add fromXML(URI) calls, for now these are copies of fromXML(File)

PreibischLab · Dec 3, 2024 · 85f1068 · 85f1068
1 parent 9805791
commit 85f1068
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diff --git a/...in/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/splitting/XmlIoSplitImgLoader.java b/...in/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/splitting/XmlIoSplitImgLoader.java
@@ -26,6 +26,7 @@
 import static mpicbg.spim.data.XmlKeys.IMGLOADER_TAG;
 
 import java.io.File;
+import java.net.URI;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
@@ -87,6 +88,43 @@ public Element toXml( final SplitImgLoader imgLoader, final File basePath )
 		return elem;
 	}
 
+	@Override
+	public SplitImgLoader fromXml(
+			final Element elem, URI basePath,
+			final AbstractSequenceDescription<?, ?, ?> sequenceDescription )
+	{
+		final HashMap< Integer, Integer > new2oldSetupId = new HashMap<>();
+		final HashMap< Integer, Interval > newSetupId2Interval = new HashMap<>();
+
+		for ( final Element setup : elem.getChild( XmlIoSplitViewerImgLoader.SETUPIDS_NAME ).getChildren( XmlIoSplitViewerImgLoader.SETUPIDS_TAG ) )
+			XmlIoSplitViewerImgLoader.setupFromXML( setup, new2oldSetupId, newSetupId2Interval );
+
+		try
+		{
+			final XmlIoSequenceDescription xmlIoSequenceDescription = new XmlIoSequenceDescription();
+			final Element sdElem = elem.getChild( xmlIoSequenceDescription.getTag() );
+			if ( sdElem == null )
+				throw new SpimDataIOException( "no <" + xmlIoSequenceDescription.getTag() + "> element found." );
+			final SequenceDescription oldSD = xmlIoSequenceDescription.fromXml( sdElem, basePath );
+
+			ImgLoader underlyingImgLoader = null;
+
+			final Element imgLoaderElem = elem.getChild( IMGLOADER_TAG );
+			final String format = imgLoaderElem.getAttributeValue( IMGLOADER_FORMAT_ATTRIBUTE_NAME );
+			final XmlIoBasicImgLoader< ? > imgLoaderIo = ImgLoaders.createXmlIoForFormat( format );
+			underlyingImgLoader = (ImgLoader)imgLoaderIo.fromXml( imgLoaderElem, basePath, oldSD );
+
+			return new SplitImgLoader( underlyingImgLoader, new2oldSetupId, newSetupId2Interval, oldSD );
+		}
+		catch( Exception e )
+		{
+			IOFunctions.println( "Unable to load underlying Sequence Description & ImgLoader, stopping." );
+			e.printStackTrace();
+			System.exit( 0 );
+			return null;
+		}
+	}
+
 	@Override
 	public SplitImgLoader fromXml(
 			final Element elem, File basePath,

diff --git a/...ibisch/mvrecon/fiji/spimdata/imgloaders/splitting/XmlIoSplitMultiResolutionImgLoader.java b/...ibisch/mvrecon/fiji/spimdata/imgloaders/splitting/XmlIoSplitMultiResolutionImgLoader.java
@@ -26,6 +26,7 @@
 import static mpicbg.spim.data.XmlKeys.IMGLOADER_TAG;
 
 import java.io.File;
+import java.net.URI;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
@@ -87,6 +88,43 @@ public Element toXml( final SplitMultiResolutionImgLoader imgLoader, final File
 		return elem;
 	}
 
