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vsnr_all.ijm
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vsnr_all.ijm
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//file parameters
suffix = ".ome.tif";
which="3D";
///////////////////
print("\\Clear");
input = getDirectory("Input directory containing raw data");
output = input+"vsnr/";
params_file = File.openDialog("VSNR parameters file");
//params_file="Z:/2020/2020_06/Bartek/2016A/vsnr3Dparams.txt";
processFolder_vsnr(input, output);
///////////////////
function processFolder_vsnr(input, output) {
setBatchMode( true );
list = getFileList(input);
createFolder(output);
for (i = 0; i < list.length; i++) {
if(endsWith(list[i], suffix)) {
processFile_vsnr(input+list[i], output+"/", "vsnr_"+substring(list[i], 0, indexOf(list[i], suffix)));
print("file done: "+ list[i]);
}
}
print("DONE");
}
function processFile_vsnr(input_file, output_subdir, output_file) {
print("Processing: " + input_file);
open(input_file);
if (which=="3D") {
getDimensions(w, h, channels, slices, frames);
if ((slices==1) & (frames>1)) Stack.setDimensions(channels, frames, frames);
run("VSNR GPU 3D", "where=[Text File (.txt)] choose="+params_file);
} else {
run("VSNR GPU 2D", "where=[Text File (.txt)] choose="+params_file);
}
//selectWindow("vsnr_"+input_file);
saveAs("Tiff", output_subdir+"/"+output_file);
close();
close();
}
function createFolder(out_dir) {
if (File.exists(out_dir)!=1) {
print("Tworzę folder: " + out_dir);
File.makeDirectory(out_dir);
} else
print("Directory exists");
}