start implementing OME-ZARR export

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

@@ -0,0 +1,52 @@
+package net.preibisch.mvrecon.fiji.spimdata.imgloaders;
+
+import java.net.URI;
+
+import org.janelia.saalfeldlab.n5.N5Reader;
+import org.janelia.saalfeldlab.n5.universe.N5Factory.StorageFormat;
+import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.OmeNgffMultiScaleMetadata;
+import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.OmeNgffMultiScaleMetadata.OmeNgffDataset;
+
+import util.URITools;
+
+public class OMEZarrAttibutes
+{
+	public static void loadOMEZarr( final N5Reader n5, final String dataset )
+	{
+		//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() );
+		final OmeNgffMultiScaleMetadata[] multiscales = n5.getAttribute( dataset, "multiscales", OmeNgffMultiScaleMetadata[].class );
+
+		if ( multiscales == null || multiscales.length == 0 )
+			throw new RuntimeException( "Could not parse OME-ZARR multiscales object. stopping." );
+
+		if ( multiscales.length != 1 )
+			System.out.println( "This dataset has " + multiscales.length + " objects, we expected 1. Picking the first one." );
+
+		//System.out.println( "AllenOMEZarrLoader.getMipmapResolutions() for " + setupId + " using " + n5properties.getPath( setupId, timePointId ) + ": found " + multiscales[ 0 ].datasets.length + " multi-resolution levels." );
+
+		//double[][] mipMapResolutions = new double[ multiscales[ 0 ].datasets.length ][ 3 ];
+		//double[] firstScale = null;
+
+		for ( int i = 0; i < multiscales[ 0 ].datasets.length; ++i )
+		{
+			final OmeNgffDataset ds = multiscales[ 0 ].datasets[ i ];
+			System.out.println( ds.coordinateTransformations.length );
+		}
+	}
+
+	public static void main( String[] args )
+	{
+		final URI uri = URITools.toURI( "s3://aind-open-data/exaSPIM_708373_2024-04-02_19-49-38/SPIM.ome.zarr/" );
+		final String dataset = "tile_x_0001_y_0001_z_0000_ch_488.zarr";
+
+		//final URI uri = URITools.toURI( "/nrs/cellmap/data/jrc_cos7-11/jrc_cos7-11.zarr/" );
+		//final String dataset = "recon-2/lm/er_palm/";
+		//final String dataset = "recon-1/em/fibsem-uint16/";
+
+		final N5Reader n5 = URITools.instantiateN5Reader( StorageFormat.ZARR, uri );
+
+		loadOMEZarr(n5, dataset);
+	}
+}