import javax.swing.*;
import java.awt.event.*;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.awt.*;



public class JFileChoose_Test extends JPanel
implements ActionListener {

    /**
     * 
     */
    private static final long serialVersionUID = 1L;

    JButton go;

    JFileChooser chooser;
    String choosertitle;
    String myDirectory;

    public JFileChoose_Test() {
        go = new JButton("Choose a Directory.");
        go.addActionListener(this);
        add(go);
    }

    public void actionPerformed(ActionEvent e) {

        // Declaring a new file chooser and setting the current directory for a default choice.
        // Selection mode is set to directories only to ensure no single file can be chosen.
        chooser = new JFileChooser();
        chooser.setCurrentDirectory(new java.io.File("."));
        chooser.setDialogTitle(choosertitle);
        chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
        //
        // disable the "All files" option.
        //
        chooser.setAcceptAllFileFilterUsed(false);
        //    
        if (chooser.showOpenDialog(this) == JFileChooser.APPROVE_OPTION) {
            System.out.println("getCurrentDirectory(): " + chooser.getCurrentDirectory());
            System.out.println("getSelectedFile() : " + chooser.getSelectedFile());
        } else {
            System.out.println("No Selection ");
        }

        myDirectory = chooser.getSelectedFile().toString();

        getFile(myDirectory);
    }

    public Dimension getPreferredSize() {
        return new Dimension(200, 200);
    }

    //Not called in the main yet because I haven't built anything that actually gets 
    // a file path, still figuring that out. However this will go to that directory path 
    // and find the first file containing "DAPI" in its file name. It will then
    // replace "DAPI" with "GFP" in the recorded string and search for the file 
    // containing that name. It then saves these two file paths for later use.
    private void getFile(String dirPath) {
        try {
            Files.find(Paths.get(dirPath), 1, (path, basicFileAttributes) - > (path.toFile().getName().contains("DAPI"))).forEach(
            dapiPath - > {
                Path gfpPath = dapiPath.resolveSibling(dapiPath.getFileName().toString().replace("DAPI", "GFP"));
                // For some reason this method is not printing out anything.
                // At this point the program just loops back to the directory selection window.
                doSomething(dapiPath, gfpPath);
            });
        } catch (IOException e) {
            e.printStackTrace();
        }
    }

    //Dummy method does nothing yet. I am first going to test it prints the 
    //correct path. Afterwards it will be built to open the files up and then 
    //run the macro I have created to go through the analysis process
    private void doSomething(Path dapiPath, Path gfpPath) {
        System.out.println(dapiPath.toAbsolutePath().toString());
        System.out.println(gfpPath.toAbsolutePath().toString());
    }

    public static void main(String s[]) {
        JFrame frame = new JFrame("");
        JFileChoose_Test panel = new JFileChoose_Test();
        frame.addWindowListener(
        new WindowAdapter() {
            public void windowClosing(WindowEvent e) {
                System.exit(0);
            }
        });

        frame.getContentPane().add(panel, "Center");
        frame.setSize(panel.getPreferredSize());
        frame.setVisible(true);
    }
}
Setting Validate Copy Format