diff --git a/pom.xml b/pom.xml index ce8b83c7..13ea5197 100644 --- a/pom.xml +++ b/pom.xml @@ -11,7 +11,7 @@ net.imglib2 imglib2-roi - 0.14.2-SNAPSHOT + 0.15.0-SNAPSHOT ImgLib2 ROI Regions of interest in ImgLib2. diff --git a/src/main/java/net/imglib2/roi/IterableRegion.java b/src/main/java/net/imglib2/roi/IterableRegion.java index 25d9785b..02d42c39 100644 --- a/src/main/java/net/imglib2/roi/IterableRegion.java +++ b/src/main/java/net/imglib2/roi/IterableRegion.java @@ -47,9 +47,10 @@ * i.e., it is assumed that all pixels outside the interval have value * {@code false}. *

- * Iterating only the pixels contained in the region is indicated by - * {@code IterableInterval}, i.e., when iterating, only the coordinates - * that are visited are interesting. There is no associated value. + * Iterating only the pixels contained in the region is done via the {@code + * IterableInterval} {@link #inside()}. (The pixel type is {@code Void} + * because, when iterating, only the coordinates that are visited are + * interesting. There is no associated value.) *

* We put interfaces {@code RandomAccessibleInterval}, extended by * {@code IterableRegion}, extended by @@ -62,5 +63,13 @@ * * @author Tobias Pietzsch */ -public interface IterableRegion< T extends BooleanType< T > > extends IterableInterval< Void >, RandomAccessibleInterval< T > -{} +public interface IterableRegion< T extends BooleanType< T > > extends RandomAccessibleInterval< T > +{ + /** + * Get an {@code IterableInterval} view of only the pixels contained in the + * region (having value {@code true}). + * + * @return iterable of the pixels in the region + */ + IterableInterval< Void > inside(); +} diff --git a/src/main/java/net/imglib2/roi/PositionableIterableInterval.java b/src/main/java/net/imglib2/roi/PositionableIterableInterval.java index 7655c3fc..629d8c26 100644 --- a/src/main/java/net/imglib2/roi/PositionableIterableInterval.java +++ b/src/main/java/net/imglib2/roi/PositionableIterableInterval.java @@ -74,7 +74,7 @@ public interface PositionableIterableInterval< T > extends IterableInterval< T > * * @return the origin to which the interval is relative. */ - public PositionableLocalizable origin(); + PositionableLocalizable origin(); /** * Make a copy of this {@link PositionableIterableInterval} which can be @@ -82,5 +82,5 @@ public interface PositionableIterableInterval< T > extends IterableInterval< T > * * @return a copy with an independent position */ - public PositionableIterableInterval< T > copy(); + PositionableIterableInterval< T > copy(); } diff --git a/src/main/java/net/imglib2/roi/PositionableIterableRegion.java b/src/main/java/net/imglib2/roi/PositionableIterableRegion.java index 45d187fe..0dcfdcae 100644 --- a/src/main/java/net/imglib2/roi/PositionableIterableRegion.java +++ b/src/main/java/net/imglib2/roi/PositionableIterableRegion.java @@ -33,11 +33,19 @@ */ package net.imglib2.roi; +import net.imglib2.Localizable; +import net.imglib2.Positionable; +import net.imglib2.roi.util.PositionableLocalizable; import net.imglib2.type.BooleanType; +import net.imglib2.type.logic.BitType; /** * An {@link IterableRegion} that can be moved around. *

+ * The iterable view of {@link #inside()} pixels can also be moved around. Its + * position is the same as the position of this {@code + * PositionableIterableRegion}. Moving one will also move the other. + *

* We put interfaces {@code RandomAccessibleInterval}, extended by * {@code IterableRegion}, extended by * {@code PositionableIterableRegion} into this sequence such that @@ -49,9 +57,48 @@ * * @author Tobias Pietzsch */ -public interface PositionableIterableRegion< T extends BooleanType< T > > - extends IterableRegion< T >, PositionableIterableInterval< Void > +public interface PositionableIterableRegion< T extends BooleanType< T > > extends IterableRegion< T >, Localizable, Positionable { + /** + * Get an {@code PositionableIterableInterval} view of only the pixels contained in the + * region (having value {@code true}). + *

