feat(csv-export): allow user to choose save location for embedded batch mode CSV

- Integrated FileChooser in save mode to let users pick where to save the example.csv
- Extracts the embedded CSV from resources and writes it to the selected location
- Automatically opens the file in the default system editor after saving

src/main/java/fr/pasteur/ida/zellige/gui/controller/MainController.java

@@ -45,6 +45,8 @@ import javafx.fxml.FXML;
 import javafx.fxml.Initializable;
 import javafx.scene.Scene;
 import javafx.scene.control.*;
+import javafx.scene.control.Label;
+import javafx.scene.control.MenuBar;
 import javafx.stage.FileChooser;
 import javafx.stage.Modality;
 import javafx.stage.Stage;
@@ -53,9 +55,10 @@ import net.imglib2.type.numeric.RealType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.File;
-import java.io.IOException;
+import java.awt.*;
+import java.io.*;
 import java.net.URL;
+import java.nio.file.Files;
 import java.text.SimpleDateFormat;
 import java.util.ArrayList;
 import java.util.Date;
@@ -122,7 +125,7 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
         constructionController.getModel().getChannelInput().bind( preprocessingController.getModel().getInput_channel() );
         constructionController.getModel().getInput().bind( preprocessingController.getModel().getInput() );
         constructionController.getModel().getFactory().bind( preprocessingController.getModel().getFactory() );
-        projectionController.getModel().getColors().bind( preprocessingController.getModel().getColors());
+        projectionController.getModel().getColors().bind( preprocessingController.getModel().getColors() );
 
         // Sets the projection display when the projection tab is clicked on.
         tabPane.getTabs().get( 2 ).selectedProperty().addListener( ( observableValue, number, newValue ) ->
@@ -159,40 +162,95 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
     }
 
     @FXML
-    private void openFileDialog() {
+    private void openFileDialog()
+    {
 
 
         BatchModeDialog dialog = new BatchModeDialog();
 
         // Create a new Stage for the dialog
         Stage dialogStage = new Stage();
-        dialogStage.setTitle("Batch Mode");
-        dialogStage.initModality( Modality.APPLICATION_MODAL);  // Blocks interaction with main window
-        dialogStage.setScene(new Scene(dialog));
+        dialogStage.setTitle( "Batch Mode" );
+        dialogStage.initModality( Modality.APPLICATION_MODAL );  // Blocks interaction with main window
+        dialogStage.setScene( new Scene( dialog ) );
 
         // Show the dialog window
         dialogStage.showAndWait();  // Use showAndWait() to wait until the dialog is closed
-
     }
 
+    /**
+     * Prompts the user to save the embedded CSV file wherever they want.
+     * Opens the file after saving, if possible.
+     */
     @FXML
-    public void openCSVExample()
+    public void saveCSVExample()
     {
-        // Open the example CSV file in the default system text editor
+        // Create FileChooser in SAVE mode
         FileChooser fileChooser = new FileChooser();
+        fileChooser.setTitle( "Save Example CSV File" );
         fileChooser.getExtensionFilters().add( new FileChooser.ExtensionFilter( "CSV Files", "*.csv" ) );
+        fileChooser.setInitialFileName( "batch_mode_csv_example.csv" );
+
+        // Show the save dialog
+        File selectedFile = fileChooser.showSaveDialog( null );
+        if ( selectedFile != null )
+        {
+            // Try extracting the embedded file to the chosen location
+            try ( InputStream inputStream = getClass().getResourceAsStream( "/batch_mode_csv_example.csv" );
+                  OutputStream outputStream = Files.newOutputStream( selectedFile.toPath() ) )
+            {
 
-        // You can specify the initial directory where the file should be saved or loaded from
-        fileChooser.setInitialDirectory( new java.io.File( "src/main/resources/" ) );
+                if ( inputStream == null )
+                {
+                    throw new FileNotFoundException( "Embedded resource 'batch_mode_csv_example.csv' not found." );
+                }
 
-        // Open the file
-        File file = fileChooser.showSaveDialog( null);
-        if ( file != null )
+                // Copy contents from resource to selected file
+                byte[] buffer = new byte[ 1024 ];
+                int length;
+                while ( ( length = inputStream.read( buffer ) ) != - 1 )
+                {
+                    outputStream.write( buffer, 0, length );
+                }
+
+                LOGGER.debug( "File saved to: {}", selectedFile.getAbsolutePath() );
+
+                // Optionally open the file
+                openFile( selectedFile );
+
+            }
+            catch ( IOException e )
+            {
+                LOGGER.debug("Something went wrong with the batch-mode CSV example");
+            }
+        }
+        else
         {
-            // Perform the necessary file operations here (e.g., writing to file)
+            System.out.println( "Save cancelled by user." );
         }
     }
 
