feat: methods for permuting metadata axes

* for use by downstream importers
saalfeldlab · May 9, 2024 · d457a1f · d457a1f
1 parent 5b01482
commit d457a1f
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diff --git a/src/main/java/org/janelia/saalfeldlab/n5/universe/metadata/MetadataUtils.java b/src/main/java/org/janelia/saalfeldlab/n5/universe/metadata/MetadataUtils.java
@@ -3,11 +3,16 @@
 import java.net.URISyntaxException;
 import java.util.Arrays;
 import java.util.HashMap;
+import java.util.Optional;
 
+import org.apache.commons.lang3.ArrayUtils;
 import org.janelia.saalfeldlab.n5.DatasetAttributes;
 import org.janelia.saalfeldlab.n5.N5URI;
 import org.janelia.saalfeldlab.n5.universe.N5TreeNode;
+import org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadata.CosemTransform;
 import org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis;
+import org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils;
+import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.NgffSingleScaleAxesMetadata;
 import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.coordinateTransformations.CoordinateTransformation;
 import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.coordinateTransformations.ScaleCoordinateTransformation;
 import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.coordinateTransformations.TranslationCoordinateTransformation;
@@ -16,17 +21,21 @@
 import com.google.gson.JsonNull;
 
 import net.imglib2.realtransform.AffineGet;
+import net.imglib2.realtransform.AffineTransform3D;
 import net.imglib2.realtransform.Scale;
 import net.imglib2.realtransform.Scale2D;
 import net.imglib2.realtransform.Scale3D;
 import net.imglib2.realtransform.ScaleAndTranslation;
 import net.imglib2.realtransform.Translation;
 import net.imglib2.realtransform.Translation2D;
 import net.imglib2.realtransform.Translation3D;
-import net.imglib2.util.Pair;
 
 public class MetadataUtils {
 
+	// duplicate variables in N5ScalePyramidExporter in n5-ij
+	public static final String DOWN_SAMPLE = "Sample";
+	public static final String DOWN_AVERAGE = "Average";
+
 	public static double[] mul(final double[] a, final double[] b) {
 
 		final double[] out = new double[a.length];
@@ -116,7 +125,7 @@ public static ScaleAndTranslation scaleTranslationFromCoordinateTransformations(
 		if (cts == null || cts.length == 0)
 			return null;
 
-		ScaleAndTranslation out = coordinateTransformToScaleAndTranslation(cts[0]);
+		final ScaleAndTranslation out = coordinateTransformToScaleAndTranslation(cts[0]);
 		for (int i = 1; i < cts.length; i++) {
 			out.preConcatenate(coordinateTransformToScaleAndTranslation(cts[i]));
 		}
@@ -218,7 +227,7 @@ public static String normalizeGroupPath(final String path) {
 	}
 
 	/**
-	 * Returns a relative group path from the child absolute path group path child 
+	 * 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.
@@ -307,4 +316,196 @@ else if (scale.length == 3)
 		return null;
 	}
 
