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src/main/java/uk/ac/franciscrickinstitute/twombli/FileUtils.java

@@ -40,12 +40,12 @@ public static boolean verifyOutputDirectoryIsEmpty(String potential) {
             return true;
         }
 
-        YesNoCancelDialog dialog = new YesNoCancelDialog(
+        YesNoDialog dialog = new YesNoDialog(
                 IJ.getInstance(),
                 "Output Directory Not Empty",
-                "The output directory is not empty. Continue and overwrite?",
+                "The output directory is not empty and this is currently a requirement for the plugin. Would you like to continue and overwrite? If you are unsure, simply make a new directory when selecting your output directory!",
                 "Delete Contents", "Cancel");
-        if (dialog.cancelPressed()) {
+        if (!dialog.yesPressed()) {
             return false;
         }
 

src/main/java/uk/ac/franciscrickinstitute/twombli/Outputs.java

@@ -0,0 +1,59 @@
+package uk.ac.franciscrickinstitute.twombli;
+
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.StandardOpenOption;
+import java.util.ArrayList;
+import java.util.List;
+
+public class Outputs {
+
+    public static void generateSummaries(Path twombli_csv_path, double alignment, int dimension, Path anamorfSummaryPath, Path hdmSummaryPath, Path gapAnalysisPath, boolean doHeader, boolean gapAnalysis, Path gap_csv_path) {
+        // Write to our twombli summary
+        try {
+            List<String> lines = new ArrayList<>();
+            List<String> anamorfEntries = Files.readAllLines(anamorfSummaryPath);
+            List<String> hdmEntries = Files.readAllLines(hdmSummaryPath);
+
+            // Conditionally write out our header
+            if (doHeader) {
+                String headerItems = anamorfEntries.get(0);
+                String[] hdmHeaderItems = hdmEntries.get(0).split(",");
+                String header = headerItems + "," + hdmHeaderItems[hdmHeaderItems.length - 1] + ",Alignment (Coherency [%]),Size";
+                lines.add(header);
+            }
+
+            // Get the data
+            String anamorfData = anamorfEntries.get(anamorfEntries.size() - 1);
+            String[] hdmData = hdmEntries.get(hdmEntries.size() - 1).split(",");
+            double hdmValue = 1 - Double.parseDouble(hdmData[hdmData.length - 1]);
+            lines.add(anamorfData + "," + hdmValue + "," + alignment + "," + dimension);
+
+            // Write
+            Files.write(twombli_csv_path, lines, StandardOpenOption.CREATE, StandardOpenOption.APPEND);
+        }
+
+        catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+
+        // Write to our gap analysis summary
+        if (gapAnalysis) {
+            try (BufferedReader reader = Files.newBufferedReader(gapAnalysisPath);
+                 BufferedWriter writer = Files.newBufferedWriter(gap_csv_path, StandardOpenOption.CREATE, StandardOpenOption.APPEND)) {
+
+                String line;
+                while ((line = reader.readLine()) != null) {
+                    writer.write(line.replace(" ", ","));
+                    writer.newLine(); // Ensure proper newline after each row
+                }
+
+            } catch (IOException e) {
+                throw new RuntimeException(e);
+            }
+        }
+    }
+}

src/main/java/uk/ac/franciscrickinstitute/twombli/ProgressCancelListener.java

@@ -0,0 +1,5 @@
+package uk.ac.franciscrickinstitute.twombli;
+
+public interface ProgressCancelListener {
+    void handleProgressBarCancelled();
+}

