//get directory

dir1 = getDirectory("Input files");
dir2 = getDirectory("Output files");

dir3 = getDirectory("Temp folder for cropping");



  extension = ".tif";
radius = 510;
  setBatchMode(true);

  
  processFolderCrop(dir1);




  n = 0;

  processFolder(dir3, dir2);


  function processFolderCrop(dir1) {
     list = getFileList(dir1);
     for (i=0; i<list.length; i++) {
          if (endsWith(list[i], "/"))
              processFolder(dir1+list[i]);
          else if (endsWith(list[i], extension))
             processImageCrop(dir1, list[i]);
      }
  }

  function processImageCrop(dir1, name) {
     open(dir1+name);
//     print(n++, name);
makeOval(512-radius, 512-radius, 2*radius, 2*radius);
setBackgroundColor(0, 0, 0);
run("Clear Outside");
saveAs(extension, dir3+name+"_Cropped");
     close();
  }



  function processFolder(dir1, dir2) {
     list = getFileList(dir1);
     for (i=0; i<list.length; i++) {
          if (endsWith(list[i], "/"))
              processFolder(dir1+list[i]);
          else if (endsWith(list[i], extension))
             Position = substring(list[i], indexOf(list[i], "_Export")-1, indexOf(list[i], "_Export"));
             if (Position < 2) {
             processImage(dir1, list[i], dir2);

             }

      }
  }

function processImage(dir1, name, dir2) {
	open(dir1+name);
	window_1 = getTitle();
	Cell= substring(name, 0, indexOf(list[i], "_Tomo"));
	Orientation = substring(name, indexOf(name, ".tif_Crop")-1, indexOf(name, ".tif_Crop"));
	//other positions
	open(dir1+Cell+"_Tomo_Area002_Export000"+Orientation+".tif_Cropped.tif");
	window_2 = getTitle();
	open(dir1+Cell+"_Tomo_Area003_Export000"+Orientation+".tif_Cropped.tif");
	window_3 = getTitle();

	orient=d2s((3-Orientation)*45, 3, "0");

newImage(Cell+"_"+orient+"_deg", "8-bit black", 1024, 2042, 1);


mergeTitle = getTitle();

makeOval(0,510,1020, 1020);
selectWindow(window_2);
run("Copy");
selectWindow(mergeTitle);
run("Paste");
makeOval(0,0, 1020,1020);
selectWindow(window_3); 
run("Copy");
selectWindow(mergeTitle);
run("Paste");
makeOval(0,1020,1020, 1020);
selectWindow(window_1);
run("Copy");
selectWindow(mergeTitle);
run("Paste");

makeRectangle(200, 250, 650, 1650);
run("Crop");

saveAs("Tiff", dir2+Cell+"_"+orient+"_deg"+".tif");
run("Close All");
}








function d2s(number, width, character) { 
        number = toString(number); // force string 
        character = toString(character); 
        for (len = lengthOf(number); len < width; len++) 
                number = character + number; 
        return number; 
}