fix a series of URI-related code that can cause issues on Windows

StephanPreibisch · StephanPreibisch · commit 10fc0ba9c39c · 2025-04-05T09:36:14.000-04:00
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/datasetmanager/FileListDatasetDefinition.java b/src/main/java/net/preibisch/mvrecon/fiji/datasetmanager/FileListDatasetDefinition.java
@@ -1296,8 +1296,8 @@ else if (resaveAsN5 || resaveAsOMEZARR )
 
 			final SequenceDescription sd = data.getSequenceDescription();
 
-			final URI xmlURI = URI.create( URITools.appendName(chosenPathXMLURI, xmlFileName ) );
-			final URI n5DatasetURI = URI.create( URITools.appendName(chosenPathDataURI, xmlFileName.subSequence( 0, xmlFileName.length() - 4 ) + (resaveAsN5 ? ".n5" : ".ome.zarr" ) ) );
+			final URI xmlURI = URITools.toURI( URITools.appendName(chosenPathXMLURI, xmlFileName ) );
+			final URI n5DatasetURI = URITools.toURI( URITools.appendName(chosenPathDataURI, xmlFileName.subSequence( 0, xmlFileName.length() - 4 ) + (resaveAsN5 ? ".n5" : ".ome.zarr" ) ) );
 
 			IOFunctions.println( (resaveAsN5 ? "N5" : "OME-ZARR" ) + " path: " + n5DatasetURI );
 
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/plugin/Split_Views.java b/src/main/java/net/preibisch/mvrecon/fiji/plugin/Split_Views.java
@@ -47,6 +47,7 @@
 import net.preibisch.mvrecon.fiji.spimdata.XmlIoSpimData2;
 import net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorer;
 import net.preibisch.mvrecon.process.splitting.SplittingTools;
+import util.URITools;
 
 public class Split_Views implements PlugIn
 {
@@ -219,7 +220,7 @@ public static boolean split( final SpimData2 data, final URI filePath )
 			return false;
 		}
 
-		return split( data, URI.create( saveAs ), new long[]{ sx, sy, sz }, new long[]{ ox, oy, oz }, minStepSize, assignIllum, optimize, addIPs, density, minPoints, maxPoints, error, exclusionRadius, choice == 0 );
+		return split( data, URITools.toURI( saveAs ), new long[]{ sx, sy, sz }, new long[]{ ox, oy, oz }, minStepSize, assignIllum, optimize, addIPs, density, minPoints, maxPoints, error, exclusionRadius, choice == 0 );
 	}
 
 	public static Pair< HashMap< String, Integer >, long[] > collectImageSizes( final AbstractSpimData< ? > data )
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/plugin/interactive/MultiResolutionSource.java b/src/main/java/net/preibisch/mvrecon/fiji/plugin/interactive/MultiResolutionSource.java
@@ -57,6 +57,7 @@
 import net.preibisch.mvrecon.headless.boundingbox.TestBoundingBox;
 import net.preibisch.mvrecon.process.deconvolution.DeconViews;
 import net.preibisch.mvrecon.process.fusion.FusionTools;
+import util.URITools;
 
 public class MultiResolutionSource implements Source< VolatileFloatType >
 {
@@ -141,9 +142,9 @@ public static void main( String[] args ) throws SpimDataException
 
 		// load drosophila
 		if ( System.getProperty("os.name").toLowerCase().contains( "mac" ) )
-			spimData = new XmlIoSpimData2().load( URI.create( "/Users/preibischs/Documents/Microscopy/SPIM/HisYFP-SPIM/dataset.xml" ) );
+			spimData = new XmlIoSpimData2().load( URITools.toURI( "/Users/preibischs/Documents/Microscopy/SPIM/HisYFP-SPIM/dataset.xml" ) );
 		else
-			spimData = new XmlIoSpimData2().load( URI.create( "/home/steffi/Desktop/HisYFP-SPIM/dataset.xml" ) );
+			spimData = new XmlIoSpimData2().load( URITools.toURI( "/home/steffi/Desktop/HisYFP-SPIM/dataset.xml" ) );
 
 		final BoundingBox boundingBox = TestBoundingBox.getBoundingBox( spimData, "My Bounding Box" );
 
