package com.github.celldynamics.quimp.plugin.protanalysis;
   
   import java.awt.event.ActionEvent;
   import java.awt.geom.Point2D;
   import java.io.FileWriter;
   import java.io.IOException;
   import java.io.PrintWriter;
   import java.nio.file.Path;
   import java.nio.file.Paths;
  import java.util.HashMap;
  import java.util.List;
  import java.util.Map;
  
  import com.github.celldynamics.quimp.QParamsQconf;
  import com.github.celldynamics.quimp.QuimpException;
  import com.github.celldynamics.quimp.filesystem.QconfLoader;
  import com.github.celldynamics.quimp.plugin.AbstractPluginOptions;
  import com.github.celldynamics.quimp.plugin.qanalysis.STmap;
  
  /**
   * Action (referenced as ActionListener) for saving tracks to csv if "Track" button is hit.
   * 
   * <p>Read:
   * <ol>
   * <li>{@link AbstractPluginOptions#paramFile}
   * <li>{@link ProtAnalysisOptions#saveTracks}
   * </ol>
   * 
   * @author p.baniukiewicz
   *
   */
  @SuppressWarnings("serial")
  public class ActionSaveTracks extends ActionTrackPoints {
  
    /**
     * Action creator.
     * 
     * @param ui reference to outer class.
     */
    public ActionSaveTracks(ProtAnalysisUi ui) {
      super(ui);
    }
  
    @Override
    public void actionPerformed(ActionEvent arg0) {
      PrintWriter pw;
      if (options.saveTracks.getValue()) {
        QconfLoader qconfLoader = ui.getModel().getQconfLoader();
        STmap[] stMap = ((QParamsQconf) qconfLoader.getQp()).getLoadedDataContainer().getQState();
        HashMap<Integer, List<Point2D>> tmpSelected = extractPoints(stMap);
        for (Map.Entry<Integer, List<Point2D>> entry : tmpSelected.entrySet()) {
          Integer cellNo = entry.getKey(); // cell number
          List<Point2D> points = entry.getValue(); // users points
          MaximaFinderquimp/plugin/protanalysis/MaximaFinder.html#MaximaFinder">MaximaFinder mf = new MaximaFinder(ui.getImagePlus().getProcessor());
          mf.setMaxima(points);
  
          TrackCollection trackCollection = getTracks(stMap, cellNo, mf);
          try {
            Path fileToSave = Paths.get(qconfLoader.getQp().getPath(), "tracks_" + cellNo + ".csv");
            pw = new PrintWriter(new FileWriter(fileToSave.toFile()));
            trackCollection.saveTracks(pw);
            pw.flush();
            pw.close();
            logger.info("Saved tracks in " + fileToSave.toString());
          } catch (IOException e) {
            new QuimpException(e, ui.getModel().getSink()).handleException(null,
                    "Exception thrown when saving maps");
            break;
          }
        }
      }
    }
  
  }