Cloud

pom.xml

@@ -5,26 +5,26 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>31.1.0</version>
+		<version>37.0.0</version>
 		<relativePath />
 	</parent>
 
 	<groupId>sc.fiji</groupId>
 	<artifactId>spim_data</artifactId>
-	<version>2.2.8-SNAPSHOT</version>
+	<version>2.3.0-SNAPSHOT</version>
 
 	<name>SPIM Data</name>
 	<description>representation of multi-angle, multi-channel (etc.) SPIM images and their registration</description>
-	<url>http://github.com/bigdataviewer/spimdata</url>
+	<url>https://github.com/bigdataviewer/spimdata</url>
 	<inceptionYear>2013</inceptionYear>
 	<organization>
 		<name>BigDataViewer</name>
-		<url>https://imagej.net/BigDataViewer</url>
+		<url>https://imagej.net/plugins/bdv</url>
 	</organization>
 	<licenses>
 		<license>
 			<name>Simplified BSD License</name>
-			<url>http://opensource.org/licenses/BSD-2-Clause</url>
+			<url>https://opensource.org/licenses/BSD-2-Clause</url>
 			<distribution>repo</distribution>
 		</license>
 	</licenses>
@@ -33,7 +33,7 @@
 		<developer>
 			<id>tpietzsch</id>
 			<name>Tobias Pietzsch</name>
-			<url>https://imagej.net/User:Pietzsch</url>
+			<url>https://imagej.net/people/tpietzsch</url>
 			<roles>
 				<role>founder</role>
 				<role>lead</role>
@@ -47,7 +47,7 @@
 		<developer>
 			<id>StephanPreibisch</id>
 			<name>Stephan Preibisch</name>
-			<url>https://imagej.net/User:StephanP</url>
+			<url>https://imagej.net/people/StephanPreibisch</url>
 			<roles>
 				<role>founder</role>
 				<role>lead</role>
@@ -60,7 +60,7 @@
 		<developer>
 			<id>ctrueden</id>
 			<name>Curtis Rueden</name>
-			<url>https://imagej.net/User:Rueden</url>
+			<url>https://imagej.net/people/ctrueden</url>
 			<roles>
 				<role>maintainer</role>
 			</roles>
@@ -69,7 +69,7 @@
 	<contributors>
 		<contributor>
 			<name>Johannes Schindelin</name>
-			<url>https://imagej.net/User:Schindelin</url>
+			<url>https://imagej.net/people/dscho</url>
 			<properties><id>dscho</id></properties>
 			<roles><role>founder</role></roles>
 		</contributor>
@@ -79,7 +79,7 @@
 		</contributor>
 		<contributor>
 			<name>Stephan Saalfeld</name>
-			<url>https://imagej.net/User:Saalfeld</url>
+			<url>https://imagej.net/people/axtimwalde</url>
 			<properties><id>axtimwalde</id></properties>
 		</contributor>
 	</contributors>
@@ -146,6 +146,8 @@
 			<groupId>net.sf.trove4j</groupId>
 			<artifactId>trove4j</artifactId>
 		</dependency>
+
+		<!-- Test dependencies -->
 		<dependency>
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>

src/main/java/mpicbg/spim/data/SpimDataExample2.java

@@ -29,6 +29,7 @@
 package mpicbg.spim.data;
 
 import java.io.IOException;
+import java.net.URI;
 import java.text.ParseException;
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -175,7 +176,7 @@ public static void exampleSequenceDescription() throws IOException, ParseExcepti
 		final Document doc = new Document( io.toXml( sequence, null ) );
 		new XMLOutputter( Format.getPrettyFormat() ).output( doc, System.out );
 
-		final SequenceDescription fromXml = io.fromXml( doc.getRootElement(), null );
+		final SequenceDescription fromXml = io.fromXml( doc.getRootElement(), ( URI ) null );
 		new XMLOutputter( Format.getPrettyFormat() ).output( new Document( new XmlIoSequenceDescription().toXml( fromXml, null ) ), System.out );
 	}
 

src/main/java/mpicbg/spim/data/XmlHelpers.java

@@ -30,6 +30,8 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.net.URI;
+import java.net.URISyntaxException;
 
 import net.imglib2.Dimensions;
 import net.imglib2.FinalDimensions;
@@ -270,7 +272,7 @@ public static File loadPath( final Element parent, final String name, final Stri
 	{
 		final Element elem = parent.getChild( name );
 		final String path = ( elem == null ) ? defaultRelativePath : elem.getText();
-		final boolean isRelative = ( elem == null ) ? true : elem.getAttributeValue( "type" ).equals( "relative" );
+		final boolean isRelative = ( elem == null ) || elem.getAttributeValue( "type" ).equals( "relative" );
 		if ( isRelative )
 		{
 			if ( basePath == null )
@@ -282,6 +284,31 @@ public static File loadPath( final Element parent, final String name, final Stri
 			return new File( path );
 	}
 