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
@@ -374,7 +374,7 @@ public boolean queryXML(
 		if ( xmlURI.trim().length() == 0 || xmlURI.trim().toLowerCase().equals( "beads" ) || 
 				xmlURI.trim().toLowerCase().equals( "fractal" ) || xmlURI.trim().toLowerCase().equals( "define" ) )
 		{
-			uri = URI.create( xmlURI );
+			uri = URI.create( xmlURI ); // URI.create is necessary here
 
 			this.data = null;
 			this.attributes = null;
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/XmlIoSpimData2.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/XmlIoSpimData2.java
@@ -104,7 +104,7 @@ public XmlIoSpimData2()
 	public void save( final SpimData2 spimData, String xmlPath ) throws SpimDataException
 	{
 		// old loading code with copying files
-		this.lastURI = URITools.toURI( xmlPath ); //URI.create( xmlPath );
+		this.lastURI = URITools.toURI( xmlPath );
 
 		try
 		{
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/interestpoints/InterestPointsN5.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/interestpoints/InterestPointsN5.java
@@ -148,7 +148,7 @@ public boolean saveInterestPoints( final boolean forceWrite )
 
 		try
 		{
-			final N5Writer n5Writer = URITools.instantiateN5Writer( StorageFormat.N5, URI.create( URITools.appendName( baseDir, baseN5 ) ) );
+			final N5Writer n5Writer = URITools.instantiateN5Writer( StorageFormat.N5, URITools.toURI( URITools.appendName( baseDir, baseN5 ) ) );
 
 			/*
 			if ( URITools.isFile( baseDir ) )
@@ -248,7 +248,7 @@ public boolean saveCorrespondingInterestPoints(boolean forceWrite)
 
 		try
 		{
-			final N5Writer n5Writer = URITools.instantiateN5Writer( StorageFormat.N5, URI.create( URITools.appendName( baseDir, baseN5 ) ) );
+			final N5Writer n5Writer = URITools.instantiateN5Writer( StorageFormat.N5, URITools.toURI( URITools.appendName( baseDir, baseN5 ) ) );
 
 			/*
 			if ( URITools.isFile( baseDir ) )
@@ -365,7 +365,7 @@ protected boolean loadInterestPoints()
 		try
 		{
 			
-			final N5Reader n5 = URITools.instantiateN5Reader( StorageFormat.N5, URI.create( URITools.appendName( baseDir, baseN5 ) ) );
+			final N5Reader n5 = URITools.instantiateN5Reader( StorageFormat.N5, URITools.toURI( URITools.appendName( baseDir, baseN5 ) ) );
 
 			/*
 			if ( URITools.isFile( baseDir ) )
@@ -474,7 +474,7 @@ protected boolean loadCorrespondences()
 	{
 		try
 		{
-			final N5Reader n5 = URITools.instantiateN5Reader( StorageFormat.N5, URI.create( URITools.appendName( baseDir, baseN5 ) ) );;
+			final N5Reader n5 = URITools.instantiateN5Reader( StorageFormat.N5, URITools.toURI( URITools.appendName( baseDir, baseN5 ) ) );;
 
 			/*
 			if ( URITools.isFile( baseDir ) )
@@ -601,7 +601,7 @@ public boolean deleteInterestPoints()
 	{
 		try
 		{
-			final N5Writer n5Writer = URITools.instantiateN5Writer( StorageFormat.N5, URI.create( URITools.appendName( baseDir, baseN5 ) ) );
+			final N5Writer n5Writer = URITools.instantiateN5Writer( StorageFormat.N5, URITools.toURI( URITools.appendName( baseDir, baseN5 ) ) );
 
 			/*
 			if ( URITools.isFile( baseDir ) )
@@ -631,7 +631,7 @@ public boolean deleteCorrespondingInterestPoints()
 	{
 		try
 		{
-			final N5Writer n5Writer = URITools.instantiateN5Writer( StorageFormat.N5, URI.create( URITools.appendName( baseDir, baseN5 ) ) );
+			final N5Writer n5Writer = URITools.instantiateN5Writer( StorageFormat.N5, URITools.toURI( URITools.appendName( baseDir, baseN5 ) ) );
 