+ * The position of the {@link #inside()} view is the same as the position of + * this {@code PositionableIterableRegion}. Moving one will also move the + * other. + * + * @return iterable of the pixels in the region + */ @Override - public PositionableIterableRegion< T > copy(); + PositionableIterableInterval< Void > inside(); + + /** + * Get the {@link Positionable}, {@link 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 {@link 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 {@link 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). + * + * @return the origin to which the interval is relative. + */ + PositionableLocalizable origin(); + + /** + * Make a copy of this {@link PositionableIterableInterval} which can be + * positioned independently. + * + * @return a copy with an independent position + */ + PositionableIterableRegion< T > copy(); } diff --git a/src/main/java/net/imglib2/roi/Regions.java b/src/main/java/net/imglib2/roi/Regions.java index bb2fc450..7c6396c4 100644 --- a/src/main/java/net/imglib2/roi/Regions.java +++ b/src/main/java/net/imglib2/roi/Regions.java @@ -60,6 +60,11 @@ public static < T > IterableInterval< T > sample( final IterableInterval< Void > return SamplingIterableInterval.create( region, img ); } + public static < T > IterableInterval< T > sample( final IterableRegion< ? > region, final RandomAccessible< T > img ) + { + return sample( region.inside(), img ); + } + /** * Given a mask and an image, return an {@link IterableInterval} over the * pixels of the image inside the mask. @@ -106,8 +111,7 @@ public static < T > IterableInterval< T > sample( final RealMaskRealInterval mas // NB: this method is not named "sample" to avoid ambiguation with sample(IterableInterval, RandomAccessible) public static < T, B extends BooleanType< B > > IterableInterval< T > sampleWithRandomAccessible( final RandomAccessible< B > mask, final RandomAccessibleInterval< T > img ) { - final IterableInterval< Void > region = iterable( Views.interval( mask, img ) ); - return sample( region, img ); + return sample( iterable( Views.interval( mask, img ) ), img ); } /** diff --git a/src/main/java/net/imglib2/roi/boundary/Boundary.java b/src/main/java/net/imglib2/roi/boundary/Boundary.java index fda6c718..489baf90 100644 --- a/src/main/java/net/imglib2/roi/boundary/Boundary.java +++ b/src/main/java/net/imglib2/roi/boundary/Boundary.java @@ -39,6 +39,7 @@ import net.imglib2.AbstractWrappedInterval; import net.imglib2.Cursor; import net.imglib2.Interval; +import net.imglib2.IterableInterval; import net.imglib2.Localizable; import net.imglib2.Point; import net.imglib2.RandomAccess; @@ -70,7 +71,8 @@ public final class Boundary< T extends BooleanType< T > > extends AbstractWrappedInterval< RandomAccessibleInterval< T > > implements IterableRegion< BoolType > { - public static enum StructuringElement + + public enum StructuringElement { FOUR_CONNECTED, EIGHT_CONNECTED @@ -84,6 +86,8 @@ public static enum StructuringElement private final int size; + private final BoundaryIterable inside; + public Boundary( final RandomAccessibleInterval< T > region ) { this( region, FOUR_CONNECTED ); @@ -108,56 +112,71 @@ public Boundary( final RandomAccessibleInterval< T > region, final StructuringEl break; } size = coords.size() / n; + inside = new BoundaryIterable(); } @Override - public long size() + public IterableInterval< Void > inside() { - return size; + return inside; } @Override - public Object iterationOrder() + public RandomAccess< BoolType > randomAccess() { - return this; + return structuringElement == FOUR_CONNECTED + ? new BoundaryRandomAccess4< T >( sourceInterval ) + : new BoundaryRandomAccess8< T >( sourceInterval ); } @Override - public BoundaryCursor cursor() + public RandomAccess< BoolType > randomAccess( final Interval interval ) { - return new BoundaryCursor(); + return randomAccess(); } - @Override - public BoundaryCursor localizingCursor() + final class BoundaryIterable extends