fix: NgffSingleScaleMetadataParser more robust

* handle situations with unusually scale/translation ordering
* or multiple scales and/or translations

see #17

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

@@ -1,8 +1,6 @@
 package org.janelia.saalfeldlab.n5.universe.metadata;
 
 import java.net.URISyntaxException;
-import java.nio.file.Path;
-import java.nio.file.Paths;
 import java.util.Arrays;
 import java.util.HashMap;
 
@@ -25,6 +23,7 @@
 import net.imglib2.realtransform.Translation;
 import net.imglib2.realtransform.Translation2D;
 import net.imglib2.realtransform.Translation3D;
+import net.imglib2.util.Pair;
 
 public class MetadataUtils {
 
@@ -112,6 +111,32 @@ public static CoordinateTransformation<?>[] buildScaleTranslationTransformList(f
 		return coordinateTransformations;
 	}
 
+	public static ScaleAndTranslation scaleTranslationFromCoordinateTransformations(final CoordinateTransformation<?>[] cts) {
+
+		if (cts == null || cts.length == 0)
+			return null;
+
+		ScaleAndTranslation out = coordinateTransformToScaleAndTranslation(cts[0]);
+		for (int i = 1; i < cts.length; i++) {
+			out.preConcatenate(coordinateTransformToScaleAndTranslation(cts[i]));
+		}
+		return out;
+	}
+
+	public static ScaleAndTranslation coordinateTransformToScaleAndTranslation(CoordinateTransformation<?> ct) {
+
+		if (ct.getType().equals(ScaleCoordinateTransformation.TYPE)) {
+			final double[] s = ((ScaleCoordinateTransformation)ct).getScale();
+			return new ScaleAndTranslation(s, new double[s.length]);
+		} else if (ct.getType().equals(TranslationCoordinateTransformation.TYPE)) {
+			final double[] t = ((TranslationCoordinateTransformation)ct).getTranslation();
+			final double[] s = new double[t.length];
+			Arrays.fill(s, 1.0);
+			return new ScaleAndTranslation(s, t);
+		}
+		return null;
+	}
+
 	/**
 	 * Returns a new {@link N5SingleScaleMetadata} equal to the baseMetadata, but with
 	 * {@link DatasetAttributes} coming from datasetMetadata.ew

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

@@ -60,8 +60,8 @@ public NgffSingleScaleAxesMetadata(final String path,
 
 		this.datasetAttributes = datasetAttributes;
 
-		// TODO generalize for translation first
 		coordinateTransformations = MetadataUtils.buildScaleTranslationTransformList(scale, translation);
+
 		this.transform = MetadataUtils.scaleTranslationTransforms(scale, translation);
 	}
 

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

@@ -8,6 +8,7 @@
 import org.janelia.saalfeldlab.n5.N5Reader;
 import org.janelia.saalfeldlab.n5.N5Writer;
 import org.janelia.saalfeldlab.n5.universe.N5TreeNode;
+import org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils;
 import org.janelia.saalfeldlab.n5.universe.metadata.N5MetadataParser;
 import org.janelia.saalfeldlab.n5.universe.metadata.N5MetadataWriter;
 import org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis;
@@ -19,6 +20,8 @@
 import com.google.gson.JsonArray;
 import com.google.gson.JsonElement;
 
+import net.imglib2.realtransform.ScaleAndTranslation;
+
 public class NgffSingleScaleMetadataParser implements N5MetadataParser<NgffSingleScaleAxesMetadata>, N5MetadataWriter<NgffSingleScaleAxesMetadata> {
 
 	private final Gson gson;
@@ -43,14 +46,9 @@ public Optional<NgffSingleScaleAxesMetadata> parseMetadata(final N5Reader n5, fi
 			if (cts == null || cts.length == 0)
 				return Optional.of(new NgffSingleScaleAxesMetadata(node.getPath(), null, null, null));
 
-			double[] scale = null;
-			double[] translation = null;
-			for (int i = 0; i < cts.length; i++) {
-				if (cts[i] instanceof ScaleCoordinateTransformation)
-					scale = ((ScaleCoordinateTransformation)cts[i]).getScale();
-				else if (cts[i] instanceof TranslationCoordinateTransformation)
-					translation = ((TranslationCoordinateTransformation)cts[i]).getTranslation();
-			}
+			final ScaleAndTranslation scaleAndTranslation = MetadataUtils.scaleTranslationFromCoordinateTransformations(cts);
+			final double[] scale = scaleAndTranslation.getScaleCopy();
+			final double[] translation = scaleAndTranslation.getTranslationCopy();
 
 			final DatasetAttributes dsetAttrs = n5.getDatasetAttributes(node.getPath());
 			if( OmeNgffMetadataParser.cOrder(dsetAttrs))