src/main/java/uk/ac/franciscrickinstitute/twombli/ProgressDialog.java

@@ -0,0 +1,110 @@
+package uk.ac.franciscrickinstitute.twombli;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import ij.gui.GUI;
+
+public class ProgressDialog extends Dialog implements WindowListener {
+
+    private final int maxProgress;
+    private final ProgressCanvas progressCanvas;
+    private final ProgressCancelListener progressCancelListener;
+
+    public ProgressDialog(Frame parent, String title, int maxProgress, ProgressCancelListener listener) {
+        super(parent, title, true);
+        this.maxProgress = maxProgress;
+        this.progressCancelListener = listener;
+
+        this.setModal(false);
+
+        // Create a canvas to draw the progress bar
+        this.progressCanvas = new ProgressCanvas(this.maxProgress);
+        this.progressCanvas.setSize(300, 30);
+
+        // Set up the dialog layout
+        setLayout(new BorderLayout());
+        add(this.progressCanvas, BorderLayout.CENTER);
+
+        // Create a cancel button
+        Button cancelButton = new Button("Cancel");
+        cancelButton.addActionListener(e -> this.handleProgressBarCancelled());
+        add(cancelButton, BorderLayout.SOUTH);
+
+        GUI.scale(this);
+        pack();
+        GUI.centerOnImageJScreen(this);
+        this.setVisible(true);
+    }
+
+    // Method to update the progress bar
+    public void updateProgress(int newProgress) {
+        this.progressCanvas.setProgress(newProgress);
+    }
+
+    private void handleProgressBarCancelled() {
+        this.progressCancelListener.handleProgressBarCancelled();
+        this.dispose();
+    }
+
+    @Override
+    public void windowOpened(WindowEvent e) {}
+
+    @Override
+    public void windowClosing(WindowEvent e) {}
+
+    @Override
+    public void windowClosed(WindowEvent e) {
+        this.handleProgressBarCancelled();
+    }
+
+    @Override
+    public void windowIconified(WindowEvent e) {}
+
+    @Override
+    public void windowDeiconified(WindowEvent e) {}
+
+    @Override
+    public void windowActivated(WindowEvent e) {}
+
+    @Override
+    public void windowDeactivated(WindowEvent e) {}
+
+    // Canvas for drawing the progress bar
+    private class ProgressCanvas extends Canvas {
+        private final int maxProgress;
+        private int currentProgress = 0;
+
+        public ProgressCanvas(int maxProgress) {
+            this.maxProgress = maxProgress;
+            this.currentProgress = 0;
+        }
+
+        public void setProgress(int progress) {
+            this.currentProgress = progress;
+            repaint();
+        }
+
+        @Override
+        public void paint(Graphics g) {
+            // Clear the canvas
+            g.setColor(Color.WHITE);
+            g.fillRect(0, 0, getWidth(), getHeight());
+
+            // Draw the progress bar background
+            g.setColor(Color.GRAY);
+            g.fillRect(0, 0, getWidth(), getHeight());
+
+            // Draw the progress based on the current value
+            g.setColor(Color.GREEN);
+            int barWidth = (int) ((getWidth() * currentProgress) / (float) maxProgress);
+            g.fillRect(0, 0, barWidth, getHeight());
+
+            // Draw the progress percentage
+            g.setColor(Color.BLACK);
+            int percent = (int) ((currentProgress / (float) maxProgress) * 100);
+            String progressText = percent + "%";
+            g.drawString(progressText, getWidth() / 2 - g.getFontMetrics().stringWidth(progressText) / 2, getHeight() / 2 + 5);
+        }
+    }
+}

src/main/java/uk/ac/franciscrickinstitute/twombli/TWOMBLIBatchRunner.java

@@ -1,5 +1,7 @@
 package uk.ac.franciscrickinstitute.twombli;
 
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.Files;
@@ -143,49 +145,12 @@ private void generateSummaries() {
             // Gather our basic info
             String filePrefix = runner.filePrefix;
             double alignment = runner.alignment;
-            double dimension = runner.dimension;
+            int dimension = runner.dimension;
             Path anamorfSummaryPath = Paths.get(this.outputPath, "masks", filePrefix + "_results.csv");
             Path hdmSummaryPath = Paths.get(this.outputPath, "hdm_csvs", filePrefix + "_ResultsHDM.csv");
             Path gapAnalysisPath = Paths.get(this.outputPath, "gap_analysis", filePrefix + "_gaps.csv");
-
-            // Write to our twombli summary
-            try {
-                List<String> lines = new ArrayList<>();
-                List<String> anamorfEntries = Files.readAllLines(anamorfSummaryPath);
-                List<String> hdmEntries = Files.readAllLines(hdmSummaryPath);
-
-                // Conditionally write out our header
-                if (doHeader) {
-                    String headerItems = anamorfEntries.get(0);
-                    String[] hdmHeaderItems = hdmEntries.get(0).split(",");
-                    String header = headerItems + "," + hdmHeaderItems[hdmHeaderItems.length - 1] + ",Alignment (Coherency [%]),Size";
-                    lines.add(header);
-                    doHeader = false;
-                }
-
-                // Get the data
-                String anamorfData = anamorfEntries.get(anamorfEntries.size() - 1);
-                String[] hdmData = hdmEntries.get(hdmEntries.size() - 1).split(",");
-                double hdmValue = 1 - Double.parseDouble(hdmData[hdmData.length - 1]);
-                lines.add(anamorfData + "," + hdmValue + "," + alignment + "," + dimension);
-
-                // Write
-                Files.write(twombliOutputPath, lines, StandardOpenOption.CREATE, StandardOpenOption.APPEND);
-            }
-
-            catch (IOException e) {
-                throw new RuntimeException(e);
-            }
-
-            // Write to our gap analysis summary
-            if (this.performGapAnalysis) {
-                try {
-                    List<String> lines = Files.readAllLines(gapAnalysisPath);
-                    Files.write(gapsOutputPath, lines, StandardOpenOption.CREATE, StandardOpenOption.APPEND);
-                } catch (IOException e) {
-                    throw new RuntimeException(e);
-                }
-            }
+            Outputs.generateSummaries(twombliOutputPath, alignment, dimension, anamorfSummaryPath, hdmSummaryPath, gapAnalysisPath, doHeader, this.performGapAnalysis, gapsOutputPath);
+            doHeader = false;
         }
     }
 }

