package com.github.celldynamics.quimp.plugin.generatemask;
   
   import java.nio.file.Path;
   import java.nio.file.Paths;
   import java.util.List;
   
   import javax.swing.JOptionPane;
   
   import com.github.celldynamics.quimp.BOAState;
  import com.github.celldynamics.quimp.Nest;
  import com.github.celldynamics.quimp.QParamsQconf;
  import com.github.celldynamics.quimp.QuimP;
  import com.github.celldynamics.quimp.QuimpException;
  import com.github.celldynamics.quimp.QuimpException.MessageSinkTypes;
  import com.github.celldynamics.quimp.Snake;
  import com.github.celldynamics.quimp.SnakeHandler;
  import com.github.celldynamics.quimp.filesystem.FileExtensions;
  import com.github.celldynamics.quimp.plugin.AbstractPluginQconf;
  import com.github.celldynamics.quimp.plugin.QuimpPluginException;
  import com.github.celldynamics.quimp.utils.QuimpToolsCollection;
  
  import ij.IJ;
  import ij.ImagePlus;
  import ij.ImageStack;
  import ij.gui.NewImage;
  import ij.gui.Roi;
  import ij.process.ImageConverter;
  import ij.process.ImageProcessor;
  import ij.process.StackConverter;
  
  /**
   * Convert QCONF files to BW masks.
   * 
   * <p>Use Snake data produced by BOA and stored in QCONF file. If run from macro it shows image and
   * save it to folder where QCONF resides. If run as API it does not do any of these two actions, use
   * {@link #getRes()} to obtain image.
   * 
   * @author p.baniukiewicz
   *
   */
  public class GenerateMask_ extends AbstractPluginQconf {
  
    private static String thisPluginName = "Generate mask";
  
    /**
     * Resulting image. (Not saved or shown if apiCall==true)
     */
    private ImagePlus res;
  
    /**
     * Executed if plugin is run from IJ. Set apiCall to false and redirect exception to IJ.
     */
    public GenerateMask_() {
      super(new GenerateMaskOptions(), thisPluginName);
    }
  
    /**
     * Constructor that allows to provide own parameters.
     * 
     * @param paramString it can be null to ask user for file or it can be parameters string like that
     *        passed in macro.
     * @throws QuimpPluginException on any error
     */
    public GenerateMask_(String paramString) throws QuimpPluginException {
      super(paramString, new GenerateMaskOptions(), thisPluginName); // will parse and fill options
    }
  
    /*
     * (non-Javadoc)
     * 
     * @see com.github.celldynamics.quimp.plugin.PluginTemplate#run(java.lang.String)
     */
    @Override
    public void run(String arg) {
      super.run(arg);
    }
  
    /*
     * (non-Javadoc)
     * 
     * @see com.github.celldynamics.quimp.plugin.IQuimpPlugin#about()
     */
    @Override
    public String about() {
      return "Generate mask plugin.\n" + "Author: Piotr Baniukiewicz\n"
              + "mail: p.baniukiewicz@warwick.ac.uk";
    }
  
    /*
     * (non-Javadoc)
     * 
     * @see com.github.celldynamics.quimp.plugin.PluginTemplate#runFromQCONF()
     */
    @Override
    protected void runFromQconf() throws QuimpException {
      GenerateMaskOptions/../../com/github/celldynamics/quimp/plugin/generatemask/GenerateMaskOptions.html#GenerateMaskOptions">GenerateMaskOptions opts = (GenerateMaskOptions) options;
      BOAState bs = qconfLoader.getBOA();
      Nest nest = bs.nest;
      int currentColor;
     // create output image
     res = NewImage.createShortImage("test", bs.boap.getWidth(), bs.boap.getHeight(),
             bs.boap.getFrames(), NewImage.FILL_BLACK);
     // get stacks reference
     ImageStack contourStack = res.getStack();
     res.setSlice(1); // set for first
     int frame; // frames counter (from 1)
     Snake snake;
     ImageProcessor contourIp; // processor taken from stack (ref)
     for (frame = 1; frame <= bs.boap.getFrames(); frame++) { // iterate over frames
       List<Integer> snakes = nest.getSnakesforFrame(frame); // find all SnakeHandlers on frame
       contourIp = contourStack.getProcessor(frame); // get processor from stack for frame
       currentColor = 1;
       for (Integer snakeID : snakes) { // iterate over SnakeHandlers
         SnakeHandler snakeH = nest.getHandlerofId(snakeID); // get SH of snakeID
         if (snakeH != null) {
           snake = snakeH.getStoredSnake(frame); // get snake from this handler and current frame
           Roi roi = snake.asFloatRoi(); // convert to ROI
           contourIp.setColor(currentColor++);
           contourIp.fill(roi); // plot on current slice
         }
       }
     }
     if (opts.binary) {
       for (int i = 1; i <= res.getImageStackSize(); i++) {
         res.getStack().getProcessor(i).threshold(0);
       }
       ImageConverter.setDoScaling(false);
       new StackConverter(res).convertToGray8();
     }
     if (!apiCall) { // do not show nor save if called from api
       res.show();
       // save in QCONF folder
       QParamsQconf/../../../../../com/github/celldynamics/quimp/QParamsQconf.html#QParamsQconf">QParamsQconf qp = (QParamsQconf) qconfLoader.getQp();
       Path filename = Paths.get(qp.getPath(), qp.getFileName() + FileExtensions.generateMaskSuffix);
       IJ.saveAsTiff(res, filename.toString());
       IJ.log("Saved in: " + filename.toString());
       if (errorSink == MessageSinkTypes.GUI) { // run form IJ not from macro
         JOptionPane.showMessageDialog(
                 IJ.getInstance(), QuimpToolsCollection
                         .stringWrap("Image saved! (" + filename.toString() + ")", QuimP.LINE_WRAP),
                 "Saved!", JOptionPane.INFORMATION_MESSAGE);
       } else {
         IJ.log("Mask generated!");
       }
     }
 
   }
 
   /**
    * Return image generated by plugin. Use with API calls.
    * 
    * <p>Return 16bit image if {@link GenerateMaskOptions#binary} is set to false with grayscale
    * indexed objects.
    * 
    * @return the res Mask image generated from loaded Qconf.
    */
   public ImagePlus getRes() {
     return res;
   }
 
   @Override
   protected void runFromPaqp() throws QuimpException {
     throw new QuimpException("Old file format is not supported");
   }
 
   /*
    * (non-Javadoc)
    * 
    * @see com.github.celldynamics.quimp.plugin.PluginTemplate#showUi(boolean)
    */
   @Override
   public void showUi(boolean val) throws Exception {
     // this method is called when no options were provided to run, paramFile is empty or null
     loadFile(options.paramFile); // if no options (run from menu) let qconfloader show file selector
     // fill this for macro recorder
     options.paramFile = qconfLoader.getQp().getParamFile().getAbsolutePath();
   }
 }