Fix the scale and translation transformations in OME-ZARR metadata

src/main/java/net/preibisch/mvrecon/fiji/plugin/resave/Resave_N5Api.java

@@ -39,6 +39,7 @@
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.stream.Collectors;
 
+import mpicbg.spim.data.sequence.VoxelDimensions;
 import org.bigdataviewer.n5.N5CloudImageLoader;
 import org.janelia.saalfeldlab.n5.Compression;
 import org.janelia.saalfeldlab.n5.DataType;
@@ -188,13 +189,15 @@ else if ( n5Params.format == StorageFormat.HDF5 )
 							}
 							else
 							{
+								VoxelDimensions vx = data.getSequenceDescription().getViewDescription( viewId ).getViewSetup().getVoxelSize();
 								// 5d OME-ZARR with dimension=1 in c and t
 								mrInfo = N5ApiTools.setupBdvDatasetsOMEZARR(
 										n5Writer,
 										viewId,
 										dataTypes.get( viewId.getViewSetupId() ),
 										dimensions.get( viewId.getViewSetupId() ),
-										//data.getSequenceDescription().getViewDescription( viewId ).getViewSetup().getVoxelSize().dimensionsAsDoubleArray(),
+										vx.dimensionsAsDoubleArray(), // resolutionS0
+										vx.unit(),
 										compression,
 										blockSize,
 										downsamplings);

src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/OMEZarrAttibutes.java

@@ -39,9 +39,7 @@
 import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.coordinateTransformations.ScaleCoordinateTransformation;
 import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.coordinateTransformations.TranslationCoordinateTransformation;
 
-import mpicbg.spim.data.sequence.VoxelDimensions;
 import net.imglib2.realtransform.AffineTransform3D;
-import net.preibisch.mvrecon.process.interestpointregistration.TransformationTools;
 import util.URITools;
 
 public class OMEZarrAttibutes
@@ -61,12 +59,6 @@ public static OmeNgffMultiScaleMetadata[] createOMEZarrMetadata(
 			final Function<Integer, String> levelToName,
 			final Function<Integer, AffineTransform3D > levelToMipmapTransform )
 	{
-		// TODO: make sure the unit is supported by OME-ZARR, if not replace it because otherwise readers will fail
-		// TODO: e.g. um -> micrometer
-		// TODO: etc.
-		// TODO: can you find out what the correct unit for 'unit unknown' is, because that is what I would replace it with, otherwise micrometer
-		// TOOD: then please also change in TransformationTools.computeCalibration
-
 		final OmeNgffMultiScaleMetadata[] meta = new OmeNgffMultiScaleMetadata[ 1 ];
 
 		// dataset name and co
@@ -85,9 +77,10 @@ public static OmeNgffMultiScaleMetadata[] createOMEZarrMetadata(
 		if ( n >= 4 )
 			axes[ index++ ] = new Axis( "channel", "c", null );
 
-		axes[ index++ ] = new Axis( "space", "z", unitXYZ );
-		axes[ index++ ] = new Axis( "space", "y", unitXYZ );
-		axes[ index++ ] = new Axis( "space", "x", unitXYZ );
+		String unit = adaptSpatialUnit( unitXYZ );
+		axes[ index ] = new Axis( "space", "z", unit );
+		axes[ index + 1 ] = new Axis( "space", "y", unit );
+		axes[ index + 2 ] = new Axis( "space", "x", unit );
 
 		// multiresolution-pyramid
 		// TODO: seem to be in XYZCT order (but in the file it seems reversed)
@@ -106,8 +99,8 @@ public static OmeNgffMultiScaleMetadata[] createOMEZarrMetadata(
 
 			for ( int d = 0; d < 3; ++d )
 			{
-				translation[ d ] = m.getTranslation()[ d ];
-				scale[ d ] = resolutionS0[ d ] * m.get( d, d );
+				translation[ d ] = resolutionS0[d] * m.getTranslation()[ d ];
+				scale[ d ] = resolutionS0[d] * m.get( d, d );
 			}
 
 			// if 4d and 5d, add 1's for C and T
@@ -137,27 +130,74 @@ public static OmeNgffMultiScaleMetadata[] createOMEZarrMetadata(
 		return meta;
 	}
 
-
-	// Note: TransformationTools.computeAverageCalibration does this reasonably correct
-	/*
-	public static double[] getResolutionS0( final VoxelDimensions vx, final double anisoF, final double downsamplingF )
+	public static double[] getResolutionS0( final double[] cal, final double anisoF, final double downsamplingF )
 	{
-		final double[] resolutionS0 = vx.dimensionsAsDoubleArray();
+		double[] resolutionS0 = Arrays.copyOf( cal, cal.length );
 
