Addition of getType() API

pom.xml

@@ -201,7 +201,10 @@ Jean-Yves Tinevez and Michael Zinsmaier.</license.copyrightOwners>
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
 		<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
 
-		<net.imglib2.imglib2.version>6.4.0</net.imglib2.imglib2.version>
+		<imglib2.version>7.0.1</imglib2.version>
+		<imglib2-realtransform.version>4.0.3</imglib2-realtransform.version>
+		<imglib2-roi.version>0.15.0</imglib2-roi.version>
+		<imglib2-cache.version>1.0.0-beta-18</imglib2-cache.version>
 	</properties>
 
 	<repositories>
@@ -226,6 +229,10 @@ Jean-Yves Tinevez and Michael Zinsmaier.</license.copyrightOwners>
 			<groupId>net.imglib2</groupId>
 			<artifactId>imglib2-realtransform</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>net.imglib2</groupId>
+			<artifactId>imglib2-cache</artifactId>
+		</dependency>
 
 		<!-- Third-party dependencies -->
 		<dependency>
@@ -240,10 +247,6 @@ Jean-Yves Tinevez and Michael Zinsmaier.</license.copyrightOwners>
 			<groupId>org.ojalgo</groupId>
 			<artifactId>ojalgo</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>net.imglib2</groupId>
-			<artifactId>imglib2-cache</artifactId>
-		</dependency>
 
 		<!-- Test dependencies -->
 		<dependency>

src/main/java/net/imglib2/algorithm/blocks/convert/ConverterBlockProcessor.java

@@ -238,6 +238,8 @@ public A update( final Object updater )
 		@Override public Cursor< T > localizingCursor() {throw new UnsupportedOperationException();}
 		@Override public Object iterationOrder() {throw new UnsupportedOperationException();}
 		@Override public RandomAccess< T > randomAccess() {throw new UnsupportedOperationException();}
-		@Override public ImgFactory< T > factory() {throw new UnsupportedOperationException();}@Override public Img< T > copy() {throw new UnsupportedOperationException();}
+		@Override public ImgFactory< T > factory() {throw new UnsupportedOperationException();}
+		@Override public Img< T > copy() {throw new UnsupportedOperationException();}
+		@Override public T getType() {throw new UnsupportedOperationException();}
 	}
 }

src/main/java/net/imglib2/algorithm/bspline/BSplineCoefficientsInterpolatorEven.java

@@ -94,6 +94,12 @@ public T get()
 		return kernel.get();
 	}
 
+	@Override
+	public T getType()
+	{
+		return kernel.type();
+	}
+
 	@Override
 	public BSplineCoefficientsInterpolatorEven<T> copy()
 	{

src/main/java/net/imglib2/algorithm/bspline/BSplineCoefficientsInterpolatorOdd.java

@@ -85,7 +85,13 @@ public T get()
 	{
 		return kernel.get();
 	}
-
+
+	@Override
+	public T getType()
+	{
+		return kernel.type();
+	}
+
 	@Override
 	public BSplineCoefficientsInterpolatorOdd<T> copy()
 	{

src/main/java/net/imglib2/algorithm/gauss/SamplingLineIterator.java

@@ -105,6 +105,12 @@ public T get()
 		return randomAccess.get();
 	}
 
+	@Override
+	public T getType()
+	{
+		return processLine.getType();
+	}
+
 	@Override
 	public SamplingLineIterator< T > copy()
 	{

src/main/java/net/imglib2/algorithm/gradient/ScaleAsFunctionOfPosition.java

@@ -77,6 +77,12 @@ public AbstractConvertedRandomAccess< T, T > randomAccess( final Interval interv
 		return randomAccess();
 	}
 
+	@Override
+	public T getType()
+	{
+		return source.getType();
+	}
+
 	public static class ScaledRandomAccess< T extends Type< T > & MulFloatingPoint > extends AbstractConvertedRandomAccess< T, T >
 	{
 
