6.1.3-alpha-4 candidate

.github/workflows/build-main.yml

@@ -18,7 +18,7 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y libblosc1
       - name: Set up Java
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: '8'
           distribution: 'zulu'

.github/workflows/build-pr.yml

@@ -16,7 +16,7 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y libblosc1
       - name: Set up Java
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: '8'
           distribution: 'zulu'

.github/workflows/platform-test.yml

@@ -35,7 +35,7 @@ jobs:
           pip install blosc --no-input --target src/test/resources
           mv src/test/resources/lib64/* src/test/resources
       - name: Set up Java
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v4
         with:
           java-version: '8'
           distribution: 'zulu'

pom.xml

@@ -5,12 +5,12 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>38.0.1</version>
+		<version>43.0.0</version>
 	</parent>
 
 	<groupId>org.janelia.saalfeldlab</groupId>
 	<artifactId>n5-viewer_fiji</artifactId>
-	<version>6.1.3-SNAPSHOT</version>
+	<version>6.1.3-alpha-4-SNAPSHOT</version>
 
 	<name>N5 Viewer for Fiji</name>
 	<description>BigDataViewer-based visualization tool for N5 datasets</description>
@@ -134,13 +134,16 @@
 		<bigdataviewer-core.version>10.6.1</bigdataviewer-core.version>
 		<bigdataviewer-vistools.version>1.0.0-beta-36</bigdataviewer-vistools.version>
 
-		<imglib2.version>7.1.1</imglib2.version>
-		<n5.version>3.3.0</n5.version>
-		<n5-aws-s3.version>4.2.1</n5-aws-s3.version>
-		<n5-google-cloud.version>4.1.1</n5-google-cloud.version>
-		<n5-ij.version>4.2.5</n5-ij.version>
-		<n5-imglib2.version>7.0.2</n5-imglib2.version>
-		<n5-universe.version>1.6.0</n5-universe.version>
+		<n5.version>4.0.0-alpha-10</n5.version>
+		<n5-aws-s3.version>4.4.0-alpha-7</n5-aws-s3.version>
+		<n5-blosc.version>2.0.0-alpha-4</n5-blosc.version>
+		<n5-google-cloud.version>5.2.0-alpha-6</n5-google-cloud.version>
+		<n5-hdf5.version>2.3.0-alpha-6</n5-hdf5.version>
+		<n5-ij.version>4.5.0-alpha-6</n5-ij.version>
+		<n5-imglib2.version>7.1.0-alpha-7</n5-imglib2.version>
+		<n5-universe.version>2.4.0-alpha-7</n5-universe.version>
+		<n5-zarr.version>2.0.0-alpha-7</n5-zarr.version>
+		<n5-zstandard.version>2.0.0-alpha-4</n5-zstandard.version>
 	</properties>
 
 	<dependencies>

src/main/java/org/janelia/saalfeldlab/n5/bdv/N5Viewer.java

@@ -80,6 +80,7 @@
 import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.NgffSingleScaleAxesMetadata;
 import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.OmeNgffMetadata;
 import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.OmeNgffMultiScaleMetadata;
+import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.OmeNgffV05Metadata;
 import org.scijava.ui.behaviour.io.InputTriggerConfig;
 import org.scijava.ui.behaviour.util.Actions;
 import org.scijava.ui.behaviour.util.InputActionBindings;
@@ -543,6 +544,12 @@ public static <T extends NumericType<T> & NativeType<T>, V extends Volatile<T> &
 						.sort(multiScaleDataset.getPaths(), multiScaleDataset.spatialTransforms3d());
 				datasetsToOpen = msd.getPaths();
 				transforms = msd.getTransforms();
+			} else if (metadata instanceof OmeNgffV05Metadata) {
+				final OmeNgffV05Metadata multiScaleDataset = (OmeNgffV05Metadata)metadata;
+				final MultiscaleDatasets msd = MultiscaleDatasets
+						.sort(multiScaleDataset.getPaths(), multiScaleDataset.spatialTransforms3d());
+				datasetsToOpen = msd.getPaths();
+				transforms = msd.getTransforms();
 			} else if (metadata instanceof N5CosemMultiScaleMetadata) {
 				final N5CosemMultiScaleMetadata multiScaleDataset = (N5CosemMultiScaleMetadata)metadata;
 				final MultiscaleDatasets msd = MultiscaleDatasets
@@ -722,7 +729,7 @@ protected static <T extends NumericType<T> & NativeType<T>> RandomAccessibleInte
 			final N5Reader n5, final String dataset) {
 
 		final CachedCellImg<?, ?> img = N5Utils.openVolatile(n5, dataset);
-		final Object t = Util.getTypeFromInterval(img);
+		final Object t = img.getType();
 		if( t instanceof LabelMultisetType ) {
 
 			final CachedCellImg<LabelMultisetType, ?> lmsImg = (CachedCellImg<LabelMultisetType, ?>)img;

src/main/java/org/janelia/saalfeldlab/n5/bdv/N5ViewerCreator.java

@@ -1,15 +1,20 @@
 package org.janelia.saalfeldlab.n5.bdv;
 
 import java.io.IOException;
+import java.util.Collections;
+import java.util.List;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
 import java.util.function.Consumer;
 
