/*  JMF_Edge_Analyzer.java

Glen Cowan
RHUL Physics Department
January 2007

This ImageJ plugin unpacks the R, G ad B pixel values of an image and sums them
to form a single intensity.  The values are put into an array.

*/

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

public class Edge_Analyzer 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) {

//  Unpack pixel contents into array; reorder vertical direction to increase upwards.

    int ncol = ip.getWidth();
    int nrow = ip.getHeight();
    System.out.println("ncol, nrow = " + ncol + "  " + nrow);
    int[] pixels = (int[])ip.getPixels();
    int[][] intensity = new int[nrow][ncol];
    int c, r, g, b;
    for(int k=0; k<ncol; k++){
      for (int j=0; j<nrow; j++){
        int l = j*ncol + k;
        c = pixels[l];
        r = (c&0xff0000)>>16;
        g = (c&0xff00)>>8;
        b = c&0xff;
        intensity[nrow-j-1][k] = r + g + b;
        System.out.println(k + "  " + j + "  " + intensity[j][k]);
      }
    }
    
// do more analysis here on the intensity array, e.g., to find edges.



    
  }          // end of run
  
}    // end of class Edge_Analyzer