package com.github.celldynamics.quimp.plugin.protanalysis;
   
   import java.awt.event.ActionEvent;
   import java.lang.reflect.Field;
   import java.util.ArrayList;
   
   import com.github.celldynamics.quimp.CellStats;
   import com.github.celldynamics.quimp.FrameStatistics;
   import com.github.celldynamics.quimp.QParamsQconf;
  import com.github.celldynamics.quimp.filesystem.QconfLoader;
  import com.github.celldynamics.quimp.filesystem.StatsCollection;
  
  import ij.gui.Plot;
  
  /**
   * Plot selected 2d data.
   * 
   * @author p.baniukiewicz
   *
   */
  @SuppressWarnings("serial")
  public class ActionPlot2d extends ProtAnalysisAbstractAction {
  
    /**
     * Action creator.
     * 
     * @param name name
     * @param desc description
     * @param ui reference to outer class.
     */
    public ActionPlot2d(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) {
      QconfLoader qconfLoader = ui.getModel().getQconfLoader();
      plot(qconfLoader);
    }
  
    void plot(QconfLoader qconfLoader) {
      int h = options.selActiveCellPlot.getValue();
      StatsCollection stats =
              ((QParamsQconf) qconfLoader.getQp()).getLoadedDataContainer().getStats();
  
      try {
        // geom plots
        if (options.chbXcentrPlot.booleanValue()) {
          plotCentroidParamVsFrame("centroid-x", stats.getStatCollection().get(h), "X");
        }
        if (options.chbYcentrPlot.booleanValue()) {
          plotCentroidParamVsFrame("centroid-y", stats.getStatCollection().get(h), "Y");
        }
        if (options.chbPersistencePlot.booleanValue()) {
          plotGeomParamVsFrame("persistance", stats.getStatCollection().get(h));
        }
  
        if (options.chbDisplPlot.booleanValue()) {
          plotGeomParamVsFrame("displacement", stats.getStatCollection().get(h));
        }
        if (options.chbDistPlot.booleanValue()) {
          plotGeomParamVsFrame("dist", stats.getStatCollection().get(h));
        }
        if (options.chbSpeedPlot.booleanValue()) {
          plotGeomParamVsFrame("speed", stats.getStatCollection().get(h));
        }
        if (options.chbPerimPlot.booleanValue()) {
          plotGeomParamVsFrame("perimiter", stats.getStatCollection().get(h));
        }
        if (options.chbElongPlot.booleanValue()) {
          plotGeomParamVsFrame("elongation", stats.getStatCollection().get(h));
        }
        if (options.chbCircPlot.booleanValue()) {
          plotGeomParamVsFrame("circularity", stats.getStatCollection().get(h));
        }
        if (options.chbAreaPlot.booleanValue()) {
          plotGeomParamVsFrame("area", stats.getStatCollection().get(h));
        }
  
        // fluo plots
        if (options.chbTotFluPlot.booleanValue()) {
          plotFluoParamVsFrame("totalFluor", stats.getStatCollection().get(h),
                  options.selActiveChannel.intValue());
        }
        if (options.chbMeanFluPlot.booleanValue()) {
          plotFluoParamVsFrame("meanFluor", stats.getStatCollection().get(h),
                  options.selActiveChannel.intValue());
        }
        if (options.chbCortexWidthPlot.booleanValue()) {
          plotFluoParamVsFrame("cortexWidth", stats.getStatCollection().get(h),
                  options.selActiveChannel.intValue());
        }
       if (options.chbCytoAreaPlot.booleanValue()) {
         plotFluoParamVsFrame("innerArea", stats.getStatCollection().get(h),
                 options.selActiveChannel.intValue());
       }
       if (options.chbTotalCytoPlot.booleanValue()) {
         plotFluoParamVsFrame("totalInnerFluor", stats.getStatCollection().get(h),
                 options.selActiveChannel.intValue());
       }
       if (options.chbMeanCytoPlot.booleanValue()) {
         plotFluoParamVsFrame("meanInnerFluor", stats.getStatCollection().get(h),
                 options.selActiveChannel.intValue());
       }
       if (options.chbCortexAreaPlot.booleanValue()) {
         plotFluoParamVsFrame("cortexArea", stats.getStatCollection().get(h),
                 options.selActiveChannel.intValue());
       }
       if (options.chbTotalCtf2Plot.booleanValue()) {
         plotFluoParamVsFrame("totalCorFluo", stats.getStatCollection().get(h),
                 options.selActiveChannel.intValue());
       }
       if (options.chbManCtfPlot.booleanValue()) {
         plotFluoParamVsFrame("meanCorFluo", stats.getStatCollection().get(h),
                 options.selActiveChannel.intValue());
       }
 