 			/*
 			if ( URITools.isFile( baseDir ) )
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/pointspreadfunctions/PointSpreadFunction.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/pointspreadfunctions/PointSpreadFunction.java
@@ -126,7 +126,7 @@ public synchronized Img< FloatType > load()
 		else
 		{
 			// load the .n5
-			final N5Reader n5Reader = URITools.instantiateN5Reader( StorageFormat.N5, URI.create( URITools.appendName( xmlBasePath, subPath ) ) );
+			final N5Reader n5Reader = URITools.instantiateN5Reader( StorageFormat.N5, URITools.toURI( URITools.appendName( xmlBasePath, subPath ) ) );
 			final Img<FloatType> img = Cast.unchecked( N5Utils.open( n5Reader, file ) );
 
 			n5Reader.close();
@@ -140,7 +140,7 @@ public synchronized boolean save()
 		if ( img == null )
 			return false;
 
-		final N5Writer n5Writer = URITools.instantiateN5Writer( StorageFormat.N5, URI.create( URITools.appendName( xmlBasePath, subPath ) ) );
+		final N5Writer n5Writer = URITools.instantiateN5Writer( StorageFormat.N5, URITools.toURI( URITools.appendName( xmlBasePath, subPath ) ) );
 
 		if ( n5Writer.datasetExists( file ) )
 			n5Writer.remove( file );
diff --git a/src/main/java/net/preibisch/mvrecon/headless/boundingbox/TestRealDataBoundingBox.java b/src/main/java/net/preibisch/mvrecon/headless/boundingbox/TestRealDataBoundingBox.java
@@ -42,6 +42,7 @@
 import net.preibisch.mvrecon.process.boundingbox.BoundingBoxMinFilterThreshold;
 import net.preibisch.mvrecon.process.deconvolution.DeconViews;
 import net.preibisch.mvrecon.process.fusion.FusionTools;
+import util.URITools;
 
 public class TestRealDataBoundingBox
 {
@@ -53,7 +54,7 @@ public static void main( String[] args ) throws SpimDataException
 		final ExecutorService service = DeconViews.createExecutorService();
 
 		// test a real scenario
-		final SpimData2 spimData = new XmlIoSpimData2().load( URI.create( "/Users/spreibi/Documents/Microscopy/SPIM/HisYFP-SPIM/dataset.xml" ) );
+		final SpimData2 spimData = new XmlIoSpimData2().load( URITools.toURI( "/Users/spreibi/Documents/Microscopy/SPIM/HisYFP-SPIM/dataset.xml" ) );
 
 		final List< ViewId > viewIds = new ArrayList< ViewId >();
 		viewIds.addAll( spimData.getSequenceDescription().getViewDescriptions().values() );
diff --git a/src/main/java/net/preibisch/mvrecon/headless/deconvolution/TestDeconvolution.java b/src/main/java/net/preibisch/mvrecon/headless/deconvolution/TestDeconvolution.java
@@ -69,6 +69,7 @@
 import net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group;
 import net.preibisch.mvrecon.process.psf.PSFCombination;
 import net.preibisch.simulation.imgloader.SimulatedBeadsImgLoader;
+import util.URITools;
 
 public class TestDeconvolution
 {
@@ -84,7 +85,7 @@ public static void main( String[] args ) throws SpimDataException
 		groups = Group.toGroups( spimData.getSequenceDescription().getViewDescriptions().values() );
 
 		// load drosophila
-		spimData = new XmlIoSpimData2().load( URI.create( "/Users/spreibi/Documents/Microscopy/SPIM/HisYFP-SPIM/dataset.xml" ) );
+		spimData = new XmlIoSpimData2().load( URITools.toURI( "/Users/spreibi/Documents/Microscopy/SPIM/HisYFP-SPIM/dataset.xml" ) );
 		groups = selectViews( spimData.getSequenceDescription().getViewDescriptions().values() );
 		groups = Group.toGroups( spimData.getSequenceDescription().getViewDescriptions().values() );
 
diff --git a/src/main/java/net/preibisch/mvrecon/headless/deconvolution/TestDeconvolutionMul.java b/src/main/java/net/preibisch/mvrecon/headless/deconvolution/TestDeconvolutionMul.java
@@ -72,6 +72,7 @@
 import net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccessibleInterval.CombineType;
 import net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group;
 import net.preibisch.mvrecon.process.psf.PSFCombination;
+import util.URITools;
 
 public class TestDeconvolutionMul
 {
@@ -80,7 +81,7 @@ public static void main( String[] args ) throws SpimDataException
 		new ImageJ();
 
