Update for Help link

To a still empty readme.

src/main/groovy/qupath/ext/basicstitching/BasicStitchingExtension.groovy

@@ -54,8 +54,7 @@ class BasicStitchingExtension implements QuPathExtension {
 
 	private void addMenuItem(QuPathGUI qupath) {
 		def menu = qupath.getMenu("Extensions>${name}", true)
-		def fileNameStitching = new MenuItem("Stitching using coordinates in file names")
-		// TODO tooltip "Coordinates are expected to be in the format ImageName[xCoordinateInMicrons, yCoordinateInMicrons].tif"
+		def fileNameStitching = new MenuItem("Basic Stitching Extension")
 		fileNameStitching.setOnAction(e -> {
 			stitchingGUI.createGUI()
 
@@ -64,22 +63,3 @@ class BasicStitchingExtension implements QuPathExtension {
 	}
 
 }
-//@ActionMenu("Extensions")
-//public class BSCommands {
-//
-//	@ActionMenu("BasicStitching")
-//	@ActionDescription("Launch BasicStitching dialog.")
-//	public final Action BSCommand;
-//
-//	/**
-//	 * Constructor.
-//	 *
-//	 * @param qupath
-//	 *            The QuPath GUI.
-//	 */
-//	private BSCommands(QuPathGUI qupath) {
-//		BSMainCommand bsCommand = new BSMainCommand(qupath);
-//		actionBSCommand = new Action(event -> bsCommand.run());
-//	}
-//
-//}

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

@@ -9,7 +9,8 @@ import javafx.stage.Modality
 import javafx.stage.DirectoryChooser
 import qupath.lib.gui.scripting.QPEx
 
-//import java.nio.file.Paths
+import java.awt.Desktop;
+
 
 import org.slf4j.Logger
 import org.slf4j.LoggerFactory
@@ -31,6 +32,7 @@ class stitchingGUI {
     static Label pixelSizeLabel = new Label("Pixel size, microns:");
     static Label downsampleLabel = new Label("Downsample:");
     static Label matchStringLabel = new Label("Matching string:");
+    static Hyperlink githubLink = new Hyperlink("GitHub ReadMe");
 
     // Map to hold the positions of each GUI element
     private static Map<Node, Integer> guiElementPositions = new HashMap<>();
@@ -85,7 +87,7 @@ class stitchingGUI {
         addPixelSizeComponents(pane);
         addDownsampleComponents(pane);
         addMatchStringComponents(pane);
-
+        addGitHubLinkComponent(pane); // Add the hyperlink component
         // Call once to set initial visibility of components
         updateComponentsBasedOnSelection(pane);
 
@@ -102,6 +104,18 @@ class stitchingGUI {
             logger.error("Row index not found for component: " + label);
         }
     }
+    // Method to add the GitHub link component
+    private static void addGitHubLinkComponent(GridPane pane) {
+        githubLink.setOnAction(e -> {
+            try {
+                Desktop.getDesktop().browse(new URI("https://github.com/MichaelSNelson/BasicStitching"));
+            } catch (Exception ex) {
+                logger.error("Error opening link", ex);
+            }
+        });
+        Integer rowIndex = guiElementPositions.get(githubLink); // Default to a high number if not set
+        pane.add(githubLink, 0, rowIndex, 2, 1); // Span 2 columns
+    }
 
     private static void initializePositions() {
         // Reset position counter
@@ -114,8 +128,14 @@ class stitchingGUI {
         guiElementPositions.put(pixelSizeLabel, currentPosition++);
         guiElementPositions.put(downsampleLabel, currentPosition++);
         guiElementPositions.put(matchStringLabel, currentPosition++);
+        guiElementPositions.put(githubLink, currentPosition++); // Assign position to hyperlink
         // Add more components as needed
     }
+
+
+
+
+
     // Method to add stitching grid components
     private static void addStitchingGridComponents(GridPane pane) {
         stitchingGridBox.getItems().clear() // Clear existing items before adding new ones

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

@@ -2,44 +2,67 @@ package qupath.ext.basicstitching.utilities
 
 import org.slf4j.LoggerFactory
 import qupath.lib.gui.QuPathGUI
-import qupath.lib.gui.dialogs.Dialogs
 import qupath.lib.images.writers.ome.OMEPyramidWriter
-import org.slf4j.Logger
 import javax.imageio.ImageIO
-import java.nio.file.Files
-import java.nio.file.Path
-import java.nio.file.Paths
 
+
+
+/**
+ * Class containing utility functions used throughout the application.
+ */
 class utilityFunctions {
+
+    /**
+     * Gets the compression type for OMEPyramidWriter based on the selected option.
+     *
+     * @param selectedOption The selected compression option as a string.
+     * @return The corresponding OMEPyramidWriter.CompressionType.
+     */
     static OMEPyramidWriter.CompressionType getCompressionType(String selectedOption) {
         switch (selectedOption) {
             case "Lossy compression":
                 return OMEPyramidWriter.CompressionType.J2K_LOSSY
             case "Lossless compression":
                 return OMEPyramidWriter.CompressionType.J2K
             default:
-                return null // or a default value
+                // Consider providing a default compression type or handling this case
+                return null
         }
     }
+
+    /**
+     * Retrieves the dimensions (width and height) of a TIFF image file.
+     *
+     * @param filePath The file path of the TIFF image.
+     * @return A map containing the 'width' and 'height' of the image, or null if an error occurs.
+     */
     static Map<String, Integer> getTiffDimensions(File filePath) {
         def logger = LoggerFactory.getLogger(QuPathGUI.class)
+
+        // Check if the file exists
         if (!filePath.exists()) {
             logger.info("File not found: $filePath")
             return null
         }
 
         try {
+            // Read the image file
             def image = ImageIO.read(filePath)
             if (image == null) {
                 logger.info("ImageIO returned null for file: $filePath")
                 return null
             }
+
+            // Return the image dimensions as a map
             return [width: image.getWidth(), height: image.getHeight()]
         } catch (IOException e) {
+            // Log and handle the error
             logger.info("Error reading the image file $filePath: ${e.message}")
             return null
         }
     }
+}
+
     //TODO Move this somewhere
 //    List<Map> prepareStitching(String folderPath, double pixelSizeInMicrons, double baseDownsample, String matchingString) {
 //        def logger = LoggerFactory.getLogger(QuPathGUI.class)
@@ -62,4 +85,4 @@ class utilityFunctions {
 //
 //        allFileRegionMaps
 //    }
-}
+//}