Add BlockProcessor.setTargetInterval(long[] pos, int[] size) with def…

…ault implementation
imglib · May 7, 2024 · c87ccee · c87ccee
1 parent aeb5385
commit c87ccee
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Showing 10 changed files with 116 additions and 38 deletions.
diff --git a/src/main/java/net/imglib2/algorithm/blocks/BlockAlgoUtils.java b/src/main/java/net/imglib2/algorithm/blocks/BlockAlgoUtils.java
@@ -85,6 +85,17 @@ CellLoader< T > cellLoader( final BlockSupplier< T > blocks )
 	}
 
 
+	// ======== INTERNAL ======================================================
+
+
+	static int safeInt( final long value )
+	{
+		if ( value > Integer.MAX_VALUE )
+			throw new IllegalArgumentException( "value too large" );
+		return ( int ) value;
+	}
+
+
 	// ======== DEPRECATED ====================================================
 
 
@@ -96,7 +107,7 @@ CellLoader< T > cellLoader( final PrimitiveBlocks< S > blocks, final UnaryBlockO
 	}
 
 	@Deprecated
-	public static < S extends NativeType< S >, T extends NativeType< T >, I, O >
+	public static < S extends NativeType< S >, T extends NativeType< T > >
 	CachedCellImg< T, ? > cellImg(
 			final PrimitiveBlocks< S > blocks,
 			final UnaryBlockOperator< S, T > operator,

diff --git a/src/main/java/net/imglib2/algorithm/blocks/BlockProcessor.java b/src/main/java/net/imglib2/algorithm/blocks/BlockProcessor.java
@@ -33,6 +33,9 @@
  */
 package net.imglib2.algorithm.blocks;
 
+import java.util.Arrays;
+
+import net.imglib2.FinalInterval;
 import net.imglib2.Interval;
 import net.imglib2.blocks.PrimitiveBlocks;
 
@@ -56,6 +59,13 @@ public interface BlockProcessor< I, O >
 
 	void setTargetInterval( Interval interval );
 
+	default void setTargetInterval( long[] srcPos, int[] size )
+	{
+		final long[] srcMax = new long[ srcPos.length ];
+		Arrays.setAll( srcMax, d -> srcPos[ d ] + size[ d ] - 1 );
+		setTargetInterval( FinalInterval.wrap( srcPos, srcMax ) );
+	}
+
 	long[] getSourcePos();
 
 	int[] getSourceSize();

diff --git a/src/main/java/net/imglib2/algorithm/blocks/BlockSupplier.java b/src/main/java/net/imglib2/algorithm/blocks/BlockSupplier.java
@@ -1,5 +1,6 @@
 package net.imglib2.algorithm.blocks;
 
+import static net.imglib2.algorithm.blocks.BlockAlgoUtils.safeInt;
 import static net.imglib2.blocks.PrimitiveBlocks.OnFallback.WARN;
 
 import java.util.Arrays;
@@ -61,7 +62,7 @@ default void copy( Interval interval, Object dest )
 	{
 		final long[] srcPos = interval.minAsLongArray();
 		final int[] size = new int[ srcPos.length ];
-		Arrays.setAll( size, d -> ( int ) interval.dimension( d ) );
+		Arrays.setAll( size, d -> safeInt( interval.dimension( d ) ) );
 		copy( srcPos, dest, size );
 	}
 
@@ -83,7 +84,7 @@ default void copy( Interval interval, Object dest )
 	 */
 	default < U extends NativeType< U > > BlockSupplier< U > andThen( UnaryBlockOperator< T, U > operator )
 	{
-		return new ConcatenatedBlockSupplier< U >( this.independentCopy(), operator.independentCopy() );
+		return new ConcatenatedBlockSupplier<>( this.independentCopy(), operator.independentCopy() );
 	}
 