AbstractWrappedInterval< Interval > implements IterableInterval< Void > { - return cursor(); - } + BoundaryIterable() + { + super( Boundary.this ); + } - @Override - public BoundaryCursor iterator() - { - return cursor(); - } + @Override + public long size() + { + return size; + } - @Override - public Void firstElement() - { - return cursor().next(); - } + @Override + public Object iterationOrder() + { + return this; + } - @Override - public RandomAccess< BoolType > randomAccess() - { - return structuringElement == FOUR_CONNECTED - ? new BoundaryRandomAccess4< T >( sourceInterval ) - : new BoundaryRandomAccess8< T >( sourceInterval ); - } + @Override + public BoundaryCursor cursor() + { + return new BoundaryCursor(); + } - @Override - public RandomAccess< BoolType > randomAccess( final Interval interval ) - { - return randomAccess(); + @Override + public BoundaryCursor localizingCursor() + { + return cursor(); + } + + @Override + public BoundaryCursor iterator() + { + return cursor(); + } + + @Override + public Void firstElement() + { + return cursor().next(); + } } final class BoundaryCursor extends Point implements Cursor< Void > @@ -246,7 +265,7 @@ static final class BoundaryConstructor< T extends BooleanType< T > > implements public BoundaryConstructor( final RandomAccessibleInterval< T > region, final StructuringElement structuringElement ) { - c = Regions.iterable( region ).localizingCursor(); + c = Regions.iterable( region ).inside().localizingCursor(); a = structuringElement == FOUR_CONNECTED ? new BoundaryRandomAccess4< T >( region ) : new BoundaryRandomAccess8< T >( region ); diff --git a/src/main/java/net/imglib2/roi/labeling/LabelRegion.java b/src/main/java/net/imglib2/roi/labeling/LabelRegion.java index 90c3ae93..6813e29d 100644 --- a/src/main/java/net/imglib2/roi/labeling/LabelRegion.java +++ b/src/main/java/net/imglib2/roi/labeling/LabelRegion.java @@ -35,6 +35,7 @@ import java.util.ArrayList; +import net.imglib2.AbstractWrappedPositionableLocalizable; import net.imglib2.FinalInterval; import net.imglib2.Interval; import net.imglib2.Positionable; @@ -44,6 +45,7 @@ import net.imglib2.RealPositionable; import net.imglib2.outofbounds.OutOfBounds; import net.imglib2.outofbounds.OutOfBoundsConstantValue; +import net.imglib2.roi.PositionableIterableInterval; import net.imglib2.roi.PositionableIterableRegion; import net.imglib2.roi.labeling.LabelRegions.LabelRegionProperties; import net.imglib2.roi.util.PositionableInterval; @@ -82,17 +84,19 @@ public class LabelRegion< T > extends PositionableInterval implements Positionab private int expectedGeneration; + private final LabelRegionIterable inside; + public LabelRegion( final LabelRegions< T > regions, final LabelRegionProperties regionProperties, final T label ) { super( new FinalInterval( regionProperties.getBoundingBoxMin(), regionProperties.getBoundingBoxMax() ) ); this.regions = regions; this.regionProperties = regionProperties; this.label = label; - expectedGeneration = regionProperties.update(); size = regionProperties.getSize(); itcodes = regionProperties.getItcodes(); centerOfMass = RealPoint.wrap( regionProperties.getCenterOfMass() ); + inside = new LabelRegionIterable(); } /** @@ -108,6 +112,7 @@ protected LabelRegion( final LabelRegion< T > other ) this.size = other.size; this.itcodes = other.itcodes; this.centerOfMass = other.centerOfMass; + this.inside = new LabelRegionIterable(); } /** @@ -117,6 +122,7 @@ protected LabelRegion( final LabelRegion< T > other ) * * @return an independent copy of this {@link LabelRegion}. */ + @Override public LabelRegion< T > copy() { return new LabelRegion<>( this ); @@ -175,41 +181,84 @@ public RandomAccess< BoolType > randomAccess( final Interval interval ) } @Override - public LabelRegionCursor cursor() + public PositionableIterableInterval< Void > inside() { - update(); - return new LabelRegionCursor( itcodes, currentOffset ); + return inside; } - @Override - public LabelRegionCursor localizingCursor() + class