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* ImgLib2: a general-purpose, multidimensional image processing library.
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* John Bogovic, Albert Cardona, Barry DeZonia, Christian Dietz, Jan Funke,
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* Martin Horn, Steffen Jaensch, Lee Kamentsky, Larry Lindsey, Melissa Linkert,
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* Jean-Yves Tinevez and Michael Zinsmaier.
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package net.imglib2.view.iteration;
import java.util.Arrays;
import java.util.Iterator;
import net.imglib2.AbstractWrappedInterval;
import net.imglib2.Cursor;
import net.imglib2.FlatIterationOrder;
import net.imglib2.Interval;
import net.imglib2.IterableInterval;
import net.imglib2.RandomAccessible;
import net.imglib2.transform.integer.BoundingBox;
import net.imglib2.transform.integer.SlicingTransform;
import net.imglib2.util.Intervals;
import net.imglib2.view.IterableRandomAccessibleInterval;
import net.imglib2.view.TransformBuilder;
import net.imglib2.view.Views;
/**
* Simplifies View cascades to provide the most efficient {@link Cursor}.
*
* @see #getEfficientIterableInterval(Interval, RandomAccessible)
*
* @author Tobias Pietzsch
*/
public class IterableTransformBuilder< T > extends TransformBuilder< T >
{
/**
* Create an {@link IterableInterval} that iterates an {@link Interval} of a
* {@link RandomAccessible}. If possible, this should return an optimized
* cursor. If not, falls back to creating an
* {@link IterableRandomAccessibleInterval}.
*
* @param interval
* the interval of {@code randomAccessible} which should be
* iterated.
* @param randomAccessible
* the {@link RandomAccessible} that should be iterated.
* @return an {@link IterableInterval} that iterates {@code interval} of
* {@code randomAccessible}.
*/
public static < S > IterableInterval< S > getEfficientIterableInterval( final Interval interval, final RandomAccessible< S > randomAccessible )
{
return new IterableTransformBuilder< S >( interval, randomAccessible ).buildIterableInterval();
}
/**
* The interval which should be iterated.
*
*
* Currently, no transformations are done on this, because the cases where
* an optimized {@link IterableInterval} can be returned do not allow for
* any transformation except a single slicing. In the future, it may become
* necessary, to propagated the interval through the transforms down the
* view hierarchy.
*/
protected Interval interval;
/**
* Create a new IterableTransformBuilder. This calls the the super
* constructor to gather and simplify transformations.
*
* @param interval
* the interval of {@code randomAccessible} which should be
* iterated.
* @param randomAccessible
* the {@link RandomAccessible} that should be iterated.
*/
public IterableTransformBuilder( final Interval interval, final RandomAccessible< T > randomAccessible )
{
super( interval, randomAccessible );
this.interval = interval;
}
/**
* An {@link IterableInterval} on {@link IterableTransformBuilder#interval
* interval} of {@link SubIntervalIterable}.
*/
private class SubInterval extends AbstractWrappedInterval< Interval > implements IterableInterval< T >
{
final long numElements;
final SubIntervalIterable< T > iterableSource;
public SubInterval( final SubIntervalIterable< T > iterableSource )
{
super( interval );
numElements = Intervals.numElements( interval );
this.iterableSource = iterableSource;
}
@Override
public long size()
{
return numElements;
}
@Override
public T firstElement()
{
return cursor().next();
}
@Override
public Object iterationOrder()
{
return iterableSource.subIntervalIterationOrder( interval );
}
@Override
public Iterator< T > iterator()
{
return cursor();
}
@Override
public Cursor< T > cursor()
{
return iterableSource.cursor( interval );
}
@Override
public Cursor< T > localizingCursor()
{
return iterableSource.localizingCursor( interval );
}
}
/**
* An {@link IterableInterval} on a slice of a {@link SubIntervalIterable}.
