test: build ngff multiscales v0.4 metadata

src/main/java/org/janelia/saalfeldlab/n5/universe/metadata/MetadataUtils.java

@@ -30,17 +30,17 @@ public class MetadataUtils {
 
 	public static double[] mul(final double[] a, final double[] b) {
 
-		final double[] out = new double[ a.length ];
-		for( int i = 0; i <  a.length; i++ )
+		final double[] out = new double[a.length];
+		for (int i = 0; i < a.length; i++)
 			out[i] = a[i] * b[i];
 
 		return out;
 	}
 
 	public static double[] mul(final double[] a, final long[] b) {
 
-		final double[] out = new double[ a.length ];
-		for( int i = 0; i <  a.length; i++ )
+		final double[] out = new double[a.length];
+		for (int i = 0; i < a.length; i++)
 			out[i] = a[i] * b[i];
 
 		return out;
@@ -91,21 +91,22 @@ public static long[] updateDownsamplingFactors(final long factor, final long[] b
 		return factors;
 	}
 
-	public static CoordinateTransformation<?>[] buildScaleTranslationTransformList( final double[] scale, final double[] translation ) {
+	public static CoordinateTransformation<?>[] buildScaleTranslationTransformList(final double[] scale, final double[] translation) {
+
 		int nTforms = 0;
-		if( scale != null )
+		if (scale != null)
 			nTforms++;
 
-		if( translation != null )
+		if (translation != null)
 			nTforms++;
 
 		final CoordinateTransformation<?>[] coordinateTransformations = new CoordinateTransformation<?>[nTforms];
 
 		int i = 0;
-		if( scale != null )
+		if (scale != null)
 			coordinateTransformations[i++] = new ScaleCoordinateTransformation(scale);
 
-		if( translation != null )
+		if (translation != null)
 			coordinateTransformations[i++] = new TranslationCoordinateTransformation(translation);
 
 		return coordinateTransformations;
@@ -120,64 +121,64 @@ public static CoordinateTransformation<?>[] buildScaleTranslationTransformList(
 	 * @param datasetMetadata dataset metadata
 	 * @return the single scale metadata
 	 */
-	public static N5SingleScaleMetadata setDatasetAttributes( final N5SingleScaleMetadata baseMetadata, final N5DatasetMetadata datasetMetadata )
-	{
-		if( baseMetadata.getPath().equals( datasetMetadata.getPath() ))
-			return new N5SingleScaleMetadata( baseMetadata.getPath(), baseMetadata.spatialTransform3d(),
+	public static N5SingleScaleMetadata setDatasetAttributes(final N5SingleScaleMetadata baseMetadata, final N5DatasetMetadata datasetMetadata) {
+
+		if (baseMetadata.getPath().equals(datasetMetadata.getPath()))
+			return new N5SingleScaleMetadata(baseMetadata.getPath(), baseMetadata.spatialTransform3d(),
 					baseMetadata.getDownsamplingFactors(), baseMetadata.getPixelResolution(), baseMetadata.getOffset(),
-					baseMetadata.unit(), datasetMetadata.getAttributes() );
+					baseMetadata.unit(), datasetMetadata.getAttributes());
 		else
 			return null;
 	}
 
-	public static N5SingleScaleMetadata[] updateChildrenDatasetAttributes( final N5SingleScaleMetadata[] baseMetadata, final N5DatasetMetadata[] datasetMetadata )
-	{
-		final HashMap<String,N5SingleScaleMetadata> bases = new HashMap<>();
-		Arrays.stream( baseMetadata ).forEach( x -> { bases.put( x.getPath(), x ); } );
+	public static N5SingleScaleMetadata[] updateChildrenDatasetAttributes(final N5SingleScaleMetadata[] baseMetadata,
+			final N5DatasetMetadata[] datasetMetadata) {
+
+		final HashMap<String, N5SingleScaleMetadata> bases = new HashMap<>();
+		Arrays.stream(baseMetadata).forEach(x -> {
+			bases.put(x.getPath(), x);
+		});
 
-		return ( N5SingleScaleMetadata[] ) Arrays.stream( datasetMetadata ).map( x -> {
-			final N5SingleScaleMetadata b = bases.get( x.getPath() );
-			if( b == null )
+		return (N5SingleScaleMetadata[])Arrays.stream(datasetMetadata).map(x -> {
+			final N5SingleScaleMetadata b = bases.get(x.getPath());
+			if (b == null)
 				return null;
 			else
-				return setDatasetAttributes( b, x );
-		} ).filter( x -> x != null ).toArray();
+				return setDatasetAttributes(b, x);
+		}).filter(x -> x != null).toArray();
 	}
 
