Merge pull request #208 from imglib/native-bool-type

Add the infrastructure for boolean[]-backed images

Author: tpietzsch

pom.xml

@@ -9,7 +9,7 @@
 	</parent>
 
 	<artifactId>imglib2</artifactId>
-	<version>5.5.1-SNAPSHOT</version>
+	<version>5.6.0-SNAPSHOT</version>
 
 	<name>ImgLib2 Core Library</name>
 	<description>A multidimensional, type-agnostic image processing library.</description>

src/main/java/net/imglib2/img/array/ArrayImgs.java

@@ -34,12 +34,14 @@
 
 package net.imglib2.img.array;
 
+import net.imglib2.img.basictypeaccess.BooleanAccess;
 import net.imglib2.img.basictypeaccess.ByteAccess;
 import net.imglib2.img.basictypeaccess.DoubleAccess;
 import net.imglib2.img.basictypeaccess.FloatAccess;
 import net.imglib2.img.basictypeaccess.IntAccess;
 import net.imglib2.img.basictypeaccess.LongAccess;
 import net.imglib2.img.basictypeaccess.ShortAccess;
+import net.imglib2.img.basictypeaccess.array.BooleanArray;
 import net.imglib2.img.basictypeaccess.array.ByteArray;
 import net.imglib2.img.basictypeaccess.array.DoubleArray;
 import net.imglib2.img.basictypeaccess.array.FloatArray;
@@ -48,6 +50,7 @@
 import net.imglib2.img.basictypeaccess.array.ShortArray;
 import net.imglib2.type.Type;
 import net.imglib2.type.logic.BitType;
+import net.imglib2.type.logic.NativeBoolType;
 import net.imglib2.type.numeric.ARGBType;
 import net.imglib2.type.numeric.complex.ComplexDoubleType;
 import net.imglib2.type.numeric.complex.ComplexFloatType;
@@ -348,6 +351,36 @@ final public static < A extends LongAccess > ArrayImg< LongType, A > longs( fina
 		return img;
 	}
 
+	/**
+	 * Create an {@link ArrayImg}&lt;{@link NativeBoolType}, {@link BooleanArray}&gt;.
+	 */
+	@SuppressWarnings( "unchecked" )
+	final static public ArrayImg< NativeBoolType, BooleanArray > booleans( final long... dim )
+	{
+		return ( ArrayImg< NativeBoolType, BooleanArray > ) new ArrayImgFactory<>( new NativeBoolType() ).create( dim );
+	}
+
+	/**
+	 * Creates an {@link ArrayImg}&lt;{@link NativeBoolType}, {@link BooleanArray}&gt;
+	 * reusing a passed byte[] array.
+	 */
+	final public static ArrayImg< NativeBoolType, BooleanArray > booleans( final boolean[] array, final long... dim )
+	{
+		return booleans( new BooleanArray( array ), dim );
+	}
+
+	/**
+	 * Creates an {@link ArrayImg}&lt;{@link NativeBoolType},
+	 * {@link BooleanAccess}&gt; using a {@link BooleanAccess} passed as argument.
+	 */
+	final public static < A extends BooleanAccess > ArrayImg< NativeBoolType, A > booleans( final A access, final long... dim )
+	{
+		final ArrayImg< NativeBoolType, A > img = new ArrayImg<>( access, dim, new Fraction() );
+		final NativeBoolType t = new NativeBoolType( img );
+		img.setLinkedType( t );
+		return img;
+	}
+
 	/**
 	 * Create an {@link ArrayImg}&lt;{@link BitType}, {@link LongArray}&gt;.
 	 */
@@ -357,6 +390,18 @@ final static public ArrayImg< BitType, LongArray > bits( final long... dim )
 		return ( ArrayImg< BitType, LongArray > ) new ArrayImgFactory<>( new BitType() ).create( dim );
 	}
 
+	/**
+	 * Creates an {@link ArrayImg}&lt;{@link NativeBoolType}, {@link LongAccess}&gt;
+	 * using a {@link LongAccess} passed as argument.
+	 */
+	final static public < A extends BooleanAccess > ArrayImg< NativeBoolType, A > bits( final A access, final long... dim )
+	{
+		final ArrayImg< NativeBoolType, A > img = new ArrayImg<>( access, dim, new Fraction( 1, 64 ) );
+		final NativeBoolType t = new NativeBoolType( img );
+		img.setLinkedType( t );
+		return img;
+	}
+
 	/**
 	 * Creates an {@link ArrayImg}&lt;{@link BitType}, {@link LongAccess}&gt;
 	 * using a {@link LongAccess} passed as argument.

