fix Save As XML

PreibischLab · Nov 7, 2024 · 6219d60 · 6219d60
1 parent 35e3a20
commit 6219d60
Show file tree

Hide file tree

Showing 3 changed files with 24 additions and 33 deletions.
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/plugin/XMLSaveAs.java b/src/main/java/net/preibisch/mvrecon/fiji/plugin/XMLSaveAs.java
@@ -22,11 +22,7 @@
  */
 package net.preibisch.mvrecon.fiji.plugin;
 
-import java.io.File;
 import java.net.URI;
-import java.net.URISyntaxException;
-
-import org.bigdataviewer.n5.N5CloudImageLoader;
 
 import bdv.img.hdf5.Hdf5ImageLoader;
 import bdv.img.n5.N5ImageLoader;
@@ -97,40 +93,30 @@ public static URI saveAs( final SpimData2 data, final String suggestedFileName )
 		IOFunctions.println( "New XML: " + newXMLPath );
 		IOFunctions.println( "New base path: " + newBaseDir );
 
-		if ( N5CloudImageLoader.class.isInstance( imgLoader ) )
-		{
-			final URI n5URI = ((N5CloudImageLoader)imgLoader).getN5URI();
-
-			IOFunctions.println( "Path of cloud N5 (stays in old location): " + n5URI );
-			data.getSequenceDescription().setImgLoader( new N5CloudImageLoader( null, n5URI, data.getSequenceDescription() ) );
-		}
-		else if ( N5ImageLoader.class.isInstance( imgLoader ) )
-		{
-			final URI n5URI = ((N5ImageLoader)imgLoader).getN5URI();
-
-			IOFunctions.println( "Path of N5 (stays in old location): " + n5URI );
-			data.getSequenceDescription().setImgLoader( new N5ImageLoader( new File( URITools.fromURI( n5URI ) ), data.getSequenceDescription() ) );
-		}
-		else if ( Hdf5ImageLoader.class.isInstance( imgLoader ) )
-		{
-			final Hdf5ImageLoader h5ImgLoader = (Hdf5ImageLoader)imgLoader;
-			final File h5File = h5ImgLoader.getHdf5File();
-
-			IOFunctions.println( "HDF5 file (stays in old location): " + h5File );
-			data.getSequenceDescription().setImgLoader( new Hdf5ImageLoader(h5File, h5ImgLoader.getPartitions(), data.getSequenceDescription()) );
-		}
-
 		data.setBasePathURI( newBaseDir );
 
 		// make sure interestpoints are saved to the new location as well
 		for ( final ViewInterestPointLists vipl : data.getViewInterestPoints().getViewInterestPoints().values() )
 			vipl.getHashMap().values().forEach( ipl ->
 			{
+				// first load
 				ipl.getInterestPointsCopy();
 				ipl.getCorrespondingInterestPointsCopy();
+
+				// then set base dir (otherwise loading fails)
 				ipl.setBaseDir( newBaseDir ); // also sets 'isModified' flags
 			});
 
+		// make sure PSF's are saved to the new location as well
+		data.getPointSpreadFunctions().getPointSpreadFunctions().values().forEach( psf ->
+		{
+			// first load
+			psf.load();
+
+			// then set base dir (otherwise loading fails)
+			psf.setBaseDir( newBaseDir );
+		});
+
 		LoadParseQueryXML.defaultXMLURI = newXMLPath.toString();
 
 		return newXMLPath;

diff --git a/src/main/java/net/preibisch/mvrecon/fiji/plugin/queryXML/GenericLoadParseQueryXML.java b/src/main/java/net/preibisch/mvrecon/fiji/plugin/queryXML/GenericLoadParseQueryXML.java
@@ -131,8 +131,6 @@ public abstract class GenericLoadParseQueryXML<
 	protected ArrayList< ActionListener > listener = null;
 	protected GenericDialog gd = null;
 
-	protected boolean isPrefetched = false;
-
 	public Button defineNewDataset = null;
 
 	/*
@@ -181,15 +179,15 @@ else if ( SplitViewerImgLoader.class.isInstance( loader ) )
 			uri = null;
 		}
 
-		if ( uri != null && !isPrefetched && ( URITools.isS3( uri ) || URITools.isGC( uri ) ) )
+		System.out.println( "ImageLoader URI: " + uri );
+
+		if ( uri != null && ( URITools.isS3( uri ) || URITools.isGC( uri ) ) )
 		{
 			IOFunctions.println( "Setting cloud fetcher threads for '" + uri + "' to: " + URITools.cloudThreads );
 			URITools.setNumFetcherThreads( data.getSequenceDescription().getImgLoader(), URITools.cloudThreads );
 
 			IOFunctions.println( "Prefetching with " + URITools.cloudThreads + " threads: for '" + uri + "'");
 			URITools.prefetch( data.getSequenceDescription().getImgLoader(), URITools.cloudThreads );
-
-			isPrefetched = true;
 		}
 
 		return data;

diff --git a/...in/java/net/preibisch/mvrecon/fiji/spimdata/pointspreadfunctions/PointSpreadFunction.java b/...in/java/net/preibisch/mvrecon/fiji/spimdata/pointspreadfunctions/PointSpreadFunction.java
@@ -48,7 +48,7 @@ public class PointSpreadFunction
 	private final static String subDirFile = "psf";
 	private final static String subPath = "psf.n5";
 
-	private final URI xmlBasePath;
+	private URI xmlBasePath;
 	private final String file;
 	private Img< FloatType > img;
 	private boolean modified;
@@ -81,6 +81,13 @@ public void setPSF( final Img< FloatType > img )
 		this.img = img;
 	}
 
+	public URI getBaseDir() { return xmlBasePath; }
+	public void setBaseDir( final URI baseDir )
+	{
+		this.xmlBasePath = baseDir;
+		this.modified = true;
+	}
+
 	public String getFile() { return file; }
 	public boolean isModified() { return modified; }
 	public synchronized boolean isLoaded() { return img != null; }