Ngff export axis order

src/main/java/org/janelia/saalfeldlab/n5/ij/N5ScalePyramidExporter.java

@@ -532,12 +532,7 @@ public <T extends RealType<T> & NativeType<T>, M extends N5DatasetMetadata, N ex
 		// get the image to save
 		final RandomAccessibleInterval<T> baseImg = getBaseImage();
 
-		final M baseMetadata;
-		if (impMeta != null)
-			baseMetadata = (M)impMeta.readMetadata(image);
-		else
-			baseMetadata = null;
-
+		final M baseMetadata = initializeBaseMetadata();
 		currentChannelMetadata = copyMetadata(baseMetadata);
 		M currentMetadata;
 
@@ -561,6 +556,7 @@ public <T extends RealType<T> & NativeType<T>, M extends N5DatasetMetadata, N ex
 			final double[] currentResolution = new double[nd];
 			System.arraycopy(baseResolution, 0, currentResolution, 0, nd);
 
+			// TODO here
 			final N multiscaleMetadata = initializeMultiscaleMetadata((M)currentMetadata, channelDataset);
 			currentTranslation = new double[nd];
 
@@ -629,6 +625,53 @@ public <T extends RealType<T> & NativeType<T>, M extends N5DatasetMetadata, N ex
 		n5.close();
 	}
 
+	@SuppressWarnings("unchecked")
+	protected <M extends N5DatasetMetadata> M initializeBaseMetadata() {
+
+		M baseMetadata = null;
+		if (impMeta != null) {
+			try {
+				baseMetadata = (M) impMeta.readMetadata(image);
+			} catch (IOException e) {
+			}
+		}
+
+		if (impMeta instanceof NgffToImagePlus) {
+
+			/*
+			 * ImagePlus axes need to be permuted before conversion to ngff (i.e. from XYCZT
+			 * to XYZCT) The data are permuted elsewhere, here we ensure the metadata
+			 * reflect that chagnge
+			 */
+			final NgffSingleScaleAxesMetadata ngffMeta = (NgffSingleScaleAxesMetadata) baseMetadata;
+			baseMetadata = (M) new NgffSingleScaleAxesMetadata(ngffMeta.getPath(), ngffMeta.getScale(),
+					ngffMeta.getTranslation(), permuteAxesForNgff(ngffMeta.getAxes()), ngffMeta.getAttributes());
+		}
+
+		return baseMetadata;
+	}
+
+	protected Axis[] permuteAxesForNgff(final Axis[] axes) {
+
+		boolean hasC = false;
+		boolean hasZ = false;
+		boolean hasT = false;
+		for (int i = 0; i < axes.length; i++) {
+			hasC = hasC || axes[i].getName().equals("c");
+			hasZ = hasZ || axes[i].getName().equals("z");
+			hasT = hasT || axes[i].getName().equals("t");
+		}
+
+		if (hasC && hasZ) {
+			if (hasT)
+				return new Axis[] { axes[0], axes[1], axes[3], axes[2], axes[4] };
+			else
+				return new Axis[] { axes[0], axes[1], axes[3], axes[2] };
+		}
+
+		return axes;
+	}
+
 	protected void initializeDataset() {
 
 		dataset = image.getShortTitle();
@@ -936,10 +979,16 @@ protected <T extends RealType<T> & NativeType<T>, M extends N5DatasetMetadata> L
 		// some metadata styles never split channels, return input image in that
 		// case
 		if (metadataStyle.equals(NONE) || metadataStyle.equals(N5Importer.MetadataCustomKey) ||
-				metadataStyle.equals(N5Importer.MetadataOmeZarrKey) ||
 				metadataStyle.equals(N5Importer.MetadataImageJKey)) {
 			return Collections.singletonList(img);
 		}
+		else if (metadataStyle.equals(N5Importer.MetadataOmeZarrKey)) {
+
+			if (image.getNChannels() > 1 && image.getNSlices() > 1)
+				return Collections.singletonList(Views.permute(img, 2, 3));
+			else
+				return Collections.singletonList(img);
+		}
 
 		// otherwise, split channels
 		final ArrayList<RandomAccessibleInterval<T>> channels = new ArrayList<>();
@@ -962,6 +1011,7 @@ protected <T extends RealType<T> & NativeType<T>, M extends N5DatasetMetadata> L
 				// make a 4d image in order XYZT
 				channelImg = Views.permute(Views.addDimension(channelImg, 0, 0), 2, 3);
 			}
+
 			channels.add(channelImg);
 		}
 
@@ -1311,16 +1361,6 @@ private static <T extends NativeType<T>> RandomAccessibleInterval<T> downsampleA
 		return BlockAlgoUtils.cellImg(blocks, dimensions, cellDimensions);
 	}
 
-	private int[] sliceBlockSize(final int exclude) {
-
-		return removeElement(chunkSize, exclude);
-	}
-
-	private long[] sliceDownsamplingFactors(final int exclude) {
-
-		return removeElement(currentAbsoluteDownsampling, exclude);
-	}
-
 	private static int[] removeElement(final int[] arr, final int excludeIndex) {
 
 		final int[] out = new int[arr.length - 1];

src/test/java/org/janelia/saalfeldlab/n5/metadata/NgffTests.java

@@ -1,36 +1,61 @@
 package org.janelia.saalfeldlab.n5.metadata;
 
+import static org.junit.Assert.assertArrayEquals;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 
+import java.io.File;
 import java.io.IOException;
+import java.nio.file.Files;
+import java.util.Arrays;
 