 		// load drosophila
-		SpimData2 spimData = new XmlIoSpimData2().load( URI.create( "Z:/Betzig/dataset.xml" ) );
+		SpimData2 spimData = new XmlIoSpimData2().load( URITools.toURI( "Z:/Betzig/dataset.xml" ) );
 		Collection< Group< ViewDescription > >groups = Group.toGroups( spimData.getSequenceDescription().getViewDescriptions().values() );
 
 		BoundingBox bb = BoundingBoxTools.maximalBoundingBox( spimData, new ArrayList<>( spimData.getSequenceDescription().getViewDescriptions().values() ), "All Views" );
diff --git a/src/main/java/net/preibisch/mvrecon/headless/definedataset/Rewrite_LuxendoXML.java b/src/main/java/net/preibisch/mvrecon/headless/definedataset/Rewrite_LuxendoXML.java
@@ -46,6 +46,7 @@
 import net.preibisch.mvrecon.fiji.spimdata.XmlIoSpimData2;
 import picocli.CommandLine;
 import picocli.CommandLine.Option;
+import util.URITools;
 
 public class Rewrite_LuxendoXML implements Callable<Void>, PlugIn
 {
@@ -126,7 +127,7 @@ public Void call() throws Exception
 			XmlIoSpimData2.initN5Writing = false;
 
 			final XmlIoSpimData2 io2 = new XmlIoSpimData2();
-			io2.save(spimDataOut, URI.create( output ) );
+			io2.save(spimDataOut, URITools.toURI( output ) );
 
 			IOFunctions.println( "done.");
 		}
diff --git a/src/main/java/net/preibisch/mvrecon/headless/fusion/OpenSeaDragonExport.java b/src/main/java/net/preibisch/mvrecon/headless/fusion/OpenSeaDragonExport.java
@@ -67,6 +67,7 @@
 import net.preibisch.mvrecon.process.export.OpenSeaDragon.OpenSeaDragonImgLib2;
 import net.preibisch.mvrecon.process.fusion.FusionTools;
 import net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval.Fusion;
+import util.URITools;
 
 public class OpenSeaDragonExport
 {
@@ -99,7 +100,7 @@ public static void main( String[] args ) throws SpimDataException, IOException
 
 		new ImageJ();
 
-		SpimData2 spimData = new XmlIoSpimData2().load( URI.create( "/Users/preibischs/Downloads/troy eberhardt/dataset.xml" ) );
+		SpimData2 spimData = new XmlIoSpimData2().load( URITools.toURI( "/Users/preibischs/Downloads/troy eberhardt/dataset.xml" ) );
 
 		testOpenSeaDragonExport( spimData, 0, 1, 2 );
 	}
diff --git a/src/main/java/net/preibisch/mvrecon/headless/fusion/TestIntensityAdjustment.java b/src/main/java/net/preibisch/mvrecon/headless/fusion/TestIntensityAdjustment.java
@@ -53,6 +53,7 @@
 import net.preibisch.mvrecon.process.fusion.intensityadjust.IntensityAdjustmentTools;
 import net.preibisch.mvrecon.process.fusion.transformed.TransformVirtual;
 import net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group;
+import util.URITools;
 
 public class TestIntensityAdjustment
 {
@@ -94,7 +95,7 @@ public static void main( String[] args ) throws SpimDataException
 		// generate 4 views with 1000 corresponding beads, single timepoint
 		// 
 		//SpimData2 spimData = SpimData2.convert( SimulatedBeadsImgLoader.spimdataExample( new int[]{ 0, 90, 135 } ) );
-		SpimData2 spimData = new XmlIoSpimData2().load( URI.create( "/Users/spreibi/Documents/BIMSB/Projects/CLARITY/Big Data Sticher/Neubias_preibisch/GridBalance/dataset.xml" ) );
+		SpimData2 spimData = new XmlIoSpimData2().load( URITools.toURI( "/Users/spreibi/Documents/BIMSB/Projects/CLARITY/Big Data Sticher/Neubias_preibisch/GridBalance/dataset.xml" ) );
 
 		System.out.println( "Views present:" );
 
diff --git a/src/main/java/net/preibisch/mvrecon/headless/fusion/TestNonRigid.java b/src/main/java/net/preibisch/mvrecon/headless/fusion/TestNonRigid.java
@@ -54,6 +54,7 @@
 import net.preibisch.mvrecon.process.fusion.FusionTools;
 import net.preibisch.mvrecon.process.fusion.transformed.TransformVirtual;
 import net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidTools;
+import util.URITools;
 
 public class TestNonRigid
 {
@@ -64,7 +65,7 @@ public static void main( String[] args ) throws SpimDataException
 		SpimData2 spimData;
 