@@ -99,6 +105,12 @@ public T get()
 			return t;
 		}
 
+		@Override
+		public T getType()
+		{
+			return t;
+		}
+
 		@Override
 		public ScaledRandomAccess< T > copy()
 		{

src/main/java/net/imglib2/algorithm/hough/HoughTransforms.java

@@ -44,6 +44,7 @@
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.algorithm.localextrema.LocalExtrema;
 import net.imglib2.algorithm.localextrema.LocalExtrema.MaximumCheck;
+import net.imglib2.type.Type;
 import net.imglib2.type.numeric.IntegerType;
 import net.imglib2.type.numeric.RealType;
 import net.imglib2.util.Intervals;
@@ -233,7 +234,28 @@ public static < T extends Comparable< T >, U extends IntegerType< U > > void vot
 			final RandomAccessibleInterval< U > votespace,
 			final int nTheta )
 	{
-		voteLines( input, votespace, nTheta, defaultRho( input ), Util.getTypeFromInterval( input ) );
+		voteLines( input, votespace, nTheta, defaultRho( input ), getTypeFromInterval( input ) );
+	}
+
+	private static <T> T getTypeFromInterval( RandomAccessibleInterval< T > rai )
+	{
+//		final T val1 = rai.randomAccess().get();
+//		final T val2 = ( T ) ( ( Type ) rai.getType() ).createVariable();
+//		System.out.println( "val1 = " + val1 );
+//		System.out.println( "val2 = " + val2 );
+
+		// TODO: The voteLines() method above used Util.getTypeFromInterval to
+		//       obtain a threshold value to call the voteLines() method below
+		//       which has a threshold argument. With the recent addition of
+		//       RandomAccessibleInterval.getType(), this breaks the tests/
+		//       However, it seems that it is a bug in the above voteLines() to
+		//       do it like this. Basically, it uses the value of the first
+		//       pixel of the image as the threshold, which looks wrong, and
+		//       depends on assumptions about how Util.getTypeFromInterval is
+		//       implemented. I now just "fixed" the test by just taking the
+		//       first pixel. But this is clearly wrong. I don't know how the
+		//       code is supposed to work though.
+		return rai.randomAccess().get();
 	}
 
 	/**
@@ -257,7 +279,7 @@ public static < T extends Comparable< T >, U extends IntegerType< U > > void vot
 			final int nTheta,
 			final int nRho )
 	{
-		voteLines( input, votespace, nTheta, nRho, Util.getTypeFromInterval( input ) );
+		voteLines( input, votespace, nTheta, nRho, getTypeFromInterval( input ) );
 	}
 
 	/**

src/main/java/net/imglib2/algorithm/interpolation/randomaccess/BSplineCoefficientsInterpolatorFactory.java

@@ -193,11 +193,11 @@ public BSplineCoefficientsInterpolator<S> create( RandomAccessible<T> f )
 				coefficients,
 				((OutOfBoundsFactory<S,RandomAccessibleInterval<S>>)oobFactory));
 
-		S type = Util.getTypeFromInterval( coefficients );
+		S type = coefficients.getType();
 		if( order % 2 == 0 )
-			return new BSplineCoefficientsInterpolatorEven<S>( order, coefExt, type.copy() );
+			return new BSplineCoefficientsInterpolatorEven<S>( order, coefExt, type.createVariable() );
 		else
-			return new BSplineCoefficientsInterpolatorOdd<S>( order, coefExt, type.copy() );
+			return new BSplineCoefficientsInterpolatorOdd<S>( order, coefExt, type.createVariable() );
 	}
 
 	@Override

src/main/java/net/imglib2/algorithm/interpolation/randomaccess/BSplineInterpolator.java

@@ -162,6 +162,12 @@ public T get()
 		return value;
 	}
 
+	@Override
+	public T getType()
+	{
+		return value;
+	}
+
 	protected void fillWeights()
 	{
 		final Neighborhood< T > rect = target.get();

src/main/java/net/imglib2/algorithm/kdtree/VolumetricSearch.java

@@ -81,7 +81,13 @@ public VolumetricSearch( final List< I > intervals )
 		final ArrayList< IntervalWrapper< I > > wrappers = new ArrayList< IntervalWrapper< I > >( intervals.size() );
 		for ( final I interval : intervals )
 			wrappers.add( new IntervalWrapper< I >( interval ) );
-		kdtree = new KDTree< IntervalWrapper< I > >( wrappers, wrappers );
+		kdtree = new KDTree<>( wrappers, wrappers );
+	}
+
+	@Override
+	public List< I > getType()
+	{
+		return new LinkedList<>();
 	}
 
 	private static class IntervalWrapper< I extends RealInterval > implements RealLocalizable
@@ -227,6 +233,12 @@ public List< I > get()
 			return find( this );
 		}
 
+		@Override
+		public List< I > getType()
+		{
+			return new LinkedList<>();
+		}
+
 		@Override
 		public VolumetricSearchRandomAccess copy()
 		{