*/
private class Slice extends AbstractWrappedInterval< Interval > implements IterableInterval< T >
{
final long numElements;
final SubIntervalIterable< T > iterableSource;
final Interval sourceInterval;
final SlicingTransform transformToSource;
final boolean hasFlatIterationOrder;
public Slice( final SubIntervalIterable< T > iterableSource, final Interval sourceInterval, final SlicingTransform transformToSource, final boolean hasFlatIterationOrder )
{
super( interval );
numElements = Intervals.numElements( interval );
this.iterableSource = iterableSource;
this.sourceInterval = sourceInterval;
this.transformToSource = transformToSource;
this.hasFlatIterationOrder = hasFlatIterationOrder;
}
@Override
public long size()
{
return numElements;
}
@Override
public T firstElement()
{
return cursor().next();
}
@Override
public Object iterationOrder()
{
return hasFlatIterationOrder ? new FlatIterationOrder( interval ) : this;
}
@Override
public Iterator< T > iterator()
{
return cursor();
}
@Override
public Cursor< T > cursor()
{
return new SlicingCursor< T >( iterableSource.cursor( sourceInterval ), transformToSource );
}
@Override
public Cursor< T > localizingCursor()
{
return new SlicingCursor< T >( iterableSource.localizingCursor( sourceInterval ), transformToSource );
}
}
/**
* Create an {@link IterableInterval} on the {@link Interval} specified in
* the constructor of the {@link RandomAccessible} specified in the
* constructor.
*/
public IterableInterval< T > buildIterableInterval()
{
if ( boundingBox != null && SubIntervalIterable.class.isInstance( source ) )
{
@SuppressWarnings( "unchecked" )
final SubIntervalIterable< T > iterableSource = ( SubIntervalIterable< T > ) source;
if ( transforms.isEmpty() )
{
if ( iterableSource.supportsOptimizedCursor( interval ) )
return new SubInterval( iterableSource );
}
else if ( transforms.size() == 1 && SlicingTransform.class.isInstance( transforms.get( 0 ) ) )
{
final SlicingTransform t = ( SlicingTransform ) transforms.get( 0 );
final int m = t.numTargetDimensions();
final int n = t.numSourceDimensions();
// Check whether the slicing can be potentially optimized.
boolean optimizable = true;
// 1.) Slice dimensions must be mapped to a contiguous range of
// target dimensions starting with dimension 0.
int firstZeroDim = 0;
for ( ; firstZeroDim < m && !t.getComponentZero( firstZeroDim ); ++firstZeroDim );
for ( int d = firstZeroDim + 1; d < m && optimizable; ++d )
if ( !t.getComponentZero( d ) )
optimizable = false;
// 2.) All slice dimensions must be mapped to a target dimension
final int[] sourceComponent = new int[ n ];
if ( optimizable )
{
Arrays.fill( sourceComponent, -1 );
for ( int d = 0; d < m; ++d )
if ( !t.getComponentZero( d ) )
sourceComponent[ t.getComponentMapping( d ) ] = d;
for ( int d = 0; d < n && optimizable; ++d )
if ( sourceComponent[ d ] < 0 )
optimizable = false;
}
if ( optimizable )
{
// System.out.println( "interval = " + Util.printInterval( interval ) );
final Interval sliceInterval = t.transform( new BoundingBox( interval ) ).getInterval();
// System.out.println( "transformed interval = " + Util.printInterval( sliceInterval ) );
if ( iterableSource.supportsOptimizedCursor( sliceInterval ) )
{
// check for FlatIterationOrder
boolean flat = FlatIterationOrder.class.isInstance( iterableSource.subIntervalIterationOrder( sliceInterval ) );
for ( int d = 0; d < n - 1; ++d )
if ( sourceComponent[ d + 1 ] <= sourceComponent[ d ] )
flat = false;
return new Slice( iterableSource, sliceInterval, t, flat );
}
}
}
}
return new IterableRandomAccessibleInterval< T >( Views.interval( build(), interval ) );
}
}