+	@SuppressWarnings("unchecked")
+	public static <M extends N5DatasetMetadata> M metadataForThisScale(final String newPath,
+			final M baseMetadata,
+			final String downsampleMethod,
+			final double[] baseResolution,
+			final double[] absoluteDownsamplingFactors,
+			final double[] absoluteScale,
+			final double[] absoluteTranslation) {
+
+		if (baseMetadata == null)
+			return null;
+
+		/**
+		 * if metadata is N5SingleScaleMetadata and not a subclass of it then this is using N5Viewer
+		 * metadata which does not have an offset
+		 */
+		if (baseMetadata.getClass().equals(N5SingleScaleMetadata.class)) {
+			return (M)buildN5VMetadata(newPath, (N5SingleScaleMetadata)baseMetadata, downsampleMethod, baseResolution, absoluteDownsamplingFactors);
+		} else if (baseMetadata instanceof N5CosemMetadata) {
+			return (M)buildCosemMetadata(newPath, (N5CosemMetadata)baseMetadata, absoluteScale, absoluteTranslation);
+
+		} else if (baseMetadata instanceof NgffSingleScaleAxesMetadata) {
+			return (M)buildNgffMetadata(newPath, (NgffSingleScaleAxesMetadata)baseMetadata, absoluteScale, absoluteTranslation);
+		} else
+			return baseMetadata;
+	}
+
+	public static N5SingleScaleMetadata buildN5VMetadata(
+			final String path,
+			final N5SingleScaleMetadata baseMetadata,
+			final String downsampleMethod,
+			final double[] baseResolution,
+			final double[] downsamplingFactors) {
+
+		/**
+		 * N5Viewer metadata doesn't have a way to directly represent offset. Rather, the half-pixel
+		 * offsets that averaging downsampling introduces are assumed when downsampling factors are
+		 * not equal to ones.
+		 *
+		 * As a result, we use downsampling factors with average downsampling, but set the factors
+		 * to one otherwise.
+		 */
+		final int nd = baseResolution.length > 3 ? 3 : baseResolution.length;
+		final double[] resolution = new double[nd];
+		final double[] factors = new double[nd];
+
+		if (downsampleMethod.equals(DOWN_AVERAGE)) {
+			System.arraycopy(baseResolution, 0, resolution, 0, nd);
+			System.arraycopy(downsamplingFactors, 0, factors, 0, nd);
+		} else {
+			for (int i = 0; i < nd; i++)
+				resolution[i] = baseResolution[i] * downsamplingFactors[i];
+
+			Arrays.fill(factors, 1);
+		}
+
+		final AffineTransform3D transform = new AffineTransform3D();
+		for (int i = 0; i < nd; i++)
+			transform.set(resolution[i], i, i);
+
+		return new N5SingleScaleMetadata(
+				path,
+				transform,
+				factors,
+				resolution,
+				baseMetadata.getOffset(),
+				baseMetadata.unit(),
+				baseMetadata.getAttributes(),
+				baseMetadata.minIntensity(),
+				baseMetadata.maxIntensity(),
+				baseMetadata.isLabelMultiset());
+
+	}
+
+	public static N5CosemMetadata buildCosemMetadata(
+			final String path,
+			final N5CosemMetadata baseMetadata,
+			final double[] absoluteResolution,
+			final double[] absoluteTranslation) {
+
+		final double[] resolution = new double[absoluteResolution.length];
+		System.arraycopy(absoluteResolution, 0, resolution, 0, absoluteResolution.length);
+
+		final double[] translation = new double[absoluteTranslation.length];
+		System.arraycopy(absoluteTranslation, 0, translation, 0, absoluteTranslation.length);
+
+		return new N5CosemMetadata(
+				path,
+				new CosemTransform(
+						baseMetadata.getCosemTransform().axes,
+						resolution,
+						translation,
+						baseMetadata.getCosemTransform().units),
+				baseMetadata.getAttributes());
+	}
+
+	public static NgffSingleScaleAxesMetadata buildNgffMetadata(
+			final String path,
+			final NgffSingleScaleAxesMetadata baseMetadata,
+			final double[] absoluteResolution,
+			final double[] absoluteTranslation) {
+
+		final double[] resolution = new double[absoluteResolution.length];
+		System.arraycopy(absoluteResolution, 0, resolution, 0, absoluteResolution.length);
+
+		final double[] translation = new double[absoluteTranslation.length];
+		System.arraycopy(absoluteTranslation, 0, translation, 0, absoluteTranslation.length);
+
+		return new NgffSingleScaleAxesMetadata(
+				path,
+				resolution,
+				translation,
+				baseMetadata.getAxes(),
+				baseMetadata.getAttributes());
+	}
+
+	@SuppressWarnings("unchecked")
+	public static <M extends N5Metadata> M permuteSpatialMetadata(final M metadata, final int[] axisPermutation) {
+
+		if (metadata == null)
+			return null;
+
+		/**
+		 * if metadata is N5SingleScaleMetadata and not a subclass of it then this is using N5Viewer
+		 * metadata which does not have an offset
+		 */
+		if (metadata.getClass().equals(N5SingleScaleMetadata.class)) {
+			return (M)permuteN5vMetadata((N5SingleScaleMetadata)metadata, axisPermutation);
+		} else if (metadata instanceof N5CosemMetadata) {
+			return (M)permuteCosemMetadata((N5CosemMetadata)metadata, axisPermutation);
+		} else if (metadata instanceof NgffSingleScaleAxesMetadata) {
+			return (M)permuteNgffMetadata((NgffSingleScaleAxesMetadata)metadata, axisPermutation);
+		} else
+			return metadata;
+	}
+
+	public static NgffSingleScaleAxesMetadata permuteNgffMetadata(final NgffSingleScaleAxesMetadata metadata, int[] axisPermutation) {
+
+		final Axis[] axes = metadata.getAxes();
+		final Axis[] axesPermuted = new Axis[axes.length];
+		for (int i = 0; i < axes.length; i++)
+			axesPermuted[i] = axes[i];
+
+		AxisUtils.permute(axesPermuted, axesPermuted, axisPermutation);
+
+		return new NgffSingleScaleAxesMetadata(
+				metadata.getPath(),
+				AxisUtils.permute(metadata.getScale(), axisPermutation),
+				AxisUtils.permute(metadata.getTranslation(), axisPermutation),
+				axesPermuted,
+				metadata.getAttributes());
+	}
+
+	public static N5CosemMetadata permuteCosemMetadata(final N5CosemMetadata metadata, int[] axisPermutation) {
+
+		final double[] newScales = AxisUtils.permute(metadata.getCosemTransform().scale, axisPermutation);
+		final double[] newTranslation = AxisUtils.permute(metadata.getCosemTransform().translate, axisPermutation);
+
+		final String[] newAxes = ArrayUtils.clone(metadata.getCosemTransform().axes);
+		AxisUtils.permute(newAxes, newAxes, axisPermutation);
+
+		final String[] newUnits = ArrayUtils.clone(metadata.getCosemTransform().units);
+		AxisUtils.permute(newUnits, newUnits, axisPermutation);
+
+		return new N5CosemMetadata(
+				metadata.getPath(),
+				new CosemTransform(newAxes, newScales, newTranslation, newUnits),
+				metadata.getAttributes());
+	}
+
+	public static N5SingleScaleMetadata permuteN5vMetadata(final N5SingleScaleMetadata metadata, int[] axisPermutation) {
+
+		final double[] newScales = AxisUtils.permute(metadata.getPixelResolution(), axisPermutation);
+		final double[] newOffset = AxisUtils.permute(metadata.getOffset(), axisPermutation);
+		final double[] newFactors = AxisUtils.permute(metadata.getDownsamplingFactors(), axisPermutation);
+
+		final AffineTransform3D offsetTform = new AffineTransform3D();
+		offsetTform.translate(newOffset);
+
+		final AffineTransform3D transform = N5SingleScaleMetadataParser.buildTransform(newFactors, newScales, Optional.of(offsetTform));
+
+		return new N5SingleScaleMetadata(
+				metadata.getPath(),
+				transform,
+				newFactors,
+				newScales,
+				newOffset,
+				metadata.unit(),
+				metadata.getAttributes());
+
+	}
+
 }
diff --git a/...rg/janelia/saalfeldlab/n5/universe/metadata/ome/ngff/v04/NgffSingleScaleAxesMetadata.java b/...rg/janelia/saalfeldlab/n5/universe/metadata/ome/ngff/v04/NgffSingleScaleAxesMetadata.java
@@ -54,15 +54,28 @@ public NgffSingleScaleAxesMetadata(final String path,
 
