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ImgMath: refactored formula constructor into class Compute,
invoked from ImgMath.compute static methods.
1 parent f5633d5 commit f68ff7a

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3 files changed

+195
-218
lines changed

3 files changed

+195
-218
lines changed

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

Lines changed: 149 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,149 @@
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package net.imglib2.algorithm.math;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.LinkedList;
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import net.imglib2.Cursor;
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import net.imglib2.RandomAccessibleInterval;
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import net.imglib2.algorithm.math.abstractions.IBinaryFunction;
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import net.imglib2.algorithm.math.abstractions.IFunction;
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import net.imglib2.algorithm.math.abstractions.ITrinaryFunction;
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import net.imglib2.algorithm.math.abstractions.IUnaryFunction;
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import net.imglib2.algorithm.math.abstractions.Util;
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import net.imglib2.converter.Converter;
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import net.imglib2.type.numeric.RealType;
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import net.imglib2.view.Views;
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public class Compute
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{
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private final IFunction operation;
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private final Converter< RealType< ? >, RealType< ? > > converter;
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public Compute( final IFunction operation )
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{
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this( operation,
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new Converter< RealType< ? >, RealType< ? > >()
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{
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@Override
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public final void convert( final RealType< ? > input, final RealType< ? > output) {
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output.setReal( input.getRealDouble() );
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}
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});
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}
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public Compute(
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final IFunction operation,
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final Converter< RealType< ? >, RealType< ? > > converter
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)
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{
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this.operation = operation;
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this.converter = converter;
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}
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public < O extends RealType< O > > RandomAccessibleInterval< O > into( final RandomAccessibleInterval< O > target )
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{
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// Recursive copy: initializes interval iterators
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final IFunction f = this.operation.copy();
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// Set temporary computation holders
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final O scrap = target.randomAccess().get().createVariable();
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f.setScrap( scrap );
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final boolean compatible_iteration_order = this.setup( f, converter );
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// Check compatible iteration order and dimensions
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if ( compatible_iteration_order )
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{
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// Evaluate function for every pixel
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for ( final O output : Views.iterable( target ) )
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f.eval( output );
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}
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else
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{
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// Incompatible iteration order
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final Cursor< O > cursor = Views.iterable( target ).cursor();
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while ( cursor.hasNext() )
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{
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cursor.fwd();
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f.eval( cursor.get(), cursor );
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}
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}
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return target;
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}
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@SuppressWarnings({ "rawtypes", "unchecked" })
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private boolean setup( final IFunction f, final Converter< ?, ? > converter )
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{
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final LinkedList< IFunction > ops = new LinkedList<>();
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ops.add( f );
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// child-parent map
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final HashMap< IFunction, IFunction > cp = new HashMap<>();
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// Collect images to later check their iteration order
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final LinkedList< RandomAccessibleInterval< ? > > images = new LinkedList<>();
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// Collect Var instances to check that each corresponds to an upstream Let
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final ArrayList< Var > vars = new ArrayList<>();
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IFunction parent = null;
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// Iterate into the nested operations
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while ( ! ops.isEmpty() )
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{
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final IFunction op = ops.removeFirst();
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cp.put( op, parent );
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parent = op;
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if ( op instanceof IterableImgSource )
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{
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final IterableImgSource iis = ( IterableImgSource )op;
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// Side effect: set the converter from input to output types
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iis.setConverter( converter );
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images.addLast( iis.rai );
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}
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else if ( op instanceof IUnaryFunction )
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{
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ops.addLast( ( ( IUnaryFunction )op ).getFirst() );
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if ( op instanceof IBinaryFunction )
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{
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ops.addLast( ( ( IBinaryFunction )op ).getSecond() );
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if ( op instanceof ITrinaryFunction )
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{
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ops.addLast( ( ( ITrinaryFunction )op ).getThird() );
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}
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}
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}
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else if ( op instanceof Var )
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{
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final Var var = ( Var )op;
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vars.add( var );
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}
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}
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// Check Vars: are they all using names declared in upstream Lets
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all: for ( final Var var : vars )
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{
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parent = var;
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while ( null != ( parent = cp.get( parent ) ) )
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{
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if ( parent instanceof Let )
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{
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Let let = ( Let )parent;
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if ( let.varName != var.name )
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continue;
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// Else, found: Var is in use
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continue all;
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}
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}
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// No upstream Let found
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throw new RuntimeException( "The Var(\"" + var.name + "\") does not read from any upstream Let. " );
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}
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return Util.compatibleIterationOrder( images );
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}
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}

