package com.github.celldynamics.quimp.plugin.randomwalk;
   
   import java.awt.FlowLayout;
   import java.awt.event.ActionEvent;
   import java.awt.event.ActionListener;
   import java.awt.event.ComponentAdapter;
   import java.awt.event.ComponentEvent;
   import java.awt.event.WindowAdapter;
   import java.awt.event.WindowEvent;
  import java.util.ArrayList;
  import java.util.Arrays;
  import java.util.List;
  
  import javax.swing.JButton;
  import javax.swing.JFrame;
  import javax.swing.JOptionPane;
  import javax.swing.JPanel;
  import javax.swing.SwingUtilities;
  
  import org.slf4j.Logger;
  import org.slf4j.LoggerFactory;
  
  import com.github.celldynamics.quimp.QuimpException.MessageSinkTypes;
  import com.github.celldynamics.quimp.utils.UiTools;
  
  import ij.IJ;
  import ij.ImagePlus;
  import ij.gui.Line;
  import ij.gui.Roi;
  import ij.plugin.frame.RoiManager;
  
  /**
   * Simple seed picker by means of ROIs. Allow to select multiple foreground objects and one
   * background. Produces {@link Seeds} structure at output.
   * 
   * <p>Add current ROI to ROI list, if nothing selected look through ROI manager and renames
   * un-renamed ROIs according to requested type (FG or BG).
   * 
   * @author p.baniukiewicz
   *
   */
  @SuppressWarnings("serial")
  public class SeedPicker extends JFrame {
  
    /**
     * The Constant LOGGER.
     */
    static final Logger LOGGER = LoggerFactory.getLogger(SeedPicker.class.getName());
  
    /**
     * Prefix for foreground ROIs.
     */
    public final String fgName = "fg";
    /**
     * Prefix for background ROI.
     */
    public final String bgName = "bg";
  
    /** The content pane. */
    private JPanel contentPane;
    /**
     * Image used for seeding. It is not modified, only its dimensions are used.
     */
    public ImagePlus image;
  
    /** The rm. */
    RoiManager rm;
  
    /** The last tool. */
    private String lastTool;
  
    /** The last line width. */
    private int lastLineWidth;
  
    /** The last fg num. */
    private int lastFgNum = 0; // cell number
  
    /** The last bg num. */
    private int lastBgNum = 0; // but this is index, cell is always 0 for BG
  
    /** The bn finish listeners. */
    // For Finish button we need specific order of ActionListeners
    private ActionListener[] bnFinishListeners = new ActionListener[2];
    /**
     * Converted seeds available after Finish.
     */
    public List<Seeds> seedsRoi = new ArrayList<>();
  
    /** The btn finish. */
    private JButton btnFinish;
  
    /**
     * Default constructor. Does not show window. Require {@link #image} to be set.
     */
    public SeedPicker() {
      this(false);
  
    }
  
   /**
    * Allow to provide image to process and disable UI. Recommended to API calls.
    * 
    * @param image image to seed, actually only size of it is required
    * @param show true to show the UI
    */
   public SeedPicker(ImagePlus image, boolean show) {
     this(show);
     this.image = image;
   }
 
   /**
    * Allow to provide image to work with.
    * 
    * @param image image to seed, actually only size of it is required
    */
   public SeedPicker(ImagePlus image) {
     this(true);
     this.image = image;
   }
 
   /**
    * Create the frame.
    * 
    * @param show true to show the UI
    */
   public SeedPicker(boolean show) {
     setDefaultCloseOperation(JFrame.HIDE_ON_CLOSE);
     setResizable(false);
     setAlwaysOnTop(true);
     setType(Type.NORMAL);
     setTitle("Select seeds");
     setVisible(show);
     // setPreferredSize(new Dimension(300, 100));
     // setBounds(100, 100, 295, 66);
     contentPane = new JPanel();
     setContentPane(contentPane);
     contentPane.setLayout(new FlowLayout(FlowLayout.LEFT, 5, 5));
 
     JButton tglbtnNewFg = new JButton("New FG");
     UiTools.setToolTip(tglbtnNewFg,
             "Create next FG label from current selection or from unassigned ROIs from Roi Manager"
                     + ". For creating one label from separated ROIs,"
                     + " add them first to Roi Manager and then use this button.");
     tglbtnNewFg.addActionListener(new ActionListener() {
       public void actionPerformed(ActionEvent e) {
         if (!increaseRois(fgName)) {
           // nothing added - add current selection
           Roi current = image.getRoi();
           if (current != null) {
             rm.add(image, current, 0);
             increaseRois(fgName);
           }
         }
       }
     });
     contentPane.add(tglbtnNewFg);
 
     JButton btnBackground = new JButton("New BG");
     UiTools.setToolTip(btnBackground,
             "Create next BG label from current selection or from unassigned ROIs from Roi Manager"
                     + ". For creating one label from separated ROIs,"
                     + " add them first to Roi Manager and then use this button.");
     btnBackground.addActionListener(new ActionListener() {
       public void actionPerformed(ActionEvent e) {
         if (!increaseRois(bgName)) {
           // nothing added - add current selection
           Roi current = image.getRoi();
           if (current != null) {
             rm.add(image, current, 0);
             increaseRois(bgName);
           }
         }
       }
     });
     contentPane.add(btnBackground);
 
     btnFinish = new JButton("Finish");
     // this listener should go first, before that from RandomWalkView
     bnFinishListeners[0] = new ActionListener() {
 
