n5vMetadataCorrection.groovy

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

/*
 * If you used Fiji to export a multi-scale image with N5Viewer metadata 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()
		.openWriter(root.getAbsolutePath());

N5SingleScaleMetadataParser metadataParser = new N5SingleScaleMetadataParser();
N5TreeNode treeRoot = N5DatasetDiscoverer.discover(n5, 
		Collections.singletonList(metadataParser),
		Collections.emptyList());

Optional node = treeRoot.getDescendant(normDatasetPath);
if (node.isPresent()) {
	
	// for each channel
	for (N5TreeNode channelNode : node.get().childrenList())
	{
		// get the highest resolution dataset
		N5SingleScaleMetadata baseTform = null;
		for (N5TreeNode c : channelNode.childrenList())
		{
			if (c.getMetadata().getPath().endsWith("s0"))
			{
				baseTform = ((N5SingleScaleMetadata)c.getMetadata());
				break;
			}
		}

		for (N5TreeNode c : channelNode.childrenList())
		{
			N5Metadata meta = c.getMetadata();
			if (meta instanceof N5SingleScaleMetadata && !meta.getPath().endsWith("s0"))
			{
				N5SingleScaleMetadata newMetadata = correct(baseTform, (N5SingleScaleMetadata)meta);
				try {
					metadataParser.writeMetadata(
							newMetadata,
							n5,
							N5URI.normalizeGroupPath(normDatasetPath + "/" + meta.getPath()));
				} catch (Exception e) { }
			}
		}
	}

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

def N5SingleScaleMetadata correct(N5SingleScaleMetadata baseTransform, N5SingleScaleMetadata tform) {

	double[] res = baseTransform.getPixelResolution();
	double[] s = tform.getPixelResolution();

	int nd = s.length;
	for( int i = 0; i < nd; i++ )
	{
		tform.getDownsamplingFactors()[i] = s[i] / res[i];	// set downsamplingFactors
		s[i] = res[i]; 										// set resolution to base resolution
		
	}
	Scale editTform = new Scale(tform.getDownsamplingFactors());
	return tform.modifySpatialTransform(tform.getPath(), editTform.inverse());
}


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.N5Metadata;
import org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadata;
import org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadataParser;

import net.imglib2.realtransform.Scale;