feat: add Downsample from bdv

Author: cmhulbert

src/main/java/org/janelia/saalfeldlab/n5/spark/util/Downsample.java

@@ -0,0 +1,97 @@
+/*
+ * Copied from bdv.export.Downsample (bigdataviewer-core), since it was removed in
+ * bigdataviewer-core 10.5.0.
+ * Original license below.
+ *
+ * #%L
+ * BigDataViewer core classes with minimal dependencies.
+ * %%
+ * Copyright (C) 2012 - 2024 BigDataViewer developers.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+package org.janelia.saalfeldlab.n5.spark.util;
+
+import net.imglib2.Cursor;
+import net.imglib2.FinalInterval;
+import net.imglib2.Interval;
+import net.imglib2.RandomAccess;
+import net.imglib2.RandomAccessible;
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.algorithm.neighborhood.Neighborhood;
+import net.imglib2.algorithm.neighborhood.RectangleNeighborhoodFactory;
+import net.imglib2.algorithm.neighborhood.RectangleNeighborhoodUnsafe;
+import net.imglib2.algorithm.neighborhood.RectangleShape;
+import net.imglib2.type.numeric.RealType;
+import net.imglib2.view.Views;
+
+public class Downsample
+{
+	/**
+	 * TODO: Revise. This is probably not very efficient
+	 */
+	public static < T extends RealType< T > > void downsample( final RandomAccessible< T > input, final RandomAccessibleInterval< T > output, final int[] factor )
+	{
+		assert input.numDimensions() == output.numDimensions();
+		assert input.numDimensions() == factor.length;
+
+		final int n = input.numDimensions();
+		final RectangleNeighborhoodFactory< T > f = RectangleNeighborhoodUnsafe.< T >factory();
+		final long[] dim = new long[ n ];
+		for ( int d = 0; d < n; ++d )
+			dim[ d ] = factor[ d ];
+		final Interval spanInterval = new FinalInterval( dim );
+
+		final long[] minRequiredInput = new long[ n ];
+		final long[] maxRequiredInput = new long[ n ];
+		output.min( minRequiredInput );
+		output.max( maxRequiredInput );
+		for ( int d = 0; d < n; ++d )
+		{
+			minRequiredInput[ d ] *= factor[ d ];
+			maxRequiredInput[ d ] *= factor[ d ];
+			maxRequiredInput[ d ] += factor[ d ] - 1;
+		}
+		final RandomAccessibleInterval< T > requiredInput = Views.interval( input, new FinalInterval( minRequiredInput, maxRequiredInput ) );
+
+		final RectangleShape.NeighborhoodsAccessible< T > neighborhoods = new RectangleShape.NeighborhoodsAccessible<>( requiredInput, spanInterval, f );
+		final RandomAccess< Neighborhood< T > > block = neighborhoods.randomAccess();
+
+		long size = 1;
+		for ( int d = 0; d < n; ++d )
+			size *= factor[ d ];
+		final double scale = 1.0 / size;
+
+		final Cursor< T > out = Views.iterable( output ).localizingCursor();
+		while( out.hasNext() )
+		{
+			final T o = out.next();
+			for ( int d = 0; d < n; ++d )
+				block.setPosition( out.getLongPosition( d ) * factor[ d ], d );
+			double sum = 0;
+			for ( final T i : block.get() )
+				sum += i.getRealDouble();
+			o.setReal( sum * scale );
+		}
+	}
+}