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BatchConvertAnyToNrrd.txt
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BatchConvertAnyToNrrd.txt
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// "BatchConvertAnyToNrrd"
//
// This macro batch all of the files in a folder hierarchy
// to nrrd format
// Adapted by Greg Jefferis from code at
// http://rsb.info.nih.gov/ij/macros/BatchProcessFolders.txt
// jefferis@gmail.com
/* Run from the command line as follows
fiji -eval '
runMacro("/Volumes/JData/JPeople/Common/CommonCode/ImageJMacros/BatchConvertAnyToNrrd.txt",
"/Volumes/JData/JPeople/Sebastian/fruitless/Registration/IS2Reg/images.unsorted/,/Volumes/JData/JPeople/Sebastian/fruitless/Registration/IS2Reg/images.unflipped/SAJ/");
' -batch --headless
*/
requires("1.42k");
file = getArgument;
dir=""
outputDir=""
//print("file = "+file);
if (file!=""){
arg = split(file,",");
if (arg.length!=2) {
exit();
} else if(arg[0]=="" || arg[1]==""){
exit();
} else {
outputDir=arg[1];
if(!endsWith(outputDir,"/")) outputDir=outputDir+"/";
if(File.isDirectory(arg[0])) {
// we're dealing with a directory
dir=arg[0];
if(!endsWith(dir,"/")) dir=dir+"/";
} else {
// single file
dir=File.getParent(arg[0])+"/";
file=File.getName(arg[0]);
processFile(dir,outputDir,file);
exit();
}
}
}
if(dir=="") dir = getDirectory("stacks directory");
if(outputDir=="") outputDir = getDirectory("output directory");
setBatchMode(true);
count = 0;
countFiles(dir);
print("Total files: "+count);
n = 0;
processFiles(dir, outputDir);
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,outputDir) {
list = getFileList(dir);
// Stops multiple processes racing each other to do the same file
shuffle(list);
for (i=0; i<list.length; i++) {
if (endsWith(list[i], "/"))
processFiles(""+dir+list[i], outputDir+list[i]);
else {
showProgress(n++, count);
processFile(dir,outputDir,list[i]);
}
}
}
function processFile(dir,outputDir,file) {
lfile=toLowerCase(file);
if (!endsWith(lfile, ".nrrd")) {
path = dir+file;
outfile=substring(file,0,lastIndexOf(file,"."))+'.nrrd';
outpath=outputDir+outfile;
lockpath=outputDir+outfile+'.lock';
if(File.exists(outpath)){
print("Skipping file: " + file + " since " + outfile + " already exists");
return;
}
if(File.exists(lockpath)){
print("Skipping file: " + file + " since someone else is working on it");
return;
}
File.saveString("",lockpath)
print("Inpath = "+path);
print("Outpath = "+outpath);
print("lockpath = "+lockpath);
open(path);
processImage();
// to save in compressed format
setKeyDown("alt");
run("Nrrd ... ", "nrrd=[" + outpath + "]");
setKeyDown("none");
close();
File.delete(lockpath);
}
}
function processImage() {
// You can make any changes to the image that you want in here
// eg flip, reverse etc
}
function shuffle(array) {
n = array.length; // The number of items left to shuffle (loop invariant).
while (n > 1) {
k = randomInt(n); // 0 <= k < n.
n--; // n is now the last pertinent index;
temp = array[n]; // swap array[n] with array[k] (does nothing if k==n).
array[n] = array[k];
array[k] = temp;
}
}
// returns a random number, 0 <= k < n
function randomInt(n) {
return n * random();
}