-	public static void updateChildrenMetadata( final N5TreeNode parent, final N5Metadata[] childrenMetadata,
-			final boolean relative )
-	{
-		final HashMap<String,N5Metadata> children = new HashMap<>();
-		Arrays.stream( childrenMetadata ).forEach( x -> {
+	public static void updateChildrenMetadata(final N5TreeNode parent, final N5Metadata[] childrenMetadata,
+			final boolean relative) {
+
+		final HashMap<String, N5Metadata> children = new HashMap<>();
+		Arrays.stream(childrenMetadata).forEach(x -> {
 			final String absolutePath;
-			if( relative )
-			{
+			if (relative) {
 				absolutePath = normalizeGroupPath(parent.getPath() + "/" + x.getPath());
 			} else {
 				absolutePath = x.getPath();
 			}
-			children.put( absolutePath, x );
+			children.put(absolutePath, x);
 		});
-		parent.childrenList().forEach( c -> {
+		parent.childrenList().forEach(c -> {
 			final N5Metadata m = children.get(MetadataUtils.normalizeGroupPath(c.getPath()));
-			if( m != null )
-				c.setMetadata( m );
+			if (m != null)
+				c.setMetadata(m);
 		});
 	}
 
-	public static String canonicalPath( final N5TreeNode parent, final String child )
-	{
-		return canonicalPath( parent.getPath(), child );
+	public static String canonicalPath(final N5TreeNode parent, final String child) {
+
+		return canonicalPath(parent.getPath(), child);
 	}
 
-	public static String canonicalPath( final String parent, final String child )
-	{
-		try
-		{
-			final N5URI url = new N5URI( "?/" + parent + "/" + child );
+	public static String canonicalPath(final String parent, final String child) {
+
+		try {
+			final N5URI url = new N5URI("?/" + parent + "/" + child);
 			return url.normalizeGroupPath();
-		}
-		catch ( final URISyntaxException e ) { }
+		} catch (final URISyntaxException e) {}
 		return null;
 	}
 
@@ -191,21 +192,24 @@ public static String normalizeGroupPath(final String path) {
 		return path;
 	}
 
-	public static String relativePath( final String parent, final String child )
-	{
-		try
-		{
-			final N5URI purl = new N5URI( "?" + parent );
-			final N5URI curl = new N5URI( "?" + child );
-			final Path ppath = Paths.get( purl.normalizeGroupPath());
-			final Path cpath = Paths.get( curl.normalizeGroupPath());
-			return ppath.relativize(cpath).toString();
-		}
-		catch ( final URISyntaxException e )
-		{
-			e.printStackTrace();
-		}
-		return null;
+	/**
+	 * Returns a relative group path from the child absolute path group path child 
+	 * the parent absolute group path.
+	 *
+	 * If the child path is not a descendent of parent, child will be returned.
+	 *
+	 * @param parent an absolute path
+	 * @param child an absolute path
+	 * @return relative path from child to parent, if it exists.
+	 */
+	public static String relativePath(final String parent, final String child) {
+
+		try {
+			final String purl = new N5URI("?" + parent).normalizeGroupPath();
+			final String curl = new N5URI("?" + child).normalizeGroupPath();
+			return new N5URI("?" + curl.replaceFirst("^"+purl, "")).normalizeGroupPath();
+		} catch (final URISyntaxException e) {}
+		return child;
 	}
 
 	/**
@@ -215,13 +219,13 @@ public static String relativePath( final String parent, final String child )
 	 * @param d exponent
 	 * @return result
 	 */
-	public static double[] pow( final double[] x, final int d )
-	{
-		final double[] y = new double[ x.length ];
-		Arrays.fill( y, 1 );
-		for ( int i = 0; i < d; i++ )
-			for ( int j = 0; j < x.length; j++ )
-				y[ j ] *= x[ j ];
+	public static double[] pow(final double[] x, final int d) {
+
+		final double[] y = new double[x.length];
+		Arrays.fill(y, 1);
+		for (int i = 0; i < d; i++)
+			for (int j = 0; j < x.length; j++)
+				y[j] *= x[j];
 
 		return y;
 	}
@@ -234,6 +238,7 @@ public static double[] pow( final double[] x, final int d )
 	 * @return a string
 	 */
 	public static String getStringNullable(final JsonElement element) {
+
 		if (element == null || element.isJsonNull())
 			return null;
 		else
@@ -252,10 +257,9 @@ public static AffineGet scaleTranslationTransforms(final double[] scale, final d
 
 		if (translation != null) {
 
-			if( scale != null ) {
+			if (scale != null) {
 				return new ScaleAndTranslation(scale, translation);
-			}
-			else {
+			} else {
 				// scale null, translation not null
 				if (translation.length == 2)
 					return new Translation2D(translation);

src/main/java/org/janelia/saalfeldlab/n5/universe/metadata/ome/ngff/v04/OmeNgffMultiScaleMetadata.java

