/*
* #%L
* ImgLib2: a general-purpose, multidimensional image processing library.
* %%
* Copyright (C) 2009 - 2014 Stephan Preibisch, Tobias Pietzsch, Barry DeZonia,
* Stephan Saalfeld, Albert Cardona, Curtis Rueden, Christian Dietz, Jean-Yves
* Tinevez, Johannes Schindelin, Lee Kamentsky, Larry Lindsey, Grant Harris,
* Mark Hiner, Aivar Grislis, Martin Horn, Nick Perry, Michael Zinsmaier,
* Steffen Jaensch, Jan Funke, Mark Longair, and Dimiter Prodanov.
* %%
* 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.array;
import net.imglib2.Cursor;
import net.imglib2.FlatIterationOrder;
import net.imglib2.Interval;
import net.imglib2.img.AbstractNativeImg;
import net.imglib2.img.Img;
import net.imglib2.type.NativeType;
import net.imglib2.util.Fraction;
import net.imglib2.util.IntervalIndexer;
import net.imglib2.util.Intervals;
import net.imglib2.view.iteration.SubIntervalIterable;
/**
* This {@link Img} stores an image in a single linear array of basic types. By
* that, it provides the fastest possible access to data while limiting the
* number of basic types stored to {@link Integer#MAX_VALUE}. Keep in mind that
* this does not necessarily reflect the number of pixels, because a pixel can
* be stored in less than or more than a basic type entry.
*
* @param <T>
* @param <A>
*
* @author Stephan Preibisch
* @author Stephan Saalfeld
* @author Stephan Saalfeld <saalfeld@mpi-cbg.de>
*/
public class ArrayImg< T extends NativeType< T >, A > extends AbstractNativeImg< T, A > implements SubIntervalIterable< T >
{
final int[] steps, dim;
// the DataAccess created by the ArrayContainerFactory
final private A data;
/**
* TODO check for the size of numPixels being < Integer.MAX_VALUE? TODO Type
* is suddenly not necessary anymore
*
* @param factory
* @param data
* @param dim
* @param entitiesPerPixel
*/
public ArrayImg( final A data, final long[] dim, final Fraction entitiesPerPixel )
{
super( dim, entitiesPerPixel );
this.dim = new int[ n ];
for ( int d = 0; d < n; ++d )
this.dim[ d ] = ( int ) dim[ d ];
this.steps = new int[ n ];
IntervalIndexer.createAllocationSteps( this.dim, this.steps );
this.data = data;
}
@Override
public A update( final Object o )
{
return data;
}
@Override
public ArrayCursor< T > cursor()
{
return new ArrayCursor< T >( this );
}
@Override
public ArrayLocalizingCursor< T > localizingCursor()
{
return new ArrayLocalizingCursor< T >( this );
}
@Override
public ArrayRandomAccess< T > randomAccess()
{
return new ArrayRandomAccess< T >( this );
}
@Override
public ArrayRandomAccess< T > randomAccess( final Interval interval )
{
return randomAccess();
}
@Override
public FlatIterationOrder iterationOrder()
{
return new FlatIterationOrder( this );
}
@Override
public ArrayImgFactory< T > factory()
{
return new ArrayImgFactory< T >();
}
@Override
public ArrayImg< T, ? > copy()
{
final ArrayImg< T, ? > copy = factory().create( dimension, firstElement().createVariable() );
final ArrayCursor< T > source = this.cursor();
final ArrayCursor< T > target = copy.cursor();
while ( source.hasNext() )
target.next().set( source.next() );
return copy;
}
/**
* {@inheritDoc}
*/
@Override
public Cursor< T > cursor( final Interval interval )
{
final int dimLength = fastCursorAvailable( interval );
assert dimLength > 0;
return new ArraySubIntervalCursor< T >( this, ( int ) offset( interval, dimLength ), ( int ) size( interval, dimLength ) );
}
private long size( final Interval interval, final int length )
{
long size = interval.dimension( 0 );
for ( int d = 1; d < length; ++d )
{
size *= interval.dimension( d );
}
return size;
}
private long offset( final Interval interval, final int length )
{
final int maxDim = numDimensions() - 1;
long i = interval.min( maxDim );
for ( int d = maxDim - 1; d >= 0; --d )
{
i = i * dimension( d ) + interval.min( d );
}
return i;
}
/**
* If method returns -1 no fast cursor is available, else the amount of dims
* (starting from zero) which can be iterated fast are returned.
*/
private int fastCursorAvailable( final Interval interval )
{
// first check whether the interval is completely contained.
if ( !Intervals.contains( this, interval ) )
return -1;
// find the first dimension in which image and interval differ
int dimIdx = 0;
for ( ; dimIdx < n; ++dimIdx )
if ( interval.dimension( dimIdx ) != dimension( dimIdx ) )
break;
if ( dimIdx == n )
return dimIdx;
// in the dimension after that, image and interval may differ
++dimIdx;
// but image extents of all higher dimensions must equal 1
for ( int d = dimIdx; d < n; ++d )
if ( interval.dimension( d ) != 1 )
return -1;
return dimIdx;
}
/**
* {@inheritDoc}
*/
@Override
public Cursor< T > localizingCursor( final Interval interval )
{
final int dimLength = fastCursorAvailable( interval );
assert dimLength > 0;
return new ArrayLocalizingSubIntervalCursor< T >( this, ( int ) offset( interval, dimLength ), ( int ) size( interval, dimLength ) );
}
/**
* {@inheritDoc}
*/
@Override
public boolean supportsOptimizedCursor( final Interval interval )
{
return fastCursorAvailable( interval ) > 0;
}
/**
* {@inheritDoc}
*/
@Override
public Object subIntervalIterationOrder( final Interval interval )
{
return new FlatIterationOrder( interval );
}
}