 		// load drosophila
-		spimData = new XmlIoSpimData2( ).load( URI.create( "/Users/preibischs/Documents/Microscopy/SPIM/HisYFP-SPIM/dataset.xml" ) );
+		spimData = new XmlIoSpimData2( ).load( URITools.toURI( "/Users/preibischs/Documents/Microscopy/SPIM/HisYFP-SPIM/dataset.xml" ) );
 
 		Pair< List< ViewId >, Interval > fused = testInterpolation( spimData, "My Bounding Box" );
 		// for bounding box1111 test 128,128,128 vs 256,256,256 (no blocks), there are differences at the edges
diff --git a/src/main/java/net/preibisch/mvrecon/headless/fusion/TestWeights.java b/src/main/java/net/preibisch/mvrecon/headless/fusion/TestWeights.java
@@ -52,6 +52,7 @@
 import net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccessibleInterval.CombineType;
 import net.preibisch.mvrecon.process.fusion.transformed.weights.ContentBasedRealRandomAccessible;
 import net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2;
+import util.URITools;
 
 public class TestWeights
 {
@@ -60,7 +61,7 @@ public static void main( String[] args ) throws SpimDataException
 		new ImageJ();
 
 		// test a real scenario
-		final SpimData2 spimData = new XmlIoSpimData2().load( URI.create( "/Users/spreibi/Documents/Microscopy/SPIM/HisYFP-SPIM/dataset.xml" ) );
+		final SpimData2 spimData = new XmlIoSpimData2().load( URITools.toURI( "/Users/spreibi/Documents/Microscopy/SPIM/HisYFP-SPIM/dataset.xml" ) );
 
 		final List< ViewId > viewIds = new ArrayList< ViewId >();
 		viewIds.addAll( spimData.getSequenceDescription().getViewDescriptions().values() );
diff --git a/src/main/java/net/preibisch/mvrecon/headless/interestpointdetection/VerifyDownsamplingCorrection.java b/src/main/java/net/preibisch/mvrecon/headless/interestpointdetection/VerifyDownsamplingCorrection.java
@@ -43,6 +43,7 @@
 import net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoG;
 import net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGParameters;
 import net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group;
+import util.URITools;
 
 public class VerifyDownsamplingCorrection
 {
@@ -51,8 +52,8 @@ public static void main( String[] args ) throws SpimDataException
 		new ImageJ();
 		IOFunctions.printIJLog = true;
 
-		final SpimData2 sdTiff = new XmlIoSpimData2().load( URI.create( "/Users/spreibi/Documents/Grants and CV/BIMSB/Projects/Big Data Sticher/TestDownsampling/TIF/dataset.xml" ) );
-		final SpimData2 sdHdf5 = new XmlIoSpimData2().load( URI.create( "/Users/spreibi/Documents/Grants and CV/BIMSB/Projects/Big Data Sticher/TestDownsampling/HDF5/dataset.xml" ) );
+		final SpimData2 sdTiff = new XmlIoSpimData2().load( URITools.toURI( "/Users/spreibi/Documents/Grants and CV/BIMSB/Projects/Big Data Sticher/TestDownsampling/TIF/dataset.xml" ) );
+		final SpimData2 sdHdf5 = new XmlIoSpimData2().load( URITools.toURI( "/Users/spreibi/Documents/Grants and CV/BIMSB/Projects/Big Data Sticher/TestDownsampling/HDF5/dataset.xml" ) );
 