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

Lines changed: 5 additions & 135 deletions
Original file line numberDiff line numberDiff line change
@@ -30,7 +30,7 @@
3030
*
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* RandomAccessibleInterval<O> result = ...
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*
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* new ImgMath<A, O>( Div<O>( Max<O>( img1, img2, img3 ), 3.0 ) ).into( result );
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* compute( div( max( img1, img2, img3 ), 3.0 ) ).into( result );
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* }
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* </pre>
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*
@@ -43,144 +43,14 @@
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*/
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public class ImgMath
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{
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private final IFunction operation;
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private final Converter< RealType< ? >, RealType< ? > > converter;
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public ImgMath( final IFunction operation )
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{
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this( operation,
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new Converter< RealType< ? >, RealType< ? > >()
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{
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@Override
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public final void convert( final RealType< ? > input, final RealType< ? > output) {
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output.setReal( input.getRealDouble() );
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}
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});
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}
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public ImgMath(
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final IFunction operation,
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final Converter< RealType< ? >, RealType< ? > > converter
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)
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{
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this.operation = operation;
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this.converter = converter;
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}
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public < O extends RealType< O > > RandomAccessibleInterval< O > into( final RandomAccessibleInterval< O > target )
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{
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// Recursive copy: initializes interval iterators
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final IFunction f = this.operation.copy();
74-
// Set temporary computation holders
75-
final O scrap = target.randomAccess().get().createVariable();
76-
f.setScrap( scrap );
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final boolean compatible_iteration_order = this.setup( f, converter );
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// Check compatible iteration order and dimensions
81-
if ( compatible_iteration_order )
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{
83-
// Evaluate function for every pixel
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for ( final O output : Views.iterable( target ) )
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f.eval( output );
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}
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else
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{
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// Incompatible iteration order
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final Cursor< O > cursor = Views.iterable( target ).cursor();
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while ( cursor.hasNext() )
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{
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cursor.fwd();
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f.eval( cursor.get(), cursor );
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}
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}
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return target;
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}
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102-
@SuppressWarnings({ "rawtypes", "unchecked" })
103-
private boolean setup( final IFunction f, final Converter< ?, ? > converter )
104-
{
105-
final LinkedList< IFunction > ops = new LinkedList<>();
106-
ops.add( f );
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// child-parent map
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final HashMap< IFunction, IFunction > cp = new HashMap<>();
110-
111-
// Collect images to later check their iteration order
112-
final LinkedList< RandomAccessibleInterval< ? > > images = new LinkedList<>();
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// Collect Var instances to check that each corresponds to an upstream Let
115-
final ArrayList< Var > vars = new ArrayList<>();
116-
117-
IFunction parent = null;
118-
119-
// Iterate into the nested operations
120-
while ( ! ops.isEmpty() )
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{
122-
final IFunction op = ops.removeFirst();
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cp.put( op, parent );
124-
parent = op;
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126-
if ( op instanceof IterableImgSource )
127-
{
128-
final IterableImgSource iis = ( IterableImgSource )op;
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// Side effect: set the converter from input to output types
130-
iis.setConverter( converter );
131-
images.addLast( iis.rai );
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}
133-
else if ( op instanceof IUnaryFunction )
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{
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ops.addLast( ( ( IUnaryFunction )op ).getFirst() );
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137-
if ( op instanceof IBinaryFunction )
138-
{
139-
ops.addLast( ( ( IBinaryFunction )op ).getSecond() );
140-
141-
if ( op instanceof ITrinaryFunction )
142-
{
143-
ops.addLast( ( ( ITrinaryFunction )op ).getThird() );
144-
}
145-
}
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}
147-
else if ( op instanceof Var )
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{
149-
final Var var = ( Var )op;
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vars.add( var );
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}
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}
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// Check Vars: are they all using names declared in upstream Lets
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all: for ( final Var var : vars )
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{
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parent = var;
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while ( null != ( parent = cp.get( parent ) ) )
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{
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if ( parent instanceof Let )
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{
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Let let = ( Let )parent;
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if ( let.varName != var.name )
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continue;
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// Else, found: Var is in use
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continue all;
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}
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}
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// No upstream Let found
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throw new RuntimeException( "The Var(\"" + var.name + "\") does not read from any upstream Let. " );
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}
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return Util.compatibleIterationOrder( images );
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}
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176-
static public final ImgMath compute( final IFunction operation )
46+
static public final Compute compute( final IFunction operation )
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{
178-
return new ImgMath( operation );
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return new Compute( operation );
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}
18050

181-
static public final ImgMath compute( final IFunction operation, final Converter< RealType< ? >, RealType< ? > > converter )
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static public final Compute compute( final IFunction operation, final Converter< RealType< ? >, RealType< ? > > converter )
18252
{
183-
return new ImgMath( operation, converter );
53+
return new Compute( operation, converter );
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}
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static public final Add add( final Object o1, final Object o2 )

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