Batch Stack Focusing

Posted by AC17 on Mar 27, 2017; 12:08pm
URL: http://imagej.273.s1.nabble.com/Batch-Stack-Focusing-tp5018376.html

Hi all,

This is my first time attempting to write a macro in image J. I would really appreciate your help with this…

I have a main directory with multiple subdirectories. Each subdirectory contains multiple images (z stacks). I would like to write a code which will take my main directory and open a subdirectory , open all the images in that subdirectory, stack the images, run the stack focusing plugin and then save the stack in the corresponding folder. I would like to loop this so that all the subdirectories within my main directory are processed.

This is what I have so far. This code runs for a few minutes but I then can’t find my saved stacks.

   dir = getDirectory("Choose Main Directory");
   setBatchMode(true);
   count = 0;
   countFiles(dir);
   n = 0;
   processFiles(dir);
   print(count+" files processed");
   
   function countFiles(dir) {
      list = getFileList(dir);
      for (i=0; i<list.length; i++) {
          if (endsWith(list[i], "/"))
              countFiles(""+dir+list[i]);
          else
              count++;
      }
  }

   function processFiles(dir) {
      list = getFileList(dir);
      for (i=0; i<list.length; i++) {
          if (endsWith(list[i], "/"))
              processFiles(""+dir+list[i]);
          else {
             showProgress(n++, count);
             path = dir+list[i];
             processFile(path);
          }
      }
  }

  function processFile(path) {
for (i=0; i<list.length; i++)
         open(path);}
         {
          run("Images to Stack", "name=Stack title=[] use");
          run("Stack Focuser ", "enter=11");
           saveAs("Tiff", "stack" );
           close();
      }

Many thanks for your help!

Amy