cosemMetadataCorrection.groovy

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

/*
 * If you used Fiji to export a multi-scale an image with COSEM 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());

N5TreeNode treeRoot = N5DatasetDiscoverer.discover(n5, 
		Collections.singletonList(new N5CosemMetadataParser()),
		Collections.emptyList());

node = treeRoot.getDescendant(normDatasetPath);
if (node.isPresent()) {

	CosemTransform baseTform = null;
	for( N5TreeNode c : node.get().childrenList())
	{
		N5Metadata meta = c.getMetadata();
		if( meta.getPath().endsWith("s0"))
		{
			baseTform = ((N5CosemMetadata)meta).getCosemTransform();
			break;
		}
	}

	for( N5TreeNode c : node.get().childrenList())
	{
		N5Metadata meta = c.getMetadata();
		if( meta instanceof N5CosemMetadata )
		{
			N5CosemMetadata cosemMeta = (N5CosemMetadata)meta;
			if( !meta.getPath().endsWith("s0"))
			{
				correct( baseTform, cosemMeta.getCosemTransform());
				n5.setAttribute(N5URI.normalizeGroupPath(normDatasetPath + "/" + meta.getPath() ), "transform", cosemMeta.getCosemTransform());
			}
		}
	}
} else {
	System.err.println("could not find : " + datasetPath);	
	return;
}
		

def correct(CosemTransform baseTransform, CosemTransform tform ) {

	double EPS = 1e-3;

	double[] res = baseTransform.scale;
	double[] s = tform.scale;
	double[] t = tform.translate;

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

	int nd = s.length;
	for( int i = 0; i < nd; i++ )
	{
		double factor = s[i] / res[i];
		t[i] = res[i] * (0.5 * factor - 0.5);
	}
}
	


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.N5CosemMetadata;
import org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadata.CosemTransform;
import org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadataParser;
import org.janelia.saalfeldlab.n5.universe.metadata.N5Metadata;