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Merge pull request #88 from imglib/ImgMath-blockread
ImgMath blockread and offset
2 parents e2fa1fe + a1f9c48 commit 2fe0ce8

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-424
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‎src/main/java/net/imglib2/algorithm/math/Add.java‎

Lines changed: 11 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -23,14 +23,21 @@ public Add( final Object... obs )
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}
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@Override
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public < O extends RealType< O > > Addition< O > reInit(
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public < O extends RealType< O > > OFunction< O > reInit(
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final O tmp,
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final Map< String, LetBinding< O > > bindings,
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final Converter< RealType< ? >, O > converter,
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final Map< Variable< O >, OFunction< O > > imgSources )
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{
32-
return new Addition< O >( tmp.copy(),
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this.a.reInit( tmp, bindings, converter, imgSources ),
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this.b.reInit( tmp, bindings, converter, imgSources ) );
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final OFunction< O > a = this.a.reInit( tmp, bindings, converter, imgSources ),
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b = this.b.reInit( tmp, bindings, converter, imgSources );
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// Optimization: remove null ops
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if ( a.isZero() )
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return b;
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if ( b.isZero() )
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return a;
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return new Addition< O >( tmp.copy(), a, b );
3542
}
3643
}

‎src/main/java/net/imglib2/algorithm/math/AndLogical.java‎

Lines changed: 42 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,42 @@
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package net.imglib2.algorithm.math;
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import java.util.Map;
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import net.imglib2.algorithm.math.abstractions.ABinaryFunction;
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import net.imglib2.algorithm.math.abstractions.ABooleanFunction;
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import net.imglib2.algorithm.math.abstractions.OFunction;
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import net.imglib2.algorithm.math.execution.LetBinding;
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import net.imglib2.algorithm.math.execution.LogicalAnd;
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import net.imglib2.algorithm.math.execution.LogicalAndBoolean;
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import net.imglib2.algorithm.math.execution.Variable;
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import net.imglib2.converter.Converter;
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import net.imglib2.type.numeric.RealType;
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public class AndLogical extends ABinaryFunction
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{
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public AndLogical( final Object c1, final Object c2 )
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{
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super( c1, c2 );
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}
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public AndLogical( final Object... c )
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{
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super( c );
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}
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@Override
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public < O extends RealType< O > > OFunction< O > reInit(
29+
final O tmp,
30+
final Map< String, LetBinding< O > > bindings,
31+
final Converter< RealType< ? >, O > converter,
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final Map< Variable< O >, OFunction< O > > imgSources )
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{
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final OFunction< O > a = this.a.reInit( tmp, bindings, converter, imgSources );
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final OFunction< O > b = this.b.reInit( tmp, bindings, converter, imgSources );
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return a instanceof ABooleanFunction< ? > && b instanceof ABooleanFunction< ? > ?
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new LogicalAndBoolean< O >( tmp.createVariable(), a, b )
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: new LogicalAnd< O >( tmp.createVariable(), a, b );
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}
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}

