositionableIterableRegion<BoolType>

Returns:

iterable of the pixels in the region

realMin

public double realMin(int d)

Specified by:

realMin in interface Interval

Specified by:

realMin in interface RealInterval

Overrides:

realMin in class PositionableInterval

realMin

public void realMin(double[] min)

Specified by:

realMin in interface RealInterval

Overrides:

realMin in class PositionableInterval

realMin

public void realMin(RealPositionable min)

Specified by:

realMin in interface RealInterval

Overrides:

realMin in class PositionableInterval

realMax

public double realMax(int d)

Specified by:

realMax in interface Interval

Specified by:

realMax in interface RealInterval

Overrides:

realMax in class PositionableInterval

realMax

public void realMax(double[] max)

Specified by:

realMax in interface RealInterval

Overrides:

realMax in class PositionableInterval

realMax

public void realMax(RealPositionable max)

Specified by:

realMax in interface RealInterval

Overrides:

realMax in class PositionableInterval

min

public long min(int d)

Specified by:

min in interface Interval

Overrides:

min in class PositionableInterval

min

public void min(long[] min)

Specified by:

min in interface Interval

Overrides:

min in class PositionableInterval

min

public void min(Positionable min)

Specified by:

min in interface Interval

Overrides:

min in class PositionableInterval

max

public long max(int d)

Specified by:

max in interface Interval

Overrides:

max in class PositionableInterval

max

public void max(long[] max)

Specified by:

max in interface Interval

Overrides:

max in class PositionableInterval

max

public void max(Positionable max)

Specified by:

max in interface Interval

Overrides:

max in class PositionableInterval

dimensions

public void dimensions(long[] dimensions)

Specified by:

dimensions in interface Dimensions

Overrides:

dimensions in class PositionableInterval

dimension

public long dimension(int d)

Specified by:

dimension in interface Dimensions

Specified by:

dimension in interface Interval

Overrides:

dimension in class PositionableInterval