Merge pull request #87 from imglib/io-package

ImgMath updates

pom.xml

@@ -200,6 +200,8 @@ Jean-Yves Tinevez and Michael Zinsmaier.</license.copyrightOwners>
 
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
 		<releaseProfiles>deploy-to-scijava</releaseProfiles>
+
+		<imglib2.version>5.10.0</imglib2.version>
 	</properties>
 
 	<repositories>

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

@@ -5,6 +5,7 @@
 import net.imglib2.algorithm.math.abstractions.ABinaryFunction;
 import net.imglib2.algorithm.math.abstractions.OFunction;
 import net.imglib2.algorithm.math.execution.Addition;
+import net.imglib2.algorithm.math.execution.LetBinding;
 import net.imglib2.algorithm.math.execution.Variable;
 import net.imglib2.converter.Converter;
 import net.imglib2.type.numeric.RealType;
@@ -24,7 +25,7 @@ public Add( final Object... obs )
 	@Override
 	public < O extends RealType< O > > Addition< O > reInit(
 			final O tmp,
-			final Map< String, O > bindings,
+			final Map< String, LetBinding< O > > bindings,
 			final Converter< RealType< ? >, O > converter,
 			final Map< Variable< O >, OFunction< O > > imgSources )
 	{

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

@@ -5,6 +5,7 @@
 import net.imglib2.algorithm.math.abstractions.ABinaryFunction;
 import net.imglib2.algorithm.math.abstractions.OFunction;
 import net.imglib2.algorithm.math.execution.Division;
+import net.imglib2.algorithm.math.execution.LetBinding;
 import net.imglib2.algorithm.math.execution.Variable;
 import net.imglib2.converter.Converter;
 import net.imglib2.type.numeric.RealType;
@@ -25,7 +26,7 @@ public Div( final Object... obs )
 	@Override
 	public < O extends RealType< O > > Division< O > reInit(
 			final O tmp,
-			final Map< String, O > bindings,
+			final Map< String, LetBinding< O > > bindings,
 			final Converter< RealType< ? >, O > converter,
 			final Map< Variable< O >, OFunction< O > > imgSources )
 	{

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

@@ -5,6 +5,7 @@
 import net.imglib2.algorithm.math.abstractions.Compare;
 import net.imglib2.algorithm.math.abstractions.OFunction;
 import net.imglib2.algorithm.math.execution.Equality;
+import net.imglib2.algorithm.math.execution.LetBinding;
 import net.imglib2.algorithm.math.execution.Variable;
 import net.imglib2.converter.Converter;
 import net.imglib2.type.numeric.RealType;
@@ -19,7 +20,7 @@ public Equal( final Object o1, final Object o2 )
 	@Override
 	public < O extends RealType< O > > OFunction< O > reInit(
 			final O tmp,
-			final Map< String, O > bindings,
+			final Map< String, LetBinding< O > > bindings,
 			final Converter< RealType< ? >, O > converter,
 			final Map< Variable< O >, OFunction< O > > imgSources )
 	{

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

@@ -0,0 +1,30 @@
+package net.imglib2.algorithm.math;
+
+import java.util.Map;
+
+import net.imglib2.algorithm.math.abstractions.AUnaryFunction;
+import net.imglib2.algorithm.math.abstractions.OFunction;
+import net.imglib2.algorithm.math.execution.Exponential;
+import net.imglib2.algorithm.math.execution.LetBinding;
+import net.imglib2.algorithm.math.execution.Variable;
+import net.imglib2.converter.Converter;
+import net.imglib2.type.numeric.RealType;
+
+public final class Exp extends AUnaryFunction
+{
+	public Exp( final Object o1 )
+	{
+		super( o1 );
+	}
+
+	@Override
+	public < O extends RealType< O > > Exponential< O > reInit(
+			final O tmp,
+			final Map< String, LetBinding< O > > bindings,
+			final Converter< RealType< ? >, O > converter,
+			final Map< Variable< O >, OFunction< O > > imgSources )
+	{
+		return new Exponential< O >( tmp.copy(),
+				this.a.reInit( tmp, bindings, converter, imgSources ) );
+	}
+}