-		// not preserving anisotropy
-		if ( Double.isNaN( anisoF ) )
-			resolutionS0[ 2 ] = resolutionS0[ 0 ];
+		if ( !Double.isNaN( anisoF ) ) {
+			// preserving anisotropy
+			resolutionS0[2] = cal[2] * anisoF;
+		}
 
 		// downsampling
 		if ( !Double.isNaN( downsamplingF ) )
 			Arrays.setAll( resolutionS0, d -> resolutionS0[ d ] * downsamplingF );
 
-		// TODO: this is a hack so the export downsampling pyramid is working
-		Arrays.setAll( resolutionS0, d -> 1 );
-
 		return resolutionS0;
 	}
-	*/
+
+	/**
+	 * Adapt various space unit namings to the units supported by Neuroglancer.
+	 * OME NGFF spec does not have any restrictions on units but Neuroglancer only supports the ones that end in meter or the US customary units.
+	 * @param unit
+	 * @return
+	 */
+	private static String adaptSpatialUnit(String unit)
+	{
+		if ( unit == null )
+			return "micrometer";
+
+		switch ( unit.toLowerCase() ) {
+			case "angstrom":
+			case "ångström":
+			case "ångströms":
+				return "angstrom";
+			case "nm":
+			case "nanometers":
+			case "nanometer":
+				return "nanometer";
+			case "mm":
+			case "millimeters":
+			case "millimeter":
+				return "millimeter";
+			case "m":
+			case "meters":
+			case "meter":
+				return "meter";
+			case "km":
+			case "kilometer":
+			case "kilometers":
+				return "kilometer";
+			case "inch":
+			case "inches":
+				return "inch";
+			case "foot":
+			case "feet":
+				return "foot";
+			case "yard":
+			case "yards":
+				return "yard";
+			case "mile":
+			case "miles":
+				return "mile";
+			case "um":
+			case "μm":
+			case "microns":
+			case "micron":
+			default:
+				return "micrometer";
+		}
+	}
 
 	public static void loadOMEZarr( final N5Reader n5, final String dataset )
 	{

src/main/java/net/preibisch/mvrecon/process/export/ExportN5Api.java

@@ -245,23 +245,21 @@ else if ( storageType == StorageFormat.N5 || storageType == StorageFormat.ZARR )
 						final Function<Integer, AffineTransform3D> levelToMipmapTransform =
 								(level) -> MipmapTransforms.getMipmapTransformDefault( mrInfoZarr[level].absoluteDownsamplingDouble() );
 
-						IOFunctions.println( "Resolution of level 0: " + Util.printCoordinates( cal ) + " " + unit ); //vx.unit() might not be OME-ZARR compatible
+						double[] resolutionS0 = OMEZarrAttibutes.getResolutionS0( cal, anisoF, downsamplingF );
+
+						IOFunctions.println( "Calibration: " + Util.printCoordinates( cal ) + " micrometer; resolution at S0: " + Util.printCoordinates( resolutionS0 ) + " " + unit);
 
 						// create metadata
 						final OmeNgffMultiScaleMetadata[] meta = OMEZarrAttibutes.createOMEZarrMetadata(
 								5, // int n
 								"/", // String name, I also saw "/"
-								cal, // double[] resolutionS0,
+								resolutionS0, // double[] resolutionS0,
 								unit, //"micrometer", //vx.unit() might not be OME-ZARR compatible // String unitXYZ, // e.g micrometer
 								mrInfoZarr.length, // int numResolutionLevels,
 								levelToName,
 								levelToMipmapTransform );
 
 						// save metadata
-
-						//org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.OmeNgffMetadata
-						// for this to work you need to register an adapter in the N5Factory class
-						// final GsonBuilder builder = new GsonBuilder().registerTypeAdapter( CoordinateTransformation.class, new CoordinateTransformationAdapter() );
 						driverVolumeWriter.setAttribute( "/", "multiscales", meta );
 					}
 				}
@@ -362,14 +360,16 @@ else if ( storageType == StorageFormat.ZARR ) // OME-Zarr export
 			final Function<Integer, AffineTransform3D> levelToMipmapTransform =
 					(level) -> MipmapTransforms.getMipmapTransformDefault( mrInfo[level].absoluteDownsamplingDouble() );
 
-			IOFunctions.println( "Resolution of level 0: " + Util.printCoordinates( cal ) + " micrometer" );
+			double[] resolutionS0 = OMEZarrAttibutes.getResolutionS0( cal, anisoF, downsamplingF );
+
+			IOFunctions.println( "Calibration: " + Util.printCoordinates( cal ) + " micrometer; resolution at S0: " + Util.printCoordinates( resolutionS0 ) + " " + unit);
 