 	/**
@@ -132,7 +133,7 @@ static < T extends NativeType< T > > BlockSupplier< T > of(
 	 * @return a {@code BlockSupplier} accessor for {@code ra}.
 	 * @param <T> pixel type
 	 */
-	static < T extends NativeType< T >, R extends NativeType< R > > BlockSupplier< T > of(
+	static < T extends NativeType< T > > BlockSupplier< T > of(
 			RandomAccessible< T > ra,
 			PrimitiveBlocks.OnFallback onFallback )
 	{

diff --git a/src/main/java/net/imglib2/algorithm/blocks/ConcatenatedBlockProcessor.java b/src/main/java/net/imglib2/algorithm/blocks/ConcatenatedBlockProcessor.java
@@ -33,7 +33,6 @@
  */
 package net.imglib2.algorithm.blocks;
 
-import java.util.function.Supplier;
 import net.imglib2.Interval;
 
 class ConcatenatedBlockProcessor< I, K, O > implements BlockProcessor< I, O >
@@ -42,8 +41,6 @@ class ConcatenatedBlockProcessor< I, K, O > implements BlockProcessor< I, O >
 
 	private final BlockProcessor< K, O > p1;
 
-	private Supplier< ConcatenatedBlockProcessor< I, K, O > > threadSafeSupplier;
-
 	public ConcatenatedBlockProcessor(
 			BlockProcessor< I, K > p0,
 			BlockProcessor< K, O > p1 )
@@ -65,6 +62,13 @@ public void setTargetInterval( final Interval interval )
 		p0.setTargetInterval( p1.getSourceInterval() );
 	}
 
+	@Override
+	public void setTargetInterval( final long[] srcPos, final int[] size )
+	{
+		p1.setTargetInterval( srcPos, size );
+		p0.setTargetInterval( p1.getSourcePos(), p1.getSourceSize() );
+	}
+
 	@Override
 	public long[] getSourcePos()
 	{

diff --git a/src/main/java/net/imglib2/algorithm/blocks/ConcatenatedBlockSupplier.java b/src/main/java/net/imglib2/algorithm/blocks/ConcatenatedBlockSupplier.java
@@ -1,10 +1,7 @@
 package net.imglib2.algorithm.blocks;
 
-import java.util.Arrays;
 import java.util.function.Supplier;
 
-import net.imglib2.FinalInterval;
-import net.imglib2.Interval;
 import net.imglib2.type.NativeType;
 import net.imglib2.util.Cast;
 import net.imglib2.util.CloseableThreadLocal;
@@ -44,20 +41,12 @@ public T getType()
 	@Override
 	public void copy( final long[] srcPos, final Object dest, final int[] size )
 	{
-//			p1.setTargetInterval( srcPos, size ); // TODO?
-		p1.setTargetInterval( interval( srcPos, size ) );
+		p1.setTargetInterval( srcPos, size );
 		final Object src = p1.getSourceBuffer();
 		p0.copy( p1.getSourcePos(), src, p1.getSourceSize() );
 		p1.compute( Cast.unchecked( src ), Cast.unchecked( dest ) );
 	}
 
-	private static Interval interval( long[] srcPos, int[] size )
-	{
-		final long[] srcMax = new long[ srcPos.length ];
-		Arrays.setAll( srcMax, d -> srcPos[ d ] + size[ d ] - 1 );
-		return FinalInterval.wrap( srcPos, srcMax );
-	}
-
 	@Override
 	public BlockSupplier< T > independentCopy()
 	{

diff --git a/src/main/java/net/imglib2/algorithm/blocks/convert/ConvertBlockProcessor.java b/src/main/java/net/imglib2/algorithm/blocks/convert/ConvertBlockProcessor.java
@@ -108,6 +108,20 @@ public void setTargetInterval( final Interval interval )
 		sourceLength = safeInt( Intervals.numElements( sourceSize ) );
 	}
 