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

@@ -5,6 +5,7 @@
 import net.imglib2.algorithm.math.abstractions.Compare;
 import net.imglib2.algorithm.math.abstractions.OFunction;
 import net.imglib2.algorithm.math.execution.IsGreaterThan;
+import net.imglib2.algorithm.math.execution.LetBinding;
 import net.imglib2.algorithm.math.execution.Variable;
 import net.imglib2.converter.Converter;
 import net.imglib2.type.numeric.RealType;
@@ -19,7 +20,7 @@ public GreaterThan( final Object o1, final Object o2 )
 	@Override
 	public < O extends RealType< O > > IsGreaterThan< O > reInit(
 			final O tmp,
-			final Map< String, O > bindings,
+			final Map< String, LetBinding< O > > bindings,
 			final Converter< RealType< ? >, O > converter,
 			final Map< Variable< O >, OFunction< O > > imgSources )
 	{

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

@@ -24,7 +24,7 @@ public If( final Object o1, final Object o2, final Object o3 )
 	@Override
 	public < O extends RealType< O > > OFunction< O > reInit(
 			final O tmp,
-			final Map< String, O > bindings,
+			final Map< String, LetBinding< O > > bindings,
 			final Converter< RealType< ? >, O > converter,
 			final Map< Variable< O >, OFunction< O > > imgSources )
 	{

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

@@ -5,6 +5,7 @@
 import net.imglib2.algorithm.math.abstractions.Util;
 import net.imglib2.converter.Converter;
 import net.imglib2.img.array.ArrayImgFactory;
+import net.imglib2.type.NativeType;
 import net.imglib2.type.numeric.RealType;
 import net.imglib2.type.numeric.real.FloatType;
 
@@ -98,6 +99,16 @@ static public final < O extends RealType< O > > RandomAccessibleInterval< O > co
 		return new Compute( operation ).into( target, converter );
 	}
 
+	static public final < O extends NativeType< O > & RealType< O > > RandomAccessibleInterval< O > computeIntoImg( final IFunction operation )
+	{
+		return compute( operation ).intoImg();
+	}
+
+	static public final < O extends NativeType< O > & RealType< O > > RandomAccessibleInterval< O > computeIntoArrayImg( final IFunction operation )
+	{
+		return compute( operation ).intoArrayImg();
+	}
+
 	static public final Add add( final Object o1, final Object o2 )
 	{
 		return new Add( o1, o2 );
@@ -138,6 +149,26 @@ static public final Div div( final Object... obs )
 		return new Div( obs );
 	}
 
+	static public final Pow pow( final Object o1, final Object o2 )
+	{
+		return new Pow( o1, o2 );
+	}
+
+	static public final Pow power( final Object... obs )
+	{
+		return new Pow( obs );
+	}
+
+	static public final Pow power( final Object o1, final Object o2 )
+	{
+		return new Pow( o1, o2 );
+	}
+
+	static public final Pow pow( final Object... obs )
+	{
+		return new Pow( obs );
+	}
+
 	static public final Max max( final Object o1, final Object o2 )
 	{
 		return new Max( o1, o2 );
@@ -178,6 +209,21 @@ static public final Min minimum( final Object... obs )
 		return new Min( obs );
 	}
 
+	static public final Log log( final Object o1 )
+	{
+		return new Log( o1 );
+	}
+
+	static public final Log logarithm( final Object o1 )
+	{
+		return new Log( o1 );
+	}
+
+	static public final Exp exp( final Object o1 )
+	{
+		return new Exp( o1 );
+	}
+
 	static public final Let let( final String varName, final Object varValue, final Object body )
 	{
 		return new Let( varName, varValue, body );
@@ -203,21 +249,41 @@ static public final Equal EQ( final Object o1, final Object o2 )
 		return new Equal( o1, o2 );
 	}
 
+	static public final Equal equal( final Object o1, final Object o2 )
+	{
+		return new Equal( o1, o2 );
+	}
+
 	static public final NotEqual NEQ( final Object o1, final Object o2 )
 	{
 		return new NotEqual( o1, o2 );
 	}
 
