Addition of getType() API

pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>34.0.0</version>
+		<version>37.0.0</version>
 		<relativePath />
 	</parent>
 
@@ -113,7 +113,7 @@ Jean-Yves Tinevez and Michael Zinsmaier.</license.copyrightOwners>
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
 		<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
 
-		<imglib2.version>6.1.0</imglib2.version>
+		<imglib2.version>7.0.0</imglib2.version>
 	</properties>
 
 	<dependencies>

src/main/java/net/imglib2/cache/IoSync.java

@@ -75,7 +75,7 @@
  * @param <V>
  *            value type
  * @param <D>
- *            value data type
+ *            value data type, see {@link CacheRemover}
  *
  * @author Tobias Pietzsch
  */

src/main/java/net/imglib2/cache/img/DiskCellCache.java

@@ -55,6 +55,7 @@
 import net.imglib2.cache.IoSync;
 import net.imglib2.img.cell.Cell;
 import net.imglib2.img.cell.CellGrid;
+import net.imglib2.img.cell.CellGrid.CellDimensionsAndSteps;
 import net.imglib2.util.Fraction;
 import net.imglib2.util.Intervals;
 
@@ -125,16 +126,14 @@ public Cell< A > get( final Long key ) throws Exception
 		if ( new File( filename ).exists() )
 		{
 			final long[] cellMin = new long[ n ];
-			final int[] cellDims = new int[ n ];
-			grid.getCellDimensions( index, cellMin, cellDims );
-			final long numEntities = entitiesPerPixel.mulCeil( Intervals.numElements( cellDims ) );
+			final CellDimensionsAndSteps dimsAndSteps = grid.getCellDimensions( index, cellMin );
+			final long numEntities = entitiesPerPixel.mulCeil( dimsAndSteps.numPixels() );
 			final long bytesize = numEntities * accessIo.getBytesPerElement();
-			try (
-					final RandomAccessFile mmFile = new RandomAccessFile( filename, "r" ); )
+			try ( final RandomAccessFile mmFile = new RandomAccessFile( filename, "r" ) )
 			{
 				final MappedByteBuffer in = mmFile.getChannel().map( MapMode.READ_ONLY, 0, bytesize );
 				final A access = accessIo.load( in, ( int ) numEntities );
-				return new Cell<>( cellDims, cellMin, access );
+				return new Cell<>( dimsAndSteps, cellMin, access );
 			}
 		}
 		else
@@ -154,9 +153,8 @@ public Cell< A > reconstruct( final Long key, final A valueData )
 	{
 		final long index = key;
 		final long[] cellMin = new long[ n ];
-		final int[] cellDims = new int[ n ];
-		grid.getCellDimensions( index, cellMin, cellDims );
-		return new Cell<>( cellDims, cellMin, valueData );
+		final CellDimensionsAndSteps dimsAndSteps = grid.getCellDimensions( index, cellMin );
+		return new Cell<>( dimsAndSteps, cellMin, valueData );
 	}
 
 	@Override

src/main/java/net/imglib2/cache/img/EmptyCellCacheLoader.java

@@ -41,10 +41,10 @@
 import net.imglib2.img.basictypeaccess.array.ArrayDataAccess;
 import net.imglib2.img.cell.Cell;
 import net.imglib2.img.cell.CellGrid;
+import net.imglib2.img.cell.CellGrid.CellDimensionsAndSteps;
 import net.imglib2.type.NativeType;
 import net.imglib2.type.PrimitiveType;
 import net.imglib2.util.Fraction;
-import net.imglib2.util.Intervals;
 
 /**
  * A {@link CacheLoader} that produces empty cells of {@link ArrayDataAccess}
@@ -84,10 +84,9 @@ public Cell< A > get( final Long key ) throws Exception
 	{
 		final long index = key;
 		final long[] cellMin = new long[ grid.numDimensions() ];
-		final int[] cellDims = new int[ grid.numDimensions() ];
-		grid.getCellDimensions( index, cellMin, cellDims );
-		final long numEntities = entitiesPerPixel.mulCeil( Intervals.numElements( cellDims ) );
-		return new Cell<>( cellDims, cellMin, creator.createArray( ( int ) numEntities ) );
+		final CellDimensionsAndSteps dimsAndSteps = grid.getCellDimensions( index, cellMin );
+		final long numEntities = entitiesPerPixel.mulCeil( dimsAndSteps.numPixels() );
+		return new Cell<>( dimsAndSteps, cellMin, creator.createArray( ( int ) numEntities ) );
 	}
 
