Stitching together multiple images within a series of folders

Posted by nebenb on Apr 26, 2018; 3:38pm
URL: http://imagej.273.s1.nabble.com/Stitching-together-multiple-images-within-a-series-of-folders-tp5020586.html

Hello,

I am trying to stitch together images of entire c.elegans worms to recreate
a 3d image of the entire worm.
Stitching them manually is easy but tedious, so I am trying to write an
ImageJ macro that will stitch them for me. All the plugins necessary are
available (pairwise stitching, run 8bit, etc) and I can get a macro to
stitch the files in a single folder if I provide the exact file names,
paths, etc within the macro. However, with my severely limited coding
knowledge, I cannot find a way to make this process generic.

Additionally, I want this macro to be propagative (not sure if this is the
right description) to the point where the user selects a 'mother' folder
with subfolders that each contain the images for a single worm (see below).
Then ImageJ would sample each 'daughter' folder, stitch those images
together, and save the result, before moving on to the next 'daughter'
folder.



MOTHER
  >DAUGHTER 1
    >worm 1_1
    >worm 1_2
    >worm 1_3
    >worm 1_4
    >worm 1_5
    >worm 1_6
    >worm 1_7
  >DAUGHTER 2
    >worm 2_1
    >worm 2_2
    >worm 2_3
    >worm 2_4
    >worm 2_5
  >DAUGHTER 3
    >worm 3_1
    >worm 3_2
    >worm 3_3
    >worm 3_4
    >worm 3_5
    >worm 3_6
etc etc


From what I have found on the web and my own trail and error I have pieced
together the following:


// This macro will takemutlipleple folders with individual
// images sequential images, sorted by sequence into folders,
// and stitch them together using the "PairwiseStitching" macro.
// The stitched images will be saved to the 'mother'
// directory with the name of the sequence-folder they were
// constructed from.


print("");
print("-- 3D Stitching --");
print("");
 mother = getDirectory("select mother directory");
print("MOTHER directory set as:");
print(mother);


// The MOTHER directory contains any number of daughter
// directories. The following sequence effectively primes
// ImageJ to be familiar with all the files within the
// 'Daughter' directories.


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

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



// The first two images are stitched together to serve as a
// template for subsequent images to be stitched on to.
// This template is saved in the MOTHER directory with the
// file name of the DAUGHTER directory.


for (i=0; i<2; i++)
   initial(daughter, mother, file1, file2);

function initial(daughter, mother, file1, file2) {
   open(daughter + list[i]);
     run("8-bit");
   open(daughter + list[i+1]);
     run("8-bit");
   print("stitching 1+2");
     run("Pairwise stitching", "first_image=file1 second_image=file2
fusion_method=[Max. Intensity] check_peaks=5 compute_overlap
subpixel_accuracy x=0.0000 y=0.0000 z=0.0000
registration_channel_image_1=[Average all channels]
registration_channel_image_2=[Average all channels]");
   saveAs("Tiff", mother + daughter);
   if (i == 2)
     exit();
   }


// With a template available, imageJ can now propagate through
// The remaining files (i<list.length) to stitch them to the template


 stitch(daughter);

for (i = 2; i < list.length; i++)
   stitch(daughter, mother, file1, file2);

function stitch(daughter, mother, file1, file2); {
   open(daughter + file1);
     run("8-bit");
   open(mother + "daughter.tif");
   print("propagative stitching");
     run("Pairwise stitching", "first_image=file1 second_image=daughter.tif
fusion_method=[Max. Intensity] check_peaks=5 compute_overlap
subpixel_accuracy x=0.0000 y=0.0000 z=0.0000
registration_channel_image_1=[Average all channels]
registration_channel_image_2=[Average all channels]");
   saveAs("Tiff", mother + daughter)
   }


//** I'm not sure if this style of naming will work, i'm not sure how to
recall



Thank you all so much for your help, in advance. I look forward to all
suggestions and criticisms.


- Ben






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