+import javax.swing.JTree;
+
 import org.janelia.saalfeldlab.n5.ij.N5Importer;
 import org.janelia.saalfeldlab.n5.metadata.N5ViewerMultichannelMetadata;
 import org.janelia.saalfeldlab.n5.metadata.imagej.ImagePlusLegacyMetadataParser;
 import org.janelia.saalfeldlab.n5.ui.DataSelection;
 import org.janelia.saalfeldlab.n5.ui.DatasetSelectorDialog;
+import org.janelia.saalfeldlab.n5.ui.N5SwingTreeNode;
 import org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadataParser;
 import org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMultiScaleMetadata;
 import org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser;
@@ -18,6 +23,7 @@
 import org.janelia.saalfeldlab.n5.universe.metadata.N5ViewerMultiscaleMetadataParser;
 import org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMetadataParser;
 import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.OmeNgffMetadataParser;
+import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.OmeNgffV05MetadataParser;
 
 import ij.ImageJ;
 
@@ -33,6 +39,7 @@
 public class N5ViewerCreator {
 
 	public static final N5MetadataParser<?>[] n5vGroupParsers = new N5MetadataParser[]{
+			new OmeNgffV05MetadataParser(),
 			new OmeNgffMetadataParser(),
 			new N5CosemMultiScaleMetadata.CosemMultiScaleParser(),
 			new N5ViewerMultiscaleMetadataParser(),
@@ -50,6 +57,8 @@ public class N5ViewerCreator {
 			new N5GenericSingleScaleMetadataParser()
 	};
 
+	private DatasetSelectorDialog dialog;
+
 	private String lastOpenedContainer = "";
 
 	final public static void main(final String... args) {
@@ -112,7 +121,7 @@ public void openViewer(
 			final Consumer<Void> cancelConsumer) {
 
 		final ExecutorService exec = Executors.newFixedThreadPool(ij.Prefs.getThreads());
-		final DatasetSelectorDialog dialog = new DatasetSelectorDialog(
+		dialog = new DatasetSelectorDialog(
 				new N5Importer.N5ViewerReaderFun(),
 				new N5Importer.N5BasePathFun(),
 				lastOpenedContainer,
@@ -138,4 +147,52 @@ public void openViewer(
 			}
 		});
 	}
+
+	public void runWithDialog(final String pathToContainer, final List<String> selectThisSubPath) {
+
+		lastOpenedContainer = pathToContainer;
+		dialog = null;
+		openViewer((e) -> e.printStackTrace());
+		if (dialog == null) {
+			throw new RuntimeException("The \"Open N5\" didn't come up when it should.");
+		} else {
+			dialog.detectDatasets();
+			if (selectThisSubPath != null) {
+				boolean isDiscoveryFinished = dialog.waitUntilDiscoveryIsFinished(60000);
+				if (isDiscoveryFinished)
+					selectTreeItem(selectThisSubPath);
+			}
+		}
+	}
+
+	public void runWithDialog( final String pathToContainer )
+	{
+		runWithDialog( pathToContainer, Throwable::printStackTrace );
+	}
+
+	public void runWithDialog( final String pathToContainer, final Consumer< Exception > exceptionHandler )
+	{
+		lastOpenedContainer = pathToContainer;
+		dialog = null;
+		openViewer( exceptionHandler );
+		dialog.openContainer( pathToContainer );
+	}
+
+	private void selectTreeItem(final List<String> itemPath) {
+
+		final JTree t = dialog.getJTree();
+		int currRow = 0;
+		for (String subPath : itemPath) {
+			for (int r = currRow; r < t.getRowCount(); ++r, ++currRow) {
+				N5SwingTreeNode n = (N5SwingTreeNode)t.getPathForRow(r).getLastPathComponent();
+				if (n.getNodeName().equals(subPath)) {
+					t.expandRow(r);
+					t.setSelectionRow(r);
+					++currRow;
+					break;
+				}
+			}
+		}
+	}
+
 }

src/test/java/org/janelia/saalfeldlab/n5/bdv/N5vAxisPermutationTests.java

@@ -22,6 +22,7 @@
 import org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer;
 import org.janelia.saalfeldlab.n5.universe.N5Factory;
 import org.janelia.saalfeldlab.n5.universe.N5TreeNode;
+import org.janelia.saalfeldlab.n5.universe.StorageFormat;
 import org.janelia.saalfeldlab.n5.universe.metadata.N5Metadata;
 import org.janelia.saalfeldlab.n5.universe.metadata.NgffTests;
 import org.junit.After;
@@ -83,11 +84,10 @@ protected String tempN5Location() throws URISyntaxException {
 	@Test
 	public void testPermutations() throws IOException {
 
-		final N5Writer zarr = new N5Factory().openWriter(containerUri.toString());
+		final N5Writer zarr = new N5Factory().openWriter(StorageFormat.ZARR2, containerUri.toString());
 		// don't check every axis permutation, but some relevant ones, and some strange ones
 		final String[] names = new String[]{
 
-				// TODO five still don't work
 				"xyz", "zyx", "yzx",
 				"xyc", "xcy", "cyx",
 				"xyt", "xty", "tyx",
@@ -145,10 +145,6 @@ protected <T extends NumericType<T> & NativeType<T>> void writeAndTest(final N5W
 		final AffineTransform3D tform = new AffineTransform3D();
 		src.getSourceTransform(0, 0, tform);
 
-		// System.out.println("");
-		// System.out.println("" + sourcesAndConverters.size());
-		// System.out.println("");
-
 		// test
 		assertEquals(dset + "size x", NgffTests.NX, dims[0]);
 		assertEquals(dset + "size y", NgffTests.NY, dims[1]);