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BatchDownsampleAmiraRespectingFolders.txt
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BatchDownsampleAmiraRespectingFolders.txt
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// "BatchConvertStacksToZProjJPGS"
//
// This macro batch processes all the amira files
// in a folder and any subfolders in that folder.
// It then saves them in the Amiramesh format using Fiji's AmiraMesh plugin
// The new file will have the same name
// If you give the same input and output folders nothing will happen
// (Slightly) Adapted by Greg Jefferis from code at
// http://rsb.info.nih.gov/ij/macros/BatchProcessFolders.txt
// v 0.1 2009-11-25
// - 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], "/")){
if(File.exists(""+outputDir+list[i]) != 1){
File.makeDirectory(""+outputDir+list[i]);
}
processFiles(""+dir+list[i], ""+outputDir+list[i]);
} else {
showProgress(n++, count);
processFile(dir,outputDir,list[i]);
}
}
}
function processFile(dir,outputDir,file) {
if (endsWith(file,".am")) {
newpath=outputDir+file;
if(File.exists(newpath)){
print("Skipping file: "+file+" since output already exists");
return;
}
path = dir+file;
open(path);
processImage();
run("AmiraMesh ...", "amirafile=["+newpath+"]");
close();
close();
}
}
function processImage() {
run("Scale...", "x=0.5 y=0.5 z=1.0 interpolation=Bilinear process create title=scaledimage");
run("8-bit");
}