centralize the URITools.toFile() method (see change in URITools @tpie…

…tzsch)
PreibischLab · Oct 11, 2024 · 3d1f5fe · 3d1f5fe
1 parent 691e863
commit 3d1f5fe
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Showing 5 changed files with 19 additions and 27 deletions.
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/datasetmanager/FileListDatasetDefinition.java b/src/main/java/net/preibisch/mvrecon/fiji/datasetmanager/FileListDatasetDefinition.java
@@ -1318,16 +1318,6 @@ else if (resaveAsN5)
 
 			data = Resave_N5Api.resaveN5( data, viewIds, n5params, false );
 
-			// Re-assemble a new SpimData object containing the subset of viewsetups and timepoints selected
-			//final SpimData2 newSpimData = Resave_TIFF.assemblePartialSpimData2( data, viewIds, chosenPathXMLURI , new ArrayList<>() );
-
-			// replace imgLoader
-			//newSpimData.getSequenceDescription().setImgLoader( new N5ImageLoader( n5DatasetURI, newSpimData.getSequenceDescription() ) );
-			//newSpimData.setBasePathURI( chosenPathXMLURI );
-
-			// replace the spimdata object
-			//data = newSpimData;
-
 			IOFunctions.println( "(" + new Date(  System.currentTimeMillis() ) + "): N5 resave finished." );
 		}
 

diff --git a/src/main/java/net/preibisch/mvrecon/fiji/plugin/XMLSaveAs.java b/src/main/java/net/preibisch/mvrecon/fiji/plugin/XMLSaveAs.java
@@ -117,7 +117,7 @@ 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( n5URI, data.getSequenceDescription() ) );
+			data.getSequenceDescription().setImgLoader( new N5ImageLoader( URITools.toFile( n5URI ), data.getSequenceDescription() ) );
 		}
 		else if ( Hdf5ImageLoader.class.isInstance( imgLoader ) )
 		{

diff --git a/src/main/java/net/preibisch/mvrecon/fiji/plugin/resave/Resave_N5Api.java b/src/main/java/net/preibisch/mvrecon/fiji/plugin/resave/Resave_N5Api.java
@@ -266,20 +266,9 @@ public static SpimData2 resaveN5(
 
 		if ( format == StorageFormat.N5 && URITools.isFile( n5Params.n5URI )) // local file
 		{
-			File f;
-			try
-			{
-				// might trigger Exception in thread "main" java.lang.IllegalArgumentException: URI is not absolute
-				f = new File( n5Params.n5URI );
-			}
-			catch ( Exception e )
-			{
-				f = new File( n5Params.n5URI.toString() );
-			}
-
 			// we need to init with File and not with URI, since otherwise the N5ImageLoader will trigger the exception above if this object is re-used
 			// this seems to not matter when opening directly from disc...
-			sdReduced.getSequenceDescription().setImgLoader( new N5ImageLoader( f, sdReduced.getSequenceDescription() ) );
+			sdReduced.getSequenceDescription().setImgLoader( new N5ImageLoader( URITools.toFile( n5Params.n5URI ), sdReduced.getSequenceDescription() ) );
 			n5Writer.close();
 		}
 		else if ( format == StorageFormat.N5 ) // some cloud location

diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ResavePopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ResavePopup.java
@@ -312,10 +312,6 @@ else if (index == 4 || index == 5) // 4 == in-place, 5 == choose path
 
 						final SpimData2 newSpimData = Resave_N5Api.resaveN5( data, viewIds, n5params, false );
 
-						// replace imgLoader
-						//newSpimData.getSequenceDescription().setImgLoader( new N5ImageLoader( n5params.n5URI, newSpimData.getSequenceDescription() ) );
-						//newSpimData.setBasePathURI( basePathURI );
-
 						// make sure interestpoints are saved to the new location as well
 						if ( index == 5 && !n5params.xmlURI.equals( panel.xml() ) )
 						{

diff --git a/src/main/java/util/URITools.java b/src/main/java/util/URITools.java
@@ -467,6 +467,23 @@ public static boolean isFile( URI uri )
 		return !hasScheme || FILE_SCHEME.asPredicate().test( scheme );
 	}
 
+	public static File toFile( final URI uri )
+	{
+		File f;
+		try
+		{
+			// might trigger Exception in thread "main" java.lang.IllegalArgumentException: URI is not absolute
+			// if it is like '/nrs/test.xml' and not 'file:/nrs/test.xml'
+			f = new File( uri );
+		}
+		catch ( Exception e )
+		{
+			f = new File( uri.toString() );
+		}
+
+		return f;
+	}
+
 	public static String removeFilePrefix( URI uri )
 	{
 		final String scheme = uri.getScheme();