 	public static < T extends NativeType< T >, A extends ArrayDataAccess< A > > EmptyCellCacheLoader< A > get(

src/main/java/net/imglib2/cache/img/LoadedCellCacheLoader.java

@@ -58,6 +58,7 @@
 import net.imglib2.img.basictypeaccess.array.ShortArray;
 import net.imglib2.img.cell.Cell;
 import net.imglib2.img.cell.CellGrid;
+import net.imglib2.img.cell.CellGrid.CellDimensionsAndSteps;
 import net.imglib2.type.NativeType;
 import net.imglib2.type.PrimitiveType;
 import net.imglib2.util.Fraction;
@@ -115,14 +116,13 @@ public Cell< A > get( final Long key ) throws Exception
 	{
 		final long index = key;
 		final long[] cellMin = new long[ grid.numDimensions() ];
-		final int[] cellDims = new int[ grid.numDimensions() ];
-		grid.getCellDimensions( index, cellMin, cellDims );
-		final long numEntities = entitiesPerPixel.mulCeil( Intervals.numElements( cellDims ) );
+		final CellDimensionsAndSteps dimsAndSteps = grid.getCellDimensions( index, cellMin );
+		final long numEntities = entitiesPerPixel.mulCeil( dimsAndSteps.numPixels() );
 		final A array = creator.createArray( ( int ) numEntities );
 		@SuppressWarnings( { "rawtypes", "unchecked" } )
-		final SingleCellArrayImg< T, ? > img = new SingleCellArrayImg( cellDims, cellMin, wrapper.wrap( array ), wrapper.wrapDirty( array ), type );
+		final SingleCellArrayImg< T, ? > img = new SingleCellArrayImg( dimsAndSteps.dimensions(), cellMin, wrapper.wrap( array ), wrapper.wrapDirty( array ), type );
 		loader.load( img );
-		return new Cell<>( cellDims, cellMin, array );
+		return new Cell<>( dimsAndSteps, cellMin, array );
 	}
 
 	public static < T extends NativeType< T >, A extends ArrayDataAccess< A > > LoadedCellCacheLoader< T, A > get(
@@ -143,7 +143,7 @@ public static < T extends NativeType< T >, A extends ArrayDataAccess< A > > Load
 	{
 		final A creator = ArrayDataAccessFactory.get( primitiveType, flags );
 		final ArrayDataAccessWrapper< A, ? > wrapper = getWrapper( primitiveType, flags );
-		return creator == null ? null : new LoadedCellCacheLoader<>( grid, type, creator, wrapper, loader );
+		return new LoadedCellCacheLoader<>( grid, type, creator, wrapper, loader );
 	}
 
 	@SuppressWarnings( "unchecked" )

src/main/java/net/imglib2/cache/img/RandomAccessibleCacheLoader.java

@@ -36,6 +36,7 @@
 import static net.imglib2.img.basictypeaccess.AccessFlags.DIRTY;
 import static net.imglib2.img.basictypeaccess.AccessFlags.VOLATILE;
 
+import java.util.Arrays;
 import java.util.Set;
 import java.util.function.Function;
 
@@ -78,11 +79,11 @@
 import net.imglib2.img.basictypeaccess.volatiles.array.VolatileShortArray;
 import net.imglib2.img.cell.Cell;
 import net.imglib2.img.cell.CellGrid;
+import net.imglib2.img.cell.CellGrid.CellDimensionsAndSteps;
 import net.imglib2.type.NativeType;
 import net.imglib2.type.PrimitiveType;
 import net.imglib2.type.NativeTypeFactory;
 import net.imglib2.util.Fraction;
-import net.imglib2.util.Intervals;
 import net.imglib2.view.Views;
 
 /**
@@ -151,22 +152,19 @@ public Cell< CA > get( final Long key ) throws Exception
 
 		final int n = grid.numDimensions();
 		final long[] cellMin = new long[ n ];
-		final int[] cellDims = new int[ n ];
 		final long[] cellMax = new long[ n ];
-
-		grid.getCellDimensions( index, cellMin, cellDims );
-		final long numEntities = entitiesPerPixel.mulCeil( Intervals.numElements( cellDims ) );
+		final CellDimensionsAndSteps dimsAndSteps = grid.getCellDimensions( index, cellMin );
+		Arrays.setAll( cellMax, d -> cellMin[ d ] + dimsAndSteps.dimensions()[ d ] - 1 );
+		final long numEntities = entitiesPerPixel.mulCeil( dimsAndSteps.numPixels() );
 		final A data = creator.createArray( ( int ) numEntities );
 		final T t = createType( data );
 		t.updateIndex( 0 );
-		for ( int d = 0; d < n; ++d )
-			cellMax[ d ] = cellMin[ d ] + cellDims[ d ] - 1;
 		for ( final T s : Views.interval( source, cellMin, cellMax ) )
 		{
 			t.set( s );
 			t.incIndex();
 		}
-		return new Cell<>( cellDims, cellMin, rewrap.apply( data ) );
+		return new Cell<>( dimsAndSteps, cellMin, rewrap.apply( data ) );
 	}
 