+	static public final NotEqual notEqual( final Object o1, final Object o2 )
+	{
+		return new NotEqual( o1, o2 );
+	}
+
 	static public final LessThan LT( final Object o1, final Object o2 )
 	{
 		return new LessThan( o1, o2 );
 	}
 
+	static public final LessThan lessThan( final Object o1, final Object o2 )
+	{
+		return new LessThan( o1, o2 );
+	}
+
 	static public final GreaterThan GT( final Object o1, final Object o2 )
 	{
 		return new GreaterThan( o1, o2 );
 	}
 
+	static public final GreaterThan greaterThan( final Object o1, final Object o2 )
+	{
+		return new GreaterThan( o1, o2 );
+	}
+
 	static public final If IF( final Object o1, final Object o2, final Object o3 )
 	{
 		return new If( o1, o2, o3 );

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

@@ -8,6 +8,7 @@
 import net.imglib2.algorithm.math.abstractions.ViewableFunction;
 import net.imglib2.algorithm.math.execution.ImgSourceIterable;
 import net.imglib2.algorithm.math.execution.ImgSourceIterableDirect;
+import net.imglib2.algorithm.math.execution.LetBinding;
 import net.imglib2.algorithm.math.execution.Variable;
 import net.imglib2.converter.Converter;
 import net.imglib2.type.numeric.RealType;
@@ -25,7 +26,7 @@ public ImgSource( final RandomAccessibleInterval< I > rai )
 	@Override
 	public < O extends RealType< O > > OFunction< O > reInit(
 			final O tmp,
-			final Map< String, O > bindings,
+			final Map< String, LetBinding< O > > bindings,
 			final Converter< RealType< ? >, O > converter,
 			final Map< Variable< O >, OFunction< O > > imgSources )
 	{

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

@@ -5,6 +5,7 @@
 import net.imglib2.algorithm.math.abstractions.Compare;
 import net.imglib2.algorithm.math.abstractions.OFunction;
 import net.imglib2.algorithm.math.execution.IsLessThan;
+import net.imglib2.algorithm.math.execution.LetBinding;
 import net.imglib2.algorithm.math.execution.Variable;
 import net.imglib2.converter.Converter;
 import net.imglib2.type.numeric.RealType;
@@ -19,7 +20,7 @@ public LessThan( final Object o1, final Object o2 )
 	@Override
 	public < O extends RealType< O > > IsLessThan< O > reInit(
 			final O tmp,
-			final Map< String, O > bindings,
+			final Map< String, LetBinding< O > > bindings,
 			final Converter< RealType< ? >, O > converter,
 			final Map< Variable< O >, OFunction< O > > imgSources )
 	{

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

@@ -62,16 +62,18 @@ static private final Object[] fixAndValidate( final Object[] obs )
 	@Override
 	public < O extends RealType< O > > LetBinding< O > reInit(
 			final O tmp,
-			final Map< String, O > bindings,
+			final Map< String, LetBinding< O > > bindings,
 			final Converter< RealType< ? >, O > converter,
 			final Map< Variable< O >, OFunction< O > > imgSources )
 	{
 		final O scrap = tmp.copy();
-		final Map< String, O > rebind = new HashMap<>( bindings );
-		rebind.put( this.varName, scrap );
+		final Map< String, LetBinding< O > > rebind = new HashMap<>( bindings );
+		// The LetBinding constructor will add itself to the rebind prior to reInit the two IFunction varValue and body.
 		return new LetBinding< O >( scrap, this.varName,
-				this.varValue.reInit( tmp, rebind, converter, imgSources ),
-				this.body.reInit( tmp, rebind, converter, imgSources ) );
+				rebind,
+				this.varValue, //this.varValue.reInit( tmp, rebind, converter, imgSources ),
+				this.body, //this.body.reInit( tmp, rebind, converter, imgSources ) );
+				converter, imgSources );
 	}
 