+    /**
+     * Opens the file in the system's default app (e.g. Notepad, Excel).
+     *
+     * @param file The file to open.
+     */
+    private void openFile( File file )
+    {
+        if ( Desktop.isDesktopSupported() )
+        {
+            try
+            {
+                Desktop.getDesktop().open( file );
+            }
+            catch ( IOException e )
+            {
+                LOGGER.debug( "Failed to open file: {}", file.getAbsolutePath() );
+            }
+        }
+    }
+
+
     @FXML
     public void saveParameters() throws IOException
     {
@@ -201,7 +259,7 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
         File file = fileChooser.showSaveDialog( null );
         if ( file != null )
         {
-            PretreatmentParameters prp = build(model.getPreprocessingModel());
+            PretreatmentParameters prp = build( model.getPreprocessingModel() );
             SelectionParameters sp = build( model.getSelectionModel() );
             ConstructionParameters[] cp = build( model.getConstructionModel() );
             ArrayList< ProjectionParameters > pp = build( model.getProjectionModel() );
@@ -210,17 +268,16 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
     }
 
 
-
-    private PretreatmentParameters build( PreprocessingModel<T> model)
+    private PretreatmentParameters build( PreprocessingModel< T > model )
     {
-        return new PretreatmentParameters(model.getChannel().get(),  model.binProperty().get() );
+        return new PretreatmentParameters( model.getChannel().get(), model.binProperty().get() );
     }
 
     private SelectionParameters build( SelectionModel model )
     {
         return new SelectionParameters(
-                model.amplitudeProperty().getValue().intValue(),
-                model.otsuProperty().getValue().intValue(),
+                model.amplitudeProperty().getValue(),
+                model.otsuProperty().getValue(),
                 model.xyBlurProperty().intValue(),
                 model.zBlurProperty().intValue(),
                 model.islandProperty().intValue() );
@@ -228,13 +285,13 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
 
     private ConstructionParameters[] build( ConstructionModel< T > model )
     {
-        ConstructionParameters[] parameters = new ConstructionParameters[2];
-        parameters[0] = new ConstructionParameters(
+        ConstructionParameters[] parameters = new ConstructionParameters[ 2 ];
+        parameters[ 0 ] = new ConstructionParameters(
                 model.c1Property().value(),
                 model.r1Property().getValue(),
                 model.st1Property().value(),
                 model.surfaceSizeProperty().get() );
-        parameters[1] = new ConstructionParameters(
+        parameters[ 1 ] = new ConstructionParameters(
                 model.c2Property().value(),
                 model.r2Property().getValue(),
                 model.st2Property().value(),
@@ -242,34 +299,29 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
         return parameters;
     }
 
-    private ArrayList< ProjectionParameters > build ( ProjectionModel<T> model)
+    private ArrayList< ProjectionParameters > build( ProjectionModel< T > model )
     {
-        ArrayList<ProjectionParameters > list = new ArrayList<>();
-        for ( int i = 0; i < getProjectionController().getModel().getReferenceSurfaces().get().size() ; i++ )
+        ArrayList< ProjectionParameters > list = new ArrayList<>();
+        for ( int i = 0; i < getProjectionController().getModel().getReferenceSurfaces().get().size(); i++ )
         {
-            ProjectionProperties<T> projectionProperties = model.getProjectionProperties().get().get( i );
-            ArrayList<ChannelProjectionParameter> channelProjectionParameters = new ArrayList<>();
+            ProjectionProperties< T > projectionProperties = model.getProjectionProperties().get().get( i );
+            ArrayList< ChannelProjectionParameter > channelProjectionParameters = new ArrayList<>();
             for ( int j = 0; j < projectionProperties.getProperties().get().size(); j++ )
             {
-                ChannelToolProperty<T> channelToolProperty = projectionProperties.getProperties().get().get( j );
+                ChannelToolProperty< T > channelToolProperty = projectionProperties.getProperties().get().get( j );
                 ChannelProjectionParameter cpp = new ChannelProjectionParameter(
                         channelToolProperty.getDeltaZ().get(),
                         channelToolProperty.getOffset().get(),
-                        channelToolProperty.getMethod().get());
-                channelProjectionParameters.add(cpp);
+                        channelToolProperty.getMethod().get() );
+                channelProjectionParameters.add( cpp );
             }
-            ProjectionParameters projectionParameter= new ProjectionParameters( channelProjectionParameters );
-            list.add(projectionParameter);
+            ProjectionParameters projectionParameter = new ProjectionParameters( channelProjectionParameters );
+            list.add( projectionParameter );
         }
         return list;
     }
 
 
-
-
-
-
-
     private File chooseFile()
     {
         FileChooser fileChooser = chooseAFile( null, "Select a Zellige parameter file"
@@ -289,7 +341,7 @@ public class MainController< T extends RealType< T > & NativeType< T > > impleme
 
     private void setParameters( ZelligeParameters parameters )
     {
-        preprocessingController.setParameters(parameters);
+        preprocessingController.setParameters( parameters );
         selectionController.setParameters( parameters );
         constructionController.setParameters( parameters );
         projectionController.setParameters( parameters );

src/main/resources/fr.pasteur.ida.zellige.gui.view/Main.fxml

@@ -32,7 +32,7 @@
        <Menu mnemonicParsing="false" text="Help">
          <items>
            <MenuItem mnemonicParsing="false" text="Zellige Wiki" />
-               <MenuItem mnemonicParsing="false" onAction="#openCSVExample" text="Batch Mode CSV file example" />
+               <MenuItem mnemonicParsing="false" onAction="#saveCSVExample" text="Batch Mode CSV file example" />
          </items>
        </Menu>
      </menus>