Extracting pixel values to results table

Posted by hjc on Jul 13, 2011; 1:15pm
URL: http://imagej.273.s1.nabble.com/Extracting-pixel-values-to-results-table-tp3683931.html

Hi

I am trying to calculate NDVI (normalise difference vegetation index) values for every pixel in a series of images in a specified folder.  I am using the macro below.  The macro runs but I cannot get it to save the values of each pixel in the results table.  When the macro is finished only the last pixel value is shown in the results table.  The NDVI values are then also not computed correctly always stating 0.

I have been able to write the results to the log screen, however this takes extremely long to process and is not feasible.  Simularly if the results is printed the macro takes extremely long.

I would appreciate any help.

Thanks
Henri

//extract surface area and ndvi over the whole plot for trees and grasses

run("Memory & Threads...", "maximum=1600 parallel=8 run");

dir1 = getDirectory("Choose Source Directory "); //prompt user for source directory

dir2 = getDirectory("Choose Destination Directory ");  //prompt user for destination directory

dir3 = getDirectory("Choose Results Directory ");  //promt user for destination directory for results file

dir4 = getDirectory("Choose NDVI Results Directory ") //promt for ndvi dir

list2 = getFileList(dir2); //get a list of the files  

setBatchMode(true);

for (z=0; z<list2.length; z++) {
      open(dir2+list2[z]);               //opens every image
      //showProgress(z+1, list2.length);  

      start = getTime();                                                   // Get current time for progress bar
     
      w = getWidth();             // Get picture width
      h = getHeight();            // Get picture height
      tt = getTitle();
      if(nResults>=0)run("Clear Results");
      print("\\Clear");           // Clears the log
      i = nResults;
     
         
      for (x=0; x<w; x++){                        // Setup nested loops to go through each x,y value in image
           
           showProgress(x+1, w);
           
           for (y=0; y<h; y++){  
           v = getPixel(x, y);                    // Get a pixel value
           r = (v & 0xff0000)>>16;                // Extract out RGB values from packed integer with pixel value
           g = (v & 0x00ff00)>>8;      
           b = (v & 0x0000ff);            
           NDVI = ((r-g)/(r+g));                  // Calculate the NDVI.
                         
         
           //print(u,tt,x+1,y+1,r,g,b,NDVI);
 
           setResult("O", i, i);
           setResult("Pr", i, x+1);
           setResult("Pc", i, y+1);
           setResult("NDVI", i, NDVI);
           //updateResults();
           //print(nResults);
       
           }
                           
        }
     
    //selectWindow("Log");
    //saveAs("Text", dir4+tt+"datandvi.txt");
    saveAs("Results", dir4+tt+"datandvi.txt");
  }