Merge branch 'master' of github.com:PreibischLab/multiview-reconstruc…

…tion
PreibischLab · Sep 9, 2024 · 878cc19 · 878cc19
2 parents d65b1df + 0ba6e36
commit 878cc19
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diff --git a/src/main/java/net/preibisch/mvrecon/fiji/plugin/resave/Resave_N5.java b/src/main/java/net/preibisch/mvrecon/fiji/plugin/resave/Resave_N5.java
@@ -200,7 +200,7 @@ else if ( URITools.isS3( n5Params.n5URI ) || URITools.isGC( n5Params.n5URI ) )*/
 				IOFunctions.println( "Downsampling: " + Util.printCoordinates( downsamplings[ s ] ) + " with relative downsampling of " + Util.printCoordinates( ds ));
 
 				final ArrayList<long[][]> allBlocks =
-						N5ResaveTools.prepareDownsampling( vidsToResave, n5Writer, level, downsamplings[ s ], ds, blockSize, compression );
+						N5ResaveTools.prepareDownsampling( vidsToResave, n5Writer, level, ds, downsamplings[ s ], blockSize, compression );
 
 				time = System.currentTimeMillis();
 

diff --git a/src/main/java/net/preibisch/mvrecon/process/resave/N5ResaveTools.java b/src/main/java/net/preibisch/mvrecon/process/resave/N5ResaveTools.java
@@ -24,9 +24,11 @@
 import mpicbg.spim.data.sequence.ViewSetup;
 import net.imglib2.FinalInterval;
 import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.type.NativeType;
 import net.imglib2.type.numeric.integer.UnsignedByteType;
 import net.imglib2.type.numeric.integer.UnsignedShortType;
 import net.imglib2.type.numeric.real.FloatType;
+import net.imglib2.util.Cast;
 import net.imglib2.util.Util;
 import net.imglib2.view.Views;
 import net.preibisch.legacy.io.IOFunctions;
@@ -200,7 +202,7 @@ public static ArrayList<long[][]> prepareDownsampling(
 				});
 
 			// set additional N5 attributes for sN dataset
-			n5.setAttribute(dataset, "downsamplingFactors", absoluteDownsampling[ level ] );
+			n5.setAttribute(dataset, "downsamplingFactors", absoluteDownsampling);
 		}
 
 		return allBlocks;
@@ -254,47 +256,27 @@ public static void createS0Datasets(
 		}
 	}
 
-	public static void resaveS0Block(
+	public static <T extends NativeType<T>> void resaveS0Block(
 			final SpimData2 data,
 			final N5Writer n5,
 			final DataType dataType,
 			final Function<long[][], String> gridBlockToDataset, // gridBlock to dataset name for s0
 			final long[][] gridBlock )
 	{
 		final ViewId viewId = new ViewId( (int)gridBlock[ 3 ][ 0 ], (int)gridBlock[ 3 ][ 1 ]);
+		final String dataset = gridBlockToDataset.apply( gridBlock );
 
-		final SetupImgLoader< ? > imgLoader = data.getSequenceDescription().getImgLoader().getSetupImgLoader( viewId.getViewSetupId() );
-
-		@SuppressWarnings("rawtypes")
-		final RandomAccessibleInterval img = imgLoader.getImage( viewId.getTimePointId() );
-
-		//final DataType dataType = n5.getAttribute( "setup" + viewId.getViewSetupId(), "dataType", DataType.class );
-		final String dataset = gridBlockToDataset.apply( gridBlock );// "setup" + viewId.getViewSetupId() + "/timepoint" + viewId.getTimePointId() + "/s0";
-
-		if ( dataType == DataType.UINT16 )
-		{
-			@SuppressWarnings("unchecked")
-			final RandomAccessibleInterval<UnsignedShortType> sourceGridBlock = Views.offsetInterval(img, gridBlock[0], gridBlock[1]);
-			N5Utils.saveNonEmptyBlock(sourceGridBlock, n5, dataset, gridBlock[2], new UnsignedShortType());
-		}
-		else if ( dataType == DataType.UINT8 )
-		{
-			@SuppressWarnings("unchecked")
-			final RandomAccessibleInterval<UnsignedByteType> sourceGridBlock = Views.offsetInterval(img, gridBlock[0], gridBlock[1]);
-			N5Utils.saveNonEmptyBlock(sourceGridBlock, n5, dataset, gridBlock[2], new UnsignedByteType());
-		}
-		else if ( dataType == DataType.FLOAT32 )
-		{
-			@SuppressWarnings("unchecked")
-			final RandomAccessibleInterval<FloatType> sourceGridBlock = Views.offsetInterval(img, 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 SetupImgLoader< ? > imgLoader = data.getSequenceDescription().getImgLoader().getSetupImgLoader( viewId.getViewSetupId() );
+		final RandomAccessibleInterval< T > img = Cast.unchecked( imgLoader.getImage( viewId.getTimePointId() ) );
+		final RandomAccessibleInterval< T > sourceGridBlock = Views.offsetInterval( img, gridBlock[ 0 ], gridBlock[ 1 ] );
+		N5Utils.saveNonEmptyBlock( sourceGridBlock, n5, dataset, gridBlock[ 2 ], img.getType().createVariable() );
+
 		System.out.println( "ViewId " + Group.pvid( viewId ) + ", written block: offset=" + Util.printCoordinates( gridBlock[0] ) + ", dimension=" + Util.printCoordinates( gridBlock[1] ) );
 	}