// Batch_Add_Z_Uncertainty.js script by Christophe Leterrier
// Add or replace Z uncertainty in ThunderSTORM localization files
// 14-10-29

importClass(Packages.java.io.File);
importClass(Packages.ij.io.DirectoryChooser);
importClass(Packages.ij.IJ);
importClass(Packages.ij.gui.GenericDialog);

// extension for input files
extFormat = "csv";
// Default Z / XY uncertainty factor
factor_def = 2;

// Dialog
var dc = new DirectoryChooser("Choose a folder");
var inDir = dc.getDirectory() + File.separator;
var inDirFile = new File(inDir);
var parDir = inDirFile.getParent() + File.separator;

var gd = new GenericDialog("Batch add Z uncertainty: options");
gd.addNumericField("Z uncertainty factor", factor_def, 1, 3, "* XY uncertainty");
gd.showDialog();
var factor = gd.getNextNumber();

if (gd.wasOKed()) {
	
	// Start
	var startTime = new Date().getTime();
	
	IJ.log("\n\n*** Batch add Z uncertainty started ***");
	IJ.log("Input folder: " + inDir);
	
	// Localize the SR folder to get the path to script functions
	var plugDir = IJ.getDirectory("imagej");
	var csPath = plugDir + "scripts" + File.separator + "NeuroCyto" + File.separator + "added macros" + File.separator + "ChriSTORM extras" + File.separator;
	
	// Batch Add Z uncertainty
	
	// Get the Func function path and load
	var FuncJS = "F-TSAddZUnc.js";
	var FuncPath = csPath + FuncJS;
	IJ.log("\nFunction path:" + plugDir + FuncJS);
	load(FuncPath);
	
	// Define input folder, define and create output folder
	var inDirFunc = inDir;
	var outDirFunc = parDir + "Locs TS Zunc" + File.separator;
	IJ.log("Function input folder: " + inDirFunc);
	IJ.log("Function output folder: " + outDirFunc);
	var outDirFuncFile = new File(outDirFunc);
	if (!outDirFuncFile.exists()) {
			outDirFuncFile.mkdir();
		}
	
	// Get the file list from the input folder, batch process them using the split function
	var fileQueueS = getExtFiles(inDirFunc, extFormat);
	for (var f = 0; f < fileQueueS.length; f++) {
		inPath = fileQueueS[f];
		TSAddZUnc(inPath, outDirFunc, factor);
	}
	
	// End
	var stopTime = new Date().getTime();
	var Time = stopTime - startTime;
	IJ.log("\n*** Batch add Z uncertainty end after " + Time / 1000 + " s ***");
	
}


function getExtFiles(dirst, inext) {
        var dir = new File(dirst); 
        var allfiles = dir.listFiles(); 
        var extFiles = new Array(); 
        for (var i = 0 ; i < allfiles.length; i++) { 
                var name = allfiles[i].getName(); 
                var ext = name.substring(name.lastIndexOf(".")+1);
                if (ext == inext) { 
                        extFiles.push(allfiles[i]); 
                } 
        } 
        return extFiles; 
}