My_Batch_Convert_Raw_Volumes.txt

  //inputDir = getDirectory("Choose Source Directory ");
  //outputDir = getDirectory("Choose Destination Directory ");
  
  
  // Modes: 1 - folder with volumes
  //        2 - List of specified files 
  //        3 - Every n-th starting from ... ending with ...
  
  mode = 3;
  
  inputDir = "G:\\DATA\\bamboo\\Input\\";
  outputDir = "G:\\DATA\\bamboo\\Output\\diff_series_new\\";

  ext = ".raw";
  
  // mode 1 parameters
  fileMask = "vol_bg_460_350_860_";
 //frameNumbers = newArray("16", "18", "20", "22", "24");
  
  // mode 3 parameters
  maskLength = 2;
  startIndex = 8;
  endIndex = 10;
  step = 2;
  
  setBatchMode(true);
  
  dimX = 460;
  dimY = 350;
  dimZ = 860;

  scaleX = 0.75;
  scaleY = 0.75;
  scaleZ = 0.75;
  
  //raw_params = "little-endian use";
  raw_params = "";
  
  
 if (mode == 1) {
    list = getFileList(inputDir); 
 }
 if (mode == 2) {
    list = newArray(frameNumbers.length);
    for (i=0; i<frameNumbers.length; i++) {
         //fileName = fileMask + toString(frameNumbers[i]) + ext ;
         fileName =  fileMask + frameNumbers[i] + ext ;
         list[i] = fileName;
    }
}
 if (mode == 3) {
  j = 0;
  list = newArray((endIndex  - startIndex) / step + 1 );
  for (i=startIndex ; i<endIndex +1 ; i=i+step) {
         fileName =  fileMask + pad(i, maskLength) + ext ;
         list[j] = fileName;
         j=j+1;
    }
 }
 
  
  //for (i=0; i<5; i++) {
  for (i=0; i<list.length; i++) {
  
  
//showMessage(list[i]);

     showProgress(i+1, list.length);
     
     
     run("Raw...", "open=" + inputDir + list[i]+ " image=[32-bit Real] width=" + toString(dimX) + " height=" + toString(dimY) + " offset=0 number=" + toString(dimZ) + " gap=0 " + raw_params);


     image1 = getTitle;
     image1ID = getImageID;


     run("8-bit");
     
     //imageCalculator("Difference create stack", image1 , image2 );

     //run("Specify...", "width=1500 height=1750 x=300 y=0");
     //run("Crop");
     
     //selectImage(image1ID );
     //close();
     
//--------------------------------------------------------
// Scaling
//--------------------------------------------------------

  width = getWidth();
  height = getHeight();
  depth = nSlices;

  width = width * scaleX;
  height = height * scaleY;
  depth = depth * scaleZ;

   run("Scale...", "x="+toString(scaleX)+ " y=" + toString(scaleY)+ " z=" + toString(scaleZ) + " width=" + toString(width) + " height=" + toString(height) + " depth=" + toString(depth) + " interpolation=Bicubic process create title=volume");
     
    idImageRes = getImageID;

    //selectImage(idImage);
    //close();
     
        
     saveAs("TIFF", outputDir+list[i]);
     //saveAs("PGM", outputDir+list[i]);
     //saveAs("Raw Data", outputDir+list[i]);
     
     run("Close All Without Saving");

  }

  showMessage("Finished");
  
 function pad(n, length) {
      str = toString(n);
      while (lengthOf(str)<length)
          str = "0" + str;
      return str;
  }