‎src/main/java/net/imglib2/algorithm/math/BlockReadSource.java‎

Lines changed: 136 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,136 @@
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package net.imglib2.algorithm.math;
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import java.util.Map;
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import java.util.stream.LongStream;
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import net.imglib2.RandomAccessible;
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import net.imglib2.algorithm.math.abstractions.IFunction;
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import net.imglib2.algorithm.math.abstractions.OFunction;
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import net.imglib2.algorithm.math.abstractions.RandomAccessOnly;
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import net.imglib2.algorithm.math.abstractions.ViewableFunction;
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import net.imglib2.algorithm.math.execution.BlockReadingSource;
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import net.imglib2.algorithm.math.execution.BlockReadingDirect;
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import net.imglib2.algorithm.math.execution.LetBinding;
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import net.imglib2.algorithm.math.execution.Variable;
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import net.imglib2.converter.Converter;
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import net.imglib2.type.numeric.RealType;
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/**
19+
* Intended for reading cuboid blocks out of an integral image.
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*
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* @author Albert Cardona
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*
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* @param <I> The {@code Type} of the {@code RandomAccessible} from which to read blocks.
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*/
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public final class BlockReadSource< I extends RealType< I > > extends ViewableFunction implements IFunction, RandomAccessOnly< I >
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{
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final private RandomAccessible< I > src;
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final private long[][] corners;
29+
final private byte[] signs;
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/**
32+
* A block centered on a particular pixel.
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*
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* @param src A {@code RandomAccessible} such as an @{code IntegralImg}, presumably a {@code RandomAccessibleInterval} that was extended with an {@code OutOfBounds} strategy.
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* @param blockRadius Array of half of the length of each side of the block.
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*/
37+
public BlockReadSource( final RandomAccessible< I > src, final long[] blockRadius )
38+
{
39+
this.src = src;
40+
this.corners = new long[ ( int )Math.pow( 2, blockRadius.length ) ][ blockRadius.length ];
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// All possible combinations to define all corners, sorted with lower dimensions being the slower-moving,
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// following Gray code (see https://en.wikipedia.org/wiki/Gray_code )
44+
for (int d = 0; d < src.numDimensions(); ++d )
45+
{
46+
final int cycle = corners.length / ( int )Math.pow( 2, d + 1 );
47+
long inc = blockRadius[ d ];
48+
for (int i = 0; i < corners.length; ++i )
49+
{
50+
if ( 0 == i % cycle) inc *= -1;
51+
corners[ i ][ d ] = inc;
52+
//System.out.println("corners[" + i + "][" + d + "] = " + corners[i][d]);
53+
}
54+
}
55+
this.signs = BlockReadSource.signsArray( src );
56+
//for (int i=0; i<signs.length; ++i)
57+
// System.out.println("signs[" + i + "] = " + signs[i]);
58+
}
59+
60+
/**
61+
* A block centered on a particular pixel.
62+
*
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* @param src A {@code RandomAccessible} such as an @{code IntegralImg}, presumably a {@code RandomAccessibleInterval} that was extended with an {@code OutOfBounds} strategy.
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* @param blockRadius Half of the length of the side of the block in every dimension.
65+
*/
66+
public BlockReadSource( final RandomAccessible< I > src, final long blockRadius )
67+
{
68+
this( src, LongStream.generate( () -> blockRadius ).limit( src.numDimensions() ).toArray() );
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}
70+
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static public byte[] signsArray( final RandomAccessible< ? > src )
72+
{
73+
switch ( src.numDimensions() )
74+
{
75+
case 1:
76+
return new byte[]{ -1, 1 };
77+
case 2:
78+
// 2D: S( (x1,y1), (x2,y2) = C( x1,y1 )
79+
// -C( x1,y2 )
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// -C( x2,y1 )
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// +C( x2,y2 )
82+
// Corners as: (x1, y1), (x1, y2), (x2, y1), (x2, y2)
83+
return new byte[]{ 1, -1, -1, 1 };
84+
case 3:
85+
// 3D: S( (x1,y1,z1) to (x2,y2,z2) ) = - C( x1, y1, z1 )
86+
// + C( x1, y1, z2 )
87+
// + C( x1, y2, z1 )
88+
// - C( x1, y2, z2 )
89+
// + C( x2, y1, z1 )
90+
// - C( x2, y1, z2 )
91+
// - C( x2, y2, z1 )
92+
// + C( x2, y2, z2 )
93+
return new byte[]{ -1, 1, 1, -1, 1, -1, -1, 1 };
94+
default:
95+
// There's a clear pattern, but I can't find the time now to break through it
96+
// Must re-read Tapias 2011 doi:10.1016/j.patrec.2010.10.007
97+
// for the use of the Mobius function for determining the sign
98+
throw new UnsupportedOperationException( "Sorry, numDimensions " + src.numDimensions() + " not supported yet." );
99+
}
100+
}
101+
102+
/**
103+
*
104+
* @param src
105+
* @param corners In coordinate moves relative to a pixel's location.
106+
*/
107+
public BlockReadSource( final RandomAccessible< I > src, final long[][] corners )
108+
{
109+
this.src = src;
110+
this.corners = corners;
111+
this.signs = BlockReadSource.signsArray( src );
112+
}
113+
114+
@SuppressWarnings("unchecked")
115+
@Override
116+
public < O extends RealType< O > > OFunction< O > reInit(
117+
final O tmp,
118+
final Map< String, LetBinding< O > > bindings,
119+
final Converter< RealType< ? >, O > converter,
120+
final Map< Variable< O >, OFunction< O > > imgSources )
121+
{
122+
if ( tmp.getClass() == src.randomAccess().get().getClass() )
123+
return new BlockReadingDirect< O >( tmp.copy(), ( RandomAccessible< O > )this.src, this.corners, this.signs );
124+
return new BlockReadingSource< I, O >(
125+
tmp.copy(),
126+
converter,
127+
this.src,
128+
this.corners,
129+
this.signs );
130+
}
131+
132+
public RandomAccessible< I > getRandomAccessible()
133+
{
134+
return this.src;
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}
136+
}

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