Minor name change updates

src/main/groovy/qupath/ext/basicstitching/functions/StitchingGUI.groovy

@@ -72,7 +72,7 @@ class StitchingGUI {
             String matchingString = matchStringField.getText() // Assuming matchStringField is accessible
             String stitchingType = stitchingGridBox.getValue()
             // Call the function with collected data
-            stitchingImplementations.stitchCore(stitchingType, folderPath, folderPath, compressionType, pixelSize, downsample, matchingString)
+            String finalImageName = stitchingImplementations.stitchCore(stitchingType, folderPath, folderPath, compressionType, pixelSize, downsample, matchingString)
             //stitchByFileName(folderPath, compressionType, pixelSize, downsample, matchingString)
         }
 

src/main/groovy/qupath/ext/basicstitching/stitching/stitchingImplementations.groovy

@@ -554,7 +554,7 @@ class stitchingImplementations {
      * @param baseDownsample The base downsample value for the stitching process.
      * @param matchingString A string to match for selecting relevant subdirectories or files.
      */
-    static void stitchCore(String stitchingType, String folderPath, String outputPath, String compressionType, double pixelSizeInMicrons, double baseDownsample, String matchingString) {
+    static String stitchCore(String stitchingType, String folderPath, String outputPath, String compressionType, double pixelSizeInMicrons, double baseDownsample, String matchingString) {
         def logger = LoggerFactory.getLogger(QuPathGUI.class)
         // Determine the stitching strategy based on the provided type
         switch(stitchingType) {
@@ -636,8 +636,9 @@ class stitchingImplementations {
                     .writePyramid(pathOutput)
 
             long endTime = System.currentTimeMillis()
-            println("Image written to ${pathOutput} in ${GeneralTools.formatNumber((endTime - startTime)/1000.0, 1)} s")
+            logger.info("Image written to ${pathOutput} in ${GeneralTools.formatNumber((endTime - startTime)/1000.0, 1)} s")
             server.close()
+            return pathOutput
         } else {
             println("No valid stitching strategy set.")
         }

src/main/groovy/qupath/ext/basicstitching/utilities/UtilityFunctions.groovy

@@ -8,6 +8,7 @@ import java.lang.reflect.Modifier
 import java.nio.file.Path
 import java.nio.file.Paths
 import java.nio.file.Files
+import java.util.stream.Stream
 
 /**
  * Class containing utility functions used throughout the application.
@@ -47,25 +48,31 @@ class UtilityFunctions {
         }
     }
 /**
- * Generates a unique file path by appending a number if the file already exists.
+ * Generates a unique file path by appending a number to the file name if a file with the
+ * same name already exists. The first instance of the file will have no number appended,
+ * while the second will have _2, the third _3, and so on.
  *
  * @param originalPath The original file path.
  * @return A unique file path.
  */
     static String getUniqueFilePath(String originalPath) {
-        Path path = Paths.get(originalPath)
-        String baseName = path.getFileName().toString().replaceAll(/\.ome\.tif$/, "")
-        Path parentDir = path.getParent()
+        Path path = Paths.get(originalPath);
+        String baseName = path.getFileName().toString().replaceAll('\\.ome\\.tif$', "");
+        Path parentDir = path.getParent();
 
-        int counter = 1
-        while (Files.exists(path)) {
-            String newFileName = "${baseName}_${counter}.ome.tif"
-            path = parentDir.resolve(newFileName)
-            counter++
+        // Start with the original base name
+        Path newPath = parentDir.resolve(baseName + ".ome.tif");
+        int counter = 2;
+
+        // If the file exists, start appending numbers
+        while (Files.exists(newPath)) {
+            newPath = parentDir.resolve(baseName + "_" + counter + ".ome.tif");
+            counter++;
         }
 
-        return path.toString()
+        return newPath.toString();
     }
+
     /**
      * Retrieves the dimensions (width and height) of a TIFF image file.
      *