+	public static URI loadPathURI( final Element parent, final String name, final String defaultRelativePath, final URI basePath )
+	{
+		final Element elem = parent.getChild( name );
+		final String path = ( elem == null ) ? defaultRelativePath : elem.getText();
+		final boolean isRelative = ( elem == null ) || elem.getAttributeValue( "type" ).equals( "relative" );
+		if ( isRelative )
+		{
+			if ( basePath == null )
+				return null;
+			else
+				return basePath.resolve( path );
+		}
+		else
+		{
+			try
+			{
+				return new URI( path );
+			}
+			catch ( URISyntaxException e )
+			{
+				return null;
+			}
+		}
+	}
+
 	public static File loadPath( final Element parent, final String name, final File basePath )
 	{
 		final Element elem = parent.getChild( name );
@@ -301,6 +328,35 @@ public static File loadPath( final Element parent, final String name, final File
 			return new File( path );
 	}
 
+	public static URI loadPathURI( final Element parent, final String name, final URI basePath )
+	{
+		final Element elem = parent.getChild( name );
+		if ( elem == null )
+			return null;
+		final String path = elem.getText();
+		final String pathType = elem.getAttributeValue( "type" );
+		final boolean isRelative = null != pathType && pathType.equals( "relative" );
+		if ( isRelative )
+		{
+			if ( basePath == null )
+				return null;
+			else
+				return basePath.resolve( path );
+		}
+		else
+		{
+			try
+			{
+				return new URI( path );
+			}
+			catch ( URISyntaxException e )
+			{
+				return null;
+			}
+		}
+	}
+
+
 	/**
 	 * @return {@code true} if the path under {@code parent/name} is stored relative, {@code false} if absolute.
 	 */
@@ -358,6 +414,38 @@ public static File getRelativePath( final File file, final File relativeToThis )
 		}
 	}
 
+	/**
+	 * @param basePath if null put the absolute path, otherwise relative to this
+	 */
+	public static Element pathElementURI( final String name, final URI path, final URI basePath )
+	{
+		final Element e = new Element( name );
+		if ( basePath == null )
+		{
+			e.setAttribute( "type", "absolute" );
+			e.setText( path.normalize().toString() );
+		}
+		else
+		{
+			// Try to build a relative path. If can't, make it absolute.
+			URI relativePath = basePath.relativize( path ).normalize();
+			if ( relativePath.equals( path ) )
+			{
+				e.setAttribute( "type", "absolute" );
+				e.setText( path.toString() );
+			}
+			else
+			{
+				if ( relativePath.toString().isEmpty() )
+					relativePath = URI.create( "." );
+				e.setAttribute( "type", "relative" );
+				e.setText( relativePath.toString() );
+			}
+		}
+
+		return e;
+	}
+
 	private static File getRelativePath( final File file, final File relativeToThis, final String relativeInitial )
 	{
 		File parent = file;

src/main/java/mpicbg/spim/data/generic/AbstractSpimData.java

@@ -29,6 +29,7 @@
 package mpicbg.spim.data.generic;
 
 import java.io.File;
+import java.net.URI;
 
 import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
 import mpicbg.spim.data.registration.ViewRegistrations;
@@ -38,15 +39,15 @@ public class AbstractSpimData< S extends AbstractSequenceDescription< ?, ?, ? >
 	/**
 	 * Relative paths in the XML should be interpreted with respect to this.
 	 */
-	private File basePath;
+	private URI basePathURI;
 
 	private S sequenceDescription;
 
 	private ViewRegistrations viewRegistrations;
 
 	public AbstractSpimData( final File basePath, final S sequenceDescription, final ViewRegistrations viewRegistrations )
 	{
-		this.basePath = basePath;
+		this.basePathURI = basePath == null ? null : basePath.toURI();
 		this.sequenceDescription = sequenceDescription;
 		this.viewRegistrations = viewRegistrations;
 	}
@@ -59,7 +60,12 @@ public AbstractSpimData( final File basePath, final S sequenceDescription, final
 	 */
 	public File getBasePath()
 	{
-		return basePath;
+		return new File( basePathURI );
+	}
+
+	public URI getBasePathURI()
+	{
+		return basePathURI;
 	}
 
 	public S getSequenceDescription()
@@ -74,7 +80,12 @@ public ViewRegistrations getViewRegistrations()
 
 	public void setBasePath( final File basePath )
 	{
-		this.basePath = basePath;
+		this.basePathURI = basePath.toURI();
+	}
+
+	public void setBasePathURI( final URI basePathURI )
+	{
+		this.basePathURI = basePathURI;
 	}
 
 	protected void setSequenceDescription( final S sequenceDescription )