From 335203e693b07794c6c424f6c5d5ec5be5d17a9c Mon Sep 17 00:00:00 2001
From: Stephan Preibisch <stephan.preibisch@gmx.de>
Date: Mon, 11 Nov 2024 09:29:00 -0500
Subject: [PATCH] remove Paths.getFileName() to hopefully fix a Windows-path
 related bug to extract the filename from a URI
 (https://forum.image.sc/t/bigstitcher-4-3-3-parsing-xml-fails-in-windows/104753/9)

---
 .../queryXML/GenericLoadParseQueryXML.java    |  5 +----
 src/main/java/util/URITools.java              | 19 ++++++++++++++++---
 2 files changed, 17 insertions(+), 7 deletions(-)

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
index 0d5db7c7..a5ef35f3 100644
--- a/src/main/java/net/preibisch/mvrecon/fiji/plugin/queryXML/GenericLoadParseQueryXML.java
+++ b/src/main/java/net/preibisch/mvrecon/fiji/plugin/queryXML/GenericLoadParseQueryXML.java
@@ -30,8 +30,6 @@
 import java.awt.event.TextEvent;
 import java.awt.event.TextListener;
 import java.net.URI;
-import java.net.URISyntaxException;
-import java.nio.file.Paths;
 import java.text.ParseException;
 import java.util.ArrayList;
 import java.util.Collections;
@@ -58,7 +56,6 @@
 import mpicbg.spim.data.sequence.Angle;
 import mpicbg.spim.data.sequence.Channel;
 import mpicbg.spim.data.sequence.Illumination;
-import mpicbg.spim.data.sequence.ImgLoader;
 import mpicbg.spim.data.sequence.Tile;
 import mpicbg.spim.data.sequence.TimePoint;
 import net.preibisch.legacy.io.IOFunctions;
@@ -715,7 +712,7 @@ protected boolean tryParsing( final URI xmlURI, final boolean parseAllTypes )
 			{
 				this.data = parseXML( xmlURI );
 
-				this.xmlFileName = Paths.get(xmlURI.getPath()).getFileName().toString();
+				this.xmlFileName = URITools.getFileName(xmlURI); //Paths.get(xmlURI.getPath()).getFileName().toString();
 
 				// which attributes
 				this.attributes = getAttributes( data, comparator );
diff --git a/src/main/java/util/URITools.java b/src/main/java/util/URITools.java
index fd2d8647..ea5251b3 100644
--- a/src/main/java/util/URITools.java
+++ b/src/main/java/util/URITools.java
@@ -35,7 +35,6 @@
 import java.io.PrintWriter;
 import java.net.URI;
 import java.net.URISyntaxException;
-import java.nio.file.Paths;
 import java.util.Date;
 import java.util.regex.Pattern;
 
@@ -671,7 +670,19 @@ public static String fromURI( final URI uri )
 
 	public static String getFileName( final URI uri )
 	{
-		return Paths.get( uri.getPath() ).getFileName().toString();
+		int l1 = uri.toString().length();
+		int l2 = l1;
+		try
+		{
+			l2 = getParentURI( uri ).toString().length();
+		}
+		catch (SpimDataIOException e)
+		{
+			IOFunctions.println( "Error getting the parent URI for '" + uri + "' in order to extract the filename. Returning entire URI as filename, even though this is most likely wrong: " + e );
+			e.printStackTrace();
+		}
+
+		return uri.toString().substring( l2, l1 );
 	}
 
 	public static String appendName( final URI uri, final String name )
@@ -744,10 +755,12 @@ public static void minimalExampleTobiS3GS() throws URISyntaxException, IOExcepti
 
 	public static void main( String[] args ) throws SpimDataException, IOException, URISyntaxException
 	{
-		URI uri1 = URITools.toURI( "s3://aind-open-data/exaSPIM_708373_2024-04-02_19-49-38/SPIM.ome.zarr" );
+		URI uri1 = URITools.toURI( "s3://aind-open-data/exaSPIM_708373_2024-04-02_19-49-38/SPIM.ome.zarr/" );
 
 		System.out.println( uri1.getHost() );
 		System.out.println( uri1.getPath() );
+		System.out.println( getFileName( uri1 ) );
+
 		System.exit( 0 );
 
 		minimalExampleTobiS3GS();