+	@Override
+	public SplitMultiResolutionImgLoader fromXml(
+			final Element elem, URI basePath,
+			final AbstractSequenceDescription<?, ?, ?> sequenceDescription )
+	{
+		final HashMap< Integer, Integer > new2oldSetupId = new HashMap<>();
+		final HashMap< Integer, Interval > newSetupId2Interval = new HashMap<>();
+
+		for ( final Element setup : elem.getChild( XmlIoSplitViewerImgLoader.SETUPIDS_NAME ).getChildren( XmlIoSplitViewerImgLoader.SETUPIDS_TAG ) )
+			XmlIoSplitViewerImgLoader.setupFromXML( setup, new2oldSetupId, newSetupId2Interval );
+
+		try
+		{
+			final XmlIoSequenceDescription xmlIoSequenceDescription = new XmlIoSequenceDescription();
+			final Element sdElem = elem.getChild( xmlIoSequenceDescription.getTag() );
+			if ( sdElem == null )
+				throw new SpimDataIOException( "no <" + xmlIoSequenceDescription.getTag() + "> element found." );
+			final SequenceDescription oldSD = xmlIoSequenceDescription.fromXml( sdElem, basePath );
+
+			MultiResolutionImgLoader underlyingImgLoader = null;
+
+			final Element imgLoaderElem = elem.getChild( IMGLOADER_TAG );
+			final String format = imgLoaderElem.getAttributeValue( IMGLOADER_FORMAT_ATTRIBUTE_NAME );
+			final XmlIoBasicImgLoader< ? > imgLoaderIo = ImgLoaders.createXmlIoForFormat( format );
+			underlyingImgLoader = (MultiResolutionImgLoader)imgLoaderIo.fromXml( imgLoaderElem, basePath, oldSD );
+
+			return new SplitMultiResolutionImgLoader( underlyingImgLoader, new2oldSetupId, newSetupId2Interval, oldSD );
+		}
+		catch( Exception e )
+		{
+			IOFunctions.println( "Unable to load underlying Sequence Description & ImgLoader, stopping." );
+			e.printStackTrace();
+			System.exit( 0 );
+			return null;
+		}
+	}
+
 	@Override
 	public SplitMultiResolutionImgLoader fromXml(
 			final Element elem, File basePath,

diff --git a/...a/net/preibisch/mvrecon/fiji/spimdata/imgloaders/splitting/XmlIoSplitViewerImgLoader.java b/...a/net/preibisch/mvrecon/fiji/spimdata/imgloaders/splitting/XmlIoSplitViewerImgLoader.java
@@ -26,6 +26,7 @@
 import static mpicbg.spim.data.XmlKeys.IMGLOADER_TAG;
 
 import java.io.File;
+import java.net.URI;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
@@ -139,6 +140,41 @@ protected static < L extends BasicImgLoader > Element createImgLoaderElement( fi
 		return imgLoaderIo.toXml( ( L ) imgLoader, basePath );
 	}
 
+	@Override
+	public SplitViewerImgLoader fromXml( final Element elem, final URI basePathURI, AbstractSequenceDescription< ?, ?, ? > sequenceDescription )
+	{
+		final HashMap< Integer, Integer > new2oldSetupId = new HashMap<>();
+		final HashMap< Integer, Interval > newSetupId2Interval = new HashMap<>();
+
+		for ( final Element setup : elem.getChild( SETUPIDS_NAME ).getChildren( SETUPIDS_TAG ) )
+			setupFromXML( setup, new2oldSetupId, newSetupId2Interval );
+
+		try
+		{
+			final XmlIoSequenceDescription xmlIoSequenceDescription = new XmlIoSequenceDescription();
+			final Element sdElem = elem.getChild( xmlIoSequenceDescription.getTag() );
+			if ( sdElem == null )
+				throw new SpimDataIOException( "no <" + xmlIoSequenceDescription.getTag() + "> element found." );
+			final SequenceDescription oldSD = xmlIoSequenceDescription.fromXml( sdElem, basePathURI );
+
+			ViewerImgLoader underlyingImgLoader = null;
+
+			final Element imgLoaderElem = elem.getChild( IMGLOADER_TAG );
+			final String format = imgLoaderElem.getAttributeValue( IMGLOADER_FORMAT_ATTRIBUTE_NAME );
+			final XmlIoBasicImgLoader< ? > imgLoaderIo = ImgLoaders.createXmlIoForFormat( format );
+			underlyingImgLoader = (ViewerImgLoader)imgLoaderIo.fromXml( imgLoaderElem, basePathURI, oldSD );
+
+			return new SplitViewerImgLoader( underlyingImgLoader, new2oldSetupId, newSetupId2Interval, oldSD );
+		}
+		catch( Exception e )
+		{
+			IOFunctions.println( "Unable to load underlying Sequence Description & ImgLoader, stopping." );
+			e.printStackTrace();
+			System.exit( 0 );
+			return null;
+		}
+	}
+
 	@Override
 	public SplitViewerImgLoader fromXml(
 			final Element elem, File basePath,