// F-LSFtxtTranslate.js script function by Christophe Leterrier
// Translate single-channel txt localization files from Sandrine to .xls ThunderSTORM localization files

importClass(Packages.java.io.File);
importClass(Packages.java.io.FileReader);
importClass(Packages.java.io.FileWriter);
importClass(Packages.java.io.BufferedReader);
importClass(Packages.java.io.BufferedWriter);
importClass(Packages.ij.IJ);
importClass(Packages.java.lang.Double);

function SLFtxtTranslate(inPath, outDir, outFormat) {
	
	// is there a header?
	var inHeader = true;
	var FWHM = 2.355;	
	var BgdADU = 100;
	// Add support for the Z uncertainty (in TS daily buil 05 may 2014)
	// fixed sigma for XY uncertainty (if fixed)
	var fixXY = 10;
	// fixed sigma for Z uncertainty (if fixed)
	var fixZ = 20;	
	var SampleMax = 100;

//	var PixelPitch = 160;
//	var ExposTime = 0.016;
//	var CpP = 1 / PpC;
//	var BgdCor = (BgdPhot / PixelPitch) * (BgdPhot / PixelPitch);
//	var EMfactor = 1.83;
	
	// Header format (if exists)
    if (inHeader == true) var inHeaderNS = ["Channel Name", "X", "Y", "Xc", "Yc", "Height", "Area", "Width", "Phi", "Ax", "BG", "I", "Frame", "Length", "Link", "Valid", "Z", "Zc", "Photons", "Lateral Localization Accuracy", "Xw", "Yw", "Xwc", "Ywc"];
	var inSep = " ";
	
	// Assign the indexes for all columns in the input format
	iX = 0;
	iY = 1;
	iZ = 2;
	
	// Define input file path
	var inFile = new File(inPath); 
	var inName = inFile.getName();
	var inNameExt = getExt("" + inName);
	IJ.log("    inName: " + inName);

	// Open input File reader
	var br = new BufferedReader(new FileReader(inFile));

	// Taste the first line to detect if 2D (all Z =0) or 3D
    if (inHeader == true) inLine = br.readLine();
	var inCells = inLine.split(inSep);	
	var zAccu = 0;
	var i = 0;	
	while ((inLine = br.readLine()) != null && i < SampleMax) {
		i++;
		inCells = inLine.split(inSep);
		zAccu = zAccu + parseFloat(inCells[iZ]);
	}
	if (zAccu == 0) 
		IJ.log("      2D file detected");
	else
		IJ.log("      3D file detected");

	// Close and reopen to get back at line 0
	br.close();
	br = new BufferedReader(new FileReader(inFile));
	// Pass header line
	if (inHeader == true) inLine = br.readLine();

	// ThunderSTORM format
	if (outFormat == "xls") {
		var sep = "\t";
		if (zAccu == 0){// 2D case
			var outHeader = ["\"frame\"","\"x [nm]\"","\"y [nm]\"","\"uncertainty_xy [nm]\""];
			var outSuffix = "_TS2D";
		}
		else {
			var outHeader = ["\"frame\"","\"x [nm]\"","\"y [nm]\"","\"z [nm]\"","\"uncertainty_xy [nm]\"", "\"uncertainty_z [nm]\""];
			var outSuffix = "_TS3D";
		}
		var includeHeader = true;	
		var outExt = ".xls";
	}


	// Prepare output file path
	var outName = inName.substring(0, inName.length()-4) + outSuffix + outExt;
	var outPath = outDir + outName;
	var outFile = new File(outPath);
	if (!outFile.exists()) {
		outFile.createNewFile();
	}
	IJ.log("      outName: " + outName);

	// Open output File writer
	var bw = new BufferedWriter(new FileWriter(outFile));	
	// Write new Header
	if (includeHeader == true) {
		var outLine = makeLineFromArray(outHeader, sep);
		bw.write(outLine);
		bw.newLine();
	}

	// Write the output file line by line
	var m = 0;
	while ((inLine = br.readLine()) != null) {

			m++;
			var inCells = inLine.split(inSep);

			// ThunderSTORM xls format
			if (outFormat == "xls") {
			
					// Build results line
				if (zAccu == 0){ // 2D case
					outLine = "1" + sep + parseFloat(inCells[iX]) + sep + parseFloat(inCells[iY]) + sep + fixXY;
				}
				else { // 3D case
					// peak width: TS has Wx and Wy (astigmatism-deformed PSF), but N-STORM has only one width W and an axial ratio Ax
					// so we calculate Wx and Wy from W and Ax
				
					outLine = "1" + sep + parseFloat(inCells[iX]) + sep + parseFloat(inCells[iY]) + sep + parseFloat(inCells[iZ]) + sep + fixXY + sep + fixZ;

				}
					
			}
			bw.write(outLine);
			bw.newLine();
		}	 
	br.close();
	bw.close();
}


function makeLineFromArray(ar, se) {
	ol = "" + ar[0];
	for (t = 1; t < ar.length; t++) {
		ol = ol + se + ar[t];
	}
	return ol;
}


function getExt(filestring){
	var namearray = filestring.split(".");
	var shortname = "";
	for (var f = 0; f < namearray.length - 1; f++) {
		shortname = shortname + namearray[f];
	}
	return [shortname, namearray[namearray.length - 1]];
}