LabelRegionIterable extends AbstractWrappedPositionableLocalizable< LabelRegion > implements PositionableIterableInterval< Void > { - return cursor(); - } + LabelRegionIterable() + { + super( LabelRegion.this ); + } - @Override - public long size() - { - update(); - return size; - } + @Override + public LabelRegionCursor cursor() + { + update(); + return new LabelRegionCursor( itcodes, currentOffset ); + } - @Override - public Void firstElement() - { - return null; - } + @Override + public LabelRegionCursor localizingCursor() + { + return cursor(); + } - @Override - public Object iterationOrder() - { - return this; + @Override + public long size() + { + return LabelRegion.this.size(); + } + + @Override + public Void firstElement() + { + return null; + } + + @Override + public Object iterationOrder() + { + return this; + } + + @Override + public LabelRegionCursor iterator() + { + return cursor(); + } + + @Override + public PositionableLocalizable origin() + { + return LabelRegion.this.origin(); + } + + @Override + public PositionableIterableInterval< Void > copy() + { + return LabelRegion.this.copy().inside(); + } + + @Override + public long min( final int d ) + { + return LabelRegion.this.min( d ); + } + + @Override + public long max( final int d ) + { + return LabelRegion.this.max( d ); + } } - @Override - public LabelRegionCursor iterator() + public long size() { - return cursor(); + update(); + return size; } @Override diff --git a/src/main/java/net/imglib2/roi/util/IterableRandomAccessibleRegion.java b/src/main/java/net/imglib2/roi/util/IterableRandomAccessibleRegion.java index 0a521e82..e805d49a 100644 --- a/src/main/java/net/imglib2/roi/util/IterableRandomAccessibleRegion.java +++ b/src/main/java/net/imglib2/roi/util/IterableRandomAccessibleRegion.java @@ -54,6 +54,8 @@ * {@link Cursor Cursors} are realized by wrapping source {@link RandomAccess * RandomAccesses} (using {@link RandomAccessibleRegionCursor}). * + * @deprecated Use {@code IterableRegionOnBooleanRAI} instead. + * * @author Tobias Pietzsch */ @Deprecated @@ -62,6 +64,8 @@ public class IterableRandomAccessibleRegion< T extends BooleanType< T > > { final long size; + private final InsideIterable inside; + public static < T extends BooleanType< T > > IterableRandomAccessibleRegion< T > create( final RandomAccessibleInterval< T > interval ) { return new IterableRandomAccessibleRegion<>( interval, Regions.countTrue( interval ) ); @@ -71,55 +75,70 @@ public IterableRandomAccessibleRegion( final RandomAccessibleInterval< T > inter { super( interval ); this.size = size; + inside = new InsideIterable(); } @Override - public long size() + public RandomAccess< T > randomAccess() { - return size; + return sourceInterval.randomAccess(); } @Override - public Void firstElement() + public RandomAccess< T > randomAccess( final Interval interval ) { - if ( size() == 0 ) - throw new NoSuchElementException(); - return cursor().next(); + return sourceInterval.randomAccess( interval ); } @Override - public Object iterationOrder() + public IterableInterval< Void > inside() { - return this; + return inside; } - @Override - public Iterator< Void > iterator() + class InsideIterable extends AbstractWrappedInterval< Interval > implements IterableInterval< Void > { - return cursor(); - } + InsideIterable() + { + super( IterableRandomAccessibleRegion.this.sourceInterval ); + } - @Override - public Cursor< Void > cursor() - { - return new RandomAccessibleRegionCursor<>( sourceInterval, size ); - } + @Override + public long size() + { + return size; + } - @Override - public Cursor< Void > localizingCursor() - { - return cursor(); - } + @Override + public Void firstElement() + { + if ( size() == 0 ) + throw new NoSuchElementException(); + return cursor().next(); + } - @Override - public RandomAccess< T > randomAccess() - { - return sourceInterval.randomAccess(); - } + @Override + public Object iterationOrder() + { + return this; + } - @Override - public RandomAccess< T > randomAccess( final Interval interval ) - { - return sourceInterval.randomAccess( interval ); + @Override + public Iterator< Void > iterator() + { + return cursor(); + } + + @Override + public Cursor< Void > cursor() + { + return new RandomAccessibleRegionCursor<>( IterableRandomAccessibleRegion.this.sourceInterval, size ); + } + + @Override + public Cursor< Void > localizingCursor() + { + return cursor(); + } } } diff --git a/src/main/java/net/imglib2/roi/util/IterableRegionOnBooleanRAI.java b/src/main/java/net/imglib2/roi/util/IterableRegionOnBooleanRAI.java index 51d1a130..d5c449f0 100644 --- a/src/main/java/net/imglib2/roi/util/IterableRegionOnBooleanRAI.java +++ b/src/main/java/net/imglib2/roi/util/IterableRegionOnBooleanRAI.java @@ -62,6 +62,8 @@ public class IterableRegionOnBooleanRAI< T extends BooleanType< T > > private final IterableInterval< T > sourceIterable; + private final InsideIterable inside; + public IterableRegionOnBooleanRAI( final RandomAccessibleInterval< T > interval ) { this( interval, Regions.countTrue( interval ) ); @@ -72,55 +74,70 @@ public IterableRegionOnBooleanRAI( final RandomAccessibleInterval< T > interval, super( interval ); this.size = size; sourceIterable = Views.iterable( interval ); + inside = new InsideIterable(); } @Override - public long size() + public RandomAccess< T > randomAccess() { - return size; + return sourceInterval.randomAccess(); } @Override - public Void firstElement() + public RandomAccess< T > randomAccess( final Interval interval ) { - if ( size() == 0 ) - throw new NoSuchElementException(); - return cursor().next(); + return sourceInterval.randomAccess( interval ); } @Override - public Object iterationOrder() + public IterableInterval< Void > inside() { - return this; + return inside; } - @Override - public Iterator< Void > iterator() + class InsideIterable extends AbstractWrappedInterval< Interval > implements IterableInterval< Void > { - return cursor(); - } + InsideIterable() + { + super( IterableRegionOnBooleanRAI.this ); + } - @Override - public Cursor< Void > cursor() - { - return new TrueCursor< T >( sourceIterable.cursor(), size ); - } + @Override + public long size() + { + return size; + } - @Override - public Cursor< Void > localizingCursor() - { - return new TrueCursor< T >( sourceIterable.localizingCursor(), size ); - } + @Override + public Void firstElement() + { + if ( size() == 0 ) + throw new NoSuchElementException(); + return cursor().next(); + } - @Override - public RandomAccess< T > randomAccess() - { - return sourceInterval.randomAccess(); - } + @Override + public Object iterationOrder() + { + return this; + } - @Override - public RandomAccess< T > randomAccess( final Interval interval ) - { - return sourceInterval.randomAccess( interval ); + @Override + public Iterator< Void > iterator() + { + return cursor(); + } + + @Override + public Cursor< Void > cursor() + { + return new TrueCursor< T >( sourceIterable.cursor(), size ); + } + + @Override + public Cursor< Void > localizingCursor() + { + return new TrueCursor< T >( sourceIterable.localizingCursor(), size ); + } } } diff --git a/src/main/java/net/imglib2/roi/util/PositionableWrappedIterableInterval.java b/src/main/java/net/imglib2/roi/util/PositionableWrappedIterableInterval.java index 90c5767a..b33d4a14 100644 --- a/src/main/java/net/imglib2/roi/util/PositionableWrappedIterableInterval.java +++ b/src/main/java/net/imglib2/roi/util/PositionableWrappedIterableInterval.java @@ -51,6 +51,7 @@ * @author Tobias Pietzsch * @author Christian Dietz */ +@Deprecated public class PositionableWrappedIterableInterval< T, S extends IterableInterval< T > > extends PositionableInterval implements PositionableIterableInterval< T > @@ -151,13 +152,7 @@ public T next() @Override public PositionableIterableIntervalCursor copy() { - return new PositionableIterableIntervalCursor( source.copyCursor() ); - } - - @Override - public PositionableIterableIntervalCursor copyCursor() - { - return copy(); + return new