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BatchProjectTif.txt
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BatchProjectTif.txt
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// "BatchConvertStacksToZProjJPGS"
//
// created by Aaron on 2011-26-10
// This macro takes all of the tifs in a folder and its subfolders
// and creates a SD Z-projection
// (Slightly) Adapted by Greg Jefferis from code at
// http://rsb.info.nih.gov/ij/macros/BatchProcessFolders.txt
// v 0.1 2007-11-07
// - first version in response to a request from Jai
requires("1.33s");
dir = getDirectory("Choose a stacks directory");
outputDir = getDirectory("Choose 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);
for (i=0; i<list.length; i++) {
if (endsWith(list[i], "/"))
processFiles(""+dir+list[i], outputDir);
else {
showProgress(n++, count);
processFile(dir,outputDir,list[i]);
}
}
}
function processFile(dir,outputDir,file) {
if (endsWith(file, ".tif")) {
if(File.exists(outputDir + substring(file,0,lengthOf(file)-4)+".jpg")==1) {
print("tif exist" + file);
return 0;
} else {
print(outputDir+substring(file,0,lengthOf(file)-4)+".jpg");
print(File.exists(outputDir+substring(file,0,lengthOf(file)-4)+".jpg"));
}
path = dir+list[i];
open(path);
processImage();
saveAs("Jpeg", outputDir+substring(file,0,lengthOf(file)-4));
close();
close();
}
}
function processImage() {
run("Z Project...", "projection=[Standard Deviation]");
run("8-bit");
// run("Flip Vertically");
}