Visualize the hemibrain and fafb together

Hemi2Fafb.java

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

import org.janelia.saalfeldlab.n5.N5DatasetDiscoverer;
import org.janelia.saalfeldlab.n5.N5FSReader;
import org.janelia.saalfeldlab.n5.N5Reader;
import org.janelia.saalfeldlab.n5.N5TreeNode;
import org.janelia.saalfeldlab.n5.hdf5.N5HDF5Reader;
import org.janelia.saalfeldlab.n5.ij.N5Importer;
import org.janelia.saalfeldlab.n5.imglib2.N5DisplacementField;
import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
import org.janelia.saalfeldlab.n5.metadata.MultiscaleMetadata;
import org.janelia.saalfeldlab.n5.metadata.N5GenericSingleScaleMetadataParser;
import org.janelia.saalfeldlab.n5.metadata.N5Metadata;
import org.janelia.saalfeldlab.n5.metadata.N5SingleScaleMetadata;

import bdv.tools.transformation.TransformedSource;
import bdv.util.BdvFunctions;
import bdv.util.BdvOptions;
import bdv.util.BdvStackSource;
import bdv.util.RandomAccessibleIntervalMipmapSource;
import bdv.util.volatiles.SharedQueue;
import bdv.util.volatiles.VolatileViews;
import bdv.viewer.Source;
import mpicbg.spim.data.sequence.FinalVoxelDimensions;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.cache.volatiles.CacheHints;
import net.imglib2.cache.volatiles.LoadingStrategy;
import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.realtransform.ExplicitInvertibleRealTransform;
import net.imglib2.realtransform.InvertibleRealTransform;
import net.imglib2.realtransform.InvertibleRealTransformSequence;
import net.imglib2.type.volatiles.VolatileUnsignedByteType;

public class Hemi2Fafb
{

	public static String FAFB_JRC18 = "/groups/saalfeld/public/jrc2018/transformations/public_transforms/JRC2018F_FAFB.h5";
	public static String  HEMI_JRC18 = "/groups/saalfeld/public/jrc2018/transformations/public_transforms/JRC2018F_JRCFIB2018F.h5";

	public static String FAFB_N5 = "/nrs/saalfeld/FAFB00/v14_align_tps_20170818_dmg.n5/volumes/raw";
	public static String FAFB_DSET = "";

	public static String HEMI_N5 = "/nrs/flyem/data/tmp/Z0115-22.export.n5/22-34";

	public static void main( String[] args ) throws Exception
	{
		final SharedQueue queue = new SharedQueue( 32 );

		final Source<?> hemiSrc = loadHemiN5Pix( HEMI_N5, queue);
		final Source< ? > hemiTransformedSrc = transformSource( hemiSrc, loadHemibrainN5ToFAFB() );
		final BdvOptions opts = BdvOptions.options().numRenderingThreads( 32 );
		final BdvStackSource< ? > bdv = BdvFunctions.show( hemiTransformedSrc, opts );

		final Source<?> fafbSrc = loadFafbUm(queue);
		BdvFunctions.show( fafbSrc, opts.addTo( bdv ) );
	}

	public static Source<?> transformSource( Source<?> src, InvertibleRealTransform transform )
	{
		System.out.println("tform src");
		final RealTransformedSource wsrc = new RealTransformedSource(src, src.getName()+" transformed" );
		wsrc.updateTransform( transform );
		wsrc.setIsTransformed( true );
		return wsrc;
	}
	
	public static Source<?> affineSource( Source<?> src, AffineTransform3D transform )
	{
		System.out.println("affine src");

		TransformedSource tsrc = new TransformedSource( src );
		tsrc.setFixedTransform( transform );
		return tsrc;
	}

	public static AffineTransform3D hemiN5ToDvid()
	{
		final AffineTransform3D toDvid = new AffineTransform3D();
		toDvid.set(
				0.0, 0.0, -1.0, 34427, 
				1.0, 0.0, 0.0, 0.0,
				0.0, 1.0, 0.0, 0.0 );
		return toDvid;
	}

	public static AffineTransform3D hemiN5ToDvidUm()
	{
		final AffineTransform3D xfm = hemiN5ToDvid();
		final AffineTransform3D res = new AffineTransform3D();
		res.scale( 0.008, 0.008, 0.008 );
		xfm.preConcatenate( res );

		return xfm;
	}
	
	public static InvertibleRealTransform loadHemibrainN5ToFAFB() throws Exception
	{
		final N5HDF5Reader n5 = new N5HDF5Reader( HEMI_JRC18, 3, 32, 32, 32 );
		final ExplicitInvertibleRealTransform dfield = N5DisplacementField.openInvertible(n5, 0);
		final InvertibleRealTransform hemi2Fafb = loadJrc2018ToFafb();

		final InvertibleRealTransformSequence seq = new InvertibleRealTransformSequence();
		seq.add( hemi2Fafb );
		seq.add( dfield );
		seq.add( hemiN5ToDvidUm().inverse() );
		return seq;
	}

	public static InvertibleRealTransform loadHemibrainN5ToJrc2018() throws Exception
	{
		final N5HDF5Reader n5 = new N5HDF5Reader( HEMI_JRC18, 3, 32, 32, 32 );
		final ExplicitInvertibleRealTransform dfield = N5DisplacementField.openInvertible(n5, 0);

		final InvertibleRealTransformSequence seq = new InvertibleRealTransformSequence();
		seq.add( dfield );
		seq.add( hemiN5ToDvidUm().inverse() );
		return seq;
	}
	