+	@Override
+	public void setTargetInterval( final long[] pos, final int[] size )
+	{
+		final int n = pos.length;
+		if ( sourcePos == null || sourcePos.length != n )
+		{
+			sourcePos = new long[ n ];
+			sourceSize = new int[ n ];
+		}
+		System.arraycopy( pos, 0, sourcePos, 0, n );
+		System.arraycopy( size, 0, sourceSize, 0, n );
+		sourceLength = safeInt( Intervals.numElements( sourceSize ) );
+	}
+
 	private static int safeInt( final long value )
 	{
 		if ( value > Integer.MAX_VALUE )

diff --git a/src/main/java/net/imglib2/algorithm/blocks/convert/ConverterBlockProcessor.java b/src/main/java/net/imglib2/algorithm/blocks/convert/ConverterBlockProcessor.java
@@ -49,6 +49,7 @@
 import net.imglib2.img.NativeImg;
 import net.imglib2.type.NativeType;
 import net.imglib2.type.NativeTypeFactory;
+import net.imglib2.util.Cast;
 import net.imglib2.util.Intervals;
 
 /**
@@ -133,6 +134,20 @@ public void setTargetInterval( final Interval interval )
 		sourceLength = safeInt( Intervals.numElements( sourceSize ) );
 	}
 
+	@Override
+	public void setTargetInterval( final long[] pos, final int[] size )
+	{
+		final int n = pos.length;
+		if ( sourcePos == null || sourcePos.length != n )
+		{
+			sourcePos = new long[ n ];
+			sourceSize = new int[ n ];
+		}
+		System.arraycopy( pos, 0, sourcePos, 0, n );
+		System.arraycopy( size, 0, sourceSize, 0, n );
+		sourceLength = safeInt( Intervals.numElements( sourceSize ) );
+	}
+
 	private static int safeInt( final long value )
 	{
 		if ( value > Integer.MAX_VALUE )
@@ -201,8 +216,8 @@ private static class WrapperImpl< T extends NativeType< T >, A > extends Abstrac
 		WrapperImpl( T type )
 		{
 			super( new long[ 0 ] );
-			final NativeTypeFactory< T, A > nativeTypeFactory = ( NativeTypeFactory< T, A > ) type.getNativeTypeFactory();
-			props = ( PrimitiveTypeProperties< ?, A > ) PrimitiveTypeProperties.get( nativeTypeFactory.getPrimitiveType() );
+			final NativeTypeFactory< T, A > nativeTypeFactory = Cast.unchecked( type.getNativeTypeFactory() );
+			props = Cast.unchecked( PrimitiveTypeProperties.get( nativeTypeFactory.getPrimitiveType() ) );
 			wrapper = nativeTypeFactory.createLinkedType( this );
 		}
 

diff --git a/src/main/java/net/imglib2/algorithm/blocks/downsample/AbstractDownsample.java b/src/main/java/net/imglib2/algorithm/blocks/downsample/AbstractDownsample.java
@@ -58,7 +58,7 @@ abstract class AbstractDownsample< T extends AbstractDownsample< T, P >, P > imp
 	// sources for every per-dimension downsampling step.
 	// dest is the tempArray of the next step, or final dest for the last step.
 	// tempArrays[0] can be used to copy the source block into.
-	private final TempArray< P > tempArrays[];
+	private final TempArray< P >[] tempArrays;
 	final int[] tempArraySizes;
 
 	private final BlockProcessorSourceInterval sourceInterval;
@@ -94,7 +94,7 @@ private static int[] downsampleDimIndices( final boolean[] downsampleInDim )
 
 	private static < P > TempArray< P >[] createTempArrays( final int steps, final PrimitiveType primitiveType )
 	{
-		final TempArray< P > tempArrays[] = new TempArray[ steps ];
+		final TempArray< P >[] tempArrays = new TempArray[ steps ];
 		tempArrays[ 0 ] = TempArray.forPrimitiveType( primitiveType );
 		if ( steps >= 2 )
 		{
@@ -148,16 +148,40 @@ public void setTargetInterval( final Interval interval )
 		}
 