src/main/java/net/imglib2/img/basictypeaccess/ArrayDataAccessFactory.java

@@ -39,8 +39,10 @@
 import java.util.Set;
 
 import net.imglib2.img.basictypeaccess.array.ArrayDataAccess;
+import net.imglib2.img.basictypeaccess.array.BooleanArray;
 import net.imglib2.img.basictypeaccess.array.ByteArray;
 import net.imglib2.img.basictypeaccess.array.CharArray;
+import net.imglib2.img.basictypeaccess.array.DirtyBooleanArray;
 import net.imglib2.img.basictypeaccess.array.DirtyByteArray;
 import net.imglib2.img.basictypeaccess.array.DirtyCharArray;
 import net.imglib2.img.basictypeaccess.array.DirtyDoubleArray;
@@ -53,13 +55,15 @@
 import net.imglib2.img.basictypeaccess.array.IntArray;
 import net.imglib2.img.basictypeaccess.array.LongArray;
 import net.imglib2.img.basictypeaccess.array.ShortArray;
+import net.imglib2.img.basictypeaccess.volatiles.array.DirtyVolatileBooleanArray;
 import net.imglib2.img.basictypeaccess.volatiles.array.DirtyVolatileByteArray;
 import net.imglib2.img.basictypeaccess.volatiles.array.DirtyVolatileCharArray;
 import net.imglib2.img.basictypeaccess.volatiles.array.DirtyVolatileDoubleArray;
 import net.imglib2.img.basictypeaccess.volatiles.array.DirtyVolatileFloatArray;
 import net.imglib2.img.basictypeaccess.volatiles.array.DirtyVolatileIntArray;
 import net.imglib2.img.basictypeaccess.volatiles.array.DirtyVolatileLongArray;
 import net.imglib2.img.basictypeaccess.volatiles.array.DirtyVolatileShortArray;
+import net.imglib2.img.basictypeaccess.volatiles.array.VolatileBooleanArray;
 import net.imglib2.img.basictypeaccess.volatiles.array.VolatileByteArray;
 import net.imglib2.img.basictypeaccess.volatiles.array.VolatileCharArray;
 import net.imglib2.img.basictypeaccess.volatiles.array.VolatileDoubleArray;
@@ -115,6 +119,14 @@ public static < A extends ArrayDataAccess< A > > A get(
 		final boolean volatil = flags.contains( VOLATILE );
 		switch ( primitiveType )
 		{
+		case BOOLEAN:
+			return dirty
+					? ( volatil
+							? ( A ) new DirtyVolatileBooleanArray( 0, true )
+							: ( A ) new DirtyBooleanArray( 0 ) )
+					: ( volatil
+							? ( A ) new VolatileBooleanArray( 0, true )
+							: ( A ) new BooleanArray( 0 ) );
 		case BYTE:
 			return dirty
 					? ( volatil

src/main/java/net/imglib2/img/basictypeaccess/BooleanAccess.java

@@ -0,0 +1,47 @@
+/*
+ * #%L
+ * ImgLib2: a general-purpose, multidimensional image processing library.
+ * %%
+ * Copyright (C) 2009 - 2018 Tobias Pietzsch, Stephan Preibisch, Stephan Saalfeld,
+ * John Bogovic, Albert Cardona, Barry DeZonia, Christian Dietz, Jan Funke,
+ * Aivar Grislis, Jonathan Hale, Grant Harris, Stefan Helfrich, Mark Hiner,
+ * Martin Horn, Steffen Jaensch, Lee Kamentsky, Larry Lindsey, Melissa Linkert,
+ * Mark Longair, Brian Northan, Nick Perry, Curtis Rueden, Johannes Schindelin,
+ * Jean-Yves Tinevez and Michael Zinsmaier.
+ * %%
+ * 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.
+ * #L%
+ */
+
+package net.imglib2.img.basictypeaccess;
+
+/**
+ * TODO
+ * 
+ * @author Curtis Rueden
+ */
+public interface BooleanAccess
+{
+	public boolean getValue( final int index );
+
+	public void setValue( final int index, final boolean value );
+}