       @Override
       public void actionPerformed(ActionEvent e) {
         try {
           if (image == null) {
             throw new RandomWalkException("No image opened with SeedPicker.");
           }
           seedsRoi = SeedProcessor.decodeSeedsfromRoiStack(Arrays.asList(rm.getRoisAsArray()),
                   fgName, bgName, image.getWidth(), image.getHeight(), image.getImageStackSize());
           dispose();
         } catch (RandomWalkException ex) {
           ex.setMessageSinkType(MessageSinkTypes.GUI);
           ex.handleException((JFrame) SwingUtilities.getRoot(contentPane),
                   "Problem with converting seeds from ROI");
         }
 
       }
     };
     btnFinish.addActionListener(new ActionListener() {
 
       @Override
       public void actionPerformed(ActionEvent e) {
         bnFinishListeners[0].actionPerformed(e);
         bnFinishListeners[1].actionPerformed(e);
       }
     });
 
     contentPane.add(btnFinish);
 
     addComponentListener(new ComponentAdapter() {
       @Override
       public void componentShown(ComponentEvent arg0) {
         openRoiManager();
         selectTools();
       }
 
       @Override
       public void componentHidden(ComponentEvent e) {
         IJ.setTool(lastTool);
         Line.setWidth(lastLineWidth);
       }
     });
     addWindowListener(new WindowAdapter() {
       @Override
       public void windowClosing(WindowEvent arg0) {
         IJ.setTool(lastTool);
         Line.setWidth(lastLineWidth);
       }
 
       @Override
       public void windowClosed(WindowEvent e) {
         IJ.setTool(lastTool);
         Line.setWidth(lastLineWidth);
       }
     });
     pack();
   }
 
   /**
    * Add Listener to Finish button that is executed as second.
    * 
    * <p>First listener prepares {@link SeedPicker#seedsRoi} structure, so second one can use it.
    * 
    * @param list listener to add as second
    */
   void addFinishController(ActionListener list) {
     bnFinishListeners[1] = list;
   }
 
   /**
    * Rename ROIs in RoiManager and increases counters.
    * 
    * @param coreName ROI to rename
    * @return true if something added
    */
   private boolean increaseRois(String coreName) {
     boolean ret = false;
     if (coreName.equals(fgName)) {
       ret = renameRois(fgName);
       if (ret) { // rename FG
         lastFgNum++; // and increase counter if anything renamed
       }
     }
     if (coreName.equals(bgName)) {
       ret = renameRois(bgName);
       if (ret) {
         lastBgNum++;
       }
     }
     return ret;
   }
 
   /**
    * Open roi manager.
    */
   private void openRoiManager() {
     rm = RoiManager.getRoiManager();
     // rm.reset();
   }
 
   /**
    * Select tools.
    */
   private void selectTools() {
     lastTool = IJ.getToolName();
     lastLineWidth = Line.getWidth();
     IJ.setTool("freeline");
     Line.setWidth(10);
 
   }
 
   /**
    * Rename ROIs in RoiManager.
    * 
    * <p>Any nonrenamed ROIS will be renamed to format corenameCell_no, where Cell is cell number and
    * no
    * is ROI number for the cell. There can be many ROIs for one cell. For background there is only
    * one object but again it cn be scribbled by many ROIs.
    * 
    * @param coreName corename ROI will be renamed to
    * @return true if anything was added.
    */
   private boolean renameRois(String coreName) {
     boolean added = false; // nothing renamed in manager
     int localIndex; // for FG will progress and match global Index, for BG always 0
     int localNum;
     if (rm == null) {
       return false;
     }
     if (coreName.equals(bgName)) {
       localIndex = 0; // do not count backgrounds ROIs
       localNum = lastBgNum;
     } else {
       localIndex = lastFgNum; // but count foreground
       localNum = 0;
     }
     List<Roi> rois = Arrays.asList(rm.getRoisAsArray());
     for (Roi roi : rois) {
       String n = roi.getName();
       if (n.startsWith(fgName) || n.startsWith(bgName)) {
         continue;
       }
       int roiIndex = rm.getRoiIndex(roi);
       rm.rename(roiIndex, coreName + localIndex + "_" + localNum);
       roi.setName(coreName + localIndex + "_" + localNum);
       localNum++;
       added = true;
     }
     if (coreName.equals(bgName)) {
       lastBgNum = localNum;
     }
     return added;
   }
 
   /**
    * Prepare for new ROI selection. Clears all counters, roi manager and Seed list.
    */
   public void reset() {
     lastFgNum = 0;
     lastBgNum = 0;
     seedsRoi.clear();
     if (rm != null) {
       if (rm.getRoisAsArray().length != 0) {
         int dialogButton = JOptionPane.YES_NO_OPTION;
         int dialogResult =
                 JOptionPane.showConfirmDialog(null, "Clear ROI manager??", "Warning", dialogButton);
         if (dialogResult == JOptionPane.YES_OPTION) {
           rm.reset();
         }
       }
     }
   }
 
 }