 		//String label = "beads4x";
 		//testLoad( sdTiff, sdHdf5, label );
diff --git a/src/main/java/net/preibisch/mvrecon/headless/quality/TestQuality.java b/src/main/java/net/preibisch/mvrecon/headless/quality/TestQuality.java
@@ -50,6 +50,7 @@
 import net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group;
 import net.preibisch.mvrecon.process.quality.FRCRealRandomAccessible;
 import net.preibisch.mvrecon.process.quality.FRCTools;
+import util.URITools;
 
 public class TestQuality
 {
@@ -65,7 +66,7 @@ public static void main( String[] args ) throws SpimDataException
 		for ( int run = 2; run <= 3; ++run )
 		{
 			// load drosophila
-			spimData = new XmlIoSpimData2().load( URI.create( "/Users/spreibi/Documents/Microscopy/SPIM/HisYFP-SPIM/dataset.xml" ) );
+			spimData = new XmlIoSpimData2().load( URITools.toURI( "/Users/spreibi/Documents/Microscopy/SPIM/HisYFP-SPIM/dataset.xml" ) );
 
 			for ( final ViewId viewId : spimData.getSequenceDescription().getViewDescriptions().values() )
 				System.out.println( Group.pvid( viewId ) );
diff --git a/src/main/java/net/preibisch/mvrecon/headless/splitting/TestSplitting.java b/src/main/java/net/preibisch/mvrecon/headless/splitting/TestSplitting.java
@@ -31,6 +31,7 @@
 import net.preibisch.mvrecon.fiji.spimdata.XmlIoSpimData2;
 import net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorer;
 import net.preibisch.mvrecon.process.splitting.SplittingTools;
+import util.URITools;
 
 public class TestSplitting
 {
@@ -49,9 +50,9 @@ public static void main( String[] args ) throws SpimDataException
 		 */
 
 		//final String file = "/Volumes/home/Data/Expansion Microscopy/dataset.xml";
-		final URI uri = URI.create( "/Users/spreibi/Documents/Microscopy/SPIM/HisYFP-SPIM/dataset.xml" );
+		final URI uri = URITools.toURI( "/Users/spreibi/Documents/Microscopy/SPIM/HisYFP-SPIM/dataset.xml" );
 
-		final URI uriOut = URI.create( uri.toString().replace( ".xml", ".split.xml" ) );
+		final URI uriOut = URITools.toURI( uri.toString().replace( ".xml", ".split.xml" ) );
 
 		System.out.println( "in: " + uri );
 		System.out.println( "out: " + uriOut );
diff --git a/src/main/java/net/preibisch/mvrecon/process/export/ExportN5Api.java b/src/main/java/net/preibisch/mvrecon/process/export/ExportN5Api.java
@@ -120,7 +120,7 @@ public class ExportN5Api implements ImgExport
 	public static int defaultBlocksizeFactorZ_H5 = 4;
 
 	StorageFormat storageType = StorageFormat.values()[ defaultOption ];
-	URI path = (defaultPathURI != null && defaultPathURI.trim().length() > 0 ) ? URI.create( defaultPathURI ) : null;
+	URI path = (defaultPathURI != null && defaultPathURI.trim().length() > 0 ) ? URITools.toURI( defaultPathURI ) : null;
 	//String baseDataset = defaultBaseDataset;
 	//String datasetExtension = defaultDatasetExtension;
 
diff --git a/src/main/java/net/preibisch/mvrecon/process/fusion/lazy/LazyAffineFusion.java b/src/main/java/net/preibisch/mvrecon/process/fusion/lazy/LazyAffineFusion.java
@@ -23,7 +23,6 @@
 
 package net.preibisch.mvrecon.process.fusion.lazy;
 
-import java.net.URI;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashMap;
@@ -56,6 +55,7 @@
 import net.preibisch.mvrecon.process.deconvolution.DeconViews;
 import net.preibisch.mvrecon.process.fusion.FusionTools;
 import net.preibisch.mvrecon.process.fusion.transformed.TransformVirtual;
+import util.URITools;
 
 /**
  * BigStitcher Affine Fusion in blocks
@@ -198,7 +198,7 @@ public static void main( String[] args ) throws SpimDataException
 	{
 		new ImageJ();
 
-		final SpimData2 data = new XmlIoSpimData2().load( URI.create( "/Users/preibischs/Documents/Microscopy/Stitching/Truman/standard/dataset.xml" ) );
+		final SpimData2 data = new XmlIoSpimData2().load( URITools.toURI( "/Users/preibischs/Documents/Microscopy/Stitching/Truman/standard/dataset.xml" ) );
 
 		final ArrayList< ViewId > viewIds = new ArrayList<>();
 
diff --git a/src/main/java/net/preibisch/mvrecon/process/fusion/lazy/LazyNonRigidFusion.java b/src/main/java/net/preibisch/mvrecon/process/fusion/lazy/LazyNonRigidFusion.java
@@ -22,7 +22,6 @@
  */
 package net.preibisch.mvrecon.process.fusion.lazy;
 
