Merge pull request #529 from saalfeldlab/feat/omengff

feat: support OmeNgff Metadata

pom.xml

@@ -82,7 +82,7 @@
 		<n5-aws-s3.version>4.1.2</n5-aws-s3.version>
 		<n5-zarr.version>1.3.1</n5-zarr.version>
 		<n5-imglib2.version>7.0.0</n5-imglib2.version>
-		<n5-universe.version>1.4.0</n5-universe.version>
+		<n5-universe.version>1.4.3</n5-universe.version>
 
 		<enforcer.skip>true</enforcer.skip>
 	</properties>
@@ -632,7 +632,7 @@
 	<mailingLists>
 		<mailingList>
 			<name>ImageJ Forum</name>
-			<archive>http://forum.imagej.net/</archive>
+			<archive>https://forum.image.sc/</archive>
 		</mailingList>
 	</mailingLists>
 

src/main/java/org/janelia/saalfeldlab/util/n5/N5Data.java

@@ -33,7 +33,7 @@
 import org.janelia.saalfeldlab.n5.N5Writer;
 import org.janelia.saalfeldlab.n5.imglib2.N5LabelMultisets;
 import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
-import org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadata;
+import org.janelia.saalfeldlab.n5.universe.metadata.N5SpatialDatasetMetadata;
 import org.janelia.saalfeldlab.n5.universe.metadata.SpatialMultiscaleMetadata;
 import org.janelia.saalfeldlab.paintera.Paintera;
 import org.janelia.saalfeldlab.paintera.cache.WeakRefVolatileCache;
@@ -624,7 +624,7 @@ public static ImagesWithTransform<LabelMultisetType, VolatileLabelMultisetType>[
 			final SharedQueue queue,
 			final int priority) throws IOException {
 
-		SpatialMultiscaleMetadata<N5SingleScaleMetadata> metadata = metadataState.getMetadata();
+		SpatialMultiscaleMetadata<N5SpatialDatasetMetadata> metadata = metadataState.getMetadata();
 		final String[] ssPaths = metadata.getPaths();
 
 		LOG.debug("Opening groups {} as multi-scale in {} ", Arrays.toString(ssPaths), metadata.getPath());

src/main/java/org/janelia/saalfeldlab/util/n5/metadata/N5PainteraDataMultiScaleGroup.java

@@ -3,11 +3,13 @@
 import net.imglib2.realtransform.AffineGet;
 import net.imglib2.realtransform.AffineTransform3D;
 import org.janelia.saalfeldlab.n5.universe.metadata.N5MultiScaleMetadata;
+import org.janelia.saalfeldlab.n5.universe.metadata.N5SpatialDatasetMetadata;
+import org.janelia.saalfeldlab.n5.universe.metadata.SpatialMultiscaleMetadata;
 
 import java.util.function.Predicate;
 import java.util.regex.Pattern;
 
-public abstract class N5PainteraDataMultiScaleGroup extends N5MultiScaleMetadata {
+public abstract class N5PainteraDataMultiScaleGroup extends SpatialMultiscaleMetadata<N5SpatialDatasetMetadata> {
 
 	public static final Predicate<String> SCALE_LEVEL_PREDICATE = Pattern.compile("^s\\d+$").asPredicate();
 	protected final N5PainteraDataMultiScaleMetadata dataGroup;

src/main/java/org/janelia/saalfeldlab/util/n5/metadata/N5PainteraDataMultiScaleMetadata.java

@@ -1,18 +1,14 @@
 package org.janelia.saalfeldlab.util.n5.metadata;
 
-import bdv.util.Affine3DHelpers;
-import com.sun.javafx.geom.transform.Affine3D;
-import net.imglib2.realtransform.AffineGet;
 import net.imglib2.realtransform.AffineTransform3D;
 import net.imglib2.realtransform.Scale3D;
 import org.janelia.saalfeldlab.n5.N5Reader;
 import org.janelia.saalfeldlab.n5.universe.N5TreeNode;
 import org.janelia.saalfeldlab.n5.universe.metadata.N5MetadataParser;
-import org.janelia.saalfeldlab.n5.universe.metadata.N5MultiScaleMetadata;
 import org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadata;
-import org.janelia.saalfeldlab.paintera.state.metadata.SingleScaleMetadataState;
+import org.janelia.saalfeldlab.n5.universe.metadata.N5SpatialDatasetMetadata;
+import org.janelia.saalfeldlab.n5.universe.metadata.SpatialMultiscaleMetadata;
 
-import java.util.Arrays;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.Optional;
@@ -21,14 +17,11 @@
 /**
  * Metadata Parser for a Paintera Data Multiscale Dataset. Namely, transforms are dependant on group metadata
  */
-public class N5PainteraDataMultiScaleMetadata extends N5MultiScaleMetadata {
+public class N5PainteraDataMultiScaleMetadata extends SpatialMultiscaleMetadata<N5SpatialDatasetMetadata> {
 
