Laboratoire RDP » Biophysics Team » FLORIVAR

//////////////////////////////////////////////////////////////////////////////////

//The script will process all your .inr.gz files in the chosen folder.

//The stacks will be saved in subfolders named as the treated lif files.

print ("===========================");

print ("==== Macro flip-vertically-mgx.ijm ====");

//Choose the directory containing your .inr.gz files//

dir = getDirectory("Choose a directory")

setBatchMode(true);

list = getFileList(dir);

print(dir);

ShortNameDir=substring(dir,0,lastIndexOf(dir,"/"));

print (ShortNameDir);

dirout=ShortNameDir+"-flipped/";

print("Creating output directory ",dirout);

File.makeDirectory(dirout);

for (FileInd=0; FileInd<list.length; FileInd++){

	FileName = list[FileInd];

	if(endsWith (FileName, ".tif")){

		print ("### Processing ",FileName," ###");

		path = dir+FileName;

		pathout = dirout+FileName;

		print("avant open", FileName,"!");

		//run("Bio-Formats Importer", "open=["+path+"] color_mode=Default view=Hyperstack stack_order=XYCZT use_virtual_stack open_all_series ");

		open(path);

		print("apres open", FileName,"!");

		run("Flip Vertically", "stack");

		saveAs("Tiff", pathout);

		print("avant close", FileName,"!");

		run("Close All");

		print("Done with", FileName,"!");

	} else {

	print("### ",FileName," Not a .tif file ###");

	};

};	

print("Done with this folder!!!");