 	@Override

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

@@ -0,0 +1,30 @@
+package net.imglib2.algorithm.math;
+
+import java.util.Map;
+
+import net.imglib2.algorithm.math.abstractions.AUnaryFunction;
+import net.imglib2.algorithm.math.abstractions.OFunction;
+import net.imglib2.algorithm.math.execution.Logarithm;
+import net.imglib2.algorithm.math.execution.LetBinding;
+import net.imglib2.algorithm.math.execution.Variable;
+import net.imglib2.converter.Converter;
+import net.imglib2.type.numeric.RealType;
+
+public final class Log extends AUnaryFunction
+{
+	public Log( final Object o1 )
+	{
+		super( o1 );
+	}
+
+	@Override
+	public < O extends RealType< O > > Logarithm< O > reInit(
+			final O tmp,
+			final Map< String, LetBinding< O > > bindings,
+			final Converter< RealType< ? >, O > converter,
+			final Map< Variable< O >, OFunction< O > > imgSources )
+	{
+		return new Logarithm< O >( tmp.copy(),
+				this.a.reInit( tmp, bindings, converter, imgSources ) );
+	}
+}

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

@@ -4,6 +4,7 @@
 
 import net.imglib2.algorithm.math.abstractions.ABinaryFunction;
 import net.imglib2.algorithm.math.abstractions.OFunction;
+import net.imglib2.algorithm.math.execution.LetBinding;
 import net.imglib2.algorithm.math.execution.Maximum;
 import net.imglib2.algorithm.math.execution.Variable;
 import net.imglib2.converter.Converter;
@@ -24,7 +25,7 @@ public Max( final Object... obs )
 	@Override
 	public < O extends RealType< O > > Maximum< O > reInit(
 			final O tmp,
-			final Map< String, O > bindings,
+			final Map< String, LetBinding< O > > bindings,
 			final Converter< RealType< ? >, O > converter,
 			final Map< Variable< O >, OFunction< O > > imgSources )
 	{

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

@@ -4,6 +4,7 @@
 
 import net.imglib2.algorithm.math.abstractions.ABinaryFunction;
 import net.imglib2.algorithm.math.abstractions.OFunction;
+import net.imglib2.algorithm.math.execution.LetBinding;
 import net.imglib2.algorithm.math.execution.Minimum;
 import net.imglib2.algorithm.math.execution.Variable;
 import net.imglib2.converter.Converter;
@@ -24,7 +25,7 @@ public Min( final Object... obs )
 	@Override
 	public < O extends RealType< O > > Minimum< O > reInit(
 			final O tmp,
-			final Map< String, O > bindings,
+			final Map< String, LetBinding< O > > bindings,
 			final Converter< RealType< ? >, O > converter,
 			final Map< Variable< O >, OFunction< O > > imgSources )
 	{

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

@@ -4,6 +4,7 @@
 
 import net.imglib2.algorithm.math.abstractions.ABinaryFunction;
 import net.imglib2.algorithm.math.abstractions.OFunction;
+import net.imglib2.algorithm.math.execution.LetBinding;
 import net.imglib2.algorithm.math.execution.Multiplication;
 import net.imglib2.algorithm.math.execution.Variable;
 import net.imglib2.converter.Converter;
@@ -24,7 +25,7 @@ public Mul( final Object... obs )
 	@Override
 	public < O extends RealType< O > > Multiplication< O > reInit(
 			final O tmp,
-			final Map< String, O > bindings,
+			final Map< String, LetBinding< O > > bindings,
 			final Converter< RealType< ? >, O > converter,
 			final Map< Variable< O >, OFunction< O > > imgSources )
 	{

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

@@ -4,6 +4,7 @@
 
 import net.imglib2.algorithm.math.abstractions.Compare;
 import net.imglib2.algorithm.math.abstractions.OFunction;
+import net.imglib2.algorithm.math.execution.LetBinding;
 import net.imglib2.algorithm.math.execution.NotEquality;
 import net.imglib2.algorithm.math.execution.Variable;
 import net.imglib2.converter.Converter;
@@ -18,7 +19,7 @@ public NotEqual( final Object o1, final Object o2) {
 	@Override
 	public < O extends RealType< O > > NotEquality< O > reInit(
 			final O tmp,
-			final Map< String, O > bindings,
+			final Map< String, LetBinding< O > > bindings,
 			final Converter< RealType< ? >, O > converter,
 			final Map< Variable< O >, OFunction< O > > imgSources )
 	{