-	private AffineTransform3D groupTransform;
-
-	public N5PainteraDataMultiScaleMetadata(final String basePath, final N5SingleScaleMetadata[] childrenMetadata, final AffineTransform3D groupTransform) {
+	public N5PainteraDataMultiScaleMetadata(final String basePath, final N5SpatialDatasetMetadata[] childrenMetadata) {
 
 		super(basePath, childrenMetadata);
-		this.groupTransform = groupTransform;
 	}
 	@Override public String unit() {
 
@@ -46,7 +39,7 @@ public static class PainteraDataMultiScaleParser implements N5MetadataParser<N5P
 			final Map<String, N5TreeNode> scaleLevelNodes = new HashMap<>();
 			for (final N5TreeNode childNode : node.childrenList()) {
 				if (N5PainteraDataMultiScaleGroup.SCALE_LEVEL_PREDICATE.test(childNode.getNodeName()) && childNode.isDataset()
-						&& childNode.getMetadata() instanceof N5SingleScaleMetadata) {
+						&& childNode.getMetadata() instanceof N5SpatialDatasetMetadata) {
 					scaleLevelNodes.put(childNode.getNodeName(), childNode);
 				}
 			}
@@ -113,7 +106,7 @@ public static class PainteraDataMultiScaleParser implements N5MetadataParser<N5P
 				);
 			}
 
-			return Optional.of(new N5PainteraDataMultiScaleMetadata(node.getPath(), resolvedChildrenMetadata, transform));
+			return Optional.of(new N5PainteraDataMultiScaleMetadata(node.getPath(), resolvedChildrenMetadata));
 		}
 	}
 }

src/main/java/org/janelia/saalfeldlab/util/n5/metadata/N5PainteraLabelMultiScaleGroup.java

@@ -37,8 +37,8 @@
 import org.janelia.saalfeldlab.n5.universe.metadata.N5MetadataParser;
 import org.janelia.saalfeldlab.n5.universe.metadata.N5MultiScaleMetadata;
 import org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadata;
+import org.janelia.saalfeldlab.n5.universe.metadata.N5SpatialDatasetMetadata;
 
-import java.io.IOException;
 import java.util.Optional;
 
 public class N5PainteraLabelMultiScaleGroup extends N5PainteraDataMultiScaleGroup {
@@ -146,12 +146,16 @@ public static class PainteraLabelMultiScaleParser implements N5MetadataParser<N5
 			final var finalFragmentSegmentAssignmentGroup = fragmentSegmentAssignment;
 			final var finalLabelToBlockLookupGroup = labelToBlockLookupGroup;
 
-			return Optional.ofNullable(dataGroup).map(dg -> new N5PainteraLabelMultiScaleGroup(
-					node.getPath(),
-					dg,
-					finalUniqueLabelsGroup, finalFragmentSegmentAssignmentGroup, finalLabelToBlockLookupGroup,
-					maxId, dg.getChildrenMetadata()[0].isLabelMultiset()
-			));
+			return Optional.ofNullable(dataGroup).map(dg -> {
+				final N5SpatialDatasetMetadata firstChild = dg.getChildrenMetadata()[0];
+				final Boolean isLabelMultiset = firstChild instanceof N5SingleScaleMetadata && ((N5SingleScaleMetadata)firstChild).isLabelMultiset();
+				return new N5PainteraLabelMultiScaleGroup(
+						node.getPath(),
+						dg,
+						finalUniqueLabelsGroup, finalFragmentSegmentAssignmentGroup, finalLabelToBlockLookupGroup,
+						maxId, isLabelMultiset
+				);
+			});
 		}
 	}
 

src/main/kotlin/org/janelia/saalfeldlab/paintera/Paintera.kt

@@ -272,7 +272,9 @@ class Paintera : Application() {
 		internal var debugMode = false
 
 		@JvmStatic
-		val n5Factory = N5FactoryWithCache().apply { cacheAttributes(true) }
+		val n5Factory = N5FactoryWithCache().apply {
+			cacheAttributes(true)
+		}
 
 		private val LOG = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass())
 

src/main/kotlin/org/janelia/saalfeldlab/paintera/state/metadata/MetadataState.kt

@@ -14,8 +14,12 @@ import org.janelia.saalfeldlab.n5.universe.metadata.N5Metadata
 import org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadata
 import org.janelia.saalfeldlab.n5.universe.metadata.N5SpatialDatasetMetadata
 import org.janelia.saalfeldlab.n5.universe.metadata.SpatialMultiscaleMetadata
+import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.NgffSingleScaleAxesMetadata
 import org.janelia.saalfeldlab.paintera.Paintera
 import org.janelia.saalfeldlab.paintera.state.metadata.MetadataState.Companion.isLabel
+import org.janelia.saalfeldlab.paintera.state.metadata.MetadataUtils.Companion.isLabelMultiset
+import org.janelia.saalfeldlab.paintera.state.metadata.MetadataUtils.Companion.offset
+import org.janelia.saalfeldlab.paintera.state.metadata.MetadataUtils.Companion.resolution
 import org.janelia.saalfeldlab.util.n5.ImagesWithTransform
 import org.janelia.saalfeldlab.util.n5.N5Data
 import org.janelia.saalfeldlab.util.n5.N5Helpers
@@ -78,20 +82,20 @@ interface MetadataState {
 