 		this.path = MetadataUtils.normalizeGroupPath(path);
 
-		this.scale = scale;
-		this.translation = translation;
+		this.scale = scale != null ? scale : ones(axes.length);
+		this.translation = translation != null ? translation : new double[axes.length];
 		this.axes = axes;
 
 		this.datasetAttributes = datasetAttributes;
 
-		coordinateTransformations = MetadataUtils.buildScaleTranslationTransformList(scale, translation);
+		coordinateTransformations = MetadataUtils.buildScaleTranslationTransformList(this.scale, this.translation);
+		if (Arrays.stream(axes).allMatch(x -> x.getType().equals(Axis.SPACE))) {
+			this.transform = MetadataUtils.scaleTranslationTransforms(this.scale, this.translation);
+		} else {
+			final int[] spaceIndexes = AxisUtils.indexes(axes, x -> x.getType().equals(Axis.SPACE));
+			final double[] spaceScale = AxisUtils.permute(this.scale, spaceIndexes);
+			final double[] spaceTranslation = AxisUtils.permute(this.translation, spaceIndexes);
+			this.transform = MetadataUtils.scaleTranslationTransforms(spaceScale, spaceTranslation);
+		}
+	}
+
+	private static double[] ones(final int N) {
 
-		this.transform = MetadataUtils.scaleTranslationTransforms(scale, translation);
+		final double[] ones = new double[N];
+		Arrays.fill(ones, 1);
+		return ones;
 	}
 
 	@Override

diff --git a/...java/org/janelia/saalfeldlab/n5/universe/metadata/ome/ngff/v04/OmeNgffMetadataParser.java b/...java/org/janelia/saalfeldlab/n5/universe/metadata/ome/ngff/v04/OmeNgffMetadataParser.java
@@ -93,13 +93,17 @@ public Optional<OmeNgffMetadata> parseMetadata(final N5Reader n5, final N5TreeNo
 				attrs[i] = dsetMeta[i].getAttributes();
 			}
 
+			// maybe axes can be flipped first?
+			ArrayUtils.reverse(ms.axes);
+
 			final NgffSingleScaleAxesMetadata[] msChildrenMeta = OmeNgffMultiScaleMetadata.buildMetadata(
 					nd, node.getPath(), ms.datasets, attrs, ms.coordinateTransformations, ms.metadata, ms.axes);
 
 			MetadataUtils.updateChildrenMetadata(node, msChildrenMeta, false);
 
 			// axes need to be flipped after the child is created
-			ArrayUtils.reverse(ms.axes);
+			// is this actually true?
+			// ArrayUtils.reverse(ms.axes);
 
 			multiscales[j] = new OmeNgffMultiScaleMetadata(ms, msChildrenMeta);
 		}

diff --git a/...nelia/saalfeldlab/n5/universe/metadata/ome/ngff/v04/OmeNgffMultiScaleMetadataMutable.java b/...nelia/saalfeldlab/n5/universe/metadata/ome/ngff/v04/OmeNgffMultiScaleMetadataMutable.java
@@ -1,12 +1,9 @@
 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;