Merge pull request #54 from PreibischLab/feature-rai-getType

Addition of getType() API

pom.xml

@@ -105,8 +105,13 @@ like Selective Plane Illumination Microscopy (SPIM) Data.</description>
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
 		<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
 
-		<bigdataviewer-core.version>10.4.12</bigdataviewer-core.version>
-		<bigdataviewer-vistools.version>1.0.0-beta-33</bigdataviewer-vistools.version>
+		<imglib2.version>7.1.0</imglib2.version>
+		<imglib2-realtransform.version>4.0.3</imglib2-realtransform.version>
+		<imglib2-cache.version>1.0.0-beta-18</imglib2-cache.version>
+		<imglib2-algorithm.version>0.15.3</imglib2-algorithm.version>
+		<imglib2-roi.version>0.15.0</imglib2-roi.version>
+		<bigdataviewer-core.version>10.6.0</bigdataviewer-core.version>
+		<bigdataviewer-vistools.version>1.0.0-beta-36</bigdataviewer-vistools.version>
 	</properties>
 
 	<repositories>
@@ -143,13 +148,6 @@ like Selective Plane Illumination Microscopy (SPIM) Data.</description>
 			<artifactId>ij</artifactId>
 		</dependency>
 
-		<!-- vistools temporary -->
-		<dependency>
-			<!-- NB: dependency:analyze erroneously flags this, but it's required -->
-			<groupId>sc.fiji</groupId>
-			<artifactId>bigdataviewer-vistools</artifactId>
-		</dependency>
-
 		<!-- ImgLib2 dependencies -->
 		<dependency>
 			<groupId>net.imglib2</groupId>
@@ -269,7 +267,7 @@ like Selective Plane Illumination Microscopy (SPIM) Data.</description>
 			<artifactId>picocli</artifactId>
 		</dependency>
 	</dependencies>
-	
+
 	<profiles>
 	<profile>
 			<id>fatjar</id>

src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/filemap2/VirtualRandomAccessibleIntervalLOCI.java

@@ -73,6 +73,12 @@ public RandomAccess< T > randomAccess(Interval interval)
 		return randomAccess();
 	}
 
+	@Override
+	public T getType()
+	{
+		return type;
+	}
+
 	private class VirtualRandomAccessLOCI extends Point implements RandomAccess< T >
 	{
 

src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/flatfield/FlatFieldCorrectedRandomAccessibleInterval.java

@@ -72,7 +72,13 @@ public RandomAccess< O > randomAccess(Interval interval)
 	{
 		return randomAccess();
 	}
-
+
+	@Override
+	public O getType()
+	{
+		return type;
+	}
+
 	private class FlatFieldCorrectedRandomAccess extends Point implements RandomAccess< O >
 	{
 		/*

src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/flatfield/VirtuallyNormalizedRandomAccessibleInterval.java

@@ -61,7 +61,13 @@ public RandomAccess< T > randomAccess(Interval interval)
 	{
 		return randomAccess();
 	}
-
+
+	@Override
+	public T getType()
+	{
+		return input.getType();
+	}
+
 	private class VirtuallyNormalizedRandomAccess extends Point implements RandomAccess< T >
 	{
 		private final T value;

src/main/java/net/preibisch/mvrecon/process/deconvolution/normalization/NormalizingRandomAccessibleInterval.java

@@ -95,6 +95,12 @@ public RandomAccess< T > randomAccess()
 	@Override
 	public RandomAccess< T > randomAccess( final Interval interval ) { return randomAccess(); }
 
+	@Override
+	public T getType()
+	{
+		return interval.getType();
+	}
+
 	@Override
 	public long min( final int d ){ return interval.min( 0 ); }
 

src/main/java/net/preibisch/mvrecon/process/fusion/transformed/AbstractTransformedIntervalRandomAccessible.java

@@ -79,4 +79,10 @@ public int numDimensions()
 	{
 		return n;
 	}
+
+	@Override
+	public FloatType getType()
+	{
+		return new FloatType();
+	}
 }

src/main/java/net/preibisch/mvrecon/process/fusion/transformed/FusedRandomAccessibleInterval.java

@@ -113,6 +113,12 @@ public RandomAccess< FloatType > randomAccess( Interval interval )
 		return randomAccess();
 	}
 
+	@Override
+	public FloatType getType()
+	{
+		return new FloatType();
+	}
+
 	@Override
 	public long min( final int d ) { return interval.min( d ); }
 

src/main/java/net/preibisch/mvrecon/process/fusion/transformed/TransformedInputGeneralRandomAccessible.java

@@ -67,6 +67,12 @@ public RandomAccess< FloatType > randomAccess( final Interval arg0 )
 		return randomAccess();
 	}
 
+	@Override
+	public FloatType getType()
+	{
+		return new FloatType();
+	}
+
 	@Override
 	public int numDimensions()
 	{

src/main/java/net/preibisch/mvrecon/process/fusion/transformed/nonrigid/grid/ModelGrid.java