 open class SingleScaleMetadataState(
 	final override var n5ContainerState: N5ContainerState,
-	final override val metadata: N5SingleScaleMetadata
-) :
-	MetadataState {
-	override var transform: AffineTransform3D = metadata.spatialTransform3d()
+	final override val metadata: N5SpatialDatasetMetadata
+) : MetadataState {
+
+	final override var transform: AffineTransform3D = metadata.spatialTransform3d()
 	override var isLabelMultiset: Boolean = metadata.isLabelMultiset
 	override var isLabel: Boolean = isLabel(metadata.attributes.dataType) || metadata.isLabelMultiset
 	override var datasetAttributes: DatasetAttributes = metadata.attributes
 	override var minIntensity = metadata.minIntensity()
 	override var maxIntensity = metadata.maxIntensity()
-	override var resolution = metadata.pixelResolution!!
-	override var translation = metadata.offset!!
-	override var unit = metadata.unit()!!
+	override var resolution = metadata.resolution
+	override var translation = metadata.offset
+	override var unit: String = metadata.unit()
 	override var reader = n5ContainerState.reader
-	override val writer :N5Writer?
+	override val writer: N5Writer?
 		get() = n5ContainerState.writer
 
 	override var group = metadata.path!!
@@ -129,11 +133,12 @@ open class SingleScaleMetadataState(
 
 open class MultiScaleMetadataState constructor(
 	override val n5ContainerState: N5ContainerState,
-	final override val metadata: SpatialMultiscaleMetadata<N5SingleScaleMetadata>
+	final override val metadata: SpatialMultiscaleMetadata<N5SpatialDatasetMetadata>
 ) : MetadataState by SingleScaleMetadataState(n5ContainerState, metadata[0]) {
 
-	private val highestResMetadata: N5SingleScaleMetadata = metadata[0]
-	override var transform: AffineTransform3D = metadata.spatialTransform3d()
+	private val highestResMetadata: N5SpatialDatasetMetadata = metadata[0]
+	final override var transform: AffineTransform3D = metadata.spatialTransform3d()
+	final override var isLabelMultiset: Boolean = metadata[0].isLabelMultiset
 	override var isLabel: Boolean = isLabel(highestResMetadata.attributes.dataType) || isLabelMultiset
 	override var resolution: DoubleArray = transform.run { doubleArrayOf(get(0, 0), get(1, 1), get(2, 2)) }
 	override var translation: DoubleArray = transform.translation
@@ -180,8 +185,7 @@ open class MultiScaleMetadataState constructor(
 class PainteraDataMultiscaleMetadataState constructor(
 	n5ContainerState: N5ContainerState,
 	var painteraDataMultiscaleMetadata: N5PainteraDataMultiScaleGroup
-) :
-	MultiScaleMetadataState(n5ContainerState, painteraDataMultiscaleMetadata) {
+) : MultiScaleMetadataState(n5ContainerState, painteraDataMultiscaleMetadata) {
 
 	val dataMetadataState = MultiScaleMetadataState(n5ContainerState, painteraDataMultiscaleMetadata.dataGroupMetadata)
 
@@ -207,13 +211,33 @@ operator fun <T> SpatialMultiscaleMetadata<T>.get(index: Int): T where T : N5Spa
 class MetadataUtils {
 
 	companion object {
+		val N5SpatialDatasetMetadata.isLabelMultiset
+			get() = when (this) {
+				is N5SingleScaleMetadata -> isLabelMultiset
+				else -> false
+			}
+
+		val N5SpatialDatasetMetadata.resolution: DoubleArray
+			get() = when (this) {
+				is N5SingleScaleMetadata -> pixelResolution!!
+				is NgffSingleScaleAxesMetadata -> scale
+				else -> DoubleArray(this.spatialTransform().numDimensions()) { 1.0 }
+			}
+
+		val N5SpatialDatasetMetadata.offset
+			get() = when (this) {
+				is N5SingleScaleMetadata -> offset!!
+				is NgffSingleScaleAxesMetadata -> translation!!
+				else -> DoubleArray(this.spatialTransform().numDimensions()) { 0.0 }
+			}
+
 		@JvmStatic
 		fun metadataIsValid(metadata: N5Metadata?): Boolean {
 			/* Valid if we are SpatialMultiscaleMetadata whose children are single scale, or we are SingleScale ourselves. */
 			return (metadata as? SpatialMultiscaleMetadata<*>)?.let {
-				it.childrenMetadata[0] is N5SingleScaleMetadata
+				it.childrenMetadata[0] is N5SpatialDatasetMetadata
 			} ?: run {
-				metadata is N5SingleScaleMetadata
+				metadata is N5SpatialDatasetMetadata
 			}
 		}
 
