Split Stack ImageJ macro to fix MetaMorph dual camera image files, by splitting them into their separate channel files

gistfile1.java

/**
 * Split Stack macro
 *
 * Fixes MetaMorph dual camera image files, by splitting them into
 * their separate channel files.
 *
 * Usage: In ImageJ, use Plugins > Macros > Run...
 *
 * Description:
 * 
 * MetaMorph 7 saves multi-camera images into a Left/Right merged
 * image.  This complicates analysis, and in fact MetaMorph's own 4D
 * reader (accessed from File > Open 4D) does not reconstruct
 * multi-camera data properly.  Therefore it's necessary to split the
 * data to make it appear as if it were obtained using a single
 * camera.
 * 
 * The split data and new "nd" file copy are saved into a "split"
 * sub-folder.  The original stacks are preserved for MetaMorph's
 * original TIF header metadata, since ImageJ destroys that metadata
 * in the split copy.
 *
 * Author: Rebecca Williams
 *
 * Contributor: Pariksheet Nanda (file renaming, documentation)
 *
 * Keywords: MetaMorph, dual camera, streaming
 *
 * Version: 2013-05-20a
 */
 
/* Settings */
indir="C:\\AALL USER IMAGES HERE\\SplitStack\\Files\\";
outdir = indir + "split" + File.separator;
channel_to_split = "cUltra 488-561";
replacement_channel_left = "GREEN";
replacement_channel_right = "RED";
no_nd_wavelengths = 0;             // at least 1 wavelength in .nd file

// Create new .nd files.  Allows multiple experiments to be processed.
nd_files = match_files(indir, ".*\\.nd$");
if (nd_files.length == 0)
   exit("No .nd files found in directory:\n" + indir);
if (! File.exists(outdir))
	File.makeDirectory(outdir);
for (i = 0; i < nd_files.length; i++)
   nd_wavelengths = save_new_nd_file(toString(indir + nd_files[i]),
                                     toString(outdir + nd_files[i]),
                                     channel_to_split,
                                     replacement_channel_left,
                                     replacement_channel_right);
if (nd_wavelengths == 0)
   no_nd_wavelengths = 1;

// Main processing loop to split image files.
if (no_nd_wavelengths)
   list = match_files(indir, ".*\\.TIF$");
else   
   list = match_files(indir, ".*_w\\d" + channel_to_split + ".*\\.TIF$");
setOption("display labels", true);
setBatchMode(true);
for (l = 0; l < list.length; l++) {
   dual_file = list[l];
      showProgress(l, list.length);
      IJ.redirectErrorMessages();
      open(indir + dual_file);
      getDimensions(xpix, ypix, nchannels, nslices, nframes);
      ID_Old = getImageID();
      newImage("D1", "8-bit black", xpix/2, ypix, nSlices);
      selectImage("D1");
      ID_1 = getImageID();
      newImage("D2", "8-bit black", xpix/2, ypix, nSlices);
      selectImage("D2");
      ID_2 = getImageID();
      for(k = 1; k <= nSlices; k++) {
         selectImage(ID_Old);
         setSlice(k);
         makeRectangle(1,1,xpix/2,ypix);
         run("Copy");
         selectImage(ID_1);
         setSlice(k);
         run("Paste");
         selectImage(ID_Old);
         setSlice(k);
         makeRectangle((xpix/2)+1, 1, xpix, ypix);
         run("Copy");
         selectImage(ID_2);
         setSlice(k);
         run("Paste");
      }
      if (no_nd_wavelengths) {
         // Special case of no wavelength information in .nd file or
         // filenames.
         // 
         // According to the MDA file format explained here:
         // http://mdc.custhelp.com/app/answers/detail/a_id/18979/kw/file%20naming
         // Wavelength `_w' is the first dimension in the MDA file
         // name, followed by stage position `_s' and then time `_t'.
         // Ignoring stage position, since one cannot use it in
         // streaming experiments.  Thus we assume wavelength preceeds
         // time.
         ti = lastIndexOf(dual_file, "_t");
         file_start = substring(dual_file, 0, ti);
         file_end = substring(dual_file, ti, lengthOf(dual_file));
         ch1_file = file_start + "_w1" + replacement_channel_left + file_end;
         ch2_file = file_start + "_w2" + replacement_channel_right + file_end;
      }
      else {
         wi = indexOf(dual_file, "_w") + lengthOf("_w");
         w1 = substring(dual_file, wi, wi+1);
         w2 = toString(parseInt(w1) + 1);
         ch1_file = replace(dual_file,
                            "_w\\d" + channel_to_split,
                            "_w" + w1 + replacement_channel_left);
         ch2_file = replace(dual_file,
                            "_w\\d" + channel_to_split,
                            "_w" + w2 + replacement_channel_right);
      }
      selectImage(ID_1);
      save(outdir + ch1_file);
      selectImage(ID_2);
      save(outdir + ch2_file);
}

