From ae1fd673df53c97dc2de0d8dd1585cdf54067f89 Mon Sep 17 00:00:00 2001
From: tpietzsch <tobias.pietzsch@gmail.com>
Date: Tue, 24 Sep 2024 12:33:19 +0200
Subject: [PATCH] Speed-up DOWN_AVERAGE downsampling for NativeType

---
 .../n5/ij/N5ScalePyramidExporter.java         | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/src/main/java/org/janelia/saalfeldlab/n5/ij/N5ScalePyramidExporter.java b/src/main/java/org/janelia/saalfeldlab/n5/ij/N5ScalePyramidExporter.java
index 51b8e780..f62380b2 100644
--- a/src/main/java/org/janelia/saalfeldlab/n5/ij/N5ScalePyramidExporter.java
+++ b/src/main/java/org/janelia/saalfeldlab/n5/ij/N5ScalePyramidExporter.java
@@ -57,6 +57,11 @@
 import javax.swing.JTextPane;
 import javax.swing.UIManager;
 
+import net.imglib2.algorithm.blocks.BlockAlgoUtils;
+import net.imglib2.algorithm.blocks.BlockSupplier;
+import net.imglib2.algorithm.blocks.downsample.Downsample;
+import net.imglib2.util.Util;
+import net.imglib2.view.fluent.RandomAccessibleIntervalView.Extension;
 import org.janelia.saalfeldlab.n5.Compression;
 import org.janelia.saalfeldlab.n5.DatasetAttributes;
 import org.janelia.saalfeldlab.n5.GzipCompression;
@@ -1282,6 +1287,10 @@ private static <T extends NumericType<T>> RandomAccessibleInterval<T> downsample
 			}
 		}
 
+		if (img.getType() instanceof NativeType) {
+			return downsampleAvgBy2NativeType((RandomAccessibleInterval) img, Util.long2int(downsampleFactors), dims);
+		}
+
 		// TODO clamping NLinearInterpFactory when relevant
 		// TODO record offset in metadata as (s-0.5)
 		final RealRandomAccessible<T> imgE = Views.interpolate(Views.extendBorder(img), new NLinearInterpolatorFactory());
@@ -1289,6 +1298,16 @@ private static <T extends NumericType<T>> RandomAccessibleInterval<T> downsample
 				new FinalInterval(dims));
 	}
 
+	private static <T extends NativeType<T>> RandomAccessibleInterval<T> downsampleAvgBy2NativeType(
+			final RandomAccessibleInterval<T> img, final int[] downsampleFactors, final long[] dimensions) {
+
+		final int[] cellDimensions = new int[] {32};
+		final BlockSupplier<T> blocks = BlockSupplier
+				.of(img.view().extend(Extension.border()))
+				.andThen(Downsample.downsample(downsampleFactors));
+		return BlockAlgoUtils.cellImg(blocks, dimensions, cellDimensions);
+	}
+
 	private int[] sliceBlockSize(final int exclude) {
 
 		return removeElement(chunkSize, exclude);