@@ -26,8 +26,6 @@
 package org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04;
 
 import java.net.URISyntaxException;
-import java.nio.file.Path;
-import java.nio.file.Paths;
 import java.util.Arrays;
 import java.util.stream.DoubleStream;
 
@@ -139,11 +137,9 @@ private static OmeNgffDataset[] buildDatasets( final String path, final NgffSing
 		for( int i = 0; i < children.length; i++ )
 		{
 			datasets[i] = new OmeNgffDataset();
-//			final Path p = Paths.get(path);
-//			final Path c = Paths.get(children[i].getPath());
-//			datasets[i].path = p.relativize(c).toString();
-			datasets[i].path = Paths.get(path).relativize(Paths.get(children[i].getPath())).toString();
+			datasets[i].path = MetadataUtils.relativePath(path, children[i].getPath());
 			datasets[i].coordinateTransformations = children[i].getCoordinateTransformations();
+
 		}
 		return datasets;
 	}

src/main/java/org/janelia/saalfeldlab/n5/universe/metadata/ome/ngff/v04/OmeNgffMultiScaleMetadataMutable.java

@@ -1,10 +1,12 @@
 package org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04;
 
+import java.net.URISyntaxException;
 import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.List;
 
 import org.janelia.saalfeldlab.n5.DatasetAttributes;
+import org.janelia.saalfeldlab.n5.N5URI;
 import org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils;
 import org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis;
 
@@ -55,8 +57,7 @@ public void addChild(final int idx, final NgffSingleScaleAxesMetadata child) {
 
 		final OmeNgffDataset dset = new OmeNgffDataset();
 		// paths are relative to this object
-		dset.path = Paths.get(getPath()).relativize(Paths.get(child.getPath())).toString();
-
+		dset.path = MetadataUtils.relativePath(getPath(), child.getPath());
 		dset.coordinateTransformations = child.getCoordinateTransformations();
 		if (idx < 0)
 		{

src/test/java/org/janelia/saalfeldlab/n5/universe/metadata/ome/ngff/v04/BuildMultiscaleTest.java

@@ -0,0 +1,65 @@
+package org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04;
+
+import static org.junit.Assert.assertEquals;
+
+import org.janelia.saalfeldlab.n5.N5URI;
+import org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis;
+import org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils;
+import org.junit.Test;
+
+public class BuildMultiscaleTest {
+
+	@Test
+	public void buildNgffMultiscale() {
+
+		testHelper("", new String[]{"s0", "s1", "s2", "s3"});
+
+		testHelper("a", new String[]{"s0", "s1", "s2", "s3"});
+		testHelper("a/b", new String[]{"s0", "s1", "s2", "s3"});
+		testHelper("a/b/c", new String[]{"s0", "s1", "s2", "s3"});
+
+		testHelper("a", new String[]{"0/s0", "0/s1", "0/s2", "0/s3"});
+	}
+
+	private static void testHelper(final String path, final String[] childPaths) {
+
+		final String downsampleMethod = "sampling";
+		final Axis[] axes = AxisUtils.buildAxes("x", "y", "z");
+		final OmeNgffMultiScaleMetadataMutable ms = new OmeNgffMultiScaleMetadataMutable(path);
+
+		for (int i = 0; i < childPaths.length; i++) {
+			final double s = Math.pow(2, i);
+			ms.addChild(buildScaleLevelMetadata(childPaths[i], new double[]{s, s, s}, axes));
+		}
+
+		final OmeNgffMultiScaleMetadata meta = new OmeNgffMultiScaleMetadata(ms.getAxes().length,
+				path, path, downsampleMethod, "0.4",
+				ms.getAxes(),
+				ms.getDatasets(), null,
+				ms.coordinateTransformations, ms.metadata, true);
+
+		for (int i = 0; i < childPaths.length; i++) {
+			assertEquals(
+					String.format("multiscale path incorrect for root: %s, child: %s", path, childPaths[i]),
+					childPaths[i], meta.getDatasets()[i].path);
+		}
+
+		// test building children from multiscales
+		// these metadata's path variables must be relative to the root
+		final NgffSingleScaleAxesMetadata[] children = OmeNgffMultiScaleMetadata.buildMetadata(3, path, null, meta);
+		for (int i = 0; i < childPaths.length; i++) {
+			// ensure the paths are equal up to normalization
+			assertEquals(
+				String.format("single scale path incorrect for root: %s, child: %s", path, childPaths[i]),
+				N5URI.normalizeGroupPath(path + "/" + childPaths[i]),
+				N5URI.normalizeGroupPath(children[i].getPath()));
+		}
+	}
+
+	private static NgffSingleScaleAxesMetadata buildScaleLevelMetadata(final String path, final double[] res,
+			final Axis[] axes) {
+
+		return new NgffSingleScaleAxesMetadata(path, res, null, axes, null);
+	}
+
+}