changes based on multiview reconstruction scale fixes

Author: cgoina

pom.xml

@@ -103,7 +103,7 @@
 		<bigdataviewer-n5.version>1.0.2</bigdataviewer-n5.version>
 
 		<spim_data.version>2.3.5</spim_data.version>
-		<multiview-reconstruction.version>8.0.0</multiview-reconstruction.version>
+		<multiview-reconstruction.version>8.0.1-SNAPSHOT</multiview-reconstruction.version>
 		<BigStitcher.version>2.5.0</BigStitcher.version>
 
 		<n5-universe.version>2.3.0</n5-universe.version>

src/main/java/net/preibisch/bigstitcher/spark/CreateFusionContainer.java

@@ -59,7 +59,7 @@ public class CreateFusionContainer extends AbstractBasic implements Callable<Voi
 {
 	private static final long serialVersionUID = -9140450542904228386L;
 
-	public static enum Compressions { Lz4, Gzip, Zstandard, Blosc, Bzip2, Xz, Raw };
+	public enum Compressions { Lz4, Gzip, Zstandard, Blosc, Bzip2, Xz, Raw };
 
 	@Option(names = { "-o", "--outputPath" }, required = true, description = "OME-ZARR/N5/HDF5 path for saving, e.g. -o /home/fused.zarr, file:/home/fused.n5 or e.g. s3://myBucket/data.zarr")
 	private String outputPathURIString = null;
@@ -365,8 +365,8 @@ else if ( storageType == StorageFormat.N5 || storageType == StorageFormat.ZARR )
 			// extract the resolution of the s0 export
 			// TODO: this is inaccurate, we should actually estimate it from the final transformn that is applied
 			// TODO: this is a hack (returns 1,1,1) so the export downsampling pyramid is working
-			final VoxelDimensions vx = new FinalVoxelDimensions( "micrometer", new double[] { 1, 1, 1 } );// dataGlobal.getSequenceDescription().getViewSetupsOrdered().iterator().next().getVoxelSize();
-			final double[] resolutionS0 = OMEZarrAttibutes.getResolutionS0( vx, anisotropyFactor, Double.NaN );
+			final VoxelDimensions vx = dataGlobal.getSequenceDescription().getViewSetupsOrdered().iterator().next().getVoxelSize();
+			final double[] resolutionS0 = OMEZarrAttibutes.getResolutionS0( vx );
 
 			System.out.println( "Resolution of level 0: " + Util.printCoordinates( resolutionS0 ) + " " + "micrometer" ); //vx.unit() might not be OME-ZARR compatiblevx.unit() );
 
@@ -410,10 +410,8 @@ else if ( storageType == StorageFormat.ZARR )
 				tps.add( new TimePoint( t ) );
 
 			// extract the resolution of the s0 export
-			// TODO: this is inaccurate, we should actually estimate it from the final transformn that is applied
-			// TODO: this is a hack (returns 1,1,1) so the export downsampling pyramid is working
-			final VoxelDimensions vx = new FinalVoxelDimensions( "micrometer", new double[] { 1, 1, 1 } );// dataGlobal.getSequenceDescription().getViewSetupsOrdered().iterator().next().getVoxelSize();
-			final double[] resolutionS0 = OMEZarrAttibutes.getResolutionS0( vx, anisotropyFactor, Double.NaN );
+			final VoxelDimensions vx = dataGlobal.getSequenceDescription().getViewSetupsOrdered().iterator().next().getVoxelSize();
+			final double[] resolutionS0 = OMEZarrAttibutes.getResolutionS0( vx );
 
 			System.out.println( "Resolution of level 0: " + Util.printCoordinates( resolutionS0 ) + " " + "m" ); //vx.unit() might not be OME-ZARR compatiblevx.unit() );
 

src/main/java/net/preibisch/bigstitcher/spark/SparkAffineFusion.java

@@ -33,7 +33,6 @@
 import java.util.concurrent.Callable;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
-import java.util.stream.Collectors;
 
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;
@@ -153,7 +152,6 @@ public enum DataTypeFusion
 	@Option(names = { "--prefetch" }, description = "prefetch all blocks required for fusion in each Spark job using unlimited threads, useful in cloud environments (default: false)")
 	protected boolean prefetch = false;
 
-
 	// TODO: add support for loading coefficients during fusion
 	@CommandLine.Option(names = { "--intensityN5Path" }, description = "N5/ZARR/HDF5 base path for loading coefficients (e.g. s3://myBucket/coefficients.n5)")
 	private String intensityN5PathURIString = null;
@@ -540,11 +538,7 @@ else if ( dataType == DataType.UINT16 )
 							return gridBlock;
 
 						// load intensity correction coefficients for all overlapping views
-
-
 						final Map< ViewId, Coefficients > coefficients;
-
-
 						if ( intensityN5PathURI != null )
 						{
 							coefficients = new HashMap<>();
@@ -598,7 +592,6 @@ else if ( dataType == DataType.UINT16 )
 							System.out.println( "Fusing block: offset=" + Util.printCoordinates( gridBlock[0] ) + ", dimension=" + Util.printCoordinates( gridBlock[1] ) );
 
 							// returns a zero-min interval
-							//blockSupplier = BlkAffineFusion.init(
 							blockSupplier = BlkAffineFusion.initWithIntensityCoefficients(
 									conv,
 									dataLocal.getSequenceDescription().getImgLoader(),

src/main/java/net/preibisch/bigstitcher/spark/SparkResaveN5.java

@@ -248,7 +248,7 @@ public Void call() throws Exception
 								viewId,
 								dataTypes.get( viewId.getViewSetupId() ),
 								dimensions.get( viewId.getViewSetupId() ),
-								//dataGlobal.getSequenceDescription().getViewDescription( viewId ).getViewSetup().getVoxelSize().dimensionsAsDoubleArray(), // TODO: this is a hack for now
+								dataGlobal.getSequenceDescription().getViewDescription( viewId ).getViewSetup().getVoxelSize().dimensionsAsDoubleArray(),
 								compression,
 								blockSize,
 								downsamplings);