     } catch (NoSuchFieldException | SecurityException | IllegalArgumentException
             | IllegalAccessException e) {
       throw new RuntimeException("Illegal field name.");
     }
 
   }
 
   /**
    * Plot geometric feature versus frame number for specified cell.
    * 
    * @param name name of the filed in {@link FrameStatistics}
    * @param stats reference to cell stats
    * @throws SecurityException on wrong filed
    * @throws NoSuchFieldException on wrong filed
    * @throws IllegalAccessException on wrong filed
    * @throws IllegalArgumentException on wrong filed
    */
   public void plotGeomParamVsFrame(String name, CellStats stats) throws NoSuchFieldException,
           SecurityException, IllegalArgumentException, IllegalAccessException {
     Plot plot = new Plot(name, "time", name);
     ArrayList<Double> ar = new ArrayList<>();
     ArrayList<Double> f = new ArrayList<>();
     for (FrameStatistics fs : stats.getFramestat()) {
       Field field = fs.getClass().getDeclaredField(name);
       ar.add((double) field.getDouble(fs));
       f.add((double) fs.frame);
     }
     plot.addPoints(f, ar, Plot.CONNECTED_CIRCLES);
     plot.show();
   }
 
   /**
    * Plot fluorescence feature versus frame number for specified cell.
    * 
    * @param name name of the filed in {@link FrameStatistics}
    * @param stats reference to cell stats
    * @param ch channel number
    * @throws SecurityException on wrong filed
    * @throws NoSuchFieldException on wrong filed
    * @throws IllegalAccessException on wrong filed
    * @throws IllegalArgumentException on wrong filed
    */
   public void plotFluoParamVsFrame(String name, CellStats stats, int ch)
           throws NoSuchFieldException, SecurityException, IllegalArgumentException,
           IllegalAccessException {
     Plot plot = new Plot(name, "time", name);
     ArrayList<Double> ar = new ArrayList<>();
     ArrayList<Double> f = new ArrayList<>();
     for (FrameStatistics fs : stats.getFramestat()) {
       Field field = fs.channels[ch].getClass().getDeclaredField(name);
       ar.add((double) field.getDouble(fs.channels[ch]));
       f.add((double) fs.frame);
     }
     plot.addPoints(f, ar, Plot.CONNECTED_CIRCLES);
     plot.show();
   }
 
   /**
    * Plot geometric feature versus frame number for specified cell.
    * 
    * <p>Plot centroid that is object not a filed like those supported by
    * {@link #plotGeomParamVsFrame(String, CellStats)}
    * 
    * @param name name of the filed in {@link FrameStatistics}
    * @param stats reference to cell stats
    * @param type X or Y for x,y coordinate
    */
   public void plotCentroidParamVsFrame(String name, CellStats stats, String type) {
     Plot plot = new Plot(name, "time", name);
     ArrayList<Double> ar = new ArrayList<>();
     ArrayList<Double> f = new ArrayList<>();
     switch (type) {
       case "X":
         for (FrameStatistics fs : stats.getFramestat()) {
           ar.add(fs.centroid.getX());
           f.add((double) fs.frame);
         }
         break;
       case "Y":
         for (FrameStatistics fs : stats.getFramestat()) {
           ar.add(fs.centroid.getY());
           f.add((double) fs.frame);
         }
         break;
       default:
         throw new IllegalArgumentException("Wrong type.");
     }
 
     plot.addPoints(f, ar, Plot.CONNECTED_CIRCLES);
     plot.show();
 
   }
 
 }