/*  Please credit Microscopy Core at NYULMC.
    v100 20161101
*/


macro "process a bunch of directories [q]" {

  mainpath = getDirectory("Choose a Directory") ;
  filelist = getFileList(mainpath);


  for (i=0; i<filelist.length; i++) {
    if ( File.isDirectory(mainpath + filelist[i])) {
     newtitle = replace(filelist[i], "\\$", "");
     newtitle = replace(newtitle, " ", "_");
     newtitle = substring(newtitle, 0, lengthOf(newtitle)-2);
     print(newtitle); //exit();  

     run("Image Sequence...", "open=[" + mainpath + filelist[i] + "Ch2] sort");
     ch2ID = getImageID();
     
     run("Image Sequence...", "open=[" + mainpath + filelist[i] + "Ch4] sort");
     ch4ID = getImageID();

     run("Image Sequence...", "open=[" + mainpath + filelist[i] + "Ph] sort");
     PhID = getImageID();

      selectImage(ch2ID);  
      setMinAndMax(32, 102);
      run("Apply LUT", "stack");
      resetMinAndMax();
      run("AVI... ", "compression=JPEG frame=3 save=" + mainpath + newtitle + "_Ch2.avi");
      rename("Ch2");

      selectImage(ch4ID);  
      setMinAndMax(32, 102);
      run("Apply LUT", "stack");
      resetMinAndMax();
      run("AVI... ", "compression=JPEG frame=3 save=" + mainpath + newtitle + "_Ch4.avi");
      rename("Ch4");

      selectImage(PhID); 
      //run("Bandpass Filter...", "filter_large=256 filter_small=0 suppress=None tolerance=5 process");
      resetMinAndMax();
      run("AVI... ", "compression=JPEG frame=3 save=" + mainpath + newtitle + "_Ph.avi");
      close();
      //  print(""+ mainpath + newtitle + "_Ch2_4");
      run("Merge Channels...", "c1=Ch4 c2=Ch2");
      run("AVI... ", "compression=JPEG frame=3 save=" + mainpath + newtitle + "_Ch2_4.avi");
      close();


    } // if
  }  // for i
 
} // end macro


function processImages() {

}