Resave a subset of a multiscale cosem dataset locally

ResaveCosemMultiscaleSubset.java

package cosem;

import java.io.IOException;
import java.util.Arrays;

import org.janelia.saalfeldlab.n5.DatasetAttributes;
import org.janelia.saalfeldlab.n5.N5Reader;
import org.janelia.saalfeldlab.n5.N5Writer;
import org.janelia.saalfeldlab.n5.ij.N5Factory;
import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
import org.janelia.saalfeldlab.n5.metadata.N5CosemMetadata;
import org.janelia.saalfeldlab.n5.metadata.N5CosemMetadata.CosemTransform;

import net.imglib2.cache.img.CachedCellImg;
import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.type.NativeType;
import net.imglib2.view.IntervalView;
import net.imglib2.view.Views;

/*
 * This is very hacky, don't trust this too much.
 */
public class ResaveCosemMultiscaleSubset
{

	public static <T extends NativeType<T>>  void main( String[] args ) throws IOException
	{
		final String n5InUrl = "https://janelia-cosem.s3.amazonaws.com/jrc_hela-2/jrc_hela-2.n5";
		final String n5OutUrl = "/home/john/projects/cosem/downloadDataSubsets/jrc-hela-2.n5";

		final N5Reader n5R = new N5Factory().openReader( n5InUrl );
		final N5Writer n5W = new N5Factory().openWriter( n5OutUrl );
		
		// edit if you want
		String[] levelList = new String[] { "s0", "s1", "s2", "s3" };
		
		double[] minPhysical = new double[] { 24400, 4400, 14342 };
		double[] maxPhysical = new double[] { 25599, 5599, 15588 };

		// image data
		String indatasetBase = "/em/fibsem-uint16";
		String outdatasetBase = "bTrainingBlock";
		saveLevels( n5R, n5W, indatasetBase, outdatasetBase, levelList, minPhysical, maxPhysical );
		

		// labels
		indatasetBase = "/labels/gt";
		outdatasetBase = "bTrainingBlock_labels";
		saveLevels( n5R, n5W, indatasetBase, outdatasetBase, levelList, minPhysical, maxPhysical );

	}
	
	public static <T extends NativeType<T>> void saveLevels(
			final N5Reader n5R,
			final N5Writer n5W,
			final String indatasetBase,
			final String outdatasetBase,
			final String[] levelList,
			final double[] minPhysical,
			final double[] maxPhysical ) throws IOException
	{
		double[] baseScale = null;
		for( String level : levelList )
		{
			System.out.println( "level: " + level );

			String indataset = indatasetBase + "/" + level;
			String outdataset = outdatasetBase + "/" + level;

			CosemTransform transform = n5R.getAttribute( indataset, "transform", N5CosemMetadata.CosemTransform.class );
			AffineTransform3D pixelToPhysical = transform.toAffineTransform3d();
			System.out.println( Arrays.toString( transform.getAffine().getRowPackedCopy()));
			
			if( baseScale == null )
				baseScale = transform.scale;

			CachedCellImg< T, ? > img = N5Utils.open( n5R, indataset );

			DatasetAttributes attrsIn = n5R.getDatasetAttributes( indataset );

			double[] tmp = new double[ 3 ];
			pixelToPhysical.applyInverse( tmp, minPhysical );

			long[] minLevel = Arrays.stream( tmp ).mapToLong( x -> (long)Math.floor( x ) ).toArray();

			pixelToPhysical.applyInverse( tmp, maxPhysical );
			long[] maxLevel = Arrays.stream( tmp ).mapToLong( x -> (long)Math.floor( x ) ).toArray();

			double[] newOffset = new double[ 3 ];
			int j = 2;
			for( int i = 0; i < 3; i++ )
			{
				newOffset[ j ] = minLevel[ i ] * transform.scale[ j ] + transform.translate[ j ];
				j--;
				
			}
			CosemTransform newTransform = new CosemTransform( transform.axes, transform.scale, newOffset, transform.units );
			
			System.out.println( "minLevel: " + Arrays.toString( minLevel ));
			System.out.println( "maxLevel: " + Arrays.toString( maxLevel ));
			System.out.println( "newOffset: " + Arrays.toString( newOffset ));

			IntervalView< T > imgCrop = Views.interval( img, minLevel, maxLevel );

			N5Utils.save( imgCrop, n5W, outdataset, attrsIn.getBlockSize(), attrsIn.getCompression() );
			n5W.setAttribute( outdataset, "transform", newTransform );
		}

	}

}