 			// create metadata
 			final OmeNgffMultiScaleMetadata[] meta = OMEZarrAttibutes.createOMEZarrMetadata(
 					3, // int n
 					omeZarrSubContainer, // String name, I also saw "/"
-					cal, // double[] resolutionS0,
-					unit, //"micrometer", //vx.unit() might not be OME-ZARR compatible // String unitXYZ, // e.g micrometer
+					resolutionS0, // double[] resolutionS0,
+					unit, // might not be OME-ZARR compatible // String unitXYZ, // e.g micrometer
 					mrInfo.length, // int numResolutionLevels,
 					(level) -> "/" + level,
 					levelToMipmapTransform );

src/main/java/net/preibisch/mvrecon/process/interestpointregistration/TransformationTools.java

@@ -320,13 +320,13 @@ public static Pair< double[], String > computeAverageCalibration(
 			else if ( unit.equalsIgnoreCase( transformedCal.getB() ) )
 				unit = transformedCal.getB();
 			else
-				unit = "inconsisistent";
+				unit = "inconsistent";
 
 			System.out.println( "Calibration (transformed): " + Util.printCoordinates( transformedCal.getA() ) + " " + transformedCal.getB() );
 		}
 
 		if ( count == 0 )
-			return new ValuePair<>( new double[] { 1, 1, 1 }, "px" );
+			return new ValuePair<>( new double[] { 1, 1, 1 }, "micrometer" );
 		else
 			return new ValuePair<>( new double[] { avgCalX / (double)count, avgCalY / (double)count, avgCalZ / (double)count }, unit );
 	}

src/main/java/net/preibisch/mvrecon/process/n5api/N5ApiTools.java

@@ -33,7 +33,6 @@
 import java.util.Collections;
 import java.util.EnumSet;
 import java.util.HashMap;
-import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.function.BiFunction;
@@ -42,7 +41,6 @@
 import org.janelia.saalfeldlab.n5.Compression;
 import org.janelia.saalfeldlab.n5.DataType;
 import org.janelia.saalfeldlab.n5.DatasetAttributes;
-import org.janelia.saalfeldlab.n5.GzipCompression;
 import org.janelia.saalfeldlab.n5.N5Writer;
 import org.janelia.saalfeldlab.n5.RawCompression;
 import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
@@ -382,7 +380,8 @@ public static MultiResolutionLevelInfo[] setupBdvDatasetsOMEZARR(
 			final ViewId viewId,
 			final DataType dataType,
 			final long[] dimensions,
-			//final double[] resolutionS0, // TODO: this is a hack (uses 1,1,1) so the export downsampling pyramid is working
+			final double[] resolutionS0,
+			final String resolutionUnit,
 			final Compression compression,
 			final int[] blockSize,
 			int[][] downsamplings )
@@ -414,25 +413,17 @@ public static MultiResolutionLevelInfo[] setupBdvDatasetsOMEZARR(
 		final Function<Integer, AffineTransform3D> levelToMipmapTransform =
 				(level) -> MipmapTransforms.getMipmapTransformDefault( mrInfo[level].absoluteDownsamplingDouble() );
 
-		// extract the resolution of the s0 export
-		//final VoxelDimensions vx = fusionGroup.iterator().next().getViewSetup().getVoxelSize();
-		//final double[] resolutionS0 = OMEZarrAttibutes.getResolutionS0( vx, anisoF, downsamplingF );
-
 		// create metadata
 		final OmeNgffMultiScaleMetadata[] meta = OMEZarrAttibutes.createOMEZarrMetadata(
 				5, // int n
 				"/", // String name, I also saw "/"
-				new double[] { 1, 1, 1 }, //resolutionS0, // double[] resolutionS0,
-				"micrometer", //vx.unit() might not be OME-ZARR compatible // String unitXYZ, // e.g micrometer
+				resolutionS0, // double[] resolutionS0,
+				resolutionUnit, //vx.unit() might not be OME-ZARR compatible // String unitXYZ, // e.g micrometer
 				mrInfo.length, // int numResolutionLevels,
 				levelToName,
 				levelToMipmapTransform );
 
 		// save metadata
-
-		//org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.OmeNgffMetadata
-		// for this to work you need to register an adapter in the N5Factory class
-		// final GsonBuilder builder = new GsonBuilder().registerTypeAdapter( CoordinateTransformation.class, new CoordinateTransformationAdapter() );
 		driverVolumeWriter.setAttribute( baseDataset, "multiscales", meta );
 
 		return mrInfo;