N5ApiTools.setupMultiResolutionPyramid() now also creates s0 ...

PreibischLab · Sep 12, 2024 · 8ebe6d1 · 8ebe6d1
1 parent ec7db26
commit 8ebe6d1
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Showing 2 changed files with 31 additions and 43 deletions.
diff --git a/src/main/java/net/preibisch/mvrecon/process/export/ExportN5API.java b/src/main/java/net/preibisch/mvrecon/process/export/ExportN5API.java
@@ -252,14 +252,6 @@ else if ( FloatType.class.isInstance( type ) )
 			// this is the relative path to the dataset inside the Zarr/N5/HDF5 container, thus using File here seems fine
 			final String dataset = new File( new File( baseDataset , title ).toString(), datasetExtension ).toString();
 
-			// create s0 dataset
-			driverVolumeWriter.createDataset(
-					dataset,
-					bb.dimensionsAsLongArray(),
-					blocksize(),
-					dataType,
-					compression );
-
 			// setup multi-resolution pyramid
 			mrInfo = N5ApiTools.setupMultiResolutionPyramid(
 					driverVolumeWriter,

diff --git a/src/main/java/net/preibisch/mvrecon/process/n5api/N5ApiTools.java b/src/main/java/net/preibisch/mvrecon/process/n5api/N5ApiTools.java
@@ -2,6 +2,7 @@
 
 import java.io.Serializable;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collection;
 import java.util.HashMap;
 import java.util.List;
@@ -212,14 +213,26 @@ public static MultiResolutionLevelInfo[] setupMultiResolutionPyramid(
 	{
 		final MultiResolutionLevelInfo[] mrInfo = new MultiResolutionLevelInfo[ downsamplings.length];
 
+		// set up s0
+		int[] relativeDownsampling = downsamplings[ 0 ].clone();
+		Arrays.setAll( relativeDownsampling, i -> 1 );
+
 		mrInfo[ 0 ] = new MultiResolutionLevelInfo(
-				viewIdToDataset.apply( viewId, 0 ), dimensionsS0.clone(), dataType, downsamplings[ 0 ], downsamplings[ 0 ], blockSize );
+				viewIdToDataset.apply( viewId, 0 ), dimensionsS0.clone(), dataType, relativeDownsampling, downsamplings[ 0 ], blockSize );
+
+		driverVolumeWriter.createDataset(
+				viewIdToDataset.apply( viewId, 0 ),
+				dimensionsS0,
+				blockSize,
+				dataType,
+				compression );
 
 		long[] previousDim = dimensionsS0.clone();
 
+		// set up s1 ... sN
 		for ( int level = 1; level < downsamplings.length; ++level )
 		{
-			final int[] relativeDownsampling = computeRelativeDownsampling( downsamplings, level );
+			relativeDownsampling = computeRelativeDownsampling( downsamplings, level );
 
 			final String datasetLevel = viewIdToDataset.apply( viewId, level );
 
@@ -313,19 +326,21 @@ public static MultiResolutionLevelInfo[] setupBdvDatasetsN5(
 			final long[] dimensions,
 			final Compression compression,
 			final int[] blockSize,
-			final int[][] downsamplings )
+			int[][] downsamplings )
 	{
 		final String s0Dataset = createBDVPath( viewId, 0, StorageType.N5 );
+		final String setupDataset = s0Dataset.substring(0, s0Dataset.indexOf( "/timepoint" ));
+		final String timepointDataset = s0Dataset.substring(0, s0Dataset.indexOf("/s0" ));
 
-		driverVolumeWriter.createDataset(
-				s0Dataset,
+		final MultiResolutionLevelInfo[] mrInfo = setupMultiResolutionPyramid(
+				driverVolumeWriter,
+				viewId,
+				viewIdToDatasetBdv( StorageType.N5 ),
+				dataType,
 				dimensions,
+				compression,
 				blockSize,
-				dataType,
-				compression );
-
-		final String setupDataset = s0Dataset.substring(0, s0Dataset.indexOf( "/timepoint" ));
-		final String timepointDataset = s0Dataset.substring(0, s0Dataset.indexOf("/s0" ));
+				downsamplings);
 
 		final Map<String, Class<?>> attribs = driverVolumeWriter.listAttributes( setupDataset );
 
@@ -357,38 +372,19 @@ public static MultiResolutionLevelInfo[] setupBdvDatasetsN5(
 		driverVolumeWriter.setAttribute(timepointDataset, "saved_completely", true );
 		driverVolumeWriter.setAttribute(timepointDataset, "multiScale", downsamplings != null && downsamplings.length != 0 );
 
-		final MultiResolutionLevelInfo[] mrInfo;
-
 		if ( downsamplings == null || downsamplings.length == 0 )
 		{
-			// set additional N5 attributes for s0 dataset
-			driverVolumeWriter.setAttribute( s0Dataset, "downsamplingFactors", new int[] {1,1,1} );
-
-			mrInfo = new MultiResolutionLevelInfo[] { new MultiResolutionLevelInfo( s0Dataset, dimensions.clone(), dataType, new int[] {1,1,1}, new int[] {1,1,1}, blockSize ) };
+			downsamplings = new int[1][ dimensions.length ];
+			Arrays.setAll( downsamplings[ 0 ], i -> 1 );
 		}
-		else
-		{
-			mrInfo = setupMultiResolutionPyramid(
-					driverVolumeWriter,
-					viewId,
-					viewIdToDatasetBdv( StorageType.N5 ),
-					dataType,
-					dimensions,
-					compression,
-					blockSize,
-					downsamplings);
 
-			driverVolumeWriter.setAttribute( s0Dataset, "downsamplingFactors", downsamplings[ 0 ] );
-
-			for ( int level = 1; level < downsamplings.length; ++level )
-			{
-				// set additional N5 attributes for s0 ... sN datasets
-				driverVolumeWriter.setAttribute( mrInfo[ level ].dataset, "downsamplingFactors", downsamplings[ level ] );
-			}
-		}
+		// set additional N5 attributes for s0 ... sN datasets
+		for ( int level = 0; level < downsamplings.length; ++level )
+			driverVolumeWriter.setAttribute( mrInfo[ level ].dataset, "downsamplingFactors", mrInfo[ level ].absoluteDownsampling );
 
 		return mrInfo;
 	}
+
 	public static void writeDownsampledBlock(
 			final N5Writer n5,
 			final MultiResolutionLevelInfo mrInfo,