/**
  *  A simple ImageJ plugin to find stars in a CCD image.
  *  Glen Cowan, RHUL Physics
  *  16 November, 2003
  */

import ij.*;
import ij.process.*;
import ij.gui.*;
import ij.plugin.filter.*;
import java.awt.*;
import java.awt.image.*;

public class Star_Finder implements PlugInFilter {

  ImagePlus imp;             // make imp available to run method

  public int setup(String arg, ImagePlus imp) {
    this.imp = imp;
    return DOES_ALL;        // claim to work on all image types
  }

  public void run(ImageProcessor ip) {

// Get info about image and set a threshold for star detection.
// Default gain is for ST-7E CCD; currently set 5 sigma threshold.

    double gain = IJ.getNumber("enter gain (e-/ADU)", 2.3);
    int ny = ip.getHeight();
    int nx = ip.getWidth();
    IJ.write("nx = " + nx);
    IJ.write("ny = " + ny);
    IJ.write("total pixels = " + nx*ny);
    ImageStatistics istat = imp.getStatistics();
    double mode = istat.dmode;
    System.out.println("mode = " + mode);
    IJ.write ("mode = " + mode);
    int threshold = (int)(mode + 5*Math.sqrt(mode/gain));
    IJ.write("threshold = " + threshold);

//  Loop over the pixels, for now just count pixels over threshold.
//  Method getPixel returns counts in ADU.

    int numPixelsOverThresh = 0;
    for (int j=0; j<ny; j++){
      for (int i=0; i<nx; i++){
        int c = ip.getPixel(i,j); 
        if ( c > threshold ) {
          System.out.println(i + "\t" + j + "\t" + c);
          numPixelsOverThresh++;

// add your code here to find stars


	  }
	}
    } 
    IJ.write("numPixelsOverThresh = " + numPixelsOverThresh);

  }          // end of run
}            // end of Star_Finder