add --surfaceBlockSize parameter that allows default 128,128 value

src/main/java/org/janelia/saalfeldlab/hotknife/SparkComputeCostMultiSem.java

@@ -151,6 +151,13 @@ public String getCostDatasetName(final int index) {
 		@Option(name = "--surfaceMaxDistance", usage = "maximum distance between the both surfaces, e.g. 30")
 		private double surfaceMaxDistance = 30;
 
+		@Option(name = "--surfaceBlockSize", usage = "surface block size in pixels, e.g. 128,128")
+		private String surfaceBlockSizeString = "128,128";
+
+		private long[] getSurfaceBlockSize() {
+			return parseCSLongArray(surfaceBlockSizeString);
+		}
+
 		@Option(name = "--localSparkBindAddress", usage = "specify Spark bind address as localhost")
 		private boolean localSparkBindAddress = false;
 
@@ -195,6 +202,9 @@ public static void computeCost(
 		System.out.println("median Z: " + options.median );
 		System.out.println("smooth cost Z: " + options.smoothCost );
 
+		final long[] surfaceBlockSize = options.getSurfaceBlockSize();
+		System.out.println("surfaceBlockSize: " + Util.printCoordinates(surfaceBlockSize) );
+
 		final N5Reader n5 = new N5FSReader(n5Path);
 		final N5Writer n5w = new N5FSWriter(costN5Path);
 
@@ -321,7 +331,8 @@ public static void computeCost(
 																  options.surfaceMaxDistance,
 																  true, // no need to permute with multi-sem
 																  false);
-			sparkSurfaceFit.callWithSparkContext(sparkContext);
+			sparkSurfaceFit.callWithSparkContext(sparkContext,
+												 options.getSurfaceBlockSize());
 		}
 	}
 

src/main/java/org/janelia/saalfeldlab/hotknife/SparkSurfaceFit.java

@@ -16,6 +16,8 @@
  */
 package org.janelia.saalfeldlab.hotknife;
 
+import com.beust.jcommander.Parameter;
+
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Paths;
@@ -1408,6 +1410,12 @@ else if ( IntegerType.class.isInstance( t ) )
 
 	public void callWithSparkContext(final JavaSparkContext sc)
 			throws IOException {
+		callWithSparkContext(sc, new long[] {128, 128});
+	}
+
+	public void callWithSparkContext(final JavaSparkContext sc,
+									 final long[] blockSize)
+			throws IOException {
 
 		final N5Reader n5 = isZarr( n5Path ) ? new N5ZarrReader( n5Path ) : new N5FSReader(n5Path);
 
@@ -1491,7 +1499,6 @@ public void callWithSparkContext(final JavaSparkContext sc)
 
 			System.out.println( "Processing scale: " + s );
 
-			final long[] blockSize = new long[] {128, 128};
 			final long[] blockPadding = new long[] {32, 32};
 
 			final double maxDeltaZ = (s == lastScaleIndex ) ? this.finalMaxDeltaZ : this.maxDeltaZ;