// CXD2TIFF_BatchProcess.txt
// 20160916 Akira Muto
// Import Hamamatsu Photonics .cxd files with the plugin Bio-Formats and then save them in a TIFF format. 
// Operation checked in ImageJ 1.50b on Windows7


destination=getDirectory("Choose a folder to save the resulted AVI files")
//destination="C:\Users\n\Desktop\\justtest\\"; //Alternatively, you can specify the folder name here. Change it accordingly. 


// Recursively lists the files in a user-specified directory.
  dir = getDirectory("Choose a folder in which you have the .cxd files");
 //dir="your folder name in full path"; //Alternatively, you can specify the folder name here. Change it accordingly. 



  count = 1;
  listFiles(dir); 

  function listFiles(dir) {
     list = getFileList(dir);
     for (i=0; i<list.length; i++) {
        if (endsWith(list[i], "/"))
           listFiles(""+dir+list[i]);
        else
           print((count++) + ": " + dir + list[i]);
	    fullpath=replace(dir,"/","\\")+list[i];
	    cxd2tiff(fullpath);
     }
  }


function cxd2tiff(fullpath){

run("Bio-Formats", "open=fullpath color_mode=Default display_metadata view=[Standard ImageJ] stack_order=XYTZC");
currentfile=getTitle();
renamedToTiff=replace(currentfile,"cxd","tif");
newTiffFilePath=destination+renamedToTiff;
saveAs("Tiff", newTiffFilePath);
close();

}