@@ -222,16 +246,16 @@ class MetadataUtils {
 			@Suppress("UNCHECKED_CAST")
 			return Optional.ofNullable(
 				(metadata as? N5PainteraDataMultiScaleGroup)?.let { PainteraDataMultiscaleMetadataState(n5ContainerState, it) }
-					?: (metadata as? SpatialMultiscaleMetadata<N5SingleScaleMetadata>)?.let { MultiScaleMetadataState(n5ContainerState, it) }
-					?: (metadata as? N5SingleScaleMetadata)?.let { SingleScaleMetadataState(n5ContainerState, it) }
+					?: (metadata as? SpatialMultiscaleMetadata<N5SpatialDatasetMetadata>)?.let { MultiScaleMetadataState(n5ContainerState, it) }
+					?: (metadata as? N5SpatialDatasetMetadata)?.let { SingleScaleMetadataState(n5ContainerState, it) }
 			)
 		}
 
 		@JvmStatic
 		fun createMetadataState(n5containerAndDataset: String): Optional<MetadataState> {
 
-			val reader  = with(Paintera.n5Factory) {
-				openWriterOrNull(n5containerAndDataset) ?: openReaderOrNull(n5containerAndDataset)?: return Optional.empty()
+			val reader = with(Paintera.n5Factory) {
+				openWriterOrNull(n5containerAndDataset) ?: openReaderOrNull(n5containerAndDataset) ?: return Optional.empty()
 			}
 
 			val n5ContainerState = N5ContainerState(reader)
@@ -246,8 +270,8 @@ class MetadataUtils {
 
 		@JvmStatic
 		fun createMetadataState(n5container: String, dataset: String?): Optional<MetadataState> {
-			val reader  = with(Paintera.n5Factory) {
-				openWriterOrNull(n5container) ?: openReaderOrNull(n5container)?: return Optional.empty()
+			val reader = with(Paintera.n5Factory) {
+				openWriterOrNull(n5container) ?: openReaderOrNull(n5container) ?: return Optional.empty()
 			}
 
 			val n5ContainerState = N5ContainerState(reader)

src/main/kotlin/org/janelia/saalfeldlab/paintera/ui/dialogs/create/CreateDataset.kt

@@ -266,7 +266,7 @@ class CreateDataset(private val currentSource: Source<*>?, vararg allSources: So
 						blockSize.asIntArray(),
 						resolution.asDoubleArray(),
 						offset.asDoubleArray(),
-						scaleLevels.stream().map { it.downsamplingFactors() }.toList().toTypedArray(),
+						scaleLevels.map { it.downsamplingFactors() }.toTypedArray(),
 						scaleLevels.stream().mapToInt { it.maxNumEntries() }.toArray()
 					)
 

src/main/kotlin/org/janelia/saalfeldlab/util/n5/N5Helpers.kt

@@ -27,6 +27,7 @@ import org.janelia.saalfeldlab.n5.hdf5.N5HDF5Reader
 import org.janelia.saalfeldlab.n5.universe.N5DatasetDiscoverer
 import org.janelia.saalfeldlab.n5.universe.N5TreeNode
 import org.janelia.saalfeldlab.n5.universe.metadata.*
+import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.OmeNgffMetadataParser
 import org.janelia.saalfeldlab.paintera.Paintera.Companion.n5Factory
 import org.janelia.saalfeldlab.paintera.control.assignment.FragmentSegmentAssignmentOnlyLocal
 import org.janelia.saalfeldlab.paintera.control.assignment.FragmentSegmentAssignmentOnlyLocal.NoInitialLutAvailable
@@ -50,7 +51,6 @@ import org.janelia.saalfeldlab.util.n5.universe.N5ContainerDoesntExist
 import org.slf4j.LoggerFactory
 import java.io.IOException
 import java.lang.invoke.MethodHandles
-import java.nio.file.Paths
 import java.util.*
 import java.util.List
 import java.util.concurrent.ExecutorService
@@ -88,6 +88,7 @@ object N5Helpers {
 	private val LOG = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass())
 
 	private val GROUP_PARSERS = List.of<N5MetadataParser<*>>(
+		OmeNgffMetadataParser(),
 		PainteraRawMultiScaleParser(),
 		PainteraLabelMultiScaleParser(),
 		PainteraDataMultiScaleParser(),