Use PrimitiveBlocks for downsampling

PreibischLab · Sep 25, 2024 · c6e0de2 · c6e0de2
1 parent 4516879
commit c6e0de2
Showing 1 changed file with 18 additions and 52 deletions.
diff --git a/src/main/java/net/preibisch/mvrecon/process/n5api/N5ApiTools.java b/src/main/java/net/preibisch/mvrecon/process/n5api/N5ApiTools.java
@@ -25,11 +25,16 @@
 import mpicbg.spim.data.sequence.ViewDescription;
 import mpicbg.spim.data.sequence.ViewId;
 import mpicbg.spim.data.sequence.ViewSetup;
-import net.imglib2.FinalInterval;
+import mpicbg.spim.data.sequence.VoxelDimensions;
+import net.imglib2.Dimensions;
 import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.algorithm.blocks.BlockAlgoUtils;
+import net.imglib2.algorithm.blocks.BlockSupplier;
+import net.imglib2.algorithm.blocks.downsample.Downsample;
 import net.imglib2.img.Img;
 import net.imglib2.img.array.ArrayImgs;
 import net.imglib2.type.NativeType;
+import net.imglib2.type.numeric.RealType;
 import net.imglib2.type.numeric.integer.IntType;
 import net.imglib2.type.numeric.integer.UnsignedByteType;
 import net.imglib2.type.numeric.integer.UnsignedShortType;
@@ -40,7 +45,6 @@
 import net.imglib2.view.Views;
 import net.preibisch.legacy.io.IOFunctions;
 import net.preibisch.mvrecon.fiji.spimdata.SpimData2;
-import net.preibisch.mvrecon.process.downsampling.lazy.LazyHalfPixelDownsample2x;
 import net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group;
 import util.Grid;
 
@@ -385,7 +389,7 @@ public static MultiResolutionLevelInfo[] setupBdvDatasetsN5(
 		return mrInfo;
 	}
 
-	public static void writeDownsampledBlock(
+	public static < T extends NativeType< T > & RealType< T > > void writeDownsampledBlock(
 			final N5Writer n5,
 			final MultiResolutionLevelInfo mrInfo,
 			final MultiResolutionLevelInfo mrInfoPreviousScale,
@@ -400,59 +404,21 @@ public static void writeDownsampledBlock(
 		final DataType dataType = mrInfo.dataType;// n5.getAttribute( datasetPreviousScale, DatasetAttributes.DATA_TYPE_KEY, DataType.class );
 		final int[] blockSize = mrInfo.blockSize;// n5.getAttribute( datasetPreviousScale, DatasetAttributes.BLOCK_SIZE_KEY, int[].class );
 
-		if ( dataType == DataType.UINT16 )
-		{
-			RandomAccessibleInterval<UnsignedShortType> downsampled = N5Utils.open(n5, datasetPreviousScale);
-
-			for ( int d = 0; d < downsampled.numDimensions(); ++d )
-				if ( mrInfo.relativeDownsampling[ d ] > 1 )
-					downsampled = LazyHalfPixelDownsample2x.init(
-						downsampled,
-						new FinalInterval( downsampled ),
-						new UnsignedShortType(),
-						blockSize,
-						d);
-
-			final RandomAccessibleInterval<UnsignedShortType> sourceGridBlock = Views.offsetInterval(downsampled, gridBlock[0], gridBlock[1]);
-			N5Utils.saveNonEmptyBlock(sourceGridBlock, n5, dataset, gridBlock[2], new UnsignedShortType());
-		}
-		else if ( dataType == DataType.UINT8 )
-		{
-			RandomAccessibleInterval<UnsignedByteType> downsampled = N5Utils.open(n5, datasetPreviousScale);
-
-			for ( int d = 0; d < downsampled.numDimensions(); ++d )
-				if ( mrInfo.relativeDownsampling[ d ] > 1 )
-					downsampled = LazyHalfPixelDownsample2x.init(
-						downsampled,
-						new FinalInterval( downsampled ),
-						new UnsignedByteType(),
-						blockSize,
-						d);
-
-			final RandomAccessibleInterval<UnsignedByteType> sourceGridBlock = Views.offsetInterval(downsampled, gridBlock[0], gridBlock[1]);
-			N5Utils.saveNonEmptyBlock(sourceGridBlock, n5, dataset, gridBlock[2], new UnsignedByteType());
-		}
-		else if ( dataType == DataType.FLOAT32 )
-		{
-			RandomAccessibleInterval<FloatType> downsampled = N5Utils.open(n5, datasetPreviousScale);;
-
-			for ( int d = 0; d < downsampled.numDimensions(); ++d )
-				if ( mrInfo.relativeDownsampling[ d ] > 1 )
-					downsampled = LazyHalfPixelDownsample2x.init(
-						downsampled,
-						new FinalInterval( downsampled ),
-						new FloatType(),
-						blockSize,
-						d);
-
-			final RandomAccessibleInterval<FloatType> sourceGridBlock = Views.offsetInterval(downsampled, gridBlock[0], gridBlock[1]);
-			N5Utils.saveNonEmptyBlock(sourceGridBlock, n5, dataset, gridBlock[2], new FloatType());
-		}
-		else
+		if ( dataType != DataType.UINT16 && dataType != DataType.UINT8 && dataType != DataType.FLOAT32 )
 		{
 			n5.close();
 			throw new RuntimeException("Unsupported pixel type: " + dataType );
 		}
+
+		final RandomAccessibleInterval<T> previousScale = N5Utils.open(n5, datasetPreviousScale);
+		final T type = previousScale.getType().createVariable();
+
+		final BlockSupplier< T > blocks = BlockSupplier.of( previousScale ).andThen( Downsample.downsample( mrInfo.relativeDownsampling ) );
+		final long[] dimensions = n5.getAttribute( dataset, DatasetAttributes.DIMENSIONS_KEY, long[].class );
+		final RandomAccessibleInterval< T > downsampled = BlockAlgoUtils.cellImg( blocks, dimensions, new int[] { 64 } );
+
+		final RandomAccessibleInterval<T> sourceGridBlock = Views.offsetInterval(downsampled, gridBlock[0], gridBlock[1]);
+		N5Utils.saveNonEmptyBlock(sourceGridBlock, n5, dataset, gridBlock[2], type);
 	}
 
 	public static ArrayList<long[][]> assembleJobs( final MultiResolutionLevelInfo mrInfo )