introduced an abstraction layer for all N5 dataset parameters and to …

…potentially expose parts of the image (5D -> 3D for OME-ZARR), this allows us to directly use the N5ImageLoader for example for reading OME-ZARR based datasets

src/main/java/bdv/img/n5/BdvN5Format.java

@@ -28,11 +28,58 @@
  */
 package bdv.img.n5;
 
-public class BdvN5Format
+import org.janelia.saalfeldlab.n5.DataType;
+import org.janelia.saalfeldlab.n5.N5Reader;
+
+import bdv.img.cache.VolatileCachedCellImg;
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.type.NativeType;
+
+public class BdvN5Format implements N5Properties
 {
 	public static final String DOWNSAMPLING_FACTORS_KEY = "downsamplingFactors";
 	public static final String DATA_TYPE_KEY = "dataType";
 
+	@Override
+	public String getPath( final int setupId )
+	{
+		return getPathName( setupId );
+	}
+
+	@Override
+	public String getPath( final int setupId, final int timepointId)
+	{
+		return getPathName( setupId, timepointId );
+	}
+
+	@Override
+	public String getPath( final int setupId, final int timepointId, final int level)
+	{
+		return getPathName( setupId, timepointId, level );
+	}
+
+	@Override
+	public DataType getDataType( final N5Reader n5, final int setupId )
+	{
+		return n5.getAttribute( getPath( setupId ), DATA_TYPE_KEY, DataType.class );
+	}
+
+	@Override
+	public double[][] getMipmapResolutions( final N5Reader n5, final int setupId )
+	{
+		return n5.getAttribute( getPath( setupId ), DOWNSAMPLING_FACTORS_KEY, double[][].class );
+	}
+
+	@Override
+	public <T extends NativeType<T>> RandomAccessibleInterval<T> extractImg(
+			final VolatileCachedCellImg<T, ?> img,
+			final int setupId,
+			final int timepointId)
+	{
+		return img;
+	}
+
+	// left the old code for compatibility 
 	public static String getPathName( final int setupId )
 	{
 		return String.format( "setup%d", setupId );

src/main/java/bdv/img/n5/N5ImageLoader.java

@@ -28,10 +28,6 @@
  */
 package bdv.img.n5;
 
-import static bdv.img.n5.BdvN5Format.DATA_TYPE_KEY;
-import static bdv.img.n5.BdvN5Format.DOWNSAMPLING_FACTORS_KEY;
-import static bdv.img.n5.BdvN5Format.getPathName;
-
 import java.io.File;
 import java.io.IOException;
 import java.net.URI;
@@ -54,6 +50,7 @@
 import bdv.cache.CacheControl;
 import bdv.cache.SharedQueue;
 import bdv.img.cache.SimpleCacheArrayLoader;
+import bdv.img.cache.VolatileCachedCellImg;
 import bdv.img.cache.VolatileGlobalCellCache;
 import bdv.util.ConstantRandomAccessible;
 import bdv.util.MipmapTransforms;
@@ -83,6 +80,7 @@
 public class N5ImageLoader implements ViewerImgLoader, MultiResolutionImgLoader
 {
 	private final URI n5URI;
+	protected final N5Properties n5properties;
 
 	// TODO: it would be good if this would not be needed
 	//       find available setups from the n5
@@ -97,6 +95,7 @@ public N5ImageLoader( final URI n5URI, final AbstractSequenceDescription< ?, ?,
 	{
 		this.n5URI = n5URI;
 		this.seq = sequenceDescription;
+		this.n5properties = createN5PropertiesInstance();
 	}
 
 	public N5ImageLoader( final File n5File, final AbstractSequenceDescription< ?, ?, ? > sequenceDescription )
@@ -120,6 +119,11 @@ public File getN5File()
 		return new File( n5URI );
 	}
 