PositionableIterableIntervalCursor( source.copy() ); } } diff --git a/src/main/java/net/imglib2/roi/util/PositionableWrappedIterableRegion.java b/src/main/java/net/imglib2/roi/util/PositionableWrappedIterableRegion.java index 715c15be..2359d43a 100644 --- a/src/main/java/net/imglib2/roi/util/PositionableWrappedIterableRegion.java +++ b/src/main/java/net/imglib2/roi/util/PositionableWrappedIterableRegion.java @@ -33,9 +33,12 @@ */ package net.imglib2.roi.util; +import net.imglib2.AbstractWrappedPositionableLocalizable; +import net.imglib2.Cursor; import net.imglib2.Interval; import net.imglib2.RandomAccess; import net.imglib2.roi.IterableRegion; +import net.imglib2.roi.PositionableIterableInterval; import net.imglib2.roi.PositionableIterableRegion; import net.imglib2.type.BooleanType; import net.imglib2.util.Intervals; @@ -48,12 +51,25 @@ * pixel type of source */ public class PositionableWrappedIterableRegion< T extends BooleanType< T > > - extends PositionableWrappedIterableInterval< Void, IterableRegion< T > > + extends PositionableInterval implements PositionableIterableRegion< T > { + private final IterableRegion< T > source; + + private final PositionableWrappedIterableRegion< T >.InsideIterable inside; + public PositionableWrappedIterableRegion( final IterableRegion< T > source ) { super( source ); + this.source = source; + inside = new InsideIterable(); + } + + private PositionableWrappedIterableRegion( final PositionableWrappedIterableRegion< T > other ) + { + super( other.source ); + this.source = other.source; + inside = new InsideIterable(); } @Override @@ -84,19 +100,125 @@ public T get() @Override public RA copy() { - return new RA( source.copyRandomAccess(), offset ); + return new RA( source.copy(), offset ); + } + } + + @Override + public PositionableWrappedIterableRegion< T > copy() + { + return new PositionableWrappedIterableRegion<>( this ); + } + + @Override + public PositionableIterableInterval< Void > inside() + { + return inside; + } + + class InsideIterable extends AbstractWrappedPositionableLocalizable< PositionableWrappedIterableRegion< T > > implements PositionableIterableInterval< Void > + { + InsideIterable() + { + super( PositionableWrappedIterableRegion.this ); } @Override - public RA copyRandomAccess() + public PositionableLocalizable origin() { - return copy(); + return PositionableWrappedIterableRegion.this.origin(); + } + + @Override + public PositionableIterableInterval< Void > copy() + { + return PositionableWrappedIterableRegion.this.copy().inside(); + } + + @Override + public Cursor< Void > cursor() + { + return new PositionableInsideCursor( inside().cursor() ); + } + + @Override + public Cursor< Void > localizingCursor() + { + return new PositionableInsideCursor( inside().localizingCursor() ); + } + + @Override + public long size() + { + return inside().size(); + } + + @Override + public Object iterationOrder() + { + return this; + } + + @Override + public long min( final int d ) + { + return PositionableWrappedIterableRegion.this.min( d ); + } + + @Override + public long max( final int d ) + { + return PositionableWrappedIterableRegion.this.max( d ); } } - @Override - public PositionableWrappedIterableRegion< T > copy() + class PositionableInsideCursor extends OffsetLocalizable< Cursor< Void > > implements Cursor< Void > { - return new PositionableWrappedIterableRegion<>( this ); + public PositionableInsideCursor( final Cursor< Void > cursor ) + { + super( cursor, currentOffset ); + } + + @Override + public Void get() + { + return null; + } + + @Override + public void jumpFwd( final long steps ) + { + source.jumpFwd( steps ); + } + + @Override + public void fwd() + { + source.fwd(); + } + + @Override + public void reset() + { + source.reset(); + } + + @Override + public boolean hasNext() + { + return source.hasNext(); + } + + @Override + public Void next() + { + return source.next(); + } + + @Override + public PositionableInsideCursor copy() + { + return new