-import java.net.URI;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -64,12 +63,13 @@
 import net.preibisch.mvrecon.process.export.DisplayImage;
 import net.preibisch.mvrecon.process.fusion.FusionTools;
 import net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval;
-import net.preibisch.mvrecon.process.fusion.transformed.TransformVirtual;
 import net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval.Fusion;
+import net.preibisch.mvrecon.process.fusion.transformed.TransformVirtual;
 import net.preibisch.mvrecon.process.fusion.transformed.nonrigid.CorrespondingIP;
 import net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidTools;
 import net.preibisch.mvrecon.process.fusion.transformed.nonrigid.SimpleReferenceIP;
 import net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGrid;
+import util.URITools;
 
 public class LazyNonRigidFusion <T extends RealType<T> & NativeType<T>> implements Consumer<RandomAccessibleInterval<T>>
 {
@@ -245,7 +245,7 @@ public static void main( String[] args ) throws SpimDataException
 	{
 		new ImageJ();
 
-		final SpimData2 spimData = new XmlIoSpimData2().load( URI.create("/Users/preibischs/Documents/Microscopy/SPIM/HisYFP-SPIM/dataset.xml") );
+		final SpimData2 spimData = new XmlIoSpimData2().load( URITools.toURI("/Users/preibischs/Documents/Microscopy/SPIM/HisYFP-SPIM/dataset.xml") );
 
 		Interval boundingBox = TestBoundingBox.getBoundingBox( spimData, "My Bounding Box" );
 		IOFunctions.println( BoundingBox.getBoundingBoxDescription( (BoundingBox)boundingBox ) );
diff --git a/src/main/java/util/URITools.java b/src/main/java/util/URITools.java

