package com.github.celldynamics.quimp.plugin.protanalysis;
   
   import java.awt.Point;
   import java.awt.event.ActionEvent;
   import java.util.Arrays;
   import java.util.List;
   import java.util.regex.Matcher;
   import java.util.regex.Pattern;
   
  import com.github.celldynamics.quimp.QParamsQconf;
  import com.github.celldynamics.quimp.filesystem.QconfLoader;
  import com.github.celldynamics.quimp.plugin.protanalysis.Prot_Analysis.PointHashSet;
  import com.github.celldynamics.quimp.plugin.qanalysis.STmap;
  
  import ij.gui.PointRoi;
  import ij.gui.Roi;
  import ij.plugin.frame.RoiManager;
  
  /**
   * Action for ROI to/from transfer.
   * 
   * @author p.baniukiewicz
   *
   */
  @SuppressWarnings("serial")
  public class ActionFromRoi extends ProtAnalysisAbstractAction {
  
    /**
     * Create action.
     * 
     * @param name name
     * @param desc tooltip
     * @param ui reference to gui manager
     */
    public ActionFromRoi(String name, String desc, ProtAnalysisUi ui) {
      super(name, desc, ui);
    }
  
    /*
     * (non-Javadoc)
     * 
     * @see
     * com.github.celldynamics.quimp.plugin.protanalysis.ProtAnalysisAbstractAction#actionPerformed(
     * java.awt.event.ActionEvent)
     */
    @Override
    public void actionPerformed(ActionEvent e) {
      int modifiers = e.getModifiers();
      PointHashSet points = ui.getModel().selected;
      points.clear(); // Here we clear points!
      RoiManager rm = RoiManager.getRoiManager();
      QconfLoader qconfLoader = ui.getModel().getQconfLoader();
      STmap[] stMap = ((QParamsQconf) qconfLoader.getQp()).getLoadedDataContainer().getQState();
      List<Roi> rois = Arrays.asList(rm.getRoisAsArray());
      int cellNo = 0;
  
      if ((modifiers & ActionEvent.CTRL_MASK) == ActionEvent.CTRL_MASK) {
        cellNo = options.selActiveCellMap.getValue();
        logger.debug("CTRL detected. Import all to current cell: " + cellNo);
      }
      for (Roi roi : rois) { // over ROIs in RoiManager
        if (!(roi instanceof PointRoi)) {
          logger.warn("ROI " + roi.getName() + " is not PointRoi");
        }
        // if NO ctrl get cell number from each ROI
        if ((modifiers & ActionEvent.CTRL_MASK) != ActionEvent.CTRL_MASK) {
          if (roi.getName().startsWith(ProtAnalysisOptions.roiPrefix)) { // our roi
            cellNo = stripCellNo(roi.getName());
            if (cellNo > stMap.length) {
              continue;
            }
            if (cellNo < 0) {
              logger.warn(
                      "Can not obtain cell index from ROI name: " + roi.getName() + " Assume cell 0");
              cellNo = 0;
            }
          }
        }
        // now each roi can contain some points (e.g. two point form one ROI object in ROI Manager)
        for (Point p : roi) {
          int tmpIndex = (int) p.getX();
          int frame = (int) Math.round(
                  p.getY() * (stMap[cellNo].getT() - 1) / stMap[cellNo].getVerticalResolution());
          // get screen coordinates (ints)
          // FIXME Why p.getY is larger than 400?? This is on tiffs as well.
          // see com.github.celldynamics.quimp.plugin.qanalysis.STmap.resize(ImagePlus),
          // (int) Math.ceil((double) res / (double) T)*T = vertRes
          try {
            int x = (int) Math.round(stMap[cellNo].getxMap()[frame][tmpIndex]);
            int y = (int) Math.round(stMap[cellNo].getyMap()[frame][tmpIndex]);
            logger.trace("name: " + roi.getName() + " point: " + p + " tmpIndex: " + tmpIndex
                    + " frame: " + frame + " cell: " + cellNo + " x: " + x + " y: " + y);
            PointCoordsimp/plugin/protanalysis/PointCoords.html#PointCoords">PointCoords point = new PointCoords(new Point(x, y), cellNo, frame);
            points.addRaw(point); // add without overwriting frame number
          } catch (ArrayIndexOutOfBoundsException ex) {
            logger.error(
                    "Point " + p + " can not be mapped to array (ArrayIndexOutOfBoundsException)");
          }
        }
 
     }
     updateCurrentView();
   }
 
   /**
    * Extract cell number from ROI name.
    * 
    * @param name roi name in format set in {@link ActionToRoi}
    * @return only cell number without additional roi number added by Fiji or -1 if number could not
    *         be retrieved.
    */
   int stripCellNo(String name) {
     // contain index and optional roi subnumber -0
     String tmp = name.substring(ProtAnalysisOptions.roiPrefix.length());
     Pattern p = Pattern.compile("^[\\d]*");
     Matcher m = p.matcher(tmp);
     if (m.find()) {
       return Integer.parseInt(m.group(0));
     }
     return -1;
   }
 
 }