PositionableInsideCursor( source.copy() ); + } } } diff --git a/src/test/java/net/imglib2/roi/util/IterableRandomAccessibleRegionBenchmarkTest.java b/src/test/java/net/imglib2/roi/util/IterableRandomAccessibleRegionBenchmarkTest.java index 396f9a26..0cea94c1 100644 --- a/src/test/java/net/imglib2/roi/util/IterableRandomAccessibleRegionBenchmarkTest.java +++ b/src/test/java/net/imglib2/roi/util/IterableRandomAccessibleRegionBenchmarkTest.java @@ -101,7 +101,7 @@ public void testIterating() { for ( final IterableRegion< BitType > region : regions ) { - final Cursor< Void > cursor = region.cursor(); + final Cursor< Void > cursor = region.inside().cursor(); while ( cursor.hasNext() ) cursor.fwd(); } diff --git a/src/test/java/net/imglib2/roi/util/IterableRegionOnBooleanRAIBenchmark.java b/src/test/java/net/imglib2/roi/util/IterableRegionOnBooleanRAIBenchmark.java index 1b5f780b..bd037b0b 100644 --- a/src/test/java/net/imglib2/roi/util/IterableRegionOnBooleanRAIBenchmark.java +++ b/src/test/java/net/imglib2/roi/util/IterableRegionOnBooleanRAIBenchmark.java @@ -87,7 +87,7 @@ public void doSetup() @Benchmark public void testIterableRandomAccessibleRegion( MyState state ) { - final Cursor< Void > c = state.irOld.cursor(); + final Cursor< Void > c = state.irOld.inside().cursor(); while ( c.hasNext() ) { c.next(); @@ -97,7 +97,7 @@ public void testIterableRandomAccessibleRegion( MyState state ) @Benchmark public void testIterableRegionOnBooleanRAI( MyState state ) { - final Cursor< Void > c = state.ir.cursor(); + final Cursor< Void > c = state.ir.inside().cursor(); while ( c.hasNext() ) { c.next(); @@ -107,7 +107,7 @@ public void testIterableRegionOnBooleanRAI( MyState state ) @Benchmark public void testIterableRandomAccessibleRegionForNonIterableView( MyState state ) { - final Cursor< Void > c = state.irViewOld.cursor(); + final Cursor< Void > c = state.irViewOld.inside().cursor(); while ( c.hasNext() ) { c.next(); @@ -117,7 +117,7 @@ public void testIterableRandomAccessibleRegionForNonIterableView( MyState state @Benchmark public void testIterableRegionOnBooleanRAIForNonIterableView( MyState state ) { - final Cursor< Void > c = state.irView.cursor(); + final Cursor< Void > c = state.irView.inside().cursor(); while ( c.hasNext() ) { c.next(); diff --git a/src/test/java/net/imglib2/roi/util/IterableRegionOnBooleanRAITest.java b/src/test/java/net/imglib2/roi/util/IterableRegionOnBooleanRAITest.java index 0437d2f5..544fa422 100644 --- a/src/test/java/net/imglib2/roi/util/IterableRegionOnBooleanRAITest.java +++ b/src/test/java/net/imglib2/roi/util/IterableRegionOnBooleanRAITest.java @@ -93,7 +93,7 @@ public void testCursorFwd() { final long count = Regions.countTrue( img ); long countIR = 0; - final Cursor< Void > c = ir.cursor(); + final Cursor< Void > c = ir.inside().cursor(); while ( c.hasNext() ) { c.fwd(); @@ -107,7 +107,7 @@ public void testCursorFwd() public void testCursorNext() { final Cursor< BitType > imgC = img.cursor(); - final Cursor< Void > irC = ir.cursor(); + final Cursor< Void > irC = ir.inside().cursor(); while ( imgC.hasNext() ) { @@ -125,14 +125,14 @@ public void testCursorNext() public void testFirstElement() { // Ensure no error is thrown - assertTrue( ir.firstElement() == null ); + assertTrue( ir.inside().firstElement() == null ); } @Test public void testCursorFwdEmptyRegion() { int count = 0; - final Cursor< Void > c = empty.cursor(); + final Cursor< Void > c = empty.inside().cursor(); while ( c.hasNext() ) { c.fwd(); @@ -148,7 +148,7 @@ public void testCursorNextEmptyRegion() final long[] originalLocation = new long[ 2 ]; final long[] newLocation = new long[ 2 ]; - final Cursor< Void > c = empty.cursor(); + final Cursor< Void > c = empty.inside().cursor(); c.fwd(); c.localize( originalLocation ); c.next(); @@ -162,6 +162,6 @@ public void testCursorNextEmptyRegion() public void testCursorFirstElementEmptyRegion() { exception.expect( NoSuchElementException.class ); - empty.firstElement(); + empty.inside().firstElement(); } }