/**
 * Modify .nd file as 2 channel and save a copy.
 *
 * @param  infile  path of input.nd file
 * @param  outfile path for output .nd file
 * @param  ch_dual name of dual channel
 * @param  ch1     name of first split channel
 * @param  ch2     name of second split channel
 * @return         number of initial wavelengths
 */
function save_new_nd_file(infile, outfile, ch_dual, ch1, ch2) {
   ch_dual = nd_safe_wavename(ch_dual);
   ch1 = nd_safe_wavename(ch1);
   ch2 = nd_safe_wavename(ch2);
   file_string = File.openAsString(infile);
   w_key = '"NWavelengths", ';
   wi = indexOf(file_string, w_key) + lengthOf(w_key);
   w_value = substring(file_string, wi, wi+1);
   if (w_value == "0") {
      no_nd_wavelengths = 1;
      file_string = replace(file_string,
                            '"DoWave", FALSE',
                            '"DoWave", TRUE');
      file_string = replace(file_string,
                            '"WaveInFileName", FALSE',
                            '"WaveInFileName", TRUE');
      do_z_1 = "";
      do_z_2 = "";
      if (indexOf(file_string, '"DoZSeries", TRUE') > -1) {
         do_z_1 = '"WaveDoZ1", TRUE\n';
         do_z_2 = '"WaveDoZ2", TRUE\n';
      }
      file_string = replace(file_string,
                            '"NWavelengths", 0\n',
                            '"NWavelengths", 2\n' +
                            '"WaveName1", "' + ch1 + '"\n' +
                            do_z_1 +
                            '"WaveName2", "' + ch2 + '"\n' +
                            do_z_2);
   }
   else {
      new_w_value = toString(parseInt(w_value) + 1);
      file_string = replace(file_string,
                            w_key + w_value,
                            w_key + new_w_value);
      do_z_1 = "";
      do_z_2 = "";
      if (indexOf(file_string, '"DoZSeries", TRUE') > -1) {
         do_z_1 = '"WaveDoZ' + w_value + '", TRUE\n';
         do_z_2 = '"WaveDoZ' + new_w_value + '", TRUE\n';
         // MetaMorph is sensitive to the position of the "WaveDoZ#"
         // key, so we have to position it after the corresponding
         // "WaveName#".
      }
      file_string = replace(file_string,
                            '"WaveDoZ' + w_value + '", TRUE\n',
                            "");
      file_string = replace(file_string,
                            '"WaveName\\d", "' + ch_dual + '"\n',
                            '"WaveName' + w_value + '", "' + ch1 + '"\n' +
                            do_z_1 +
                            '"WaveName' + new_w_value + '", "' + ch2 + '"\n' +
                            do_z_2);
   }
   File.saveString(file_string, outfile);
   return toString(w_value);
}

/**
 * Replace illegal characters from WaveName value for .nd file.
 * 
 * @param  string channel name in MetaMorph
 * @return        string of safe channel name
 */
function nd_safe_wavename(string) {
   return replace(string, "[-/\]", "_");
}

/**
 * Filter file list with RegEx.
 * 
 * @param  directory path where files are located
 * @param  regexp    desired match expression
 * @return           array file list
 */
function match_files(directory, regexp) {
   all_file_list = getFileList(directory);
   match_file_list = newArray();
   for (i = 0; i < all_file_list.length; i++) {
      file = all_file_list[i];
      if (matches(file, regexp))
         match_file_list = Array.concat(match_file_list, file);
   }
   return match_file_list;
}


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