+import org.janelia.saalfeldlab.n5.DatasetAttributes;
 import org.janelia.saalfeldlab.n5.N5Exception;
 import org.janelia.saalfeldlab.n5.N5FSReader;
+import org.janelia.saalfeldlab.n5.N5Reader;
+import org.janelia.saalfeldlab.n5.ij.N5Importer;
+import org.janelia.saalfeldlab.n5.ij.N5ScalePyramidExporter;
+import org.janelia.saalfeldlab.n5.universe.N5Factory;
 import org.janelia.saalfeldlab.n5.universe.metadata.NgffMultiScaleGroupAttributes;
 import org.janelia.saalfeldlab.n5.universe.metadata.NgffMultiScaleGroupAttributes.MultiscaleDataset;
+import org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis;
 import org.junit.Assert;
-import org.junit.Before;
+import org.junit.BeforeClass;
 import org.junit.Test;
 
+
+import ij.ImagePlus;
+import ij.gui.NewImage;
+
 public class NgffTests {
-
-	private N5FSReader n5;
 
-	@Before
-	  public void setUp() throws IOException {
+	private final String n5Root = "src/test/resources/ngff.n5";
+
+	private static File baseDir;
+
+	@BeforeClass
+	public static void setup() {
+
+		try {
+			baseDir = Files.createTempDirectory("ngff-tests-").toFile();
+			baseDir.deleteOnExit();
+
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+	}
 
-		final String n5Root = "src/test/resources/ngff.n5";
-		n5 = new N5FSReader(n5Root);
-	  }
+	@Test
+	public void testNgffGroupAttributeParsing() {
 
-	  @Test
-	  public void testNgffGroupAttributeParsing() {
+		final double eps = 1e-9;
+		try( final N5FSReader n5 = new N5FSReader(n5Root) ) {
 
-		  final double eps = 1e-9;
-		  try {
-			NgffMultiScaleGroupAttributes[] multiscales = n5.getAttribute("ngff_grpAttributes", "multiscales", NgffMultiScaleGroupAttributes[].class );
+			NgffMultiScaleGroupAttributes[] multiscales = n5.getAttribute("ngff_grpAttributes", "multiscales",
+					NgffMultiScaleGroupAttributes[].class);
 			Assert.assertEquals("one set of multiscales", 1, multiscales.length);
-			
+
 			MultiscaleDataset[] datasets = multiscales[0].datasets;
 			Assert.assertEquals("num levels", 6, datasets.length);
 
@@ -48,6 +73,67 @@ public void testNgffGroupAttributeParsing() {
 			fail("Ngff parsing failed");
 			e.printStackTrace();
 		}
-	  }
+	}
+
+	@Test
+	public void testNgffExportAxisOrder() {
+
+		testNgfffAxisOrder("xyczt", new int[] { 10, 8, 6, 4, 2 });
+
+		testNgfffAxisOrder("xyzt", new int[] { 10, 8, 1, 4, 2 });
+		testNgfffAxisOrder("xyct", new int[] { 10, 8, 6, 1, 2 });
+		testNgfffAxisOrder("xycz", new int[] { 10, 8, 6, 4, 1 });
+
+		testNgfffAxisOrder("xyc", new int[] { 10, 8, 6, 1, 1 });
+		testNgfffAxisOrder("xyz", new int[] { 10, 8, 1, 4, 1 });
+		testNgfffAxisOrder("xyt", new int[] { 10, 8, 1, 1, 2 });
+	}
+
+	public void testNgfffAxisOrder(final String dataset, int[] size) {
+
+		final int nx = size[0];
+		final int ny = size[1];
+		final int nc = size[2];
+		final int nz = size[3];
+		final int nt = size[4];
+
+		final String metadataType = N5Importer.MetadataOmeZarrKey;
+		final String compressionType = N5ScalePyramidExporter.RAW_COMPRESSION;
+
+		final ImagePlus imp = NewImage.createImage("test", nx, ny, nz * nc * nt, 8, NewImage.FILL_BLACK);
+		imp.setDimensions(nc, nz, nt);
+
+		final N5ScalePyramidExporter writer = new N5ScalePyramidExporter();
+		writer.setOptions(imp, baseDir.getAbsolutePath(), dataset, N5ScalePyramidExporter.ZARR_FORMAT, "64", false,
+				N5ScalePyramidExporter.DOWN_SAMPLE, metadataType, compressionType);
+		writer.run();
+
+		final long[] expectedDims = Arrays.stream(new long[] { nx, ny, nz, nc, nt }).filter(x -> x > 1).toArray();
+
+		try (final N5Reader n5 = new N5Factory().openReader(baseDir.getAbsolutePath())) {
+
+			assertTrue(n5.exists(dataset));
+			assertTrue(n5.datasetExists(dataset + "/s0"));
+
+			final DatasetAttributes dsetAttrs = n5.getDatasetAttributes(dataset + "/s0");
+			assertArrayEquals("dimensions", expectedDims, dsetAttrs.getDimensions());
+
+			int i = 0;
+			final Axis[] axes = n5.getAttribute(dataset, "multiscales[0]/axes", Axis[].class);
+
+			if (nt > 1)
+				assertEquals("t", axes[i++].getName());
+
+			if (nc > 1)
+				assertEquals("c", axes[i++].getName());
+
+			if (nz > 1)
+				assertEquals("z", axes[i++].getName());
+
+			assertEquals("y", axes[i++].getName());
+			assertEquals("x", axes[i++].getName());
+		}
+
+	}
 
 }