src/main/java/net/imglib2/img/basictypeaccess/array/AbstractBooleanArray.java

@@ -0,0 +1,79 @@
+/*
+ * #%L
+ * ImgLib2: a general-purpose, multidimensional image processing library.
+ * %%
+ * Copyright (C) 2009 - 2018 Tobias Pietzsch, Stephan Preibisch, Stephan Saalfeld,
+ * John Bogovic, Albert Cardona, Barry DeZonia, Christian Dietz, Jan Funke,
+ * Aivar Grislis, Jonathan Hale, Grant Harris, Stefan Helfrich, Mark Hiner,
+ * Martin Horn, Steffen Jaensch, Lee Kamentsky, Larry Lindsey, Melissa Linkert,
+ * Mark Longair, Brian Northan, Nick Perry, Curtis Rueden, Johannes Schindelin,
+ * Jean-Yves Tinevez and Michael Zinsmaier.
+ * %%
+ * 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.
+ * #L%
+ */
+
+package net.imglib2.img.basictypeaccess.array;
+
+import net.imglib2.img.basictypeaccess.BooleanAccess;
+
+/**
+ *
+ * @author Curtis Rueden
+ */
+public abstract class AbstractBooleanArray< A extends AbstractBooleanArray< A > > implements BooleanAccess, ArrayDataAccess< A >
+{
+	protected boolean[] data;
+
+	public AbstractBooleanArray( final int numEntities )
+	{
+		this.data = new boolean[ numEntities ];
+	}
+
+	public AbstractBooleanArray( final boolean[] data )
+	{
+		this.data = data;
+	}
+
+	@Override
+	public boolean getValue( final int index )
+	{
+		return data[ index ];
+	}
+
+	@Override
+	public void setValue( final int index, final boolean value )
+	{
+		data[ index ] = value;
+	}
+
+	@Override
+	public boolean[] getCurrentStorageArray()
+	{
+		return data;
+	}
+
+	@Override
+	public int getArrayLength() {
+		return data.length;
+	}
+}

src/main/java/net/imglib2/img/basictypeaccess/array/BooleanArray.java

@@ -0,0 +1,58 @@
+/*
+ * #%L
+ * ImgLib2: a general-purpose, multidimensional image processing library.
+ * %%
+ * Copyright (C) 2009 - 2018 Tobias Pietzsch, Stephan Preibisch, Stephan Saalfeld,
+ * John Bogovic, Albert Cardona, Barry DeZonia, Christian Dietz, Jan Funke,
+ * Aivar Grislis, Jonathan Hale, Grant Harris, Stefan Helfrich, Mark Hiner,
+ * Martin Horn, Steffen Jaensch, Lee Kamentsky, Larry Lindsey, Melissa Linkert,
+ * Mark Longair, Brian Northan, Nick Perry, Curtis Rueden, Johannes Schindelin,
+ * Jean-Yves Tinevez and Michael Zinsmaier.
+ * %%
+ * 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.
+ * #L%
+ */
+
+package net.imglib2.img.basictypeaccess.array;
+
+/**
+ *
+ * @author Curtis Rueden
+ */
+public class BooleanArray extends AbstractBooleanArray< BooleanArray >
+{
+	public BooleanArray( final int numEntities )
+	{
+		super( numEntities );
+	}
+
+	public BooleanArray( final boolean[] data )
+	{
+		super( data );
+	}
+
+	@Override
+	public BooleanArray createArray( final int numEntities )
+	{
+		return new BooleanArray( numEntities );
+	}
+}

src/main/java/net/imglib2/img/basictypeaccess/array/DirtyBooleanArray.java

@@ -0,0 +1,81 @@
+/*
+ * #%L
+ * ImgLib2: a general-purpose, multidimensional image processing library.
+ * %%
+ * Copyright (C) 2009 - 2018 Tobias Pietzsch, Stephan Preibisch, Stephan Saalfeld,
+ * John Bogovic, Albert Cardona, Barry DeZonia, Christian Dietz, Jan Funke,
+ * Aivar Grislis, Jonathan Hale, Grant Harris, Stefan Helfrich, Mark Hiner,
+ * Martin Horn, Steffen Jaensch, Lee Kamentsky, Larry Lindsey, Melissa Linkert,
+ * Mark Longair, Brian Northan, Nick Perry, Curtis Rueden, Johannes Schindelin,
+ * Jean-Yves Tinevez and Michael Zinsmaier.
+ * %%
+ * 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.
+ * #L%
+ */
+
+package net.imglib2.img.basictypeaccess.array;
+
+import net.imglib2.Dirty;
+
+/**
+ *
+ * @author Curtis Rueden
+ */
+public class DirtyBooleanArray extends AbstractBooleanArray< DirtyBooleanArray > implements Dirty
+{
+	protected boolean dirty = false;
+
+	public DirtyBooleanArray( final int numEntities )
+	{
+		super( numEntities );
+	}
+
+	public DirtyBooleanArray( final boolean[] data )
+	{
+		super( data );
+	}
+
+	@Override
+	public void setValue( final int index, final boolean value )
+	{
+		dirty = true;
+		data[ index ] = value;
+	}
+
+	@Override
+	public DirtyBooleanArray createArray( final int numEntities )
+	{
+		return new DirtyBooleanArray( numEntities );
+	}
+
+	@Override
+	public boolean isDirty()
+	{
+		return dirty;
+	}
+
+	@Override
+	public void setDirty()
+	{
+		dirty = true;
+	}
+}