Original file line number	Diff line number	Diff line change
`@@ -47,6 +47,7 @@`
`47`	`47`	`import net.preibisch.mvrecon.fiji.spimdata.XmlIoSpimData2;`
`48`	`48`	`import net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorer;`
`49`	`49`	`import net.preibisch.mvrecon.process.splitting.SplittingTools;`
	`50`	`+import util.URITools;`
`50`	`51`
`51`	`52`	`public class Split_Views implements PlugIn`
`52`	`53`	`{`
`@@ -219,7 +220,7 @@ public static boolean split( final SpimData2 data, final URI filePath )`
`219`	`220`	`return false;`
`220`	`221`	`}`
`221`	`222`
`222`		`- return split( data, URI.create( saveAs ), new long[]{ sx, sy, sz }, new long[]{ ox, oy, oz }, minStepSize, assignIllum, optimize, addIPs, density, minPoints, maxPoints, error, exclusionRadius, choice == 0 );`
	`223`	`+ return split( data, URITools.toURI( saveAs ), new long[]{ sx, sy, sz }, new long[]{ ox, oy, oz }, minStepSize, assignIllum, optimize, addIPs, density, minPoints, maxPoints, error, exclusionRadius, choice == 0 );`
`223`	`224`	`}`
`224`	`225`
`225`	`226`	`public static Pair< HashMap< String, Integer >, long[] > collectImageSizes( final AbstractSpimData< ? > data )`
Original file line number	Diff line number	Diff line change
`@@ -374,7 +374,7 @@ public boolean queryXML(`
`374`	`374`	`if ( xmlURI.trim().length() == 0 \|\| xmlURI.trim().toLowerCase().equals( "beads" ) \|\|`
`375`	`375`	`xmlURI.trim().toLowerCase().equals( "fractal" ) \|\| xmlURI.trim().toLowerCase().equals( "define" ) )`
`376`	`376`	`{`
`377`		`- uri = URI.create( xmlURI );`
	`377`	`+ uri = URI.create( xmlURI ); // URI.create is necessary here`
`378`	`378`
`379`	`379`	`this.data = null;`
`380`	`380`	`this.attributes = null;`
Original file line number	Diff line number	Diff line change
`@@ -104,7 +104,7 @@ public XmlIoSpimData2()`
`104`	`104`	`public void save( final SpimData2 spimData, String xmlPath ) throws SpimDataException`
`105`	`105`	`{`
`106`	`106`	`// old loading code with copying files`
`107`		`- this.lastURI = URITools.toURI( xmlPath ); //URI.create( xmlPath );`
	`107`	`+ this.lastURI = URITools.toURI( xmlPath );`
`108`	`108`
`109`	`109`	`try`
`110`	`110`	`{`
Original file line number	Diff line number	Diff line change
`@@ -148,7 +148,7 @@ public boolean saveInterestPoints( final boolean forceWrite )`
`148`	`148`
`149`	`149`	`try`
`150`	`150`	`{`
`151`		`- final N5Writer n5Writer = URITools.instantiateN5Writer( StorageFormat.N5, URI.create( URITools.appendName( baseDir, baseN5 ) ) );`
	`151`	`+ final N5Writer n5Writer = URITools.instantiateN5Writer( StorageFormat.N5, URITools.toURI( URITools.appendName( baseDir, baseN5 ) ) );`
`152`	`152`
`153`	`153`	`/*`
`154`	`154`	`if ( URITools.isFile( baseDir ) )`
`@@ -248,7 +248,7 @@ public boolean saveCorrespondingInterestPoints(boolean forceWrite)`
`248`	`248`
`249`	`249`	`try`
`250`	`250`	`{`
`251`		`- final N5Writer n5Writer = URITools.instantiateN5Writer( StorageFormat.N5, URI.create( URITools.appendName( baseDir, baseN5 ) ) );`
	`251`	`+ final N5Writer n5Writer = URITools.instantiateN5Writer( StorageFormat.N5, URITools.toURI( URITools.appendName( baseDir, baseN5 ) ) );`
`252`	`252`
`253`	`253`	`/*`
`254`	`254`	`if ( URITools.isFile( baseDir ) )`
`@@ -365,7 +365,7 @@ protected boolean loadInterestPoints()`
`365`	`365`	`try`
`366`	`366`	`{`
`367`	`367`
`368`		`- final N5Reader n5 = URITools.instantiateN5Reader( StorageFormat.N5, URI.create( URITools.appendName( baseDir, baseN5 ) ) );`
	`368`	`+ final N5Reader n5 = URITools.instantiateN5Reader( StorageFormat.N5, URITools.toURI( URITools.appendName( baseDir, baseN5 ) ) );`
`369`	`369`
`370`	`370`	`/*`
`371`	`371`	`if ( URITools.isFile( baseDir ) )`
`@@ -474,7 +474,7 @@ protected boolean loadCorrespondences()`
`474`	`474`	`{`
`475`	`475`	`try`
`476`	`476`	`{`
`477`		`- final N5Reader n5 = URITools.instantiateN5Reader( StorageFormat.N5, URI.create( URITools.appendName( baseDir, baseN5 ) ) );;`
	`477`	`+ final N5Reader n5 = URITools.instantiateN5Reader( StorageFormat.N5, URITools.toURI( URITools.appendName( baseDir, baseN5 ) ) );;`
`478`	`478`
`479`	`479`	`/*`
`480`	`480`	`if ( URITools.isFile( baseDir ) )`
`@@ -601,7 +601,7 @@ public boolean deleteInterestPoints()`
`601`	`601`	`{`
`602`	`602`	`try`
`603`	`603`	`{`
`604`		`- final N5Writer n5Writer = URITools.instantiateN5Writer( StorageFormat.N5, URI.create( URITools.appendName( baseDir, baseN5 ) ) );`
	`604`	`+ final N5Writer n5Writer = URITools.instantiateN5Writer( StorageFormat.N5, URITools.toURI( URITools.appendName( baseDir, baseN5 ) ) );`
`605`	`605`
`606`	`606`	`/*`
`607`	`607`	`if ( URITools.isFile( baseDir ) )`
`@@ -631,7 +631,7 @@ public boolean deleteCorrespondingInterestPoints()`
`631`	`631`	`{`
`632`	`632`	`try`
`633`	`633`	`{`
`634`		`- final N5Writer n5Writer = URITools.instantiateN5Writer( StorageFormat.N5, URI.create( URITools.appendName( baseDir, baseN5 ) ) );`
	`634`	`+ final N5Writer n5Writer = URITools.instantiateN5Writer( StorageFormat.N5, URITools.toURI( URITools.appendName( baseDir, baseN5 ) ) );`
`635`	`635`
`636`	`636`	`/*`
`637`	`637`	`if ( URITools.isFile( baseDir ) )`