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

@@ -277,8 +277,8 @@ public < O extends RealType< O >, C extends RealType< C > > RandomAccessibleInte
 	{
 		if ( null == inConverter )
 			inConverter = Util.genericRealTypeConverter();
-		
-		final O outputType = target.randomAccess().get().createVariable();		
+
+		final O outputType = target.randomAccess().get().createVariable();
 		final boolean are_same_type = computingType.getClass() == outputType.getClass();
 
 		if ( null == outConverter && !are_same_type )
@@ -372,6 +372,12 @@ public RandomAccess< O > randomAccess( final Interval interval )
 			{
 				return this.randomAccess();
 			}
+
+			@Override
+			public O getType()
+			{
+				return outputType;
+			}
 		}, interval );
 	}
 

src/main/java/net/imglib2/algorithm/math/execution/FunctionCursor.java

@@ -98,7 +98,13 @@ public FunctionCursor(
 		this.scrapO = outputType.createVariable();
 		this.reset();
 	}
-
+
+	@Override
+	public O getType()
+	{
+		return scrapO;
+	}
+
 	private final class FunctionSamplerConverter implements Sampler< O >
 	{	
 		@Override
@@ -110,6 +116,12 @@ public final O get()
 
 		@Override
 		public final Sampler< O > copy() { return null; }
+
+		@Override
+		public O getType()
+		{
+			return scrapO;
+		}
 	}
 
 	private final class FunctionSamplerDirect implements Sampler< C >
@@ -122,6 +134,12 @@ public final C get()
 
 		@Override
 		public final Sampler< C > copy() { return null; }
+
+		@Override
+		public C getType()
+		{
+			return scrapC;
+		}
 	}
 
 	@Override

src/main/java/net/imglib2/algorithm/math/execution/FunctionRandomAccess.java

@@ -132,6 +132,12 @@ public O get()
 			this.outConverter.convert( this.f.eval( this.point ), outputType );
 			return this.outputType;
 		}
+
+		@Override
+		public O getType()
+		{
+			return outputType;
+		}
 	}
 
 	private final class FunctionSamplerDirect implements Sampler< O >
@@ -171,6 +177,12 @@ public final O get()
 		{
 			return this.f.eval( this.point );
 		}
+
+		@Override
+		public O getType()
+		{
+			return outputType;
+		}
 	}
 
 	@Override
@@ -179,6 +191,12 @@ public O get()
 		return this.sampler.get();
 	}
 
+	@Override
+	public O getType()
+	{
+		return outputType;
+	}
+
 	@Override
 	public RandomAccess< O > copy()
 	{

src/main/java/net/imglib2/algorithm/math/execution/FunctionRandomAccessDouble.java

@@ -87,6 +87,12 @@ public final O get()
 			this.scrap.setReal( this.f.evalDouble( this.point ) );
 			return this.scrap;
 		}
+
+		@Override
+		public O getType()
+		{
+			return scrap;
+		}
 	}
 
 	@Override
@@ -95,6 +101,12 @@ public O get()
 		return this.sampler.get();
 	}
 
+	@Override
+	public O getType()
+	{
+		return this.sampler.getType();
+	}
+
 	@Override
 	public RandomAccess< O > copy()
 	{

src/main/java/net/imglib2/algorithm/math/execution/IterableRandomAccessibleFunction.java

@@ -173,4 +173,10 @@ public Cursor< O > localizingCursor()
 	{
 		return this.cursor();
 	}
+
+	@Override
+	public O getType()
+	{
+		return outputType;
+	}
 }

src/main/java/net/imglib2/algorithm/math/execution/KDTreeRadiusSource.java

@@ -99,6 +99,13 @@ public O get()
 		return this.outsideO;
 	}
 
+
+	@Override
+	public O getType()
+	{
+		return this.scrap;
+	}
+
 	@Override
 	public RandomAccess< O > copy()
 	{

src/main/java/net/imglib2/algorithm/neighborhood/DiamondNeighborhood.java

@@ -120,6 +120,12 @@ public T get()
 			return source.get();
 		}
 
+		@Override
+		public T getType()
+		{
+			return source.getType();
+		}
+
 		@Override
 		public void fwd()
 		{
@@ -435,4 +441,9 @@ public LocalCursor localizingCursor()
 		return cursor();
 	}
 
+	@Override
+	public T getType()
+	{
+		return sourceRandomAccess.getType();
+	}
 }