 		if ( destSizeChanged )
+			recomputeTempArraySizes();
+	}
+
+	protected void recomputeTempArraySizes()
+	{
+		int size = safeInt( Intervals.numElements( sourceSize ) );
+		tempArraySizes[ 0 ] = size;
+		for ( int i = 1; i < steps; ++i )
+		{
+			final int d = downsampleDims[ i - 1 ];
+			size = size / sourceSize[ d ] * destSize[ d ];
+			tempArraySizes[ i ] = size;
+		}
+	}
+
+	@Override
+	public void setTargetInterval( final long[] pos, final int[] size )
+	{
+		boolean destSizeChanged = false;
+		for ( int d = 0; d < n; ++d )
 		{
-			int size = safeInt( Intervals.numElements( sourceSize ) );
-			tempArraySizes[ 0 ] = size;
-			for ( int i = 1; i < steps; ++i )
+			sourcePos[ d ] = downsampleInDim[ d ] ? pos[ d ] * 2 - 1 : pos[ d ];
+
+			final int tdim = safeInt( size[ d ] );
+			if ( tdim != destSize[ d ] )
 			{
-				final int d = downsampleDims[ i - 1 ];
-				size = size / sourceSize[ d ] * destSize[ d ];
-				tempArraySizes[ i ] = size;
+				destSize[ d ] = tdim;
+				sourceSize[ d ] = downsampleInDim[ d ] ? tdim * 2 + 1 : tdim;
+				destSizeChanged = true;
 			}
 		}
+
+		if ( destSizeChanged )
+			recomputeTempArraySizes();
 	}
 
 	static int safeInt( final long value )

diff --git a/src/main/java/net/imglib2/algorithm/blocks/downsample/AbstractDownsampleHalfPixel.java b/src/main/java/net/imglib2/algorithm/blocks/downsample/AbstractDownsampleHalfPixel.java
@@ -35,7 +35,6 @@
 
 import net.imglib2.Interval;
 import net.imglib2.type.PrimitiveType;
-import net.imglib2.util.Intervals;
 
 abstract class AbstractDownsampleHalfPixel< T extends AbstractDownsampleHalfPixel< T, P >, P > extends AbstractDownsample< T, P >
 {
@@ -68,16 +67,27 @@ public void setTargetInterval( final Interval interval )
 		}
 
 		if ( destSizeChanged )
+			recomputeTempArraySizes();
+	}
+
+	@Override
+	public void setTargetInterval( final long[] pos, final int[] size )
+	{
+		boolean destSizeChanged = false;
+		for ( int d = 0; d < n; ++d )
 		{
-			int size = safeInt( Intervals.numElements( sourceSize ) );
-			tempArraySizes[ 0 ] = size;
-			for ( int i = 1; i < steps; ++i )
+			sourcePos[ d ] = downsampleInDim[ d ] ? pos[ d ] * 2 : pos[ d ];
+
+			final int tdim = safeInt( size[ d ] );
+			if ( tdim != destSize[ d ] )
 			{
-				final int d = downsampleDims[ i - 1 ];
-				size = size / sourceSize[ d ] * destSize[ d ];
-				tempArraySizes[ i ] = size;
+				destSize[ d ] = tdim;
+				sourceSize[ d ] = downsampleInDim[ d ] ? tdim * 2 : tdim;
+				destSizeChanged = true;
 			}
 		}
-	}
 
+		if ( destSizeChanged )
+			recomputeTempArraySizes();
+	}
 }
diff --git a/src/main/java/net/imglib2/algorithm/blocks/transform/AbstractTransformProcessor.java b/src/main/java/net/imglib2/algorithm/blocks/transform/AbstractTransformProcessor.java
@@ -116,7 +116,7 @@ abstract class AbstractTransformProcessor< T extends AbstractTransformProcessor<
 	public void setTargetInterval( final Interval interval )
 	{
 		interval.min( destPos );
-		Arrays.setAll( destSize, d -> ( int ) interval.dimension( d ) );
+		Arrays.setAll( destSize, d -> safeInt( interval.dimension( d ) ) );
 
 		final RealInterval bounds = estimateBounds( interval );
 		switch ( interpolation )