Cloud

pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>37.0.0</version>
+		<version>38.0.1</version>
 		<relativePath />
 	</parent>
 
@@ -146,7 +146,8 @@
 		<imglib2.version>7.0.3</imglib2.version>
 		<imglib2-realtransform.version>4.0.3</imglib2-realtransform.version>
 		<imglib2-cache.version>1.0.0-beta-18</imglib2-cache.version>
-		<imglib2-algorithm.version>0.15.2</imglib2-algorithm.version>
+		<imglib2-algorithm.version>0.15.3</imglib2-algorithm.version>
+		<spim_data.version>2.3.0</spim_data.version>
 
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
 		<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>

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

@@ -34,6 +34,7 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.net.URI;
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
@@ -80,7 +81,7 @@
 
 public class N5ImageLoader implements ViewerImgLoader, MultiResolutionImgLoader
 {
-	private final File n5File;
+	private final URI n5URI;
 
 	// TODO: it would be good if this would not be needed
 	//       find available setups from the n5
@@ -89,17 +90,33 @@ public class N5ImageLoader implements ViewerImgLoader, MultiResolutionImgLoader
 	/**
 	 * Maps setup id to {@link SetupImgLoader}.
 	 */
-	private final Map< Integer, SetupImgLoader > setupImgLoaders = new HashMap<>();
+	private final Map< Integer, SetupImgLoader< ?, ? > > setupImgLoaders = new HashMap<>();
 
-	public N5ImageLoader( final File n5File, final AbstractSequenceDescription< ?, ?, ? > sequenceDescription )
+	public N5ImageLoader( final URI n5URI, final AbstractSequenceDescription< ?, ?, ? > sequenceDescription )
 	{
-		this.n5File = n5File;
+		this.n5URI = n5URI;
 		this.seq = sequenceDescription;
 	}
 
+	public N5ImageLoader( final File n5File, final AbstractSequenceDescription< ?, ?, ? > sequenceDescription )
+	{
+		this( n5File.toURI(), sequenceDescription );
+	}
+
+	public N5ImageLoader( final N5Reader n5Reader, final URI n5URI, final AbstractSequenceDescription< ?, ?, ? > sequenceDescription )
+	{
+		this( n5URI, sequenceDescription );
+		n5 = n5Reader;
+	}
+
+	public URI getN5URI()
+	{
+		return n5URI;
+	}
+
 	public File getN5File()
 	{
-		return n5File;
+		return new File( n5URI );
 	}
 
 	private volatile boolean isOpen = false;
@@ -134,14 +151,17 @@ private void open()
 
 				try
 				{
-					this.n5 = new N5FSReader( n5File.getAbsolutePath() );
+					if ( n5 == null )
+					{
+						n5 = new N5FSReader( getN5File().getAbsolutePath() );
+					}
 
 					int maxNumLevels = 0;
 					final List< ? extends BasicViewSetup > setups = seq.getViewSetupsOrdered();
 					for ( final BasicViewSetup setup : setups )
 					{
 						final int setupId = setup.getId();
-						final SetupImgLoader setupImgLoader = createSetupImgLoader( setupId );
+						final SetupImgLoader< ?, ? > setupImgLoader = createSetupImgLoader( setupId );
 						setupImgLoaders.put( setupId, setupImgLoader );
 						maxNumLevels = Math.max( maxNumLevels, setupImgLoader.numMipmapLevels() );
 					}
@@ -190,7 +210,7 @@ public void close()
 	}
 
 	@Override
-	public SetupImgLoader getSetupImgLoader( final int setupId )
+	public SetupImgLoader< ?, ? > getSetupImgLoader( final int setupId )
 	{
 		open();
 		return setupImgLoaders.get( setupId );
@@ -405,6 +425,8 @@ public A loadArray( final long[] gridPosition, final int[] cellDimensions ) thro
 		return new N5CacheArrayLoader<>( n5, pathName, attributes, DataTypeProperties.of( attributes.getDataType() ) );
 	}
 
+	// TODO: replace ndArrayCopy(...) below with new SubArrayCopy from imglib2 core ???
+
 	/**
 	 * Like `System.arrayCopy()` but for flattened nD arrays.
 	 *

src/main/java/bdv/img/n5/XmlIoN5ImageLoader.java

@@ -28,15 +28,22 @@
  */
 package bdv.img.n5;
 
+import static mpicbg.spim.data.XmlKeys.IMGLOADER_FORMAT_ATTRIBUTE_NAME;
+
 import java.io.File;
+import java.net.URI;
+import java.util.regex.Pattern;
+
+import org.janelia.saalfeldlab.n5.N5FSReader;
+import org.jdom2.Element;
+
+import mpicbg.spim.data.SpimDataInstantiationException;
 import mpicbg.spim.data.XmlHelpers;
 import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
 import mpicbg.spim.data.generic.sequence.ImgLoaderIo;
+import mpicbg.spim.data.generic.sequence.ImgLoaders;
 import mpicbg.spim.data.generic.sequence.XmlIoBasicImgLoader;
-import org.jdom2.Element;
-
-import static mpicbg.spim.data.XmlHelpers.loadPath;
-import static mpicbg.spim.data.XmlKeys.IMGLOADER_FORMAT_ATTRIBUTE_NAME;
+import net.imglib2.util.Cast;
 
 @ImgLoaderIo( format = "bdv.n5", type = N5ImageLoader.class )
 public class XmlIoN5ImageLoader implements XmlIoBasicImgLoader< N5ImageLoader >
@@ -53,9 +60,40 @@ public Element toXml( final N5ImageLoader imgLoader, final File basePath )
 
 	@Override
 	public N5ImageLoader fromXml( final Element elem, final File basePath, final AbstractSequenceDescription< ?, ?, ? > sequenceDescription )
+	{
+		return fromXml( elem, basePath.toURI(), sequenceDescription );
+	}
+
+	@Override
+	public N5ImageLoader fromXml( final Element elem, final URI basePathURI, final AbstractSequenceDescription< ?, ?, ? > sequenceDescription )
 	{
 //		final String version = elem.getAttributeValue( "version" );
-		final File path = loadPath( elem, "n5", basePath );
-		return new N5ImageLoader( path, sequenceDescription );
+		final URI uri = XmlHelpers.loadPathURI( elem, "n5", basePathURI );
+
+		// try to open with N5FSReader if URI is a file
+		try
+		{
+			final String scheme = uri.getScheme();
+			final boolean hasScheme = scheme != null;
+			if ( !hasScheme || FILE_SCHEME.asPredicate().test( scheme ) )
+			{
+				final N5FSReader n5 = new N5FSReader( new File( uri ).getAbsolutePath() );
+				return new N5ImageLoader( n5, uri, sequenceDescription );
+			}
+		}
+		catch ( Exception e ) {}
+
+		// try to open with "bdv.n5.cloud" format, if XmlIo for that can be discovered
+		try
+		{
+			final XmlIoBasicImgLoader< ? > io = ImgLoaders.createXmlIoForFormat( "bdv.n5.cloud" );
+			return Cast.unchecked( io.fromXml( elem, basePathURI, sequenceDescription ) );
+		}
+		catch ( SpimDataInstantiationException e )
+		{
+			return null;
+		}
 	}
+
+	private final static Pattern FILE_SCHEME = Pattern.compile("file", Pattern.CASE_INSENSITIVE);
 }