minors fixes

src/main/java/plugins/ylemontag/matlabxserver/MatlabXServerDeamon.java

@@ -100,6 +100,11 @@ public class MatlabXServerDeamon extends Plugin implements MatlabInterpreter
 			newErr.setStackTrace(err.getStackTrace());
 			throw newErr;
 		}
+        catch(InterruptedException err) {
+            MatlabCommandException newErr = new MatlabCommandException(err);
+            newErr.setStackTrace(err.getStackTrace());
+            throw newErr;
+        }
 	}
 
 	/**
@@ -413,9 +418,11 @@ public class MatlabXServerDeamon extends Plugin implements MatlabInterpreter
 
 	/**
 	 * Let the user draw a ROI on the given sequence, and return the corresponding mask
+	 * @throws InterruptedException
 	 */
 	private void executeROIMask(MatFileReader reader, MatFileWriter writer, MatlabSession session)
-			throws IOException, InterruptedException {
+		throws IOException, InterruptedException
+	{
 		Sequence fig = retrieveFigureIndex(session).get(reader.getData("h_fig").getAsInt32());
 		if(fig==null) {
 			return;
@@ -433,16 +440,18 @@ public class MatlabXServerDeamon extends Plugin implements MatlabInterpreter
 
 	/**
 	 * Convert a pair ROI+sequence into a Matlab boolean mask
+	 * @throws InterruptedException
 	 */
 	private static MLArrays.Logical convertToMatlabBooleanMask(String name, Sequence seq, ROI roi)
-			throws MLIOException, InterruptedException {
+		throws MLIOException, InterruptedException
+	{
 		// Return an empty array if no ROI is given
 		if(roi==null) {
 			return new MLArrays.Logical(name, new boolean[0]);
 		}
 
 		// Extract the boolean mask (in Icy's format)
-		boolean[] mask = ((ROI2D)roi).getBooleanMask(seq.getBounds());
+		boolean[] mask = ((ROI2D)roi).getBooleanMask(seq.getBounds2D(), false);
 
 		// Convert the Icy boolean mask into a Matlab boolean mask (i.e. essentially
 		// swap the X and Y dimensions)