+	/**
+	 * @return a class that creates the pathnames for the setupId, timePointId and multiresolution levels
+	 */
+	public N5Properties createN5PropertiesInstance() { return new BdvN5Format(); }
+
 	private volatile boolean isOpen = false;
 	private SharedQueue createdSharedQueue;
 	private VolatileGlobalCellCache cache;
@@ -219,11 +223,10 @@ public void close()
 
 	private < T extends NativeType< T >, V extends Volatile< T > & NativeType< V > > SetupImgLoader< T, V > createSetupImgLoader( final int setupId ) throws IOException
 	{
-		final String pathName = getPathName( setupId );
 		final DataType dataType;
 		try
 		{
-			dataType = n5.getAttribute( pathName, DATA_TYPE_KEY, DataType.class );
+			dataType = n5properties.getDataType( n5, setupId );
 		}
 		catch ( final N5Exception e )
 		{
@@ -258,10 +261,9 @@ public SetupImgLoader( final int setupId, final T type, final V volatileType ) t
 		{
 			super( type, volatileType );
 			this.setupId = setupId;
-			final String pathName = getPathName( setupId );
 			try
 			{
-				mipmapResolutions = n5.getAttribute( pathName, DOWNSAMPLING_FACTORS_KEY, double[][].class );
+				mipmapResolutions = n5properties.getMipmapResolutions( n5, setupId );
 			}
 			catch ( final N5Exception e )
 			{
@@ -289,7 +291,7 @@ public Dimensions getImageSize( final int timepointId, final int level )
 		{
 			try
 			{
-				final String pathName = getPathName( setupId, timepointId, level );
+				final String pathName = n5properties.getPath( setupId, timepointId, level );
 				final DatasetAttributes attributes = n5.getDatasetAttributes( pathName );
 				return new FinalDimensions( attributes.getDimensions() );
 			}
@@ -330,7 +332,7 @@ private < T extends NativeType< T > > RandomAccessibleInterval< T > prepareCache
 		{
 			try
 			{
-				final String pathName = getPathName( setupId, timepointId, level );
+				final String pathName = n5properties.getPath( setupId, timepointId, level );
 				final DatasetAttributes attributes = n5.getDatasetAttributes( pathName );
 				final long[] dimensions = attributes.getDimensions();
 				final int[] cellDimensions = attributes.getBlockSize();
@@ -340,7 +342,9 @@ private < T extends NativeType< T > > RandomAccessibleInterval< T > prepareCache
 				final CacheHints cacheHints = new CacheHints( loadingStrategy, priority, false );
 
 				final SimpleCacheArrayLoader< ? > loader = createCacheArrayLoader( n5, pathName );
-				return cache.createImg( grid, timepointId, setupId, level, cacheHints, loader, type );
+				final VolatileCachedCellImg<T, ?> img = cache.createImg( grid, timepointId, setupId, level, cacheHints, loader, type );
+
+				return n5properties.extractImg( img, setupId, timepointId );
 			}
 			catch ( final IOException | N5Exception e )
 			{

src/main/java/bdv/img/n5/N5Properties.java

@@ -0,0 +1,20 @@
+package bdv.img.n5;
+
+import org.janelia.saalfeldlab.n5.DataType;
+import org.janelia.saalfeldlab.n5.N5Reader;
+
+import bdv.img.cache.VolatileCachedCellImg;
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.type.NativeType;
+
+public interface N5Properties
+{
+	// in case of OME-ZARR, it has an underlying 5D container
+	public < T extends NativeType<T> > RandomAccessibleInterval<T> extractImg( final VolatileCachedCellImg<T, ?> img, final int setupId, final int timepointId );
+
+	public DataType getDataType( final N5Reader n5, final int setupId );
+	public double[][] getMipmapResolutions( final N5Reader n5, final int setupId );
+	public String getPath( final int setupId );
+	public String getPath( final int setupId, final int timepointId );
+	public String getPath( final int setupId, final int timepointId, final int level );
+}