	public static InvertibleRealTransform loadJrc2018ToHemibrain() throws Exception
	{
		N5HDF5Reader n5 = new N5HDF5Reader( HEMI_JRC18, 3, 32, 32, 32 );
		return N5DisplacementField.openInvertible(n5, 0).inverse();
	}
	
	public static InvertibleRealTransform loadFafbToJrc2018() throws Exception
	{
		N5HDF5Reader n5 = new N5HDF5Reader( FAFB_JRC18, 3, 32, 32, 32 );
		return N5DisplacementField.openInvertible(n5, 0);
	}
	
	public static InvertibleRealTransform loadJrc2018ToFafb() throws Exception
	{
		N5HDF5Reader n5 = new N5HDF5Reader( FAFB_JRC18, 3, 32, 32, 32 );
		return N5DisplacementField.openInvertible(n5, 0).inverse();
	}

	public static Source< ? > loadHemiN5Pix( final SharedQueue queue ) throws IOException
	{
		return loadHemiN5Pix( HEMI_N5, queue );
	}

	public static Source< ? > loadFafbNm( final SharedQueue queue ) throws IOException
	{
		N5Reader n5 = new N5FSReader( FAFB_N5 );
		return getRandomAccessibleIntervalMipmapSourceV( n5, FAFB_DSET, "fafb", queue, false, new double[] {4,4,40} );
	}

	public static Source< ? > loadFafbUm( final SharedQueue queue ) throws IOException
	{
		N5Reader n5 = new N5FSReader( FAFB_N5 );
		return getRandomAccessibleIntervalMipmapSourceV( n5, FAFB_DSET, "fafb", queue, false, new double[] {0.004, 0.004 ,0.04} );
	}

	public static Source< ? > loadHemiN5Pix( final String hemiN5Path, final SharedQueue queue ) throws IOException
	{
		N5Reader n5hemi = new N5FSReader( hemiN5Path );
		return getRandomAccessibleIntervalMipmapSourceV( n5hemi, "hemibrain", "hemibrain", queue );
	}
	
	public static Source< ? > loadHemiN5Um( final String hemiN5Path, final SharedQueue queue ) throws IOException
	{
		N5Reader n5hemi = new N5FSReader( hemiN5Path );
		return getRandomAccessibleIntervalMipmapSourceV( n5hemi, "hemibrain", "hemibrain", queue, true, new double[] {0.004, 0.004, 0.004 });
	}
	
	public static Source<?> getRandomAccessibleIntervalMipmapSourceV(
			final N5Reader n5, final String dataset, final String name, final SharedQueue queue ) throws IOException
	{
		return getRandomAccessibleIntervalMipmapSourceV( n5, dataset, name, queue, true );
	}
	
	public static Source<?> getRandomAccessibleIntervalMipmapSourceV(
			final N5Reader n5, final String dataset, final String name, final SharedQueue queue, boolean relativeScales ) throws IOException
	{
		return getRandomAccessibleIntervalMipmapSourceV( n5, dataset, name, queue, relativeScales, new double[]{1,1,1} );
	}

	public static Source<?> getRandomAccessibleIntervalMipmapSourceV(
			final N5Reader n5, final String dataset, final String name, final SharedQueue queue, boolean relativeScales, double[] res ) throws IOException
	{
		N5GenericSingleScaleMetadataParser metaParser = new N5GenericSingleScaleMetadataParser(
				"min", "max",
				"resolution", "offset", "unit",
				"downsamplingFactors");

		N5DatasetDiscoverer disc = new N5DatasetDiscoverer( n5, Collections.singletonList(metaParser), Arrays.asList( N5Importer.GROUP_PARSERS));
		N5TreeNode node = disc.discoverAndParseRecursive("/");
		N5Metadata meta = node.getMetadata();
		MultiscaleMetadata<N5SingleScaleMetadata> ms = (MultiscaleMetadata)meta;

		int N = ms.getPaths().length;
		double[][] scales = new double[N][];
		final RandomAccessibleInterval< ? >[] scaleLevelImgs = new RandomAccessibleInterval[ scales.length ];
		int i = 0;
		for ( N5SingleScaleMetadata scaleMeta : ms.getChildrenMetadata() )
		{
			N5Utils.openVolatile( n5, scaleMeta.getPath() );
//			scales[i] = scaleMeta.getPixelResolution();
			scales[i] = scaleMeta.getDownsamplingFactors();
			for( int d = 0; d < 3; d++ )
			{
				scales[i][d] *= res[d];
			}

			System.out.println( String.format( "s%d", i ) + " " + Arrays.toString(scales[i]));
			i++;
		}

		for ( int s = 0; s < scales.length; ++s )
		{
			RandomAccessibleInterval<?> rai = N5Utils.openVolatile( n5, getScaleGroupPath( s ) );
			scaleLevelImgs[ s ] = VolatileViews.wrapAsVolatile( rai, queue, 
					new CacheHints(LoadingStrategy.VOLATILE, 0, true));
		}

		final RandomAccessibleIntervalMipmapSource< ? > source = 
				new RandomAccessibleIntervalMipmapSource(
				scaleLevelImgs,
				new VolatileUnsignedByteType(),
				scales,
				new FinalVoxelDimensions("", 1, 1, 1 ),
				name );

		return source;	
	}

	public static String getScaleGroupPath( final int scale )
	{
		return String.format( "s%d", scale );
	} 

}