From d4d704655c5fd8633104a7a382b36c25f2765a65 Mon Sep 17 00:00:00 2001
From: Stephan Preibisch <stephan.preibisch@gmx.de>
Date: Mon, 11 Nov 2024 16:20:57 -0500
Subject: [PATCH] continuing with OME-ZARR support

---
 .../spimdata/imgloaders/OMEZarrAttibutes.java | 71 +++++++++++++++++++
 1 file changed, 71 insertions(+)

diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/OMEZarrAttibutes.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/OMEZarrAttibutes.java
index 1bacd957..99bd737b 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/OMEZarrAttibutes.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/OMEZarrAttibutes.java
@@ -23,16 +23,84 @@
 package net.preibisch.mvrecon.fiji.spimdata.imgloaders;
 
 import java.net.URI;
+import java.util.function.Function;
 
+import org.janelia.saalfeldlab.n5.DatasetAttributes;
 import org.janelia.saalfeldlab.n5.N5Reader;
 import org.janelia.saalfeldlab.n5.universe.N5Factory.StorageFormat;
+import org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis;
 import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.OmeNgffMultiScaleMetadata;
 import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.OmeNgffMultiScaleMetadata.OmeNgffDataset;
+import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.OmeNgffMultiScaleMetadata.OmeNgffDownsamplingMetadata;
+import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.coordinateTransformations.CoordinateTransformation;
+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 net.imglib2.realtransform.AffineTransform3D;
 import util.URITools;
 
 public class OMEZarrAttibutes
 {
+	/**
+	 * 
+	 * @param n - num dimensions, 3-5 makes sense here (zyx to tczyx; TODO: which order?)
+	 * @param numResolutionLevels - number of multiresolution levels (e.g. s0, s1, s2 would be 3), always includes full res
+	 * @return
+	 */
+	public static OmeNgffMultiScaleMetadata[] createOMEZarrMetadata(
+			final int n,
+			final int numResolutionLevels,
+			final Function<Integer, String> levelToName,
+			final Function<Integer, AffineTransform3D> levelToMipmapTransform )
+	{
+		final OmeNgffMultiScaleMetadata[] meta = new OmeNgffMultiScaleMetadata[ 1 ];
+
+		// dataset name
+		final String path = null;
+		final String name = "setup0_timepoint5"; // I also saw "/"
+		final String type = null;
+
+		// axis descriptions
+		// TODO: for some reason they are in TCZYX order
+		final Axis[] axes = new Axis[ n ];
+
+		int index = 0;
+
+		if ( n >= 5 )
+			axes[ index++ ] = new Axis( "time", "t", "millisecond" );
+
+		if ( n >= 4 )
+			axes[ index++ ] = new Axis( "channel", "c", null );
+
+		axes[ index++ ] = new Axis( "space", "z", "micrometer" );
+		axes[ index++ ] = new Axis( "space", "y", "micrometer" );
+		axes[ index++ ] = new Axis( "space", "x", "micrometer" );
+
+		// multiresolution-pyramid
+		// TODO: for some reason in XYZCT order (but in the file it seems reversed)
+		final OmeNgffDataset[] datasets = new OmeNgffDataset[ numResolutionLevels ];
+
+		for ( int s = 0; s < numResolutionLevels; ++s )
+		{
+			datasets[ s ] = new OmeNgffDataset();
+
+			datasets[ s ].path = levelToName.apply( s );
+
+			datasets[ s ].coordinateTransformations = new CoordinateTransformation[ 2 ];
+			datasets[ s ].coordinateTransformations[ 0 ] = new ScaleCoordinateTransformation( new double[] { } ); // TODO
+			datasets[ s ].coordinateTransformations[ 1 ] = new TranslationCoordinateTransformation( new double[] { } ); // TODO
+		}
+
+		// just saw these being null everywhere
+		final DatasetAttributes[] childrenAttributes = null;
+		final CoordinateTransformation<?>[] coordinateTransformations = null; // I also saw ScaleTransform [1,1,1]
+		final OmeNgffDownsamplingMetadata metadata = null;
+		
+		meta[ 0 ] = new OmeNgffMultiScaleMetadata( n, path, name, type, "0.4", axes, datasets, childrenAttributes, coordinateTransformations, metadata );
+
+		return meta;
+	}
+
 	public static void loadOMEZarr( final N5Reader n5, final String dataset )
 	{
 		//org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.OmeNgffMetadata
@@ -60,6 +128,9 @@ public static void loadOMEZarr( final N5Reader n5, final String dataset )
 
 	public static void main( String[] args )
 	{
+		//final URI uri = URITools.toURI( "https://storage.googleapis.com/jax-public-ngff/KOMP/adult_lacZ/ndp/Moxd1/23420_K35061_FGut.zarr/0/" );
+		//final String dataset = "/";
+
 		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";