fix: project and landmark file parsin

* clean up whitespace and scheme when drag+drop
saalfeldlab · Nov 29, 2023 · 8b80dca · 8b80dca
1 parent 4288aa1
commit 8b80dca
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Showing 2 changed files with 54 additions and 13 deletions.
diff --git a/src/main/java/bdv/gui/BigWarpInitDialog.java b/src/main/java/bdv/gui/BigWarpInitDialog.java
@@ -62,6 +62,7 @@
 import bigwarp.transforms.metadata.N5TransformMetadataParser;
 import bigwarp.transforms.metadata.N5TransformTreeCellRenderer;
 import ij.IJ;
+import ij.ImageJ;
 import ij.ImagePlus;
 import ij.Macro;
 import ij.Prefs;
@@ -164,6 +165,26 @@ public BigWarpInitDialog( final String title, final DatasetService datasetServic
 		};
 	}
 
+	public static void main( String[] args ) {
+
+		final ImageJ ij = new ImageJ();
+//		runBigWarp( "/home/john/tmp/boats_lm.csv",
+//				new String[]{ "/home/john/tmp/boats.tif", "/home/john/tmp/boats.tif" },
+//				new String[]{ "true", "false" },
+//				null);
+
+//		runBigWarp( "/home/john/tmp/boats_lm2.csv",
+//				new String[]{ "/home/john/tmp/boats.tif", "/home/john/tmp/boats-HR.tif" },
+//				new String[]{ "true", "false" },
+//				null);
+
+//		runBigWarp( "file:///home/john/Documents/presentations/20231130_BdvCommunity/demo/boats-hr-project.json ",
+//				null,
+//				null,
+//				null);
+
+		new BigWarpInitDialog("bigwarp test").createAndShow();
+	}
 
 	public void setInitialRecorderState( final boolean initialRecorderState )
 	{
@@ -172,10 +193,11 @@ public void setInitialRecorderState( final boolean initialRecorderState )
 
 	public static < T extends NativeType<T> > BigWarp<?> runBigWarp( final String projectLandmarkPath, final String[] images, final String[] moving, final String[] transforms )
 	{
+		final String projectLandmarkPathTrim = projectLandmarkPath == null ? null : projectLandmarkPath.trim();
 		final BigWarpData< T > data = BigWarpInit.initData();
-		final boolean haveProjectLandmarkArg = projectLandmarkPath != null && !projectLandmarkPath.isEmpty();
-		final boolean haveProject = haveProjectLandmarkArg && projectLandmarkPath.endsWith(".json");
-		final boolean haveLandmarks = haveProjectLandmarkArg && projectLandmarkPath.endsWith(".csv");
+		final boolean haveProjectLandmarkArg = projectLandmarkPathTrim != null && !projectLandmarkPathTrim.isEmpty();
+		final boolean haveProject = haveProjectLandmarkArg && projectLandmarkPathTrim.trim().endsWith(".json");
+		final boolean haveLandmarks = haveProjectLandmarkArg && projectLandmarkPathTrim.trim().endsWith(".csv");
 
 		final int nThreads = IJ.getInstance() != null ? Prefs.getThreads() : 1;
 		final BigWarpViewerOptions bwOpts = ( BigWarpViewerOptions ) BigWarpViewerOptions.options().numRenderingThreads( nThreads );
@@ -238,9 +260,9 @@ public static < T extends NativeType<T> > BigWarp<?> runBigWarp( final String pr
 
 			bw = new BigWarp<>( data, bwOpts, new ProgressWriterIJ() );
 			if( haveProject )
-				bw.loadSettings( projectLandmarkPath, true );
+				bw.loadSettings( projectLandmarkPathTrim, true );
 			else if( haveLandmarks )
-				bw.loadLandmarks(projectLandmarkPath);
+				bw.loadLandmarks( projectLandmarkPathTrim );
 		}
 		catch ( final SpimDataException e )
 		{
@@ -269,7 +291,7 @@ public <T extends NativeType<T>> void runBigWarp()
 
 		final BigWarpData< T > data = BigWarpInit.initData();
 
-		projectLandmarkPath = projectLandmarkPath == null ? projectPathTxt.getText() : projectLandmarkPath;
+		projectLandmarkPath = projectLandmarkPath == null ? projectPathTxt.getText().trim() : projectLandmarkPath;
 		final boolean haveProjectLandmarkArg = projectLandmarkPath != null && !projectLandmarkPath.isEmpty();
 		final boolean haveProject = haveProjectLandmarkArg && projectLandmarkPath.endsWith(".json");
 		final boolean haveLandmarks = haveProjectLandmarkArg && projectLandmarkPath.endsWith(".csv");

diff --git a/src/main/java/bigwarp/BigWarp.java b/src/main/java/bigwarp/BigWarp.java
@@ -40,6 +40,7 @@
 import java.io.IOException;
 import java.lang.reflect.Field;
 import java.lang.reflect.InvocationTargetException;
+import java.net.URI;
 import java.net.URISyntaxException;
 import java.text.SimpleDateFormat;
 import java.util.ArrayList;
@@ -4074,10 +4075,19 @@ protected void loadLandmarks()
 
 	public void loadLandmarks( final String filename )
 	{
-		final File file = new File( filename );
-		setLastDirectory( file.getParentFile() );
 
-		if( filename.endsWith( "csv" ))
+		final String filenameTrim = filename.trim();
+		String name = filenameTrim;
+		try {
+			final URI uri = new URI( filenameTrim );
+			if( !uri.getScheme().isEmpty())
+				name = uri.getSchemeSpecificPart();
+		}
+		catch ( URISyntaxException e ) { }
+
+		final File file = new File( name );
+		setLastDirectory( file.getParentFile() );
+		if( name.endsWith( "csv" ))
 		{
 			try
 			{
@@ -4088,7 +4098,7 @@ public void loadLandmarks( final String filename )
 				e1.printStackTrace();
 			}
 		}
-		else if( filename.endsWith( "json" ))
+		else if( name.endsWith( "json" ))
 		{
 			TransformWriterJson.read( file, this );
 		}
@@ -4301,10 +4311,19 @@ public void loadSettings( final String jsonOrXmlFilename ) throws IOException,
 	public void loadSettings( final String jsonOrXmlFilename, boolean overwriteSources ) throws IOException,
 			JDOMException
 	{
-		if ( jsonOrXmlFilename.endsWith( ".xml" ) )
+		final String filenameTrim = jsonOrXmlFilename.trim();
+		String name = filenameTrim;
+		try {
+			final URI uri = new URI( filenameTrim );
+			if( uri != null && uri.getScheme() != null )
+				name = uri.getSchemeSpecificPart();
+		}
+		catch ( URISyntaxException e ) { }
+
+		if ( name.endsWith( ".xml" ) )
 		{
 			final SAXBuilder sax = new SAXBuilder();
-			final Document doc = sax.build( jsonOrXmlFilename );
+			final Document doc = sax.build( name );
 			final Element root = doc.getRootElement();
 
 			/* add default sources if present */
@@ -4338,7 +4357,7 @@ public void loadSettings( final String jsonOrXmlFilename, boolean overwriteSourc
 		{
 			final BigwarpSettings settings = getSettings();
 			settings.setOverwriteSources( overwriteSources );
-			settings.read( new JsonReader( new FileReader( jsonOrXmlFilename ) ) );
+			settings.read( new JsonReader( new FileReader( name ) ) );
 
 			// TODO I may need this
 //			Executors.newSingleThreadExecutor().execute(new Runnable() {