Merge remote-tracking branch 'github/janelia1' into janelia2

src/main/java/net/imglib2/type/volatiles/AbstractVolatileNativeNumericType.java

+/*
+ * #%L
+ * ImgLib2: a general-purpose, multidimensional image processing library.
+ * %%
+ * Copyright (C) 2009 - 2012 Stephan Preibisch, Stephan Saalfeld, Tobias
+ * Pietzsch, Albert Cardona, Barry DeZonia, Curtis Rueden, Lee Kamentsky, Larry
+ * Lindsey, Johannes Schindelin, Christian Dietz, Grant Harris, Jean-Yves
+ * Tinevez, Steffen Jaensch, Mark Longair, Nick Perry, and Jan Funke.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ *
+ * The views and conclusions contained in the software and documentation are
+ * those of the authors and should not be interpreted as representing official
+ * policies, either expressed or implied, of any organization.
+ * #L%
+ */
+
+package net.imglib2.type.volatiles;
+
+import net.imglib2.type.NativeType;
+import net.imglib2.type.numeric.NumericType;
+
+/**
+ * Abstract base class for {@link VolatileNumericType}s that wrap
+ * {@link NativeType native} {@link NumericType}s.
+ *
+ * @param <N>
+ *            wrapped {@link NativeType native} {@link NumericsType}.
+ * @param <T>
+ *            type of derived concrete class.
+ *
+ * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
+ * @author Stephan Saalfeld <saalfelds@janelia.hhmi.org>
+ */
+public abstract class AbstractVolatileNativeNumericType< N extends NumericType< N > & NativeType< N >, T extends AbstractVolatileNativeNumericType< N, T > >
+	extends AbstractVolatileNumericType< N, T >
+	implements NativeType< T >
+{
+	public AbstractVolatileNativeNumericType( final N t, final boolean valid )
+	{
+		super( t, valid );
+	}
+
+	@Override
+	public int getEntitiesPerPixel()
+	{
+		return t.getEntitiesPerPixel();
+	}
+
+	@Override
+	public void updateIndex( final int i )
+	{
+		t.updateIndex( i );
+	}
+
+	@Override
+	public int getIndex()
+	{
+		return t.getIndex();
+	}
+
+	@Override
+	public void incIndex()
+	{
+		t.incIndex();
+	}
+
+	@Override
+	public void incIndex( final int increment )
+	{
+		t.incIndex( increment );
+	}
+
+	@Override
+	public void decIndex()
+	{
+		t.decIndex();
+	}
+
+	@Override
+	public void decIndex( final int decrement )
+	{
+		t.decIndex( decrement );
+	}
+}

src/main/java/net/imglib2/type/volatiles/VolatileARGBType.java

+package net.imglib2.type.volatiles;
+
+import net.imglib2.Volatile;
+import net.imglib2.img.NativeImg;
+import net.imglib2.img.NativeImgFactory;
+import net.imglib2.img.basictypeaccess.IntAccess;
+import net.imglib2.img.basictypeaccess.volatiles.VolatileIntAccess;
+import net.imglib2.img.basictypeaccess.volatiles.VolatileShortAccess;
+import net.imglib2.img.basictypeaccess.volatiles.array.VolatileIntArray;
+import net.imglib2.type.numeric.ARGBType;
+import net.imglib2.type.numeric.integer.UnsignedShortType;
+
+/**
+ * A {@link Volatile} variant of {@link UnsignedShortType}. It uses an
+ * underlying {@link UnsignedShortType} that maps into a
+ * {@link VolatileShortAccess}.
+ *
+ * @author Stephan Saalfeld <saalfelds@janelia.hhmi.org>
+ * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
+ */
+public class VolatileARGBType extends AbstractVolatileNativeNumericType< ARGBType, VolatileARGBType >
+{
+	final protected NativeImg< ?, ? extends VolatileIntAccess > img;
+
+	private static class WrappedARGBType extends ARGBType
+	{
+		public WrappedARGBType( final NativeImg< ?, ? extends IntAccess > img )
+		{
+			super( img );
+		}
+		
+		public WrappedARGBType( final IntAccess access )
+		{
+			super( access );
+		}
+
+		public void setAccess( final IntAccess access )
+		{
+			dataAccess = access;
+		}
+	}
+
+	// this is the constructor if you want it to read from an array
+	public VolatileARGBType( final NativeImg< ?, ? extends VolatileIntAccess > img )
+	{
+		super( new WrappedARGBType( img ), false );
+		this.img = img;
+	}
+
+	// this is the constructor if you want to specify the dataAccess
+	public VolatileARGBType( final VolatileIntAccess access )
+	{
+		super( new WrappedARGBType( access ), access.isValid() );
+		this.img = null;
+	}
+
+	// this is the constructor if you want it to be a variable
+	public VolatileARGBType( final int value )
+	{
+		this( new VolatileIntArray( 1, true ) );
+		set( value );
+	}
+
+	// this is the constructor if you want it to be a variable
+	public VolatileARGBType()
+	{
+		this( 0 );
+	}
+
+	public void set( final int value )
+	{
+		get().set( value );
+	}
+
+	@Override
+	public void updateContainer( final Object c )
+	{
+		final VolatileIntAccess a = img.update( c );
+		( ( WrappedARGBType ) t ).setAccess( a );
+		setValid( a.isValid() );
+	}
+
+	@Override
+	public NativeImg< VolatileARGBType, ? extends VolatileIntAccess > createSuitableNativeImg( final NativeImgFactory< VolatileARGBType > storageFactory, final long[] dim )
+	{
+		throw new UnsupportedOperationException();
+	}
+
+	@Override
+	public VolatileARGBType duplicateTypeOnSameNativeImg()
+	{
+		return new VolatileARGBType( img );
+	}
+
+	@Override
+	public VolatileARGBType createVariable()
+	{
+		return new VolatileARGBType();
+	}
+
+	@Override
+	public VolatileARGBType copy()
+	{
+		final VolatileARGBType v = createVariable();
+		v.set( this );
+		return v;
+	}
+}

src/main/java/net/imglib2/type/volatiles/VolatileUnsignedShortType.java

@@ -25,6 +25,7 @@ public class VolatileUnsignedShortType extends AbstractVolatileNativeRealType< U
 		{
 			super( img );
 		}
+		
 		public WrappedUnsignedShortType( final ShortAccess access )
 		{
 			super( access );