omeZarrMetadataCorrection.groovy

#@ File(styles="both") root
#@ String(value="/") datasetPath

/*
 * If you used Fiji to export a multi-scale OME-Zarr image using average downsampling
 * between approximately March 13 and April 15 2024, the translation metadata may be incorrect.
 * 
 * Running this script will correct the metadata.
 * 
 * John Bogovic
 */

String normDatasetPath = N5URI.normalizeGroupPath(datasetPath);

N5Writer n5 = new N5Factory()
		.gsonBuilder(OmeNgffMetadataParser.gsonBuilder())
		.openWriter(root.getAbsolutePath());

N5TreeNode treeRoot = N5DatasetDiscoverer.discover(n5, 
		Collections.singletonList(new N5GenericSingleScaleMetadataParser()),
		Collections.singletonList(new OmeNgffMetadataParser()));


Optional<N5TreeNode> node = treeRoot.getDescendant(datasetPath == "/" ? "" : datasetPath);
if (node.isPresent()) {

	N5Metadata metadata = node.get().getMetadata();
	if (!(metadata instanceof OmeNgffMetadata)) {
		System.err.println("Could not find NGFF metadata at: " + datasetPath);
		return;
	}

	final OmeNgffMetadata ngffMeta = (OmeNgffMetadata)metadata;

	ScaleCoordinateTransformation baseScale = null;
	for( OmeNgffDataset dataset : ngffMeta.multiscales[0].datasets ) {

		ValuePair<ScaleCoordinateTransformation, TranslationCoordinateTransformation> tforms = getTransformsMulti(dataset);
		if( baseScale == null )
		{
			baseScale = tforms.getA();
			continue;
		}
		correct(baseScale, tforms);

		Optional<N5TreeNode> childNode = treeRoot.getDescendant(normDatasetPath + "/" + dataset.path);
		if(childNode.isPresent())
		{
			N5Metadata childMetadata = childNode.get().getMetadata();
			if( childMetadata instanceof NgffSingleScaleAxesMetadata )
			{
				NgffSingleScaleAxesMetadata ngffChildMetadata = (NgffSingleScaleAxesMetadata)childMetadata;
				final ValuePair<ScaleCoordinateTransformation, TranslationCoordinateTransformation> tformsArray = getTransformsArray(ngffChildMetadata);
				correct(baseScale, tformsArray);

				n5.setAttribute(
						N5URI.normalizeGroupPath(normDatasetPath + "/" + dataset.path), 
						"coordinateTransformations", ngffChildMetadata.getCoordinateTransformations());
			}
		}
	}

	// write the new metadata out
	n5.setAttribute(normDatasetPath, "multiscales", ngffMeta.multiscales);

}
else {
	System.err.println("could not find : " + datasetPath);
}



def correct(ScaleCoordinateTransformation baseScale, ValuePair tforms) {

	EPS = 1e-3;
	ScaleCoordinateTransformation scale = tforms.getA();
	TranslationCoordinateTransformation translation = tforms.getB();

	res = baseScale.getScale();
	s = scale.getScale();
	t = translation.getTranslation();

	if( t[0] < 0.1 * EPS * s[0] )
		return;

	int nd = scale.getScale().length;
	if( translation.getTranslation().length != nd )
	{
		System.err.println("scale and translation different lengths");
		return;
	}
		
	for( int i = 0; i < nd; i++ )
	{
		double factor = s[i] / res[i];
		t[i] = res[i] * (0.5 * factor - 0.5);
	}

}	

def ValuePair validateTransforms(String path, CoordinateTransformation[] coordinateTransformations ) {

	numTforms = coordinateTransformations.length;
	if (numTforms != 2) {
		System.err.println("Nothing to do, need 2 transforms. There are " + numTforms + " transforms at " + path);
		return null;
	}

	CoordinateTransformation<?> fst = coordinateTransformations[0];
	CoordinateTransformation<?> snd = coordinateTransformations[1];
	
	if (!(fst instanceof ScaleCoordinateTransformation)) {
		System.err.println("First transform not a scale transformation");
		return null;
	}

	if (!(snd instanceof TranslationCoordinateTransformation)) {
		System.err.println("Second transform not a translation transformation");
		return null;
	}			

	ScaleCoordinateTransformation scale = (ScaleCoordinateTransformation)fst;
	TranslationCoordinateTransformation translation = (TranslationCoordinateTransformation)snd;

	return new ValuePair(scale, translation);
}


def ValuePair getTransformsMulti(OmeNgffDataset dataset) {
	return validateTransforms(dataset.path, dataset.coordinateTransformations)
}

def ValuePair getTransformsArray(NgffSingleScaleAxesMetadata meta) {

	return validateTransforms(meta.getPath(), meta.getCoordinateTransformations());
}


import java.io.File;
import java.util.Collections;
import java.util.Optional;

import org.janelia.saalfeldlab.n5.N5URI;
import org.janelia.saalfeldlab.n5.N5Writer;
import org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer;
import org.janelia.saalfeldlab.n5.universe.N5Factory;
import org.janelia.saalfeldlab.n5.universe.N5TreeNode;
import org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser;
import org.janelia.saalfeldlab.n5.universe.metadata.N5Metadata;
import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.NgffSingleScaleAxesMetadata;
import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.OmeNgffMetadata;
import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.OmeNgffMultiScaleMetadata.OmeNgffDataset;
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.util.ValuePair;

import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.OmeNgffMetadataParser;