Update to ImgLib2 version 5.1.0

And make the necessary code changes for the revised API.

As part of this update, the MorphologyUtils.createSuitableFactory method
was removed in favor of the new Util.getSuitableImgFactory method.

Author: ctrueden

pom.xml

@@ -10,7 +10,7 @@
 	</parent>
 
 	<artifactId>imglib2-algorithm</artifactId>
-	<version>0.8.3-SNAPSHOT</version>
+	<version>0.9.0-SNAPSHOT</version>
 
 	<name>ImgLib2 Algorithms</name>
 	<description>Useful image processing algorithms.</description>
@@ -200,6 +200,7 @@ Jean-Yves Tinevez and Michael Zinsmaier.</license.copyrightOwners>
 		<!-- NB: Deploy releases to the ImageJ Maven repository. -->
 		<releaseProfiles>deploy-to-imagej</releaseProfiles>
 
+		<imglib2.version>5.1.0</imglib2.version>
 		<imglib2-realtransform.version>2.0.0-beta-39</imglib2-realtransform.version>
 		<jitk-tps.version>3.0.0</jitk-tps.version>
 		<ojalgo.version>43.0</ojalgo.version>

src/main/java/net/imglib2/algorithm/binary/Thresholder.java

@@ -77,7 +77,7 @@ public static final < T extends Type< T > & Comparable< T >> Img< BitType > thre
 		try
 		{
 			final ImgFactory< BitType > bitFactory = factory.imgFactory( new BitType() );
-			final Img< BitType > target = bitFactory.create( source, new BitType() );
+			final Img< BitType > target = bitFactory.create( source );
 
 			final Converter< T, BitType > converter;
 			if ( above )

src/main/java/net/imglib2/algorithm/componenttree/BuildComponentTree.java

@@ -342,8 +342,8 @@ private BuildComponentTree( final RandomAccessibleInterval< T > input, final Par
 		final long[] dimensions = new long[ input.numDimensions() ];
 		input.dimensions( dimensions );
 
-		final ImgFactory< BitType > imgFactory = new ArrayImgFactory< BitType >();
-		visited = imgFactory.create( dimensions, new BitType() );
+		final ImgFactory< BitType > imgFactory = new ArrayImgFactory<>( new BitType() );
+		visited = imgFactory.create( dimensions );
 		visitedRandomAccess = visited.randomAccess();
 
 		neighborhood = new Neighborhood( dimensions );

src/main/java/net/imglib2/algorithm/componenttree/mser/MserPartialComponentGenerator.java

@@ -87,7 +87,7 @@ public MserPartialComponentGenerator( final T maxValue, final RandomAccessibleIn
 		this.maxValue = maxValue;
 		dimensions = new long[ input.numDimensions() ];
 		input.dimensions( dimensions );
-		linkedList = imgFactory.create( dimensions, new LongType() );
+		linkedList = imgFactory.create( dimensions );
 	}
 
 	@Override

src/main/java/net/imglib2/algorithm/componenttree/pixellist/PixelListPartialComponentGenerator.java

@@ -86,7 +86,7 @@ final class PixelListPartialComponentGenerator< T extends Type< T > > implements
 		this.maxValue = maxValue;
 		dimensions = new long[ input.numDimensions() ];
 		input.dimensions( dimensions );
-		linkedList = imgFactory.create( dimensions, new LongType() );
+		linkedList = imgFactory.create( dimensions );
 	}
 
 	@Override

src/main/java/net/imglib2/algorithm/dog/DifferenceOfGaussian.java

@@ -91,7 +91,7 @@ public static < I extends NumericType< I >, T extends NumericType< T > & NativeT
 			final ExecutorService service )
 	{
 		final T type = Util.getTypeFromInterval( dog );
-		final Img< T > g1 = Util.getArrayOrCellImgFactory( dog, type ).create( dog, type );
+		final Img< T > g1 = Util.getArrayOrCellImgFactory( dog, type ).create( dog );
 		final long[] translation = new long[ dog.numDimensions() ];
 		dog.min( translation );
 		DoG( sigmaSmaller, sigmaLarger, input, Views.translate( g1, translation ), dog, service );

src/main/java/net/imglib2/algorithm/dog/DogDetection.java

@@ -344,7 +344,7 @@ public ArrayList< Point > getPeaks()
 			else
 				service = executorService;
 
-			dogImg = Util.getArrayOrCellImgFactory( interval, type ).create( interval, type );
+			dogImg = Util.getArrayOrCellImgFactory( interval, type ).create( interval );
 			final long[] translation = new long[ interval.numDimensions() ];
 			interval.min( translation );
 			dogImg = Views.translate( dogImg, translation );

src/main/java/net/imglib2/algorithm/edge/SubpixelEdgelDetection.java

@@ -111,7 +111,7 @@ public static < T extends RealType< T > > ArrayList< Edgel > getEdgels(
 		for ( int d = 0; d < n; ++d )
 			dim[ d ] = input.dimension( d );
 		dim[ n ] = n;
-		final Img< T > gradients = factory.create( dim, input.randomAccess().get() );
+		final Img< T > gradients = factory.create( dim );
 
 		// Compute partial derivatives of input in all dimension. This requires
 		// a border of 1 pixel with respect to the input image

src/main/java/net/imglib2/algorithm/floydsteinberg/FloydSteinbergDithering.java

@@ -182,12 +182,12 @@ public String getErrorMessage()
 
 	public Img< FloatType > createErrorDiffusionKernel( final int numDimensions )
 	{
-		final ArrayImgFactory< FloatType > factory = new ArrayImgFactory< FloatType >();
+		final ArrayImgFactory< FloatType > factory = new ArrayImgFactory<>( new FloatType() );
 
 		// for 2d we take the values from the literature
 		if ( numDimensions == 2 )
 		{
-			final Img< FloatType > kernel = factory.create( new long[] { 3, 3 }, new FloatType() );
+			final Img< FloatType > kernel = factory.create( 3, 3 );
 
 			final RandomAccess< FloatType > cursor = kernel.randomAccess();
 
@@ -212,7 +212,7 @@ public Img< FloatType > createErrorDiffusionKernel( final int numDimensions )
 
 			return kernel;
 		}
-		final Img< FloatType > kernel = factory.create( Util.getArrayFromValue( 3L, numDimensions ), new FloatType() );
+		final Img< FloatType > kernel = factory.create( Util.getArrayFromValue( 3L, numDimensions ) );
 		final Cursor< FloatType > cursor = kernel.cursor();
 
 		final int numValues = ( int ) ( kernel.size() / 2 );

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

@@ -107,12 +107,12 @@ public AbstractGauss( final double[] sigma, final RandomAccessible< T > input, f
 		final Interval intervalTmp = getTemporaryImgSize();
 
 		if ( numDimensions > 1 )
-			tmp1 = factory.create( intervalTmp, getProcessingType() );
+			tmp1 = factory.create( intervalTmp );
 		else
 			tmp1 = null;
 
 		if ( numDimensions > 2 )
-			tmp2 = factory.create( intervalTmp, getProcessingType() );
+			tmp2 = factory.create( intervalTmp );
 		else
 			tmp2 = null;
 	}