@@ -157,4 +157,10 @@ public RealRandomAccess< NumericAffineModel3D > realRandomAccess()
 
 	@Override
 	public RealRandomAccess< NumericAffineModel3D > realRandomAccess( final RealInterval interval ) { return realRandomAccess(); }
+
+	@Override
+	public NumericAffineModel3D getType()
+	{
+		return new NumericAffineModel3D();
+	}
 }

src/main/java/net/preibisch/mvrecon/process/fusion/transformed/nonrigid/grid/VirtualGrid.java

@@ -66,6 +66,12 @@ public RandomAccess< NumericAffineModel3D > randomAccess(
 		return randomAccess();
 	}
 
+	@Override
+	public NumericAffineModel3D getType()
+	{
+		return new NumericAffineModel3D();
+	}
+
 	@Override
 	public int numDimensions()
 	{

src/main/java/net/preibisch/mvrecon/process/fusion/transformed/weightcombination/CombineWeightsRandomAccessibleInterval.java

@@ -110,6 +110,12 @@ public RandomAccess< FloatType > randomAccess( Interval interval )
 		return randomAccess();
 	}
 
+	@Override
+	public FloatType getType()
+	{
+		return new FloatType();
+	}
+
 	@Override
 	public long min( final int d ) { return interval.min( d ); }
 

src/main/java/net/preibisch/mvrecon/process/fusion/transformed/weights/BlendingRealRandomAccessible.java

@@ -84,4 +84,10 @@ public RealRandomAccess<FloatType> realRandomAccess( final RealInterval interval
 	{
 		return realRandomAccess();
 	}
+
+	@Override
+	public FloatType getType()
+	{
+		return new FloatType();
+	}
 }

src/main/java/net/preibisch/mvrecon/process/fusion/transformed/weights/ContentBasedFFTRealRandomAccessible.java

@@ -197,4 +197,9 @@ public static void main( String[] args ) throws IncompatibleTypeException
 		ImageJFunctions.show( cb.getContentBasedImg() );
 	}
 
+	@Override
+	public FloatType getType()
+	{
+		return new FloatType();
+	}
 }

src/main/java/net/preibisch/mvrecon/process/fusion/transformed/weights/ContentBasedRealRandomAccessible.java

@@ -108,6 +108,12 @@ public RealRandomAccess<FloatType> realRandomAccess( final RealInterval interval
 		return entropyRRA.realRandomAccess( interval );
 	}
 
+	@Override
+	public FloatType getType()
+	{
+		return new FloatType();
+	}
+
 	@Override
 	public int numDimensions() { return entropy.numDimensions(); }
 

src/main/java/net/preibisch/mvrecon/process/fusion/transformed/weights/InterpolatingNonRigidRasteredRandomAccessible.java

@@ -70,4 +70,10 @@ public RandomAccess< T > randomAccess()
 
 	@Override
 	public RandomAccess< T > randomAccess( final Interval interval ) { return randomAccess(); }
+
+	@Override
+	public T getType()
+	{
+		return realRandomAccessible.getType();
+	}
 }

src/main/java/net/preibisch/mvrecon/process/fusion/transformed/weights/NonRigidRasteredRandomAccessible.java

@@ -78,4 +78,10 @@ public RandomAccess< T > randomAccess()
 
 	@Override
 	public RandomAccess< T > randomAccess( final Interval interval ) { return randomAccess(); }
+
+	@Override
+	public T getType()
+	{
+		return realRandomAccessible.getType();
+	}
 }

src/main/java/net/preibisch/mvrecon/process/fusion/transformed/weights/TransformedRasteredRandomAccessible.java

@@ -65,4 +65,10 @@ public RandomAccess< T > randomAccess()
 
 	@Override
 	public RandomAccess< T > randomAccess( final Interval interval ) { return randomAccess(); }
+
+	@Override
+	public T getType()
+	{
+		return realRandomAccessible.getType();
+	}
 }

src/main/java/net/preibisch/mvrecon/process/quality/FRCRealRandomAccessible.java

@@ -161,6 +161,12 @@ public RealRandomAccess<FloatType> realRandomAccess( final RealInterval interval
 		return realRandomAccess();
 	}
 
+	@Override
+	public FloatType getType()
+	{
+		return new FloatType();
+	}
+
 	public RealRandomAccessible< FloatType > getRealRandomAccessible()
 	{
 		final NearestNeighborSearch< FloatType > search = new NearestNeighborSearchOnKDTree<>( new KDTree<>( qualityList ) );

src/main/java/util/StackingRealRandomAccessible.java

@@ -355,6 +355,12 @@ public StackingRealRandomAccess realRandomAccess( final RealInterval interval )
 		return realRandomAccess();
 	}
 
+	@Override
+	public T getType()
+	{
+		return source.getType();
+	}
+
 	@Override
 	public int numDimensions()
 	{