add compute block size as it is very useful and more explanations

src/main/java/net/preibisch/mvrecon/fiji/plugin/resave/ParametersResaveN5.java

@@ -22,6 +22,7 @@
  */
 package net.preibisch.mvrecon.fiji.plugin.resave;
 
+import java.awt.Color;
 import java.awt.Font;
 import java.net.URI;
 import java.net.URISyntaxException;
@@ -42,29 +43,36 @@
 import bdv.export.ProposeMipmaps;
 import fiji.util.gui.GenericDialogPlus;
 import mpicbg.spim.data.sequence.ViewSetup;
+import net.imglib2.Dimensions;
 import net.preibisch.legacy.io.IOFunctions;
+import net.preibisch.mvrecon.fiji.plugin.util.GUIHelper;
 
 public class ParametersResaveN5
 {
 	public static String[] compressions = new String[]{ "Bzip2", "Gzip", "Lz4", "Raw (no compression)", "Xz" };
 	public static int defaultBlockSize = 64;
 	public static int defaultBlockSizeXY = 128;
 	public static int defaultCompression = 1;
+
+	public static int defaultBlockSizeFactorX = 16;
+	public static int defaultBlockSizeFactorY = 16;
+	public static int defaultBlockSizeFactorZ = 1;
+
 	public static int defaultNumThreads = Math.max( 1, Runtime.getRuntime().availableProcessors() - 1 );
 
 	public URI xmlURI, n5URI;
 
+	public int[] blockSizeFactor;
 	public int[][] resolutions, subdivisions;
 	public Map< Integer, ExportMipmapInfo > proposedMipmaps;
 
 	public Compression compression;
 	public int numCellCreatorThreads = 1;
 
-	//public boolean saveXML = true; // mostly important for cluster-based re-saving
-	//public boolean saveData = true; // mostly important for cluster-based re-saving
-
-	//public boolean setFinishedAttributeInN5 = true; // required if double-checking that all ViewId were written
-	//final public static String finishedAttrib = "saved_completely"; // required if double-checking that all ViewId were written
+	public static URI createN5URIfromXMLURI( final URI xmlURI )
+	{
+		return URI.create( xmlURI.toString().subSequence( 0, xmlURI.toString().length() - 4 ) + ".n5" );
+	}
 
 	public static ParametersResaveN5 getParamtersIJ(
 			final Collection< ViewSetup > setupsToProcess )
@@ -82,11 +90,6 @@ public static ParametersResaveN5 getParamtersIJ(
 		return getParamtersIJ( xmlURI, n5URI, setupsToProcess, askForPaths );
 	}
 
-	public static URI createN5URIfromXMLURI( final URI xmlURI )
-	{
-		return URI.create( xmlURI.toString().subSequence( 0, xmlURI.toString().length() - 4 ) + ".n5" );
-	}
-
 	public static ParametersResaveN5 getParamtersIJ(
 			final URI xmlURI,
 			final URI n5URI,
@@ -108,13 +111,27 @@ public static ParametersResaveN5 getParamtersIJ(
 				row[ 1 ] = ParametersResaveN5.defaultBlockSizeXY;
 		}
 
+		final long[] maxDimensions = setupsToProcess.iterator().next().getSize().dimensionsAsLongArray();
+
+		setupsToProcess.forEach( viewSetup ->
+		{
+			for ( int d = 0; d < maxDimensions.length; ++d )
+				maxDimensions[ d ] = Math.max( maxDimensions[ d ], viewSetup.getSize().dimension( d ) );
+		} );
+
 		final GenericDialogPlus gdp = new GenericDialogPlus( "Options" );
 
 		gdp.addMessage( "N5 saving options", new Font( Font.SANS_SERIF, Font.BOLD, 13 ) );
 
 		gdp.addChoice( "Compression", compressions, compressions[ defaultCompression ] );
 		gdp.addStringField( "Downsampling_factors", ProposeMipmaps.getArrayString( autoMipmapSettings.getExportResolutions() ), 40 );
 		gdp.addStringField( "Block_size (all the same)", ProposeMipmaps.getArrayString( autoMipmapSettings.getSubdivisions() ), 40 );
+		gdp.addSlider( "Compute_block_size_factor_X", 1, 128, defaultBlockSizeFactorX );
+		gdp.addSlider( "Compute_block_size_factor_Y", 1, 128, defaultBlockSizeFactorY );
+		gdp.addSlider( "Compute_block_size_factor_Z", 1, 128, defaultBlockSizeFactorZ );
+		gdp.addMessage( "Defines how many blocks are written at once; e.g. 4,4,1 & blockSize 128,128,32 means each thread writes 512,512,32 chunks.\n"
+				+ "For optimal performance, the size in XY is as large as each XY plane, as usually entire planes must be read.", GUIHelper.smallStatusFont );
+		gdp.addMessage( "Max dimensions of the images that will be re-saved: " + Arrays.toString( maxDimensions ), GUIHelper.smallStatusFont, Color.red );
 		gdp.addNumericField( "Number_of_threads (CPUs:" + Runtime.getRuntime().availableProcessors() + ")", defaultNumThreads, 0 );
 
 		if ( askForPaths )
@@ -134,6 +151,11 @@ public static ParametersResaveN5 getParamtersIJ(
 		final String subsampling = gdp.getNextString();
 		final String chunkSizes = gdp.getNextString();
 
+		final int blockSizeFactorX = defaultBlockSizeFactorX = Math.max( 1, (int)Math.round( gdp.getNextNumber() ) );
+		final int blockSizeFactorY = defaultBlockSizeFactorY = Math.max( 1, (int)Math.round( gdp.getNextNumber() ) );
+		final int blockSizeFactorZ = defaultBlockSizeFactorZ = Math.max( 1, (int)Math.round( gdp.getNextNumber() ) );
+
+		n5params.blockSizeFactor = new int[] { blockSizeFactorX, blockSizeFactorY, blockSizeFactorZ };
 		n5params.numCellCreatorThreads = defaultNumThreads = Math.max( 1, (int)Math.round( gdp.getNextNumber() ) );
 
 		if ( askForPaths )

src/main/java/net/preibisch/mvrecon/fiji/plugin/resave/Resave_N5.java

@@ -183,7 +183,6 @@ else if ( URITools.isS3( n5Params.n5URI ) || URITools.isGC( n5Params.n5URI ) )*/
 			//
 			// Save remaining downsampling levels (s1 ... sN)
 			//
-
 			for ( int level = 1; level < downsamplings.length; ++level )
 			{
 				final int s = level;