Merge pull request #63 from PreibischLab/omezarr

OME-ZARR support for BigStitcher fusion

Author: StephanPreibisch

src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/OMEZarrAttibutes.java

@@ -23,10 +23,13 @@
 package net.preibisch.mvrecon.fiji.spimdata.imgloaders;
 
 import java.net.URI;
+import java.net.URISyntaxException;
+import java.util.Arrays;
 import java.util.function.Function;
 
 import org.janelia.saalfeldlab.n5.DatasetAttributes;
 import org.janelia.saalfeldlab.n5.N5Reader;
+import org.janelia.saalfeldlab.n5.universe.N5Factory;
 import org.janelia.saalfeldlab.n5.universe.N5Factory.StorageFormat;
 import org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis;
 import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.OmeNgffMultiScaleMetadata;
@@ -36,6 +39,7 @@
 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 mpicbg.spim.data.sequence.VoxelDimensions;
 import net.imglib2.realtransform.AffineTransform3D;
 import util.URITools;
 
@@ -59,7 +63,7 @@ public static OmeNgffMultiScaleMetadata[] createOMEZarrMetadata(
 		final OmeNgffMultiScaleMetadata[] meta = new OmeNgffMultiScaleMetadata[ 1 ];
 
 		// dataset name and co
-		final String path = null;
+		final String path = "";
 		final String type = null;
 
 		// axis descriptions
@@ -102,7 +106,7 @@ public static OmeNgffMultiScaleMetadata[] createOMEZarrMetadata(
 			// if 4d and 5d, add 1's for C and T
 			for ( int d = 3; d < n; ++d )
 			{
-				translation[ d ] = 1.0;
+				translation[ d ] = 0.0;
 				scale[ d ] = 1.0;
 			}
 
@@ -126,6 +130,22 @@ public static OmeNgffMultiScaleMetadata[] createOMEZarrMetadata(
 		return meta;
 	}
 
+	// TODO: this is inaccurate, we should actually estimate it from the final transformn that is applied
+	public static double[] getResolutionS0( final VoxelDimensions vx, final double anisoF, final double downsamplingF )
+	{
+		final double[] resolutionS0 = vx.dimensionsAsDoubleArray();
+
+		// not preserving anisotropy
+		if ( Double.isNaN( anisoF ) )
+			resolutionS0[ 2 ] = resolutionS0[ 0 ];
+
+		// downsampling
+		if ( !Double.isNaN( downsamplingF ) )
+			Arrays.setAll( resolutionS0, d -> resolutionS0[ d ] * downsamplingF );
+
+		return resolutionS0;
+	}
+
 	public static void loadOMEZarr( final N5Reader n5, final String dataset )
 	{
 		//org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.OmeNgffMetadata
@@ -151,8 +171,19 @@ public static void loadOMEZarr( final N5Reader n5, final String dataset )
 		}
 	}
 
-	public static void main( String[] args )
+	public static void main( String[] args ) throws URISyntaxException
 	{
+		final URI uri2 = URITools.toURI("https://keller-data.int.janelia.org/s12a/samples_for_stitching/Live%20zebra%20fish%20stitched/Live%20zebra%20plane%206/dataset.n5");///setup0/time;t0/");
+		System.out.println( uri2.toString() );
+
+		//FileSystemKeyValueAccess kva = new FileSystemKeyValueAccess( FileSystems.getDefault() );
+		
+		String s = uri2.toString();
+		N5Factory f = new N5Factory();
+		N5Reader r = f.openFileSystemReader( s );
+		r.close();
+		System.exit( 0 );
+
 		//final URI uri = URITools.toURI( "https://storage.googleapis.com/jax-public-ngff/KOMP/adult_lacZ/ndp/Moxd1/23420_K35061_FGut.zarr/0/" );
 		//final String dataset = "/";
 

src/main/java/net/preibisch/mvrecon/process/export/DisplayImage.java

@@ -29,7 +29,7 @@
 import fiji.util.gui.GenericDialogPlus;
 import ij.ImagePlus;
 import ij.gui.GenericDialog;
-import mpicbg.spim.data.sequence.ViewId;
+import mpicbg.spim.data.sequence.ViewDescription;
 import net.imglib2.Interval;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.exception.ImgLibException;
@@ -90,7 +90,7 @@ public < T extends RealType< T > & NativeType< T > > boolean exportImage(
 			final double downsampling,
 			final double anisoF,
 			final String title,
-			final Group< ? extends ViewId > fusionGroup )
+			final Group< ? extends ViewDescription > fusionGroup )
 	{
 		// do nothing in case the image is null
 		if ( img == null )

src/main/java/net/preibisch/mvrecon/process/export/ExportLarge2DTIFF.java

@@ -36,14 +36,12 @@
 import ch.epfl.biop.kheops.ometiff.OMETiffPyramidizerExporter;
 import fiji.util.gui.GenericDialogPlus;
 import mpicbg.spim.data.sequence.ViewDescription;
-import mpicbg.spim.data.sequence.ViewId;
 import net.imglib2.FinalInterval;
 import net.imglib2.Interval;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.converter.ColorChannelOrder;
 import net.imglib2.converter.Converters;
 import net.imglib2.img.display.imagej.ImageJFunctions;
-import net.imglib2.multithreading.SimpleMultiThreading;
 import net.imglib2.position.FunctionRandomAccessible;
 import net.imglib2.realtransform.AffineTransform3D;
 import net.imglib2.type.NativeType;
@@ -99,7 +97,7 @@ public <T extends RealType<T> & NativeType<T>> boolean exportImage(
 			final double downsampling,
 			final double anisoF,
 			final String title,
-			final Group<? extends ViewId> fusionGroup )
+			final Group<? extends ViewDescription> fusionGroup )
 	{
 		// hack to make the interval divisable by 16 (see https://imagesc.zulipchat.com/#narrow/stream/212929-general/topic/Writing.20large.202D.20TIFFs)
 		if ( imgInterval.dimension( 0 ) % 16 != 0 || imgInterval.dimension( 1 ) % 16 != 0 )