src/main/java/uk/ac/franciscrickinstitute/twombli/TWOMBLIConfigurator.java

@@ -1,7 +1,6 @@
 package uk.ac.franciscrickinstitute.twombli;
 
 import javax.swing.*;
-import java.io.File;
 import java.util.ArrayList;
 import java.util.Arrays;
 

src/main/java/uk/ac/franciscrickinstitute/twombli/TWOMBLIRunner.java

@@ -74,15 +74,21 @@ public class TWOMBLIRunner implements Command {
     @Parameter
     public int minimumGapDiameter = 0;
 
-    @Parameter(type = ItemIO.OUTPUT)
-    public ImagePlus output;
-
-    @Parameter(type = ItemIO.OUTPUT)
+    @Parameter(type=ItemIO.OUTPUT)
     public double alignment;
 
-    @Parameter(type = ItemIO.OUTPUT)
+    @Parameter(type=ItemIO.OUTPUT)
     public int dimension;
 
+    @Parameter(type=ItemIO.OUTPUT)
+    public ImagePlus maskImage;
+
+    @Parameter(type=ItemIO.OUTPUT)
+    public ImagePlus hdmImage;
+
+    @Parameter(type=ItemIO.OUTPUT)
+    public ImagePlus gapImage;
+
     // Magic number declarations
     private static final double HIGH_CONTRAST_THRESHOLD = 120.0;
     private static final double LOW_CONTRAST_THRESHOLD = 0.0;
@@ -188,16 +194,14 @@ public void run() {
         ImagePlus maskImage = IJ.openImage(new File(finalMaskImagePath).getAbsolutePath());
         this.runOrientationJ(maskImage);
 
-        // Close non-essential windows
-//        this.closeNonImages();
-
         // Gap analysis
         maskImage = IJ.openImage(new File(finalMaskImagePath).getAbsolutePath());
         this.performGapAnalysis(gapAnalysisDirectory, maskImage);
 
         // Output handling
-//        this.closeNonImages();
-        this.output = maskImage;
+        this.maskImage = maskImage;
+        this.hdmImage = IJ.openImage(hdmDirectory + File.separator + this.filePrefix + "_hdm.png");
+        this.gapImage = IJ.openImage(gapAnalysisDirectory + File.separator + this.filePrefix + "_gap.png");
     }
 
     private void detectRidges(ImagePlus inputImage, String maskImage) {
@@ -317,7 +321,9 @@ private void runAnamorf(String maskImageDirectory) {
                 File propsFile = new File(this.anamorfPropertiesFile);
                 props.loadFromXML(Files.newInputStream(propsFile.toPath()));
             }
-        } catch (IOException ex) {
+        }
+
+        catch (IOException ex) {
             ex.printStackTrace();
             return;
         }
@@ -468,18 +474,20 @@ private void performGapAnalysis(String gapAnalysisDirectory, ImagePlus maskImage
         File individualGapAnalysisFile = new File(individualGapAnalysisFilePath);
         try (BufferedWriter bw = new BufferedWriter(new FileWriter(individualGapAnalysisFile))) {
             bw.write(this.filePrefix + " " + mean + " " + standardDeviation + " " + fivePercentile + " " + fiftyPercentile + " " + ninetyFivePercentile);
-        } catch (IOException e) {
+        }
+        catch (IOException e) {
             e.printStackTrace();
         }
 
         // Write the array to file
-        String individualGapAnalysisArrayFilePath = gapAnalysisDirectory + File.separator + this.filePrefix + "_area_arrays.csv";
+        String individualGapAnalysisArrayFilePath = gapAnalysisDirectory + File.separator +  this.filePrefix + "_area_arrays.csv";
         File individualGapAnalysisArrayFile = new File(individualGapAnalysisArrayFilePath);
         try (BufferedWriter bw = new BufferedWriter(new FileWriter(individualGapAnalysisArrayFile))) {
             for (double area : areas) {
                 bw.write(area + "\n");
             }
-        } catch (IOException e) {
+        }
+        catch (IOException e) {
             e.printStackTrace();
         }
         WindowManager.setTempCurrentImage(null);