 	public static < T extends NativeType< T >, A extends ArrayDataAccess< A >, CA extends ArrayDataAccess< CA > > RandomAccessibleCacheLoader< T, A, CA > get(

src/main/java/net/imglib2/cache/img/SingleCellArrayImg.java

@@ -178,6 +178,12 @@ public RandomAccess< T > randomAccess( final Interval interval )
 		return randomAccess();
 	}
 
+	@Override
+	public T getType()
+	{
+		return linkedType;
+	}
+
 	class CellArrayRandomAccess extends AbstractLocalizable implements RandomAccess< T >
 	{
 		final T type;
@@ -208,6 +214,12 @@ public T get()
 			return type;
 		}
 
+		@Override
+		public T getType()
+		{
+			return type;
+		}
+
 		@Override
 		public void fwd( final int d )
 		{
@@ -363,6 +375,12 @@ public T get()
 			return type;
 		}
 
+		@Override
+		public T getType()
+		{
+			return type;
+		}
+
 		@Override
 		public boolean hasNext()
 		{
@@ -450,6 +468,12 @@ public T get()
 			return type;
 		}
 
+		@Override
+		public T getType()
+		{
+			return type;
+		}
+
 		@Override
 		public void fwd()
 		{

src/main/java/net/imglib2/cache/img/optional/AccessOptions.java

@@ -33,8 +33,10 @@
  */
 package net.imglib2.cache.img.optional;
 
+import java.util.Set;
 import java.util.function.BiConsumer;
 import net.imglib2.Dirty;
+import net.imglib2.img.basictypeaccess.AccessFlags;
 import org.scijava.optional.Options;
 import org.scijava.optional.Values;
 
@@ -67,6 +69,13 @@ default T volatileAccesses( final boolean volatil )
 		return setValue( "volatileAccesses", volatil );
 	}
 
+	default T accessFlags( final Set< AccessFlags > flags )
+	{
+		final boolean dirty = flags.contains( AccessFlags.DIRTY );
+		final boolean volatil = flags.contains( AccessFlags.VOLATILE );
+		return ( ( AccessOptions< T > ) dirtyAccesses( dirty ) ).volatileAccesses( volatil );
+	}
+
 	interface Val extends Values
 	{
 		default void forEach( BiConsumer< String, Object > action )

src/main/java/net/imglib2/cache/ref/GuardedStrongRefLoaderRemoverCache.java

@@ -72,6 +72,8 @@
  *            key type
  * @param <V>
  *            value type
+ * @param <D>
+ *            value data type, see {@link CacheRemover}
  *
  * @author Tobias Pietzsch
  */

src/main/java/net/imglib2/cache/util/IntervalKeyLoaderAsLongKeyLoader.java

@@ -33,8 +33,8 @@
  */
 package net.imglib2.cache.util;
 
+import java.util.Arrays;
 import java.util.function.Function;
-import java.util.stream.IntStream;
 
 import net.imglib2.FinalInterval;
 import net.imglib2.Interval;
@@ -79,10 +79,10 @@ public Cell< A > get( final Long key )
 
 		final int n = grid.numDimensions();
 		final long[] cellMin = new long[ n ];
-		final int[] cellDims = new int[ n ];
-		grid.getCellDimensions( index, cellMin, cellDims );
-		final long[] cellMax = IntStream.range( 0, n ).mapToLong( d -> cellMin[ d ] + cellDims[ d ] - 1 ).toArray();
-		final A result = intervalKeyLoader.apply( new FinalInterval( cellMin, cellMax ) );
-		return new Cell<>( cellDims, cellMin, result );
+		final long[] cellMax = new long[ n ];
+		final CellGrid.CellDimensionsAndSteps dimsAndSteps = grid.getCellDimensions( index, cellMin );
+		Arrays.setAll( cellMax, d -> cellMin[ d ] + dimsAndSteps.dimensions()[ d ] - 1 );
+		final A result = intervalKeyLoader.apply( FinalInterval.wrap( cellMin, cellMax ) );
+		return new Cell<>( dimsAndSteps, cellMin, result );
 	}
 }